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Organizing Committee:
Tamara Bintener, Charandeep Singh, Diana Charles El Assal, Ganna Androsova, Sarah Nickels,
Zoé Hanss, and Egle Danileviciute
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Contents Acknowledgements .............................................................................................................................................. 4
Welcome Letter .................................................................................................................................................... 5
A word from the student representatives ............................................................................................................ 7
For your future… ................................................................................................................................................... 9
General Information ........................................................................................................................................... 11
Getting Here? ................................................................................................................................................. 12
Social Event..................................................................................................................................................... 13
Sponsors ............................................................................................................................................................. 15
Luxembourg Institute of healthy (LIH) ........................................................................................................... 17
Greiner Bio-One .............................................................................................................................................. 18
PeproTech ....................................................................................................................................................... 19
Thermo Fisher Scientific ................................................................................................................................. 20
Eppendorf ....................................................................................................................................................... 21
BIORAD ........................................................................................................................................................... 22
Promega ......................................................................................................................................................... 23
Scientific programme ......................................................................................................................................... 25
Thursday, 24th November .............................................................................................................................. 26
Friday, 25th November ................................................................................................................................... 27
Workshop ....................................................................................................................................................... 29
Keynote Speakers ............................................................................................................................................... 31
Dr. Uwe Ohler ................................................................................................................................................. 32
Dr. Nicola Zamboni ......................................................................................................................................... 33
Dr. Steffen Scholpp ......................................................................................................................................... 34
Dr. Liliana Bernardino ..................................................................................................................................... 35
Abstracts ............................................................................................................................................................. 37
Talks ................................................................................................................................................................ 39
Posters ............................................................................................................................................................ 58
FIN....................................................................................................................................................................... 89
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Acknowledgements The organization committee of the Life Sciences PhD Days 2015 would like to acknowledge the support of the University of Luxembourg, Luxembourg Centre of Systems Biomedicine and Luxembourg Institute of Health.
We would like to give our special thanks to the Luxembourg Institute of Health for providing the
prize money of the three best talks.
They are also grateful for the support from the following sponsors:
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Welcome Letter by Prof. Dr. Serge Haan
Dear external guests, PhD candidates, PIs, colleagues,
I wish to welcome you to the PhD days 2016!
Again, our PhD candidates organized this interesting and stimulating event which aims at fostering
interactions between the candidates in the different Life Science discipline.
Currently, the Doctoral School in Systems and Molecular Biomedicine of the University of Luxembourg
encompasses about 75 PhD candidates and more will join our programme in the context of the PRIDE
scheme. In addition, there are some other changes ahead of us. With the establishment of a faculty-
wide doctoral school at the FSTC, the Doctoral School in Science and Engineering (DSSE), our doctoral
school in biomedicine will now become one of 8 foreseen programmes of the DSSE, including
computer science and computer engineering, computational sciences, mathematics, physics as well
as three programmes in engineering. We thus expect stronger interactions between PhD candidates
but also between PIs involved in the different programmes. Having a new faculty-wide doctoral
school will of course lead to changes in the functioning of the school and the already existing
programmes. Again we will have a transition period in which we need to display some flexibility. I am
sure that the investment of the many people involved in this initiative will help us to reach our
primary goals:
help our PhD candidates increase their knowledge in their different areas of interest
provide an interactive and interdisciplinary environment
ensure a high quality of the PhD theses and supervision
further increase the employability of our candidates
As always, I would like to take the opportunity to thank the people who contribute to the day to day
functioning of the school as well as its development, such as the my colleagues in the member’s
council, Karsten Hiller, Eric van Dyck and Alex Skupin. I also thank all the PIs who actively contribute
to functioning of the school. Special thanks also go to our secretary, Magali Guillaume, who ensures
the day to day operation of our school. Of course I would also like to thank our leaving as well as
incoming PhD candidate representatives, Anne Dirkse, Sean Sapcariu, Anna Monzel and Jonathan
Arias. Last but not least I thank the organising committee of the PhD days 2016 for organising this
event. I am pretty sure that it will be very well received by most participants and guest.
Enjoy the PhD days 2016!
Serge Haan
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A word from the student representatives
Dear PhD students,
We are Jonathan Arias and Anna Monzel and as the new student representatives, we are delighted
to welcome you to this year’s PhD days. First of all we would like to thank you for your trust and
confidence by choosing us as your student representatives. We hope to properly put forward your
ideas that will help to constantly improve our doctoral program. Our former representatives Anne
Dirkse and Sean Sapcariu created many valuable academic activities and we hope to consolidate
them as traditions of our student council.
During this year we will continue to organize the coffee with Rudi, pizza club and PhD retreat.
We intend to increase your participation in our activities and for that we will arrange regular
meetings. During these events we will brainstorm about current and future aspects relevant for you.
We are very excited to continuously contribute to improve our doctoral program and improve your
experience as student.
Best regards
Anna & Jonathan
© Michel Brumat
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For your future…
EURAXESS Luxembourg provides free advice and guidance to researchers moving to or from Luxembourg to
develop their research career.
In particular, it offers essential advice to help newcomers in all the administrative procedures and practical
information related to issues of daily life in Luxembourg, such as:
• visas;
• jobs & funding on the EURAXESS job portal;
• housing;
• taxes & social security;
• family matters & life in Luxembourg.
EURAXESS Luxembourg is part of EURAXESS, a pan-European network with over 260 service centres located in
40 countries.
Its aim is to enhance researchers' mobility within and towards Europe and to contribute to making Europe a
centre of excellence in research.
The EURAXESS Luxembourg network is managed by the:
In partnership with:
National Contact Point:
University of Luxembourg
International Relations office – Euraxess
Barbara Daniel
T : +352 466644-6681
Planning to settle in Luxembourg? Check the Foreign Researchers Guide to
Luxembourg.
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General Information
“Everything you need to know before.”
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Getting Here?
The PhD Days 2016 will take place at the Maison du Savoir (MSA) room 3.530 (3rd floor)
Maison du Savoir (number 1 on the map)
GPS : 49.504839 | 5.948214 http://wwwfr.uni.lu/contact/campus_de_belval
2, avenue de l'Université L-4365 Esch-sur-Alzette
By Car See map Free less-then-three-hours parking at Belval Plaza during working hours of the Belval Plaza shopping centre. Outdoor parking areas and underground car parks are available throughout the campus, particularly P+R Belval Université.
By Bus The following bus lines are servicing several stops on Belval Campus: Belval Plaza, Belval-Université, Belvaux Um Bedding, Esch/Alzette Av.Rock'N'Roll Esch/Alzette Av. Hauts-
Fourneaux
By Train, "Belval-Université" Train Stop Trains departing every 15 minutes from
Luxembourg Central Station are direct
to "Belval-Université" - line is connection-
free via Esch-sur-Alzette. Get information
on train schedules on the CFL’s website.
Maison du Savoir
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Social Event
Quiz Night! @ Biotech II
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Sponsors
“Silent gratitude isn't much use to anyone.”
- G.B. Stern
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Luxembourg Institute of healthy (LIH)
Luxembourg Institute of Health: Research dedicated to life.
The Luxembourg Institute of Health is a public research organisation at the forefront of biomedical sciences.
With its strong expertise in population health, oncology, infection and immunity as well as storage and
handling of biological samples, its research activities are dedicated to people’s health. At the Luxembourg
Institute of Health, more than 300 individuals are working together, aiming at investigating disease
mechanisms and developing new diagnostics, innovative therapies and effective tools to implement
personalised medicine. The institution is the first supplier of public health information in Luxembourg, a strong
cooperation partner in local and international projects and an attractive training place for ambitious early-
stage researchers
We would also like to thank the Luxembourg Institute of Health for providing the prize money for the three
best talks.
www.lih.lu
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Greiner Bio-One
Follow our mascot: Theo Tube!
Our company, Greiner Bio-One, is a global player. With a workforce of around 1,800, 23 branches and numerous sales partners, our presence spans more than 100 countries.
Our BioScience expertise lies in the development of products for universities and research organizations, as well as for the diagnostics, biotechnology and pharmaceutical industries.
BioScience is a leading supplier of specialist products for the analysis of cell cultures and microplates. Some of our latest innovations are:
CELLdiscTM, for mass cell culture;
SAL 10-6 Triple-Packed products;
CELLviewTM Slide, for high-resolution microscopy;
Datamatrix Cryo’sTM, for biobanking.
Your Power for Health
Our research department develops innovative products and system solutions. Its work is geared towards the needs of our markets and is carried out in close collaboration with our cooperation partners.
Our products are innovative, efficient and of high quality, thereby complying with our customers' requirements.
Our goal is healthy and sustainable growth. The long-term prospect of success always lies at the heart of our strategies.
For more information, please visit our website: www.gbo.com
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PeproTech
Supporting Life Science Research since 1988, PeproTech is the trusted source for the development and
manufacture of high quality cytokine products for the life-science and cell therapy markets. Over the past 27
years the company has grown into a global enterprise with state-of-the-art manufacturing facilities in the US,
and offices around the world.
With over 2,000 products PeproTech has developed and refined innovative protocols to ensure quality,
reliability and consistency.
Our mission is to provide the highest quality products that address the needs of today’s scientists and
researchers.
We pride ourselves on being a trusted partner within the scientific community.
• Research Use Only proteins and antibodies
• GMP-Compliant products for Cell, Gene and Tissue Therapy
• Animal Free Cytokine Range
• ELISA kits
• Media Kits / Supplements
Contact PeproTech to request a quote or discuss your research requirements:
020 7610 3062
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Thermo Fisher Scientific
The World Leader in Serving Science
As the world’s leader in serving science, Thermo Fisher Scientific is a driving force in the research, healthcare,
industrial and applied markets, generating more than USD 17 billion in annual revenue.
No other company can match our range of customer touch points – technologically, geographically or
commercially. We help our customers in finding cures for cancer, protecting the environment, making sure
our food is safe and moving forward with thousands of important projects that improve millions of lives.
At Thermo Fisher Scientific, each one of our 50,000 extraordinary minds has a unique story to tell. Join us and
contribute to our singular mission - enabling our customers to make the world healthier, cleaner and safer.
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Eppendorf
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Bio-Rad
Bio-Rad Laboratories has played a leading role in the advancement of scientific discovery for 60 years by
providing a broad range of innovative tools and services to the life science research and clinical diagnostic
markets. Bio-Rad’s Life Science Group develops, manufactures, markets and supports a wide range of
laboratory instruments, apparatus and consumables used for research in genomics, proteomics, cell biology
and food safety.
In many of these areas Bio-Rad is both a leading supplier and a pioneer. For example, in our efforts to advance
the capabilities of PCR, Bio-Rad introduced the first commercially available droplet-based digital PCR platform;
a system that has gone on to be cited in over 250 peer reviewed publications.
In cell biology we have made life in the lab easier with the S3™ Cell Sorter and the new ZOE™ Fluorescent Cell
Imager alongside an extensive range of performance guaranteed immunology antibodies.
For the study of proteins, Bio-Rad has a wide range of innovative chromatography, electrophoresis, western
blotting and imaging systems as well as multiplex immunoassays are helping accelerate discovery and give
greater confidence in results.
We operate globally with dedicated offices in over 75 countries, distributing, servicing and providing technical
and customer support for over 10,000 products. For complete details of our comprehensive range of products
contact your local office or visit www.discover.bio-rad.com
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Promega
With a portfolio of more than 3,000 products covering the fields of genomics, protein analysis and expression,
cellular analysis, drug discovery and genetic identity, Promega is a global leader in providing innovative
solutions and technical support to life scientists in academic, industrial and government settings.
Promega products are used by life scientists who are asking fundamental questions about biological processes
as well as by scientists who are applying scientific knowledge to diagnose and treat diseases, discover new
therapeutics, and use genetics and DNA testing for human identification.
Promega holds significant intellectual property rights and licenses in several key areas that form a foundation
for its diverse portfolio including:
- Bioluminescence, including engineered luciferases, luciferase reporter vectors and luciferase
substrates
- Short tandem repeat (STR) detection for STR-based cell line authentication, human identification, cell
and tissue characterization, and mixed sample detection
- HaloTag® protein labeling and capture technology
- Cell Health and Metabolism Assays
- NanoLuc luciferase technologies from gene reporter assays to protein:protein interaction in living cells
and beyond.
Contact Details
Promega Benelux
Schipholweg 1, 2316XB Leiden, The Netherlands – Tel: +31 71 532 4244 – Fax: +31 71 532 4907 – web:
www.promega.com
Sales Representative: Mrs. Marylène Focant, PhD
Account Manager – Bruxelles, Wallonie & Luxembourg Mobile: +32 476 57 20 28
E-mail: [email protected]
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Scientific programme
“Let’s get serious”
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Thursday, 24th November 8:30
Welcome - Registration 8:45
9:00 Opening talk
9:15
Short presentation of 1st year PhD students 9:30
9:45
10:00 Dr. Uwe Ohler
Computational Biology of Post-transcriptional Gene Regulation 10:15
10:30
10:45 Coffee Break 30 minutes 11:00
11:15
PhD student presentations: Deborah Gérard Daniela Antonelli Florence Servais Antoun Al Absi
11:30
11:45
12:00
12:15
12:30
12:45
Lunch Break +
Poster Session
13:00
13:15
13:30
13:45
14:00 Dr. Nicola Zamboni
On the quest from metabolic phenotypes to molecular mechanisms 14:15
14:30
14:45 PhD Student presentations : Linda Wampach
Loise Wandera Diana C. El Assal
15:00
15:15
15:30
15:45 First Day Closing Words
16:00 Poster Session (even numbers)
+ Coffee Break
16:15
16:30
16:45
17:00
Workshop with Dr. Nicola Zamboni MSA 4.070 (4th floor)
19:00
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Friday, 25th November 8:30
Welcome - Registration 8:45
9:00 Day 2 Opening Talk
9:15 Dr. Steffen Scholpp
The Wnt morphogenetic field - about ligand transport, advection and signaling 9:30
9:45
10:00 PhD Student presentations : Hélène Erasimus Ursula Heins Marroquin
10:15
10:30
10:45 Coffee Break 30 minutes 11:00
11:15 PhD Student presentations :
Remon Soliman Elie Daher Malte Herold Giulia Cesi
11:30
11:45
12:00
12:15
12:30
12:45 Lunch Break
+ Poster Session (odd numbers)
13:00
13:15
13:30
13:45
14:00 Dr. Liliana Bernardino
Nanomedicine approaches to modulate neural stem cells in brain repair 14:15
14:30
14:45 PhD Student presentations: Dheeraj Reddy Bobbili Fatima Liliana Monteiro Anna Monzel
15:00
15:15
15:30
15:45 Coffee Break 30 minutes 16:00
16:15 PhD Student presentations : Bruno Filipe Rodrigues Santos Shankari Nadupalli
16:30
16:45
17:00 Last Day Closing Words
17:30
Social Event @ Biotech II
late
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Workshop Thursday, 24th November 17:00
We would like to thank Dr. Nicola Zamboni for offering the following workshops. If time allows, both
workshops will be held.
WORKSHOP 1
A brains-on, hands-off workshop on systems biology of metabolism
Metabolism is fun and there are plenty of things to discover on its architecture and regulation. The true
limitations aren’t technical, but conceptual. Hence, I’d like to have a brainstorming session on the meaning
of data. Starting from what we all learned in biochemistry, we’ll make our way to hypothesis-driven analysis
of metabolic networks. The workshop is very interactive, and active thinking is a must to profit the most.
WORKSHOP 2
13C-metabolic flux analysis
13C-MFA analysis is the major method to measure intracellular metabolic fluxes, and it’s increasingly
penetrating cell biology. I’ll try to explain the basics, best practice, common errors and – if time allows – give
a sneak previews on current development.
Where? MSA, room 4.070 (4th floor)
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Keynote Speakers
“The Best way to conquer stage fright
is to know what you’re talking about.”
– Michael H Mescon
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Dr. Uwe Ohler Thursday, November 24 at 10:00
(Computational Regulatory Genomics)
Since 2012, Uwe Ohler has been Professor at the Max Delbrueck Center in
Berlin, with a primary appointment in the Department of Biology and a
secondary appointment in the Department of Computer Science at Humboldt
University Berlin.
He studied computer science with a minor in biology at the University of
Erlangen-Nuremberg in Germany, graduating in 1996. During a student
research project involving computational DNA sequence analyis, he became
fascinated with computational biology.
In 1998, he started his PhD research at the Chair for Pattern Recognition
(Professor Heinrich Niemann) at the same university. He was a Boehringer
Ingelheim pre-doctoral fellow from 1998-2001 and a visiting researcher with
the Berkeley Drosophila Genome Project (Professor Gerald Rubin). He obtained
his PhD with distinction in 2002 for the McPromoter system for computational
identification of promoters in eukaryotic genomes.
Before returning to Germany, Uwe lived in the US for more than a decade and followed his interests in gene
regulation and applied machine learning. From 2002-2004, he worked as a postdoctoral researcher in the
Department of Biology (Professor Chris Burge) at the Massachusetts Institute of Technology, where he was
also a member of the cross-departmental Computational and Systems Biology Initiative. In 2005, he joined the
faculty of the Institute of Genome Sciences & Policy at Duke University, Durham NC, USA, where he received
tenure in 2011. He taught in the cross-departmental graduate program in Computational Biology &
Bioinformatics, and was core faculty of the Duke Center for Systems Biology. During this time, he received
fellowships from the Alfred P Sloan Foundation, as well as HFSP, NSF CAREER, and NIH Transformative
Research awards.
Computational Biology of Post-transcriptional Gene Regulation Uwe Ohler
A variety of deep sequencing protocols now allow us to interrogate many aspects of gene regulation. This has
boosted our ability to explore regulatory protein-RNA interactions via RNA-binding proteins (RBPs) and to
track RNA through the post-transcriptional processing steps that these RBPs control: Looking beyond steady-
state RNAseq now makes it possible to track RNA from nascent transcription to translation. I will present an
overview of the field and some of our recent contributions to develop new algorithms and apply them to gain
insight into regulatory mechanisms.
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Dr. Nicola Zamboni Thursday, November 24 at 14:00
(Systems Biology of Metabolism)
Nicola Zamboni graduated in the group of Jay Bailey at the Institute of
Biotechnology of ETH Zurich in the field of metabolic engineering and 13C
metabolic flux analysis. As a PostDoc in Stanford, he developed and applied
metabolomics-based approaches for unraveling metabolic changes in
eukaryotic cells. Since 2005, he’s an independent PI at the Institute of
Molecular Systems Biology in Zurich. His lab focuses on the development of
mass spectrometry and computational methods to characterize metabolic
dynamics in complex systems and reverse engineer cellular regulation.
On the quest from metabolic phenotypes to molecular mechanisms Nicola Zamboni1
1 Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
Metabolism plays a pivotal role in all cellular processes by providing building blocks and energy for
biosynthesis and participating in decision-making. In many biomedical areas such as oncology, toxicology,
immunology, stem cell research, etc., metabolism is currently regarded as a key driver and a differentiating
factor to be exploited in diagnostics and selective therapy. Historically, the discovery of aberrant metabolism
has been mainly accomplished at the genetic level, e.g. by identifying specific enzyme mutations in primary
cancers, by finding upregulation of atypical (embryonic) isoforms at expression level, or screening for
sensitivity to RNAi in cell lines or mice. Albeit highly valuable, these approaches suffer from intrinsic limitations
in scope and sensitivity.
Our lab approaches metabolism bottom-up, which means from a phenotypic and functional perspective on
the basis of metabolite levels and fluxes assayed with stable tracers. Over the past years, we analyzed > 3’000
experiments (>800’000 samples) in all of the aforementioned areas. Overall, it has become routine to profile
large cohorts and discover metabolic alterations in virtually any study. This massive capacity unlocked a realm
of novel opportunities. Fueled by this wealth of information, our research focus shifted from data generation
to functional interpretation of the results, i.e. to the generation of testable hypotheses from high-throughput
metabolomics.
I’ll illustrate this process on the basis of recently published study on T cell metabolism [1] and give an overview
on current efforts to abridge data to mechanisms.
[1] Geiger et al, L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity, Cell 167 (3), 829-842.
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Dr. Steffen Scholpp Friday, November 25 at 9:15
(Biology of Brain Development)
Steffen Scholpp is group leader at the Karlsruhe Institute of Technology
(Karlsruhe, Baden-Wuerttemberg, Germany). He obtained a PhD in
Developmental Neurobiology at the Ruprecht-Karls University of
Heidelberg and continued his career as Postdoctoral researcher at Max
Planck institute in Dresden (2003-2004) and in the Centre for
Developmental Neurobiology of Kings College in London (2005-2009). Dr.
Steffen Scholpp is interested in the early development of the brain
particularly towards the development of the thalamus. His group recently
assigned a new organising function to the transverse Zona Limitans
Intrathalamica boundary and termed it therefore as the mid-diencephalic
organiser (MDO). This region expresses several important signalling
molecules, including those of the Hedgehog and Wnt families. Through the
release of these signaling factors, the MDO orchestrates the development
of the thalamus.
The Wnt morphogenetic field - about ligand transport, advection and signaling Steffen Scholpp (Karlsruhe Institute of Technology (KIT))
After secretion, developmental signals known as morphogens must travel relatively long distances to form a
concentration gradient that the responding tissue uses to acquire positional information. The role of
morphogen transport and endocytic trafficking in this process is the subject of intense debate. Wnt proteins
regulate developmental processes, tissue regeneration and stem cell maintenance. It has been postulated that
Wnt/β-catenin signalling form concentration gradients across responsive tissues and act as morphogens.
However, little is known about the transport mechanism for these lipid-modified signalling proteins in
vertebrates.
Here we show that Wnt8a is transported on short, actin-based filopodia to contact responding cells and
activate signalling during neural plate formation in zebrafish (1,2). Cdc42/N-Wasp regulates the formation of
these Wnt-positive filopodia. Enhanced formation of filopodia increases the effective signalling range of Wnt
by facilitating spreading. Consistently, reduction in filopodia leads to a restricted distribution of the ligand and
a limited signalling range. Using a numerical simulation, we provide evidence that such a short-range transport
system for Wnt has long-range signalling function.
After contact by Wnt/β-catenin positive filopodia, a multi-protein complex at the plasma membrane assembles clustering membrane-bound receptors and intracellular signal transducers into the so-called Lrp6-signalosome. Our imaging studies in live zebrafish embryos show that the signalosome is a highly dynamic structure, which is continuously assembled and disassembled by a Dvl2-mediated endocytic process (2). We show that this endocytic process is not only essential for ligand-receptor internalization but also for signaling. We conclude that a cytoneme-based transport system for Wnt and subsequent endocytosis is important for
Wnt/β-catenin signaling and controls anteroposterior patterning of the neural plate during vertebrate
gastrulation. (1) Stanganello et al., Nature Comms., 2015; (2) Stanganello end Scholpp. J. Cell Sci., 2016; (3) Hagemann, et al., J.Cell Sci., 2014
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Dr. Liliana Bernardino Friday, November 25 at 16:00
(Brain Repair Mechanisms)
Liliana Bernardino obtained a PhD in Molecular Biology at the University
of Coimbra (2008). The experimental work was conducted at the Center
for Neuroscience and Cell Biology (CNC) under the supervision of Dr. João
Malva; Institute of Pharmacological Research Mario Negri (Milan, Italy)
under the supervision of Dr. Annamaria Vezzani and at the Department
of Anatomy and Neurobiology, University of Southern Denmark
(Denmark) under the supervision of Dr. Jens Zimmer. The main goal of her
doctoral and postdoctoral studies was to find new therapeutic strategies,
targeting neuroinflammation processes, which could promote
neuroprotection and neurogenesis. She has published 26 peer-review
international articles, 5 book chapters, 56 abstracts published in
conference proceedings and she has 4 pending patents. She was the
principal investigator of 4 research projects funded by the Foundation for
Science and Technology (FCT), Calouste Gulbenkian Foundation and
“Medalhas de Honra L’Oreal”; and a member of the research team of 7
projects funded by the FCT. Currently, Liliana is the leader scientist of several research projects that aim to
boost brain repair in the context of brain ischemic stroke and in Parkinson’s disease.
Nanomedicine approaches to modulate neural stem cells in brain repair Liliana Bernardino
Parkinson's disease (PD), a neurodegenerative disorder characterized by the selective degeneration of the
nigrostriatal dopaminergic pathway, is a major socio-economic burden in modern society. While there is
presently no cure for PD, enhancing the number of neural stem cells (NSCs) and/or stimulating their
differentiation into new neurons are promising therapeutic strategies. Many proneurogenic factors have been
implicated in controlling NSCs activity, including several microRNAs. However, actual strategies described for
the intracellular delivery of microRNAs involve mostly unspecific or inefficient platforms. Recently, we
developed miR-124 loaded nanoparticles (NPs) able to efficiently deliver miR-124 into neural stem/progenitor
cells and boost neuronal differentiation and maturation in vitro. In vivo, the intracerebroventricular injection
of miR-124 NPs increased the number of new neurons in the olfactory bulb of healthy and 6-hydroxidopamine
(6-OHDA) treated mice, a model for PD. Importantly, miR-124 NPs enhanced the migration of new neurons
into the 6-OHDA lesioned striatum, culminating in motor function improvement. Given the recent advent of
clinical trials for miR-based therapies and the theranostic applications of our NPs, we expect to support the
clinical translation of our delivery platform in the context of PD and other neurodegenerative diseases which
may benefit from enhancing microRNA levels.
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Abstracts
“The abstract of a paper is the only part of the paper
that is published in conference proceedings.”
Andrade, C. (2011). How to write a good abstract for a scientific paper or conference presentation. Indian Journal of Psychiatry, 53(2), 172–175.
http://doi.org/10.4103/0019-5545.82558
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Talks
Thursday, November 24th
1. Derivation of gene regulatory networks from temporal epigenomic and transcriptomic profiles during mesenchymal lineage commitment
Deborah Gérard
2. Development of a mass spectrometry-based clinical assay for ERCC1/XPF proteins
Daniela Antonelli
3. Identification and characterization of microRNAs targeting the IL-6/STAT3 pathway
Florence Servais
4. Tumor actin cytoskeleton remodeling: a novel mechanism for cancer cells to escape from natural killer cell-mediated cell death
Antoun Al Absi
5. Metagenomic assessment of the neonatal microbiome colonization Linda Wampach
6. Towards understanding wetland ecohydrology from mapping evapotranspiration using satellite data
Loise Wandera
7. Constraint-based computational modelling of bioenergetic pathway switching in synaptic mitochondria from Parkinson’s disease patients
Diana C. El Assal
Friday, November 25th
8. Identification of novel molecular targets for TMZ-based therapies against glioblastoma: A comprehensive shRNA-based screen of DNA Damage Response factors
Hélène Erasimus
9. Towards small-molecule therapies for a juvenile form of Batten disease Ursula Heins Marroquin
10. Characterisation of two protein repair enzymes and their effect on calcium signalling
Remon Soliman
11. Data-driven development in the smart city. Generative design for refugees camps in Luxembourg.
Elie Daher
12. Integrated multi-omics for understanding niche ecology of distinct populations in microbial consortia
Malte Herold
13. Detection, characterization and function of extracellular vesicles in resistant melanoma
Giulia Cesi
14. Identification of risk factors for Parkinson’s disease by the means of large-scale genomic analysis.
Dheeraj Reddy Bobbili
15. Metabolic requirements of induced pluripotent stem cell derived dopaminergic neurons
Fatima Liliana Monteiro
16. A novel approach to derive human midbrain-specific organoids from neuroepithelial stem cells
Anna Monzel
17. Mitochondrial phenotypes of the A30P mutation in alpha-synuclein gene patient-derived cellular model of Parkinson’s disease
Bruno Filipe Rodrigues Santos
18. Stress modulated bulkphotovoltaic effect in Transition metal doped Lithium Niobate
Shankari Nadupalli
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Derivation of gene regulatory networks from temporal epigenomic and transcriptomic profiles during mesenchymal lineage commitment
Deborah Gérard, Florian Schmidt, Aurelien Ginolhac, Marcel H. Schulz, Thomas Sauter, Lasse Sinkkonen Identification of cell type-specific key regulators of cellular differentiation and of the gene regulatory networks (GRNs) they control has implications for a wide range of applications. Temporal data on expression profiles and context-specific open chromatin states can significantly improve GRN construction but remain difficult to integrate. We have generated time-series transcriptomic and epigenomic data during the differentiation of bone marrow adipocytes and osteoblasts from their shared mesenchymal precursor cells using RNA-seq and ChIP-seq for several histone modifications, in order to identify the GRNs underlying these differentiation processes, and to better understand their dynamics over time. Multipotent ST2 stromal cells were differentiated for 15 days either into adipocytes or osteoblasts and RNA and chromatin were collected at 6 different time points. RNA-seq analysis identifies over 30,000 expressed transcripts and ChIP-Seq for histone H3 lysine 27 acetylation (H3K27ac) identifies over 46,000 active enhancer regions controlling their expression. Expression levels of most transcripts correlate with their H3K4me3 and H3K36me3 signals, suggesting that their expression is largely controlled at the transcriptional level. Over 10% of the transcripts and enhancers exhibit significant changes over time with osteoblasts showing somewhat slower dynamics than adipocytes. The identified time point-specific open chromatin regions were annotated for transcription factor binding affinities and a novel machine learning approach was used to build dynamic regulatory networks that make full use of these time-series data. In parallel, to further prioritize the identified regulatory genes we mapped super-enhancers with dynamic profiles during differentiation and associated them to target genes using correlation between expression and epigenomic data. Among the key regulatory genes controlled by dynamic super-enhancers, we identified both transcription factors (TFs) and micro-RNA genes. They influence the differentiation of both of the lineages and we propose them as regulators of the mesenchymal multipotency. Keywords: Gene regulatory networks, epigenomics, super-enhancers, adipocytes, osteoblasts November 24th: 11:15 Deborah Gérard
[email protected] 4th year of my PhD
41
Development of a mass spectrometry-based clinical assay for ERCC1/XPF proteins Daniela Antonelli, Sara Rosati, Yeoun Jin Kim
ERCC1 protein, a key player of the nucleotide excision repair (NER) pathway, repairs DNA lesions caused by platinum-based chemotherapy drugs. Due to the lack of an antibody that specifically recognizes ERCC1 protein, a potential predicitve biomarker of platinum-based chemotherapy efficacy in lung cancer, there is the need to develop a robust and reliable clinical assay as alternative to the immunohistochemistry (IHC) assay used so far to assess ERCC1 protein expression level in biospecimens. Here we present a targeted mass spectrometry (MS)-based assay to detect ERCC1 protein and its binding partner XPF. Combining the immunoaffinity enrichment with targeted mass spectromety we provide higher specificity compared to the conventional immunoassay. We used ERCC1 and XPF proteotypic peptides (PTPs) as surrogates of the proteins and stable isotopically labeled (SIL) peptides as internal standards. Our results show ERCC1 and XPF proteotypic peptide detection by mass spectrometry after immunoenrichment of ERCC1 protein from cancer cells. The strength of this study is to guide clinicians’ therapeutic decisions towards patient-tailored treatment strategies. Keywords: ERCC1, XPF, Immunoaffinity, Mass Spectrometry
November, 24th: 11:35 Daniela Antonelli [email protected]
3rd year of my PhD
42
Identification and characterization of microRNAs targeting the IL-6/STAT3 pathway Servais, F; Kirchmeyer, M; Hamdorf, M; Haan, C; Kreis, S; Behrmann, I
IL-6 plays important roles in the regulation of liver functions and promotes the development of hepatocellular carcinoma (HCC), the most common primary liver cancer. Little is known about miRNAs regulating key players of IL-6 signal transduction. Therefore, our aim is to identify such miRNAs in a miRNA mimics screen (540 mimics) and to elucidate their effects on this pathway. Two rounds of Luciferase assay screenings have been done in two different kinds of cells. For the first screen we used Hek293T cells (kidney-derived cells) stably transduced with a construct containing the secreted Cypridina luciferase gene under the control of six STAT-responsive elements. Out of 540 mimics, we selected 129 which up- or down-regulated luciferase activity and used them in a second round of selection in Hep3B cells (HCC cell line) engineered to express the secreted Cypridina luciferase under the control of the rPAP1 promoter specific for STAT3. Overall, almost 90% of the mimics showed the same effect (up- or down-regulation) on the pathway in both screening approaches. Currently, we are further testing 33 mimic candidates by western blot analysis, validating (potential) effects on STAT3 phosphorylation and/or expression levels of STAT3 and other signaling molecules of the IL-6 signaling pathway. Those results, complementing our analyses of cytokine-induced miRNome changes, may contribute to the identification of novel regulatory circuits regarding the IL-6/STAT3 signaling pathway. Keywords: Mimic screening, miRNA, IL-6, Luciferase assay, JAK/STAT November, 24th: 11:55 Florence Servais
[email protected] 4th year of my PhD
43
Tumor actin cytoskeleton remodeling: a novel mechanism for cancer cells to escape from natural killer cell-mediated cell death
Antoun Al Absi, Coralie Guerin, Céline Hoffmann, Xianqing Mao, Flora Moreau, Salem Chouaib, Guy Berchem, Bassam Janji, Clément Thomas
Tumor actin cytoskeleton remodeling: a novel mechanism for cancer cells to escape from natural killer cell-mediated cell death Natural killers cells (NKs) are effectors of the innate immune system that destroy cancer cells through the directed secretion of granzyme B and perforin. This process requires the formation of a specialized cell-cell interaction region termed the immune synapse (IS). Previous reports have established that the formation of the IS largely rely on sequential rearrangement of actin filaments within NKs. In contrast, there is a gap of knowledge regarding the organization and role of the tumor cell actin cytoskeleton during NK attack. We showed that actin of NK-resistant tumor cells accumulate at the IS. Using the high-throughput ImageStream®X Mark II Imaging Flow Cytometer, we found that the majority of cells belonging to the resistant cell lines respond to NK cell attack by local accumulation of actin near the IS. Furthermore, we show that actin accumulation is associated with a partial blocking of NK granules at the synapse and a reduced transfer of their cytolytic molecules to the target tumor cell. In addition actin accumulation is also accompanied by an increased density of MHC class 1 inhibitory ligands, HLA-ABC at the IS, a process which likely contributes to reduce tumor cell susceptibility to NK. Moreover, our data suggest that the ability of cancer cells to respond to NK attack by fast remodeling their actin cytoskeleton is associated with their EMT status. We extended these data by analyzing a large panel of breast cancer cells and showing that mesenchymal cells are significantly more resistant to NK-mediated cell death as compared to epithelial cells. Together our data suggest that the tumor cell actin cytoskeleton has to critical role in breast cancer cell escape from NK cell-mediated cell death. The identification of signaling pathways and actin regulators involved in these processes will allow to develop innovative strategies to revert cancer cell resistance to NKs.
Keywords: Actin cytoskeleton, natural killer, immune synapse, EMT, cytotoxicity, granzyme B November, 24th: 12:15 Antoun AL ABSI
[email protected] 3rd year of my PhD
44
Metagenomic assessment of the neonatal microbiome colonization Linda Wampach, Anna Heintz-Buschart, Shaman Narayanasamy, Malte Herold, Anne Kaysen, Angela Hogan, Lutz Bindl,
Jean Bottu, Carine de Beaufort and Paul Wilmes Perturbations to the colonization process of the human gastrointestinal tract induced by caesarean section delivery have been suggested to result in adverse health effects later in life. Although many studies focus on the microbial colonization and succession of the gastrointestinal microbiome during infancy, far less is known about the earliest time after delivery and the potential transfer of neonatal colonizers from mother to infant. Previously, we observed that fundamental differences in the microbiome were observable as early as 3 days after birth between delivery modes. In a follow-up study, we analyzed the gastrointestinal microbiome of 12 infants, either delivered vaginally or by caesarean section, on days 1, 3 and 5 after birth as well as the maternal vaginal and gastrointestinal microbiomes. This time, we applied high-throughput random shotgun sequencing (metagenomics), with specifically adapted methods to minimize the impact of potential contaminants. We observed again differences between both delivery modes as early as 3 days after birth. Furthermore, it was possible to link microbial populations between samples from mothers and infants in order to trace back the potential source of microbial colonization. To date, this is the earliest metagenomic assessment of the neonatal gastrointestinal microbiome. Keywords: Neonatal colonization, microbiome, metagenomics November, 24th: 14:45 Linda Wampach
[email protected] 4th year of my PhD
45
Towards understanding wetland ecohydrology from mapping evapotranspiration using satellite data
Wandera Nangira Loise, Kaniska Mallick
Remote Sensing and Eco-hydrological Modelling, Department ERIN, Luxembourg Institute of Science and Technology (LIST)
Wetlands as an ecosystem are continuously receiving recognition for their high biodiversity and for their important hydrological functions in groundwater recharge, nutrient cycling and flood alleviation. Hence these are important ecosystems that not only impact the regional hydrological cycle but also the surrounding ecological communities. The spectre of frequent drought and climate extremes might significantly alter the thermal regime of wetlands, which is expected to reflect the seasonal evapotranspiration (E) of these ecosystems. Large scale characterization wetland E is therefore critical to understand the integrated impact of environmental and ecohydrological factors in the evaporative depletion of the wetlands. Thermal remote sensing from Earth observation platforms has become the most significant method for estimating and monitoring spatially distributed E and water stress over the natural surfaces. Since E is an endothermic process, increasing E rates decrease the temperature of a surface and vice-versa. Based on the surface energy balance principle, the measurements of surface temperature with thermal infrared (TIR) sensors can be used to provide diagnostic assessments of E and surface moisture status without the need for additional information on precipitation or soil pedotransfer functions as commonly required in distributed hydrological models for E simulation. Retrospective maps of E highlight the water stressed pockets in an ecosystem, and with the further help of physically-based E models it could be possible to identify the probable feedbacks between wetland E and prevailing environmental as well as ecohydrological conditions. Here we demonstrate the conceptual framework of wetland E estimation using satellite data. Initially, we assess the efficiency of one prognostic and one diagnostic model for simulating E under varying seasonal conditions, spring and summer using ground observations before applying on satellite data. The preliminary results showed the models to produce good correlation (R2= 0.54 to 0.86) and acceptable agreement (RMSE 23 to 88 W m-2 The overall performance of the models appears to be promising for wetland E mapping using polar orbiting and geostationary satellites. Keywords: Earth observations, Evapotranspiration, Mapping, Wetlands November, 24th: 15:05 Loise Wandera
[email protected] 3rd year of my PhD
46
Constraint-based computational modelling of bioenergetic pathway switching in synaptic mitochondria from Parkinson’s disease patients
Diana C. El Assal, Caroline May, Peter Barbuti, Silvia Bolognin, Averina Nicolae, Fatima Monteiro, Lemmer R.P. El Assal, Swagatika Sahoo, Longfei Mao, Jens Schwamborn, Rejko Kruger, Ines Thiele, Katrin Marcus and Ronan M.T. Fleming
Degeneration of substantia nigra pars compacta dopaminergic neurons is one of the hallmarks of Parkinson’s disease. These neurons have a highly complex axonal arborisation and a high energy demand, so any reduction in ATP synthesis could lead to an imbalance between supply and demand, thereby impeding normal neuronal bioenergetic requirements. Synaptic mitochondria exhibit increased vulnerability to dysfunction in Parkinson’s disease. After biogenesis in and transport from the cell body, synaptic mitochondria become highly dependent upon oxidative phosphorylation. We applied a systems biochemistry approach to identify the metabolic pathways used by neuronal mitochondria for energy generation. The mitochondrial component of an existing manual reconstruction of human metabolism (Recon 2.04) was extended with manual curation of the biochemical literature and specialised using omics data from Parkinson’s disease patients and controls, to generate reconstructions of synaptic and asynaptic mitochondrial metabolism. These reconstructions were converted into stoichiometrically and flux-consistent constraint-based computational models. These models predict that Parkinson’s disease is accompanied by an increase in the rate of glycolysis and a decrease in the rate of oxidative phosphorylation within synaptic mitochondria. This is consistent with independent experimental reports of a compensatory switching of bioenergetic pathways in the striatum of post-mortem Parkinson’s disease patients. Ongoing work, in the context of the SysMedPD project (http://sysmedpd.eu) is aimed at computational prediction of mitochondrial drug targets to slow the progression of neurodegeneration in the subset of Parkinson’s disease patients with overt mitochondrial dysfunction. Keywords: Parkinson's disease; computational models; mitochondria; glycolysis; oxidative phosphorylation; synaptic November, 24th: 15:25 Diana C. El Assal
[email protected] 3rd year of my PhD
47
Identification of novel molecular targets for TMZ-based therapies against glioblastoma: A comprehensive shRNA-based screen of DNA Damage Response
factors Hélène Erasimus, Sabrina Fritah, Serge Haan, Barbara Klink, Petr V. Nazarov , Simone P. Niclou, Eric Van Dyck
Despite surgical resection and genotoxic treatment with ionizing radiation and the DNA alkylating agent temozolomide (TMZ), glioblastoma (GBM) remains one of the most lethal cancers, due in great part to the action of DNA repair factors that drive resistance and lead to tumor relapse. Important features of these mechanisms include the inherent redundancy and complexity of the many DNA repair pathways activated as part of the DNA damage response (DDR) to DNA damage. Understanding the molecular details of the DNA repair mechanisms that operate to remove lesions induced by TMZ and identifying novel pharmacological targets remains vital tasks to improve GBM treatment. Our experimental strategy to reach these goals consisted in large-scale, loss-of-function RNAi screens for DDR genes that are required for the survival of GBM cells to TMZ. Pooled shRNAs targeting more than 500 DDR genes were introduced into selected GBM-derived, cancer stem-like cells (CSCs), as well as into control non-cancer cells, followed by identification of the genes that appear essential to the survival of CSCs under TMZ treatment, but dispensable to non-cancer cells. Two major screens were carried out to reflect the clinical benefit conferred by epigenetic inactivation of the MGMT gene encoding a crucial factor for the repair of TMZ-induced lesions, on the response of GBM patients to TMZ – one with MGMT-positive cells and one where MGMT was depleted through pharmacological inhibition. The first goal has been reached and potential DDR targets that could sensitize cancer cells to TMZ have been identified. We are now validating very promising genes and we will elucidate the molecular mechanisms by which this gene operates to confer cellular resistance to TMZ. Keywords: Glioblastoma, DNA damage, chemoresistance November, 25th: 10:00 Hélène Erasimus
[email protected] 4th year of my PhD
48
Towards small-molecule therapies for a juvenile form of Batten disease Ursula Heins-Marroquin, Paul P. Jung, Alexander D. Crawford, Carole L. Linster
The ATP13A2/PARK9/CLN12 gene encodes a lysosomal P5-type ATPase and several mutations in this gene lead to an autosomal recessive form of early-onset Parkinsonism, called Kufor-Rakeb syndrome (KRS). Recently, the mutation c.2429C>G in exon 22 of ATP13A2 was identified in members of a Belgian family diagnosed with neuronal ceroid lipofuscinosis (NCL), also known as Batten disease. The link between KRS and NCL pathogenesis is further supported by studies in animal models, but the exact molecular mechanism of ATP13A2 function in the disease pathogenesis is not understood. For this reason, we launched functional studies for the ATP13A2 protein, mainly in the context of the juvenile form of NCL (JNCL). ATP13A2 is highly conserved across multiple species, suggesting an important role in a fundamental biological process. We have developed disease models for the ATP13A2 form of Batten disease in budding yeast and zebrafish. The results already obtained with these models point at an implication of ATP13A2 in heavy metal resistance, with potentially different pathways involved for different types of metal. In parallel, we aim to exploit the combination of both models for a more rapid identification of bioactive compounds with therapeutic potential as orphan drug candidates for JNCL. Keywords: ATP13A2, CLN12, Batten disease, Kufor-Rakeb syndrome, Metal homeostasis, yeast, zebrafish November, 25th: 10:20 Ursula Heins Marroquin
[email protected] 2nd year of my PhD
49
Characterisation of two protein repair enzymes and their effect on calcium signalling
Remon Soliman and Carole Linster Under physiological conditions, aspartyl and asparaginyl residues in protein are prone to spontaneous isomerization leading to formation of isoaspartyl residues that, in turn, may generate conformational change, loss of function and enhanced protein degradation. Protein L-isoaspartyl methyltransferase (PCMT1) is a repair enzyme that specifically recognizes isoaspartyl residues and initiates their conversion to aspartate. Although the catalytic function of PCMT1 is known, many of its physiological implications are not well understood. Interestingly, homozygous deletion of PCMT1 gene in mice leads to massive seizure events and eventually to a premature death. Zebrafish is a well-established model organism for developmental biology, and also for investigations of neurological disorders such as epilepsy. During its evolution, zebrafish has undergone a genome duplication leading to two orthologs of PCMT1, namely PCMT and PCMT-like. In this study, we used a morpholinos-based strategy to knockdown both PCMT and PCMT-like genes in order to obtain a better overview of the physiological function(s) of the PCMT, notably at the brain level. Whereas electroencephalography analysis did not show any statistical difference between morphant and control larvae, calcium flux (another indicator of seizures) showed strong impairment in the brain of morphants only. Similar results were obtained through analysis of mammalian HT22 cells where the PCMT1 gene was knocked-out. These results clearly show a trade-off between PCMT1 function and calcium signalling. Hence, as calcium homeostasis and regulated calcium signalling pathways are prerequisite for normal brain function, repair PIMT-dependant mechanism seems to be a keystone to avoid calcium-related neurological disorders.
Keywords: Isoaspartyl, protein damage, zebrafish, calcium signalling
November, 25th: 11:15 Remon Soliman [email protected]
4th year of my PhD
50
Data-driven development in the smart city. Generative design for refugees camps in Luxembourg.
Elie Daher, Sylvain Kubicki, Annie Guerriero The talk will be presenting a result of a research addressing computational design as a key technological asset in the development of the smart city. In particular, the research targets context-aware adaptation to usage requirements at urban fragment level. Indeed, cities’ policy makers have to take into account many factors in a development policy, such as situational, technical or human-related factors as well anticipating future usages. Moreover, nowadays cities are key resources to answer growing humanitarian needs in term of sheltering and camps. Indeed they are increasing due to different factors related to nature or human activities. This is true also in Luxembourg, where a 2016’s public program aims to develop three container villages. The objective of this work is to help policy makers and humanitarian people in the optimization of the spatial design of camps. The use of parametric modeling approach enables the optimization of space layout planning. It is applied on a case study allowing policy makers to explore scenarios for the decision-making in the camp space planning. Keywords: Parametric modeling, generative design, humanitarian needs, data-driven design November, 25th: 11:35 Elie Daher
[email protected] 1st year of my PhD
51
Integrated multi-omics for understanding niche ecology of distinct populations in microbial consortia
Malte Herold, Emilie L. Mueller, Shaman Narayanasamy, Patrick May, Anna Heintz-Buschart, Paul Wilmes Microbial communities are ubiquitous and are primarily shaped by the niche breadths of their constituent populations. However, a detailed understanding of niche ecology is typically lacking. Integrated multi-omic analyses offer the prospect of resolving fundamental and realised niches in situ. We have recently developed a suite of wet- and dry-lab methods, which allow the systematic molecular characterisation of microbial consortia to allow unprecedented deep insights into microbial community structure and function. Here, we apply these methods to resolve resource usage by distinct microbial populations within lipid accumulating microbial consortia sampled from the surface of an anoxic tank of a biological wastewater treatment plant over weekly timeframes. The application of state-of-the-art reference-independent binning approaches to the metagenomic data enabled the reconstruction of population-level genomes which provide a platform for integration of functional omics data, i.e. the metatranscriptomes, metaproteomes and (meta )metabolome. Using these approaches, we were able to track patterns of gene expressions and resource usage of distinct populations over time and link the observed patterns to overall community dynamics. This allowed unprecedented insights into the niche ecology of constituent populations which is fundamental to our understanding of community dynamics. Keywords: microbial communities, niche ecology, meta-transcriptomics, meta-genomics November, 25th: 11:55 Malte Herold
[email protected] 2nd year of my PhD
52
Detection, characterization and function of extracellular vesicles in resistant melanoma
G. Cesi1, D. Philippidou1, F. Bernardin2, Y.J.Kim2, Guillaume Van Niel3 and S. Kreis1
1Signal Transduction Laboratory, Life Sciences Research Unit, Faculty of Science, Technology and Communication, University of Luxemburg,
2Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health, Luxembourg, Luxembourg 3Institut Curie, Paris, France
Extracellular vesicles are nano-sized structures that are released by all cell types under both physiological and pathological conditions. It has been shown that different diseases can induce specific changes in the levels of extracellular vesicles secretion so that different amounts and/or different content profiles can be studied and potentially used as biomarkers. As extracellular vesicles can be released by “donor” cells and taken up by “recipient” cells, it has been hypothesized that they are important players in influencing key biological functions by delivering and transporting cytokines, growth factors, proteins, mRNAs and microRNAs. Recently, extracellular vesicles have also been identified as new messengers in transferring drug resistance to still sensitive or “drug-naïve” cells. In melanoma patients, drug resistance is a pressing clinical problem. Despite the promising initial results obtained with vemurafenib and dabrafenib (BRAF kinase inhibitors) in the clinic, it soon became evident that these molecules were not able to provide durable responses, as resistance to treatment soon develops within months in almost all patients. The aim of my project is to understand the potential involvement of extracellular vesicles in the “spreading” of drug resistance. The content of the extracellular vesicles released by melanoma cells and their corresponding cells that have been made drug resistant will be analyzed. Preliminary results show that sensitive melanoma cells acquire the drug resistant phenotype if co-cultured with extracellular vesicles released by resistant cells. This suggests an involvement of extracellular vesicles in propagating important tumorigenic properties. Keywords: extracellular vesicles, melanoma, drug resistance November, 25th: 12:15 Giulia Cesi
[email protected] 4th year of my PhD
53
Identification of risk factors for Parkinson’s disease by the means of large-scale genomic analysis.
Dheeraj Reddy Bobbili To unravel the genetic factors besides the known PD genes such as LRRK2 gene for autosomal dominant and PARK2 gene for autosomal recessive PD, we used a 2 stage approach. We used the whole genome sequencing data available from 17 one-generational pedigrees as a discovery cohort and the whole exome sequencing data available as a part of Parkinson Progression Markers Initiative (PPMI) as a replication cohort. We identified genes harboring rare, deleterious variants that are segregating with disease in the familial data and also showing significantly higher burden in the PD cases from PPMI data. Keywords: Genetics, parkinson, rare variants November, 25th: 14:45 Dheeraj Reddy Bobbili
[email protected] 3rd year of my PhD
54
Metabolic requirements of induced pluripotent stem cell derived dopaminergic neurons
F. L. Monteiro , A. Nicolae, C. Gulersonmez , E. Lucumi Moreno , Z. Zhang, D. El Assal, M. Oliveira, A. Harms , I. Thiele, E. Glaab, T. Hankemeier and R. M. T. Fleming
A hallmark of Parkinson's disease (PD) is degeneration of nigrostriatal dopaminergic neurons (DN), but the biochemical mechanisms underlying dopaminergic neuronal death in PD are not completely understood. Dopaminergic neurons derived from induced pluripotent stem cells (iPSCs) represent a promising platform for studying the neuronal metabolism in vitro. Exchange of metabolites can be evaluated by measuring the changes in the cultivation media caused by substrate uptake and product secretion. Due to the heterogeneous nature of the iPSC-derived DN cell culture, it is difficult to assign the observed changes to a particular cell type. To evaluate which observations are specific to DN metabolism, condition-specific genome-scale metabolic models of an iPSC-derived DN and a mixed cell culture containing DN are generated. The workflow involves several steps: (1) build a network reconstruction based on omics data from iPSC-derived DN cultures; (2) include information on manually curated genes and reactions; (3) convert a generic reconstruction into a computational model using a generic human reconstruction as template; (4) apply media composition constraints to the metabolic models to simulate the experimental conditions (context-specific model); (5) analyse the resulting model with COBRA toolbox methods using a set of functions implementing biochemical functionality and network property testing. Following iterative rounds of reconstruction, model prediction and experimental testing and refinement, metabolite uptake and secretion rates were predicted, compared with exometabolomics measurements. Keywords: iPSC-derived Dopaminergic neurons, exometabolomics, COBRA November, 25th:15:05 Fatima Liliana Monteiro
[email protected] 3rd year of my PhD
55
A novel approach to derive human midbrain-specific organoids from
neuroepithelial stem cells
Anna S Monzel1, Lisa M Smits1, Kathrin Hemmer1, Siham Hachi2, Edinson Lucumi Moreno2, Thea van Wuellen1, Ronan M Fleming2, Silvia Bolognin1, Jens C Schwamborn1,3 1Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Developmental and Cellular Biology, Esch-Belval, Luxembourg, 2Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Systems Biochemistry, Esch-Belval, Luxembourg, 3Correspondence: Jens C. Schwamborn, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
Research on human brain development and neurological diseases is limited by the lack of advanced experimental in vitro models that truly recapitulate the complexity of the human brain. Although animal models most closely recapitulate human physiology, they often fail to model neurodevelopmental and neurodegenerative disorders, and the success rate of clinical trials based on these models has been disappointing. Here, we show a novel and robust human brain organoid system that is highly specific to the midbrain, and which is derived from regionally patterned neuroepithelial stem cells. The midbrain organoid system has the potential to be used for advanced in vitro disease modeling and therapy development. Keywords: midbrain organoids, 3D culture, stem cells
November, 25th:15:25 Anna Monzel
[email protected] 1st year of my PhD
56
Mitochondrial phenotypes of the A30P mutation in alpha-synuclein gene patient-derived cellular model of Parkinson’s disease
Bruno Santos, Peter Barbuti, Ibrahim Boussaad, Andreas Hummel, Rejko Krüger In this study, we aim to generate and characterise patient-derived midbrain dopaminergic neurons (mDANs) of a carrier of the A30P mutation in the alpha-synuclein (SNCA) gene causing autosomal dominantly inherited Parkinson’s disease (PD). Our goal is to establish A30P-alpha-synuclein-associated phenotypes, with focus on mitochondria, which could be addressed on a comprehensive imaging-based HCS/HTS on our automated system. In 1998, our group discovered one of these point mutations of SNCA, an Alanine to Proline mutation at position 30 (A30P). This was confirmed upon autopsy with the presence of Lewy Bodies, Lewy neurites and abundant alpha-synuclein aggregates. We generated a patient-derived cellular model of SNCA with the A30P point mutation, by obtaining fibroblasts from the index patient, an age-matched gender-matched non-PD control, and the unaffected brother of the patient. We reprogrammed these fibroblasts using retroviruses, and generated induced pluripotent stem cells (iPSCs). From these iPSCs, we used small molecules to differentiate these iPSCs into neural precursor cells (smNPCs), and then further differentiated these cells into mDANs. These generated mDANs were then used to assess the mitochondria effects from A30P α-syn. We successfully obtained enriched cultures of ≥85% neurons (CD200+/CD49f-) when analysed using FACS. From these, approximately 20% were confirmed by immunocytochemistry as being midbrain (FoxA2+) dopaminergic (TH+), and demonstrate the capability to actively fire and release dopamine, all characteristics of a good model for PD. We were also able to identify mitochondria respiration impairment, and a reduced protein level of some complexes on the patient cells. We were able to generate a robust, repeatable, standardised model for the A30P familial case of PD. Mitochondria phenotypic differences were identified and consistently obtained, and can now be integrated on our automated image-based HCS/HTS system.
Keywords: alpha-synuclein, Parkinson Diesease, Mitochondria, iPSCs, mDANs November, 25th: 16:15 Bruno Filipe Rodrigues Santos
[email protected] 2nd year of my PhD
57
Stress modulated bulkphotovoltaic effect in Transition metal doped Lithium Niobate
Shankari Nadupalli, Torsten Granzow When a ferroelectric is homogeneously illuminated with a specific wavelength range, a steady state photo current can be observed, even without any interfaces present in the system. This, so called Bulk photovoltaic effect (BPVE) relies on the non-centrosymmetry of the ferroelectric crystal. Iron doped lithium niobate (Fe: LiNbO3) is a prototypical material for the BPVE. The opto-electronic excitation originates from the donor-dopant center (Fe) in LiNbO3 to the nearest Nb small free polaron, stimulating a non-thermalized ballistic transport of charge through the crystal, until it thermalizes in the span of 10^-13 s. A model has been proposed [1] for Fe: LiNbO3 on non-isotropic excitation of Fe2+ to NbNb5+. However the contributions of factors that affect the BPVE and electron charge transport mechanism are not entirely understood. The objective of this talk is to focus on identifying factors that are at the origin of the BPVE, i.e. donor center absorption, focusing more on the contribution of interatomic distances and polaronic charge transport both which are susceptible to mechanical stress. The contribution of the interatomic distances will be explained via stress modulation of BPVE constants which also reflect in the XRD spectra; and the NbNb5+ polaron charge transport will be discussed by understanding the shift of the polaron energy via Raman spectroscopy under uniaxial stress. The mechanism of electron transition probability in Fe:LiNbO3 will further be discussed based on the above results. [1] O. Schirmer et al., Phys. Rev. B 83, 165106 (2011). Keywords: Bulk photovoltaic effect, charge transport, Polarons, Lithium Niobate November, 25th: 16:35 Shankari Nadupalli
[email protected] 3rd year of my PhD
58
Posters
4th Year Posters
1. The tumor suppressor Testin is a centrosomal and midbody protein involved in cytokinesis
Coralie Mazzacavallo
2. The PD patient specific genetic background complements LRRK2-G2019S pathogenesis in hNESC
Sarah Nickels
3. LRRK2-G2019S related Parkinson's disease modelling with CRISPR-Cas9 and hiPS
Xiaobing Qing
4. Effect of STAT-activating cytokines on the mRNA transcriptome and miRNome of non-neoplastic and cancerous colon-, liver- and skin-derived cell lines
Florence Servais
5. The actin binding protein Tes goes to the nucleus Raffaella Vaccaroli
3rd Year Posters
6. Tumor actin cytoskeleton remodeling: a novel mechanism for cancer cells to escape from natural killer cell-mediated cell death
Antoun Al Absi
7. Exploring Therapeutic Value of the Candidate Drug Target Regulator of G-Protein Signalling 4 (RGS4) for Parkinson’s Disease
Amer Ashrafi
8. Metagenomic Integration and Computational Modeling of Microbial Community Metabolism in Crohn’s Disease
Eugen Bauer
9. Identification of risk factors for Parkinson’s disease by the means of large-scale genomic analysis
Dheeraj Reddy Bobbili
10. Influence of pesticide toxicokinetic parameters on the association between plasma and hair concentration
Caroline Chata
11. Impact of neonatal maternal separation on neuropathic pain behaviour and spinal nociceptive processing -a support of the mismatch hypothesis?
Genty Julien
12. Bulk Photovoltaic effect in Transition Metal doped polar oxide ceramics Shankari Nadupalli
13. Characterization of the Immune Mechanisms Involved in Microglia Activation
Carole Lara Veiga De Sousa
14. Linear Dynamic Network Reconstruction from Heterogeneous Datasets Zuogong Yue
59
2nd Year Posters
15. A multi-scale model of melanoma growth Marco Albrecht
16. Study-driven bias effects on disease-specific network extraction Ganna Androsova
17. Impact of DNA repair on GBM biology and resistance to Temozolomide: DNA repair gene expression study in patient biopsies
Matthieu Gobin
18. A study of the molecular mechanisms underlying the response of human colorectal adenocarcinoma enterocytes to prebiotics and probiotics
Kacy Greenhalgh
19. Decoding Calcium signals, new perspective on single cell dynamics. Kamil Grzyb
20. Double mutant GBA-PARK2 patient-derived cellular models to study the effects of GBA as a modifier of familial Parkinson’s disease
Zoé Hanss
21. Evaluation of zebrafish as a potential model for comorbidities associated with Dravet syndrome
Maxime Jacmin
22. Diabetic multi-scale model predicts drug metabolism at the whole-body level
Patricia Martins Conde
23. Midbrain organoids as a model to study Parkinson's disease Lisa Smits
1st Year Posters
24. Characterization of CD8 T cells during HIV infection using 18 color flow cytometry
Philipp Adams
25. PerMET: Creating and simulating personalized intestinal community metabolic models through metagenomics data integration
Federico Baldini
26. Data-driven development in the smart city. Generative design for refugees camps in Luxembourg.
Elie Daher
27. Mechanisms of acquired resistance to BRAF kinase inhibitors in melanoma Ines Kozar
28. Patient-derived cellular model of the D620N mutation of VPS35 (PARK17) Simone Larsen
29. Molecular and functional characterization of the unconventional interaction partners of CXCR7 and their role in virus-associated tumorigenesis
Max Meyrath
60
The tumor suppressor Testin is a centrosomal and midbody protein involved in cytokinesis
C.Mazzacavallo, E.Hadzic, A.Maiser, C.Laurini, M.Catillon, M.Koffa, S.Haan and C.Ampe
Tes is a LIM domain protein which has been described as a potential tumor suppressor. Tes is also a scaffold protein and has partners such as zyxin, talin and other actin regulatory proteins. Tes localizes to focal adhesions and stress fibers, where it participates in the regulation of the actin cytoskeleton, thereby playing a role in cell spreading and motility. Recently, we describe a novel cellular localization of Tes that occurs in cell division process. We show that during early stages of mitosis, Tes localizes in centrosomes. In anaphase, Tes localizes in the midzone and in late telophase and cytokinesis Tes localizes to the central part of the midbody which corresponds to an intercellular bridge composed of overlapping and antiparallel microtubules. Originating from the mitotic spindle, this bridge results from the tightening of the contractile, actin filament ring. Using structured illumination microscopy, we have shown that Tes localizes to the bulge of the midbody. Using RNAi as well as overexpression experiments in combination with live imaging, we have assessed the role of Tes during mitosis. Keywords: Cytoskeleton, Testin, mitosisl midbody
Coralie Mazzacavallo [email protected]
4th year of my PhD Poster number: 1
61
The PD patient specific genetic background complements LRRK2-G2019S pathogenesis in hNESC
S.L. Nickels, J. Walter, X. Qing, J. Jarazo, D. Gerard, P. Antony, A. Ginolhac, L. Sinkkonen, T. Sauter, J. C. Schwamborn Parkinson’s disease (PD) is a complex progressive incurable neurodegenerative disorder with multiple genetic predispositions. The most prevalent mutation, LRRK2-G2019S, is linked to familial and sporadic PD and different polymorphisms are associated with its age of onset. LRRK2-G2019S has, amongst other, been linked to impaired neurogenesis. Because of the multiple origins of PD, the incomplete penetrance of LRRK2-G2019S and the high variability of its phenotypes, we hypothesize that modifiers within the PD genetic background of neural stem cells act as susceptibility factors for developing PD. To address the question about LRRK2-G2019S pathogenicity we used 17 different iPSC-derived neuroepithelial stem cell lines originating from human patients or healthy donors. Isogenic control lines are used to differ between LRRK2-G2019S dependent and genetic background specific phenotypes. We could demonstrate that LRRK2-G2019S indeed leads to neural stem cell deregulations. Patient lines are altered in cell death, mitosis, and αSYN and Tau protein expression. Interestingly, these changes are only partly LRRK2-G2019S dependent, highlighting the contribution of the PD genetic background. Transcriptomic analysis identified different genes that might act as genetic modifiers responsible for the observed phenotypes. One of the genes showed promising effects on rescuing increased cell death and decreased mitosis. We conclude that there are susceptibility factor, within the PD genetic background that could potentially be used as a new target for early diagnosis and treatment strategies in PD. Keywords: Parkinson’s disease, LRRK2-G2019S, Neural stem cells, Genetic background, Susceptibility factors
Sarah Nickels [email protected]
3rd year of my PhD Poster number: 2
62
LRRK2-G2019S related Parkinson's disease modelling with CRISPR-Cas9 and hiPS Xiaobing QING, Jens Schwamborn
The dominant G2019S mutation of Leucine-Rich Repeat Kinase 2 (LRRK2) is related to Parkinson’s Disease (PD). To further study the pathologies of LRRK2-G2019S, here we introduced this point mutation into wildtype human induced pluripotent stem cells (hiPSCs) using CRISPR-Cas9 together with piggyBac. Unlike CRE-LoxP, which will leave 34bp exogenous nucleotides after excision, piggyBac can remove the selection cassette by over-expressing transposase without leaving any exogenous nucleotide. Dopaminergic (DA) neurons differentiated from LRRK2-G2019S hiPSCs showed decreased neurites length and complexity compared to the DAs from wildtype hiPSCs. These PD-related phenotypes can be rescued by conditionally inhibiting LRRK2 kinase activity. These findings based on genome edited hiPS in vitro model confirm LRRK2-G2019S mutation's effects on the DAs and provide new insights into PD therapy. Keywords: CRISPR, piggyBac, mDA, LRRK2-G2019S
Xiaobing Qing [email protected]
4th year of my PhD Poster number: 3
63
Effect of STAT-activating cytokines on the mRNA transcriptome and miRNome of non-neoplastic and cancerous colon-, liver- and skin-derived cell lines
Servais, F; Kirchmeyer, M; Philippidou, D; Margue, C; Hamdorf, M; Haan, C; Nazarov, P; Vallar, L; Casper, M; Glanemann M; Lammert, F; Kreis, S; Behrmann, I
IL-6 plays important roles in the regulation of liver functions and the development of hepatocellular carcinoma (HCC), the most common primary liver cancer. As the contribution of IL-6-induced miRNAs to these effects is largely unknown, we studied the effects of IL-6 on the miRNome of hepatoma cell lines and primary human hepatocytes. Although IL-6 (and Hyper-IL-6) induces the differential expression of many (65) miRNAs in primary hepatocytes, only very few miRNAs change their expression level significantly in HepG2 and HuH-7 hepatoma cell lines. In contrast, we have previously observed that Interferon-γ (IFN-γ) has a profound effect on the miRNome of melanoma cells (Schmitt et al., Cell Comm. Sign. 2012). To further investigate possible cytokine-, cell type- and/or tissue-specificities, we analyzed by microarray the effects of STAT1 and STAT3-activating cytokines (IFN-γ and IL-27 / Hyper-IL-6 and OSM) on both the miRNome and mRNA transcriptome of non-neoplastic and cancerous cell lines, derived from human liver, colon and skin. In general, miRNA samples show a higher variability than mRNA samples. Differences between arrays is mostly caused by cell-type effects rather than cytokine-mediated effects which only play a minor role, as reflected on the global clustering patterns. We could show that STAT1-activating cytokines IFN-γ and IL-27 have a stronger “general” effect on the different cell types, i.e. they strongly upregulated a similar set of genes in a broad range of cells. In contrast, the effects of STAT3-activating cytokines HIL-6 and OSM seem to be more restricted to particular cell types. The regulation and roles of selected JAK/STAT-related miRNAs with potential relevance for HCC are currently further analyzed, as well as the characterization of cell-type dependent or independent STAT1- and/or STAT3-regulated miRNAs. Keywords: Cytokine, JAK/STAT, Microarray, miRNA, mRNA
Florence Servais [email protected]
4th year of my PhD Poster number: 4
64
The actin binding protein Tes goes to the nucleus Raffaella Vaccaroli*, Marie Catillon*, Ilona Kesisova*, Ermin Hadzic**, Aliaksandr Halavatyi**, , Elisabeth Schaffner-
Reckinger*, Christophe Ampe***, Maria Koffa* Tes is a LIM domain protein that has been described as a potential tumor suppressor, as well as an actor in the regulation of the actin cytoskeleton. In the cytoplasm, Tes is involved in different cellular processes and has been linked to cell migration, cell spreading as well as the regulation of the actin cytoskeleton. Similar to other actin-binding proteins, Tes shuttles between the cytoplasm and the nucleus. While different functions have been associated with Tes in the cytoplasm, its nuclear function and import-export mechanism is presently not understood. Here, we provide evidence that Tes is able to undergo nucleo-cytoplasmic transport via a CRM1 exportin-dependent mechanism. Using fluorescence microscopy, we identified and characterized a nuclear export signal (NES) at the N-terminus of Tes, suggesting that its nuclear export is an active mechanism. Immunoprecipitation studies together with quantitative mass spectrometry have shown that that Tes is submitted to a classical import mechanism relying on Importin α and β transport receptors and dependent on Ran GTPase. Moreover we have identified a nuclear localization signal (NLS) within the PET domain of the protein. Collectively, these findings allowed us to gain new insight about nucleo-cytoplasmic shuttling of Tes. However, as for many others actin binding protein capable to localize in the nucleus, Tes nuclear function is still not described. Keywords: Actin, Nuclear actin binding protein, Cytoskeleton, Nuclear transport
Raffaella Vaccaroli [email protected]
4th year of my PhD Poster number: 5
65
Tumor actin cytoskeleton remodeling: a novel mechanism for cancer cells to escape from natural killer cell-mediated cell death
Antoun Al Absi, Coralie Guerin, Céline Hoffmann, Xianqing Mao, Flora Moreau, Salem Chouaib, Guy Berchem, Bassam Janji, Clément Thomas
Tumor actin cytoskeleton remodeling: a novel mechanism for cancer cells to escape from natural killer cell-mediated cell death Natural killers cells (NKs) are effectors of the innate immune system that destroy cancer cells through the directed secretion of granzyme B and perforin. This process requires the formation of a specialized cell-cell interaction region termed the immune synapse (IS). Previous reports have established that the formation of the IS largely rely on sequential rearrangement of actin filaments within NKs. In contrast, there is a gap of knowledge regarding the organization and role of the tumor cell actin cytoskeleton during NK attack. We showed that actin of NK-resistant tumor cells accumulate at the IS. Using the high-throughput ImageStream®X Mark II Imaging Flow Cytometer, we found that the majority of cells belonging to the resistant cell lines respond to NK cell attack by local accumulation of actin near the IS. Furthermore, we show that actin accumulation is associated with a partial blocking of NK granules at the synapse and a reduced transfer of their cytolytic molecules to the target tumor cell. In addition actin accumulation is also accompanied by an increased density of MHC class 1 inhibitory ligands, HLA-ABC at the IS, a process which likely contributes to reduce tumor cell susceptibility to NK. Moreover, our data suggest that the ability of cancer cells to respond to NK attack by fast remodeling their actin cytoskeleton is associated with their EMT status. We extended these data by analyzing a large panel of breast cancer cells and showing that mesenchymal cells are significantly more resistant to NK-mediated cell death as compared to epithelial cells. Together our data suggest that the tumor cell actin cytoskeleton has to critical role in breast cancer cell escape from NK cell-mediated cell death. The identification of signaling pathways and actin regulators involved in these processes will allow to develop innovative strategies to revert cancer cell resistance to NKs.
Keywords: Actin cytoskeleton, natural killer, immune synapse, EMT, cytotoxicity, granzyme B
Antoun AL ABSI [email protected]
3rd year of my PhD Poster number: 6
66
Exploring Therapeutic Value of the Candidate Drug Target Regulator of G-Protein Signalling 4 (RGS4) for Parkinson’s Disease
Amer Ashrafi, Pierre Garcia, Heike Kollmus, Klaus Schughart, Manuel Buttini, Enrico Glaab Parkinson's disease (PD) is one of the most frequent age-related neurodegenerative disorders and represents a major economic and social burden for health care systems in aging societies. Although existing drug therapies, focusing on restoring dopamine levels in the brain reduced due to neurodegeneration, can alleviate some of the main symptoms, a gradual loss of efficacy and several adverse effects limit their utility. Non-dopaminergic protein drug targets are therefore being investigated to develop adjuvant treatments for currently insufficiently or inadequately addressed symptoms of PD. One of the recently proposed candidate targets is RGS4, a regulator of G-protein signalling-4 involved in the control of striatal long-term depression. A study shows that mice lacking RGS4 were less impaired in the 6-OHDA model of Parkinson’s disease (Lerner et al., 2012), suggesting it as an effective potential target of non-dopaminergic strategy for treating PD. The use of the 6-OHDA mouse model allows us to well characterize RGS4 and validate it as a putative target in PD in ultimate goal of developing and validating the neuroprotective effect of new selective RGS4-inhibiting experimental therapeutics Keywords: Parkinson's disease, non-dopaminergic, RGS4, 6-OHDA mouse model
Amer Ashrafi [email protected]
3rd year of my PhD Poster number: 7
67
Metagenomic Integration and Computational Modeling of Microbial Community Metabolism in Crohn’s Disease
Eugen Bauer and Ines Thiele Most microbiota-associated diseases, such as Crohn’s disease (CD), are connected to an ecological imbalance of the underlying microbial community, consisting of hundreds of different species [1]. Systems biology approaches are promising to investigate the metabolic interactions between gut microbes in a systematic manner to unravel novel mechanistic insights in these complex diseases. In this study, we create patient-specific computational models of the gut microbiota to evaluate differences between healthy controls and CD patients. We retrieved publicly available metagenomic sequence reads of healthy individuals and CD patients from a previous study [1]. The reads were mapped onto a predefined set of 321 microbial genomes [2] to create an abundance profile for each microbe. Metabolic reconstructions were retrieved from a collection of experimentally refined and validated models. To simulate metabolic interactions, the models were integrated in an agent-based-modeling framework [3], representing microbes as replicating individuals, dynamically changing spatial metabolite concentration by secretion and absorption. The initial number of individuals per microbe was scaled according to their mapped abundance, thus creating personalized microbiota models of each human individual. Different diets were simulated by adding initial compound concentrations of daily intake. Microbiota and concentration dynamics were simulated for 12 hours and subsequently analyzed. The microbe abundance after simulation reflected differences between the healthy controls and the CD patients. Furthermore, the metabolite concentrations, emerged from the interactions within the microbes, were indicative for the differences between the healthy and disease group. Throughout the simulation, the ecological interactions between species increased, leading to a complex metabolic exchange between the microbes. The combination of metagenomic data with metabolic models results in personalized microbiota models which show several emergent properties: First, a metabolic profile of the community can be simulated and second, the interaction profile of each microbiota can be assessed. Our analysis framework could be applied for various sequencing data to gain new ecological insights. 1. Qin, J., et al., A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 2010. 464(7285): p. 59-65. 2. Bauer, E., et al., Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Microbiome, 2015. 3(1): p. 1-13. 3. Bauer, E. and J. Zimmermann. BacArena: Modeling Framework for Cellular Communities in their Environments. 2016; Available from: https://cran.r-project.org/web/packages/BacArena/.
Keywords: Microbiome, Crohn's disease, Metabolic interactions, Systems biology, Metagenomics
Eugen Bauer [email protected]
3rd year of my PhD Poster number: 8
68
Identification of risk factors for Parkinson’s disease by the means of large-scale genomic analysis.
Dheeraj Reddy Bobbili To unravel the genetic factors besides the known PD genes such as LRRK2 gene for autosomal dominant and PARK2 gene for autosomal recessive PD, we used a 2 stage approach. We used the whole genome sequencing data available from 17 one-generational pedigrees as a discovery cohort and the whole exome sequencing data available as a part of Parkinson Progression Markers Initiative (PPMI) as a replication cohort. We identified genes harboring rare, deleterious variants that are segregating with disease in the familial data and also showing significantly higher burden in the PD cases from PPMI data. Keywords: Genetics, parkinson, rare variants November, 25th: 14:45 Dheeraj Reddy Bobbili
[email protected] 3rd year of my PhD
Poster number: 9
69
Influence of pesticide toxicokinetic parameters on the association between plasma and hair concentration
Chata C, Hardy EM, Grova N, Palazzi P, Emond C, Appenzeller BMR Aims: Mainly used for the detection of medical and illicit drugs, hair analysis is increasingly used for the assessment of human exposure to pollutants thanks to recent progresses in analytical techniques which allowed the detection of low levels of concentration. Although the relationship between chemicals intake and resulting concentration in hair remains incompletely elucidated, the transfer from blood to hair bulb is generally considered the main route of incorporation in hair. Mechanisms of absorption, distribution and metabolization into blood should modulate the transfer of chemicals depending on their toxicokinetic parameters, resulting in different “blood to hair concentration” ratios. The present work investigated the correlation between “blood and hair concentration” and “toxicokinetic parameters” of more than twenty pesticides from different chemical classes in animal models submitted to controlled exposure. Methods: Two animal experiments were performed on the same strain (Lister Hooded). The first one was conducted to observe the relationship between hair and blood concentration. Hence, rats were administered pesticides by gavage over a 90 days-period, 3 times per week, at 7 different levels plus one control group. Each level of exposure consisted of n=8 animals. Animals’ hair was collected at the end of the experiment by shaving. The second one provided toxicokinetic parameters of pesticides into blood. Rats were administered pesticides by gavage of a single dose and blood was sampled at different times using a catheter in the caudal vein. Toxicokinetic was established with 20 different time points with a 12-repetition for each in order to reduce individual variability. After hair sample decontamination, pulverization and extraction, both parents and metabolites were analyzed by GC-MS/MS. Blood was immediately turned into plasma, and after extraction, the same compounds were analyzed also by GC-MS/MS. Results: The data obtained for all the investigated compounds demonstrated significant association between plasma and hair concentrations (P value of 2.97E-45 and Rpearson of 0.875), with the exception of 3 outliers. For all the target compounds, toxicokinetic parameters (such as Cmax, tmax, Cmin, elimination half-life, area under the curve) were investigated in order to understand the influence of these parameters on the association between plasma and hair concentration. Conclusions: Our results support that the concentration of chemicals in hair depends on the respective concentration in plasma and suggest that for most pesticides, the transfer from blood to hair would not represent a limiting step in the incorporation and that toxicokinetic parameters influence hair incorporation. Keywords: Hair Plasma Toxicokinetic
Caroline Chata [email protected]
3rd year of my PhD Poster number: 10
70
Impact of neonatal maternal separation on neuropathic pain behaviour and spinal nociceptive processing -a support of the mismatch hypothesis?
Genty J, Anton F, HaneschU Aim of investigation Aversive early life (AEL) events lead to long-term alterations of neural and immune systems and may predispose individuals to pain processing dysfunctions. Neuropathic pain is a debilitating condition occurring after nerve damage and presents a substantial comorbidity with psychiatric disorders. We assessed the impact of AEL on neuropathic pain and the expression of nociceptionrelated spinal biomarkers in adult rats. Methods AEL was induced with Maternal Separation (MS) after birth. At adult age, noxious sensitivity was tested during normal and neuropathic condition induced by Chronic Constriction Injury (CCI). Then, animal were sacrificed and spinal cord levels L4-L5 were removed, total RNA was extracted, and RT-qPCR was performed. Results MS per se had no impact on pain thresholds. However, animals undergoing MS were less sensitive to mechanical and thermal stimulation after CCI. MS up-regulated NMDA receptor sub-unit and the EAAT3 transporter mRNAs. 21 days after surgery, their levels were slightly decreased in CCI group but not in MS+CCI. EAAT2 and GFAP expression were unchanged. Iba1 levels were decreased. In both glial cell types, CCI provoked an increased expression of markers which was reduced in MS animals. MS alone slightly reduced IL-1β mRNA levels but had no influence on IL- 6 expression. For both cytokines, mRNA levels were upregulated following CCI. In animals undergoing MS, this increase was delayed for IL-1β but no difference could be detected for IL-6. MS prevented GDNF mRNA decrease seen after CCI. Interestingly, in CCI+MS the initially CCIdriven NGF increase shortly after CCI was prevented as well as the later decrease at d21. Conclusions Behavioural data show that AEL protects from neuropathy-induced noxious hypersensitivity. This is supported by the alterations in mRNA expression profiles of mediators involved in pain transmission. Indeed, spinal biochemical marker expression could, at least to some extent, explain the changes in pain behaviour.
Keywords: Early life stress, chronic constriction injury, nociception
Genty Julien [email protected] 3rd year of my PhD
Poster number: 11
71
Bulk Photovoltaic effect in Transition Metal doped polar oxide ceramics Shankari Nadupalli* , Torsten Granzow
One of the most fundamental aspects of photo-ferroelectric behaviour is the light-induced charge transport. In this context, it is essential to take into account the bulk photovoltaic effect (BPVE). Unlike normal photovoltaic effect in semiconductors that rely on the separation of charge carriers at p-n-junctions where voltage created can never exceed the band gap energy, the BPVE scales with sample thickness and can create an arbitrarily high voltage. There are several competing propositions for the mechanism driving the charge carriers. For Fe:LiNbO3, the most prominent material with a large BPVE, a recent model [1] is based on the transition of the electron from an Fe-donor to a small free Nb polaron state with the transition probability depending on interatomic distances. Both interatomic distances and phonon spectrum are susceptible to mechanical stress. This poster will elucidate the origin of the BPVE by determining the short-circuit current of LiNbO3:Fe at different levels of uniaxial compressive stress under homogeneous illumination. The full stress-dependence of the BPVE is quantified via the piezo-photovoltaic tensor. The stress-dependence of the phonon spectrum is determined by Raman spectroscopy and the changes in interatomic distances by structural characterization. [1] O. Schirmer et al., Phys. Rev. B 83, 165106 (2011).
Keywords: Bulk Photovoltaic effect, Lithium Niobate, Polaron, Charge transport
Shankari Nadupalli [email protected]
3rd year of my PhD Poster number: 12
72
Characterization of the Immune Mechanisms Involved in Microglia Activation C. Sousa, D. Coowar, A. Golebiewska, R. Balling, J.C. Schwamborn, K. Biber, A. Michelucci
Microglia are a specialized population of tissue macrophages resident in the central nervous system (CNS) parenchyma specifically adapted to the unique properties of the CNS. Microglia dynamically scan their environment ready to react to any disturbance of the homeostatic equilibrium. Under physiological conditions, microglia play critical functions during neuronal development, adult neurogenesis and in modulating synaptic transmission. Yet, microglia dysfunction has been associated to several neurodegenerative and neuroinflammatory disorders, therefore an effective microglial function is crucial for proper CNS development and homeostasis in both physiological and threatening conditions. In response to inflammatory stimuli, microglia undergo significant genetic and functional changes. The extent of the molecular changes occurring during the inflammatory process and whether such changes might be beneficial or detrimental to neuronal parenchyma under different CNS diseases is a milestone in research. Recently, genome-wide sequencing technologies together with the ability to purify microglial and other brain cell populations from their proper environment led to the identification of gene signatures selectively and specifically expressed by resident microglia. Here, we take advantage of these signatures to characterize the mechanisms involved in the activation and immune function of microglial cells ex vivo and in vitro under resting as well as under specific inflammatory conditions. Our studies are imperative to fill major gaps in the understanding of microglia biology in both health and disease, such as Parkinson’s disease, and could provide therapeutic options to tune the normal homeostatic functions of microglia. Keywords: Microglia, Inflammation, Genome-wide
Carole Lara Veiga de Sousa [email protected] 3rd year of my PhD
Poster number: 13
73
Linear Dynamic Network Reconstruction from Heterogeneous Datasets Zuogong Yue, Johan Thunberg, Jorge Goncalves
This paper provides a method for reconstruction of linear dynamic networks from heterogeneous datasets. Those datasets contain 1) data from several replicates of an experiment; 2) measurements from linear dynamical systems subjected to different experimental conditions, e.g., changes/perturbations in parameters, different disturbance or noise. A main assumption is that the underlying network topology, identified from data sets, is the same for all experiments. An ARMAX model is adopted to parameterize a general linear dynamic network representation, which provides the Granger Causality graph as a special case. The identification is performed by integrating all available datasets, which resorts to simultaneous group sparsity selections to assure both the sparsity of network topology and the consistency of topologies over datasets (not parameters). In terms of numerical computation, besides classical convexation methods, Sparse Bayesian Learning is also used to give a better approximate to the cardinality optimization problem. In terms of this treatment, simultaneous integration of various datasets in system identification has the potential to avoid non-identifiability issues typically arising when only a single dataset is used. Keywords: dynamic network, causality, biological time-series, heterogeneous datasets
Zuogong Yue [email protected]
3rd year of my PhD Poster number: 14
74
A multi-scale model of melanoma growth Marco Albrecht
Tumour progression in tissues is a complex phenomenon and several models try to capture its main characteristics. Cancer cells interact with their mechanical surrounding and are affected by concentration gradients. 3 years ago, the innovative “thermodynamically constrained averaging theory” (TCAT) found its application in cancer modelling and provides the base for this PhD project. A multi-phase liquid system describes cell populations and the interstitial fluid. The extracellular matrix is modelled as elastic porous media. The model can simulate a necrotic core and can switch easily between compact and invasive growth. The model is supposed to link pharmacokinetics and biochemical signalling networks with the tissue level in order to predict therapy success or tumour recurrence in patients with melanoma. Keywords: Bio mechanics, multi-scale model, tumour stroma interaction, microenvironment, porous media, Systems Biology, tumour growth, thermodynamically constrained averaging theory
Marco Albrecht [email protected]
2nd year of my PhD Poster number: 15
75
Study-driven bias effects on disease-specific network extraction Ganna Androsova, Reinhard Schneider, Roland Krause
Many works on disease-specific networks from protein-protein interactions report abundant proteins such as ubiquitin and TP53 as key findings. Due the small-world and scale-free properties of biological networks, extraction of relevant sub-networks poses a challenge in specificity as hubs are likely to be encountered often. The extreme degree of some proteins is driven by a study bias due to raised interest in key regulators like TP53 which occurs frequently in disease-relevant networks not associated with cancer, often flagged as key regulator. We evaluated the impact of the degree distribution on the retrieval of relevant networks for understudied syndromes for which little information is available. We compared performance of well-known algorithms for construction of disease-specific networks by simulation. An existing list of condition-related molecules is the most specifically connected by the shortest path, which does not introduce false positives in typically settings. First-neighborhood retrieval adds interacting partners that potentially may be involved in the syndrome of interest, while introducing swaths of irrelevant hubs and false positives. Random walks using Markov chains of different lengths comprise a trade-off performance between first-neighborhood and shortest path. We alleviate the study bias problem by introducing a degree-discounted network, thereby reducing the frequency of hub retrieval. Keywords: networks, study bias, protein-protein interaction
Ganna Androsova [email protected]
2nd year of my PhD Poster number: 16
76
Impact of DNA repair on GBM biology and resistance to Temozolomide: DNA repair gene expression study in patient biopsies
Matthieu Gobin, Petr Nazarov, Marco Timmer, Simone Niclou, Eric Van Dyck Despite surgical resection and the combination of ionizing radiation and chemotherapy with temozolomide (TMZ), a DNA methylating agent introduced in 2005, glioblastoma multiforme (GBM) remains a lethal disease associated with poor prognosis (the median survival is about 15 months); patients inevitably display tumor relapse due in great part to the development of resistance to chemoradiation mediated by DNA repair mechanisms. Our aim is to propose novel molecular targets and strategies in the fight against GBM, based on the identification of the DNA repair machineries that i) are altered during glioblastoma genesis and ii) mediate resistance to TMZ-induced DNA damage, and tumor relapse. To this end, we carried out a gene expression analysis in clinical samples. Specifically, using the nCounter technology (Nanostring), we measured the mRNA expression levels of a selection of genes encompassing the major DNA repair pathways and cell cycle-related factors, in paired primary and recurrent biopsies from GBM patients. Stratification of our cohort led to the identification of a specific signature that segregates groups of primary and recurrent tumors, and the observation that specific DNA repair pathways are deregulated in primary GBM compared to healthy control tissue. In order to propose novel strategies targeting DNA repair based on genotoxics and the inhibition/depletion of selected DNA repair factors, we are currently analyzing the impact of targeting the most promising candidate genes in GBM cell lines. Our study carries the long-term prospect of proposing novel, targeted strategies for the treatment of GBM patients. Keywords: Glioblastoma, DNA repair, human biopsies, nCounter gene expression analysis, TMZ
Matthieu Gobin [email protected]
2nd year of my PhD Poster number: 17
77
A study of the molecular mechanisms underlying the response of human colorectal adenocarcinoma enterocytes to prebiotics and probiotics
Kacy Greenhalgh, Joëlle V. Fritz, Elisabeth Letellier, Audrey Frachet Bour1, Joanna Baginska , Pranjul Shah, Mahesh S. Desai, Enrico Glaab, Christian Jäger, Serge Haan, Paul Wilmes
The majority of the microorganisms constituting the human microbiome inhabit the gastrointestinal tract (GIT) where they play essential roles in governing human health. A variety of diseases including colorectal cancer (CRC) are associated with dysbiosis, a pathological imbalance in the intestinal microbiota. Apart from endogenous microbial consortia, diets supplemented with prebiotics, are thought to have a major effect on GIT microbiota and are inversely correlated with the risk of developing CRC. Furthermore, the use of probiotics including Lactobacillus rhamnosus GG (LGG) has been found to exhibit anti-cancer effects. Here, we study the synergistic effects of probiotic bacterial strains, namely Bacteroides caccae (B. caccae) and LGG as well as several prebiotic dietary components (mainly soy and diosgenin), on primary intestinal cell lines of the human GIT. Using the microfluidics-based GIT co-culture model called HuMiX (human microbial crosstalk) and specific relevant in vitro human cellular culture assays, we are investigating the effects of two prebiotics in combination or alone with two probiotic bacterial strains on different intestinal cell lines; namely conventional cell lines such as Caco-2 and HT-29 as well as primary established cell linesT-6, T20 and T18. More specifically, we are using the HuMiX model to investigate the effects of pre- and probiotics on the human and microbial transcriptome. A thorough mechanistic understanding of the interplay between dietary habits, bacterial metabolism and human physiology is required to understand the role of pre-and probiotics and apply them appropriately in CRC therapies and prevention. In this context, this project will likely result in recommendations for dietary and probiotic- based interventions to modulate the microbiota-host relationship in order to reduce the expression of pro-carcinogenic genes and reduce pro-inflammatory responses that have been found to play a pivotal role in CRC.
Keywords: Gastrointestinal microbiome, Prebiotics, Probiotics, RNAseq
Kacy Greenhalgh [email protected]
2nd year of my PhD Poster number: 18
78
Decoding calcium signaling Kamil Grzyb
The Ca2+ signaling pathway translates external signals into intracellular responses often by increasing the cytosolic Ca2+ concentration in a stimulus-dependent temporal pattern typically referred to as Ca2+ oscillations. Recent findings confirmed the stochastic nature of this calcium spiking dynamics and linear relationship between the standard deviation s and the average period Tav, with pathway specific slopes indicating a non-trivial and well-defined signature. We plan to use the well-established relation between temporal Ca2+ dynamics and NF-kB caused by CaM activation resulting in nuclear translocation of NF-kB and further downstream transcription in order to characterize Ca2+ spiking of HMLER and iPS cells. For this purpose we will use recently at the LCSB established Ca2+ patch clamp framework to induce well-controlled stochastic Ca2+ dynamics in cell populations. Further single cell analysis of Ca2+ dynamics driven cells will reveal transcriptional characteristics for each given Ca2+ signature profile. By extending existing multiscale model of intracellular Ca2+ dynamics with a transcriptional module we plan to integrate the obtained data and develop a decoding model
Keywords: Calcium - secondary messenger
Kamil Grzyb [email protected] 2nd year of my PhD
Poster number: 19
79
Double mutant GBA-PARK2 patient-derived cellular models to study the effects of GBA as a modifier of familial Parkinson’s disease
Zoé Hanss, Ibrahim Boussaad, Peter Barbuti, Stefano Goldwurm, Rejko Krüger
Mutations in the GBA1 gene, encoding the beta-glucocerebrosidase (GCase), are an important and common
risk factor for both familial and sporadic Parkinson’s disease (PD). Carriers of one mutated allele of GBA have
an up to 20-fold increased risk to develop PD. In patient harbouring also familial PD mutation, the presence of
a mutation in GBA could lead to an aggravated phenotype of the disease.
Here, we aim to investigate the effects of the GBA p.N370S mutation on stem cell based neuronal models
derived from fibroblasts of a PD patient harbouring a deletion of the exon 3 of Parkin and the N370S GBA
mutation. These fibroblasts have been reprogrammed into induced pluripotent stem cells (iPSC), then further
differentiated into small neuronal precursor cells (smNPC) to finally generate midbrain-specific dopaminergic
neurons. These cellular models have been fully characterized in order to assure the quality of the models used
for phenotyping. At iPSC stage, isogenic control will be created with correction of the GBA p.N370S mutation
by CRISPR Cas9 using double nickase strategy.
Phenotyping these different cell lines in terms of GCase protein level and activity, mitochondrial dynamics,
lysosomal activity and interplay with α-synuclein will allow us to assess the involvement of mutant GCase in
the physiopathology of the disease. Exploring the effects of GBA mutation in the context of monogenic PD
with well-known mutation will open new perspectives in the comprehension of combined effects of different
genes in the same individual.
Keywords: GBA, Parkin, familial Parkinson's disease, iPSC, dopaminergic neurons, CRISPR Cas9
Zoé Hanss [email protected]
2nd year of my PhD Poster number: 20
80
Evaluation of zebrafish as a potential model for comorbidities associated with Dravet syndrome
Maxime Jacmin, Alexander D. Crawford Dravet Syndrome (DS), also called severe myoclonic epilepsy of infancy (SMEI), is one of the most frequent form of pharmacoresistant epilepsy with an incidence of 1/30,000. Indeed, more than 40 medications have been approved but about 30% of all epilepsy patients do not respond adequately to any of the available anti-epileptic drugs (AEDs) and amongst them, the Dravet Syndrome patients. Approximately 80% of Dravet patients are genetically predisposed to the disease by presenting de novo mutations in the SCN1A gene encoding the Nav1.1 sodium channel alpha subunit and the mortality rate is 20% in children. Moreover, another hallmark of Dravet syndrome is that most patients have to cope not only with the disease itself but also with many additional medical problems that may be associated with epilepsy. Indeed, apart from psychiatric disorders as depression and anxiety, many patients suffer from impaired cognitive performance caused either by the disease itself and/or by the side effects of the medications prescribed. Recent studies on zebrafish have demonstrated its ability to be a promising in vivo model for biomedical research. Indeed, his genome has high homology (up to 80%) with most human sequences and, interestingly, 85% of the known epilepsy genes are found in the zebrafish genome. In this view, the zebrafish is becoming a relevant genetic model organism for human Dravet Syndrome. In order to reach this aim, this project will focus on the cognitive functions of zebrafish Dravet models in order to find similarities between cognition impairments in human patients and our zebrafish model. Then, we will expose zebrafish and mouse DS models to AEDs and novel anti-epileptic compounds known to suppress seizures in that models with the hope that we can find a new treatment working in human DS patients. Keywords: Dravet Syndrome ; comorbidities ; zebrafish ; mouse ; antiepileptic drugs
Maxime Jacmin [email protected]
2nd year of my PhD Poster number: 21
81
Diabetic multi-scale model predicts drug metabolism at the whole-body level Patricia Martins Conde, Thomas Sauter, Thomas Pfau
The incidence of Diabetes Mellitus has increased rapidly in the last years. It is estimated that more than 300 million people are suffering from this disease. Therefore it is of extreme importance to analyse deeply Diabetes processes and to find drugs and drug combinations that are more effective against this disease. Constraint Based Modelling (CBM) of metabolic networks is a well suited approach to study metabolic diseases such as Diabetes Mellitus. Despite the great detail of CBM models, they only offer a static perspective of metabolism at the cellular level. In order to associate the complex interplay between cellular metabolism at the systems perspective, higher level models are needed. Bearing that in mind, we aim to link whole-body physiologically-based pharmacokinetic-pharmacodynamics (PBPK-PD) and tissue CBM models in order to establish a dynamic multi-scale whole-body model. The multi-scale whole body model will consist of multiple contextualized CBM models which interact via the PBPK-PD model. The contextualized models will be reconstructed using algorithms previously developed in our group. By combining the whole body PBPK-PD model with tissue specific CBM models, it allows the simultaneous analysis of whole-body distributions and inter-tissue interactions. To ensure that the model represents physiological conditions as well as disease conditions, we will incorporate available data i.e. metabolite data from patients into the models. By mapping genetic defects at the cellular level, we will be able to determine the effect that these defects have at the whole-body model. More precisely we will be able to assess how glucose and insulin levels change during Diabetes at the whole-body level. Additionally, in silico prediction of Diabetic drugs efficiency, will allow to decrease the duration of pharmaceutical R&D, while less volunteers are needed. In silico prediction becomes even more important when specific populations are target, such as infants, elderlies and pregnant women. Keywords: multi-scale, CBM, dynamic, diabetes
Patricia Martins Conde [email protected]
2nd year of my PhD Poster number: 22
82
Midbrain organoids as a model to study Parkinson's disease Lisa M. Smits, Anna S. Monzel, Silvia Bolognin, Jens C. Schwamborn
The identification and optimisation of new in vitro approaches mirroring tissue complexity of the human brain are intense areas of stem cell research. The aim of this study is to establish a novel 3D cell culture system with midbrain identity. These midbrain-specific organoids will be useful to investigate the conditions that are responsible for neurodegenerative disorders like Parkinson’s disease (PD). Neuroepithelial stem cells (NESCs) generated from PD patient-specific induced pluripotent stem cells (iPSCs) have been used as a starting cell population. The cells were kept in a 3D environment and cultured under neuronal differentiation conditions. Midbrain-specific organoids were analysed with regard to morphology, gene expression and electrophysiological functionality. After 70 days of culture organoids revealed mature midbrain derived neural subtypes. Immunohistochemistry proofed the presence of neuronal, astroglial and oligodendrocyte differentiation. Furthermore, the recordings of microelectrode arrays showed electrophysiological activity of the midbrain-specific organoids. We established a novel 3D cell culture system approach that results in the generation of midbrain-specific organoids that feature tissue complexity similar to the human brain. With this, the effect of well characterised mutations can be analysed for the first time in an optimised in vitro environment. This will lead to new insights into PD. Keywords: Parkinson's disease, midbrain organoids, 3D cell culture
Lisa Smits [email protected]
2nd year of my PhD Poster number: 23
83
Characterization of CD8 T cells during HIV infection using 18 color flow cytometry Adams P.1; Iserentant G.1; Pannus P.2; Vanham G.2; Devaux C.1
1Luxembourg institute of Health; 2Institute of Tropical Medicine, Antwerp
Introduction: There is an urgent need for developing an HIV cure overcoming the current limitations of anti retroviral treatment. The current knowledge points to the direction that a combination of both CD8 T-cell function and phenotype should be elicited to achieve virus control. Characterization of cytotoxic CD8 + T cells in HIV-1 controllers merits further investigation to unravel the cellular subsets responsible for an effective and durable immune response. To this end we set up, validated and screened different patient groups using 18 color flow cytometry panels. Material and Methods: Phenotyping of peripheral blood monouclear cells from healthy donors (HD), therapy-naïve HIV-infected patients, HIV-infected patients under antiretroviral therapy and controller populations using 18-color flow cytometry on a FACSFortessa (BD Bioscience). Stimulation was achieved by either PMA/Ionomycin or Consensus GAG peptide pools for six hours using Brefeldin and Monesin as Golgi Transport blockers. Dead cells, monocytes and B lymphocytes were gated out to characterize CD8 T cells regarding cytotoxicity, activation, polyfunctionality, exhaustion and senescence. Results: The validation of the panels showed intracellular detection of IL-2, IFN-y, TNF-α and MIP-1β. Screening of HIV controllers delivered higher populations of CD8+CD56+perforin+ and granzyme B. Overall production of Granzyme B was especially pronounced in the viremic controller (77,53% as compared to 11,44% in the HD). Presence of a HLA-DR+CD38- subpopulation in the CD8 subsets was clearly confirmed (44,21% as compared to 3,53%). Conclusion: Flow cytometry panels were established and validated. Furthermore first screening of HIV controllers could confirm presence of HIV-specific cytotoxic subsets in these rare patients. Keywords: HIV Cure, polyfuntionality, CD8 T cells
Philipp Adams [email protected]
1st year of my PhD Poster number: 24
84
PerMET: Creating and simulating personalized intestinal community metabolic models trough metagenomics data integration
Federico Baldini and Ines Thiele Everyday people are assuming drugs that will not help them or that might even be harmful to them. The reason for this is that each individual is different from another, but, treatments do not reflect this complexity of variation between patients. That is why personalized medicine has been defined as the new frontier in medicine. Personalized medicine requires a smooth integration between data collection and advanced modeling techniques to deal with the complexity created by the availability of such big scale data. The field of systems biology, especially with metabolic and agent based modeling, provides powerful techniques for modeling cell behavior, as well as communities of different organisms. In parallel, recent advances in genomics, transcriptomics and proteomics made it possible to obtain a multiplicity of experimental data. Here we present PerMET, a pipeline that aims to integrate METagenomic data with a resource of genome scale METabolic models of the intestinal microbiota. The final goal is to understand and compare the microbe-microbe and host-microbe interactions present in the gut of healthy controls and disease patients through creation and simulation of personalized models to find key markers for pathological states and possible “personalized” intervention strategies. Keywords: metabolic modeling, agent based modeling, microbiota, metagenomics, data integration, healthy and disease, pipeline
Federico Baldini [email protected]
1st year of my PhD Poster number: 25
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Data-driven development in the smart city. Generative design for refugees camps in Luxembourg.
Elie Daher, Sylvain Kubicki, Annie Guerriero The poster will a result of a research addressing computational design as a key technological asset in the development of the smart city. In particular, the research targets context-aware adaptation to usage requirements at urban fragment level. Indeed, cities’ policy makers have to take into account many factors in a development policy, such as situational, technical or human-related factors as well anticipating future usages. Moreover, nowadays cities are key resources to answer growing humanitarian needs in term of sheltering and camps. Indeed they are increasing due to different factors related to nature or human activities. This is true also in Luxembourg, where a 2016’s public program aims to develop three container villages. The objective of this work is to help policy makers and humanitarian people in the optimization of the spatial design of camps. The use of parametric modeling approach enables the optimization of space layout planning. It is applied on a case study allowing policy makers to explore scenarios for the decision-making in the camp space planning. Keywords: Parametric modeling, generative design, humanitarian needs, data-driven design
Elie Daher [email protected]
1st year of my PhD Poster number: 26
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Mechanisms of acquired resistance to BRAF kinase inhibitors in melanoma Ines Kozar, Christiane Margue, Demetra Philippidou, Giulia Cesi, Stephanie Kreis
Cutaneous melanoma is the most aggressive skin cancer that emerges from the unrestrained proliferation of melanocytes. Although, this malignancy accounts for only 1% of all skin cancers, it is responsible for the vast majority of skin cancer related deaths. Interestingly, up to 50% of patients with sporadic melanoma harbour activating mutations in the protein kinase BRAF, with V600E being the most predominant mutation. Consequently, targeting mutant BRAF using BRAF inhibitors (BRAFi), has slightly increased the overall survival of patients with metastatic melanoma. Despite these promising results, the efficacy of BRAFi is limited by the rapidly emerging resistance to treatment. In order to understand the mechanisms underlying the resistance to BRAFi, we used in vitro melanoma cell models consisting of drug-sensitive and drug-resistant cells, which have been generated in our laboratory. Firstly, we performed whole exome sequencing to analyse variants in the coding part of the genome that might be responsible for the onset of resistance. Secondly, a microarray analysis was implemented with the aim to describe changes in the transcriptome and the miRNome that might play a role in resistance. Finally, we tested additional kinase inhibitors in order to identify novel drug combinations with the intention to overcome resistance. Keywords: melanoma, resistance, vemurafenib, dabrafenib, BRAF V600E, microRNAs, kinase inhibitors, whole exome sequencing, microarrays
Ines Kozar [email protected]
1st year of my PhD Poster number: 27
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Patient-derived cellular model of the D620N mutation of VPS35 (PARK17) Simone Larsen1, Peter A. Barbuti1, Peter A. Silbur2,3, Stephen A. Wood2, George Mellick2, Rejko Krüger1,4,5
1 - Clinical and Experimental Neuroscience, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Luxembourg 2- Eskitis Institute for Drug Discovery, Griffith University, Nathan, 3- The University of Queensland Centre for Clinical Research, Herston, Queensland, Australia 4 - Centre Hospitalier de Luxembourg (CHL), Luxembourg 5 - Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University Clinics Tübingen, 72076 Tübingen, Germany
The VPS35 D620N mutation is an autosomal-dominant cause of familial Parkinson’s disease (PD). The VPS35
protein, encoded by the VPS35 gene located at the PARK17 locus, is a component of the retromer complex
and is implicated in the sorting and trafficking of various proteins in the endosomal pathway. The D620N
mutation is known to interfere with endosomal trafficking which may lead to impaired autophagy and
subsequent mitochondria dysfunction.
The aim of this project is to study the cellular phenotype of midbrain dopaminergic (mDA) neurons derived
from patient’s induced pluripotent stem cells (iPSC) carrying the VPS35 D620N mutation.
The patient’s fibroblasts were reprogrammed into pluripotency. The induced pluripotent stem cells (iPSCs) will
then undergo gene correction using Crispr-mediated technology to generate an isogenic cell line in which we
have corrected the patient’s heterozygous mutation, and inserted this mutation into age- and gender-matched
controls. Two nucleases will be used to correct/insert the mutation: the Cpf1 and the spCas9. The isogenic
iPSC will be differentiated into small molecule neuroprecursor cells (smNPC) and further specified into mDA
neurons.
We aim to focus on the autophagy pathway, mitochondria phenotype and alpha-synuclein aggregation in mDA
neurons by using live cell imaging techniques, biochemical and functional assays. Consequently, our objective
is to rescue that phenotype using high-throughput screening of compounds.
Keywords: Parkinson's disease, retromer complex, patient-derived cellular model, gene editing
Simone Larsen [email protected]
1st year of my PhD Poster number: 28
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Molecular and functional characterization of the unconventional interaction partners of CXCR7 and their role in virus-associated tumorigenesis Max Meyrath, Martyna Szpakowska, Alain Vanderplasschen, Markus Ollert and Andy Chevigné
CXCR7 is an atypical and enigmatic chemokine receptor playing crucial roles in numerous physiological
processes but also in viral infection and cancer. To date, the exact functions and signaling properties of
CXCR7 are still a matter of debate. Unlike other chemokine receptors, CXCR7 is proposed to act as a
scavenging receptor for its ligands, to trigger arrestin-dependent signaling and possibly classical G-protein
mediated signaling.
Besides its two endogenous chemokines CXCL11 and CXCL12 and the virus-encoded chemokine vCCL2,
accumulating evidence suggest that CXCR7 interacts with several non-chemokine ligands such as the pro-
angiogenic peptide Adrenomedullin (ADM). Furthermore, calcitonin receptor like receptor (CLR) and receptor
activity modifying proteins (RAMPs), constituting the main ADM receptor, might crosstalk with CXCR7
conferring the receptor alternative functions. While the interactions of CXCR7 with classical chemokine ligands
are now well characterized, little is known about the interdependence of ADM and the membrane interacting
partners with CXCR7, the signaling pathways activated as well as their roles in viral infection and
tumorigenesis.
This PhD project aims at unravelling the role and impact of CLR and RAMPs on the binding, scavenging and
signaling properties of CXCR7 towards the different ligands ADM, CXCL12, CXCL11 and vCCL2. Additionally,
by using state-of-the-art techniques like BRET, we will inquire the ability of CXCR7 to heterodimerize with
CLR and RAMPs. Lastly, since CXCR7 and RAMPs were described to be upregulated upon infection by several
tumorigenic viruses, a detailed expression profile of all the ligands and partners of CXCR7 in a herpesvirus-
induced cancer model will be determined and will help to reveal the role of CXCR7 in viral associated
tumorigenesis. This project will allow improving our level of understanding of CXCR7 regulation and
functions and will open new therapeutic directions for selective CXCR7 inhibition. Keywords: Chemokine receptors, CXCR7, signalling, heterodimerization, adrenomedullin, RAMPs, CLR, BRET
Max Meyrath [email protected]
1st year of my PhD Poster number: 29
89
FIN.
“Parting is such sweet sorrow
that I shall say goodnight till it be morrow.” – William Shakespeare, Romeo and Juliet
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Closing words
As all good things come to end, we must say goodbye to every each of you who enjoyed the Life
Sciences PhD days 2016 together with us.
What makes the event great is the people who contribute to it. This year we had a big support from
a number of different organizations. Our special appreciation goes to the Luxembourg Institute of
Health for providing the prizes for the three best PhD students’ talks and immense contribution of
the sponsors: Greiner Bio-One, PeproTech, ThermoFisher Scientific, Eppendorf, Promega and Bio-
Rad.
This year we had an exceptional opportunity to hear the talks of four wonderful scientists: Dr. Liliana
Bernardino, Dr. Nicola Zamboni, Dr. Uwe Ohler and Dr. Steffen Scholpp as well as attend the
presentations and seeing the posters of those who just made their first steps into the scientific
community by pursuing their doctorate degrees.
As a result of our work, we hope that new networks were built, new collaborations were established
and knowledge have been shared. We as (future) scientists are stronger together!
Thank you very much for being remarkable participants in the Life Sciences PhD days 2016!
If you have feedback, feel free to contact us:
E-mail: [email protected]
Facebook page: https://www.facebook.com/PhDdays2016/
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PhD Days 2016: Statistics
because everyone loves statistics!
Overall: Institute & Position
PhD students: Year & Activity
39%
23%2%
25%
11% LCSB
LIH
LIST
LSRU
Other
10%
12%
58%
8%
12%
MasterStudentOther
PhD Student
PI
Postdoctoralresearcher
31%
25%
25%
19% 1st year
2nd year
3rd year
4th year
18%
7%
31%
44%
Give a talk
Give a talkAND presenta posterPresent aposter
simply enjoythe PhD days
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PhD Days 2015: Pictures
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Notes
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