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Defective post-transcriptional gene regulation
Neil Renwick MD, PhD
Laboratory of Translational RNA Biology
Department of Pathology and Molecular Medicine
SEAMO Innovation Showcase 2015
MBChB
PhD
FCAPMCTSK08
Path to research independence in Translational RNA Biology
DTMH
Research theme: Using RNA to diagnose and treat disease
Post-transcriptional gene regulation
DNA RNA PROTEIN
miRNAs
RBPs
miRNA gene mutations
1) miR-96-related non-syndromic hearing loss
RNA-binding proteins
2) FMR1 loss of expression resulting in Fragile X Syndrome3) RBM20-related Dilated Cardiomyopathy4) RBM10-related Cleft Palate5) TDP43-related Amyotrophic Lateral Sclerosis6) FUS-related Amyotrophic Lateral Sclerosis
RNAs
1) Likely many TBD
Post-transcriptional diseases
Post-transcriptional gene regulation
DNA RNA PROTEIN
miRNAs
RBPs
5 ng -
(or less)
sequence annotation and analysis
upload sequence file on RNAworld (300 mio reads) barcode extraction (20 x 15 mio reads, validated)small RNA annotation (iterative process)
miRNAs 13,300,000 (88.2%)
none 298,000 (2.0%)
rRNA 382,000 (2.5%)
snoRNA 161,048 (1.1%)
std cali 254,941 (1.7%)
tRNA 218,229 (1.3%)
clustering, heat map (log2 expression)differential expressiondiscriminant analysis
Post-transcriptional gene regulation
DNA RNA PROTEIN
miRNAs
RBPs
Illustration of PAR-CLIP method
4-thiouridine
5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 510
2000000
4000000
6000000
8000000
10000000
12000000
14000000
16000000
18000000
Library 5:TDP43 library annotation by read length.non nannotated mito_genome
genome pET28a_plasmid
pET16B_plasmid RNL2_insert
BICC1_insert concatamers
tRNA_prec tRNA
std_cali snRNA_prec
snRNA snoRNA_prec
snoRNA scRNA_prec
scRNA scaRNA_prec
scaRNA rRNA_prec
rRNA plasmid
piRNA other_ncRNA_prec
other_ncRNA Ome_cali
mt_tRNA mt_rRNA
mt_mRNA mRNA_gene
mRNA mirtron
miRNA marker
long_cali l incRNA_gene
lincRNA doubtful_snoRNA
doubtful_miRNA circRNA
alt_cali adapterRead length (nt)
Re
du
nd
an
t re
ad
co
un
t
TDP-43 PAR-CLIP
Projects
1) miRNA reannotation (other RNAs)2) miRNA-based diagnostics for NETs (cancer biology)3) RBP pathomechanisms (TDP-43)4) Rare disease genetics (RNA-based mutation identification)
Yrs 1-2
Set up functional laboratory and recruitObtain preliminary fundingWrite first and senior author manuscriptsTalk to senior investigators
Yrs 3-5
Develop collaborations (models)Present nationallySelect topic for larger research award application
Directions and plan
Lab members
Xiaojing Yang (research associate)Kathrin Tyryshkin (data analyst)Bryony Dorrington (path 499 student)Betty Li (path 499 student)Tiandra Ceyhan (summer student)Dakota Gustafson (summer student)Shane Mooney (summer student)Francine Milone (volunteer)
Collaborators
Thomas Tuschl, The Rockefeller University (RNA biology)Yao-Tseng Chen, Weill Cornell Medical College (rare tumors)Lev Goldfarb, National Institutes of Health (genetics)Fyodor Platonov, North-Eastern Federal University (rare diseases)Andrew Craig, Queen’s University (cancer biology)
Acknowledgments
Start up
Department of Pathology and Molecular MedicineQU School of MedicineSEAMO
Competitive
AHSC AFP Innovation FundCFI JELFMRI ORF-RI ProgramQU KGH Clare Nelson Bequest FundQU SARC GrantSFARI
Funding
