Lecture 1: Cancer Biology for Modellers · 2013-12-07 · Cancer Biology for Modellers Paul Macklin, Ph.D. 16 August 2010 Lecturer University of Dundee. ... – B. Albertset al. Molecular

Lecture 1: Lecture 1: Cancer Biology

for ModellersPaul Macklin, Ph.D.

16 August 2010

Lecturer

University of Dundee

Motivation

• To be effective biomathematicians, we need to “speak biology” as well mathematics and “speak biology” as well mathematics and programming.

– Helps in communicating with team members

– Biological understanding helps inform:

• Model formulation and analysis

• Evaluation of modelling predictions

• Parameter estimation

• Calibration

• relates to image processing

• Need to understand what you’re seeing (histopathology)

Lecture Outline

• Cell organisation

• Tissue organisation• Tissue organisation

• Maintaining tissue structure

• Cell birth and death

• Cell signalling

• Cell motility

• Oncogenes and tumour suppressor genes• Oncogenes and tumour suppressor genes

• Abusing the system: cancer progression

• Coming next

• References and resources

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Cell Organisation

• Bilipid layer surrounding cytoplasm– Permeable to small molecules– Requires active transport of others– Requires active transport of others

• Ion pumps control cell volume, pH, etc.

– Impermeable to larger proteins

• Cytoskeleton provides structure

• Organelles embedded in the cytoplasm to perform specialised functions

• Relatively rigid nucleus in the centre• Relatively rigid nucleus in the centre

• Receptors on cell surface:– Mediate cell-microenvironment communication

by binding to ligands– Mechanically link cell cytoskeleton to membrane

and microenvironment

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Tissue Organisation

•• Typical tissue microstructure in an organ:Typical tissue microstructure in an organ:

–– Epithelial tissue (epithelium)Epithelial tissue (epithelium)

•• Sheets of specialised cells that perform the work of the Sheets of specialised cells that perform the work of the •• Sheets of specialised cells that perform the work of the Sheets of specialised cells that perform the work of the organ (secretory products, filtration, etc.)organ (secretory products, filtration, etc.)

–– Loose connective tissue (stroma)Loose connective tissue (stroma)

•• Extracellular matrix (ECM) supports the organExtracellular matrix (ECM) supports the organ

•• Contains blood vessels, lymphatics, nervesContains blood vessels, lymphatics, nerves

–– Tissues separated by basement membrane (BM)Tissues separated by basement membrane (BM)

–– Often a Often a lumen lumen (fluid(fluid-- or airor air--filled cavity)filled cavity)

•• Transports secretory products from/to epithelium Transports secretory products from/to epithelium

•• stromastroma--BMBM--epithelium microstructure: designed to epithelium microstructure: designed to maximise surface area of epitheliummaximise surface area of epithelium--lumen interfacelumen interface

•• Notable biophysics and transport:Notable biophysics and transport:

–– BM is a physical barrier to cell motion between tissues BM is a physical barrier to cell motion between tissues

–– Oxygen, glucose, and growth factors can only reach Oxygen, glucose, and growth factors can only reach epithelium by diffusionepithelium by diffusion

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Maintaining Tissue Structure:Mechanics

• Mesenchymal cells (e.g., fibroblasts) can move freely in the stroma, secrete and degrade ECM

• Epithelial cells are polarised:

– Anisotropic adhesion receptor distribution

– Integrins on base for cell-BM adhesion

• Heterophilic adhesion

– No adhesion receptors on apex

– E-cadherins on basolateral sides for cell-cell adhesion

• Homophilic adhesion

• Mechanics determine tissue geometry:

– Balance of cell-cell and cell-BM strength

– Distribution of cell receptors likely help in determine curvature

– Mechanics of cell-BM adhesion, stresses, BM-to-ECM coupling likely determines BM curvature.

Maintaining Tissue Structure:Population Dynamics

•• Cell populations must be maintained in Cell populations must be maintained in homeostasishomeostasis–– Proliferation to replace aged cellsProliferation to replace aged cells–– Proliferation to replace aged cellsProliferation to replace aged cells

–– Apoptosis to remove damaged cells, or those out Apoptosis to remove damaged cells, or those out of placeof place

•• Adhesion receptors are not merely mechanical:Adhesion receptors are not merely mechanical:–– EE--cadherin helps detect presence/absence of cadherin helps detect presence/absence of

neighboursneighbours•• Trigger proliferation when missing a neighbour (ETrigger proliferation when missing a neighbour (E--

cadherin/βcadherin/β--catenin)catenin)cadherin/βcadherin/β--catenin)catenin)

•• Suppress cell cycle when attached to neighbours Suppress cell cycle when attached to neighbours (block Cyclin D1, etc.)(block Cyclin D1, etc.)

–– Integrins detect detachment from BMIntegrins detect detachment from BM•• Trigger apoptosis (anoikis)Trigger apoptosis (anoikis)

–– (This is why they’re (This is why they’re receptorsreceptors. . ☺☺☺☺☺☺☺☺))

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Cell Birth and Death:Proliferation

•• TightlyTightly--controlled cellcontrolled cell--cycle:cycle:–– G0G0: quiescent “resting state” : quiescent “resting state”

–– SS: Synthesis of new DNA: Synthesis of new DNA–– SS: Synthesis of new DNA: Synthesis of new DNA

–– G2G2: “gap” phase : “gap” phase –– final prep for divisionfinal prep for division

–– MM: mitosis phase: mitosis phase•• DNA divided into two daughter nuclei (mitosis)DNA divided into two daughter nuclei (mitosis)

•• Cytoplasm and organelles divided into Cytoplasm and organelles divided into daughter cells (cytokinesis) daughter cells (cytokinesis)

–– G1G1: “gap” or “growth” phase : “gap” or “growth” phase –– daughter cells daughter cells grow in volume, then exit cyclegrow in volume, then exit cyclegrow in volume, then exit cyclegrow in volume, then exit cycle

–– Note 1Note 1: Some biologists treat G0+G1 as long, : Some biologists treat G0+G1 as long, variablevariable--length G1 phase (often seen in flow length G1 phase (often seen in flow cytometry)cytometry)

–– Note 2Note 2: Others treat G1 as relatively fixed : Others treat G1 as relatively fixed length, with G0 of variable length (useful for length, with G0 of variable length (useful for KiKi--67 matching)67 matching)

Cell Birth and Death:Proliferation

•• Checkpoints provide opportunities for:Checkpoints provide opportunities for:–– Cycle arrest: Restriction checkpoint R at G1/SCycle arrest: Restriction checkpoint R at G1/S–– Cycle arrest: Restriction checkpoint R at G1/SCycle arrest: Restriction checkpoint R at G1/S

–– DNA error checking and repairDNA error checking and repair

–– Apoptosis for irreparable damageApoptosis for irreparable damage

•• Cycle progression controlled by Cycle progression controlled by intracellular signallingintracellular signallingintracellular signallingintracellular signalling–– Cyclins and cyclinCyclins and cyclin--dependent kinases (CDKs)dependent kinases (CDKs)

–– Connected to other signalling networksConnected to other signalling networks

Cell Birth and Death:Apoptosis

•• Apoptosis: orderly cell deathApoptosis: orderly cell death

–– SelfSelf--regulated, in response to signalling eventsregulated, in response to signalling events–– SelfSelf--regulated, in response to signalling eventsregulated, in response to signalling events

–– Early processes:Early processes:

•• Mitochondria lose membrane potential, integrity Mitochondria lose membrane potential, integrity

•• PrePre--positioned caspases are activated (cleaved), begin degrading positioned caspases are activated (cleaved), begin degrading cellcell

–– Orderly cell volume shrinkingOrderly cell volume shrinking

•• requires active N+, Ka+ pumps!requires active N+, Ka+ pumps!•• requires active N+, Ka+ pumps!requires active N+, Ka+ pumps!

Cell Birth and Death:Apoptosis

•• Apoptosis: orderly cell death (continued)Apoptosis: orderly cell death (continued)–– DNA is chopped into piecesDNA is chopped into pieces–– DNA is chopped into piecesDNA is chopped into pieces

–– Organelles disassembledOrganelles disassembled

–– Cell contents encapsulated into apoptotic bodiesCell contents encapsulated into apoptotic bodies•• Protects surrounding cells from otherwise damaging reactionsProtects surrounding cells from otherwise damaging reactions

–– Cell lyses to release apoptotic bodiesCell lyses to release apoptotic bodies

–– Apoptotic bodies phagocytosedApoptotic bodies phagocytosed

–– Entire process requires energy!Entire process requires energy!–– Entire process requires energy!Entire process requires energy!

Cell Birth and Death:Necrosis and Calcification

•• Necrosis: uncontrolled cell deathNecrosis: uncontrolled cell death–– Can occur due to energy depletion (hypoxia or Can occur due to energy depletion (hypoxia or hypoglycemiahypoglycemia), mechanical ), mechanical

injury, chemical stressors, failure during apoptosis, etc. injury, chemical stressors, failure during apoptosis, etc. injury, chemical stressors, failure during apoptosis, etc. injury, chemical stressors, failure during apoptosis, etc. –– Uncontrolled cell volumeUncontrolled cell volume

•• No energy for N+, Ka+ pumpsNo energy for N+, Ka+ pumps•• Cell swells, then burstsCell swells, then bursts•• Cell contents released into microenvironmentCell contents released into microenvironment

–– No orderly disassembly of nucleus, organelles, etc.No orderly disassembly of nucleus, organelles, etc.–– Generally no Generally no phagocytosisphagocytosis–– Calcification:Calcification:

•• Ca+ pumps not activeCa+ pumps not active•• Solid cell fraction replaced by calcium phosphate and Solid cell fraction replaced by calcium phosphate and oxolateoxolate cyrstalscyrstals•• Hard Hard microcalcificationsmicrocalcifications resultsresults

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Cell Signalling

• Cells are regulated by internal signalling networks

– DNA transcribes RNA– DNA transcribes RNA

– RNA encodes proteins

– Proteins:

• Assemble into structures

• Perform “duties”

• Transmit information through reactions

– Network:

• Redundancies

• Feedback loops

• Signal amplification

Cell Signalling:Two examples

• HIF signalling:

– Cells create hypoxia-inducible factors (HIFs)– Cells create hypoxia-inducible factors (HIFs)

• Big example: HIF-1α

– Ordinarily, O2 tags these for degradation

– During hypoxia, HIFs accumulate � HIFs as O2 sensors

– Trigger downstream transcription

• Decreased cell adhesion• Decreased cell adhesion

• Increased motility

• Glycolysis

• Temporary resistance to apoptosis

• VEGF secretion

Cell Signalling:Two examples

• EGFR signalling

– Epidermal growth factor (EGF) – Epidermal growth factor (EGF) binds to EGFR receptor

– Ligated EGFR receptors dimerise

– Dimerised EGFR receptors phorphorylate intracellular proteins

– Downstream actions:

• Transcription

• Increased motility

• Increased proliferation

• Cell survival

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Cell Motility

• Actin polymerisation and depolymerisation:

– Actin monomers join or leave chains to grow or shrink the cytoskeleton

• Cell signalling can nucleate biased polymerisation (e.g., in response to a gradient)Cell signalling can nucleate biased polymerisation (e.g., in response to a gradient)

– EGFR � Src � N-Wasp � Arp2/3 nucleation � …

• Actin fibres deform and extend cell membrane, forming a pseudopod (“false foot”)

– Filopodium: finger-like projection

– Lamellipodium: sheet-like projection

• Cells focally secrete MMPs from invadopodia:

– Degrade ECM

– Break integrin bonds

– Create space for motion

• Cell forms new focal adhesion on leading edge• Cell forms new focal adhesion on leading edge

• Actin polymers broken down in trailing edge (depolymerisation)

• Cell contracts to pull towards leading edge

• Protrusion – Adhesion – Contraction – Retraction cycles

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Oncogenes and Tumour Suppressor Genes

• Oncogenes:

– Proliferation-promoting genes : “gas pedal”

– Examples:– Examples:

• Growth factor secretion (including autocrine): EGF, PDGF, VEGF

• Internal promotion of cell cycle: β-catenin promotes transcription of Cyclin D1

• Counter-act TSGs: MDM2 degerades p53

• Growth factor receptors: EGFR / ErbB

• Downstream regulators of receptor pathways: Ras, Raf, Src

• Tumour suppressor genes (TSGs):

– Impede proliferation : “brake pedal”

– Examples:

• Block oncogenic signals: VHL helps degrade HIF-1α

• Regulate cell cycle / create inhibitory signals: Rb impedes cell cycle, promotes arrest at G1/S• Regulate cell cycle / create inhibitory signals: Rb impedes cell cycle, promotes arrest at G1/S

• Repair DNA damage: TP53 impedes cell cycle to allow DNA repair at G1/S

• Promote apoptosis: p53 can trigger apoptosis

– Knudson 2-hit hypothesis:

• You have 2 copies of each TSG, so need to eliminate both copies to lose function

– Discovered in studying Rb (retinoblastoma) TSG

– Mitigating factor: loss of heterozygosity

– Mitigating factor: partial loss of function

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Abusing the system:Carcinogenesis

•• Mutations and/or epigenetic events:Mutations and/or epigenetic events:

–– DownDown--regulate apoptosis (lose TSGs)regulate apoptosis (lose TSGs)

•• No No anoikisanoikis –– cells can survive in the lumencells can survive in the lumenNo No anoikisanoikis –– cells can survive in the lumencells can survive in the lumen

•• p53 mutation p53 mutation –– cells can ignore apoptosis signalscells can ignore apoptosis signals

–– UpUp--regulate proliferation (regulate proliferation (oncogenesoncogenes))

•• Decreased contact inhibition Decreased contact inhibition –– proliferate even in the presence of proliferate even in the presence of neighboursneighbours

•• Increased secretion of growth signals Increased secretion of growth signals �� selfself--signallingsignalling

•• “stuck switches”“stuck switches”

–– HER2 HER2 –– can can dimerisedimerise without binding without binding ligandligand

»» increases increases signallingsignalling activityactivity

–– KK--rasras mutation mutation –– constitutive active, allowing EGFR signalling with EGF constitutive active, allowing EGFR signalling with EGF

•• Consequences:Consequences:•• Consequences:Consequences:

–– Increased survival fitness versus normal cellsIncreased survival fitness versus normal cells

–– Forms a colony of Forms a colony of hyperproliferativehyperproliferative cellscells

•• Mechanics:Mechanics:

–– Mechanical pressure, stresses created by proliferating cellsMechanical pressure, stresses created by proliferating cells

–– Net outward flux of cells as mass grows Net outward flux of cells as mass grows –– Darcy’s lawDarcy’s law

–– Net inward fluid fluxNet inward fluid flux

Abusing the system:Avascular Growth

•• Can only receive substrates by diffusion from the stromaCan only receive substrates by diffusion from the stroma

–– Substrate gradientsSubstrate gradients

–– HypoxiaHypoxia–– HypoxiaHypoxia

–– HyperglycemiaHyperglycemia

•• Consequences:Consequences:

–– Viable rim thickness related to diffusion length scaleViable rim thickness related to diffusion length scale

–– Heterogeneous growth rates Heterogeneous growth rates –– relationship with oxygen and relationship with oxygen and glucose (cell energetics)glucose (cell energetics)

–– Inner band of hypoxic cellsInner band of hypoxic cells

•• HIF signalling HIF signalling

–– Interior necrotic coreInterior necrotic coreInterior necrotic coreInterior necrotic core

•• Mechanics:Mechanics:

–– Outward fluid flux from necrotic core due to lysisOutward fluid flux from necrotic core due to lysis

–– Inward cell flux due to reduced interior strainInward cell flux due to reduced interior strain

–– Steady tumour volume:Steady tumour volume:

•• Cell flux out of viable rim ≈ fluid flux from necrotic coreCell flux out of viable rim ≈ fluid flux from necrotic core

Abusing the system:Angiogenesis

•• Hypoxic cells release angiogenic factorsHypoxic cells release angiogenic factors

•• VEGF diffuses into stromaVEGF diffuses into stroma•• VEGF diffuses into stromaVEGF diffuses into stroma

•• Endothelial cells respond to VEGFEndothelial cells respond to VEGF

–– Degrade vessel wallsDegrade vessel walls

–– Chemotaxis (up Chemotaxis (up ∇∇∇∇∇∇∇∇VEGF), haptotaxis (up VEGF), haptotaxis (up ∇∇∇∇∇∇∇∇ECM)ECM)

–– Increased proliferationIncreased proliferation

–– Temporary suspension of anoikis (to facilitate survival until new basal Temporary suspension of anoikis (to facilitate survival until new basal lamina surrounds mature vessels)lamina surrounds mature vessels)

•• New vessels grow towards tumour, generally towards the VEGF New vessels grow towards tumour, generally towards the VEGF gradientgradientgradientgradient

•• New vessels crossNew vessels cross--link (anastomose)link (anastomose)

•• New blood flow in the vessels New blood flow in the vessels –– new substrate transport to fuel new substrate transport to fuel further tumour growthfurther tumour growth

•• Vessels mature: pericytes recruited, deposit basal lamina around Vessels mature: pericytes recruited, deposit basal lamina around vesselsvessels

Abusing the system:Vascular Growth & Invasion

•• New vessels fuel rapid New vessels fuel rapid tumour growthtumour growthtumour growthtumour growth

•• BM deformation and stressBM deformation and stress

•• Hypoxic stress remainsHypoxic stress remains

–– Glycolysis Glycolysis

–– AcidosisAcidosis–– AcidosisAcidosis

–– Selection pressuresSelection pressures

Abusing the system:Vascular Growth & Invasion

•• MutationsMutations

–– AcidAcid--resistantresistant

–– BM and ECM degradation (by MMPs)BM and ECM degradation (by MMPs)–– BM and ECM degradation (by MMPs)BM and ECM degradation (by MMPs)

–– MotilityMotility

•• Invasion into stromaInvasion into stroma

–– By growth and by motilityBy growth and by motility

–– CoCo--option of blood vesselsoption of blood vessels

•• Sustained tissue stressSustained tissue stress

–– Collapsed blood vesselsCollapsed blood vessels–– Collapsed blood vesselsCollapsed blood vessels

–– New rounds of angiogenesisNew rounds of angiogenesis

•• MetastasisMetastasis

–– Travel through blood vessels and lymphaticsTravel through blood vessels and lymphatics

–– Extravasation, growth of new tumourExtravasation, growth of new tumour

–– Possible role of metastatic nichePossible role of metastatic niche

Lecture Outline





• Cell signalling

• Cell motility



• Coming next

• References and Resources

Coming Next:

•• Lecture 1:Lecture 1:

–– Cancer biology for modellersCancer biology for modellers–– Cancer biology for modellersCancer biology for modellers


–– An agentAn agent--based cell model; application to DCISbased cell model; application to DCIS


–– Parameter estimation, patientParameter estimation, patient--specific calibrationspecific calibration–– Parameter estimation, patientParameter estimation, patient--specific calibrationspecific calibration


–– Numerical method, simulation resultsNumerical method, simulation results

Lecture Outline





• Cell signalling

• Cell motility



• Coming next


Some References

• Some biology texts:– P. Macklin. Biological background. In: V. Cristini and J. Lowengrub. Multiscale

Modeling of Cancer. Cambridge University Press, Cambridge, UK, 2010. Chapter 2, Modeling of Cancer. Cambridge University Press, Cambridge, UK, 2010. Chapter 2, pages 8-24. ISBN 978-0521884426. (in press)

– B. Alberts et al. Molecular Biology of the Cell. Garland Science, New York, NY USA, 5th edition, 2007. ISBN 978-0815341116.

– M. Knowles and P. Selby, eds., Introduction to the Cellular and Molecular Biology of Cancer. Oxford Univ. Press, Oxford, UK, 4th edition, 2005. ISBN 0-19-852563-X.

• Also see some great modelling texts by Wodarz & Komarova, Anderson et al.

• Some great websites:– Cell biology and animations: http://www.johnkyrk.com/

– SIU histology: http://www.siumed.edu/~dking2/

– Zoomified histology: http://www.meddean.luc.edu/lumen/MedEd/Histo/virtualhistology.htm

Contact Information:

•• Email:Email:

–– [email protected]@maths.dundee.ac.uk–– [email protected]@maths.dundee.ac.uk

•• Web:Web:

–– http://www.maths.dundee.ac.uk/macklinhttp://www.maths.dundee.ac.uk/macklin

•• (new but under construction)(new but under construction)•• (new but under construction)(new but under construction)

–– http://biomathematics.shis.uth.tmc.eduhttp://biomathematics.shis.uth.tmc.edu

•• (old but already built)(old but already built)

Documents

Lecture 1: Cancer Biology for Modellers · 2013-12-07 · Cancer Biology for Modellers Paul Macklin, Ph.D. 16 August 2010 Lecturer University of Dundee. ... – B. Albertset al. Molecular