BS3 ADVANCED BIOCHEMISTRY

PHYSIOPATHOLOGY

Course C0: FROM MOLECULES TO

PATHOLOGIES AND FROM
PATHOLOGIES TO MOLECULES

TUMORIGENESIS AS A MODEL
Pr Germain TRUGNAN
with the help of Dr Lan Trang VU
 OUTLINE

1- Life, biomolecules and cells. Physiopathology relies on dysfunctionning molecules and cells
2- Tumorigenesis as a model for physiopathology studies
3- Cell communication and signaling
4- Cell fate : physiology and pathology
5- General mechanisms of cell communication deregulation
6- A global map of cell deregulation in cancers
7- From physiopathology to therapeutic molecules
1- Life, biomolecules and cells. Physiopathology relies on dysfunctionning molecules and cells

Lighting
bolts

H20 NH3
Aleksandr Oparine John Haldane Stanley Miller CH4 H2 To vacuum
1924 1929 1953
Sampling
Cold
Fresh
Formaldehyde water

Formic acid Sampling

water
Hydrogen Cyanide
Abiotic Syntheses Sarcosine
Effluents boiler
Acetic acid
Chirality
Glycine collection
Polymers Lactic acid
Replication Alanine

Catalysis Urea
Aspartate
Nucleotides
etc…
1- Life, biomolecules and cells. Physiopathology relies on dysfunctionning molecules and cells

From molecules to proto-cells

compartimentation
1
3
5 6

4
2
coacervates vesicles growth division

myristoleic acid bicine

geranylgeranyl phosphoric acid

n-decylphosphonic acid Plausible mechanism...

Plausible prebiotic amphiphiles
1- Life, biomolecules and cells. Physiopathology relies on dysfunctionning molecules and cells

From proto-cells to life animals

algae mushrooms
plants

eucaryotes

proto-cell
LUCA
Archae
(procaryotes)

proto-cellule

Charles
DARWIN LUCA : Last Universal Bacteria
(procaryotes)
1809-1882 Common Ancestor
2- Tumorigenesis as a model for physiopathology studies
2- Tumorigenesis as a model for physiopathology studies
- It’s a major public health problem
Cancer represents around 1/5 of death in Vietnam (lung, breast, colon, prostate…)
WHO report 2020 : total population = 97 338 583; new cases = 182 563; number of deaths = 122 690
2- Tumorigenesis as a model for physiopathology studies

- It’s a major public health problem

- It allows to discuss many biological and medical questions

Biologically, cancer results from

a global cell dysfonctionning:
uncontrolled cell proliferation,
capacity to resist apoptosis,
capacity to locally invade a
tissue, capacity to produce
distant metastasis.
2- Tumorigenesis as a model for physiopathology studies
Cell dysfunctions Tissue dysfunctions

Vascular cells
Primary tumor cells

Connective tissue
(fibroblasts)

Extracellular Matrix Immune cells

Tumorigenesis is a pathology of cell and tissue communication

3- cell communication and signalization
3- cell communication and signalization

Incoming information Cell and tissue Outgoing information

Integration
ions
Hormones
Hydrophilic ...
hydrophobic

Growth factors Gene expression

ex : TGFa changes
Anti-growth
factors. ex : TGFb
Intracellular
Survival factors Topology of
Traffic
Cytokines expression
ex : IGF1 Secretion

Death Factors
Protein synthesis
ex : FasL Level of
or degradation
expression
Drugs

Cells Cell homeostasis

changes

Extracellular Matrix
3- cell communication and signalization
SIGNALS ARE TRANSDUCED BY RECEPTORS THAT ENGAGE SIGNALING PATHWAYS

Cells Anti-growth
factors. ex : TGFb
E-cadherins
TGFbR
Extracellular matrix Gene expression
changes
integrins
Intracellular
Growth
ER-Golgi- Traffic
Factors
endosomes Secretion
ex : TGFa
lysosomes
RTK membrane
Protein synthesis
or degradation

Hydrophilic
Cell homeostasis
hormones 7-TMR changes
Lipophilic cytosol
hormones nucleus
RTK
Survival factors
mitochondrion
ex : IGF1
channel
ions Fas
Cytokine-R Death factors
Cytokines
ex : FasL
3- cell communication and signalization
FINAL TARGETS

Cells Anti-growth
factors. ex : TGFb
E-cadherins Gene expression Differentiation
changes and cell
TGFbR
functionnality
Extracellular matrix
Intracellular
integrins Traffic
Secretion
Growth
Factors ER-Golgi-
endosomes
ex : TGFa Cell proliferation
lysosomes
RTK (cycle) membrane

Protein synthesis
Hydrophilic or degradation
hormones
7-TMR
Lipophilic
hormones Cell homeostasis cytosol
changes nucleus
RTK
Cell death
Survival factors apoptosis
ex : IGF1
canal
ions Fas
Cytokine-R mitochondrion Death factors
Cytokines
ex : FasL
3- cell communication and signalization
SUMMARY

Incoming information Cell and tissue Outgoing information

Integration
4- cell fate : physiology and pathology
4- cell fate : physiology and pathology
The fate of any cell consist in either one of three possibilities

SIGNAUX
1 proliferation
2 differentiation
(execution of specialized functions
3 Death (apoptosis, necrosis...)
1
3
2

A cell become cancerous when at least one of these processes is altered

4- cell fate : physiology and pathology

- All biological and physiological functions depend on cell communication

- A huge number of pathologies is associated with cell communication dysfunction

Synaptic transmission Infections

Immune response Inflammation
Muscle contraction Endocrinopathies
Hormonal regulations Neuropathies
Cardiopathies
Cell growth and proliferation
Gut pathologies
Embryonic development
Kidney pathologies
…………
…………

Tumorigenesis

Therapeutic strategies are increasingly based on pathophysiological knowledge

5- General mechanisms of cell communication deregulation
5- General mechanisms of cell communication deregulation
1- DISCOVERY AND CHARACTERIZATION OF ONCOGENES (1)
Communication dysfunction is related to mutations on genes essential for cell maintenance
Discovery of these genes derived from studies on cancers caused by viruses
Comparative analysis of RSV and ALV virus genomes explains the
RSV ALV
exclusive transforming capacity of RSV

ALV

RSV
gag pol env src

Viral structural Reverse

proteins transcriptase Envelope tyrosine kinase
Protease Integrase glycoproteins Src

RSV genome contains an additional gene src encoding a 60 kDa

tyrosine kinase. This gene alone confers transforming capacity of
RSV. It is absolutely not involved in virus replication.
Virus replication with Virus replication without
host cell transformation host cell transformation
Transfection of src into chicken fibroblasts induces sarcoma

src gene is the first discovered oncogene

5- General mechanisms of cell communication deregulation
1- DISCOVERY AND CHARACTERIZATION OF ONCOGENES (2)
Where is this src gene coming from ?

Hypothesis: This gene has been captured by viruses during their passages on host cells
This hypothesis has been confirmed and this leads to the definition of proto-oncogene:
A proto-oncogene is a highly expressed gene from a normal cell, extremely conserved during evolution, ensuring
central functions in normal cell signalization.
Integration of a proto-oncogene in viral genome results in an abnormal expression or regulation that will drive
tumorigenesis. Raf proto-oncogene protein
In this condition, the proto-oncogene becomes an oncogene
An example of proto-oncogene (Raf) activation through an Regulatory domain Kinase domain
integration in the viral genome that eliminate the
regulatory domain of the normal protein Raf oncogene protein
Convention : c-onc means proto-oncogene
GAG Kinase domain
and v-onc, the viral abnormal oncogene

This concept can be generalized to non-viral cancers (representing the vast majority of cancers)

Human bladder carcinoma Tumoral ADN transfection into normal Tumoral phenotype of
ADN extraction from tumoral cells
cells ( mouse fibroblastes) transfected cells
5- General mechanisms of cell communication deregulation
1- DISCOVERY AND CHARACTERIZATION OF ONCOGENES (3)
A very large number of proto-oncogenes having important functions in normal cells (house-keeping genes) has been
discovered. Abnormal activity of these genes is associated with tumorigenesis.

Growth factors
Growth factor receptors
b Chain of PDGF
EGF-receptor FGF subtype
CSF-receptor

EGF-receptor

Protein-tyrosine
kinases

Small G proteins

Serine-threonine kinases

Transcription factors Other nuclear factors

5- General mechanisms of cell communication deregulation
2- ACTIVATION MECHANISMS of PROTO-ONCOGENES (1)

Oncogenes are activated forms of proto-oncogenes. Three mechanisms are involved.

CHROMOSOME
DELETION OR GENIC AMPLIFICATION REARRANGEMENT
POINT MUTATION

ADN

ARN
Hyperactive protein Normal protein Normal protein
produced in normal produced in huge produced in huge Hyperactive or hyper-
quantity quantity quantity due to the transcribed fusion
proximity of a strong protein
enhancer
Examples Examples Examples
ras c-myc c-erbB bcr/abl myc
erbB K-ras c-myb
src
5- General mechanisms of cell communication deregulation
2- ACTIVATION MECHANISMS of PROTO-ONCOGENES (1)
RAS-ACTIVATING POINT MUTATION

aa-10 aa-15 This mutation inactivate Ras protein GTPase activity

Gly Ala Gly Gly Val Gly that becomes permanently activate, resulting in an
impaired regulation. Cell proliferation cannot be
ras wt GGC GCC GGC GGT GTG GGC controled.
Val
ras oncogene GGC GCC GTC GGT GTG GGC

Pr G. TRUGNAN, UPMC, FMPMC

5- General mechanisms of cell communication deregulation
2- ACTIVATION MECHANISMS of PROTO-ONCOGENES (1)
TRANSLOCATIONS abl
c-myc

c-myc
IgH IgH/myc

8 14
5- General mechanisms of cell communication deregulation
3- DISCOVERY AND CHARACTERIZATION OF INACTIVATION MECHANISMS OF ANTI-ONCOGENES

Somatic hybridization between normal and tumor cells

may results in the production of non-tumorigenic cells

Genes from the genome of normal cells

contain information that suppress cancer
phenotype

Example of tumor suppressor proteins: p53, pRb, DCC, WT1

6- A global map of cell deregulation in cancers
6- A global map of cell deregulation in cancers

→
anti-proliferative signals

→
Proliferative signals

→
Immune capabilities
→

Cell energy resources

→
apoptosis Cell immortality
→→

Genome instability

→
Inflammation
→

angiogenesis
→

Invading capacities
and metastasis
6- A global map of cell deregulation in cancers
7- From physiopathology to therapeutic molecules
7- From physiopathology to therapeutic molecules
A long way to go…

High throughput sequencing

Bioinformatics
Genomics and proteomics
Mass spectrometry
Genes
RMN
Proteins Structure determination RX
and 3D Modeling
structure-function Molecular Dynamics
Target identification
relationships
Target caracterization
Virtual screening
Ligands Ligand conception
identification Pharmacophore
Selection and diversity

Generation of active molecules

Selectivity profile
Optimization Toxicology

Formulation /
« Lead »…. delivery
7- From physiopathology to therapeutic molecules

A very very long way to go and more…

10 000 100 10
Tested Drug 1
Screened
molecules candidates DRUG
molecules

Clinical Legal procedures

Reseach Commercialization and
Exploratory pre-clinical Administration
Industrial Authorization pharmacovigilance
research Tests
development
0 5 years 10 years 15 years 20 years + 5 years max

Patent
application
Patent
expiration

« Nous partîmes cinq cents; mais par un prompt renfort

Nous nous vîmes trois mille en arrivant au port » P. Corneille
7- From physiopathology to therapeutic molecules
 Organization for Projects
Group 1

Group 6

Group 5

Group 2

Group 4 Group 3
USTH BS3 Physiopathology