Transcript Population Genetics I

Announcements
1. Pick up study guide today - some time in lab for questions
2. Pick up problem set 8 - first 2 questions graded, due start of lab next
week.
3. Please let me know if you have a final exam scheduling conflict; we
need to reschedule your final ASAP.
4. Reminder on grades - Probable adjustment after final
5. Check your t-test numbers with Jason or myself; be sure your statistics
are correct before concluding your unknowns; email OK - lab report
due Fri. 12/6 at start of lecture.
6. End of class today - consult with other groups re. were any of your
worms dumpy?
Using the “t distribution” table
1. The numerator when calculating t should always be a positive value ie. use absolute value of (mean 1 - mean 2) or just the difference
between the two means
2. If your t value is greater than the value in the table (under the p=0.05
column), then there is less than a 5% probability that there is no
significant difference.
Another way to say this: if t > than table value, there IS a significant
difference.
You should determine how small the probability is that your means
do not significantly differ: what is the lowest p in which your t value
is larger than table value?
In example, t value was greater than table value at p=0.005;
therefore, < 0.5% chance there is NO difference.
Review of lecture 36
2 of 3 main checkpoints in the cell cycle
1.
1. G1/S
Is cell the correct size?
Is DNA damaged?
2. G2/M
Is DNA fully replicated?
Is DNA damage repaired?
2.
What proteins regulate arrest vs. proceed?
2 kinds of proteins:
1) kinases - cdk’s
2) Cyclins - complex with cdk’s
What do these proteins do when complexed together?
Modify (+P) target proteins needed for either replication (S) or
mitosis (M)
Example of target protein that must be modified in order
for cell cycle to proceed from G1 to S:
Rb (retinoblastoma) normally puts brakes on cell cycle; once
modified, releases E2F and cell cycle proceeds
How does p53 arrest cell cycle?
Is a transcription factor that activates p21 which inhibits cdkG1 cyclin; Rb is not +P/ modified
Severe Sunburn example
1) Healthy individual - skin peels:
UV irradiation from sun causes mutation in DNA (generates T dimers
and inhibits normal replication); in response to DNA damage, p53 levels
increase. p53 will either cause cell cycle to arrest or if too much
damage (this case), trigger apoptosis (programmed cell death); dying
skin cells = peeling skin.
2) Individual/cells with p53 mutation - why skin cancer?
No ability to trigger apoptosis; therefore no peeling skin. This failure to
arrest DNA-damaged cells, or kill them off, will be repeated in
subsequent cell cycles permitting other mutations to accumulate,
culminating in neoplastic transformation... tumor formation and cancer.
Overview of lecture 37
I. Tumor suppressors - normally arrest cell cycle
II. Proto-/Oncogenes - normally promote cell cycle
III. Translocations and Genomic instability
IV. Colon cancer results form series of mutations
V. Carcinogens
Breast Cancer Tumor Suppressors
• A small proportion of breast cancer is heritable. Two
genes are associated with predisposition to
developing breast cancer.
– BRCA1 on chromosome 17
– BRCA2 on chromosome 13
• Normal function of both is in repair of ds DNA breaks.
Tumor suppressors - normally suppress
unregulated cell growth: Rb is brake on cell cycle;
p53 also can arrest cell cycle
KEY POINT To promote development of cancer, are
mutations in one or both alleles of a tumor-suppressor
gene needed?
II. Oncogenes
• Arise from mutation in normal gene called a proto-oncogene;
these promote cell division
• Dominant mutation: one copy is sufficient to cause cancer.
(different than tumor-suppressors) - when switched on
permanently, uncontrolled cell division.
• First link between specific genes and cancer was proposed by
Francis Peyton Rous in 1910 (Nobel Prize, 1966): cell-free
extracts from chicken tumors injected into healthy chickens
caused new tumors. Some “agent” and substance must be
transmitting disease; now known that a virus and DNA/gene are
responsible.
Rous Sarcoma Virus (RSV)
• Discovered by Harold Varmus and Bishop, 1975-76 (Nobel Prize,
1989).
• A transforming retrovirus (TRV): a cancer-causing single-stranded
RNA virus that uses reverse transcriptase enzyme to make
ssDNA, then ds DNA, which integrates into host DNA.
• Note: not all retroviruses are TRV’s, not all oncogenes caused by
viruses.
• 100’s of oncogenes now known.
• RSV captured c-src gene from chickens during infection and it is
now in viral genome in slightly modified form. Now, upon
infection, the virus’ v-src transforms chicken cells into sarcomas
Southern Blots Probed with viral src Gene
Revealed Cellular Origin of Oncogenes
Infected
chicken #1
Infected
chicken #2
Uninfected chicken
(Negative Control)
v-src
c-src
Proto-oncogene
SURPRISE!
Origin of Transforming Retroviruses
Capsid protein Reverse Transcriptase Envelope Protein
c- onc
v-onc
Mutation creates oncogene
Converting a proto-oncogene
into an oncogene
1. Point mutations - example of ras, next slide
2. Translocations - example of CML/Philadelphia chromosome
3. Overexpression - c-onc may acquire new promoter or
enhancer - increase in transcription.
Ras Proto-oncogene
• Mutated in 30% of all cancers.
• A “molecular switch” in the signal transduction
pathway connecting growth factors to gene
expression controlling cell proliferation:
GF  receptor   Ras    TF  target genes
 cell division.
• A single amino acid change in Ras protein can cause
constant stimulation of the pathway, even in the
absence of growth factors.
KEY POINT To promote development of cancer, are
mutations in one or both alleles of a proto-oncogene
needed?
III. Translocations and genomic instability
**-A reciprocal
translocation
between chr. 9
and 22
c-abl proto-oncogene becomes part of bcr gene and this
hybrid bcr/c-abl oncogene is transcriptionally active; cell cycle becomes
deregulated - results in CML, chronic myelogenous leukemia. Single
white blood cell with translocation event may act as origin.
Genomic instability
Events resulting in genomic alterations that are characteristic
of cancerous cells - gains/losses of chromosomes,
rearrangements, amplification/deletion of genetic material
-- caused by 1) defects in DNA repair and replication,
2 ) abnormal chromosome segregation, 3) defects in cellcycle control
Example: 15% of colon cancer cases are HNPCC
(hereditary nonpolyposis colon cancer)
-see changes in microsatellite DNA throughout genome, resulting
in thousands of mutations
Intense debate on role that genomic instability plays in cancer:
cause vs. consequence of malignancy
IV. Cancers Usually Result from a
Series of Mutations in a Single Cell
Tumor suppressor
oncogene Tumor suppressors
Normal -> proliferating -> benign -> intermed. -> late -> cancerous -> colon
epithelium
adenoma adenoma adenoma adenoma
cancer
with villi
Tumor Progression: Evolution at the
Cellular Level
Benign tumor (polyp in
epithelial cells) is confined
by basal lamina; then
additional mutation occurs.
Malignant tumor (carcinoma
in epithelial cells) grows
very fast, becomes invasive,
and metastasizes.
Cancer Cells Evade Two “Safety”
Mechanisms Built into the Cell Cycle
1. Once p53 is inactivated, cells with DNA damage don’t
arrest from G1 and don’t undergo apoptosis.
2. Telomerase enzyme is activated, avoiding the limit to
cell divisions imposed by telomere shortening.
V. Carcinogens
•Chemicals are responsible for more cancers than viruses.
•Most are pro-carcinogens - must be converted metabolically to become
active carcinogens; then they bind DNA and cause point mutations
•Historically, first seen in 1700’s - scrotal skin cancer in people who
worked as chimney sweeps as children.
•Now, radiologists and farmers develop skin cancer; insulation workers
develop lung cancer, etc..
•Chemical carcinogens (tobacco smoke and diet) responsible for 50-60%
of cancer-related deaths.
-30% of cancer deaths related to smoking (cigarettes)
- polycyclic hydrocarbons are converted in cells and cause
mutations to DNA
Genetic testing and
predicting/treating cancer
Predictive testing
Do you want to know if you have a mutation in a tumorsuppressor gene or proto-oncogene? An increased
chance of developing cancer, but no clear answer if you
will or will not get cancer.
- what if it involves predisposition to a cancer
where medical surveillance could detect cancer early?
breast cancer vs. pancreatic cancer???
Testing for treatment/prognosis
difference in how you view a small breast tumor
depending on whether it has a mutation in p53 or not???
Know limitations and utilities of these tests