lecture 14 and 15 - cancer

regulatory genes

regulatory genes control

➢ Genome maintenance and repair

➢ Cell division (mitosis)

➢ Cell fate (differentiation)

➢ Cell survival (metabolism and apoptosis)

Cells have a limited lifespan.

➢ arise from stem cell population

➢ perform a specific job

➢ undergo a tidy packing-up process when they wear out

apoptosis

CANCER CELLS ARISE FROM

DNA damage

cancers are

sporadic

sporadic

the most common form of cancer—comprising 75% to 90% of cases—developing by chance, not through inherited genes, as a result of somatic mutations that accumulate over time.

epigenetic

how your behaviors and environment, such as diet and stress, cause changes that affect the way your genes work without altering the underlying DNA sequence.

Once enough

mutations effect

one cell,

it begins

to change.

Mutations

accumulate

faster and faster.

disrupted pathways

cell fate

cell survival

genome maintenance

cell fate

cell survival

genome maintenance

alterations

point mutations

copy number variants

chromosome rearrangements anupliody

changes in gene expression

point mutations

copy number variants

chromosome rearrangements anupliody

changes in gene expression

symptoms

biomarkers

imaging

mutation detection

Standard somatic cells

Only expresses a standard set of genes

related to the cell’s job

• Differentiated to perform a certain job,

  takes a standard shape

• Anchored, with contact inhibition

  (cells don’t divide unless connected)

• Damaged cells undergo programmed

  cell death (apoptosis)

• Cell division tightly regulated or inhibited

cancerous cells

Gene expression patterns change, proteins are mutated, new

proteins appear on the surface

• Shape changes, fewer connections to surrounding cells, irregular

  growth patterns

• Loss of contact inhibition, pressure on surrounding cells, mobility

  (cells lose anchors and start moving around– metastasis

• Apoptosis mechanisms disabled

• Unregulated cell division

What’s the problem?

Cells become less effective at doing their job.

Tissues deform and become less effective at

doing their job.

Rogue cells can start new tumors elsewhere,

disrupting other tissue

CANCEROUS CELLS UNDERGO

UNREGULATED MITOSIS

Mitosis

cell cloning

Unlike meiosis, mitosis just duplicates a cell exactly.

The two daughter cells are genetic copies of the parent.

do ALL cells undergo mitosis?

No, most stay in G1 or G0…

think of this as “daily life” phase for cells.

Multiple proteins

(encoded by genes!) keep mitosis under control.

cell cycle

CHECKPOINT PROTEINS PREVENT CELLS

FROM

DIVIDING UNLESS STRICT CONDITIONS ARE MET

Analogy for checkpoints:

gates in a parking lot or at a

train crossing.

❖ Prevent moving forward

unless fee is paid (signal is

received).

❖ Prevent moving forward if

conditions are unsafe

❖ Will never open if you

don’t have the right

permissions!

CELL CYCLE STAGES

CELL CYCLE CHECKPOINTS

Checkpoint 1:

Is there DNA

damage?

(Y/N-

Checkpoint 2:

Is new DNA copy

OK? (Y/N)

Are we big enough

for division? (Y/N)

Checkpoint 3

(metaphase):

Are all our

chromosomes lined

up and correctly

attached to fibers?

(Y/N)

Tumor suppressor proteins at each

checkpoint

prevent the cell from going any

further in the cycle until…

WHAT IF THE ANSWER IS “NO?”

• tumor or whatever

• …the problem is fixed.

Then the tumor suppressors turn

off, and cell cycle continues

…the problem is

irreparable

Then the tumor suppressors cause

the cell to commit apoptosis

WHAT WOULD HAPPEN IF MITOSIS OCCURRED WITHOUT FIRST

ENSURING DNA WAS PROPERLY COPIED?

A. The cell would divide unevenly

B. The cell couldn’t divide at all

C. The nuclear membrane would prevent chromosomes from moving to

the center

D. Some chromosomes could get missorted (nondisjunction)

E. DNA could be mutated due to mistakes in the DNA synthesis stage (DNA

replication)

Remember how mutations

occur:

❖ DNA template has

chemical damage

❖ DNA polymerase

makes a new strand

with mistakes

❖ Daughter cells now

have new mutations

WHAT WOULD HAPPEN IF MITOSIS KEPT GOING WITHOUT

FIRST ENSURING ALL CHROMOSOMES ARE LINED UP AND

ATTACHED TO SPINDLE FIBERS?

A. The cell would divide unevenly

B. The cell couldn’t divide at all

C. The nuclear membrane would prevent chromosomes from moving to

the center

D. Some chromosomes could get missorted (nondisjunction)

E. DNA would be mutated

GENE EXPRESSION PATTERNS ALSO

CHANGE

Leukemia

affects white blood cells. In leukemia,

useless cancer cells flood the bloodstream and

crowd out the vital red and white blood cells

microarray

• measures

  the expression of

  genes. Each square

  represents one gene.

• measures if genes are

  turned on MORE or LESS

  in cancer cells than in

  normal cells.

genes in microarray\

• This gene is expressed at higher levels in this

cancerous cell than in normal white blood cells.

• This gene is expressed at lower levels in this

cancerous cell than in normal white blood cells.

Leukemia affects white blood cells. In leukemia,

useless cancer cells flood the bloodstream and

crowd out the vital red and white blood cells.

• If there’s no change, it’s light

pastel

We’re interested in the overall expression

pattern of the chosen genes.

This could indicate dedifferentiation.

It means the cells aren’t making the correct

set of proteins for their specific duties.

dedifferentiation

a transient process by which cells become less specialized and return to an earlier cell state within the same lineage.

Cancer results from

multiple mutations, mostly spontaneous (not inherited),

accumulated over a lifetime

Mutations in cell cycle genes allow unregulated growth

• Mutations in DNA repair genes allow

mutations to accumulate more rapidly

• Mutations in cell-death genes

make the cancer cells harder to kill

• Mutations in cell-cell adhesion genes allow

allow cancer cells to break away and stat new tumors

(metastasis)

• Mutations in metabolism genes allow

cancer cells to steal more resources from the body

Exposure to anything that damages DNA (mutagens)

increases cancer risk

• DNA damage causes mutations

• DNA repair proteins can become overwhelmed and can also become mutated

Untreated cancer is ultimately fatal because

the tumor cells take up resources and do not contribute to keeping the body alive.

• The tumor cells press on and distort surrounding organs– altered structure means they become less

and less able to perform their functions.

• death occurs from organ failure

Everyone’s cancer is unique

Spontaneous mutations are different in each person

• Tumors are heterogenous

• Which means even in the same tumor, different cells have different mutations!

Everyone’s cancer is unique which makes cancer

• hard to detect. We can screen for commonly mutated genes, or other biomarkers, or changes in

overall gene expression.

• Hard to treat with a one-drug-fits-all approach. Treatment uses a variety of approaches:

• Chemotherapy: kill all currently dividing cells (which also kills healthy cells, causing the drastic side effects like

hair loss), encourage apoptosis (cell death)

• Radiation and surgery: remove as many abnormal cells as possible

• New techniques to specifically target tumor cells

MOST INHERITED RISK FACTORS FOR

CANCER ARE

REGULATORY GENES

REGULATORY GENES

control the expression of other genes, acting as "on/off" switches or volume knobs for protein production

You must know the

Example: inheriting mutation X increases risk of

cancer Y by 150% (1.5).

Base rate of getting cancer Y: 0.5% (0.005)

Calculate increased risk:

0.005 x 2.5 (1 + increased risk) = 0.0125

Your new risk of getting cancer Y because of

mutation X: 1.5%

INHERITING ONE BROKEN

ALLELE SPEEDS UP PROCESS OF

CANCER FORMATION

Inherited risk factors are

mutations in tumor

suppressor genes. The second mutation is

much easier to acquire when you already

have one.

Most common: 50% age*

➢ p53 30

➢ BRCA 1 or 2 50s

➢ Rb 1-2

nherited risk factors accoun

for only 5-10% of

cancer cases.

Most do not increase risk this drastically, either.

BOTH NATURAL PROCESSES AND

CARCINOGENS DAMAGE DNA

WHICH CAN

CAUSE NEW MUTATIONS

Natural mutagens:

Oxygen tobacco smoke

Oxygen

X-rays

UV radiation

Chemistry*

Avoidable mutagens

tobacco smoke

industrial chemicals / pollutions

alchohol

OXYGEN CAN CREATE

“FREE RADICALS”

(OR ROS) THAT DAMAGE DNA BASES

If the DNA is DAMAGED

during replication,

the cell

creates a mutation.

The G and C have switched

positions and the code is

changed.

Cells make antioxidants to

help absorb ROS before

they damage DNA.

antioxidants

substances—including vitamins (C, E), minerals (selenium), and enzymes—that protect cells by delaying or preventing damage caused by harmful free radicals (oxidative stress).

These mutations cause point mutations

anywhere in the genome

point mutations

a genetic alteration where a single nucleotide base pair in the DNA sequence is substituted, inserted, or deleted.

UV LIGHT ALTERS DNA STRUCTURE,

CREATING

ABNORMAL CHEMICAL BONDS CALLED

PYRIMIDINE DIMERS

Pyrimidine dimer

Two Ts or two Cs on same strand

form a covalent bond

Sometimes incorrect repair results

in Cs being converted to Ts.

ENZYMES CONSTANTLY SCAN

THE DNA FOR MISTAKES.

MISTAKES ARE FIXED BY CHOPPING OUT A PORTION OF ONE

DNA STRAND AND USING THE OTHER STRAND TO REBUILD IT

These enzymes can fix:

• Mismatches

• Chemically damaged bases

• Thymine dimers

Cannot fix

• Double-stranded backbone

breaks

• Double-stranded backbone

breaks

a severe form of DNA damage occurring when both sugar-phosphate backbones of the DNA helix are severed simultaneously or within close proximity.

CHEMICALS CAN CREATE CROSSLINKS,

ABNORMAL COVALENT BONDS BETWEEN

DNA STRANDS

Nitrogen Mustard ICL

Moiyomycin C ICL

Psoralen ICL

Cisplatin ICL

Trying to separate the

strands can

break the backbone

X-RAYS AND RADIATION CAN BREAK

THE

DNA BACKBONE

Highly energetic particles

rip

through cells like mini

wrecking balls!

If both sides of the DNA

backbone are broken, it’s

harder to fix– why?

CRISPR-CAS9 WORKS BY

CREATING

DELIBERATE DNA BACKBONE BREAKS

(WE CAN CONTROL EXACTLY WHERE)

DNA cleavage

the breaking of the covalent sugar-phosphate backbone that links nucleotides in a DNA strand, resulting in smaller fragments

knock in vs knock out in DNA cleavage

Knock-out (KO) and knock-in (KI) are DNA editing techniques that use cleavage to alter genomes. Knock-out uses cleavage to disrupt a gene (loss of function) via error-prone repair, while knock-in uses cleavage to insert specific DNA sequences (gain of function) via precise repair. KO is faster and more efficient, whereas KI is generally more complex. 

ZeClinics +3

Provide an intact template with

with the

change we want.

Force cell to use HR to repair to

edit a change into a gene.

example of chemotherapy drugs disrupting the cell

Taxol (paclitaxel)

disrupts spindle

formation.

Anaphase goes

badly wrong!

(some cells “freeze”

in this phase and die)

Cytokinesis in

multiple regions

results in 2+

aneuploid cells

which die

NEWER TECHNIQUES INVOLVE

GENETICALLY

MODIFYING A PATIENT’S CELLS TO HELP THE IMMUNE

SYSTEM DETECT AND FIGHT THE CANCER

Chimeric antigen receptor

CAR cell therapy enables a patients T cells attack cancer cells.

What are environmental factors that can increase your risk of cancer, and why?

• Radiation (UV light, X-rays, ionizing radiation): causes DNA strand breaks, pyrimidine dimers, and base modifications that can lead to permanent mutations if not repaired correctly.

• Chemical carcinogens (tobacco smoke, asbestos, benzene, aflatoxins): these molecules can directly alkylate or intercalate DNA, causing miscoding during replication.

• Viral infections (HPV, Hepatitis B/C, EBV): oncogenic viruses can insert viral DNA near proto-oncogenes, produce proteins that inactivate tumor suppressors (e.g., HPV's E6 protein degrades p53), or drive chronic inflammation that increases replication errors.

• Chronic inflammation: increases reactive oxygen species (ROS), which oxidize DNA bases (e.g., 8-oxoguanine), leading to transversion mutations.

• Poor diet / obesity: excess calories increase cell proliferation rates and hormonal signaling (e.g., insulin/IGF-1), raising the chance of replication errors.

➢ Why does inheriting mutations in DNA repair genes give you a strong predisposition to developing cancer?

DNA repair genes encode the cellular machinery that fixes replication errors and damage from environmental mutagens. If you inherit a defective copy of a repair gene (e.g., BRCA1/2, MSH2/MLH1 in Lynch syndrome), every cell in your body starts life with already-compromised repair capacity. This means:

• Errors that would normally be corrected now persist as permanent mutations.

• Mutations accumulate far faster than in someone with normal repair.

• The threshold for hitting the critical set of driver mutations needed for cancer is reached much sooner and more easily.

• You don't need an environmental "first hit" to disable repair — it's already impaired from birth.

This is why BRCA1/2 carriers have dramatically elevated lifetime risks of breast and ovarian cancer.

➢ Why would inheriting a mutation in a tumor suppressor gene like p53 or Rb give

you a strong predisposition to developing cancer?

Tumor suppressor genes act as brakes on cell division. Most cells carry two functional copies (two alleles). Under Knudson's "two-hit hypothesis", both copies must be inactivated to lose suppressor function.

If you inherit one mutant copy (one hit already present in every cell):

• You only need one somatic mutation in any susceptible cell to completely lose function, versus two in the general population.

• The probability of that second hit occurring in at least one cell over a lifetime is very high.

• p53 ("guardian of the genome") normally halts the cell cycle and triggers apoptosis in response to DNA damage — lose it, and damaged cells divide unchecked.

• Rb normally prevents the cell cycle from advancing past G1 — lose it, and cells proliferate even without proper growth signals.

This is why Li-Fraumeni syndrome (inherited p53 mutation) and familial retinoblastoma (inherited Rb mutation) cause very early-onset, multiple cancers.

➢ How many cancers (%) are caused by mutations that are NOT inherited, but accumulate over the course of a lifetime?

Approximately ~90–95% of all cancers are caused by somatic mutations — mutations that are not inherited, but accumulate over a lifetime in individual cells due to replication errors, environmental exposures, and random stochastic events. Only ~5–10% of cancers are strongly linked to inherited germline mutations.

➢ Why are all cancers genetically different?

Each cancer arises from a unique cell that accumulated a unique sequence of mutations over time, influenced by:

• The cell type of origin (a lung epithelial cell vs. a B-lymphocyte have different baseline gene expression and vulnerabilities).

• The specific mutagens the individual was exposed to (e.g., tobacco causes C→A transversions; UV causes C→T transitions).

• Random replication errors — DNA polymerase makes ~1 error per 10⁹ bp, and which specific bases are hit is stochastic.

• The order in which mutations accumulate alters which subsequent mutations are selected for.

Because the path to cancer involves hitting multiple driver genes through random processes in a unique individual environment, no two cancers will ever have exactly the same mutational profile.

➢ Why are cancer cells in the same tumor genetically different?

• The founding tumor cell continues to divide and accumulate new mutations after transformation.

• Cancer cells have increased genomic instability (often due to defective repair or checkpoint genes), so daughter cells mutate at higher-than-normal rates.

• Different subclones within the tumor evolve independently through clonal evolution and natural selection — some subclones may acquire resistance to therapy, faster proliferation, or invasive capacity.

• Spatial differences in the tumor microenvironment (oxygen, nutrients, immune pressure) apply different selective pressures on different regions of the tumor.

This heterogeneity is clinically important because it means a biopsy from one region may not represent the whole tumor, and it underlies the development of drug resistance.