BIMM 134: Biology of Cancer

Directly from notes

[start wk.1] Cancer is the _____ leading cause of death in the US.

Cancer is the second leading cause of death in the US.

Note: All diseases show a statistically significant decrease in 2023 compared to 2022, except CANCER…

Men: most likeky

1. Prostate

2. Lung Cancer

   1. Lung Cancer is the deadliest, yet the most avoidable (not smoking).

3. Colon Cancer

4. Pancreatic Cancer

   1. Pancreatic (survival rate is low, hard to detect, and very aggressive cancer)

Cancer Death Incidence in Male

Lung Cancer is the most deadliest, yet the most avoidable (not smoking). Prostate Colon Pancreatic (survival rate is low, hard to detect, very aggressive cancer)

Cause of Lung Cancer

• Approximately ___ of lung cancer related deaths attributed to tobacco use

• Approximately ___ of all cancer related deaths attributed to tobacco use

• Approximately 90% of lung cancer related deaths attributed to tobacco use

• Approximately 1/3 of all cancer related deaths attributed to tobacco use

Female: most likely

1. Breast Cancer

2. Lung Cancer

3. Colon Cancer

4. Pancreas

Cancer Death Incidence in Female

1. Lung Cancer is the most deadliest, yet the most avoidable (not smoking).

2. Breast

3. Pancreatic (survival rate is low, hard to detect, very aggressive cancer)

4. Colon

Education - Lung Cancer

*Other cancer declining rates: Colorectal, Breast, and Prostate…..why???

• A decrease in lung cancer deaths correlates to decrease of cigarette consumption

• Note: Females in US lagging in this compared to male

• Other cancer declining rates: Colorectal, Breast, and Prostate…..why???

  • Education

  • Sceening

  • Treatment

• Not much change in the other ones…………

Metastasis leads to ___% of cancer-related deaths

Metastasis leads to 95% of cancer-related deaths

At the time of diagnosis, approximately what % of cancers have already metastasized?

Up to 70% of patients with invasive cancer have metastases at diagnosis.

Approximately what % of US Budget has been spent on cancer research (pre-Trump)?

0.1%

What is Cancer?

• “Cancer” actually > >>>100 forms of disease

  • PATIENT SPECIFIC mutations; Genetically unstable; Intratumor variations/variations in metastases

• Basic processes/pathways that produce this diversity are the same

  • CELL DIVISION/CELL DEATH/CELL DIFFERENTIATION/Metabolism

• Cancer development is a multistep process; Cells must acquire multiple mutations (4-7) for malignant transformation

  • ONE “RENEGADE CELL”

  • DECADES TO DEVELOP

How can we combat this diversity in cancer among patients?

• GENOMICS;PROTEOMICS; PHARMACOGENETICS

  • “New proteomics (proteins) and genomics (DNA and RNA) arrays can distinguish between cancer severities and predict the most effective treatments.”

• Development of patient/tumor-specific diagnosis/treatments

  • “If you overtreat patients, it can piss off the tumor.”

  • You don’t want to overtreat; cancer can be “sticky”

Basic processes/pathways that produce this diversity the same: Cancer

• Increase proliferation/decrease senescence

  • senescence: the condition or process of deterioration with age.

• Increase survival/decrease apoptosis

• Decrease differentiation

• Increase cell motility (metastasis)

“Cancer development is a multistep process; Cells must acquire ____ (4-7) for malignant transformation”

Cancer development is a multistep process; Cells must acquire multiple mutations (4-7) for malignant transformation

Malignant vs. Benign Tumors

• Benign (not cancer) tumor cells grow
  only locally and cannot spread by invasion or metastasis

• Malignant (cancer) cells invade neighboring tissues, enter blood vessels, and metastasize to different sites

Cancer Classification

Carcinomas

• The most common cancer type with >80% of cancer-related deaths

• Two-types (not needed to know):

  • Squamous cell carcinomas

    • derived from cells forming protective layer from underlying cells (ex skin,cervix)

  • Adenocarcinomas:

    • Derived from cells lining secretory cells (ex. Mucous producing cells within lung,colon, prostate)

• Some tumors have mixture of these and several are separately classified

Sarcomas

Derived from connective tissues like bone,fat,etc

Hematopoietic

Derived from blood producing cells

• Leukemias are circulating malignancies

• Lymphomas derived from B and T lymphocytes

  • Usually solid masses in lymph tissue

Tumor Grade vs. Stage

• Tumor Grade: Appearance of cells in biopsy

• Tumor Stage: How far the cancer has spread

What does a pathologist look for?

• Mitotic rate

  • How many/fast cells are dividing

    • Increased mitotic rate = worse grade

• Nuclear grade

  • abnormal nuclei = worse grade

• Cellular differentiation

  • Loss of cell specialization=worse grade

• Surgical margins

  • How close are tumor cells to the surgical edge

  • Positive=cells at edge=worse prognosis

Cancer Progression Stages

• Many cancers have somewhat predictable mutational patterns

• Colon cancer highly characterized

TNM STAGING

• PRIMARY TUMOR

• ABSENCE/PRESENCE REGIONAL LYMPH NODES

• ABSENCE/PRESENCE DISTANT METASTASIS

Stage	Description	Example of TNM
I	localized	T2N0MO (Patient 1)
II or III	Regional spread	T3N2MO (Patient 2)
IV	Distant Metastasis	T3N2M1 (Patient )

^Need to know!!

SIMPLIFIED TNM EXAMPLES

Patient 1 Biopsy: well-differentiated;low mitotic index; good surgical margins (LOW GRADE);

Gene screen Estrogen receptor +; Her2+; progesterone receptor +

Patient 2 Biopsy: poorly differentiated; high mitotic index good surgical margins (High GRADE)

Gene screen Estrogen receptor +; Her2+; progesterone receptor +

Patient 3 Biopsy: poorly differentiated; high mitotic index poor surgical margins (High GRADE)

Gene screen Estrogen receptor neg; Her2 neg; progesterone receptor neg(TRIPLE NEGATIVE)

Stage	Description	Example of TNM
I	localized	T2N0MO (Patient 1)
II or III	Regional spread	T3N2MO (Patient 2)
IV	Distant Metastasis	T3N2M1 (Patient )

Obesity vs. Cancer

• Fat produces factors that increase the likelihood that cells will develop mutations.

• These factors represent Carcinogens: Cancer Promoters

Exercise vs Cancer

• IN CONTRAST, exercise decreases the risk of cancer and cancer progression

• Decreases circulating cancer promoters

• Increases immune response against cancer.... "poisons the tumor-promoting microenvironment

Carcinogens

1. Mutagens: Directly mutate DNA/RNA

   • Include tobacco; UV radiation

2. Promoters: Increase the likelihood of mutations

   • Substances that increase proliferation, cell damage, inflammation e.g., Alcohol;hormones

3. A combination often results in a synergistic increase in cancer incidence

Alcohol + Smoking

• Alcohol caused cell damage and stimulates cell proliferation

• Smoking leads to DNA mutation

• Work synergistically to produce greater effect than acting singly

Oncogenes vs Tumor Suppressors

Oncogene

• Gain of function (stuck accelerator)

• Dominant phenotype

Tumor Suppressors

• Loss of function

• Recessive phenotype

• Generally, a combination of activation of oncogenes and inactivation of tumor suppressor genes lead to lack of growth control and unrestrained proliferation

Proto-oncogene vs Oncogenic Ras

• Proto-oncogene: Ras with normal function

• Oncogenic Ras: Increase Ras activity, increase in proliferation

Telomeres, telomerase, and cellular “immortality

• Telomeres are a repeated sequence at the ends of the chromosomes that protect the chromosomes from damage

• Cancer cells re-express telomerase leading to unlimited cell division: Endless tank of gas

Apoptosis

• Cell death

• Cancer cells decrease apoptosis via several mechanisms including

• Gain of anti-apoptotic proteins (e.g. Bcl-2)

• loss of pro-apoptotic proteins (e.g.BAX or p53)

Angiogenesis

• Tumors are limited in growth to around 1-2mm due to limited diffusion of oxygen/nutrients and removal of waste

• In response, cancer cells initiate an “angiogenic switch”

  • Increasing release of pro-angiogenic molecules (e.g. VEGF)

  • Decreasing release of anti-angiogenic molecules (e.g. thrombospondin)

Angiogenesis results in…

• Resulting in new blood vessel growth

• Growth of cancer

• Invasion into the bloodstream

• Metastasis

Summary of main hallmarks of cancer

Gain of an oncogene

• Example: RAS

  • Car analogy: stuck accelerator

Loss of tumor suppressor

• Example: Loss of p53

  • Car analogy: cutting the brakes

Cell immortalization

• Example: Loss of telomerase

  • Car analogy: running out of gas (or electric charge..)

Loss of apoptosis

• Example: Loss of p53

Angiogenesis: growth of blood vessels into tumor

• Example: Increase in VEGF

Metastasis: Spread to distant sites

• Example: loss of E-cadherin

Warburg effect: Aerobic glycolysis

The Warburg effect is when cells preferentially use glycolysis to produce energy even in the presence of oxygen, leading to lactate production (aerobic glycolysis).

[end of wk.1] Reverse Warburg effect

Instead of cancer cells doing glycolysis themselves, nearby stromal cells (like fibroblasts) do glycolysis and feed the cancer cells.

[start of wk.2] Enzyme-linked Receptors: Tyrosine Kinase receptors

• Many growth factors (insulin, epidermal growth factor, fibroblast growth factor) use this type of receptor

• Important for control of cell division and growth

• These are often mutated in cancer cells

Signal Transduction: Phosphorylation Cascade

• Adding or removing P to molecules is used to activate/deactivate molecules

• Protein Kinases: Add phosphates

• Protein phosphatases: Remove P

• Tyrosine Kinases: Add phosphates to tyrosines

• Serine/threonine Kinases: Add phosphates to serine/threonines

• Dual kinase:has both tyrosine kinase and ser/thr kinase activity

• Lipid kinase: Add phosphates to lipids

Tyrosine Kinase receptors

• Family of related receptors

• Share common extracellular and intracellular protein domains

INCREASED COMPLEXITY

• Some signals can activate several receptors

• Some receptors activated by multiple ligand Intracellular pathway convergence and divergence

• Intracellular pathways can have numerous cellular effects depending on pathways that are activated

EGF-RTK-RAS-MAPK Pathway

• EGF binds to EGF Receptor

• Binding causes conformational change in receptor exposing extracellular dimerization domain

RTK-RAS-MAPK Pathway

• EGF binds to EGFR

• Binding causes conformational change in receptor

• Exposing extracellular dimerization domain

• Receptor dimerization

• Autophosphorylation of key tyrosines needed for recruitment of signal molecules

• Phosphorylation of key tyrosine levels result in binding/activation of numerous intracellular molecules

• Helps explains activation of multiple downstream pathways/cellular effects

INCREASED COMPLEXITY

• Some signals can activate several receptors

• Some receptors activated by multiple ligand Intracellular pathway convergence and divergence

• Intracellular pathways can have numerous cellular effects depending on pathways that are activated

Intracellular protein interactions

• Intracellular protein interactions Mediated by specific protein modular domains

• SH2 (Src homology 2) 100 amino acids

• Interact with specific amino acids located near P tyrosine

• SH3 (Src homology ) 50 amino acids

• Interact with proline and hyrdophobic residues on proteins

Protein recruitment to membrane/receptor

• Protein recruitment to the membrane/receptor Adaptor GRB2 binds to EGFR via the SH2 domain

• SH3 domains of GRB2 bind SOS (son of sevenless), which recruits SOS to the membrane

  • SOS is a GEF( Guanine-nucleotide exchange factor)

  • Transfers a GTP to Ras: activates Ras

• Results in RAS binding/activation

  • RAS is subsequently inactivated by GAP (GTPase) proteins, which hydrolyze GTP to GDP

RAS Modifications

• Addition of a farnesyl lipid and methylation to RAS targets thought to be necessary for full RAS activity

• Farnesyl transferase inhibitors have been tested in clinical trials

RTK-RAS-MAPK Pathway

• Ras now recruits RAF and other proteins to membrane

• RAF is a serine/threonine kinase

• RAF (MAPKKK) adds P and activates

• MEK (MAPKK) MEK is a tyrosine and ser/thre kinase

• MEK adds P and activates MAPK (also called ERK: extracellular signal-related Kinase)

  • Activated MAPK translocates to nucleus and activates transcription factors

  • These include AP-1 (Fos/Jun) and Myc:Max

  • Activate many genes (e.g. cyclins) promoting cell cycle/cell division

Alternative MAPK pathways

• JNK and P38 MAPK pathways

• Respond to cellular damage/stress

• Usually trigger apoptosis

• Type and severity of signals can lead to either

• Cellular survival or Cellular death

RAS-PI3K-AKT Pathway

• RAS can also activate other pathways that often mutated in human cancers, including PI3K/AKT pathway

• RAS activated Phosphatidylinositol-3-kinase (PI3K:Lipid Kinase):This kinase attaches phosphates to lipids,in this case, to PIP2, producing PIP3

• PIP3 binds a serine/threonine kinases and PDK-1 and AKT(PKB): PDK1 activated AKT

• Phosphorylation of AKT/PKB leads to phosphorylation/activation other substrates resulting in

• Decrease apoptosis/increased survival

• Increase in protein synthesis

RAS-PI3K-AKT-mTOR Pathway

Note: mTOR is also a serine threonine kinase

• Activation of the serine/threonine kinase,mTOR, (mechanistic/mammalian target of rapamycin),

• leads to activation of many cancer hallmarks

• proliferation

• motility/metastasis,

• angiogenesis, and decreased apoptosis

• Studies suggest that the disruption of the PI3K pathway is one of the most common pathways mutated in human cancers

• loss of PTEN (a phosphatase) the most abundant tumor suppressor mutation

• PTEN converts PIP3 back to PIP2 inhibiting pathway

Point mutations vs Gene Amplification

• Point mutations

  • deletions of the receptor causing ligand-independent dimerization/activation

• Gene amplification

  • overexpression of receptors; ligand-independent dimerization/activation

• Conversion from paracrine to autocrine signaling pattern

  • Cancer likes autocrine; to be independent

EGF Receptors and Ligands

• Two main receptors

• (HER1)(erB1)

• HER2(erB2)

HER2

• Over expression of HER2 common in breast cancer

• Expression associated with poor prognosis

• Over expression of HER2 results in ligand-independent HER2 dimerization/activation of Ras-MAPK and PI3K-AKT pathways

RAS mutation

• RAS normally only sends signals when a positive growth signal is sent to the cell

• Then RAS becomes quickly deactivated

• Ras point mutations prevent Ras interaction with GAPs (GTPase activating proteins)

• Prevents (decreases) hydrolysis of GTP

• Ras remains in activated state for extended periods of time

• most RAS mutations are within codons

  • 12,13,61

• Codon 12 mutations predominate in lung,colorectal and pancreatic cancers

  • High prevalence of a G12C (Glycine to cysteine) mutation is associated with Lung adenocarcinoma (LUAD)

  • High prevalence of a G12D (Glycine to Aspartate) mutation is strongly associated with pancreatic (PDAC) and colorectal cancer (CRC)

⭐RAS therapeutics : Undruggable target…???…️

• Ras has been considered “undruggable” because

• GTP binding pocket relatively inaccessible

• High affinity for GTP

• High levels of cytoplasmic GTP

⭐ Two inhibitors targeted G12C mutations in NSCLC have gained FDA approval

Sotorasib (2021) and Adagrasib (2022)

RAS therapeutics RAS G12C mutations in NSCLC

• These small molecules covalently bind to the cysteine in the G12C mutation in the switch-II GTP binding pocket preventing/decreasing activation

• They do not greatly affect wild-type RAS or other RAS mutations

RAS therapeutics RAS G12D mutations in Pancreatic cancers

• Development of RMC-6236