Understanding Cancer Biology

• Cancer is a leading cause of death worldwide, with some cancers increasing in incidence in certain age groups in the US, such as colorectal cancers under 50, prostate cancer, and breast cancer in women under 40.
• Only 5-10% of breast cancers are linked to family history.

Definitions

• Cancer is a clone of cells with aberrant growth or impaired death in common.
• A benign tumor remains clustered and is relatively non-aggressive, like adenomas.
• Carcinomas arise from epithelial cells, for example, breast carcinomas.
• Dysplasia is the abnormal growth of cells, but not necessarily a tumor.
• Hyperplasia is increased cell growth.
• A malignant tumor is an aggressive, metastasizing tumor that has accumulated multiple genetic changes, like adenocarcinomas.
• Malignant transformation is the process of changes that convert a normal cell to a cancerous cell.
• Mutation is a change in the DNA sequence that is fixed as cells divide.
• Sarcomas are connective/soft tissue cancers.
• A tumor is a collection of cells, including cancerous cells, and can be solid or leukemic.
• Leukemias arise from blood cells; some can form solid tumors, for example, plasmacytoma.
• Necrotic cell death is non-apoptotic and usually due to an environmental stimulus.

Phosphorylation

• Phosphorylation is the addition of a phosphate group from ATP to a protein on serine, threonine, or tyrosine.
• Serine, threonine, and tyrosine are three amino acids that can be phosphorylated or unphosphorylated.
• A kinase is an enzyme that adds phosphate groups to proteins on serine, threonine, or tyrosine
• An enzyme is a protein that facilitates a chemical reaction.
• Phosphatases are enzymes that remove phosphate groups from proteins on serine, threonine, or tyrosine.
• Growth factors signal from outside the cell to the nucleus through a phosphorylation cascade, where each step activates the next.
• A growth factor binds to a receptor tyrosine kinase (RTK) on the cell membrane.
• Receptors undergo phosphorylation, which activates intracellular signaling proteins.
• A phosphorylation cascade transmits the signal to the nucleus (RasRafMEKERK).
• ERK phosphorylates transcription factors like Myc, leading to increased expression of genes that promote cell growth and division.
• In cancer, mutations can hyperactivate signaling, leading to unchecked proliferation, survival, and tumor formation.
• This may result from the increased presence of growth factors.
• A mutant Ras stays “on,” driving constant signaling.
• Overactive Myc leads to uncontrolled cell division.
• Loss of tumor suppressors like p53 and Rb removes braking mechanisms.

Types of Proteins that Control Cell Cycle

• Growth factors like IL-6, EGF, and PDGF interact with cell surface receptors.
• Growth factor receptors, such as HER2/Neu, activate various signal transduction pathways.
• HER2/Neu is a transmembrane tyrosine kinase receptor involved in cell growth that is abnormally activated in some cancers, like breast cancer.
• Signal transduction factors like Abl, Src, and ALK kinases activate secondary messengers inside the cell, amplifying the signal and helping transmit it within the cell.
• Transcription factors, such as NF-B and AhR, are activated once a signal has been transduced in a cell.
• Transcription factors bind to specific DNA sequences to activate or repress gene transcription, which leads to the production of proteins that control cell function.
• AhR is a ligand-activated transcription factor that detects environmental toxins and regulates gene expression and is involved in cell migration, metastasis, and cancer stem cell formation.
• Anti-apoptosis factors, such as the BCL family, inhibit apoptosis.
• BCL-2 is an anti-apoptosis protein often up-regulated in cancer to facilitate cell survival.
• Cell cycle control proteins (cyclins) accumulate during different phases of the cell cycle and bind to CDKs.
• CDK-cyclin complexes phosphorylate target proteins that drive the progression of the cell cycle from one phase to the next.
• DNA repair/elongation proteins include telomerase.

Hallmarks of Cancer

• Hallmarks of cancer represent the changes that occur in cells when they become malignant and some of the agents that cause those changes, such as microbiome changes.
• The most generic hallmarks: aberrant cell growth, defective cell death, identity crisis (invasion, metastasis, loss of contact inhibition), and alteration of microenvironment.

Aberrant Cell Growth

• Aberrant cell growth involves sustaining proliferative signaling and evading growth suppressors.
• The four main stages of the cell cycle are G1, S, G2, and M.
• G1 involves growth and the synthesis of components required for DNA synthesis.
• S involves DNA synthesis and increased transcription, translation, and metabolism.
• G2 prepares for mitosis and doubles chromosomes.
• M involves mitosis and cell division.
• Each phase is controlled tightly by a cascade of activation and inactivation of kinases and transcription factors.
• The process is regulated by outside forces like hormones/growth factors and by inside forces.
• Factors relevant to cell cycle control (can go out of whack in cancer) are cyclins, cyclin-dependent kinases, tumor suppressor genes, E2F, and oncogenes.
• Cyclins are proteins that regulate the cell cycle at various checkpoints and are activated or inactivated by kinases, for example, cyclin D, cyclin E, and cyclin A.
• Cyclins regulate CDKs, which drive cell cycle progression, so overexpression of certain cyclins or hyperactivation of CDKs can push cells through the cycle unchecked, which promotes cancerous growth.
• Cyclin-dependent kinases (CDKs) are kinases that must associate with cyclins to be activated.
• CDKs work with cyclins to phosphorylate down-stream targets during cell growth.
• CDKs are involved in regulating cell cycle checkpoints.
• CDKs may interact with tumor suppressor proteins like Rb.
• A tumor suppressor gene is a gene whose protein product down-regulates cell growth or induces apoptosis.
• P53 is a tumor suppressor gene that regulates cell growth and can initiate apoptosis, hence it is “guardian of the genome”.
• P53 halts the cell cycle for DNA repair or triggers apoptosis if damage is severe.
• The Retinoblastoma gene (Rb) is a tumor suppressor gene that restricts the cell cycle.
• Rb controls the G1/S checkpoint by inhibiting E2F.
• E2F is a transcription factor required for DNA synthesis that is inhibited by the Rb tumor suppressor protein.
• Mutations in either gene removes “brakes” of cell cycles, allowing unchecked proliferation.
• An oncogene is a gene that has the potential to cause cancer and results from mutation, amplification, or chromosomal translocation.
• Myc is an oncogene and transcription factor that promotes cell growth and proliferation by upregulating genes needed for metabolism and division; when mutated or overexpressed, it drives excessive cell division.

Defective Cell Death

• Defective cell death involves apoptosis

Apoptosis

• Apoptosis is an active process of cell suicide characterized by cell shrinkage and DNA fragmentation.
• Apoptosis functions as a fail-safe mechanism.
• At various points in the cell cycle, the cell checks for appropriate cell function/accurate copying of DNA.
• If defective, the cell can activate the apoptosis pathway to prevent mutations from being replicated.
• DNA is wound around histones, and caspases cleave at the nucleosome during apoptosis.
• A nucleosome is a length of DNA coiled around a core of 4 histones that occur about every 200 bp.
• A caspase (Cysteine Aspartate-specific Proteases) is a protease enzyme that plays a central role in apoptosis.
• Initiator caspases trigger apoptosis by activating executioner caspases.
• Executioner caspases break down cellular components, leading to cell death.
• Inflammatory caspases are involved in immune response.
• An endonuclease is an enzyme that cleaves DNA.
• The Intrinsic (mitochondrial) pathway is triggered by internal stress, such as DNA damage or oxidative stress.
• P53 can activate the pathway by increasing Bax/Bak, which creates pores in the mitochondrial membrane, releasing cytochrome C into the cytoplasm.
• Cytochrome C binds to APAF1, undergoes conformational change, and assembles into the apoptosome (multiprotein complex).
• APAF1 is apoptosis protease activating factor 1.
• The apoptosome activates caspases to degrade cellular components, leading to cell death.
• The Extrinsic (death receptor) pathway is triggered by external signals, which bind to their respective death receptors.
• The extrinsic pathway activates caspase-8, which directly activates executioner caspases or amplifies apoptosis via the intrinsic path.
• Apoptosis is a balance between Bax + caspases (death) vs Bcl-2 (life).
• When BCL-2 is up-regulated in cancer, this prolongs cell life by preventing death.
• Apoptosis pathway disruptions in cancer include reduced expression of death signal/receptor.
• Defects/mutations in p53 prevent activation of the intrinsic pathway.
• Reduced expression of caspases prevents cell degradation.
• Increased expression of IAPs (inhibitors of apoptosis proteins) prevents cell death by inhibiting caspases.
• There is a disrupted balance between Bcl-2 (life) and Bax + caspases (death).
• Overexpression of antiapoptotic proteins like Bcl-2 prevents the mitochondrion from developing pores and releasing cytochrome C.
• Under expression of proapoptotic proteins like Bax also disrupts the balance.

Enabling Replicative Immortality via Telomerase

• Telomerase is an enzyme that contains a single strand of RNA and extends the ends of chromosomes (telomeres) during DNA replication and is often over-expressed in cancers.
• Telomeres are protective caps at the ends of chromosomes.
• In normal cells, telomeres shorten with each cell division, eventually triggering growth arrest or apoptosis.
• In cancer cells, telomerase is reactivated, allowing them to maintain telomere length and divide indefinitely.
• Over-expression of telomerase, which is found in ~90% of human cancers, provides immortality, enabling tumors to grow uncontrollably.
• Therapeutic options: telomerase inhibitors, immunotherapies targeting telomerase-expressing cells.

Cancer Stem Cells

• Cancer stem cells are a subpopulation of tumor cells that function as a single, self-renewing cell/clone that drives tumor growth, metastasis, and treatment resistance.
• Normal tumor cells are more differentiated and less able to self-renew or sustain tumor growth.
• Cancer stem cells represent a very small % of the tumor, but like to metastasize.
• A clone is the offspring of a single cell.
• Cancer stem cells are able to self-renew (create more CSCs) and differentiate into various cell types that make up the tumor, allowing them to sustain tumor growth over time even after the majority is killed by therapy.
• Cancer stem cells are often more aggressive and have a high capacity to initiate tumor formation.
• Cancer stem cells are more resistant to chemotherapy, radiation, and targeted therapies compared to other tumor cells, for example, AhR drives the chemoresistance.
• Cancer stem cells have enhanced migratory and invasive abilities, allowing them to spread to distant organs and form secondary tumors (metastasis).
• Cancer stem cells interact with the tumor microenvironment (e.g., immune cells), which helps them evade immune surveillance.

Identity Crises

• Identity crises involve activating invasion and metastasis.

Activating Invasion and Metastasis

• Epithelial to Mesenchymal transition is the process where epithelial cells (which are tightly adherent and form structured layers) transition into mesenchymal cells (more migratory and less adhesive).
• EMT enables cancer cells to become more invasive and metastatic, which facilitates the spread of cancer and contributes to poor prognosis and therapy resistance.
• EMT plays a critical role in cancer progression, particularly metastasis, resulting in the loss of epithelial traits and the gaining of mesenchymal traits.
• Loss of epithelial traits: cell-cell adhesion, tight junctions (which maintains tissue structure).
• Gaining mesenchymal traits: increased motility, invasiveness, and resistance to apoptosis, allows cancer cells to invade surrounding tissues and enter bloodstream, leading to metastasis.
• EMT provides resistance to chemotherapy and radiation b/c of the promotion of stem-like properties.
• AhR drives human tumor metastasis through the activation of EMT signaling, enhancing the cell migration/invasion, and making tumor cells more like CSCs so they can evade treatment.

Alteration of the Microenvironment

• Alteration of the microenvironment involves inducing or accessing vasculature.

Inducing or Accessing Vasculature

• Angiogenesis is the process by which new blood vessels are formed from existing ones, which helps tumors grow/spread.
• Angiogenesis provides the tumor with nutrients and oxygen, facilitates growth and survival, enables metastasis (allows cancer cells to enter the bloodstream), and enhances resistance to therapies.
• Vascular endothelial growth factor (VEGF) is a protein that plays a role in angiogenesis.
• Anti-VEGF drugs are used in some cancer treatments.

Genome Instability and Mutation

• Genome instability is an increased rate of mutations, which can result from factors like defective DNA repair, errors during cell division, or environmental stress such as radiation or toxins.
• Mutations can lead to the loss of DNA repair mechanisms, activation of oncogenes (promoting uncontrolled cell growth), or the inactivation of tumor suppressor genes.

Polymorphic Microbiomes

• The microbiome is in aggregate the microbial population in a given organ such as the gut, oral cavity, or skin.
• An imbalance in the microbiome can contribute to cancer.
• The microbiome increases inflammation, which drives cancer because it creates a microenvironment that promotes genomic instability.
• The microbiome produces carcinogenic metabolites, which directly damage DNA.
• The microbiome affects host metabolism, affecting hormone or immune pathways.
• The microbiome impairs the body’s ability to recognize and attack tumor cells.
• The microbiome enhances or reduces the efficacy of cancer treatments.
• Gut infections are prevalent in some cancers, for example, colorectal carcinomas.

Viruses, Oncogenesis, and Cancer

• Proto-oncogene expression or function is disrupted by deletion or point mutation in the coding sequence, resulting in a hyperactive protein produced in normal amounts.
• Proto-oncogene expression or function is disrupted by gene amplification, which results in a normal protein greatly overproduced.
• Gene amplification: process by which multiple copies of the same oncogene are passed on from cell to daughter cell and amplification of genes involved in growth result in aberrant cell cycling.
• Proto-oncogene expression or function is disrupted by chromosome rearrangement, resulting in a nearby strong enhancer causing a normal protein to be overproduced.
• Proto-oncogene expression or function is disrupted by inversion resulting in fusion to an actively transcribed gene greatly overproduces/hyperactivates fused protein.
• Proto-oncogene expression or function is disrupted by methylation of tumor suppressor genes.

Proto-Oncogenes

• A proto-oncogene is a normal cellular gene (c-gene) that influences cell growth and division, cell death, and homing.
• When proto-oncogenes mutate, they can lead to malignancy (oncogene).
• Viruses acquire these genes to aid propagation.
• Rous sarcoma virus Src proto-oncogene
• c-myc: proto-oncogene regulated by c-Rel protein and encodes a transcription factor that represses p27, an inhibitor of the cell cycle.
• c-Rel: proto-oncogene which codes for a member of the NF-B family of transcription factors.
• c-Src: proto-oncogene which codes for a protein kinase involved in intracellular signaling.
• c-Src is homologous with v-Src in the Plymouth Rock hen (viral version).
• C-oncogenes or proto-oncogenes are the mammalian (normal) version.
• “Oncogene” is used to refer to the mutated form of a c-oncogene in cancer.
• K-Ras: proto-oncogene which helps regulate protein phosphorylation; activated by binding to a small molecule, guanine triphosphate (GTP).
• K-Ras is associated with ~50% of tumors with mutations.
• Oncogene-personalized cancer treatments

Chromosomal Abnormalities

• Gene translocation is the exchange of genetic material from one chromosome to a non-homologous chromosome, resulting in an unusual rearrangement of chromosomes, for example, the bcr-Abl, chromosome 9 to chromosome 13 translocation, i.e., the Philadelphia chromosome.
• Src Homology (SH2) domain: part of a protein enabling it to bind to other proteins with phosphorylated tyrosine.
• Cancers associated with translocation include Chronic Myelogenous Leukemia, a cancer of myeloid blood cells resulting from a translocation of the ABL gene to the BCR regulatory region resulting in a fusion protein of BCR-ABL, i.e., the Philadelphia Chromosome
• Gene inversion: a chromosomal rearrangement in which a part of a chromosome is reversed end to end.

Micro RNA

• OncomiR: a microRNA (miRNA) that contributes to cancer.
• Increased miRNA expression leads to decreased tumor suppressor gene expression.
• Decreased miRNA expression leads to increased oncogene expression.
• Metastatic miRNAs: epithelial to mesenchymal transition (EMT) causes metastasis after initiation and progression in tumor cells, and miRNAs play a role.
• Oncogenic miRNAs promote tumor development by negatively inhibiting tumor suppressor genes and/or genes that control cell differentiation or apoptosis.
• Tumor suppressor miRNAs target oncogenes in cell differentiation, invasion, apoptosis, proliferation, and metastasis.

Cancer-Causing Viruses

• Human Papilloma Virus (HPV): a transmissible virus that causes warts and the majority of cervical cancers.
• HPV infects cervical cells and integrates DNA into the host genome using viral replication proteins.
• High-risk HPV strains inactivate tumor suppressor proteins (p53 and Rb), leading to uncontrolled cell growth, genetic instability, and the development of precancerous legions.
• The Gardasil (HPV) vaccine is highly effective in preventing infection.
• The incidence of HPV-associated oral cancers has increased over time, while cervical cancer rates have decreased.