Block 2 Flashcards
Cancer
What is cancer?
uncontrolled, clonal (arising from a single transformed progenitor cell) proliferation of cells uncoordinated with normal tissue proliferations that continues in the absence of stimuli
Benign vs. malignant tumors?
non-cancerous, slow growing, distinct borders (capsulated)
don’t invade surrounding tissue or spread
cells are normal
can still cause health issues
cancerous, grow quickly, irregular borders (non-capsulated)
invade surrounding tissue and spread
cells have large, dark nuclei, can have abnormal shape
often cause death
How can benign tumors cause health issues?
- compression of surrounding tissues and organs
ex) pituitary adenoma pressing on optic nerve - obstruction of passages (blood vessels, airways, digestive tracts)
- hormonal effects: tumors in endocrine glands can disrupt hormone levels
Tumor grade vs. stage?
appearance of cancer cells: nuclear atypia (high N:C ratio), cellular pleomorphism (variation in size and shape), polarity: poorly organized, loss of tissue architecture, tend to grow/spread faster (more mitosis), necrosis
poorly differentiated = higher grade = more abnormal looking
extent of tumor spread from the primary site
high stage = spread to distant parts of the body
TNM staging: tumor size (T1-T4), lymph node number/localization (N1-N3), metastasis (M0-M1)
How are cancers named?
tissue of origin and if they are malignant or benign
malignant: -carcinoma, -sarcoma
benign: -oma
How does cancer lead to death?
- local growth: space filling lesions that can impinge crucial structures and obstruct normal flow (nerves, blood vessels, GI) ; bleeding, infection
- metastasis: replacing normal, functioning tissue; most common = lungs, liver, bones (no immune cells), brain (LOF)
- secretion factors: secrete biological molecules that lead to physiologic dysfunction: pro-clotting factors (cut off blood supply), tumor necrosis factor (cachexia: muscle wasting, fat loss)
What are the three conditions associated with secretion of factors?
Trousseau’s Syndrome: secretion of tissue factor that lead to coagulation
Paraneoplastic Syndrome: secretion of hormones not normally made by those cells that leads to hypercalcemia, hypoglycemia
Cancer Cachexia: pro-inflammatory molecules (TNF) and catabolic factors produced by tumor suppresses appeptite; loss of skeletal muscle and adipose tissue from proteolysis, lipolysis, and futile cycling
What are the agents of mutation that initiate cancer development?
- chemicals: carcinogens can initiate cancer (mutagens) or promote its growth (stimulators): cigarette smoke, alcohol
- UV radiation: also mutagenic (pyrimidine dimers)
- Microbial: viruses (HPV), bacteria (H Pylori), parasites can encode oncogenes or proteins that disable tumor suppressors, can cause chronic inflammation with injury repair, cause immunosuppression
What are the two types of carcinogens?
initiators (mutagens) and promoters (stimulator of growth): need both
inflammation: ROS are mutagenic, growth factors, pro-angiogenic factors
consequences of proliferation
- DNA replication errors
- Telomere shortening
What are the Hallmarks of Cancer?
KEEP dividing/proliferating + avoid being killed
1. sustained proliferative signaling
2. evading growth suppressors
3. avoiding immune destruction
4. enabling replicative immortality
5. tumor-promoting inflammation
6. activating invasion & metastasis
7. inducing or accessing vasculature
8. genome instability and mutation
9. resisting cell death
10. deregulating cellular metabolism
Sustaining proliferative signaling
mutations in growth factor signal transduction cascade (oncogenes)
- Growth Factors: increased expression that permits autocrine signaling
- TGF-alpha, FGF - Receptors: activation without growth factors
- EGF-R in lung - Signal transduction
- RAS: always active + GTP-bound - Transcription Factors: activates cell cycle genes
- MYC: amplifications in breast, colon
translocations in Burkitt Lymphoma - Cell cycle increases
Evading growth suppressors
Together with sustained proliferative signaling (oncogene mutations), you
need co-occurring evasion of growth suppressors (tumor suppressor mutations) to drive tumor development
dysfunction of various genes that arrest the cell cycle: Rb (blocks DNA synthesis) + p53 (regulates cell cycle, DNA repair, apoptosis)
What drives cancer growth?
genetic mishaps: translocation, mutation, amplification, deletion
epigenetic changes: histone modification, DNA methylation
genetic mutations can cause epigenetic changes
Tumor suppressor genes vs. oncogenes?
inhibit cell proliferation and promote apoptosis (p53, BRCA1, BRCA2, Rb); both need to be mutated to lose function
mutations promote cell growth and proliferation (GOF); one mutation required; MYC, RAS, Abl
What is loss of heterozygosity?
one copy of the tumor suppressor gene is lost (inherited or spontaneous); loss of the other copy via mutation or deletion results in inactivation
most common is p53: impaired cell cycle regulation, DNA repair, apoptosis
Resisting Cell Death
genetic changes in the intrinsic apoptosis pathway are very common in cancer
1. anti-apoptotic oncogenes (amplification): BCL2, BCL-xL, MCL-1
2. pro-apoptotic (mutations/decrease expression) tumor suppressor: Bax, Bak
Activating Invasion/Metastasis
tumors are most lethal when they spread
steps
1. epithelial-mesenchymal transition (EMT)
2. invade (leave current tissue)
3. intravasate (get into bloodstream)
4. circulate (move to another place)
5. extravasate (out of bloodstream)
6. colonize (start growing in new tissue)
Why do micrometastases stay dormant?
- anti-growth signals in normal tissue
- incapable of activating angiogenesis
- tumor-suppressing action of immune system
What is the key process of invasion/metastasis?
EMT: epithelial to mesenchymal transition = lose organization, cell-to-cell adhesion, and attachment to basement membrane and gain migratory and invasive properties
Marker epithelial cells: E-cadherin
Marker mesenchymal cells: N-cadherin, vimentin
Enabling Replicative Immortality
increased telomerase expression in cancer cells keeps telomeres long so they can keep dividing and avoid senescence
Tumor-promoting inflammation
not oncogenic itself but allow mutations in other genes during normal cell division
cancer cell can benefit from inflammation
inflammatory cells release ROS cause mutation, and they can also supply growth factors and other tumor survival factors
Deregulating cellular energetics
Warburg effect – cancer cells shift from oxidative phosphorylation to aerobic
glycolysis/lactic acid fermentation to gain biomass: use these breakdown products to make
building blocks for the cell to keep growing (nucleotides, amino acids, lipids)
Inducing Angiogenesis
Tumors need access to nutrients to survive/spread – get this from making new
blood vessels (angiogenesis) via vascular endothelial growth factor (VEGF)
neovasculature is aberrant
- excessive vessel branching
- distorted/enlarged vessels
- erratic blood flow
- leakiness
Genome instability/mutation
not oncogenic itself but allow mutations in other genes during normal cell division
Cancer cells often have mutations in DNA repair genes – cells develop more mutations, genetic diversity often helps them keep growing
ex) mismatch repair: hereditary non-polyposis colon cancer (HNPCC)
nucleotide excision: XP
recombination repair: breast, ovarian
Avoiding Immune Response
T cells recognize neoantigens, tumor associated antigens, and unconventional tumor antigens
cancer cell needs to fend off the immune system’s attempt to kill it, so they suppress immune cell activation by increasing expression of checkpoint proteins PD-1,PD-L1, CTLA-4
New Hallmarks of cancer?
- Unlocking phenotypic plasticity
- Nonmutational epigenetic programming
- Polymorphic microbiomes
- Senescent cells
Unlocking phenotypic plasticity
cancer cells are able to evade terminal differentiation and keep dividing by
1. staying in an immature cell type (blocked differentiation)
2. reverting from a mature to a more immature cell type (de-differentiation)
3. reverting to a different cell type altogether (trans-differentiation)
Nonmutational epigenetic programming
enabling, not oncogenic
components of the tumor microenvironment (hypoxia, interactions with surrounding cells) can induce epigenetic changes that affect gene transcription (oncogenes)
Polymorphic microbiomes
enabling, not oncogenic
microbes can either prevent or promote tumor development (damage DNA directly)
can directly interact with cancer cells to enable them to sustain proliferative signaling or evade growth suppressors
Senescent cells
cells in proliferative arrest secrete pro-proliferative factors, avoid apoptosis, promote angiogenesis, Senescence Associated Secretory Profile (SASP) promote inflammation
Difference between driver and passenger mutations?
driver: mutation that is critical to and responsible for the development of cancer (cells without it die)
passenger: mutation that has no effect on tumor growth/fitness
How many drivers do tumors have?
5-6 +/- 2 mutations: oncogenes, tumor suppressors, telomerase
therefore develops in older individuals who accumulate more mutations
Exception = chromothripsis: chromosome shattering in a single event
Which tissues have higher risk of acquiring driver mutations?
organs with higher tissue/stem cell replacement will have higher risk of cancer because more cell divisions means higher likelihood of acquiring mutations + tumors forming
Why is understanding the genetic basis of cancer critical?
diagnosis and treatment
1. precision medicine: prescribing patients a specific treatment regimen based on genetic make up of their tumor (driver can be targeted with drug or certain chemos)
2. cells with the same driver mutations respond to the same therapies even in different tissues (Gleevec = BCR-ABL inhibitor treats both chronic myelogenous leukemia and GI stromal tumors with 9:22 translocation)
Why is tumor heterogeneity important?
the fact that tumors have multiple/diverse drivers makes it much harder to treat
- hetero within a tumor, across patients
- even if you target one driver, tumor can compensate
What is the difference between intertumoral and intratumoral heterogeneity?
inter: variability between tumors across patients from environmental factors, germline genetic variation, somatic mutations
intra: variability within the cells of a tumor; picking up passenger mutations during clonal proliferation
How does intratumoral heterogeneity manifest itself?
spatial: genetically diverse tumor cell subpopulations can be distributed across multiple sites or even at a single anatomical location in the same patient
temporal: genetic diversity can change over time
How does exposure to cancer therapies increase the genomic complexity of tumors?
- genetic changes may develop in response to therapy (de novo)
ex) ROS1 drug resistance - genetic changes may be present before therapy
mutations acquired can be on-target (new mutation in oncogene that renders drug ineffective) or off-target (diff. oncogene)
cases also exist where different mutations are seen in different sites of metastatic disease
How can we profile tumor heterogeneity?
Fluorescence in situ hybridization (FISH): DNA probes to hybridize to specific DNA regions to asses gene amplifications
Immunohistochemistry (IHC): antibodies to detect protein expression
DNA sequencing
Sanger: single region, very slow, one strand at a time, need 20% VAF for detection
NGS: many genes of interest examined in parallel, high throughput, can detect low frequency genetic variants
Why calculate the VAF?
useful to determine the predicted abundance of a mutation within the tumor: higher VAF = more cells with the mutation
What is the VAF?
variant allelic fraction: fraction of total sequencing reads at a specific genomic position that contain the variant
non-tumor tissue:
no variant: 0%
heterozygous: 50%
tumor tissue:
no variant: 0%
heterozygous variant: 50%
loss of heterozygosity: 100%
What factors influence the VAF?
- ratio of malignant to normal cells in the sample
- whether variant is present in all malignant cells or only a subclone
- whether the gene has an abnormal number of copies in the malignant cells
How do you treat cancer?
- surgery: physical removal
- radiation: induce DNA damage in cancer cells
- cytotoxic chemotherapy: drugs that cause DNA damage or inhibit mitosis
- molecularly targeted therapy: drugs that target mutant proteins in cancer cells
- immunotherapy: drugs that allow immune system to remove cancer cells
How does targeted therapy work?
easier to turn off an oncogene than turn on a tumor suppressor
most targeted therapies are kinase inhibitors: small molecule binds to ATP pocket
ex) Gleevac binds in BCR-ABL pocket
How does tumors avoid immune surveillance?
T-cells engage with target cells by binding to an antigen on the target cell via its T-cell receptor; checkpoints to prevent hyperactivation of T-cells
cancer overexpresses these so T-cells can’t induce death
Which immune checkpoints are expressed on T-cells and tumor cells?
T-cells: PD-1, CTLA-4
Tumor: PD-L1
How does immunotherapy work?
checkpoint inhibitors enable T-cells to become activated when they encounter cancer cells
checkpoints inhibitors are more effective when the cancers have a high mutational burden = more neoantigens (foreign), more T-cell infiltration, more tumor clearance
What are TILs?
tumor infiltrating lymphocytes: increase abundance of immune cells that can get into the tumor and clear cancer cells
1. isolate T-cells from tumor
2. multiply T-cells + insert
What are CAR T-Cells?
- get T-cells from patient’s blood, engineer them to produce chimeric antigen receptors (CARs) direct against antigens that are expression on cancer cells
chimeric = receptors both bind antigen and induce signaling to activate T-cell
used for blood cancers (CD19, B-cell marker)
What is personalized medicine?
sequencing patients’ tumors to inform prognosis/treatment
- identify both driver and passenger mutations
- predict disease prognosis, therapies
- helps determine if therapies are working
What are the main ways targeted therapies can work?
- directly turning off mutated oncogene (EGFR inhibitors in lung cancer)
- mutations in the tumor confer sensitivity to a non-direct therapy (patients with high mutational burden are more sensitive to immunotherapy)
Germline vs. somatic mutations
Germline: passed down from parents, present in every cell
- present in normal and tumor tissue
Somatic: only present in specific tissues
- more common in tumors
What is circulating tumor DNA?
– tumor-derived DNA released from cancer cells
- Less invasive/easier to obtain than solid tumor biopsies
- If more than one tumor (metastases), get information about multiple sites at once
(but harder to tell where the DNA is coming from)
- Potential to detect a new site of metastasis before it shows up on imaging
Sporadic vs. hereditary vs. familial cancers?
cancer that occurs due to spontaneous mutations that accumulate over a person’s lifetime; typically diagnosed at an older age
caused by a single genetic change in the germline; pattern of specific, recurring cancer types across multiple generations; diagnosed at younger age
cancer that appears to occur more frequently in families than expected compared to rates in the general population (clustering); shared genetics/enivronment; no pattern of genetic transmission
What are features suggestive of hereditary cancer?
- multiple primary tumors in the same organ (same breast)
- multiple primary tumors in different organs (breast + ovarian)
- bilateral primary tumors in paired organs (separate cancers in both breasts)
- multifocality within a single organ (multiple genetically-related tumors in the same breast)
- younger age at cancer diagnosis than others in the general population
- family history
Which inheritance pattern is most common in hereditary cancer predisposition syndrome?
autosomal dominant: normally one hit in the tumor suppressor genes
incomplete penetrance is common (genotype doesn’t express phenotype) because other factors
variable expressivity: extent a genotype is expressed at the phenotypic level = type of cancer, age of onset in families because of other factors
What are BRCA1 and BRCA2? What is their role in Hereditary Breast and Ovarian Cancer Syndrome?
tumor suppressor proteins in the homologous recombination (HR) DNA repair pathway
inactivation leads to defective repair of DSB
associated with breast, ovarian, prostate, and pancreatic cancer
What is PARP?
enzyme in BER pathway that repairs single-stranded breaks
tumors with BRCA1/2 are sensitive to inhibitors because they cause apoptosis
What is Lynch Syndrome?
caused by germline mutations in MLH1, MSH2, MSH6, PMS2 = genes involved in mismatch repair
associated with colorectal, uterine, stomach cancer
sensitive to immunotherapy (microsatellite instability-high): higher mutational burden, more neoantigens on tumor cells, more immune cell infiltration
