MS523.L20.Cancer Genetics.Q2.22.pptx

Lecture: Cancer Genetics Presenter: Dr. Darl Swartz Course: Human Genetics MS523 Date: 12/2/22 12/12/ Dr. Darl Ray. Swartz 1 Objectives: 1. 2. 3. 4. 5. Define neoplasm, benign tumor and malignant tumor. Describe the histological/pathological types of cancer. Discriminate between germ-line and s...

Lecture: Cancer Genetics Presenter: Dr. Darl Swartz Course: Human Genetics MS523 Date: 12/2/22 12/12/ Dr. Darl Ray. Swartz 1 Objectives: 1. 2. 3. 4. 5. Define neoplasm, benign tumor and malignant tumor. Describe the histological/pathological types of cancer. Discriminate between germ-line and somatic mutations that cause cancer. Explain the Vogelgram diagram in relation to cancer theory. Describe the evolution of a cancer cell population during disease development. 6. Describe the functional mechanisms involved in the formation of oncogenes and tumor suppressor genes. 7. Describe the most prevalent oncogenes. 8. Describe the most prevalent tumor suppressor genes. 9. Explain the two-hit hypothesis for tumor suppressor genes. 10. Distinguish between driver genes and follower genes during cancer evolution. 11. Explain the genetic instability of cancer and how this relates to cancer evolution. 12. Describe the current state of cancer genomic diagnostics and its 12/12/2 Dr. Darl Ray. Swartz practical use in patient treatment. 2 Outline: I. II. III. IV. 12/12/2 Cancer Basics Oncogenes Tumor Suppressor Genes Genetic Instability in Cancer and Diagnostics Dr. Darl Ray. Swartz 3 Cancer Basics 12/12/2 Dr. Darl Ray. Swartz 4 Cancer Basics A) Human body averages 37 trillion somatic cells maintained mostly throughout life including senescent cells and repair/replacement cells 1) Senescent cells (Go) mostly in CNS, cardiac muscle, and skeletal muscle 2) Repair/replacement cells (mitotic) mostly in epithelia and blood cells 3) Normal changes in adult body size result from cell hypertrophy/accretion rather cell proliferation 4) Age or disease-related changes in body size result from mis-regulation of cell growth and/or cell proliferation (a) Atrophy > decrease in body size (b) Hypertrophy > increase in body size (i) Mostly via an increase in cell number 12/12/2 Dr. Darl Ray. Swartz associated with mis-regulation of the cell 5 Cancer Basics B) Cancer is a neoplasm (new growth) associated with a disease state 1) Tumor is a cancerous disease where a new population of cells has acquired the ability to proliferate 2) Tumors can be benign or malignant (a) Benign is not invasive – stays where it originated (b) Malignant is invasive – metastasizes and invades and grows in distant tissues (i) More likely to be lethal 12/12/2 Dr. Darl Ray. Swartz 6 Cancer Basics C) Cancers are classified based upon tissue type where cancer originated and location where originated 1) Primary = tissue type where originated 2) Secondary = metastasized into other tissue type but maintains same tissue type 3) Tissue type cancers (a) Carcinoma > epithelial origin (i) Glandular epithelium > adenocarcinoma (ii)Squamous epithelium > squamous cell carcinoma (b) Sarcoma > connective and muscle tissue origin (mesoderm derived) (c)Myeloma > plasma cell origin (d) Leukemia > leukocyte origin The new World Health Organization classification of lung tumo E. Brambilla*, W.D. Travis#, T.V. Colby}, B. Corrinz, Y. Shimosa (e) Lymphoma > Lymph (lymphocyte) Eur Respir J 2001; 18: 1059–1068 organ origin (spleen, nodes, thymus, and 12/12/2 Dr. Darl Ray. Swartz 7 Cancer Basics D) Cancers are more prevalent in tissues/organs that are highly proliferative 1) More times a cell divides, the more likely to have a mistake (mutation) in the cell cycle, mostly in epithelia E) Cancers have a genetic component but mono-genetic inheritance is rare 1) 5 – 10% of cancers are germ-line linked 2) Mono-genic cancers are typically autosomal dominant and increase risk of developing cancer over proband’s lifetime 12/12/2 Dr. Darl Ray. Swartz (a) Cancer occurs earlier than 8 Cancer Basics F) Most cancers involve somatic mutations that occur over a life-time 1) Induced by environmental mutagens (a) Tobacco smoke induces base modification and subsequent repair causing a point mutation (G > T) (b) UV-light induced base cross-linking and subsequent repair causing a point mutation (C > T) (c) Chronic inflammation caused by microbial infections from excessive cytokines and chemokines (i) Viruses > HBV, HCV, HPV, Epstein-Barr (ii) Bacteria > H. plyori 2) Age-associated changes in the epigenome and/or clonal population evolution from 12/12/2 Dr. Darl Ray. Swartz slowly growing benign tumors 9 Cancer Basics G) Cancers evolve 1) Originate from somatic mutation in cancer stem cell 2) Subsequent offspring via mitosis gives clones carrying same mutation (a) Cancer stem cells in some cancers 12/12/2 Dr. Darl Ray. Swartz NATURE REVIEWS | CANCER VOLUME 12 | NOVEMBER 2012 | 76710 Cancer Basics G) Cancers evolve 3) Mutation give selective advantage for proliferation and/or inhibition of senescence/apoptosis (a) Variants typically can survive hypoxic environment better than normal cells (i) Bias metabolism more towards anaerobic glycolysis 4) Cancer evolution involves cell population genetics (a) Increase population size by proliferation (b) Increase genetic diversity by additional mutations (c) Most variants may die off but a few remain 12/12/2 Darl Ray. Swartz (d) Combination of a and bDr.in a few clonal 11 Cancer Basics G) Cancers evolve Front. Physiol., 03 September 2013 | https://doi.org/10.3389/fphys.2013.002 The evolution of genome-scale models of cancer metabolism Nathan E. Lewis1* and Alyaa M. Abdel-Haleem2 12/12/2 Dr. Darl Ray. Swartz 12 Cancer Basics G) Cancers evolve 5) As cancer grows and evolves, it becomes more difficult to treat by various anticancer drugs (a) Drug-resistant clones exist in the population and expand upon drug treatment 6) Clones have slow growth advantage of about 0.4% (compared to 0%) for normal tissues resulting in slow growth of tumor 7) As mutations increase, growth rate may increase 8) Mutations generally occur in genes involved in cell proliferation of the cell cycle (a) Growth promoting pathways affecting mostly G1 (i) Proto-oncogenes have gain of function mutation to give oncogenes (b) DNA damage pathways that halt the cell cycle (i) Tumor suppressors have loss of function mutations allowing the 13 12/12/2 Dr. Darl Ray. Swartz cell cycle to proceed even though there is DNA damage Cancer Basics G) Cancers evolve 8) Mutations generally occur in genes involved in cell proliferation of the cell cycle Tumor suppressors primarily involved in DNA damage/repair and apoptosis 12/12/2 Proto-oncogenes primarily involved regulation of growth Dr. Darl Ray. Swartz 14 Cancer Basics H) Research done on colo-rectal cancers by Bert Vogelstein and colleagues developed the Vogelgram to describe the histological and genetic changes involved in tumorigenesis Tumor-suppressor genes Proto-oncogenes 12/12/2 Dr. Darl Ray. Swartz 15 Cancer Basics I) Major concepts for the genetics of cancer theory: 1) There are two types of mutant cancer genes (a) Oncogenes (b) Tumor suppressor 2) Cancers exhibit genetic instability (a) Increasing mutagenesis (b) Nearly all tumors end up with chromosomal numerical and/or structural aberrations 3) Cancer genes are involved in cellular pathways that favor survival in harsh environments (a) Avascular tissue subject to hypoxia (b) Drug resistance 4) Different types of cancers harbor a variety of cancer genes (a) The two major types of mutations are common but additional mutations are cancer-type specific 5) Cancer genes can be used to inform presences of disease for early 12/12/2 Darl Ray. Swartz diagnostics and developmentDr.of treatment options 16 I. Oncogenes 12/12/2 Dr. Darl Ray. Swartz 17 I. Oncogenes A) Mutant forms of proto-oncogenes B) Proto-oncogenes code for proteins involved in cell growth and differentiation C) Mutation to oncogenes typically results in a gain of function or increase in activity compared to proto-oncogene 1) Autosomal dominant effect D) Most result from somatic mutations via SNVs, gene duplication/amplification, and translocations E) Originally discovered in viruses that can cause cancer 1) Avian Rous sarcoma virus 2) Retrovirus incorporation into host genome resulted in mutation of protooncogene to oncogene 12/12/2 Dr. Darl Ray. Swartz 18 I. Oncogenes F) RAS (Retrovirus Associated DNA Sequence) was the first intrinsic somatic human gene discovered 1) Codes for a small GTPase involved in cell growth signaling (3 human genes with one having alternative splicing (NRAS, KRAS, HRAS) 2) Activating SNV mutations increase basal activity by slowing GTPase activity and thus maintaining active state for a longer period of time 3) Signals downstream through MAPK pathway to transcription factors to stimulate cell growth and proliferation 12/12/2 Dr. Darl Ray. Swartz 19 I. Oncogenes G) MYC (MYeloCytomatosis) mutant genes were found in myeloma, neuroblastoma, and lung carcinoma resulting from larger scale mutations that increased the amount of protein 1) Codes for a transcription factor that activates expression of cell growth and death pathways 2) Proto-oncogene > oncogene involves complex genomic rearrangements that increase the amount of the protein (a) Gene duplications/amplification 12/12/2 Dr. Darl Ray. Swartz (b) Translocation to different 20 I. Oncogenes H) ERBB2 (Erythroblastosis oncogene B/HER2/Neu) is an epidermal growth factor receptor (receptor tyrosine kinase) 1) Proto-oncogene > oncogene via gene duplication/amplification via segmental duplications in chromosome 17 2) Increased signaling for growth because of an increase in copy number 3) Many other cancer genes show increased copy number in cancers and are mostly involved in cell cycle regulation during growth 4) Commonly tested in breast cancers via immunocytochemistry for 12/12/2 Dr. Darl Ray. Swartz increased protein amount (HER2+) 21 I. Oncogenes K) Chromosomal translocations that place genes proximal to active promoters involved in many liquid (leukemias and lymphomas) cancers 1) Reciprocal translocation (Philadelphia Chromosome) and the ABL gene (a) ABL gene translocated proximal to an active promoter for the BCR gene resulting in chronic myeloid leukemia 2) Reciprocal translocation is involved in Ewing’s sarcoma again involving translocation of a gene to an active promotor in an RNA binding protein involved in RNA processing and transport 12/12/2 Dr. Darl Ray. Swartz 22 I. Oncogenes L) PIK3CA (PhosphatidylInositol 3 Kinase) variants associated with many cancer types through its role in phospholipid signaling 1) Activating point mutations 2) Amplifications 3) Combinations of both 12/12/2 Dr. Darl Ray. Swartz 23 . Tumor Suppressors TP53 binding to DNA 12/12 24 . Tumor Suppressors A) Normal protein that mutates resulting in loss of function 1) Mostly autosomal recessive in action 2) Dosage effects with higher cancer incidence for homozygous than heterozygotes B) Original epidemiological studies on retinoblastoma led to the two hithypothesis 1) Heterozygote with germ line mutation (first hit) 2) Homozygosity with somatic mutation (second hit) 3) Disease progressing requires both hits 4) Can have somatic mutations for both 12/12/20 Dr. Darl Ray. Swartz hits but will have delayed onset 25 . Tumor Suppressors C) Normal tumor suppressor genes involved in many cellular processes Study of genomic aberrations and gene expression profiling in Merkel cell carcinoma Thesis · January 2002 Mireille Van Gele Ghent University 1) Maintenance of genetic integrity (DNA damage repair) 2) Regulation of progression of the cell cycle (mostly inhibitory) 3) Differentiation 4) Growth inhibitory signaling 5) Programmed cell death 12/12/20 Dr. Darl Ray. Swartz 26 . Tumor Suppressors D) A few are “driver genes” that start the clone down the path to more mutations giving other “follower genes” that further facilitate cancer cell survival 1) Driver genes (a) Rb (b) APC (c)P53 2) Follower genes (a) MDM2 (b) PTEN (c)SMAD4 (d) CDKN2A (e) BRCA1 and BRCA2 12/12/20 Dr. Darl Ray. Swartz 27 . Tumor Suppressors E) Mutations that result in loss of function include: 1) Substitutions that result in a missense, non-conservative amino acid at active site 2) Nonsense mutations 3) Small indels that alter the reading frame 4) Splice mutations 5) Deletions of exons or entire genes F) Most mutations are somatic 12/12/20 Dr. Darl Ray. Swartz 28 . Tumor Suppressors G) Rb (retinoblastoma) was the first tumor suppressor gene discovered through linkage analysis 1) Discovered as gene causing cancer of the retina mostly in the young 2) Heritable form of cancer caused by germ line first hit (a) Inherited or de-novo germ line mutation 3) Mutation via gene loss by deletions or loss of heterozygosity by homologous recombinationmediated DNA repair 4) Requires loss or inactivation of both functional alleles for cancer to develop 12/12/20 5) Rb phosphorylation involved Dr.inDarl Ray. Swartz 29 . Tumor Suppressors H) APC (Adenomatous Polyposis Coli) is a gene that causes/is associated with colorectal cancer 1) Heritable form following germ-line first hit model 2) Involved in regulation of the canonical Wnt pathway growth 3) Mutations mostly form like Rb I) TP53 (Tumor Protein 53) gene codes for the p53 gene 1) Heritable variant causes Li-Fraumeni syndrome in autosomal dominant fashion (a)Leads to early onset sarcomas 2) Variants found in all types of cancer resulting from somatic mutations 3) Most variants develop via single nucleotide substitution 4) P53 involved in inhibiting cell cycle progression, upregulation (via transcriptional regulation) of DNA repair enzymes and stimulating apoptosis 12/12/20 Dr. Darl Ray. Swartz 30 . Tumor Suppressors K) MDM2 (Mouse Double Minute 2 homolog) is involved in inhibition of p53 function and its mutation to oncogenes 1) Mutations result from amplification of gene or mutations in the promoter region (a) Endgame is increased expression of the protein 2) Functions as ubiquitin ligase (E3) that sends p53 to the proteasome 3) Upregulation results in decreased p53 levels L) PTEN (Phosphatase and Tensin Homolog) is associated with many cancers 1) Normal protein is involved in regulation of phospholipid signaling through its phosphatase activity 2) Loss of functions results in increases 12/12/20 Darl Ray. Swartz signaling for growth through Dr. PI3K signaling 31 . Tumor Suppressors M)SMAD4 (? Mothers Against Decapentaplegic homolog 4) is the transducer of TGF-beta signaling to the nucleus and variants are associated with cancer 1) Involved in differentiation and apoptosis 2) Variants result in loss of these growth inhibitory signals 3) Variants appear later during cancer development 12/12/20 Dr. Darl Ray. Swartz 32 . Tumor Suppressors N) CDKN2A (Cyclin-Dependent Kinase Inhibitor 2A) gene codes for two proteins involved in cell cycle regulation 1) P16 inhibits CDK4/CDK6 that downstream leads to activation of Rb (a) Inactivation mutations leads to over activation of Rb 2) P14art activates p53 (a) Inactivation leads to lack of activation of p53 12/12/20 Dr. Darl Ray. Swartz 33 . Tumor Suppressors O) BRCA1 and BRCA2 variants are associated with breast and ovarian cancer 1) Involved in homologous recombination ds break DNA repair during S/G2 and spindle assembly during prometaphase 2) Discovered through classical linkage studies 3) Variant with loss of function allow for genetic instability 4) Inheritance is autosomal dominant with reproductive history (decrease) Long version history age- dependent penetrance Short version history 12/12/20 Dr. Darl Ray. Swartz 34 Genetic Instability in Cancer 12/12 Dr. Darl Ray. Swartz 35 enetic Instability in Cancer and Diagnostics A) Loss of cell cycle control and DNA repair pathways results in escalating levels of mutation B) Observe differences in karyotype between clones within a given cancer or cancer cell line C) Can have significant genetic drift within a cancer cell line over months to years of culture/experimentation 1) Problem with cancer cell models as they can become moving targets Karyotype of the T47D breast cancer cell line 12/12/ Dr. Darl Ray. Swartz 36 enetic Instability in Cancer and Diagnostics D) Observe numerous aneuploidies and structural aberrations E) Can have double minute chromosomes from fracturing of chromosomes during the cell cycle 1) Circular dsDNA lacking centromeres and frequently contain oncogenes lacking transcriptional regulatory (inhibitory) elements F) As the cancer cell population becomes larger the genetic variation becomes greater 1) Need to sample several clones via karyotyping and genomically/sequencce G) Bottom line > detect as early as possible for targeted removal by drugs or surgery H) Current diagnostics use biopsy for 12/12/ Ray. Swartz pathological/molecular analysis Dr.toDarlidentify Advances in Cellular Neurobiology, 198 37 enetic Instability in Cancer and Diagnostics I) Genomic analysis for cancer moving towards NGS (short read sequencing) panel to cover more genes 1) DNA, DNA methylation, RNA 2) FDA-approved NGS sequencing panels for diagnostic use in 2017 for 324 – 468 cancer variants (a) Both somatic (specimen specific) and gametic (inherited) 3) Objective is to use in early diagnostics for more specific treatment options 4) Several clinical trials completed or in progress (a) Like other precision genomic medicine efforts they are not wellliked by physicians and currently a challenge for insurance coverage Journal of Experimental & Clinical Cancer Research (2018) 37:47 12/12/ Dr. Darl Ray. Swartz 38 enetic Instability in Cancer and Diagnostics J) Working towards using cell-free (cf) nucleic acids shed by the cancer cells and found in plasma 1) cfDNA is being developed and allows for more closely defining the cancer-causing variants, drug resistance, and treatment progress (a) Can be for variant identification (b) Can analyze for methylation 2) cfRNA to observe unique or over-expressed genes 3) Current clinical trials underway show: (a) An increase in sensitivity with increase severity of disease (Stage 1 at ca 18% to Stage IV 90+%) (b) Can distinguish different types and subtypes of cancer 12/12/ Dr. Darl Ray. Swartz 39 enetic Instability in Cancer Diagnostics https://www.cancer.gov/about-cancer/treatment/research/car-t-c K) Personalized cancer treatment via CAR-T therapy 1) CAR = chimeric antigen receptors 2) Engineered receptors to cancer cell antigens and expressed in T-cells (a) Use patient’s T-cells and incorporate receptor gene into genome (b) Can engineer receptors to patient’s specific cancer antigen (c)T-cells are cytotoxic T-cells that kill the cancer cells 3) Many highly successful in treating blood (liquid) cancers but are not effective for solid tumors (a) Potentially accessibility issue of cancer cell antigens in solid tissue 40 12/12/ Dr. Darl Ray. Swartz 4) Need to suppress immune system to prevent enetic Instability in Cancer Diagnostics L) Cancers evolve and become resistant to anti-cancer drugs Single Agent and Synergistic Activity of the "First-in-Class” Dual PI3K/BRD4 Inhibitor SF1126 with Sorafenib in Hepatocellular Carcinoma. Mol Cancer Ther; 15(11) November 2016 Figure 5. Antitumor effect of SF1126 and sorafenib in human xenografts. A and C, 8 106 SK-Hep1 cells (A) or 10 106 Huh7 (C) cells were injected subcutaneously in NSG mice. After 15 days of SK-Hep1 or 25 days of Huh 7 tumor implantation when tumor volume reached up to approximately 50 mm3 mice were divided in to four groups (n 1⁄4 7–8 mice per group). Mice in group 1, treated with acidified water (vehicle control); Group 2, treated with SF1126 (50 mg/kg/day), injected subcutaneously; Group 3, treated with sorafenib (25 mg/kg) injected intraperitoneally; and Group 4, SF1126 þ sorafenib (50 and 25 mg/kg, respectively), 6 days a week for 3 weeks. Arrow indicates the treatment start date (P Why does the tumor area begin to 0.001). 12/12/ increase after 30 – 35 days of drug treatment??? Dr. Darl Ray. Swartz 41 Copyright Notice All materials found on Geisinger Commonwealth School of Medicine’s course and project sites may be subject to copyright protection, and may be restricted from further dissemination, retention or copying. Disclosure I have no financial relationship with a commercial entity producing health-care related products and/or services.