Genetics Lecture 10.PDF

Genetics Lecture 10 – Cancer and Genomic Medicine Question Conversion of a proto-oncogene to an oncogene involves a ___ mutation - Hypomorphic (loss of function) - Hypermorphic (gain of function) - Isomorphic (silent) Clinical Case - Evelyn, 22 months - Has a white reflection in her left eye (leukoc...

Genetics Lecture 10 – Cancer and Genomic Medicine Question Conversion of a proto-oncogene to an oncogene involves a ___ mutation - Hypomorphic (loss of function) - Hypermorphic (gain of function) - Isomorphic (silent) Clinical Case - Evelyn, 22 months - Has a white reflection in her left eye (leukocoria) - Also is slightly cross-eyed (strabismus) - No family history of eye problems - Other eye also has a tumour upon examination Hereditary Cancer Syndrome - Cancer syndromes where the “first hit” in a TSG is inherited as a constitutional mutation - Classic example (Knudson) is Hereditary Retinoblastoma – OMIM 180200 - Inherited mutation in the RB1 TS gene on one copy of Chr 13q14 in all cells (incl. retina) - Subsequent “2nd hit” in RB1 in retinal cells lead to retinoblastoma tumour - There is also a sporadic form of retinoblastoma where the two hits occur de novo (somatic) – accounts for ~2/3 of cases (hereditary is less common) - In sporadic retinoblastoma, the tumours are generally unilateral (one eye) whereas in hereditary RB the tumours are often bilateral or multiple per eye (multifocal) Tumour Suppressor Genes - Typically need change in both alleles for malignant transformation - Recessive amorph/hypomorphic (loss of function) mutations - Knudson’s two-hit hypothesis: (Sporadic – have a normal cell that gets 1 “hit”, the chances of getting a second hit are low, but if it occurs then both copies are affected. Inherited mutation – already have the first hit, so the chances of both copies being affected is equal to the probability of the first hit in a sporadic mutation) Loss of Heterozygosity (LOH) - A (TSG) locus that is heterozygous in a normal cell becomes homozygous (or) in derived cancer cell - Loss of the “good” gene copy - Most important mechanism of 2nd hit in hereditary cancer syndromes* - Most commonly occurs due to mistakes during mitosis: o Acquired UPD (uniparental disomy – 2 copies from 1 parrent) (pictured) (copy neutral) o Monosomy (by nondisjunction) - hemizygous o Gene conversion (copy neutral) – hybrid Chr (hybridisation – 2 copies of gene on bad chromosome) o Mitotic recombination between parental homologs (copy neutral) o Deletion Question Samples of Evelyn’s blood and tumour DNA were extracted and the RB1 gene was analysed for wildtype (WT) and mutant (M) alleles. What would you expect her pattern to be? a) Blood homozygous WT, tumour heterozygous (Blood WT/WT, Tumour WT/M) b) Blood heterozygous, tumour homozygous M (Blood WT/M1, Tumour M1/M1) (LOH – more likely she has same mutation) c) Blood homozygous WT, tumour homozygous M (Blood WT/WT, Tumour M1/M1) d) Blood heterozygous, tumour compound heterozygous M (different mutations) (Blood WT/M1, Tumour M1/M1) Retinoblastoma - Only 10% of children with retinoblastoma have a positive family history - 95% risk for RB (high penetrance) - De novo mutation in the parental (usually paternal) germ line accounts for the other (approximately 3/4) of hereditary retinoblastoma - Hereditary cancer syndrome patients are also prone to other forms of cancer. For retinoblastoma this includes pineoblastoma, osteosarcoma and melanoma Other Hereditary Cancer Syndromes - Familial Adenomatous Polyposis (FAP) o OMIM 175100 – APC - Chr5q21 o Colon polyps that become malignant by ~40 o Extracolonic manifestations - Lynch Syndrome (Hereditary NonPolyposis Colon Cancer - HNPCC) o Usually MLH1 (Chr3p22)or MSH2 (Chr2p21) o Early onset (avg 44) colon cancer, often multiple tumours and often multiple forms of cancer - Li-Fraumeni Syndrome o OMIM 151623 - TP53 – Chr17p13 o Multiple forms of cancer o 50% have cancer by 30, 90% by 65 Question: Are hereditary cancer syndromes inherited in a dominant or recessive patter? Why? Pattern is autosomal dominant because they already have 1 hit so the chances of a second hit are very high – “matter of time” Hereditary Breast Cancer (HBC) - ~ 5% of breast cancer - Suggested if multiple 1st degree relatives affected - Germ-line mutations in cancer susceptibility genes o BRCA1 or 2 - mutations in 25% HBC o Others: ATM, CHEK2, p53, PTEN, LKB1 o Many susceptibility genes unknown BRCA1 - Tumour Suppressor Gene - Germ line inherited non-functioning allele in 1 homolog of Ch17 (Knudson’s first hit) - Subsequent somatic mutation in BRCA1 in the other homologue of Ch 17 of one breast cell - Potential for Neoplastic Transformation Breast Cancer – Summary - Breast cancer is a “genetic disease” in the sense that DNA change in somatic cell DNA drives neoplasia BUT o Some families have an inherited tendency to develop breast cancer o Most breast cancers are sporadic (not hereditary) o Deregulated genes and pathways result in acquisition of six hallmarks of cancer o Complex interplay between different factors o Heterogeneous disease with many subtypes o Limited number of genes are used clinically in prognosis or management but this is changing Cancer Progression - Remember! o It is never a single mutation that causes cancer; rather, cancer is the result of the accumulation of several genetic and chromosomal changes o Often accompanied by reversible epigenetic modifications which perturb the function of 100s-1000s of genes – impact cellular control pathways - Balance is important: o Uncontrolled growth (tumour) is common and ≠ cancer o If balance between cell division/growth and apoptosis is disrupted can get undifferentiated tumour – more likely to become malignant Question: Match the cancer to the oncogene or TSG - Burkitt’s Lymphoma - MYC - Breast cancer (female) – BRCA2 - FAP - APC - APML - PML-RARα - Lynch Syndrome (HNPCC) – MLH1 - Li-Fraumeni Syndrome – TP53 - Prostate cancer – BRCA1 - CML - BCR-ABL Question: Should screening for BRCA1/BRCA2 be encouraged to prevent breast cancer? Screening – is hard BRCA1 – 24 exons – 1863 aa protein BRCA2 – 28 exons – 3418 aa protein Thousands of different mutations BreastCheck Screening in Ireland - Mammography every 2 yrs for women 50-69 o 1 in 25 require follow up ultrasound - Staging TNM, biopsy, grading (1-4) (differentiation) - Molecular profiling - If criteria met family history & BRCA/TP53 testing (Crumlin/St James’s) o Carrier probability 10% or more Breast Cancer – Molecular (gene expression) Profiling - Evaluation of multiple genes/proteins in parallel - ER, PR, HER2, etc.. - Different approaches & platforms e.g. o Expression micro-array profiling o Quantitative RT-PCR for multiple genes – e.g. Oncotype DX o Genome sequencing o Immunohistochemistry - Basic science + high throughput clinical studies - Research versus clinical practice - Guide patient management: - Surgery/radiation/hormone/chemo (inclpharmacogenetics) Next Generation Sequencing – how it works RNA sequencing – gene expression profiling of cancers Whole Exome Sequencing NGS and Personalised medicine Cancer genome resources - Causation - Progression - Recurrence - Treatment response - Risk prediction - Therapeutic development Challenges of NGS in clinical medicine and public health - Data analysis and interpretation - Informed consent - Data protection - Genetic literacy - Managing incidental results - Computational power - Costs and who pays? - Equality in benefits and burdens - Discrimination by insurance companies - Consequences of sequencing healthy people Is it worth it? - Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature (2018) - “The current health economic evidence base to support the more widespread use of WES and WGS in clinical practice is very limited. Studies that carefully evaluate the costs, effectiveness, and cost-effectiveness of these tests are urgently needed to support their translation into clinical practice”. Yes if used correctly: - A 2018 study found the mean total cost of NGS for targeted gene panels in clinical practice in France was estimated to 607€ (±207) in somatic genetics and 550€ (±140) in germline oncogenetic analysis. https://www.nature.com/articles/s41431-017-0081-3 - A 2018 meta-analysis found that WGS/WES was better at diagnosing clinically relevant genetic abnormalities in children than chromosomal microarray https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037748/ - WES of children with suspected monogenic conditions at first genetics appointment would have saved €4k per additional diagnosis versus standard diagnostic pathway https://www.ncbi.nlm.nih.gov/pubmed/28759686 Things to Remember 1. Hereditary (predisposition to) cancer (hereditary cancer syndromes) accounts for about 5-10% of all cancer. Hereditary Breast Cancer – accounts for about for 5% of breast cancer and BRCA1 & 2 are most common genes 2. Hereditary/familial cancer syndromes are inherited in an autosomal dominant fashion 3. There are various mechanisms for the “2nd hit” to occur in cancer, including mutation, amplification, chromosomal rearrangement, epigenetic changes and loss of heterozygosity 4. Loss of heterozygosity (LOH) is the most common mechanism for the “2nd hit” to occur in familial cancer syndromes, is usually associated with loss of TSG function, and is often seen as part of the malignant progression of sporadic tumours 5. Molecular (gene expression) profiling is useful for assessing breast cancer prognosis and guiding optimal therapeutic selection and patient management. It has the potential to help delineate subsets of other cancers that are likely to be more responsive to various therapeutic regimens and to guide the optimal selection of agents for each individual 6. Cancer genomics and NGS technologies hold immense potential for the design of personalised/precision medicine treatments for cancer, but there are issues to be overcome for clinical practice including data analysis and interpretation, managing incidental results and ethical concerns including data protection