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TEMPLATE DESIGN © 2008 www.PosterPresentations.com For a gene pair (A,B) and a (large) set of tumours, let • |S A |: the subset of tumours carrying alterations in A; • |S B |: the subset of tumours carrying alterations in B; • |S AB |: the subset of tumours carrying alterations in both A and B; • X: a random variable that counts the co-occurrence of alterations in A and B. We compute the statistical significance for the mutual exclusivity for alterations in A and B based on the probability of observing at most |S AB | tumours (out of |S B | tumours) showing co-occurrence of the alterations (with |S A | tumours). We estimate this probability P[X |S AB |] as: [ |S AB |] = 1 − P[X > |S AB |], where P[X > |S AB | ] is computed using the hypergeometric probability mass function for X = k > |S AB |: > = − − = +1 . This “1-hypergeometric test” p-value (Equation 1) is used to infer SL pairs (at p<0.05) and rank them by their p-values. Identifying Genetic Vulnerabilities in Cancers Driven by Defects in DNA-damage Response Authors’ Affiliations OPTIONAL LOGO HERE OPTIONAL LOGO HERE 3. Prediction of Synthetic Lethal Partners of DDR Defects 1. Background Cancers Driven by Defects in DNA-damage Response (DDR) • Defects – e.g. via mutations, copy-number loss or underexpression – of DNA-damage repair genes BRCA1 and BRCA2 are highly penetrant and significantly increase the risk of breast (by 60-80%) and ovarian (35%) cancers [1]. • Together with defects in • the DNA-damage sensor ATM, • the apoptosis effector TP53, and • PTEN and CDH1 that closely regulate DDR, these defects account for considerable proportions of sporadic breast (63%) and ovarian (85%) cancers. 2. Our Approach Mutually Exclusive Genetic Alterations Identify Synthetic Lethal Gene Pairs Genetic Vulnerabilities Arising from DDR Defects Sriganesh Srihari, Murugan Kalimutho, Jitin Singla, Aimee Davidson, Limsoon Wong, Peter T. Simpson, Kum Kum Khanna and Mark A. Ragan SS, AD, MAR: Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia. MK, KK: QIMR-Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4006, Australia. JS: Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089-2910, USA LW: Department of Computer Science, National University of Singapore, Singapore 117417. PTS: The University of Queensland, School of Medicine and Centre for Clinical Research, Brisbane, Queensland 4006, Australia. Our hypothesis: Genes altered in a mutually exclusive manner to DDR defects in cancer cells constitute the synthetic lethal partners of DDR genes, and if targeted in conjunction with DDR defects could induce cancer cell death. 5. Pathway-based Models for Targeting Synthetic Lethal Partners of DDR Defects in Cancer Funding Acknowledgements Proportions of cancers carrying mutations, homozygous deletions or underexpression in six DDR genes ATM, BRCA1, BRCA2, CDH1, PTEN and TP53. Data from The Cancer Genome Atlas (TCGA) for Breast Invasive Carcinoma and Ovarian Serous Cystadenocarcinoma: Key References 1. Liu et al., A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Res 2014, 42(10):6106-27. 2. Srihari et al., Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology Direct 2015, 10:57. • Research funded by Australian National Health and Medical Research Council grants# 1028742, 1080985 to MAR, PTS and Dr Nicola Waddell (QIMR-Berghofer). • Travel support to SS from: • Institute for Molecular Bioscience (UQ), • The Ian Potter Foundation Australia (grant# 20160303) • AACR Scholar-in-Training Award – Supported by Susan G. Komen • Despite defects in DDR, cancer cells tolerate damage to their DNA and continue to survive and proliferate. • This is effected by rewiring of the DDR signalling network and by (clonally) selecting optimal combinations of genetic alterations that are amenable to cell survival. • However, this exposes genetic vulnerabilities that could be capitalized for selective targeting of cancer cells. • In particular, via triggering significant DNA damage (genomic catastrophe) in cancer cells. Synthetic Lethality (SL): A combination between two genetic events (typically affecting two different genes) in which their co- occurrence results in severe loss of viability or death of the cell, although the cell remains viable when only one of the two events occurs [1]. DDR Partner Observation from a large set of tumours: DDR Partner (Equation 1) Genomic copy-number and gene-expression datasets from four sporadic cancers, breast, prostrate, ovarian and uterine from TCGA, composing a total of 3980 tumour samples. Cancer Genomic Gene expression Total Breast 847 1182 2029 Prostate 152 471 623 Ovarian 562 266 828 Uterine 443 57 500 Total 2004 1976 3980 • Deletion/downregulation of A – Deletion/downregulation of B • Deletion/downregulation of A – Amplification/upregulation of B Distribution of DDR genes for involvement in SL combinations: Parallel pathways model: •The SL partner, typically a tumour suppressor compensates for the loss of DDR gene. •Targeting it results in complete loss of DDR functions, resulting in genomic catastrophe and cell death. Negative feedback-loop model: •In the presence of a DDR gene in the negative feedback loop, the SL partner, typically an oncogene, is upregulated to drive the pathway signals. •However, in the event of DDR loss, upregulation of the partner could be detrimental to cell survival, which cancer cells avoid. •Targeting the partner shunts off the signal, and decreases cell viability. 4. Experimental Validation of Predictions Effect of BRF2 Knockdown in Breast Cancer Cell Lines • siRNA-mediated knockdown of BRF2 reduces cell proliferation, in particular up to 70% in MDA-MB-453 cell line. • BRF2 could be a DDR-context-dependent oncogene. Examples of identified SL partners of DDR genes and their network: This poster is the intellectual property of the author/presenter. Contact them at [email protected] for permission to reprint and/or distribute. Network of 718 genes synthetic lethal to the six DDR genes Survival analysis based on 43 shortlisted genes in ER-negative / basal-like breast tumours Statistical Model to Infer Synthetic Lethal Gene Pairs Bioinformatic Set-up and Datasets
