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For a gene pair (A,B) and a (large) set of tumours, let

• |SA|: the subset of tumours carrying alterations in A;

• |SB|: the subset of tumours carrying alterations in B;

• |SAB|: 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

|SAB| tumours (out of |SB| tumours) showing co-occurrence of

the alterations (with |SA| tumours).

We estimate this probability P[X |SAB|] as:

𝑃[𝑋 |SAB|] = 1 − P[X > |SAB|],

where P[X > |SAB| ] is computed using the hypergeometric

probability mass function for X = k > |SAB|:

𝑃 𝑋 > 𝑆𝐴𝐵 =

𝑆𝐴𝑘

𝑆 − 𝑆𝐴𝑆𝐵 − 𝑘

𝑆𝑆𝐵

𝑆𝐵

𝑘= 𝑆𝐴𝐵 +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

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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 s.srihari@uq.edu.au 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