Abstract 67: An integrated copy number and gene expression genomics analysis and RNAi approach identifies and validates the KIFC1 kinesin as a malignant cell selective target in triple negative breast cancer
Authors: Patel Nirmesh S. , Drosopoulos Konstantinos , Weekes Daniel , Noel Elodie , Mirza Hasan , Rashid Mamunur , de Rinaldis Emanuele , Brasó Maristany Fara , Mathew Sumi , Francesch Domenech Erika , Gazinska Patrycja , Noor Farzana , Quist Jelmar , Marlow Rebecca , Grigoriadis Anita , Linardopoulos Spiros , Tutt Andrew N. 
Published: July 2016

Abstract
Triple negative breast cancers (TNBCs) lack oestrogen (ER), progesterone (PR) and human epidermal growth factor 2 (HER2) receptors, and have limited targeted treatment options. Large scale genomic and transcriptomic studies have advanced our understanding of the changes which occur in TNBCs. However, the substantial number of copy number and gene expression alterations present in TNBCs makes it difficult to identify putative drivers, biomarkers and/or therapeutic targets of the disease. To overcome this problem, we have carried out an integrative computational and RNAi based approach to identify genes required for proliferation of TNBC.
Copy number and gene expression alterations were analysed using Affymetrix Human Exon HTS1.0 and SNP6.0 data of 152 primary breast tumours enriched for a TNBC phenotype and 9 normal breast epithelium. These analyses revealed 141 candidate genes whose upregulated gene expression is copy number driven in TNBC. The functional dependence on each of these genes was subsequently examined using RNAi in an array of 17 breast cancer and non-malignant cell lines using 6-8 cell lines per gene covering the widest possible range of expression levels for that gene. We validated a malignant cell specific functional dependence on 37 of the 141 genes using this method.
STRING analysis of validated hits reveals a subset of genes involved in the process of cell division and mitosis including the previously characterised mitotic kinase TTK. Of these, we further validated KIFC1 (HSET) which is known to play a role in clustering supernumerary centrosomes, a common occurrence in breast cancer. We show that siRNA and shRNA mediated depletion of KIFC1 decreases cell viability and clonogenic ability specifically in centrosome amplified cell lines, which can be rescued upon introduction of an si/shRNA resistant KIFC1. KIFC1 depletion also produces a high level of catastrophic multipolar mitoses in centrosome amplified but not in non-amplified cell lines. Furthermore, in-vivo studies show that inducible depletion of KIFC1 suppresses tumour growth of centrosome amplified cell line xenografts.
Our work has identified and functionally validated novel drivers, and potential therapeutic targets in TNBC. The data presented here shows KIFC1, a druggable kinesin motor protein is a promising target for therapeutic intervention being expressed through gene copy gain in a significant proportion of TNBCs. We validate its role in cancer-specific amplified centrosome clustering showing KIFC1 plays an essential role in aiding the survival of breast cancer cells that have supernumerary centrosomes in both in-vitro and in-vivo contexts.
Citation Format: Nirmesh S. Patel, Konstantinos Drosopoulos, Daniel Weekes, Elodie Noel, Hasan Mirza, Mamunur Rashid, Emanuele de Rinaldis, Fara Brasó Maristany, Sumi Mathew, Erika Francesch Domenech, Patrycja Gazinska, Farzana Noor, Jelmar Quist, Rebecca Marlow, Anita Grigoriadis, Spiros Linardopoulos, Andrew N. Tutt. An integrated copy number and gene expression genomics analysis and RNAi approach identifies and validates the KIFC1 kinesin as a malignant cell selective target in triple negative breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 67.