Hani Choudhry

Graduate Research Prize Winners Autumn 2014

Hani Choudhry

I received my BSc in Biochemistry from King Abdulaziz University in Jeddah, Saudi Arabia in 2006, and an MSc in Molecular Medicine with Distinction in 2009 from the University of Sheffield School of Medicine. I joined the Wellcome Trust Centre for Human Genetics in January 2010. For my DPhil in Clinical Medicine, I have been supervised by Prof Sir Peter Ratcliffe and Dr David Mole in NDM, as well as Prof Adrian Harris (Oncology) and Prof Ioannis Ragoussis (McGill University), who are leaders in cancer genomics and hypoxia biology.

My research project aimed to improve understanding of the transcriptional regulation of the non-coding transcriptome in hypoxia.  Hypoxia pathways are associated with the pathogenesis of both ischaemic and neoplastic diseases. To date, pan-genomic analyses of these transcriptional responses have focused on protein-coding genes and microRNAs. However, the role of other classes of non-coding RNAs, in particular long non-coding RNAs (lncRNAs) in the hypoxia response is largely uncharacterised. I performed an integrated genomic analysis of both non-coding and coding transcripts using next generation sequencing.

The analyses have revealed that hypoxia profoundly regulated all RNA classes; in addition, a significant number of previously non-annotated (and largely hypoxia upregulated) transcripts were identified, including novel intergenic transcripts and natural antisense transcripts. My findings extend the role of the hypoxic transcriptional response in cancer into the spectrum of non-coding transcripts, and provide new insights into molecular roles of hypoxia-regulated lncRNAs. Furthermore, these results indicate a new role for HIF transcriptional pathways in the regulation of nuclear structure and that this contributes to the pro-tumorigenic hypoxia-phenotype in breast cancer.

During my postgraduate tenure, I have received a number of awards including 2014 AACR Scholar-in-Training Award at the San Antonio Breast Cancer Annual Symposium (SABCS),  the OECI-EurocanPlatform Translational Cancer Research Fellowship,  2014 Tumour Profile Grant Award Affymetrix, Inc., the Susan G. Komen for the Cure Award and Proffered Paper Award for Non-coding RNA in cancers in the 23rd Biennial European Association for Cancer Research Congress,  the ASHG/Charles J. Epstein Trainee Award for Excellence in Human Genetics Research (SF) 2013,  the National Cancer Research Institute (NCRI) Prize Award 2013, the Best Paper in Medical Sciences in the 6th SIC, and  in 2011 Selected to participate in the prestigious 61st Landau Meeting of Nobel Laureates dedicated to Physiology/Medicine.

Currently, I am an Assistant Professor of Medical and Cancer Genomics at King Abdulaziz University, a Principal Investigator at King Fahd Center for Medical Research, and an Associate Scientist at the Center of Innovation for Personalized Medicine, where my research focuses on understanding the role and function of non-coding RNA in hypoxia, as well as  clinical applications of cancer genomics.

Publications

Textbook

Next Generation Sequencing in Cancer Research Volume 1: Decoding the Cancer Genome, Editors: Wu Wei & Hani Choudhry, Springer-USA, 2013, 398 pages, 
ISBN 978-1-4614-7644 -3 
http://www.springer.com/biomed/cancer/book/978-1-4614-7644-3

Papers

Choudhry, H., Schödel, J., Oikonomopoulos, S., Camps, C., Grampp, S., Harris, A. L., Ratcliffe, P. J., Ragoussis, J. & Mole, D. R. 2014. Extensive regulation of the non‐coding transcriptome by hypoxia: role of HIF in releasing paused RNApol2. EMBO reports, 15, 70-76.

Camps, C., Saini, H. K., Mole, D. R., Choudhry, H., Reczko, M., Guerra-Assunção, J. A., Tian, Y.-M., Buffa, F. M., Harris, A. L. & Hatzigeorgiou, A. G. 2014. Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Molecular Cancer, 13, 28.

Choudhry, H., Albukhari, A., Schodel, J., Oikonomopoulos, S., Haider, S., Ratcliffe, P., Ragousis, I., Mole, D. & Harris, A. 2014. 54: Proffered Paper: Hypoxic regulation of the long non-coding transcriptome in breast cancer. European Journal of Cancer, 50, S14.