Dr Sushila Rigas

Professional biography

I am a geneticist and bioinformatician with research interests in characterising genes and variants in cancers.

I have worked on research projects characterising DNA variants in cancers and I now run a research group focused on identifying functional and regulatory DNA and RNA variants that may affect risk of breast cancer and other cancers. We collaborate with Dr Francesco Crea's group within the Open University, identifying long non-coding RNAs (lncRNA) variants putatively underlying risk of prostate and other cancers. I have also collaborated with Professor Angela Cox (University of Sheffield) on the identification of regulatory DNA variants in apoptosis genes associated with breast cancer risk and Professor Nicola J Camp (University of Utah, USA).

My first post-doctoral position was in Professor Angela Cox's group, where we were the first to identify that the Caspase 8 gene (Casp8) was associated with risk of breast cancer and subsequently identify CASP8 and other apoptosis DNA variants (Yorkshire Cancer Research, Cancer Research UK, Breast Cancer Campaign, and the Wellcome Trust). Whilst doing my PhD (The role of p14ARF in familial and sporadic melanoma, funded by Imperial Cancer Research now called Cancer Research UK) in Professor D Timothy Bishop and Professor Julia Newton-Bishops's group with Professor Margaret A Knowles (University of Leeds), I was the first to: comprehensively screen for deletions on chromosome 9p in melanoma families and in sporadic melanomas (at a time when it was difficult for detect deletions and loss of heterozygosity, LOH); to identify p14ARF [CDKN2A-ARF gene (exon 1β)] as a tumour suppressor gene; identify the MTAP to KIAA1 gene region as important in melanoma aetiology and a candidate locus for the location of a tumour suppressor gene; and contributed to being the first to identify that introns are important in disease with the detection of a splicing variant (IVS2-105) in melanoma families.

Tools: genetic (e.g. high throughput PCR, allelic discrimination, sequencing, MLPA, qPCR), molecular (e.g. cell culture, flow cytometry, tissue microdissection/cores), and bioinformatics: R programming, data mining using publicly available online databases e.g. dbSNP, Ensembl, UCSC, GEO etc. Mainly gene expression tools.

Key words: cancer, breast cancer, genetics, clinical research/samples, gene expression, sequencing, molecular science, epidemiology, bioinformatics, data mining, DNA variants, RNA variants, DNA characterisation, RNA expression, protein expression.

Membership of societies

• The European Association for Cancer Research (EACR), Nottingham, UK (from 2018)
• The British Association for Cancer Research (BACR), Leeds, UK (from 2018)
• The Genetics Society, London, UK (from 2017)
• Participated in the Breast Cancer Association Consortium (BCAC, UK), North of England Genetic Epidemiology Group (NEGEG, UK), and the Melanoma Genetics Consortium (GenoMEL, UK)

Awards

• Two research poster prizes 2009, Yorkshire Cancer Research Annual Science Meeting (Harrogate)
• Research Team of the Year 2008, Awarded by Baroness Fookes of Plymouth DBE DL, patron of the Breast Cancer Campaign (House of Lords)
• Sarah Jane Cross memorial prize, University of Wales, Aberystwyth 1997
• Academic excellence letter, Biological Sciences, University of Wales, Aberystwyth 1997

Qualifications

• PGC HEP, Postgraduate Certificate in Higher Education Practice, University of Bradford, 2016
• PhD, School of Medicine, University of Leeds (Leeds Institute of Cancer and Pathology, Section of Epidemiology and Biostatisics), St James' Hospital, 2004
  • The role of p14ARF in familial and sporadic melanoma
• BSc. (HONS) 1st, Genetics, Aberystwyth University, Wales, 2000
  • Familial hypercholesterolaemia, causitive role in atherosclerosis, other risk factors, and treatment

Research interests

Genetics and bioinformatics lab for clinical research

Aims

Using genetic wet lab techniques, and bioinformatics tools and programming, we aim to develop biomarkers and treatment targets by:

• characterising DNA and RNA (including lnRNA) variants
• identifying hub and driver genes
• identifying differentially expressed genes (DEGs) and expressed quantitative trait loci's (eQTLs) and gene signatures
• identifying novel variants that are functional in the risk of cancers
• understanding epigenetic alterations
• identifying novel variants and genes correlated with cancer survival 
• using clinical tissue and blood samples, and data derived from these types of samples

Bioinformatics

• R programming
• online databases
• gene networks and functions
• survival plots
• cell pathway analyses
• single cell sequencing analysis and supporting training and collaboration with EMBL-EBI with Wendi Bacon

Research Projects

• EZH2 as a therapeutic target for aggressive prostate cancer.
• Identification of functional variants in breast and other cancers with putative shared aetiology.
• Epigenetics and non-coding RNAs as novel therapeutic targets for incurable neuroendocrine prostate cancer.
• Identification of lncRNAs that drive liver cancer development and metastases using the cBioPortal database and R programming. 
• Identification of variants in MOG Antibody Disease (MOGAD), Neuromyelitis optica spectrum disorder (NMOSD), Neuromyelitis optica (NMO) and related neurological/autoimmune disorders.

Funding

PhD student highlights

• 3 Minute Thesis (3MT) OU Student Conference 2019: two winning students
• Grant: The Genetics Society training grant (2018) awarded
• OpenLearn article: Big data and bioinformatics: Powerful tools for decoding DNA (2017)
• OU/BBC Tomorrows World video: Medicine is about to get personal (2017)

Teaching interests

OU modules

• SDK100 Science and health (level 1, 60 credits)
• SK299 Human biology (level 2, 60 credits) - module chair
• S290 Investigating human health and disease (level 2, 60 credits)

Previous Universities

I have taught on Undergraduate and Graduate degree programmes, and supervised MSc degrees and undergraduate final year projects. I also designed and delivered active learning into the curriculums. 

• Clinical Sciences at the University of Bradford (2013 - 2016)
• Medical School of Sheffield University (2005 - 2013)

Teaching Qualifications

• PGC HEP, Postgraduate Certificate in Higher Education Practice, University of Bradford (2016)
• Fellow of the Higher education Academy (FHEA) from 2016
• Associate Fellow of the Higher Education (AFHEA) from 2013

Impact and engagement

We have developed a LINUX server machine with algorithms and data for breast, ovarian and prostate cancers analysis. We hope to analyse this data further and include data on more cancers.

We aim to work towards developing:

• personalised screening tools (blood tests)
• biomarkers
• novel treatment targets
• assessing genetic risk of cancers

External collaborations

Professor Angela Cox, University of Sheffield, UK (member of the Breast Cancer Consortium, UK)

Dr Anita Grigoriadis, Kings College London, UK

International links

​Professor Nicola J. Camp, University of Utah, USA

Dr Luca Quagliata, Thermo Fisher Scientific, and University of Basel, Switzerland

Professor Yuzhuo Wang, BC Cancer Agency, University of British Columbia, Canada