Staff Profile

I graduated from the University of Manchester in 2009 with a First Class Master of Pharmacy (MPharm) degree. I subsequently completed my professional registration with the General Pharmaceutical Council (GPhC). In 2015 I completed my PhD studies in precision medicine approaches to treat the genetic renal stone disease, cystinuria (Newcastle University). My PhD focussed on rare gene mutations leading to altered protein structure in proximal tubular transport proteins.

My postdoctoral research focussed on the functional analysis of GWAS variants in the musculoskeletal disease, osteoarthritis. In the laboratory of Professor John Loughlin (Newcastle University) I used a combination of human patient joint tissues and cartilage cell models to determine the gene targets of common intergenic variants associated with disease. This involved using a range of Cas9 genome and epigenome editing approaches. 

As of August 2021, I am a Versus Arthritis Career Development and Academic Track Fellow within the Skeletal Research Group (SRG) at the International Centre for Life (Newcastle University). My research focusses on the epigenetic control of RUNX2, the gene encoding the master-regulator of long bone development. Variation in the expression of this transcription factor is linked to multiple common traits including facial morphology, height, hip shape and femoral neck length, and to complex age-related diseases such as osteoarthritis and osteoporosis. I investigate tissue-specific gene enhancers to understand the control of this gene in bone and cartilage throughout hip development (using human foetal samples in collaboration with the MRC-Wellcome funded Human Developmental Biology Resource) and in age-associated hip disease (using human arthroplasty tissues in collaboration with the Newcastle Hospitals NHS Foundation Trust).

I am particularly interested in the interplay between genetic variation and epigenetic state, and how this can impact gene expression at a molecular level, by altering transcription factor binding. I currently co-supervise two PhD students Mr Jack Roberts (funded by the Ruth and Lionel Jacobsen Charitable Trust) and Ms Yulia Kehayova (funded by the MRC-Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing). Both student projects focus on applying molecular genetic approaches to conduct post-GWAS functional studies using a range of dCas9 technologies in relevant cell types to identify causal genes in complex diseases.

Techniques

• CRISPR-Cas9 and dCas9 epigenome editing in cell lines and primary cells.
• DNA methylation sequencing, arrays, and targeted quantification using short-read sequencing in-house.
• Allelic quantification of gene transcripts, gene reporter assays, in vitro DNA methylation, qPCR
• ATAC sequencing.

Esteem Indicators

OARSI Young Investigator Award for highest rated abstract. Identification of novel methylation quantitative trait loci (mQTLs) and functional characterisation using CRISPR-Cas9 and gene expression analysis prioritizes PLEC as an OA risk gene. OARSI world congress, Liverpool, April 2018.

Invited workshop presentation. In vitro CRISPR-Cas9 genome and epigenome editing in OA. 2^nd International Workshop on the Epigenetics of Osteoarthritis. Trinity College, Dublin, Ireland. November 6^th, 2018.

Bone and Joint Research Specialty Editor (from April 2019)

Chair of the Gordon Research Seminar "Cartilage Biology and Pathology" 2023, Tuscany, Italy. 

Grants and Awards

Versus Arthritis Career Development Fellowship: “Genetic and epigenetic effects in development, ageing, and disease of the human hip” (2021-2026); Principal Investigator.

JGW Patterson Foundation Pump Priming Grant: “Molecular genetic and epigenetic analysis of the chromosome 4p16.3 osteoarthritis risk locus” (2019-2020); Co-Investigator.

MRC-Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA) PhD Studentship Grant: “Epigenetic, genetic and functional analysis of the growth differentiation factor 5 gene GDF5 in developmental dysplasia of the hip and in osteoarthritis; from development of the musculoskeletal system through to ageing” (2018-2022); Co-Investigator.

MRC-Versus Arthritis Centre for Integrated Research into Musculoskeletal Ageing (CIMA) Postdoctoral Development Bursary. Award to develop techniques and generate preliminary data for subnuclear proteomics profiling in collaboration with Professor Matthias Trost, Newcastle University.

OARSI Young Investigator Award for highest rated abstract 2021. “Genetic and epigenetic interplay fine-tunes expression of TGFB1, encoding Tgf-β1, contributing to osteoarthritis risk”.

Wellcome Trust Institutional Strategic Support Fund (ISSF). “Broadening our Horizons” funding to attend Keystone Symposium, Whistler BC, Canada.

CIMA prize for postdoctoral oral presentation “Novel methylation quantitative trait loci (mQTLs) in osteoarthritis”.

OARSI Young Investigator Award for highest rated abstract 2019. “Identification of novel methylation quantitative trait loci (mQTLs) and functional characterisation using CRISPR-Cas9 and gene expression analysis prioritizes PLEC as an OA risk gene”.

Public Engagement

“Gene Editing: The Good, The Bad, and The Ugly”. Genetics Matters, International Centre for Life, Newcastle upon Tyne. 23^rd February 2019.

Laboratory Supervision

Miss Yulia Kehayova (MRes/PhD Student)

Mr Jack Roberts (PhD Student)

Miss Abby Brumwell (PhD Student)

Dr Utsav Das (PhD Student)

• Rice SJ, Brumwell A, Falk J, Kehayova YS, Casement J, Parker E, Hofer IMJ, Shepherd C, Loughlin J. Genetic risk of osteoarthritis operates during human skeletogenesis. Human Molecular Genetics 2023, 32(13), 2124-2138.
• Aubourg G, Rice SJ, Bruce-Wootton P, Loughlin J. Genetics of osteoarthritis. Osteoarthritis and Cartilage 2022, 30(5), 636-649.
• Brumwell A, Aubourg G, Hussain J, Parker E, Deehan DJ, Rice SJ, Loughlin J. Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk. Arthritis Research & Therapy 2022, 24, 189.
• Kehayova YS, Wilkinson JM, Rice SJ, Loughlin J. Mediation of the Same Epigenetic and Transcriptional Effect by Independent Osteoarthritis Risk–Conferring Alleles on a Shared Target Gene, COLGALT2. Arthritis & Rheumatology 2023, 75(6), 910-922.
• Devane J, Ott E, Olinger EG, Epting D, Decker E, Friedrich A, Bachmann N, Renschler G, Eisenberger T, Briem-Richter A, Grabhorn EF, Powell L, Wilson IJ, Rice SJ, Miles CG, Wood K, Trivedi P, Hirschfield G, Pietrobattista A, Wohler E, Mezina A, Sobreira N, Agolini E, Maggiore G, Dahmer-Heath M, Yilmaz A, Boerries M, Metzger P, Schell C, Grunewald I, Konrad M, Konig J, Schlevogt B, Sayer JA, Bergmann C. Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations. American Journal of Human Genetics 2022, 109(5), 928-943.
• Harvey NC, Clegg PD, Dennison EM, Greenhaff P, Griffin SJ, Gregson CL, Jackson MJ, Lord JM, McCloskey EV, Stevenson E, Tobias JH, Ward KA, Cooper C, Brook M, Curtis EM, Faber BG, Fuggle NR, Linaker C, Naylor AJ, Pearse C, Rice S, Wilkinson D. UKRI MRC National Musculoskeletal Ageing Network: strategic prioritisation to increase healthy lifespan and minimise physical frailty. Archives of Osteoporosis 2022, 17(1), 147.
• Al Alawi I, Powell L, Rice SJ, Al Riyami MS, Al-Riyami M, Al Salmi I, Sayer JA. Case Report: A Novel In-Frame Deletion of GLIS2 Leading to Nephronophthisis and Early Onset Kidney Failure. Frontiers in Genetics 2021, 12, 791495.
• Rice SJ, Roberts JB, Tselepi M, Brumwell A, Falk J, Steven C, Loughlin J. Genetic and Epigenetic Fine-Tuning of TGFB1 Expression Within the Human Osteoarthritic Joint. Arthritis and Rheumatology 2021, 73(10), 1866-1877.
• Kehayova YS, Watson E, Wilkinson JM, Loughlin J, Rice SJ. Genetic and Epigenetic Interplay Within a COLGALT2 Enhancer Associated With Osteoarthritis. Arthritis and Rheumatology 2021, 73(10), 1856-1865.
• Boer CG, Yau MS, Rice SJ, Coutinho de Almeida R, Cheung K, Styrkarsdottir U, Southam L, Broer L, Wilkinson JM, Uitterlinden AG, Zeggini E, Felson D, Loughlin J, Young M, Capellini TD, Meulenbelt I, van Meurs JBJ. Genome-wide association of phenotypes based on clustering patterns of hand osteoarthritis identify WNT9A as novel osteoarthritis gene. Annals of the Rheumatic Diseases 2021, 80(3), 367-375.
• Powell L, Olinger E, Wedderburn S, Ramakumaran VS, Kini U, Clayton-Smith J, Ramsden SC, Rice SJ, Barroso-Gil M, Wilson I, Cowley L, Johnson S, Harris E, Montgomery T, Bertoli M, Boltshauser E, Sayer JA. Identification of LAMA1 mutations ends diagnostic odyssey and has prognostic implications for patients with presumed Joubert syndrome. Brain Communications 2021, 3(3), fcab163.
• Parker E, Hofer IMJ, Rice SJ, Earl L, Anjum SA, Deehan DJ, Loughlin J. Multi‐Tissue Epigenetic and Gene Expression Analysis Combined With Epigenome Modulation Identifies RWDD2B as a Target of Osteoarthritis Susceptibility. Arthritis and Rheumatology 2021, 73(1), 100-109.
• Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nature Reviews Rheumatology 2020, 16, 268-281.
• Sorial AK, Hofer IM, Tselepi M, Cheung K, Parker E, Deehan DJ, Rice SJ, Loughlin J. Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC. Osteoarthritis and Cartilage 2020, 28(11), 1448-1458.
• Al-Hamed MH, Alsahan N, Rice SJ, Edwards N, Nooreddeen E, Alotaibi M, Kurdi W, Alnemer M, Altaleb N, Ali W, Al-Numair N, Almejaish N, Sayer JA, Imtiaz F. Bialleleic PKD1 mutations underlie early-onset autosomal dominant polycystic kidney disease in Saudi Arabian families. Pediatric Nephrology 2019, 34, 1615-1623.
• Willows J, Al Badi M, Richardson C, Al Sinani A, Edwards N, Rice SJ, Sayer JA. Case Report: Investigation and molecular genetic diagnosis of familial hypomagnesaemia: a case report . F1000Research 2019, 8, 666.
• Rice SJ, Cheung K, Reynard LN, Loughlin J. Discovery and analysis of methylation quantitative trait loci (mQTLs) mapping to novel osteoarthritis genetic risk signals. Osteoarthritis and Cartilage 2019, 27(10), 1545-1556.
• Klein JC, Keith A, Rice SJ, Shepherd C, Agarwal V, Loughlin J, Shendure J. Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nature Communications 2019, 10, 2434.
• Rice SJ, Cheung K, Reynard LN, Loughlin J. Identification and analysis of novel methylation quantitative trait loci (mQTLs) in osteoarthritis. In: Osteoarthritis and Cartilage. 2019, Toronto, Canada: Elsevier.
• Rice SJ, Tselepi M, Sorial AK, Aubourg G, Shepherd C, Almarza D, Skelton AJ, Pangou I, Deehan DJ, Reynard L, Loughlin J. Prioritization of PLEC and GRINA as osteoarthritis risk genes through the identification and characterization of novel methylation quantitative trait loci. Arthritis and Rheumatology 2019, 71(8), 1285-1296.
• Alkanderi S, Molinari E, Shaheen R, Elmaghloob Y, Stephen LA, Sammut V, Ramsbottom SA, Srivastava S, Cairns G, Edwards N, Rice SJ, Ewida N, Alhashem A, White K, Miles CG, Steel DH, Alkuraya FS, Ismail S, Sayer JA. ARL3 Mutations Cause Joubert Syndrome by Disrupting Ciliary Protein Composition. The American Journal of Human Genetics 2018, 103(4), 612-620.
• Fearn A, Allison B, Rice SJ, Edwards N, Halbritter J, Bourgeois S, Pastor-Arroyo EM, Hildebrandt F, Tasic V, Wagner CA, Hernando N, Sayer JA, Werner A. Clinical, biochemical, and pathophysiological analysis of SLC34A1 mutations. Physiological Reports 2018, 6(12), e13715.
• Delpiano L, Thomas JJ, Yates AR, Rice SJ, Gray MA, Saint-Criq V. Esomeprazole Increases Airway Surface Liquid pH in Primary Cystic Fibrosis Epithelial Cells. Frontiers in Pharmacology 2018, 9, 1462.
• Rice SJ, Aubourg G, Sorial AK, Almarza D, Tselepi M, Deehan DJ, Reynard LN, Loughlin J. Identification of a novel, methylation-dependent, RUNX2 regulatory region associated with osteoarthritis risk. Human Molecular Genetics 2018, 27(19), 3464-3474.
• Rice SJ, Sorial AK, Aubourg G, Shepherd C, Tselepi M, Almarza D, Skelton AJ, Deehan D, Reynard LN, Loughlin J. Identification of novel methylation quantitative trait loci (mqtls) and functional characterization using CRISPR/CAS9 and gene expression analysis prioritizes PLEC as an OA risk gene. In: 2018 OARSI World Congress on Osteoarthritis Promoting Clinical and Basic Research in Osteoarthritis. 2018, Liverpool: Elsevier.
• Rice SJ, Aubourg G, Sorial AK, Deehan D, Loughlin J, Reynard LN. Epigenetic and transcriptional effects operate on the SUPT3H and RUNX2 genes residing at the chromosome 6p21.1 osteoarthritis susceptibility locus and correlate with the association signal. In: 2017 OARSI World Congress. 2017, Las Vegas, NV, USA.
• Edwards N, Rice SJ, Raman S, Hynes AM, Srivastava S, Moore I, Al-Hamed M, Xu Y, Santibanez-Koref M, Thwaites DT, Gale D, Sayer JA. A novel LMX1B mutation in a family with end-stage renal disease of ‘unknown cause’. Clinical Kidney Journal 2015, 8(1), 113-119.
• Rhodes HL, Yarram L, Rice SJ, Tabaksert A, Edwards N, Hartley A, Woodward MN, Smithson SL, Tomson C, Welsh GI, Williams M, Thwaites DT, Sayer JA, Coward RJM. Clinical and genetic analysis of patients with cystinuria in the UK. Clinical Journal of the American Society of Nephrology 2015, 10(7), 1235-1245.
• Halbritter J, Baum M, Hynes AM, Rice SJ, Thwaites DT, Gucev ZS, Fisher B, Spaneas L, Porath JD, Braun DA, Wassner AJ, Nelson CP, Tasic V, Sayer JA, Hildebrandt F. Fourteen Monogenic Genes Account for 15% of Nephrolithiasis/Nephrocalcinosis. Journal of the American Society of Nephrology 2015, 26(3), 543-551.
• Rice SJ, Thwaites DT, Halbritter J, Sayer JA. Cystinuria revisited: presentations with calcium-containing stones demands vigilance and screening in the stone clinic. Medical & Surgical Urology 2014, 3(3), 1-2.