I am a Versus Arthritis-funded Research Associate in the lab of Professor John Loughlin within the Skeletal Research Group. We are based at the International Centre for Life, and our group focuses on osteoarthritis (OA) susceptibility loci, identified primarily through genome-wide association studies (GWAS). Using a range of molecular biology techniques, including CRISPR-Cas9, dCas9, RT-PCR, pyrosequencing, luciferase reporter assays, and siRNA knockdown, I investigate the functional effect of polymorphisms on gene expression. This project has involved the study of DNA methylation (DNAm) levels in various tissues of the articulating joints in late-stage OA patients, and the investigation of how a methylation quantitative trait locus (mQTL) can influence gene expression (eQTL). I am particularly interested in these effects in OA upon the gene RUNX2, the transcription factor responsible for skeletogenesis. Now, in collaboration with the MRC-Wellcome funded Human Developmental Biology Resource (HDBR) we are investigating the impact of DNAm in development, upon the integrity of cartilage in ageing.

I completed my MPharm degree at the University of Manchester in 2009, and successfully gained my professional registration with the GPhC. Following on from this, my interest in pharmacogenetics brought me to Newcastle University, where I completed a PhD project investigating the effect of rare missense mutations upon the structure and function of renal transport proteins.

Research Interests

Aberrant epigenetic gene regulation in osteoarthritis.

Epigenetic prioritisation of OA risk loci

The function of OA-associated mQTLs in developmental limb tissues

Current Work

dCas9 epigenome editing in chondrocyte cell lines, primary cells, and MSCs. 

Gene regulation by OA-associated methylation quantitative trait loci (mQTLs)

Functional analysis of GWAS loci using a range of molecular genetics techniques.

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)

Reviewer for Arthritis Research and Therapy, Applied Biochemistry and Biotechnology, and The Dunhill Medical Trust.

Chair of the Gordon Research Seminar "Cartilage Biology and Pathology" 2021, Tuscany, Italy. 

Current Grants: Co-Investigator (John Loughlin Principle Investigator):

Pump Priming Grant. Molecular genetic and epigenetic analysis of the chromosome 4p16.3 osteoarthritis risk locus. (June 2019-June 2020; Source: JGW Patterson Foundation; Amount: £48,722).

MRes/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. (September 2018-August 2022; Source: CIMA; Amount: £120,000).  

Public Engagement

Gene Editing: The Good, The Bad, and The Ugly. Genetics Matters, International Centre for Life, Newcastle upon Tyne. 23^rd February 2019 (Invited oral communication).

Laboratory Supervision

Miss Yulia Kehayova (CIMA MRes/PhD Student)

Mr Jack Roberts (Research Technician)

Miss Abby Brumwell (CIMA Research Technician)

• Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nature Reviews Rheumatology 2020, 16, 268-281.
• 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 T, 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 2020. In Press.
• 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.
• 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, 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, 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.
• 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.
• 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, Epub ahead of print.
• 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, 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.
• 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.
• 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.
• 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.
• 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.
• 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-Smith L, Rice SJ, Tabaksert A, Edwards N, Smithson S, Woodward MN, Tomson C, Welsh GI, Williams M, Thwaites D, Sayer JA, Coward RJM. Clinical and Genetic Analysis of a Cohort of English Cystinuria Patients. In: 52nd ERA-EDTA Congress. 2015, London, UK: Oxford University Press.
• 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 S, Edwards N, Sayer J, Thwaites D. The Effect of a Novel rBAT Mutation on the Expression and Function of System b(o,+). In: Experimental Biology 2015. 2015, Boston, USA: Federation of American Societies for Experimental Biology.
• Rice SJ, Edwards N, Sayer JA, Thwaites DT. The novel rBAT mutation Y579D and activity of the amino acid transporter System b^0,+. In: Physiology 2015. 2015, Cardiff: The Physiological Society.
• 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.