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Cambridge Immunology Network


Clinician Scientist Group Leader, The Francis Crick Institute 

Honorary Consultant Gastroenterologist, Royal Free London NHS Foundation Trust


James Lee is a gastroenterologist with a clinical interest in inflammatory bowel disease (IBD) and a background in genetics, genomics and immunology. He is also a member of the UK and International IBD Genetics Consortia. His research interests include the genetic and biological determinants of prognosis in autoimmune, inflammatory and infectious diseases - as distinct from those pathways that drive disease development - and in better understanding how genetic variation contributes to complex disease biology. He currently holds a Wellcome Trust Intermediate Clinical Fellowship and in which he plans to investigate the role of previously uncharacterised long non-coding RNAs in the immune system - having shown that several of them lie within IBD-associated genetic loci. James will be based at the University of Cambridge and will spend half of his Fellowship at Harvard University.


Key publications: 

A blood-based prognostic biomarker in inflammatory bowel disease

Biasci D*, Lee JC* , Noor NM, Pombal DR, Hou M, Lewis N, Ahmad T, Hart A, Parkes M, McKinney EF, Lyons PA, Smith KGC. [* denotes joint first authors, denotes co-corresponding authors]. Gut. In press



Predicting outcomes for Crohn’s disease using a molecular biomarker (PROFILE): protocol for a multi-centre, randomised, biomarker-stratified trial.

Parkes M, Noor NM, Dowling F, Leung H, Bond S, Whitehead L, Upponi S, Kinnon P, Sandham AP, Lyons PA, McKinney EF, Smith KGC, Lee JC.  [ denotes co-corresponding authors] BMJ Open. 5;8(12):e026767 (2018)



Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease.

Lee JC* , Biasci D*, Roberts R, Gearry RB, Mansfield JC, Ahmad T, Prescott NJ, Satsangi J, Wilson DC, Jostins L, Anderson CA; UK IBD Genetics Consortium., Traherne JA, Lyons PA, Parkes M, Smith KGC. [* denotes joint first authors, denotes co-corresponding authors] Nat Genet. 49: 262-268 (2017)



Genome-wide association study implicates immune activation of multiple integrin genes in IBD.

de Lange KM*, Moutsianas L*, Lee JC*, Lamb CA, Luo Y, Kennedy NA, Jostins L, Rice DL, Gutierrez-Achury J, Ji SG, Heap G, Nimmo ER, Edwards C, Henderson P, Mowat C, Sanderson J, Satsangi J, Simmons A, Wilson DC, Tremelling M, Hart A, Mathew CG, Newman WG, Parkes M, Lees CW, Uhlig H, Hawkey C, Prescott NJ, Ahmad T, Mansfield JC, Anderson CA, Barrett JC. [* denotes joint first authors] Nat Genet. 49: 256-261 (2017)



Association between genetic variation in FOXO3 and reductions in inflammation and disease activity in inflammatory polyarthritis.

Viatte S*, Lee JC*, Fu B, Espéli M, Lunt M, De Wolf JN, Wheeler L, Reynolds JA, Castelino M, Symmons DP, Lyons PA, Barton A, Smith KGC. [* denotes joint first authors] Arthritis Rheumatol. 68(11):2629-2636. (2016)



In vivo characterization of Linc-p21 reveals functional cis-regulatory DNA elements. Groff AF, Sanchez-Gomez DB, Soruco MML, Gerhardinger C, Barutcu AR, Li E, Elcavage L, Plana O, Sanchez LV, Lee JC, Sauvageau M, Rinn JL. Cell Reports 23;16(8):2178-86. (2016)



Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway.

Lee JC, Espéli M, Anderson CA, Linterman MA, Pocock JM, Williams NJ, Roberts R, Viatte S, Fu B, Peshu N, Hien TT, Phu NH, Wesley E, Edwards C, Ahmad T, Mansfield JC, Gearry R, Dunstan S, Williams TN, Barton A, Vinuesa CG, UK IBD Genetics Consortium, Parkes M, Lyons PA, Smith KGC. Cell 155(1):57-69 (2013)



Gene-expression profiling of CD8 T-cells predicts prognosis in patients with Crohn disease and ulcerative colitis.

Lee JC, Lyons PA, McKinney EF, Sowerby JM, Carr EJ, Bredin F, Rickman HM, Ratlamwala H, Hatton A, Rayner TF, Parkes M, Smith KGC. J Clin Invest. 121(10):4170-4179. (2011)



Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.

Barrett JC, Lee JC, Lees CW, Prescott NJ, Anderson CA, Phillips A, Wesley E, Parnell K, Zhang H, Drummond H, Nimmo ER, Massey D, Blaszczyk K, Elliott T, Cotterill L, Dallal H, Lobo AJ, Mowat C, Sanderson JD, Jewell DP, Newman WG, Edwards C, Ahmad T, Mansfield JC, Satsangi J, Parkes M, Mathew CG; Wellcome Trust Case Control Consortium 2, Donnelly P, Peltonen L, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Craddock N, Deloukas P, Duncanson A, Jankowski J, Markus HS, Mathew CG, McCarthy MI, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Samani N, Trembath RC, Viswanathan AC, Wood N, Spencer CC, Barrett JC, Bellenguez C, Davison D, Freeman C, Strange A, Donnelly P, Langford C, Hunt SE, Edkins S, Gwilliam R, Blackburn H, Bumpstead SJ, Dronov S, Gillman M, Gray E, Hammond N, Jayakumar A, McCann OT, Liddle J, Perez ML, Potter SC, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P, Deloukas P, Peltonen L, Mathew CG, Blackwell JM, Brown MA, Corvin A, McCarthy MI, Spencer CC, Attwood AP, Stephens J, Sambrook J, Ouwehand WH, McArdle WL, Ring SM, Strachan DP. Nat Genet. 41(12):1330-4. (2009)

Other Professional Activities

Public Involvement/Engagement


Dr James Lee works with patient groups (e.g. Crohn's and Colitis UK), participates in public events (e.g. Cambridge Science Festival, Harvard Science cafe), prepares articles for patient magazines
( and mainstream press (including Huffington Post), and is involved in establishing and training a "Patient Champion" on the trial management group of the PROFILE trial.  

Dr James  Lee
Available for consultancy


Person keywords: 
B cells
co-stimulatory molecules
T cells