Contact information

Telephone
+44 (0) 1865 222412 (Renata Sojka)

PA
Renata Sojka
renata.sojka@rdm.ox.ac.uk

DPhil Projects Available

2026 Simmons Group: Engineering Intestinal Mesenchymal Niches to Promote Epithelial Barrier Health Through Life — Radcliffe Department of Medicine

Alison Simmons

PhD FRCP FMedSci

Director of the MRC Translational Immune Discovery Unit

Consultant Physician
Professor of Gastroenterology

Key publications

Spatial fibroblast niches define Crohn's fistulae.

McGregor C. et al, (2026), Nature, 649, 703 - 712

Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis.

Gupta T. et al, (2024), Cancer Cell, 42, 797 - 814.e15

Spatiotemporal analysis of human intestinal development at single-cell resolution.

Fawkner-Corbett D. et al, (2021), Cell, 184, 810 - 826.e23

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis.

Corridoni D. et al, (2020), Nat Med, 26, 1480 - 1490

Colonic epithelial cell diversity in health and inflammatory bowel disease.

Parikh K. et al, (2019), Nature, 567, 49 - 55

Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets.

Aulicino A. et al, (2018), Nat Commun, 9

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.

Kinchen J. et al, (2018), Cell, 175, 372 - 386.e17

Recent publications

Spatial fibroblast niches define Crohn's fistulae.

McGregor C. et al, (2026), Nature, 649, 703 - 712

Author Correction: Spatial fibroblast niches define Crohn's fistulae.

McGregor C. et al, (2025), Nature, 648

Immune-epithelial-stromal networks define the cellular ecosystem of the small intestine in celiac disease.

FitzPatrick MEB. et al, (2025), Nat Immunol, 26, 947 - 962

Type I IFN-activated lung monocytes and macrophages as initiators and drivers of fibrosis at the alveolar barrier in IPF

Nathwani V. et al, (2025)

Human Enteric Glia Diversity in Health and Disease: New Avenues for the Treatment of Hirschsprung Disease.

Windster JD. et al, (2025), Gastroenterology, 168, 965 - 979.e12

Goblet cell differentiation subgroups in colorectal cancer.

Abdullayeva G. et al, (2024), Proc Natl Acad Sci U S A, 121

Biologic Therapy for Inflammatory Bowel Disease: Real-World Comparative Effectiveness and Impact of Drug Sequencing in 13 222 Patients within the UK IBD BioResource.

Kapizioni C. et al, (2024), J Crohns Colitis, 18, 790 - 800

Mechanisms and management of loss of response to anti-TNF therapy for patients with Crohn's disease: 3-year data from the prospective, multicentre PANTS cohort study.

Chanchlani N. et al, (2024), Lancet Gastroenterol Hepatol, 9, 521 - 538

Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitis.

Gupta T. et al, (2024), Cancer Cell, 42, 797 - 814.e15

Baseline Expression of Immune Gene Modules in Blood is Associated With Primary Response to Anti-TNF Therapy in Crohn's Disease Patients.

Bai BYH. et al, (2024), J Crohns Colitis, 18, 431 - 445

GSDMB is increased in IBD and regulates epithelial restitution/repair independent of pyroptosis.

Rana N. et al, (2024), Cell, 187, 1011 - 1015

HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44+ Natural Killer Cells in Ulcerative Colitis.

Baumdick ME. et al, (2023), Gastroenterology, 165, 946 - 962.e13

A robust deep learning workflow to predict CD8 + T-cell epitopes.

Lee CH. et al, (2023), Genome Med, 15

A Roadmap for the Human Gut Cell Atlas.

Zilbauer M. et al, (2023), Nat Rev Gastroenterol Hepatol, 20, 597 - 614

Anti-TNF Biologicals Enhance the Anti-Inflammatory Properties of IgG N-Glycome in Crohn's Disease.

Hanić M. et al, (2023), Biomolecules, 13

Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila.

Matute JD. et al, (2023), J Exp Med, 220

A systems approach evaluating the impact of SARS-CoV-2 variant of concern mutations on CD8+ T cell responses.

Buckley PR. et al, (2023), Immunother Adv, 3

Pathogenesis of Fistulating Crohn's Disease: A Review.

McGregor CGC. et al, (2023), Cell Mol Gastroenterol Hepatol, 15, 1 - 11

Lymphatic endothelia stakeout cryptic stem cells.

Antanaviciute A. et al, (2022), Cell Stem Cell, 29, 1292 - 1293

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility.

Sazonovs A. et al, (2022), Nat Genet, 54, 1275 - 1283

Author Correction: Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease.

Serra EG. et al, (2022), Nat Commun, 13

Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens.

Buckley PR. et al, (2022), Brief Bioinform, 23

HLA-dependent variation in SARS-CoV-2 CD8 + T cell cross-reactivity with human coronaviruses.

Buckley PR. et al, (2022), Immunology, 166, 78 - 103

Multicentre derivation and validation of a colitis-associated colorectal cancer risk prediction web tool.

Curtius K. et al, (2022), Gut, 71, 705 - 715

Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion.

Aulicino A. et al, (2022), Commun Biol, 5

GSDMB is increased in IBD and regulates epithelial restitution/repair independent of pyroptosis.

Rana N. et al, (2022), Cell, 185, 283 - 298.e17

A robust deep learning platform to predict CD8+ T-cell epitopes

Lee C. et al, (2022)

Isolation of human fetal intestinal cells for single-cell RNA sequencing.

Fawkner-Corbett D. et al, (2021), STAR Protoc, 2

Interferon-Gamma-Producing CD8+ Tissue Resident Memory T Cells Are a Targetable Hallmark of Immune Checkpoint Inhibitor-Colitis.

Sasson SC. et al, (2021), Gastroenterology, 161, 1229 - 1244.e9

A Pilot Study on Automatic Three-Dimensional Quantification of Barrett's Esophagus for Risk Stratification and Therapy Monitoring.

Ali S. et al, (2021), Gastroenterology, 161, 865 - 878.e8

Common heritage of fibroblasts.

Antanaviciute A. et al, (2021), Nat Immunol, 22, 944 - 946

Bone Morphogenetic Protein Pathway Antagonism by Grem1 Regulates Epithelial Cell Fate in Intestinal Regeneration.

Koppens MAJ. et al, (2021), Gastroenterology, 161, 239 - 254.e9

IL-6 effector function of group 2 innate lymphoid cells (ILC2) is NOD2 dependent.

Hardman CS. et al, (2021), Sci Immunol, 6

Thiopurine monotherapy is effective in ulcerative colitis but significantly less so in Crohn's disease: long-term outcomes for 11 928 patients in the UK inflammatory bowel disease bioresource.

Stournaras E. et al, (2021), Gut, 70, 677 - 686

Spatiotemporal analysis of human intestinal development at single-cell resolution.

Fawkner-Corbett D. et al, (2021), Cell, 184, 810 - 826.e23

Author Correction: A dynamic CD2-rich compartment at the outer edge of the immunological synapse boosts and integrates signals.

Demetriou P. et al, (2021), Nat Immunol, 22

Multi-Modal Characterization of Monocytes in Idiopathic Pulmonary Fibrosis Reveals a Primed Type I Interferon Immune Phenotype.

Fraser E. et al, (2021), Front Immunol, 12

HLA-dependent variation in SARS-CoV-2 CD8+ T cell cross-reactivity with human coronaviruses

Buckley P. et al, (2021)

FAECAL MICROBIOTA TRANSPLANT FOR REFRACTORY CHECKPOINT INHIBITOR IMMUNOTHERAPY-RELATED COLITIS

Cheung V. et al, (2021), GUT, 70, A89 - A89

Paracrine signalling by cardiac calcitonin controls atrial fibrogenesis and arrhythmia.

Moreira LM. et al, (2020), Nature, 587, 460 - 465

Paracrine signalling by cardiac calcitonin controls atrial fibrogenesis and arrhythmia.

Moreira LM. et al, (2020), Nature, 587, 460 - 465

Inflammatory Bowel Disease Through the Lens of Single-cell RNA-seq Technologies.

Corridoni D. et al, (2020), Inflamm Bowel Dis, 26, 1658 - 1668

Homologous and heterologous re-challenge with Salmonella Typhi and Salmonella Paratyphi A in a randomised controlled human infection model.

Gibani MM. et al, (2020), PLoS Negl Trop Dis, 14

A dynamic CD2-rich compartment at the outer edge of the immunological synapse boosts and integrates signals.

Demetriou P. et al, (2020), Nat Immunol, 21, 1232 - 1243

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis.

Corridoni D. et al, (2020), Nat Med, 26, 1480 - 1490

Evasion of MAIT cell recognition by the African Salmonella Typhimurium ST313 pathovar that causes invasive disease.

Preciado-Llanes L. et al, (2020), Proc Natl Acad Sci U S A, 117, 20717 - 20728

Calcitonin paracrine signaling controls atrial fibrogenesis and arrhythmia

MOREIRA LM. et al, (2020), Nature

Epithelial-derived gasdermin D mediates nonlytic IL-1β release during experimental colitis.

Bulek K. et al, (2020), J Clin Invest, 130, 4218 - 4234

Immune checkpoint inhibitor-related colitis assessment and prognosis: can IBD scoring point the way?

Cheung VTF. et al, (2020), Br J Cancer, 123, 207 - 215

Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease.

Serra EG. et al, (2020), Nat Commun, 11

Stem Cells and Organoid Technology in Precision Medicine in Inflammation: Are We There Yet?

Tran F. et al, (2020), Front Immunol, 11

HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease.

Sazonovs A. et al, (2020), Gastroenterology, 158, 189 - 199

Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.

Lee CH. et al, (2020), Front Immunol, 11

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.

Lee CH. et al, (2020), Front Immunol, 11

Remission of Inflammatory Bowel Disease in Glucose-6-Phosphatase 3 Deficiency by Allogeneic Haematopoietic Stem Cell Transplantation.

Bolton C. et al, (2020), J Crohns Colitis, 14, 142 - 147

IMMUNE CHECKPOINT INHIBITOR-RELATED COLITIS ASSESSMENT AND PROGNOSIS: CAN UCEIS, MAYO AND NANCY INDEX SCORING POINT THE WAY?

Cheung VT. et al, (2020), GASTROENTEROLOGY, 158, S535 - S536

Immune checkpoint inhibitor-related colitis assessment and prognosis: can inflammatory bowel disease scoring point the way?

Cheung VTF. et al, (2020), JOURNAL OF CROHNS & COLITIS, 14, S286 - S288

Immunotherapy-related hepatitis: real-world experience from a tertiary centre.

Cheung V. et al, (2019), Frontline Gastroenterol, 10, 364 - 371

17th International Congress of Immunology, 19-23 October 2019, Beijing, China.

(2019), Eur J Immunol, 49 Suppl 3, 1 - 2223

R-spondin 3 promotes stem cell recovery and epithelial regeneration in the colon.

Harnack C. et al, (2019), Nat Commun, 10

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Contact information

DPhil Projects Available

Alison Simmons

Key publications

Recent publications