Contact information

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

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

Research groups

Simmons Group: Intestinal Immunity in Health and Disease

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), Nature Medicine, 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), Nature Communications, 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, E7 - E7

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

FitzPatrick MEB. et al, (2025), Nature Immunology, 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), Proceedings of the National Academy of Sciences, 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), Journal of Crohn's and 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), The Lancet Gastroenterology & Hepatology, 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), Journal of Crohn's and 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 Medicine, 15

A Roadmap for the Human Gut Cell Atlas

Zilbauer M. et al, (2023), Nature Reviews Gastroenterology & Hepatology, 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, 954 - 954

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

Buckley PR. et al, (2023), Immunotherapy Advances, 3

Pathogenesis of Fistulating Crohn’s Disease: A Review

McGregor CGC. et al, (2023), Cellular and Molecular Gastroenterology and Hepatology, 15, 1 - 11

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

Matute JD. et al, (2023), The Journal of experimental medicine, 220

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

Lee CH. et al, (2022)

Lymphatic endothelia stakeout cryptic stem cells

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

Lymphatic endothelia stakeout cryptic stem cells

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

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

Serra EG. et al, (2022), Nature Communications, 13

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

Buckley PR. et al, (2022), Briefings in Bioinformatics, 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), Communications Biology, 5

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

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

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

Fawkner-Corbett D. et al, (2021), STAR Protocols, 2, 100890 - 100890

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), Nature Immunology, 22, 944 - 946

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

Buckley PR. et al, (2021)

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), Science Immunology, 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

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

Fraser E. et al, (2021), Frontiers in Immunology, 12

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), Nature Immunology, 22, 99 - 99

FAECAL MICROBIOTA TRANSPLANT FOR REFRACTORY CHECKPOINT INHIBITOR IMMUNOTHERAPY-RELATED COLITIS

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

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

Tran F. et al, (2020), Frontiers in Immunology, 11

Paracrine signalling by cardiac calcitonin controls atrial fibrogenesis and arrhythmia

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

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

Lee CH. et al, (2020), Frontiers in Immunology, 11

The battle for iron in enteric infections.

Sousa Gerós A. et al, (2020), Immunology, 161, 186 - 199

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 Neglected Tropical Diseases, 14, e0008783 - e0008783

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

Demetriou P. et al, (2020), Nature Immunology, 21, 1232 - 1243

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

Corridoni D. et al, (2020), Inflammatory bowel diseases, 26, 1658 - 1668

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

Corridoni D. et al, (2020), Nature Medicine, 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), Proceedings of the National Academy of Sciences, 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), The Journal of clinical investigation, 130, 4218 - 4234

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

Cheung VTF. et al, (2020), British Journal of 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), Nature Communications, 11

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

Bolton C. et al, (2020), Journal of Crohn's and Colitis, 14, 142 - 147

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

Lee CH. et al, (2020), Frontiers in immunology, 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

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 Gastroenterology, 10, 364 - 371

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

(2019), European journal of immunology, 49 Suppl 3, 1 - 2223

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

Harnack C. et al, (2019), Nature Communications, 10

More publications