T cell clonal expansions in ileal Crohn's disease are associated with smoking behaviour and postoperative recurrence.

T cell clonal expansions are present in the inflamed mucosa of patients with Crohn's disease (CD) and may be implicated in postoperative recurrence after ileocolonic resection.
Methods: T cell receptor (TCR) analysis was performed in 57 patients included in a prospective multicentre cohort. Endoscopic recurrence was defined by a Rutgeerts score >i0. DNA and mRNA were extracted from biopsies collected from the surgical specimen and endoscopy, and analysed by high throughput sequencing and microarray, respectively.
Results: TCR repertoire in the mucosa of patients with CD displayed diverse clonal expansions. Active smokers at time of surgery had a significantly increased proportion of clonal expansions as compared with non-smokers (25.9%vs17.9%, p=0.02). The percentage of high frequency clones in the surgical specimen was significantly higher in patients with recurrence and correlated with postoperative endoscopic recurrence (area under the curve (AUC) 0.69, 95% CI 0.54 to 0.83). All patients with clonality above 26.8% (18/57) had an endoscopic recurrence. These patients with a high clonality were more frequently smokers than patients with a low clonality (61% vs 23%, p=0.005). The persistence of a similar TCR repertoire at postoperative endoscopy was associated with smoking and disease recurrence. Patients with high clonality showed increased expression of genes associated with CD8 T cells and reduced expression of inflammation-related genes. Expanded clones were found predominantly in the CD8 T cell compartment.
Conclusion: Clonal T cell expansions are implicated in postoperative endoscopic recurrence. CD patients with increased proportion of clonal T cell expansions in the ileal mucosa represent a subgroup associated with smoking and where pathogenesis appears as T cell driven.
Trial Registration Number: NCT03458195.
Competing Interests: Competing interests: MA received honoraria from Abbvie, MSD, Janssen, Takeda, Pfizer, Novartis, Ferring, Tillots, Celgene and Genentech/Roche. SN received honoraria from MSD, Abbvie, Takeda, Janssen, HAC Pharma, Tillots, Ferring and Novartis. AB received honoraria from MSD, Abbvie, Ferring, Takeda, Vifor Pharma, Sanofi‐Aventis, Hospira and Janssen. BP received honoraria from AbbVie, MSD, Takeda, Janssen, Bioagaran and Ferring. MF received honoraria from AbbVie, MSD, Takeda, Janssen, Pfizer, Ferring and Boehringer. HS received unrestricted study grants: Danone, Biocodex and Enterome; board membership, consultancy, or lecture fees: Carenity, Abbvie, Astellas, Danone, Ferring, Mayoly Spindler, MSD, Novartis, Roche, Tillots, Enterome, Maat, BiomX, Biose, Novartis and Takeda; cofunder of Nextbiotix. XT received honoraria from Abbvie, MSD, Takeda, Ferring, Norgine and Janssen. PS received honoraria from Takeda, MSD, Biocodex, Ferring and Abbvie, and non-financial support from Takeda. CA, MN, HB, VC, AMC, AS, CS and NB declare no competing interest.
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