Phage-Display Immunoprecipitation Sequencing Reveals Distinct Antibody Signatures Against Bacterial Flagellins Associated With Treatment Response in Crohn's Disease.

INTRODUCTION

Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.

METHODS

Thirty-nine patients with active CD (Harvey-Bradshaw Index > 4 or fecal calprotectin > 150 μg/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22, and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.

RESULTS

Using PhIP-Seq analysis, only the antiflagellin antibodies' library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (Harvey-Bradshaw Index ≤ 4 and fecal calprotectin ≤ 150) vs nonremission at all time points ( P < 0.05). Of the 55 antiflagellin antibodies analyzed, 15 showed consistent >1.5-fold overrepresentation in nonremission samples, with high conservation of amino-acid sequences and targeting of Clostridiales , Lachnospiraceae , or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while nonremission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semiessential amino acids biosynthesis (q < 0.05).

DISCUSSION: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.