A comprehensive single-cell analysis of nearly 1 million cells from patients with inflammatory bowel disease uncovered key cellular and molecular signatures that corresponded with response to anti–tumor necrosis factor therapy. The study represented the largest longitudinal therapeutic atlas examining adalimumab treatment in both Crohn's disease and ulcerative colitis. 

In the study, published in Nature Immunology, researchers analyzed 216 gut biopsies from 41 patients (16 with Crohn's disease [CD], 22 with ulcerative colitis [UC], and 3 healthy controls) across five gut regions: terminal ileum, ascending colon, descending colon, sigmoid, and rectum. The study generated detailed profiles of 109 distinct cell states across immune, stromal, and epithelial compartments.

Patient Characteristics:

• Mean age: patients with CD = 36 years (standard deviation [SD] = 10.6), patients with UC = 33 years (SD = 10.10).
• Mean disease duration: patients with CD = 96 months, patients with UC = 73 months
• Gender distribution: 19 males, 22 females
• All patients were biologic-naive prior to initiating adalimumab.

Disease-Specific Differences:

• CD showed specific expansion of Th1 cells and PLCG2-high enterocytes
• UC demonstrated greater expansion of IgG-positive plasma cells and plasmablasts
• Both conditions shared similar tumor necrosis factor (TNF) pathway gene expression patterns.

TNF Receptor Expression:

• TNFRSF1A (TNFR1) was mainly found in epithelial, stromal, and myeloid cells
• TNFRSF1B (TNFR2) was preferentially expressed in immune cells
• Myeloid cells had highest expression of both receptors.

Remission Predictors:

• Higher baseline epithelial cell frequency was associated with remission in CD
• In UC, colonic goblet cells were more abundant at baseline in remission groups
• CD remission was associated with increased baseline abundance of C1Q-high IL1B-low macrophages expressing TREM2
• Both CD and UC remission groups showed higher baseline expression of MHC class I and II and interferon-response genes across multiple epithelial cell states.

Treatment Response Patterns:

• In remission cases, successful treatment led to epithelial reconstitution and decreased immune cell presence
• Nonremission in CD showed persistent myeloid-myeloid and CD4-positive T cell–myeloid interactions
• UC nonremission was characterized by increased plasmacytoid dendritic cells, multi-compartmental interferon signaling, distinct fibroblast recruitment signatures, specific T–helper cell responses, IgG-skewed plasmablasts.

The researchers employed multiple analytical techniques:

• Single-cell RNA sequencing
• Multiplexed imaging
• Spatial transcriptomics
• Flow cytometry
• RNAscope for spatial validation.

Remission Criteria: For CD (two out of three required):

• Harvey-Bradshaw Index < 5
• No macroscopic ulcers
• Nancy histological score ≤ 1.

For UC (two out of three required):

• Simple Clinical Colitis Activity Index ≤ 2
• Ulcerative Colitis Endoscopic Index of Severity ≤ 1
• Nancy histological score ≤ 1.

Sample Collection Protocol:

• Biopsies were processed within 2 hours of collection
• Samples were cryopreserved in liquid nitrogen
• Parallel samples were collected for histology
• Adalimumab trough levels were monitored to exclude antibody-mediated therapy failure.

The researchers extended their analysis to rheumatoid arthritis, finding shared inflammatory pathways that could inform treatment strategies across immune-mediated inflammatory diseases.

For nonresponders showing increased interferon signaling, JAK or p19 inhibition emerged as potential alternative therapeutic options. The study found cell state abundances showed stronger correlations with histological inflammation features compared with clinical or endoscopic measures.

Conflict of interest disclosures can be found in the study.