BIRC3 Gene Variants Disrupt RIPK1 Signaling, Driving Monogenic Crohn’s Disease: New Insights and Therapeutic Avenues

Highlight

• Identification of rare, damaging BIRC3 variants in patients with monogenic Crohn’s disease (CD) across ages.
• BIRC3 deficiency disrupts receptor-interacting protein kinase 1 (RIPK1) ubiquitylation, leading to increased intestinal epithelial cell death through autophosphorylation of RIPK1.
• Functional and transcriptomic analyses in cellular, mouse, and zebrafish models demonstrate dysregulated TNF signaling and spontaneous intestinal inflammation due to BIRC3 variants.
• Pharmacological inhibition of RIPK1 or caspases mitigates intestinal inflammation, highlighting RIPK1 as a viable therapeutic target in BIRC3-deficient CD.

Study Background

Crohn’s disease (CD), a chronic inflammatory bowel disease, manifests as segmental inflammation primarily affecting the intestinal mucosa, leading to significant morbidity. While CD is generally considered polygenic, recent advances have uncovered monogenic forms often presenting in pediatric populations. Tumor necrosis factor (TNF) signaling is a crucial mediator of intestinal inflammation; dysregulation within its pathway can exacerbate epithelial damage and disease severity. The BIRC3 gene encodes cellular inhibitor of apoptosis protein 2 (cIAP2), an important negative regulator that modulates TNF receptor signaling through ubiquitylation of receptor-interacting protein kinase 1 (RIPK1). Despite extensive studies on TNF pathway components, human BIRC3 variants have not previously been implicated in CD pathogenesis. This research aimed to elucidate the role of BIRC3 variants in intestinal inflammation and identify new molecular targets for intervention.

Study Design

This multi-center study screened exome sequences from CD patients, both pediatric and adult-onset, for rare BIRC3 variants. Functional pathogenicity assessments were conducted using a multidisciplinary approach: cellular assays; mouse intestinal organoids; induced pluripotent stem cell (iPSC)-derived intestinal organoids; knock-in mouse models harboring specific BIRC3 variants such as p.H312Y; knockout mouse models; and knockout zebrafish models. Transcriptomic analyses of organoids and in vivo models provided insights into gene expression changes. The therapeutic potential of targeting aberrant pathways was assessed via small-molecule inhibitors of RIPK1 and caspases.

Key Findings

The study identified 14 CD patients from 10 unrelated families harboring rare, damaging variants in BIRC3. Notably, the p.H312Y cIAP2 variant was recurrent in multiple patients, including the index case. Functional experiments revealed that BIRC3 deficiency impaired the ubiquitylation of RIPK1, leading to its autophosphorylation, which precipitates increased epithelial cell death—a central driver of gut barrier disruption and inflammation.

The p.H312Y variant cIAP2 protein demonstrated mislocalization within cells, underscoring its defective regulatory function. Correspondingly, a knock-in mouse model heterozygous for this variant (cIAP2H312Y/+) exhibited exacerbated colitis upon chemical induction, while ciap1 heterozygous knockout zebrafish spontaneously developed colitis, affirming the mutation’s pathogenicity across species.

Transcriptomic profiling of BIRC3-deficient mouse intestinal organoids and zebrafish models uncovered inappropriate, sustained activation of TNF-responsive genes without external stimuli, indicating a loss of crucial negative feedback in inflammatory signaling pathways.

Crucially, treatment with RIPK1 kinase inhibitors or caspase inhibitors attenuated inflammation and epithelial cell death in BIRC3-deficient organoids and the cIAP2H312Y/+ mouse model, suggesting a targeted therapeutic approach for patients harboring these variants.

Expert Commentary

This work robustly illuminates a novel genetic cause of monogenic CD implicating BIRC3 variants that compromise epithelial integrity via dysregulated RIPK1 signaling. It aligns with emerging paradigms where epithelial cell death contributes fundamentally to inflammatory bowel disease pathogenesis, particularly in genetically predisposed individuals.

The use of diverse model organisms and state-of-the-art organoid systems strengthens the mechanistic link between BIRC3 dysfunction and intestinal inflammation. Notably, the identification of pharmacologically targetable pathways provides an exciting groundwork for precision therapeutics in CD, which conventionally relies on broadly immunosuppressive therapies.

However, translation to human clinical use will require validation in larger cohorts and clinical trials to delineate efficacy and safety profiles of RIPK1 inhibitors in this genetic subtype. The heterogeneity of CD implies that BIRC3 variant screening could become an important tool in the genetic diagnosis and personalized management of affected patients.

Conclusion

This study conclusively establishes BIRC3 deficiency as a cause of monogenic Crohn’s disease characterized by faulty RIPK1 regulation and increased intestinal epithelial cell death. The discovery of rare BIRC3 variants across pediatric and adult-onset CD patients expands the genetic landscape of this disease.

By elucidating the underlying molecular mechanisms and demonstrating the therapeutic impact of RIPK1 inhibition, the research offers a promising avenue for new targeted therapies aiming to restore epithelial balance and control inflammation. These findings highlight the importance of integrating genetic testing into clinical practice to enable personalized treatment strategies in Crohn’s disease.

Funding and Clinical Trials

The research was supported by multi-institutional collaborations and grants, details of which can be found at the original publication. No current clinical trials specifically targeting BIRC3 variants in CD were reported; however, interest in RIPK1 inhibitors is growing and may lead to relevant studies in the near future.

References

Li Q, Nambu R, Yaqiang H, et al. BIRC3 (Encoding Cellular Inhibitor of Apoptosis Protein 2) Variants Result in Dysregulated Receptor-Interacting Protein Kinase 1 Signaling Leading to Increased Epithelial Cell Death and Are Associated With Monogenic Crohn’s Disease. Gastroenterology. 2026 Jun 23. PMID: 42335979. Available from: https://pubmed.ncbi.nlm.nih.gov/42335979/

Additional literature on RIPK1 inhibitors, TNF signaling modulation, and monogenic inflammatory bowel disease pathogenesis was reviewed to contextualize these findings within the current field.