Novel Gene Variants of ZFYVE21 and Dysregulated Innate Immunity

Human gene data has fundamentally transformed our understanding of human disease. However, a major barrier for leveraging genomic data lies in the fact that many immune conditions, in particular autoimmune disease, often show complex etiologies. Many candidate risk genes show low explained heritability, complicating discovery of pathogenic mechanisms. Identification of monogene defects that strongly contribute to disease pathologies carries broad relevance for understanding the complex basis of autoimmunity. We have discovered novel loss-of-function (LOF) gene defect in a gene called ZFYVE21. ZFYVE21 is an ancient endosome-associated protein that shows increased expression in cells showing high endo- phagocytic activity like macrophages (MΦ). We previously identified ZFYVE21 as an essential mediator of NF- κB. Affected individuals with LOF of ZFYVE21 developed mucosal pathologies including ulcerative colitis (UC), a form of inflammatory bowel disease (IBD), and patient PBMCs showed signs of immune dysregulation including overexuberant innate signaling and impaired bacterial killing. We call this uncharacterized condition, ZFYVE21-Associated Disorder (ZAD). In preliminary studies, we explored how LOF of ZFYVE21 dysregulates innate immunity. Via a team approach, we collaborated with an IBD specialist, immune geneticist, structural biologist, and microbiologist. We harmonized in silico, in vitro, and in vivo approaches, and we generated 2 new mouse models including conditional loss of ZFYVE21 and mice systemically reconstituted with ZFYVE21 gene variants. Using our team approach, we preliminarily found that LOF of ZFYVE21 led to a MΦ intrinsic defect causing exacerbated colitis in vivo. These studies informed a new hypothesis that LOF of ZFYVE21 promotes MΦ dysfunction. Pathogen control processes including innate signaling and bacterial killing are essential for intestinal homeostasis. In 2 non-overlapping Specific Aims, we explore these processes as a basis for explaining immune dysregulation and development of mucosal immune pathologies with LOF of ZFYVE21. In Aim 1, we will explore how mutant ZFYVE21 proteoforms affects innate signaling, and in Aim 2 we will define how loss of ZFYVE21 protein stability impairs bacterial killing. We identified ZFYVE21 as a novel immune regulator in humans. Gene defects in ZFYVE21 have not been described for any human immune condition. Leveraging the strong effects of the ZFYVE21 gene defect, we pair biochemical, functional, and in vivo approaches to understand new mechanisms by which ZFYVE21 contributes to human immune pathologies. Project Number: 1R01AI195738-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of Allergy and Infectious Diseases (NIAID) | Principal Investigator: Dan Jane-Wit (+1 co-PI) | Institution: YALE UNIVERSITY, NEW HAVEN, CT | Award Amount: $778,828 | Activity Code: R01 | Study Section: Special Emphasis Panel[ZRG1 IIDA-A (81)] View on NIH RePORTER: https://reporter.nih.gov/project-details/1R01AI19573801