RAG genomic variation causes autoimmune diseases through specific structure-based mechanisms of enzyme dysregulation
Neshatul Haque,
Tomoki Kawai,
Brian D. Ratnasinghe,
Jessica B. Wagenknecht,
Raul Urrutia,
Luigi D. Notarangelo,
Michael T. Zimmermann
Affiliations
Neshatul Haque
Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
Tomoki Kawai
Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20817, USA
Brian D. Ratnasinghe
Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
Jessica B. Wagenknecht
Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
Raul Urrutia
Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
Luigi D. Notarangelo
Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20817, USA; Corresponding author
Michael T. Zimmermann
Bioinformatics Research and Development Laboratory, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Corresponding author
Summary: Interpreting genetic changes observed in individual patients is a critical challenge. The array of immune deficiency syndromes is typically caused by genetic variation unique to individuals. Therefore, new approaches are needed to interpret functional variation and accelerate genomics interpretation. We constructed the first full-length structural model of human RAG recombinase across four functional states of the recombination process. We functionally tested 182 clinically observed RAG missense mutations. These experiments revealed dysfunction due to recombinase dysfunction and altered chromatin interactions. Structural modeling identified mechanical and energetic roles for each mutation. We built regression models for RAG1 (R2 = 0.91) and RAG2 (R2 = 0.97) to predict RAG activity changes. We applied our model to 711 additional RAG variants observed in population studies and identified a subset that may impair RAG function. Thus, we demonstrated a fundamental advance in the mechanistic interpretation of human genetic variations spanning from rare and undiagnosed diseases to population health.
