Pseudo-observations of longevity improve detection of resilience-associated genes in the Radiation Late Effects Cohort of rhesus macaques.

Non-human primates are an ideal model for interrogating the genetic basis of human lifespan and resilience due to their long lifespan compared to other model organisms, development of similar age-related chronic conditions, and genetic similarity. However, like humans, statistical methods for modeling survival suffer from the challenges of dealing with non-proportionality of hazards, large numbers of living individuals that must be censored, and loss-to-follow-up over studies that may last a decade or more. Here we overcome these challenges through the use of pseudo-observations of Restricted Mean Survival Time as a measure of resilience to the acute challenge of radiation exposure and chronic challenges of aging and a Western-style diet in rhesus macaques (Macaca mulatta) from the Wake Forest Non-Human Primate Radiation Late Effects Cohort. Our whole-exome analysis used Genome-wide Efficient Mixed Model Association (GEMMA) to identify variants associated with longevity, and a subsequent Gene Set Enrichment Analysis (GSEA) highlighted the cadherin and integrin signaling pathways as central to this resilience. As dysregulation of cell adhesion and extracellular matrix signaling is central to the development of fibrosis, we tested the functional relevance of these signals using a targeted Combined Annotation Dependent Depletion (CADD) score-weighted Sequence Kernel Association Test-Optimal (SKAT-O) analysis of GSEA leading-edge genes from both the cadherin and integrin pathways. This linked variant burden in PCDHGA5, PCDHGA3, PCDHGB2, PCDHA11, and PSENEN to the severity of myocardial fibrosis, and in IBSP, PDGFD, and LAMC2 to the severity of pulmonary fibrosis observed at necropsy. Critically, we note that the genetic variants are not caused by the radiation but rather create an underlying risk for disease that is then exacerbated by the acute and persistent stressors challenging these animals' intrinsic resilience. The success of this method in identifying biologically relevant genetic variants underlying survival in animals undergoing a strong challenge to their resilience highlights not only the role of genes predisposing animals to fibrosis in lifespan, but the overall utility of pseudo-observations in overcoming the limitations of survival analyses in humans and other long-lived species.