Shixiang Sun

Mutations accumulate with age in most human tissues. While some undergo clonal expansion and contribute to disease, the mutational burden tolerated by a normal cell without functional decline remains unknown. Here, we repeatedly treat proliferating human primary fibroblasts with the point mutagen N -ethyl- N -nitrosourea, and analyze mutation burden by single-cell whole-genome sequencing. Mutation burden increases linearly to ~56,000 single-nucleotide variants per cell, with only a modest reduction in growth rate. We detect negative selection against potentially deleterious coding and noncoding variants, including mutations affecting pathways important for cell growth and maintenance. These findings suggest that selective depletion of harmful variants helps proliferating cells maintain function despite an extreme mutation burden. Because most adult tissues are largely nondividing and cannot remove damaging mutations through a growth disadvantage, somatic mutations that accumulate during aging may have pronounced functional consequences in vivo.

Recent advances in ultra-accurate sequencing technologies have revealed that somatic mutations accumulate throughout the human lifespan and may contribute to both normal aging and disease. These mutations are highly diverse, often non-recurrent, and functionally heterogeneous, making their biological impact difficult to evaluate systematically. Although many studies have profiled somatic mutations in individual tissues or limited cohorts, a centralized and scalable platform that integrates discoveries and supports functional interpretation has been lacking. To address this gap, we present SomaMutDB 2.0 (https://somamutdb.org/SomaMutDB/), a substantially expanded database cataloging 8.9 million mutations (8.57 million SNVs and 0.29 million INDELs) from 10 852 samples of 607 human subjects across 47 studies. Beyond expanded data coverage, SomaMutDB 2.0 introduces a comprehensive functional annotation framework applying 22 predictive models spanning coding, regulatory, expression-based, and ensemble predictors to systematically assess mutational impact. Users can browse pre-annotated variants through an interactive interface or upload their own variants for real-time analysis. Notably, all results are contextualized against mutations from normal, non-diseased tissues in the database, enabling more meaningful interpretation than raw scores alone. Together, these advances establish SomaMutDB 2.0 as the most comprehensive resource currently available for characterizing somatic mosaicism and its functional impact on human health and aging.

Somatic mutation is now recognized as a cause of multiple human diseases other than cancer. Osteoarthritis (OA), a highly prevalent age-related disease, has been associated with increased chromosomal abnormalities in articular cartilage. Here we characterize the somatic mutational landscape of chondrocytes during normal aging and in affected cartilage of patients with OA. We used single-cell whole-genome sequencing to analyze single-nucleotide variants (SNVs) and small insertions and deletions (InDels) in 100 chondrocytes isolated from the cartilage of hip femoral heads of 17 research participants aged 26−90 years, including 9 patients with OA and 8 non-OA donors. Both SNVs and InDels accumulate with age in chondrocytes with a clock-like mutational signature. Surprisingly, the age-related accumulation rate in OA chondrocytes is lower than that in non-OA control chondrocytes. Differences in mutational signatures and Gene Ontology term enrichment were found between OA and non-OA control samples. In this study, to understand the role of somatic mutation in the pathogenesis of OA, we characterized somatic SNV and InDel mutations. With further progress in analytical approaches, structural variations in the chondrocyte genome are also expected to provide valuable information.

Aneuploidy, an abnormal number of chromosomes, is a hallmark of cancer and has been proposed as an initiating event in tumorigenesis. In glioblastoma (GBM), a highly aggressive brain tumor, cells almost universally display gain of chromosome 7 and loss of chromosome 10. However, it remains unclear whether these alterations arise de novo during malignant transformation or reflect pre-existing chromosomal instability in normal brain tissue. Here, we used single-nucleus whole-genome sequencing (snWGS) on 225 NeuN-negative (non-neuronal) cortical nuclei from 12 healthy individuals and 6 GBM patients, including matched tumor cores and non-tumor brain regions. In healthy brains, approximately 15% of glial nuclei harbored somatic aneuploidies, most often involving chromosome arms, with recurrent 16p alterations detected in up to 3% of nuclei from both healthy controls and GBM non-tumor tissue. These findings establish 16p is a hotspot of structural variation in adult glia. Non-tumor regions in GBM patients closely resembled healthy controls in aneuploidy burden and chromosomal instability metrics and lacked hallmark tumor alterations. In contrast, GBM tumors exhibited significantly elevated aneuploidy (~50%), enrichment for canonical chromosomal instability-driven events, and sex-specific karyotype patterns, consistent with transformation-associated chromosomal instability. Thus, aneuploidy is a recurrent but constrained feature of normal adult glia, whereas chromosome instability and GBM-defining aneuploidies emerge only during malignant transformation.

At more than 200 years, the maximum lifespan of the bowhead whale exceeds that of all other mammals. The bowhead is also the second-largest animal on Earth¹, reaching over 80,000 kg. Despite its very large number of cells and long lifespan, the bowhead is not highly cancer-prone, an incongruity termed Peto’s paradox². Here, to understand the mechanisms that underlie the cancer resistance of the bowhead whale, we examined the number of oncogenic hits required for malignant transformation of whale primary fibroblasts. Unexpectedly, bowhead whale fibroblasts required fewer oncogenic hits to undergo malignant transformation than human fibroblasts. However, bowhead whale cells exhibited enhanced DNA double-strand break repair capacity and fidelity, and lower mutation rates than cells of other mammals. We found the cold-inducible RNA-binding protein CIRBP to be highly expressed in bowhead fibroblasts and tissues. Bowhead whale CIRBP enhanced both non-homologous end joining and homologous recombination repair in human cells, reduced micronuclei formation, promoted DNA end protection, and stimulated end joining in vitro. CIRBP overexpression in Drosophila extended lifespan and improved resistance to irradiation. These findings provide evidence supporting the hypothesis that, rather than relying on additional tumour suppressor genes to prevent oncogenesis^3,4,5, the bowhead whale maintains genome integrity through enhanced DNA repair. This strategy, which does not eliminate damaged cells but faithfully repairs them, may be contributing to the exceptional longevity and low cancer incidence in the bowhead whale.

Aging is the main risk factor for Parkinson’s disease (PD), yet our understanding of how age-related mechanisms contribute to PD pathophysiology remains limited. We conducted a longitudinal analysis of blood samples from the Parkinson’s Progression Markers Initiative cohort to investigate DNA damage in PD. Patients with PD exhibited disrupted DNA repair pathways and biased suppression of longer transcripts, indicating age-related, transcription-stalling DNA damage. Notably, at the intake visit, this DNA damage signature was detected only in patients with more severe progression of motor symptoms over 3 years, suggesting its potential as a predictor of disease severity. We validated this signature in independent PD cohorts and confirmed increased DNA damage in peripheral blood cells and dopamine neurons of the substantia nigra pars compacta in postmortem PD brains. Our study sheds light on an aging-related mechanism in PD pathogenesis and identifies potential markers of disease progression, providing a diagnostic platform to prognosticate disease progression.

We discovered a uniquely high spontaneous somatic mutational load in peripheral blood mononuclear cells (PBMCs) of Xeroderma Pigmentosum group C (XP-C) patients, characterized by elevated single nucleotide variants associated with mutation signatures SBS8 and SBS32, as well as an enrichment of single-nucleotide cytosine deletions. This hypermutability was markedly lower in fibroblasts, suggesting a replication-dependent mechanism of mutagenesis due to deficient global genome nucleotide excision repair (GG-NER). Our findings reveal distinct molecular subtypes within XP defined by spontaneous mutational load in normal blood cells and demonstrate that the exceptionally high mutation burden in XP-C leukemia originates from mutations already present prior to malignant transformation.