Biology subjects

Evrony, G. D.

Publications and source records attributed to Evrony, G. D..

3 recordsLinked to original sources

bioRxiv2025

Divergent somatic mutation patterns among human cerebellar neuron types

Neurons in the human brain accumulate somatic mutations with age. However, it is largely unknown how somatic mutation rates and patterns vary among the brains diverse types of neurons. Characterizing this variability is critical for elucidating the role of genome integrity in human brain function and disease. Moreover, the significant physiological differences among the brains cell types provides an opportunity to learn more general underlying factors that determine mutation rates and patterns. Here, we utilized high-fidelity duplex DNA sequencing to profile somatic mutation processes across the lifespan in the two major cell types of the human cerebellum, Purkinje neurons and granule neurons, which have dramatically different sizes, functions, and physiologies. Surprisingly, these cell types exhibited similar rates of substitution mutations, including similar rates of signature SBS5 that is responsible for most mutations in the body yet whose mechanism remains unknown. However, we identified differences in Purkinje and granule neurons patterns of substitutions and in their rates and patterns of insertions and deletions, with transcription playing a key role in mediating these differences. Our work indicates that different types of neurons in the brain can differ in their aging-related somatic mutation processes. Our results further suggest that key features that distinguish Purkinje neurons from granule neurons, such as cell size, metabolic rates, and neuronal firing rates, are unlikely to be intrinsic determinants of the total substitution mutation rate and of signature SBS5, which is the most prevalent aging-related mutational process.

genomics↗

bioRxiv2023

High-fidelity, Large-scale Targeted Profiling of Microsatellites

Microsatellites are highly mutable sequences that can serve as markers for relationships among individuals or cells within a population. The accuracy and resolution of reconstructing these relationships depends on the fidelity of microsatellite profiling and the number of microsatellites profiled. However, current methods for targeted profiling of microsatellites incur significant "stutter" artifacts that interfere with accurate genotyping, and sequencing costs preclude whole-genome microsatellite profiling of a large number of samples. We developed a novel method for accurate and cost-effective targeted profiling of a panel of > 150,000 microsatellites per sample, along with a computational tool for designing large-scale microsatellite panels. Our method addresses the greatest challenge for microsatellite profiling -- "stutter" artifacts -- with a low-temperature hybridization capture that significantly reduces these artifacts. We also developed a computational tool for accurate genotyping of the resulting microsatellite sequencing data that uses an ensemble approach integrating three microsatellite genotyping tools, which we optimize by analysis of de novo microsatellite mutations in human trios. Altogether, our suite of experimental and computational tools enables high-fidelity, large-scale profiling of microsatellites, which may find utility in diverse applications such as lineage tracing, population genetics, ecology, and forensics.

genomics↗

bioRxiv2023

Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other genetic diseases1-4. Almost all of these mosaic mutations begin as nucleotide mismatches or damage in only one of the two strands of the DNA prior to becoming double-strand mutations if unrepaired or misrepaired5. However, current DNA sequencing technologies cannot resolve these initial single-strand events. Here, we developed a single-molecule, long-read sequencing method that achieves single-molecule fidelity for single-base substitutions when present in either one or both strands of the DNA. It also detects single-strand cytosine deamination events, a common type of DNA damage. We profiled 110 samples from diverse tissues, including from individuals with cancer-predisposition syndromes, and define the first single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumors deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples deficient in only polymerase proofreading. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. Since the double-strand DNA mutations interrogated by prior studies are only the endpoint of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable new studies of how mutations arise in a variety of contexts, especially in cancer and aging.

genomics↗