Biology subjects

Maslov, A. Y.

Publications and source records attributed to Maslov, A. Y..

15 recordsLinked to original sources

bioRxiv2026

Metallothionein loss in cancer cells contributes to increased mutations through defective DNA repair and metabolic imbalance

Understanding which genes are involved in mutagenesis is essential for developing cancer prevention and treatment strategies; establishing protectors of the genome has revolutionized cancer biology. Here, we describe metallothionein (MT) proteins as previously uncharacterized protectors against mutagenesis. MT is a heavy metal binding protein essential for zinc homeostasis and protection against heavy metal cytotoxicity. Because zinc binds approximately 10-15% of the proteome and is critical for processes such as DNA repair and mitochondrial health, MT loss is expected to disrupt these processes. We hypothesized that MT loss induces genomic instability by impairing DNA repair and mitochondrial function. In this study, the consequences of MT deficiency in high-grade serous ovarian cancer (HGSC) were investigated by knockdown of the most highly expressed MT, MT2A. Loss of MT2A resulted in the impaired DNA repair pathway base excision repair (BER), leading to increased mutagenesis. MT2A deficiency produced mitochondrial dysfunction, characterized by a decrease in mitochondrial membrane potential, glycolysis, oxidative phosphorylation, amino acids, and an imbalance of nucleobases. Together, these defects reflect cellular states associated with increased cancer aggressiveness. These findings identify MT as a fundamental hub maintaining genomic and metabolic integrity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/736843v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1af4adeorg.highwire.dtl.DTLVardef@15c588forg.highwire.dtl.DTLVardef@1ba5181org.highwire.dtl.DTLVardef@13d150b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data

Loss of chromosome Y (LOY) is the most common aneuploidy in aging men and is increasingly recognized as a marker of aging and genomic instability. Because LOY occurs in mosaic form, its degree reflects the fraction of cells lacking the Y chromosome. Existing SNP-array- and sequencing-based methods rely largely on single genomic features and indirect transformations to estimate this fraction. We developed BaySeq-Y, a Bayesian method that directly estimates LOY mosaicism from sequencing data using VCF files with read depth (DP) and allelic depth (AD). Within a rigorous Bayesian framework, BaySeq-Y integrates complementary LOY-associated genomic features, including decreased read depth and allelic imbalance, and can additionally leverage haplotype phasing to improve precision. In simulations and fluorescence in situ hybridization validation (FISH), BaySeq-Y provided accurate estimates and outperformed existing methods. Applications to ROSMAP and GTEx supported its biological relevance through transcriptomic validation, demonstrating its utility for quantifying LOY across diverse sequencing datasets.

bioinformatics↗

bioRxiv2025

Uniquely high spontaneous mutational load in blood cells of XP-C patients

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.

genomics↗

bioRxiv2025

Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver

Aneuploidy is a hallmark of cancers, including high-grade glioma (GBM), one of the most aggressive brain tumors. To assess whether increased aneuploidy already occurs in normal brain tissue of GBM patients, we performed single-nucleus whole-genome sequencing on 225 non-neuronal cortical nuclei from 12 disease-free individuals and 6 GBM patients, in the latter analyzing both tumor and non-tumor distal regions. Somatic aneuploidy was found in approximately 15% of non-neuronal nuclei in the adult human cortex, with recurrent chromosome 16p aneuploidy in up to 4% of nuclei. In contrast, about 51% of GBM tumor nuclei showed frequent aneuploidy of chromosomes 7 and 10, consistent with known GBM profiles. Notably, non-tumor brain regions from GBM patients exhibited aneuploidy frequencies and patterns similar to controls, including recurrent 16p involvement. These findings indicate that somatic aneuploidy in non-neuronal cells is a normal feature of the adult human brain and not linked to increased GBM risk.

cancer biology↗

bioRxiv2025

RNA sequence analysis of somatic mutations in aging and Parkinson's Disease

Parkinsons Disease (PD) is an age-related neurodegenerative disorder that has been associated with increased DNA damage. To test if PD is associated with increased somatic mutations, we analyzed RNA-seq data in whole blood from 5 visits of the Parkinsons Progression Markers Initiative for clonally amplified somatic variants. Comprehensive analysis of RNA-sequencing data revealed a total of 5,927 somatic variants (2.4 variants per sample on average). Mutation frequencies were significantly elevated in PD subjects as compared to age-matched controls at the time of the last visit. This was confirmed by RNA analysis of substantia nigra. By contrast, the fraction of carriers with clonal hematopoiesis, was significantly reduced in old PD patients as compared to old healthy controls. These results indicate that while the overall mutation rate is higher in PD, specific clonally amplified mutations are protective against PD, as has been found for Alzheimers Disease.

genetics↗

bioRxiv2024

Single-cell analysis of the somatic mutational landscape in human chondrocytes during aging and in osteoarthritis

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 of OA patients. Thus far no systematic attempt has been made to characterize the somatic mutational landscape of chondrocytes during normal aging and in affected cartilage of OA patients. Here we used single-cell whole genome sequencing to quantitatively analyze single-nucleotide variants (SNVs) and small insertions and deletions (InDels) in 100 single chondrocytes isolated from the cartilage of hip femoral heads of 17 subjects aged from 26 to 90 years, including 9 OA patients and 8 non-OA donors. Both SNVs and InDels were found to accumulate with age in chondrocytes with a clock-like mutational signature. Surprisingly, the age-related accumulation rate of these mutations was found to be lower in OA chondrocytes compared with chondrocytes from non-OA control subjects.

genomics↗

bioRxiv2024

Detection of genome structural variation in normal cells and tissues by single molecule sequencing

Rare genome structural-variants (SVs) in somatic cells and tissues are difficult to measure in bulk DNA because library preparation can create chimeric junctions that mimic authentic events. Based on our previous Single-Molecule Mutation sequencing (SMM-seq) assay, we developed a new method, SMM-SV-seq, which combines a chimera-suppressing library preparation with duplex confirmation of breakpoint-supporting molecules. Using libraries from mixtures of human and Drosophila DNA, we show a remaining artifact rate of 1.52 +/- 0.53 detectable cross-species chimeras per billion bases, providing an empirical background for correcting breakpoint frequencies. In a benchmark of evaluable homozygous germline deletions in the GM24385 cell line, SMM-SV-seq achieved 81.4% precision and 85.7% recall, exceeding the precision of established short-read callers while maintaining comparable recall. The assay detected dose-associated increases in SV-breakpoint frequencies in cells treated with bleomycin, a known clastogen. Biological relevance was demonstrated by a significantly greater irradiation-associated increase in translocation-like breakpoint frequencies in the BRCA1 185delAG-heterozygous mammary epithelial clone than in its isogenic wild-type control. These results establish SMM-SV-seq as a practical assay for calibrated, duplex-confirmed detection of rare somatic SV breakpoints directly in bulk DNA from non-clonal cell populations.

genomics↗

bioRxiv2024

Negative Selection Allows DNA Mismatch Repair-Deficient Mouse Fibroblasts In Vitro to Tolerate High Levels of Somatic Mutations

Substantial numbers of somatic mutations have been found to accumulate with age in different human tissues. Clonal cellular amplification of some of these mutations can cause cancer and other diseases. However, it is as yet unclear if and to what extent an increased burden of random mutations can affect cellular function without clonal amplification. We tested this in cell culture, which avoids the limitation that an increased mutation burden in vivo typically leads to cancer. We performed single-cell whole-genome sequencing of primary fibroblasts from DNA mismatch repair (MMR) deficient Msh2-/- mice and littermate control animals after long-term passaging. Apart from analyzing somatic mutation burden we analyzed clonality, mutational signatures, and hotspots in the genome, characterizing the complete landscape of somatic mutagenesis in normal and MMR-deficient mouse primary fibroblasts during passaging. While growth rate of Msh2-/-fibroblasts was not significantly different from the controls, the number of de novo single-nucleotide variants (SNVs) increased linearly up until at least 30,000 SNVs per cell, with the frequency of small insertions and deletions (INDELs) plateauing in the Msh2-/- fibroblasts to about 10,000 INDELS per cell. We provide evidence for negative selection and large-scale mutation-driven population changes, including significant clonal expansion of preexisting mutations and widespread cell-strain-specific hotspots. Overall, our results provide evidence that increased somatic mutation burden drives significant cell evolutionary changes in a dynamic cell culture system without significant effects on growth. Since similar selection processes against mutations preventing organ and tissue dysfunction during aging are difficult to envision, these results suggest that increased somatic mutation burden can play a causal role in aging and diseases other than cancer.

genomics↗

bioRxiv2024

Evidence for negative selection in human primary fibroblasts to tolerate high somatic mutation loads upon treatment with multiple low doses of N-ethyl-N-nitrosourea

Advanced sequencing has revealed that thousands of mutations accumulate with age in most human tissues. While some can clonally expand and cause disease, the maximum mutation load a cell can tolerate without functional decline is unknown. We addressed this by repeatedly treating proliferating human primary fibroblasts with a low dose of the mutagen N-ethyl-N-nitrosourea and quantifying somatic mutation burden using single-cell whole-genome sequencing. Mutation load increased linearly to [~]56,000 single-nucleotide variants per cell with only a slight reduction in growth rate. Analysis showed negative selection against potentially deleterious mutations in coding and non-coding regions, including sequences tied to pathways essential for cell growth and identity. This selective removal of harmful variants likely enables cells to maintain growth functions despite extreme mutation burden. Because most adult tissues are non-dividing and cannot benefit from negative selection based on growth, mutations that accumulate during aging may have pronounced functional consequences.

genetics↗

bioRxiv2023

Reduced frequency of clonal hematopoiesis in Parkinson's disease

To test if clonal hematopoiesis of indeterminate potential (CHIP) is associated with the incidence of Parkinsons Disease (PD), we analyzed blood whole exome sequencing data from 171 healthy controls and 335 PD subjects in the Parkinsons Progression Markers Initiative. We observed an age-related increase of CHIP carriers in the healthy controls. Surprisingly, the percentage of CHIP carriers was significantly lower in old PD patients than in age-matched controls.

genetics↗

bioRxiv2022

Analysis of somatic mutations in senescent cells using single-cell whole-genome sequencing

SO_SCPLOWUMMARYC_SCPLOWSomatic mutations accumulate in multiple organs and tissues during aging and are a known cause of cancer. Here we tested whether mutations accumulate during replicative senescence. Cellular senescence is also a possible cause of functional decline in aging, yet also acts as an anti-cancer mechanism in vivo. Using single-cell whole-genome sequencing, we compared mutation burdens between early passage and deeply senescent human fibroblasts. The results showed that single-nucleotide variations and small insertions and deletions increased in senescent cells by about two-fold, but have the same spectrum as early passage cells, while it has been known that particular mutational signatures are found in tumor cells. In contrast, aneuploidies were observed in half the senescent cells, but largely absent in early passage cells. Thus, the patterns of mutations among senescent, normal-aged and tumor cells differ significantly.

genomics↗

bioRxiv2019

Single-cell whole-genome sequencing reveals mutational landscapes of DNA mismatch repair deficiency in mouse primary fibroblasts

DNA Mismatch repair (MMR) deficiency is a major cause of hereditary non-polyposis colorectal cancer, and is also associated with increased risk of several other cancers. This is generally ascribed to the role of MMR in avoiding mutations by correcting DNA replication errors. In MMR knockout mice very high frequencies of somatic mutations, up until 100-fold of background, have been reported. However, these results have been obtained using bacterial reporter transgenes, which are not representative for the genome overall, and mutational patterns of MMR deficiency remain largely unknown. To fill this knowledge gap, we performed single-cell whole-genome sequencing of lung fibroblasts of Msh2-/- and wild-type mice. We observed a 4-fold increase of somatic single nucleotide variants (SNVs) in the fibroblasts of Msh2-/- mice compared to those of wild-type mice. The SNV signature of Msh2 deficiency was found to be driven by C>T and T>C transitions. By comparing it to human cancer signatures, we not only confirmed the inferred MMR-deficiency-related etiology of several cancer signatures but also suggested that MMR deficiency is likely the cause of a cancer signature with its etiology previously unknown. We also observed a 7-fold increase of somatic small insertions and deletions (INDELs) in the Msh2-/- mice. An elevated INDEL frequency has also been found in human MMR-related cancers. INDELs and SNVs distributed differently across genomic features in the Msh2-/- and control cells, with evidence of selection pressure and repair preference. These results provide insights into the landscape of somatic mutations in normal somatic cells caused by MMR deficiency.\n\nSignificanceOur results show that MMR deficiency in the mouse is associated with a much lower elevation of somatic mutation rates than previously reported and provides the first MMR whole-genome mutational landscapes in normal somatic cells in vivo.

genomics↗

bioRxiv2019

Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver

Accumulating somatic mutations have been implicated in age-related cellular degeneration and death. Because of their random nature and low abundance, somatic mutations are difficult to detect except in single cells or clonal lineages. Here we show that in single hepatocytes from human liver, an organ normally exposed to high levels of genotoxic stress, somatic mutation frequencies are high and increase substantially with age. Significantly lower mutation frequencies were observed in liver stem cells and organoids derived from them. These results could explain the increased age-related incidence of liver disease in humans and stress the importance of stem cells in maintaining genome integrity.

genomics↗

bioRxiv2019

Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

Introductory paragraphThe accumulation of mutations in somatic cells have been implicated as a cause of ageing since the 1950s1,2. Yet, attempts to establish a causal relationship between somatic mutations and ageing have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide detailed, genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan, from newborns to centenarians, using a recently developed, highly accurate single-cell whole-genome sequencing method3. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, located at immunoglobulin genes associated with somatic hypermutation. B cell-specific mutation signatures were observed associated with development, ageing or somatic hypermutation (SHM). The SHM signature strongly correlated with the signature found in human chronic lymphocytic leukemia and malignant B-cell lymphomas4, indicating that even in B cells of healthy individuals the potential cancer-causing events are already present. We also identified multiple mutations in sequence features relevant to cellular function, i.e., transcribed genes and gene regulatory regions. Such mutations increased significantly during ageing, but only at approximately half the rate of the genome average, indicating selection against mutations that impact B cell function. This first full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.

genomics↗

bioRxiv2019

Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation

Activation of retrotransposons and their insertions into new genomic locations, i.e., retrotranspositions (RTs), have been identified in about 50% of tumors. However, the landscape of RTs in different, normal somatic cell types in humans remains largely unknown. Using single-cell whole-genome sequencing we identified 528 RT events, including LINE-1 (L1), and Alu, in 164 single cells and clones of fibroblasts, neurons, B lymphocytes, hepatocytes and liver stem cells, of 29 healthy human subjects aged from 0 to 106 years. The frequency of RTs was found to vary from <1 on average per cell in primary fibroblasts to 7.8 per cell in hepatocytes. Somewhat surprisingly, RT frequency does not increase with age, which is in contrast to other types of spontaneous mutation. RTs were found significantly more likely to insert in or close to target genes of the Polycomb Repressive Complex 2 (PRC2), which represses most of the genes encoding developmental regulators through H3K27me3 histone modification in embryonic stem cells. Indeed, when directly comparing RT frequency between differentiated liver hepatocytes with liver stem cells, the latter were almost devoid of RTs. These results indicate that spontaneous RTs are associated with cellular differentiation and occur, possibly, as a consequence of the transient chromatin transition of differentiation-specific genes from a transcriptionally repressed to activated state during the differentiation process.

genomics↗