Biology subjects

Heguy, A.

Publications and source records attributed to Heguy, A..

18 recordsLinked to original sources

bioRxiv2026

Cyclin D-CDK4/6 couple proliferation to membrane and mitochondrial protein supply through a DeSI1 phospho-switch

Cyclin D-CDK4/6 complexes drive cell-cycle entry through an RB-E2F-dependent transcriptional program, but how they coordinate proliferation with the membrane and organelle protein supply required for growth is unclear. We identify DeSI1 as a cyclin D-CDK4/6 substrate whose phosphorylation at S25 converts a latent homodimer into an active monomeric deubiquitylase that recognizes hydrophobic proteins such as those bearing transmembrane domains and mitochondrial targeting sequences. Phosphorylated DeSI1 extends the lifetime of newly synthesized hydrophobic proteins that support membrane and mitochondrial capacity. Constitutive DeSI1 activation uncouples this proteostatic program from metabolic supply, creating a cytidine-nucleotide supply-demand imbalance associated with impaired CTP-dependent phospholipid homeostasis, cardiolipin depletion, and mitochondrial decompensation - defects that cytidine reverses. In mice, constitutive DeSI1 activation causes progressive cerebellar degeneration with membrane-protein accumulation, respiratory-chain loss, and phospholipid depletion. These findings define a post-translational mechanism coupling cell-cycle entry to membrane and mitochondrial capacity, and reveal the cost of uncoupling this program from its metabolic support.

cell biology↗

bioRxiv2025

Cardiomyocyte-specific plakophilin-2 loss is sufficient to induce aging and senescence of nonmyocytes. Relevance to arrhythmogenic cardiomyopathy.

IntroductionPathogenic variants in PKP2 are the most common cause of familial arrhythmogenic right ventricular cardiomyopathy (ARVC). ObjectiveTo test whether PKP2 deficiency only in cardiomyocytes is sufficient to provoke premature aging and pro-inflammatory senescence in non-myocytes, cardiac resident cells. MethodsWe studied mice with cardiomyocyte-specific, tamoxifen-activated loss of PKP2 (PKP2cKO) using conventional and multiplex imaging, cytokine arrays, epigenetic clocks, spatial transcriptomics, expansion and structured illumination microscopy, and correlative data analysis. We examined non-myocytes and cardiomyocytes for premature aging and senescence. ResultsWe observed senescence-associated heterochromatin foci (SAHFs) and p21 staining in non-myocytes. Cytokines in media of non-myocyte cells were consistent with senescence-associated secretory phenotype (SASP). Epigenetic clocks identified premature aging. Multiplex immunohistochemistry showed non-myocyte cells in niches, intermingled with cardiomyocytes. Spatial transcriptomics showed over-representation of SASP-related transcripts, predominantly in myocyte-rich areas of the left ventricle. SAHFs, p21 staining and increased epigenetic age were not found in cardiomyocytes from PKP2cKO hearts, though we observed structural features associated to premature aging. Cross-reference analysis showed correlation between the PKP2cKO cardiac proteome and that of mice 5 or 6 times their chronological age, as well as transcriptional signatures of neurodegenerative diseases. ConclusionLoss of PKP2 expression only in adult cardiac myocytes is sufficient to induce pro-inflammatory senescence in non-myocytes, and overall premature cardiac aging. This is the first study to intersect cellular senescence and premature aging in desmosomal arrhythmogenic cardiomyopathies. We speculate that cell-agnostic molecular signatures, biomarkers, and pharmacology of senescence and of neurodegenerative diseases may be relevant to diagnose or treat PKP2-ARVC. UNSTRUCTURED ABSTRACTPathogenic variants in PKP2 are the most common cause of familial arrhythmogenic right ventricular cardiomyopathy. We used the PKP2cKO model (cardiomyocyte-specific, tamoxifen-activated PKP2 knockout) to examine whether PKP2 deficiency only in cardiomyocytes is sufficient to provoke premature aging and pro-inflammatory senescence in non-myocyte, cardiac resident cells. Through a variety of methods, we identified senescence-associated heterochromatin foci (SAHFs), p21 staining, and cytokines consistent with senescence-associated secretory phenotype (SASP) in cells and media of non-myocytes. Epigenetic clocks identified premature aging. Spatial transcriptomics showed over-representation of SASP-related transcripts, predominantly in myocyte-rich areas of the left ventricle. SAHFs, p21 staining and epigenetics suggesting advanced age were not found in cardiomyocytes, though we observed structural features associated to premature aging. Cross-reference analysis showed correlation between the PKP2cKO cardiac proteome and that of mice 5 or 6 times their chronological age, as well as transcriptional signatures of neurodegenerative diseases. HIGHLIGHTSO_LIPKP2-ARVC is a leading cause of sudden unexpected death in the young. C_LIO_LIThe molecular path from the variant of a gene to the clinical disease remains unclear. An inflammatory component has been postulated. C_LIO_LIWe show that loss of PKP2 only in myocytes is sufficient to induce a pro-inflammatory senescence in non-myocytes and premature aging of cardiac cells. C_LIO_LISimilarities to the molecular profile of neurodegenerative diseases and novel paths to therapy are discussed. C_LI

physiology↗

bioRxiv2025

Clonal Heterogeneity in Human Pancreatic Ductal Adenocarcinoma and Its Impact on Tumor Progression

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer characterized by profound desmoplasia and cellular heterogeneity, which cannot be fully resolved using traditional bulk sequencing approaches. To understand the contribution of this heterogeneity to PDAC biology, we analyzed a large cohort of primary human PDAC samples (n = 62), profiling 443,451 single cells and 53,236 spatial transcriptomic spots using a combined single-cell RNA sequencing and spatial transcriptomics approach. Our analysis revealed significant intratumoral heterogeneity, with multiple genetically distinct neoplastic clones co-existing within individual tumors. These clones exhibited diverse transcriptional states and subtype profiles, challenging the traditional binary classification of PDAC into basal and classical subtypes; instead, our findings support a transcriptional continuum influenced by clonal evolution and spatial organization. Additionally, these clones each interacted uniquely with surrounding cell types in the tumor microenvironment. Phylogenetic analysis uncovered a rare but consistent classical-to-basal clonal transition associated with MYC amplification and immune response depletion, which were validated experimentally, suggesting a mechanism driving the emergence of a more aggressive basal clonal phenotype. Spatial analyses further revealed dispersed clones enriched for epithelial-to-mesenchymal transition (EMT) activity and immune suppression, correlating with metastatic potential and colonization of lymph node niches. These dispersed clones tended to transition toward a basal phenotype, contributing to disease progression. Our findings highlight the critical role of clonal diversity, transcriptional plasticity, and TME interactions in shaping human PDAC biology. This work provides new insights into the molecular and spatial heterogeneity of PDAC and offers potential avenues for therapeutic intervention targeting clonal evolution and the mechanisms driving metastasis.

cancer biology↗

bioRxiv2024

A genome wide code to define cell-type specific CTCF binding and chromatin organization

CTCF-mediated chromatin folding plays a key role in gene regulation, however the mechanisms controlling chromatin organization across cell states are not fully elucidated. Comprehensive analyses reveal that CTCF binding stability and cohesin overlap in mice and humans, are regulated by species specific differences in CTCF binding site (CBS) accessibility and enrichment of motifs corresponding to expressed TFs. By analyzing TFs, we confirm the co-operativity and competitiveness of TF/CTCF binding, which we further validate by allele specific analysis of SNPs. TF motif enrichment at CTCF bound sites is determined by cell state-specific transcriptional programs, which either stabilize or destabilize CTCF binding, as reflected by changing TF concentration. To examine CTCF binding in the context of nucleosome positioning, we performed single molecule nano-NOMe-seq. Subsetting reveals a continuum of binding states for CTCF, which are differentially represented at accessible versus inaccessible CBSs. As expected, CTCF degradation leads to a progressive loss of binding and nucleosome repositioning giving profiles similar to CTCF free CBSs. We also observe a similar time dependent effect when the cohesin subcomponent, SSC1 is degraded although CTCF remains bound, indicating that cohesin mediates CTCF-associated nucleosome repositioning. Stratified analysis of CTCF signal strength and accessibility reveals that in the presence of cohesin, CTCF strength contributes to nucleosome repositioning and chromatin insulation independent of accessibility. However, cobound TFs can uncouple the relationship between signal strength and nucleosome repositioning, without affecting the connection between repositioning and insulation. These studies identify mechanisms underlying cell state-specific CTCF profiles, linked to local and long-range chromatin organization.

genomics↗

bioRxiv2023

MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer

Aberrations in the capacity of DNA/chromatin modifiers and transcription factors to bind non-coding regions can lead to changes in gene regulation and impact disease phenotypes. However, identifying distal regulatory elements and connecting them with their target genes remains challenging. Here, we present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover novel cis regulatory elements (CREs) in a 1Mb region around every promoter in the genome. MethNet identifies clusters of highly ranked CREs, referred to as hubs, which contribute to the regulation of multiple genes and significantly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPRi based scRNA Perturb-seq validated the functional impact of CREs. Thus, MethNet-identified CREs represent a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots.

cancer biology↗

bioRxiv2023

Integrative Multi-omic Profiling of Two Human Decedents Receiving Pig Heart Xenografts Reveals Strong Perturbations in Early Immune-Cell and Cellular Metabolism Responses.

BackgroundRecent advances in xenotransplantation in living and decedent humans using pig xenografts have laid promising groundwork towards future emergency use and first in human trials. Major obstacles remain though, including a lack of knowledge of the genetic incompatibilities between pig donors and human recipients which may led to harmful immune responses against the xenograft or dysregulation of normal physiology. In 2022 two pig heart xenografts were transplanted into two brain-dead human decedents with a minimized immunosuppression regime, primarily to evaluate onset of hyper-acute antibody mediated rejection and sustained xenograft function over 3 days. MethodsWe performed multi-omic profiling to assess the dynamic interactions between the pig and human genomes in the first two pig heart-xenografts transplants into human decedents. To assess global and specific biological changes that may correlate with immune-related outcomes and xenograft function, we generated transcriptomic, lipidomic, proteomic and metabolomics datasets, across blood and tissue samples collected every 6 hours over the 3-day procedures. ResultsSingle-cell datasets in the 3-day pig xenograft-decedent models show dynamic immune activation processes. We observe specific scRNA-seq, snRNA-seq and geospatial transcriptomic changes of early immune-activation leading to pronounced downstream T-cell activity and hallmarks of early antibody mediated rejection (AbMR) and/or ischemia reperfusion injury (IRI) in the first xenograft recipient. Using longitudinal multiomic integrative analyses from blood in addition to antigen presentation pathway enrichment, we also observe in the first xeno-heart recipient significant cellular metabolism and liver damage pathway changes that correlate with profound physiological dysfunction whereas, these signals are not present in the other xenograft recipient. ConclusionsSingle-cell and multiomics approaches reveal fundamental insights into early molecular immune responses indicative of IRI and/or early AbMR in the first human decedent, which was not evident in the conventional histological evaluations.

systems biology↗

bioRxiv2022

Inflammation in the tumor-adjacent lung as a predictor of clinical outcome in lung adenocarcinoma

Early-stage lung adenocarcinoma is typically treated by surgical resection of the tumor. While in the majority of cases surgery can lead to cure, approximately 30% of patients progress. Despite intense efforts to map the genetic landscape of early-stage lung tumors, there has been limited success in discovering accurate biomarkers that can predict clinical outcomes. Meanwhile, the role of the tumor-adjacent tissue in cancer progression has been largely ignored. To test whether tumor-adjacent tissue can be informative of progression-free survival and to probe the underlying molecular pathways involved, we designed a multi-omic study in both tumor and matched tumor-adjacent histologically normal lung tissue from the same patient. Our study includes 143 treatment naive stage I cases with long-term patient follow-up and is, to our knowledge, the largest such study with the longest follow-up. We performed a comprehensive histologic characterization of all tumors, mapped the mutational landscape and probed the transcriptome of both tumor and adjacent normal tissue. We evaluated the predictive power of each data modality and showed that the transcriptome of tumor-adjacent histologically normal lung tissue is the only reliable predictor of clinical outcome. Unbiased discovery of co-expressed gene modules revealed that inflammatory pathways are upregulated in the tumor-adjacent tissue of patients at high risk for disease progression. Furthermore, single-cell transcriptome analysis in the tumor-adjacent lung demonstrated that progression-associated inflammatory signatures were broadly expressed by both immune and non-immune cells including mesothelial cells, alveolar type 2 cells and fibroblasts, CD1 dendritic cells and MAST cells. Collectively, our studies suggest that molecular profiling of tumor-adjacent tissue can identify patients that are at high risk for disease progression.

bioinformatics↗

bioRxiv2022

De novo assembly and annotation of the singing mouse genome

BackgroundDeveloping genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits.Specifically, organisms that exhibit unique, accessible phenotypes-of-interests, allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alstons singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. ResultsUsing PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. ConclusionsThese resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.

genomics↗

bioRxiv2022

Lupus disease flares are concordant with immune responses to blooms of lipoglycan-expressing Ruminococcus blautia gnavus strains arising from unstable gut microbiota communities

Whereas genetic susceptibility for Systemic Lupus Erythematosus has been well explored, the precipitants for clinical disease flares remain a mystery. To investigate for dynamic-relationships between gut-microbial communities and Lupus disease activity, we performed taxonomic surveys of fecal 16S rRNA gene amplicon-libraries from Lupus patients and healthy volunteers, obtained at serial timepoints over many months to several years. Individual Lupus patients commonly displayed imbalances in alpha and beta microbiota-diversity, which were uniquely different from healthy individuals as well as from other Lupus patients. Moreover, multivariate analysis of sequential Lupus libraries documented community-wide ecological microbiota instability overtime, most pronounced in patients with Lupus Nephritis LN), a severe form associated with worse prognosis. Lupus gut communities displayed transient spikes of pathogenic bacterial species, with by far the most prevalent being blooms of Ruminococcus blautia gnavus (RG), occurring in nearly half of LN patients often concordant with disease activity flares. RG strains isolated during disease flares, but not those isolated from healthy individuals or patients with inflammatory bowel disease, commonly expressed a novel, highly immunogenic cell wall-associated lipoglycan with conserved structural features that include a diacyl glycerol anchor. Cross-reactive antigenic determinants on these lipoglycans were recognized by murine monoclonal antibodies, and by spontaneously arising Lupus serum IgG antibodies with peak serum antibody responses also concordant with RG blooms. As SLE is frequently characterized by remitting-relapsing disease, despite appropriate treatment, we speculate that gut blooms of pathogenic bacteria, that impair gut barrier function and stoke systemic inflammation, directly contribute to immunopathogenesis.

immunology↗

bioRxiv2022

Single-Cell RNA Sequencing Reveals the Effects of Chemotherapy on Human Pancreatic Adenocarcinoma and its Tumor Microenvironment

The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. We performed single-cell RNA sequencing on freshly collected human PDAC samples either before or after chemotherapy. Overall, we found a heterogeneous mixture of basal and classical cancer cell subtypes, along with distinct cancer-associated fibroblast and macrophage subpopulations. Strikingly, classical and basal-like cancer cells exhibited similar transcriptional responses to chemotherapy, and did not demonstrate a shift towards a basal-like transcriptional program among treated samples. We observed decreased ligand-receptor interactions in treated samples, particularly TIGIT on CD8+ T cells and its receptor on cancer cells, and identified TIGIT as the major inhibitory checkpoint molecule of CD8+ T cells. Our results suggest that chemotherapy profoundly impacts the PDAC TME and may promote resistance to immunotherapy.

cancer biology↗

bioRxiv2022

Delta-Omicron recombinant SARS-CoV-2 in a transplant patient treated with Sotrovimab

BackgroundThe emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. MethodsMulti-method amplicon and metagenomic sequencing of a clinical swab and the in vitro grown virus allowed for high-confidence detection of a novel recombinant variant. Mutational, phylogeographic, and structural analyses determined features of the recombinant genome and spike protein. Neutralization assays using infectious as well as pseudotyped viruses and point mutants thereof defined the recombinants sensitivity to a panel of monoclonal antibodies and sera from vaccinated and/or convalescent individuals. ResultsA novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5-Delta AY.45 and a 3-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D. ConclusionsRecombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others)

microbiology↗

bioRxiv2022

Little skate genome exposes the gene regulatory mechanisms underlying the evolution of vertebrate locomotion

The little skate Leucoraja erinacea, a cartilaginous fish, displays pelvic fin driven walking-like behaviors using genetic programs and neuronal subtypes similar to those of land vertebrates. However, mechanistic studies on little skate motor circuit development have been limited, due to a lack of high-quality reference genome. Here, we generated an assembly of the little skate genome, containing precise gene annotation and structures, which allowed post-genome analysis of spinal motor neurons (MNs) essential for locomotion. Through interspecies comparison of mouse, skate and chicken MN transcriptomes, shared and divergent MN expression profiles were identified. Conserved MN genes were enriched for early-stage nervous system development. Comparison of accessible chromatin regions between mouse and skate MNs revealed conservation of the potential regulators with divergent transcription factor (TF) networks through which expression of MN genes is differentially regulated. TF networks in little skate MNs are much simpler than those in mouse MNs, suggesting a more fine-grained control of gene expression operates in mouse MNs. These findings suggest conserved and divergent mechanisms controlling MN development system of vertebrates during evolution and the contribution of intricate gene regulatory networks in the emergence of sophisticated motor system in tetrapods.

evolutionary biology↗

bioRxiv2022

Clostridia isolated from helminth-colonized humans promote hatching of Trichuris muris

Soil transmitted intestinal worms known as helminths colonize over 1.5 billion people worldwide. Although helminth colonization has been associated with altered composition of the gut microbiota, such as increases in Clostridia, individual species have not been isolated and characterized. Here, we isolated and sequenced the genome of 13 Clostridia from the Orang Asli, an indigenous population in Malaysia with high prevalence of helminth infections. Metagenomic analysis of 650 fecal samples from urban and rural Malaysians revealed higher prevalence and abundance of these isolates compared to individuals in the United States, with Peptostreptococcaceae family members displaying a specific association with helminth colonization. Remarkably, Peptostreptococcaceae isolated from the Orang Asli displayed superior capacity to induce hatching of eggs from the murine helminth Trichuris muris. These findings support a model in which helminths select for gut colonization of microbes that in turn support their life cycle by promoting egg hatching.

microbiology↗

bioRxiv2020

iCellR: Combined Coverage Correction and Principal Component Alignment for Batch Alignment in Single-Cell Sequencing Analysis

Under-sampling RNA molecules and low-coverage sequencing in some single cell sequencing technologies introduce zero counts (also known as drop-outs) into the expression matrices. This issue may complicate the processes of dimensionality reduction and clustering, often forcing distinct cell types to falsely resemble one another, while eliminating subtle, but important differences. Considering the wide range in drop-out rates from different sequencing technologies, it can also affect the analysis at the time of batch/sample alignment and other downstream analyses. Therefore, generating an additional harmonized gene expression matrix is important. To address this, we introduce two separate batch alignment methods: Combined Coverage Correction Alignment (CCCA) and Combined Principal Component Alignment (CPCA). The first method uses a coverage correction approach (analogous to imputation) in a combined or joint fashion between multiple samples for batch alignment, while also correcting for drop-outs in a harmonious way. The second method (CPCA) skips the coverage correction step and uses k nearest neighbors (KNN) for aligning the PCs from the nearest neighboring cells in multiple samples. Our results of nine scRNA-seq PBMC samples from different batches and technologies shows the effectiveness of both these methods. All of our algorithms are implemented in R, deposited into CRAN, and available in the iCellR package.

bioinformatics↗

bioRxiv2018

The translatome of adult cortical axons is regulated by learning in vivo

Local translation can support memory consolidation by supplying new proteins to synapses undergoing plasticity. Translation in adult forebrain dendrites is an established mechanism of synaptic plasticity and is regulated by learning, yet there is no evidence for learning-regulated protein synthesis in adult forebrain axons, which have traditionally been believed to be incapable of translation. Here we show that axons in the adult rat amygdala contain translation machinery, and use translating ribosome affinity purification (TRAP) with RNASeq to identify mRNAs in cortical axons projecting to the amygdala, over 1200 of which were regulated during consolidation of associative memory. Mitochondrial and translation-related genes were upregulated, whereas synaptic, cytoskeletal, and myelin-related genes were downregulated; the opposite effects were observed in the cortex. Our results demonstrate that learning-regulated axonal translation occurs in the adult forebrain, and support the likelihood that local translation is more a rule than an exception in neuronal processes.

neuroscience↗

bioRxiv2018

Molecular features of premenopausal breast cancers in Latin American women: pilot results from the PRECAMA study

BackgroundIn Latin America (LA), there is a high incidence rate of breast cancer (BC) in premenopausal women, and the genomic features of these BC remain unknown. Here, we aim to characterize the molecular features of BC in young LA women within the framework of the PRECAMA study, a multicenter population-based case-control study on breast cancer in premenopausal women.\n\nMethodsPathological tumor tissues were collected from incident cases from four LA countries. Immunohistochemistry (IHC) was performed centrally for ER, PR, HER2, Ki67, EGFR, CK5/6 and p53 protein markers. Targeted deep sequencing was done on genomic DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour tissues and their paired blood samples to screen for somatic mutations in eight genes frequently mutated in BC. A subset of samples was analyzed by exome sequencing to identify somatic mutational signatures.\n\nResultsThe majority of cases were positive for ER or PR (168/233; 72%) and there were 21% triple negative (TN) cases, mainly of basal type. Most tumors were positive for Ki67 (189/233; 81%). In 126 sequenced cases, TP53 and PIK3CA were the most frequently mutated genes (32.5% and 21.4%, respectively), followed by AKT1 (9.5%). TP53 mutations were more frequent in HER2-enriched and TN IHC subtypes, while PIK3CA/AKT1 mutations were more frequent in ER positive tumors, as expected. Interestingly, a higher proportion of G:C>T:A mutations was observed in TP53 gene in PRECAMA cases compared to TCGA and METABRIC breast cancer series (27% vs 14%). Exome-wide mutational patterns in 10 TN cases revealed alterations in signaling transduction pathways and major contributions of mutational signatures caused by altered DNA repair pathways.\n\nConclusionsThis pilot results on PRECAMA tumors gives a preview of the molecular features of premenopausal BC in LA. Although, the overall mutation burden was as expected from data in other populations, mutational patterns observed in TP53 and exome-wide suggested possible differences in mutagenic processes giving rise to these tumors compared to other populations. Further omics analyses of a larger number of cases in the near future will allow investigating relationships between these molecular features and risk factors.

cancer biology↗

bioRxiv2018

Experimental analysis of exome-scale mutational signature of glycidamide, the reactive metabolite of acrylamide

Acrylamide, a probable human carcinogen, is ubiquitously present in the human environment, with sources including heated starchy foods, coffee and cigarette smoke. Humans are also exposed to acrylamide occupationally. Acrylamide is genotoxic, inducing gene mutations and chromosomal aberrations in various experimental settings. Covalent haemoglobin adducts were reported in acrylamide-exposed humans and DNA adducts in experimental systems. The carcinogenicity of acrylamide has been attributed to the effects of glycidamide, its reactive and mutagenic metabolite capable of inducing rodent tumors at various anatomical sites. In order to characterize the pre-mutagenic DNA lesions and global mutation spectra induced by acrylamide and glycidamide, we combined DNA-adduct and whole-exome sequencing analyses in an established exposure-clonal immortalization system based on mouse embryonic fibroblasts. Sequencing and computational analysis revealed a unique mutational signature of glycidamide, characterized by predominant T:A>A:T transversions, followed by T:A>C:G and C:G>A:T mutations exhibiting specific trinucleotide contexts and significant transcription strand bias. Computational interrogation of human cancer genome sequencing data indicated that a combination of the glycidamide signature and an experimental benzo[a]pyrene signature are nearly equivalent to the COSMIC tobacco-smoking related signature 4 in lung adenocarcinomas and squamous cell carcinomas. We found a more variable relationship between the glycidamide- and benzo[a]pyrene-signatures and COSMIC signature 4 in liver cancer, indicating more complex exposures in the liver. Our study demonstrates that the controlled experimental characterization of specific genetic damage associated with glycidamide exposure facilitates identifying corresponding patterns in cancer genome data, thereby underscoring how mutation signature laboratory experimentation contributes to the elucidation of cancer causation.\n\nA 40-word summaryInnovative experimental approaches identify a novel mutational signature of glycidamide, a metabolite of the probable human carcinogen acrylamide. The results may elucidate the cancer risks associated with exposure to acrylamide, commonly found in tobacco smoke, thermally processed foods and beverages.

genomics↗

bioRxiv2017

Genome-Scale Mutational Signatures Of Aflatoxin In Cells, Mice And Human Tumors

Aflatoxin B1 (AFB1) is a mutagen and IARC Group 1 carcinogen that causes hepatocellular carcinoma (HCC). Here we present the first whole genome data on the mutational signatures of AFB1 exposure from a total of > 40,000 mutations in four experimental systems: two different human cell lines, and in liver tumors in wild-type mice and in mice that carried a hepatitis B surface antigen transgene - this to model the multiplicative effects of aflatoxin exposure and hepatitis B in causing HCC. AFB1 mutational signatures from all four experimental systems were remarkably similar. We integrated the experimental mutational signatures with data from newly-sequenced HCCs from Qidong County, China, a region of well-studied aflatoxin exposure. This indicated that COSMIC mutational signature 24, previously hypothesized to stem from aflatoxin exposure, indeed likely represents AFB1 exposure, possibly combined with other exposures. Among published somatic mutation data, we found evidence of AFB1 exposure in 0.7% of HCCs treated in North America, 1% of HCCs from Japan, but 16% of HCCs from Hong Kong. Thus, aflatoxin exposure apparently remains a substantial public health issue in some areas. This aspect of our study exemplifies the promise of future widespread resequencing of tumor genomes in providing new insights into the contribution of mutagenic exposures to cancer incidence.

cancer biology↗