RESUMO
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features, including intellectual disability, developmental and speech delay, and hypotonia, and affects multiple organ systems. KAT6A is the enzymatic core of a histone-acetylation protein complex; however, the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n = 8) and control (n = 14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23% (14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, and HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
Assuntos
Epigênese Genética , Histonas , Humanos , Histonas/genética , Histonas/metabolismo , Proteômica , Cromatina , Mutação , Fatores de Transcrição/genética , Proteínas de Homeodomínio/genética , Histona Acetiltransferases/genética , Histona Acetiltransferases/metabolismoRESUMO
BACKGROUND: Asian American and Pacific Islander (AAPI) melanoma patients have higher mortality than non-Hispanic White (NHW) patients. Treatment delays may contribute, but whether AAPI patients have longer time from diagnosis to definitive surgery (TTDS) is unknown. OBJECTIVES: Investigate TTDS differences between AAPI and NHW melanoma patients. METHODS: Retrospective review of AAPI and NHW melanoma patients in the National Cancer Database (NCD) (2004-2020). The association of race with TTDS was evaluated by multivariable logistic regression, controlling for sociodemographic characteristics. RESULTS: Of 354,943 AAPI and NHW melanoma patients identified, 1155 (0.33%) were AAPI. AAPI patients had longer TTDS for stage I, II, and III melanoma (P < .05 for all). Adjusting for sociodemographic factors, AAPI patients had 1.5 times the odds of a TTDS between 61 and 90 days and twice the odds of a TTDS >90 days. Racial differences in TTDS persisted in Medicare and private insurance types. Uninsured AAPI patients had the longest TTDS (mean, 53.26 days), while those with private insurance had the shortest TTDS (mean, 34.92 days; P < .001 for both). LIMITATION: AAPI patients comprised 0.33% of the sample. CONCLUSIONS: AAPI melanoma patients have increased odds of treatment delays. Associated socioeconomic differences should inform efforts to reduce disparities in treatment and survival.
Assuntos
Asiático , Acessibilidade aos Serviços de Saúde , Melanoma , População das Ilhas do Pacífico , Neoplasias Cutâneas , Tempo para o Tratamento , Idoso , Humanos , Asiático/estatística & dados numéricos , Estudos Transversais , Medicare/estatística & dados numéricos , Melanoma/epidemiologia , Melanoma/etnologia , Melanoma/terapia , Estados Unidos/epidemiologia , Neoplasias Cutâneas/epidemiologia , Neoplasias Cutâneas/etnologia , Neoplasias Cutâneas/terapia , Acessibilidade aos Serviços de Saúde/estatística & dados numéricosRESUMO
BACKGROUND: Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes they affect, from single basepair modifications by DNMT1 to whole genome structural changes by PRM1/2. Patterns of DNA methylation are related to a diverse set of epigenetic features across this full range of epigenetic scale, making DNA methylation valuable for mapping regions of general epigenetic dysregulation. However, existing methods are unable to accurately identify regions of differential methylation across this full range of epigenetic scale directly from DNA methylation data. RESULTS: To address this, we developed DMRscaler, a novel method that uses an iterative windowing procedure to capture regions of differential DNA methylation (DMRs) ranging in size from single basepairs to whole chromosomes. We benchmarked DMRscaler against several DMR callers in simulated and natural data comparing XX and XY peripheral blood samples. DMRscaler was the only method that accurately called DMRs ranging in size from 100 bp to 1 Mb (pearson's r = 0.94) and up to 152 Mb on the X-chromosome. We then analyzed methylation data from rare-disease cohorts that harbor chromatin modifier gene mutations in NSD1, EZH2, and KAT6A where DMRscaler identified novel DMRs spanning gene clusters involved in development. CONCLUSION: Taken together, our results show DMRscaler is uniquely able to capture the size of DMR features across the full range of epigenetic scale and identify novel, co-regulated regions that drive epigenetic dysregulation in human disease.
Assuntos
Metilação de DNA , Epigênese Genética , Cromatina , Epigenômica , Genoma , HumanosRESUMO
TDP-43 proteinopathy is very prevalent among the elderly (affecting at least 25% of individuals over 85â¯years of age) and is associated with substantial cognitive impairment. Risk factors implicated in age-related TDP-43 proteinopathy include commonly inherited gene variants, comorbid Alzheimer's disease pathology, and thyroid hormone dysfunction. To test parameters that are associated with aging-related TDP-43 pathology, we performed exploratory analyses of pathologic, genetic, and biochemical data derived from research volunteers in the University of Kentucky Alzheimer's Disease Center autopsy cohort (nâ¯=â¯136 subjects). Digital pathologic methods were used to discriminate and quantify both neuritic and intracytoplasmic TDP-43 pathology in the hippocampal formation. Overall, 46.4% of the cases were positive for TDP-43 intracellular inclusions, which is consistent with results in other prior community-based cohorts. The pathologies were correlated with hippocampal sclerosis of aging (HS-Aging) linked genotypes. We also assayed brain parenchymal thyroid hormone (triiodothyronine [T3] and thyroxine [T4]) levels. In cases with SLCO1A2/IAPP or ABCC9 risk associated genotypes, the T3/T4 ratio tended to be reduced (pâ¯=â¯.051 using 2-tailed statistical test), and in cases with low T3/T4 ratios (bottom quintile), there was a higher likelihood of HS-Aging pathology (pâ¯=â¯.025 using 2-tailed statistical test). This is intriguing because the SLCO1A2/IAPP and ABCC9 risk associated genotypes have been associated with altered expression of the astrocytic thyroid hormone receptor (protein product of the nearby gene SLCO1C1). These data indicate that dysregulation of thyroid hormone signaling may play a role in age-related TDP-43 proteinopathy.
Assuntos
Encéfalo/patologia , Proteinopatias TDP-43/genética , Tiroxina , Tri-Iodotironina , Idoso , Idoso de 80 Anos ou mais , Envelhecimento , Encéfalo/metabolismo , Feminino , Predisposição Genética para Doença , Humanos , Masculino , Pessoa de Meia-Idade , Transportadores de Ânions Orgânicos/genética , Polimorfismo de Nucleotídeo Único , Fatores de Risco , Receptores de Sulfonilureias/genética , Proteinopatias TDP-43/metabolismo , Proteinopatias TDP-43/patologia , Tiroxina/análise , Tiroxina/genética , Tiroxina/metabolismo , Tri-Iodotironina/análise , Tri-Iodotironina/genética , Tri-Iodotironina/metabolismoRESUMO
ABCC9 genetic polymorphisms are associated with increased risk for various human diseases including hippocampal sclerosis of aging. The main goals of this study were 1 > to detect the ABCC9 variants and define the specific 3' untranslated region (3'UTR) for each variant in human brain, and 2 > to determine whether a polymorphism (rs704180) associated with risk for hippocampal sclerosis of aging pathology is also associated with variation in ABCC9 transcript expression and/or splicing. Rapid amplification of ABCC9 cDNA ends (3'RACE) provided evidence of novel 3' UTR portions of ABCC9 in human brain. In silico and experimental studies were performed focusing on the single nucleotide polymorphism, rs704180. Analyses from multiple databases, focusing on rs704180 only, indicated that this risk allele is a local expression quantitative trait locus (eQTL). Analyses of RNA from human brains showed increased ABCC9 transcript levels in individuals with the risk genotype, corresponding with enrichment for a shorter 3' UTR which may be more stable than variants with the longer 3' UTR. MicroRNA transfection experiments yielded results compatible with the hypothesis that miR-30c causes down-regulation of SUR2 transcripts with the longer 3' UTR. Thus we report evidence of complex ABCC9 genetic regulation in brain, which may be of direct relevance to human disease. ABCC9 gene variants are associated with increased risk for hippocampal sclerosis of aging (HS-Aging--a prevalent brain disease with symptoms that mimic Alzheimer's disease). We describe novel ABCC9 variants in human brain, corresponding to altered 3'UTR length, which could lead to targeting by miR-30c. We also determined that the HS-Aging risk mutation is associated with variation in ABCC9 transcript expression.
Assuntos
Envelhecimento/patologia , Encefalopatias/genética , Hipocampo/patologia , Doenças Neurodegenerativas/genética , Receptores de Sulfonilureias/genética , Idoso de 80 Anos ou mais , Encefalopatias/patologia , Feminino , Regulação da Expressão Gênica/genética , Predisposição Genética para Doença , Humanos , Masculino , MicroRNAs/genética , Doenças Neurodegenerativas/patologia , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Esclerose/genética , Esclerose/patologiaRESUMO
BACKGROUND & OBJECTIVE: The legacy of colonialism includes ongoing trauma and disruption of traditional teachings on relationality, which has contributed to Indigenous populations being disproportionately exposed to gender-based violence (GBV). GBV in Indigenous populations is explored to consider gender-specific findings and points of resilience in relational networks. PARTICIPANTS & SETTING: Included articles sampled Indigenous groups in Canada, US, Mexico, Guatemala, and Israel. All participants self-identified as Indigenous, and were either GBV survivors or service providers working in GBV contexts. METHODS: A scoping review was conducted in OVID Medline, Embase, APA Psycinfo, and Informit Indigenous Collection, using keywords for Indigenous peoples, gender concepts, and GBV. Articles were screened and extracted by two reviewers; a third reviewer resolved conflicts. RESULTS: Our search yielded one mixed-method study and seven qualitative studies, all published since 2016. North American studies identified colonial, patriarchal disruptions (e.g. residential schools) to positive pre-contact gender norms (e.g. non-hierarchical roles) that contribute to emerging GBV. Studies conducted in Guatemala and Israel also described local patriarchal cultures contributing to GBV. Lack of understanding of the Two-Spirit identity (i.e. supra-binary gender identity used by Indigenous persons) led to harmful attitudes and stigma. Interpersonal support and return to traditional matriarchal practices were identified as key resilience processes. CONCLUSIONS: There is limited literature on Indigenous gender concepts and GBV, particularly regarding GBV against males and Two-Spirit persons. Colonization-related violence and/or patriarchal gender norms were identified as precursors for GBV. Decolonization processes should be further explored to address GBV in Indigenous populations.
Assuntos
Violência de Gênero , Resiliência Psicológica , Humanos , Masculino , Feminino , Identidade de Gênero , Violência , Pesquisa QualitativaRESUMO
Background: Bloom Syndrome (BSyn) is an autosomal recessive disorder caused by biallelic germline variants in BLM, which functions to maintain genomic stability. BSyn patients have poor growth, immune defects, insulin resistance, and a significantly increased risk of malignancies, most commonly hematologic. The malignancy risk in carriers of pathogenic variants in BLM (BLM variant carriers) remains understudied. Clonal hematopoiesis of indeterminate potential (CHIP) is defined by presence of somatic mutations in leukemia-related genes in blood of individuals without leukemia and is associated with increased risk of leukemia. We hypothesize that somatic mutations driving clonal expansion may be an underlying mechanism leading to increased cancer risk in BSyn patients and BLM variant carriers. Methods: To determine whether de novo or somatic variation is increased in BSyn patients or carriers, we performed and analyzed exome sequencing on BSyn and control trios. Results: We discovered that both BSyn patients and carriers had increased numbers of low-frequency, putative somatic variants in CHIP genes compared to controls. Furthermore, BLM variant carriers had increased numbers of somatic variants in DNA methylation genes compared to controls. There was no statistical difference in the numbers of de novo variants in BSyn probands compared to control probands. Conclusion: Our findings of increased CHIP in BSyn probands and carriers suggest that one or two germline pathogenic variants in BLM could be sufficient to increase the risk of clonal hematopoiesis. These findings warrant further studies in larger cohorts to determine the significance of CHIP as a potential biomarker of aging, cancer, cardiovascular disease, morbidity and mortality.
RESUMO
ASXL1 (additional sex combs-like 1) plays key roles in epigenetic regulation of early developmental gene expression. De novo protein-truncating mutations in ASXL1 cause Bohring-Opitz syndrome (BOS; OMIM #605039), a rare neurodevelopmental condition characterized by severe intellectual disabilities, distinctive facial features, hypertrichosis, increased risk of Wilms tumor, and variable congenital anomalies, including heart defects and severe skeletal defects giving rise to a typical BOS posture. These BOS-causing ASXL1 variants are also high-prevalence somatic driver mutations in acute myeloid leukemia. We used primary cells from individuals with BOS (n = 18) and controls (n = 49) to dissect gene regulatory changes caused by ASXL1 mutations using comprehensive multiomics assays for chromatin accessibility (ATAC-seq), DNA methylation, histone methylation binding, and transcriptome in peripheral blood and skin fibroblasts. Our data show that regardless of cell type, ASXL1 mutations drive strong cross-tissue effects that disrupt multiple layers of the epigenome. The data showed a broad activation of canonical Wnt signaling at the transcriptional and protein levels and upregulation of VANGL2, which encodes a planar cell polarity pathway protein that acts through noncanonical Wnt signaling to direct tissue patterning and cell migration. This multiomics approach identifies the core impact of ASXL1 mutations and therapeutic targets for BOS and myeloid leukemias.
Assuntos
Deficiência Intelectual , Neoplasias Renais , Humanos , Deficiência Intelectual/genética , Deficiência Intelectual/patologia , Mutação , Epigênese Genética , Multiômica , Via de Sinalização Wnt/genética , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Fatores de Transcrição/genética , Neoplasias Renais/genéticaRESUMO
Over three percent of people carry a dominant pathogenic mutation, yet only a fraction of carriers develop disease (incomplete penetrance), and phenotypes from mutations in the same gene range from mild to severe (variable expressivity). Here, we investigate underlying mechanisms for this heterogeneity: variable variant effect sizes, carrier polygenic backgrounds, and modulation of carrier effect by genetic background (epistasis). We leveraged exomes and clinical phenotypes from the UK Biobank and the Mt. Sinai Bio Me Biobank to identify carriers of pathogenic variants affecting cardiometabolic traits. We employed recently developed methods to study these cohorts, observing strong statistical support and clinical translational potential for all three mechanisms of variable penetrance and expressivity. For example, scores from our recent model of variant pathogenicity were tightly correlated with phenotype amongst clinical variant carriers, they predicted effects of variants of unknown significance, and they distinguished gain- from loss-of-function variants. We also found that polygenic scores predicted phenotypes amongst pathogenic carriers and that epistatic effects can exceed main carrier effects by an order of magnitude.
RESUMO
BACKGROUND: The human chromosome 19q13.32 is a gene rich region and has been associated with multiple phenotypes, including late onset Alzheimer's disease (LOAD) and other age-related conditions. OBJECTIVE: Here we developed the first humanized mouse model that contains the entire TOMM40 and APOE genes with all intronic and intergenic sequences including the upstream and downstream regions. Thus, the mouse model carries the human TOMM40 and APOE genes and their intact regulatory sequences. METHODS: We generated the APOE-TOMM40 humanized mouse model in which the entire mouse region was replaced with the human (h)APOE-TOMM40 loci including their upstream and downstream flanking regulatory sequences using recombineering technologies. We then measured the expression of the human TOMM40 and APOE genes in the mice brain, liver, and spleen tissues using TaqMan based mRNA expression assays. RESULTS: We investigated the effects of the '523' polyT genotype (S/S or VL/VL), sex, and age on the human TOMM40- and APOE-mRNAs expression levels using our new humanized mouse model. The analysis revealed tissue specific and shared effects of the '523' polyT genotype, sex, and age on the regulation of the human TOMM40 and APOE genes. Noteworthy, the regulatory effect of the '523' polyT genotype was observed for all studied organs. CONCLUSION: The model offers new opportunities for basic science, translational, and preclinical drug discovery studies focused on the APOE genomic region in relation to LOAD and other conditions in adulthood.
Assuntos
Doença de Alzheimer , Apolipoproteínas E , Humanos , Animais , Camundongos , Apolipoproteínas E/genética , Genótipo , Fenótipo , Íntrons , Expressão Gênica , Doença de Alzheimer/genética , Doença de Alzheimer/metabolismo , Predisposição Genética para Doença , Proteínas do Complexo de Importação de Proteína Precursora MitocondrialRESUMO
Arboleda-Tham Syndrome (ARTHS) is a rare genetic disorder caused by heterozygous, de novo truncating mutations in Lysine(K) acetyltransferase 6A (KAT6A). ARTHS is clinically heterogeneous and characterized by several common features including intellectual disability, developmental and speech delay, hypotonia and affects multiple organ systems. KAT6A is highly expressed in early development and plays a key role in cell-type specific differentiation. KAT6A is the enzymatic core of a histone-acetylation protein complex, however the direct histone targets and gene regulatory effects remain unknown. In this study, we use ARTHS patient (n=8) and control (n=14) dermal fibroblasts and perform comprehensive profiling of the epigenome and transcriptome caused by KAT6A mutations. We identified differential chromatin accessibility within the promoter or gene body of 23%(14/60) of genes that were differentially expressed between ARTHS and controls. Within fibroblasts, we show a distinct set of genes from the posterior HOXC gene cluster (HOXC10, HOXC11, HOXC-AS3, HOXC-AS2, HOTAIR) that are overexpressed in ARTHS and are transcription factors critical for early development body segment patterning. The genomic loci harboring HOXC genes are epigenetically regulated with increased chromatin accessibility, high levels of H3K23ac, and increased gene-body DNA methylation compared to controls, all of which are consistent with transcriptomic overexpression. Finally, we used unbiased proteomic mass spectrometry and identified two new histone post-translational modifications (PTMs) that are disrupted in ARTHS: H2A and H3K56 acetylation. Our multi-omics assays have identified novel histone and gene regulatory roles of KAT6A in a large group of ARTHS patients harboring diverse pathogenic mutations. This work provides insight into the role of KAT6A on the epigenomic regulation in somatic cell types.
RESUMO
Hospitalized patients have an increased risk of developing hospital-acquired sacral pressure injury (HASPI). However, it is unknown whether SARS-CoV-2 infection affects HASPI development. To explore the role of SARS-CoV-2 infection in HASPI development, we conducted a single institution, multi-hospital, retrospective study of all patients hospitalized for ≥5 days from March 1, 2020 to December 31, 2020. Patient demographics, hospitalization information, ulcer characteristics, and 30-day-related morbidity were collected for all patients with HASPIs, and intact skin was collected from HASPI borders in a patient subset. We determined the incidence, disease course, and short-term morbidity of HASPIs in COVID-19(+) patients, and characterized the skin histopathology and tissue gene signatures associated with HASPIs in COVID-19 disease. COVID-19(+) patients had a 63% increased HASPI incidence rate, HASPIs of more severe ulcer stage (OR 2.0, p<0.001), and HASPIs more likely to require debridement (OR 3.1, p=0.04) compared to COVID-19(-) patients. Furthermore, COVID-19(+) patients with HASPIs had 2.2x increased odds of a more severe hospitalization course compared to COVID-19(+) patients without HASPIs. HASPI skin histology from COVID-19(+) patients predominantly showed thrombotic vasculopathy, with the number of thrombosed vessels being significantly greater than HASPIs from COVID-19(-) patients. Transcriptional signatures of a COVID-19(+) sample subset were enriched for innate immune responses, thrombosis, and neutrophil activation genes. Overall, our results suggest that immunologic dysregulation secondary to SARS-CoV-2 infection, including neutrophil dysfunction and abnormal thrombosis, may play a pathogenic role in development of HASPIs in patients with severe COVID-19.
Assuntos
COVID-19 , Úlcera por Pressão , Trombose , Humanos , COVID-19/epidemiologia , Úlcera por Pressão/epidemiologia , SARS-CoV-2 , Estudos Retrospectivos , Úlcera , Ativação de Neutrófilo , Incidência , Trombose/epidemiologia , Trombose/etiologia , HospitaisRESUMO
Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. Uncovering the genetic basis of complex, quantitative traits such as starvation resistance is technically challenging. We developed a synthetic-population (re)sequencing approach using molecular inversion probes (MIP-seq) to measure relative fitness during and after larval starvation in Caenorhabditis elegans. We applied this competitive assay to 100 genetically diverse, sequenced, wild strains, revealing natural variation in starvation resistance. We confirmed that the most starvation-resistant strains survive and recover from starvation better than the most starvation-sensitive strains using standard assays. We performed genome-wide association (GWA) with the MIP-seq trait data and identified three quantitative trait loci (QTL) for starvation resistance, and we created near isogenic lines (NILs) to validate the effect of these QTL on the trait. These QTL contain numerous candidate genes including several members of the Insulin/EGF Receptor-L Domain (irld) family. We used genome editing to show that four different irld genes have modest effects on starvation resistance. Natural variants of irld-39 and irld-52 affect starvation resistance, and increased resistance of the irld-39; irld-52 double mutant depends on daf-16/FoxO. DAF-16/FoxO is a widely conserved transcriptional effector of insulin/IGF signaling (IIS), and these results suggest that IRLD proteins modify IIS, although they may act through other mechanisms as well. This work demonstrates efficacy of using MIP-seq to dissect a complex trait and it suggests that irld genes are natural modifiers of starvation resistance in C. elegans.
Assuntos
Proteínas de Caenorhabditis elegans , Inanição , Animais , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Fatores de Transcrição Forkhead/metabolismo , Estudo de Associação Genômica Ampla , Insulina/metabolismo , Inanição/genéticaRESUMO
Although dermatology is one of the most competitive specialties to match into, there is limited transparency in the residency match process. In this retrospective cohort study of 2234 allopathic medical graduates, we identify applicant characteristics associated with matching into research oriented dermatology programs. Many of the statistically significant variables in our study, including PhD/MD status, graduating from a Top-25 NIH funded medical school, increasing total number of pre-residency publications (PRPs), and increasing number of high-impact PRPs, correlate with future academic employment. Although literature shows an association between an increasing number of first author PRPs and future academic employment, we did not find number of first or last author PRPs to be predictive of matching into a research oriented residency program. A more comprehensive evaluation of an applicant's research output, considering both the final products of an applicant's research endeavors and an applicant's role in various projects, may better approximate an applicant's commitment to academics.