keyword
https://read.qxmd.com/read/38536233/integrative-methylome-and-transcriptome-analysis-reveals-epigenetic-regulation-of-fusobacterium-nucleatum-in-laryngeal-cancer
#1
JOURNAL ARTICLE
Xiaohui Yuan, Hui-Ching Lau, Huiying Huang, Chi-Yao Hsueh, Hongli Gong, Liang Zhou
The aetiological mechanisms of Fusobacterium nucleatum in laryngeal cancer remain unclear. This study aimed to reveal the epigenetic signature induced by F. nucleatum in laryngeal squamous cell carcinoma (LSCC). Combined analysis of methylome and transcriptome data was performed to address the functional role of F. nucleatum in laryngeal cancer. Twenty-nine differentially expressed methylation-driven genes were identified by mapping the methylation levels of significant differential methylation sites to the expression levels of related genes...
March 2024: Microbial Genomics
https://read.qxmd.com/read/38532825/heterogeneity-of-dna-methylation-profiles-and-copy-number-alterations-in-10782-adult-type-glioblastomas-idh-wildtype
#2
JOURNAL ARTICLE
David E Reuss, Daniel Schrimpf, Asan Cherkezov, Abigail K Suwala, Tereza Lausová, Matija Snuderl, David Capper, Martin Sill, David T W Jones, Stefan M Pfister, Felix Sahm, Andreas von Deimling
The morphological patterns leading to the diagnosis of glioblastoma may also commonly be observed in several other distinct tumor entities, which can result in a mixed bag of tumors subsumed under this diagnosis. The 2021 WHO Classification of CNS Tumors has separated several of these entities from the diagnosis of glioblastoma, IDH-wildtype. This study determines the DNA methylation classes most likely receiving the diagnosis glioblastoma, IDH wildtype according to the definition by the WHO 2021 Classification and provides comparative copy number analyses...
January 2024: Free neuropathology
https://read.qxmd.com/read/38532526/paternal-aging-impacts-expression-and-epigenetic-markers-as-early-as-the-first-embryonic-tissue-lineage-differentiation
#3
JOURNAL ARTICLE
Michelle M Denomme, Blair R McCallie, Mary E Haywood, Jason C Parks, William B Schoolcraft, Mandy G Katz-Jaffe
BACKGROUND: Advanced paternal age (APA) is associated with adverse outcomes to offspring health, including increased risk for neurodevelopmental disorders. The aim of this study was to investigate the methylome and transcriptome of the first two early embryonic tissue lineages, the inner cell mass (ICM) and the trophectoderm (TE), from human blastocysts in association with paternal age and disease risk. High quality human blastocysts were donated with patient consent from donor oocyte IVF cycles from either APA (≥ 50 years) or young fathers...
March 26, 2024: Human Genomics
https://read.qxmd.com/read/38530405/integrative-network-analysis-of-differentially-methylated-regions-to-study-the-impact-of-gestational-weight-gain-on-maternal-metabolism-and-fetal-neonatal-growth
#4
JOURNAL ARTICLE
Perla Pizzi Argentato, João Victor da Silva Guerra, Liania Alves Luzia, Ester Silveira Ramos, Mariana Maschietto, Patrícia Helen de Carvalho Rondó
Integrative network analysis (INA) is important for identifying gene modules or epigenetically regulated molecular pathways in diseases. This study evaluated the effect of excessive gestational weight gain (EGWG) on INA of differentially methylated regions, maternal metabolism and offspring growth. Brazilian women from "The Araraquara Cohort Study" with adequate pre-pregnancy body mass index were divided into EGWG (n=30) versus adequate gestational weight gain (AGWG, n=45) groups. The methylome analysis was performed on maternal blood using the Illumina MethylationEPIC BeadChip...
2024: Genetics and Molecular Biology
https://read.qxmd.com/read/38522508/epigenetic-modifications-of-cfdna-in-liquid-biopsy-for-the-cancer-care-continuum
#5
JOURNAL ARTICLE
Jodie Wong, Rohit Muralidhar, Liang Wang, Chiang-Ching Huang
This review provides a comprehensive overview of the latest advancements in the clinical utility of liquid biopsy, with a particular focus on epigenetic approaches aimed at overcoming challenges in cancer diagnosis and treatment. It begins by elucidating key epigenetic terms, including methylomics, fragmentomics, and nucleosomics. The review progresses to discuss methods for analyzing circulating cell-free DNA (cfDNA) and highlights recent studies showcasing the clinical relevance of epigenetic modifications in areas such as diagnosis, drug treatment response, minimal residual disease (MRD) detection, and prognosis prediction...
March 22, 2024: Biomedical Journal
https://read.qxmd.com/read/38521043/mixtures-of-per-and-polyfluoroalkyl-substances-pfas-alter-sperm-methylation-and-long-term-reprogramming-of-offspring-liver-and-fat-transcriptome
#6
JOURNAL ARTICLE
DruAnne L Maxwell, Oladele A Oluwayiose, Emily Houle, Katherine Roth, Karolina Nowak, Savni Sawant, Amanda L Paskavitz, Wanqing Liu, Katherine Gurdziel, Michael C Petriello, J Richard Pilsner
Male fertility has been declining worldwide especially in countries with high levels of endocrine disrupting chemicals (EDCs). Per- and polyfluorinated alkyl Substances (PFAS) have been classified as EDCs and have been linked to adverse male reproductive health. The mechanisms of these associations and their implications on offspring health remain unknown. The aims of the current study were to assess the effect of PFAS mixtures on the sperm methylome and transcriptional changes in offspring metabolic tissues (i...
March 16, 2024: Environment International
https://read.qxmd.com/read/38519892/exploring-the-ageing-methylome-in-the-model-insect-nasonia-vitripennis
#7
JOURNAL ARTICLE
K Brink, C L Thomas, A Jones, T W Chan, E B Mallon
BACKGROUND: The ageing process is a multifaceted phenomenon marked by the gradual deterioration of cellular and organismal functions, accompanied by an elevated susceptibility to diseases. The intricate interplay between genetic and environmental factors complicates research, particularly in complex mammalian models. In this context, simple invertebrate organisms have been pivotal, but the current models lack detectable DNA methylation limiting the exploration of this critical epigenetic ageing mechanism...
March 22, 2024: BMC Genomics
https://read.qxmd.com/read/38516266/methylome-wide-and-meqtl-analysis-helps-to-distinguish-treatment-response-from-non-response-and-pathogenesis-markers-in-schizophrenia
#8
JOURNAL ARTICLE
Binithamol K Polakkattil, Neetha N Vellichirammal, Indu V Nair, Chandrasekharan M Nair, Moinak Banerjee
Schizophrenia is a complex condition with entwined genetic and epigenetic risk factors, posing a challenge to disentangle the intermixed pathological and therapeutic epigenetic signatures. To resolve this, we performed 850K methylome-wide and 700K genome-wide studies on the same set of schizophrenia patients by stratifying them into responders, non-responders, and drug-naïve patients. The key genes that signified the response were followed up using real-time gene expression studies to understand the effect of antipsychotics at the gene transcription level...
2024: Frontiers in Psychiatry
https://read.qxmd.com/read/38510975/comprehensive-analysis-of-m-6-a-methylome-alterations-after-azacytidine-plus-venetoclax-treatment-for-acute-myeloid-leukemia-by-nanopore-sequencing
#9
JOURNAL ARTICLE
Zaifeng Zhang, Lili Zhang, Jiangtao Li, Ru Feng, Chang Li, Ye Liu, Gaoyuan Sun, Fei Xiao, Chunli Zhang
N6 adenosine methylation (m6 A), one of the most prevalent internal modifications on mammalian RNAs, regulates RNA transcription, stabilization, and splicing. Growing evidence has focused on the functional role of m6 A regulators on acute myeloid leukemia (AML). However, the global m6 A levels after azacytidine (AZA) plus venetoclax (VEN) treatment in AML patients remain unclear. In our present study, bone marrow (BM) sample pairs (including pre-treatment [AML] and post-treatment [complete remission (CR)] samples) were harvested from three AML patients who had achieved CR after AZA plus VEN treatment for Nanopore direct RNA sequencing...
December 2024: Computational and Structural Biotechnology Journal
https://read.qxmd.com/read/38486452/the-super-pangenome-of-populus-unveil-genomic-facets-for-its-adaptation-and-diversification-in-widespread-forest-trees
#10
JOURNAL ARTICLE
Tingting Shi, Xinxin Zhang, Yukang Hou, Changfu Jia, Xuming Dan, Yulin Zhang, Yuanzhong Jiang, Qiang Lai, Jiajun Feng, Jianju Feng, Tao Ma, Jiali Wu, Shuyu Liu, Lei Zhang, Zhiqin Long, Liyang Chen, Nathaniel R Street, Pär K Ingvarsson, Jianquan Liu, Tongming Yin, Jing Wang
Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pan-genes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions...
March 13, 2024: Molecular Plant
https://read.qxmd.com/read/38486226/multi-omics-provide-insights-into-the-regulation-of-dna-methylation-in-pear-fruit-metabolism
#11
JOURNAL ARTICLE
Chao Gu, Mao-Song Pei, Zhi-Hua Guo, Lei Wu, Kai-Jie Qi, Xue-Ping Wang, Hong Liu, Zhongchi Liu, Zhaobo Lang, Shaoling Zhang
BACKGROUND: Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved...
March 14, 2024: Genome Biology
https://read.qxmd.com/read/38471723/enhanced-medullary-and-extramedullary-granulopoiesis-sustain-the-inflammatory-response-in-lupus-nephritis
#12
JOURNAL ARTICLE
Eleni Zervopoulou, Maria Grigoriou, Stavros A Doumas, Danae Yiannakou, Pavlos Pavlidis, Gilles Gasparoni, Jörn Walter, Anastasia Filia, Harikleia Gakiopoulou, Aggelos Banos, Ioannis Mitroulis, Dimitrios T Boumpas
OBJECTIVES: In SLE, deregulation of haematopoiesis is characterised by inflammatory priming and myeloid skewing of haematopoietic stem and progenitor cells (HSPCs). We sought to investigate the role of extramedullary haematopoiesis (EMH) as a key player for tissue injury in systemic autoimmune disorders. METHODS: Transcriptomic analysis of bone marrow (BM)-derived HSPCs from patients with SLE and NZBW/F1 lupus-prone mice was performed in combination with DNA methylation profile...
March 11, 2024: Lupus Science & Medicine
https://read.qxmd.com/read/38471632/integrative-epigenome-transcriptome-analysis-unravels-cancer-specific-over-expressed-genes-potentially-regulating-immune-microenvironment-in-clear-cell-renal-cell-carcinoma
#13
JOURNAL ARTICLE
Nikhil Gadewal, Abhiram Natu, Siddhartha Sen, Sukanya Rauniyar, Virupaksha Bastikar, Sanjay Gupta
BACKGROUND: Clear cell Renal Cell Carcinoma (ccRCC) is the frequently diagnosed histological life-threatening tumor subtype in the urinary system. Integrating multi-omics data is emerging as a tool to provide a comprehensive view of biology and disease for better therapeutic interventions. METHOD: We have integrated freely available ccRCC data sets of genome-wide DNA methylome, transcriptome, and active histone modification marks, H3K27ac, H3K4me1, and H3K4me3 specific ChIP-seq data to screen genes with higher expression...
March 10, 2024: Biochimica et Biophysica Acta. General Subjects
https://read.qxmd.com/read/38471085/whole-genome-dna-methylation-profiling-of-intrahepatic-cholangiocarcinoma-reveals-prognostic-subtypes-with-distinct-biological-drivers
#14
JOURNAL ARTICLE
Haotian Liao, Xing Chen, Haichuan Wang, Youpei Lin, Lu Chen, Kefei Yuan, Mingheng Liao, Hanyu Jiang, Jiajie Peng, Zhenru Wu, Jiwei Huang, Jiaxin Li, Yong Zeng
Intrahepatic cholangiocarcinoma (iCCA) is the second most prevalent primary liver cancer. While the genetic characterization of iCCA has led to targeted therapies for treating tumors with FGFR2 alterations and IDH1/2 mutations, only a limited number of patients can benefit from these strategies. Epigenomic profiles have emerged as potential diagnostic and prognostic biomarkers for improving treatment of cancers. In this study, we conducted whole-genome bisulfite sequencing on 331 iCCAs integrated with genetic, transcriptomic, and proteomic analyses, demonstrating the existence of four DNA methylation subtypes of iCCAs (S1-S4) that exhibited unique post-operative clinical outcomes...
March 12, 2024: Cancer Research
https://read.qxmd.com/read/38470455/a-preliminary-investigation-of-epigenome-wide-dna-methylation-and-temperament-during-infancy
#15
JOURNAL ARTICLE
John Leri, Jingwen Liu, Maria Kelly, Darlene A Kertes
This study provides preliminary evidence for an epigenetic architecture of infant temperament. At 12 months of age, blood was collected and assayed for DNA methylation and maternally reported infant temperament was assessed using the Infant Behavior Questionnaire in 67 mother-infant dyads. Epigenome-wide analyses showed that the higher order temperament dimensions Surgency and Negative Affect were associated with DNA methylation. The epigenetic signatures of Surgency and Negative Affect were situated at genes involved in synaptic signaling and plasticity...
April 2024: Developmental Psychobiology
https://read.qxmd.com/read/38468866/dna-methylation-landscapes-in-dipg-reveal-methylome-variability-that-can-be-modified-pharmacologically
#16
JOURNAL ARTICLE
Ashley R Tetens, Allison M Martin, Antje Arnold, Orlandi V Novak, Adrian Idrizi, Rakel Tryggvadottir, Jordyn Craig-Schwartz, Athanasia Liapodimitri, Kayleigh Lunsford, Michael I Barbato, Charles G Eberhart, Adam C Resnick, Eric H Raabe, Michael A Koldobskiy
BACKGROUND: Diffuse intrinsic pontine glioma (DIPG) is a uniformly lethal brainstem tumor of childhood, driven by histone H3 K27M mutation and resultant epigenetic dysregulation. Epigenomic analyses of DIPG have shown global loss of repressive chromatin marks accompanied by DNA hypomethylation. However, studies providing a static view of the epigenome do not adequately capture the regulatory underpinnings of DIPG cellular heterogeneity and plasticity. METHODS: To address this, we performed whole-genome bisulfite sequencing on a large panel of primary DIPG specimens and applied a novel framework for analysis of DNA methylation variability, permitting the derivation of comprehensive genome-wide DNA methylation potential energy landscapes that capture intrinsic epigenetic variation...
2024: Neuro-oncology advances
https://read.qxmd.com/read/38464935/network-based-analysis-of-heterogeneous-patient-matched-brain-and-extracranial-melanoma-metastasis-pairs-reveals-three-homogeneous-subgroups
#17
JOURNAL ARTICLE
Konrad Grützmann, Theresa Kraft, Matthias Meinhardt, Friedegund Meier, Dana Westphal, Michael Seifert
Melanoma, the deadliest form of skin cancer, can metastasize to different organs. Molecular differences between brain and extracranial melanoma metastases are poorly understood. Here, promoter methylation and gene expression of 11 heterogeneous patient-matched pairs of brain and extracranial metastases were analyzed using melanoma-specific gene regulatory networks learned from public transcriptome and methylome data followed by network-based impact propagation of patient-specific alterations. This innovative data analysis strategy allowed to predict potential impacts of patient-specific driver candidate genes on other genes and pathways...
December 2024: Computational and Structural Biotechnology Journal
https://read.qxmd.com/read/38464476/the-lemon-genome-and-dna-methylome-unveil-epigenetic-regulation-of-citric-acid-biosynthesis-during-fruit-development
#18
JOURNAL ARTICLE
Hang Yu, Chao Zhang, Chuang Lu, Yana Wang, Congcong Ge, Guixiang Huang, Haifeng Wang
Citric acid gives lemons their unique flavor, which impacts their sensory traits and market value. However, the intricate process of citric acid accumulation during lemon fruit growth remains incompletely understood. Here, we achieved a chromosomal-level genome assembly for the 'Xiangshui' lemon variety, spanning 364.85 Mb across nine chromosomes. This assembly revealed 27 945 genes and 51.37% repetitive sequences, tracing the divergence from citron 2.85 million years ago. DNA methylome analysis of lemon fruits across different developmental stages revealed significant variations in DNA methylation...
March 2024: Horticulture Research
https://read.qxmd.com/read/38464472/dna-methylome-analysis-reveals-novel-insights-into-active-hypomethylated-regulatory-mechanisms-of-temperature-dependent-flower-opening-in-osmanthus-fragrans
#19
JOURNAL ARTICLE
Shiwei Zhong, Huijun Zhu, Wenle Li, Dan Wu, Yunfeng Miao, Bin Dong, Yiguang Wang, Zhen Xiao, Qiu Fang, Jinping Deng, Hongbo Zhao
Short-term ambient low temperature (ALT) stimulation is necessary for Osmanthus fragrans to facilitate continued flower opening after floral bud development reaches maturity. DNA methylation, a vital epigenetic modification, regulates various biological processes in response to temperature fluctuations. However, its role in temperature-driven flower opening remains elusive. In this study, we identified the pivotal timeframe during which O. fragrans promptly detected temperature cues. Using whole-genome bisulfite sequencing, we explored global DNA hypomethylation during this phase, with the most significant changes occurring in CHH sequence contexts...
March 2024: Horticulture Research
https://read.qxmd.com/read/38464217/comparison-of-ccrm-dependent-methylation-in-caulobacter-crescentus-and-brucella-abortus-by-nanopore-sequencing
#20
Maxwell Campbell, Ian Scott Barton, R Martin Roop, Peter Chien
UNLABELLED: Bacteria rely on DNA methylation for restriction-modification systems and epigenetic control of gene expression. Here, we use direct detection of methylated bases by nanopore sequencing to monitor global DNA methylation in Alphaproteobacteria, where use of this technique has not yet been reported. One representative of this order, Caulobacter crescentus , relies on DNA methylation to control cell cycle progression, but it is unclear whether other members of this order, such as Brucella abortus , depend on the same systems...
March 2, 2024: bioRxiv
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