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Integrative multi-omics analysis identified FUT9 and MS4A3 as novel immune-phenotype and prognosis biomarkers for colorectal cancer and analyze the role of FUT9 in oncoimmunology
Colorectal cancer (CRC) is one of the most common malignant tumors worldwide. Patients with different immunophenotypes of CRC could achieve different effect of immunotherapy and yield different prognosis. With the advancement of bioinformatics, multi-omics analysis …
Read PDFAdvanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease
Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the …
Read PDFCharacterizing heterogeneous cis-regulatory elements in gene regulatory programs associated with breast cancer
<h4>Background</h4>Cis-regulatory elements (CREs) control oncogene expression and malignant phenotypes. The high clinicopathological heterogeneity of cancer cannot be explained by gene expression alone, being attributed to CRE heterogeneity. However, characterizing cancer-associated CREs is challenging. To address …
Read PDFDistinct trajectory of gut microbiota driven by a human oral commensal: insights from a murine study
<h4>Background</h4>Oral microbes modulate the gut microbiota. <i>Haemophilus parainfluenzae</i>, a core human oral commensal with immunomodulatory properties, is reduced in autoimmune diseases, while mitigating Sjögren's syndrome-like disease with improved oral microbiota in female NOD mice. However, …
Read PDFARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response
AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles …
Read PDFMineral encapsulation of microorganisms in calcified oral biofilms: implications for immune dysregulation and vascular calcification
Oral biofilms represent highly organized microbial ecosystems embedded within extracellular matrices enriched with calcium and phosphate ions that promote the nucleation of calcium phosphate minerals, including hydroxyapatite. During plaque mineralization, microorganisms may become incorporated within …
Read PDFRNA polymerase II coordinates histone deacetylation at active promoters
Nucleosomes at promoters of active genes are marked by specific histone post-translational modifications and histone variants. These features are thought to promote the formation and maintenance of an "open" chromatin environment that is suitable for …
Read PDFMulti-omics biomarkers in female fertility: from oocyte quality to endometrial receptivity and clinical translation
High-throughput omics technologies have transformed our understanding of female reproductive biology, revealing molecular interactions governing oocyte maturation, ovarian reserve, endometrial receptivity, and embryo development, yet most findings remain fragmented and insufficiently translated into clinical practice. …
Read PDFEpigenetic modifications in vascular inflammation
Vascular inflammation is closely associated with the onset and progression of diseases, playing a pivotal role in the development of numerous acute and chronic conditions. The pathophysiological processes underlying vascular inflammation are highly complex, involving …
Read PDFAdvancements in DNA methylation technologies and their application in cancer diagnosis
DNA methylation is a common epigenetic modification that maintains the integrity of the DNA sequence while profoundly influencing gene expression and phenotypic variation. Aberrant DNA methylation has been associated with the onset and progression of …
Read PDFIntegrating Omics Data and AI for Cancer Diagnosis and Prognosis
Cancer is one of the leading causes of death, making timely diagnosis and prognosis very important. Utilization of AI (artificial intelligence) enables providers to organize and process patient data in a way that can lead …
Read PDFN4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development
N4-acetylcytidine (ac4C) is a post-transcriptional RNA modification that plays a crucial role in the epitranscriptome, influencing gene expression and cellular function. This modification occurs at the cytosine base, where an acetyl group is installed to …
Read PDFEmerging technologies of single-cell multi-omics
The heterogeneity of the hematopoietic system was largely veiled by traditional bulk sequencing methods, which measure the averaged signals from mixed cellular populations. In contrast, single-cell sequencing has enabled the direct measurement of individual signals …
Read PDFMultimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations
BACKGROUND: Accurately identifying functionally distinct tumor cell subpopulations remains a critical challenge in cancer research. While single-cell epigenomics assays provide powerful insights into tumor heterogeneity beyond gene expression, computational limitations have hindered their application. METHODS: …
Read PDFDefining the role of natural killer cells in acute myeloid leukemia through the lens of single-cell omics
This review explores the alterations in natural killer (NK) cell function in acute myeloid leukemia (AML) and their implications for disease progression and therapeutic outcomes. As key effectors of innate immunity, NK cells are critical …
Read PDFOxidized LDL Induces Pro-Inflammatory Transcriptomic and Epigenomic Responses in Human CD4<sup>+</sup> T Cells
Elevated circulating low-density lipoprotein cholesterol (LDL-C) is a key risk factor for coronary artery disease (CAD). The pathogenesis of CAD is multifactorial, driven by heritable and lifestyle-related risk factors. Although CD4<sup>+</sup> T cells are one …
Read PDFCorrigendum: The maternal microbiome programs the m<sup>6</sup>A epitranscriptome of the mouse fetal brain and intestine
[This corrects the article DOI: 10.3389/fcell.2022.882994.].
Read PDFEditorial: Interaction between genes and the environment in skin aging
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