Maintenance of a genome requires DNA repair integrated with chromatin remodeling. We have analyzed six transcriptome data sets and one set on translational regulation known remodeling genes in synchronized human cells. These are available through our new database: www.dnarepairgenes.com. Genes that similar transcription profiles at least two generally agree well protein profiles. In brief, long patch base excision (BER) is enriched for S phase genes, whereas short BER uses essentially...

Genome-wide gene expression analyses of the human somatic cell cycle have indicated that set cycling genes differ between primary and cancer cells. By identifying dependent in HaCaT keratinocytes comparing these with previously identified genes, we three distinct groups genes. First, housekeeping enriched for known functions; second, type-specific HaCaT-specific third, Polycomb-regulated These are specifically upregulated during DNA replication, consistent being epigenetically silenced other...

Abstract Background The expression of microRNAs (miRNAs) is a promising prognostic and diagnostic tool in hepatocellular carcinoma (HCC). Here we performed small RNA sequencing (sRNA-seq) tissue, serum exosomes to investigate changes miRNA between the different sample types correlated with clinical parameters. We also gene arrays on tumor normal tissue. Results Paired revealed consistent positive correlation miR-21 indicating that could be exported from tissue circulation via exosomes. found...

The historically recent domestication of fishes has been essential to meet the protein demands a growing human population. Selection for traits interest during is complex process whose epigenetic basis poorly understood. Cytosine hydroxymethylation increasingly recognized as an important DNA modification involved in regulation. In present study, we investigated if plays role fish and demonstrated first time at genome-wide level single nucleotide resolution that muscle hydroxymethylome...

Here, we analyze the viral landscape in blood and tissue from 4,918 metastatic cancer patients across 38 solid types Hartwig Medical Foundation (HMF) cohort, largest pan-cancer study on cancer. Using a coverage-based filtering approach, detected 25 unique genera 32 different types, with total of 747 virus-positive samples. We 336 samples 29 dominated by Torque teno virus Alphatorquevirus. The were Alphapapillomavirus Roseolovirus. was significantly enriched genital, anal, colorectal cancers...

Abstract Background This study aimed to investigate the potential of circulating small RNAs (sRNAs) as predictive biomarkers for future colorectal cancer (CRC). The analyzed serum samples from pre-diagnostic CRC patients in two prospective biobanks. Methods Serum 142 patients, Finnish Maternity Cohort (FMC) and HUNT Study (HUNT2), were subjected RNA sequencing. compared sRNA expression cases with controls, considering diverse classes. Results Analysis revealed miRNA patterns notable...

UNG is the major uracil-DNA glycosylase in mammalian cells and involved both error-free base excision repair of genomic uracil mutagenic uracil-processing at antibody genes. However, regulation these different processes currently not well understood. The gene encodes two isoforms, UNG1 UNG2, each possessing unique N-termini that mediate translocation to mitochondria nucleus, respectively. A strict subcellular localization isoform has been widely accepted despite a lack models study them...

Abstract Multiple myeloma (MM) is an incurable cancer of terminally differentiated plasma cells that proliferate in the bone marrow. miRNAs are promising biomarkers for risk stratification MM and several shown to have a function disease pathogenesis. However, date, surprisingly few miRNA-mRNA interactions been described functionally validated MM. In this study, we performed miRNA-seq mRNA-seq on CD138 + isolated from marrow aspirates 86 patients identify novel between sRNAs mRNAs. We...

Kisspeptin regulates puberty and reproduction onset, acting upstream of the brain–pituitary–gonad (HPG) axis. This study aimed to test a kisspeptin-based hormonal therapy on cultured Senegalese sole (G1) breeders, known have reproductive dysfunctions. A single intramuscular injection KISS2-10 decapeptide (250 µg/kg) was tested in females males during season, gonad maturation, sperm motility, plasma levels gonadotropins (Fsh Lh) sex steroids (11-ketotestosterone, testosterone estradiol), as...

Metastatic colorectal cancer (mCRC) presents significant challenges in clinical management due to its heterogeneity and variable response treatment. In this study, we conducted comprehensive small RNA (sRNA) sequencing analyses identify sRNA biomarkers associated with survival treatment mCRC patients. We measured serum sRNAs before after chemotherapy a discovery cohort of 189 Our analysis revealed 25 microRNAs (miRNA) as significantly overall at baseline. found that 11 the miRNAs were also...

MicroRNAs (miRNAs) are promising prognostic and diagnostic biomarkers due to their high stability in blood. Here we investigate the expression of miRNAs other noncoding (nc) RNAs serum rectal cancer patients. Serum from 96 patients was profiled using small RNA sequencing correlated with clinicopathological characteristics Multiple classes were detected, including fragments tRNAs, snoRNAs, long ncRNAs, RNAs. Several miRNAs, miRNA variants (isomiRs) ncRNAs differentially expressed between...

In vertebrates, the somatotropic axis comprising pituitary gland, liver and muscle plays a major role in myogenesis.Its output terms of growth is highly affected by nutritional environmental cues, thus likely epigenetically regulated.Hydroxymethylation emerging as DNA modification that modulates gene expression but holistic characterization hydroxymethylome has not been investigated to date.Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissuespecific...

Interleukin-32 (IL-32) is a nonclassical cytokine expressed in cancers, inflammatory diseases, and infections. Its expression regulated by two different oxygen sensing systems; HIF1α cysteamine dioxygenase (ADO), indicating that IL-32 may be involved the response to hypoxia. We here demonstrate endogenously expressed, intracellular interacts with components of mitochondrial respiratory chain promotes oxidative phosphorylation. Knocking out three myeloma cell lines reduced survival...

DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner depends on genomic context and varies considerably across taxa. This modification was first found nuclear genomes eukaryote several decades ago it has also been described mitochondrial DNA. It recently shown extensively methylated mammals other vertebrates. Our current knowledge fish very limited, especially non-model teleosts. In this study, using whole-genome bisulfite sequencing, we...

Multiple myeloma (MM) is a hematological cancer characterized by accumulation of malignant plasma cells in the bone marrow. The patients are immune suppressed and suffer from recurrent chronic infections. Interleukin-32 non-conventional, pro-inflammatory cytokine expressed subgroup MM with poor prognosis. IL-32 has also been shown to promote proliferation survival cells. Here we show that activation toll-like receptors (TLRs) promotes expression through NFκB activation. In patient-derived...

Improved transcriptomic sequencing technologies now make it possible to perform longitudinal experiments, thus generating a large amount of data. Currently, there are no dedicated or comprehensive methods for the analysis these experiments. In this article, we describe our TimeSeries Analysis pipeline (TiSA) which combines differential gene expression, clustering based on recursive thresholding, and functional enrichment analysis. Differential expression is performed both temporal...

Infections are common in plasma cell cancer multiple myeloma (MM) due to disease-related immune deficiencies and treatment. Myeloma cells express Toll-like receptors (TLRs), TLR activation has been shown induce proliferative pro-survival signals cells. MM is a complex heterogeneous disease, expression levels of TLRs as well downstream signaling components likely differ between patients. Here, we show that large cohort patients, TLR1, TLR4, TLR6, TLR9, TLR10 the most highly expressed primary...

Understanding microbial communities' roles in human health and disease requires methods that accurately characterize the composition their activity effects within biological samples. We present sMETASeq (small RNA Metagenomics by Sequencing), a novel method uses sequencing of small RNAs to jointly measure host expression create metagenomic profiles detect bacterial RNAs. evaluated performance on mock community demonstrated its use different samples, including colon cancer, oral leukoplakia,...

Lung cancer (LC) incidence is increasing globally and altered levels of microRNAs (miRNAs) in blood may contribute to identification individuals with LC. We identified miRNAs differentially expressed peripheral at LC diagnosis evaluated, pre‐diagnostic specimens, how long before expression changes such candidate could be detected. upregulated plasma specimens from a hospital‐based study sample 128 patients confirmed 62 suspected but negative (FalsePos). then evaluated the or serum 360 future...

Small RNAs (sRNAs), a heterogenous group of non-coding RNAs, are emerging as promising molecules for cancer patient risk stratification and players in tumour pathogenesis. Here, we have studied microRNAs (miRNAs) other sRNAs relation to survival disease severity multiple myeloma.We comprehensively characterised sRNA expression myeloma patients by performing sRNA-sequencing on cells isolated from bone marrow aspirates 86 patients. The profiles were correlated with the patients' clinical data...

Diabetes is a heterogeneous disease and precise diagnosis of diabetes subgroups necessary to initiate proper early treatment clinical management the disease. Circulating small RNAs (sRNAs) are potentially diagnostic biomarkers in diseases, including diabetes. Here we aimed examine whether profiles circulating sRNAs differed between patients with autoimmune non-autoimmune non-diabetic controls.This cross-sectional case-control study included participants from third survey HUNT study.We...

(1) Background: Analysis of tumor DNA by next-generation sequencing (NGS) plays various roles in the classification and management cancer. This study aimed to assess performance two similar large, comprehensive gene panels with a focus on clinically relevant variant detection mutation burden (TMB) assessment; (2) Methods: from 19 diagnostic small cell lung cancer biopsies an AcroMetrix™ assessment sample >500 mutations were sequenced using Oncomine™ Comprehensive Assay Plus (OCAP) Ion...

Abstract Introduction Blood biomarkers for early detection of lung cancer (LC) are in demand. There few studies the full microRNome serum asymptomatic subjects that later develop LC. Here we searched novel microRNA blood from non-cancer, ever-smokers populations up to eight years before diagnosis. Methods Serum samples 98,737 two prospective population studies, HUNT2 and HUNT3, were considered initially. Inclusion criteria cases were: ever-smokers; no known at study entrance; 0–8 sampling LC...