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Winata, H.

Publications and source records attributed to Winata, H..

4 recordsLinked to original sources

LCR-modules: a collection of workflows for cancer genome analysis

The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10,800 samples.

bioinformatics↗

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

SummaryThe price, quality and throughout of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data- visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust testing and consistent verifications of inputs, outputs and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data. AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.

bioinformatics↗

Calcium-dependent transcriptional profiles of human pancreatic islet cells reveal functional diversity in islet subpopulations

Aims/hypothesisPancreatic islets depend on cytosolic calcium to trigger the secretion of glucoregulatory hormones and regulate the transcription of genes important for the response to stimuli. To date, there has not been an attempt to profile calcium-regulated gene expression in all islet cell types. Our aim was to construct a large single-cell transcriptomic dataset from human islets exposed to conditions that would acutely induce or inhibit intracellular calcium signalling, while preserving biological heterogeneity. MethodsWe exposed intact human islets from three donors to the following conditions: (1) 2.8 mM glucose; (2) 25 mM glucose and 40 mM KCl to maximally stimulate calcium signalling; and (3) 25 mM glucose, 40 mM KCl and 5 mM EGTA (calcium chelator) to inhibit calcium signalling, for 1 hour. We sequenced 43,909 cells from all islet cell types, and further subsetted the cells to form an endocrine cell-specific dataset of 32,486 cells expressing INS, GCG, SST or PPY. We compared transcriptomes across conditions to determine the differentially expressed calcium-regulated genes in each endocrine cell type, and in each endocrine cell subcluster of alpha and beta cells. ResultsBased on the number of calcium-regulated genes, we found that each alpha and beta cell cluster had a different magnitude of calcium response. We also showed that a polyhormonal cluster expressing INS, GCG, and SST is defined by calcium-regulated genes specific to this cluster. Finally, we identified the gene PCDH7 from the beta cell clusters that had the highest number of calcium-regulated genes, and showed that cells expressing cell surface PCDH7 protein have enhanced glucose-stimulated insulin secretory function. ConclusionsHere we use our single-cell dataset to show that human islets have cell-type-specific calcium-regulated gene expression profiles, some of them specific to subpopulations. In our dataset, we identify PCDH7 as a novel marker of beta cells having an increased number of calcium-regulated genes and enhanced insulin secretory function. Data availabilityA searchable and user-friendly format of the data in this study, specifically designed for rapid mining of single-cell RNA sequencing data, is available at https://lynnlab.shinyapps.io/Hislet_2023/. The raw data files are available at NCBI Gene Expression Omnibus (GSE196715).

physiology↗

Type 2 diabetes susceptibility gene GRK5 regulates physiological pancreatic β-cell proliferation via phosphorylation of HDAC5 in mice

ObjectiveDiabetes onset is accompanied with {beta}-cell deficiency, and thus restoring functional {beta}-cell mass is a promising therapy for those with diabetes. However, the regulatory mechanisms controlling {beta}-cell mass are not fully understood. Previously, we demonstrated that the transcription factor SOX4 is required for {beta}-cell proliferation in the prediabetic state. To elucidate potential mechanisms by which SOX4 regulates {beta}-cell mass, we performed RNA sequencing (RNA-seq) using pancreatic {beta}-cell specific SOX4 knockout mice ({beta}SOX4 KO). The RNA-seq revealed decreased expression of GRK5, a known type 2 diabetes susceptibility gene whose association with diabetes has not been fully elucidated. Therefore, we aimed to clarify the function of GRK5 in pancreatic {beta} cells. MethodsWe generated a novel pancreatic {beta} cell-specific GRK5 knockout mass ({beta}GRK5 KO) and evaluated glucose tolerance and metabolic changes by body weight measurement, oral glucose tolerance test, and insulin tolerance test. The number of pancreatic {beta} cells was quantified by immunohistochemistry. Glucose loading and Ca2+ imaging was performed on isolated islets to evaluate insulin secretory capacity. To elucidate the mechanism of {beta}GRK5 on {beta} cell mass regulation, we performed RNA-seq of isolated islets and identified the signaling pathways that could be regulated by GRK5. Furthermore, in vitro experiments were conducted using human islets and mouse {beta}GRK5 KO islets to clarify the direct effects of GRK5 on these pathways. Results{beta}GRK5 KO islets showed impaired glucose tolerance and insulin secretion, but no change in body weight or insulin resistance, suggesting that the main cause of impaired glucose tolerance is impaired insulin secretion. Isolated islets showed no abnormalities in insulin secretory capacity or changes in calcium influx, but histologically showed a decrease in {beta} cell mass. Consistent with the decreased {beta} cell mass in {beta}GRK5 KO, the cell cycle inhibitor gene Cdkn1a was upregulated in {beta}GRK5 KO islets; this phenocopies the {beta}SOX4 KO. Furthermore, we found that Grk5 positively regulates facultative increases in {beta} cell mass through activity-dependent phosphorylation of HDAC5 and subsequent transcription of immediate early genes (IEGs) such as Nr4a1, Fosb, Junb, Arc, Egr1 and Srf. ConclusionsOur results suggest that GRK5 is associated with type 2 diabetes through regulation of {beta} cell mass. GRK5 could become a potential target of cell therapy to preserve functional {beta} cells during the progression towards frank diabetes.

physiology↗