Search Results - EGA European Genome-Phenome Archive

Single-Cell Genomic Analysis of Gastrointestinal Cancer

Our study aimed to define the heterogeneity of gastrointestinal cancers at a single-cell resolution. We subjected single-cell suspensions derived from surgical resections of gastrointestinal cancer tissue, paired normal tissue, peripheral blood mononuclear cells (PBMCs) or their ex vivo cultures to high-throughput microfluidics based single-cell RNA and DNA sequencing. We analyzed the features of the tumor microenvironment including fibroblasts, endothelial cells, macrophages and lymphocytes to determine their contribution to tumor growth and progression. We also characterized the mechanisms of immunosuppression in these tumors. This analysis led to novel insights into the biology of the microenvironment and also enabled the identification of new treatment targets.

Study phs001818

Bulk RNASeq of metastatic colorectal cancer organoids with ATOH1 knockout

Bulk RNA sequencing was performed on mCRC organoids subjected to cetuximab treatment, comparing ATOH1 knockout and control conditions. The dataset is intended to elucidate the contribution of ATOH1-regulated secretory cell population to cetuximab persistence mechanisms.

Dataset EGAD50000002060

CSER: Evaluating Utility and Improving Implementation of Genomic Sequencing for Pediatric Cancer Patients in the Diverse Population and Healthcare Settings of Texas: The KidsCanSeq Study

Through this Clinical Sequencing Evidence-Generating Research (CSER) with Enhanced Diversity project we are completing a clinical study (The Texas KidsCanSeq Study) comparing the results of targeted cancer panel sequencing versus genome-scale testing in pediatric cancer patients across diverse clinical settings. We will compare the targeted pediatric cancer panel to germline whole exome sequencing (WES) of unselected childhood cancer patients. We will also compare an RNA/DNA targeted pediatric cancer panel versus WES, transcriptome sequencing and copy number array of FFPE tumor samples for the subset of patients with high-risk tumors. Exome sequencing is performed from a blood or saliva sample of the pediatric age (0-18) patient. We are building on our success completing the CSER program BASIC3 exome sequencing trial (which included 60% Hispanic and African-American patients from a single large academic center) in this large multi-institutional study of an even more diverse patient population from six pediatric oncology healthcare settings across Texas. Data from the Texas KidsCanSeq study will be submitted through the CSER Data Coordinating Center for access in NIH-supported databases.

Study phs002378

Super enhancers define regulatory subtypes and cell identity in neuroblastoma - RNA-seq

Half of the children diagnosed with neuroblastoma have high-risk disease, disproportionately contributing to overall childhood cancer-related deaths. In addition to recurrent gene mutations, there is increasing evidence supporting the role of epigenetic deregulation in disease pathogenesis. Yet, comprehensive cis-regulatory network descriptions from neuroblastoma tissues are lacking. Here, using genome-wide H3K27ac profiles across 60 neuroblastomas, covering the different clinical and molecular subtypes, we identified four major super enhancer-driven epigenetic subtypes and their underlying master regulatory networks. Three of these subtypes recapitulated known clinical groups, namely MYCN amplified, MYCN non-amplified high-risk and MYCN non-amplified low-risk neuroblastomas. The fourth subtype, exhibiting mesenchymal characteristics, shared features with multipotent Schwann cell precursors, was induced by RAS activation and enriched in relapsed disease. Notably, CCND1, a disease essential gene, was regulated by both mesenchymal and adrenergic regulatory networks converging on distinct super-enhancer modules. Together, this reveals subtype-specific super-enhancer regulation in neuroblastoma.

Study EGAS00001004552

Strand-seq of hematopoietic stem and progenitor cells along human aging

Somatic mosaicism (SM), referring to the presence of somatic mutations in sub-populations of cells within healthy individuals, is associated with an increased risk of a variety of diseases, including cancer. Blood is at particularly high risk of SM, given its rapid turnover and functionally- heterogeneous cell-type composition. While the roles of point mutations and large-scale rearrangements in blood SM have been scrutinised in recent years, the functional impact of mosaic structural variants (mSVs) remains poorly understood. Using haplotype-resolved single-cell multi-omics based on Strand-seq technology, we explored the mSV landscape of human hematopoietic stem and progenitor cells (HSPCs).

Dataset EGAD00001009402

Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

We profile the adult human CNS from distinct regions, sex and ages, for chromatin accessibility at the single-nuclei level. Tissue was collected from 20 different donors (10 male, 10 female) within the ages of 34 to 74 years old. Additionally we performed Single-cell nanoCUT&Tag H3K27ac and H3K27me3 profiling for 4 of the donors and multiome single cell assay (RNA-seq+ATAC-seq) for 2 of the donors. Each donor donated fresh frozen white matter from the following three tissue regions: primary motor cortex (Brodmann area 4, BA4), arbor vitae cerebelli (CB) and fasciculi cuneatus and gracilis from and cervical spinal cord (CSC). Tissue was processed semi-randomly, ensuring that each batch of experiments had a representation of both sexes and all three tissue regions. Completed libraries were again randomly multiplexed during sequencing to minimize batch effects. We also performed micro-C,2 replicates, of iPS human derived cell cultures of human oligodendrocyte precursor cells (hOPC).

Dataset EGAD50000000410

Upper cortical layer-driven network impairment in schizophrenia - 10x genomics v3 snRNA-seq and Visium spatial transcriptomics datasets

This dataset contains 10x Genomics v3 3’ single nuclei RNA sequencing (24 human schizophrenia and control samples) and 10x Genomics Visium spatial transcriptomics (14 human schizophrenia and control samples) datasets. Files are in .bam format, output of the cellranger v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.1/using/count) for snRNA-seq and spaceranger v1.1.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/1.1/using/count) for Visium samples. Reads were mapped against Release 97 of human genome from Ensembl (http://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz http://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz). More details on sample processing are available in the biorXiv pre-print (https://doi.org/10.1101/2020.11.17.386458) and upcoming publication in Science Advances. BAM files can be converted to fastq files using bamtofastq tool (https://support.10xgenomics.com/docs/bamtofastq) with downstream remapping using tools and genomes of choice.

Dataset EGAD00001009173

BLUEPRINT: Epigenetic programming during monocyte to macrophage differentiation and trained innate immunity

Monocyte differentiation into macrophages represents a cornerstone process for host defense. Concomitantly, immunological imprinting of either tolerance or trained immunity determines the functional fate of macrophages and susceptibility to secondary infections. Transcriptomes (RNA-Seq) and epigenomes (ChIP-Seq H3K4me1,H3K4me3,H3K27ac) in four primary cell types: monocytes, in vitro differentiated naive, tolerized and trained macrophages were characterized. Inflammatory and metabolic pathways were modulated in macrophages, including decreased inflammasome activation, and pathways functionally implicated in trained immunity were identified. Strikingly, B-glucan training elicits an exclusive epigenetic signature, revealing a complex network of enhancers and promoters. Analysis of transcription factor motifs in DNase I hypersensitive sites at cell-type specific epigenetic loci unveiled differentiation and treatment specific repertoires. Altogether, this study provides a resource to understand the epigenetic changes that underlie innate immunity in humans.

Dataset EGAD00001001011

Whole genome bisufite sequencing of smoking and non-smoking mother-child pairsBisufite sequencing, RNA-seq and ChIP-Seq data of whole blood samples from smoking and non-smoking mothers and their children at gestation/birth and follow-up years.

Whole-blood samples of 16 mother-child pairs with differing maternal smoking behaviour were bisulfite treated and sequenced with deep coverage to identify smoking-associated differentially methylated regions.RNA-sequencing and ChIP-sequencing of 4 chromatin marks complete the data set and allow for integrative analyses, functional region annotation and to study the impact of epigenetic changes on gene expression.Longitudinal data spanning several years provides the means to investigate the stability of observed differences of all data types.

Study EGAS00001000455

SU2C-MARK Lung Cancer Consortium - Checkpoint Blockade Response Project

Immune checkpoint inhibitors have become a critical part of the armamentarium against advanced Non-Small Cell Lung Cancer (NSCLC). While early studies have identified Tumor Mutation Burden (TMB) and PD-L1 staining as important biomarkers of response, they remain imperfect predictors. Here we describe a multi-institutional effort as part of the SU2C-MARK Lung Cancer Consortium in which Whole Exome Sequencing (WES) - and in select cases, RNA sequencing – was performed on a large collection of NSCLC samples prior to immune checkpoint blockade therapy, along with matched clinical response data following therapy. (Profiling of a small number of on- or post-treatment samples was also performed.) We anticipate this dataset to be of high value for the development of a deep understanding of the molecular determinants of immune checkpoint blockade response as well as the discovery of novel biomarkers.

Study phs002822

Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

Study phs003638

RNA sequencing and Illumina 2.5M SNP array data collected from 675 commonly used human cancer cell lines.

Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels2–4, the transcriptome – which represents the active program of a cell – remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines.

Study EGAS00001000610

Hyperdiploid Acute Lymphoblastic Leukemia RNA-Seq

Few genetic drivers of children with hyperdiploid precursor B-cell acute lymphoblastic leukemia (ALL) have been identified to date. In an effort to detect novel genomic rearrangements that could be promoting leukemogenesis in this subset of patients, we sequenced ribosomal RNA-depleted transcriptomes isolated from 5 hyperdiploid acute lymphoblastic leukemia samples. In addition to looking for novel genomic rearrangements, we also sought to identify transcripts that could be created as a result of a novel posttranscriptional process. Surprisingly, we identified transcripts created as the result of exon circularization. The results of our studies are present in the paper "Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types" published in PLoS ONE (PMID: 22319583).

Study phs000522

single-cell RNA-seq Case-Control study of children progressing to Type1 diabetes

Single-cell RNA sequencing was carried out on four selected PBMC samples of Finnish children at risk of developing Type 1 diabetes and their gender age and HLA matched control children using 10X genomic platform. All four Case children were positive for multiple islet specific autoantibodies and two of them also progressed to clinical disease during the follow up whereas the control children remain negative for all autoantibodies. Age at seroconversion for Case 2, 3, 5, and 9 children is 12, 18, 24, and 18 months, respectively. Age at sampling, in months, for the pairs was as follows (Case/Control): pair 2:24/24; pair 3: 12/18; pair 5: 12/12; pair 9:24/18.

Study EGAS00001004070

Bacterial Vaginosis, Cervical Immune Cells and HIV Susceptibility

This was a cross-sectional study to characterize cervical immune cell composition and activation status in the presence versus absence of bacterial vaginosis (BV) using bulk messenger RNA sequencing (mRNA-Seq). Women enrolled in a longitudinal, open cohort study and engaged in a sex work in Mombasa, Kenya, were eligible. On the day of enrollment, participants self-collected vaginal swabs for generation of Gram-stained slide. The slides were scored from 0-10 using the method of Nugent and Hillier; in this system, women with scores of 0-3 are considered to have normal vaginal flora, those with scores of 4-6 are considered to have intermediate flora, and those with scores of 7-10 are considered to have BV. For this study, only women with normal flora (Nugent scores 0-3) or BV (Nugent scores 7-10) were eligible. Participants underwent speculum-assisted pelvic examination and collection of cervical biopsy specimens using Tischler forceps. Biopsies were placed immediately in ice cold medium and transferred to the laboratory where they were weighed and transferred to freezing medium (10% DMSO + fetal bovine serum) and cooled slowly overnight. Samples were shipped from Kenya to the United States in liquid nitrogen dry shippers, collagenase digested into single cell suspensions, and sorted on a FACS aria to enrich for a population of live, CD45+ cells. Sorted samples (N=17 with BV and N=13 without BV) were immediately lysed and processed using the Takara SMART-Seq v4 Ultra Low Input RNA Kit for sequencing. Library generation was completed using the manufacturer's instructions and sequencing performed on an Illumina NextSeq500 platform using Illumina NextSeq 500/550 High Output v2.5 (150 Cycles). The FASTQ files generated and BV status (N=9 with BV and N=12 without BV that passed quality control) of the donor sample will be available on dbGaP. We identified over 1000 differentially expressed genes between women with versus without BV at an adjusted p-value of <0.05 (listed under "gene names" below).

Study phs002329

11936 results for "cancer rna-seq"

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