Search Results - EGA European Genome-Phenome Archive

Investigating Delayed-Onset Drug Hypersensitivity Reactions Prospectively

Delayed-type drug hypersensitivity reactions (dtDHR) are significant causes of morbidity and mortality, but the origin, phenotype and function of pathogenic T cells across the spectrum of severity are unknown. Research has been hampered by several barriers. We leveraged recent technical advancements to study skin-resident memory T cells (TRM) versus recruited T cell subsets in the pathogenesis of severe systemic forms of disease, Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) and drug reaction with eosinophilia and systemic symptoms (DRESS), and skin-limited disease, morbilliform drug eruption (MDE). As part of the overarching study, we used single cell RNA sequencing (scRNA-seq) with CITE sequencing and TCR sequencing on prospectively collected skin and blood samples from patients with SJS/TEN and MDE patients. We compared this to healthy controls obtained from discarded skin from surgeries and discarded blood collars from a blood donation center. These data are included here in dbGaP database. The overarching study also performed bulk transcriptional profiling and microscopic analysis of clinical skin samples, as well as a mouse model of MDE (PMID: 39042477). Together, the data supported clonal expansion and recruitment of cytotoxic CD8+ T cells (identified using the mean normalized expression of NKG7, GNLY, GZMA, GZMB, and PRF1) from circulation into skin, along with both expanded and non-expanded cytotoxic CD8+ skin TRM in SJS/TEN whereas MDE displayed a cytotoxic T cell profile without expansion or recruitment of cytotoxic CD8+ T cells from circulation implicating TRM as the potential cause of disease. Concurrently, MDE displayed a pro-Treg signature, highlighted by CCR8 and TNFRSF4 (OX40), which promotes Treg survival compared to SJS/TEN.

Study phs003344

Exploiting immune cell receptor information to quantify index switching in single cell transcriptome sequencing experiment

By offering high sequencing speed and ultra-high-throughput at a low price, Illumina next-generation sequencing platforms has been widely adopted in recent years. However, an experiment with multiplexed library could be at risk of molecular recombination, known as “index switching”, which causes certain amount of reads to be assigned to an incorrect library. It is reported that a new advance, exclusion amplification (ExAmp) in conjunction with the patterned flow cell technology introduced on HiSeq 3000/HiSeq 4000/HiSeq X sequencing systems, potentially suffers from a higher rate of index switching than conventional bridge amplification. We took advantage of the diverse but highly cell-unique expression of immune cell receptors to quantify index switching on single cell RNA-seq data that were sequenced on HiSeq 3500 and HiSeq 4000. By utilizing the unique T-cell receptor (TCR) expression, we could quantify the spread-of-signal from many different wells (n=51 from total three batches) due to index switching. We used TraCer to reconstruct full-length TCR from all samples, and then used Kallisto to quantify TCR gene expression. We found index switching in all three batches of experiments investigated. The median percentage of incorrectly detected markers was estimated to be 4.2% (interquartile range (IQR): 2.0%-8.7%). We did not detect any consistent pattern of certain indices to be more prone for switching than others, suggesting that index switching is a stochastic process. We confirm that index switching is a problem that affects all samples run in multiplexed libraries on Illumina HiSeq 3500 and HiSeq 4000 platforms.

Study EGAS00001002911

Monocyte and macrophage lipid accumulation results in downregulated type-I interferon responses

Macrophages are critical components of atherosclerotic lesions and their pro- and anti-inflammatory responses influence atherogenesis. Type-I interferons (IFNs) are cytokines that play an essential role in antiviral responses and inflammatory activation and have been shown to promote atherosclerosis. Although the impact of type-I IFNs on macrophage foam cell formation is well-documented, the effect of lipid accumulation in monocytes and macrophages on type-I IFN responses remains unknown. Here we examined IFN stimulated (ISG) and non-ISG inflammatory gene expression in mouse and human macrophages that were loaded with acetylated LDL (acLDL), as a model for foam cell formation. We found that acLDL loading in mouse and human macrophages specifically suppressed expression of ISGs and IFN-β secretion, but not other pro-inflammatory genes. The downregulation of ISGs could be rescued by exogenous IFN-β supplementation. Activation of the cholesterol-sensing nuclear liver X receptor (LXR) recapitulated the cholesterol-initiated type-I IFN suppression. Additional analyses of murine in vitro and in vivo generated foam cells confirmed the suppressed IFN signalling pathways and suggest that this phenotype is mediated via downregulation of interferon regulatory factor binding at gene promoters. Finally, RNA-seq analysis of monocytes of familial hypercholesterolemia (FH) patients also showed type-I IFN suppression which was restored by lipid-lowering therapy and not present in monocytes of healthy donors. Taken together, we define type-I IFN suppression as an athero-protective characteristic of foamy macrophages. These data provide new insights into the mechanisms that control inflammatory responses in hyperlipidaemic settings and can support future therapeutic approaches focusing on reprogramming of macrophages to reduce atherosclerotic plaque progression and improve stability.

Study EGAS00001005955

Identification of the dismal subtype of B-ALL with dysregulation of CDX2 and UBTF

PURPOSE: Advance in the knowledge of genomic basis of B-cell acute lymphoblastic leukemia (B-ALL) has changed the treatment approaches and diagnostic assays and improved their outcome. Despite the recent development of next generation sequencing approaches, there are still some cases that their drivers are unknown. We aimed to define and describe the characteristics of an additional B-ALL subtype by integrating genomic, transcriptomic, and epigenomic approach. METHODS: More than 2,000 B-ALL cases of RNA-seq data from from Eastern Cooperative Oncology Group (ECOG) and the American College of Radiology Imaging Network (ACRIN) (n=764), the Children's Oncology Group (COG), Munich Leukemia Laboratory (MLL) (n=280), and other several collaborators were analyzed to identify the new subtype. Whole genome sequence was performed to detect mutations, stractural variants, and copy number alterations. The tridimentional analysis of chromatin was performed with HiChIP. RESULTS: We identified the new high-risk B-ALL subtype “CDX2/UBTF” that exhibited unique gene expression profiles, which is enriched in female (77.3%), adolescents and young adults (52.6%), and relapse cohort (3.3%). CD10 negativity and IgM positivity are hallmarks of this subtype with NTRK3 expression that can be an effective marker at diagnostic approach and a potential targeted therapy with TRK and mulkinase inbitors, larotrectinib and entrectinib. Genetically, two different alterations define CDX2/UBTF. One is UBTF-ATXN7L3 fusions caused by deletion of 17q21.31, and the other is extopic CDX2 expression through the enhancer hijacking mechanism induced by deletion of 13q12.2. Other genomic features include gain of 1q and PAX5 rearrangement (PAX5-ZCCHC7), might induce upregulation of histone cluster genes and PAX5. CONCLUSION: We described the novel B-ALL subtype “CDX2/UBTF” that has unique clinical and genomic characteristics.

Study EGAS00001005863

Whole exome and RNA sequencing of organoid samples derived from TRACERx patients

Immune checkpoint blockade in non-small cell lung cancer (NSCLC) rarely leads to complete tumour remission, suggesting that tumours harbour subpopulations of cancer cells that can escape immune predation. However, while tumours consist of multiple genetically distinct clones, the extent to which separate tumour subclones differ intrinsically in their functional capacity for immune evasion remains largely unexplored. This has been challenging to address due to an inability to isolate and propagate individual tumour subclones from human cancers. Here, we leverage the multi-region TRACERx lung cancer evolution study to generate a patient-derived platform that allows the functional analysis of immune escape at single clone resolution. We generated libraries of >20 separate NSCLC organoid lines per patient by isolating individual (clonal) organoids established from multiple spatially separated tumour regions. Each organoid subline was co-cultured with autologous tumour infiltrating lymphocytes (TIL) to evaluate their capacity to elicit a T cell response. Organoid lines derived from separate tumour regions, or from single clones within individual regions, differ vastly in their capacity to elicit a T cell response, showing the coexistence of intrinsically immune evading (‘hot’) and non-evading (‘cold’) clones in the same primary tumour. Organoid lines escaping T cell recognition represent genetically and transcriptionally unique subclones with a distinct evolutionary history, showing that evolutionary sculpting of subclonal diversity can have functional consequences for anti-tumour immunity. Notably, the identification of immune-evasive subclones would not have been possible using computational approaches alone, highlighting the unique value of functional co-culture platforms. This patient-derived functional co-culture platform reveals that tumour evolution can give rise to distinct cancer clones with intrinsic differences in immune evasion capacity and provides an approach to prospectively identify, isolate and characterise immune evading subclones from patients with cancer.

Study EGAS00001008092

single cell RNA sequencing and ATAC sequencing, and Whole Genome sequencing of ALS patients

To investigate ALS pathology at the cellular level, we conducted a multiome (single-nucleus RNA sequencing and assay for transposase-accessible chromatin using sequencing) analysis using the motor cortex and spinal cord of patients with ALS and control individuals.

Study JGAS000852

Using RNA-sequencing to characterize the resistance to lirafugratinib

In addition to Exome-sequencing, we used RNA-sequencing to also characterize resistance to lirafugratinib with whole exome sequencing in patients with FGFR2-driven cancers, treated in the phase 1/2 ReFocus trial (NCT04526106) and enrolled in the UNLOCK program at Gustave Roussy

Study EGAS50000001370

Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

Human intestinal organoids co-cultured with pro-inflammatory (M1) or anti-inflammatory (M2) human macrophages for 48 hours. 3 days after the co-culture alive cells were sorted and processed for single cell RNA sequencing

Study EGAS50000000467

Bulk RNA sequencing of 36 multi-region IPMN–PDAC tumours comprising 160 sequencing runs

This dataset contains bulk RNA sequencing data generated from 36 multi-region tumour samples obtained from patients with intraductal papillary mucinous neoplasms (IPMN) and associated pancreatic ductal adenocarcinoma (PDAC). A total of 160 sequencing runs are included. Libraries were prepared from poly(A)-selected RNA and sequenced on an Illumina platform. The data are provided as raw sequencing files for downstream transcriptomic analyses.

Dataset EGAD50000002215

scMultiomics of ARID1B+/+ (control) and ARID1B+/- human telencephalic organoids at D120

This dataset contains scMultiomics (scRNAseq + scATACseq) data of human telencephalic organoids, at day 120, from 3 different sequencing runs (libraries), as follows (please see cell line clone nomenclature in original publication): 1. Library 233269(RNA)/235293(ATAC): Pat.1 ARID1B+/- clone 1a (9 pooled organoids). 2. Library 233270(RNA)/235294(ATAC): HD.1 ARID1B+/+ clone 3a (9 pooled organoids). 3. Library 233271(RNA)/235295(ATAC): HD.1 ARID1B+/- clone 3b (8 pooled organoids).

Dataset EGAD50000000499

RNASeq profiles of ROBUST clinical trial and processed WGS mutation calls output

The dataset contains RNAseq profiles of 1040 patients from the ROBUST clinical trial (NCT02285062). The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and total RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. RNAseq libraries (75PE, 50M) were constructed using Illumina TruSeq RNA Access method. Fastq files are included. Also includes processed WGS mutation calls output.

Dataset EGAD50000000482

RNAseq profiles from the CheckMate-142 clinical trial

The dataset contains RNAseq profiles of 57 patients from the CheckMate-142 clinical trial. The Allprep DNA/RNA FFPE kit was used to simultaneously purify genomic DNA and RNA from formalin-fixed, paraffin embedded (FFPE) tissue sections. Baseline tumor tissue samples were processed using the Illumina TruSeq RNA Access in-solution hybrid capture panel and underwent subsequent NGS on the Illumina NovaSeq platform. Fastq files are included.

Dataset EGAD50000000609

RNA sequencing data of pediatric KMT2A-rearranged acute lymphoblastic leukemia (set 1)

The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of two KMT2A-r ALL patients (ALLT-325, ALLT-346). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

Dataset EGAD50000002582

RNA sequencing data of pediatric hyperdiploid acute lymphoblastic leukemia

The dataset includes RNA sequencing FASTQ files from diagnostic tumor samples of four hyperdiploid ALL patients (ALLT-315, ALLT-320, ALLT-329, ALLT-347). NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) was used in library preparation, and Globin-Zero Gold rRNA Removal Kit (Illumina) was utilized for rRNA removal. The diagnostic tumor samples were sequenced using Illumina Novaseq 6000, and the target sequencing depth was 21 Gb per sample.

Dataset EGAD50000002595

Whole genome and RNA sequencing of cutaneous melanoma metastases

Whole genome sequencing of cutaneous melanoma skin and brain metastases and matched normal DNA, as well as RNA sequencing of material from the skin and brain metastases. In addition, RNA sequencing was performed for Dabrafenib and Trametinib treated patient-derived xenografts, together with untreated and vehicle treated controls.

Dataset EGAD00001004130

Single-cell RNA sequencing of erythroid and megakaryocytic acute myeloid leukemia patient cells

Single-cell RNA sequencing was performed on bone marrow mononuclear cells of a patient with acute myeloid leukemia with erythroid differentiation of the blasts and on peripheral blood mononuclear cells of a patient with acute myeloid leukemia with megakaryocytic differentiation of the blasts. The dataset contains raw fastq files of these two samples with single-cell RNA sequencing performed using the 10x Genomics platform.

Dataset EGAD00001009865

Whole transcriptome RNA sequencing on bone marrow and peripheral blood samples from patients with acute myeloid leukemia at diagnosis or relapse.

One hundred cryopreserved bone marrow and peripheral blood samples from patients with acute myeloid leukemia (AML) with 10-90% blasts were selected from the biobank of the Department of Hematology of Leiden University Medical Center (LUMC). The AML cases cover all subtypes, and specifically include known subtype-defining balanced chromosomal translocations according to the WHO classification. The samples were obtained from 96 patients and include three pairs of de novo and relapsed AML and one pair of de novo and presumed therapy-related AML (tAML). Total RNA was isolated from mononuclear cells without prior enrichment for leukemic blasts. The quality and integrity of total RNA was checked and RNA libraries were prepared using the TruSeq RNA library preparation kit v2 (Illumina, San Diego, CA) in an ISO/IEC 17025-accredited protocol. This workflow started with enrichment of messenger RNA by oligo dT magnetic beads. After fragmentation, cDNA synthesis was performed, followed by adaptor ligation and PCR amplification. Paired-end sequencing with a read length of 126 bp was performed on an Illumina HiSeq 2500 v4 sequencer to at least 12.5 Gbp per sample. Image analysis, base calling, and quality check was performed with Illumina data analysis pipeline RTA v1.18.64 and Bcl2fastq v1.8.4. RNAseq reads are provided in compressed Sanger FASTQ format.

Dataset EGAD00001004187

Combined – whole blood and skin fibroblasts - transcriptomic analysis in Psoriatic arthritis.

Whole blood RNA sequencing was performed longitudinally in 27 subjects with PsA at the beginning, one month and six months after treatment and response to therapy was defined at 6 months. As control groups 7 healthy individuals and 9 subjects with rheumatoid arthritis were recruited combined with public RNA-sequencing datasets from patients with psoriasis and systemic lupus erythematous. Differential expression analysis and weighted gene co-expression network analysis were performed to identify gene expression signatures, while deconvolution and flow cytometry to characterize the peripheral blood immune cell profile. RNA sequencing of skin fibroblasts was performed in a subset of affected (n=3) and healthy individuals (n=3) combined with CellChat to identify the blood-skin fibroblasts interaction network.

Study EGAS00001006288

12312 results for "cancer rna-seq"

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