3743 results for "RNA AND sequencing OR transcriptome"

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• Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma

  Background:Malignant pleural mesothelioma (MPM) is a heterogeneous cancer. Better knowledge of molecular and cellular intra-tumor heterogeneity throughout the thoracic cavity is required to develop efficient therapies. This study focuses on molecular intra-tumor heterogeneity using the largest series to date in MPM and is the first to report on the multi-omics profiling of a substantial series of multi-site tumor samples. Methods:Intra-tumor heterogeneity was investigated in 16 patients from whom biopsies were taken at distinct anatomical sites. The paired biopsies collected from apex, side wall, costo-diaphragmatic or highest metabolic sites as well as 5 derived cell lines were screened using targeted sequencing. Whole exome sequencing, RNA sequencing, and DNA methylation were performed on a subset of the cohort for deep characterization. Molecular classification, recently defined histo-molecular gradients, and cell populations of the tumor microenvironment were assessed. Results:Sequencing analysis identified heterogeneous variants notably in NF2, a key tumor suppressor gene of mesothelial carcinogenesis. Subclonal tumor populations were shared among paired biopsies, suggesting a polyclonal dissemination of the tumor. Transcriptome analysis highlighted dysregulation of cell adhesion and extracellular matrix pathways, linked to changes in histo-molecular gradient proportions between anatomic sites. Methylome analysis revealed contribution of epigenetic mechanisms in two patients. Finally, significant changes in the expression of immune mediators and genes related to immunological synapse, as well as differential infiltration of immune populations in the tumor environment were observed and led to a switch from a hot to a cold immune profile in three patients. Conclusions:This comprehensive analysis reveals patient-dependent spatial intra-tumor heterogeneity at the genetic, transcriptomic and epigenetic levels and in the immune landscape of the tumor microenvironment. Results support

  Study EGAS00001005328

• Count Me In (CMI): The Angiosarcoma (ASC) Project (CMI-ASCproject)

  Count Me In - The Angiosarcoma Project: A Patient-Partnered Research Initiative to Accelerate Research in a Rare Sarcoma The Angiosarcoma Project (ASCproject) is a research study that directly engages angiosarcoma patients online and empowers them to accelerate cancer research by sharing medical information and clinical samples. Angiosarcoma is an exceedingly rare soft tissue sarcoma with an incidence of ~300 newly diagnosed cases per year in the United States. This low incidence has impeded large-scale research efforts in this disease that are strongly needed to catalyze research and improve clinical outcomes. The Angiosarcoma Project, launched in March 2017, has demonstrated the feasibility of directly engaging geographically dispersed patients to democratize research and establish a large patient cohort to characterize the genomic and clinical landscape of a rare disease. Angiosarcoma patients living in the US or Canada can access the study and consent online through an online portal (ASCproject.org). Enrolled patients are mailed saliva and blood draw kits, which can be used to extract germline DNA and cell-free DNA (cfDNA), respectively. The study team contacts participants' healthcare institutions to obtain medical records and a portion of archived tumor samples. All received tumor samples are subjected to centralized histological re-review by an expert pathologist to confirm a diagnosis of angiosarcoma. Whole exome sequencing is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing is performed on tumor RNA. De-identified data, including linked genomic, clinical, and patient-reported data, are shared via public databases on a recurring pre-publication basis. Participants are regularly provided updates on the study.

  Study phs001931

• Count Me In (CMI): The Metastatic Breast Cancer (MBC) Project (CMI-MBCproject)

  Count Me In - The Metastatic Breast Cancer Project: A Patient-Driven Research Initiative to Accelerate Metastatic Breast Cancer Research The Metastatic Breast Cancer Project is a research study that directly engages patients with metastatic breast cancer via social media and advocacy groups and empowers them to accelerate cancer research by sharing their samples and clinical information. Our goal is to create a publicly available dataset of genomic, molecular, clinical, and patient-reported data to enable research. Patients in the US or Canada may register online. Registered patients are sent an online consent form that asks for permission to obtain and analyze their medical records, tumor tissue, saliva, and blood samples. Once enrolled, patients are sent a saliva kit and asked to mail back a saliva sample, which is used to extract germline DNA. Study staff contact participants' medical providers and obtain medical records and a portion of their stored tumor biopsies. Patients may be asked to mail in a blood sample, which is used to extract cell free DNA (cfDNA). Whole exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing is performed on tumor RNA. Clinically annotated genomic data are used to study specific patient cohorts (including outliers) and to identify mechanisms of response and resistance to therapies. All de-identified data, including genomic, clinical, and patient-reported data, are shared via public databases on a pre-publication and recurring basis as it is generated. The latest data release in cBioPortal is available here. Study updates are shared with participants regularly.

  Study phs001709

• The Adhesion GPCR ADGRL2 Engages Galpha13 to Enable Epidermal Differentiation

  We sought to determine the role of ADGRL2 in epidermal homeostasis. Primary neonatal foreskin keratinocytes were obtained from discarded surgical samples at a California hospital. Samples were anonymous and not selected. ADGRL2, working through GNA13, was found to promote epidermal differentiation through the ADGRL2 intracellular loop 3 (ICL3) loop, using the methods of RNA-seq and Perturb-seq.

  Study phs004223

• A Phase Ib/II Study of Regorafenib and Paclitaxel in Beyond First-line Advanced Esophagogastric Carcinoma (REPEAT)

  Regorafenib showed promising results in gastric cancer. We aimed to assess the tolerability of regorafenib and paclitaxel in advanced esophagogastric cancer (EGC) patients refractory to first-line treatment and explore potential biomarkers.. We performed enzyme-linked immunosorbent assay measurements of galectin-1, RNA sequencing, and shallow wholegenome sequencing of metastatic tumor biopsies for biomarker analyses.

  Study EGAS00001006054

• Genomic and transcriptomic profiling of signalling networks in follicular lymphoma

  This dataset is composed of sequencing data from 16 patients diagnosed with follicular lymphoma, who developed transformed disease and for whom representative frozen tumor biopsy samples were available. For 14 patients there is paired material from both disease stages. DNA and RNA libraries were constructed and captured with a kinome bait library (Agilent Technologies), before sequencing on an Illumina platform.

  Study EGAS00001002175

• The genomic landscape of Burkitt Lymphoma

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of Burkitt Lymphomas . Burkitt lymphomas are the most common B-cell lymphomas in childhood. Analyses were performed in concordance with the guidelines of the ICGC. The results define the genomic landscape of structural variants, somatic single nucleotide variants and mutational signatures in these lymphomas.

  Study EGAS00001002198

• RNA-seq data of bone marrow CD34-positive cells from 57 patients with myelodysplastic syndromes (MDS) and 5 healthy individuals (62 participants in total)

  Genetic mutations in hematopoietic neoplasms, seen in disease-specific and non-specific ways, are key drivers in pathogenesis. Typically, these mutations alone don't cause neoplasms; rather, multiple mutations or breakdowns in regulatory mechanisms occur, progressing the disease through stages. Genetic mutation patterns vary even within subtypes, suggesting shared gene expression abnormalities from different mutations may drive neoplasm development. Identifying these "common factors" is vital for effective molecular-targeted therapy development. Our study aims to elucidate neoplasm pathogenesis by analyzing patient genetic abnormalities, pinpointing "common factors" in each subtype for novel targeted therapy development.

  Study JGAS000724

• COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

  To investigate the immune response and mechanisms associated with severe COVID-19, we performed single-cell RNA-seq on nasopharyngeal and bronchial samples from 19 clinically well-characterized patients with moderate or critical disease and from 5 healthy controls. We identified airway epithelial cell types and states vulnerable to SARS-CoV-2 infection. In COVID-19 patients, epithelial cells showed an average threefold increase in expression of the SARS-CoV-2 entry receptor ACE2, which correlated with interferon signals by immune cells. Compared with moderate cases, critical cases exhibited stronger interactions between epithelial and immune cells, as indicated by ligand–receptor expression profiles, and activated immune cells , including inflammatory macrophages expressing CCL2, CCL3, CCL20, CXCL1, CXCL3, CXCL10, IL8, IL1B and TNF . The transcriptional differences in critical cases compared with moderate cases likely contribute to clinical observations of heightened inflammatory tissue damage, lung injury and respiratory failure. Our data suggest that pharmacologic inhibition of the CCR1 and/or CCR5 pathways may suppress immune hyperactivation in critical COVID-19.

  Dataset EGAD00001006339

• Reproducibility of 10x Genomics single cell RNA sequencing method in the immune cell environment

  Study EGAS00001005905