Genomics and Transcriptomics of Human Insulinoma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA397244 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genomics and Transcriptomics of Human Insulinoma
| PRJNA397245 | ENA
Project description:<p><b>The Genomics and Transcriptomics of Human Insulinoma</b><br/> The common forms of diabetes - Types 1 and 2 - ultimately result from a deficiency of insulin-producing pancreatic beta cells. The Genomics and Transcriptomics of Human Insulinoma study was performed in order to identify novel approaches to inducing human pancreatic beta cells to replicate and regenerate. As a corollary, developing drugs that are able to expand human beta cell mass in people with diabetes should reverse diabetes. Unfortunately, identifying druggable pathways that can enhance human beta cell replication has been a major challenge. In 2017, there is only one class of drugs - the harmine analogues - that can induce human beta cells to replicate, and in this case, higher replication rates are desirable. Thus, identifying additional drugs and druggable pathways is a priority in diabetes research.</p> <p>Insulinomas are rare, benign adenomas of the pancreatic beta cell that cause excess insulin production and hypoglycemia: exactly the opposite of Types 1 and 2 diabetes. Beta cell proliferation rates in insulinomas are abnormally high. Thus, the premise for The Genomics and Transcriptomics of Human Insulinoma study is that benign human insulinomas hold the genomic and transcriptomic "recipe", and the repertoire of druggable pathways, that can be exploited to induce regeneration or replication of human beta cells in diabetes. Because, insulinomas are so rare, are almost always benign (non-malignant), and are easily resected by laparoscopic surgery, little attention has been paid to understanding the genomics or transcriptomics of insulinoma. There are at present only three published studies employing next-gen sequencing in insulinoma (<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=24326773">PMID:24326773</a>; <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=25787250">PMID:25787250</a>; and <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=25763608">PMID:25763608</a>). These studies contained 10, 7 and 8 insulinomas, respectively, and highlighted likely mutations in YY1 and MEN1. Our goal was to markedly expand the database and to add RNAseq to these earlier studies. </p> <p>The Genomics and Transcriptomics of Human Insulinoma study, in press in Nature Communications in 2017, reports next-gen sequencing on 38 insulinomas, by far the largest series of human insulinomas subjected to next-gen sequencing. This includes paired (genomic plus tumor) whole exome sequencing on 26 human insulinomas (22 sequenced at Mount Sinai, 4 downloaded from Cao <i>et al</i>, <a hre="https://www.ncbi.nlm.nih.gov/pubmed/?term=24326773">PMID:24326773</a>), and 25 sets of RNAseq from insulinomas, some of which also had paired whole exome seq, and some of which did not. The insulinoma RNAseq was compared to RNAseq from 22 sets of FACS-sorted normal human beta cells. Since insulinomas are so rare, the 38 insulinomas were collected by several investigators at several institutions over several decades, but most (22 whole exome sets, and all RNAseq) were sequenced at the Icahn School of Medicine at Mount Sinai in New York. </p> <p>The current dataset contains whole exome seq and RNAseq on the 11 insulinomas harvested at Mount Sinai. The four from Cao <i>et al</i> can be retrieved from Cao <i>et al</i> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=24326773"> PMID:24326773</a>. Fastq files from the remaining 23 insulinomas will be added as the local IRBs and Institutional Certifications are acquired. Complete patient data are provided in our Nature Communications report. Going forward, our intention is to expand this series, with the goal of sequencing 100 human insulinomas. These will be added to dbGaP as they accrue.</p> <p>Paired-end whole exome seq (mean usable sequencing depth 79X and 105X for blood and insulinoma, respectively) was performed using an Illumina HiSeq 2500. Insulinoma and sorted normal beta cell RNAseq was performed on Ribozero and polyA paired end libraries using the Illumina HiSeq 2500. Complete sequencing and bioinformatic details are provided in our Nature Communications report.</p> <p>The principal findings from the study are that although each insulinoma has a different set of presumptive driver mutations, the majority converge on genes that are members of the Polycomb Complex, Trithorax Complex and other epigenetic modifying enzymes. In addition, 20% of insulinomas have copy number loss or loss of heterozygosity of all or most of chromosome 11, and the majority display abnormalities in CpG methylation and imprinting control on the imprinted Chr 11 p15.5-15.4 region that contains <a href="https://www.ncbi.nlm.nih.gov/gene/?term=INS">INS</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/?term=IGF2">IGF2</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/?term=CDKN1C">CDKN1C</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/?term=KCNQ1">KCNQ1</a>, and other genes involved in beta cell specification and proliferation. </p>
| phs001422 | dbGaP
Project description:This study includes spatial transcriptomics on the human lumbar spinal cord using the 10x Genomics Visium platform. Frozen sections of spinal cord were placed on Visium slide arrays and processed using the 10x Genomics workflow, followed by alignment and quantification using the spaceranger package.
2023-01-31 | GSE222322 | GEO
Project description:Transcriptional responses of human insulinoma cells to acute cytokine exposure
| PRJNA553835 | ENA
Project description:Visium (10x Genomics) spatially resolved transcriptomics data generated from normal and Idiopathic Pulmonary Fibrosis (IPF) lung parenchyma tissues collected from human donors. The fresh-frozen tissues that were analyzed were from four healthy control (HC) subjects and from four IPF patients. For each IPF patient, three different tissues were selected representing areas of mild (“B1”), moderate (“B2\") or severe (“B3”) fibrosis within the same donor, as determined by histological inspection of Hematoxylin and Eosin (H&E)-stained samples. Data from a total of 25 tissue sections, from 16 unique lung tissue blocks. The lung tissues were collected post-mortem (HC donors) or during lung transplant/resection (IPF patients) after obtaining informed consent. The study protocols were approved by the local human research ethics committee (HC: Lund, permit number Dnr 2016/317; IPF: Gothenburg, permit number 1026-15) and the samples are anonymized and cannot/should not be traced back to individual donors.
2024-05-28 | E-MTAB-14121 | biostudies-arrayexpress
Project description:This clinical trial studies the effectiveness of a web-based cancer education tool called Helping Oncology Patients Explore Genomics (HOPE-Genomics) in improving patient knowledge of personal genomic testing results and cancer and genomics in general. HOPE-Genomics is a web-based education tool that teaches cancer/leukemia patients, and patients who may be at high-risk for developing cancer, about genomic testing and provide patients with information about their own genomic test results. The HOPE-Genomics tool may improve patient’s genomic knowledge and quality of patient-centered care. In addition, it may also improve education and care quality for future patients.
| 2378933 | ecrin-mdr-crc
Project description:We have shown that increased β-cell proliferation in functioning pancreatic neuroendocrine tumors (insulinomas) correlated with reduced expression of the long non-coding RNA Meg3 and increased expression of the oncogenic receptor c-Met. To investigate the target binding sites of Meg3 in and around the c-Met gene, we did ChIRP-Seq using biotinylated probes from the mouse Meg3 RNA sequence. This would help us better understand how Meg3 regulates ithe expression of c-Met to control β-cell proliferation in insulinoma cells.
2017-09-20 | GSE99798 | GEO
Project description:We have shown that increased β-cell proliferation in functioning pancreatic neuroendocrine tumors (insulinomas) correlated with expression of phosphorylated isoform of the transcription factor HLXB9 which is an embryonic beta-cell differentiation factor (HLXB9 is also known as HB9, MNR2, and MNX1). To investigate the target genes of phospho-HLXB9 we did ChIP-seq using anti-HB9-PO4. This would help us better understand how phospho-HLXB9 regulates its targets and affects β-cell proliferation in insulinoma cells.
2015-09-30 | GSE61432 | GEO
Project description:Genomics and transcriptomics of boar taint in pigs
| PRJNA362224 | ENA
Project description:Spatial transcriptomics (Visium, Spatial 3' V1, 10x Genomics) analysis of heart tissues from Lactobacillus casei cell wall extract (LCWE)-injected mice and control PBS-injected mice
2021-09-14 | GSE178799 | GEO