Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis

ABSTRACT: CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis

PROVIDER: PRJNA301209 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis [Affy_500K]

Project description:Since ESCC is a complex and heterogeneous disease, it is increasingly important that analyses combine the evaluation of alterations in DNA, including somatic copy number alterations (SCNA), which distinguished from germ line copy number variants, allelic imbalance and LOH, and RNA, including those that occur in both mRNA and miRNA on the same specimen. Thus, in order to better understand their potential interactions in the development of cancers, in the present study, we studied alterations at DNA level as well as expression of mRNA and target miRNA in tumors and their matched normal tissues from 56 ESCC cases on a candidate tumor suppressor gene CSMD1 to characterize there alterations in this gene for import insights into the cellular detect that cause the complex disease, ESCC.

2018-10-31 | GSE74704 | GEO

CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis [Affy_SNP5]

2018-10-31 | GSE74703 | GEO

CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-10-31 | GSE74705 | GEO

RNA-seq of CSMD1 enhancer CRISPRi in LUHMES cells and differentiated neurons

Project description:we performed lentiviral CRISPR interference (CRISPRi) by recruiting dCas9 fused with the KRAB domain to the CSMD1 enhancer (fam3) in the neuronal precursor cell line – Lund human mesencephalic (LUHMES). Given that the expression of CSMD1 was not detectable in LUHMES cells we differentiated these cells into neurons. Differentiated neurons with CRISPRi of CSMD1 enhancer showed significantly higher expression of CSMD1 than control.

2022-06-30 | E-MTAB-8027 | biostudies-arrayexpress

<i>CSMD1</i> Shows Complex Patterns of Somatic Copy Number Alterations and Expressions of mRNAs and Target Micro RNAs in Esophageal Squamous Cell Carcinoma.

Project description:BackgroundHuman Cub and Sushi Multiple Domains 1 (CSMD1) is a novel candidate tumor-suppressor gene that codes for multiple domains, including complement regulatory and adhesion proteins, and has recently been shown to have alterations in multiple cancers. We investigated CSMD1 in esophageal squamous cell carcinoma (ESCC) by performing an integrated analysis on somatic copy number alterations (CNAs), including copy-number gain or loss, allelic imbalance (AI), loss of heterozygosity (LOH), and the expressions of mRNA and its target miRNAs on specimens from the same patients with ESCC.Results(i) Two-thirds of ESCC patients had all three types of alterations studied-somatic DNA alterations in 70%, and abnormal expressions of CSMD1 RNA in 69% and in target miRNAs in 66%; patterns among these alterations were complex. (ii) In total, 97% of 888 CSMD1 SNPs studied showed somatic DNA alterations, with most located near exons 4-11, 24-25, 39-40, 55-56, and 69-70. (iii) In total, 68% of SNPs with a CNA were correlated with expression of CSMD1. (iv) A total of 33 correlations between non-coding SNPs and expression of CSMD1 target miRs were found.ConclusionsOur results indicate that the CSMD1 gene may play a role in ESCC through complex patterns of DNA alterations and RNA and miRNA expressions. Alterations in some somatic SNPs in non-coding regions of CSMD1 appear to influence expression of this gene and its target miRNAs.

| S-EPMC9599939 | biostudies-literature

RNA sequencing of fibroblasts with or without CSMD1 knockdown

Project description:CSMD1 gene, mapping to human chromosomal region 8p23, encodes a transmembrane protein with an extracellular region containing 14 CUB and 28 sushi domains, a transmembrane domain and a cytoplasmic domain with a putative tyrosine phosphorylation site.The loss of CSMD1 has been found to be associated with enhanced cell proliferation, migration and poor prognosis in head and neck squamous cell carcinoma (HNSCCs), lung squamous cell carcinoma (SCCs), melanoma, and breast cancer, suggesting its role as a tumor suppresser.However, its role in hypertrophic scar has not been uncovered. So we decided using fibroblasts to see its transcriptomes changing after CSMD1 knockdown.

2021-08-18 | GSE176551 | GEO

Rare mutations in the complement regulatory gene CSMD1 are associated with male and female infertility

Project description:Infertility in men and women is a common and complex genetic trait with shared biological bases between the sexes. We performed a series of rare variant analyses across 73,185 women and men to identify genes that contribute to primary gonadal dysfunction and identified CSMD1 as a strong candidate in both sexes. CSMD1 is a complement regulatory protein on chromosome 8p23. In order to interpret and support our genetic findings, we performed detailed transcriptomic and protein-based experiments which found CSMD1 enriched at the germ-cell/somatic-cell interface in both male and female gonads. We then performed a battery of tests on Csmd1 knockout mice. Knockout males show increased rates of infertility, and present testes with severe histological degeneration and significantly increased deposition of complement C3 protein. Knockout females show significant reduction in ovarian quality and breeding success, as well as impaired branching of the mammary glands. Furthermore, double knockout of Csmd1 and C3 leads to an unexpected and non-additive reduction in breeding success, suggesting that CSMD1 and the complement pathway play an important role in the normal postnatal development of the gonads in both sexes.

2019-09-04 | GSE136769 | GEO

Homo sapiens

Project description:CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis [Affy_500K]

| PRJNA301208 | ENA

Homo sapiens

Project description:CSMD1 shows complex somatic alterations in esophageal squamous cell carcinoma based on a pilot integrated analysis [Affy_SNP5]

| PRJNA301206 | ENA

Human esophageal dysplasia (16 cases) vs. esophageal squamous cell carcinoma (59 cases)

Project description:Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations. Two group experiment, esophageal dysplasia vs. esophageal squamous cell carcinoma. Biological replicates: 16 dysplasias vs. 59 carcinomas

2013-04-29 | E-GEOD-46452 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data