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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE74703 | GEO | 2018/10/31

REPOSITORIES: GEO

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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

An association study between somatic alterations and eQTL in immunity, DNA repair and inflammation pathways in esophageal squamous cell carcinoma (ESCC)

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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

Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma

Project description:Genomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors. In the current study we focus on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using results from 500K SNP, mRNA, and miRNA arrays in 30 cases from a high-risk region of China.

2016-02-29 | GSE66274 | GEO

Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma

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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.

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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.

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Prevalence of Copy-number neutral LOH in glioblastomas revealed by analysis of laser-microdissected tissues

2009-03-01 | GSE10922 | GEO

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

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

| PRJNA301209 | ENA

Prevalence of Copy-number neutral LOH in glioblastomas revealed by analysis of laser-microdissected tissues

Project description:We have employed a laser capture microdissection technique and single nucleotide polymorphism arrays to characterize genomic alterations associated with the development of glioblastomas. Combined analysis of LOH and copy number revealed that more than half of the identified 254 LOH loci showed no copy number alteration, indicating the presence of copy-number neutral LOH Keywords: DNA copy number, Loss of heterozygosity Affymetrix 50K SNP mapping arrays were used to profile 14 primary glioblastomas (GBMs) with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair.

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