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Intergenic risk variant rs56258221 skews the fate of naive CD4+ T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis

ABSTRACT: We correlated comprehensive T cell phenotyping data from peripheral blood to the corresponding genotype of different disease-associated and T cell related SNPs. This revealed significantly increased frequencies of naive CD4+ T cells (CD4+ TN) and T helper 17 (TH17) cells in carriers of intergenic SNP rs56258221 (BACH2/MIR4464) as compared to non-carriers. Functional experiments identified CD4+ TN from SNP-carriers to rather polarize towards pro-inflammatory subsets than into regulatory T cells (TREG). *** Due to data privacy concerns fastq files have not been uploaded ***

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Christian Casar

PROVIDER: E-MTAB-14103 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Intergenic risk variant rs56258221 skews the fate of naive CD4+ T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis

Project description:We correlated comprehensive T cell phenotyping data from peripheral blood to the corresponding genotype of different disease-associated and T cell related SNPs. This revealed significantly increased frequencies of naive CD4+ T cells (CD4+ TN) and T helper 17 (TH17) cells in carriers of intergenic SNP rs56258221 (BACH2/MIR4464) as compared to non-carriers. Functional experiments identified CD4+ TN from SNP-carriers to rather polarize towards pro-inflammatory subsets than into regulatory T cells (TREG). *** Due to data privacy concerns fastq files have not been uploaded ***

2024-04-22 | E-MTAB-14013 | biostudies-arrayexpress

SNP microarray-based PGS significantly improves the clinical outcome for translocation carriers

Project description:This was a retrospective comparison study of SNP-based preimplantation genetic screening (SNP-PGS) and FISH-based preimplantation genetic diagnosis (FISH-PGD) for 575 couples in total with chromosome translocations, including 169 couples treated by SNP-PGS between October 2011 and August 2012, and 406 couples treated by FISH- PGD between January 2005 and October 2011. In total, 773 blastocysts obtained from 169 couples were biopsied and frozen, embryo transfer was carried out on the balanced embryos. The PGS results and pregnancy outcomes were compared with those of FISH-PGD for 406 translocation carriers with 3,968 embryos biopsied on day 3. Of the 773 biopsied blastocysts, reliable SNP-PGS results were obtained for 717 (92.76%). For Robertsonian translocation carriers, the rate of normal/balanced embryos, embryos with translocation-related abnormalities, and embryos with abnormalities unrelated to a translocation were 57.80%, 23.39% and 18.81%, respectively. In reciprocal translocation carriers, the rate of normal/balanced embryos, embryos with translocation-related abnormalities and embryos with abnormalities unrelated to translocation were 35.47%, 52.10% and 12.42%, respectively. There was no significant differences in patient age, basal endocrine level and the average number of retrieved oocytes and good quality day 3 embryos before biopsy in the SNP-PGS group compared with the FISH-PGD group. The number of embryos biopsied in the FISH-PGD group was higher than in the SNP-PGS group. However, the pregnancy rate with successful delivery per oocyte retrieval and the implantation rate were both lower in the FISH-PGD group than in the SNP-PGS group. The spontaneous abortion rate was higher in the FISH-PGD group than in the SNP-PGS group. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from trophectoderm cells.

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Glioma Proteome explored by LC/MS/MS

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