Project description:We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3’ and/or 5’ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5’ differences and in support of this we report that a 5’ isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5’ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes
Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.
Project description:Approximately 1% of chronic lymphocytic leukemia (CLL) cases harbor a translocation juxtaposing the immunoglobulin heavy chain (IGH) and B-cell lymphoma 3 (BCL3) loci. Aiming at comprehensive molecular characterization of IGH::BCL3-positive B-cell neoplasms we here investigated samples from 84 patients using FISH, whole genome and targeted sequencing and DNA methylation analyses. Junctional sequences obtained in 27 patients showed breakpoints upstream of BCL3 in all CLL cases. IGH breaks were presumably driven by aberrant class-switch recombination in 26/27 cases, frequently involving IGHA (12/26). Notably, 95% (78/82) of patients carried an unmutated IGHV with significant CLL stereotype subset #8 enrichment. Trisomy 12 (61%, 51/83) and mutations affecting NOTCH1 (32%, 25/79), BRAF (14%, 11/79) and FBXW7 (14%, 11/79) were frequent aberrations. DNA methylation analysis assigned 77% (51/66) of patients with IGH::BCL3-translocation with at least 60% tumor cell content to the naive B-cell-like group but unraveled a distinct and during follow-up stable signature resembling in part plasma cell-like epigenetic features. A binary DNA methylation classifier using 20 CpGs could distinguish IGH::BCL3-translocated CLL samples from other CLL subtypes. In an efficacy cohort of 3832 previously untreated patients from GCLLSG trials, IGH::BCL3 was associated with shorter progression-free survival (PFS) and overall survival (OS) in 28 patients when treated with chemoimmunotherapy, but not in those receiving venetoclax. Our findings highlight the genetic and epigenetic homogeneity of IGH::BCL3-translocated CLL samples and their differences from other types of CLL suggesting IGH::BCL3 leukemic B-cell neoplasms to be a biological distinct subtype of CLL.
