4986 results for "*oma"

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• Hepatocellular Carcinoma Spatial transcriptomics Data Access Committee

  This is the DAC for study ST HCC

  Dac EGAC50000000635

• Comprehensive genetic landscape, immune checkpoint profiling, and establishment of patient-derived xenograft (PDX) of metachronous brain tumors from constitutive mismatch repair deficiency with a biallelic variant on MSH6

  Constitutional mismatch repair deficiency (CMMRD) syndrome is a rare genetic disorder caused by biallelic pathogenic variants in mismatch repair genes (PMS2, MSH6, MLH1, or MSH2) resulting in the development of a variety of different tumors, including brain neoplasms. This study molecularly characterized a Brazilian child with CMMRD, harboring two metachronous brain tumors (medulloblastoma and high-grade glioma), and established a patient-derived xenograft (PDX) of the CMMRD-associated brain tumor. Keywords: Brazil, Constitutional mismatch repair deficiency syndrome, exome, MSH6, medulloblastoma, high-grade glioma.

  Study EGAS50000000351

• TTFields Glioblastoma Data Access Committee, Charité – Universitätsmedizin Berlin

  This Data Access Committee is responsible for reviewing and approving data access requests for genomic and associated clinical data from patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. The DAC ensures that any data use is consistent with the patients’ informed consent, the study’s ethical approval and applicable data protection regulations. Approved applicants may use the data only for biomedical research on brain tumours and related methods, must not attempt re-identification of participants, and may not share the data with unauthorized third parties

  Dac EGAC50000000843

• Recurrent COPA mutation drives R-spondin-independent Wnt activation in intestinal tumors

  The majority of intestinal tumors harbor mutations in canonical Wnt pathway genes such as APC, whereas the lack of such alterations in a subset of tumors implies alternative tumorigenic routes. Here, we identify recurrent in-frame deletion in COPA, frequently co-occurring with USP9X truncating mutation, in small intestinal adenoma and adenocarcinoma. Patient-derived and CRISPR-engineered small intestinal organoids carrying COPA in-frame deletions exhibit R-spondin-independent yet Wnt ligand-dependent growth, maintaining LGR5 expression without canonical Wnt drivers. Mechanistically, COPA mutation stabilizes frizzled co-receptor LRP6 irrespective of R-spondin, sustaining Wnt pathway activation under growth factor-restricted conditions. USP9X loss further potentiates this phenotype. Unlike canonical Wnt pathway members, COPA encodes the alpha-subunit of coatomer complex I, which engages in vesicle trafficking with little prior linkage to intestinal tumorigenesis. Our findings establish COPA mutation as a novel and atypical intestinal tumor driver and implicate USP9X loss as a cooperating lesion.

  Study JGAS000868

• DAC for study CMMRD–associated high-grade glioma

  This Data Access Committee (DAC) is responsible for de-identified, summarized somatic variant call data derived from paired tumor–blood Whole-exome sequencing of human samples in a glioma research study. Access requests are approved without additional restrictions and are granted solely for health-related research purposes.

  Dac EGAC50000000855

• Relapse CHL study

  Classical Hodgkin Lymphoma (CHL) is characterized by a complex tumor microenvironment (TME) that supports disease progression. While immune cell recruitment by Hodgkin and Reed–Sternberg (HRS) cells is well-documented, the role of non-malignant B cells in relapse remains unclear. Using single-cell RNA sequencing (scRNA-seq) on paired diagnostic and relapsed CHL samples, we identified distinct shifts in B cell populations, particularly an enrichment of naïve B cells and a reduction of memory B cells in early-relapse compared to late-relapse and newly diagnosed CHL. The enrichment of naïve B cells in early relapse biopsies was confirmed in independent validation cohorts using scRNA-seq and immunohistochemistry. Notably, naïve B cells in early-relapse samples exhibited high expression of LGALS9, an immunosuppressive molecule known to interact with T cell immunoglobulin and mucin domain 3 (TIM-3) on regulatory T cells (Tregs). Cell-cell interaction analysis revealed the importance of interactions between LGALS9+ naïve B cells and TIM-3+ Tregs in the early-relapse setting. Spatial analysis by imaging mass cytometry confirmed close proximity of LGALS9+ naïve B cells with TIM-3⁺ CD4⁺ T cells and HRS cells, pointing to their role in shaping an immunosuppressive niche. Our findings highlight a previously unrecognized population of LGALS9⁺ naïve B cells with immunoregulatory potential in early-relapse CHL and provide new insights into the spatial and transcriptional architecture of the relapsed TME in CHL.

  Study EGAS00001008222

• WES of Mino-VEN-R Mantle Cell Lymphoma Cells

  This project investigates the genetic basis of therapy resistance in mantle cell lymphoma (MCL) using whole exome sequencing (WES) of the Mino_VEN_R cell line, a model of resistance to pirtobrutinib, a non-covalent BTK inhibitor. Our study suggested that drug-tolerant persister (DTP) cells evade therapy through metabolic and phenotypic reprogramming. By analyzing the exome profile of resistant cells, this study aims to identify mutations associated with treatment escape and cellular plasticity. The findings will contribute to a better understanding of resistance mechanisms and support the development of more effective therapeutic strategies.

  Study EGAS50000001088

• RNAseq of MCL cell lines

  This study profiles the transcriptomic response of the Mino-VEN-R and Jeko-BTK-R mantle cell lymphoma (MCL) cell lines to pirtobrutinib (PBN) treatment using bulk RNA sequencing. Mino-VEN-R models drug-tolerant persister (DTP) cells that arise during exposure to non-covalent BTK inhibitors. Building on our recent findings that DTP cells undergo metabolic and phenotypic state transitions governed by TCA cycle reprogramming, this dataset aims to capture gene expression changes associated with treatment-induced plasticity. The results contribute to a broader multi-omic framework exploring mechanisms of resistance and therapeutic vulnerability in MCL.

  Study EGAS50000001087

• RNaseq of mantle cell lymphoma patient samples

  This study presents bulk RNA sequencing data from 78 clinical mantle cell lymphoma (MCL) samples. Following rigorous quality control and batch effect correction to account for sample type and redundancy, 62 samples from 59 patients were included in the final analysis. The transcriptomic profiles capture the molecular diversity across both solid and liquid tumor contexts and support investigations into the phenotypic plasticity and metabolic states of drug-tolerant persister (DTP) cells.

  Study EGAS50000001086

• Lymphoma_primary_patient_drug_perturbed_RNASeq_samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET-762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dac EGAC50000000578