5526 results for "*oma"

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• Single-cell tracking reveals tumor-reactive T cell plasticity during melanoma TIL therapy

  Using 10x genomics 5' Single Cell Immune Profiling kit for single-cell RNA and TCR sequencing, we tracked the transcriptional alterations and fate decisions of tumor-reactive T cells through longitudinal sample obtained from patients undergo-ing TIL therapy. We performed single-cell RNA and single-cell TCR sequencing (scRNA-seq and scTCR-seq) of CD45+ CD3+ tumor-infiltrating lymphocytes from the baseline tumor (pre-ACT), during and after TIL expansion protocol (intermediate product and TIL product, respectively), as well as after cell transfer in blood (PBMC 7dpt) or from metastatic lesions (post-ACT). Samples were derived from patients enrolled in a phase I clinical trial (NCT04165967) that inves-tigated ACT-TIL therapy in combination with nivolumab therapy for metastatic melanoma. Additionally, we established a tumor reactivity assay by co-culturing TIL products with autologous single-cell suspensions of tumor material or short cultured primary melanoma cell lines derived from the tumor material. Reactive T cells were identified by IFNɣ and TNF⍺ expression and sorted to sequence TCRβ genes.

  Study EGAS50000000967

• Single cell RNA and TCR sequencing of adoptive cell transfer using tumor infiltrating lymphocyte.

  This dataset contains two experiments. 1) Single cell RNA and TCR sequencing of tumor infiltrating lymphocites from 7 patients across 5 timepoints: from the baseline tumor (pre-ACT, 7), during and after TIL expansion protocol (intermediate product and TIL product, respectively, 7 each), as well as after cell transfer in blood (PBMC 7dpt, 7) or from metastatic lesions after therapy (post-ACT, 1 patient with one leason and 4 patient with two lesions). Samples were derived from patients with metastatic melanoma which were enrolled in a phase I clinical trial (NCT04165967). The raw reads are available as compressed fastq files. 2) TCRb sequences of the bulk TIL product or TCRb reads derived from an in vitro coculturing assay of TIL product with autologous tumor material and subsequent isolation of IFNɣ and TNF⍺ positive T cells. For some patients multiple autologous tumor material sources could be tested including pre-ACT, post-ACT or tumor lesion derived cell lines. The raw reads are available as compressed fastq files.

  Dataset EGAD50000001408

• MDACC GBM Data Access Committee

  Retrospective global-omics analyses of an anti-PD-L1 treated cohort of newly diagnosed glioblastoma.

  Dac EGAC50000000477

• Transcriptomic characterization of breast cancer cells in a luminal-hybrid state

  Background: We have previously identified a subset of early human breast epithelial progenitors that, despite their luminal affiliation, are enriched for basal markers, including CD146 and keratin 14 (K14). This simultaneous presence of both lineages thus defines a luminal-hybrid state. As luminal progenitors are generally proposed as a cell of origin of breast carcinoma, we examined how cells within this luminal hybrid state relate to breast cancer malignancy. Findings: We first analyzed two patient-derived xenograft (PDX)-derived breast cancer cell lines by dividing cell populations based on CD146-expression by FACS and found that this marker defines a cellular state with increased expression of a selection of luminal hybrid markers, including KRT14. When subjecting the sorted cells to in vitro transwell filter analysis, CD146HI/K14HI luminal hybrid state cells were less invasive. Knocking out either CD146- or K14-expression by CRISPR/Cas9 on a CD146/K14-positive background did not affect the in vivo tumorigenic potential, nor the differentiation state. However, when subjecting the respective sorted populations to a soft agar colony formation assay or as in vivo xenografts, CD146HI/K14HI cells exhibited more growth and metastasis, suggesting that the luminal hybrid state contributes to malignant properties. Conclusions: Our findings demonstrate that multiple components of the luminal hybrid state provide distinct properties to tumor malignancy. The fact that breast cancer can reflect a significant part of the original breast gland differentiation hierarchy may add weight to the argument that the search for novel strategies for treating basal-like breast cancer should include manipulation of cellular differentiation states.

  Dataset EGAD50000002857

• Transcriptomics analysis of biopsy and resected material from HCC and matched non-tumor

  We hypothesize that pre-analytical handling such as surgery procedure and cold ischemia have significant effects on omics data derived from liver and liver tumor tissue that may confound classification of tumor subtypes of hepatocellular carcinoma. This study is aimed at revealing such effects by comparing resection samples with patient matched biopsy samples in a multi-omics analysis.

  Study EGAS50000001602

• FGFR2b Prevalence in Biliary Tract Cancers

  Patients with intrahepatic cholangiocarcinoma (iCCA) often have limited effective treatment options after first-line therapy. Actionable driver mutations are present in only a small subset of patients with iCCA; therefore, therapeutic strategies such as antibody–drug conjugates (ADCs) that do not exclusively rely on presence of specific oncogenic mutations may be particularly attractive. However, there is a critical lack of knowledge regarding prevalent and actionable cell-surface targets in iCCA. We applied a novel isoform-resolved proteogenomic discovery framework for profiling cell surface targets and identified FGFR2b, a splicing isoform of FGFR2, as a therapeutic target in iCCA that is highly-expressed, tumor-enriched, localized to the membrane, and associated with prognosis. FGFR2b is the dominant isoform in iCCA, and it was present in all patients with FGFR2 fusions. These findings provide a strong rationale for further research and therapeutic development of FGFR2b-targeted biologics, including therapeutic antibodies and ADCs, in iCCA.

  Study EGAS50000002012

• Tumoral immune microenvironment profiling in B-cell non-Hodgkin lymphoma stratifies patients in different prognostic groups

  Dac EGAC50000001065

• RNAseq and WES of CHC patients years before HCC development

  We conducted a nested case–control study within a prospective liver biopsy biobank at the University Hospital Basel. Patients with chronic hepatitis C (CHC) who developed hepatocellular carcinoma (HCC) during follow-up (index cases, CHC-HCC) were identified and 1:2 propensity score-matched to CHC controls without HCC (controls, CHC-nonHCC). Matching included clinical, demographic, and virological risk factors for HCC. Liver biopsies were analyzed using RNA and whole-exome sequencing.

  Dataset EGAD50000001591

• Targeted DNA sequencing of 60 non-Hodgkin lymphoma biopsies using a custom gene panel for hematological malignancies: raw (FASTQ) data

  Targeted DNA sequencing was performed on 60 non-Hodgkin lymphoma (NHL) samples using a custom next-generation sequencing panel targeting the coding regions of 190 genes recurrently mutated in hematological malignancies. Libraries were sequenced on an Illumina NovaSeq 6000 platform using 2 × 150 bp paired-end reads. The dataset includes the raw sequencing data (FASTQ files) for all 60 samples.

  Dataset EGAD50000002845

• scRNAseq and spatial transcriptomics data of melanoma samples

  Paired-end 10x single-cell RNA sequencing and Visium spatial transcriptomics data from samples derived from 11 melanoma patients. Sequencing was performed on the Illumina NovaSeq 6000 using 10xGenomics Chromium Next GEM Single-Cell 5 Reagent Kits v2 or 10xGenomics Visium Gene Expression kit.

  Dataset EGAD50000002902