5495 results for "*oma"

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• RASA2 deletion rescues immune synapse dysfunction, enhancing CAR T cell efficacy against DMGs

  Methods: We compared the efficacy of B7-H3 CAR T-cells between SJ-DIPGX7c (DMG) and U87-MG (adult glioblastoma) patient-derived cell lines and showed impaired efficacy both in vitro and in vivo. We performed live-cell imaging and single-cell RNA sequencing to investigate deficiencies in immune synapse (IS) formation between CAR T-cells and DMGs. Lastly, we genetically deleted RASA2, a negative regulator of T cell activation, and evaluated the resulting impact on IS formation and quality, as well as in vitro and in vivo functionality. Sample preparation and sequencing For single cell RNA sequencing, two sets of co-culture arrays were prepared: (1) 2.5×106 Ctrl T cells were co-cultured with 2.5×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG) and (2) 1×106 CAR T-cells were co-cultured with 4×106 tumor cells (SJ-DIPGX7c, SJ-DIPGX9c, SJ-DIPGX37c, D425, ST1, and U87-MG). Both co-culture arrays were incubated at 37°C 5% CO2 for 16 hours. Co-cultures were enzymatically digested with Accutase (Thermofisher; A1110501) for 10 min at room temperature, and cells were filtered by using Miltenyi dead cell removal kit (Miltenyi; 130-090-101). Highly viable cells were recovered and prepared using the Fixation Kit (PARSE Bioscience) according to manufacturer ‘s protocol. After fixation, the cell count was determined by using a Neubauer hemocytometer. A total of 1.14×105 cells from 12 coculture conditions were used, resulting in approximately 9.5×104 cells per condition. These cells were subjected to the Single Cell Whole Transcriptomic kit v2 (PARSE Bioscience) for library construction. Libraries were subsequently sequenced using the Illumina NovaSeq 6000 platform, generating paired-end 200 bp reads.

  Dataset EGAD50000002785

• CUP-COMP DAC

  The Carcinoma of Unknown Primary (CUP): A comparison across tissue and liquid biomarkers (CUP-COMP) study (NCT: NCT04750109) was sponsored by The Christie NHS Foundation Trust and funded by Innovate UK. Data generated include: A) Whole genome sequencing* of paired germline blood and tumour tissue B) Whole genome sequencing *of germline blood only C) Next-generation sequencing of circulating tumour DNA (FoundationOne Liquid CDX) D) Next-generation sequencing of tumour tissue (FoudationOne CDX) *Whole genome sequencing - germline sample at 30x coverage and somatic sample at 75x coverage performed by Illumina NovaSeq 6000 instrument in the 150bp PE read mode.

  Dac EGAC50000000610

• DAC policy The Kids Research Institute Australia

  DAC policy related to the study: Visium CytAssist Spatial Gene Expression analysis for FFPE glioblastoma samples. Committee: Raelene Endersby raelene.endersby@thekids.org.au Anya Jones anya.jones@thekids.org.au Emma Stone emma.stone@thekids.org.au

  Dac EGAC50000000734

• Multi-omic signatures in multiple myeloma

  Multiple myeloma (MM) is a genetically and clinically heterogeneous plasma-cell malignancy. Quadruplet therapy, combining anti-CD38 antibodies, immunomodulatory drugs, proteasome inhibitors, and dexamethasone, is now the standard induction treatment for newly diagnosed multiple myeloma (NDMM). To gain a comprehensive view of molecular changes in MM and their association with treatment response in this new standard care, we performed a multi-omic study of 423 NDMM from the MIDAS trial.

  Study EGAS50000001573

• Comprehensive gene expression analysis in renal cell carcinoma

  The goal is to elucidate the mechanisms of tumor initiation and progression, identify gene signatures associated with drug efficacy and adverse effects, and develop more accurate and reliable diagnostic methods and therapeutic targets.

  Study JGAS000913

• Investigating adaptive immune responses in MM patients treated with belantamab mafodotin

  We used single-cell CITE + VDJ sequencing and CapTCRseq to investigate the adaptive immune response, specifically the role of T cells and tumor-reactive gamma delta T cells, in multiple myeloma patients treated with belantamab mafodotin from the on-going Algonquin clinical trial (NCT03715478).

  Study EGAS50000001889

• Identification of broadly tumor-reactive γδ TCRs from multiple myeloma

  We used single-cell CITE + TCR sequencing to identify tumor-reactive gamma delta TCR sequences from multiple myeloma patient bone marrow samples.

  Study EGAS50000001888

• Single-cell sequencing of Belamaf treated MM patients

  Single-cell CITE + VDJ sequencing of bone marrow samples from relapsed/refractory multiple myeloma patients prior to and following one round (28 days) of treatment with belantamab mafodotin from the on-going Algonquin clinical trial (NCT03715478).

  Dataset EGAD50000002742

• Targeted bulk TCR sequencing of Belamaf treated MM patients

  Targeted bulk TCR sequencing from peripheral blood mononuclear cell (PBMC) and plasma cell-free DNA (cfDNA) samples from relapsed/refractory multiple myeloma patients being treated with belantamab mafodotin from the on-going Algonquin clinical trial (NCT03715478).

  Dataset EGAD50000002743

• Targeted bulk TCR sequencing of MM patients

  Targeted bulk TCR sequencing of longitudinally collected peripheral blood buffy coat samples from two multiple myeloma patients.

  Dataset EGAD50000002744

• Single-cell sequencing MM patients

  Single-cell CITE + VDJ sequencing of bone marrow samples collected from a mix of diagnosis and relapsed/refractory multiple myeloma patients undergoing standard of care treatment which were used for the development of PreGame.

  Dataset EGAD50000002745

• 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

• RNA-seq of adult T-cell leukemia-lymphoma patient-derived xenograft (PDX) models treated with the MALT1 protease inhibitor CRD-1441551

  To elucidate the therapeutic effect of MALT1 protease inhibition in adult T-cell leukemia/lymphoma (ATL), we performed RNA-seq on tumor tissues from five ATL patient-derived xenograft (PDX) models. NOG mice engrafted with each PDX model were treated with the MALT1 protease inhibitor CRD-1441551 or vehicle for 21 days, in biological triplicate (n = 3 per condition; 30 samples in total). Mouse-derived reads were removed and the remaining human reads were aligned to the human reference genome (hg19). These data underlie the gene-expression analyses reported in the associated publication.

  Study JGAS000921

• Impact of Mutated CTCF DNA binding sites of Topologically associating domains on nearby Cancer Gene Regulation: A Multi-Omics Analysis

  Cutaneous squamous cell carcinoma (cSCC) is the most common lethal malignancy world-wide. Due in most part to the extremely high mutational burden (TMB) in cSCC, making sense of it’s non-coding and regulatory regional genomic variation has lagged that of other far less common cancers. This study presents the first investigation of mutations at CCCTC-binding factor binding sites (CTCFbs) of Topologically associating domains (TAD) across defined cSCC progression stages—primary non-metastatic (PNM), primary metastat-ic (PM), and lymph node metastasis (LNM).

  Study EGAS50000001686

• CTCF Binding Site Mutations: Linking Topologically Associated Domains Dysregulation to Cutaneous Squamous Cell Carcinoma Progression

  Fresh tumor tissue from nodal metastases (n = 41) was harvested during surgery and immediately snap-frozen. A total of 72/75 cSCC, WGS samples were included in the analysis (refer to QC section), comprising primary tumors (both metastatic (PM (n = 16)) and non-metastatic (PNM (n = 15)), as well as lymph node metastases (LNM (n = 41)). The metastatic cohort included matched PM and LNM samples for 13 patients. The PNM group had to meet the following criteria: absence of metastases at > 24 months follow-up after resection of the primary or negative sentinel lymph node biopsy at time of resection or histologically negative neck dissection. Somatic variant analysis was performed using DRAGEN pipeline version 4.3.6 on the Illumina Connected Analytics (ICA) v2 environment using in house shell scripting. Tumor-normal paired analyses were carried out in three stages: alignment, variant calling, and integrative somatic analysis. Further information on the somatic calling is available at https://help.dragen.illumina.com/product-guides/dragen-v4.3/dragen-dna-pipeline/small-variant-calling/somatic-mode.

  Dataset EGAD50000002416

• IMC-F106C-101 dose escalation

  Brenetafusp is an ImmTAC bispecific (PRAME×CD3) targeting the cancer testis antigen PRAME. In this phase 1 study (NCT04262466), 126 HLA-A*02:01+ patients with advanced solid tumors received weekly IV doses from 0.3-320 mcg. The primary objective was to identify the maximum tolerated dose (MTD) or recommended phase 2 dose (RP2D); additional objectives included pharmacokinetics, pharmacodynamics, and preliminary anti-tumor activity. Brenetafusp demonstrated manageable safety and preliminary efficacy in PRAME+ tumors. A phase 3 trial in metastatic cutaneous melanoma is ongoing

  Study EGAS50000001976