8432 results for "canc*"

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• Colorectal Microenvironment Spatial Mapping

  In colorectal cancer (CRC), interactions between tumor and immune cells within the tumor microenvironment are critical drivers of tumorigenesis, immune evasion, prognosis, and therapeutic response. Therefore, a deeper understanding of the spatial organization of cancer and immune cells within the CRC microenvironment is urgently needed. In this study, we aimed to characterize distinct cell populations and patterns of spatial gene expression associated with CRC tumorigenesis and immune infiltration. Spatial transcriptomics (ST) was performed on CRC and adjacent normal tissues to investigate the patterns of gene expression. Integrative ST data and publicly available single-cell RNA sequencing (scRNA-seq) data analysis tools were used for data integration, dimension reduction, clustering, and differential expression analysis. This study identified novel immunosuppressive cell populations and immune regulatory factors in CRC. Further functional validation of these findings will be essential to assess their potential as therapeutic targets.

  Study EGAS00001008254

• Organoid_Derivation_Project___GRCh38___TGS

  Generation of normal and cancer organoids for sequencing as part of the WTSI-CRUK international collaboration with NCI (in HCMI) to generate the next generation of cancer cell lines.

  Study EGAS00001007349

• Endocrine therapy reprogramming of breast cancer facilitates metastatic escape via upregulation of P-Rex1/Rac1 signalling

  The estrogen receptor (ER) drives growth in ~70% of breast cancers, and endocrine therapies prevent recurrence. However, 30% of patients recur, with many fatal cases occurring late (after >5 years), presenting a challenge due to their often non-proliferative nature and limited options. To study this, we generated slow-growing resistant cells that form small primary tumours but readily metastasize. Single-cell RNA sequencing (scRNAseq) revealed that endocrine therapy reprograms these cells, notably upregulating the Rac1 signalling component P-Rex1. We found in clinical cohorts that P-Rex1 in high in ER+ breast cancer. Intravital imaging demonstrated that Rac1 signalling is active in ER+ cells following endocrine therapy. Targeting the Rac1 pathway with small molecule inhibitors (NSC23766, R-ketorolac) reduced survival and motility in resistant cells, inhibited in vivo Rac1 activity, and reduced tumour burden when combined with tamoxifen in a drug-refractory patient-derived xenograft. This work identifies the P-Rex1/Rac1 axis, as a potential therapeutic target for late recurring ER+ breast cancer.

  Study EGAS00001008353

• Single-cell RNA-seq of murine splenocytes from Bcl6tg/+ and Cd70-/-; Bcl6tg/+ diffuse large B-cell lymphoma mouse models and Cd70-/- and wild-type controls.

  Study EGAS00001007570

• Single-cell and spatial transcriptomic profiling of peritoneal metastasis of gastric cancer

  Peritoneal metastasis is associated with disease progression and poor prognosis in gastric cancer. This study uses single-cell RNA sequencing and spatial transcriptomics to characterize the cellular composition, tumor microenvironment heterogeneity, and potential therapeutic vulnerabilities in peritoneal metastasis of gastric cancer. Human peritoneal metastatic samples and humanized mouse models engrafted with human gastric cancer cells were analyzed to investigate tumor and immune microenvironment features.

  Study EGAS50000001875

• Single-cell analysis for metastatic gastric adenocarcinoma

  Intra-tumoral heterogeneity (ITH) is the fundamental property of cancer, however, the origins of ITH remain poorly understood. Here we performed single-cell RNA sequencing of peritoneal carcinomatosis (PC) from patients with advanced gastric adenocarcinoma (GAC), constructed a transcriptome map of 45,048 PC cells, profiled the transcriptome states of diverse tumor cell lineages and types, incisively explored ITH of PC tumor cells, and identified significant correlates with patient survival.

  Study EGAS00001004443

• Pan Prostate Cancer Group data

  The Pan Prostate Cancer Group intends to provide breakthrough advances from the analysis of a very large series of Whole Genome DNA data, contributed by many of the leading scientists and clinicians working in prostate cancer genomics generating Whole Genome DNA Sequence (WGS) data from prostate cancer patients. The accumulated data, collected and compared in a common format including common storage, re-analysis through a single pipeline, and investigation to achieve a variety of scientific goals, are presented in this series. This project will provide a global framework for the future analysis of even larger series of genomes as costs of DNA sequencing, storage, and sequence analysis decrease. In addition to these WGS data from different clinical categories, ethnicities, levels of aggressiveness, and disease managed by different treatments with information linked to long-term clinical follow up, we intend to add additional layers of data, including transcriptome and methylation data. The current data series focuses primarily on the analysis of WGS data. For further information, please refer to https://panprostate.org/, and The Pan Prostate Cancer Group Data Sharing Policy, EGAP00001003712.

  Study EGAS00001002876

• TLS-associated B cell repertoire shaping and response to immune checkpoint inhibitors in patients with renal cell cancer

  All raw and processed data necessary to reproduce main and supplementary figures related to the article. 4 datasets: Ig-inferred with MiXCR from bulk RNAseq of ccRCC tumors (n=95) ; Ig-targeted capture in bulk (Immunoverse) from ccRCC tumors & blood before and after treatment paired patient’ samples (n=96) ; Ig-targeted capture in spatial transcriptomics (SpatialVDJ) from ccRCC tumor sections (n=4) ; Ig-inferred with MiXCR in spatial transcriptomics from ccRCC tumor sections included in Meyan et al, 2022, Immunity paper (n=12). Scripts are available on GitHub (github.com/GuiPupier/Ig_TLS_ICI). Note that additional files not deposited in EGA are available in a complementary Zenodo repository (named "title - Additional files supporting the EGA submission").

  Study EGAS50000002165

• Structural Forms of ERBB2 Amplification and Their Clinical Significance in EAC Brain Metastases

  We characterized the genomic architecture, evolutionary history, and tumor microenvironment of EAC brain metastases from 65 patients using whole-genome sequencing, single-cell spatial transcriptomics, and ERBB2 fluorescence in situ hybridization. We retrospectively identified patients who underwent neurosurgical resection for brain metastases arising from esophageal adenocarcinoma. Whole-genome sequencing was performed using a hybrid strategy that combined Oxford Nanopore long-read sequencing with Illumina short-read sequencing to enable high-resolution detection of copy number alterations and complex structural variants. This study identifies ERBB2 amplification as a dominant genomic feature of esophageal adenocarcinoma brain metastases and demonstrates that the structural organization of this amplicon is associated with clinical behavior.

  Study EGAS50000001593

• Germline ALK variant in patient with neurodisability and neuroblastoma

  Anaplastic Lymphoma Kinase (ALK) is a transmembrane receptor tyrosine kinase involved in nervous system development. Germline ALK mutations are the commonest cause of hereditary neuroblastoma, usually without a neurodevelopmental phenotype. We report a child with congenital low- risk neuroblastoma, developmental delay, feeding difficulties, poor growth and a de novo heterozygous, germline F1174L ALK mutation. The child was treated with the 3rd generation ALK inhibitor lorlatinib from 6 years of age, with marked symptom improvement. To our knowledge this is the first report of both this germline ALK mutation and use of an ALK inhibitor to treat the associated phenotype.

  Study EGAS50000001885