{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["HiSeq X Ten;ILLUMINA, NextSeq 500;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003751"],"sample_count":["102"],"description":["EGA dataset EGAD00001003751"],"repository":["EGA"],"title":["Raw DNA and RNA data from breast cancer organoids, control samples and biopsies"],"pubmed_abstract":["Developing strategies to enhance cancer prevention is a paramount goal, particularly given recent concerns about surgical treatment of preinvasive states such as ductal carcinoma in situ. Promoting effective immunosurveillance by leukocytes that scan for nascent neoplastic transformations represents a potential means to achieve this goal. Because most breast cancers arise within the ductal epithelium, enhancing protective immunosurveillance will likely necessitate targeting one or more of the distinctive lymphocyte types found in these sites under normal conditions. Here, we have characterized the intraepithelial lymphocyte compartment of non-cancerous human breast tissue and identified a subset of T lymphocytes that can be pharmacologically targeted to enhance their responses to breast cancer cells. Specifically, Vδ2(+) γδ T cells were consistently present in preparations of mammary ductal epithelial organoids and they proliferated in response to zoledronic acid, an aminobisphosphonate drug. Vδ2(+) T cells from breast ductal organoids produced the antitumor cytokine IFNγ and efficiently killed bisphosphonate-pulsed breast carcinoma cells. These findings demonstrate the potential for exploiting the ability of Vδ2(+) γδ T cells to respond to FDA-approved bisphosphonate drugs as a novel immunotherapeutic approach to inhibit the outgrowth of breast cancers."],"pubmed_title":["Analysis of Immune Cells from Human Mammary Ductal Epithelial Organoids Reveals Vδ2+ T Cells That Efficiently Target Breast Carcinoma Cells in the Presence of Bisphosphonate."],"pubmed_authors":["Zumwalde Nicholas A NA, Haag Jill D JD, Sharma Deepak D, Mirrielees Jennifer A JA, Wilke Lee G LG, Gould Michael N MN, Gumperz Jenny E JE"],"name_synonyms":["Vasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, 225., MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["Controlling, Complete, preventive therapy, Whole Genome, Malignant Neoplasm, reference sample, whole blood, Malignancy, prophylaxis, Neoplasms, Complete Genome Sequencing, Benign Neoplasm, Genome Sequencing, Benign Neoplasms, Cancers, Tumor, Malignant, Organoid., Sequencing, prevention, Malignant Neoplasms, Neoplasias, preventive measures, whole transcriptome, Complete Genome, Benign, Organoid, control, Whole, Neoplasm, Malignancies, prevention and control, Neoplasia, Controlled, Cancer, Tumors"],"pubmed_title_synonyms":["Breast Carcinoma, Human Mammary Neoplasm, Carcinoma, Carcinoma of breast NOS, human being, Breast Carcinomas, determination, CANCER, carcinoma of breast, BREAST, Neoplasms, Modern, number, Mammary Cancers, Human Mammary Neoplasms, Tumor, Cell, presence., Human, Breast Malignant Neoplasm, Breast Malignant Tumor, count in organism, Homo sapiens, epithelial, Mammary Carcinomas, Breast Tumor, chemical analysis, Neoplasm, Human Mammary Carcinoma, NOS, cancer of the breast, Carcinoma of the Breast, breast carcinoma, Mammary carcinoma, Malignant Neoplasm of Breast, Man, epitheliocyte, Carcinomas, Mammary Neoplasms, Human Mammary, Breast Neoplasm, Man (Taxonomy), Mammary Neoplasm, Carcinoma of breast NOS (disorder), Mammary Carcinoma, Human Mammary Carcinomas, Cancers, human, Cancer of the Breast, CA - Carcinoma of breast, Carcinoma of Breast, Organoid, breast cancer, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, Modern Man, Breast Tumors, Breast Cancer, Breast Malignant Tumors, Carcinoma of breast (disorder), Cancer of Breast, assay, Breast, cancer, Breast Malignant Neoplasms, breast, Tumors, Cancer"],"pubmed_abstract_synonyms":["malignant tumor of the breast, Breasts, Product, CGP 42446A, Lactiferous gland, mammary neoplasm, Human Mammary Neoplasms, Tumor, glandula mammaria, Mucosal T Lymphocyte, prevention, intraepithelial T cell, ductal epithelium, T Lymphocyte, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], Pharmaceutical Product, symptoms, Atypical Ductal, cancer of the breast, Intraepithelial T Lymphocyte, prevention and control, treatment, average, BC, Mammary Neoplasms, malignant neoplasm of breast, Dendritic Epithelial T Cell, Man (Taxonomy), Tissue, Human Mammary Carcinomas, SCAN, preventive measures, CA - Carcinoma of breast, T Cells, Organoid, malignant neoplasm, cancer of breast, medicine, Pharmaceutical, disease management, Therapies, Intraepithelial T Lymphocytes, Carcinoma of breast (disorder), Malignancies, Lymphoid, Gamma Delta T Lymphocytes, mammary cancer, Gamma Delta T Lymphocyte, Breast Malignant Neoplasms, Tumors, mamma, Therapy, Ductal Hyperplasias, screening, Carcinoma, Noninfiltrating Intraductal Carcinoma, preventive therapy, Hyperplasia, \"breast neoplasm\" EXACT [MTH:120], Zoledronate, CANCER, Dendritic Epithelial T Cells, Modern, Intraductal, Benign, breast ductal carcinoma in situ, Hyperplasias, epithelial, Lobe of mammary gland, Ductal Hyperplasia, Corpuscles, IEL, NOS, Lymphoid Cell, simple tissue, Pharmaceutic, breast carcinoma, CGP-42'446, Mammary carcinoma, Malignant Neoplasm of Breast, Carcinomas, Blood Cell, Intraductal Carcinoma, Mucosal T Cells, CGP42446, Gamma Delta T Cell, signs, Benign Neoplasms, White Blood Corpuscles, \"mammary neoplasm\" RELATED [], CGP-42446, Treatments, human, Malignant Neoplasms, White Blood Cells, Corpuscle, intraepithelial T-cell, breast cancer, Breast Tumors, Cells, Breast Malignant Tumors, White, T Cell, Blood Corpuscles, cancer, Mucosal T Lymphocytes, mammary region, primary breast cancer, Carcinoma of breast NOS, CGP 42'446, human being, Neoplasms, BREAST, Benign Neoplasm, Intraepithelial T Cell, Goal, Mammary Cancers, CGP 42446, Malignant, White Blood Corpuscle, Human, Breast Malignant Tumor, Atypical Ductal Hyperplasia, Homo sapiens, Breast Tumor, \"mammary tumor\" EXACT [CSP2005:2016-0671], breast tumor, Ductal Carcinoma In Situ, Carcinoma of the Breast, Zometa, Atypical, Blood Corpuscle, Man, Drugs, Human Mammary, Malignancy, Mammary Neoplasm, Carcinoma of breast NOS (disorder), Mammary Carcinoma, Noninfiltrating Intraductal, mammary part of chest, Intraepithelial Lymphocyte, Cancer of the Breast, Neoplasias, drugs, Malignant Tumor of Breast, Mammary, Mammary Cancer, Intraepithelial T Cells, intraepithelial lymphocyte, Preparation, Breast, T Lymphocytes, mammary tumor, Lymphocyte, Cancer, Pharmaceuticals, Products, Breast Carcinoma, Human Mammary Neoplasm, 2-(Imidazol-1-yl)-1-hydroxyethylidene-1, Leukocyte, Breast Carcinomas, findings, Malignant Neoplasm, carcinoma of breast, drug, Gamma Delta T Cells, Medications, \"breast tumor\" EXACT [NCI2004_11_17:C2910], Brustdruese, Cell, Atypical Ductal Hyperplasias, Breast Malignant Neoplasm, duct epithelium, Mucosal, MT, Cytokine, Mammary Carcinomas, Neoplasm, Human Mammary Carcinoma, Zoledronic Acid Anhydrous, Lymphoid Cells, epitheliocyte, Blood Cells, Noninfiltrating Intraductal Carcinomas, primary cancer, Breast Neoplasm, CGP42'446, Pharmaceutic Preparations, prophylaxis, 1-bisphosphonic acid, Lobe of breast, Noninfiltrating, Lymphocytes, Cancers, malignant tumor, Drug, Mucosal T Cell, Preparations, Carcinoma of Breast, Therapeutic, breast., control, Intraepithelial, Modern Man, Breast Cancer, White Blood, Treatment, Cancer of Breast, DCIS, Pharmaceutical Products, White Blood Cell, Neoplasia, breast, Intraductal Carcinomas, Pharmaceutical Preparation"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-UMCU-14-09-2017-12:12:35:225-409 - samples","description":"Whole genome sequencing data for primary tumors, matching control material from blood and their corresponding organoid.\nWhole transcriptome data for organoids.","dates":{"updated":"2020-09-22 11:26:00"},"accession":"EGAD00001003751","cross_references":{"TAXONOMY":["9606"],"pubmed":["26811335"],"EGA":["EGAC00001000432","EGAS00001002158"]}}