{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Transcriptome Analysis"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001004809"],"host":["EGA"],"description":["EGA study EGAS00001004809"],"dataset_title":["Early breast cancer (WES)","Validated Single-cell RNA sequencing in early breast cancer","Early breast cancer (WGS)","CITE-seq of early breast cancer"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["primary breast cancer, malignant tumor of the breast, d230, Neoplasms, mammary neoplasm, Mammary Cancers, dTAFII250, Human Mammary Neoplasms, Tumor, EfW1, Human, dmTAF[[II]]230, Breast Malignant Tumor, dmTAF1, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], Taf230, Breast Tumor, responsivity, \"mammary tumor\" EXACT [CSP2005:2016-0671], breast tumor, cancer of the breast, DmF2, Fs(3)Hor, TAF250, lod, BC, reactivity, Mammary Neoplasms, malignant neoplasm of breast, Taf200, DmelCG2684, Human Mammary, dTAF[[II]]250, TFIID TAF250, cel, cell, Mammary Neoplasm, Mammary Carcinoma, Human Mammary Carcinomas, Taf1p, NTef2, Cancer of the Breast, dTAF250, cancer of breast, Malignant Tumor of Breast, Mammary, Mammary Cancer, TAF, Breast, mammary cancer, mammary tumor, Tumors, Cancer, Breast Carcinoma, Human Mammary Neoplasm, Carcinoma, dTAF[[II]]230, TAF[[II]]250, Breast Carcinomas, \"breast neoplasm\" EXACT [MTH:120], TAF200, l(3)84Ab, BG:DS00004.13, TAFII-250, TAF250/230, \"breast tumor\" EXACT [NCI2004_11_17:C2910], Cell, Fs(3)Sz11, dTAF230, Breast Malignant Neoplasm, TAFII250, Mammary Carcinomas, p230, Neoplasm, TAF[[II]]250/230, TFIID, Human Mammary Carcinoma, NOS, Malignant Neoplasm of Breast, Carcinomas, Taf[[II]]250, Breast Neoplasm, TAF[[II]]230, Immunotherapies, TAF[II]250, Cancers, Breast Malignant Neoplasms., \"mammary neoplasm\" RELATED [], CG17603, Lds, TAF[[II]], early, DmelCG17603, Taf250, breast cancer, SR3-5, Horka, Breast Tumors, Breast Cancer, CG2684, Breast Malignant Tumors, Fs(3)Horka, Cancer of Breast, response, cancer, TAF230, breast, TAF1"],"description_synonyms":["malignant tumor of the breast, Materials, T-cell surface antigen T4/Leu-3, Myeloid, PNT-P1, DmelCG17077, mammary neoplasm, Human Mammary Neoplasms, EY3-1, Pnt, Tumor, Cell Interactions, dmTAF[[II]]230, L3T4, png, Communications, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], responsivity, Ly-4, cancer of the breast, Cell-to-Cell, D-ets-2, 3520, Pnt-P1, BC, treatment, Mammary Neoplasms, malignant neoplasm of breast, increased, Gene Expressions, TFIID TAF250, Biopsies, cel, non-developmental growth of a unicellular organism, Cell to Cell Interaction, Human Mammary Carcinomas, metabolic process resulting in cell growth, PMNC, Communication, cancer of breast, malignant neoplasm, disease management, Therapies, cellular growth, myeloid cell, Malignancies, mammary cancer, Breast Malignant Neoplasms, Tumors, Therapy, Carcinoma, dTAF[[II]]230, \"breast neoplasm\" EXACT [MTH:120], SLEB2, T-cell surface antigen T4|Leu-3, metabolism resulting in cell growth, TAF200, D-Ets-2, ets94F, 0123/09, PMN cell, TAFII-250, TAF250/230, TAFII250, Interaction, Benign, non-developmental cell growth, Chemotherapy, Genetic Materials, NOS, dendroid, Malignant Neoplasm of Breast, PD1, Genetic Material, PD-1, Carcinomas, pntP2, Immunotherapies, Factors, Cell Communications, Pharmacotherapy, Pointed-P1, p32, T-cell surface glycoprotein CD4, Ets94F, dendriform, Benign Neoplasms, CD4mut, \"mammary neoplasm\" RELATED [], CG17603, TAF[[II]], Treatments, hPD-1, Malignant Neoplasms, ptd, Phenotypes, PntP2, white blood cell, hPD-l, breast cancer, Patient, Taf250, Material, SR3-5, PntP1, Breast Tumors, hSLE1, E(E2F)3D, Cells, Breast Malignant Tumors, Cistron, PNTP2, other neoplasm, tamo, cancer, PNTP1, TAF230, accessory, polymorphonuclear cell, PARK1, primary breast cancer, 0998/12, d230, PARK4, chemotherapy, Neoplasms, ETS2, Ets2, Benign Neoplasm, Mammary Cancers, Gene, dTAFII250, pharmacotherapy, Pharmacotherapies, EfW1, Malignant, Transcription Factor, supernumerary, Chemotherapies, Human, Breast Malignant Tumor, DMPOINT1A, pntegfr, 0608/07, dmTAF1, Breast Tumor, Taf230, Cell-to-Cell Interactions, \"mammary tumor\" EXACT [CSP2005:2016-0671], breast tumor, MAL, Drug Therapies, TAF250, reactivity, Taf200, NACP, Transcription, Human Mammary, dTAF[[II]]250, Genetic, pointed-RC, Malignancy, growth of cell, Cell Interaction, Mammary Neoplasm, cell, Mammary Carcinoma, Cell-to-Cell Interaction, Taf1p, Expressions, CD279, EK3-2, Cancer of the Breast, Neoplasias, dTAF250, l(3)07825, Malignant Tumor of Breast, Mammary, Mammary Cancer, Clients, CG17077, Expression, Breast, TAF, mammary tumor, l(3)j1B7, Myeloid Cell, Cancer, Breast Carcinoma, Human Mammary Neoplasm, TAF[[II]]250, Ets, Breast Carcinomas, Malignant Neoplasm, immune cell, Leu2, l(3)84Ab, BG:DS00004.13, function, Factor, \"breast tumor\" EXACT [NCI2004_11_17:C2910], Cistrons, Client, Cell, dTAF230, Breast Malignant Neoplasm, cell expansion, MT, Mammary Carcinomas, T-cell differentiation antigen L3T4, p230, Neoplasm, TAF[[II]]250/230, Human Mammary Carcinoma, TFIID, pnt-P1, pnt-P2, l(3)s118306, Taf[[II]]250, Breast Neoplasm, primary cancer, leucocyte, TAF[[II]]230, dendroidal, increased number, TAF[II]250, Cancers, Breast Malignant Neoplasms., malignant tumor, Drug, present in greater numbers in organism, Ets58AB, DmelCG17603, Therapeutic, Breast Cancer, PPP1R145, CD4, Cancer of Breast, Treatment, pharmacologic therapy, response, CD8, Interactions, Neoplasia, POINT, breast, TAF1, CG8705"],"additional_accession":[]},"is_claimable":false,"name":"BIOKEY: A single-cell catalogue of the dynamic changes underlying Checkpoint Immunotherapy response in Early Breast Cancer","description":"Checkpoint immunotherapy combined with neoadjuvant chemotherapy improves complete pathologic response in a subset of breast cancer patients. Here, we applied single-cell profiling to tumor biopsies collected before and during anti-PD1 therapy. One-third of tumors exhibited proliferative T-cells expanding along CD8+ or CD4+ lineages, which were either characterized by increased cytotoxicity and exhaustion or improved T-helper function, respectively. Lineage tracing in non-expanding tumors revealed at which point in the lineage T-cells were impaired, while gene expression modeling along these lineages revealed novel genes and underlying transcription factors involved in T-cell expansion. Interestingly, different dendritic and myeloid cell phenotypes could either stimulate or inhibit expanding T-cells, while cell-to-cell communication revealed an integrated immune context highly predictive of T-cell expansion, consisting of immune-stimulatory/-inhibitory interactions between cancer and various immune cell types. Our data yield unprecedented insights into the dynamic changes underlying checkpoint immunotherapy response in breast cancer.","dates":{"updated":"2021-04-12 10:49:16"},"accession":"EGAS00001004809","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001007058","EGAD00001007057","EGAD00001006608","EGAD00001007056","EGAC00001001808"]}}