EGAGenomicsCancer Genomicshttps://ega-archive.org/studies/EGAS00001006502EGAEGA study EGAS000010065027 samples RNA-seq raw data9 samples variant calling datarestrictedEGArosette, chemical analysis., leaf whorl, assay, determinationlambdatop, HBGFR, Stem Cells, dev, Oligodendrocyte, Profiles, Tumor, Diagnosis, Preoligodendrocyte, Grade I Astrocytomas, x1fgfr, Mutations, 5730420M11Rik, p110-alpha, DmelCG8318, dmTAF[[II]]230, Subependymal Giant Cell Astrocytoma, Malignant Gangliogliomas, CEK, type I, Cerebral Astrocytoma, symptoms, Pilocytic Astrocytoma, Whole Transcriptome, Transcriptome Sequencing, Eask, Tumor Microenvironments, notch, peripheral type, DNT of the cerebellum, Piloid astrocytoma, Fgf-r, FLG, rosette, SET, cek, CNS tumor, E030030H24Rik, TFIID TAF250, cel, Pre Oligodendrocytes, neoplasm of the central nervous system, leaf whorl, composition, Hspy, PMNC, Ax, fgfr-1, D17Mit170, Signatures, Astrocytoma, flg, BTL/FGFR2, DmelCG4299, MCAP, Fibrillary, set, Expression Signature, co, Xotch, grade I astrocytic tumour, childhood ganglioglioma, Protoplasmic Astrocytomas, Tk2, NECD, Diagnose, l(1)N, single organism signaling, Tumors, rosette-forming glioneuronal tumor, close to, screening, dTAF[[II]]230, Pilocytic, Chp, Oligodendrocyte Progenitor Cells, Cerebral Astrocytomas, Co, CGC cell, Exome, familial, TAF200, bFGF-R-1, PMN cell, Tl3, Tl2, Anaplastic, Diagnoses, DmIKKgamma, Postmortem, Benign, XFGFR-1, dIKK, Recklinghausen's disease, Expression Signatures, shd, Mixed Oligoastrocytomas, Expression Profile, fa, Grade I Astrocytoma, Complete Transcriptome, Gemistocytic Astrocytomas, HLA-DR-associated protein II, neural precursor cell, DI-2, FGFR-1, content, I-2Dm, IKK-gamma, signs, Grade III Astrocytomas, Benign Neoplasms, cerebellar granule neuron, Malignant Neoplasms, I-2PP1, Phenotypes, white blood cell, TAF-IBETA, clone 1.12, Taf250, Cells, Subependymal Giant Cell, Whole Exome Sequencing, Glioma, TAF-Ibeta, notch-1, l(3)00208, WSS, TAN1, other neoplasm, Protoplasmic, TAF230, Grade II Astrocytoma, HRTFDS, Neoplasms, number, dIKK-gamma, pilocytic, KAL2, Pleomorphic Xanthoastrocytomas, morphology, Cancer Microenvironment, Neural Stem, DmIKK-gamma, kal2, Screening, rosette-forming glioneuronal tumour, Antemortem, Juvenile Pilocytic Astrocytoma, bfgfr, Pre-Oligodendrocyte, l(1)Ax, anatomy, Complete, Exome Sequencings, dTAF[[II]]250, fgfr1, Oligodendrocyte Progenitor Cell, cell, FGFBR, Profile, Gangliogliomas, 2pp2a, Diagnoses and Examinations, Nf-1, NFNS, VRNF, Sequencing, CG10574, CG6714, Gemistocytic, Neoplasias, dTAF250, Whole Exome, 2PP2A, tumour cell, Xanthoastrocytoma, Whole, FGFR, OGD, tumor of the central nervous system, dSET, dSet, Intracranial Ganglioglioma, MCM, NF1, NF-1, nf1, von Reklinghausen disease, constitutitional genetic, Methylations, CT13012, neural progenitor cell, Cancer, Pilocytic Astrocytomas, 16-178, Antemortem Diagnoses, 16-55, FLT2, neuronal stem cell, findings, cou, Complete Exome Sequencings, grupo, Malignant Neoplasm, ogd, FLT-2, Precursor, Progenitor Cells, anon-EST:Liang-1.12, BG:DS00004.13, dtk2, compositionality, Cell, xfgfr1, N-SAM, dTAF230, near to, whole transcriptome, IKKgamma, Exome Sequencing, Lr, fgf-r, CWS5, I-2PP2A, chemical analysis, Gene Expression Signatures, Dm I-2, spl, Neoplasm, adult ganglioglioma, TAF[[II]]250/230, flt2, 1.1, oligodendrocyte/type-2 astrocyte progenitor cell, nd, Oligodendrocyte Precursor, Taf[[II]]250, leucocyte, Grade I, ensemble, Dmikkgamma, Intracranial Astrocytomas, Von Recklinghausen disease, neural stem progenitor cell, Childhood, Cancers, MFR, CG16910, CG32134, CT20816, Pre-Oligodendrocytes, caPI3K, CLOVE, signalling process, Nerven-Stammzelle, Mixed Oligoastrocytoma, Gene Expression Profiles, vicinity of, structure, Bra, Benign Gangliogliomas, O-2A/OPC, central nervous system neoplasm (disease), Dtk2, Fibrillary Astrocytoma, Microenvironments, hereditary, Neoplasia, IPP2A2, Antemortem Diagnosis, xnotch, determination, Feature, dFGFR, Gene Expression Profile, central nervous system tumor, histology, PI3K, Astrocytomas, composed of, neoplasm of central nervous system, CD331, Grade II Astrocytomas, NOTCH, DFGF-R1, p110alpha, Precursor Cell, anatomy and histology, Btl, IKKg, DFR2, KEY, Key, Gemistocytic Astrocytoma, neoplasm of CNS, me75, tumor cell, TAF-I, Complete Exome Sequencing, Whole Transcriptome Sequencing, type 1 neurofibromatosis, benign, Dfr-2, tumor of the CNS, T1, genetic, IGAAD, notch1-a, DmelCG10574, Astroglioma, Transcriptomes, Malignancies, MCMTC, EG:140G11.1, Flt-2, swb, Cancer Microenvironments, phapii, dysembryoplastic neuroepithelial tumour of cerebellum, Oligoastrocytoma, Expression Profiles, Astrocytic, CG8318, StF-IT-1, oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell, TAFII-250, TAF250/230, RGNT, Fgfr-1, central nervous system neoplasm, Gene Expression, TAFII250, grade I astrocytic neoplasm, Screenings, Stem Cell, grade I astrocytoma, Examinations and Diagnoses, Kenny, Gliomas, Postmortem Diagnosis, dNF1, neuronal precursor cell, Transcriptome Profiles, Diagnoses and Examination, xnotch1, Postmortem Diagnoses, Anaplastic Astrocytoma, histopathology, DmelCG32134, Childhood Cerebral, Protoplasmic Astrocytoma, XFGFRA2, CG4299, CNS neoplasm, Features, CG17603, TAF[[II]], Intracranial, DmelCG16910, SR3-5, c-fgr, inherited genetic, Fibrillary Astrocytomas, Transcriptome Sequencings, i2pp2a, n[fah], Neural Stem Cell, Gruppe, polymorphonuclear cell, Malignant Neoplasms., d230, Grade II, Complete Exome, Transcriptome Profile, Microenvironment, EG:163A10.2, Progenitor Cell, Benign Neoplasm, Gene, dTAFII250, neurofibromatosis, Malignant, EfW1, presence, PHAPII, NSC, dmTAF1, Taf230, Mass, HH2, Low, Oligodendrocyte Precursors, l(1)3Cb, neurale Stammzelle, dmIKKgamma, IKK[[gamma]], Cerebral, Progenitor, Oligodendrocyte Progenitors, Neural, TAF250, neural stem cell, study, flt-2, Intracranial Gangliogliomas, WES, Taf200, 0844/01, Malignancy, BFGFR, DmelCG3936, ipp2a2, Intracranial Astrocytoma, granule cell of the cerebellum, Childhood Cerebral Astrocytomas, dysembryoplastic neuroepithelial tumor of cerebellum, astrocytoma, Taf1p, dNotch, Oligodendrocyte Precursor Cell, Anaplastic Astrocytomas, X1FGFR, Juvenile Pilocytic, Grade III Astrocytoma, IKK, grupos, taf-ibeta, Characteristics, AW208770, NICD, TAF, Astrocytic Gliomas, FGFR1, Grade III, Childhood Cerebral Astrocytoma, TAF[[II]]250, Transcriptome, 6330412C24Rik, immune cell, igaad, D-FGFR, p110, l(3)84Ab, Precursors, Astrogliomas, Juvenile Pilocytic Astrocytomas, Examination and Diagnoses, Pleomorphic, group, Juvenile, neurofibromatosis type 1 microdeletion syndrome, count in organism, pilocytic astrocytoma, Characteristic, Benign Ganglioglioma, Mass Screenings, DmHD-311, p230, I2PP2A, Pleomorphic Xanthoastrocytoma, Ganglioglioma, TFIID, rare (European definition), Mixed, Gene Expression Signature, methylation, tumor of central nervous system, Precursor Cells, Complete Transcriptome Sequencing, TAF[[II]]230, distinct, tumor of CNS, Rest, brain/spinal cord tumor, Astrocytic Glioma, TAF[II]250, O2A/OPC, Malignant Ganglioglioma, Oligodendrocyte Progenitor, Progenitors, dSET/TAF-Ibeta, 2610030F17Rik, DmelCG17603, approaches, Preoligodendrocytes, AW494271, HD-311, assay, Signature, CG3936, AA407739, groupe, grade I astrocytic tumor, TAF1falseImmune microenvironment and lineage tracing help deciphering Rosette-forming GlioNeuronal Tumors: a multi-omic analysis of 9 casesRosette-forming GlioNeuronal Tumor (RGNT) is a rare central nervous system neoplasm containing two components, glial and neuronal. The delineation of histological diagnosis of RGNT from similar low-grade tumors such as pilocytic astrocytoma (PA) and ganglioglioma (GG) may be challenging. We performed here a comprehensive molecular analysis of a cohort of tumors with same histology features to identify molecular characteristics of RGNT. A cohort of 9 rosette-forming tumors histologically-diagnosed were analyzed at molecular level using multimodal approaches as Whole Exome Sequencing (WES), RNAseq and methylome. In our cohort, 3 tumors were plotted within the Methylation Class-RGNT (MC-RGNT) characterized by FGFR1 mutation associated with PIK3CA or NF1 mutations. Transcriptome analysis was performed in 7 cases. RNAseq identified a “Hot†and a “Cold†transcriptomic group; the latter includes the 3 MC-RGNT and 1 MC-Pilocytic Astrocytoma and exhibited a “Cold†immune tumor microenvironment in comparison with the “Hot†group. The distinct immune cell content of both groups was confirmed by quantitative immunostainings. Get Set Enrichment Analysis showed that the “Cold†group had upregulated NOTCH pathway and mainly oligodendrocyte precursor cell and neuronal phenotypes while the “Hot†group exhibited predominantly astrocytic and neural stem cell phenotypes. In silico deconvolution identified the cerebellar granule cell lineage as a putative origin and as the cell context to understand the effects of genetic alterations and NOTCH signaling. Histological diagnosis of rosette-forming tumors encompasses heterogeneous tumor entities. Our study identified distinct tumor cell contexts and microenvironments as key features to better understand and manage these neoplasms.2022-09-05 09:43:41EGAS000010065029606EGAD00001009266EGAD00001009265EGAC00001002814