Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA272408 | ENA |
REPOSITORIES: ENA
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Project description:Rosette-forming glioneuronal tumour (RGNT) of the IV ventricle is a very recent entity, recognized in the latest WHO classification of Central Nervous System Tumors. It is composed by two distinct features: a glial component, with typical characteristics of pilocytic astrocytoma, and a component forming neurocytic rosettes, with eosinophilic regions positive for synaptofisin and/or perivascular rosettes. Herein, we describe a 33-year-old man with RGNT arising in a peculiar location, namely the spinal cord. We further performed an extensive immunohistochemistry and molecular analysis, using array-CGH (aCGH), whole exome and cancer-related hotspot sequencing, in order to better understand its underlying biology. The histology revealed a WHO grade I RGNT typically found in the fourth-ventricle. Immunoreactivity for synaptophysin and neurofilament protein was noted in the neurocytic component, whereas the glial component exhibited positivity for GFAP and S-100. Neurocytic component was found negative for GFAP. Mitoses were rare, and there was no necrosis present. Across all mutational analyses, there were detected somatic mutations in 4 genes: MLL2, CNNM3, PCDHGC4 and SCN1A. The tumor exhibited a microsatellite stable (MSS) phenotype. Array-CGH (aCGH) showed loss in 1p and gain of 1q, as well as gain of the whole chromosomes 7, 9 and 16. Moreover, we observed focal gains/losses in the chromosomes 1, 2, 3, 6, 7, 11, 14, 17, 22 and 23. Local amplifications in 9q34.2 (region with no genes mapped) and 19p13.3 (region encompassing the gene SBNO2) were identified. Additionally, we verified the KIAA1549-BRAF fusion, typically found in pilocytic astrocytomas, through aCGH, RT-PCR and FISH. Our comprehensive molecular profiling of a RGNT case suggests the existence of a unique genetic pathway for the development of these tumors: KIAA1549-BRAF fusion is a possible driver by constitutively activating MAPK pathway, and MLL2 mutation may lead to profound changes in the methylome. Taken together, these mechanisms may increase survival and/or tumorigenic capacity of cells, leading to the development of this rare entity. Two-color Agilent 8x60K array CGH (aCGH) was performed in the rosette-forming glioneuronal tumour (CY3) and reference DNA (CY5 - DNA extracted from leucocytes of the patient).
2015-07-13 | E-GEOD-64891 | biostudies-arrayexpress
Project description:Rosette-forming glioneuronal tumour (RGNT) of the IV ventricle is a very recent entity, recognized in the latest WHO classification of Central Nervous System Tumors. It is composed by two distinct features: a glial component, with typical characteristics of pilocytic astrocytoma, and a component forming neurocytic rosettes, with eosinophilic regions positive for synaptofisin and/or perivascular rosettes. Herein, we describe a 33-year-old man with RGNT arising in a peculiar location, namely the spinal cord. We further performed an extensive immunohistochemistry and molecular analysis, using array-CGH (aCGH), whole exome and cancer-related hotspot sequencing, in order to better understand its underlying biology. The histology revealed a WHO grade I RGNT typically found in the fourth-ventricle. Immunoreactivity for synaptophysin and neurofilament protein was noted in the neurocytic component, whereas the glial component exhibited positivity for GFAP and S-100. Neurocytic component was found negative for GFAP. Mitoses were rare, and there was no necrosis present. Across all mutational analyses, there were detected somatic mutations in 4 genes: MLL2, CNNM3, PCDHGC4 and SCN1A. The tumor exhibited a microsatellite stable (MSS) phenotype. Array-CGH (aCGH) showed loss in 1p and gain of 1q, as well as gain of the whole chromosomes 7, 9 and 16. Moreover, we observed focal gains/losses in the chromosomes 1, 2, 3, 6, 7, 11, 14, 17, 22 and 23. Local amplifications in 9q34.2 (region with no genes mapped) and 19p13.3 (region encompassing the gene SBNO2) were identified. Additionally, we verified the KIAA1549-BRAF fusion, typically found in pilocytic astrocytomas, through aCGH, RT-PCR and FISH. Our comprehensive molecular profiling of a RGNT case suggests the existence of a unique genetic pathway for the development of these tumors: KIAA1549-BRAF fusion is a possible driver by constitutively activating MAPK pathway, and MLL2 mutation may lead to profound changes in the methylome. Taken together, these mechanisms may increase survival and/or tumorigenic capacity of cells, leading to the development of this rare entity.
2015-07-13 | GSE64891 | GEO
Project description:Genome and transcriptome sequence data from a rosette-forming glioneuronal tumor (RGNT) patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study
| EGAD00001015320 | EGA
Project description:Glioneuronal tumor with CLIP2-MET fusion: A case report
| PRJNA597892 | ENA
Project description:We report an infantile case of midline ‘supratentorial ependymoma ZFTA fusion-positive’ involving both the infra- and the supra-tentorial compartments (i.e., cerebellar vermis, pons and midbrain). The radiological features, i.e., the upward displacement and compression of the supratentorial anatomical structures and the infiltrative margins of the tumour towards the cerebellar vermis, suggested an infratentorial origin of the lesion with secondary involvement of the supratentorial compartment. This case adds to the limited literature of non-hemispheric ‘supratentorial ependymoma ZFTA fusion-positive’ occurring in midline structures, both supratentorial (pineal region, thalamus) and infratentorial (cervico-medullary region and spinal cord), and in the cerebellum. These cases highlight the need to consider this entity in the differential diagnosis of paediatric non-hemispheric lesions and raise the question of whether the inclusion of the location within the WHO definition of this tumour type may be too restrictive
2023-01-01 | GSE220932 | GEO
Project description:Genome-wide DNA methylation profiling of 30 low-grade neuroepithelial tumors with FGFR1 alterations including rosette-forming glioneuronal tumor, pilocytic astrocytoma, dysembryoplastic neuroepithelial tumor, and extraventricular neurocytoma. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 30 low-grade neuroepithelial tumors with FGFR1 alterations including kinase domain tandem duplication, in-frame fusion with TACC1, and hotspot missense mutation within the intracellular tyrosine kinase domain.
2020-08-19 | GSE152653 | GEO
Project description:Glioneuronal tumor (GN) is one type of biphasic central nervous system (CNS) tumor that exhibits both glial and neuronal immunohistological characteristics. We report a case of glioneuronal tumor (GN) with a discovery of novel gene fusion of CLIP2-MET resulting from aberrant chromosome 7 abnormalities. The tumor exhibited typical characteristics on histological examinations. We executed an elaborate genomic study on this case including whole-exome sequencing and RNA sequencing. Genomic analysis of the tumor revealed aberrations in chromosomes 1 and 7 and a CLIP2-MET fusion. Further analysis of the upregulated genes revealed substantial connections with MAPK pathway activation. We concluded that the chromosome 7 abnormalities prompted CLIP2-MET gene fusion which successively leads to MAPK pathway activation. We deliberated that MAPK pathway activation is responsible for the oncogenesis of GN based on our case and other previously reported ones.
2019-12-28 | GSE142668 | GEO
Project description:Rosette-forming marine heterotroph
| PRJNA18315 | ENA
Project description:Among the vertebrates, teleost and urodele amphibians are capable of regenerating their central nervous system. We have used crush injury method on zebrafish spinal cord, which is a common mammalian mode of injury in spinal cord. To identify the molecular mechanisms of the underlying cellular events during regeneration of zebrafish spinal cord, we have employed high density oligonucleotide microarrays and profiled the temporal transcriptome dynamics during the entire phenomenon. A total of 3842 genes expressed differentially with significant fold changes during spinal cord regeneration. Cluster analysis revealed event specific dynamic expression of genes related to inflammation, cell death, cell migration, cell proliferation, neurogenesis, neural patterning and axonal regrowth. We have also validated the expression pattern of 14 genes (which include inflammatory regulators, cell cycle regulators, pattern forming genes and signaling molecules) by different methodologies. Spatio-temporal analysis of STAT3 expression suggested its possible function in controlling inflammation and cell proliferation. Genes involved in the proliferating neural progenitors and their dorso-ventral patterning (sox2 and dbx2) are differentially expressed. Injury induced cell proliferation is controlled by many cell cycle regulators and some of them also show their common expression in other regenerating systems like fin, heart and retina. We also reported unusual expression pattern of certain pathway genes like one carbon folate metabolism and N-glycan biosynthesis which have not been reported during regeneration of spinal cord. Genes like stat3, socs3, atf3, mmp9 and sox11, which are known to control peripheral nervous system (PNS) regeneration in mammals, are also upregulated in zebrafish spinal cord injury (SCI) thus creating PNS like environment after injury. Our study provides a comprehensive genetic blue print of diverse cellular response(s) during regeneration of zebrafish spinal cord that could be used to induce successful regeneration in mammals. The spinal cord has been injured by crushing dorso-ventrally for 1 sec with a number 5 Dumont forceps at the level of 15th/16th vertebrae. Later the wound were sealed by placing a suture. Both spinal cord injured and sham operated fish were allowed to regenerate and the progress of regeneration was observed after 1, 3, 7, 10 and 15 days of injury. Zebrafishes were anesthetized deeply for 5 minutes in 0.1% tricaine (MS222; Sigma, USA) and approximately 1mm length of spinal cord both rostrally and caudally from injury epicenter were dissected out from 50-60 fishes in each batch and pooled for RNA extraction.
2012-12-01 | E-GEOD-39295 | biostudies-arrayexpress