Glioneuronal tumor with CLIP2-MET fusion: A case report
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ABSTRACT:
PROVIDER: PRJNA597892 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10775585_1.fastq.gz | Fastqsanger.gz | |||
| SRR10775585_2.fastq.gz | Fastqsanger.gz | |||
| SRR10775586_1.fastq.gz | Fastqsanger.gz | |||
| SRR10775586_2.fastq.gz | Fastqsanger.gz | |||
| SRR10775587_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:Oncogenic gene fusions have been identified in many cancers and many serve as biomarkers or targets for therapy. Here we identify six different melanocytic tumors with genomic rearrangements of MET fusing the kinase domain of MET in-frame to six different N-terminal partners. These tumors lack activating mutations in other established melanoma oncogenes. We functionally characterize two of the identified fusion proteins (TRIM4-MET and ZKSCAN1-MET) and find that they constitutively activate the mitogen-activated protein kinase (MAPK), phosphoinositol-3 kinase (PI3K), and phospholipase C gamma 1 (PLCγ1) pathways. The MET inhibitors cabozantinib (FDA-approved for progressive medullary thyroid cancer) and PF-04217903 block their activity at nanomolar concentrations. MET fusion kinases thus provide a potential therapeutic target for a rare subset of melanoma for which currently no targeted therapeutic options currently exist.
2015-12-01 | GSE67841 | GEO
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).
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Project description:Purpose: Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8% cases). A 2-month-old female patient presented with a mass arising in the fibula which was excised at our surgical center. This is only the eighth case of MNTI affecting an extremity, and the first reported in the fibula. To understand better the etiology of this MNTI, we used high-throughput sequencing technology to carry out an exhaustive genomic, transcriptomic and epigenetic characterization on the excised primary tumor and a derived cell line. Methods: RNA was extracted from the flash frozen tumor and paired-end RNA-Seq was performed to identify potential oncogenic fusion genes and to quantify gene expression in the MNTI transcriptome. Genomic DNA was extracted from the tumor and from a sample of the patient's blood and whole-exome sequencing was done to detect somatic and germline variants. Copy number variation in the MNTI was determined by comparative genomic hybridization (CGH) of DNA from the tumor and blood to a SNP array. A cell line was derived from the tumor and was tested for sensitivity to a panel of compounds targeting epigenetic regulators. Results: Whole-exome analysis indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16INK4A, D74A). SNP-array CGH revealed the tumor to be euploid, with no detectable gene copy number variants. Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells (GEO acession: GSE28875) and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed. Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. The derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators. Conclusions: In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case.
2016-08-29 | GSE84430 | GEO
Project description:Purpose: Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8% cases). A 2-month-old female patient presented with a mass arising in the fibula which was excised at our surgical center. This is only the eighth case of MNTI affecting an extremity, and the first reported in the fibula. To understand better the etiology of this MNTI, we used high-throughput sequencing technology to carry out an exhaustive genomic, transcriptomic and epigenetic characterization on the excised primary tumor and a derived cell line. Methods: RNA was extracted from the flash frozen tumor and paired-end RNA-Seq was performed to identify potential oncogenic fusion genes and to quantify gene expression in the MNTI transcriptome. Genomic DNA was extracted from the tumor and from a sample of the patient's blood and whole-exome sequencing was done to detect somatic and germline variants. Copy number variation in the MNTI was determined by comparative genomic hybridization (CGH) of DNA from the tumor and blood to a SNP array. A cell line was derived from the tumor and was tested for sensitivity to a panel of compounds targeting epigenetic regulators. Results: Whole-exome analysis indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16INK4A, D74A). SNP-array CGH revealed the tumor to be euploid, with no detectable gene copy number variants. Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells (GEO acession: GSE28875) and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed. Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. The derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators. Conclusions: In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case.
2016-08-29 | GSE84428 | GEO
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