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Wang Y, Huang J, Yin X, Xu Q, Sun Y, Yao Y, Xiong J. Development and validation of a 23-gene expression signature for molecular subtyping of medulloblastoma in a long-term Chinese cohort. Acta Neurochir (Wien) 2024; 166:72. [PMID: 38329556 DOI: 10.1007/s00701-024-05922-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 11/16/2023] [Indexed: 02/09/2024]
Abstract
PURPOSE Medulloblastoma is the most common childhood malignant brain tumor and is a leading cause of cancer-related death in children. Recent transcriptional studies have shown that medulloblastomas comprise at least four molecular subgroups, each with distinct demographics, genetics, and clinical outcomes. Medulloblastoma subtyping has become critical for subgroup-specific therapies. The use of gene expression assays to determine the molecular subgroup of clinical specimens is a long-awaited application of molecular biology for this pediatric cancer. METHODS In the current study, we established a medulloblastoma transcriptome database of 460 samples retrieved from three published datasets (GSE21140, GSE37382, and GSE37418). With this database, we identified a 23-gene signature that is significantly associated with the medulloblastoma subgroups and achieved a classification accuracy of 95.2%. RESULTS The 23-gene signature was further validated in a long-term cohort of 142 Chinese medulloblastoma patients. The 23-gene signature classified 21 patients as WNT (15%), 41 as SHH (29%), 16 as Group 3 (11%), and 64 as Group 4 (45%). For patients of WNT, SHH, Group 3, and Group 4, 5-year overall-survival rate reached 80%, 62%, 27%, and 47%, respectively (p < 0.0001), meanwhile 5-year progression-free survival reached 80%, 52%, 27%, and 45%, respectively (p < 0.0001). Besides, SHH/TP53-mutant tumors were associated with worse prognosis compared with SHH/TP53 wild-type tumors and other subgroups. We demonstrated that subgroup assignments by the 23-gene signature and Northcott's NanoString assay were highly comparable with a concordance rate of 96.4%. CONCLUSIONS In conclusion, we present a novel gene signature that is capable of accurately and reliably assigning FFPE medulloblastoma samples to their molecular subgroup, which may serve as an auxiliary tool for medulloblastoma subtyping in the clinic. Future incorporation of this gene signature into prospective clinical trials is warranted to further evaluate its clinical.
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Affiliation(s)
- Yuyuan Wang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai, 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Jianhan Huang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai, 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Xian Yin
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Qinghua Xu
- Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd, Hangzhou, 31100, Zhejiang Province, China
- Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Shanghai, 200092, China
| | - Yifeng Sun
- Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd, Hangzhou, 31100, Zhejiang Province, China
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, China
- Neurosurgical Institute of Fudan University, Shanghai, 200040, China
- Shanghai Clinical Medical Center of Neurosurgery, Shanghai, 200040, China
- Shanghai Key Laboratory of Brain Function and Restoration and Neural Regeneration, Shanghai, 200040, China
| | - Ji Xiong
- Department of Pathology, Huashan Hospital, Fudan University, No. 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
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das Chagas PF, de Sousa GR, Veronez LC, Martins-da-Silva A, Corrêa CAP, Cruzeiro GAV, Nagano LFP, Queiroz RGDP, Marie SKN, Brandalise SR, Scrideli CA, Tone LG, Valera ET. Identification of ITPR1 as a Hub Gene of Group 3 Medulloblastoma and Coregulated Genes with Potential Prognostic Values. J Mol Neurosci 2021; 72:633-641. [PMID: 34822110 DOI: 10.1007/s12031-021-01942-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/04/2021] [Indexed: 01/03/2023]
Abstract
The Group 3 Medulloblastoma (Grp3-MB) is an aggressive molecular subtype with a high incidence of metastasis and deaths. In this study, were used an RNA sequencing data (RNA-Seq) from a Brazilian cohort of MBs to identify hub genes associated with the metastatic risk. Data validation were performed by using multiple large datasets from MBs (GSE85217, GSE37418, and EGAS00001001953). DESeq2 package in R software was used to identify the differentially expressed genes (DEGs) in our RNA-Seq data. The DEGs data were accessed to construct the modules/graphs of co-expression and to identify hub genes through Cytoscape platform. The coregulated genes were enriched by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and the protein-protein interaction (PPI) network was visualized by Cytoscape. The Kaplan-Meier plotter and ROC curves were used to validate the diagnostic and prognostic values of specific biomarkers identified through this model. We identified that inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) as a downregulated hub gene, with a high diagnostic accuracy to Grp3-MBs and associated with tumor metastasis. In addition, we identified genes significantly correlated with ITPR1 that were associated with metastasis in Grp3-MB (ATP1A2, MTTL7A, and RGL1) and worst overall survival in MBs (ANTXR1 and RGL1). Our findings suggest that the ITPR1 hub gene is potentially involved in the metastatic process for Grp3-MB. Our data also provide evidence of targets that may serve as prognostic predictors and/or regulators for the metastatic process that maybe explored for further research of individualized therapy to Grp3-MBs.
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Affiliation(s)
- Pablo Ferreira das Chagas
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.
| | - Graziella Ribeiro de Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Luciana Chain Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Andrea Martins-da-Silva
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Carolina Alves Pereira Corrêa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luis Fernando Peinado Nagano
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Rosane Gomes de Paula Queiroz
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Cellular and Molecular Biology, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de SãoPaulo, São Paulo, SP, Brazil
| | | | - Carlos Alberto Scrideli
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.,Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.,Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
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Villegas-Ruíz V, Olmos-Valdez K, Castro-López KA, Saucedo-Tepanecatl VE, Ramírez-Chiquito JC, Pérez-López EI, Medina-Vera I, Juárez-Méndez S. Identification and Validation of Novel Reference Genes in Acute Lymphoblastic Leukemia for Droplet Digital PCR. Genes (Basel) 2019; 10:genes10050376. [PMID: 31108950 PMCID: PMC6562415 DOI: 10.3390/genes10050376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
Droplet digital PCR is the most robust method for absolute nucleic acid quantification. However, RNA is a very versatile molecule and its abundance is tissue-dependent. RNA quantification is dependent on a reference control to estimate the abundance. Additionally, in cancer, many cellular processes are deregulated which consequently affects the gene expression profiles. In this work, we performed microarray data mining of different childhood cancers and healthy controls. We selected four genes that showed no gene expression variations (PSMB6, PGGT1B, UBQLN2 and UQCR2) and four classical reference genes (ACTB, GAPDH, RPL4 and RPS18). Gene expression was validated in 40 acute lymphoblastic leukemia samples by means of droplet digital PCR. We observed that PSMB6, PGGT1B, UBQLN2 and UQCR2 were expressed ~100 times less than ACTB, GAPDH, RPL4 and RPS18. However, we observed excellent correlations among the new reference genes (p < 0.0001). We propose that PSMB6, PGGT1B, UBQLN2 and UQCR2 are housekeeping genes with low expression in childhood cancer.
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Affiliation(s)
- Vanessa Villegas-Ruíz
- Experimental Oncology Laboratory, Research Department, National Institute of Pediatrics, Mexico City 04530, Mexico.
| | - Karina Olmos-Valdez
- Experimental Oncology Laboratory, Research Department, National Institute of Pediatrics, Mexico City 04530, Mexico.
| | | | | | | | - Eleazar Israel Pérez-López
- Experimental Oncology Laboratory, Research Department, National Institute of Pediatrics, Mexico City 04530, Mexico.
| | - Isabel Medina-Vera
- Research Methodology Department, National Institute of Pediatrics, Mexico City 04530, Mexico.
| | - Sergio Juárez-Méndez
- Experimental Oncology Laboratory, Research Department, National Institute of Pediatrics, Mexico City 04530, Mexico.
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Jiménez-Ávila CE, Villegas-Ruíz V, Zapata-Tarres M, Rubio-Portillo AE, Pérez López EI, Zenteno JC, Juárez-Méndez S. Centromere-associated protein E expresses a novel mRNA isoform in acute lymphoblastic leukemia. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2018; 9:43-54. [PMID: 30515258 PMCID: PMC6261922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/12/2018] [Indexed: 06/09/2023]
Abstract
The alternative splicing plays an important role to generate protein diversity. Recent studies have shown alterations in alternative splicing, resulting in loss, gain or changes of functions in the resulting protein. Specific products of alternative splicing are known to contribute in cancer-related mechanisms, such as angiogenesis, migration, adhesion and cell proliferation, among others. We using high-density microarrays reported a CENP-E as a one of significant transcript expressed and potentially is alternatively spliced in cancer. We focus in validate alternative splicing of CENP-E transcript using RT-PCR and sequencing in different cancer cell lines. We performed RT-PCR using specific primers designed to delimit the non-reported alternative splicing in CENP-E transcript. Our results showed the co-expression of the variant one and two of CENP-E in all cell lines evaluated. We detected more expression of variant one than two. Moreover, we identify an alternative 5'splice site of CENP-E in the exon 38 and was observed in RoVa cell line. Additionally, we characterized alternative skipping from exon 20 (NAT-CENP-E), these alternative splicing was observed in all cell lines evaluated except RoVa. Finally, we corroborate alternative mRNA splicing in leukemia patients using quantitative RT-PCR, in 71.8% of the patients NAT-CENP-E is downregulated and 28.2% is overexpressed.
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Affiliation(s)
- Cindy E Jiménez-Ávila
- Experimental Oncology Laboratory, Research Department, National Institute of PediatricsMexico City, Mexico
| | - Vanessa Villegas-Ruíz
- Experimental Oncology Laboratory, Research Department, National Institute of PediatricsMexico City, Mexico
- Genetics Department-Research Unit, Institute of Ophthalmology, “Conde de Valenciana”Mexico City, Mexico
| | | | - Alejandra E Rubio-Portillo
- Experimental Oncology Laboratory, Research Department, National Institute of PediatricsMexico City, Mexico
| | - Eleazar I Pérez López
- Experimental Oncology Laboratory, Research Department, National Institute of PediatricsMexico City, Mexico
| | - Juan C Zenteno
- Genetics Department-Research Unit, Institute of Ophthalmology, “Conde de Valenciana”Mexico City, Mexico
- Biochemistry Department, Faculty of Medicine, UNAMMexico City, Mexico
| | - Sergio Juárez-Méndez
- Experimental Oncology Laboratory, Research Department, National Institute of PediatricsMexico City, Mexico
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