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Ordónez-Rubiano EG, Cómbita A, Baldoncini M, Payán-Gómez C, Gómez-Amarillo DF, Hakim F, Camargo J, Zorro-Sepúlveda V, Luzzi S, Zorro O, Parra-Medina R. Cellular Senescence in Diffuse Gliomas: From Physiopathology to Possible Treatments. World Neurosurg 2024; 191:138-148. [PMID: 39233309 DOI: 10.1016/j.wneu.2024.08.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 09/06/2024]
Abstract
Cellular senescence in gliomas is a complex process that is induced by aging and replication, ionizing radiation, oncogenic stress, and the use of temozolomide. However, the escape routes that gliomas must evade senescence and achieve cellular immortality are much more complex, in which the expression of telomerase and the alternative lengthening of telomeres, as well as the mutation of some proto-oncogenes or tumor suppressor genes, are involved. In gliomas, these molecular mechanisms related to cellular senescence can have a tumor-suppressing or promoting effect and are directly involved in tumor recurrence and progression. From these cellular mechanisms related to cellular senescence, it is possible to generate targeted senostatic and senolytic therapies that improve the response to currently available treatments and improve survival rates. This review aims to summarize the mechanisms of induction and evasion of cellular senescence in gliomas, as well as review possible treatments with therapies targeting pathways related to cellular senescence.
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Affiliation(s)
- Edgar G Ordónez-Rubiano
- Department of Neurological Surgery, Fundación Universitaria de Ciencias de la Salud (FUCS), Hospital de San José - Sociedad de Cirugía de Bogotá, Bogotá, Colombia; School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia; Department of Neurosurgery, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia.
| | - Alba Cómbita
- Department of Neurosurgery, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia; Department of Microbiology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Matías Baldoncini
- School of Medicine, Laboratory of Microsurgical Neuroanatomy, Second Chair of Gross Anatomy, University of Buenos Aires, Buenos Aires, Argentina; Department of Neurological Surgery, Hospital San Fernando, Buenos Aires, Argentina
| | - César Payán-Gómez
- Dirección Académica, Universidad Nacional de Colombia, Sede de La Paz, La Paz, Colombia
| | - Diego F Gómez-Amarillo
- Department of Neurosurgery, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Fernando Hakim
- Department of Neurosurgery, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Julián Camargo
- Department of Neurosurgery, Hospital Universitario Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | | | - Sabino Luzzi
- Neurosurgery Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Oscar Zorro
- Department of Neurological Surgery, Fundación Universitaria de Ciencias de la Salud (FUCS), Hospital de San José - Sociedad de Cirugía de Bogotá, Bogotá, Colombia
| | - Rafael Parra-Medina
- Department of Pathology, Instituto Nacional de Cancerología, Bogotá, Colombia; Research Institute, Fundación Universitaria de Ciencias de la Salud (FUCS), Hospital de San José - Sociedad de Cirugía de Bogotá, Bogotá, Colombia
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2
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Phadnis S, Wang X, Daw NC, Herzog CE, Subbiah IM, Zaky W, Gouda MA, Morani AC, Amini B, Harrison DJ, Piha-Paul SA, Meric-Bernstam F, Gorlick R, Schwartz CL, Subbiah V. Everolimus in combination with vandetanib in children, adolescents, and young adults: a phase I study. ESMO Open 2023; 8:101609. [PMID: 37879233 PMCID: PMC10774869 DOI: 10.1016/j.esmoop.2023.101609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/14/2023] [Accepted: 06/22/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Combined use of inhibitors of mammalian target of rapamycin (mTOR) and vascular endothelial growth factor (VEGF-2) receptors is a potential strategy to overcome resistance to either class of drugs when used alone. PATIENTS AND METHODS We designed a phase 1 trial to test the drug combination of a multikinase VEGF receptor 2 inhibitor, vandetanib, and an mTOR inhibitor, everolimus, in a pediatric and young adult patient cohort with advanced cancers. Exceptional responders were probed for tumor mutational profile to explore possible molecular mechanisms of response. RESULTS Among 21 enrolled patients, clinical benefit was observed in 38% (one patient with partial response and eight patients with stable disease) with a median progression-free survival of 3.3 months. The most common treatment-related adverse event was rash (n = 13). Other treatment-related toxicities included diarrhea, fatigue, hypertension, QT prolongation, hypertriglyceridemia/hypercholesterolemia, transaminitis, thrombocytopenia, and weight loss. None of the patients experienced dose-limiting toxicities. Three exceptional responders were analyzed and were found to harbor genetic alterations including kinase insert domain receptor (KDR) Q472H mutation, EWSR1-CREB3L1, CDKN2A/B loss, and ASPL/ASPSCR1-TFE3 fusion. CONCLUSIONS The combination of vandetanib and everolimus showed early activity and tolerable toxicity profile in pediatric patients with advanced cancers.
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Affiliation(s)
- S Phadnis
- Division of Pediatrics, Children's of Alabama at The University of Alabama, Birmingham
| | - X Wang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - N C Daw
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston
| | - C E Herzog
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston
| | - I M Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston; Sarah Cannon Research Institute (SCRI), Nashville
| | - W Zaky
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston
| | - M A Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - A C Morani
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston
| | - B Amini
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - D J Harrison
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston
| | - S A Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - R Gorlick
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston
| | - C L Schwartz
- Children's Hospital of Wisconsin, Milwaukee, USA
| | - V Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston; Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston; Sarah Cannon Research Institute (SCRI), Nashville.
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Foss-Skiftesvik J, Li S, Rosenbaum A, Hagen CM, Stoltze UK, Ljungqvist S, Hjalmars U, Schmiegelow K, Morimoto L, de Smith AJ, Mathiasen R, Metayer C, Hougaard D, Melin B, Walsh KM, Bybjerg-Grauholm J, Dahlin AM, Wiemels JL. Multi-ancestry genome-wide association study of 4069 children with glioma identifies 9p21.3 risk locus. Neuro Oncol 2023; 25:1709-1720. [PMID: 36810956 PMCID: PMC10484172 DOI: 10.1093/neuonc/noad042] [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: 12/12/2022] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date. METHODS Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes. RESULTS Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8). CONCLUSIONS In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Adam Rosenbaum
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | | | - Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Sally Ljungqvist
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Ulf Hjalmars
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Libby Morimoto
- Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, California, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - David Hougaard
- Section for Neonatal Genetics, Statens Serum Institute, Copenhagen, Denmark
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Kyle M Walsh
- Division of Neuro-Epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | | | - Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
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Sanchez A, Lhuillier J, Grosjean G, Ayadi L, Maenner S. The Long Non-Coding RNA ANRIL in Cancers. Cancers (Basel) 2023; 15:4160. [PMID: 37627188 PMCID: PMC10453084 DOI: 10.3390/cancers15164160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
ANRIL (Antisense Noncoding RNA in the INK4 Locus), a long non-coding RNA encoded in the human chromosome 9p21 region, is a critical factor for regulating gene expression by interacting with multiple proteins and miRNAs. It has been found to play important roles in various cellular processes, including cell cycle control and proliferation. Dysregulation of ANRIL has been associated with several diseases like cancers and cardiovascular diseases, for instance. Understanding the oncogenic role of ANRIL and its potential as a diagnostic and prognostic biomarker in cancer is crucial. This review provides insights into the regulatory mechanisms and oncogenic significance of the 9p21 locus and ANRIL in cancer.
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Affiliation(s)
| | | | | | - Lilia Ayadi
- CNRS, Université de Lorraine, IMoPA, F-54000 Nancy, France
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Youn BJ, Cheong HS, Namgoong S, Kim LH, Baek IK, Kim JH, Yoon SJ, Kim EH, Kim SH, Chang JH, Kim SH, Shin HD. Asian-specific 3'UTR variant in CDKN2B associated with risk of pituitary adenoma. Mol Biol Rep 2022; 49:10339-10346. [PMID: 36097105 DOI: 10.1007/s11033-022-07796-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/13/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Previous genomewide association studies (GWASs), single nucleotide polymorphisms (SNPs) on cyclin-dependent kinase inhibitor 2 A (CDKN2A), cyclin-dependent kinase inhibitor 2B (CDKN2B), and cyclin-dependent kinase inhibitor 2B antisense RNA1 (CDKN2B-AS1) were reported as risk loci for glioma, a subgroup of the brain tumor. To further characterize this association with the risk of brain tumors in a Korean population, we performed a fine-mapping association study of CDKN2A, CDKN2B, and CDKN2B-AS1. METHODS AND RESULTS A total of 17 SNPs were selected and genotyped in 1,439 subjects which were comprised of 959 patients (pituitary adenoma 335; glioma 324; meningioma 300) and 480 population controls (PCs). We discovered that a 3'untranslated region (3'UTR) variant, rs181031884 of CDKN2B (Asian-specific variant), had significant association with the risk of pituitary adenoma (PA) (Odds ratio = 0.58, P = 0.00003). Also, rs181031884 appeared as an independent causal variant among the significant variants in CDKN2A and CDKN2B, and showed dose-dependent effects on PA. CONCLUSIONS Although further studies are needed to verify the impact of this variant on PA susceptibility, our results may help to understand CDKN2B polymorphism and the risk of PA.
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Affiliation(s)
- Byeong Ju Youn
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea.,Forensic DNA Division, National Forensic Service, 26460, Wonju, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea
| | - In Ki Baek
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea.,Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui Hyun Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sun Ho Kim
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, 04107, Seoul, Republic of Korea. .,Department of Genetic Epidemiology, SNP Genetics Inc, Seoul, Republic of Korea. .,Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
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6
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Deacu M, Docu Axelerad A, Popescu S, Topliceanu TS, Aschie M, Bosoteanu M, Cozaru GC, Cretu AM, Voda RI, Orasanu CI. Aggressiveness of Grade 4 Gliomas of Adults. Clin Pract 2022; 12:701-713. [PMID: 36136867 PMCID: PMC9498876 DOI: 10.3390/clinpract12050073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Grade 4 adult gliomas are IDH-mutant astrocytomas and IDH-wildtype glioblastomas. They have a very high mortality rate, with survival at 5 years not exceeding 5%. We aimed to conduct a clinical imaging and morphogenetic characterization of them, as well as to identify the main negative prognostic factors that give them such aggressiveness. We conducted a ten-year retrospective study. We followed the clinical, imaging, and morphogenetic aspects of the cases. We analyzed immunohistochemical markers (IDH1, Ki-67, and nestin) and FISH tests based on the CDKN2A gene. The obtained results were analyzed using SPSS Statistics with the appropriate parameters. The clinical aspects representing negative prognostic factors were represented by patients’ comorbidities: hypertension (HR = 1.776) and diabetes mellitus/hyperglycemia (HR = 2.159). The lesions were mostly supratentorial, and the temporal lobe was the most affected. The mean volume was 88.05 cm3 and produced a midline shift with an average of 8.52 mm. Subtotal surgical resection was a negative prognostic factor (HR = 1.877). The proliferative index did not influence survival rate, whereas CDKN2A gene mutations were shown to have a major impact on survival. We identified the main negative prognostic factors that support the aggressiveness of grade 4 gliomas: patient comorbidities, type of surgical resection, degree of cell differentiation, and CDKN2A gene mutations.
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Affiliation(s)
- Mariana Deacu
- Clinical Service of Pathology, Departments of Pathology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
- Faculty of Medicine, “Ovidius” University of Constanta, 900470 Constanta, Romania
| | - Any Docu Axelerad
- Faculty of Medicine, “Ovidius” University of Constanta, 900470 Constanta, Romania
- Department of Neurology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
| | - Steliana Popescu
- Faculty of Medicine, “Ovidius” University of Constanta, 900470 Constanta, Romania
- Department of Radiology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
| | - Theodor Sebastian Topliceanu
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology (CEDMOG), “Ovidius” University of Constanta, 900591 Constanta, Romania
| | - Mariana Aschie
- Clinical Service of Pathology, Departments of Pathology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
- Faculty of Medicine, “Ovidius” University of Constanta, 900470 Constanta, Romania
- Academy of Medical Sciences of Romania, 030167 Bucharest, Romania
| | - Madalina Bosoteanu
- Clinical Service of Pathology, Departments of Pathology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
- Faculty of Medicine, “Ovidius” University of Constanta, 900470 Constanta, Romania
| | - Georgeta Camelia Cozaru
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology (CEDMOG), “Ovidius” University of Constanta, 900591 Constanta, Romania
- Clinical Service of Pathology, Departments of Genetics, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
| | - Ana Maria Cretu
- Clinical Service of Pathology, Departments of Pathology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology (CEDMOG), “Ovidius” University of Constanta, 900591 Constanta, Romania
| | - Raluca Ioana Voda
- Clinical Service of Pathology, Departments of Pathology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology (CEDMOG), “Ovidius” University of Constanta, 900591 Constanta, Romania
| | - Cristian Ionut Orasanu
- Clinical Service of Pathology, Departments of Pathology, “Sf. Apostol Andrei” Emergency County Hospital, 900591 Constanta, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology (CEDMOG), “Ovidius” University of Constanta, 900591 Constanta, Romania
- Correspondence: ; Tel.: +40-72-281-4037
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7
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Perez‐Becerril C, Wallace AJ, Schlecht H, Bowers NL, Smith PT, Gokhale C, Eaton H, Charlton C, Robinson R, Charlton RS, Evans DG, Smith MJ. Screening of potential novel candidate genes in schwannomatosis patients. Hum Mutat 2022; 43:1368-1376. [PMID: 35723634 PMCID: PMC9540472 DOI: 10.1002/humu.24424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 06/10/2022] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
Schwannomatosis comprises a group of hereditary tumor predisposition syndromes characterized by, usually benign, multiple nerve sheath tumors, which frequently cause severe pain that does not typically respond to drug treatments. The most common schwannomatosis‐associated gene is NF2, but SMARCB1 and LZTR1 are also associated. There are still many cases in which no pathogenic variants (PVs) have been identified, suggesting the existence of as yet unidentified genetic risk factors. In this study, we performed extended genetic screening of 75 unrelated schwannomatosis patients without identified germline PVs in NF2, LZTR1, or SMARCB1. Screening of the coding region of DGCR8, COQ6, CDKN2A, and CDKN2B was carried out, based on previous reports that point to these genes as potential candidate genes for schwannomatosis. Deletions or duplications in CDKN2A, CDKN2B, and adjacent chromosome 9 region were assessed by multiplex ligation‐dependent probe amplification analysis. Sequencing analysis of a patient with multiple schwannomas and melanomas identified a novel duplication in the coding region of CDKN2A, disrupting both p14ARF and p16INK4a. Our results suggest that none of these genes are major contributors to schwannomatosis risk but the possibility remains that they may have a role in more complex mechanisms for tumor predisposition.
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Affiliation(s)
- Cristina Perez‐Becerril
- School of Biological Sciences, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Andrew J. Wallace
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Philip T. Smith
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Carolyn Gokhale
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Helen Eaton
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Chris Charlton
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Rachel Robinson
- North East and Yorkshire Genomic Laboratory HubSt James's University HospitalLeedsUK
| | - Ruth S. Charlton
- North East and Yorkshire Genomic Laboratory HubSt James's University HospitalLeedsUK
| | - D. Gareth Evans
- School of Biological Sciences, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
| | - Miriam J. Smith
- School of Biological Sciences, Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
- Manchester Centre for Genomic Medicine, St Mary's HospitalManchester University NHS Foundation TrustManchesterUK
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8
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Brandner S, McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Leal ES, Faulkner CL, Palmer A, Wragg C, Jefferies S, Vale L, Higgins JPT, Kurian KM. Diagnostic accuracy of 1p/19q codeletion tests in oligodendroglioma: A comprehensive meta-analysis based on a Cochrane systematic review. Neuropathol Appl Neurobiol 2022; 48:e12790. [PMID: 34958131 PMCID: PMC9208578 DOI: 10.1111/nan.12790] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
Codeletion of chromosomal arms 1p and 19q, in conjunction with a mutation in the isocitrate dehydrogenase 1 or 2 gene, is the molecular diagnostic criterion for oligodendroglioma, IDH mutant and 1p/19q codeleted. 1p/19q codeletion is a diagnostic marker and allows prognostication and prediction of the best drug response within IDH-mutant tumours. We performed a Cochrane review and simple economic analysis to establish the most sensitive, specific and cost-effective techniques for determining 1p/19q codeletion status. Fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) test methods were considered as reference standard. Most techniques (FISH, chromogenic in situ hybridisation [CISH], PCR, real-time PCR, multiplex ligation-dependent probe amplification [MLPA], single nucleotide polymorphism [SNP] array, comparative genomic hybridisation [CGH], array CGH, next-generation sequencing [NGS], mass spectrometry and NanoString) showed good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma, irrespective of whether FISH or PCR-based LOH was used as the reference standard. Both NGS and SNP array had a high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. Our findings suggest that G banding is not a suitable test for 1p/19q analysis. Within these limits, considering cost per diagnosis and using FISH as a reference, MLPA was marginally more cost-effective than other tests, although these economic analyses were limited by the range of available parameters, time horizon and data from multiple healthcare organisations.
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Affiliation(s)
- Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Neurodegenerative Disease, Queen Square Instituite of NeurologyUniversity College LondonLondonUK
| | - Alexandra McAleenan
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Hayley E. Jones
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Ashleigh Kernohan
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Tomos Robinson
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Claire L. Faulkner
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | | | - Luke Vale
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Julian P. T. Higgins
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Kathreena M. Kurian
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Bristol Medical School: Brain Tumour Research Centre, Public Health SciencesUniversity of BristolBristolUK
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Shafi O, Siddiqui G. Tracing the origins of glioblastoma by investigating the role of gliogenic and related neurogenic genes/signaling pathways in GBM development: a systematic review. World J Surg Oncol 2022; 20:146. [PMID: 35538578 PMCID: PMC9087910 DOI: 10.1186/s12957-022-02602-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 02/16/2023] Open
Abstract
Background Glioblastoma is one of the most aggressive tumors. The etiology and the factors determining its onset are not yet entirely known. This study investigates the origins of GBM, and for this purpose, it focuses primarily on developmental gliogenic processes. It also focuses on the impact of the related neurogenic developmental processes in glioblastoma oncogenesis. It also addresses why glial cells are at more risk of tumor development compared to neurons. Methods Databases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving glioblastoma, gliogenesis, neurogenesis, stemness, neural stem cells, gliogenic signaling and pathways, neurogenic signaling and pathways, and astrocytogenic genes. Results The origin of GBM is dependent on dysregulation in multiple genes and pathways that accumulatively converge the cells towards oncogenesis. There are multiple layers of steps in glioblastoma oncogenesis including the failure of cell fate-specific genes to keep the cells differentiated in their specific cell types such as p300, BMP, HOPX, and NRSF/REST. There are genes and signaling pathways that are involved in differentiation and also contribute to GBM such as FGFR3, JAK-STAT, and hey1. The genes that contribute to differentiation processes but also contribute to stemness in GBM include notch, Sox9, Sox4, c-myc gene overrides p300, and then GFAP, leading to upregulation of nestin, SHH, NF-κB, and others. GBM mutations pathologically impact the cell circuitry such as the interaction between Sox2 and JAK-STAT pathway, resulting in GBM development and progression. Conclusion Glioblastoma originates when the gene expression of key gliogenic genes and signaling pathways become dysregulated. This study identifies key gliogenic genes having the ability to control oncogenesis in glioblastoma cells, including p300, BMP, PAX6, HOPX, NRSF/REST, LIF, and TGF beta. It also identifies key neurogenic genes having the ability to control oncogenesis including PAX6, neurogenins including Ngn1, NeuroD1, NeuroD4, Numb, NKX6-1 Ebf, Myt1, and ASCL1. This study also postulates how aging contributes to the onset of glioblastoma by dysregulating the gene expression of NF-κB, REST/NRSF, ERK, AKT, EGFR, and others.
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Affiliation(s)
- Ovais Shafi
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan.
| | - Ghazia Siddiqui
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
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McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Spencer Leal E, Faulkner CL, Palmer A, Wragg C, Jefferies S, Brandner S, Vale L, Higgins JP, Kurian KM. Diagnostic test accuracy and cost-effectiveness of tests for codeletion of chromosomal arms 1p and 19q in people with glioma. Cochrane Database Syst Rev 2022; 3:CD013387. [PMID: 35233774 PMCID: PMC8889390 DOI: 10.1002/14651858.cd013387.pub2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Complete deletion of both the short arm of chromosome 1 (1p) and the long arm of chromosome 19 (19q), known as 1p/19q codeletion, is a mutation that can occur in gliomas. It occurs in a type of glioma known as oligodendroglioma and its higher grade counterpart known as anaplastic oligodendroglioma. Detection of 1p/19q codeletion in gliomas is important because, together with another mutation in an enzyme known as isocitrate dehydrogenase, it is needed to make the diagnosis of an oligodendroglioma. Presence of 1p/19q codeletion also informs patient prognosis and prediction of the best drug treatment. The main two tests in use are fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) assays (also known as PCR-based short tandem repeat or microsatellite analysis). Many other tests are available. None of the tests is perfect, although PCR-based LOH is expected to have very high sensitivity. OBJECTIVES To estimate the sensitivity and specificity and cost-effectiveness of different deoxyribonucleic acid (DNA)-based techniques for determining 1p/19q codeletion status in glioma. SEARCH METHODS We searched MEDLINE, Embase and BIOSIS up to July 2019. There were no restrictions based on language or date of publication. We sought economic evaluation studies from the results of this search and using the National Health Service Economic Evaluation Database. SELECTION CRITERIA We included cross-sectional studies in adults with glioma or any subtype of glioma, presenting raw data or cross-tabulations of two or more DNA-based tests for 1p/19q codeletion. We also sought economic evaluations of these tests. DATA COLLECTION AND ANALYSIS We followed procedures outlined in the Cochrane Handbook for Diagnostic Test Accuracy Reviews. Two review authors independently screened titles/abstracts/full texts, performed data extraction, and undertook applicability and risk of bias assessments using QUADAS-2. Meta-analyses used the hierarchical summary ROC model to estimate and compare test accuracy. We used FISH and PCR-based LOH as alternate reference standards to examine how tests compared with those in common use, and conducted a latent class analysis comparing FISH and PCR-based LOH. We constructed an economic model to evaluate cost-effectiveness. MAIN RESULTS We included 53 studies examining: PCR-based LOH, FISH, single nucleotide polymorphism (SNP) array, next-generation sequencing (NGS), comparative genomic hybridisation (CGH), array comparative genomic hybridisation (aCGH), multiplex-ligation-dependent probe amplification (MLPA), real-time PCR, chromogenic in situ hybridisation (CISH), mass spectrometry (MS), restriction fragment length polymorphism (RFLP) analysis, G-banding, methylation array and NanoString. Risk of bias was low for only one study; most gave us concerns about how patients were selected or about missing data. We had applicability concerns about many of the studies because only patients with specific subtypes of glioma were included. 1520 participants contributed to analyses using FISH as the reference, 1304 participants to analyses involving PCR-based LOH as the reference and 262 participants to analyses of comparisons between methods from studies not including FISH or PCR-based LOH. Most evidence was available for comparison of FISH with PCR-based LOH (15 studies, 915 participants): PCR-based LOH detected 94% of FISH-determined codeletions (95% credible interval (CrI) 83% to 98%) and FISH detected 91% of codeletions determined by PCR-based LOH (CrI 78% to 97%). Of tumours determined not to have a deletion by FISH, 94% (CrI 87% to 98%) had a deletion detected by PCR-based LOH, and of those determined not to have a deletion by PCR-based LOH, 96% (CrI 90% to 99%) had a deletion detected by FISH. The latent class analysis suggested that PCR-based LOH may be slightly more accurate than FISH. Most other techniques appeared to have high sensitivity (i.e. produced few false-negative results) for detection of 1p/19q codeletion when either FISH or PCR-based LOH was considered as the reference standard, although there was limited evidence. There was some indication of differences in specificity (false-positive rate) with some techniques. Both NGS and SNP array had high specificity when considered against FISH as the reference standard (NGS: 6 studies, 243 participants; SNP: 6 studies, 111 participants), although we rated certainty in the evidence as low or very low. NGS and SNP array also had high specificity when PCR-based LOH was considered the reference standard, although with much more uncertainty as these results were based on fewer studies (just one study with 49 participants for NGS and two studies with 33 participants for SNP array). G-banding had low sensitivity and specificity when PCR-based LOH was the reference standard. Although MS had very high sensitivity and specificity when both FISH and PCR-based LOH were considered the reference standard, these results were based on only one study with a small number of participants. Real-time PCR also showed high specificity with FISH as a reference standard, although there were only two studies including 40 participants. We found no relevant economic evaluations. Our economic model using FISH as the reference standard suggested that the resource-optimising test depends on which measure of diagnostic accuracy is most important. With FISH as the reference standard, MLPA is likely to be cost-effective if society was willing to pay GBP 1000 or less for a true positive detected. However, as the value placed on a true positive increased, CISH was most cost-effective. Findings differed when the outcome measure changed to either true negative detected or correct diagnosis. When PCR-based LOH was used as the reference standard, MLPA was likely to be cost-effective for all measures of diagnostic accuracy at lower threshold values for willingness to pay. However, as the threshold values increased, none of the tests were clearly more likely to be considered cost-effective. AUTHORS' CONCLUSIONS In our review, most techniques (except G-banding) appeared to have good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma against both FISH and PCR-based LOH as a reference standard. However, we judged the certainty of the evidence low or very low for all the tests. There are possible differences in specificity, with both NGS and SNP array having high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. The economic analysis should be interpreted with caution due to the small number of studies.
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Affiliation(s)
- Alexandra McAleenan
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Hayley E Jones
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ashleigh Kernohan
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tomos Robinson
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne , UK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emmelyn Spencer Leal
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire L Faulkner
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology Sciences, Southmead Hospital, Bristol, UK
| | - Sarah Jefferies
- Department of Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
| | - Luke Vale
- Institute of Health & Society, Newcastle University, Newcastle upon Tyne, UK
| | - Julian Pt Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- Bristol Medical School: Brain Tumour Research Centre, Public Health Sciences, University of Bristol, Bristol, UK
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Wan D, Wang S, Xu Z, Zan X, Liu F, Han Y, Jiang M, Wu A, Zhi Q. PRKAR2A-derived circular RNAs promote the malignant transformation of colitis and distinguish patients with colitis-associated colorectal cancer. Clin Transl Med 2022; 12:e683. [PMID: 35184406 PMCID: PMC8858608 DOI: 10.1002/ctm2.683] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Emerging studies have proved that colonic inflammation caused by refractory inflammatory bowel disease (IBD) can initiate the colitis-associated cancer (CAC), but the transition from inflammation to carcinoma is still largely unknown. METHODS In this study, mouse colitis and CAC models were established, and the RNA-seq by circRNA microarray was employed to identify the differentially expressed circRNAs and mRNAs in different comparisons (DSS vs. NC and AOM/DSS vs. DSS). The bioinformatics analyses were used to search the common characteristics in mouse colitis and CAC. RESULTS The K-means clustering algorithm packaged these differential expressed circRNAs into subgroup analysis, and the data strongly implied that mmu_circ_0001109 closely correlated to the pro-inflammatory signals, while mmu_circ_0001845 was significantly associated with the Wnt signalling pathway. Our subsequent data in vivo and in vitro confirmed that mmu_circ_0001109 could exacerbate the colitis by up-regulating the Jak-STAT3 and NF-kappa B signalling pathways, and mmu_circ_0001845 promoted the CAC transformation through the Wnt signalling pathway. By RNA blasting between mice and humans, the human RTEL1- and PRKAR2A-derived circRNAs, which might be considered as homeotic circRNAs of mmu_circ_0001109 and mmu_circ_0001845, respectively, were identified. The clinical data revealed that RTEL1-derived circRNAs had no clinical significance in human IBD and CAC. However, three PRKAR2A-derived circRNAs, which had the high RNA similarities to mmu_circ_0001845, were remarkably up-regulated in CAC tissue samples and promoted the transition from colitis to CAC. CONCLUSIONS Our results suggested that these human PRKAR2A-derived circRNAs could be novel candidates for distinguishing CAC patients and predicted the prognosis of CAC.
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Affiliation(s)
- Daiwei Wan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Sentai Wang
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhihua Xu
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Min Jiang
- Department of OncologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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12
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Śledzińska P, Bebyn MG, Furtak J, Kowalewski J, Lewandowska MA. Prognostic and Predictive Biomarkers in Gliomas. Int J Mol Sci 2021; 22:ijms221910373. [PMID: 34638714 PMCID: PMC8508830 DOI: 10.3390/ijms221910373] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022] Open
Abstract
Gliomas are the most common central nervous system tumors. New technologies, including genetic research and advanced statistical methods, revolutionize the therapeutic approach to the patient and reveal new points of treatment options. Moreover, the 2021 World Health Organization Classification of Tumors of the Central Nervous System has fundamentally changed the classification of gliomas and incorporated many molecular biomarkers. Given the rapid progress in neuro-oncology, here we compile the latest research on prognostic and predictive biomarkers in gliomas. In adult patients, IDH mutations are positive prognostic markers and have the greatest prognostic significance. However, CDKN2A deletion, in IDH-mutant astrocytomas, is a marker of the highest malignancy grade. Moreover, the presence of TERT promoter mutations, EGFR alterations, or a combination of chromosome 7 gain and 10 loss upgrade IDH-wildtype astrocytoma to glioblastoma. In pediatric patients, H3F3A alterations are the most important markers which predict the worse outcome. MGMT promoter methylation has the greatest clinical significance in predicting responses to temozolomide (TMZ). Conversely, mismatch repair defects cause hypermutation phenotype predicting poor response to TMZ. Finally, we discussed liquid biopsies, which are promising diagnostic, prognostic, and predictive techniques, but further work is needed to implement these novel technologies in clinical practice.
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Affiliation(s)
- Paulina Śledzińska
- Department of Thoracic Surgery and Tumors, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 85-067 Torun, Poland
- The F. Lukaszczyk Oncology Center, Molecular Oncology and Genetics Department, Innovative Medical Forum, 85-796 Bydgoszcz, Poland
| | - Marek G Bebyn
- The F. Lukaszczyk Oncology Center, Molecular Oncology and Genetics Department, Innovative Medical Forum, 85-796 Bydgoszcz, Poland
- Faculty of Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland
| | - Jacek Furtak
- Department of Neurosurgery, 10th Military Research Hospital and Polyclinic, 85-681 Bydgoszcz, Poland
- Franciszek Lukaszczyk Oncology Center, Department of Neurooncology and Radiosurgery, 85-796 Bydgoszcz, Poland
| | - Janusz Kowalewski
- Department of Thoracic Surgery and Tumors, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 85-067 Torun, Poland
| | - Marzena A Lewandowska
- Department of Thoracic Surgery and Tumors, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 85-067 Torun, Poland
- The F. Lukaszczyk Oncology Center, Molecular Oncology and Genetics Department, Innovative Medical Forum, 85-796 Bydgoszcz, Poland
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13
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Xu S, Wang Z, Ye J, Mei S, Zhang J. Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade Glioma. Front Oncol 2021; 11:729103. [PMID: 34568059 PMCID: PMC8458946 DOI: 10.3389/fonc.2021.729103] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022] Open
Abstract
Lower-grade glioma (LGG) is characterized by genetic and transcriptional heterogeneity, and a dismal prognosis. Iron metabolism is considered central for glioma tumorigenesis, tumor progression and tumor microenvironment, although key iron metabolism-related genes are unclear. Here we developed and validated an iron metabolism-related gene signature LGG prognosis. RNA-sequence and clinicopathological data from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) were downloaded. Prognostic iron metabolism-related genes were screened and used to construct a risk-score model via differential gene expression analysis, univariate Cox analysis, and the Least Absolute Shrinkage and Selection Operator (LASSO)-regression algorithm. All LGG patients were stratified into high- and low-risk groups, based on the risk score. The prognostic significance of the risk-score model in the TCGA and CGGA cohorts was evaluated with Kaplan-Meier (KM) survival and receiver operating characteristic (ROC) curve analysis. Risk- score distributions in subgroups were stratified by age, gender, the World Health Organization (WHO) grade, isocitrate dehydrogenase 1 (IDH1) mutation status, the O6-methylguanine-DNA methyl-transferase (MGMT) promoter-methylation status, and the 1p/19q co-deletion status. Furthermore, a nomogram model with a risk score was developed, and its predictive performance was validated with the TCGA and CGGA cohorts. Additionally, the gene set enrichment analysis (GSEA) identified signaling pathways and pathological processes enriched in the high-risk group. Finally, immune infiltration and immune checkpoint analysis were utilized to investigate the tumor microenvironment characteristics related to the risk score. We identified a prognostic 15-gene iron metabolism-related signature and constructed a risk-score model. High risk scores were associated with an age of > 40, wild-type IDH1, a WHO grade of III, an unmethylated MGMT promoter, and 1p/19q non-codeletion. ROC analysis indicated that the risk-score model accurately predicted 1-, 3-, and 5-year overall survival rates of LGG patients in the both TCGA and CGGA cohorts. KM analysis showed that the high-risk group had a much lower overall survival than the low-risk group (P < 0.0001). The nomogram model showed a strong ability to predict the overall survival of LGG patients in the TCGA and CGGA cohorts. GSEA analysis indicated that inflammatory responses, tumor-associated pathways, and pathological processes were enriched in high-risk group. Moreover, a high risk score correlated with the infiltration immune cells (dendritic cells, macrophages, CD4+ T cells, and B cells) and expression of immune checkpoint (PD1, PDL1, TIM3, and CD48). Our prognostic model was based on iron metabolism-related genes in LGG, can potentially aid in LGG prognosis, and provides potential targets against gliomas.
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Affiliation(s)
- Shenbin Xu
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Department of Gastroenterology Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zefeng Wang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Juan Ye
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shuhao Mei
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianmin Zhang
- Department of Neurosurgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Brain Research Institute, Zhejiang University, Hangzhou, China
- Collaborative Innovation Center for Brain Science, Zhejiang University, Hangzhou, China
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14
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Cusenza VY, Bisagni A, Rinaldini M, Cattani C, Frazzi R. Copy Number Variation and Rearrangements Assessment in Cancer: Comparison of Droplet Digital PCR with the Current Approaches. Int J Mol Sci 2021; 22:ijms22094732. [PMID: 33946969 PMCID: PMC8124143 DOI: 10.3390/ijms22094732] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
The cytogenetic and molecular assessment of deletions, amplifications and rearrangements are key aspects in the diagnosis and therapy of cancer. Not only the initial evaluation and classification of the disease, but also the follow-up of the tumor rely on these laboratory approaches. The therapeutic choice can be guided by the results of the laboratory testing. Genetic deletions and/or amplifications directly affect the susceptibility or the resistance to specific therapies. In an era of personalized medicine, the correct and reliable molecular characterization of the disease, also during the therapeutic path, acquires a pivotal role. Molecular assays like multiplex ligation-dependent probe amplification and droplet digital PCR represent exceptional tools for a sensitive and reliable detection of genetic alterations and deserve a role in molecular oncology. In this manuscript we provide a technical comparison of these two approaches with the golden standard represented by fluorescence in situ hybridization. We also describe some relevant targets currently evaluated with these techniques in solid and hematologic tumors.
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Affiliation(s)
- Vincenza Ylenia Cusenza
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Alessandra Bisagni
- Pathology Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
| | - Monia Rinaldini
- Medical Genetics Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (M.R.); (C.C.)
| | - Chiara Cattani
- Medical Genetics Unit, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy; (M.R.); (C.C.)
| | - Raffaele Frazzi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale—IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy;
- Correspondence:
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15
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Zhang L, Li X, Lu J, Qian Y, Qian T, Wu X, Xu Q. The EGFR Polymorphism Increased the Risk of Hepatocellular Carcinoma Through the miR-3196-Dependent Approach in Chinese Han Population. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2021; 14:469-476. [PMID: 33935511 PMCID: PMC8079348 DOI: 10.2147/pgpm.s304524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022]
Abstract
Background Previous studies have shown that epidermal growth factor receptor (EGFR) promotes cell proliferation through the PI3K-Akt-mTOR signaling pathway and participates in the occurrence and development of hepatocellular carcinoma (HCC). Here, we focused on the functional polymorphism of EGFR in the 3ʹ-untranslated region (UTR), aiming to reveal the potential mechanisms by which functional polymorphism is associated with the risk and development of HCC in the Han Chinese population. Methods This study was a hospital-based case-control study. A total of 600 patients were enrolled, and another 600 healthy volunteers served as controls. The miR-associated SNPs in EGFR were screened, and genotyping was performed by TaqMan allele differential analysis. In this study, genotyping, real-time PCR, cell transfection and double luciferase reporter gene were used for subsequent analysis. Results HBV/HCV infection instead of alcohol exposure, smoking exposure, hypertension or diabetes mellitus was associated with an increased risk of HCC. Compared with TT genotypes, TG and GG genotypes of EGFR rs884225 were significantly associated with reduced HCC risk. The stratified analysis of association between rs884225 and HCC subgroup feature reveal a highly correlation with tumor size. Furthermore, qRT-PCR confirmed that EGFR rs884225, TG and GG genotypes were more likely to bind to miR-3196 and down-regulate EGFR level in cells, thereby inhibiting cell proliferation. Conclusion This study suggested that EGFR rs884225 is associated with a reduced risk of liver cancer and may be a developing biomarker.
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Affiliation(s)
- Li Zhang
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
| | - Xiaoping Li
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
| | - Jiang Lu
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
| | - Yi Qian
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
| | - Tao Qian
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
| | - Xing Wu
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
| | - Qinghua Xu
- Department of Hepatobiliary and Pancreatic Surgery, LiYang People's Hospital, LiYang, 213300, Jiangsu, People's Republic of China
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CAMTA1, a novel antitumor gene, regulates proliferation and the cell cycle in glioma by inhibiting AKT phosphorylation. Cell Signal 2020; 79:109882. [PMID: 33316386 DOI: 10.1016/j.cellsig.2020.109882] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022]
Abstract
Identifying biomarkers for the early diagnosis of glioma and elucidating the molecular mechanisms underlying the development of this cancer are of considerable clinical importance. Recently, studies performing microarray profiling of genes to identify distinct gene signatures reported specific subtypes with predictive and prognostic relevance. Thus, we performed deep sequencing on a total of 26 glioma tissue samples to identify the frequently mutated of oncogenes and tumor suppressors in gliomas. A total of 2306 single-nucleotide polymorphisms (SNPs) and 2010 insertion and deletion sites (indels) were found by aligning sequencing information from 26 glioma samples with sequences from the normal human gene database (GRCh37/hg19). GSEA results suggest that an underexpressed gene, calmodulin binding transcription activator 1 (CAMTA1), participates in the cell proliferation and cell cycle regulation of glioma cells. Moreover, overexpression of CAMTA1 in glioma cells notably inhibited cell growth, migration, invasion and cell cycle and enhanced temozolomide (TMZ)-induced cell apoptosis in glioma cells, while CAMTA1 overexpression decreased the ITGA5, ITGB1, p-AKT, p-FAK, and Myc protein levels, suggesting that the signaling pathways of these proteins might be involved in the cellular functions of CAMTA1 in glioma. Moreover, overexpression of CAMTA1 attenuated the growth and tumorigenesis of glioma in vivo. In summary, we identified high-frequency mutant genes in glioma and provided an experimental basis for a novel mechanism by which CAMTA1 may serve as a tumor suppressor in glioma.
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Critical role of HOX transcript antisense intergenic RNA (HOTAIR) in gliomas. J Mol Med (Berl) 2020; 98:1525-1546. [PMID: 32978667 DOI: 10.1007/s00109-020-01984-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
Despite extensive research, gliomas are associated with high morbidity and mortality, mainly attributed to the rapid growth rate, excessive invasiveness, and molecular heterogeneity, as well as regenerative potential of cancer stem cells. Therefore, elucidation of the underlying molecular mechanisms and the identification of potential molecular diagnostic and prognostic biomarkers are of paramount importance. HOX transcript antisense intergenic RNA (HOTAIR) is a well-studied long noncoding RNA, playing an emerging role in tumorigenesis of several human cancers. A growing amount of preclinical and clinical evidence highlights the pro-oncogenic role of HOTAIR in gliomas, mainly attributed to the enhancement of proliferation and migration, as well as inhibition of apoptosis. In vitro and in vivo studies demonstrate that HOTAIR modulates the activity of specific transcription factors, such as MXI1, E2F1, ATF5, and ASCL1, and regulates the expression of cell cycle-associated genes along with related signaling pathways, like the Wnt/β-catenin axis. Moreover, it can interact with specific miRNAs, including miR-326, miR-141, miR-148b-3p, miR-15b, and miR-126-5p. Of importance, HOTAIR has been demonstrated to enhance angiogenesis and affect the permeability of the blood-tumor barrier, thus modulating the efficacy of chemotherapeutic agents. Herein, we provide evidence on the functional role of HOTAIR in gliomas and discuss the benefits of its targeting as a novel approach toward glioma treatment.
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The Genetic Architecture of Gliomagenesis-Genetic Risk Variants Linked to Specific Molecular Subtypes. Cancers (Basel) 2019; 11:cancers11122001. [PMID: 31842352 PMCID: PMC6966482 DOI: 10.3390/cancers11122001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies have identified 25 germline genetic loci that increase the risk of glioma. The somatic tumor molecular alterations, including IDH-mutation status and 1p/19q co-deletion, have been included into the WHO 2016 classification system for glioma. To investigate how the germline genetic risk variants correlate with the somatic molecular subtypes put forward by WHO, we performed a meta-analysis that combined findings from 330 Swedish cases and 876 controls with two other recent studies. In total, 5,103 cases and 10,915 controls were included. Three categories of associations were found. First, variants in TERT and TP53 were associated with increased risk of all glioma subtypes. Second, variants in CDKN2B-AS1, EGFR, and RTEL1 were associated with IDH-wildtype glioma. Third, variants in CCDC26 (the 8q24 locus), C2orf80 (close to IDH), LRIG1, PHLDB1, ETFA, MAML2 and ZBTB16 were associated with IDH-mutant glioma. We therefore propose three etiopathological pathways in gliomagenesis based on germline variants for future guidance of diagnosis and potential functional targets for therapies. Future prospective clinical trials of patients with suspicion of glioma diagnoses, using the genetic variants as biomarkers, are necessary to disentangle how strongly they can predict glioma diagnosis.
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Viana-Pereira M, Moreno DA, Linhares P, Amorim J, Nabiço R, Costa S, Vaz R, Reis RM. Replication of GWAS identifies RTEL1, CDKN2A/B, and PHLDB1 SNPs as risk factors in Portuguese gliomas patients. Mol Biol Rep 2019; 47:877-886. [PMID: 31721021 DOI: 10.1007/s11033-019-05178-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
Abstract
Diffuse gliomas are the most common malignant primary brain tumors and remain incurable. A better knowledge of the tumor etiology is required. Specific single nucleotides polymorphisms (SNPs) rs4977756 (CDKN2A/B), rs6010620 (RTEL1), rs498872 (PHLDB1), rs2736100 (TERT), and rs4295627 (CCDC26) have been associated with glioma susceptibility and are potential risk biomarkers. This study aimed to analyze five SNPs associated with glioma susceptibility, in the Portuguese population. SNPs were genotyped using the Sequenom MassARRAY platform in 127 gliomas and 180 controls. Unconditional logistic regression models were used to calculate odds ratio (OR) and 95% confidence intervals. The false-positive report probability was also assessed. The associations between polymorphisms and survival were evaluated using the log-rank test. It was found that the AG and GG genotypes of the rs4977756 (CDKN2A/B) were associated with an increased risk of gliomas (OR 1.85 and OR 2.38) and glioblastomas (OR 2.77 and OR 3.94). The GA genotype of the rs6010620 (RTEL1) was associated with a decreased risk of glioblastomas (OR 0.45). We also observed that the GA genotype of the rs498872 (PHLDB1) was associated with an increased risk of gliomas (OR 2.92) and glioblastomas (OR 2.39). No significant risk associations were found for the rs2736100 (TERT) and rs4295627 (CCDC26). In addition, the genotype AA of the rs498872 (PHLDB1) was associated with poor overall survival of gliomas patients (AA vs. GA, p = 0.037). The rs6010620 (RTEL1), rs4977756 (CDKN2A/B), and rs498872 (PHLDB1) are associated with glioma risk in the Portuguese population and these data may contribute to understanding gliomas etiology.
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Affiliation(s)
- Marta Viana-Pereira
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Minho, Portugal
| | | | - Paulo Linhares
- Department of Neurosurgery, Hospital S. João, Porto, Portugal.,Faculty of Medicine, University of Porto, Porto, Portugal
| | - Júlia Amorim
- Department of Oncology, Hospital de Braga, Braga, Portugal
| | - Rui Nabiço
- Department of Oncology, Hospital de Braga, Braga, Portugal
| | - Sandra Costa
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Minho, Portugal
| | - Rui Vaz
- Department of Neurosurgery, Hospital S. João, Porto, Portugal.,Faculty of Medicine, University of Porto, Porto, Portugal
| | - Rui Manuel Reis
- School of Medicine, Life and Health Sciences Research Institute (ICVS), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Minho, Portugal. .,Barretos Cancer Hospital, Molecular Oncology Research Center, Barretos, SP, Brazil.
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Niu B, Liang C, Lu Y, Zhao M, Chen Q, Zhang Y, Zheng L, Chou KC. Glioma stages prediction based on machine learning algorithm combined with protein-protein interaction networks. Genomics 2019; 112:837-847. [PMID: 31150762 DOI: 10.1016/j.ygeno.2019.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 05/25/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Glioma is the most lethal nervous system cancer. Recent studies have made great efforts to study the occurrence and development of glioma, but the molecular mechanisms are still unclear. This study was designed to reveal the molecular mechanisms of glioma based on protein-protein interaction network combined with machine learning methods. Key differentially expressed genes (DEGs) were screened and selected by using the protein-protein interaction (PPI) networks. RESULTS As a result, 19 genes between grade I and grade II, 21 genes between grade II and grade III, and 20 genes between grade III and grade IV. Then, five machine learning methods were employed to predict the gliomas stages based on the selected key genes. After comparison, Complement Naive Bayes classifier was employed to build the prediction model for grade II-III with accuracy 72.8%. And Random forest was employed to build the prediction model for grade I-II and grade III-VI with accuracy 97.1% and 83.2%, respectively. Finally, the selected genes were analyzed by PPI networks, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and the results improve our understanding of the biological functions of select DEGs involved in glioma growth. We expect that the key genes expressed have a guiding significance for the occurrence of gliomas or, at the very least, that they are useful for tumor researchers. CONCLUSION Machine learning combined with PPI networks, GO and KEGG analyses of selected DEGs improve our understanding of the biological functions involved in glioma growth.
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Affiliation(s)
- Bing Niu
- School of Life Sciences, Shanghai University, Shanghai 200444, China; Gordon Life Science Institute, Boston, MA 02478, USA.
| | - Chaofeng Liang
- Department of Neurosurgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yi Lu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Manman Zhao
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qin Chen
- School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Yuhui Zhang
- Renji Hospital, Medical School, Shanghai Jiaotong University, 160 Pujian Rd, New Pudong District, Shanghai 200127, China; Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
| | - Linfeng Zheng
- Department of Radiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China; Department of Radiology, Shanghai First People's Hospital, Baoshan Branch, Shanghai 200940, China.
| | - Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; Gordon Life Science Institute, Boston, MA 02478, USA.
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González-Castro TB, Juárez-Rojop IE, López-Narváez ML, Tovilla-Zárate CA, Genis-Mendoza AD, Pérez-Hernández N, Martínez-Magaña JJ, Rodríguez-Pérez JM. Genetic Polymorphisms of CCDC26 rs891835, rs6470745, and rs55705857 in Glioma Risk: A Systematic Review and Meta-analysis. Biochem Genet 2019; 57:583-605. [DOI: 10.1007/s10528-019-09911-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/07/2019] [Indexed: 01/03/2023]
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Andersson U, Degerman S, Dahlin AM, Wibom C, Johansson G, Bondy ML, Melin BS. The association between longer relative leukocyte telomere length and risk of glioma is independent of the potentially confounding factors allergy, BMI, and smoking. Cancer Causes Control 2018; 30:177-185. [PMID: 30560391 DOI: 10.1007/s10552-018-1120-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/06/2018] [Indexed: 12/28/2022]
Abstract
PURPOSE Previous studies have suggested an association between relative leukocyte telomere length (rLTL) and glioma risk. This association may be influenced by several factors, including allergies, BMI, and smoking. Previous studies have shown that individuals with asthma and allergy have shortened relative telomere length, and decreased risk of glioma. Though, the details and the interplay between rLTL, asthma and allergies, and glioma molecular phenotype is largely unknown. METHODS rLTL was measured by qPCR in a Swedish population-based glioma case-control cohort (421 cases and 671 controls). rLTL was related to glioma risk and health parameters associated with asthma and allergy, as well as molecular events in glioma including IDH1 mutation, 1p/19q co-deletion, and EGFR amplification. RESULTS Longer rLTL was associated with increased risk of glioma (OR = 1.16; 95% CI 1.02-1.31). Similar to previous reports, there was an inverse association between allergy and glioma risk. Specific, allergy symptoms including watery eyes was most strongly associated with glioma risk. High body mass index (BMI) a year prior diagnosis was significantly protective against glioma in our population. Adjusting for allergy, asthma, BMI, and smoking did not markedly change the association between longer rLTL and glioma risk. rLTL among cases was not associated with IDH1 mutation, 1p/19q co-deletion, or EGFR amplification, after adjusting for age at diagnosis and sex. CONCLUSIONS In this Swedish glioma case-control cohort, we identified that long rLTL increases the risk of glioma, an association not confounded by allergy, BMI, or smoking. This highlights the complex interplay of the immune system, rLTL and cancer risk.
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Affiliation(s)
- Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden.
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umea University, Umea, Sweden
| | - Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - Gunnar Johansson
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - Melissa L Bondy
- Department of Medicine, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Beatrice S Melin
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
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Damasceno S, Menezes NBD, Rocha CDS, Matos AHBD, Vieira AS, Moraes MFD, Martins AS, Lopes-Cendes I, Godard ALB. Transcriptome of the Wistar audiogenic rat (WAR) strain following audiogenic seizures. Epilepsy Res 2018; 147:22-31. [DOI: 10.1016/j.eplepsyres.2018.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 08/27/2018] [Indexed: 12/18/2022]
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Shi J, Dong B, Zhou P, Guan W, Peng Y. Functional network analysis of gene-phenotype connectivity associated with temozolomide. Oncotarget 2017; 8:87554-87567. [PMID: 29152101 PMCID: PMC5675653 DOI: 10.18632/oncotarget.20848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023] Open
Abstract
Rationale Glioma has a poor survival rate in patients even with aggressive treatment. Temozolomide (TMZ) is the standard chemotherapeutic choice for treating glioma, but TMZ treatment consistently leads to high resistance. Aim To investigate the underlying mechanisms of TMZ action with new therapeutic regimens in glioma. Methods and results The biological effects of TMZ mainly depend on the three following DNA repair systems: methylguanine methyltransferase (MGMT), mismatch repair (MMR) and base excision repair (BER). Based on related genes in these three systems, web-based tools containing data compiled from open-source databases, including DrugBank, STRING, WebGestalt and ClueGO, were queried, and five common genes along with the top fifteen pathways, including the glioma pathway, were identified. A genomic analysis of the six genes identified in the glioma pathway by cBioPortal indicated that TMZ might exert biological effects via interaction with the tumor protein P53(TP53) signaling axis. Finally, a survival analysis with the six genes in glioma cases (low-grade glioma and glioblastoma multiforme) was conducted using OncoLnc, which might provide directions for the future exploration of prognosis in glioma. Conclusions This study indicates that a functional network analysis resembles a "BioGPS", with the ability to draw a web-based scientific map that can productively and cost-effectively associate TMZ with its primary and secondary biological targets.
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Affiliation(s)
- Jia Shi
- Department of Neurosurgery, The Third Affiliated Hospital of Soochow University, Changzhou City, 213003, China
| | - Bo Dong
- Department of Neurosurgery, The Third Affiliated Hospital of Soochow University, Changzhou City, 213003, China
| | - Peng Zhou
- Department of Neurosurgery, The Third Affiliated Hospital of Soochow University, Changzhou City, 213003, China
| | - Wei Guan
- Department of Neurosurgery, The Third Affiliated Hospital of Soochow University, Changzhou City, 213003, China
| | - Ya Peng
- Department of Neurosurgery, The Third Affiliated Hospital of Soochow University, Changzhou City, 213003, China
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EGFR Amplification and IDH Mutations in Glioblastoma Patients of the Northeast of Morocco. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8045859. [PMID: 28785587 PMCID: PMC5530437 DOI: 10.1155/2017/8045859] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/11/2017] [Indexed: 02/06/2023]
Abstract
Glioblastomas are the most frequent and aggressive primary brain tumors which are expressing various evolutions, aggressiveness, and prognosis. Thus, the 2007 World Health Organization classification based solely on the histological criteria is no longer sufficient. It should be complemented by molecular analysis for a true histomolecular classification. The new 2016 WHO classification of tumors of the central nervous system uses molecular parameters in addition to histology to reclassify these tumors and reduce the interobserver variability. The aim of this study is to determine the prevalence of IDH mutations and EGFR amplifications in the population of the northeast region of Morocco and then to compare the results with other studies. Methods. IDH1 codon 132 and IDH2 codon 172 were directly sequenced and the amplification of exon 20 of EGFR gene was investigated by qPCR in 65 glioblastoma tumors diagnosed at the University Hospital of Fez between 2010 and 2014. Results. The R132H IDH1 mutation was observed in 8 of 65 tumor samples (12.31%). No mutation of IDH2 was detected. EGFR amplification was identified in 17 cases (26.15%). Conclusion. A systematic search of both histological and molecular markers should be requisite for a good diagnosis and a better management of glioblastomas.
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Relation between Established Glioma Risk Variants and DNA Methylation in the Tumor. PLoS One 2016; 11:e0163067. [PMID: 27780202 PMCID: PMC5079592 DOI: 10.1371/journal.pone.0163067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/01/2016] [Indexed: 01/08/2023] Open
Abstract
Genome-wide association studies and candidate gene studies have identified several genetic variants that increase glioma risk. The majority of these variants are non-coding and the mechanisms behind the increased risk in carriers are not known. In this study, we hypothesize that some of the established glioma risk variants induce aberrant DNA methylation in the developing tumor, either locally (gene-specific) or globally (genome-wide). In a pilot data set including 77 glioma patients, we used Illumina beadchip technology to analyze genetic variants in blood and DNA methylation in matched tumor samples. To validate our findings, we used data from the Cancer Genome Atlas, including 401 glioblastoma patients. Consensus clustering identified the glioma CpG island methylator phenotype (gCIMP) and two additional subgroups with distinct patterns of global DNA methylation. In the pilot dataset, gCIMP was associated with two genetic variants in CDKN2B-AS1, rs1412829 and rs4977756 (9p21.3, p = 8.1 x 10-7 and 4.8 x 10-5, respectively). The association was in the same direction in the TCGA dataset, although statistically significant only when combining individuals with AG and GG genotypes. We also investigated the relation between glioma risk variants and DNA methylation in the promoter region of genes located within 30 kb of each variant. One association in the pilot dataset, between the TERT risk variant rs2736100 and lower methylation of cg23827991 (in TERT; p = 0.001), was confirmed in the TCGA dataset (p = 0.001). In conclusion, we found an association between rs1412829 and rs4977756 (9p21.3, CDKN2B-AS1) and global DNA methylation pattern in glioma, for which a trend was seen also in the TCGA glioblastoma dataset. We also found an association between rs2736100 (in TERT) and levels of methylation at cg23827991 (localized in the same gene, 3.3 kbp downstream of the risk variant), which was validated in the TCGA dataset. Except for this one association, we did not find strong evidence for gene-specific DNA methylation mediated by glioma risk variants.
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