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D’Aguanno S, Buczkowicz P. Editorial: Methods in cancer genetics. Front Oncol 2023; 13:1227854. [PMID: 37469406 PMCID: PMC10353300 DOI: 10.3389/fonc.2023.1227854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Affiliation(s)
- Simona D’Aguanno
- Preclinical Models and New Therapeutic Agents Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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2
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Mirzaei G, Petreaca RC. Distribution of copy number variations and rearrangement endpoints in human cancers with a review of literature. Mutat Res 2022; 824:111773. [PMID: 35091282 DOI: 10.1016/j.mrfmmm.2021.111773] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs) which include deletions, duplications, inversions, translocations, and other forms of chromosomal re-arrangements are common to human cancers. In this report we investigated the pattern of these variations with the goal of understanding whether there exist specific cancer signatures. We used re-arrangement endpoint data deposited on the Catalogue of Somatic Mutations in Cancers (COSMIC) for our analysis. Indeed, we find that human cancers are characterized by specific patterns of chromosome rearrangements endpoints which in turn result in cancer specific CNVs. A review of the literature reveals tissue specific mutations which either drive these CNVs or appear as a consequence of CNVs because they confer an advantage to the cancer cell. We also identify several rearrangement endpoints hotspots that were not previously reported. Our analysis suggests that in addition to local chromosomal architecture, CNVs are driven by the internal cellular or nuclear physiology of each cancer tissue.
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Affiliation(s)
- Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University at Marion, Marion, OH, 43302, USA
| | - Ruben C Petreaca
- Department of Molecular Genetics, The Ohio State University at Marion, Marion, OH, 43302, USA; Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH, 43210, USA.
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3
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Sasaki S, Takeda M, Hirose T, Fujii T, Itami H, Uchiyama T, Morita K, Matsuda R, Yamada S, Nakagawa I, Ohbayashi C. Correlation of MTAP Immunohistochemistry With CDKN2A Status Assessed by Fluorescence In Situ Hybridization and Clinicopathological Features in CNS WHO Grade 2 and 3 Meningiomas: A Single Center Cohort Study. J Neuropathol Exp Neurol 2021; 81:117-126. [PMID: 34897475 DOI: 10.1093/jnen/nlab127] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CDKN2A homozygous deletion has occasionally been reported in atypical and anaplastic meningiomas and is considered as one of the genetic alterations commonly involved in their recurrence and malignant progression. Methylthioadenosine phosphorylase (MTAP) immunohistochemistry is a promising surrogate marker for CDKN2A homozygous deletion in different cancers but has not been examined in meningiomas. We performed CDKN2A FISH and MTAP immunohistochemistry on specimens from 30 patients with CNS WHO grade 2 (n = 27) and 3 (n = 3) meningiomas, including specimens from primary and recurrent tumors and then determined whether MTAP immunohistochemistry correlated with CDKN2A homozygous deletion and clinicopathological features. CDKN2A homozygous deletion was detected in 12% (3/26) of CNS WHO grade 2 and 67% (2/3) of CNS WHO grade 3 meningiomas; 3 cases exhibited temporal and/or spatial heterogeneity. MTAP loss was in excellent concordance with CDKN2A homozygous deletion (sensitivity; 100%, specificity; 100%). MTAP loss/CDKN2A homozygous deletion correlated with cellular proliferation (mitotic rate; p = 0.001, Ki-67 labeling index; p = 0.03) and poor prognosis (overall survival; p = 0.01, progression free survival; p < 0.001). Thus, MTAP immunostaining can be a surrogate marker for CDKN2A homozygous deletion in meningiomas, and MTAP loss/CDKN2A homozygous deletion may be an important prognostic factor for meningiomas.
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Affiliation(s)
- Shoh Sasaki
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
| | - Maiko Takeda
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
| | - Takanori Hirose
- Department of Diagnostic Pathology, Hyogo Cancer Center, Akashi, Hyogo, Japan (TH)
| | - Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
| | - Hiroe Itami
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
| | - Tomoko Uchiyama
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
| | - Kohei Morita
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
| | - Ryosuke Matsuda
- Department of Neurosurgery, Nara Medical University, Nara, Japan (RM, SY, IN)
| | - Shuichi Yamada
- Department of Neurosurgery, Nara Medical University, Nara, Japan (RM, SY, IN)
| | - Ichiro Nakagawa
- Department of Neurosurgery, Nara Medical University, Nara, Japan (RM, SY, IN)
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan (SS, MT, TF, HI, TU, KM, CO)
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4
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Hoogstrate Y, Komor MA, Böttcher R, van Riet J, van de Werken HJG, van Lieshout S, Hoffmann R, van den Broek E, Bolijn AS, Dits N, Sie D, van der Meer D, Pepers F, Bangma CH, van Leenders GJLH, Smid M, French PJ, Martens JWM, van Workum W, van der Spek PJ, Janssen B, Caldenhoven E, Rausch C, de Jong M, Stubbs AP, Meijer GA, Fijneman RJA, Jenster GW. Fusion transcripts and their genomic breakpoints in polyadenylated and ribosomal RNA-minus RNA sequencing data. Gigascience 2021; 10:6458609. [PMID: 34891161 PMCID: PMC8673554 DOI: 10.1093/gigascience/giab080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/08/2021] [Accepted: 11/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Fusion genes are typically identified by RNA sequencing (RNA-seq) without elucidating the causal genomic breakpoints. However, non-poly(A)-enriched RNA-seq contains large proportions of intronic reads that also span genomic breakpoints. RESULTS We have developed an algorithm, Dr. Disco, that searches for fusion transcripts by taking an entire reference genome into account as search space. This includes exons but also introns, intergenic regions, and sequences that do not meet splice junction motifs. Using 1,275 RNA-seq samples, we investigated to what extent genomic breakpoints can be extracted from RNA-seq data and their implications regarding poly(A)-enriched and ribosomal RNA-minus RNA-seq data. Comparison with whole-genome sequencing data revealed that most genomic breakpoints are not, or minimally, transcribed while, in contrast, the genomic breakpoints of all 32 TMPRSS2-ERG-positive tumours were present at RNA level. We also revealed tumours in which the ERG breakpoint was located before ERG, which co-existed with additional deletions and messenger RNA that incorporated intergenic cryptic exons. In breast cancer we identified rearrangement hot spots near CCND1 and in glioma near CDK4 and MDM2 and could directly associate this with increased expression. Furthermore, in all datasets we find fusions to intergenic regions, often spanning multiple cryptic exons that potentially encode neo-antigens. Thus, fusion transcripts other than classical gene-to-gene fusions are prominently present and can be identified using RNA-seq. CONCLUSION By using the full potential of non-poly(A)-enriched RNA-seq data, sophisticated analysis can reliably identify expressed genomic breakpoints and their transcriptional effects.
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Affiliation(s)
- Youri Hoogstrate
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Malgorzata A Komor
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - René Böttcher
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Department of Life Sciences, Barcelona Supercomputing Center, Barcelona 08034, Spain
| | - Job van Riet
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Harmen J G van de Werken
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands.,Cancer Computational Biology Center, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | - Evert van den Broek
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands.,Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen 9713GZ, The Netherlands
| | - Anne S Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Natasja Dits
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - Daoud Sie
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | | | | | - Chris H Bangma
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | | | - Marcel Smid
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Pim J French
- Department of Neurology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | - Peter J van der Spek
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | | | | | | | | | - Andrew P Stubbs
- Department of Pathology, Erasmus Medical Center, Rotterdam 3015GD, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam 3015GD, The Netherlands
| | - Guido W Jenster
- Department of Urology, Erasmus Medical Center Cancer Institute, Wytemaweg 80, Rotterdam 3015GD, The Netherlands
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5
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Hu Q, Qin Y, Ji S, Shi X, Dai W, Fan G, Li S, Xu W, Liu W, Liu M, Zhang Z, Ye Z, Zhou Z, Yang J, Zhuo Q, Yu X, Li M, Xu X. MTAP deficiency-induced metabolic reprogramming creates a vulnerability to co-targeting de novo purine synthesis and glycolysis in pancreatic cancer. Cancer Res 2021; 81:4964-4980. [PMID: 34385182 DOI: 10.1158/0008-5472.can-20-0414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/18/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022]
Abstract
Methylthioadenosine phosphorylase (MTAP) is a key enzyme associated with the salvage of methionine and adenine that is deficient in 20%-30% of pancreatic cancer. Our previous study revealed that MTAP-deficiency indicates a poor prognosis for pancreatic ductal adenocarcinoma (PDAC) patients. In this study, bioinformatics analysis of The Cancer Genome Atlas (TCGA) data indicated that PDACs with MTAP deficiency display a signature of elevated glycolysis. Metabolomics studies showed that that MTAP deletion-mediated metabolic reprogramming enhanced glycolysis and de novo purine synthesis in pancreatic cancer cells. Western blot analysis revealed that MTAP knockout stabilized hypoxia-inducible factor 1α (HIF-1α) protein via posttranslational phosphorylation. RIO kinase 1 (RIOK1), a downstream kinase upregulated in MTAP-deficient cells, interacted with and phosphorylated HIF-1α to regulate its stability. In vitro experiments demonstrated that the glycolysis inhibitor 2-deoxy-D-glucose (2-DG) and the de novo purine synthesis inhibitor L-alanosine synergized to kill MTAP-deficient pancreatic cancer cells. Collectively, these results reveal that MTAP deficiency drives pancreatic cancer progression by inducing metabolic reprogramming, providing a novel target and therapeutic strategy for treating MTAP-deficient disease.
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Affiliation(s)
- Qiangsheng Hu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Yi Qin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
- Cancer Research Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shunrong Ji
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xiuhui Shi
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Weixing Dai
- Cancer Research Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guixiong Fan
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Shuo Li
- Shanghai Pancreatic Cancer Institute, Shanghai, China
| | - Wenyan Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wensheng Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Mengqi Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Zheng Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Zeng Ye
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Zhijun Zhou
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Jingxuan Yang
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Qifeng Zhuo
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Min Li
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.
| | - Xiaowu Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
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6
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Magallón-Lorenz M, Fernández-Rodríguez J, Terribas E, Creus-Batchiller E, Romagosa C, Estival A, Perez Sidelnikova D, Salvador H, Villanueva A, Blanco I, Carrió M, Lázaro C, Serra E, Gel B. Chromosomal translocations inactivating CDKN2A support a single path for malignant peripheral nerve sheath tumor initiation. Hum Genet 2021; 140:1241-1252. [PMID: 34059954 DOI: 10.1007/s00439-021-02296-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/24/2021] [Indexed: 12/22/2022]
Abstract
Malignant peripheral nerve sheath tumors (MPNST) are aggressive soft tissue sarcomas with poor prognosis, developing either sporadically or in persons with neurofibromatosis type 1 (NF1). Loss of CDKN2A/B is an important early event in MPNST progression. However, many reported MPNSTs exhibit partial or no inactivation of CDKN2A/B, raising the question of whether there is more than one molecular path for MPNST initiation. We present here a comprehensive genomic analysis of MPNST cell lines and tumors to explore in depth the status of CDKN2A. After accounting for CDKN2A deletions and point mutations, we uncovered a previously unnoticed high frequency of chromosomal translocations involving CDKN2A in both MPNST cell lines and primary tumors. Most identified translocation breakpoints were validated by PCR amplification and Sanger sequencing. Many breakpoints clustered in an intronic 500 bp hotspot region adjacent to CDKN2A exon 2. We demonstrate the bi-allelic inactivation of CDKN2A in all tumors (n = 15) and cell lines (n = 8) analyzed, supporting a single molecular path for MPNST initiation in both sporadic and NF1-related MPNSTs. This general CDKN2A inactivation in MPNSTs has implications for MPNST diagnostics and treatment. Our findings might be relevant for other tumor types with high frequencies of CDKN2A inactivation.
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Affiliation(s)
- Miriam Magallón-Lorenz
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP)-PMPPC, Badalona, 08916, Barcelona, Spain
| | - Juana Fernández-Rodríguez
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Ernest Terribas
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP)-PMPPC, Badalona, 08916, Barcelona, Spain.,Oncohematology Area, Health Research Institute of the Balearic Islands (IdISBa), Palma de Mallorca, Illes Balears, Spain
| | - Edgar Creus-Batchiller
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cleofe Romagosa
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.,Pathology Department, Hospital Universitari Vall d'Hebron and Vall d'Hebron Research Institut (VHIR), 08035, Barcelona, Spain.,Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Estival
- B-ARGO Group, Catalan Institute of Oncology - Hospital Universitari Germans Tries i Pujol, Badalona, 08916, Barcelona, Spain
| | - Diana Perez Sidelnikova
- Plastic Surgery Service, Functional Sarcoma Unit, ICO-HUB, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Héctor Salvador
- Pediatric Oncology Department, Sant Joan de Déu Barcelona Children's Hospital, 08950, Barcelona, Spain
| | - Alberto Villanueva
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance (ProCURE), ICO-IDIBELL, L'Hospitalet del Llobregat, 08908, Barcelona, Spain
| | - Ignacio Blanco
- Programa d'Assessorament i Genètica Clínica, Hospital Universitari Germans Trias i Pujol, Badalona, 08916, Barcelona, Spain
| | - Meritxell Carrió
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP)-PMPPC, Badalona, 08916, Barcelona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Program in Molecular Mechanisms and Experimental Therapy in Oncology (ONCOBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Eduard Serra
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP)-PMPPC, Badalona, 08916, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
| | - Bernat Gel
- Hereditary Cancer Group, Germans Trias i Pujol Research Institute (IGTP)-PMPPC, Badalona, 08916, Barcelona, Spain. .,Departament de Fonaments Clínics, Universitat de Barcelona, 08036, Barcelona, Spain.
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7
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Funakoshi Y, Hata N, Takigawa K, Arita H, Kuga D, Hatae R, Sangatsuda Y, Fujioka Y, Sako A, Umehara T, Yoshitake T, Togao O, Hiwatashi A, Yoshimoto K, Iwaki T, Mizoguchi M. Clinical significance of CDKN2A homozygous deletion in combination with methylated MGMT status for IDH-wildtype glioblastoma. Cancer Med 2021; 10:3177-3187. [PMID: 33838014 PMCID: PMC8124111 DOI: 10.1002/cam4.3860] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVE Accumulating evidence from recent molecular diagnostic studies has indicated the prognostic significance of various genetic markers for patients with glioblastoma (GBM). To evaluate the impact of such genetic markers on prognosis, we retrospectively analyzed the outcomes of patients with IDH-wildtype GBM in our institution. In addition, to assess the impact of bevacizumab (BEV) treatment, we compared overall survival (OS) between the pre- and post-BEV eras. METHODS We analyzed the data of 100 adult patients (over 18 years old) with IDH-wildtype GBM from our database between February 2006 and October 2018. Genetic markers, such as MGMT methylation status, EGFR amplification, CDKN2A homozygous deletion, and clinical factors were analyzed by evaluating the patients' OS. RESULTS CDKN2A homozygous deletion showed no significant impact on OS in patients with methylated MGMT status (p = 0.5268), whereas among patients with unmethylated MGMT status, there was a significant difference in OS between patients with and without CDKN2A homozygous deletion (median OS: 14.7 and 16.9 months, respectively, p = 0.0129). This difference was more evident in the pre-BEV era (median OS: 10.1 and 15.6 months, respectively, p = 0.0351) but has become nonsignificant in the post-BEV era (median OS: 16.0 and 16.9 months, respectively, p = 0.1010) due to OS improvement in patients with CDKN2A homozygous deletion. However, these findings could not be validated in The Cancer Genome Atlas cohort. CONCLUSIONS MGMT and CDKN2A status subdivided our cohort into three race-specific groups with different prognoses. Our findings indicate that BEV approval in Japan led to OS improvement exclusively for patients with concurrent unmethylated MGMT status and CDKN2A homozygous deletion.
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Affiliation(s)
- Yusuke Funakoshi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Takigawa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideyuki Arita
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Aki Sako
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toru Umehara
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tadamasa Yoshitake
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Osamu Togao
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akio Hiwatashi
- Department of Clinical Radiology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.,Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Toru Iwaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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8
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MTAP-deficiency could predict better treatment response in advanced lung adenocarcinoma patients initially treated with pemetrexed-platinum chemotherapy and bevacizumab. Sci Rep 2020; 10:843. [PMID: 31965001 PMCID: PMC6972892 DOI: 10.1038/s41598-020-57812-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022] Open
Abstract
To investigate the predictive value of methylthioadenosine phosphorylase (MTAP) on treatment response and survival in advanced lung adenocarcinoma. MTAP expression was detected by immunohistochemistry. Treatment response and survival were compared according to MTAP expression level. The results indicated MTAP-low expression was observed in 61.2% (101/165) of all patients. The objective response rate and disease control rate improved in the MTAP-low group (64.4% vs 46.9%, p = 0.035; 92.1% vs. 79.7%, p = 0.03; respectively). The median progression-free survival and survival time in the MTAP-low group were significantly lower than that in the MTAP-high group (8.1 vs. 13.1 months, p = 0.002; 22 vs. 32 months, p = 0.044). Multivariate analysis demonstrated that brain metastasis (HR 1.55, p = 0.046), thoracic radiation (HR 0.52, p = 0.026), and MTAP-low expression (HR 1.36, p = 0.038) were independent factors on survival. It is concluded that MTAP-low expression could predict improved treatment response but worsened survival in advanced lung adenocarcinoma.
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9
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Pelosi G, Sabella G, Cannone M, Balladore E, Papanikolaou N, Incarbone M, Zompatori M, Harari S, Bedini AV. Parietal Pleura-Based Malignant Perivascular Epithelioid Cell Neoplasm Protruding Into Serous Cavity: A Hitherto Unrecognized Occurrence. J Thorac Oncol 2019; 15:462-466. [PMID: 31812753 DOI: 10.1016/j.jtho.2019.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/20/2019] [Accepted: 11/22/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy; Interhospital Pathology Division, IRCCS MultiMedica, Milan, Italy.
| | - Giovanna Sabella
- Interhospital Pathology Division, IRCCS MultiMedica, Milan, Italy
| | - Maria Cannone
- Interhospital Pathology Division, IRCCS MultiMedica, Milan, Italy
| | | | | | | | - Maurizio Zompatori
- Department of Radiology, San Giuseppe Hospital, IRCCS MultiMedica, Milan, Italy
| | - Sergio Harari
- Department of Medical Sciences and Division of Pneumology, San Giuseppe Hospital, IRCCS MultiMedica, Milan, Italy
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Zeng J, Johnson A, Shufean MA, Kahle M, Yang D, Woodman SE, Vu T, Moorthy S, Holla V, Meric-Bernstam F. Operationalization of Next-Generation Sequencing and Decision Support for Precision Oncology. JCO Clin Cancer Inform 2019; 3:1-12. [PMID: 31550176 PMCID: PMC6874004 DOI: 10.1200/cci.19.00089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2019] [Indexed: 12/18/2022] Open
Abstract
Genomic testing has become a part of routine oncology care and plays critical roles in diagnosis, prognostic assessment, and treatment selection. Thus, in parallel, the variety of genomic testing providers and sequencing platforms has grown exponentially. Selection of the best-fit panel for each case can be daunting, with many factors to consider. Among them is whether alteration interpretation and therapy/clinical trial matching are included and/or sufficient. In this article, we review some common commercially available sequencing platforms for the genes and types of alterations tested, samples needed, and reporting content provided. We review publicly available resources for a do-it-yourself approach to alteration interpretation when it is not provided or when supplemental research is needed, along with resources to identify genomically matched treatment options that are approved and/or investigational. However, with both commercially provided interpretation and publicly available resources, there are still caveats and limitations that can stem from insufficient or ambiguous nomenclature as well as from the presentation of information. Use cases in which clinical decision making was affected are discussed. After treatment options are identified, it is important to assess the level of evidence for use within the patient's tumor type and molecular profile. However, numerous level-of-evidence scales have been published in recent years, so we provide a publicly available tool to facilitate interoperability. The level of evidence, along with other factors, such as allelic frequency and copy number, can be used to prioritize treatment options when multiple are identified.
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Affiliation(s)
- Jia Zeng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Amber Johnson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Md Abu Shufean
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Kahle
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dong Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Thuy Vu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shhyam Moorthy
- The University of Texas MD Anderson Cancer Center, Houston, TX
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