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Prashanth S, Radha Maniswami R, Rajajeyabalachandran G, Jegatheesan SK. SETDB1, an H3K9-specific methyltransferase: An attractive epigenetic target to combat cancer. Drug Discov Today 2024; 29:103982. [PMID: 38614159 DOI: 10.1016/j.drudis.2024.103982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) is an important epigenetic regulator catalyzing histone H3 lysine 9 (H3K9) methylation, specifically di-/tri-methylation. This regulation promotes gene silencing through heterochromatin formation. Aberrant SETDB1 expression, and its oncogenic role is evident in many cancers. Thus, SETDB1 is a valid target with novel therapeutic benefits. In this review, we explore the structural and biochemical features of SETDB1, its regulatory mechanisms, and its role in various cancers. We also discuss recent discoveries in small molecules targeting SETDB1 and provide suggestions for future research.
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Affiliation(s)
- Seema Prashanth
- Informatics, AI & ML, Jubilant Biosys Ltd., Bangalore, India
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Ma T, Xu F, Hou Y, Shu Y, Zhao Z, Zhang Y, Bai L, Feng L, Zhong L. SETDB1: Progress and prospects in cancer treatment potential and inhibitor research. Bioorg Chem 2024; 145:107219. [PMID: 38377821 DOI: 10.1016/j.bioorg.2024.107219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/03/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
SET domain bifurcated methyltransferase 1 (SETDB1) serves as a histone lysine methyltransferase, catalyzing the di- and tri-methylation of histone H3K9. Mounting evidence indicates that the abnormal expression or activity of SETDB1, either through amplification or mutation, plays a crucial role in tumorigenesis and progression. This is particularly evident in the context of tumor immune evasion and resistance to immune checkpoint blockade therapy. Furthermore, there is a robust association between SETDB1 dysregulation and an unfavorable prognosis across various types of tumors. The oncogenic role of SETDB1 primarily arises from its methyltransferase function, which contributes to the establishment of a condensed and transcriptionally inactive heterochromatin state. This results in the inactivation of genes that typically hinder cancer development and silencing of retrotransposons that could potentially trigger an immune response. These findings underscore the substantial potential for SETDB1 as an anti-tumor therapeutic target. Nevertheless, despite significant strides in recent years in tumor biology research, challenges persist in SETDB1-targeted therapy. To better facilitate the development of anti-tumor therapy targeting SETDB1, we have conducted a comprehensive review of SETDB1 in this account. We present the structure and function of SETDB1, its role in various tumors and immune regulation, as well as the advancements made in SETDB1 antagonists. Furthermore, we discuss the challenges encountered and provide perspectives for the development of SETDB1-targeted anti-tumor therapy.
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Affiliation(s)
- Tingnan Ma
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Feifei Xu
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China; State Key Laboratory of Southwestern Chinese Medicine Resources; Key Laboratory of Standardization of Chinese Herbal Medicines of Ministry of Education, Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Yingying Hou
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Yongquan Shu
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Zhipeng Zhao
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Yaru Zhang
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Lan Bai
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China.
| | - Lu Feng
- Department of Emergency, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610041, China.
| | - Lei Zhong
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China.
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Febres-Aldana CA, Fanaroff R, Offin M, Zauderer MG, Sauter JL, Yang SR, Ladanyi M. Diffuse Pleural Mesothelioma: Advances in Molecular Pathogenesis, Diagnosis, and Treatment. Annu Rev Pathol 2024; 19:11-42. [PMID: 37722697 DOI: 10.1146/annurev-pathol-042420-092719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Diffuse pleural mesothelioma (DPM) is a highly aggressive malignant neoplasm arising from the mesothelial cells lining the pleural surfaces. While DPM is a well-recognized disease linked to asbestos exposure, recent advances have expanded our understanding of molecular pathogenesis and transformed our clinical practice. This comprehensive review explores the current concepts and emerging trends in DPM, including risk factors, pathobiology, histologic subtyping, and therapeutic management, with an emphasis on a multidisciplinary approach to this complex disease.
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Affiliation(s)
- Christopher A Febres-Aldana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Rachel Fanaroff
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jennifer L Sauter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA; ,
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Xu M, Tu Y, Bi W, Lundberg MZ, Klooster I, Fletcher JA, Ou WB. SETDB1 tumour suppressor roles in near-haploid mesothelioma involve TP53. Br J Cancer 2023; 129:531-540. [PMID: 37369845 PMCID: PMC10403575 DOI: 10.1038/s41416-023-02330-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 05/17/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Mutational inactivation of the SETDB1 histone methyltransferase is found in a subset of mesothelioma, particularly in cases with near-haploidy and TP53 mutations. However, the tumourigenic consequences of SETDB1 inactivation are poorly understood. METHODS In this study, we investigated SETDB1 tumour suppressor functions in mesothelioma and explored biologic relationships between SETDB1 and TP53. RESULTS Immunoblotting of early passage cultures showed that SETDB1 was undetectable in 7 of 8 near-haploid mesotheliomas whereas SETDB1 expression was retained in each of 13 near-diploid mesotheliomas. TP53 aberrations were present in 5 of 8 near-haploid mesotheliomas compared to 2 of 13 near-diploid mesotheliomas, and BAP1 inactivation was demonstrated only in near-diploid mesotheliomas, indicating that near-haploid and near-diploid mesothelioma have distinct molecular and biologic profiles. Lentiviral SETDB1 restoration in near-haploid mesotheliomas (MESO257 and MESO542) reduced cell viability, colony formation, reactive oxygen species levels, proliferative marker cyclin A expression, and inhibited growth of MESO542 xenografts. The combination of SETDB1 restoration with pemetrexed and/or cisplatin treatment additively inhibited tumour growth in vitro and in vivo. Furthermore, SETDB1 restoration upregulated TP53 expression in MESO542 and MESO257, whereas SETDB1 knockdown inhibited mutant TP53 expression in JMN1B near-haploid mesothelioma cells. Likewise, TP53 knockdown inhibited SETDB1 expression. Similarly, immunoblotting evaluations of ten near-diploid mesothelioma biopsies and analysis of TCGA expression profiles showed that SETDB1 expression levels paralleled TP53 expression. CONCLUSION These findings demonstrate that SETDB1 inactivation in near-haploid mesothelioma is generally associated with complete loss of SETDB1 protein expression and dysregulates TP53 expression. Targeting SETDB1 pathways could be an effective therapeutic strategy in these often untreatable tumours.
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Affiliation(s)
- Mengting Xu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yuqing Tu
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Wenhui Bi
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Meijun Z Lundberg
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Isabella Klooster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jonathan A Fletcher
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wen-Bin Ou
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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Felley-Bosco E. Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and Immunotherapy. Cancers (Basel) 2023; 15:cancers15112969. [PMID: 37296931 DOI: 10.3390/cancers15112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Recent high-throughput RNA sequencing technologies have confirmed that a large part of the non-coding genome is transcribed. The priority for further investigations is nevertheless generally given in cancer to coding sequences, due to the obvious interest of finding therapeutic targets. In addition, several RNA-sequencing pipelines eliminate repetitive sequences, which are difficult to analyze. In this review, we shall focus on endogenous retroviruses. These sequences are remnants of ancestral germline infections by exogenous retroviruses. These sequences represent 8% of human genome, meaning four-fold the fraction of the genome encoding for proteins. These sequences are generally mostly repressed in normal adult tissues, but pathological conditions lead to their de-repression. Specific mesothelioma-associated endogenous retrovirus expression and their association to clinical outcome is discussed.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, Zürich University Hospital, 8091 Zurich, Switzerland
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Vannucchi M, Pennati V, Mencaroni C, Defraia C, Bardhi L, Castiglione F, Bellan C, Comin CE. KRAS Mutations Are Associated with Shortened Survival in Patients with Epithelioid Malignant Pleural Mesothelioma. Cancers (Basel) 2023; 15:cancers15072072. [PMID: 37046732 PMCID: PMC10093256 DOI: 10.3390/cancers15072072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive malignancy of the pleural surface that includes three major histologic subtypes, epitheliod, sarcomatoid and biphasic. Epithelioid mesothelioma is usually associated with better prognosis. The genetic mechanisms driving MPM, the possible target mutations and the correlation with overall survival remain largely unsettled. We performed target exome sequencing in 29 cases of MPM aimed at identifying somatic mutations and, eventually, their correlation with phenotypic traits and prognostic significance. We found that KRAS mutations, occurring in 13.7% of cases, were associated with shortened median survival (7.6 versus 32.6 months in KRAS wild-type; p = 0.005), as it was the occurrence of any ≥3 mutations (7.6 versus 37.6 months; p = 0.049). Conversely, the presence of KDR single nucleotide polymorphism p.V297I (rs2305948) resulted in a favorable variable for survival (NR versus 23.4 months; p = 0.026). With the intrinsic limitations of a small number of cases and patient heterogeneity, results of this study contribute to the characterization of the mutation profile of MPM and the impact of selected somatic mutations, and possibly KDR polymorphism, on prognosis.
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Affiliation(s)
- Margherita Vannucchi
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
- Correspondence:
| | - Veronica Pennati
- Division of Pathological anatomy, Department of Medical and Surgical Critical Care, University of Florence, 50121 Florence, Italy
| | - Clelia Mencaroni
- Division of Pathological anatomy, Department of Medical and Surgical Critical Care, University of Florence, 50121 Florence, Italy
| | - Chiara Defraia
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Ledi Bardhi
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Francesca Castiglione
- Division of Pathological anatomy, Department of Medical and Surgical Critical Care, University of Florence, 50121 Florence, Italy
| | - Cristiana Bellan
- Section of Pathology, Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Camilla Eva Comin
- Department of Experimental and Clinical Medicine, Section of Surgery, Histopathology and Molecular Pathology, University of Florence, 50121 Florence, Italy
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Paajanen J, Bueno R, De Rienzo A. The Rocky Road from Preclinical Findings to Successful Targeted Therapy in Pleural Mesothelioma. Int J Mol Sci 2022; 23:13422. [PMID: 36362209 PMCID: PMC9658134 DOI: 10.3390/ijms232113422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/19/2023] Open
Abstract
Pleural mesothelioma (PM) is a rare and aggressive disease that arises from the mesothelial cells lining the pleural cavity. Approximately 80% of PM patients have a history of asbestos exposure. The long latency period of 20-40 years from the time of asbestos exposure to diagnosis, suggests that multiple somatic genetic alterations are required for the tumorigenesis of PM. The genomic landscape of PM has been characterized by inter- and intratumor heterogeneity associated with the impairment of tumor suppressor genes such as CDKN2A, NF2, and BAP1. Current systemic therapies have shown only limited efficacy, and none is approved for patients with relapsed PM. Advances in understanding of the molecular landscape of PM has facilitated several biomarker-driven clinical trials but so far, no predictive biomarkers for targeted therapies are in clinical use. Recent advances in the PM genetics have provided optimism for successful molecular strategies in the future. Here, we summarize the molecular mechanism underlying PM pathogenesis and review potential therapeutic targets.
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Affiliation(s)
| | - Raphael Bueno
- The Thoracic Surgery Oncology Laboratory and The International Mesothelioma Program, Division of Thoracic Surgery and the Lung Center, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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Lin X, Xiao M, Chen Z, Ding C, Zhang T, Li Q, Xu Y. Pancancer Analyses Reveal Genomics and Clinical Characteristics of the SETDB1 in Human Tumors. Journal of Oncology 2022; 2022:1-40. [PMID: 35656340 PMCID: PMC9152430 DOI: 10.1155/2022/6115878] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022]
Abstract
Background. Malignant tumor is one of the most common diseases that seriously affect human health. The prior literature has reported the biological function and potential therapeutic targets of SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) as an oncogene. However, SETDB1 has rarely been analyzed from a pan-cancer perspective. Methods. Bioinformatics analysis tools and databases, including GeneCards, National Center for Biotechnology Information (NCBI), UniProt, Illustrator for Biological Sequences (IBS), Human Protein Atlas (HPA), GEPIA, TIMER2, Sangerbox 3.0, UALCAN, Kaplan-Meier (K-M) plotter, cBioPortal, Catalogue Of Somatic Mutations In Cancer (COSMIC), PhosphoSitePlus, TISIDB, STRING, and GeneMANIA, were utilized to clarify the biological functions and clinical significance of SETDB1 from a pan-cancer perspective. Results. In this study, the pan-cancer analysis demonstrated that SETDB1 showed significantly differential expression in most tumor tissues and paracancerous tissues, and SETDB1 expression was associated with clinicopathological features and clinical prognosis. We also found that SETDB1 mutations occurred in most tumors and were related to tumorigenesis. In addition, DNA methylation of SETDB1 primarily occurred at the cg10444928 site and was associated with prognosis in several human tumors. The predicted phosphorylation site of SETDB1 was Ser1006. We found that SETDB1 was significantly related to the specific tumor-infiltrating immune cell populations and expression of clinically targetable immune checkpoints and may be a promising immunotherapy target. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses also indicated that SETDB1 may function as crucial regulator in carcinogenesis of human cancers. Conclusions. SETDB1 is an important oncogene involved in tumorigenesis and tumor progression through different biological mechanisms. Furthermore, SETDB1 may be a potential therapeutic target for cancer treatment.
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Offin M, Yang SR, Egger J, Jayakumaran G, Spencer RS, Lopardo J, Nash GM, Cercek A, Travis WD, Kris MG, Ladanyi M, Sauter JL, Zauderer MG. Molecular Characterization of Peritoneal Mesotheliomas. J Thorac Oncol 2022; 17:455-460. [PMID: 34648949 PMCID: PMC8882128 DOI: 10.1016/j.jtho.2021.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Malignant peritoneal mesothelioma (MPeM) is clinically distinct and less studied than malignant pleural mesothelioma. We report the genomic and immunophenotypic features of a prospectively collected MPeM cohort. METHODS Next-generation sequencing (NGS) was performed on MPeM tumors. Genomic near-haploidization (GNH) was assessed. WT1, BAP1, mesothelin, VISTA, and programmed death-ligand 1 were evaluated by immunohistochemistry (IHC) when tissue was available. Overall survival was stratified by selected genomic and IHC features. RESULTS A total of 50 consented patients with MPeM (45 epithelioid, 5 nonepithelioid) were studied exhibiting common alterations in BAP1 (60%; 30 of 50), NF2 (24%; 12 of 50) SETD2 (22%; 11 of 50), and TP53 (16%; 8 of 50). A total of 76% (38 of 50) of specimens were assessable for allele-specific copy number analysis; 8% (3 of 38) had GNH. IHC positivity rates were 93% (37 of 40) for mesothelin, 96% (46 of 48) for WT1, 50% (19 of 38) for programmed death-ligand 1, and 89% (34 of 38) for VISTA. BAP1 loss by IHC was observed in 76% (29 of 38), including five wild-type on NGS. Combining NGS and IHC for BAP1, overall survival was worse with alteration or loss compared with wild-type or retained in all patients (n = 37 versus 13, 43.8 versus 117.3 mo, p = 0.04) Three of 30 patients had a pathogenic germline variant: POT1 I78T, MUTYH R109Y, and BAP1 E402∗. CONCLUSIONS MPeM has distinct biology and genomic composition. CDKN2A/B alterations were rare in MPeM, whereas BAP1, NF2, TP53, SETD2, and LATS2 were common. BAP1 alteration/loss was associated with shorter survival when all patients were included. A notable minority of specimens had GNH associated with NF2, TP53, and SETDB1 mutations. Pathogenic germline mutations were found in 3 of 30 patients.
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Affiliation(s)
- Michael Offin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York.
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacklynn Egger
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rowanne S Spencer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jessica Lopardo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Garrett M Nash
- Department of Colorectal Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Weill Cornell Medical College, New York, New York; Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark G Kris
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jennifer L Sauter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marjorie G Zauderer
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
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Hajj GNM, Cavarson CH, Pinto CAL, Venturi G, Navarro JR, Lima VCCD. Malignant pleural mesothelioma: an update. J Bras Pneumol 2021; 47:e20210129. [PMID: 34909922 PMCID: PMC8836658 DOI: 10.36416/1806-3756/e20210129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/11/2021] [Indexed: 12/14/2022] Open
Abstract
Malignant mesotheliomas are rare types of cancers that affect the mesothelial surfaces, usually the pleura and peritoneum. They are associated with asbestos exposure, but due to a latency period of more than 30 years and difficult diagnosis, most cases are not detected until they reach advanced stages. Treatment options for this tumor type are very limited and survival ranges from 12 to 36 months. This review discusses the molecular physiopathology, current diagnosis, and latest therapeutic options for this disease.
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Affiliation(s)
- Glaucia N M Hajj
- Instituto International de Pesquisa, A.C. Camargo Cancer Center, São Paulo (SP), Brasil.,Instituto Nacional de Oncogenômica e Inovação Terapêutica, São Paulo (SP), Brasil
| | - Carolina H Cavarson
- Instituto International de Pesquisa, A.C. Camargo Cancer Center, São Paulo (SP), Brasil.,Instituto Nacional de Oncogenômica e Inovação Terapêutica, São Paulo (SP), Brasil
| | | | - Gabriela Venturi
- Instituto International de Pesquisa, A.C. Camargo Cancer Center, São Paulo (SP), Brasil.,BP Mirante, São Paulo (SP), Brasil
| | | | - Vladmir C Cordeiro de Lima
- Instituto Nacional de Oncogenômica e Inovação Terapêutica, São Paulo (SP), Brasil.,Rede D'Or, São Paulo (SP), Brasil
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Johnson BW, Takahashi K, Cheng YY. Preclinical Models and Resources to Facilitate Basic Science Research on Malignant Mesothelioma - A Review. Front Oncol 2021; 11:748444. [PMID: 34900693 PMCID: PMC8660093 DOI: 10.3389/fonc.2021.748444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/25/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant mesothelioma is an aggressive cancer with poor prognosis, predominantly caused by human occupational exposure to asbestos. The global incidence of mesothelioma is predicted to increase as a consequence of continued exposure to asbestos from a variety of sources, including construction material produced in the past in developed countries, as well as those currently being produced in developing countries. Mesothelioma typically develops after a long latency period and consequently it is often diagnosed in the clinic at an advanced stage, at which point standard care of treatment, such as chemo- and radio-therapy, are largely ineffective. Much of our current understanding of mesothelioma biology, particularly in relation to disease pathogenesis, diagnosis and treatment, can be attributed to decades of preclinical basic science research. Given the postulated rising incidence in mesothelioma cases and the limitations of current diagnostic and treatment options, continued preclinical research into mesothelioma is urgently needed. The ever-evolving landscape of preclinical models and laboratory technology available to researchers have made it possible to study human disease with greater precision and at an accelerated rate. In this review article we provide an overview of the various resources that can be exploited to facilitate an enhanced understanding of mesothelioma biology and their applications to research aimed to improve the diagnosis and treatment of mesothelioma. These resources include cell lines, animal models, mesothelioma-specific biobanks and modern laboratory techniques/technologies. Given that different preclinical models and laboratory technologies have varying limitations and applications, they must be selected carefully with respect to the intended objectives of the experiments. This review therefore aims to provide a comprehensive overview of the various preclinical models and technologies with respect to their advantages and limitations. Finally, we will detail about a highly valuable preclinical laboratory resource to curate high quality mesothelioma biospecimens for research; the biobank. Collectively, these resources are essential to the continued advancement of precision medicine to curtail the increasing health burden caused by malignant mesothelioma.
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Affiliation(s)
| | - Ken Takahashi
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
| | - Yuen Yee Cheng
- Asbestos Diseases Research Institute, Sydney, NSW, Australia
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12
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Shamseddin M, Obacz J, Garnett MJ, Rintoul RC, Francies HE, Marciniak SJ. Use of preclinical models for malignant pleural mesothelioma. Thorax 2021; 76:1154-1162. [PMID: 33692175 PMCID: PMC8526879 DOI: 10.1136/thoraxjnl-2020-216602] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/16/2021] [Accepted: 02/26/2021] [Indexed: 01/08/2023]
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive cancer most commonly caused by prior exposure to asbestos. Median survival is 12-18 months, since surgery is ineffective and chemotherapy offers minimal benefit. Preclinical models that faithfully recapitulate the genomic and histopathological features of cancer are critical for the development of new treatments. The most commonly used models of MPM are two-dimensional cell lines established from primary tumours or pleural fluid. While these have provided some important insights into MPM biology, these cell models have significant limitations. In order to address some of these limitations, spheroids and microfluidic chips have more recently been used to investigate the role of the three-dimensional environment in MPM. Efforts have also been made to develop animal models of MPM, including asbestos-induced murine tumour models, MPM-prone genetically modified mice and patient-derived xenografts. Here, we discuss the available in vitro and in vivo models of MPM and highlight their strengths and limitations. We discuss how newer technologies, such as the tumour-derived organoids, might allow us to address the limitations of existing models and aid in the identification of effective treatments for this challenging-to-treat disease.
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Affiliation(s)
- Marie Shamseddin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Joanna Obacz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Robert Campbell Rintoul
- Department of Oncology, University of Cambridge, Cambridge, Cambridgeshire, UK
- Department of Thoracic Oncology, Royal Papworth Hospital NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | | | - Stefan John Marciniak
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, Cambridgeshire, UK
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13
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Obacz J, Yung H, Shamseddin M, Linnane E, Liu X, Azad AA, Rassl DM, Fairen-Jimenez D, Rintoul RC, Nikolić MZ, Marciniak SJ. Biological basis for novel mesothelioma therapies. Br J Cancer 2021; 125:1039-1055. [PMID: 34226685 PMCID: PMC8505556 DOI: 10.1038/s41416-021-01462-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/13/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Mesothelioma is an aggressive cancer that is associated with exposure to asbestos. Although asbestos is banned in several countries, including the UK, an epidemic of mesothelioma is predicted to affect middle-income countries during this century owing to their heavy consumption of asbestos. The prognosis for patients with mesothelioma is poor, reflecting a failure of conventional chemotherapy that has ultimately resulted from an inadequate understanding of its biology. However, recent work has revolutionised the study of mesothelioma, identifying genetic and pathophysiological vulnerabilities, including the loss of tumour suppressors, epigenetic dysregulation and susceptibility to nutrient stress. We discuss how this knowledge, combined with advances in immunotherapy, is enabling the development of novel targeted therapies.
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Affiliation(s)
- Joanna Obacz
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Henry Yung
- UCL Respiratory, Division of Medicine Rayne Institute, University College London, London, UK
| | - Marie Shamseddin
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Saffron Walden, UK
| | - Emily Linnane
- Adsorption & Advanced Materials Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Xiewen Liu
- Adsorption & Advanced Materials Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Arsalan A Azad
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Doris M Rassl
- Department of Histopathology, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - David Fairen-Jimenez
- Adsorption & Advanced Materials Laboratory, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Robert C Rintoul
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Thoracic Oncology, Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine Rayne Institute, University College London, London, UK
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
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14
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Markouli M, Strepkos D, Piperi C. Structure, Activity and Function of the SETDB1 Protein Methyltransferase. Life (Basel) 2021; 11:life11080817. [PMID: 34440561 PMCID: PMC8397983 DOI: 10.3390/life11080817] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) is a prominent member of the Suppressor of Variegation 3–9 (SUV39)-related protein lysine methyltransferases (PKMTs), comprising three isoforms that differ in length and domain composition. SETDB1 is widely expressed in human tissues, methylating Histone 3 lysine 9 (H3K9) residues, promoting chromatin compaction and exerting negative regulation on gene expression. SETDB1 has a central role in normal physiology and nervous system development, having been implicated in the regulation of cell cycle progression, inactivation of the X chromosome, immune cells function, expression of retroelements and formation of promyelocytic leukemia (PML) nuclear bodies (NB). SETDB1 has been frequently deregulated in carcinogenesis, being implicated in the pathogenesis of gliomas, melanomas, as well as in lung, breast, gastrointestinal and ovarian tumors, where it mainly exerts an oncogenic role. Aberrant activity of SETDB1 has also been implicated in several neuropsychiatric, cardiovascular and gastrointestinal diseases, including schizophrenia, Huntington’s disease, congenital heart defects and inflammatory bowel disease. Herein, we provide an update on the unique structural and biochemical features of SETDB1 that contribute to its regulation, as well as its molecular and cellular impact in normal physiology and disease with potential therapeutic options.
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15
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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16
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Lorenzini E, Ciarrocchi A, Torricelli F. Molecular Fingerprints of Malignant Pleural Mesothelioma: Not Just a Matter of Genetic Alterations. J Clin Med 2021; 10:jcm10112470. [PMID: 34199544 PMCID: PMC8199660 DOI: 10.3390/jcm10112470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/21/2021] [Accepted: 05/29/2021] [Indexed: 12/12/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a clinical emergency of our time. Being strongly associated with asbestos exposure, incidence of this cancer is ramping up these days in many industrialized countries and it will soon start to increase in many developing areas where the use of this silicate derivate is still largely in use. Deficiency of reliable markers for the early identification of these tumors and the limited efficacy of the currently available therapeutic options are the basis of the impressive mortality rate of MPM. These shortcomings reflect the very poor information available about the molecular basis of this disease. Results of the recently released deep profiling studies point to the epigenome as a central element in MPM development and progression. First, MPM is characterized by a low mutational burden and a highly peculiar set of mutations that hits almost exclusively epigenetic keepers or proteins controlling chromatin organization and function. Furthermore, asbestos does not seem to be associated with a distinctive mutational signature, while the precise mapping of epigenetic changes caused by this carcinogen has been defined, suggesting that alterations in epigenetic features are the driving force in the development of this disease. Last but not least, consistent evidence also indicates that, in the setting of MPM, chromatin rewiring and epigenetic alterations of cancer cells heavily condition the microenvironment, including the immune response. In this review we aim to point to the relevance of the epigenome in MPM and to highlight the dependency of this tumor on chromatin organization and function. We also intend to discuss the opportunity of targeting these mechanisms as potential therapeutic options for MPM.
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Affiliation(s)
- Eugenia Lorenzini
- Laboratory of Translational Research, Azienda USL—IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (E.L.); (A.C.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL—IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (E.L.); (A.C.)
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL—IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy; (E.L.); (A.C.)
- Correspondence:
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Napoli F, Listì A, Zambelli V, Witel G, Bironzo P, Papotti M, Volante M, Scagliotti G, Righi L. Pathological Characterization of Tumor Immune Microenvironment (TIME) in Malignant Pleural Mesothelioma. Cancers (Basel) 2021; 13:2564. [PMID: 34073720 PMCID: PMC8197227 DOI: 10.3390/cancers13112564] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 02/08/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and highly aggressive disease that arises from pleural mesothelial cells, characterized by a median survival of approximately 13-15 months after diagnosis. The primary cause of this disease is asbestos exposure and the main issues associated with it are late diagnosis and lack of effective therapies. Asbestos-induced cellular damage is associated with the generation of an inflammatory microenvironment that influences and supports tumor growth, possibly in association with patients' genetic predisposition and tumor genomic profile. The chronic inflammatory response to asbestos fibers leads to a unique tumor immune microenvironment (TIME) composed of a heterogeneous mixture of stromal, endothelial, and immune cells, and relative composition and interaction among them is suggested to bear prognostic and therapeutic implications. TIME in MPM is known to be constituted by immunosuppressive cells, such as type 2 tumor-associated macrophages and T regulatory lymphocytes, plus the expression of several immunosuppressive factors, such as tumor-associated PD-L1. Several studies in recent years have contributed to achieve a greater understanding of the pathogenetic mechanisms in tumor development and pathobiology of TIME, that opens the way to new therapeutic strategies. The study of TIME is fundamental in identifying appropriate prognostic and predictive tissue biomarkers. In the present review, we summarize the current knowledge about the pathological characterization of TIME in MPM.
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Affiliation(s)
- Francesca Napoli
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
| | - Angela Listì
- Thoracic Oncology Unit, San Luigi Hospital, 10043 Orbassano, Italy;
| | - Vanessa Zambelli
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
| | - Gianluca Witel
- Department of Medical Sciences, University of Turin, City of Health and Science, 10126 Torino, Italy;
| | - Paolo Bironzo
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
- Thoracic Oncology Unit, San Luigi Hospital, 10043 Orbassano, Italy;
| | - Mauro Papotti
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
- Pathology Unit, City of Health and Science, 10126 Torino, Italy
| | - Marco Volante
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
| | - Giorgio Scagliotti
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
- Thoracic Oncology Unit, San Luigi Hospital, 10043 Orbassano, Italy;
| | - Luisella Righi
- Department of Oncology, University of Turin, 10043 Orbassano, Italy; (F.N.); (V.Z.); (P.B.); (M.P.); (M.V.); (G.S.)
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18
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Strepkos D, Markouli M, Klonou A, Papavassiliou AG, Piperi C. Histone Methyltransferase SETDB1: A Common Denominator of Tumorigenesis with Therapeutic Potential. Cancer Res 2021; 81:525-534. [PMID: 33115801 DOI: 10.1158/0008-5472.can-20-2906] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/06/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022]
Abstract
Epigenetic regulation of gene expression has been ultimately linked to cancer development, with posttranslational histone modifications representing attractive targets for disease monitoring and therapy. Emerging data have demonstrated histone lysine (K) methylation by methyltransferase SETDB1 as a common denominator of gene regulation in several cancer types. SETDB1 reversibly catalyzes the di- and trimethylation of histone 3 (H3) K9 in euchromatic regions of chromosomes, inhibiting gene transcription within these regions and promoting a switch from euchromatic to heterochromatic states. Recent studies have implicated aberrant SETDB1 activity in the development of various types of cancers, including brain, head and neck, lung, breast, gastrointestinal, ovarian, endometrial and prostate cancer, mesothelioma, melanoma, leukemias, and osteosarcoma. Although its role has not been fully elucidated in every case, most data point toward a pro-oncogenic potential of SETDB1 via the downregulation of critical tumor-suppressive genes. Less commonly, however, SETDB1 can also acquire a tumor-suppressive role, depending on cancer type and stage. Here we provide an updated overview of the cellular and molecular effects underlying SETDB1 activity in cancer development and progression along with current targeting strategies in different cancer types, with promising effects either as a standalone therapy or in conjunction with other therapeutic agents.
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Affiliation(s)
- Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexia Klonou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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19
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Abstract
Hürthle cell lesions have been a diagnostic conundrum in pathology since they were first recognized over a century ago. Controversy as to the name of the cell, the origin of the cell, and even which cells in particular may be designated as such still challenge pathologists and confound those treating patients with a diagnosis of "Hürthle cell" anything within the diagnosis, especially if that anything is a sizable mass lesion. The diagnosis of Hürthle cell adenoma (HCA) or Hürthle cell carcinoma (HCC) has typically relied on a judgement call by pathologists as to the presence or absence of capsular and/or vascular invasion of the adjacent thyroid parenchyma, easy to note in widely invasive disease and a somewhat subjective diagnosis for minimally invasive or borderline invasive disease. Diagnostic specificity, which has incorporated a sharp increase in molecular genetic studies of thyroid tumor subtypes and the integration of molecular testing into preoperative management protocols, continues to be challenged by Hürthle cell neoplasia. Here, we provide the improving yet still murky state of what is known about Hürthle cell tumor genetics, clinical management, and based upon what we are learning about the genetics of other thyroid tumors, how to manage expectations, by pathologists, clinicians, and patients, for more actionable, precise classifications of Hürthle cell tumors of the thyroid.
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Affiliation(s)
- David G. McFadden
- Division of Endocrinology, Department of Internal Medicine, Department of Biochemistry, Program in Molecular Medicine, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Peter M. Sadow
- Departments of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
- *Correspondence: Peter M. Sadow,
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20
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Saha N, Muntean AG. Insight into the multi-faceted role of the SUV family of H3K9 methyltransferases in carcinogenesis and cancer progression. Biochim Biophys Acta Rev Cancer 2020; 1875:188498. [PMID: 33373647 DOI: 10.1016/j.bbcan.2020.188498] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
Growing evidence implicates histone H3 lysine 9 methylation in tumorigenesis. The SUV family of H3K9 methyltransferases, which include G9a, GLP, SETDB1, SETDB2, SUV39H1 and SUV39H2 deposit H3K9me1/2/3 marks at euchromatic and heterochromatic regions, catalyzed by their conserved SET domain. In cancer, this family of enzymes can be deregulated by genomic alterations and transcriptional mis-expression leading to alteration of transcriptional programs. In solid and hematological malignancies, studies have uncovered pro-oncogenic roles for several H3K9 methyltransferases and accordingly, small molecule inhibitors are being tested as potential therapies. However, emerging evidence demonstrate onco-suppressive roles for these enzymes in cancer development as well. Here, we review the role H3K9 methyltransferases play in tumorigenesis focusing on gene targets and biological pathways affected due to misregulation of these enzymes. We also discuss molecular mechanisms regulating H3K9 methyltransferases and their influence on cancer. Finally, we describe the impact of H3K9 methylation on therapy induced resistance in carcinoma. Converging evidence point to multi-faceted roles for H3K9 methyltransferases in development and cancer that encourages a deeper understanding of these enzymes to inform novel therapy.
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Affiliation(s)
- Nirmalya Saha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Andrew G Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America.
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21
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Torricelli F, Lococo F, Di Stefano TS, Lorenzini E, Piana S, Valli R, Rena O, Veronesi G, Billè A, Ciarrocchi A. Deep Sequencing Analysis Identified a Specific Subset of Mutations Distinctive of Biphasic Malignant Pleural Mesothelioma. Cancers (Basel) 2020; 12:E2454. [PMID: 32872534 DOI: 10.3390/cancers12092454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Malignant Pleural Mesothelioma (MPM) is a heterogeneous disease. Morphologically, three different phenotypes are distinguishable: epithelioid (e-), sarcomatoid (s-) and biphasic (biph-) MPM, the latest, being a mixture of e- and s-MPM cells. Being an intermediate entity, management of biph-MPM, remains debatable and controversial, with different guidelines recommending distinct approaches. Identification of biph-MPM associated genetic alterations, through deep sequencing analysis, may provide useful tools to understand these lesions. A retrospective cohort of 69 surgically resected MPMs, 39 biph-MPMs (56.5%) and 30 e-MPMs (43.5%) was selected. A separate set of 16 biph-MPM was used as validation set. Deep sequencing analysis on an MPM-specific custom panel (MPM_geneset) comprising 1041 amplicons spanning 34 genes was performed. A total of 588 variants and 5309 mutational events were detected. In total, 91.3% of MPMs showed at least one mutation and 76.8% showed co-occurrence of more than one alteration. Mutations in MXRA5 (p = 0.05) and NOD2 (p = 0.018) were significantly associated with biph-MPM both in the training and validation cohort and correlated with the extent of the sarcomatoid component. Mutations in NOD2 and XRCC6 correlated with patients’ survival. We demonstrated that biph-MPM are associated with a specific mutation set, and that genetic analysis at diagnosis may improve patients’ risk stratification.
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Abstract
The global incidence of malignant mesothelioma (MM) causes considerable disease burden, suffering and health care costs. Beside preventive measures and ban the use of asbestos, early diagnosis would largely improve the chance of curative treatment. Current histologic criteria, however, requiring presence of invasion in the surrounding fatty tissue fail to identify MM in sufficiently early stage. Unilateral accumulation of pleural effusion is one of the earliest clinical manifestations of MM that occurs in approximately 90% of the patients. Therapeutic thoracocenthesis is necessary to remove the fluid and to relieve patients’ symptoms. This effusion is easily accessible and offers early and minimally invasive diagnosis by combining cytology with immunologic, molecular- and biomarker analyses. Typically, the fluid is rich in malignant cells and cell groups, but incipient stages of the disease may be difficult to recognize as the malignant cells can be masked by presence of inflammatory or reactive mesothelial cells. Recurrent, hemorrhagic and cell rich effusion should always be suspicious for MM and adequately prepared and analyzed to provide necessary information for subsequent therapy. Importantly, early detection of MM by integrating cytology and molecular approaches has high sensitivity and positive predictive value and has a major impact on patient survival. Thus, a conclusive positive MM cytology should lead to treatment without delay. This review summarizes molecular and diagnostic criteria of MM diagnosis.
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Affiliation(s)
- Anders Hjerpe
- Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Sulaf Abd Own
- Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - Katalin Dobra
- Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital, Stockholm, Sweden
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23
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Abbott DM, Bortolotto C, Benvenuti S, Lancia A, Filippi AR, Stella GM. Malignant Pleural Mesothelioma: Genetic and Microenviromental Heterogeneity as an Unexpected Reading Frame and Therapeutic Challenge. Cancers (Basel) 2020; 12:cancers12051186. [PMID: 32392897 PMCID: PMC7281319 DOI: 10.3390/cancers12051186] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Mesothelioma is a malignancy of serosal membranes including the peritoneum, pleura, pericardium and the tunica vaginalis of the testes. Malignant mesothelioma (MM) is a rare disease with a global incidence in countries like Italy of about 1.15 per 100,000 inhabitants. Malignant Pleural Mesothelioma (MPM) is the most common form of mesothelioma, accounting for approximately 80% of disease. Although rare in the global population, mesothelioma is linked to industrial pollutants and mineral fiber exposure, with approximately 80% of cases linked to asbestos. Due to the persistent asbestos exposure in many countries, a worldwide progressive increase in MPM incidence is expected for the current and coming years. The tumor grows in a loco-regional pattern, spreading from the parietal to the visceral pleura and invading the surrounding structures that induce the clinical picture of pleural effusion, pain and dyspnea. Distant spreading and metastasis are rarely observed, and most patients die from the burden of the primary tumor. Currently, there are no effective treatments for MPM, and the prognosis is invariably poor. Some studies average the prognosis to be roughly one-year after diagnosis. The uniquely poor mutational landscape which characterizes MPM appears to derive from a selective pressure operated by the environment; thus, inflammation and immune response emerge as key players in driving MPM progression and represent promising therapeutic targets. Here we recapitulate current knowledge on MPM with focus on the emerging network between genetic asset and inflammatory microenvironment which characterize the disease as amenable target for novel therapeutic approaches.
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Affiliation(s)
- David Michael Abbott
- Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy;
| | - Chandra Bortolotto
- Unit of Radiology, Department of Intensive Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy;
| | - Silvia Benvenuti
- Candiolo Cancer Institute, FPO—IRCCS—Str. Prov.le 142, km. 3,95—10060 Candiolo (TO), Italy;
| | - Andrea Lancia
- Unit of Radiation Therapy, Department of Medical Sciences and Infective Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy; (A.L.); (A.R.F.)
| | - Andrea Riccardo Filippi
- Unit of Radiation Therapy, Department of Medical Sciences and Infective Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy; (A.L.); (A.R.F.)
| | - Giulia Maria Stella
- Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, 27100 Pavia, Italy;
- Correspondence:
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24
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Hung YP, Dong F, Dubuc AM, Dal Cin P, Bueno R, Chirieac LR. Molecular characterization of localized pleural mesothelioma. Mod Pathol 2020; 33:271-280. [PMID: 31371807 PMCID: PMC7359734 DOI: 10.1038/s41379-019-0330-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/31/2022]
Abstract
Localized pleural mesothelioma is a rare solitary circumscribed pleural tumor that is microscopically similar to diffuse malignant pleural mesothelioma. However, the molecular characteristics and nosologic relationship with its diffuse counterpart remain unknown. In a consecutive cohort of 1110 patients with pleural mesotheliomas diagnosed in 2005-2018, we identified six (0.5%) patients diagnosed with localized pleural mesotheliomas. We gathered clinical history, evaluated the histopathology, and in select cases performed karyotypic analysis and targeted next-generation sequencing. The cohort included three women and three men (median age 63; range 28-76), often presenting incidentally during radiologic evaluation for unrelated conditions. Neoadjuvant chemotherapy was administered in two patients. All tumors (median size 5.0 cm; range 2.7-13.5 cm) demonstrated gross circumscription (with microscopic invasion into lung, soft tissue, and/or rib in four cases), mesothelioma histology (four biphasic and two epithelioid types), and mesothelial immunophenotype. Of four patients with at least 6-month follow-up, three were alive (up to 8.9 years). Genomic characterization identified several subgroups: (1) BAP1 mutations with deletions of CDKN2A and NF2 in two tumors; (2) TRAF7 mutations in two tumors, including one harboring trisomies of chromosomes 3, 5, 7, and X; and (3) genomic near-haploidization, characterized by extensive loss of heterozygosity sparing chromosomes 5 and 7. Localized pleural mesotheliomas appear genetically heterogeneous and include BAP1-mutated, TRAF7-mutated, and near-haploid subgroups. While the BAP1-mutated subgroup is similar to diffuse malignant pleural mesotheliomas, the TRAF7-mutated subgroup overlaps genetically with adenomatoid tumors and well-differentiated papillary mesotheliomas, in which recurrent TRAF7 mutations have been described. Genomic near-haploidization, identified recently in a subset of diffuse malignant pleural mesotheliomas, suggests a novel mechanism in the pathogenesis of both localized pleural mesothelioma and diffuse malignant pleural mesothelioma. Our findings describe distinctive genetic features of localized pleural mesothelioma, with both similarities to and differences from diffuse malignant pleural mesothelioma.
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Affiliation(s)
- Yin P. Hung
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Fei Dong
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Raphael Bueno
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lucian R. Chirieac
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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25
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Abstract
Malignant mesothelioma is associated with the exposure to asbestos fibers. Recent discovery of the BAP1 cancer syndrome, a Mendelian disorder with high-penetrance autosomal dominant inheritance fostered the genotyping for nucleotide-level or larger structural alteration of germline DNA. Inherited heterozygous mutations of the BAP1 gene increase the susceptibility to carcinogenic fibers, leading to a concept of gene x environment interaction (GxE) as a pathogenetic mechanism of mesothelioma. Several studies on cohorts of unselected patients with mesothelioma or on familial/early-onset cohorts of mesothelioma cases converged on BAP1 as the more frequent germline mutated gene, followed by other genes involved in DNA repair and homologous recombination. Evidence has been emerging that patients with mesothelioma carrying germline mutations of BAP1 and of other genes, such as those involved in DNA repair and tumor suppressor genes, have better prognosis and higher chemosensitivity when compared with patients with germline wildtype Bap1. We report here a germline genomic analysis targeted 22 genes in a cohort of 101 Japanese patients irrespective of asbestos exposure, age at diagnosis, or personal or family history of cancer. By comparing the results with the Human Genetic Variation Database (HGVD) and the Genome Aggregation Database (gnomAD) we selected rare germline variants with a Combined Annotation Dependent Depletion (CADD) >20. We show here that 31 of 101 subjects were carrying 25 rare variants in 14 genes, neither reported in the HGVD nor in the gnomAD database for 14/25 variants. Besides pathogenic variants of BAP1, rare missense variants were found in genes encoding lysine-specific histone methyltransferase SETD2 and SETDB1 and genes encoding subunits of the mSWI/SNF chromatin remodeling complex. The complete scenario of the genetic background consisting of pathogenic germline variants required for the predisposition and GxE for pathogenesis of mesothelioma appears complex, and further large-scale studies are warranted.
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Affiliation(s)
- Yoshie Yoshikawa
- Department of Genetic, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Mitsuru Emi
- Department of Genetic, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan.,University of Hawai'i Cancer Center, Honolulu, HI, USA
| | - Takashi Nakano
- Center for Respiratory Medicine, Otemae Hospital, Chuo-ku, Osaka, Japan
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26
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Batham J, Lim PS, Rao S. SETDB-1: A Potential Epigenetic Regulator in Breast Cancer Metastasis. Cancers (Basel) 2019; 11:cancers11081143. [PMID: 31405032 PMCID: PMC6721492 DOI: 10.3390/cancers11081143] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
The full epigenetic repertoire governing breast cancer metastasis is not completely understood. Here, we discuss the histone methyltransferase SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) and its role in breast cancer metastasis. SETDB1 serves as an exemplar of the difficulties faced when developing therapies that not only specifically target cancer cells but also the more elusive and aggressive stem cells that contribute to metastasis via epithelial-to-mesenchymal transition and confer resistance to therapies.
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Affiliation(s)
- Jacob Batham
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia
| | - Pek Siew Lim
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia.
| | - Sudha Rao
- Melanie Swan Memorial Translational Centre, Faculty of Sci-Tech, University of Canberra, Bruce ACT 2617, Australia.
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27
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Fitzgerald RC, Rhodes JM. Ingested asbestos in filtered beer, in addition to occupational exposure, as a causative factor in oesophageal adenocarcinoma. Br J Cancer 2019; 120:1099-1104. [PMID: 31068670 PMCID: PMC6738048 DOI: 10.1038/s41416-019-0467-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 03/21/2019] [Accepted: 04/02/2019] [Indexed: 02/06/2023] Open
Abstract
Oesophageal adenocarcinoma has become much more common over the past 50 years, particularly in Britain, with an unexplained male to female ratio of > 4:1. Given the use of asbestos filtration in commercial brewing and reports of its unregulated use in British public houses in the 1970’s to clear draught beer “slops”, we have assessed the hypothesis that ingested asbestos could be a causative factor for this increased incidence. Importantly, occupational asbestos exposure increases the risk of adenocarcinoma but not squamous cell carcinoma of the oesophagus. The presence of asbestos fibres was consistently reported in filtered beverages including beers in the 1970s and asbestos bodies have been found in gastrointestinal tissue, particularly oesophageal tissue, at autopsy. There is no reported association between the intake of alcohol and oesophageal adenocarcinoma but studies would mostly have missed exposure from draught beer before 1980. Oesophageal adenocarcinoma has some molecular similarities to pleural mesothelioma, a condition that is largely due to inhalation of asbestos fibres, including predominant loss of tumour suppressor genes rather than an increase of classical oncogenic drivers. Trends in incidence of oesophageal adenocarcinoma and mesothelioma are similar, rising rapidly over the past 50 years but now plateauing. Asbestos ingestion, either from beer consumed before around 1980, or from occupational exposure, seems a plausible causative factor for oesophageal adenocarcinoma. If this is indeed the case, its incidence should fall back to a low baseline by around 2050.
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Affiliation(s)
- Rebecca C Fitzgerald
- MRC Cancer Unit,Hutchison-MRC Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, USA
| | - Jonathan M Rhodes
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, The Henry Wellcome Laboratory, Nuffield Building, Crown St., Liverpool, L69 3GE, UK.
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28
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Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, Tarpey P, Danilova L, Drill E, Gibb EA, Bowlby R, Kanchi R, Osmanbeyoglu HU, Sekido Y, Takeshita J, Newton Y, Graim K, Gupta M, Gay CM, Diao L, Gibbs DL, Thorsson V, Iype L, Kantheti H, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Sallé F, Fujimoto J, Husain AN, Silveira HC, Rusch VW, Rintoul RC, Pass H, Kindler H, Zauderer MG, Kwiatkowski DJ, Bueno R, Tsao AS, Creaney J, Lichtenberg T, Leraas K, Bowen J, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson AG, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M. Integrative Molecular Characterization of Malignant Pleural Mesothelioma. Cancer Discov 2018; 8:1548-1565. [PMID: 30322867 DOI: 10.1158/2159-8290.cd-18-0804] [Citation(s) in RCA: 368] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/06/2018] [Accepted: 10/10/2018] [Indexed: 01/26/2023]
Abstract
Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity. We also report strong expression of the immune-checkpoint gene VISTA in epithelioid MPM, strikingly higher than in other solid cancers, with implications for the immune response to MPM and for its immunotherapy. Our findings highlight new avenues for further investigation of MPM biology and novel therapeutic options. SIGNIFICANCE: Through a comprehensive integrated genomic study of 74 MPMs, we provide a deeper understanding of histology-independent determinants of aggressive behavior, define a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity, and discovered strong expression of the immune-checkpoint gene VISTA in epithelioid MPM.See related commentary by Aggarwal and Albelda, p. 1508.This article is highlighted in the In This Issue feature, p. 1494.
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Affiliation(s)
- Julija Hmeljak
- Department of Pathology and Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Chip Stewart
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David Heiman
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Patrick Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Ludmila Danilova
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Esther Drill
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ewan A Gibb
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Rupa Kanchi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hatice U Osmanbeyoglu
- Computational Systems Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yoshitaka Sekido
- Division of Cancer Biology, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | | | - Yulia Newton
- Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California
| | - Kiley Graim
- Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California
| | - Manaswi Gupta
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Carl M Gay
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Lisa Iype
- Institute for Systems Biology, Seattle, Washington
| | | | - David T Severson
- Division of Thoracic Surgery, The Lung Center and International Mesothelioma Program, Brigham and Women's Hospital, Boston, Massachusetts
| | - Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrice Desmeules
- Department of Pathology, Quebec Heart and Lung Institute, Quebec, Canada
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Lucian R Chirieac
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aliya N Husain
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Henrique C Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Sao Paulo, Brazil
| | - Valerie W Rusch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Harvey Pass
- Department of Cardiothoracic Surgery, NYU Langone Medical Center, New York, New York
| | - Hedy Kindler
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center and Biological Sciences, Chicago, Illinois
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David J Kwiatkowski
- Division of Pulmonary Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and International Mesothelioma Program, Brigham and Women's Hospital, Boston, Massachusetts
| | - Anne S Tsao
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jenette Creaney
- School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia
| | - Tara Lichtenberg
- The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kristen Leraas
- The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Jay Bowen
- The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | | | - Ina Felau
- National Cancer Institute, Bethesda, Maryland
| | | | - Rehan Akbani
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Lauren A Byers
- Division of Thoracic Surgery, The Lung Center and International Mesothelioma Program, Brigham and Women's Hospital, Boston, Massachusetts
| | - Michael S Noble
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Jonathan A Fletcher
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Bruce W Robinson
- School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Marc Ladanyi
- Department of Pathology and Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
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29
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Abstract
Asbestos fibers are naturally occurring silicates that have been extensively used in the past, including house construction, but because of their toxicity, their use has been banned in 63 countries. Despite this, more than one million metric tons of asbestos are still consumed annually in countries where asbestos use has not been banned. Asbestos-related disease incidence is still increasing in several countries, including those countries that banned the use of asbestos more than 30 years ago. We highlight here recent knowledge obtained in experimental models about the mechanisms leading to tumor development following asbestos exposure, including genetic and epigenetic changes. Importantly, the landscape of alterations observed experimentally in tumor samples is consistent with alterations observed in clinical tumor samples; therefore, studies performed on early/precancer stages should help inform secondary prevention, which remains crucial in the absence of an efficient primary prevention. Knowledge gathered on asbestos should also help address future challenges, especially in view of the increased production of new materials that may behave similarly to asbestos fibers.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology , University Hospital Zurich , Sternwartstrasse 14 , 8091 Zürich , Switzerland
| | - Marion MacFarlane
- MRC Toxicology Unit , University of Cambridge , Hodgkin Building, Leicester LE1 9HN , United Kingdom
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30
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Sun Z, Chadwick BP. Loss of SETDB1 decompacts the inactive X chromosome in part through reactivation of an enhancer in the IL1RAPL1 gene. Epigenetics Chromatin 2018; 11:45. [PMID: 30103804 PMCID: PMC6088404 DOI: 10.1186/s13072-018-0218-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/10/2018] [Indexed: 01/04/2023] Open
Abstract
Background The product of dosage compensation in female mammals is the inactive X chromosome (Xi). Xi facultative heterochromatin is organized into two different types, one of which is defined by histone H3 trimethylated at lysine 9 (H3K9me3). The rationale for this study was to assess SET domain bifurcated 1 (SETDB1) as a candidate for maintaining this repressive modification at the human Xi. Results Here, we show that loss of SETDB1 does not result in large-scale H3K9me3 changes at the Xi, but unexpectedly we observed striking decompaction of the Xi territory. Close examination revealed a 0.5 Mb region of the Xi that transitioned from H3K9me3 heterochromatin to euchromatin within the 3′ end of the IL1RAPL1 gene that is part of a common chromosome fragile site that is frequently deleted or rearranged in patients afflicted with intellectual disability and other neurological ailments. Centrally located within this interval is a powerful enhancer adjacent to an ERVL-MaLR element. In the absence of SETDB1, the enhancer is reactivated on the Xi coupled with bidirectional transcription from the ERVL-MaLR element. Xa deletion of the enhancer/ERVL-MaLR resulted in loss of full-length IL1RAPL1 transcript in cis, coupled with trans decompaction of the Xi chromosome territory, whereas Xi deletion increased detection of full-length IL1RAPL1 transcript in trans, but did not impact Xi compaction. Conclusions These data support a critical role for SETDB1 in maintaining the ERVL-MaLR element and adjacent enhancer in the 3′ end of the IL1RAPL1 gene in a silent state to facilitate Xi compaction. Electronic supplementary material The online version of this article (10.1186/s13072-018-0218-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhuo Sun
- Department of Biological Science, Florida State University, 319 Stadium Drive, King 3076, Tallahassee, FL, 32306-4295, USA
| | - Brian P Chadwick
- Department of Biological Science, Florida State University, 319 Stadium Drive, King 3076, Tallahassee, FL, 32306-4295, USA.
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31
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Hjerpe A, Abd-Own S, Dobra K. Cytopathologic Diagnosis of Epithelioid and Mixed-Type Malignant Mesothelioma: Ten Years of Clinical Experience in Relation to International Guidelines. Arch Pathol Lab Med 2018; 142:893-901. [DOI: 10.5858/arpa.2018-0020-ra] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Katalin Dobra
- From the Department of Laboratory Medicine, Division of Pathology, Karolinska University Hospital, Huddinge, Stockholm, Sweden
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32
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Sage AP, Martinez VD, Minatel BC, Pewarchuk ME, Marshall EA, MacAulay GM, Hubaux R, Pearson DD, Goodarzi AA, Dellaire G, Lam WL. Genomics and Epigenetics of Malignant Mesothelioma. High Throughput 2018; 7:E20. [PMID: 30060501 PMCID: PMC6163664 DOI: 10.3390/ht7030020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/19/2018] [Accepted: 07/25/2018] [Indexed: 12/11/2022] Open
Abstract
Malignant mesothelioma is an aggressive and lethal asbestos-related disease. Diagnosis of malignant mesothelioma is particularly challenging and is further complicated by the lack of disease subtype-specific markers. As a result, it is especially difficult to distinguish malignant mesothelioma from benign reactive mesothelial proliferations or reactive fibrosis. Additionally, mesothelioma diagnoses can be confounded by other anatomically related tumors that can invade the pleural or peritoneal cavities, collectively resulting in delayed diagnoses and greatly affecting patient management. High-throughput analyses have uncovered key genomic and epigenomic alterations driving malignant mesothelioma. These molecular features have the potential to better our understanding of malignant mesothelioma biology as well as to improve disease diagnosis and patient prognosis. Genomic approaches have been instrumental in identifying molecular events frequently occurring in mesothelioma. As such, we review the discoveries made using high-throughput technologies, including novel insights obtained from the analysis of the non-coding transcriptome, and the clinical potential of these genetic and epigenetic findings in mesothelioma. Furthermore, we aim to highlight the potential of these technologies in the future clinical applications of the novel molecular features in malignant mesothelioma.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Michelle E Pewarchuk
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
| | - Gavin M MacAulay
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Roland Hubaux
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
| | - Dustin D Pearson
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Aaron A Goodarzi
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Graham Dellaire
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
- Departments of Pathology and Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.
- Canadian Environmental Exposures in Cancer (CE2C) Network, Dalhousie University, P.O. BOX 15000, Halifax, NS B3H 4R2, Canada.
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33
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Kim JE, Kim D, Hong YS, Kim KP, Yoon YK, Lee DH, Kim SW, Chun SM, Jang SJ, Kim TW. Mutational Profiling of Malignant Mesothelioma Revealed Potential Therapeutic Targets in EGFR and NRAS. Transl Oncol 2018; 11:268-274. [PMID: 29413759 PMCID: PMC5884183 DOI: 10.1016/j.tranon.2018.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/29/2022] Open
Abstract
Pemetrexed and platinum (PP) combination chemotherapy is the current standard first-line therapy for treatment of malignant mesothelioma (MM). However, a useful predictive biomarker for PP therapy is yet to be found. Here, we performed targeted exome sequencing to profile somatic mutations and copy number variations in 12 MM patients treated with PP therapy. We identified 187 somatic mutations in 12 patients (65 synonymous, 102 missense, 2 nonsense, 5 splice site, and 13 small coding insertions/deletions). We identified somatic mutations in 23 genes including BAP1, TP53, NRAS, and EGFR. Interestingly, rare NRAS p.Q61K and EGFR exon 19 deletions were observed in 2 patients. We also found somatic chromosomal copy number deletions in CDKN2A and CDKN2B genes. Genetic alteration related to response after PP therapy was not found. Somatic mutation profiling in MM patients receiving PP therapy revealed genetic alterations in potential therapeutic targets such as NRAS and EGFR. No alterations in genes with potential predictive role for PP therapy were found.
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Affiliation(s)
- Jeong Eun Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul. Korea
| | - Deokhoon Kim
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea; Department of Pathology, University of Ulsan college of Medicine, Asan Medical Center, Seoul, Korea
| | - Yong Sang Hong
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul. Korea
| | - Kyu-Pyo Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul. Korea
| | - Young Kwang Yoon
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Dae Ho Lee
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul. Korea
| | - Sang-We Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul. Korea
| | - Sung-Min Chun
- Department of Pathology, University of Ulsan college of Medicine, Asan Medical Center, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, University of Ulsan college of Medicine, Asan Medical Center, Seoul, Korea
| | - Tae Won Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul. Korea.
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Mendez P, Fang LT, Jablons DM, Kim IJ. Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues. Sci Rep 2017; 7:4055. [PMID: 28642587 PMCID: PMC5481435 DOI: 10.1038/s41598-017-04419-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
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Affiliation(s)
- Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Li Tai Fang
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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Yoon JH, Kim TW, Mendez P, Jablons DM, Kim IJ. Mobile Genome Express (MGE): A comprehensive automatic genetic analyses pipeline with a mobile device. PLoS One 2017; 12:e0174696. [PMID: 28403238 PMCID: PMC5389793 DOI: 10.1371/journal.pone.0174696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/13/2017] [Indexed: 01/19/2023] Open
Abstract
The development of next-generation sequencing (NGS) technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE) that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.
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Affiliation(s)
- Jun-Hee Yoon
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Thomas W. Kim
- CureSeq Inc., Brisbane, California, United States of America
| | - Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - David M. Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (IJK); (DMJ)
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, California, United States of America
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (IJK); (DMJ)
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Karanth AV, Maniswami RR, Prashanth S, Govindaraj H, Padmavathy R, Jegatheesan SK, Mullangi R, Rajagopal S. Emerging role of SETDB1 as a therapeutic target. Expert Opin Ther Targets 2017; 21:319-331. [PMID: 28076698 DOI: 10.1080/14728222.2017.1279604] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Epigenetic changes lead to aberrant gene expression in cancer. SETDB1, a histone lysine methyltransferase plays an important role in methylation and gene silencing. Aberrant histone methylation at H3K9 by SETDB1 promotes silencing of tumor suppressor genes and thus contributes to carcinogenesis. Recent studies indicate that SETDB1 is abnormally expressed in various human cancer conditions which contributed to enhanced tumor growth and metastasis. Hence, SETDB1 appears to be a promising epigenetic target for therapeutic intervention. Areas covered: In this article, the structural features, localization and functions of SETDB1 are reviewed. Also, an overview of the role of SETDB1 in cancer and other disease mechanisms, the currently studied inhibitors for SETDB1 are mentioned. Expert opinion: Silencing of tumor suppressor genes due to excessive trimethylation at H3K9 by amplified SETDB1 levels is found in various cancerous conditions. Since epigenetic changes are reversible, SETDB1 holds promise as an important therapeutic target for cancer. Therefore, a better understanding of the role of SETDB1 and its interaction with various proteins in cancer-related mechanisms along with therapeutic interventions specific for SETDB1 may improve targeted cancer therapy.
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Dang J, Mendez P, Lee S, Kim JW, Yoon JH, Kim TW, Sailey CJ, Jablons DM, Kim IJ. Development of a robust DNA quality and quantity assessment qPCR assay for targeted next-generation sequencing library preparation. Int J Oncol 2016; 49:1755-65. [PMID: 27511764 PMCID: PMC5021246 DOI: 10.3892/ijo.2016.3654] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/01/2016] [Indexed: 01/18/2023] Open
Abstract
Next-generation sequencing (NGS) is becoming a standard for genetic analyses of clinical samples. DNAs retrieved from formalin-fixed, paraffin-embedded (FFPE) tissue specimens are commonly degraded, and specimens such as core biopsies are sometimes too small to obtain enough DNA for NGS applications. Thus, it is important to measure both the DNA quantity and quality accurately from clinical samples. However, there is no standard method for DNA quantity and quality analyses for NGS library preparation. We tested four different methods (PicoGreen, Qubit® fluorometry, TaqMan and SYBR-Green-based qPCR assay) and compared each to RNase P TaqMan as a reference control. We found that SYBR-Green-based qPCR assay provides a consistent and accurate DNA quantification while keeping its cost relatively low and the throughput high. We designed a dual-probe SYBR-Green qPCR assay for DNA quantity and quality assessment for targeted NGS library preparation. This assay provides a Dscore (degradation score) of the interrogated DNA by analyzing two different sizes of amplicons. We show an example of a clinical sample with a very high Dscore (high degradation). With a regular DNA quantification, without considering the degradation status, no correct NGS libraries were obtained. However, after optimizing the library condition by considering its poor DNA quality, a reasonably good library and sequencing results were obtained. In summary, we developed and presented a new DNA quantity and quality analysis qPCR assay for the targeted NGS library preparation. This assay may be mostly efficient for the clinical samples with high degradation and poor DNA quality.
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Affiliation(s)
| | - Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94115, USA
| | | | | | - Jun-Hee Yoon
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94115, USA
| | | | - Charles J. Sailey
- CureSeq Inc., Brisbane, CA 94005, USA
- Purity Laboratories, Lake Oswego, OR 97035, USA
- Molecular Testing Labs, Vancouver, WA 98684, USA
| | - David M. Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94115, USA
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94115, USA
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA 94115, USA
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94115, USA
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Hylebos M, Van Camp G, van Meerbeeck JP, Op de Beeck K. The Genetic Landscape of Malignant Pleural Mesothelioma: Results from Massively Parallel Sequencing. J Thorac Oncol 2016; 11:1615-26. [PMID: 27282309 DOI: 10.1016/j.jtho.2016.05.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/27/2016] [Accepted: 05/22/2016] [Indexed: 12/18/2022]
Abstract
Malignant pleural mesothelioma (MPM) is a rare yet aggressive tumor that is causally associated with-mostly professional-asbestos exposure. Given the long latency between exposure and disease, and because asbestos is still being used, MPM will remain a global health issue for decades to come. Notwithstanding the increasing incidence of MPM and the fact that patients with MPM face a poor prognosis, currently available treatment options are limited. To enable the development of novel targeted therapies, identification of the genetic alterations underlying MPM will be crucial. The first studies reporting on the genomic background of MPM identified recurrent somatic mutations in a number of tumor suppressor genes (i.e., cyclin-dependent kinase inhibitor 2A gene [CDKN2A], neurofibromin 2 (merlin) gene [NF2], and BRCA1 associated protein 1 gene [BAP1]). More recently, massively parallel sequencing strategies have been used and have provided a more genome-wide view on the genetic landscape of MPM. This review summarizes their results, describing alterations that cluster mainly in four pathways: the tumor protein p53/DNA repair, cell cycle, mitogen-activated protein kinase, and phosphoinisitide 3-kinase (PI3K)/AKT pathways. As these pathways are important during tumor development, they provide interesting candidates for targeting with novel drugs.
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Affiliation(s)
- Marieke Hylebos
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Antwerp, Belgium.
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Jan P van Meerbeeck
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium; Thoracic Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Antwerp, Belgium
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Andujar P, Lacourt A, Brochard P, Pairon JC, Jaurand MC, Jean D. Five years update on relationships between malignant pleural mesothelioma and exposure to asbestos and other elongated mineral particles. J Toxicol Environ Health B Crit Rev 2016; 19:151-172. [PMID: 27705546 DOI: 10.1080/10937404.2016.1193361] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite the reduction of global asbestos consumption and production due to the ban or restriction of asbestos uses in more than 50 countries since the 1970s, malignant mesothelioma remains a disease of concern. Asbestos is still used, imported, and exported in several countries, and the number of mesothelioma deaths may be expected to increase in the next decades in these countries. Asbestos exposure is the main risk factor for malignant pleural mesothelioma, but other types of exposures are linked to the occurrence of this type of cancer. Although recent treatments improve the quality of life of patients with mesothelioma, malignant pleural mesothelioma remains an aggressive disease. Recent treatments have not resulted in appreciable improvement in survival, and thus development of more efficient therapies is urgently needed. The development of novel therapeutic strategies is dependent on our level of knowledge of the physiopathological and molecular changes that mesothelial cells acquired during the neoplastic process. During the past 5 years, new findings have been published on the etiology, epidemiology, molecular changes, and innovative treatments of malignant pleural mesothelioma. This review aims to update the findings of recent investigations on etiology, epidemiology, and molecular changes with a focus on (1) attributable risk of asbestos exposure in men and women and (2) coexposure to other minerals and other elongated mineral particles or high aspect ratio nanoparticles. Recent data obtained on genomic and gene alterations, pathways deregulations, and predisposing factors are summarized.
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Affiliation(s)
- Pascal Andujar
- a Institut Santé Travail Paris-Est , Université Paris-Est , Créteil , France
- b CHI Créteil , Service de Pneumologie et Pathologie Professionnelle, DHU A-TVB , Créteil , France
- c INSERM U955 , Equipe 4 , Créteil , France
- d Universite Paris-Est Créteil , Faculté de Médecine , Créteil , France
| | - Aude Lacourt
- e INSERM U1219 , EPICENE , Bordeaux , France
- f ISPED , Université de Bordeaux , Bordeaux , France
| | - Patrick Brochard
- f ISPED , Université de Bordeaux , Bordeaux , France
- g CHU Bordeaux , Bordeaux , France
| | - Jean-Claude Pairon
- a Institut Santé Travail Paris-Est , Université Paris-Est , Créteil , France
- b CHI Créteil , Service de Pneumologie et Pathologie Professionnelle, DHU A-TVB , Créteil , France
- c INSERM U955 , Equipe 4 , Créteil , France
- d Universite Paris-Est Créteil , Faculté de Médecine , Créteil , France
| | - Marie-Claude Jaurand
- h INSERM , UMR-1162, Génomique fonctionnelle des tumeurs solides , Paris , France
- i Université Paris Descartes , Labex Immuno-Oncology , Sorbonne Paris Cité, Paris , France
- j Université Paris Diderot , IUH , Paris , France
- k Université Paris 13 , Sorbonne Paris Cité , Bobigny , France
| | - Didier Jean
- h INSERM , UMR-1162, Génomique fonctionnelle des tumeurs solides , Paris , France
- i Université Paris Descartes , Labex Immuno-Oncology , Sorbonne Paris Cité, Paris , France
- j Université Paris Diderot , IUH , Paris , France
- k Université Paris 13 , Sorbonne Paris Cité , Bobigny , France
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