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Feng X, He S, Chen Y, Zhang L. Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression. Genes Genomics 2024; 46:637-646. [PMID: 38470543 DOI: 10.1007/s13258-024-01508-8] [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: 10/09/2023] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Breast cancer type 1 susceptibility protein/breast cancer type 2 susceptibility protein-containing complex subunit 3 (BRCC3), a deubiquitinase (DUBs), is overexpressed in various cancers. However, the underlying biological roles of BRCC3 in adenocarcinoma colon (COAD) have yet to be decrypted. OBJECTIVE In this work, we explored the potential biological function of BRCC3 in the natural process of COAD cells. METHODS The expression levels of BRCC3 in COAD tissues and cell lines were investigated via quantitative real time polymerase chain reaction and western blotting analyses. Meanwhile, short hairpin RNAs targeting BRCC3 (sh-BRCC3) or mesenchymal-epithelial transition factor (MET) (sh-MET) were used to investigate the biological function, including proliferation, apoptosis, migration, invasion, and epithelial-mesenchymal transition (EMT) progression in COAD cells. Furthermore, the expression levels of EMT-related biomarkers were detected with western blotting analysis. Furthermore, we also performed Co-IP assay to identify the correlation between BRCC3 and MET. RESULTS BRCC3 expression was increased in COAD tissues and cell lines. ShRNA-mediated downmodulation of BRCC3 in COAD cell lines induced EMT progression. BRCC3 knockdown resulted in decreased migration as well as invasion and increased apoptosis of SW480 and Lovo cells. Besides, MET was regulated by BRCC3 and involved in the migration, invasion, and EMT in SW480 and Lovo cells. Finally, we uncovered that the overexpressed MET reversed the effects of BRCC3 knockdown in COAD cell development. CONCLUSIONS BRCC3 acted as a critical factor in the development of COAD by deubiquitinating and stabilizing MET, which might provide an emerging biomarker for the therapeutic and diagnosis strategy of COAD.
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Affiliation(s)
- Xiu Feng
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China
| | - Shengnan He
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China
| | - Ying Chen
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
| | - Liang Zhang
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
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2
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Li Y, Jiang C, Liu Q, Zhou P, Tian D, Zeng Y, Xiang M. USP15 facilitates the progression of bladder cancer by amplifying the activation of the NF-κB signaling pathway. Aging (Albany NY) 2024; 16:6757-6772. [PMID: 38656882 PMCID: PMC11087123 DOI: 10.18632/aging.205696] [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: 08/15/2023] [Accepted: 11/21/2023] [Indexed: 04/26/2024]
Abstract
USP15, a pivotal member of the deubiquitinase family, plays a crucial role in orchestrating numerous vital biological processes, including the regulation of NF-κB signaling pathway and deubiquitination of proto-oncogenes. In various cancers, USP15 has been validated to exhibit up-regulated expression, impacting the initiation and progression of cancer. However, its precise mechanism in bladder cancer remains elusive. Our study shed light on the significant overexpression of USP15 in bladder cancer cells compared to normal bladder cells, correlating with a poorer prognosis for bladder cancer patients. Strikingly, attenuation of USP15 expression greatly attenuated the proliferation, migration, and invasion of bladder cancer cells. Moreover, upregulation of USP15 was found to drive cancer progression through the activation of the NF-κB signaling pathway. Notably, USP15 directly deubiquitinates BRCC3, heightening its expression level, and subsequent overexpression of BRCC3 counteracted the antitumoral efficacy of USP15 downregulation. Overall, our findings elucidated the carcinogenic effects of USP15 in bladder cancer, primarily mediated by the excessive activation of the NF-κB signaling pathway, thereby promoting tumor development. These results underscore the potential of USP15 as a promising therapeutic target for bladder cancer in the future.
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Affiliation(s)
- Yun Li
- Department of Ophthalmology, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chenghang Jiang
- Department of Emergency Medicine, Emergency and Critical Care Center, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Quanqi Liu
- Department of Urology, Jinhua Hospital Affiliated to Zhejiang University School of Medicine, Jinhua, China
| | - Pengfei Zhou
- Department of Urology, Jinhua Hospital Affiliated to Zhejiang University School of Medicine, Jinhua, China
| | - Daxue Tian
- Department of Urology, Jinhua Hospital Affiliated to Zhejiang University School of Medicine, Jinhua, China
| | - Ying Zeng
- Department of Ophthalmology, The First Affiliated Hospital, Sun-Yat-sen University, Guangzhou, China
| | - Mingfeng Xiang
- Department of Urology, Second Affiliated Hospital of Nanchang University, Nanchang, China
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3
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Abstract
Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying that system has yet to be achieved. Towards this goal, we measured 147,153 pairwise interactions among genes implicated in PARP inhibitor (PARPi) response. Evaluating genetic interactions at this scale, with and without exposure to PARPi, revealed hierarchical organization of the pathways and complexes that maintain genome stability during normal growth and defined changes that occur upon accumulation of DNA lesions due to cytotoxic doses of PARPi. We uncovered unexpected relationships among DNA repair genes, including context-specific buffering interactions between the minimally characterized AUNIP and BRCA1-A complex genes. Our work thus establishes a foundation for mapping differential genetic interactions in mammalian cells and provides a comprehensive resource for future studies of DNA repair and PARP inhibitors.
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Affiliation(s)
- Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jia Ling
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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4
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Tao H, Liao Y, Yan Y, He Z, Zhou J, Wang X, Peng J, Li S, Liu T. BRCC3 Promotes Tumorigenesis of Bladder Cancer by Activating the NF-κB Signaling Pathway Through Targeting TRAF2. Front Cell Dev Biol 2021; 9:720349. [PMID: 34604222 PMCID: PMC8481630 DOI: 10.3389/fcell.2021.720349] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
NF-κB signaling is very important in cancers. However, the role of BRCC3-associated NF-κB signaling activation in bladder cancer remains to be characterized. Western blotting and IHC of tissue microarray were used to confirm the abnormal expression of BRCC3 in bladder cancer. Growth curve, colony formation, soft agar assay and Xenograft model were performed to identify the role of BRCC3 over-expression or knock-out in bladder cancer. Further, RNA-Seq and luciferase reporter assays were used to identify the down-stream signaling pathway. Finally, co-immunoprecipitation and fluorescence confocal assay were performed to verify the precise target of BRCC3. Here, we found that high expression of BRCC3 promoted tumorigenesis through targeting the TRAF2 protein. BRCC3 expression is up-regulated in bladder cancer patients which indicates a negative prognosis. By in vitro and in vivo assays, we found genetic BRCC3 ablation markedly blocks proliferation, viability and migration of bladder cancer cells. Mechanistically, RNA-Seq analysis shows that NF-κB signaling is down-regulated in BRCC3-deficient cells. BRCC3 binds to and synergizes with TRAF2 to activate NF-κB signaling. Our results indicate that high BRCC3 expression activates NF-κB signaling by targeting TRAF2 for activation, which in turn facilitates tumorigenesis in bladder cancer. This finding points to BRCC3 as a potential target in bladder cancer patients.
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Affiliation(s)
- Huangheng Tao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.,State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education (KLOBM), School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yixiang Liao
- Jingzhou Hospital, Yangtze University, Jingzhou, China.,The Second Clinical Medical College, Yangtze University, Jingzhou, China
| | - Youji Yan
- Jingzhou Hospital, Yangtze University, Jingzhou, China.,The Second Clinical Medical College, Yangtze University, Jingzhou, China
| | - Zhiwen He
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiajie Zhou
- Jingzhou Hospital, Yangtze University, Jingzhou, China.,The Second Clinical Medical College, Yangtze University, Jingzhou, China
| | - Xinghuan Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianping Peng
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shangze Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.,School of Medicine, Chongqing University, Chongqing, China
| | - Tao Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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5
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Abstract
Deubiquitinases (DUBs) are enzymes that control the stability, interactions or localization of most cellular proteins by removing their ubiquitin modification. In recent years, some DUBs, such as USP7, USP9X and USP10, have been identified as promising therapeutic targets in hematological malignancies. Importantly, some potent inhibitors targeting the oncogenic DUBs have been developed, showing promising inhibitory efficacy in preclinical models, and some have even undergone clinical trials. Different DUBs perform distinct function in diverse hematological malignancies, such as oncogenic, tumor suppressor or context-dependent effects. Therefore, exploring the biological roles of DUBs and their downstream effectors will provide new insights and therapeutic targets for the occurrence and development of hematological malignancies. We summarize the DUBs involved in different categories of hematological malignancies including leukemia, multiple myeloma and lymphoma. We also present the recent development of DUB inhibitors and their applications in hematological malignancies. Together, we demonstrate DUBs as potential therapeutic drug targets in hematological malignancies.
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Affiliation(s)
- Hu Lei
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jiaqi Wang
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiacheng Hu
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qian Zhu
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingli Wu
- Department of Pathophysiology, International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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6
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Barabino SML, Citterio E, Ronchi AE. Transcription Factors, R-Loops and Deubiquitinating Enzymes: Emerging Targets in Myelodysplastic Syndromes and Acute Myeloid Leukemia. Cancers (Basel) 2021; 13:cancers13153753. [PMID: 34359655 PMCID: PMC8345071 DOI: 10.3390/cancers13153753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary The advent of DNA massive sequencing technologies has allowed for the first time an extensive look into the heterogeneous spectrum of genes and mutations underpinning myelodysplastic syndromes (MDSs) and acute myeloid leukemia (AML). In this review, we wish to explore the most recent advances and the rationale for the potential therapeutic interest of three main actors in myelo-leukemic transformation: transcription factors that govern myeloid differentiation; RNA splicing factors, which ensure proper mRNA maturation and whose mutations increase R-loops formation; and deubiquitinating enzymes, which contribute to genome stability in hematopoietic stem cells (HSCs). Abstract Myeloid neoplasms encompass a very heterogeneous family of diseases characterized by the failure of the molecular mechanisms that ensure a balanced equilibrium between hematopoietic stem cells (HSCs) self-renewal and the proper production of differentiated cells. The origin of the driver mutations leading to preleukemia can be traced back to HSC/progenitor cells. Many properties typical to normal HSCs are exploited by leukemic stem cells (LSCs) to their advantage, leading to the emergence of a clonal population that can eventually progress to leukemia with variable latency and evolution. In fact, different subclones might in turn develop from the original malignant clone through accumulation of additional mutations, increasing their competitive fitness. This process ultimately leads to a complex cancer architecture where a mosaic of cellular clones—each carrying a unique set of mutations—coexists. The repertoire of genes whose mutations contribute to the progression toward leukemogenesis is broad. It encompasses genes involved in different cellular processes, including transcriptional regulation, epigenetics (DNA and histones modifications), DNA damage signaling and repair, chromosome segregation and replication (cohesin complex), RNA splicing, and signal transduction. Among these many players, transcription factors, RNA splicing proteins, and deubiquitinating enzymes are emerging as potential targets for therapeutic intervention.
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7
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Pelizzo G, Chiricosta L, Mazzon E, Zuccotti GV, Avanzini MA, Croce S, Lima M, Bramanti P, Calcaterra V. Discovering Genotype Variants in an Infant with VACTERL through Clinical Exome Sequencing: A Support for Personalized Risk Assessment and Disease Prevention. Pediatr Rep 2021; 13:45-56. [PMID: 33466296 PMCID: PMC7838983 DOI: 10.3390/pediatric13010006] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022] Open
Abstract
Congenital anomalies may have an increased risk of noncommunicable diseases (NCDs) We performed a clinical exome analysis in an infant affected by "Vertebral, Anorectal, Cardiac, Tracheoesophageal, Genitourinary, and Limb" (VACTERL) malformation association to identify potential biomarkers that may be helpful for preventing malignancy risk or other chronic processes. Among the variants, six variants that may be linked with VACTERL were identified in the exome analysis. The variants c.501G>C on OLR1 and c.-8C>G on PSMA6 were previously associated with myocardial infarction. The variants c.1936A>G on AKAP10 and c.575A>G on PON1 are linked to defects in cardiac conduction and artery disease, respectively. Alterations in metabolism were also suggested by the variants c.860G>A on EPHX2 and c.214C>A on GHRL. In addition, three variants associated with colon cancer were discovered. Specifically, the reported variants were c.723G>A on CCND1 and c.91T>A on AURKA proto-oncogenes as well as c.827A>C in the tumor suppressor PTPRJ. A further inspection identified 15 rare variants carried by cancer genes. Specifically, these mutations are located on five tumor suppressors (SDHA, RB1CC1, PTCH1, DMBT1, BCR) and eight proto-oncogenes (MERTK, CSF1R, MYB, ROS1, PCM1, FGFR2, MYH11, BRCC3) and have an allele frequency lower than 0.01 in the Genome Aggregation Database (GnomAD). We observed that the cardiac and metabolic phenotypic traits are linked with the genotype of the patient. In addition, the risk of developing neoplasia cannot be excluded a priori. Long-term surgical issues of patients with VATER syndrome could benefit from the clinical exome sequencing of a personalized risk assessment for the appearance of further disease in pubertal timing and adult age.
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Affiliation(s)
- Gloria Pelizzo
- Pediatric Surgery Unit, Ospedale dei Bambini “Vittore Buzzi”, 20154 Milano, Italy
- Department of Biomedical and Clinical Science “L. Sacco”, University of Milano, 20157 Milano, Italy;
- Correspondence:
| | - Luigi Chiricosta
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (L.C.); (E.M.); (P.B.)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (L.C.); (E.M.); (P.B.)
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Science “L. Sacco”, University of Milano, 20157 Milano, Italy;
- Department of Pediatrics, Ospedale dei Bambini “Vittore Buzzi”, 20154 Milano, Italy;
| | - Maria Antonietta Avanzini
- Immunology and Transplantation Laboratory, Cell Factory, Pediatric Hematology Oncology Unit, Department of Maternal and Children’s Health, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy; (M.A.A.); (S.C.)
| | - Stefania Croce
- Immunology and Transplantation Laboratory, Cell Factory, Pediatric Hematology Oncology Unit, Department of Maternal and Children’s Health, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy; (M.A.A.); (S.C.)
| | - Mario Lima
- Pediatric Surgery Unit, S. Orsola Hospital, University of Bologna, 40138 Bologna, Italy;
| | - Placido Bramanti
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (L.C.); (E.M.); (P.B.)
| | - Valeria Calcaterra
- Department of Pediatrics, Ospedale dei Bambini “Vittore Buzzi”, 20154 Milano, Italy;
- Pediatrics and Adolescentology Unit, Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
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8
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Nguyen DTT, Lu Y, Chu KL, Yang X, Park SM, Choo ZN, Chin CR, Prieto C, Schurer A, Barin E, Savino AM, Gourkanti S, Patel P, Vu LP, Leslie CS, Kharas MG. HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells. Nat Commun 2020; 11:2026. [PMID: 32332729 PMCID: PMC7181745 DOI: 10.1038/s41467-020-15814-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 05/27/2019] [Accepted: 03/25/2020] [Indexed: 01/16/2023] Open
Abstract
The cell-context dependency for RNA binding proteins (RBPs) mediated control of stem cell fate remains to be defined. Here we adapt the HyperTRIBE method using an RBP fused to a Drosophila RNA editing enzyme (ADAR) to globally map the mRNA targets of the RBP MSI2 in mammalian adult normal and malignant stem cells. We reveal a unique MUSASHI-2 (MSI2) mRNA binding network in hematopoietic stem cells that changes during transition to multipotent progenitors. Additionally, we discover a significant increase in RNA binding activity of MSI2 in leukemic stem cells compared with normal hematopoietic stem and progenitor cells, resulting in selective regulation of MSI2's oncogenic targets. This provides a basis for MSI2 increased dependency in leukemia cells compared to normal cells. Moreover, our study provides a way to measure RBP function in rare cells and suggests that RBPs can achieve differential binding activity during cell state transition independent of gene expression.
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Affiliation(s)
- Diu T T Nguyen
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yuheng Lu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Blavatnik Institute of System Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Karen L Chu
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell School of Medical Sciences, New York, NY, 10065, USA
| | - Xuejing Yang
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sun-Mi Park
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Zi-Ning Choo
- Weill Cornell School of Medical Sciences, New York, NY, 10065, USA
| | | | - Camila Prieto
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ersilia Barin
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Angela M Savino
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Saroj Gourkanti
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Payal Patel
- Weill Cornell School of Medical Sciences, New York, NY, 10065, USA
| | - Ly P Vu
- Terry Fox Laboratory, British Columbia Cancer Research Centre, Vancouver, BC, V5Z 1L3, Canada
- Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, V5A 1S6, Canada
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Center for Cell Engineering, Center for Stem Cell Biology, Center for Experimental Therapeutics, Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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9
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Ballout RA, Dickerson C, Wick MJ, Al-Sweel N, Openshaw AS, Srivastava S, Swanson LC, Bramswig NC, Kuechler A, Hong B, Fleming LR, Curry K, Robertson SP, Andersen EF, El-Hattab AW. Int22h1/Int22h2-mediated Xq28 duplication syndrome: de novo duplications, prenatal diagnoses, and additional phenotypic features. Hum Mutat 2020; 41:1238-1249. [PMID: 32112660 DOI: 10.1002/humu.24009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 11/13/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/11/2022]
Abstract
Int22h1/Int22h2-mediated Xq28 duplication syndrome is a relatively new X-linked intellectual disability syndrome, arising from duplications of the subregion flanked by intron 22 homologous regions 1 and 2 on the q arm of chromosome X. Its primary manifestations include variable cognitive deficits, distinct facial dysmorphia, and neurobehavioral abnormalities that mainly include hyperactivity, irritability, and autistic behavior. Affected males are hemizygous for the duplication, which explains their often more severe manifestations compared with heterozygous females. In this report, we describe the cases of nine individuals recently identified having the syndrome, highlighting unique and previously unreported findings of this syndrome. Specifically, we report for the first time in this syndrome, two cases with de novo duplications, three receiving prenatal diagnosis with the syndrome, and three others having atypical versions of the duplication. Among the latter, one proband has a shortened version spanning only the centromeric half of the typical duplication, while the other two cases have a nearly identical length duplication as the classical duplication, with the exception that their duplication's breakpoints are telomerically shifted by about 0.2 Mb. Finally, we shed light on two new manifestations in this syndrome, vertebral anomalies and multiple malignancies, which possibly expand the phenotypic spectrum of the syndrome.
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Affiliation(s)
- Rami A Ballout
- Lipoprotein Metabolism Section, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.,Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Cheryl Dickerson
- WakeMed Physician Practices, Maternal-Fetal Medicine, Raleigh, North Carolina
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Najla Al-Sweel
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | - Amanda S Openshaw
- ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | | | - Lindsay C Swanson
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts
| | - Nuria C Bramswig
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Bo Hong
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | - Leah R Fleming
- St. Luke's Children's Genetics and Metabolic Clinic, Boise, Idaho
| | - Kathryn Curry
- St. Luke's Children's Genetics and Metabolic Clinic, Boise, Idaho
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Erica F Andersen
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Cytogenetics and Genomic Microarray, Salt Lake City, Utah
| | - Ayman W El-Hattab
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
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10
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Mylonas E, Yoshida K, Frick M, Hoyer K, Christen F, Kaeda J, Obenaus M, Noerenberg D, Hennch C, Chan W, Ochi Y, Shiraishi Y, Shiozawa Y, Zenz T, Oakes CC, Sawitzki B, Schwarz M, Bullinger L, le Coutre P, Rose-Zerilli MJJ, Ogawa S, Damm F. Single-cell analysis based dissection of clonality in myelofibrosis. Nat Commun 2020; 11:73. [PMID: 31911629 DOI: 10.1038/s41467-019-13892-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/28/2019] [Indexed: 12/29/2022] Open
Abstract
Cancer development is an evolutionary genomic process with parallels to Darwinian selection. It requires acquisition of multiple somatic mutations that collectively cause a malignant phenotype and continuous clonal evolution is often linked to tumor progression. Here, we show the clonal evolution structure in 15 myelofibrosis (MF) patients while receiving treatment with JAK inhibitors (mean follow-up 3.9 years). Whole-exome sequencing at multiple time points reveal acquisition of somatic mutations and copy number aberrations over time. While JAK inhibition therapy does not seem to create a clear evolutionary bottleneck, we observe a more complex clonal architecture over time, and appearance of unrelated clones. Disease progression associates with increased genetic heterogeneity and gain of RAS/RTK pathway mutations. Clonal diversity results in clone-specific expansion within different myeloid cell lineages. Single-cell genotyping of circulating CD34 + progenitor cells allows the reconstruction of MF phylogeny demonstrating loss of heterozygosity and parallel evolution as recurrent events. Myelofibrosis is a myeloproliferative neoplasm. Here, the authors show the clonal evolution of myelofibrosis during JAK inhibitor therapy, revealing how the treatment results in an increase in clonal complexity and a gain of RAS pathway mutations.
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11
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Abstract
During the past decade, substantial progress has been made in the field of the genetics of myelodysplastic syndromes (MDS). These comprise a group of chronic myeloid neoplasms with abnormal cell morphology and progression to acute myeloid leukemia (AML), where revolutionary sequencing technologies have played a major role. Through extensive sequencing of a large number of MDS genomes, a comprehensive registry of driver mutations involved in the pathogenesis of MDS has been revealed, along with their impacts on clinical phenotype and prognosis. The most frequently affected molecules are involved in DNA methylations, chromatin modification, RNA splicing, transcription, signal transduction, cohesin regulation, and DNA repair. These mutations show strong positive and negative correlations with each other, suggesting the presence of functional interactions between mutations, which dictate disease progression. Because these mutations are associated with disease phenotype, drug response, and clinical outcomes, it is essential to be familiar with MDS genetics not only for better understanding of MDS pathogenesis but also for management of patients.
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Affiliation(s)
- Seishi OGAWA
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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12
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Meyer T, Jahn N, Lindner S, Röhner L, Dolnik A, Weber D, Scheffold A, Köpff S, Paschka P, Gaidzik VI, Heckl D, Wiese S, Ebert BL, Döhner H, Bullinger L, Döhner K, Krönke J. Functional characterization of BRCC3 mutations in acute myeloid leukemia with t(8;21)(q22;q22.1). Leukemia 2019; 34:404-415. [PMID: 31576005 PMCID: PMC7214237 DOI: 10.1038/s41375-019-0578-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 02/20/2019] [Revised: 06/28/2019] [Accepted: 07/29/2019] [Indexed: 12/16/2022]
Abstract
BRCA1/BRCA2-containing complex 3 (BRCC3) is a Lysine 63-specific deubiquitinating enzyme (DUB) involved in inflammasome activity, interferon signaling, and DNA damage repair. Recurrent mutations in BRCC3 have been reported in myelodysplastic syndromes (MDS) but not in de novo AML. In one of our recent studies, we found BRCC3 mutations selectively in 9/191 (4.7%) cases with t(8;21)(q22;q22.1) AML but not in 160 cases of inv(16)(p13.1q22) AML. Clinically, AML patients with BRCC3 mutations had an excellent outcome with an event-free survival of 100%. Inactivation of BRCC3 by CRISPR/Cas9 resulted in improved proliferation in t(8;21)(q22;q22.1) positive AML cell lines and together with expression of AML1-ETO induced unlimited self-renewal in mouse hematopoietic progenitor cells in vitro. Mutations in BRCC3 abrogated its deubiquitinating activity on IFNAR1 resulting in an impaired interferon response and led to diminished inflammasome activity. In addition, BRCC3 inactivation increased release of several cytokines including G-CSF which enhanced proliferation of AML cell lines with t(8;21)(q22;q22.1). Cell lines and primary mouse cells with inactivation of BRCC3 had a higher sensitivity to doxorubicin due to an impaired DNA damage response providing a possible explanation for the favorable outcome of BRCC3 mutated AML patients.
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Affiliation(s)
- Tatjana Meyer
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Nikolaus Jahn
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Stefanie Lindner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Linda Röhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Anna Dolnik
- Department of Hematology, Oncology, and Tumorimmunology, Charité University Medicine, Berlin, Germany
| | - Daniela Weber
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Annika Scheffold
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Simon Köpff
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Peter Paschka
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Verena I Gaidzik
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Dirk Heckl
- Department of Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Sebastian Wiese
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Tumorimmunology, Charité University Medicine, Berlin, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Jan Krönke
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany.
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13
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Hurtado AM, Luengo-Gil G, Chen-Liang TH, Amaral F, Batta K, Palomo L, Lumbreras E, Przychodzen B, Caparros E, Amigo ML, Dıez-Campelo M, Zamora L, Salido Fierrez EJ, Maciejewski JP, Ortuño FJ, Vicente V, Del Canizo M, Sole F, Ferrer-Marin F, Wiseman DH, Jerez A. Transcriptomic rationale for synthetic lethality-targeting ERCC1 and CDKN1A in chronic myelomonocytic leukaemia. Br J Haematol 2018; 182:373-383. [PMID: 29797327 DOI: 10.1111/bjh.15408] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022]
Abstract
Despite the absence of mutations in the DNA repair machinery in myeloid malignancies, the advent of high-throughput sequencing and discovery of splicing and epigenetics defects in chronic myelomonocytic leukaemia (CMML) prompted us to revisit a pathogenic role for genes involved in DNA damage response. We screened for misregulated DNA repair genes by enhanced RNA-sequencing on bone marrow from a discovery cohort of 27 CMML patients and 9 controls. We validated 4 differentially expressed candidates in CMML CD34+ bone marrow selected cells and in an independent cohort of 74 CMML patients, mutationally contextualized by targeted sequencing, and assessed their transcriptional behavior in 70 myelodysplastic syndrome, 66 acute myeloid leukaemia and 25 chronic myeloid leukaemia cases. We found BAP1 and PARP1 down-regulation to be specific to CMML compared with other related disorders. Chromatin-regulator mutated cases showed decreased BAP1 dosage. We validated a significant over-expression of the double strand break-fidelity genes CDKN1A and ERCC1, independent of promoter methylation and associated with chemorefractoriness. In addition, patients bearing mutations in the splicing component SRSF2 displayed numerous aberrant splicing events in DNA repair genes, with a quantitative predominance in the single strand break pathway. Our results highlight potential targets in this disease, which currently has few therapeutic options.
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Affiliation(s)
- Ana M Hurtado
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Gines Luengo-Gil
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Tzu H Chen-Liang
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Fabio Amaral
- Leukaemia Biology Laboratory, Cancer Research UK, Manchester Institute, University of Manchester, Manchester, UK
| | - Kiran Batta
- Division of Cancer Sciences, Cancer Research UK, Manchester Institute, University of Manchester, Manchester, UK
| | - Laura Palomo
- Josep Carreras Leukaemia- Research Institute, ICO-Hospital Germans Trias i Pujol, Badalona, Spain
| | - Eva Lumbreras
- Department of Haematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Bartlomiej Przychodzen
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, USA
| | - Eva Caparros
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Marıa L Amigo
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Maria Dıez-Campelo
- Department of Haematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Lurdes Zamora
- Josep Carreras Leukaemia- Research Institute, ICO-Hospital Germans Trias i Pujol, Badalona, Spain
| | | | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, USA
| | | | - Vicente Vicente
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Marıa Del Canizo
- Department of Haematology, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Francesc Sole
- Josep Carreras Leukaemia- Research Institute, ICO-Hospital Germans Trias i Pujol, Badalona, Spain
| | | | - Daniel H Wiseman
- Leukaemia Biology Laboratory, Cancer Research UK, Manchester Institute, University of Manchester, Manchester, UK
| | - Andres Jerez
- Haematology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
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14
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Nieborowska-Skorska M, Maifrede S, Dasgupta Y, Sullivan K, Flis S, Le BV, Solecka M, Belyaeva EA, Kubovcakova L, Nawrocki M, Kirschner M, Zhao H, Prchal JT, Piwocka K, Moliterno AR, Wasik M, Koschmieder S, Green TR, Skoda RC, Skorski T. Ruxolitinib-induced defects in DNA repair cause sensitivity to PARP inhibitors in myeloproliferative neoplasms. Blood 2017; 130:2848-2859. [PMID: 29042365 PMCID: PMC5746670 DOI: 10.1182/blood-2017-05-784942] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [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: 05/12/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023] Open
Abstract
Myeloproliferative neoplasms (MPNs) often carry JAK2(V617F), MPL(W515L), or CALR(del52) mutations. Current treatment options for MPNs include cytoreduction by hydroxyurea and JAK1/2 inhibition by ruxolitinib, both of which are not curative. We show here that cell lines expressing JAK2(V617F), MPL(W515L), or CALR(del52) accumulated reactive oxygen species-induced DNA double-strand breaks (DSBs) and were modestly sensitive to poly-ADP-ribose polymerase (PARP) inhibitors olaparib and BMN673. At the same time, primary MPN cell samples from individual patients displayed a high degree of variability in sensitivity to these drugs. Ruxolitinib inhibited 2 major DSB repair mechanisms, BRCA-mediated homologous recombination and DNA-dependent protein kinase-mediated nonhomologous end-joining, and, when combined with olaparib, caused abundant accumulation of toxic DSBs resulting in enhanced elimination of MPN primary cells, including the disease-initiating cells from the majority of patients. Moreover, the combination of BMN673, ruxolitinib, and hydroxyurea was highly effective in vivo against JAK2(V617F)+ murine MPN-like disease and also against JAK2(V617F)+, CALR(del52)+, and MPL(W515L)+ primary MPN xenografts. In conclusion, we postulate that ruxolitinib-induced deficiencies in DSB repair pathways sensitized MPN cells to synthetic lethality triggered by PARP inhibitors.
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Affiliation(s)
| | - Silvia Maifrede
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Yashodhara Dasgupta
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Katherine Sullivan
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Sylwia Flis
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Department of Pharmacology, National Medicines Institute, Warsaw, Poland
| | - Bac Viet Le
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Martyna Solecka
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Elizaveta A Belyaeva
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lucia Kubovcakova
- Department of Biomedicine, University Hospital Basel/University of Basel, Basel, Switzerland
| | - Morgan Nawrocki
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Huaqing Zhao
- Department of Clinical Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
| | - Josef T Prchal
- School of Medicine, University of Utah, Salt Lake City, UT
| | - Katarzyna Piwocka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Alison R Moliterno
- Division of Hematology, Department of Medicine, School of Medicine, The Johns Hopkins University, Baltimore, MD; and
| | - Mariusz Wasik
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen, Germany
| | - Tony R Green
- Cambridge Institute for Medical Research
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, and
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom; and
| | - Radek C Skoda
- Department of Biomedicine, University Hospital Basel/University of Basel, Basel, Switzerland
| | - Tomasz Skorski
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
- Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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15
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Marneth AE, Prange KHM, Al Hinai ASA, Bergevoet SM, Tesi N, Janssen-Megens EM, Kim B, Sharifi N, Yaspo ML, Kuster J, Sanders MA, Stoetman ECG, Knijnenburg J, Arentsen-Peters TCJM, Zwaan CM, Stunnenberg HG, van den Heuvel-Eibrink MM, Haferlach T, Fornerod M, Jansen JH, Valk PJM, van der Reijden BA, Martens JHA. C-terminal BRE overexpression in 11q23-rearranged and t(8;16) acute myeloid leukemia is caused by intragenic transcription initiation. Leukemia 2017; 32:828-836. [PMID: 28871137 DOI: 10.1038/leu.2017.280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/16/2017] [Accepted: 08/10/2017] [Indexed: 01/05/2023]
Abstract
Overexpression of the BRE (brain and reproductive organ-expressed) gene defines a distinct pediatric and adult acute myeloid leukemia (AML) subgroup. Here we identify a promoter enriched for active chromatin marks in BRE intron 4 causing strong biallelic expression of a previously unknown C-terminal BRE transcript. This transcript starts with BRE intron 4 sequences spliced to exon 5 and downstream sequences, and if translated might code for an N terminally truncated BRE protein. Remarkably, the new BRE transcript was highly expressed in over 50% of 11q23/KMT2A (lysine methyl transferase 2A)-rearranged and t(8;16)/KAT6A-CREBBP cases, while it was virtually absent from other AML subsets and normal tissues. In gene reporter assays, the leukemia-specific fusion protein KMT2A-MLLT3 transactivated the intragenic BRE promoter. Further epigenome analyses revealed 97 additional intragenic promoter marks frequently bound by KMT2A in AML with C-terminal BRE expression. The corresponding genes may be part of a context-dependent KMT2A-MLLT3-driven oncogenic program, because they were higher expressed in this AML subtype compared with other groups. C-terminal BRE might be an important contributor to this program because in a case with relapsed AML, we observed an ins(11;2) fusing CHORDC1 to BRE at the region where intragenic transcription starts in KMT2A-rearranged and KAT6A-CREBBP AML.
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Affiliation(s)
- A E Marneth
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - K H M Prange
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - A S A Al Hinai
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - S M Bergevoet
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - N Tesi
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - E M Janssen-Megens
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - B Kim
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - N Sharifi
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - M L Yaspo
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Kuster
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - M A Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - E C G Stoetman
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - J Knijnenburg
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - T C J M Arentsen-Peters
- Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - C M Zwaan
- Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - H G Stunnenberg
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
| | - M M van den Heuvel-Eibrink
- Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands.,Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - T Haferlach
- MLL Munich Leukemia Laboratory, Munich, Germany
| | - M Fornerod
- Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - J H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - P J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - B A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, The Netherlands
| | - J H A Martens
- Department of Molecular Biology, Faculty of Science, RIMLS, Radboud University, Nijmegen, The Netherlands
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16
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Rosewick N, Durkin K, Artesi M, Marçais A, Hahaut V, Griebel P, Arsic N, Avettand-Fenoel V, Burny A, Charlier C, Hermine O, Georges M, Van den Broeke A. Cis-perturbation of cancer drivers by the HTLV-1/BLV proviruses is an early determinant of leukemogenesis. Nat Commun 2017; 8:15264. [PMID: 28534499 PMCID: PMC5457497 DOI: 10.1038/ncomms15264] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Human T-cell leukaemia virus type-1 (HTLV-1) and bovine leukaemia virus (BLV) infect T- and B-lymphocytes, respectively, provoking a polyclonal expansion that will evolve into an aggressive monoclonal leukaemia in ∼5% of individuals following a protracted latency period. It is generally assumed that early oncogenic changes are largely dependent on virus-encoded products, especially TAX and HBZ, while progression to acute leukaemia/lymphoma involves somatic mutations, yet that both are independent of proviral integration site that has been found to be very variable between tumours. Here, we show that HTLV-1/BLV proviruses are integrated near cancer drivers which they affect either by provirus-dependent transcription termination or as a result of viral antisense RNA-dependent cis-perturbation. The same pattern is observed at polyclonal non-malignant stages, indicating that provirus-dependent host gene perturbation contributes to the initial selection of the multiple clones characterizing the asymptomatic stage, requiring additional alterations in the clone that will evolve into full-blown leukaemia/lymphoma. Human T-cell leukaemia virus type-1 and bovine leukaemia virus infect T and B lymphocytes and lead to aggressive leukaemia. Here, the authors show these proviruses integrate near cancer drivers perturbing transcription termination or antisense RNA-dependent interaction, suggesting post-transcriptional mechanisms in some cases.
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Affiliation(s)
- Nicolas Rosewick
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Keith Durkin
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Maria Artesi
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Ambroise Marçais
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, 149-161 rue de Sèvres, Paris 75010, France
| | - Vincent Hahaut
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3
| | - Natasa Arsic
- Vaccine and Infectious Disease Organization, VIDO-Intervac, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Canada S7N 5E3
| | - Véronique Avettand-Fenoel
- Laboratoire de Virologie, AP-HP, Hôpital Necker-Enfants Malades, Université Paris Descartes, Sorbonne Paris Cité, EA7327, 149 rue de Sèvres, Paris 75010, France
| | - Arsène Burny
- Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Olivier Hermine
- Service d'hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance publique hôpitaux de Paris, 149-161 rue de Sèvres, Paris 75010, France.,INSERM U1163-ERL8254, Institut Imagine, 24 B Boulevard du Montparnasse, Paris 75010, France
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium
| | - Anne Van den Broeke
- Unit of Animal Genomics, GIGA-R, Université de Liège (ULg), Avenue de l'Hôpital 11, B34, Liège 4000, Belgium.,Laboratory of Experimental Hematology, Institut Jules Bordet, Université Libre de Bruxelles (ULB), Boulevard de Waterloo 121, Brussels 1000, Belgium
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17
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Abstract
SETBP1 is a SET-binding protein regulating self-renewal potential through HOXA-protein activation. Somatic SETBP1 mutations were identified by whole exome sequencing in several phenotypes of myelodysplastic/myeloproliferative neoplasms (MDS/MPN), including atypical chronic myeloid leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic leukemia as well as in secondary acute myeloid leukemia (sAML). Surprisingly, its recurrent somatic activated mutations are located at the identical positions of germline mutations reported in congenital Schinzel-Giedion syndrome. In general, somatic SETBP1 mutations have a significant clinical impact on the outcome as poor prognostic factor, due to downstream HOXA-pathway as well as associated aggressive types of chromosomal defects (-7/del(7q) and i(17q)), which is consistent with wild-type SETBP1 activation in aggressive types of acute myeloid leukemia and leukemic evolution. Biologically, mutant SETBP1 attenuates RUNX1 and activates MYB. The studies of mouse models confirmed biological significance of SETBP1 mutations in myeloid leukemogenesis, particularly associated with ASXL1 mutations. SETBP1 is a major oncogene in myeloid neoplasms, which cooperates with various genetic events and causes distinct phenotypes of MDS/MPN and sAML.
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MESH Headings
- Animals
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Chromosome Deletion
- Chromosomes, Human, Pair 7/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/genetics
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/metabolism
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/mortality
- Leukemia, Myeloid, Chronic, Atypical, BCR-ABL Negative/therapy
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/metabolism
- Leukemia, Myelomonocytic, Chronic/mortality
- Leukemia, Myelomonocytic, Chronic/therapy
- Leukemia, Myelomonocytic, Juvenile
- Mice
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Proto-Oncogene Proteins c-myb/genetics
- Proto-Oncogene Proteins c-myb/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
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Affiliation(s)
- Hideki Makishima
- Department of Pathology and Tumor Biology, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
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Makishima H, Yoshizato T, Yoshida K, Sekeres MA, Radivoyevitch T, Suzuki H, Przychodzen B, Nagata Y, Meggendorfer M, Sanada M, Okuno Y, Hirsch C, Kuzmanovic T, Sato Y, Sato-Otsubo A, LaFramboise T, Hosono N, Shiraishi Y, Chiba K, Haferlach C, Kern W, Tanaka H, Shiozawa Y, Gómez-Seguí I, Husseinzadeh HD, Thota S, Guinta KM, Dienes B, Nakamaki T, Miyawaki S, Saunthararajah Y, Chiba S, Miyano S, Shih LY, Haferlach T, Ogawa S, Maciejewski JP. Dynamics of clonal evolution in myelodysplastic syndromes. Nat Genet 2017; 49:204-12. [PMID: 27992414 DOI: 10.1038/ng.3742] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
To elucidate differential roles of mutations in myelodysplastic syndromes (MDS), we investigated clonal dynamics using whole-exome and/or targeted sequencing of 699 patients, of whom 122 were analyzed longitudinally. Including the results from previous reports, we assessed a total of 2,250 patients for mutational enrichment patterns. During progression, the number of mutations, their diversity and clone sizes increased, with alterations frequently present in dominant clones with or without their sweeping previous clones. Enriched in secondary acute myeloid leukemia (sAML; in comparison to high-risk MDS), FLT3, PTPN11, WT1, IDH1, NPM1, IDH2 and NRAS mutations (type 1) tended to be newly acquired, and were associated with faster sAML progression and a shorter overall survival time. Significantly enriched in high-risk MDS (in comparison to low-risk MDS), TP53, GATA2, KRAS, RUNX1, STAG2, ASXL1, ZRSR2 and TET2 mutations (type 2) had a weaker impact on sAML progression and overall survival than type-1 mutations. The distinct roles of type-1 and type-2 mutations suggest their potential utility in disease monitoring.
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Hsu JS, Kwan JSH, Pan Z, Garcia-Barcelo MM, Sham PC, Li M. Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes. Bioinformatics 2016; 32:3065-3071. [PMID: 27354691 DOI: 10.1093/bioinformatics/btw381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 06/14/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Exome sequencing studies have facilitated the detection of causal genetic variants in yet-unsolved Mendelian diseases. However, the identification of disease causal genes among a list of candidates in an exome sequencing study is still not fully settled, and it is often difficult to prioritize candidate genes for follow-up studies. The inheritance mode provides crucial information for understanding Mendelian diseases, but none of the existing gene prioritization tools fully utilize this information. RESULTS We examined the characteristics of Mendelian disease genes under different inheritance modes. The results suggest that Mendelian disease genes with autosomal dominant (AD) inheritance mode are more haploinsufficiency and de novo mutation sensitive, whereas those autosomal recessive (AR) genes have significantly more non-synonymous variants and regulatory transcript isoforms. In addition, the X-linked (XL) Mendelian disease genes have fewer non-synonymous and synonymous variants. As a result, we derived a new scoring system for prioritizing candidate genes for Mendelian diseases according to the inheritance mode. Our scoring system assigned to each annotated protein-coding gene (N = 18 859) three pathogenic scores according to the inheritance mode (AD, AR and XL). This inheritance mode-specific framework achieved higher accuracy (area under curve = 0.84) in XL mode. CONCLUSION The inheritance-mode specific pathogenicity prioritization (ISPP) outperformed other well-known methods including Haploinsufficiency, Recessive, Network centrality, Genic Intolerance, Gene Damage Index and Gene Constraint scores. This systematic study suggests that genes manifesting disease inheritance modes tend to have unique characteristics. AVAILABILITY AND IMPLEMENTATION ISPP is included in KGGSeq v1.0 (http://grass.cgs.hku.hk/limx/kggseq/), and source code is available from (https://github.com/jacobhsu35/ISPP.git). CONTACT mxli@hku.hkSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | | | - Pak Chung Sham
- Department of Psychiatry Centre for Genomics Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Miaoxin Li
- Department of Psychiatry Centre for Genomics Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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