1
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Yang L, Zhang X, Wang F, Zhang L, Li J, Yue JX. NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with Nanopore direct RNA sequencing. J Genet Genomics 2024:S1673-8527(24)00183-8. [PMID: 39004399 DOI: 10.1016/j.jgg.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024]
Abstract
Nanopore direct RNA sequencing (DRS) provides the direct access to native RNA strands with full-length information, shedding light on rich qualitative and quantitative properties of gene expression profiles. Here with NanoTrans, we present an integrated computational framework that comprehensively covers all major DRS-based application scopes, including isoform clustering and quantification, poly(A) tail length estimation, RNA modification profiling, and fusion gene detection. In addition to its merit in providing such a streamlined one-stop solution, NanoTrans also shines in its workflow-orientated modular design, batch processing capability, all-in-one tabular and graphic report output, as well as automatic installation and configuration supports. Finally, by applying NanoTrans to real DRS datasets of yeast, Arabidopsis, as well as human embryonic kidney and cancer cell lines, we further demonstrated its utility, effectiveness, and efficacy across a wide range of DRS-based application settings.
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Affiliation(s)
- Ludong Yang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Xinxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China
| | - Fan Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China; Department of Medical Oncology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 223200, China
| | - Li Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.
| | - Jing Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.
| | - Jia-Xing Yue
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, China.
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2
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Testa U, Pelosi E, Castelli G, Leone G. Recent Advances in The Definition of the Molecular Alterations Occurring in Multiple Myeloma. Mediterr J Hematol Infect Dis 2024; 16:e2024062. [PMID: 38984097 PMCID: PMC11232684 DOI: 10.4084/mjhid.2024.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024] Open
Abstract
Multiple myeloma (MM) is a disorder of the monoclonal plasma cells and is the second most common hematologic malignancy. MM initiation and progression are dependent upon complex genomic abnormalities. The current pathogenic model of MM includes two types of primary events, represented by chromosome translocations or chromosome number alterations resulting in hyperdiploidy. These primary molecular events are observed both in MM and in monoclonal gammopathy, its premalignant precursor. Subsequent genetic events allow the progression of monoclonal gammopathy to MM and, together with primary events, contribute to the genetic complexity and heterogeneity of MM. Newer therapies have considerably improved patient outcomes; however, MM remains an incurable disease and most patients experience multiple relapses. The dramatic progresses achieved in the analysis of the heterogeneous molecular features of different MM patients allowed a comprehensive molecular classification of MM and the definition of an individualized prognostic model to predict an individual MM patient's response to different therapeutic options. Despite these progresses, prognostic models fail to identify a significant proportion of patients destined to early relapse. Treatment strategies are increasingly. Based on disease biology, trials are enriched for high-risk MMs, whose careful definition and categorization requires DNA sequencing studies.
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Affiliation(s)
- Ugo Testa
- Istituto Superiore di Sanità, Roma, Italy
| | | | | | - Giuseppe Leone
- Department of Radiological and Hematological Sciences, Catholic University, Rome, Italy
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3
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Brouze M, Czarnocka-Cieciura A, Gewartowska O, Kusio-Kobiałka M, Jachacy K, Szpila M, Tarkowski B, Gruchota J, Krawczyk P, Mroczek S, Borsuk E, Dziembowski A. TENT5-mediated polyadenylation of mRNAs encoding secreted proteins is essential for gametogenesis in mice. Nat Commun 2024; 15:5331. [PMID: 38909026 PMCID: PMC11193744 DOI: 10.1038/s41467-024-49479-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 05/31/2024] [Indexed: 06/24/2024] Open
Abstract
Cytoplasmic polyadenylation plays a vital role in gametogenesis; however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of four TENT5 poly(A) polymerases in mouse fertility and gametogenesis. TENT5B and TENT5C play crucial yet redundant roles in oogenesis, with the double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP knock-in females display a gain-of-function infertility effect, with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, as shown by the sterility in males following the knockout of either gene. Finally, Tent5a knockout substantially lowers fertility, although the underlying mechanism is not directly related to gametogenesis. Through direct RNA sequencing, we discovered that TENT5s polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motif analysis and reporter mRNA assays reveal that the presence of an endoplasmic reticulum-leader sequence represents the primary determinant of TENT5-mediated regulation.
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Affiliation(s)
- Michał Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | | | - Olga Gewartowska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Monika Kusio-Kobiałka
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
| | - Kamil Jachacy
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Marcin Szpila
- Genome Engineering Facility, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Bartosz Tarkowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Jakub Gruchota
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Paweł Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Ewa Borsuk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, 02-109, Poland.
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland.
- Laboratory of Embryology, Institute of Developmental Biology and Biomedical Research, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland.
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4
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Resnati M, Pennacchio S, Viviani L, Perini T, Materozzi M, Orfanelli U, Bordini J, Molteni R, Nuvolone M, Da Vià M, Lazzaroni F, Bolli N, Cenci S, Milan E. TENT5C/FAM46C modulation in vivo reveals a trade-off between antibody secretion and tumor growth in multiple myeloma. Haematologica 2024; 109:1966-1972. [PMID: 38385303 PMCID: PMC11141651 DOI: 10.3324/haematol.2023.284299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/13/2024] [Indexed: 02/23/2024] Open
Abstract
Not available.
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Affiliation(s)
- Massimo Resnati
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Sara Pennacchio
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Lisa Viviani
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Tommaso Perini
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy; Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milano
| | - Maria Materozzi
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Ugo Orfanelli
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Jessica Bordini
- B-cell Neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano
| | - Raffaella Molteni
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy; Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, Pavia
| | - Matteo Da Vià
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano
| | - Francesca Lazzaroni
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano
| | - Niccolò Bolli
- Hematology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy; Università degli Studi di Milano, Milano. Italy
| | - Simone Cenci
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy; University Vita-Salute San Raffaele, Milano
| | - Enrico Milan
- Age Related Diseases Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milano, Italy; University Vita-Salute San Raffaele, Milano.
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5
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Yang K, Zhu T, Yin J, Zhang Q, Li J, Fan H, Han G, Xu W, Liu N, Lv X. The non-canonical poly(A) polymerase FAM46C promotes erythropoiesis. J Genet Genomics 2024; 51:594-607. [PMID: 38403115 DOI: 10.1016/j.jgg.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The post-transcriptional regulation of mRNA is a crucial component of gene expression. The disruption of this process has detrimental effects on the normal development and gives rise to various diseases. Searching for novel post-transcriptional regulators and exploring their roles are essential for understanding development and disease. Through a multimodal analysis of red blood cell trait genome-wide association studies (GWAS) and transcriptomes of erythropoiesis, we identify FAM46C, a non-canonical RNA poly(A) polymerase, as a necessary factor for proper red blood cell development. FAM46C is highly expressed in the late stages of the erythroid lineage, and its developmental upregulation is controlled by an erythroid-specific enhancer. We demonstrate that FAM46C stabilizes mRNA and regulates erythroid differentiation in a polymerase activity-dependent manner. Furthermore, we identify transcripts of lysosome and mitochondria components as highly confident in vivo targets of FAM46C, which aligns with the need of maturing red blood cells for substantial clearance of organelles and maintenance of cellular redox homeostasis. In conclusion, our study unveils a unique role of FAM46C in positively regulating lysosome and mitochondria components, thereby promoting erythropoiesis.
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Affiliation(s)
- Ke Yang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China; The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
| | - Tianqi Zhu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jiaying Yin
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Qiaoli Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Jing Li
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hong Fan
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Gaijing Han
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Weiyin Xu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China
| | - Nan Liu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Liangzhu Laboratory, Zhejiang University, Hangzhou, Zhejiang 311121, China; Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang 311121, China.
| | - Xiang Lv
- The State Key Laboratory for Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Medical Epigenetics Research Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
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6
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Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024; 56:1080-1106. [PMID: 38689093 PMCID: PMC11148060 DOI: 10.1038/s12276-024-01224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
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Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
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7
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Ma WX, Wang SW, Fan QW, Wang YY, Chu CQ, Liu D, Guo Z, Tang JH, Wen JG. Mild hypothermia reduces lipopolysaccharide-induced microglial activation via down-regulation of Tent5c. Biochem Biophys Res Commun 2024; 706:149767. [PMID: 38484570 DOI: 10.1016/j.bbrc.2024.149767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/09/2024] [Indexed: 03/24/2024]
Abstract
Microglial activation is a critical factor in the pathogenesis and progression of neuroinflammatory diseases. Mild hypothermia, known for its neuroprotective properties, has been shown to alleviate microglial activation. In this study, we explore the differentially expressed (DE) mRNAs and long non-coding RNAs (lncRNAs) in BV-2 microglial cells under different conditions: normal temperature (CN), mild hypothermia (YT), normal temperature with lipopolysaccharide (LPS), and mild hypothermia with LPS (LPS + YT). Venn analysis revealed 119 DE mRNAs that were down-regulated in the LPS + YT vs LPS comparison but up-regulated in the CN vs LPS comparison, primarily enriched in Gene Ontology terms related to immune and inflammatory responses. Furthermore, through Venn analysis of YT vs CN and LPS + YT vs LPS comparisons, we identified 178 DE mRNAs and 432 DE lncRNAs. Among these transcripts, we validated the expression of Tent5c at the protein and mRNA levels. Additionally, siRNA-knockdown of Tent5c attenuated the expression of pro-inflammatory genes (TNF-α, IL-1β, Agrn, and Fpr2), cellular morphological changes, NLRP3 and p-P65 protein levels, immunofluorescence staining of p-P65 and number of cells with ASC-speck induced by LPS. Furthermore, Tent5c overexpression further potentiated the aforementioned indicators in the context of mild hypothermia with LPS treatment. Collectively, our findings highlight the significant role of Tent5c down-regulation in mediating the anti-inflammatory effects of mild hypothermia.
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Affiliation(s)
- Wen-Xian Ma
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Shao-Wen Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Qian-Wen Fan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Yue-Yue Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Chao-Qun Chu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Dong Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China
| | - Zhen Guo
- Hunan Provincial Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical University, Changsha, 410219, China
| | - Ji-Hui Tang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China.
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, 230032, China.
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8
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Lai G, De Grossi F, Catusi I, Pesce E, Manfrini N. Dissecting the Puzzling Roles of FAM46C: A Multifaceted Pan-Cancer Tumour Suppressor with Increasing Clinical Relevance. Cancers (Basel) 2024; 16:1706. [PMID: 38730656 PMCID: PMC11083040 DOI: 10.3390/cancers16091706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
FAM46C is a well-established tumour suppressor with a role that is not completely defined or universally accepted. Although FAM46C expression is down-modulated in several tumours, significant mutations in the FAM46C gene are only found in multiple myeloma (MM). Consequently, its tumour suppressor activity has primarily been studied in the MM context. However, emerging evidence suggests that FAM46C is involved also in other cancer types, namely colorectal, prostate and gastric cancer and squamous cell and hepatocellular carcinoma, where FAM46C expression was found to be significantly reduced in tumoural versus non-tumoural tissues and where FAM46C was shown to possess anti-proliferative properties. Accordingly, FAM46C was recently proposed to function as a pan-cancer prognostic marker, bringing FAM46C under the spotlight and attracting growing interest from the scientific community in the pathways modulated by FAM46C and in its mechanistic activity. Here, we will provide the first comprehensive review regarding FAM46C by covering (1) the intracellular pathways regulated by FAM46C, namely the MAPK/ERK, PI3K/AKT, β-catenin and TGF-β/SMAD pathways; (2) the models regarding its mode of action, specifically the poly(A) polymerase, intracellular trafficking modulator and inhibitor of centriole duplication models, focusing on connections and interdependencies; (3) the regulation of FAM46C expression in different environments by interferons, IL-4, TLR engagement or transcriptional modulators; and, lastly, (4) how FAM46C expression levels associate with increased/decreased tumour cell sensitivity to anticancer agents, such as bortezomib, dexamethasone, lenalidomide, pomalidomide, doxorubicin, melphalan, SK1-I, docetaxel and norcantharidin.
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Affiliation(s)
- Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Federica De Grossi
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Ilaria Catusi
- SC Clinical Pathology, SS Medical Genetics Laboratory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy; (G.L.); (F.D.G.); (E.P.)
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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9
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Miglierina E, Ordanoska D, Le Noir S, Laffleur B. RNA processing mechanisms contribute to genome organization and stability in B cells. Oncogene 2024; 43:615-623. [PMID: 38287115 PMCID: PMC10890934 DOI: 10.1038/s41388-024-02952-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2024]
Abstract
RNA processing includes post-transcriptional mechanisms controlling RNA quality and quantity to ensure cellular homeostasis. Noncoding (nc) RNAs that are regulated by these dynamic processes may themselves fulfill effector and/or regulatory functions, and recent studies demonstrated the critical role of RNAs in organizing both chromatin and genome architectures. Furthermore, RNAs can threaten genome integrity when accumulating as DNA:RNA hybrids, but could also facilitate DNA repair depending on the molecular context. Therefore, by qualitatively and quantitatively fine-tuning RNAs, RNA processing contributes directly or indirectly to chromatin states, genome organization, and genome stability. B lymphocytes represent a unique model to study these interconnected mechanisms as they express ncRNAs transcribed from key specific sequences before undergoing physiological genetic remodeling processes, including V(D)J recombination, somatic hypermutation, and class switch recombination. RNA processing actors ensure the regulation and degradation of these ncRNAs for efficient DNA repair and immunoglobulin gene remodeling while failure leads to B cell development alterations, aberrant DNA repair, and pathological translocations. This review highlights how RNA processing mechanisms contribute to genome architecture and stability, with emphasis on their critical roles during B cell development, enabling physiological DNA remodeling while preventing lymphomagenesis.
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Affiliation(s)
- Emma Miglierina
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Delfina Ordanoska
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France
| | - Sandrine Le Noir
- UMR CNRS 7276, Inserm 1262, Université de Limoges: Contrôle de la Réponse Immune B et des Lymphoproliférations, Team 2, B-NATION: B cell Nuclear Architecture, Immunoglobulin genes and Oncogenes, Limoges, France
| | - Brice Laffleur
- University of Rennes, Inserm, EFS Bretagne, CHU Rennes, UMR, 1236, Rennes, France.
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10
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Zhang YT, Shen G, Zhuo LC, Yang X, Wang SY, Ruan TC, Jiang C, Wang X, Wang Y, Yang YH, Shen Y. Novel variations in TENT5D lead to teratozoospermia in infertile patients. Andrology 2024. [PMID: 38228861 DOI: 10.1111/andr.13589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024]
Abstract
PURPOSE Teratozoospermia is the main pathogenic factor of male infertility. However, the genetic etiology of teratozoospermia is largely unknown. This study aims to clarify the relationship between novel variations in TENT5D and teratozoospermia in infertile patients. MATERIALS AND METHODS Two infertile patients were enrolled. Routine semen analysis of patients and normal controls was conducted with the WHO guidelines. Whole-exome sequencing (WES) was conducted to identify pathogenic variants in the two patients. Morphology and ultrastructure analysis of spermatozoa in the two patients was determined by Papanicolaou staining, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The functional effect of the identified variants was analyzed by immunofluorescence staining and western blotting. The expression of TENT5D in different germ cells was detected by immunofluorescence staining. RESULTS Two new hemizygous variations, c.101C > T (p.P34L) and c.125A > T (p.D42V), in TENT5D were detected in two patients with male infertility. Morphology analysis showed abnormalities in spermatozoa morphology in the two patients, including multiple heads, headless, multiple tails, coiled, and/or bent flagella. Ultrastructure analysis showed that most of the spermatozoa exhibited missing or irregularly arranged '9+2' structures. Further functional experiments confirmed the abrogated TENT5D protein expression in patients. In addition, both p.P34L and p.D42V substitutions resulted in a conformational change of the TENT5D protein. We precisely analyzed the subcellular localization of TENT5D in germ cells in humans and mice. And we found that TENT5D was predominantly detected in the head and flagellum of elongating spermatids and epididymal spermatozoa. CONCLUSIONS Our results showed further evidence of a relationship between TENT5D mutation and human male infertility, providing new genetic insight for use in the diagnosis and treatment of male infertility.
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Affiliation(s)
- Ying-Teng Zhang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Gan Shen
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Liang-Chai Zhuo
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xue Yang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Su-Yan Wang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Tie-Chao Ruan
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Chuan Jiang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiang Wang
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yan Wang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Yi-Hong Yang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, Chengdu, China
| | - Ying Shen
- Department of Obstetrics/Gynecology, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
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11
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Song Y, Zhang N, Zhang Y, Wang J, Lv Q, Zhang J. Single-Cell Transcriptome Analysis Reveals Development-Specific Networks at Distinct Synchronized Antral Follicle Sizes in Sheep Oocytes. Int J Mol Sci 2024; 25:910. [PMID: 38255985 PMCID: PMC10815039 DOI: 10.3390/ijms25020910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The development of the ovarian antral follicle is a complex, highly regulated process. Oocytes orchestrate and coordinate the development of mammalian ovarian follicles, and the rate of follicular development is governed by a developmental program intrinsic to the oocyte. Characterizing oocyte signatures during this dynamic process is critical for understanding oocyte maturation and follicular development. Although the transcriptional signature of sheep oocytes matured in vitro and preovulatory oocytes have been previously described, the transcriptional changes of oocytes in antral follicles have not. Here, we used single-cell transcriptomics (SmartSeq2) to characterize sheep oocytes from small, medium, and large antral follicles. We characterized the transcriptomic landscape of sheep oocytes during antral follicle development, identifying unique features in the transcriptional atlas, stage-specific molecular signatures, oocyte-secreted factors, and transcription factor networks. Notably, we identified the specific expression of 222 genes in the LO, 8 and 6 genes that were stage-specific in the MO and SO, respectively. We also elucidated signaling pathways in each antral follicle size that may reflect oocyte quality and in vitro maturation competency. Additionally, we discovered key biological processes that drive the transition from small to large antral follicles, revealing hub genes involved in follicle recruitment and selection. Thus, our work provides a comprehensive characterization of the single-oocyte transcriptome, filling a gap in the mapping of the molecular landscape of sheep oogenesis. We also provide key insights into the transcriptional regulation of the critical sizes of antral follicular development, which is essential for understanding how the oocyte orchestrates follicular development.
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Affiliation(s)
| | | | | | | | | | - Jiaxin Zhang
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.S.)
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12
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Mancino M, Lai G, De Grossi F, Cuomo A, Manganaro L, Butta GM, Ferrari I, Vicenzi E, Poli G, Pesce E, Oliveto S, Biffo S, Manfrini N. FAM46C Is an Interferon-Stimulated Gene That Inhibits Lentiviral Particle Production by Modulating Autophagy. Microbiol Spectr 2023; 11:e0521122. [PMID: 37358411 PMCID: PMC10434054 DOI: 10.1128/spectrum.05211-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/02/2023] [Indexed: 06/27/2023] Open
Abstract
FAM46C is a multiple myeloma (MM) tumor suppressor whose function is only starting to be elucidated. We recently showed that in MM cells FAM46C triggers apoptosis by inhibiting autophagy and altering intracellular trafficking and protein secretion. To date, both a physiological characterization of FAM46C role and an assessment of FAM46C-induced phenotypes outside of MM are lacking. Preliminary reports suggested an involvement of FAM46C with regulation of viral replication, but this was never confirmed. Here, we show that FAM46C is an interferon-stimulated gene and that the expression of wild-type FAM46C in HEK-293T cells, but not of its most frequently found mutant variants, inhibits the production of both HIV-1-derived and HIV-1 lentiviruses. We demonstrate that this effect does not require transcriptional regulation and does not depend on inhibition of either global or virus-specific translation but rather mostly relies on FAM46C-induced deregulation of autophagy, a pathway that we show to be required for efficient lentiviral particle production. These studies not only provide new insights on the physiological role of the FAM46C protein but also could help in implementing more efficient antiviral strategies on one side and lentiviral particle production approaches on the other. IMPORTANCE FAM46C role has been thoroughly investigated in MM, but studies characterizing its role outside of the tumoral environment are still lacking. Despite the success of antiretroviral therapy in suppressing HIV load to undetectable levels, there is currently no HIV cure, and treatment is lifelong. Indeed, HIV continues to be a major global public health issue. Here, we show that FAM46C expression in HEK-293T cells inhibits the production of both HIV and HIV-derived lentiviruses. We also demonstrate that such inhibitory effect relies, at least in part, on the well-established regulatory role that FAM46C exerts on autophagy. Deciphering the molecular mechanism underlying this regulation will not only facilitate the understanding of FAM46C physiological role but also give new insights on the interplay between HIV and the cellular environment.
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Affiliation(s)
- Marilena Mancino
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lara Manganaro
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Giacomo M. Butta
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Ivan Ferrari
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Guido Poli
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University School of Medicine, Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Stefania Oliveto
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
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13
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Zhou P, Li W, Zuo S, Ma R, Yuan X, Zhu Z. Pathogenesis, clinical characteristics and personalized managements of multiple myeloma with chromosome 1 abnormalities. Leuk Lymphoma 2023; 64:1373-1388. [PMID: 37300424 DOI: 10.1080/10428194.2023.2216325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
Multiple myeloma (MM) is a biologically heterogeneous malignancy defined by the proliferation of monoclonal plasma cells. Despite the tremendous advancement in MM treatment over the past decades, relapse remains a major problem which is inevitable for most patients. In particular, a partial of patients with early relapse and poor outcomes are classified as a high-risk group. Apart from the clinical stage, genetic aberrations are now recognized as important prognostic factors for identifying high-risk patients. Chromosome 1 abnormalities (C1As), particularly 1q21 gain or amplification, have been identified as common genetic aberrations in patients with MM and are often considered unfavorable prognostic markers for progression-free survival and overall survival. However, more effective therapeutic approaches are still needed to overcome the negative impact of C1As. Therefore, we summarize the prevalence, pathogenesis, clinical significance and present therapeutic condition of C1As in MM, and attempt to conclude the precise and personalized management for patients with C1As.
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Affiliation(s)
- Pan Zhou
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P.R. China
| | - Weiya Li
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P.R. China
| | - Suqiong Zuo
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P.R. China
| | - Rongjun Ma
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P.R. China
| | - Xiaoli Yuan
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P.R. China
| | - Zunmin Zhu
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, P.R. China
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14
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Zhang W, Wu C, Geng S, Wang J, Yan C, Zhang X, Zhang JJ, Wu F, Pang Y, Zhong Y, Wang J, Fu W, Huang X, Wang W, Lyu X, Huang Y, Jing H. FAM46C-mediated tumor heterogeneity predicts extramedullary metastasis and poorer survival in multiple myeloma. Aging (Albany NY) 2023; 15:3644-3677. [PMID: 37155154 PMCID: PMC10449297 DOI: 10.18632/aging.204697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/22/2023] [Indexed: 05/10/2023]
Abstract
Cancers originate from a single cell according to Nowell's theory of clonal evolution. The enrichment of the most aggressive clones has been developed and the heterogeneity arises for genomic instability and environmental selection. Multiple myeloma (MM) is a multiple relapse plasma cell cancer generated from bone marrow. Although there were accumulating researches in multiple myeloma pathogenesis, the heterogeneity remains poorly understood. The participants enrolled in this study were 4 EMP+ (EMP, Extramedullary plasmacytoma) and 2 EMP- primarily untreated MM patients. Single cell RNA sequencing and analysis were conducted for the single cell suspension, which was sorted by flow cytometry from peripheral blood mononuclear cells or bone marrow cells. In our research, the results of single cell RNA sequencing show that FAM46C determines MM tumor heterogeneity predicting extramedullary metastasis by influencing RNA stability. Further, we integrated and analyzed 2280 multiple myeloma samples from 7 independent datasets, which uncover that FAM46C mediated tumor heterogeneity predicts poorer survival in multiple myeloma.
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Affiliation(s)
- Weilong Zhang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Chaoling Wu
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Shuang Geng
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
| | - Jing Wang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Changjian Yan
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Xiannian Zhang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
| | - Jia-jia Zhang
- Department of Hematology, Beijing Chaoyang Hospital West, Capital Medical University, Beijing 100054, China
| | - Fan Wu
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
| | - Yuhong Pang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
| | - Yuping Zhong
- Department of Hematology, Beijing Chaoyang Hospital West, Capital Medical University, Beijing 100054, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100190, China
| | - Wei Fu
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Xin Huang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Wenming Wang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
| | - Xiaoqing Lyu
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
| | - Yanyi Huang
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
- Beijing Advanced Innovation Center for Genomics (ICG), School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100084, China
| | - Hongmei Jing
- Department of Hematology, Biodynamic Optical Imaging Center (BIOPIC) and Lymphoma Research Center, Third Hospital, Peking University, Beijing 100084, China
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15
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Flietner E, Yu M, Poudel G, Veltri AJ, Zhou Y, Rajagopalan A, Feng Y, Lasho T, Wen Z, Sun Y, Patnaik MM, Callander NS, Asimakopoulos F, Wang D, Zhang J. Molecular characterization stratifies VQ myeloma cells into two clusters with distinct risk signatures and drug responses. Oncogene 2023; 42:1751-1762. [PMID: 37031341 PMCID: PMC10367583 DOI: 10.1038/s41388-023-02684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
Multiple myeloma (MM) is a cancer of malignant plasma cells in the bone marrow and extramedullary sites. We previously characterized a VQ model for human high-risk MM. The various VQ lines display different disease phenotypes and survival rates, suggesting significant intra-model variation. Here, we use whole-exome sequencing and copy number variation (CNV) analysis coupled with RNA-Seq to stratify the VQ lines into corresponding clusters: Group A cells had monosomy chromosome (chr) 5 and overexpressed genes and pathways associated with sensitivity to bortezomib (Btz) treatment in human MM patients. By contrast, Group B VQ cells carried recurrent amplification (Amp) of chr3 and displayed high-risk MM features, including downregulation of Fam46c, upregulation of cancer growth pathways associated with functional high-risk MM, and expression of Amp1q and high-risk UAMS-70 and EMC-92 gene signatures. Consistently, in sharp contrast to Group A VQ cells that showed short-term response to Btz, Group B VQ cells were de novo resistant to Btz in vivo. Our study highlights Group B VQ lines as highly representative of the human MM subset with ultrahigh risk.
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Affiliation(s)
- Evan Flietner
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Mei Yu
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA
| | - Govinda Poudel
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Yun Zhou
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Adhithi Rajagopalan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yubin Feng
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Terra Lasho
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, 55902, USA
| | - Zhi Wen
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Yuqian Sun
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, 55902, USA
| | - Natalie S Callander
- Division of Hematology/Oncology, Department of Medicine, UW Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Fotis Asimakopoulos
- Division of Blood and Marrow Transplantation, Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Demin Wang
- Versiti Blood Research Institute, Milwaukee, WI, 53226, USA.
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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16
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Liu S, Chen H, Yin Y, Lu D, Gao G, Li J, Bai XC, Zhang X. Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. SCIENCE ADVANCES 2023; 9:eadf5583. [PMID: 37018411 PMCID: PMC10075960 DOI: 10.1126/sciadv.adf5583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.
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Affiliation(s)
- Shun Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Yin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guoming Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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17
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Ohguchi Y, Ohguchi H. DIS3: The Enigmatic Gene in Multiple Myeloma. Int J Mol Sci 2023; 24:ijms24044079. [PMID: 36835493 PMCID: PMC9958658 DOI: 10.3390/ijms24044079] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/01/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Recent studies have revealed the genetic aberrations involved in the initiation and progression of various cancers, including multiple myeloma (MM), via next-generation sequencing analysis. Notably, DIS3 mutations have been identified in approximately 10% of patients with MM. Moreover, deletions of the long arm of chromosome 13, that includes DIS3, are present in approximately 40% of patients with MM. Regardless of the high incidence of DIS3 mutations and deletions, their contribution to the pathogenesis of MM has not yet been determined. Herein, we summarize the molecular and physiological functions of DIS3, focusing on hematopoiesis, and discuss the characteristics and potential roles of DIS3 mutations in MM. Recent findings highlight the essential roles of DIS3 in RNA homeostasis and normal hematopoiesis and suggest that the reduced activity of DIS3 may be involved in myelomagenesis by increasing genome instability.
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Affiliation(s)
- Yasuyo Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Hiroto Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
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18
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Liudkovska V, Krawczyk PS, Brouze A, Gumińska N, Wegierski T, Cysewski D, Mackiewicz Z, Ewbank JJ, Drabikowski K, Mroczek S, Dziembowski A. TENT5 cytoplasmic noncanonical poly(A) polymerases regulate the innate immune response in animals. SCIENCE ADVANCES 2022; 8:eadd9468. [PMID: 36383655 PMCID: PMC9668313 DOI: 10.1126/sciadv.add9468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Innate immunity is the first line of host defense against pathogens. Here, through global transcriptome and proteome analyses, we uncover that newly described cytoplasmic poly(A) polymerase TENT-5 (terminal nucleotidyltransferase 5) enhances the expression of secreted innate immunity effector proteins in Caenorhabditis elegans. Direct RNA sequencing revealed that multiple mRNAs with signal peptide-encoding sequences have shorter poly(A) tails in tent-5-deficient worms. Those mRNAs are translated at the endoplasmic reticulum where a fraction of TENT-5 is present, implying that they represent its direct substrates. Loss of tent-5 makes worms more susceptible to bacterial infection. Notably, the role of TENT-5 in innate immunity is evolutionarily conserved. Its orthologs, TENT5A and TENT5C, are expressed in macrophages and induced during their activation. Analysis of macrophages devoid of TENT5A/C revealed their role in the regulation of secreted proteins involved in defense response. In summary, our study reveals cytoplasmic polyadenylation to be a previously unknown component of the posttranscriptional regulation of innate immunity in animals.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksandra Brouze
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz Wegierski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zuzanna Mackiewicz
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jonathan J Ewbank
- Aix Marseille University, INSERM, CNRS, CIML, Turing Centre for Living Systems, Marseille, France
| | - Krzysztof Drabikowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
- Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma. Nat Commun 2022; 13:5469. [PMID: 36115844 PMCID: PMC9482638 DOI: 10.1038/s41467-022-33142-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
Oncogenic RAS mutations are common in multiple myeloma (MM), an incurable malignancy of plasma cells. However, the mechanisms of pathogenic RAS signaling in this disease remain enigmatic and difficult to inhibit therapeutically. We employ an unbiased proteogenomic approach to dissect RAS signaling in MM. We discover that mutant isoforms of RAS organize a signaling complex with the amino acid transporter, SLC3A2, and MTOR on endolysosomes, which directly activates mTORC1 by co-opting amino acid sensing pathways. MM tumors with high expression of mTORC1-dependent genes are more aggressive and enriched in RAS mutations, and we detect interactions between RAS and MTOR in MM patient tumors harboring mutant RAS isoforms. Inhibition of RAS-dependent mTORC1 activity synergizes with MEK and ERK inhibitors to quench pathogenic RAS signaling in MM cells. This study redefines the RAS pathway in MM and provides a mechanistic and rational basis to target this mode of RAS signaling. RAS mutations are commonly found in multiple myeloma (MM). Here, the authors show that oncogenic RAS mutations activate mTORC1 signalling in MM and combining mTORC1 and MEK/ERK inhibitors synergize to improve survival in preclinical models.
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Centrosome Defects in Hematological Malignancies: Molecular Mechanisms and Therapeutic Insights. BLOOD SCIENCE 2022; 4:143-151. [DOI: 10.1097/bs9.0000000000000127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022] Open
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21
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Luo S, Su T, Zhou X, Hu WX, Hu J. Chromosome 1 instability in multiple myeloma: Aberrant gene expression, pathogenesis, and potential therapeutic target. FASEB J 2022; 36:e22341. [PMID: 35579877 DOI: 10.1096/fj.202200354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/25/2022] [Indexed: 11/11/2022]
Abstract
Multiple myeloma (MM), the terminally differentiated B cells malignancy, is widely considered to be incurable since many patients have either developed drug resistance or experienced an eventual relapse. To develop precise and efficient therapeutic strategies, we must understand the pathogenesis of MM. Thus, unveiling the driver events of MM and its further clonal evolution will help us understand this complicated disease. Chromosome 1 instabilities are the most common genomic alterations that participate in MM pathogenesis, and these aberrations of chromosome 1 mainly include copy number variations and structural changes. The chromosome 1q gains/amplifications and 1p deletions are the most frequent structural changes of chromosomes in MM. In this review, we intend to focus on the genes that are affected by chromosome 1 instability: some tumor suppressors were lost or down regulated in 1p deletions, and others that contributed to tumorigenesis were upregulated in 1q gains/amplifications. We have summarized their biological function as well as their roles in the MM pathogenesis, hoping to uncover potential novel therapeutical targets and promote the development of future therapeutic approaches.
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Affiliation(s)
- Saiqun Luo
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Tao Su
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiang Zhou
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Wei-Xin Hu
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
| | - Jingping Hu
- Molecular Biology Research Center, School of Life Sciences, Central South University, Changsha, China
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22
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Hanamura I. Multiple myeloma with high-risk cytogenetics and its treatment approach. Int J Hematol 2022; 115:762-777. [PMID: 35534749 PMCID: PMC9160142 DOI: 10.1007/s12185-022-03353-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 12/13/2022]
Abstract
Despite substantial advances in anti-myeloma treatments, early recurrence and death remain an issue in certain subpopulations. Cytogenetic abnormalities (CAs) are the most widely accepted predictors for poor prognosis in multiple myeloma (MM), such as t(4;14), t(14;16), t(14;20), gain/amp(1q21), del(1p), and del(17p). Co-existing high-risk CAs (HRCAs) tend to be associated with an even worse prognosis. Achievement of sustained minimal residual disease (MRD)-negativity has recently emerged as a surrogate for longer survival, regardless of cytogenetic risk. Information from newer clinical trials suggests that extended intensified treatment can help achieve MRD-negativity in patients with HRCAs, which may lead to improved outcomes. Therapy should be considered to include a 3- or 4-drug induction regimen (PI/IMiD/Dex or PI/IMiD/Dex/anti-CD38 antibody), auto-transplantation, and consolidation/maintenance with lenalidomide ± a PI. Results from ongoing clinical trials for enriched high-risk populations will reveal the precise efficacy of the investigated regimens. Genetic abnormalities of MM cells are intrinsic critical factors determining tumor characteristics, which reflect the natural course and drug sensitivity of the disease. This paper reviews the clinicopathological features of genomic abnormalities related to adverse prognosis, focusing on HRCAs that are the most relevant in clinical practice, and outline current optimal therapeutic approaches for newly diagnosed MM with HRCAs.
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Affiliation(s)
- Ichiro Hanamura
- Division of Hematology, Department of Internal Medicine, Aichi Medical University, 1 Karimata, Yazako, Nagakute, Aichi, 480-1195, Japan.
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23
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Turner DJ, Saveliev A, Salerno F, Matheson LS, Screen M, Lawson H, Wotherspoon D, Kranc KR, Turner M. A functional screen of RNA binding proteins identifies genes that promote or limit the accumulation of CD138+ plasma cells. eLife 2022; 11:e72313. [PMID: 35451955 PMCID: PMC9106329 DOI: 10.7554/elife.72313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 04/21/2022] [Indexed: 12/02/2022] Open
Abstract
To identify roles of RNA binding proteins (RBPs) in the differentiation or survival of antibody secreting plasma cells we performed a CRISPR/Cas9 knockout screen of 1213 mouse RBPs for their ability to affect proliferation and/or survival, and the abundance of differentiated CD138 + cells in vitro. We validated the binding partners CSDE1 and STRAP as well as the m6A binding protein YTHDF2 as promoting the accumulation of CD138 + cells in vitro. We validated the EIF3 subunits EIF3K and EIF3L and components of the CCR4-NOT complex as inhibitors of CD138 + cell accumulation in vitro. In chimeric mouse models YTHDF2-deficient plasma cells failed to accumulate.
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Affiliation(s)
- David J Turner
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute (NCI)FrederickUnited States
| | - Alexander Saveliev
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Fiamma Salerno
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Louise S Matheson
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Michael Screen
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
| | - Hannah Lawson
- Laboratory of Haematopoietic Stem Cell and Leukaemia Biology, Queen Mary University of LondonLondonUnited Kingdom
| | - David Wotherspoon
- Laboratory of Haematopoietic Stem Cell and Leukaemia Biology, Queen Mary University of LondonLondonUnited Kingdom
| | - Kamil R Kranc
- Laboratory of Haematopoietic Stem Cell and Leukaemia Biology, Queen Mary University of LondonLondonUnited Kingdom
| | - Martin Turner
- Immunology Programme, The Babraham Institute,Babraham Research CampusCambridgeUnited Kingdom
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24
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Deng J, Xiao W, Wang Z. FAM46C as a Potential Marker for Pan-Cancer Prognosis and Predicting Immunotherapeutic Efficacy. Front Genet 2022; 13:810252. [PMID: 35222533 PMCID: PMC8864238 DOI: 10.3389/fgene.2022.810252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/18/2022] [Indexed: 12/28/2022] Open
Abstract
Background:FAM46C is a common mutated gene in tumours. A comprehensive understanding of the relationship between FAM46C expression and pan-cancer can guide clinical prognosis and broaden the immunotherapeutic targets.Methods: Data from The Cancer Genome Atlas and Genotype-Tissue Expression (GTEx) databases were obtained, and gene expression of different tumour types and stages was analysed. Immunohistochemical analysis was performed to detect differences in the FAM46C protein levels in normal and cancerous tissues. The genetic variation of FAM46C was characterised using cBioPortal. The clinical prognostic value of FAM46C and the impact of FAM46C expression levels on the prognosis of patients with different types of cancer were assessed based on Kaplan–Meier and Cox regression analyses. Gene set enrichment analysis (GSEA) was used to analyse the pathways associated with FAM46C. Correlations between FAM46C expression levels and immune infiltration were assessed using the TIMER2 database and CIBERSORT algorithm, and correlations between FAM46C expression and the ESTIMATE, immune and stromal scores were analysed using the ESTIMATE algorithm. In addition, we also analysed the correlation between FAM46C expression and immune activation, suppression genes and immune chemokines.Results: The expression level of FAM46C was correlated with the prognosis of most tumours, and low expression levels often suggested a poor prognosis. FAM46C was positively correlated with the abundance of CD4+ T cells, CD8+ T cells and plasma B lymphocytes in the tumour microenvironment. FAM46C exhibited a strong correlation with immunomodulatory pathways, immunomodulatory factors and immune markers. In addition, high FAM46C expression correlated with tumour mutational burden in acute myeloid leukaemia and microsatellite instability in endometrial cancer.Conclusion: Our study suggests that FAM46C can be a potential prognostic marker for pan-cancer, is closely associated with immune regulation and may be an immune checkpoint to guide future clinical immunotherapy.
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Affiliation(s)
- Jiehua Deng
- Centre of Imaging Diagnosis, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Wei Xiao
- Department of Clinical Medicine, Medical College of Shihezi University, Shihezi, China
| | - Zheng Wang
- Centre of Imaging Diagnosis, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
- *Correspondence: Zheng Wang,
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25
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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26
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Cutler SD, Knopf P, Campbell CJV, Thoni A, El Hassan MA, Forward N, White D, Wagner J, Goudie M, Boudreau JE, Kennedy BE, Gujar S, Gaston D, Elnenaei MO. DMG26: A Targeted Sequencing Panel for Mutation Profiling to Address Gaps in the Prognostication of Multiple Myeloma. J Mol Diagn 2021; 23:1699-1714. [PMID: 34562616 DOI: 10.1016/j.jmoldx.2021.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/15/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022] Open
Abstract
Multiple myeloma presents with numerous primary genomic lesions that broadly dichotomize cases into hyperdiploidy or IgH translocated. Clinically, these large alterations are assessed by fluorescence in situ hybridization (FISH) for risk stratification at diagnosis. Secondary focal events, including indels and single-nucleotide variants, are also reported; however, their clinical correlates are poorly described, and FISH has insufficient resolution to assess many of them. In this study, we examined the exonic sequences of 26 genes reported to be mutated in >1% of patients with myeloma using a custom panel. We sequenced these exons to approximately 1000 times in a cohort of 76 patients from Atlantic Canada with detailed clinical correlates and in four multiple myeloma cell lines. Across the 76 patients, 255 mutations and 33 focal copy number variations were identified. High-severity mutations and mutations predicted by FATHMM-XF to be pathogenic identified patients with significantly reduced progression-free survival. These mutations were mutually exclusive from the Revised International Staging System high-risk FISH markers and were independent of all biochemical parameters of the Revised International Staging System. Applying our panel to patients classified by FISH to be standard risk successfully reclassified patients into high- and standard-risk groups. Furthermore, three patients in our cohort each had two high-risk markers; two of these patients developed plasma cell leukemia, a rare and severe clinical sequela of multiple myeloma.
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Affiliation(s)
- Samuel D Cutler
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Philipp Knopf
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Clinton J V Campbell
- Pathology & Molecular Medicine, Faculty of Health Sciences, McMaster University, Toronto, Ontario, Canada
| | - Andrea Thoni
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada; Pathology & Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | | | - Nicholas Forward
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Darrell White
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Julie Wagner
- Pathology & Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Marissa Goudie
- Pathology & Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Jeanette E Boudreau
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Barry E Kennedy
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shashi Gujar
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia, Canada; Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - Daniel Gaston
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada; Pathology & Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada; Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada.
| | - Manal O Elnenaei
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada; Pathology & Laboratory Medicine, Nova Scotia Health, Halifax, Nova Scotia, Canada; Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada.
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27
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Eldefrawy F, Xu HS, Pusch E, Karkoura A, Alsafy M, Elgendy S, Williams SM, Navara K, Guo TL. Modulation of folliculogenesis in adult laying chickens by bisphenol A and bisphenol S: Perspectives on ovarian morphology and gene expression. Reprod Toxicol 2021; 103:181-190. [PMID: 34147626 DOI: 10.1016/j.reprotox.2021.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/25/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Both bisphenol A (BPA) and its analog bisphenol S (BPS) are industrial chemicals that have been used to make certain plastic products applied in chicken farms, including food and water containers. They are endocrine disrupting chemicals (EDCs) with xenoestrogenic activities and affect reproductive success in many ways. It was hypothesized that BPA and BPS could adversely affect the folliculogenesis in chickens due to their disruption of the estrogen responses, using either genomic or non-genomic mechanisms. This study investigated the deleterious effects of BPA and BPS on the ovaries when adult layer chickens were orally treated with these EDCs at 50 μg/kg body weight, the reference dose for chronic oral exposure of BPA established by the U.S. EPA. The chickens in both BPA and BPS-treated groups showed a decreased number of the preovulatory follicles. BPA-treated chickens showed a significant decrease in the diameter of F1. Additionally, both BPA and BPS treatments increased the infiltrations of lymphocytes and plasma cells in ovaries. Moreover, it was found that the ovaries of BPS-treated chickens weighed the most among the groups. RNA sequencing and subsequent pathway enrichment analysis of differentially expressed genes revealed that both BPA- and BPS-treatment groups showed significant changes in gene expression and pathways related to reproduction, immune function and carcinogenesis. Taken together, both BPA and BPS are potentially carcinogenic and have deleterious effects on the fertility of laying chickens by inducing inflammation, suggesting that BPS may not be a safe replacement for BPA.
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Affiliation(s)
- Fatma Eldefrawy
- Department of Anatomy and Embryology, College of Veterinary Medicine, Alexandria University, Egypt; Department of Veterinary Biomedical Sciences, University of Georgia, Athens, GA, United States
| | - Hannah Shibo Xu
- Department of Veterinary Biomedical Sciences, University of Georgia, Athens, GA, United States
| | - Elizabeth Pusch
- Department of Poultry Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Ashraf Karkoura
- Department of Anatomy and Embryology, College of Veterinary Medicine, Alexandria University, Egypt
| | - Mohamed Alsafy
- Department of Anatomy and Embryology, College of Veterinary Medicine, Alexandria University, Egypt
| | - Samir Elgendy
- Department of Anatomy and Embryology, College of Veterinary Medicine, Alexandria University, Egypt
| | - Susan M Williams
- Department of Population Health, Poultry Diagnostic and Research Center, University of Georgia, Athens, GA, United States
| | - Kristen Navara
- Department of Poultry Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA, United States
| | - Tai L Guo
- Department of Veterinary Biomedical Sciences, University of Georgia, Athens, GA, United States.
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28
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Perini T, Materozzi M, Milan E. The Immunity-malignancy equilibrium in multiple myeloma: lessons from oncogenic events in plasma cells. FEBS J 2021; 289:4383-4397. [PMID: 34117720 DOI: 10.1111/febs.16068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/13/2021] [Accepted: 06/10/2021] [Indexed: 11/29/2022]
Abstract
Multiple myeloma (MM) is a malignancy of plasma cells (PC) that grow within the bone marrow and maintain massive immunoglobulin (Ig) production. Disease evolution is driven by genetic lesions, whose effects on cell biology and fitness underlie addictions and vulnerabilities of myeloma cells. Several genes mutated in myeloma are strictly involved in dictating PC identity and antibody factory function. Here, we evaluate the impact of mutations in IRF4, PRDM1, and XBP1, essential transcription factors driving the B to PC differentiation, on MM cell biology and homeostasis. These factors are highly specialized, with limited overlap in their downstream transcriptional programs. Indeed, IRF4 sustains metabolism, survival, and proliferation, while PRDM1 and XBP1 are mainly responsible for endoplasmic reticulum expansion and sustained Ig secretion. Interestingly, IRF4 undergoes activating mutations and translocations, while PRDM1 and XBP1 are hit by loss-of-function events, raising the hypothesis that containment of the secretory program, but not its complete extinction, may be beneficial to malignant PCs. Finally, recent studies unveiled that also the PRDM1 target, FAM46C/TENT5C, an onco-suppressor uniquely and frequently mutated or deleted in myeloma, is directly and potently involved in orchestrating ER homeostasis and secretory activity. Inactivating mutations found in this gene and its interactors strengthen the notion that reduced secretory capacity confers advantage to myeloma cells. We believe that dissection of the evolutionary pressure on genes driving PC-specific functions in myeloma will disclose the cellular strategies by which myeloma cells maintain an equilibrium between antibody production and survival, thus unveiling novel therapeutic targets.
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Affiliation(s)
- Tommaso Perini
- Age related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy.,University Vita-Salute San Raffaele, Milano, Italy.,Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - Maria Materozzi
- Age related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy.,Department of Medicine, Surgery and Neurosciences, University of Siena, Italy
| | - Enrico Milan
- Age related Diseases Unit, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milano, Italy.,University Vita-Salute San Raffaele, Milano, Italy
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29
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Li W, Guo L, Tang W, Ma Y, Wang X, Shao Y, Zhao H, Ying J. Identification of DNA methylation biomarkers for risk of liver metastasis in early-stage colorectal cancer. Clin Epigenetics 2021; 13:126. [PMID: 34108011 PMCID: PMC8190869 DOI: 10.1186/s13148-021-01108-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022] Open
Abstract
Background Liver metastases can occur even in CRC patients who underwent curative surgery. While evidence suggested that adjuvant chemotherapy can help to reduce the occurrence of liver metastases for certain patients, it is not a recommended routine as the side effects outweigh the potential benefits, especially in Stage II CRC patients. This study aims to construct a model for predicting liver metastasis risk using differential methylation signals in primary CRC tumors, which can facilitate the decision for adjuvant chemotherapy. Methods Fifty-nine stage I/II and IV CRC patients were enrolled. Primary tumor, adjacent normal tissue, and metastatic tumor tissues were subject to targeted bisulfite sequencing for DNA methylation. The Least Absolute Shrinkage and Selection Operator (LASSO) algorithm was used to identify potential DMRs for predicting liver metastasis of CRC. Results We identified a total of 241,573 DMRs by comparing the DNA methylation profile of primary tumors of stage II patients who developed metastasis to those who were metastasis-free during the follow up period. 213 DMRs were associated with poor prognosis, among which 182 DMRS were found to be hypermethylated in the primary tumor of patients with metastases. Furthermore, by using the LASSO regression model, we identified 23 DMRs that contributed to a high probability of liver metastasis of CRC. The leave-one-out cross validation (LOOCV) was used to evaluate model predictive performance at an AUC of 0.701. In particular, 7 out of those 23 DMRs were found to be in the promoter region of genes that were previously reported prognostic biomarkers in diverse tumor types, including TNNI2, PAX8, GUF1, KLF4, EVI2B, CEP112, and long non-coding RNA AC011298. In addition, the model was also able to distinguish metastases of different sites (liver or lung) at an AUC of 0.933. Conclusion We have identified DNA methylation biomarkers associated with the risk of cancer liver metastasis in early-stage CRC patients. A risk prediction model based on those epigenetic markers was proposed for outcome assessment. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01108-3.
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Affiliation(s)
- Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | | | - Yutong Ma
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Xiaonan Wang
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China.
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Comprehensive CRISPR-Cas9 screens identify genetic determinants of drug responsiveness in multiple myeloma. Blood Adv 2021; 5:2391-2402. [PMID: 33950175 DOI: 10.1182/bloodadvances.2020003541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
The introduction of new drugs in the past years has substantially improved outcome in multiple myeloma (MM). However, the majority of patients eventually relapse and become resistant to one or multiple drugs. While the genetic landscape of relapsed/ resistant multiple myeloma has been elucidated, the causal relationship between relapse-specific gene mutations and the sensitivity to a given drug in MM has not systematically been evaluated. To determine the functional impact of gene mutations, we performed combined whole-exome sequencing (WES) of longitudinal patient samples with CRISPR-Cas9 drug resistance screens for lenalidomide, bortezomib, dexamethasone, and melphalan. WES of longitudinal samples from 16 MM patients identified a large number of mutations in each patient that were newly acquired or evolved from a small subclone (median 9, range 1-55), including recurrent mutations in TP53, DNAH5, and WSCD2. Focused CRISPR-Cas9 resistance screens against 170 relapse-specific mutations functionally linked 15 of them to drug resistance. These included cereblon E3 ligase complex members for lenalidomide, structural genes PCDHA5 and ANKMY2 for dexamethasone, RB1 and CDK2NC for bortezomib, and TP53 for melphalan. In contrast, inactivation of genes involved in the DNA damage repair pathway, including ATM, FANCA, RAD54B, and BRCC3, enhanced susceptibility to cytotoxic chemotherapy. Resistance patterns were highly drug specific with low overlap and highly correlated with the treatment-dependent clonal evolution in patients. The functional association of specific genetic alterations with drug sensitivity will help to personalize treatment of MM in the future.
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Zhang H, Zhang SH, Hu JL, Wu YT, Ma XY, Chen Y, Yu B, Liao S, Huang H, Gao S. Structural and functional characterization of multiple myeloma associated cytoplasmic poly(A) polymerase FAM46C. Cancer Commun (Lond) 2021; 41:615-630. [PMID: 34048638 PMCID: PMC8286142 DOI: 10.1002/cac2.12163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 03/28/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Multiple myeloma (MM) is a hematologic malignancy characterized by the accumulation of aberrant plasma cells within the bone marrow. The high frequent mutation of family with sequence similarity 46, member C (FAM46C) is closely related with the occurrence and progression of MM. Recently, FAM46C has been identified as a non‐canonical poly(A) polymerase (PAP) that functions as a tumor suppressor in MM. This study aimed to elucidate the structural features of this novel non‐canonical PAP and how MM‐related mutations affect the structural and biochemical properties of FAM46C, eventually advancing our understandings towards FAM46C mutation‐related MM occurrence. Methods We purified and crystallized a mammalian FAM46C construct, and solved its structure. Next, we characterized the property of FAM46C as a PAP through a combination of structural analysis, site‐directed mutagenesis and biochemical assays, and by comparison with its homolog FAM46B. Finally, we structurally analyzed MM‐related FAM46C mutations and tested the enzymatic activity of corresponding mutants. Results We determined the crystal structure of a mammalian FAM46C protein at 2.35 Å, and confirmed that FAM46C preferentially consumed adenosine triphosphate (ATP) and extended A‐rich RNA substrates. FAM46C showed a weaker PAP activity than its homolog FAM46B, and this difference was largely dependent on the residue variance at particular sites. Of them, residues at positions 77, 290, and 298 of mouse FAM46C were most important for the divergence in enzymatic activity. Among the MM‐associated FAM46C mutants, those residing at the catalytic site (D90G and D90H) or putative RNA‐binding site (I155L, S156F, D182Y, F184L, Y247V, and M270V) showed abolished or compromised PAP activity of FAM46C, while N72A and S248A did not severely affect the PAP activity. FAM46C mutants D90G, D90H, I155L, S156F, F184L, Y247V, and M270V had significantly lower inhibitory effect on apoptosis of RPMI‐8226 cells as compared to wild‐type FAM46C. Conclusions FAM46C is a prokaryotic‐like PAP with preference for A‐rich RNA substrates, and showed distinct enzymatic efficiency with its homolog FAM46B. The MM‐related missense mutations of FAM46C lead to various structural and biochemical outcomes to the protein.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shi-Hui Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, P. R. China
| | - Yu-Tong Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, P. R. China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510530, P. R. China
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32
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Lu M, Wu Y, Gao W, Tian Y, Wang G, Liu A, Chen W. Novel Non-coding RNA Analysis in Multiple Myeloma Identified Through High-Throughput Sequencing. Front Genet 2021; 12:625019. [PMID: 34108986 PMCID: PMC8181418 DOI: 10.3389/fgene.2021.625019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
This study aimed to explore the potential effects of novel non-coding ribose nucleic acids (ncRNAs) in patients with multiple myeloma (MM). The gene expression profile of plasma cells was used for sequence analysis to explore the expression pattern of ncRNAs in MM. The expression patterns of non-coding RNAs in MM were analyzed by RNA sequencing (whole-transcriptome-specific RNA sequencing). Next, the expression of the selected ncRNAs was verified by quantitative real-time polymerase chain reaction. Further, the lncRNA-associated competitive endogenous RNA network in MM was elucidated using deep RNA-seq. Differentially expressed (DE) ncRNAs were significantly regulated in patients with MM. DE target lncRNAs were analyzed by cis and trans targeting prediction. Two new lncRNAs were shown to be related to MM oncogenes. MSTRG.155519 played a carcinogenic role in myeloma by targeting CEACAM1; MSTRG.13132 was related to FAM46C. Finally, the network of lncRNA–mRNA–miRNA in MM was constructed in this study. The expression of non-coding RNAs through sequence and functional analyses might be helpful for further studies on the pathogenesis of MM and the development of new MM-targeted therapy for non-coding RNAs.
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Affiliation(s)
- Minqiu Lu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.,Department of Hematology, Beijing Jishuitan Hospital, Fourth Medical College of Peking University, Beijing, China
| | - Yin Wu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Wen Gao
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Ying Tian
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Guorong Wang
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Aijun Liu
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Wenming Chen
- Department of Hematology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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33
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Lizárraga D, García-Gasca A. The Placenta as a Target of Epigenetic Alterations in Women with Gestational Diabetes Mellitus and Potential Implications for the Offspring. EPIGENOMES 2021; 5:epigenomes5020013. [PMID: 34968300 PMCID: PMC8594713 DOI: 10.3390/epigenomes5020013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is a pregnancy complication first detected in the second or third trimester in women that did not show evident glucose intolerance or diabetes before gestation. In 2019, the International Diabetes Federation reported that 15.8% of live births were affected by hyperglycemia during pregnancy, of which 83.6% were due to gestational diabetes mellitus, 8.5% were due to diabetes first detected in pregnancy, and 7.9% were due to diabetes detected before pregnancy. GDM increases the susceptibility to developing chronic diseases for both the mother and the baby later in life. Under GDM conditions, the intrauterine environment becomes hyperglycemic, while also showing high concentrations of fatty acids and proinflammatory cytokines, producing morphological, structural, and molecular modifications in the placenta, affecting its function; these alterations may predispose the baby to disease in adult life. Molecular alterations include epigenetic mechanisms such as DNA and RNA methylation, chromatin remodeling, histone modifications, and expression of noncoding RNAs (ncRNAs). The placenta is a unique organ that originates only in pregnancy, and its main function is communication between the mother and the fetus, ensuring healthy development. Thus, this review provides up-to-date information regarding two of the best-documented (epigenetic) mechanisms (DNA methylation and miRNA expression) altered in the human placenta under GDM conditions, as well as potential implications for the offspring.
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The Interaction of the Tumor Suppressor FAM46C with p62 and FNDC3 Proteins Integrates Protein and Secretory Homeostasis. Cell Rep 2021; 32:108162. [PMID: 32966780 DOI: 10.1016/j.celrep.2020.108162] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/23/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
FAM46C is a non-canonical poly(A) polymerase uniquely mutated in up to 20% of multiple myeloma (MM) patients, implying a tissue-specific tumor suppressor function. Here, we report that FAM46C selectively stabilizes mRNAs encoding endoplasmic reticulum (ER)-targeted proteins, thereby concertedly enhancing the expression of proteins that control ER protein import, folding, N-glycosylation, and trafficking and boosting protein secretion. This role requires the interaction with the ER membrane resident proteins FNDC3A and FNDC3B. In MM cells, FAM46C expression raises secretory capacity beyond sustainability, inducing ROS accumulation, ATP shortage, and cell death. FAM46C activity is regulated through rapid proteasomal degradation or the inhibitory interaction with the ZZ domain of the autophagic receptor p62 that hinders its association with FNDC3 proteins via sequestration in p62+ aggregates. Altogether, our data disclose a p62/FAM46C/FNDC3 circuit coordinating sustainable secretory activity and survival, providing an explanation for the MM-specific oncosuppressive role of FAM46C and uncovering potential therapeutic opportunities against cancer.
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35
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Xiong S, Chng WJ, Zhou J. Crosstalk between endoplasmic reticulum stress and oxidative stress: a dynamic duo in multiple myeloma. Cell Mol Life Sci 2021; 78:3883-3906. [PMID: 33599798 PMCID: PMC8106603 DOI: 10.1007/s00018-021-03756-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/19/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023]
Abstract
Under physiological and pathological conditions, cells activate the unfolded protein response (UPR) to deal with the accumulation of unfolded or misfolded proteins in the endoplasmic reticulum. Multiple myeloma (MM) is a hematological malignancy arising from immunoglobulin-secreting plasma cells. MM cells are subject to continual ER stress and highly dependent on the UPR signaling activation due to overproduction of paraproteins. Mounting evidence suggests the close linkage between ER stress and oxidative stress, demonstrated by overlapping signaling pathways and inter-organelle communication pivotal to cell fate decision. Imbalance of intracellular homeostasis can lead to deranged control of cellular functions and engage apoptosis due to mutual activation between ER stress and reactive oxygen species generation through a self-perpetuating cycle. Here, we present accumulating evidence showing the interactive roles of redox homeostasis and proteostasis in MM pathogenesis and drug resistance, which would be helpful in elucidating the still underdefined molecular pathways linking ER stress and oxidative stress in MM. Lastly, we highlight future research directions in the development of anti-myeloma therapy, focusing particularly on targeting redox signaling and ER stress responses.
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Affiliation(s)
- Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
- Centre for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore.
| | - Jianbiao Zhou
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
- Centre for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
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36
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Gewartowska O, Aranaz-Novaliches G, Krawczyk PS, Mroczek S, Kusio-Kobiałka M, Tarkowski B, Spoutil F, Benada O, Kofroňová O, Szwedziak P, Cysewski D, Gruchota J, Szpila M, Chlebowski A, Sedlacek R, Prochazka J, Dziembowski A. Cytoplasmic polyadenylation by TENT5A is required for proper bone formation. Cell Rep 2021; 35:109015. [PMID: 33882302 DOI: 10.1016/j.celrep.2021.109015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/23/2021] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Osteoblasts orchestrate bone formation through the secretion of type I collagen and other constituents of the matrix on which hydroxyapatite crystals mineralize. Here, we show that TENT5A, whose mutations were found in congenital bone disease osteogenesis imperfecta patients, is a cytoplasmic poly(A) polymerase playing a crucial role in regulating bone mineralization. Direct RNA sequencing revealed that TENT5A is induced during osteoblast differentiation and polyadenylates mRNAs encoding Col1α1, Col1α2, and other secreted proteins involved in osteogenesis, increasing their expression. We postulate that TENT5A, possibly together with its paralog TENT5C, is responsible for the wave of cytoplasmic polyadenylation of mRNAs encoding secreted proteins occurring during bone mineralization. Importantly, the Tent5a knockout (KO) mouse line displays bone fragility and skeletal hypomineralization phenotype resulting from quantitative and qualitative collagen defects. Thus, we report a biologically relevant posttranscriptional regulator of collagen production and, more generally, bone formation.
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Affiliation(s)
- Olga Gewartowska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Goretti Aranaz-Novaliches
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic
| | - Paweł S Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Monika Kusio-Kobiałka
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Bartosz Tarkowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Frantisek Spoutil
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic; Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, Prague, Czech Republic
| | - Oldrich Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic
| | - Olga Kofroňová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic
| | - Piotr Szwedziak
- Laboratory of Structural Cell Biology, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Dominik Cysewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Jakub Gruchota
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Marcin Szpila
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic; Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, Prague, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 142 20 Prague 4, Czech Republic; Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, Prague, Czech Republic
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
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37
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Cardona-Benavides IJ, de Ramón C, Gutiérrez NC. Genetic Abnormalities in Multiple Myeloma: Prognostic and Therapeutic Implications. Cells 2021; 10:336. [PMID: 33562668 PMCID: PMC7914805 DOI: 10.3390/cells10020336] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Some genetic abnormalities of multiple myeloma (MM) detected more than two decades ago remain major prognostic factors. In recent years, the introduction of cutting-edge genomic methodologies has enabled the extensive deciphering of genomic events in MM. Although none of the alterations newly discovered have significantly improved the stratification of the outcome of patients with MM, some of them, point mutations in particular, are promising targets for the development of personalized medicine. This review summarizes the main genetic abnormalities described in MM together with their prognostic impact, and the therapeutic approaches potentially aimed at abrogating the undesirable pathogenic effect of each alteration.
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Affiliation(s)
- Ignacio J. Cardona-Benavides
- Hematology Department, University Hospital, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, 37007 Salamanca, Spain; (I.J.C.-B.); (C.d.R.)
- Cancer Research Center-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Cristina de Ramón
- Hematology Department, University Hospital, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, 37007 Salamanca, Spain; (I.J.C.-B.); (C.d.R.)
- Cancer Research Center-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
| | - Norma C. Gutiérrez
- Hematology Department, University Hospital, Institute of Biomedical Research of Salamanca (IBSAL), University Hospital of Salamanca, 37007 Salamanca, Spain; (I.J.C.-B.); (C.d.R.)
- Cancer Research Center-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
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38
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Manfrini N, Mancino M, Miluzio A, Oliveto S, Balestra M, Calamita P, Alfieri R, Rossi RL, Sassoè-Pognetto M, Salio C, Cuomo A, Bonaldi T, Manfredi M, Marengo E, Ranzato E, Martinotti S, Cittaro D, Tonon G, Biffo S. FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy. Cancer Res 2020; 80:4693-4706. [PMID: 32963011 DOI: 10.1158/0008-5472.can-20-1357] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/15/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022]
Abstract
Multiple myeloma is a plasma cell neoplasm characterized by the production of unfolded immunoglobulins, which cause endoplasmic reticulum (ER) stress and sensitivity to proteasome inhibition. The genomic landscape of multiple myeloma is characterized by the loss of several genes rarely mutated in other cancers that may underline specific weaknesses of multiple myeloma cells. One of these is FAM46C that is lost in more than 10% of patients with multiple myeloma. We show here that FAM46C is part of a new complex containing the ER-associated protein FNDC3A, which regulates trafficking and secretion and, by impairing autophagy, exacerbates proteostatic stress. Reconstitution of FAM46C in multiple myeloma cells that had lost it induced apoptosis and ER stress. Apoptosis was preceded by an increase of intracellular aggregates, which was not linked to increased translation of IgG mRNA, but rather to impairment of autophagy. Biochemical analysis showed that FAM46C requires interaction with ER bound protein FNDC3A to reside in the cytoplasmic side of the ER. FNDC3A was lost in some multiple myeloma cell lines. Importantly, depletion of FNDC3A increased the fitness of FAM46C-expressing cells and expression of FNDC3A in cells that had lost it recapitulated the effects of FAM46C, inducing aggregates and apoptosis. FAM46C and FNDC3A formed a complex that modulates secretion routes, increasing lysosome exocytosis. The cellular landscape generated by FAM46C/FNDC3A expression predicted sensitivity to sphingosine kinase inhibition. These results suggest that multiple myeloma cells remodel their trafficking machinery to cope with ER stress. SIGNIFICANCE: This study identifies a new multiple myeloma-specific tumor suppressor complex that regulates autophagy and unconventional secretion, highlighting the sensitivity of multiple myeloma cells to the accumulation of protein aggregates.
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Affiliation(s)
- Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Marilena Mancino
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Clinical Sciences and Community, University of Milan, Milan, Italy
| | - Annarita Miluzio
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Stefania Oliveto
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Matteo Balestra
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy.,Department of Biological Sciences, University of Milan, Milan, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Riccardo L Rossi
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy
| | - Marco Sassoè-Pognetto
- Department of Neuroscience "Rita Levi Montalcini," University of Turin, Torino, Italy
| | - Chiara Salio
- Department of Veterinary Sciences, University of Turin, Grugliasco, Torino, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Novara, Italy.,ISALIT, Novara, Italy.,Department of Translation Medicine, University of Piemonte Orientale, Novara, Italy
| | - Emilio Marengo
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, Novara, Italy.,ISALIT, Novara, Italy.,Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Elia Ranzato
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Simona Martinotti
- Department of Sciences and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Functional Genomics of Cancer Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi," Milan, Italy. .,Department of Biological Sciences, University of Milan, Milan, Italy
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Liang T, Ye X, Yan D, Deng C, Li Z, Tian B. FAM46B Promotes Apoptosis and Inhibits Glycolysis of Prostate Cancer Through Inhibition of the MYC-LDHA Axis. Onco Targets Ther 2020; 13:8771-8782. [PMID: 32943883 PMCID: PMC7478375 DOI: 10.2147/ott.s258724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/18/2020] [Indexed: 12/24/2022] Open
Abstract
Objective Increased dependence on glycolysis is a known element of cancer. This study was designed to examine critical glycolysis components including transcription factor MYC and its downstream target lactate dehydrogenase A (LDHA), potential upstream regulators of glycolysis such as family with sequence similarity 46 member B (FAM46B), and the impact of the abundance of these proteins on apoptosis and glycolysis in prostate cancer. Materials and Methods A total of 70 primary prostate cancer patient samples were compared to normal tissues for FAM46B and LDHA expression and the corresponding patients’ survival was monitored for 60 months. Prostate cancer cell lines were employed for protein expression manipulation, glucose uptake and LDH assays, and apoptosis measurements. A xenograft mouse model was used to quantify the role of FAM46B and LDHA on tumor growth in vivo. Results FAM46B expression was reduced in prostate tumor tissue compared to normal tissue and prostate cancer patients who expressed low amounts of FAM46B had shortened average lifespans compared to those who expressed higher amounts of FAM46B (p=0.008). FAM46B overexpression reduced glucose uptake, decreased LDH activity, and induced apoptosis in prostate cancer cell lines while FAM46B shRNA increased MYC levels in a non-malignant prostate cell line (P69). Conversely, forced expression of LDHA in LNCaP cells produced an increase in glycolysis markers with a corresponding decrease in apoptosis. FAM46B-overexpressing xenografts had starkly blunted growth which was restored with co-overexpression of LDHA. Conclusion FAM46B plays a central role in regulating glycolysis and apoptosis in prostate cancer and operates through the regulation of LDHA via MYC. FAM46B’s keystone status in prostate cancer makes it a potential, robust biomarker for prostate cancer prognosis and a promising therapeutic target.
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Affiliation(s)
- Tao Liang
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Xuxiao Ye
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Dongliang Yan
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Chao Deng
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Zuowei Li
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
| | - Binqiang Tian
- Department of Urology, Shanghai Sixth People's Hospital East Affiliated to Shanghai University of Medicine & Health Sciences, Shanghai 201306, People's Republic of China
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40
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Mishima Y, Mishima Y, Shirouchi Y, Nishimura N, Yokoyama M, Okabe T, Inoue N, Uryu H, Fukuta T, Hatake K, Terui Y. The clonal evolution during long-term clinical course of multiple myeloma. Int J Hematol 2020; 113:279-284. [PMID: 32864713 DOI: 10.1007/s12185-020-02979-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 10/23/2022]
Abstract
Somatic gene mutations related to acceleration disease and clonal evolution in multiple myeloma strongly influence severe clinical outcomes. In this study, we traced the transition of somatic mutations during the clinical course of myeloma patients over a long-term follow-up period (8.5 year average). Seven myeloma cases treated with immuno-chemotherapy at our institution were analyzed with clinical courses and the results of FISH and G-band analyses. Furthermore, the target sequences in regard to 121 genes, related to driver mutations or acceleration of disease in myeloma, were performed using bone marrow myeloma samples by next-generation sequencing, Ion Proton™ System. We detected a relationship between an increase in the dominant mutated gene (e.g., TP53, DIS3, FAM46C, KDM6B, and EGR1) and poor prognosis. In particular, clonal escalation of the TP53 mutation could not be overcome by any treatment. The selection of a combination treatment conducted in conjunction with the monitoring of gene mutations is appropriate for long-term survival. Our data demonstrate that long-term follow-up of somatic gene mutations during the clinical course of myeloma is helpful in the development of an effective treatment strategy.
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Affiliation(s)
- Yuko Mishima
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan. .,Division of Clinical Research, The Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Yuji Mishima
- Division of Clinical Research, The Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuko Shirouchi
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Noriko Nishimura
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Masahiro Yokoyama
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Takashi Okabe
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Norihito Inoue
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Hideki Uryu
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Takanori Fukuta
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Kiyohiko Hatake
- Department of Hematology, International University of Health and Welfare, School of Medicine, Mita Hospital, Tokyo, Japan
| | - Yasuhito Terui
- Department of Hematology Oncology, The Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-ku, Tokyo, 135-8550, Japan.,Division of Clinical Research, The Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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41
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Kazazian K, Haffani Y, Ng D, Lee CMM, Johnston W, Kim M, Xu R, Pacholzyk K, Zih FSW, Tan J, Smrke A, Pollett A, Wu HST, Swallow CJ. FAM46C/TENT5C functions as a tumor suppressor through inhibition of Plk4 activity. Commun Biol 2020; 3:448. [PMID: 32807875 PMCID: PMC7431843 DOI: 10.1038/s42003-020-01161-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/20/2020] [Indexed: 12/17/2022] Open
Abstract
Polo like kinase 4 (Plk4) is a tightly regulated serine threonine kinase that governs centriole duplication. Increased Plk4 expression, which is a feature of many common human cancers, causes centriole overduplication, mitotic irregularities, and chromosomal instability. Plk4 can also promote cancer invasion and metastasis through regulation of the actin cytoskeleton. Herein we demonstrate physical interaction of Plk4 with FAM46C/TENT5C, a conserved protein of unknown function until recently. FAM46C localizes to centrioles, inhibits Plk4 kinase activity, and suppresses Plk4-induced centriole duplication. Interference with Plk4 function by FAM46C was independent of the latter's nucleotidyl transferase activity. In addition, FAM46C restrained cancer cell invasion and suppressed MDA MB-435 cancer growth in a xenograft model, opposing the effect of Plk4. We demonstrate loss of FAM46C in patient-derived colorectal cancer tumor tissue that becomes more profound with advanced clinical stage. These results implicate FAM46C as a tumor suppressor that acts by inhibiting Plk4 activity.
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Affiliation(s)
- Karineh Kazazian
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada.,Department of Surgical Oncology, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Yosr Haffani
- Laboratory of Physiopathology, Alimentation and Biomolecules LR17ES03, Higher Institute of Biotechnology, Sidi Thabet, University of Manouba, Ariana, 2020, Tunisia
| | - Deanna Ng
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Chae Min Michelle Lee
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Wendy Johnston
- Department of Radiation Oncology, University of Toronto, Toronto, ON, M5T 1P5, Canada
| | - Minji Kim
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Roland Xu
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Karina Pacholzyk
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Francis Si-Wah Zih
- Department of Surgical Oncology, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Julie Tan
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Alannah Smrke
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada
| | - Aaron Pollett
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hannah Sun-Tsi Wu
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Carol Jane Swallow
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, M5G 1X5, Canada. .,Department of Surgical Oncology, University of Toronto, Toronto, ON, M5G 2M9, Canada.
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42
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Zheng C, Ouyang YC, Jiang B, Lin X, Chen J, Dong MZ, Zhuang X, Yuan S, Sun QY, Han C. Non-canonical RNA polyadenylation polymerase FAM46C is essential for fastening sperm head and flagellum in mice†. Biol Reprod 2020; 100:1673-1685. [PMID: 31087039 DOI: 10.1093/biolre/ioz083] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/24/2019] [Accepted: 05/13/2019] [Indexed: 01/21/2023] Open
Abstract
Family with sequence similarity 46, member C (FAM46C) is a highly conserved non-canonical RNA polyadenylation polymerase that is abundantly expressed in human and mouse testes and is frequently mutated in patients with multiple myeloma. However, its physiological role remains largely unknown. In this study, we found that FAM46C is specifically localized to the manchette of spermatids in mouse testes, a transient microtubule-based structure mainly involved in nuclear shaping and intra-flagellar protein traffic. Gene knockout of FAM46C in mice resulted in male sterility, characterized by the production of headless spermatozoa in testes. Sperm heads were intermittently found in the epididymides of FAM46C knockout mice, but their fertilization ability was severely compromised based on the results of intracytoplasmic sperm injection assays. Interestingly, our RNA-sequencing analyses of FAM46C knockout testes revealed that mRNA levels of only nine genes were significantly altered compared to wild-type ones (q < 0.05). When considering alternate activities for FAM46C, in vitro assays demonstrated that FAM46C does not exhibit protein kinase or AMPylation activity against general substrates. Together, our data show that FAM46C in spermatids is a novel component in fastening the sperm head and flagellum.
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Affiliation(s)
- Chunwei Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Savaid Medical School, Beijing, China
| | - Ying-Chun Ouyang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Binjie Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ming-Zhe Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xinjie Zhuang
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China
| | - Shuiqiao Yuan
- Family Planning Research Institute, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Savaid Medical School, Beijing, China
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43
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Zhang S, Yang Y, Hua Y, Hu C, Zhong Y. NCTD elicits proapoptotic and antiglycolytic effects on colorectal cancer cells via modulation of Fam46c expression and inhibition of ERK1/2 signaling. Mol Med Rep 2020; 22:774-782. [PMID: 32468032 PMCID: PMC7339822 DOI: 10.3892/mmr.2020.11151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer is a digestive tract malignancy and the third leading cause of cancer‑related mortality worldwide. Norcantharidin (NCTD), the demethylated form of cantharidin, has been reported to possess anticancer properties. Family‑with‑sequence‑similarity‑46c (Fam46c), a non‑canonical poly(A) polymerase, has been reported to be critical in NCTD‑mediated effects in numerous types of cancer, including hepatoma. In the current study, it was found that Fam46c expression was reduced in colorectal cancer tissues and cells. Treatment with NCTD was observed to significantly enhance apoptosis and inhibit glycolysis in colorectal cancer cells. In addition, Fam46c and cleaved caspase 3 expression levels were found to be increased in response to NCTD treatment, in contrast to tumor‑specific pyruvate kinase M2 and phosphorylated ERK expression, which was reduced. Importantly, overexpression of Fam46c exerted similar effects as NCTD treatment on the apoptosis and glycolysis of colorectal cancer cells, whereas Fam46c knockdown strongly attenuated the effect of NCTD. Moreover, epidermal growth factor, which acts as an agonist of ERK1/2 signaling, weakened the effects of NCTD on colorectal cancer cells. Taken together, the results indicated that NCTD promotes apoptosis and suppresses glycolysis in colorectal cancer cells by possibly targeting Fam46c and inhibiting ERK1/2 signaling, hence suggesting that Fam46c may act as a tumor suppressor in colorectal cancer. Thus, the present study identified a novel therapeutic target of NCTD in the clinical treatment of colorectal cancer.
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Affiliation(s)
- Shiqiang Zhang
- Shanghai University of Traditional Chinese Medicine, Shanghai 200082, P.R. China
- Department of Oncology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai 200082, P.R. China
| | - Yun Yang
- Shanghai University of Traditional Chinese Medicine, Shanghai 200082, P.R. China
- Department of Oncology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai 200082, P.R. China
| | - Yunwei Hua
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai 200082, P.R. China
| | - Chen Hu
- School of Life Sciences and Technology, Tongji University, Shanghai 200082, P.R. China
| | - Yi Zhong
- Department of Oncology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai 200082, P.R. China
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44
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Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1622. [PMID: 33145994 PMCID: PMC7988573 DOI: 10.1002/wrna.1622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
Abstract
Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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45
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A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing. Nat Rev Mol Cell Biol 2020; 21:542-556. [PMID: 32483315 DOI: 10.1038/s41580-020-0246-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2020] [Indexed: 01/06/2023]
Abstract
RNA tailing, or the addition of non-templated nucleotides to the 3' end of RNA, is the most frequent and conserved type of RNA modification. The addition of tails and their composition reflect RNA maturation stages and have important roles in determining the fate of the modified RNAs. Apart from canonical poly(A) polymerases, which add poly(A) tails to mRNAs in a transcription-coupled manner, a family of terminal nucleotidyltransferases (TENTs), including terminal uridylyltransferases (TUTs), modify RNAs post-transcriptionally to control RNA stability and activity. The human genome encodes 11 different TENTs with distinct substrate specificity, intracellular localization and tissue distribution. In this Review, we discuss recent advances in our understanding of non-canonical RNA tails, with a focus on the functions of human TENTs, which include uridylation, mixed tailing and post-transcriptional polyadenylation of mRNAs, microRNAs and other types of non-coding RNA.
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46
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Lin HH, Lo YL, Wang WC, Huang KY, I KY, Chang GW. Overexpression of FAM46A, a Non-canonical Poly(A) Polymerase, Promotes Hemin-Induced Hemoglobinization in K562 Cells. Front Cell Dev Biol 2020; 8:414. [PMID: 32528962 PMCID: PMC7264091 DOI: 10.3389/fcell.2020.00414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/05/2020] [Indexed: 01/11/2023] Open
Abstract
FAM46A belongs to the FAM46 subfamily of the nucleotidyltransferase-fold superfamily and is predicted to be a non-canonical poly(A) polymerase. FAM46A has been linked to several human disorders including retinitis pigmentosa, bone abnormality, cancer, and obesity. However, its molecular and functional characteristics are largely unknown. We herein report that FAM46A is expressed in cells of the hematopoietic system and plays a role in hemin-induced hemoglobinization. FAM46A is a nucleocytoplasmic shuttle protein modified by Tyr-phosphorylation only in the cytosol, where it is closely associated with ER. On the other hand, it is located proximal to the chromatin regions of active transcription in the nucleus. FAM46A is a cell cycle-dependent poly-ubiquitinated short-lived protein degraded mostly by proteasome and its overexpression inhibits cell growth and promotes hemin-induced hemoglobinization in K562 cell. Site-directed mutagenesis experiments confirm the non-canonical poly(A) polymerase activity of FAM46A is essential for enhanced hemin-induced hemoglobinization. In summary, FAM46A is a novel poly(A) polymerase that functions as a critical intracellular modulator of hemoglobinization.
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Affiliation(s)
- Hsi-Hsien Lin
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Anatomic Pathology, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan
| | - Yu-Ling Lo
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Chih Wang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Yeh Huang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Yu I
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Gin-Wen Chang
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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47
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Structural and Functional Analyses of the FAM46C/Plk4 Complex. Structure 2020; 28:910-921.e4. [PMID: 32433990 DOI: 10.1016/j.str.2020.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
FAM46C, a non-canonical poly(A) polymerase, is frequently mutated in multiple myeloma. Loss of function of FAM46C promotes cell survival of multiple myeloma, suggesting a tumor-suppressive role. FAM46C is also essential for fastening sperm head and flagellum, indispensable for male fertility. The molecular mechanisms of these functions of FAM46C remain elusive. We report the crystal structure of FAM46C to provide the basis for its poly(A) polymerase activity and rationalize mutations associated with multiple myeloma. In addition, we found that FAM46C interacts directly with the serine/threonine kinase Plk4, the master regulator of centrosome duplication. We present the structure of FAM46C in complex with the Cryptic Polo-Box 1-2 domains of Plk4. Our structure-based mutational analyses show that the interaction with Plk4 recruits FAM46C to centrosomes. Our data suggest that Plk4-mediated localization of FAM46C enables its regulation of centrosome structure and functions, which may underlie the roles for FAM46C in cell proliferation and sperm development.
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48
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Hu JL, Liang H, Zhang H, Yang MZ, Sun W, Zhang P, Luo L, Feng JX, Bai H, Liu F, Zhang T, Yang JY, Gao Q, Long Y, Ma XY, Chen Y, Zhong Q, Yu B, Liao S, Wang Y, Zhao Y, Zeng MS, Cao N, Wang J, Chen W, Yang HT, Gao S. FAM46B is a prokaryotic-like cytoplasmic poly(A) polymerase essential in human embryonic stem cells. Nucleic Acids Res 2020; 48:2733-2748. [PMID: 32009146 PMCID: PMC7049688 DOI: 10.1093/nar/gkaa049] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 01/11/2023] Open
Abstract
Family with sequence similarity (FAM46) proteins are newly identified metazoan-specific poly(A) polymerases (PAPs). Although predicted as Gld-2-like eukaryotic non-canonical PAPs, the detailed architecture of FAM46 proteins is still unclear. Exact biological functions for most of FAM46 proteins also remain largely unknown. Here, we report the first crystal structure of a FAM46 protein, FAM46B. FAM46B is composed of a prominently larger N-terminal catalytic domain as compared to known eukaryotic PAPs, and a C-terminal helical domain. FAM46B resembles prokaryotic PAP/CCA-adding enzymes in overall folding as well as certain inter-domain connections, which distinguishes FAM46B from other eukaryotic non-canonical PAPs. Biochemical analysis reveals that FAM46B is an active PAP, and prefers adenosine-rich substrate RNAs. FAM46B is uniquely and highly expressed in human pre-implantation embryos and pluripotent stem cells, but sharply down-regulated following differentiation. FAM46B is localized to both cell nucleus and cytosol, and is indispensable for the viability of human embryonic stem cells. Knock-out of FAM46B is lethal. Knock-down of FAM46B induces apoptosis and restricts protein synthesis. The identification of the bacterial-like FAM46B, as a pluripotent stem cell-specific PAP involved in the maintenance of translational efficiency, provides important clues for further functional studies of this PAP in the early embryonic development of high eukaryotes.
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Affiliation(s)
- Jia-Li Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - He Liang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hong Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ming-Zhu Yang
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, P.R. China.,Laboratory for Functional Genomics and Systems Biology, The Berlin Institute for Medical Systems Biology, 13092 Berlin, Germany
| | - Peng Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jian-Xiong Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Huajun Bai
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Fang Liu
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Tianpeng Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jin-Yu Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qingsong Gao
- Laboratory for Functional Genomics and Systems Biology, The Berlin Institute for Medical Systems Biology, 13092 Berlin, Germany
| | - Yongkang Long
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Xiao-Yan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Bing Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuang Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Nan Cao
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jichang Wang
- MOE Key Laboratory for Stem Cells and Tissue Engineering, Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Huang-Tian Yang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Laboratory of Molecular Cardiology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510530, China
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49
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Pathogenic diversity of RNA variants and RNA variation-associated factors in cancer development. Exp Mol Med 2020; 52:582-593. [PMID: 32346127 PMCID: PMC7210288 DOI: 10.1038/s12276-020-0429-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/13/2020] [Accepted: 03/23/2020] [Indexed: 01/30/2023] Open
Abstract
Recently, with the development of RNA sequencing technologies such as next-generation sequencing (NGS) for RNA, numerous variations of alternatively processed RNAs made by alternative splicing, RNA editing, alternative maturation of microRNA (miRNA), RNA methylation, and alternative polyadenylation have been uncovered. Furthermore, abnormally processed RNAs can cause a variety of diseases, including obesity, diabetes, Alzheimer’s disease, and cancer. Especially in cancer development, aberrant RNAs caused by deregulated RNA modifiers or regulators are related to progression. Accumulating evidence has reported that aberrant RNAs promote carcinogenesis in many cancers, including liver cancer, leukemia, melanoma, lung cancer, breast cancer, and other cancers, in which abnormal RNA processing occurs in normal cells. Therefore, it is necessary to understand the precise roles and mechanisms of disease-related RNA processing in various cancers for the development of therapeutic interventions. In this review, the underlying mechanisms of variations in the RNA life cycle and the biological impacts of RNA variations on carcinogenesis will be discussed, and therapeutic strategies for the treatment of tumor malignancies will be provided. We also discuss emerging roles of RNA regulators in hepatocellular carcinogenesis. A single gene can generate a variety of RNA products, and changes in this final RNA output can directly contribute to cancer onset and progression. The initial transcription of each DNA sequence yields a raw RNA strand that subsequently undergoes a variety of modification processes that shape its function. Hee Doo Yang and Suk Woo Nam, The Catholic University of Korea, Seoul, have reviewed the potential impact of these mechanisms on malignancy. Some cancers, for example, express RNA sequences that have been inappropriately edited by an enzymatic process called splicing, yielding abnormal RNAs that drive metastasis. Other tumors contain RNAs with atypical chemical modifications, or in which individual nucleotides have been enzymatically converted into other nucleotides. A deeper understanding of these RNA alterations and their impacts could lead to more effective and targeted cancer treatments.
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50
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Bilska A, Kusio-Kobiałka M, Krawczyk PS, Gewartowska O, Tarkowski B, Kobyłecki K, Nowis D, Golab J, Gruchota J, Borsuk E, Dziembowski A, Mroczek S. Immunoglobulin expression and the humoral immune response is regulated by the non-canonical poly(A) polymerase TENT5C. Nat Commun 2020; 11:2032. [PMID: 32341344 PMCID: PMC7184606 DOI: 10.1038/s41467-020-15835-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 03/28/2020] [Indexed: 02/06/2023] Open
Abstract
TENT5C is a non-canonical cytoplasmic poly(A) polymerase highly expressed by activated B cells to suppress their proliferation. Here we measure the global distribution of poly(A) tail lengths in responsive B cells using a Nanopore direct RNA-sequencing approach, showing that TENT5C polyadenylates immunoglobulin mRNAs regulating their half-life and consequently steady-state levels. TENT5C is upregulated in differentiating plasma cells by innate signaling. Compared with wild-type, Tent5c−/− mice produce fewer antibodies and have diminished T-cell-independent immune response despite having more CD138high plasma cells as a consequence of accelerated differentiation. B cells from Tent5c−/− mice also have impaired capacity of the secretory pathway, with reduced ER volume and unfolded protein response. Importantly, these functions of TENT5C are dependent on its enzymatic activity as catalytic mutation knock-in mice display the same defect as Tent5c−/−. These findings define the role of the TENT5C enzyme in the humoral immune response. Regulating polyadenylation is important for mRNA stability, which can in turn affect B cell maturation and humoral immune responses. Here the authors use Nanopore poly(A) sequencing to explore the importance of the cytoplasmic poly(A) polymerase TENT5C, particularly in the production of immunoglobulins.
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Affiliation(s)
- Aleksandra Bilska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Monika Kusio-Kobiałka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Paweł S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Olga Gewartowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Bartosz Tarkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Kamil Kobyłecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Dominika Nowis
- Genomic Medicine, Medical University of Warsaw, Banacha 1a, 02-097, Warsaw, Poland.,Laboratory of Experimental Medicine, Center of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Jakub Golab
- Department of Immunology, Medical University of Warsaw, Banacha 1a, 02-097, Warsaw, Poland.,Centre of Preclinical Research, Medical University of Warsaw, Banacha 1a, 02-097, Warsaw, Poland
| | - Jakub Gruchota
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Ewa Borsuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.,Department of Embryology, Institute of Zoology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland. .,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland. .,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland. .,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
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