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Wang Z, Wu D, Xu X, Yu G, Li N, Wang X, Li JL, Dean J. DIS3 ribonuclease is essential for spermatogenesis and male fertility in mice. Development 2024; 151:dev202579. [PMID: 38953252 PMCID: PMC11266750 DOI: 10.1242/dev.202579] [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: 12/01/2023] [Accepted: 06/07/2024] [Indexed: 07/03/2024]
Abstract
Spermatogonial stem cell (SSC) self-renewal and differentiation provide foundational support for long-term, steady-state spermatogenesis in mammals. Here, we have investigated the essential role of RNA exosome associated DIS3 ribonuclease in maintaining spermatogonial homeostasis and facilitating germ cell differentiation. We have established male germ-cell Dis3 conditional knockout (cKO) mice in which the first and subsequent waves of spermatogenesis are disrupted. This leads to a Sertoli cell-only phenotype and sterility in adult male mice. Bulk RNA-seq documents that Dis3 deficiency partially abolishes RNA degradation and causes significant increases in the abundance of transcripts. This also includes pervasively transcribed PROMoter uPstream Transcripts (PROMPTs), which accumulate robustly in Dis3 cKO testes. In addition, scRNA-seq analysis indicates that Dis3 deficiency in spermatogonia significantly disrupts RNA metabolism and gene expression, and impairs early germline cell development. Overall, we document that exosome-associated DIS3 ribonuclease plays crucial roles in maintaining early male germ cell lineage in mice.
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Affiliation(s)
- Zhengpin Wang
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Di Wu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaojiang Xu
- Integrative Bioinformatics Support Group, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Guoyun Yu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nana Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Xiao Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Li S, Dermawan JK, Seavey CN, Ma S, Antonescu CR, Rubin BP. Epithelioid hemangioendothelioma (EHE) with WWTR1::TFE3 gene fusion, a novel fusion variant. Genes Chromosomes Cancer 2024; 63:e23226. [PMID: 38380774 PMCID: PMC11293803 DOI: 10.1002/gcc.23226] [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: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Epithelioid hemangioendothelioma (EHE) is a rare endothelial sarcoma associated with a high incidence of metastases and for which there are no standard treatment options. Based on disease-defining mutations, most EHEs are classified into two subtypes: WWTR1::CAMTA1-fused EHE or YAP1::TFE3-fused EHE. However, rare non-canonical fusions have been identified in clinical samples of EHE cases and are challenging to classify. In this study, we report the identification of a novel WWTR1::TFE3 fusion variant in an EHE patient using targeted RNA sequencing. Histologically, the tumor exhibited hybrid morphological characteristics between WWTR1::CAMTA1-fused EHE and YAP1::TFE3-fused EHE. In addition to the driver fusion, there were six additional secondary mutations identified, including a loss-of-function FANCA mutation. Furthermore, in vitro studies were conducted to investigate the tumorigenic function of the WWTR1::TFE3 fusion protein in NIH3T3 cells and demonstrated that WWTR1::TFE3 promotes colony formation in soft agar. Finally, as the wild-type WWTR1 protein relies on binding the TEAD family of transcription factors to affect gene transcription, mutation of the WWTR1 domain of the fusion protein to inhibit such binding abrogates the transformative effect of WWTR1::TFE3. Overall, we describe a novel gene fusion in EHE with a hybrid histological appearance between the two major genetic subtypes of EHE. Further cases of this very rare subtype of EHE will need to be identified to fully elucidate the clinical and pathological characteristics of this unusual subtype of EHE.
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Affiliation(s)
- Shuo Li
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Caleb N Seavey
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of General Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, PRISM Program, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Shuang Ma
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Brian P Rubin
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
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3
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Zaki MS, Abdel-Ghafar SF, Abdel-Hamid MS. A missense variant in EXOSC8 causes exon skipping and expands the phenotypic spectrum of pontocerebellar hypoplasia type 1C. J Hum Genet 2024; 69:79-84. [PMID: 38017281 PMCID: PMC10810757 DOI: 10.1038/s10038-023-01207-4] [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: 07/10/2023] [Revised: 08/29/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023]
Abstract
Pontocerebellar hypoplasia (PCH) is a rare heterogeneous neurodegenerative disorder affecting the pons and cerebellum and is currently classified into 17 types (PCH1-PCH17). PCH1 is distinguishable from other types by the association of spinal motor neuron dysfunction. Based on the underlying genetic etiology, PCH1 is further classified into 6 different subtypes (PCH1 A-F). Of them, PCH type 1C is caused by pathogenic variants in EXOSC8 gene and so far, only four families have been described in the literature. In this study, we report a new patient with PCH1 who proved by whole-exome sequencing to harbor a novel homozygous missense variant in the splice region of EXOSC8 gene (c.238 G > A; p.Val80Ile). Studying mRNA of the patient confirmed that this variant results in skipping of exon 5 of the gene and early protein truncation. Our patient presented with the main clinical findings of PCH type 1C including psychomotor retardation, spasticity, spinal muscle atrophy, and respiratory problems. However, unlike most of the reported cases, he did not develop hearing or visual impairment and displayed a longer survival. In addition, our patient had dysmorphic facies, nystagmus, congenital esotropia and contractures which were infrequently described in patients with EXOSC8. Diaphragmatic hernia, dilated lateral ventricles, hypoplastic temporal lobes, and thinning of the brain stem were additional new findings noted in our patient. This study presents the fifth family with this extremely rare type of PCH and expands the associated clinical and brain imaging findings.
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Affiliation(s)
- Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
| | - Sherif F Abdel-Ghafar
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.
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4
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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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5
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Li C, Chen L, Pan G, Zhang W, Li SC. Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram. Nat Commun 2023; 14:5528. [PMID: 37684230 PMCID: PMC10491683 DOI: 10.1038/s41467-023-41259-w] [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: 10/13/2022] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Breakage-fusion-bridge (BFB) is a complex rearrangement that leads to tumor malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out the possibility of BFBs entangled with other structural variations, that is, complex BFBs. We propose an algorithm Ambigram to identify complex BFB and reconstruct the rearranged structure of the local genome during the cancer subclone evolution process. Ambigram handles data from short, linked, long, and single-cell sequences, and optical mapping technologies. Ambigram successfully deciphers the gold- or silver-standard complex BFBs against the state-of-the-art in multiple cancers. Ambigram dissects the intratumor heterogeneity of complex BFB events with single-cell reads from melanoma and gastric cancer. Furthermore, applying Ambigram to liver and cervical cancer data suggests that the BFB mechanism may mediate oncovirus integrations. BFB also exists in noncancer genomics. Investigating the complete human genome reference with Ambigram suggests that the BFB mechanism may be involved in two genome reorganizations of Homo Sapiens during evolution. Moreover, Ambigram discovers the signals of recurrent foldback inversions and complex BFBs in whole genome data from the 1000 genome project, and congenital heart diseases, respectively.
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Affiliation(s)
- Chaohui Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Guangze Pan
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Wenqian Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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6
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Sterrett MC, Farchi D, Strassler SE, Boise LH, Fasken MB, Corbett AH. In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2023; 13:jkad049. [PMID: 36861343 PMCID: PMC10411580 DOI: 10.1093/g3journal/jkad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/05/2023] [Accepted: 02/10/2023] [Indexed: 03/03/2023]
Abstract
The RNA exosome is a conserved molecular machine that processes/degrades numerous coding and non-coding RNAs. The 10-subunit complex is composed of three S1/KH cap subunits (human EXOSC2/3/1; yeast Rrp4/40/Csl4), a lower ring of six PH-like subunits (human EXOSC4/7/8/9/5/6; yeast Rrp41/42/43/45/46/Mtr3), and a singular 3'-5' exo/endonuclease DIS3/Rrp44. Recently, several disease-linked missense mutations have been identified in structural cap and core RNA exosome genes. In this study, we characterize a rare multiple myeloma patient missense mutation that was identified in the cap subunit gene EXOSC2. This missense mutation results in a single amino acid substitution, p.Met40Thr, in a highly conserved domain of EXOSC2. Structural studies suggest that this Met40 residue makes direct contact with the essential RNA helicase, MTR4, and may help stabilize the critical interaction between the RNA exosome complex and this cofactor. To assess this interaction in vivo, we utilized the Saccharomyces cerevisiae system and modeled the EXOSC2 patient mutation into the orthologous yeast gene RRP4, generating the variant rrp4-M68T. The rrp4-M68T cells show accumulation of certain RNA exosome target RNAs and show sensitivity to drugs that impact RNA processing. We also identified robust negative genetic interactions between rrp4-M68T and specific mtr4 mutants. A complementary biochemical approach revealed that Rrp4 M68T shows decreased interaction with Mtr4, consistent with these genetic results. This study suggests that the EXOSC2 mutation identified in a multiple myeloma patient impacts the function of the RNA exosome and provides functional insight into a critical interface between the RNA exosome and Mtr4.
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Affiliation(s)
- Maria C Sterrett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, School of Medicine, Emory University, Atlanta, GA 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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7
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Wu D, Dean J. RNA exosome ribonuclease DIS3 degrades Pou6f1 to promote mouse pre-implantation cell differentiation. Cell Rep 2023; 42:112047. [PMID: 36724075 PMCID: PMC10387129 DOI: 10.1016/j.celrep.2023.112047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/24/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Mammalian development is precisely controlled by cell differentiation. Identifying new regulators and investigating their interactions provide insight into genetic networks defining pre-implantation development. We established a knockout mouse model of Dis3, an exosome associated ribonuclease. Homozygous Dis3 null embryos arrest at the morula stage of development. Using single-embryo RNA sequencing (RNA-seq), we observed persistence of Pou6f1 mRNA in homozygous null Dis3 embryos and that the cognate protein represses transcription of Nanog and Cdx2. The resultant defects in cell differentiation disrupt the morula-to-blastocyst transition and are embryonic lethal. Microinjection of Dis3 mRNA into zygotes rescues the phenotype. Point mutations of Dis3 ribonuclease in individual blastomeres prevents their incorporation into embryos. To overcome the paucity of embryos, we derived homozygous Dis3 null mouse embryonic stem cells to identify additional gene targets of POU6F1. Our findings delineate a regulatory pathway of DIS3-POU6F1 in pre-implantation mammalian embryogenesis.
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Affiliation(s)
- Di Wu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA.
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8
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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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9
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Dumontet C, Demangel D, Galia P, Karlin L, Roche L, Fauvernier M, Golfier C, Laude M, Leleu X, Rodon P, Roussel M, Azaïs I, Doyen C, Slama B, Manier S, Decaux O, Pertesi M, Beaumont M, Caillot D, Boyle EM, Cliquennois M, Cony‐Makhoul P, Doncker A, Dorvaux V, Petillon MO, Fontan J, Hivert B, Leduc I, Leyronnas C, Macro M, Maigre M, Mariette C, Mineur P, Rigaudeau S, Royer B, Vincent L, Mckay J, Perrial E, Garderet L. Clinical characteristics and outcome of 318 families with familial monoclonal gammopathy: A multicenter Intergroupe Francophone du Myélome study. Am J Hematol 2023; 98:264-271. [PMID: 36588407 PMCID: PMC10107808 DOI: 10.1002/ajh.26785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/10/2022] [Accepted: 10/24/2022] [Indexed: 01/03/2023]
Abstract
Familial forms of monoclonal gammopathy, defined as multiple myeloma (MM) or Monoclonal Gammopathy of Undetermined Significance (MGUS), are relatively infrequent and most series reported in the literature describe a limited number of families. MM rarely occurs in a familial context. MGUS is observed much more commonly, which can in some cases evolve toward full-blown MM. Although recurrent cytogenetic abnormalities have been described in tumor cells of sporadic cases of MM, the pathogenesis of familial MM remains largely unexplained. In order to identify genetic factors predisposing to familial monoclonal gammopathy, the Intergroupe Francophone du Myélome identified 318 families with at least two confirmed cases of monoclonal gammopathy. There were 169 families with parent/child pairs and 164 families with cases in at least two siblings, compatible with an autosomal transmission. These familial cases were compared with sporadic cases who were matched for age at diagnosis, sex and immunoglobulin isotype, with 10 sporadic cases for each familial case. The gender distribution, age and immunoglobulin subtypes of familial cases were unremarkable in comparison to sporadic cases. With a median follow-up of 7.4 years after diagnosis, the percentage of MGUS cases having evolved to MM was 3%. The median overall survival of the 148 familial MM cases was longer than that of matched sporadic cases, with projected values of 7.6 and 16.1 years in patients older and younger than 65 years, respectively. These data suggest that familial cases of monoclonal gammopathy are similar to sporadic cases in terms of clinical presentation and carry a better prognosis.
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Affiliation(s)
- Charles Dumontet
- Hospices Civils de LyonLyonFrance
- CRCL, UMR INSERM 1052/CNRS 5286/University of Lyon‐FranceLyonFrance
| | | | | | | | | | | | | | | | | | | | | | | | | | - Borhane Slama
- Clinical Hematology DepartmentCH AvignonAvignonFrance
| | | | - Olivier Decaux
- Hematology DepartmentCHU Rennes, Inserm UMR1236RennesFrance
| | - Maroulio Pertesi
- Genetic Cancer Susceptibility, International Agency for Research on CancerLyonFrance
- Department of Laboratory MedicineHematology and Transfusion MedicineLundSweden
| | | | - Denis Caillot
- Clinical Hematology DepartmentHôpital F. Mitterrand, CHU DijonDijonFrance
| | - Eileen M. Boyle
- Perlmutter Cancer CenterNYU Langone HealthNew YorkNew YorkUSA
| | | | | | | | - Véronique Dorvaux
- Clinical Hematology DepartmentCHR Metz‐ThionvilleMetz‐ThionvilleFrance
| | | | - Jean Fontan
- Hematology DepartmentCHU BesançonBesançonFrance
| | | | | | | | | | - Michel Maigre
- Internal Medicine DepartmentCH ChartresChartresFrance
| | | | - Philippe Mineur
- Clinical Hematology DepartmentGrand Hôpital de CharleroiCharleroiBelgium
| | | | - Bruno Royer
- Clinical Hematology and Cell Therapy DepartmentAmiensFrance
| | | | - James Mckay
- Genetic Cancer Susceptibility, International Agency for Research on CancerLyonFrance
| | - Emeline Perrial
- CRCL, UMR INSERM 1052/CNRS 5286/University of Lyon‐FranceLyonFrance
| | - Laurent Garderet
- HU PITIE SALPETRIERE APHPParisFrance
- Centre de Recherche Saint‐Antoine‐Team Hematopoietic and Leukemic DevelopmentSorbonne Université‐INSERM, UMR_S 938ParisFrance
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10
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Gritti I, Basso V, Rinchai D, Corigliano F, Pivetti S, Gaviraghi M, Rosano D, Mazza D, Barozzi S, Roncador M, Parmigiani G, Legube G, Parazzoli D, Cittaro D, Bedognetti D, Mondino A, Segalla S, Tonon G. Loss of ribonuclease DIS3 hampers genome integrity in myeloma by disrupting DNA:RNA hybrid metabolism. EMBO J 2022; 41:e108040. [PMID: 36215697 PMCID: PMC9670201 DOI: 10.15252/embj.2021108040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/25/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023] Open
Abstract
The ribonuclease DIS3 is one of the most frequently mutated genes in the hematological cancer multiple myeloma, yet the basis of its tumor suppressor function in this disease remains unclear. Herein, exploiting the TCGA dataset, we found that DIS3 plays a prominent role in the DNA damage response. DIS3 inactivation causes genomic instability by increasing mutational load, and a pervasive accumulation of DNA:RNA hybrids that induces genomic DNA double-strand breaks (DSBs). DNA:RNA hybrid accumulation also prevents binding of the homologous recombination (HR) machinery to double-strand breaks, hampering DSB repair. DIS3-inactivated cells become sensitive to PARP inhibitors, suggestive of a defect in homologous recombination repair. Accordingly, multiple myeloma patient cells mutated for DIS3 harbor an increased mutational burden and a pervasive overexpression of pro-inflammatory interferon, correlating with the accumulation of DNA:RNA hybrids. We propose DIS3 loss in myeloma to be a driving force for tumorigenesis via DNA:RNA hybrid-dependent enhanced genome instability and increased mutational rate. At the same time, DIS3 loss represents a liability that might be therapeutically exploited in patients whose cancer cells harbor DIS3 mutations.
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Affiliation(s)
- Ilaria Gritti
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Veronica Basso
- Division of Immunology, Transplantation and Infectious DiseaseIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | | | - Federica Corigliano
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Silvia Pivetti
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Marco Gaviraghi
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Dalia Rosano
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Davide Mazza
- Experimental Imaging CenterIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Sara Barozzi
- IFOM, The FIRC Institute of Molecular OncologyMilanoItaly
| | - Marco Roncador
- Department of Data SciencesDana Farber Cancer InstituteBostonMAUSA,Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Giovanni Parmigiani
- Department of Data SciencesDana Farber Cancer InstituteBostonMAUSA,Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Gaelle Legube
- MCD, Centre de Biologie Intégrative (CBI), CNRSUniversity of ToulouseToulouseFrance
| | | | - Davide Cittaro
- Center for Omics Sciences @OSR (COSR)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Davide Bedognetti
- Cancer Research DepartmentSidra MedicineDohaQatar,Dipartimento di Medicina Interna e Specialità MedicheUniversità degli Studi di GenovaGenoaItaly
| | - Anna Mondino
- Division of Immunology, Transplantation and Infectious DiseaseIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Simona Segalla
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly,Center for Omics Sciences @OSR (COSR)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly,Università Vita‐Salute San RaffaeleMilanItaly
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11
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Saadoune C, Nouadi B, Hamdaoui H, Chegdani F, Bennis F. Multiple Myeloma: Bioinformatic Analysis for Identification of Key Genes and Pathways. Bioinform Biol Insights 2022; 16:11779322221115545. [PMID: 35958298 PMCID: PMC9358573 DOI: 10.1177/11779322221115545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/26/2022] [Indexed: 01/02/2023] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy in which monoclonal plasma cells multiply in the bone marrow and monoclonal immunoglobulins are overproduced in older people. Several molecular and cytogenetic advances allow scientists to identify several genetic and chromosomal abnormalities that cause the disease. The comprehension of the pathophysiology of MM requires an understanding of the characteristics of malignant clones and the changes in the bone marrow microenvironment. This study aims to identify the central genes and to determine the key signaling pathways in MM by in silico approaches. A list of 114 differentially expressed genes (DEGs) is important in the prognosis of MM. The DEGs are collected from scientific publications and databases (https://www.ncbi.nlm.nih.gov/). These data are analyzed by Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) software (https://string-db.org/) through the construction of protein-protein interaction (PPI) networks and enrichment analysis of the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, by CytoHubba, AutoAnnotate, Bingo Apps plugins in Cytoscape software (https://cytoscape.org/) and by DAVID database (https://david.ncifcrf.gov/). The analysis of the results shows that there are 7 core genes, including TP53; MYC; CDND1; IL6; UBA52; EZH2, and MDM2. These top genes appear to play a role in the promotion and progression of MM. According to functional enrichment analysis, these genes are mainly involved in the following signaling pathways: Epstein-Barr virus infection, microRNA pathway, PI3K-Akt signaling pathway, and p53 signaling pathway. Several crucial genes, including TP53, MYC, CDND1, IL6, UBA52, EZH2, and MDM2, are significantly correlated with MM, which may exert their role in the onset and evolution of MM.
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Affiliation(s)
- Chaimaa Saadoune
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Badreddine Nouadi
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Hasna Hamdaoui
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco.,Laboratory of Medical Genetics, University Hospital Center Tangier-Tetouan-Al Hoceima, Tangier, Morocco
| | - Fatima Chegdani
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Faiza Bennis
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Aïn Chock, Hassan II University of Casablanca, Casablanca, Morocco
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Gadd S, Huff V, Skol AD, Renfro LA, Fernandez CV, Mullen EA, Jones CD, Hoadley KA, Yap KL, Ramirez NC, Aris S, Phung QH, Perlman EJ. Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study. Cell Rep Med 2022; 3:100644. [PMID: 35617957 PMCID: PMC9244995 DOI: 10.1016/j.xcrm.2022.100644] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/23/2022] [Accepted: 05/04/2022] [Indexed: 12/15/2022]
Abstract
Over the last decade, sequencing of primary tumors has clarified the genetic underpinnings of Wilms tumor but has not affected therapy, outcome, or toxicity. We now sharpen our focus on relapse samples from the umbrella AREN03B2 study. We show that over 40% of relapse samples contain mutations in SIX1 or genes of the MYCN network, drivers of progenitor proliferation. Not previously seen in large studies of primary Wilms tumors, DIS3 and TERT are now identified as recurrently mutated. The analysis of primary-relapse tumor pairs suggests that 11p15 loss of heterozygosity (and other copy number changes) and mutations in WT1 and MLLT1 typically occur early, but mutations in SIX1, MYCN, and WTX are late developments in some individuals. Most strikingly, 75% of relapse samples had gain of 1q, providing strong conceptual support for studying circulating tumor DNA in clinical trials to better detect 1q gain earlier and monitor response.
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Affiliation(s)
- Samantha Gadd
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew D Skol
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA
| | - Lindsay A Renfro
- Division of Biostatistics, University of Southern California, Los Angeles, CA 90007, USA
| | - Conrad V Fernandez
- Department of Pediatrics, IWK Health Centre and Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Elizabeth A Mullen
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Boston, MA 02215, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kai Lee Yap
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA
| | - Nilsa C Ramirez
- Institute for Genomic Medicine and Biopathology Center, Nationwide Children's Hospital, Departments of Pathology and Pediatrics, Ohio State University, Columbus, OH 43205, USA
| | - Sheena Aris
- Biospecimen Research Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Quy H Phung
- Biospecimen Research Group, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Robert H. Lurie Cancer Center, Northwestern University, 225 East Chicago Avenue, Box 17, Chicago, IL 60611, USA.
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13
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Zhang T, Wang LL, Guan J, Zhou Y, Cheng P, Zou L. MicroRNA-125a/b-5p promotes malignant behavior in multiple myeloma cells and xenograft tumor growth by targeting DIS3. Kaohsiung J Med Sci 2022; 38:574-584. [PMID: 35394705 DOI: 10.1002/kjm2.12534] [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: 09/26/2021] [Revised: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 11/11/2022] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy with a high prevalence and is characterized by the clonal expansion of malignant plasma cells. As a new tumor suppressor, defective in sister chromatid joining (DIS3) was reported to be a gene closely related to MM. This study elucidated the biological functions and underlying mechanisms of DIS3 in MM. DIS3 mRNA and protein levels were detected using RT-qPCR and western blotting, respectively. Methyl thiazolyl tetrazolium assays, flow cytometry analyses, Transwell assays, and wound healing assays were performed to detect the proliferation, apoptosis, invasion, and migration of MM cells. The binding relationship between miR-125a/b-5p and DIS3 was verified using luciferase reporter assays and RNA pulldown assays. Xenograft tumor models were established in nude mice to investigate the effects of miR-125a/b-5p and DIS3 on tumor growth in vivo. DIS3 levels were downregulated in MM cells, and DIS3 upregulation inhibited the malignant behaviors of MM cells. Mechanistically, miR-125a/b-5p directly targeted the 3' untranslated region of DIS3. The expression of miR-125a/b-5p was upregulated in MM cells, miR-125a/b-5p knockdown inhibited the malignant behaviors of MM cells, and the inhibitory effect was reversed by DIS3 downregulation. The results of in vivo experiments indicated that miR-125a/b-5p promoted tumor growth by downregulating DIS3. Overall, miR-125a/b-5p promotes MM cellular processes and xenograft tumor growth by targeting DIS3.
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Affiliation(s)
- Ting Zhang
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Lan-Lan Wang
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Jun Guan
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Ying Zhou
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Ping Cheng
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Liang Zou
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
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Taniue K, Tanu T, Shimoura Y, Mitsutomi S, Han H, Kakisaka R, Ono Y, Tamamura N, Takahashi K, Wada Y, Mizukami Y, Akimitsu N. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. Int J Mol Sci 2022; 23:496. [PMID: 35008922 PMCID: PMC8745236 DOI: 10.3390/ijms23010496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The RNA exosome is a multi-subunit ribonuclease complex that is evolutionally conserved and the major cellular machinery for the surveillance, processing, degradation, and turnover of diverse RNAs essential for cell viability. Here we performed integrated genomic and clinicopathological analyses of 27 RNA exosome components across 32 tumor types using The Cancer Genome Atlas PanCancer Atlas Studies' datasets. We discovered that the EXOSC4 gene, which encodes a barrel component of the RNA exosome, was amplified across multiple cancer types. We further found that EXOSC4 alteration is associated with a poor prognosis of pancreatic cancer patients. Moreover, we demonstrated that EXOSC4 is required for the survival of pancreatic cancer cells. EXOSC4 also repressed BIK expression and destabilized SESN2 mRNA by promoting its degradation. Furthermore, knockdown of BIK and SESN2 could partially rescue pancreatic cells from the reduction in cell viability caused by EXOSC4 knockdown. Our study provides evidence for EXOSC4-mediated regulation of BIK and SESN2 mRNA in the survival of pancreatic tumor cells.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Shuhei Mitsutomi
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Nobue Tamamura
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Kenji Takahashi
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yusuke Mizukami
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
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15
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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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16
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Alaterre E, Vikova V, Kassambara A, Bruyer A, Robert N, Requirand G, Bret C, Herbaux C, Vincent L, Cartron G, Elemento O, Moreaux J. RNA-Sequencing-Based Transcriptomic Score with Prognostic and Theranostic Values in Multiple Myeloma. J Pers Med 2021; 11:jpm11100988. [PMID: 34683129 PMCID: PMC8541503 DOI: 10.3390/jpm11100988] [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: 09/02/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/11/2022] Open
Abstract
Multiple myeloma (MM) is the second most frequent hematological cancer and is characterized by the clonal proliferation of malignant plasma cells. Genome-wide expression profiling (GEP) analysis with DNA microarrays has emerged as a powerful tool for biomedical research, generating a huge amount of data. Microarray analyses have improved our understanding of MM disease and have led to important clinical applications. In MM, GEP has been used to stratify patients, define risk, identify therapeutic targets, predict treatment response, and understand drug resistance. In this study, we built a gene risk score for 267 genes using RNA-seq data that demonstrated a prognostic value in two independent cohorts (n = 674 and n = 76) of newly diagnosed MM patients treated with high-dose Melphalan and autologous stem cell transplantation. High-risk patients were associated with the expression of genes involved in several major pathways implicated in MM pathophysiology, including interferon response, cell proliferation, hypoxia, IL-6 signaling pathway, stem cell genes, MYC, and epigenetic deregulation. The RNA-seq-based risk score was correlated with specific MM somatic mutation profiles and responses to targeted treatment including EZH2, MELK, TOPK/PBK, and Aurora kinase inhibitors, outlining potential utility for precision medicine strategies in MM.
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Affiliation(s)
- Elina Alaterre
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
| | - Veronika Vikova
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
| | - Alboukadel Kassambara
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Diag2Tec, 34395 Montpellier, France
| | - Angélique Bruyer
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Diag2Tec, 34395 Montpellier, France
| | - Nicolas Robert
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
| | - Guilhem Requirand
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
| | - Caroline Bret
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
| | - Charles Herbaux
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
- Department of Clinical Hematology, CHU Montpellier, 34395 Montpellier, France;
| | - Laure Vincent
- Department of Clinical Hematology, CHU Montpellier, 34395 Montpellier, France;
| | - Guillaume Cartron
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
- Department of Clinical Hematology, CHU Montpellier, 34395 Montpellier, France;
- IGMM, UMR CNRS-UM 5535, 34090 Montpellier, France
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Jérôme Moreaux
- Institute of Human Genetics, UMR 9002 CNRS-UM, 34395 Montpellier, France; (E.A.); (V.V.); (A.K.); (A.B.); (C.B.); (C.H.)
- Department of Biological Hematology, CHU Montpellier, 34395 Montpellier, France; (N.R.); (G.R.)
- UFR de Médecine, University of Montpellier, 34003 Montpellier, France;
- IUF, Institut Universitaire de France, 75005 Paris, France
- Correspondence: ; Tel.: +33-(0)4-67-33-79-03
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Co-evolution of tumor and immune cells during progression of multiple myeloma. Nat Commun 2021; 12:2559. [PMID: 33963182 PMCID: PMC8105337 DOI: 10.1038/s41467-021-22804-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate MM and its immune environment, we apply single cell RNA and linked-read whole genome sequencing to profile 29 longitudinal samples at different disease stages from 14 patients. Here, we collect 17,267 plasma cells and 57,719 immune cells, discovering patient-specific plasma cell profiles and immune cell expression changes. Patients with the same genetic alterations tend to have both plasma cells and immune cells clustered together. By integrating bulk genomics and single cell mapping, we track plasma cell subpopulations across disease stages and find three patterns: stability (from precancer to diagnosis), and gain or loss (from diagnosis to relapse). In multiple patients, we detect “B cell-featured” plasma cell subpopulations that cluster closely with B cells, implicating their cell of origin. We validate AP-1 complex differential expression (JUN and FOS) in plasma cell subpopulations using CyTOF-based protein assays, and integrated analysis of single-cell RNA and CyTOF data reveals AP-1 downstream targets (IL6 and IL1B) potentially leading to inflammation regulation. Our work represents a longitudinal investigation for tumor and microenvironment during MM progression and paves the way for expanding treatment options. Clonal evolution in multiple myeloma (MM) needs to be understood in both the tumor and its microenvironment. Here the authors perform single-cell multi-omics profiling of samples from MM patients at different stages, finding transitions in the immune cell composition throughout progression.
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Treatment Strategies Considering Micro-Environment and Clonal Evolution in Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13020215. [PMID: 33435539 PMCID: PMC7827913 DOI: 10.3390/cancers13020215] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/03/2021] [Accepted: 01/06/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Multiple myeloma is an uncurable hematological malignancy, although the prognosis of myeloma patients is getting better using proteasome inhibitors (PIs), immune modulatory drugs (IMiDs), monoclonal antibodies (MoAbs), and cytotoxic agents. Drug resistance makes myeloma difficult to treat and it can be subdivided into two broad categories: de novo and acquired. De novo drug resistance is associated with the bone marrow microenvironment including bone marrow stromal cells, the vascular niche and endosteal niche. Acquired drug resistance is related to clonal evolution and non-genetic diversity. The initial treatment plays the most important role considering de novo and acquired drug resistance and should contain PIs, IMIDs, MoAbs, and autologous stem cell transplantation because these treatments improve the bone marrow microenvironment and might prevent clonal evolution via sustained deep response including minimal residual disease negativity. Abstract Multiple myeloma is an uncurable hematological malignancy because of obtained drug resistance. Microenvironment and clonal evolution induce myeloma cells to develop de novo and acquired drug resistance, respectively. Cell adhesion-mediated drug resistance, which is induced by the interaction between myeloma and bone marrow stromal cells, and soluble factor-mediated drug resistance, which is induced by cytokines and growth factors, are two types of de novo drug resistance. The microenvironment, including conditions such as hypoxia, vascular and endosteal niches, contributes toward de novo drug resistance. Clonal evolution was associated with acquired drug resistance and classified as branching, linear, and neutral evolutions. The branching evolution is dependent on the microenvironment and escape of immunological surveillance while the linear and neutral evolution is independent of the microenvironment and associated with aggressive recurrence and poor prognosis. Proteasome inhibitors (PIs), immunomodulatory drugs (IMiDs), monoclonal antibody agents (MoAbs), and autologous stem cell transplantation (ASCT) have improved prognosis of myeloma via improvement of the microenvironment. The initial treatment plays the most important role considering de novo and acquired drug resistance and should contain PIs, IMIDs, MoAb and ASCT. This review summarizes the role of anti-myeloma agents for microenvironment and clonal evolution and treatment strategies to overcome drug resistance.
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Wen S, Liu T, Zhang H, Zhou X, Jin H, Sun M, Yun Z, Luo H, Ni Z, Zhao R, Fan B. Whole-Exome Sequencing Reveals New Potential Mutations Genes for Primary Mucosa-Associated Lymphoid Tissue Lymphoma Arising From the Kidney. Front Oncol 2021; 10:609839. [PMID: 33585230 PMCID: PMC7873889 DOI: 10.3389/fonc.2020.609839] [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: 10/02/2020] [Accepted: 11/25/2020] [Indexed: 12/31/2022] Open
Abstract
Low-grade B cell lymphomas of mucosa-associated lymphoid tissue (MALT) lymphomas involving the kidney were extremely rare, genetic alteration or molecular features was not yet explored, which may lead to limited choices for postoperative adjuvant or targeted. Whole-exome sequencing based tumor mutation profiling was performed on the tumor sample from a 77-year-old female presenting with discomfort at the waist was pathologically diagnosed as MALT lymphomas in the right kidney. We identified 101 somatic SNVs, and the majority of the identified SNVs were located in CDS and intronic regions. A total of 190 gain counts of CNVs with a total size of 488,744,073 was also investigated. After filtering with the CGC database, seven predisposing genes (ARID4A, COL2A1, FANCL, ABL2, HSP90AB1, FANCA, and DIS3) were found in renal MALT specimen. Furthermore, we compared somatic variation with known driver genes and validated three mutational driver genes including ACSL3, PHOX2B, and ADCY1. Sanger sequencing of germline DNA revealed the presence of a mutant base T of PHOX2B and a mutant base C of ADCY1 in the sequence, which were discovered for the first time in MALT lymphomas involving the kidney. Moreover, immunohistochemical analysis revealed that tumor cells were positive for CD20, CD79a, PAX5, CD21, and CD23, and expression of CD3, CD5, and CD8 were observed in reactive T lymphocytes surrounding tumor cells. These findings illustrated that concurrent aberrant PHOX2B and ADCY1 signaling may be a catastrophic event resulting in disease progression and inhibition of the putative driver mutations may be alternative adjuvant therapy for MALT lymphoma in the kidney which warrants further clinical investigation.
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Affiliation(s)
- Shuang Wen
- Department of Pathology, Dalian Friendship Hospital, Dalian, China
| | - Tianqing Liu
- Department of Pathology, Dalian Friendship Hospital, Dalian, China
| | - Hongshuo Zhang
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Xu Zhou
- Section of Experimental Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Huidan Jin
- Department of Anaesthesiology, Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Man Sun
- Department of Clinical Medicine, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhifei Yun
- Department of Clinical Medicine, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hong Luo
- Department of Clinical Medicine, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ze Ni
- Department of Pharmacy, Zhongshan College of Dalian Medical University, Dalian, China
| | - Rui Zhao
- Department of Pharmacy, Zhongshan College of Dalian Medical University, Dalian, China
| | - Bo Fan
- Department of Urology, Second Affiliated Hospital of Dalian Medical University, Dalian, China
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20
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Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
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Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
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21
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Fazel E, Fattahpour S, Abdali H, Nasiri J, Sedghi M. Understanding the impact of DIS3 cancer-associated mutations by in silico structure modeling. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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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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23
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Wermuth PJ, Jimenez SA. Molecular characteristics and functional differences of anti-PM/Scl autoantibodies and two other distinct and unique supramolecular structures known as "EXOSOMES". Autoimmun Rev 2020; 19:102644. [PMID: 32801042 DOI: 10.1016/j.autrev.2020.102644] [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: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023]
Abstract
The term "exosome" has been applied to three distinct supramolecular entities, namely the PM/Scl autoantibodies or "RNA exosomes", transforming DNA fragments termed "DNA exosomes", and small size extracellular vesicles knows as "exosomes". Some of the molecular components of the "PM/Scl exosome complex" or "RNA exosome" are recognized by specific autoantibodies present in the serum from some Systemic Sclerosis (SSc), polymyositis (PM) and polymyositis SSc (PM/Scl) overlap syndrome patients. On the other hand, one of the most active focuses of laboratory investigation in the last decade has been the biogenesis and role of extracellular vesicles known as "exosomes". The remarkable ability of these "exosome" vesicles to alter the cellular phenotype following fusion with target cells and the release of their macromolecular cargo has revealed a possible role in the pathogenesis of numerous diseases, including malignant, inflammatory, and autoimmune disorders and may allow them to serve as theranostic agents for personalized and precision medicine. The indiscriminate use of the term "exosome" to refer to these three distinct molecular entities has engendered great confusion in the scientific literature. Here, we review the molecular characteristics and functional differences between the three molecular structures identified as "exosomes". Given the rapidly growing scientific interest in extravesicular exosomes, unless a solution is found the confusion in the literature resulting from the use of the term "exosomes" will markedly increase.
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Affiliation(s)
- Peter J Wermuth
- Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
| | - Sergio A Jimenez
- Jefferson Institute of Molecular Medicine and Scleroderma Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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24
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Wu D, Dean J. EXOSC10 sculpts the transcriptome during the growth-to-maturation transition in mouse oocytes. Nucleic Acids Res 2020; 48:5349-5365. [PMID: 32313933 DOI: 10.1093/nar/gkaa249] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/28/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Growing mammalian oocytes accumulate substantial amounts of RNA, most of which is degraded during subsequent meiotic maturation. The growth-to-maturation transition begins with germinal vesicle or nuclear envelope breakdown (GVBD) and is critical for oocyte quality and early development. The molecular machinery responsible for the oocyte transcriptome transition remains unclear. Here, we report that an exosome-associated RNase, EXOSC10, sculpts the transcriptome to facilitate the growth-to-maturation transition of mouse oocytes. We establish an oocyte-specific conditional knockout of Exosc10 in mice using CRISPR/Cas9 which results in female subfertility due to delayed GVBD. By performing multiple single oocyte RNA-seq, we document dysregulation of several types of RNA, and the mRNAs that encode proteins important for endomembrane trafficking and meiotic cell cycle. As expected, EXOSC10-depleted oocytes have impaired endomembrane components including endosomes, lysosomes, endoplasmic reticulum and Golgi. In addition, CDK1 fails to activate, possibly due to persistent WEE1 activity, which blocks lamina phosphorylation and disassembly. Moreover, we identified rRNA processing defects that cause higher percentage of developmentally incompetent oocytes after EXOSC10 depletion. Collectively, we propose that EXOSC10 promotes normal growth-to-maturation transition in mouse oocytes by sculpting the transcriptome to degrade RNAs encoding growth-phase factors and, thus, support the maturation phase of oogenesis.
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Affiliation(s)
- Di Wu
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jurrien Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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25
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Alagpulinsa DA, Szalat RE, Poznansky MC, Shmookler Reis RJ. Genomic Instability in Multiple Myeloma. Trends Cancer 2020; 6:858-873. [PMID: 32487486 DOI: 10.1016/j.trecan.2020.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Genomic instability (GIN), an increased tendency to acquire genomic alterations, is a cancer hallmark. However, its frequency, underlying causes, and disease relevance vary across different cancers. Multiple myeloma (MM), a plasma cell malignancy, evolves through premalignant phases characterized by genomic abnormalities. Next-generation sequencing (NGS) methods are deconstructing the genomic landscape of MM across the continuum of its development, inextricably linking malignant transformation and disease progression with increasing acquisition of genomic alterations, and illuminating the mechanisms that generate these alterations. Although GIN drives disease evolution, it also creates vulnerabilities such as dependencies on 'superfluous' repair mechanisms and the induction of tumor-specific antigens that can be targeted. We review the mechanisms of GIN in MM, the associated vulnerabilities, and therapeutic targeting strategies.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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26
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Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus 2020; 10:21-32. [PMID: 30724665 PMCID: PMC6380420 DOI: 10.1080/19491034.2019.1578600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.
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Affiliation(s)
- Karissa L Milbury
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Biplab Paul
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Azra Lari
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Claire Fowler
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Ben Montpetit
- b Department of Cell Biology , University of Alberta , Edmonton , Canada.,c Department of Viticulture and Enology , University of California , Davis , CA , USA
| | - Peter C Stirling
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada.,d Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
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27
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Chu B, Bao L, Wang Y, Lu M, Shi L, Gao S, Fang L, Xiang Q, Liu X. CD27 antigen negative expression indicates poor prognosis in newly diagnosed multiple myeloma. Clin Immunol 2020; 213:108363. [PMID: 32120013 DOI: 10.1016/j.clim.2020.108363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/19/2019] [Accepted: 02/17/2020] [Indexed: 12/20/2022]
Abstract
To investigate the role of CD27 in multiple myeloma(MM), bone marrow samples from 165 newly diagnosed MM were analysed by flow cytometry. CD27- group (n = 93) had higher level of plasma cell proportion (37.00% vs 22.50%, p < .05), β2-MG (5.42 vs 3.20 mg/L, p < .05), calcium (2.45 vs 2.28 mmol/L, p < .05),higher percentage of ISS stage III (49.46% vs 22.22%, p < .05) and patients with ≥2 high-risk cytogenetics (24.73% vs 15.28%, p < .05) than CD27+ group (n = 72). After 4 cycles of chemotherapy, the overall response rate in CD27- group were lower than CD27+ group (56.67% vs 73.02%,p < .05). After a median follow-up of 18 months, progression-free survival was significantly shorter in CD27- group than in CD27+ group (22 vs 40 months, p < .05), so was overall survival (median OS not reached, p < .05). Gene sequencing showed more adverse mutations in CD27- group than CD27+ group.
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Affiliation(s)
- Bin Chu
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Li Bao
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China.
| | - Yutong Wang
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Minqiu Lu
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Lei Shi
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Shan Gao
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Lijuan Fang
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Qiuqing Xiang
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
| | - Xi Liu
- Department of hematology, Beijing Jishuitan Hospital, Beijing, China
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28
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Exon-4 Mutations in KRAS Affect MEK/ERK and PI3K/AKT Signaling in Human Multiple Myeloma Cell Lines. Cancers (Basel) 2020; 12:cancers12020455. [PMID: 32079091 PMCID: PMC7072554 DOI: 10.3390/cancers12020455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 01/12/2023] Open
Abstract
Approximately 20% of multiple myeloma (MM) cases harbor a point mutation in KRAS. However, there is still no final consent on whether KRAS-mutations are associated with disease outcome. Specifically, no data exist on whether KRAS-mutations have an impact on survival of MM patients at diagnosis in the era of novel agents. Direct blockade of KRAS for therapeutic purposes is mostly impossible, but recently a mutation-specific covalent inhibitor targeting KRASp.G12C entered into clinical trials. However, other KRAS hotspot-mutations exist in MM patients, including the less common exon-4 mutations. For the current study, the coding regions of KRAS were deep-sequenced in 80 newly diagnosed MM patients, uniformely treated with three cycles of bortezomib plus dexamethasone and cyclophosphamide (VCD)-induction, followed by high-dose chemotherapy and autologous stem cell transplantation. Moreover, the functional impact of KRASp.G12A and the exon-4 mutations p.A146T and p.A146V on different survival pathways was investigated. Specifically, KRASWT, KRASp.G12A, KRASp.A146T, and KRASp.A146V were overexpressed in HEK293 cells and the KRASWT MM cell lines JJN3 and OPM2 using lentiviral transduction and the Sleeping Beauty vector system. Even though KRAS-mutations were not correlated with survival, all KRAS-mutants were found capable of potentially activating MEK/ERK- and sustaining PI3K/AKT-signaling in MM cells.
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29
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Pertesi M, Went M, Hansson M, Hemminki K, Houlston RS, Nilsson B. Genetic predisposition for multiple myeloma. Leukemia 2020; 34:697-708. [PMID: 31913320 DOI: 10.1038/s41375-019-0703-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 12/24/2019] [Indexed: 12/14/2022]
Abstract
Multiple myeloma (MM) is the second most common blood malignancy. Epidemiological family studies going back to the 1920s have provided evidence for familial aggregation, suggesting a subset of cases have an inherited genetic background. Recently, studies aimed at explaining this phenomenon have begun to provide direct evidence for genetic predisposition to MM. Genome-wide association studies have identified common risk alleles at 24 independent loci. Sequencing studies of familial cases and kindreds have begun to identify promising candidate genes where variants with strong effects on MM risk might reside. Finally, functional studies are starting to give insight into how identified risk alleles promote the development of MM. Here, we review recent findings in MM predisposition field, and highlight open questions and future directions.
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Affiliation(s)
- Maroulio Pertesi
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Kari Hemminki
- Department of Cancer Epidemiology, German Cancer Research Center, Im Neuenheimer Feld, Heidelberg, Germany.,Faculty of Medicine and Biomedical Center, Charles University in Prague, 30605, Pilsen, Czech Republic
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden. .,Broad Institute, 415 Main Street, Cambridge, MA, 02142, USA.
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30
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Abstract
The evolutionarily conserved RNA exosome is a multisubunit ribonuclease complex that processes and/or degrades numerous RNAs. Recently, mutations in genes encoding both structural and catalytic subunits of the RNA exosome have been linked to human disease. Mutations in the structural exosome gene EXOSC2 cause a distinct syndrome that includes retinitis pigmentosa, hearing loss, and mild intellectual disability. In contrast, mutations in the structural exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are related autosomal recessive, neurodegenerative diseases. In addition, mutations in the structural exosome gene EXOSC9 cause a PCH-like disease with cerebellar atrophy and spinal motor neuronopathy. Finally, mutations in the catalytic exosome gene DIS3 have been linked to multiple myeloma, a neoplasm of plasma B cells. How mutations in these RNA exosome genes lead to distinct, tissue-specific diseases is not currently well understood. In this chapter, we examine the role of the RNA exosome complex in human disease and discuss the mechanisms by which mutations in different exosome subunit genes could impair RNA exosome function and give rise to diverse diseases.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
| | - Derrick J Morton
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Emily G Kuiper
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephanie K Jones
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Sara W Leung
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Anita H Corbett
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
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31
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Pertesi M, Vallée M, Wei X, Revuelta MV, Galia P, Demangel D, Oliver J, Foll M, Chen S, Perrial E, Garderet L, Corre J, Leleu X, Boyle EM, Decaux O, Rodon P, Kolb B, Slama B, Mineur P, Voog E, Le Bris C, Fontan J, Maigre M, Beaumont M, Azais I, Sobol H, Vignon M, Royer B, Perrot A, Fuzibet JG, Dorvaux V, Anglaret B, Cony-Makhoul P, Berthou C, Desquesnes F, Pegourie B, Leyvraz S, Mosser L, Frenkiel N, Augeul-Meunier K, Leduc I, Leyronnas C, Voillat L, Casassus P, Mathiot C, Cheron N, Paubelle E, Moreau P, Bignon YJ, Joly B, Bourquard P, Caillot D, Naman H, Rigaudeau S, Marit G, Macro M, Lambrecht I, Cliquennois M, Vincent L, Helias P, Avet-Loiseau H, Moreno V, Reis RM, Varkonyi J, Kruszewski M, Vangsted AJ, Jurczyszyn A, Zaucha JM, Sainz J, Krawczyk-Kulis M, Wątek M, Pelosini M, Iskierka-Jażdżewska E, Grząśko N, Martinez-Lopez J, Jerez A, Campa D, Buda G, Lesueur F, Dudziński M, García-Sanz R, Nagler A, Rymko M, Jamroziak K, Butrym A, Canzian F, Obazee O, Nilsson B, Klein RJ, Lipkin SM, McKay JD, Dumontet C. Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma. Leukemia 2019; 33:2324-2330. [PMID: 30967618 PMCID: PMC6756025 DOI: 10.1038/s41375-019-0452-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/04/2019] [Accepted: 02/08/2019] [Indexed: 01/23/2023]
Affiliation(s)
- Maroulio Pertesi
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
- Department of Laboratory Medicine, Division of Hematology and Transfusion medicine, Lund University, Lund, Sweden
| | - Maxime Vallée
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Xiaomu Wei
- Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | | | - Perrine Galia
- ProfilExpert, Lyon, France
- Hospices Civils de Lyon, Lyon, France
| | | | - Javier Oliver
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria; Institute of Biomedical Research in Malaga (IBIMA), CIMES, University of Málaga, Málaga, Spain
| | - Matthieu Foll
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Siwei Chen
- Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Emeline Perrial
- INSERM 1052, CNRS 5286, CRCL, Lyon, France
- University of Lyon, Lyon, France
| | - Laurent Garderet
- INSERM, UMR_S 938, Paris, France
- AP-HP, Hôpital Saint Antoine, Departement d'hematologie et de therapie cellulaire, Paris, France
- Sorbonne Universites, UPMC Univ Paris 06, UMR_S 938, Paris, France
| | - Jill Corre
- IUC-Oncopole and CRCT INSERM U1037, Toulouse, France
| | - Xavier Leleu
- Inserm CIC 1402 & Service d'Hématologie et Thérapie Cellulaire, CHU La Miletrie, Poitiers, France
| | | | - Olivier Decaux
- Service de Medecine Interne, CHU Rennes, Rennes, France
- Faculte de Medecine, Universite de Rennes 1, Rennes, France
- INSERM UMR U1236, Rennes, France
| | - Philippe Rodon
- Unite d'Hematologie et d'Oncologie, Centre Hospitalier, Perigueux, France
| | | | - Borhane Slama
- Service d'Onco hematologie, CH Avignon, Avignon, France
| | - Philippe Mineur
- Hematologie et pathologies de la coagulation, Grand Hôpital de Charleroi, Charleroi, Belgium
| | - Eric Voog
- Centre Jean Bernard, Institut Inter-regional de Cancerologie, Le Mans, France
| | - Catherine Le Bris
- Service post urgences, CHU de FORT DE FRANCE, pôle RASSUR, Martinique, France
| | - Jean Fontan
- Hopital Jean Minjoz, CHRU Besançon, Besançon, France
| | - Michel Maigre
- Service d'Hemato-Oncologie, CHU Chartres, Chartres, France
| | - Marie Beaumont
- Hematologie clinique et therapie cellulaire, CHU Amiens, Amiens, France
| | | | - Hagay Sobol
- Cancer Genetics Department, Paoli-Calmettes Institute, Aix-Marseille University, Marseille, France
| | | | - Bruno Royer
- Service d'Immuno-hematologie, Hôpital Saint Louis, Paris, France
| | - Aurore Perrot
- Service d'Hematologie, CHU de Nancy, Universite de Lorraine, Vandoeuvre les Nancy, Nancy, France
| | | | | | | | - Pascale Cony-Makhoul
- Service d'Hematologie, Centre Hospitalier Annecy Genevois, Epagny Metz-Tessy, France
| | | | | | | | - Serge Leyvraz
- Departement d'oncologie, CHUV, Lausanne, Switzerland
| | - Laurent Mosser
- Unite d'oncologie medicale, Pôle medical 2, Hôpital Jacques Puel, Rodez, France
| | | | - Karine Augeul-Meunier
- Service Hematologie, Institut de Cancerologie Lucien Neuwirth, Saint-Priest-en-Jarez, France
| | | | - Cécile Leyronnas
- Institut Daniel Hollard, Groupe Hospitalier Mutualiste de Grenoble, Grenoble, France
| | - Laurent Voillat
- Service hemato/oncologie, CH William Morey, Chalon sur Saône, France
| | | | - Claire Mathiot
- Intergroupe Francophone du Myelome (IFM), Bobigny, France
| | | | | | | | - Yves-Jean Bignon
- Laboratoire de Biologie Medicale OncoGènAuvergne; Departement d'oncogenetique, UMR INSERM 1240, Centre Jean Perrin, Clermont-Ferrand, France
| | - Bertrand Joly
- Service d'hematologie clinique, Pôle medecine de specialite, Centre Hospitalier Sud Francilien (CHSF), Corbeil-Essonnes, France
| | | | | | - Hervé Naman
- Hematologie - Oncologie medicale, Centre Azureen de Cancerologie, Mougins, France
| | - Sophie Rigaudeau
- Service d'Hematologie et d'Oncologie, CHU de Versailles, Le Chesnay, France
| | - Gérald Marit
- INSERM U1035, Universite de Bordeaux, Bordeaux, France
| | - Margaret Macro
- Hematologie Clinique, IHBN-CHU CAEN (University Hospital), Caen, France
| | - Isabelle Lambrecht
- Rheumatology Department, Maison Blanche Hospital, Reims University Hospitals, Reims, France
| | - Manuel Cliquennois
- Unite d'Hematologie clinique, Groupement des hôpitaux de l'Institut Catholique (GHICL), Universite Catholique de Lille, Lille, France
| | - Laure Vincent
- Departement d'hematologie clinique, CHU de Montpellier, Montpellier, France
| | - Philippe Helias
- Service d'Oncologie medicale, CHU de La Guadeloupe, Pointe-a-Pitre, Guadeloupe
| | - Hervé Avet-Loiseau
- Laboratory for Genomics in Myeloma, Institut Universitaire du Cancer and University Hospital, Centre de Recherche en Cancerologie de Toulouse, Toulouse, France
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Unit of Biomarkers and Susceptibility, Cancer Prevention and Control Program, IDIBELL, Catalan Institute of Oncology; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Rui Manuel Reis
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Judit Varkonyi
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | | | - Annette Juul Vangsted
- Department of Haematology, Rigshospitalet, Copenhagen University, Copenhagen, Denmark
| | - Artur Jurczyszyn
- Jagiellonian University Medical College, Department of Hematology, Cracow, Poland
| | - Jan Maciej Zaucha
- Gdynia Oncology Center, Gdynia and Department of Oncological Propedeutics, Medical University of Gdańsk, Gdańsk, Poland
| | - Juan Sainz
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Malgorzata Krawczyk-Kulis
- Department of Bone Marrow Transplantation and Hematology-Oncology M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology Gliwice Branch, Gliwice, Poland
| | - Marzena Wątek
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
- Holycross Cancer Center of Kielce, Hematology Clinic, Kielce, Poland
| | - Matteo Pelosini
- Department of Oncology, Transplants and Advanced Technologies, Section of Hematology, Pisa University Hospital, Pisa, Italy
| | | | - Norbert Grząśko
- Department of Experimental Hemato-oncology, Medical University of Lubli, Poland; Department of Hematology, St. John's Cancer Centre, Polish Myeloma Study Group, Lublin, Poland
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital 12 de Octubre, Universidad Complutense; CNIO, Madrid, Spain
| | - Andrés Jerez
- Hematology and Medical Oncology Department, Hospital Morales Meseguer, IMIB, Murcia, Spain
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Gabriele Buda
- Holycross Cancer Center of Kielce, Hematology Clinic, Kielce, Poland
| | - Fabienne Lesueur
- Inserm U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France
| | | | - Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Arnon Nagler
- Hematology Division, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Marcin Rymko
- Department of Hematology, Copernicus Hospital, Torun, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | | | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ofure Obazee
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Björn Nilsson
- Department of Laboratory Medicine, Division of Hematology and Transfusion medicine, Lund University, Lund, Sweden
| | - Robert J Klein
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - James D McKay
- Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France.
| | - Charles Dumontet
- ProfilExpert, Lyon, France.
- Hospices Civils de Lyon, Lyon, France.
- INSERM 1052, CNRS 5286, CRCL, Lyon, France.
- University of Lyon, Lyon, France.
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Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. Cell 2019; 173:1663-1677.e21. [PMID: 29906447 DOI: 10.1016/j.cell.2018.05.041] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/26/2018] [Accepted: 05/17/2018] [Indexed: 01/08/2023]
Abstract
The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.
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33
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Saramago M, da Costa PJ, Viegas SC, Arraiano CM. The Implication of mRNA Degradation Disorders on Human DISease: Focus on DIS3 and DIS3-Like Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:85-98. [PMID: 31342438 DOI: 10.1007/978-3-030-19966-1_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA degradation is considered a critical posttranscriptional regulatory checkpoint, maintaining the correct functioning of organisms. When a specific RNA transcript is no longer required in the cell, it is signaled for degradation through a number of highly regulated steps. Ribonucleases (or simply RNases) are key enzymes involved in the control of RNA stability. These enzymes can perform the RNA degradation alone or cooperate with other proteins in RNA degradation complexes. Important findings over the last years have shed light into eukaryotic RNA degradation by members of the RNase II/RNB family of enzymes. DIS3 enzyme belongs to this family and represents one of the catalytic subunits of the multiprotein complex exosome. This RNase has a diverse range of functions, mainly within nuclear RNA metabolism. Humans encode two other DIS3-like enzymes: DIS3L (DIS3L1) and DIS3L2. DIS3L1 also acts in association with the exosome but is strictly cytoplasmic. In contrast, DIS3L2 acts independently of the exosome and shows a distinctive preference for uridylated RNAs. These enzymes have been shown to be involved in important cellular processes, such as mitotic control, and associated with human disorders like cancer. This review shows how the impairment of function of each of these enzymes is implicated in human disease.
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Affiliation(s)
- Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Paulo J da Costa
- Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, Lisboa, Portugal.,Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisbon, Lisboa, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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34
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Dos Santos RF, Quendera AP, Boavida S, Seixas AF, Arraiano CM, Andrade JM. Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:101-155. [PMID: 30340785 DOI: 10.1016/bs.pmbts.2018.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.
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Affiliation(s)
- Ricardo F Dos Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ana P Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia Boavida
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André F Seixas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - José M Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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35
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Subclonal evolution in disease progression from MGUS/SMM to multiple myeloma is characterised by clonal stability. Leukemia 2018; 33:457-468. [PMID: 30046162 PMCID: PMC6365384 DOI: 10.1038/s41375-018-0206-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/01/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022]
Abstract
Multiple myeloma (MM) is a largely incurable haematological malignancy defined by the clonal proliferation of malignant plasma cells (PCs) within the bone marrow. Clonal heterogeneity has recently been established as a feature in MM, however, the subclonal evolution associated with disease progression has not been described. Here, we performed whole-exome sequencing of serial samples from 10 patients, providing new insights into the progression from monoclonal gammopathy of undetermined significance (MGUS) and smouldering MM (SMM), to symptomatic MM. We confirm that intraclonal genetic heterogeneity is a common feature at diagnosis and that the driving events involved in disease progression are more subtle than previously reported. We reveal that MM evolution is mainly characterised by the phenomenon of clonal stability, where the transformed subclonal PC populations identified at MM are already present in the asymptomatic MGUS/SMM stages. Our findings highlight the possibility that PC extrinsic factors may play a role in subclonal evolution and MGUS/SMM to MM progression.
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36
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Robinson SR, Viegas SC, Matos RG, Domingues S, Bedir M, Stewart HJS, Chevassut TJ, Oliver AW, Arraiano CM, Newbury SF. DIS3 isoforms vary in their endoribonuclease activity and are differentially expressed within haematological cancers. Biochem J 2018; 475:2091-2105. [PMID: 29802118 PMCID: PMC6024818 DOI: 10.1042/bcj20170962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/16/2018] [Accepted: 05/24/2018] [Indexed: 11/17/2022]
Abstract
DIS3 (defective in sister chromatid joining) is the catalytic subunit of the exosome, a protein complex involved in the 3'-5' degradation of RNAs. DIS3 is a highly conserved exoribonuclease, also known as Rrp44. Global sequencing studies have identified DIS3 as being mutated in a range of cancers, with a considerable incidence in multiple myeloma. In this work, we have identified two protein-coding isoforms of DIS3. Both isoforms are functionally relevant and result from alternative splicing. They differ from each other in the size of their N-terminal PIN (PilT N-terminal) domain, which has been shown to have endoribonuclease activity and tether DIS3 to the exosome. Isoform 1 encodes a full-length PIN domain, whereas the PIN domain of isoform 2 is shorter and is missing a segment with conserved amino acids. We have carried out biochemical activity assays on both isoforms of full-length DIS3 and the isolated PIN domains. We find that isoform 2, despite missing part of the PIN domain, has greater endonuclease activity compared with isoform 1. Examination of the available structural information allows us to provide a hypothesis to explain this altered behaviour. Our results also show that multiple myeloma patient cells and all cancer cell lines tested have higher levels of isoform 1 compared with isoform 2, whereas acute myeloid leukaemia and chronic myelomonocytic leukaemia patient cells and samples from healthy donors have similar levels of isoforms 1 and 2. Taken together, our data indicate that significant changes in the ratios of the two isoforms could be symptomatic of haematological cancers.
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Affiliation(s)
- Sophie R Robinson
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, U.K
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Susana Domingues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marisa Bedir
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, U.K
| | - Helen J S Stewart
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, U.K
| | - Timothy J Chevassut
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, U.K
| | - Antony W Oliver
- School of Life Sciences, Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, U.K
| | - Cecilia M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Sarah F Newbury
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, U.K.
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37
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Singh P, Saha U, Paira S, Das B. Nuclear mRNA Surveillance Mechanisms: Function and Links to Human Disease. J Mol Biol 2018; 430:1993-2013. [PMID: 29758258 DOI: 10.1016/j.jmb.2018.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Production of export-competent mRNAs involves transcription and a series of dynamic processing and modification events of pre-messenger RNAs in the nucleus. Mutations in the genes encoding the transcription and mRNP processing machinery and the complexities involved in the biogenesis events lead to the formation of aberrant messages. These faulty transcripts are promptly eliminated by the nuclear RNA exosome and its cofactors to safeguard the cells and organisms from genetic catastrophe. Mutations in the components of the core nuclear exosome and its cofactors lead to the tissue-specific dysfunction of exosomal activities, which are linked to diverse human diseases and disorders. In this article, we examine the structure and function of both the yeast and human RNA exosome complex and its cofactors, discuss the nature of the various altered amino acid residues implicated in these diseases with the speculative mechanisms of the mutation-induced disorders and project the frontier and prospective avenues of the future research in this field.
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Affiliation(s)
- Pragyan Singh
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Upasana Saha
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India.
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38
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Ryu D, Kim HJ, Joung JG, Lee HO, Bae JS, Kim SJ, Kim H, Park WY, Kim K. Comprehensive genomic profiling of IgM multiple myeloma identifies IRF4 as a prognostic marker. Oncotarget 2018; 7:47127-47133. [PMID: 27223072 PMCID: PMC5216929 DOI: 10.18632/oncotarget.9478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/28/2016] [Indexed: 12/11/2022] Open
Abstract
Immunoglobulin M multiple myeloma (IgM MM) is an extremely rare subtype of multiple myeloma with a poor clinical outcome. In this study, bone marrow aspirates of MM patients, including two cases of IgM MM, were analyzed by whole exome sequencing and RNA sequencing. Recurrent somatic mutations in the NRAS, KRAS, CCND1, DIS3, and TP53 genes were found in IgM MM and other types of MM, in agreement with previous studies. Overall transcription profiles of IgM and other types of MM clustered together, but separate from normal blood or peripheral plasma cells. Among the differentially expressed genes in IgM MM, IRF4 was highly expressed in IgM as well as in a subset of other types of MM patients. Thus, IRF4 is an independent prognostic factor for general MM patients. Taken together, the somatic mutation and transcriptome profiles support the idea that IgM MM can be classified as an aggressive MM subtype.
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Affiliation(s)
- Daeun Ryu
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jin Kim
- Department of Laboratory Medicine & Genetics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Seol Bae
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Haesu Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kihyun Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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39
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Mutzbauer G, Maurus K, Buszello C, Pischimarov J, Roth S, Rosenwald A, Chott A, Geissinger E. SYK expression in monomorphic epitheliotropic intestinal T-cell lymphoma. Mod Pathol 2018; 31:505-516. [PMID: 29052597 DOI: 10.1038/modpathol.2017.145] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 09/02/2017] [Accepted: 09/11/2017] [Indexed: 01/02/2023]
Abstract
Monomorphic epitheliotropic intestinal T-cell lymphoma (MEITL), formerly known as type II enteropathy associated T-cell lymphoma (type II EATL), is a rare, aggressive primary intestinal T-cell lymphoma with a poor prognosis and an incompletely understood pathogenesis. We collected 40 cases of MEITL and 27 cases of EATL, formerly known as type I EATL, and comparatively investigated the T-cell receptor (TCR) itself and associated signaling molecules using immunohistochemistry, amplicon deep sequencing and bisulfite pyrosequencing. The TCR showed both an αβ-T-cell origin (30%) and a γδ-T-cell derivation (55%) resulting in a predominant positive TCR phenotype in MEITL compared with the mainly silent TCR phenotype in EATL (65%). The immunohistochemical expression of the spleen tyrosine kinase (SYK) turned out to be a distinctive feature of MEITL (95%) compared with EATL (0%). Aberrant SYK overexpression in MEITL is likely caused by hypomethylation of the SYK promoter, while no common mutations in the SYK gene or in its promoter could be detected. Using amplicon deep sequencing, mutations in DNMT3A, IDH2, and TET2 were infrequent events in MEITL and EATL. Immunohistochemical expression of linker for activation of T-cells (LAT) subdivided MEITL into a LAT expressing subset (33%) and a LAT silent subset (67%) with a potentially earlier disease onset in LAT-positive MEITL.
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Affiliation(s)
- Grit Mutzbauer
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Katja Maurus
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Clara Buszello
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | | | - Sabine Roth
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany.,Comprehensive Cancer Center Mainfranken, University and University Hospital, Wuerzburg, Germany
| | - Andreas Chott
- Institute of Pathology and Microbiology, Wilhelminenspital, Vienna, Austria
| | - Eva Geissinger
- Institute of Pathology, University of Wuerzburg, Wuerzburg, Germany.,Comprehensive Cancer Center Mainfranken, University and University Hospital, Wuerzburg, Germany
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40
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Han J, van Hoof A. The RNA Exosome Channeling and Direct Access Conformations Have Distinct In Vivo Functions. Cell Rep 2018; 16:3348-3358. [PMID: 27653695 DOI: 10.1016/j.celrep.2016.08.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 06/06/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022] Open
Abstract
The RNA exosome is a 3'-5' ribonuclease complex that is composed of nine core subunits and an essential catalytic subunit, Rrp44. Two distinct conformations of Rrp44 were revealed in previous structural studies, suggesting that Rrp44 may change its conformation to exert its function. In the channeling conformation, (Rrp44(ch)), RNA accesses the active site after traversing the central channel of the RNA exosome, whereas in the other conformation, (Rrp44(da)), RNA gains direct access to the active site. Here, we show that the Rrp44(da) exosome is important for nuclear function of the RNA exosome. Defects caused by disrupting the direct access conformation are distinct from those caused by channel-occluding mutations, indicating specific functions for each conformation. Our genetic analyses provide in vivo evidence that the RNA exosome employs a direct-access route to recruit specific substrates, indicating that the RNA exosome uses alternative conformations to act on different RNA substrates.
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Affiliation(s)
- Jaeil Han
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 1.212, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 1.212, Houston, TX 77030, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 1.212, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 1.212, Houston, TX 77030, USA.
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41
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Hirsch B, Endris V, Lassmann S, Weichert W, Pfarr N, Schirmacher P, Kovaleva V, Werner M, Bonzheim I, Fend F, Sperveslage J, Kaulich K, Zacher A, Reifenberger G, Köhrer K, Stepanow S, Lerke S, Mayr T, Aust DE, Baretton G, Weidner S, Jung A, Kirchner T, Hansmann ML, Burbat L, von der Wall E, Dietel M, Hummel M. Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics. Virchows Arch 2018; 472:557-565. [PMID: 29374318 PMCID: PMC5924673 DOI: 10.1007/s00428-017-2288-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/05/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022]
Abstract
The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.
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Affiliation(s)
- B Hirsch
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany. .,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
| | - V Endris
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - S Lassmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - W Weichert
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - N Pfarr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Technical University Munich (TUM), Munich, Germany
| | - P Schirmacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Medicine Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - V Kovaleva
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - M Werner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute for Surgical Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Breisacherstraße 115A, 79106, Freiburg, Germany
| | - I Bonzheim
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - F Fend
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - J Sperveslage
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology and Neuropathology, University Hospital Tuebingen, Eberhard-Karls-University, Liebermeisterstraße 8, 72076, Tuebingen, Germany
| | - K Kaulich
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - A Zacher
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - G Reifenberger
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - K Köhrer
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Stepanow
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Department of Neuropathology, Heinrich Heine University Duesseldorf and Biological and Medical Research Center (BMFZ), Genomics and Transcriptomics Laboratory, Heinrich Heine University Duesseldorf, 40225, Duesseldorf, Germany
| | - S Lerke
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - T Mayr
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - D E Aust
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - G Baretton
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstraße 74, 01307, Dresden, Germany
| | - S Weidner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - A Jung
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - T Kirchner
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Institute of Pathology, Ludwig-Maximilians University Munich, Thalkirchner Straße 36, 80337, Munich, Germany
| | - M L Hansmann
- German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Dr. Senckenberg Institute of Pathology, University Hospital, Goethe-University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - L Burbat
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - E von der Wall
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Dietel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - M Hummel
- Campus Mitte, Institute of Pathology, Charité-University Medicine Berlin, Virchowweg 15, 10117, Berlin, Germany.,German Cancer Consortium (DKTK) Partner Site, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
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Chiappetta C, Mancini M, Lessi F, Aretini P, De Gregorio V, Puggioni C, Carletti R, Petrozza V, Civita P, Franceschi S, Naccarato AG, Rocca CD, Mazzanti CM, Di Cristofano C. Whole-exome analysis in osteosarcoma to identify a personalized therapy. Oncotarget 2017; 8:80416-80428. [PMID: 29113313 PMCID: PMC5655208 DOI: 10.18632/oncotarget.19010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/20/2017] [Indexed: 11/25/2022] Open
Abstract
Osteosarcoma is the most common pediatric primary non-hematopoietic bone tumor. Survival of these young patients is related to the response to chemotherapy and development of metastases. Despite many advances in cancer research, chemotherapy regimens for osteosarcoma are still based on non-selective cytotoxic drugs. It is essential to investigate new specific molecular therapies for osteosarcoma to increase the survival rate of these patients. We performed exomic sequence analyses of 8 diagnostic biopsies of patients with conventional high grade osteosarcoma to advance our understanding of their genetic underpinnings and to correlate the genetic alteration with the clinical and pathological features of each patient to identify a personalized therapy. We identified 18,275 somatic variations in 8,247 genes and we found three mutated genes in 7/8 (87%) samples (KIF1B, NEB and KMT2C). KMT2C showed the highest number of variations; it is an important component of a histone H3 lysine 4 methyltransferase complex and it is one of the histone modifiers previously implicated in carcinogenesis, never studied in osteosarcoma. Moreover, we found a group of 15 genes that showed variations only in patients that did not respond to therapy and developed metastasis and some of these genes are involved in carcinogenesis and tumor progression in other tumors. These data could offer the opportunity to get a key molecular target to identify possible new strategies for early diagnosis and new therapeutic approaches for osteosarcoma and to provide a tailored treatment for each patient based on their genetic profile.
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Affiliation(s)
- Caterina Chiappetta
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
| | - Massimiliano Mancini
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
| | | | | | | | - Chiara Puggioni
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
| | - Raffaella Carletti
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
| | - Vincenzo Petrozza
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
| | | | | | | | - Carlo Della Rocca
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
| | | | - Claudio Di Cristofano
- UOC of Pathology, Department of Medical-Surgical Sciences and Bio-Technologies, Sapienza University of Rome, Latina, Italy
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43
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Lee KJ, Lee KH, Yoon KA, Sohn JY, Lee E, Lee H, Eom HS, Kong SY. Chromothripsis in Treatment Resistance in Multiple Myeloma. Genomics Inform 2017; 15:87-97. [PMID: 29020724 PMCID: PMC5637343 DOI: 10.5808/gi.2017.15.3.87] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 08/17/2017] [Accepted: 08/29/2017] [Indexed: 12/24/2022] Open
Abstract
Multiple myeloma (MM) is a malignant disease caused by an abnormal proliferation of plasma cells, of which the prognostic factors include chromosomal abnormality, β-2 microglobulin, and albumin. Recently, the term chromothripsis has emerged, which is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event. Many studies have shown an association of chromothripsis with the prognosis in several cancers; however, few studies have investigated it in MM. Here, we studied the association between chromothripsis-like patterns and treatment resistance or prognosis. First, we analyzed nine MM cell lines (U266, MM.1S, RPMI8226, KMS-11, KMS-12-BM, KMS-12-PE, KMS-28-BM, KMS-28-PE, and NCI-H929) and bone marrow samples of four patients who were diagnosed with MM by next-generation sequencing-based copy number variation analysis. The frequency of the chromothripsis-like pattern was observed in seven cell lines. We analyzed the treatment-induced chromothripsis-like patterns in KMS-12-BM and KMS-12-PE cells. As a result, breakpoints and chromothripsis-like patterns were increased after drug treatment in the relatively resistant KMS-12-BM. We further analyzed the patients’ results according to the therapeutic response, which was divided into sensitive and resistant, as suggested by the International Myeloma Working Group. The chromothripsis-like pattern was more frequently observed in the resistant group. In the sensitive group, the frequency of the chromothripsis-like pattern decreased after treatment, whereas the resistant group showed increased chromothripsis-like patterns after the treatment. These results suggest that the chromothripsis-like pattern is associated with treatment response in MM.
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Affiliation(s)
- Kyoung Joo Lee
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Korea
| | - Ki Hong Lee
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Korea
| | - Kyong-Ah Yoon
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
| | - Ji Yeon Sohn
- Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang 10408, Korea
| | - Eunyoung Lee
- Center for Hematologic Malignancy, National Cancer Center, Goyang 10408, Korea
| | - Hyewon Lee
- Center for Hematologic Malignancy, National Cancer Center, Goyang 10408, Korea.,Precision Medicine Branch, Division of Precision Medicine, National Cancer Center, Goyang 10408, Korea
| | - Hyeon-Seok Eom
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Korea.,Center for Hematologic Malignancy, National Cancer Center, Goyang 10408, Korea
| | - Sun-Young Kong
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang 10408, Korea.,Department of Laboratory Medicine, Center for Diagnostic Oncology, Research Institute and Hospital, National Cancer Center, Goyang 10408, Korea.,Center for Hematologic Malignancy, National Cancer Center, Goyang 10408, Korea.,Translational Research Branch, Division of Translational Science, National Cancer Center, Goyang 10408, Korea
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44
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Abstract
OBJECTIVES This integrative review describes the genomic variants that have been found to be associated with poor prognosis in patients diagnosed with multiple myeloma (MM). Second, it identifies MM genetic and genomic changes using next-generation sequencing, specifically whole-genome sequencing or exome sequencing. DATA SOURCE A search for peer-reviewed articles through PubMed, EBSCOhost, and DePaul WorldCat Libraries Worldwide yielded 33 articles that were included in the final analysis. CONCLUSION The most commonly reported genetic changes were KRAS, NRAS, TP53, FAM46C, BRAF, DIS3, ATM, and CCND1. These genetic changes play a role in the pathogenesis of MM, prognostication, and therapeutic targets for novel therapies. IMPLICATIONS FOR NURSING PRACTICE MM genetics and genomics are expanding rapidly; oncology nurse clinicians must have basic competencies in genetics and genomics to help patients understand the complexities of genetic and genomic alterations and be able to refer patients to appropriate genomic professionals if needed.
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45
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Hoskins JW, Ibrahim A, Emmanuel MA, Manmiller SM, Wu Y, O’Neill M, Jia J, Collins I, Zhang M, Thomas JV, Rost LM, Das S, Parikh H, Haake JM, Matters GL, Kurtz RC, Bamlet WR, Klein A, Stolzenberg-Solomon R, Wolpin BM, Yarden R, Wang Z, Smith J, Olson SH, Andresson T, Petersen GM, Amundadottir LT. Functional characterization of a chr13q22.1 pancreatic cancer risk locus reveals long-range interaction and allele-specific effects on DIS3 expression. Hum Mol Genet 2016; 25:4726-4738. [PMID: 28172817 PMCID: PMC5815622 DOI: 10.1093/hmg/ddw300] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/08/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple common susceptibility loci for pancreatic cancer. Here we report fine-mapping and functional analysis of one such locus residing in a 610 kb gene desert on chr13q22.1 (marked by rs9543325). The closest candidate genes, KLF5, KLF12, PIBF1, DIS3 and BORA, range in distance from 265-586 kb. Sequencing three sub-regions containing the top ranked SNPs by imputation P-value revealed a 30 bp insertion/deletion (indel) variant that was significantly associated with pancreatic cancer risk (rs386772267, P = 2.30 × 10-11, OR = 1.22, 95% CI 1.15-1.28) and highly correlated to rs9543325 (r2 = 0.97 in the 1000 Genomes EUR population). This indel was the most significant cis-eQTL variant in a set of 222 histologically normal pancreatic tissue samples (β = 0.26, P = 0.004), with the insertion (risk-increasing) allele associated with reduced DIS3 expression. DIS3 encodes a catalytic subunit of the nuclear RNA exosome complex that mediates RNA processing and decay, and is mutated in several cancers. Chromosome conformation capture revealed a long range (570 kb) physical interaction between a sub-region of the risk locus, containing rs386772267, and a region ∼6 kb upstream of DIS3 Finally, repressor regulatory activity and allele-specific protein binding by transcription factors of the TCF/LEF family were observed for the risk-increasing allele of rs386772267, indicating that expression regulation at this risk locus may be influenced by the Wnt signaling pathway. In conclusion, we have identified a putative functional indel variant at chr13q22.1 that associates with decreased DIS3 expression in carriers of pancreatic cancer risk-increasing alleles, and could therefore affect nuclear RNA processing and/or decay.
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Affiliation(s)
- Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abdisamad Ibrahim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mickey A. Emmanuel
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah M. Manmiller
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yinglun Wu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maura O’Neill
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Janelle V. Thomas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren M. Rost
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jefferson M. Haake
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Gail L. Matters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - William R. Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Alison Klein
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology, the Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ronit Yarden
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jill Smith
- Department of Medicine, Georgetown University Hospital, Washington, DC, and Department of Medicine, Penn State University College of Medicine, Hershey PA, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gloria M. Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Neri A, Todoerti K, Lionetti M, Simeon V, Barbieri M, Nozza F, Vona G, Pompa A, Baldini L, Musto P. Primary plasma cell leukemia 2.0: advances in biology and clinical management. Expert Rev Hematol 2016; 9:1063-1073. [DOI: 10.1080/17474086.2016.1244002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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47
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Manier S, Salem KZ, Park J, Landau DA, Getz G, Ghobrial IM. Genomic complexity of multiple myeloma and its clinical implications. Nat Rev Clin Oncol 2016; 14:100-113. [DOI: 10.1038/nrclinonc.2016.122] [Citation(s) in RCA: 293] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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48
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A compendium of DIS3 mutations and associated transcriptional signatures in plasma cell dyscrasias. Oncotarget 2016; 6:26129-41. [PMID: 26305418 PMCID: PMC4694891 DOI: 10.18632/oncotarget.4674] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
DIS3 is a catalytic subunit of the human exosome complex, containing exonucleolytic (RNB) and endonucleolytic (PIN) domains, recently found mutated in multiple myeloma (MM), a clinically and genetically heterogeneous form of plasma cell (PC) dyscrasia. We analyzed by next-generation sequencing (NGS) the DIS3 PIN and RNB domains in purified bone marrow PCs from 164 representative patients, including 130 cases with MM, 24 with primary PC leukemia and 10 with secondary PC leukemia. DIS3 mutations were found respectively in 18.5%, 25% and 30% of cases. Identified variants were predominantly missense mutations localized in the RNB domain, and were often detected at low allele frequency. DIS3 mutations were preferentially carried by IGH-translocated/nonhyperdiploid patients. Sequential analysis at diagnosis and relapse in a subset of cases highlighted some instances of increasing DIS3 mutation burden during disease progression. NGS also revealed that the majority of DIS3 variants in mutated cases were comparably detectable at transcriptional level. Furthermore, gene expression profiling analysis in DIS3-mutated patients identified a transcriptional signature suggestive for impaired RNA exosome function. In conclusion, these data further support the pathological relevance of DIS3 mutations in plasma cell dyscrasias and suggest that DIS3 may represent a potential tumor suppressor gene in such disorders.
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49
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Keppler S, Weiβbach S, Langer C, Knop S, Pischimarov J, Kull M, Stühmer T, Steinbrunn T, Bargou R, Einsele H, Rosenwald A, Leich E. Rare SNPs in receptor tyrosine kinases are negative outcome predictors in multiple myeloma. Oncotarget 2016; 7:38762-38774. [PMID: 27246973 PMCID: PMC5122427 DOI: 10.18632/oncotarget.9607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/04/2016] [Indexed: 12/25/2022] Open
Abstract
Multiple myeloma (MM) is a plasma cell disorder that is characterized by a great genetic heterogeneity. Recent next generation sequencing studies revealed an accumulation of tumor-associated mutations in receptor tyrosine kinases (RTKs) which may also contribute to the activation of survival pathways in MM. To investigate the clinical role of RTK-mutations in MM, we deep-sequenced the coding DNA-sequence of EGFR, EPHA2, ERBB3, IGF1R, NTRK1 and NTRK2 which were previously found to be mutated in MM, in 75 uniformly treated MM patients of the "Deutsche Studiengruppe Multiples Myelom". Subsequently, we correlated the detected mutations with common cytogenetic alterations and clinical parameters. We identified 11 novel non-synonymous SNVs or rare patient-specific SNPs, not listed in the SNP databases 1000 genomes and dbSNP, in 10 primary MM cases. The mutations predominantly affected the tyrosine-kinase and ligand-binding domains and no correlation with cytogenetic parameters was found. Interestingly, however, patients with RTK-mutations, specifically those with rare patient-specific SNPs, showed a significantly lower overall, event-free and progression-free survival. This indicates that RTK SNVs and rare patient-specific RTK SNPs are of prognostic relevance and suggests that MM patients with RTK-mutations could potentially profit from treatment with RTK-inhibitors.
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Affiliation(s)
- Sarah Keppler
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Susann Weiβbach
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Christian Langer
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Stefan Knop
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Jordan Pischimarov
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Miriam Kull
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Thorsten Stühmer
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Torsten Steinbrunn
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Ralf Bargou
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
| | - Ellen Leich
- Institute of Pathology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken (CCC MF), University Hospital Würzburg, Würzburg, Germany
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Szczepińska T, Kalisiak K, Tomecki R, Labno A, Borowski LS, Kulinski TM, Adamska D, Kosinska J, Dziembowski A. DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts. Genome Res 2015; 25:1622-33. [PMID: 26294688 PMCID: PMC4617959 DOI: 10.1101/gr.189597.115] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 07/16/2015] [Indexed: 01/13/2023]
Abstract
Human DIS3, the nuclear catalytic subunit of the exosome complex, contains exonucleolytic and endonucleolytic active domains. To identify DIS3 targets genome-wide, we combined comprehensive transcriptomic analyses of engineered HEK293 cells that expressed mutant DIS3, with Photoactivatable Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP) experiments. In cells expressing DIS3 with both catalytic sites mutated, RNAs originating from unannotated genomic regions increased ∼2.5-fold, covering ∼70% of the genome and allowing for thousands of novel transcripts to be discovered. Previously described pervasive transcription products, such as Promoter Upstream Transcripts (PROMPTs), accumulated robustly upon DIS3 dysfunction, representing a significant fraction of PAR-CLIP reads. We have also detected relatively long putative premature RNA polymerase II termination products of protein-coding genes whose levels in DIS3 mutant cells can exceed the mature mRNAs, indicating that production of such truncated RNA is a common phenomenon. In addition, we found DIS3 to be involved in controlling the formation of paraspeckles, nuclear bodies that are organized around NEAT1 lncRNA, whose short form was overexpressed in cells with mutated DIS3. Moreover, the DIS3 mutations resulted in misregulation of expression of ∼50% of transcribed protein-coding genes, probably as a secondary effect of accumulation of various noncoding RNA species. Finally, cells expressing mutant DIS3 accumulated snoRNA precursors, which correlated with a strong PAR-CLIP signal, indicating that DIS3 is the main snoRNA-processing enzyme. EXOSC10 (RRP6) instead controls the levels of the mature snoRNAs. Overall, we show that DIS3 has a major nucleoplasmic function in shaping the human RNA polymerase II transcriptome.
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Affiliation(s)
- Teresa Szczepińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Katarzyna Kalisiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Anna Labno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Lukasz S Borowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Tomasz M Kulinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Dorota Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Center for Biostructure Research, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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