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Terradas M, Schubert SA, Viana-Errasti J, Ruano D, Aiza G, Nielsen M, Marciel P, Tops CM, Parra G, Morreau H, Torrents D, van Leerdam ME, Capellá G, de Miranda NFCC, Valle L, van Wezel T. Germline NPAT inactivating variants as cause of hereditary colorectal cancer. Eur J Hum Genet 2024; 32:871-875. [PMID: 38778081 PMCID: PMC11219789 DOI: 10.1038/s41431-024-01625-8] [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: 02/05/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Two independent exome sequencing initiatives aimed to identify new genes involved in the predisposition to nonpolyposis colorectal cancer led to the identification of heterozygous loss-of-function variants in NPAT, a gene that encodes a cyclin E/CDK2 effector required for S phase entry and a coactivator of histone transcription, in two families with multiple members affected with colorectal cancer. Enrichment of loss-of-function and predicted deleterious NPAT variants was identified in familial/early-onset colorectal cancer patients compared to non-cancer gnomAD individuals, further supporting the association with the disease. Previous studies in Drosophila models showed that NPAT abrogation results in chromosomal instability, increase of double strand breaks, and induction of tumour formation. In line with these results, colorectal cancers with NPAT somatic variants and no DNA repair defects have significantly higher aneuploidy levels than NPAT-wildtype colorectal cancers. In conclusion, our findings suggest that constitutional inactivating NPAT variants predispose to mismatch repair-proficient nonpolyposis colorectal cancer.
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Affiliation(s)
- Mariona Terradas
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Stephanie A Schubert
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julen Viana-Errasti
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gemma Aiza
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Paula Marciel
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Genís Parra
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gabriel Capellá
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Laura Valle
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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2
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Sakano Y, Matoba D, Noda T, Kobayashi S, Yamada D, Tomimaru Y, Takahashi H, Uemura M, Doki Y, Eguchi H. Clinical significance of ribosomal protein S15 expression in patients with colorectal cancer liver metastases. JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES 2024. [PMID: 38838053 DOI: 10.1002/jhbp.12012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
BACKGROUND Liver metastasis is the most frequently observed distant metastasis of colorectal cancer, and the residual liver recurrence rate after hepatic resection is still high. To explore the mechanism of liver metastasis to discover potential new treatments, we assessed the relationship between the expression of differentially expressed genes (DEGs) and prognosis in patients with colorectal cancer liver metastasis (CRLM). METHODS The gene expression dataset was extracted from The Cancer Genome Atlas and the Gene Expression Omnibus. Significance analysis of DEGs between tumor and normal samples of colorectum, liver, and lung was conducted. A total of 80 CRLM patients were studied to assess the expression of RPS15, characteristics, and outcomes. We examined the relationships of RPS15 expression to cell viability and apoptosis in vitro and vivo. RESULTS Significance analysis identified 33 DEGs. In our cohorts, the overall survival rates were significantly lower in the high-RPS15-expression group, and high expression of RPS15 was an independent and unfavorable prognostic factor in recurrence-free survival and overall survival. Knockdown of RPS15 expression reduced the proliferative capacity of colorectal cancer cells and increased BAX-induced apoptotic cell death. CONCLUSIONS RPS15 expression is an independent prognostic factor for CRLM patients and might be a novel therapeutic target for CRLM.
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Affiliation(s)
- Yoshihiro Sakano
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Daijiro Matoba
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takehiro Noda
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shogo Kobayashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Daisaku Yamada
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yoshito Tomimaru
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidenori Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
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3
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Wang M, Vulcano S, Xu C, Xie R, Peng W, Wang J, Liu Q, Jia L, Li Z, Li Y. Potentials of ribosomopathy gene as pharmaceutical targets for cancer treatment. J Pharm Anal 2024; 14:308-320. [PMID: 38618250 PMCID: PMC11010632 DOI: 10.1016/j.jpha.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/29/2023] [Accepted: 10/07/2023] [Indexed: 04/16/2024] Open
Abstract
Ribosomopathies encompass a spectrum of disorders arising from impaired ribosome biogenesis and reduced functionality. Mutation or dysexpression of the genes that disturb any finely regulated steps of ribosome biogenesis can result in different types of ribosomopathies in clinic, collectively known as ribosomopathy genes. Emerging data suggest that ribosomopathy patients exhibit a significantly heightened susceptibility to cancer. Abnormal ribosome biogenesis and dysregulation of some ribosomopathy genes have also been found to be intimately associated with cancer development. The correlation between ribosome biogenesis or ribosomopathy and the development of malignancies has been well established. This work aims to review the recent advances in the research of ribosomopathy genes among human cancers and meanwhile, to excavate the potential role of these genes, which have not or rarely been reported in cancer, in the disease development across cancers. We plan to establish a theoretical framework between the ribosomopathy gene and cancer development, to further facilitate the potential of these genes as diagnostic biomarker as well as pharmaceutical targets for cancer treatment.
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Affiliation(s)
- Mengxin Wang
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Rehabilitation Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Stephen Vulcano
- Autoimmunity and Inflammation Program, HSS Research Institute, Hospital for Special Surgery New York, New York, NY, 10021, USA
| | - Changlu Xu
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Renjian Xie
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Medical Information Engineering, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Weijie Peng
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Jie Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, Institute for Liver Diseases of Anhui Medical University, School of Pharmacy, Anhui Medical University, Hefei, 230032, China
| | - Qiaojun Liu
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
| | - Lee Jia
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhi Li
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, CA, 90095, USA
| | - Yumei Li
- Key Laboratory of Biomaterials and Biofabrication in Tissue Engineering of Jiangxi Province, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
- School of Basic Medicine, Gannan Medical University, Ganzhou, Jiangxi, 341000, China
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4
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Da Costa L, Mohandas N, David-NGuyen L, Platon J, Marie I, O'Donohue MF, Leblanc T, Gleizes PE. Diamond-Blackfan anemia, the archetype of ribosomopathy: How distinct is it from the other constitutional ribosomopathies? Blood Cells Mol Dis 2024:102838. [PMID: 38413287 DOI: 10.1016/j.bcmd.2024.102838] [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: 11/15/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
Diamond-Blackfan anemia (DBA) was the first ribosomopathy described in humans. DBA is a congenital hypoplastic anemia, characterized by macrocytic aregenerative anemia, manifesting by differentiation blockage between the BFU-e/CFU-e developmental erythroid progenitor stages. In 50 % of the DBA cases, various malformations are noted. Strikingly, for a hematological disease with a relative erythroid tropism, DBA is due to ribosomal haploinsufficiency in 24 different ribosomal protein (RP) genes. A few other genes have been described in DBA-like disorders, but they do not fit into the classical DBA phenotype (Sankaran et al., 2012; van Dooijeweert et al., 2022; Toki et al., 2018; Kim et al., 2017 [1-4]). Haploinsufficiency in a RP gene leads to defective ribosomal RNA (rRNA) maturation, which is a hallmark of DBA. However, the mechanistic understandings of the erythroid tropism defect in DBA are still to be fully defined. Erythroid defect in DBA has been recently been linked in a non-exclusive manner to a number of mechanisms that include: 1) a defect in translation, in particular for the GATA1 erythroid gene; 2) a deficit of HSP70, the GATA1 chaperone, and 3) free heme toxicity. In addition, p53 activation in response to ribosomal stress is involved in DBA pathophysiology. The DBA phenotype may thus result from the combined contributions of various actors, which may explain the heterogenous phenotypes observed in DBA patients, even within the same family.
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Affiliation(s)
- L Da Costa
- Service d'Hématologie Biologique (Hematology Diagnostic Lab), AP-HP, Hôpital Bicêtre, F-94270 Le Kremlin-Bicêtre, France; University of Paris Saclay, F-94270 Le Kremlin-Bicêtre, France; University of Paris Cité, F-75010 Paris, France; University of Picardie Jules Verne, F-80000 Amiens, France; Inserm U1170, IGR, F-94805 Villejuif/HEMATIM UR4666, F-80000 Amiens, France; Laboratory of Excellence for Red Cells, LABEX GR-Ex, F-75015 Paris, France.
| | | | - Ludivine David-NGuyen
- Service d'Hématologie Biologique (Hematology Diagnostic Lab), AP-HP, Hôpital Bicêtre, F-94270 Le Kremlin-Bicêtre, France
| | - Jessica Platon
- Inserm U1170, IGR, F-94805 Villejuif/HEMATIM UR4666, F-80000 Amiens, France
| | - Isabelle Marie
- Service d'Hématologie Biologique (Hematology Diagnostic Lab), AP-HP, Hôpital Bicêtre, F-94270 Le Kremlin-Bicêtre, France
| | - Marie Françoise O'Donohue
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Thierry Leblanc
- Service d'immuno-hématologie pédiatrique, Hôpital Robert-Debré, F-75019 Paris, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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5
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Gelfo V, Venturi G, Zacchini F, Montanaro L. Decoding Ribosome Heterogeneity: A New Horizon in Cancer Therapy. Biomedicines 2024; 12:155. [PMID: 38255260 PMCID: PMC10813612 DOI: 10.3390/biomedicines12010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The traditional perception of ribosomes as uniform molecular machines has been revolutionized by recent discoveries, revealing a complex landscape of ribosomal heterogeneity. Opposing the conventional belief in interchangeable ribosomal entities, emerging studies underscore the existence of specialized ribosomes, each possessing unique compositions and functions. Factors such as cellular and tissue specificity, developmental and physiological states, and external stimuli, including circadian rhythms, significantly influence ribosome compositions. For instance, muscle cells and neurons are characterized by distinct ribosomal protein sets and dynamic behaviors, respectively. Furthermore, alternative forms of ribosomal RNA (rRNAs) and their post-transcriptional modifications add another dimension to this heterogeneity. These variations, orchestrated by spatial, temporal, and conditional factors, enable the manifestation of a broad spectrum of specialized ribosomes, each tailored for potentially distinct functions. Such specialization not only impacts mRNA translation and gene expression but also holds significant implications for broader biological contexts, notably in the realm of cancer research. As the understanding of ribosomal diversity deepens, it also paves the way for exploring novel avenues in cellular function and offers a fresh perspective on the molecular intricacies of translation.
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Affiliation(s)
- Valerio Gelfo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Federico Zacchini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
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Valle L, Monahan KJ. Genetic predisposition to gastrointestinal polyposis: syndromes, tumour features, genetic testing, and clinical management. Lancet Gastroenterol Hepatol 2024; 9:68-82. [PMID: 37931640 DOI: 10.1016/s2468-1253(23)00240-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 11/08/2023]
Abstract
Gastrointestinal tract polyposis is characterised by the presence of multiple polyps, particularly in the colorectum, and encompasses both cancer predisposition genetic syndromes and non-syndromic clinical manifestations. The sources of the heterogeneity observed in polyposis syndromes relate to genetic cause, mode of inheritance, polyp burden and histological type, and spectrum and frequency of extracolonic manifestations. These features determine the clinical management of carriers, including strategies for cancer prevention and early detection, and oncological treatments. Despite substantial progress in identifying the genetic causes of polyposis, a large proportion of cases remain genetically unexplained. Although some of these cases might be due to lifestyle, environmental factors, or cancer treatments, it is likely that additional polyposis predisposition genes will be identified. This Review provides an overview of the known syndromes and genes, genetic testing, and clinical management of patients with polyposis, and recent advances and challenges in the field of gastrointestinal polyposis.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Programme, Catalan Institute of Oncology, Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Kevin J Monahan
- The St Mark's Centre for Familial Intestinal Cancer Lynch Syndrome & Family Cancer Clinic & Polyposis Registry, St Mark's Hospital, London, UK; Imperial College, London, UK.
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7
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Olkinuora A, Nieminen TT, Douglas S, Kauppinen A, Kontro M, Väänänen J, Kankainen M, Ristimäki A, Mäkinen M, Lahermo P, Heckman C, Saarela J, Salonen M, Lepistö A, Järvinen H, Mecklin JP, Kilpivaara O, Wartiovaara-Kautto U, Porkka K, Peltomäki P. Identification of DHX40 as a candidate susceptibility gene for colorectal and hematological neoplasia. Leukemia 2023; 37:2301-2305. [PMID: 37696923 PMCID: PMC10624609 DOI: 10.1038/s41375-023-02021-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023]
Affiliation(s)
- Alisa Olkinuora
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
| | - Taina T Nieminen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
| | - Suvi Douglas
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Anni Kauppinen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
| | - Mika Kontro
- Department of Hematology, Helsinki University Hospital, Comprehensive Cancer Center and University of Helsinki, 00014, Helsinki, Finland
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, 00014, Helsinki, Finland
| | - Juho Väänänen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Matti Kankainen
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, 00029, Helsinki, Finland
- Hematology Research Unit Helsinki, University of Helsinki, 00014, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Department of Pathology, HUSLAB, HUS Diagnostic Center, Helsinki University Hospital and University of Helsinki, 00014, Helsinki, Finland
| | - Markus Mäkinen
- Research Unit of Cancer and Translational Medicine, Department of Pathology, 90014, University of Oulu, and Department of Pathology, Oulu University Hospital, OYS, 90029, Oulu, Finland
| | - Päivi Lahermo
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
| | - Caroline Heckman
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Janna Saarela
- HiLIFE Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014, Helsinki, Finland
- Centre for Molecular Medicine Norway, NCMM, University of Oslo, 0318, Oslo, Norway
| | - Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland
- Folkhälsan Research Center, 00290, Helsinki, Finland
| | - Anna Lepistö
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Department of Abdominal Surgery, Helsinki University Hospital and University of Helsinki, 00014, Helsinki, Finland
| | - Heikki Järvinen
- Department of Abdominal Surgery, Helsinki University Hospital and University of Helsinki, 00014, Helsinki, Finland
| | - Jukka-Pekka Mecklin
- Department of Education & Research and Surgery, Jyväskylä Central Hospital, 40620, Jyväskylä, Finland
- Department of Sports & Health Sciences, Jyväskylä University, 40014, Jyväskylä, Finland
| | - Outi Kilpivaara
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, 00029, Helsinki, Finland
| | - Ulla Wartiovaara-Kautto
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
- Department of Hematology, Helsinki University Hospital, Comprehensive Cancer Center and University of Helsinki, 00014, Helsinki, Finland
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital, Comprehensive Cancer Center and University of Helsinki, 00014, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
- HUSLAB Laboratory of Genetics, HUS Diagnostic Center, HUS, Helsinki University Hospital, 00029, Helsinki, Finland.
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8
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Abbass MA, Plesec T, Church JM. A Different Way to Think About Syndromes of Hereditary Colorectal Cancer. Dis Colon Rectum 2023; 66:1339-1346. [PMID: 37163656 DOI: 10.1097/dcr.0000000000002772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
BACKGROUND Hereditary colorectal cancer is an increasingly complex field in which the commoner syndromes are being augmented by rarer genetic presentations contributing to familial polyposis and colorectal cancer. Coming to grips with the complexity is difficult because of the phenotypic and genotypic overlap between syndromes. OBJECTIVE This study aimed to describe a new way of thinking about syndromes of hereditary colorectal cancer based on their embryonic tissue of origin. DATA SOURCES Articles were searched through PubMed and MEDLINE. STUDY SELECTION The terms "hereditary colorectal cancer," "syndromes of hereditary colorectal cancer," and "hereditary polyposis" were used to direct the search. RESULTS Primarily endoderm-derived syndromes were different from mesoderm-derived syndromes in their genetics, molecular biology, histology, and clinical course. LIMITATIONS There is considerable phenotypic and genotypic overlap between syndromes, even when considering embryonic tissue of origin. CONCLUSIONS Thinking about hereditary syndromes of colorectal cancer from the perspective of embryonic tissue of origin provides a fresh look at phenotype and genotype that opens new areas of exploration. UNA FORMA DIFERENTE DE PENSAR SOBRE LOS SNDROMES DEL CNCER COLORRECTAL HEREDITARIO ANTECEDENTES:El cáncer colorrectal hereditario es un campo cada vez más complejo donde los síndromes más comunes se ven aumentados por presentaciones genéticas más raras que contribuyen a la poliposis familiar y al cáncer colorrectal. Hacer frente a esta complejidad resulta difícil debido a la superposición fenotípica y genotípica entre los síndromes.OBJETIVO:En este artículo, describimos una nueva forma de pensar sobre los síndromes de cáncer colorrectal hereditario en función del origen de su tejido embrionario.FUENTES DE DATOS:Se realizaron búsquedas de artículos en Pubmed y Medline.SELECCIÓN DE ESTUDIOS:Se utilizaron los términos "cáncer colorrectal hereditario", "síndromes de cáncer colorrectal hereditario", "poliposis hereditaria" para dirigir la búsqueda.RESULTADOS:Principalmente los síndromes derivados del endodermo fueron diferentes a los síndromes derivados del mesodermo en su genética, biología molecular, histología y curso clínico.LIMITACIONES:Existe una superposición fenotípica y genotípica considerable entre los síndromes, incluso cuando se considera el tejido de origen embrionario.CONCLUSIÓN:Pensar en los síndromes hereditarios del cáncer colorrectal desde la perspectiva del tejido embrionario de origen proporciona una nueva mirada al fenotipo y al genotipo que abre nuevas áreas de exploración. (Traducción-Dr Osvaldo Gauto ).
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Affiliation(s)
- Mohammad Ali Abbass
- Department of Colorectal Surgery, Northwestern University, Chicago, Illinois
| | - Thomas Plesec
- Department of Pathology, Cleveland Clinic Foundation, Cleveland, Ohio
| | - James M Church
- Division of Colorectal Surgery, Columbia University Medical Center, New York, New York
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9
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Iskander D, Roy NBA, Payne E, Drasar E, Hennessy K, Harrington Y, Christodoulidou C, Karadimitris A, Batkin L, de la Fuente J. Diamond-Blackfan anemia in adults: In pursuit of a common approach for a rare disease. Blood Rev 2023; 61:101097. [PMID: 37263874 DOI: 10.1016/j.blre.2023.101097] [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: 11/22/2022] [Revised: 04/19/2023] [Accepted: 05/07/2023] [Indexed: 06/03/2023]
Abstract
Diamond-Blackfan anemia (DBA) is a rare bone marrow failure syndrome, usually caused by loss-of function variants in genes encoding ribosomal proteins. The hallmarks of DBA are anemia, congenital anomalies and cancer predisposition. Although DBA usually presents in childhood, the prevalence in later life is increasing due to an expanding repertoire of implicated genes, improvements in genetic diagnosis and increasing life expectancy. Adult patients uniquely suffer the manifestations of end-organ damage caused by the disease and its treatment, and transition to adulthood poses specific issues in disease management. To standardize and optimize care for this rare disease, in this review we provide updated guidance on the diagnosis and management of DBA, with a specific focus on older adolescents and adults. Recommendations are based upon published literature and our pooled clinical experience from three centres in the United Kingdom (U·K.). Uniquely we have also solicited and incorporated the views of affected families, represented by the independent patient organization, DBA U.K.
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Affiliation(s)
- Deena Iskander
- Centre for Haematology, Department of Immunology & Inflammation, Imperial College London, London W12 0NN, UK.
| | - Noémi B A Roy
- Oxford University Hospitals NHS Foundation Trust and University of Oxford, OX3 9DU, UK
| | - Elspeth Payne
- UCL Cancer Institute, Dept of Hematology, London WC1 E6BT, UK; Dept of Hematology, University College Hospital London, NW1 2BU, UK
| | - Emma Drasar
- Whittington Health NHS Trust and University College Hospital London, N19 5NF, UK
| | - Kelly Hennessy
- Department of Paediatrics, St. Mary's Hospital, Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - Yvonne Harrington
- Department of Paediatrics, St. Mary's Hospital, Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - Chrysi Christodoulidou
- Centre for Haematology, Department of Immunology & Inflammation, Imperial College London, London W12 0NN, UK
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Immunology & Inflammation, Imperial College London, London W12 0NN, UK
| | - Leisa Batkin
- DBA, UK 71-73 Main Street, Palterton, Chesterfield, S44 6UR, UK
| | - Josu de la Fuente
- Department of Paediatrics, St. Mary's Hospital, Imperial College Healthcare NHS Trust, London W2 1NY, UK.
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10
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Bonjoch L, Fernandez-Rozadilla C, Alvarez-Barona M, Lopez-Novo A, Herrera-Pariente C, Amigo J, Bujanda L, Remedios D, Dacal A, Cubiella J, Balaguer F, Fernández-Bañares F, Carracedo A, Jover R, Castellvi-Bel S, Ruiz-Ponte C. BMPR2 as a Novel Predisposition Gene for Hereditary Colorectal Polyposis. Gastroenterology 2023; 165:162-172.e5. [PMID: 36907526 DOI: 10.1053/j.gastro.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/27/2023] [Accepted: 03/05/2023] [Indexed: 03/14/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) is one of the most prevalent tumors worldwide, with incidence quickly increasing (particularly in the context of early-onset cases), despite important prevention efforts, mainly in the form of population-wide screening programs. Although many cases present a clear familial component, the current list of hereditary CRC genes leaves a considerable proportion of the cases unexplained. METHODS In this work, we used whole-exome sequencing approaches on 19 unrelated patients with unexplained colonic polyposis to identify candidate CRC predisposition genes. The candidate genes were then validated in an additional series of 365 patients. CRISPR-Cas9 models were used to validate BMPR2 as a potential candidate for CRC risk. RESULTS We found 8 individuals carrying 6 different variants in the BMPR2 gene (approximately 2% of our cohort of patients with unexplained colonic polyposis). CRISPR-Cas9 models of 3 of these variants showed that the p.(Asn442Thrfs∗32) truncating variant completely abrogated BMP pathway function in a similar way to the BMPR2 knockout. Missense variants p.(Asn565Ser), p.(Ser967Pro) had varying effects on cell proliferation levels, with the former impairing cell control inhibition via noncanonical pathways. CONCLUSIONS Collectively, these results support loss-of-function BMPR2 variants as candidates to be involved in CRC germline predisposition.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Ceres Fernandez-Rozadilla
- Instituto de Investigacion Sanitaria de Santiago, Grupo de Medicina Xenomica, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Miriam Alvarez-Barona
- Instituto de Investigacion Sanitaria de Santiago, Grupo de Medicina Xenomica, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Anael Lopez-Novo
- Instituto de Investigacion Sanitaria de Santiago, Grupo de Medicina Xenomica, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Cristina Herrera-Pariente
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Jorge Amigo
- Instituto de Investigacion Sanitaria de Santiago, Grupo de Medicina Xenomica, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Luis Bujanda
- Hospital Universitario de Donostia, Instituto Biodonostia, Universidad del Pais Vasco, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, San Sebastián, Spain
| | - David Remedios
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Ourense, Spain
| | - Andrés Dacal
- Department of Gastroenterology, Hospital Lucus Augusti, Lugo, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Joaquín Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Ourense, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Fernando Fernández-Bañares
- Hospital Universitari Mutua Terrassa, Barcelona, Spain; Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas, Ourense, Madrid, Spain
| | - Angel Carracedo
- Instituto de Investigacion Sanitaria de Santiago, Grupo de Medicina Xenomica, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Rodrigo Jover
- Digestive Medicine Department, Instituto de Investigación Biomédica, Hospital General Universitario de Alicante, Departamento de Medicina Clínica, Universidad Miguel Hernández, Alicante, Spain
| | - Sergi Castellvi-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomediques August Pi i Sunyer, Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas, Hospital Clinic, University of Barcelona, Barcelona, Spain.
| | - Clara Ruiz-Ponte
- Instituto de Investigacion Sanitaria de Santiago, Grupo de Medicina Xenomica, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain.
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11
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Garutti M, Foffano L, Mazzeo R, Michelotti A, Da Ros L, Viel A, Miolo G, Zambelli A, Puglisi F. Hereditary Cancer Syndromes: A Comprehensive Review with a Visual Tool. Genes (Basel) 2023; 14:1025. [PMID: 37239385 PMCID: PMC10218093 DOI: 10.3390/genes14051025] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Hereditary cancer syndromes account for nearly 10% of cancers even though they are often underdiagnosed. Finding a pathogenic gene variant could have dramatic implications in terms of pharmacologic treatments, tailored preventive programs, and familiar cascade testing. However, diagnosing a hereditary cancer syndrome could be challenging because of a lack of validated testing criteria or because of their suboptimal performance. In addition, many clinicians are not sufficiently well trained to identify and select patients that could benefit from a genetic test. Herein, we searched the available literature to comprehensively review and categorize hereditary cancer syndromes affecting adults with the aim of helping clinicians in their daily clinical practice through a visual tool.
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Affiliation(s)
- Mattia Garutti
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Lorenzo Foffano
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Roberta Mazzeo
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Anna Michelotti
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Lucia Da Ros
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Alessandra Viel
- Unit of Oncogenetics and Genomics CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Gianmaria Miolo
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
| | - Alberto Zambelli
- Medical Oncology and Hematology Unit, IRCCS—Humanitas Research Hospital, Rozzano, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20072 Milan, Italy
| | - Fabio Puglisi
- CRO Aviano, National Cancer Institute, IRCCS, 33081 Aviano, Italy
- Department of Medicine, University of Udine, 33100 Udine, Italy
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12
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Genetic Predisposition to Colorectal Cancer: How Many and Which Genes to Test? Int J Mol Sci 2023; 24:ijms24032137. [PMID: 36768460 PMCID: PMC9916931 DOI: 10.3390/ijms24032137] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
Colorectal cancer is one of the most common tumors, and genetic predisposition is one of the key risk factors in the development of this malignancy. Lynch syndrome and familial adenomatous polyposis are the best-known genetic diseases associated with hereditary colorectal cancer. However, some other genetic disorders confer an increased risk of colorectal cancer, such as Li-Fraumeni syndrome (TP53 gene), MUTYH-associated polyposis (MUTYH gene), Peutz-Jeghers syndrome (STK11 gene), Cowden syndrome (PTEN gene), and juvenile polyposis syndrome (BMPR1A and SMAD4 genes). Moreover, the recent advances in molecular techniques, in particular Next-Generation Sequencing, have led to the identification of many new genes involved in the predisposition to colorectal cancers, such as RPS20, POLE, POLD1, AXIN2, NTHL1, MSH3, RNF43 and GREM1. In this review, we summarized the past and more recent findings in the field of cancer predisposition genes, with insights into the role of the encoded proteins and into the associated genetic disorders. Furthermore, we discussed the possible clinical utility of genetic testing in terms of prevention protocols and therapeutic approaches.
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13
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Shen C, Chen Z, Zhang Y, Xu W, Peng R, Jiang J, Zuo W, Fan Y, Zheng B. Biochemical and clinical effects of RPS20 expression in renal clear cell carcinoma. Oncol Rep 2022; 49:22. [PMID: 36484407 PMCID: PMC9773015 DOI: 10.3892/or.2022.8459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC) remains one of the most lethal urinary tumors in East Asia despite great advancements in treatment strategies in recent years. Ribosomal protein S20 (RPS20) is considered a new oncogene; however, little information is available on its expression, regulation and biological function in patients with RCC. In the present study, 43 pairs of human RCC and neighboring normal renal tissues were examined for protein expression and immunohistochemistry examination of RPS20. Lentiviral transduction was also employed to create RPS20 knockdown cell lines for downstream cellular experiments. MTT, flow cytometry, wound healing, colony formation and invasion assays were used to examine how RPS20 affected kidney renal clear cell carcinoma (KIRC) cell behavior. Western blotting was used to detect cycle‑related proteins (CDK4 and cyclin D1), Wnt‑related proteins (N‑cadherin and E‑cadherin) and signaling proteins [phosphorylated (p)‑AKT and p‑ERK]. The functions of RPS20 in vivo were examined in 786‑O cells with RPS20 knockdown. RPS20 was significantly overexpressed in tumor tissues compared with its expression in the corresponding normal tissues. RPS20 expression was linked to tumor stage, differentiation grade, tumor size and lymph node metastasis, and it had an independent prognostic value in KIRC. Since RCC cell proliferation, migration and invasion were suppressed when RPS20 was knocked down, the formation of renal tumors in vivo was markedly slowed down. In RPS20 knockdown cell lines, CDK4, cyclin D1 and E‑cadherin were downregulated, while N‑cadherin expression was increased. RPS20 was also observed to be involved in controlling the activation of the ERK and mTOR signaling pathways. In summary, the present study showed that RPS20 increased cell proliferation in RCC by activating the AKT‑mTOR and ERK‑MAPK signaling pathways, which suggests that RPS20 may be a therapeutic and prognostic target for RCC.
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Affiliation(s)
- Cheng Shen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Zhan Chen
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yong Zhang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Wei Xu
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Rui Peng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Jie Jiang
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Medical Research Center, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Wenjing Zuo
- Department of Orthopedics, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yihui Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, Jiangsu 226001, P.R. China,Dr Yihui Fan, Department of Pathogenic Biology, School of Medicine, Nantong University, 20 Xisi Road, Chongchuan District, Nantong, Jiangsu 226001, P.R. China, E-mail:
| | - Bing Zheng
- Department of Urology, The Second Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China,Correspondence to: Dr Bing Zheng, Department of Urology, The Second Affiliated Hospital of Nantong University, 6 North Road, Haierxiang, Nantong, Jiangsu 226001, P.R. China, E-mail:
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14
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Styk J, Buglyó G, Pös O, Csók Á, Soltész B, Lukasz P, Repiská V, Nagy B, Szemes T. Extracellular Nucleic Acids in the Diagnosis and Progression of Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14153712. [PMID: 35954375 PMCID: PMC9367600 DOI: 10.3390/cancers14153712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Colorectal cancer (CRC) is a disease that usually shows no evident clinical symptoms in the early stages, often leading to late diagnosis. Over the past few years, a new approach based on liquid biopsy has gained far-reaching applications in less-invasive CRC diagnosis and management, allowing for the use of extracellular nucleic acids as promising biomarkers to detect CRC at an early stage and monitor disease recurrence. That is why an up-to-date review and discussion of in-depth liquid biopsy-derived DNA and RNA biomarkers is essential. We hereby offer an overview of known predisposing genetic factors for developing sporadic and hereditary CRC, and an extensive repertoire of available extracellular DNA/RNA molecules with their potential clinical applications and shortcomings. Our review may be of value to experts dealing with CRC at the molecular level as well as to clinical professionals aiming for a better understanding of state-of-the-art techniques in CRC diagnosis and management. Abstract Colorectal cancer (CRC) is the 3rd most common malignant neoplasm worldwide, with more than two million new cases diagnosed yearly. Despite increasing efforts in screening, many cases are still diagnosed at a late stage, when mortality is high. This paper briefly reviews known genetic causes of CRC (distinguishing between sporadic and familial forms) and discusses potential and confirmed nucleic acid biomarkers obtainable from liquid biopsies, classified by their molecular features, focusing on clinical relevance. We comment on advantageous aspects such as better patient compliance due to blood sampling being minimally invasive, the possibility to monitor mutation characteristics of sporadic and hereditary CRC in a disease showing genetic heterogeneity, and using up- or down-regulated circulating RNA markers to reveal metastasis or disease recurrence. Current difficulties and thoughts on some possible future directions are also discussed. We explore current evidence in the field pointing towards the introduction of personalized CRC management.
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Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Correspondence:
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Ondrej Pös
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
| | - Ádám Csók
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Beáta Soltész
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Peter Lukasz
- Department of Surgery, Transplantation and Gastroenterology, Semmelweis University, 1082 Budapest, Hungary;
| | - Vanda Repiská
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
- Medirex Group Academy, n.p.o., 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (G.B.); (Á.C.); (B.S.)
| | - Tomáš Szemes
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia; (O.P.); (B.N.); (T.S.)
- Geneton Ltd., 841 04 Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 05 Bratislava, Slovakia
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15
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Djursby M, Hansen TVO, Wadt KAW, Madsen MB, Berchtold LA, Lautrup CK, Markholt S, Jensen UB, Krogh LN, Lundsgaard M, Gerdes AM, Nilbert M, Therkildsen C. Clinical implications of genetic testing in familial intermediate and late-onset colorectal cancer. Hum Genet 2022; 141:1925-1933. [PMID: 35904628 DOI: 10.1007/s00439-022-02470-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
Abstract
The genetic background of familial, late-onset colorectal cancer (CRC) (i.e., onset > age 50 years) has not been studied as thoroughly as other subgroups of familial CRC, and the proportion of families with a germline genetic predisposition to CRC remains to be defined. To define the contribution of known or suggested CRC predisposition genes to familial late-onset CRC, we analyzed 32 well-established or candidate CRC predisposition genes in 75 families with late-onset CRC. We identified pathogenic or likely pathogenic variants in five patients in MSH6 (n = 1), MUTYH (monoallelic; n = 2) and NTHL1 (monoallelic; n = 2). In addition, we identified a number of variants of unknown significance in particular in the lower penetrant Lynch syndrome-associated mismatch repair (MMR) gene MSH6 (n = 6). In conclusion, screening using a comprehensive cancer gene panel in families with accumulation of late-onset CRC appears not to have a significant clinical value due to the low level of high-risk pathogenic variants detected. Our data suggest that only patients with abnormal MMR immunohistochemistry (IHC) or microsatellite instability (MSI) analyses, suggestive of Lynch syndrome, or a family history indicating another cancer predisposition syndrome should be prioritized for such genetic evaluations. Variants in MSH6 and MUTYH have previously been proposed to be involved in digenic or oligogenic hereditary predisposition to CRC. Accumulation of variants in MSH6 and monoallelic, pathogenic variants in MUTYH in our study indicates that digenic or oligogenic inheritance might be involved in late-onset CRC and warrants further studies of complex types of inheritance.
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Affiliation(s)
- Malene Djursby
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin A W Wadt
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Majbritt Busk Madsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lukas Adrian Berchtold
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Charlotte Kvist Lautrup
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Sara Markholt
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Malene Lundsgaard
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Anne Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mef Nilbert
- Clinical Research Centre, Copenhagen University Hospital, Amager and Hvidovre Hospital, Copenhagen, Denmark.,Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Christina Therkildsen
- Clinical Research Centre, Copenhagen University Hospital, Amager and Hvidovre Hospital, Copenhagen, Denmark.,HNPCC Register, Gastro Unit, Copenhagen University Hospital, Amager and Hvidovre Hospital, Copenhagen, Denmark
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16
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Elhamamsy AR, Metge BJ, Alsheikh HA, Shevde LA, Samant RS. Ribosome Biogenesis: A Central Player in Cancer Metastasis and Therapeutic Resistance. Cancer Res 2022; 82:2344-2353. [PMID: 35303060 PMCID: PMC9256764 DOI: 10.1158/0008-5472.can-21-4087] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/01/2022] [Accepted: 03/16/2022] [Indexed: 01/07/2023]
Abstract
Ribosomes are a complex ensemble of rRNA and ribosomal proteins that function as mRNA translation machines. Ribosome biogenesis is a multistep process that begins in the nucleolus and concludes in the cytoplasm. The process is tightly controlled by multiple checkpoint and surveillance pathways. Perturbations in these checkpoints and pathways can lead to hyperactivation of ribosome biogenesis. Emerging evidence suggests that cancer cells harbor a specialized class of ribosomes (onco-ribosomes) that facilitates the oncogenic translation program, modulates cellular functions, and promotes metabolic rewiring. Mutations in ribosomal proteins, rRNA processing, and ribosome assembly factors result in ribosomopathies that are associated with an increased risk of developing malignancies. Recent studies have linked mutations in ribosomal proteins and aberrant ribosomes with poor prognosis, highlighting ribosome-targeted therapy as a promising approach for treating patients with cancer. Here, we summarize various aspects of dysregulation of ribosome biogenesis and the impact of resultant onco-ribosomes on malignant tumor behavior, therapeutic resistance, and clinical outcome. Ribosome biogenesis is a promising therapeutic target, and understanding the important determinants of this process will allow for improved and perhaps selective therapeutic strategies to target ribosome biosynthesis.
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Affiliation(s)
- Amr R. Elhamamsy
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Brandon J. Metge
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Heba A. Alsheikh
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lalita A. Shevde
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rajeev S. Samant
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama.,O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham VA Medical Center, Birmingham, Alabama.,Corresponding Author: Rajeev S. Samant, The University of Alabama at Birmingham, WTI 320E, 1824 6th Avenue South, Birmingham, AL 35233. Phone: 205-975-6262; E-mail:
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17
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Azevedo ALKD, Gomig THB, Giner IS, Batista M, Marchini FK, Lima RS, de Andrade Urban C, Sebastião APM, Cavalli IJ, Ribeiro EMDSF. Comprehensive analysis of the large and small ribosomal proteins in breast cancer: Insights on proteomic and transcriptomic expression patterns, regulation, mutational landscape, and prognostic significance. Comput Biol Chem 2022; 100:107746. [DOI: 10.1016/j.compbiolchem.2022.107746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022]
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18
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Changes in the Transcriptome Caused by Mutations in the Ribosomal Protein uS10 Associated with a Predisposition to Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23116174. [PMID: 35682850 PMCID: PMC9181716 DOI: 10.3390/ijms23116174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
A number of mutations in the RPS20 gene encoding the ribosomal protein uS10 have been found to be associated with a predisposition to hereditary non-polyposis colorectal carcinoma (CRC). We transfected HEK293T cells with constructs carrying the uS10 minigene with mutations identical to those mentioned above and examined the effects of the produced proteins on the cellular transcriptome. We showed that uS10 with mutations p.V50SfsX23 or p.L61EfsX11 cannot be incorporated into 40S ribosomal subunits, while the protein with the missense mutation p.V54L functionally replaces the respective endogenous protein in the 40S subunit assembly and the translation process. The comparison of RNA-seq data obtained from cells producing aberrant forms of uS10 with data for those producing the wild-type protein revealed overlapping sets of upregulated and downregulated differently expressed genes (DEGs) related to several pathways. Among the limited number of upregulated DEGs, there were genes directly associated with the progression of CRC, e.g., PPM1D and PIGN. Our findings indicate that the accumulation of the mutant forms of uS10 triggers a cascade of cellular events, similar to that which is triggered when the cell responds to a large number of erroneous proteins, suggesting that this may increase the risk of cancer.
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Skopelitou D, Srivastava A, Miao B, Kumar A, Dymerska D, Paramasivam N, Schlesner M, Lubinski J, Hemminki K, Försti A, Reddy Bandapalli O. Whole exome sequencing identifies novel germline variants of SLC15A4 gene as potentially cancer predisposing in familial colorectal cancer. Mol Genet Genomics 2022; 297:965-979. [PMID: 35562597 PMCID: PMC9250485 DOI: 10.1007/s00438-022-01896-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 04/02/2022] [Indexed: 11/25/2022]
Abstract
About 15% of colorectal cancer (CRC) patients have first-degree relatives affected by the same malignancy. However, for most families the cause of familial aggregation of CRC is unknown. To identify novel high-to-moderate-penetrance germline variants underlying CRC susceptibility, we performed whole exome sequencing (WES) on four CRC cases and two unaffected members of a Polish family without any mutation in known CRC predisposition genes. After WES, we used our in-house developed Familial Cancer Variant Prioritization Pipeline and identified two novel variants in the solute carrier family 15 member 4 (SLC15A4) gene. The heterozygous missense variant, p. Y444C, was predicted to affect the phylogenetically conserved PTR2/POT domain and to have a deleterious effect on the function of the encoded peptide/histidine transporter. The other variant was located in the upstream region of the same gene (GRCh37.p13, 12_129308531_C_T; 43 bp upstream of transcription start site, ENST00000266771.5) and it was annotated to affect the promoter region of SLC15A4 as well as binding sites of 17 different transcription factors. Our findings of two distinct variants in the same gene may indicate a synergistic up-regulation of SLC15A4 as the underlying genetic cause and implicate this gene for the first time in genetic inheritance of familial CRC.
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Affiliation(s)
- Diamanto Skopelitou
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aayushi Srivastava
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Beiping Miao
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abhishek Kumar
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104 India
| | - Dagmara Dymerska
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Kari Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Asta Försti
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Obul Reddy Bandapalli
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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21
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Surya A, Sarinay-Cenik E. Cell autonomous and non-autonomous consequences of deviations in translation machinery on organism growth and the connecting signalling pathways. Open Biol 2022; 12:210308. [PMID: 35472285 PMCID: PMC9042575 DOI: 10.1098/rsob.210308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/31/2022] [Indexed: 01/09/2023] Open
Abstract
Translation machinery is responsible for the production of cellular proteins; thus, cells devote the majority of their resources to ribosome biogenesis and protein synthesis. Single-copy loss of function in the translation machinery components results in rare ribosomopathy disorders, such as Diamond-Blackfan anaemia in humans and similar developmental defects in various model organisms. Somatic copy number alterations of translation machinery components are also observed in specific tumours. The organism-wide response to haploinsufficient loss-of-function mutations in ribosomal proteins or translation machinery components is complex: variations in translation machinery lead to reduced ribosome biogenesis, protein translation and altered protein homeostasis and cellular signalling pathways. Cells are affected both autonomously and non-autonomously by changes in translation machinery or ribosome biogenesis through cell-cell interactions and secreted hormones. We first briefly introduce the model organisms where mutants or knockdowns of protein synthesis and ribosome biogenesis are characterized. Next, we specifically describe observations in Caenorhabditis elegans and Drosophila melanogaster, where insufficient protein synthesis in a subset of cells triggers cell non-autonomous growth or apoptosis responses that affect nearby cells and tissues. We then cover the characterized signalling pathways that interact with ribosome biogenesis/protein synthesis machinery with an emphasis on their respective functions during organism development.
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Affiliation(s)
- Agustian Surya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Elif Sarinay-Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
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van Dooijeweert B, Kia SK, Dahl N, Fenneteau O, Leguit R, Nieuwenhuis E, van Solinge W, van Wijk R, Da Costa L, Bartels M. GATA-1 Defects in Diamond-Blackfan Anemia: Phenotypic Characterization Points to a Specific Subset of Disease. Genes (Basel) 2022; 13:genes13030447. [PMID: 35328001 PMCID: PMC8949872 DOI: 10.3390/genes13030447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/13/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
Diamond−Blackfan anemia (DBA) is one of the inherited bone marrow failure syndromes marked by erythroid hypoplasia. Underlying variants in ribosomal protein (RP) genes account for 80% of cases, thereby classifying DBA as a ribosomopathy. In addition to RP genes, extremely rare variants in non-RP genes, including GATA1, the master transcription factor in erythropoiesis, have been reported in recent years in patients with a DBA-like phenotype. Subsequently, a pivotal role for GATA-1 in DBA pathophysiology was established by studies showing the impaired translation of GATA1 mRNA downstream of the RP haploinsufficiency. Here, we report on a patient from the Dutch DBA registry, in which we found a novel hemizygous variant in GATA1 (c.220+2T>C), and an Iranian patient with a previously reported variant in the initiation codon of GATA1 (c.2T>C). Although clinical features were concordant with DBA, the bone marrow morphology in both patients was not typical for DBA, showing moderate erythropoietic activity with signs of dyserythropoiesis and dysmegakaryopoiesis. This motivated us to re-evaluate the clinical characteristics of previously reported cases, which resulted in the comprehensive characterization of 18 patients with an inherited GATA-1 defect in exon 2 that is presented in this case-series. In addition, we re-investigated the bone marrow aspirate of one of the previously published cases. Altogether, our observations suggest that DBA caused by GATA1 defects is characterized by distinct phenotypic characteristics, including dyserythropoiesis and dysmegakaryopoiesis, and therefore represents a distinct phenotype within the DBA disease spectrum, which might need specific clinical management.
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Affiliation(s)
- Birgit van Dooijeweert
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
- Department of Pediatric Hematology, van Creveldkliniek, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Sima Kheradmand Kia
- Laboratory for Red Blood Cell Diagnostics, Sanquin, 1006 AD Amsterdam, The Netherlands;
- Peyvand Lab Complex, Shiraz 7363871347, Iran
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Children’s Hospital, 751 85 Uppsala, Sweden;
| | - Odile Fenneteau
- AP-HP, Service d’Hématologie Biologique, Hôpital Robert Debré, University of Paris Cité, Hematim EA 4666, UPJV, F-75019 Paris, France; (O.F.); (L.D.C.)
| | - Roos Leguit
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Edward Nieuwenhuis
- Department of Pediatrics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands;
| | - Wouter van Solinge
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
| | - Richard van Wijk
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
| | - Lydie Da Costa
- AP-HP, Service d’Hématologie Biologique, Hôpital Robert Debré, University of Paris Cité, Hematim EA 4666, UPJV, F-75019 Paris, France; (O.F.); (L.D.C.)
| | - Marije Bartels
- Department of Pediatric Hematology, van Creveldkliniek, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Pediatrics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands;
- Correspondence:
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23
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Garcia FADO, de Andrade ES, de Campos Reis Galvão H, da Silva Sábato C, Campacci N, de Paula AE, Evangelista AF, Santana IVV, Melendez ME, Reis RM, Palmero EI. New insights on familial colorectal cancer type X syndrome. Sci Rep 2022; 12:2846. [PMID: 35181726 PMCID: PMC8857274 DOI: 10.1038/s41598-022-06782-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Familial colorectal cancer type X (FCCTX) is a heterogeneous colorectal cancer predisposition syndrome that, although displays a cancer pattern similar to Lynch syndrome, is mismatch repair proficient and does not exhibit microsatellite instability. Besides, its genetic etiology remains to be elucidated. In this study we performed germline exome sequencing of 39 cancer-affected patients from 34 families at risk for FCCTX. Variant classification followed the American College of Medical Genetics and Genomics (ACMG) guidelines. Pathogenic/likely pathogenic variants were identified in 17.65% of the families. Rare and potentially pathogenic alterations were identified in known hereditary cancer genes (CHEK2), in putative FCCTX candidate genes (OGG1 and FAN1) and in other cancer-related genes such as ATR, ASXL1, PARK2, SLX4 and TREX1. This study provides novel important clues that can contribute to the understanding of FCCTX genetic basis.
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Affiliation(s)
- Felipe Antonio de Oliveira Garcia
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | - Edilene Santos de Andrade
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | | | - Natália Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil. .,Department of Genetics, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
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Nonmalignant Features Associated with Inherited Colorectal Cancer Syndromes-Clues for Diagnosis. Cancers (Basel) 2022; 14:cancers14030628. [PMID: 35158896 PMCID: PMC8833640 DOI: 10.3390/cancers14030628] [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: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/23/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Familiarity with nonmalignant features and comorbidities of cancer predisposition syndromes may raise awareness and assist clinicians in the diagnosis and interpretation of molecular test results. Genetic predisposition to colorectal cancer (CRC) should be suspected mainly in young patients, in patients with significant family histories, multiple polyps, mismatch repair-deficient tumors, and in association with malignant or nonmalignant comorbidities. The aim of this review is to describe the main nonmalignant comorbidities associated with selected CRC predisposition syndromes that may serve as valuable diagnostic clues for clinicians and genetic professionals. Abstract Genetic diagnosis of affected individuals and predictive testing of their at-risk relatives, combined with intensive cancer surveillance, has an enormous cancer-preventive potential in these families. A lack of awareness may be part of the reason why the underlying germline cause remains unexplained in a large proportion of patients with CRC. Various extracolonic features, mainly dermatologic, ophthalmic, dental, endocrine, vascular, and reproductive manifestations occur in many of the cancer predisposition syndromes associated with CRC and polyposis. Some are mediated via the WNT, TGF-β, or mTOR pathways. However the pathogenesis of most features is still obscure. Here we review the extracolonic features of the main syndromes, the existing information regarding their prevalence, and the pathways involved in their pathogenesis. This knowledge could be useful for care managers from different professional disciplines, and used to raise awareness, enable diagnosis, and assist in the process of genetic testing and interpretation.
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Miao B, Skopelitou D, Srivastava A, Giangiobbe S, Dymerska D, Paramasivam N, Kumar A, Kuświk M, Kluźniak W, Paszkowska-Szczur K, Schlesner M, Lubinski J, Hemminki K, Försti A, Bandapalli OR. Whole-Exome Sequencing Identifies a Novel Germline Variant in PTK7 Gene in Familial Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23031295. [PMID: 35163215 PMCID: PMC8836109 DOI: 10.3390/ijms23031295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/02/2022] [Accepted: 01/18/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequently diagnosed malignancy worldwide. Only 5% of all CRC cases are due to germline mutations in known predisposition genes, and the remaining genetic burden still has to be discovered. In this study, we performed whole-exome sequencing on six members of a Polish family diagnosed with CRC and identified a novel germline variant in the protein tyrosine kinase 7 (inactive) gene (PTK7, ENST00000230419, V354M). Targeted screening of the variant in 1705 familial CRC cases and 1674 healthy elderly individuals identified the variant in an additional familial CRC case. Introduction of this variant in HT-29 cells resulted in increased cell proliferation, migration, and invasion; it also caused down-regulation of CREB, p21 and p53 mRNA and protein levels, and increased AKT phosphorylation. These changes indicated inhibition of apoptosis pathways and activation of AKT signaling. Our study confirmed the oncogenic function of PTK7 and supported its role in genetic predisposition of familial CRC.
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Affiliation(s)
- Beiping Miao
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Diamanto Skopelitou
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Aayushi Srivastava
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Sara Giangiobbe
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
| | - Dagmara Dymerska
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (D.D.); (M.K.); (W.K.); (K.P.-S.); (J.L.)
| | - Nagarajan Paramasivam
- Computational Oncology, Molecular Diagnostics Program, National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany;
| | - Abhishek Kumar
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Institute of Bioinformatics, International Technology Park, Bengaluru 560066, India
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Magdalena Kuświk
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (D.D.); (M.K.); (W.K.); (K.P.-S.); (J.L.)
| | - Wojciech Kluźniak
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (D.D.); (M.K.); (W.K.); (K.P.-S.); (J.L.)
| | - Katarzyna Paszkowska-Szczur
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (D.D.); (M.K.); (W.K.); (K.P.-S.); (J.L.)
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, 71252 Szczecin, Poland; (D.D.); (M.K.); (W.K.); (K.P.-S.); (J.L.)
| | - Kari Hemminki
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
- Correspondence: (K.H.); (O.R.B.); Tel.: +49-6221-421809 (O.R.B.); Fax: +49-6221-424639 (O.R.B.)
| | - Asta Försti
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Obul Reddy Bandapalli
- Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (B.M.); (D.S.); (A.S.); (S.G.); (A.K.); (A.F.)
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence: (K.H.); (O.R.B.); Tel.: +49-6221-421809 (O.R.B.); Fax: +49-6221-424639 (O.R.B.)
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Li R, Pu J, Cai Y, Zheng K, Qin X, Zhang Z, Xu X. Proteomic characteristics of PM 2.5-induced differentially expressed proteins in k-ras-silenced HBE cells. Toxicol Mech Methods 2022; 32:431-438. [PMID: 35014587 DOI: 10.1080/15376516.2022.2028328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The human bronchial epithelial cells (HBE) and K-ras-silenced HBE cells were treated with fine particulate matter (PM2.5) samples from Taiyuan for 24 h. To screen the proteomic characteristics of PM2.5-induced differentially expressed proteins (DEPs), the Q Exactive mass spectrometer was used. Gene ontology (GO) analysis, Kyoto encyclopedia of genes and genomes (KEGG) analysis, functional prediction, protein-protein interaction (PPI) network analysis, and visualization of differential protein interactions were performed. 251 DEPs in K-ras silenced cells and 535 DEPs in normal HBE cells were identified, respectively. KEGG analysis showed that the differentially expressed proteins of PM2.5-treated cells were related to the biosynthesis of ribosomes, antibiotics, and amino acids. On the other hand, K-ras silenced cells were related to metabolic pathways, RNA transport, and DNA replication. Through the construction of a PPI network, the top 10 hub proteins were screened from the two cell groups, among which MRPL13, RPS20, and EIF1AX were of great significance. Our results indicated that the K-ras gene plays an important role in PM2.5-induced DEPs, and the findings provide a scientific basis for the further study of PM2.5 toxic mechanisms and biomarkers.
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Affiliation(s)
- Runbing Li
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Jiening Pu
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Ying Cai
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Kai Zheng
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Xiaoyun Qin
- Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
| | - Zhaohui Zhang
- School of Public Health, University of South China, Hengyang, China
| | - Xinyun Xu
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Institute of environment and health, Shenzhen, China
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Lipton JM, Molmenti CLS, Desai P, Lipton A, Ellis SR, Vlachos A. Early Onset Colorectal Cancer: An Emerging Cancer Risk in Patients with Diamond Blackfan Anemia. Genes (Basel) 2021; 13:56. [PMID: 35052397 PMCID: PMC8774389 DOI: 10.3390/genes13010056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022] Open
Abstract
Diamond Blackfan anemia (DBA) is a rare inherited bone marrow failure syndrome, the founding member of a class of disorders known as ribosomopathies. Most cases result from loss of function mutations or deletions in 1 of 23 genes encoding either a small or large subunit-associated ribosomal protein (RP), resulting in RP haploinsufficiency. DBA is characterized by red cell hypoplasia or aplasia, poor linear growth and congenital anomalies. Small case series and case reports demonstrate DBA to be a cancer predisposition syndrome. Recent analyses from the Diamond Blackfan Anemia Registry of North America (DBAR) have quantified the cancer risk in DBA. These studies reveal the most prevalent solid tumor, presenting in young adults and in children and adolescents, to be colorectal cancer (CRC) and osteogenic sarcoma, respectively. Of concern is that these cancers are typically detected at an advanced stage in patients who, because of their constitutional bone marrow failure, may not tolerate full-dose chemotherapy. Thus, the inability to provide optimal therapy contributes to poor outcomes. CRC screening in individuals over the age of 50 years, and now 45 years, has led to early detection and significant improvements in outcomes for non-DBA patients with CRC. These screening and surveillance strategies have been adapted to detect familial early onset CRC. With the recognition of DBA as a moderately penetrant cancer risk syndrome a rational screening and surveillance strategy will be implemented. The downstream molecular events, resulting from RP haploinsufficiency and leading to cancer, are the subject of significant scientific inquiry.
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Affiliation(s)
- Jeffrey M. Lipton
- Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, New Hyde Park, NY 11040, USA; (P.D.); (A.V.)
- Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA; (C.L.S.M.); (A.L.)
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Christine L. S. Molmenti
- Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA; (C.L.S.M.); (A.L.)
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Division of Epidemiology, Department of Occupational Medicine, Epidemiology and Prevention, Great Neck, NY 11021, USA
| | - Pooja Desai
- Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, New Hyde Park, NY 11040, USA; (P.D.); (A.V.)
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Alexander Lipton
- Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA; (C.L.S.M.); (A.L.)
| | - Steven R. Ellis
- Department of Biochemistry and Molecular Biology, University of Louisville, Louisville, KY 40202, USA;
| | - Adrianna Vlachos
- Division of Hematology/Oncology and Cellular Therapy, Cohen Children’s Medical Center, New Hyde Park, NY 11040, USA; (P.D.); (A.V.)
- Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA; (C.L.S.M.); (A.L.)
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
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Deregulation of ribosomal proteins in human cancers. Biosci Rep 2021; 41:230380. [PMID: 34873618 PMCID: PMC8685657 DOI: 10.1042/bsr20211577] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ribosome, the site for protein synthesis, is composed of ribosomal RNAs (rRNAs) and ribosomal proteins (RPs). The latter have been shown to have many ribosomal and extraribosomal functions. RPs are implicated in a variety of pathological processes, especially tumorigenesis and cell transformation. In this review, we will focus on the recent advances that shed light on the effects of RPs deregulation in different types of cancer and their roles in regulating the tumor cell fate.
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Rafter P, Gormley IC, Purfield D, Parnell AC, Naderi S, Berry DP. Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle. BMC Genomics 2021; 22:757. [PMID: 34688258 PMCID: PMC8542340 DOI: 10.1186/s12864-021-08075-2] [Citation(s) in RCA: 3] [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: 04/23/2021] [Accepted: 10/07/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process. RESULTS A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit. CONCLUSIONS The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.
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Affiliation(s)
- Pierce Rafter
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Isobel Claire Gormley
- School of Mathematics and Statistics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Deirdre Purfield
- Department of Biological Sciences, Munster Technological University Institute, Cork, Bishopstown, Ireland
| | - Andrew C Parnell
- Hamilton Institute, Insight Centre for Data Analytics, Maynooth University, Kildare, Ireland
| | - Saeid Naderi
- Irish Cattle Breeding Federation, Cork, Bandon, Ireland
| | - Donagh P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Cork, Fermoy, Ireland.
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Olkinuora AP, Peltomäki PT, Aaltonen LA, Rajamäki K. From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet 2021; 30:R206-R224. [PMID: 34329396 PMCID: PMC8490010 DOI: 10.1093/hmg/ddab208] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/12/2022] Open
Abstract
Hereditary colorectal cancer (CRC) syndromes attributable to high penetrance mutations represent 9-26% of young-onset CRC cases. The clinical significance of many of these mutations is understood well enough to be used in diagnostics and as an aid in patient care. However, despite the advances made in the field, a significant proportion of familial and early-onset cases remains molecularly uncharacterized and extensive work is still needed to fully understand the genetic nature of CRC susceptibility. With the emergence of next-generation sequencing and associated methods, several predisposition loci have been unraveled, but validation is incomplete. Individuals with cancer-predisposing mutations are currently enrolled in life-long surveillance, but with the development of new treatments, such as cancer vaccinations, this might change in the not so distant future for at least some individuals. For individuals without a known cause for their disease susceptibility, prevention and therapy options are less precise. Herein, we review the progress achieved in the last three decades with a focus on how CRC predisposition genes were discovered. Furthermore, we discuss the clinical implications of these discoveries and anticipate what to expect in the next decade.
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Affiliation(s)
- Alisa P Olkinuora
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Päivi T Peltomäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
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Xu P, Sun D, Gao Y, Jiang Y, Zhong M, Zhao G, Chen J, Wang Z, Liu Q, Hong J, Chen H, Chen YX, Fang JY. Germline mutations in a DNA repair pathway are associated with familial colorectal cancer. JCI Insight 2021; 6:148931. [PMID: 34549727 PMCID: PMC8492347 DOI: 10.1172/jci.insight.148931] [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: 02/22/2021] [Accepted: 07/30/2021] [Indexed: 12/18/2022] Open
Abstract
Aiming to identify rare high-penetrance mutations in new genes for the underlying predisposition in familial colorectal cancer (CRC), we performed whole-exome sequencing in 24 familial CRCs. Mutations in genes that regulate DNA repair (RMI1, PALB2, FANCI) were identified that were related to the Fanconi anemia DNA repair pathway. In one pedigree, we found a nonsense mutation in CHEK2. CHEK2 played an essential role in cell cycle and DNA damage repair. Somatic mutation analysis in CHEK2 variant carriers showed mutations in TP53, APC, and FBXW7. Loss of heterozygosity was found in carcinoma of CHEK2 variant carrier, and IHC showed loss of Chk2 expression in cancer tissue. We identified a second variant in CHEK2 in 126 sporadic CRCs. A KO cellular model for CHEK2 (CHEK2KO) was generated by CRISPR/Cas9. Functional experiments demonstrated that CHEK2KO cells showed defective cell cycle arrest and apoptosis, as well as reduced p53 phosphorylation, upon DNA damage. We associated germline mutations in genes that regulate the DNA repair pathway with the development of CRC. We identified CHEK2 as a regulator of DNA damage response and perhaps as a gene involved in CRC germline predisposition. These findings link CRC predisposition to the DNA repair pathway, supporting the connection between genome integrity and cancer risk.
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Affiliation(s)
- Pingping Xu
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Danfeng Sun
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Yaqi Gao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Yi Jiang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | | | | | | | | | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Hong
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Haoyan Chen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Ying-Xuan Chen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease
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Tapak L, Afshar S, Afrasiabi M, Ghasemi MK, Alirezaei P. Application of Genetic Algorithm-Based Support Vector Machine in Identification of Gene Expression Signatures for Psoriasis Classification: A Hybrid Model. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5520710. [PMID: 34540995 PMCID: PMC8443357 DOI: 10.1155/2021/5520710] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Psoriasis is a chronic autoimmune disease impairing significantly the quality of life of the patient. The diagnosis of the disease is done via a visual inspection of the lesional skin by dermatologists. Classification of psoriasis using gene expression is an important issue for the early and effective treatment of the disease. Therefore, gene expression data and selection of suitable gene signatures are effective sources of information. METHODS We aimed to develop a hybrid classifier for the diagnosis of psoriasis based on two machine learning models of the genetic algorithm and support vector machine (SVM). The method also conducts gene signature selection. A publically available gene expression dataset was used to test the model. RESULTS A number of 181 probe sets were selected among the original 54,675 probes using the hybrid model with a prediction accuracy of 100% over the test set. A number of 10 hub genes were identified using the protein-protein interaction network. Nine out of 10 identified genes were found in significant modules. CONCLUSIONS The results showed that the genetic algorithm improved the SVM classifier performance significantly implying the ability of the proposed model in terms of detecting relevant gene expression signatures as the best features.
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Affiliation(s)
- Leili Tapak
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
- Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Mohammad Kazem Ghasemi
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Pedram Alirezaei
- Department of Dermatology, Psoriasis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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A Transcriptomic Approach Reveals Selective Ribosomal Remodelling in the Tumour Versus the Stromal Compartment of Metastatic Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13164188. [PMID: 34439343 PMCID: PMC8394399 DOI: 10.3390/cancers13164188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary In this study, we analyzed a cohort of six colorectal cancer patients harboring KRAS mutations and with wild-type BRAF from a transcriptional perspective, with the aim of elucidating the role of the stromal cells in tumor progression. Specifically, paraffin-embedded specimens were subjected to microdissection and hybridized on Agilent-026652 microarrays to compare the gene expression of tumor samples composed of neoplastic epithelial samples against the neighboring stromal tissue. A paired rank-product test led to the detection of 193 differentially expressed genes. Subsequent functional enrichment analysis pointed to extracellular matrix constituents, angiogenesis, and cell migration as the main biological processes enhanced in stromata, while the tumor compartment was characterized by an overexpression of many ribosomal protein genes. A further gene set enrichment analysis against a comprehensive ribosomal protein gene set finally revealed that only cytosolic ribosomes (80S) were affected by such upregulation, while mitochondrial ribosomes were virtually unaltered. Abstract Because of its high incidence and poor prognosis, colorectal cancer (CRC) represents an important health issue in several countries. As with other carcinomas, the so-called tumour microenvironment (TME) has been shown to play key roles in CRC progression and related therapeutical outcomes, even though a deeper understanding of the underlying molecular mechanisms is needed to devise new treatment strategies. For some years now, omics technologies and consolidated bioinformatics pipelines have allowed scientists to access large amounts of biologically relevant information, even when starting from small tissue samples; thus, in order to shed new light upon the role of the TME in CRC, we compared the gene expression profiles of 6 independent tumour tissues (all progressed towards metastatic disease) to the expression profile of the surrounding stromata. To do this, paraffin-embedded whole tissues were first microdissected to obtain samples enriched with tumour and stromal cells, respectively. Afterwards, RNA was extracted and analysed using a microarray-based approach. A thorough bioinformatics analysis was then carried out to identify transcripts differentially expressed between the two groups and possibly enriched functional terms. Overall, 193 genes were found to be significantly downregulated in tumours compared to the paired stromata. The functional analysis of the downregulated gene list revealed three principal macro areas of interest: the extracellular matrix, cell migration, and angiogenesis. Conversely, among the upregulated genes, the main alterations detected by the functional annotation were related to the ribosomal proteins (rProteins) of both the large (60S) and small (40S) subunits of the cytosolic ribosomes. Subsequent gene set enrichment analysis (GSEA) confirmed the massive overexpression of most cytosolic—but not mitochondrial—ribosome rProteins.
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Mur P, Bonifaci N, Díez-Villanueva A, Munté E, Alonso MH, Obón-Santacana M, Aiza G, Navarro M, Piñol V, Brunet J, Tomlinson I, Capellá G, Moreno V, Valle L. Non-Lynch Familial and Early-Onset Colorectal Cancer Explained by Accumulation of Low-Risk Genetic Variants. Cancers (Basel) 2021; 13:3857. [PMID: 34359758 PMCID: PMC8345397 DOI: 10.3390/cancers13153857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 01/07/2023] Open
Abstract
A large proportion of familial and/or early-onset cancer patients do not carry pathogenic variants in known cancer predisposing genes. We aimed to assess the contribution of previously validated low-risk colorectal cancer (CRC) alleles to familial/early-onset CRC (fCRC) and to serrated polyposis. We estimated the association of CRC with a 92-variant-based weighted polygenic risk score (wPRS) using 417 fCRC patients, 80 serrated polyposis patients, 1077 hospital-based incident CRC patients, and 1642 controls. The mean wPRS was significantly higher in fCRC than in controls or sporadic CRC patients. fCRC patients in the highest (20th) wPRS quantile were at four-fold greater CRC risk than those in the middle quantile (10th). Compared to low-wPRS fCRC, a higher number of high-wPRS fCRC patients had developed multiple primary CRCs, had CRC family history, and were diagnosed at age ≥50. No association with wPRS was observed for serrated polyposis. In conclusion, a relevant proportion of mismatch repair (MMR)-proficient fCRC cases might be explained by the accumulation of low-risk CRC alleles. Validation in independent cohorts and development of predictive models that include polygenic risk score (PRS) data and other CRC predisposing factors will determine the implementation of PRS into genetic testing and counselling in familial and early-onset CRC.
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Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Nuria Bonifaci
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
| | - Anna Díez-Villanueva
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Elisabet Munté
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
| | - Maria Henar Alonso
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Mireia Obón-Santacana
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Virginia Piñol
- Gastroenterology Unit, Hospital Universitario de Girona Dr Josep Trueta, 17007 Girona, Spain;
- School of Medicine, University of Girona, 17071 Girona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- School of Medicine, University of Girona, 17071 Girona, Spain
- Catalan Institute of Oncology, IDIBGi, 17007 Girona, Spain
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK;
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Victor Moreno
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
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36
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Hinoi T. Cancer Genomic Profiling in Colorectal Cancer: Current Challenges in Subtyping Colorectal Cancers Based on Somatic and Germline Variants. J Anus Rectum Colon 2021; 5:213-228. [PMID: 34395933 PMCID: PMC8321592 DOI: 10.23922/jarc.2021-009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/17/2021] [Indexed: 11/30/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease caused by the accumulation of multistep genetic alterations under the influence of genomic instability. Different backgrounds of genomic instability, such as chromosomal instability, microsatellite instability, hypermutated-single nucleotide variants, and genome stable-induced transformation in the colonic epithelium, can result in adenomas, adenocarcinomas, and metastatic tumors. Characterization of molecular subtypes and establishment of treatment policies based on each subtype will lead to better treatment outcomes and an improved selection of molecularly targeted agents. In Japan, cancer precision medicine has been introduced in the National Health Insurance program through the addition of the cancer genomic profiling (CGP) examination. It has also become possible to access a large amount of genomic information, including information on pathogenic somatic and germline variants, incomparable to conventional diagnostic tests. This information enables us to apply research data to clinical decision-making, benefiting patients and their healthy family members. In this article, we discuss the important molecules and signaling pathways presumed to be the driver genes of CRC progression and the signal transduction system in which they are involved. Molecular subtypes of CRC based on CGP examinations and gene expression profiles have been established in The Cancer Genome Atlas Network with the advent of next-generation sequencing technology. We will also discuss the recommended management of secondary/germline findings, pathogenic germline variants, and presumed germline pathogenic variants obtained from CGP examination and review the current challenges to better understand these data in a new era of cancer genomic medicine.
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Affiliation(s)
- Takao Hinoi
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Hiroshima, Japan
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37
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Sugai T, Osakabe M, Habano W, Tanaka Y, Eizuka M, Sugimoto R, Yanagawa N, Matsumoto T, Suzuki H. A genome-wide analysis of the molecular alterations occurring in the adenomatous and carcinomatous components of the same tumor based on the adenoma-carcinoma sequence. Pathol Int 2021; 71:582-593. [PMID: 34263942 PMCID: PMC8518074 DOI: 10.1111/pin.13129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022]
Abstract
Identification of molecular alterations occurring in the adenomatous and carcinomatous components within the same tumor would greatly enhance understanding of the neoplastic progression of colorectal cancer. We examined somatic copy number alterations (SCNAs) and mRNA expression at the corresponding loci involved in the adenoma–carcinoma sequence in the isolated adenomatous and cancer glands of the same tumor in 15 cases of microsatellite‐stable “carcinoma in adenoma,” using genome‐wide SNP and global gene expression arrays. Multiple copy‐neutral loss of heterozygosity events were detected at 4q13.2, 15q15.1, and 14q24.3 in the adenomatous component and at 4q13.2, 15q15.1, and 14q24.3 in the carcinomatous component. There were significant differences in the copy number (CN) gain frequencies at 20q11.21–q13.33, 8q13.3, 8p23.1, and 8q21.2–q22.2 between the adenomatous and carcinomatous components. Finally, we found a high frequency of five genotypes involving CN gain with upregulated expression of the corresponding gene (RPS21, MIR3654, RSP20, SNORD54, or ASPH) in the carcinomatous component, whereas none of these genotypes were detected in the adenomatous component. This finding is interesting in that CN gain with upregulated gene expression may enhance gene function and play a crucial role in the progression of an adenoma into a carcinomatous lesion.
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Affiliation(s)
- Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Wataru Habano
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Yoshihito Tanaka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Makoto Eizuka
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Ryo Sugimoto
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Naoki Yanagawa
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, Shiwagun'yahabachou, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, Shiwagun'yahabachou, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, School of Medicine, Sapporo Medical University, Cyuuouku, Sapporo, Japan
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38
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Lam KK, Thean LF, Cheah PY. Advances in colorectal cancer genomics and transcriptomics drive early detection and prevention. Int J Biochem Cell Biol 2021; 137:106032. [PMID: 34182137 DOI: 10.1016/j.biocel.2021.106032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/20/2022]
Abstract
Colorectal carcinoma (CRC) is a high incidence cancer and leading cause of cancer mortality worldwide. The advances in genomics and transcriptomics in the past decades have improved the detection and prevention of CRC in familial CRC syndromes. Nevertheless, the ultimate goal of personalized medicine for sporadic CRC is still not within reach due no less to the difficulty in integrating population disparity and clinical data to combat what essentially is a very heterogenous disease. This minireview highlights the achievement of the past decades and present possible direction in the hope of early detection and metastasis prevention for reducing CRC-associated morbidity and mortality.
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Affiliation(s)
- Kuen Kuen Lam
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Lai Fun Thean
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore
| | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore.
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39
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Thompson BA, Snow AK, Koptiuch C, Kohlmann WK, Mooney R, Johnson S, Huff CD, Yu Y, Teerlink CC, Feng BJ, Neklason DW, Cannon-Albright LA, Tavtigian SV. A novel ribosomal protein S20 variant in a family with unexplained colorectal cancer and polyposis. Clin Genet 2021; 97:943-944. [PMID: 32424863 DOI: 10.1111/cge.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Bryony A Thompson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Angela K Snow
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Wendy K Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Ryan Mooney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Sara Johnson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig C Teerlink
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, Utah, USA
| | - Deborah W Neklason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Lisa A Cannon-Albright
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA.,Research and Development Service, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
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40
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Loss of m 1acp 3Ψ Ribosomal RNA Modification Is a Major Feature of Cancer. Cell Rep 2021; 31:107611. [PMID: 32375039 DOI: 10.1016/j.celrep.2020.107611] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/03/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022] Open
Abstract
The ribosome is an RNA-protein complex that is essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We identify a cancer-specific single-nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of patients with colorectal carcinoma (CRC) and present across >22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m1acp3Ψ), a >1-billion-years-conserved RNA modification at the peptidyl decoding site of the ribosome. A subset of CRC tumors we call hypo-m1acp3Ψ shows sub-stoichiometric m1acp3Ψ modification, unlike normal control tissues. An m1acp3Ψ knockout model and hypo-m1acp3Ψ patient tumors share a translational signature characterized by highly abundant ribosomal proteins. Thus, m1acp3Ψ-deficient rRNA forms an uncharacterized class of "onco-ribosome" which may serve as a chemotherapeutic target for treating cancer patients.
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41
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Exome sequencing of early-onset patients supports genetic heterogeneity in colorectal cancer. Sci Rep 2021; 11:11135. [PMID: 34045552 PMCID: PMC8159954 DOI: 10.1038/s41598-021-90590-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/12/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is a complex disease that can be caused by a spectrum of genetic variants ranging from low to high penetrance changes, that interact with the environment to determine which individuals will develop the disease. In this study, we sequenced 20 early-onset CRC patients to discover novel genetic variants that could be linked to the prompt disease development. Eight genes, CHAD, CHD1L, ERCC6, IGTB7, PTPN13, SPATA20, TDG and TGS1, were selected and re-sequenced in a further 304 early onset CRC patients to search for rare, high-impact variants. Although we found a recurring truncating variant in the TDG gene shared by two independent patients, the results obtained did not help consolidate any of the candidates as promising CRC predisposing genes. However, we found that potential risk alleles in our extended list of candidate variants have a tendency to appear at higher numbers in younger cases. This supports the idea that CRC onset may be oligogenic in nature and may show molecular heterogeneity. Further, larger and robust studies are thus needed to unravel the genetics behind early-onset CRC development, coupled with novel functional analyses and omic approaches that may offer complementary insight.
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Heald B, Hampel H, Church J, Dudley B, Hall MJ, Mork ME, Singh A, Stoffel E, Stoll J, You YN, Yurgelun MB, Kupfer SS. Collaborative Group of the Americas on Inherited Gastrointestinal Cancer Position statement on multigene panel testing for patients with colorectal cancer and/or polyposis. Fam Cancer 2021; 19:223-239. [PMID: 32172433 DOI: 10.1007/s10689-020-00170-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multigene panel tests for hereditary cancer syndromes are increasingly utilized in the care of colorectal cancer (CRC) and polyposis patients. However, widespread availability of panels raises a number of questions including which patients should undergo testing, which genes should be included on panels, and the settings in which panels should be ordered and interpreted. To address this knowledge gap, key questions regarding the major issues encountered in clinical evaluation of hereditary CRC and polyposis were designed by the Collaborative Group of the Americas on Inherited Gastrointestinal Cancer Position Statement Committee and leadership. A literature search was conducted to address these questions. Recommendations were based on the best available evidence and expert opinion. This position statement addresses which genes should be included on a multigene panel for a patient with a suspected hereditary CRC or polyposis syndrome, proposes updated genetic testing criteria, discusses testing approaches for patients with mismatch repair proficient or deficient CRC, and outlines the essential elements for ordering and disclosing multigene panel test results. We acknowledge that critical gaps in access, insurance coverage, resources, and education remain barriers to high-quality, equitable care for individuals and their families at increased risk of hereditary CRC.
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Affiliation(s)
- Brandie Heald
- Sanford R Weiss, MD, Center for Hereditary Colorectal Neoplasia, Cleveland Clinic, Cleveland, OH, USA.
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine and the Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - James Church
- Sanford R Weiss, MD, Center for Hereditary Colorectal Neoplasia, Cleveland Clinic, Cleveland, OH, USA
| | - Beth Dudley
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Maureen E Mork
- Department of Clinical Cancer Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aparajita Singh
- Department of Medicine, Division of Gastroenterology, University of California San Francisco, San Francisco, CA, USA
| | - Elena Stoffel
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jessica Stoll
- Gastrointestinal Cancer Risk and Prevention Clinic, University of Chicago, Chicago, IL, USA
| | - Y Nancy You
- Department of Clinical Cancer Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sonia S Kupfer
- Gastrointestinal Cancer Risk and Prevention Clinic, University of Chicago, Chicago, IL, USA
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43
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Yang X, Han B, Zhang R, Su Y, Hosseini DK, Wu H, Yang M, Sun H. Development and validation of a RNA binding protein-associated prognostic model for head and neck squamous cell carcinoma. Aging (Albany NY) 2021; 13:7975-7997. [PMID: 33758106 PMCID: PMC8034976 DOI: 10.18632/aging.202848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 03/13/2021] [Indexed: 12/13/2022]
Abstract
Evidence shows that defects in RNA-binding proteins (RBPs) are closely related to the occurrence and development of HNSCC. We obtained 502 tumors and 44 normal samples from the TCGA database, among which 190 differentially expressed RBPs were screened. Finally, a prognostic model containing nine RBPs (CELF2, CPEB1, DDX39B, EIF3L, EZH2, KHDRBS3, RNASE10, RNASE3 and SIDT1) was produced. Further analysis showed that the overall survival rate in the high-risk group was lower than that in the low-risk group. The area under the ROC curve (AUC) in the training and testing groups was significant (3-year AUC, 0.735 vs 0.796; 5-year AUC, 0.821 vs 0.804). In addition, a comprehensive analysis of nine identified RBPs showed that most of them were related to the OS of HNSCC patients, and three of them (CELF2, EZH2, and SIDT1) were differentially expressed in HNSCC and control tissues at the protein level. In addition, our data revealed that the identified RBPs are highly interconnected, with high frequency copy number changes in HNSCC samples. GSEA indicated that the abnormal biological processes related to RNA and the activation of some classical tumor signaling pathways were important driving forces for the development of HNSCC. Our results provide novel insights into the pathogenesis of HNSCC, among which nine RBP markers have potential application value in clinical decision-making and individualized treatment of HNSCC.
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Affiliation(s)
- Xiuping Yang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.,Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Baoai Han
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Runshi Zhang
- Department of Clinical Laboratory, Xi'an No. 1 Hospital, Xi'an 710000, China
| | - Yuan Su
- Department of Clinical Laboratory, Xi'an Labor Union Hospital, Xi'an 710000, China
| | - Davood K Hosseini
- Department of Internal Medicine, Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Han Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Minlan Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Haiying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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44
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Daca Alvarez M, Quintana I, Terradas M, Mur P, Balaguer F, Valle L. The Inherited and Familial Component of Early-Onset Colorectal Cancer. Cells 2021; 10:cells10030710. [PMID: 33806975 PMCID: PMC8005051 DOI: 10.3390/cells10030710] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
Early-onset colorectal cancer (EOCRC), defined as that diagnosed before the age of 50, accounts for 10–12% of all new colorectal cancer (CRC) diagnoses. Epidemiological data indicate that EOCRC incidence is increasing, despite the observed heterogeneity among countries. Although the cause for such increase remains obscure, ≈13% (range: 9–26%) of EOCRC patients carry pathogenic germline variants in known cancer predisposition genes, including 2.5% of patients with germline pathogenic variants in hereditary cancer genes traditionally not associated with CRC predisposition. Approximately 28% of EOCRC patients have family history of the disease. This article recapitulates current evidence on the inherited syndromes that predispose to EOCRC and its familial component. The evidence gathered support that all patients diagnosed with an EOCRC should be referred to a specialized genetic counseling service and offered somatic and germline pancancer multigene panel testing. The identification of a germline pathogenic variant in a known hereditary cancer gene has relevant implications for the clinical management of the patient and his/her relatives, and it may guide surgical and therapeutic decisions. The relative high prevalence of hereditary cancer syndromes and familial component among EOCRC patients supports further research that helps understand the genetic background, either monogenic or polygenic, behind this increasingly common disease.
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Affiliation(s)
- Maria Daca Alvarez
- Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain;
| | - Isabel Quintana
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
| | - Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28029 Madrid, Spain
- Correspondence: (F.B.); (L.V.); Tel.: +34-932275400 (ext. 5418) (F.B.); +34-93-260-7145 (L.V.)
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, 08908 Barcelona, Spain; (I.Q.); (M.T.); (P.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: (F.B.); (L.V.); Tel.: +34-932275400 (ext. 5418) (F.B.); +34-93-260-7145 (L.V.)
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45
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de Paula AE, Galvão HDCR, Bonatelli M, Sabato C, Fernandes GC, Berardinelli GN, Andrade CEM, Neto MC, Romagnolo LGC, Campacci N, Scapulatempo-Neto C, Reis RM, Palmero EI. Clinicopathological and molecular characterization of Brazilian families at risk for Lynch syndrome. Cancer Genet 2021; 254-255:82-91. [PMID: 33647816 DOI: 10.1016/j.cancergen.2021.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/14/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022]
Abstract
Lynch syndrome (LS), is the most common hereditary colorectal cancer syndrome. However, it is poorly characterized in Brazil. Therefore, we aimed to determine the spectrum of pathogenic variants in Mismatch Repair (MMR) genes and investigate the MLH1 promotor methylation role as a second hit in LS tumors. Tumor screening through microsatellite instability and immunohistochemistry for MMR proteins was performed in 323 cases who met clinical criteria. BRAF-V600E and MLH1 promoter methylation were analyzed for all MLH1-deficient tumors. Patients with MMR deficient tumor proceeded to germline genetic testing. MMR deficient tumors were detected in 41% of patients recruited. About half of patients carried a pathogenic germline variant. Two recurrent variants in MLH1 and three novel pathogenic variants were identified. Furthermore, pathogenic germline variants with concomitant somatic MLH1 hypermethylation were found in 6% of cases. Predictive genetic testing was offered to 387 relatives. Overall, 127 tumors were diagnosed in 100 LS patients, from 62 unrelated families. Our molecular data provide new information about the spectrum of MMR mutations, which contributes to a better characterization of LS in Brazil. Furthermore, we call attention to the possibility of failure in the diagnosis of germline MLH1 mutation carriers when somatic MLH1 hypermethylation is used to rule out LS.
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Affiliation(s)
| | | | - Murilo Bonatelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristina Sabato
- Molecular Diagnosis Laboratory, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | | | | | | | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Rui Manuel Reis
- Molecular Diagnosis Laboratory, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inêz Palmero
- Molecular Diagnosis Laboratory, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Pele Pequeno Principe Research Institute, Curitiba, Brazil; Faculdades Pequeno Principe, Curitiba, Brazil.
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46
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Reza AMMT, Yuan YG. microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins. Cells 2021; 10:110. [PMID: 33435549 PMCID: PMC7827472 DOI: 10.3390/cells10010110] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3' untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5' untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.
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Affiliation(s)
- Abu Musa Md Talimur Reza
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Yu-Guo Yuan
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Li T, Hui W, Halike H, Gao F. RNA Binding Protein-Based Model for Prognostic Prediction of Colorectal Cancer. Technol Cancer Res Treat 2021; 20:15330338211019504. [PMID: 34080453 PMCID: PMC8182183 DOI: 10.1177/15330338211019504] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a kind of gastrointestinal tumor with serious high morbidity and mortality. Several reports have implicated the disorder of RNA-binding proteins (RBPs) in plenty of tumors, associating it to tumorigenesis and disease progression. The study is intended to construct novel prognostic biomarkers associated with CRC patients. METHODS Data of gene expression was acquired from the TCGA database, prognosis-related genes were selected. Besides, we analyzed GO and KEGG pathways. Univariate and multivariate Cox analyses were performed to generate a prognostic-related gene signature, which was evaluated by the Kaplan-Meier (K-M) and the Receiver Operating Characteristic (ROC) curve. The independent prognostic factor was established by survival analysis. GSE38832 dataset was used to validate the signature. Finally, expression of 8 genes was further confirmed by qRT-PCR in SW480 and SW620 cell lines. RESULTS We obtained 224 differentially expressed RBPS in total, of which 78 were downregulated and 146 were upregulated. Univariate COX analysis was conducted in the TCGA cohort to select 13 RBPs with P < 0.005, stepwise multivariate COX regression analysis was used to construct an 8-RBP signature (TERT, PPARGC1A, BRCA1, CELF4, TDRD7, LUZP4, PNLDC1, ZC3H12C). Based on the model, systematic analysis illustrated that a high risk score was obviously connected to a poor prognosis. The prognostic value of the risk score was validated in GSE38832 dataset, indicating that the risk model was accurate and effective. The prognostic signature-based risk score was identified as an independent prognostic indicator for CRC. The expression results of qRT-PCR were consistent with the results of differential expression analysis. CONCLUSIONS The eight-RBP signature can predict the survival of CRC patients and potentially act as CRC prognostic biomarker.
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Affiliation(s)
- Ting Li
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
| | - Wenjia Hui
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
| | - Halina Halike
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
| | - Feng Gao
- Department of Gastroenterology, People’s Hospital of Xinjiang Uygur
Autonomous Region, Urumqi, Xinjiang Province, China
- Feng Gao, PhD, Department of
Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi
830000, Xinjiang Province, China.
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te Paske IBAW, Ligtenberg MJL, Hoogerbrugge N, de Voer RM. Candidate Gene Discovery in Hereditary Colorectal Cancer and Polyposis Syndromes-Considerations for Future Studies. Int J Mol Sci 2020; 21:E8757. [PMID: 33228212 PMCID: PMC7699508 DOI: 10.3390/ijms21228757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
To discover novel high-penetrant risk loci for hereditary colorectal cancer (hCRC) and polyposis syndromes many whole-exome and whole-genome sequencing (WES/WGS) studies have been performed. Remarkably, these studies resulted in only a few novel high-penetrant risk genes. Given this observation, the possibility and strategy to identify high-penetrant risk genes for hCRC and polyposis needs reconsideration. Therefore, we reviewed the study design of WES/WGS-based hCRC and polyposis gene discovery studies (n = 37) and provide recommendations to optimize discovery and validation strategies. The group of genetically unresolved patients is phenotypically heterogeneous, and likely composed of distinct molecular subtypes. This knowledge advocates for the screening of a homogeneous, stringently preselected discovery cohort and obtaining multi-level evidence for variant pathogenicity. This evidence can be collected by characterizing the molecular landscape of tumors from individuals with the same affected gene or by functional validation in cell-based models. Together, the combined approach of a phenotype-driven, tumor-based candidate gene search might elucidate the potential contribution of novel genetic predispositions in genetically unresolved hCRC and polyposis.
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Affiliation(s)
- Iris B. A. W. te Paske
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Richarda M. de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
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Nait Slimane S, Marcel V, Fenouil T, Catez F, Saurin JC, Bouvet P, Diaz JJ, Mertani HC. Ribosome Biogenesis Alterations in Colorectal Cancer. Cells 2020; 9:E2361. [PMID: 33120992 PMCID: PMC7693311 DOI: 10.3390/cells9112361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022] Open
Abstract
Many studies have focused on understanding the regulation and functions of aberrant protein synthesis in colorectal cancer (CRC), leaving the ribosome, its main effector, relatively underappreciated in CRC. The production of functional ribosomes is initiated in the nucleolus, requires coordinated ribosomal RNA (rRNA) processing and ribosomal protein (RP) assembly, and is frequently hyperactivated to support the needs in protein synthesis essential to withstand unremitting cancer cell growth. This elevated ribosome production in cancer cells includes a strong alteration of ribosome biogenesis homeostasis that represents one of the hallmarks of cancer cells. None of the ribosome production steps escape this cancer-specific dysregulation. This review summarizes the early and late steps of ribosome biogenesis dysregulations described in CRC cell lines, intestinal organoids, CRC stem cells and mouse models, and their possible clinical implications. We highlight how this cancer-related ribosome biogenesis, both at quantitative and qualitative levels, can lead to the synthesis of ribosomes favoring the translation of mRNAs encoding hyperproliferative and survival factors. We also discuss whether cancer-related ribosome biogenesis is a mere consequence of cancer progression or is a causal factor in CRC, and how altered ribosome biogenesis pathways can represent effective targets to kill CRC cells. The association between exacerbated CRC cell growth and alteration of specific steps of ribosome biogenesis is highlighted as a key driver of tumorigenesis, providing promising perspectives for the implementation of predictive biomarkers and the development of new therapeutic drugs.
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Affiliation(s)
- Sophie Nait Slimane
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Virginie Marcel
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Tanguy Fenouil
- Institute of Pathology EST, Hospices Civils de Lyon, Site-Est Groupement Hospitalier- Est, 69677 Bron, France;
| | - Frédéric Catez
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Christophe Saurin
- Gastroenterology and Genetic Department, Edouard Herriot Hospital, Hospices Civils de Lyon, 69008 Lyon, France;
| | - Philippe Bouvet
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Hichem C. Mertani
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
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Hua X, Chen J, Ge S, Xiao H, Zhang L, Liang C. Integrated analysis of the functions of RNA binding proteins in clear cell renal cell carcinoma. Genomics 2020; 113:850-860. [PMID: 33169673 DOI: 10.1016/j.ygeno.2020.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/16/2020] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBPs) dysregulation is involved in the processes of various tumors. However, the roles of RBPs in clear cell renal cell carcinoma (ccRCC) remain poorly understand. In present study, we first performed consensus clustering and identified two clusters, of which cluster 2 was closely correlated with the malignancy of ccRCC. Differentially expressed RBPs between normal and tumor tissues were obtained, comprising 71 up-regulated and 44 down-regulated ones. Then, ten hub genes were selected and validated using The Human Protein Atlas database and receiver operating characteristic curves, showing good diagnostic value for cancers. Besides, we identified ten RBPs with the most useful prognostic values, and were used to construct a risk score model. The model could be used to stratify patients with different prognosis and phenotype distributions. The model showed good performance and can be used as a complementation for clinical factors to guide clinical practice in the future.
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Affiliation(s)
- Xiaoliang Hua
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Juan Chen
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, the College of Laboratory Medicine, Chongqing Medical University, 400016, Chongqing, China
| | - Shengdong Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Haibing Xiao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China
| | - Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei, China; The Institute of Urology, Anhui Medical University, Hefei, China.
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