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Ji R, Wei L, Zan Y, Li X, Ma S, Ma L, He X, Wang L, Ding Y. ABI3BP promotes renal aging through Klotho-mediated ferroptosis. J Transl Med 2024; 22:514. [PMID: 38812032 PMCID: PMC11134664 DOI: 10.1186/s12967-024-05300-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
The aging process of the kidneys is accompanied with several structural diseases. Abnormal fiber formation disrupts the balance of kidney structure and function, causing to end-stage renal disease and subsequent renal failure. Despite this, the precise mechanism underlying renal damage in aging remains elusive. In this study, ABI3BP gene knockout mice were used to investigate the role of ABI3BP in renal aging induced by irradiation. The results revealed a significant increase in ABI3BP expression in HK2 cells and kidney tissue of aging mice, with ABI3BP gene knockout demonstrating a mitigating effect on radiation-induced cell aging. Furthermore, the study observed a marked decrease in Klotho levels and an increase in ferroptosis in renal tissue and HK2 cells following irradiation. Notably, ABI3BP gene knockout not only elevated Klotho expression but also reduced ferroptosis levels. A significant negative correlation between ABI3BP and Klotho was established. Further experiments demonstrated that Klotho knockdown alleviated the aging inhibition caused by ABI3BP downregulation. This study identifies the upregulation of ABI3BP in aged renal tubular epithelial cells, indicating a role in promoting ferroptosis and inducing renal aging by inhibiting Klotho expression.
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Affiliation(s)
- Ren Ji
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Lin Wei
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Yuxin Zan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiao Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Shinan Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Liming Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xiju He
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Li Wang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
- Urology Department, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Yan Ding
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
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2
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Feng Y, Han X, Zhang Z, Qiao H, Tang H. ABI3BP is a prognosis biomarker related with clinicopathological features and immunity infiltration of lung tumor. Front Genet 2023; 13:1085785. [PMID: 36744181 PMCID: PMC9894588 DOI: 10.3389/fgene.2022.1085785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Background: The primary factor of cancer mortality is lung tumor. ABI3BP gene encodes an extracellular matrix bind protein associated to multiplication and derivation. However, the prognosis score of ABI3BP for lung tumor and its relation with immunity cellular infiltration for lung tumor have not been reported. Methods: Public repository systems (Timer, GEPIA, TCGA, HPA) were utilized to explore expression of ABI3BP for lung tumor, and explored the relation of ABI3BP and clinicopathological parameters. TCGA information set was utilized for cox analysis for data with one or more variables of ABI3BP for lung tumor. STRING was utilized to explore ABI3BP regulatory networks. GO/KEGG enrichment analysis as well as enrichment analysis of gene sets were carried out for ABI3BP co-expression via R package. And finally we explored the relation of expression of ABI3BP and lung tumor immunity invasion, exploring the influence of ABI3BP level of expression on immunotreatment and whether immunity invasion would affect the prognosis of patients with lung tumor. Results: ABI3BP is downregulated in LUAD and LUSC, and associated to lung tumor phase and prognosis. Univariate and multivariate cox regression showed that ABI3BP was an independent prognostic factor in patients with lung tumors. The extracellular matrix protein-coding gene and the ABI3BP-related gene were intersected to obtain 10 hub genes. On the basis of GO/KEGG enrichment analysis, hub genes are closely associated to immunity-associated pathways including T cell receptor signaling pathway, immune response-activating cell surface receptor signaling pathway. Finally, the expression of ABI3BP is closely related to immune cell infiltration and immune cell marker set, and the expression of ABI3BP can help predict the therapeutic effect of immune checkpoint inhibitors and improve the prognosis of patients. Conclusion: ABI3BP could be a new target for lung tumor that could be utilized as a diagnostic and therapeutic tool.
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Affiliation(s)
- Yan Feng
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Xiaolei Han
- Department of Health Office, Qingdao Municipal Hospital, Qingdao, China
| | - Zhe Zhang
- Department of Thoracic Surgery, Qingdao Municipal Hospital, Qingdao, China
| | - Han Qiao
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Huaping Tang
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao, China,*Correspondence: Huaping Tang,
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3
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Nong B, Guo M, Wang W, Songyang Z, Xiong Y. Comprehensive Analysis of Large-Scale Transcriptomes from Multiple Cancer Types. Genes (Basel) 2021; 12:1865. [PMID: 34946814 PMCID: PMC8701385 DOI: 10.3390/genes12121865] [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: 10/15/2021] [Revised: 11/21/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Various abnormalities of transcriptional regulation revealed by RNA sequencing (RNA-seq) have been reported in cancers. However, strategies to integrate multi-modal information from RNA-seq, which would help uncover more disease mechanisms, are still limited. Here, we present PipeOne, a cross-platform one-stop analysis workflow for large-scale transcriptome data. It was developed based on Nextflow, a reproducible workflow management system. PipeOne is composed of three modules, data processing and feature matrices construction, disease feature prioritization, and disease subtyping. It first integrates eight different tools to extract different information from RNA-seq data, and then used random forest algorithm to study and stratify patients according to evidences from multiple-modal information. Its application in five cancers (colon, liver, kidney, stomach, or thyroid; total samples n = 2024) identified various dysregulated key features (such as PVT1 expression and ABI3BP alternative splicing) and pathways (especially liver and kidney dysfunction) shared by multiple cancers. Furthermore, we demonstrated clinically-relevant patient subtypes in four of five cancers, with most subtypes characterized by distinct driver somatic mutations, such as TP53, TTN, BRAF, HRAS, MET, KMT2D, and KMT2C mutations. Importantly, these subtyping results were frequently contributed by dysregulated biological processes, such as ribosome biogenesis, RNA binding, and mitochondria functions. PipeOne is efficient and accurate in studying different cancer types to reveal the specificity and cross-cancer contributing factors of each cancer.It could be easily applied to other diseases and is available at GitHub.
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Affiliation(s)
- Baoting Nong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
| | - Mengbiao Guo
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
| | - Weiwen Wang
- School of Mathematics, Sun Yat-sen University, Guangzhou 510006, China;
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; (B.N.); (M.G.); (Z.S.)
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4
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Xiong Y, Xi S, Gara SK, Shan J, Gao J, Zhang M, Shukla V, Wang R, Hoang CD, Chen H, Schrump DS. Hookah Smoke Mediates Cancer-Associated Epigenomic and Transcriptomic Signatures in Human Respiratory Epithelial Cells. JTO Clin Res Rep 2021; 2:100181. [PMID: 34790904 PMCID: PMC8479631 DOI: 10.1016/j.jtocrr.2021.100181] [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: 01/27/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Although communal smoking of hookah by means of water pipes is perceived to be a safe alternative to cigarette smoking, the effects of hookah smoke in respiratory epithelia have not been well characterized. This study evaluated epigenomic and transcriptomic effects of hookah smoke relative to cigarette smoke in human respiratory epithelial cells. Methods Primary normal human small airway epithelial cells from three donors and cdk4 and hTERT-immortalized small airway epithelial cells and human bronchial epithelial cells were cultured for 5 days in normal media with or without cigarette smoke condensates (CSCs) or water pipe condensates (WPCs). Cell count, immunoblot, RNA sequencing, quantitative real-time reverse-transcriptase polymerase chain reaction, methylation-specific polymerase chain reaction, and quantitative chromatin immunoprecipitation techniques were used to compare effects of hookah and cigarette smoke on cell proliferation, global histone marks, gene expression, and promoter-related chromatin structure. Results CSC and WPC decreased global H4K16ac and H4K20me3 histone marks and mediated distinct and overlapping cancer-associated transcriptome signatures and pathway modulations that were cell line dependent and stratified across lung cancer cells in a histology-specific manner. Epiregulin encoding a master regulator of EGFR signaling that is overexpressed in lung cancers was up-regulated, whereas FILIP1L and ABI3BP encoding mediators of senescence that are repressed in lung cancers were down-regulated by CSC and WPC. Induction of epiregulin and repression of FILIP1L and ABI3BP by these condensates coincided with unique epigenetic alterations within the respective promoters. Conclusions These findings support translational studies to ascertain if hookah-mediated epigenomic and transcriptomic alterations in cultured respiratory epithelia are detectable and clinically relevant in hookah smokers.
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Affiliation(s)
- Yin Xiong
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sichuan Xi
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sudheer Kumar Gara
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jigui Shan
- The Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James Gao
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mary Zhang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Vivek Shukla
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Ruihong Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Chuong D Hoang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Haobin Chen
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
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5
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The Depletion of ABI3BP by MicroRNA-183 Promotes the Development of Esophageal Carcinoma. Mediators Inflamm 2020; 2020:3420946. [PMID: 32774142 PMCID: PMC7399787 DOI: 10.1155/2020/3420946] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Background Esophageal cancer (EC), as a serious threat to human life and health, is one of the most common cancers around the world. Many studies have suggested that many microRNAs are involved in tumorigenesis and progression. Methods To search for a novel and promising predictive therapeutic target or biomarker to achieve the goal of the early diagnosis and treatment of EC, we used the EC cell lines Eca-109 and KYSE-150 and normal human esophageal epithelial cells (HEECs) to investigate the effect of ABI3BP on EC. Results We found that ABI family member 3 binding protein (ABI3BP) was downregulated in EC and suppressed the proliferation, activity, migration, and invasion of EC cells. ABI3BP was downregulated by miR-183, which plays the role of an oncogene. Conclusion ABI3BP and miR-183 can be considered potential biomarkers for the diagnosis of patients with EC and can be effective targets for antitumor therapy.
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6
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Delfín DA, DeAguero JL, McKown EN. The Extracellular Matrix Protein ABI3BP in Cardiovascular Health and Disease. Front Cardiovasc Med 2019; 6:23. [PMID: 30923710 PMCID: PMC6426741 DOI: 10.3389/fcvm.2019.00023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/20/2019] [Indexed: 01/31/2023] Open
Abstract
ABI3BP is a relatively newly identified protein whose general biological functions are not yet fully defined. It is implicated in promoting cellular senescence and cell-extracellular matrix interactions, both of which are of vital importance in the cardiovascular system. ABI3BP has been shown in multiple studies to be expressed in the heart and vasculature, and to have a role in normal cardiovascular function and disease. However, its precise role in the cardiovascular system is not known. Because ABI3BP is present in the cardiovascular system and is altered in cardiovascular disease states, further investigation into ABI3BP's biological and biochemical importance in cardiovascular health and disease is warranted.
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Affiliation(s)
- Dawn A. Delfín
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States
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7
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Horpaopan S, Kirfel J, Peters S, Kloth M, Hüneburg R, Altmüller J, Drichel D, Odenthal M, Kristiansen G, Strassburg C, Nattermann J, Hoffmann P, Nürnberg P, Büttner R, Thiele H, Kahl P, Spier I, Aretz S. Exome sequencing characterizes the somatic mutation spectrum of early serrated lesions in a patient with serrated polyposis syndrome (SPS). Hered Cancer Clin Pract 2017; 15:22. [PMID: 29213343 PMCID: PMC5707812 DOI: 10.1186/s13053-017-0082-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/21/2017] [Indexed: 01/01/2023] Open
Abstract
Background Serrated or Hyperplastic Polyposis Syndrome (SPS, HPS) is a yet poorly defined colorectal cancer (CRC) predisposition characterised by the occurrence of multiple and/or large serrated polyps throughout the colon. A serrated polyp-CRC sequence (serrated pathway) of CRC formation has been postulated, however, to date only few molecular signatures of serrated neoplasia (BRAF, KRAS, RNF43 mutations, CpG Island Methylation, MSI) have been described in a subset of SPS patients and neither the etiology of the syndrome nor the distinct genetic alterations during tumorigenesis have been identified. Methods To identify somatic point mutations in potential novel candidate genes of SPS-associated lesions and the involved pathways we performed exome sequencing of eleven early serrated polyps obtained from a 41 year-old female patient with clinically confirmed SPS. For data filtering and analysis, standard pipelines were used. Somatic mutations were identified by comparison with leukocyte DNA and were validated by Sanger sequencing. Results The BRAF p.V600E or KRAS p.G12D mutation was identified in six polyps (~50%) and not found in polyps from the distal colon. In addition, we found seven unique rare somatic alterations of seven different genes in four serrated tumours, all of which are missense variants. The variant in ABI3BP and CATSPERB are predicted to be deleterious. No established cancer gene or candidate genes related to serrated tumorigenesis were affected. Conclusions Somatic mutations seem to be rare events in early hyperplastic and serrated lesions of SPS patients. Neither frequently affected genes nor enrichment of specific pathways were observed. Thus, other alterations such as non-coding variants or epigenetic changes might be the major driving force of tumour progression in SPS. Electronic supplementary material The online version of this article (10.1186/s13053-017-0082-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand.,Center of Excellence in Medical Biotechnology, Naresuan University, Phitsanulok, Thailand
| | - Jutta Kirfel
- Institute of Pathology, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Kloth
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Robert Hüneburg
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.,Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | | | - Glen Kristiansen
- Institute of Pathology, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Christian Strassburg
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.,Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Jacob Nattermann
- Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.,Department of Internal Medicine I, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Institute of Medical Genetics and Pathology, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | | | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Philip Kahl
- Heinz-Werner-Seifert-Institut für Dermatopathologie Bonn, Bonn, Germany
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany.,Institute of Human Genetics, Center for Hereditary Tumor Syndromes, University of Bonn, Sigmund-Freud-Str. 25, D-53127 Bonn, Germany
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8
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Radder JE, Gregory AD, Leme AS, Cho MH, Chu Y, Kelly NJ, Bakke P, Gulsvik A, Litonjua AA, Sparrow D, Beaty TH, Crapo JD, Silverman EK, Zhang Y, Berndt A, Shapiro SD. Variable Susceptibility to Cigarette Smoke-Induced Emphysema in 34 Inbred Strains of Mice Implicates Abi3bp in Emphysema Susceptibility. Am J Respir Cell Mol Biol 2017; 57:367-375. [PMID: 28441029 DOI: 10.1165/rcmb.2016-0220oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is caused by a complex interaction of environmental exposures, most commonly cigarette smoke, and genetic factors. Chronic cigarette smoke exposure in the mouse is a commonly used animal model of COPD. We aimed to expand our knowledge about the variable susceptibility of inbred strains to this model and test for genetic variants associated with this trait. To that end, we sought to measure differential susceptibility to cigarette smoke-induced emphysema in the mouse, identify genetic loci associated with this quantitative trait, and find homologous human genes associated with COPD. Alveolar chord length (CL) in 34 inbred strains of mice was measured after 6 months of exposure to cigarette smoke. After testing for association, we connected a murine candidate locus to a published meta-analysis of moderate-to-severe COPD. We identified deleterious mutations in a candidate gene in silico and measured gene expression in extreme strains. A/J was the most susceptible strain in our survey (Δ CL 7.0 ± 2.2 μm) and CBA/J was the least susceptible (Δ CL -0.3 ± 1.2 μm). By integrating mouse and human genome-wide scans, we identified the candidate gene Abi3bp. CBA/J mice harbor predicted deleterious variants in Abi3bp, and expression of the gene differs significantly between CBA/J and A/J mice. This is the first report of susceptibility to cigarette smoke-induced emphysema in 34 inbred strains of mice, and Abi3bp is identified as a potential contributor to this phenotype.
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Affiliation(s)
- Josiah E Radder
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alyssa D Gregory
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adriana S Leme
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael H Cho
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yanxia Chu
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Neil J Kelly
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Per Bakke
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- 4 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Augusto A Litonjua
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 5 School of Public Health and.,6 School of Medicine, Boston University, Boston, Massachusetts.,7 Veterans Affairs Boston Healthcare System, Boston, Massachusetts
| | - Terri H Beaty
- 8 Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
| | - James D Crapo
- 9 Department of Radiology, National Jewish Health, Denver, Colorado
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine, and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
| | - Yingze Zhang
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Annerose Berndt
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Steven D Shapiro
- 1 Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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9
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Yang H, Chen W, Shi J, Huang D, Li J, Hu B, Zhang M, Wang Z, Fei J. Knockout of Abi3bp in mice does not affect their olfactory function, mental state and NNK-induced lung tumorigenesis. Acta Biochim Biophys Sin (Shanghai) 2016; 48:820-6. [PMID: 27521794 DOI: 10.1093/abbs/gmw071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/25/2016] [Indexed: 01/19/2023] Open
Abstract
Abi3bp was originally discovered as Abi3-Src homology 3 (SH3) binding protein and has been proved to have a broad expression profile in adult tissues. Although previous studies have indicated that Abi3bp may be associated with cancer suppression, cell senescence, dendritic refinement and mental disorder, most conclusions achieved were based on in vitro model or genome-wide association study. In this work, we constructed an Abi3bp-deficient mouse model and observed phenotypic changes. The generated Abi3bp-knockout mice are viable and fertile, develop normally and exhibit no significant differences in anxiety or depression-like behaviors, olfactory function and tumor incidence. These data suggest that the function of Abi3bp in in vitro models does not translate to a similar role in the intact animal. Its depletion may be compensated by other genes, which needs to be addressed in future studies.
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Affiliation(s)
- Hua Yang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Weidong Chen
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jiahao Shi
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Dandan Huang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Jun Li
- Shanghai Engineering Research Center of Model Organisms/Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Binyang Hu
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Mengjie Zhang
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Zhugang Wang
- Shanghai Engineering Research Center of Model Organisms/Shanghai Research Center for Model Organisms, Shanghai 201203, China
| | - Jian Fei
- School of Life Science and Technology, Tongji University, Shanghai 200092, China Shanghai Engineering Research Center of Model Organisms/Shanghai Research Center for Model Organisms, Shanghai 201203, China
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10
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Perlis RH, Huang J, Purcell S, Fava M, Rush AJ, Sullivan PF, Hamilton SP, McMahon FJ, Schulze TG, Schulze T, Potash JB, Zandi PP, Willour VL, Penninx BW, Boomsma DI, Vogelzangs N, Middeldorp CM, Rietschel M, Nöthen M, Cichon S, Gurling H, Bass N, McQuillin A, Hamshere M, Craddock N, Sklar P, Smoller JW. Genome-wide association study of suicide attempts in mood disorder patients. Am J Psychiatry 2010; 167:1499-507. [PMID: 21041247 PMCID: PMC3795390 DOI: 10.1176/appi.ajp.2010.10040541] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Family and twin studies suggest that liability for suicide attempts is heritable and distinct from mood disorder susceptibility. The authors therefore examined the association between common genomewide variation and lifetime suicide attempts. METHOD The authors analyzed data on lifetime suicide attempts from genomewide association studies of bipolar I and II disorder as well as major depressive disorder. Bipolar disorder subjects were drawn from the Systematic Treatment Enhancement Program for Bipolar Disorder cohort, the Wellcome Trust Case Control Consortium bipolar cohort, and the University College London cohort. Replication was pursued in the NIMH Genetic Association Information Network bipolar disorder project and a German clinical cohort. Depression subjects were drawn from the Sequential Treatment Alternatives to Relieve Depression cohort, with replication in the Netherlands Study of Depression and Anxiety/Netherlands Twin Register depression cohort. RESULTS Strongest evidence of association for suicide attempt in bipolar disorder was observed in a region without identified genes (rs1466846); five loci also showed suggestive evidence of association. In major depression, strongest evidence of association was observed for a single nucleotide polymorphism in ABI3BP, with six loci also showing suggestive association. Replication cohorts did not provide further support for these loci. However, meta-analysis incorporating approximately 8,700 mood disorder subjects identified four additional regions that met the threshold for suggestive association, including the locus containing the gene coding for protein kinase C-epsilon, previously implicated in models of mood and anxiety. CONCLUSIONS The results suggest that inherited risk for suicide among mood disorder patients is unlikely to be the result of individual common variants of large effect. They nonetheless provide suggestive evidence for multiple loci, which merit further investigation.
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Affiliation(s)
- Roy H Perlis
- Department of Psychiatry, Massachusetts General Hospital, Boston, 02114, USA.
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Abstract
Olfactory sensory neurons synapse with mitral cells to form stereotyped connections in the olfactory bulb (OB). Mitral cell apical dendrites receive input from olfactory sensory neurons expressing the same odorant receptor. During development, this restricted dendritic targeting of mitral cells is achieved through eliminating elaborated dendritic trees to a single apical dendrite. Through a genome-wide microarray screen, we identified TARSH (Target of NESH SH3) as a transiently expressed molecule in mitral cells during the dendritic refinement period. TARSH expression is restricted to pyramidal neurons along the main olfactory pathway, including the anterior olfactory nucleus and piriform cortex. The dynamic TARSH expression is not altered when odor-evoked activity is blocked by naris closure or in AC3 knockout mice. We also demonstrate that TARSH is a secreted protein. In dissociated OB cultures, secreted TARSH promotes the reduction of mitral cell dendritic complexity and restricts dendritic branching and outgrowth of interneurons. Dendritic morphological changes were also observed in mitral cells overexpressing TARSH themselves. We propose that TARSH is part of the genetic program that regulates mitral cell dendritic refinement.
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Affiliation(s)
- Ting-Wen Cheng
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California, Davis, CA 95616, USA
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Implication of p53-dependent cellular senescence related gene, TARSH in tumor suppression. Biochem Biophys Res Commun 2009; 380:807-12. [DOI: 10.1016/j.bbrc.2009.01.171] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 01/25/2009] [Indexed: 11/21/2022]
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Latini FRM, Hemerly JP, Oler G, Riggins GJ, Cerutti JM. Re-expression of ABI3-binding protein suppresses thyroid tumor growth by promoting senescence and inhibiting invasion. Endocr Relat Cancer 2008; 15:787-99. [PMID: 18559958 PMCID: PMC2742300 DOI: 10.1677/erc-08-0079] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Loss of ABI gene family member 3-binding protein (ABI3BP) expression may be functionally involved in the pathogenesis of cancer. Previous reports have indicated a loss of expression in lung cancer and a presumed role in inducing cellular senescence. We show here that ABI3BP expression is significantly decreased in most malignant thyroid tumors of all types. To better understand ABI3BP's role, we created a model by re-expressing ABI3BP in two thyroid cancer cell lines. Re-expression of ABI3BP in thyroid cells resulted in a decrease in transforming activity, cell growth, cell viability, migration, invasion, and tumor growth in nude mice. ABI3BP re-expression appears to trigger cellular senescence through the p21 pathway. Additionally, ABI3BP induced formation of heterochromatin 1-binding protein gamma-positive senescence-associated (SA) heterochromatin foci and accumulation of SA beta-galactosidase. The combination of a decrease in cell growth, invasion, and other effects upon ABI3BP re-expression in vitro helps to explain the large reduction in tumor growth that we observed in nude mice. Together, our data provide evidence that the loss of ABI3BP expression could play a functional role in thyroid tumorigenesis. Activation of ABI3BP or its pathway may represent a possible basis for targeted therapy of certain cancers.
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Affiliation(s)
- Flavia R. M. Latini
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics; Federal University of São Paulo, SP, Brazil
| | - Jefferson P. Hemerly
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics; Federal University of São Paulo, SP, Brazil
| | - Gisele Oler
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics; Federal University of São Paulo, SP, Brazil
| | - Gregory J. Riggins
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Janete M. Cerutti
- Genetic Bases of Thyroid Tumors Laboratory, Division of Genetics, Department of Morphology and Genetics; Federal University of São Paulo, SP, Brazil
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Uekawa N, Nishioka T, Terauchi K, Ohta S, Sugimoto M, Shimada JI, Maruyama M. Generation and characterization of novel monoclonal antibodies against murine and human TARSH proteins. Hybridoma (Larchmt) 2007; 26:381-5. [PMID: 18158782 DOI: 10.1089/hyb.2007.0520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
TARSH/Abi3bp was originally isolated as a novel target of NESH-SH3 by a two-hybrid yeast system. We have already identified murine TARSH (mTARSH) as a cellular senescence-related gene because of its robust induction in the early phase of mouse embryonic fibroblast cellular senescence. We have also revealed that the expression of this gene was dramatically reduced in human lung cancer cell lines and primary lung tumor, while it was predominantly expressed in normal conditions. This evidence suggests that TARSH is involved in both stress-induced senescence and prevention of cancer development; however, little is known about its molecular mechanisms. To reveal the further physiological function of this molecule, we established rat anti-TARSH monoclonal antibodies (MAb). Recombinant His-tagged partial mouse TARSH protein was expressed in Escherichia coli, affinity purified and used as an antigen to immunize rats. Hybridomas were screened by enzyme-linked immunosorbent assay, and we generated six stable hybridoma cell lines that produced antibody against murine TARSH protein, including three clones that represented cross-reactivity with human TARSH. We determined their isotypes and further examined capabilities or limitations in immunoblotting, immunoprecipitation, and immunofluorescence microscopy, realizing the most suitable antibody for each application. These MAbs should therefore be very useful tools for the study of TARSH expression and for following biological function in cellular senescence and tumor suppression.
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Affiliation(s)
- Natsuko Uekawa
- Department of Mechanism of Aging, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, Obu-City, Aichi, Japan
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Guimarães GS, Latini FRM, Camacho CP, Maciel RMB, Dias-Neto E, Cerutti JM. Identification of candidates for tumor-specific alternative splicing in the thyroid. Genes Chromosomes Cancer 2006; 45:540-53. [PMID: 16493598 DOI: 10.1002/gcc.20316] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing is the differential processing of exon junctions to produce a new transcript variant from one gene. Some aberrant splicing, however, has been shown to be cancer specific. Identification of these specific splice variations will provide important insight into the molecular mechanism of normal cellular physiology as well as the disease processes. To gain knowledge about whether alternative splicing is linked to thyroid tumorigenesis, we used our prediction database to select targets for analysis. Fifteen putatively new alternative splicing isoforms were selected on the basis of their expression in thyroid libraries and/or their origin in genes previously associated with carcinogenesis. Using a set of 66 normal, benign, and malignant thyroid tissue samples, new splicing events were confirmed by RT-PCR for 13 of 15 genes (a validation rate of 87%). In addition, new alternative splicing isoforms not predicted by the system and not previously described in public databases were identified. Five genes (PTPN18, ABI3BP, PFDN5, SULF2, and ST5) presented new and/or additional unpredicted isoforms differentially expressed between malignant and benign or normal thyroid tissues, confirmed by sequencing. PTPN18, ABI3BP, and PFDN5 revealed a statistically significant differential splicing profile. In addition, real-time PCR analysis revealed that expression of an alternative PFDN5 variant was higher in malignant lesions than in benign lesions or normal tissues.
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Affiliation(s)
- Gustavo S Guimarães
- Laboratory of Molecular Endocrinology, Department of Medicine, Federal University of São Paulo, Brazil
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Terauchi K, Shimada J, Uekawa N, Yaoi T, Maruyama M, Fushiki S. Cancer-associated loss of TARSH gene expression in human primary lung cancer. J Cancer Res Clin Oncol 2005; 132:28-34. [PMID: 16205947 DOI: 10.1007/s00432-005-0032-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Accepted: 08/18/2005] [Indexed: 11/27/2022]
Abstract
PURPOSE We have previously identified mouse Tarsh as one of the cellular senescence-related genes and showed the loss of expression of TARSH mRNA in four human lung cancer cell lines. TARSH is a presumptive signal transduction molecule interacting with NESH, which is implicated to have some roles in lung cancer metastasis. METHODS The amplification of complete ORF-encoding TARSH cDNA was done with reverse transcription-PCR. Northern blotting was carried out using TARSH cDNA probes. To clarify the relationship between TARSH and lung cancer, we quantified TARSH mRNA expression in 15 human lung cancer cell lines and 32 primary non-small cell lung cancers. RESULTS We first determined the complete ORF-encoding cDNA sequence which is expressed in the human lung. On the Northern hybridization analysis, TARSH was strongly expressed in the human lung. The expression of TARSH mRNA is remarkably downregulated in all the lung cancer cell lines examined. Furthermore, TARSH expression was significantly low in all of the tumor specimens when compared to the expression in corresponding non-neoplastic lung tissue specimens. CONCLUSION The cancer-associated transcriptional inactivation of TARSH suggests that TARSH could be used as a biomarker for lung cancer development as well as a molecular adjunct for lung carcinogenesis in human.
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Affiliation(s)
- Kunihiko Terauchi
- Department of Cardiovascular and Thoracic Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku, 602-8566, Kyoto, Japan
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