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Liu Y, Hoskins I, Geng M, Zhao Q, Chacko J, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Rao S, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of Translation Efficiency Covariation (TEC), identifying coordinated translation patterns across cell types. We nominate potential mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and helps uncover gene functions. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish translational covariation as a conserved organizing principle of mammalian transcriptomes.
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Affiliation(s)
- Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Geng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kangsheng Qi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Yochen Zhong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Sail Biomedicines, Cambridge, MA, 02141, USA
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2
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de Boer E, Marcelis C, Neveling K, van Beusekom E, Hoischen A, Klein WM, de Leeuw N, Mantere T, Melo US, van Reeuwijk J, Smeets D, Spielmann M, Kleefstra T, van Bokhoven H, Vissers LE. A complex structural variant near SOX3 causes X-linked split-hand/foot malformation. HGG ADVANCES 2023; 4:100200. [PMID: 37216008 PMCID: PMC10196709 DOI: 10.1016/j.xhgg.2023.100200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Split-hand/foot malformation (SHFM) is a congenital limb defect most typically presenting with median clefts in hands and/or feet, that can occur in a syndromic context as well as in isolated form. SHFM is caused by failure to maintain normal apical ectodermal ridge function during limb development. Although several genes and contiguous gene syndromes are implicated in the monogenic etiology of isolated SHFM, the disorder remains genetically unexplained for many families and associated genetic loci. We describe a family with isolated X-linked SHFM, for which the causative variant could be detected after a diagnostic journey of 20 years. We combined well-established approaches including microarray-based copy number variant analysis and fluorescence in situ hybridization coupled with optical genome mapping and whole genome sequencing. This strategy identified a complex structural variant (SV) comprising a 165-kb gain of 15q26.3 material ([GRCh37/hg19] chr15:99795320-99960362dup) inserted in inverted position at the site of a 38-kb deletion on Xq27.1 ([GRCh37/hg19] chrX:139481061-139518989del). In silico analysis suggested that the SV disrupts the regulatory framework on the X chromosome and may lead to SOX3 misexpression. We hypothesize that SOX3 dysregulation in the developing limb disturbed the fine balance between morphogens required for maintaining AER function, resulting in SHFM in this family.
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Affiliation(s)
- Elke de Boer
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Ellen van Beusekom
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willemijn M. Klein
- Department of Medical Imaging, Radiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Uirá S. Melo
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Dominique Smeets
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, 23562 Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
- Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Radboudumc University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
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3
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Li Q, Wang Y, Liu F, Wang H, Fan Y. LRSAM1 E3 Ubiquitin Ligase Promotes Choriocarcinoma Progression and Metastasis via p53/p21 Signaling Impediment. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1926605. [PMID: 36093406 PMCID: PMC9453058 DOI: 10.1155/2022/1926605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/06/2022] [Accepted: 08/10/2022] [Indexed: 11/18/2022]
Abstract
Objective The E3 ubiquitin ligase LRSAM1 (LRSAM1) was involved in many cancers, but whether it exerts anti- or protumor efficacies on choriocarcinoma cellular structures remains unknown. We wanted to explore the efficacies of aberrant LRSAM1 expression on human choriocarcinoma cellular structures and the underlying mechanisms. Methods LRSAM1 mRNA expressions in choriocarcinoma lines of cells JEG-3 and JAR cellular structures, as well as HTR8/sev8 human trophoblastic cell line cellular structures, were assessed using assay analysis of quantitative real-time polymerase chain reactions. We compared cell proliferation, migratory flow, invasive force, adhesion, and apoptotic process between cellular structures infected with si-LRSAM1 plasmids versus negative controls using CCK-8, clone formation, Transwell, adhesion, and flow cytometry assays. Protein expressions of LRSAM1, E-cadherin, and N-cadherin (indicators of epithelial-mesenchymal transformation) and p53/p21 pathway components were quantitated using a Western blot assay. The morphology of tumor lesions was observed in xenografted nude mice using immunohistochemistry (IHC) analyses. Results LRSAM1 was markedly overexpressed within JEG-3 and JAR choriocarcinoma cellular structures compared to HTR8/sev8 trophoblast cellular structures. Compared to si-NC, LRSAM1 knockdown robustly restricted cell proliferating, migratory flow, invasive force, and adhesion and fueled apoptotic cell process in JEG-3 as well as JAR cellular structures and suppressed tumor growth, as evidenced by the reduction in tumor volume and weight in naked mice inoculated with transfected cellular structures. Compared to si-negative control (si-NC), si-LRSAM1 significantly decreased Ki67 (a proliferating indicator) and N-cadherin expressions but reduced E-cadherin expression in JEG-3 and JAR cellular structures. Blocking the p53/p21 pathway by pifithrin-a (a p53 restrictor) successfully reversed the anti-inhibitory effect of LRSAM1 depletion, resulting in enhanced proliferating and metastasis in JEG-3 and JAR cellular structures. Conclusion LRSAM1 exerts tumorigenic roles in choriocarcinoma. Via the activating of the p53/p21 pathway of signaling and impediment of choriocarcinoma cell proliferating, migratory flow, and invasive force, LRSAM1 knockdown slows the course of the disease. For choriocarcinoma diagnosis and treatment, it serves as a new therapeutic target.
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Affiliation(s)
- Qiumin Li
- Department of Obstetrics, Shaanxi Provincial People's Hospital, China
| | - Ying Wang
- Department of Obstetrics, Shaanxi Provincial People's Hospital, China
| | - Feifei Liu
- Department of Obstetrics, Shaanxi Provincial People's Hospital, China
| | - Haili Wang
- Department of Obstetrics, Shaanxi Provincial People's Hospital, China
| | - Yangyang Fan
- Department of Obstetrics, Shaanxi Provincial People's Hospital, China
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4
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Jang H, Stevens P, Gao T, Galperin E. The leucine-rich repeat signaling scaffolds Shoc2 and Erbin: cellular mechanism and role in disease. FEBS J 2021; 288:721-739. [PMID: 32558243 PMCID: PMC7958993 DOI: 10.1111/febs.15450] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/28/2020] [Accepted: 06/10/2020] [Indexed: 12/12/2022]
Abstract
Leucine-rich repeat-containing proteins (LRR proteins) are involved in supporting a large number of cellular functions. In this review, we summarize recent advancements in understanding functions of the LRR proteins as signaling scaffolds. In particular, we explore what we have learned about the mechanisms of action of the LRR scaffolds Shoc2 and Erbin and their roles in normal development and disease. We discuss Shoc2 and Erbin in the context of their multiple known interacting partners in various cellular processes and summarize often unexpected functions of these proteins through analysis of their roles in human pathologies. We also review these LRR scaffold proteins as promising therapeutic targets and biomarkers with potential application across various pathologies.
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Affiliation(s)
- HyeIn Jang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Payton Stevens
- Center for Cancer and Cell Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Tianyan Gao
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
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5
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Chen H, Cao W, Chen J, Liu D, Zhou L, Du F, Zhu F. miR-218 contributes to drug resistance in multiple myeloma via targeting LRRC28. J Cell Biochem 2021; 122:305-314. [PMID: 33417267 DOI: 10.1002/jcb.29684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/13/2020] [Indexed: 01/09/2023]
Abstract
Multiple myeloma (MM) is a malignant neoplasm featured by obvious drug resistance and poor prognosis. MicroRNAs (miRNAs) are a class of small noncoding RNAs with crucial roles in many biological processes including cancer initiation and progression. The current study aims to investigate the pathogenic role and molecular mechanism of miRNAs in MM drug resistance. In the present study, The expression profile of miRNAs in MM samples was analyzed by microarray and real-time polymerase chain reaction. Protein expressions were detected by Western blot analysis. Cell apoptosis was detected by the Annexin V staining assay. The interaction between miRNA and the targeting mRNA was assessed using Dual luciferase reporter assay. Herein, we show that expression profile of miRNAs is deregulated in MM. miR-218, one of the most aberrational miRNAs in MM, is significantly decreased in MM cells compared to peripheral blood mononuclear cell (PBMC). Genetic manipulation reveals miR-218 control the response of MM cells to anticancer drug bortezomib (BTZ). Overexpression of miR-218 causes a significant aberrant genes expression including leucine rich repeat containing 28 (LRRC28). Mechanistic study shows that miR-218 control the drug response through mediating the expression of LRRC28 in MM cells. Overexpression of LRRC28 significantly reserves miR-218-mediated cell response to BTZ. Taken together, miR-218 is decreased in MM that contributes to BTZ resistance via targeting LRRC28, which might be used as a novel therapeutic target for multiple myeloma.
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Affiliation(s)
- Haifei Chen
- Department of Hematology, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Weiling Cao
- Department of Pharmacy, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Jiao Chen
- Department of Hematology, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Danbo Liu
- Department of Hematology, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Lingyun Zhou
- Department of Hematology, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Fang Du
- Department of Hematology, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Feiqi Zhu
- Cognitive Impairment Ward of Neurology Department, Shenzhen Luohu People's Hospital, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
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6
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Rivière T, Bader A, Pogoda K, Walzog B, Maier-Begandt D. Structure and Emerging Functions of LRCH Proteins in Leukocyte Biology. Front Cell Dev Biol 2020; 8:584134. [PMID: 33072765 PMCID: PMC7536344 DOI: 10.3389/fcell.2020.584134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/01/2020] [Indexed: 01/10/2023] Open
Abstract
Actin-dependent leukocyte trafficking and activation are critical for immune surveillance under steady state conditions and during disease states. Proper immune surveillance is of utmost importance in mammalian homeostasis and it ensures the defense against pathogen intruders, but it also guarantees tissue integrity through the continuous removal of dying cells or the elimination of tumor cells. On the cellular level, these processes depend on the precise reorganization of the actin cytoskeleton orchestrating, e.g., cell polarization, migration, and vesicular dynamics in leukocytes. The fine-tuning of the actin cytoskeleton is achieved by a multiplicity of actin-binding proteins inducing, e.g., the organization of the actin cytoskeleton or linking the cytoskeleton to membranes and their receptors. More than a decade ago, the family of leucine-rich repeat (LRR) and calponin homology (CH) domain-containing (LRCH) proteins has been identified as cytoskeletal regulators. The LRR domains are important for protein-protein interactions and the CH domains mediate actin binding. LRR and CH domains are frequently found in many proteins, but strikingly the simultaneous expression of both domains in one protein only occurs in the LRCH protein family. To date, one LRCH protein has been described in drosophila and four LRCH proteins have been identified in the murine and the human system. The function of LRCH proteins is still under investigation. Recently, LRCH proteins have emerged as novel players in leukocyte function. In this review, we summarize our current understanding of LRCH proteins with a special emphasis on their function in leukocyte biology.
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Affiliation(s)
- Thibaud Rivière
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Almke Bader
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kristin Pogoda
- Department of Physiology, Medical Faculty, Augsburg University, Augsburg, Germany
| | - Barbara Walzog
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Daniela Maier-Begandt
- Institute of Cardiovascular Physiology and Pathophysiology, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Walter Brendel Center of Experimental Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
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7
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Pian L, Huang X, Zhao M, Zhang Y, Qin C, Zhang J, Zhang J, Wang Q. Leucine-rich repeat and sterile alpha motif containing 1 promotes the oncogenic growth of human hepatocellular carcinoma cells. Cancer Cell Int 2019; 19:255. [PMID: 31592239 PMCID: PMC6775663 DOI: 10.1186/s12935-019-0976-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/23/2019] [Indexed: 01/07/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC), the most common primary cancer of the liver, is one of the most common malignancies and the leading cause of cancer-related death worldwide. Leucine-rich repeat and sterile alpha motif containing 1 (LRSAM1) is an E3 ubiquitin ligase involved in diverse cellular activities, including the regulation of cargo sorting, cell adhesion and antibacterial autophagy. The role of LRSAM1 in HCC remains unknown. Methods In this study, we reviewed the TCGA database and then performed gain-of-function and loss-of-function analyses of LRSAM1 in HCC cell lines. Results We found that the mRNA expression level of LRSAM1 was significantly increased in clinical HCC tissues in the TCGA database. Transient LRSAM1 knockdown in several human HCC cell lines led to reduced growth in conventional culture conditions. Stable LRSAM1 knockdown in HepG2 cells led to impaired anchorage-independent growth whereas its stable ectopic overexpression yielded the opposite effects. LRSAM1 overexpression in HepG2 cells enhanced in vivo tumorigenicity, whereas LRSAM1 knockdown in this cell line significantly impaired tumor growth. Conclusions Our data suggest that LRSAM1 promotes the oncogenic growth of human HCC cells, although the underlying mechanisms remain to be explored.
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Affiliation(s)
- Lili Pian
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China.,2Henan University Joint National Laboratory for Antibody Drug Engineering, School of Medicine, Henan University, Jinming District, Kaifeng, 475004 People's Republic of China
| | - Xiaofeng Huang
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China
| | - Min Zhao
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China
| | - Yaolin Zhang
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China
| | - Cheng Qin
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China
| | - Jiyan Zhang
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China
| | - Jun Zhang
- 2Henan University Joint National Laboratory for Antibody Drug Engineering, School of Medicine, Henan University, Jinming District, Kaifeng, 475004 People's Republic of China
| | - Qingyang Wang
- Beijing Institute of Brain Sciences, East 0749, 27# Taiping Road, Haidian District, Beijing, 100850 China
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8
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Chen L, König B, Liu T, Pervaiz S, Razzaque YS, Stauber T. More than just a pressure relief valve: physiological roles of volume-regulated LRRC8 anion channels. Biol Chem 2019; 400:1481-1496. [DOI: 10.1515/hsz-2019-0189] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/27/2019] [Indexed: 12/29/2022]
Abstract
Abstract
The volume-regulated anion channel (VRAC) is a key player in the volume regulation of vertebrate cells. This ubiquitously expressed channel opens upon osmotic cell swelling and potentially other cues and releases chloride and organic osmolytes, which contributes to regulatory volume decrease (RVD). A plethora of studies have proposed a wide range of physiological roles for VRAC beyond volume regulation including cell proliferation, differentiation and migration, apoptosis, intercellular communication by direct release of signaling molecules and by supporting the exocytosis of insulin. VRAC was additionally implicated in pathological states such as cancer therapy resistance and excitotoxicity under ischemic conditions. Following extensive investigations, 5 years ago leucine-rich repeat-containing family 8 (LRRC8) heteromers containing LRRC8A were identified as the pore-forming components of VRAC. Since then, molecular biological approaches have allowed further insight into the biophysical properties and structure of VRAC. Heterologous expression, siRNA-mediated downregulation and genome editing in cells, as well as the use of animal models have enabled the assessment of the proposed physiological roles, together with the identification of new functions including spermatogenesis and the uptake of antibiotics and platinum-based cancer drugs. This review discusses the recent molecular biological insights into the physiology of VRAC in relation to its previously proposed roles.
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Affiliation(s)
- Lingye Chen
- Institut für Chemie und Biochemie , Freie Universität Berlin , Thielallee 63 , D-14195 Berlin , Germany
| | - Benjamin König
- Institut für Chemie und Biochemie , Freie Universität Berlin , Thielallee 63 , D-14195 Berlin , Germany
| | - Tianbao Liu
- Institut für Chemie und Biochemie , Freie Universität Berlin , Thielallee 63 , D-14195 Berlin , Germany
| | - Sumaira Pervaiz
- Institut für Chemie und Biochemie , Freie Universität Berlin , Thielallee 63 , D-14195 Berlin , Germany
| | - Yasmin S. Razzaque
- Institut für Chemie und Biochemie , Freie Universität Berlin , Thielallee 63 , D-14195 Berlin , Germany
| | - Tobias Stauber
- Institut für Chemie und Biochemie , Freie Universität Berlin , Thielallee 63 , D-14195 Berlin , Germany
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9
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Fukamachi K, Hagiwara Y, Futakuchi M, Alexander DB, Tsuda H, Suzui M. Evaluation of a biomarker for the diagnosis of pancreas cancer using an animal model. J Toxicol Pathol 2019; 32:135-141. [PMID: 31404387 PMCID: PMC6682554 DOI: 10.1293/tox.2018-0062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/27/2019] [Indexed: 12/03/2022] Open
Abstract
Many approaches have been taken to identify new biomarkers of pancreatic ductal
carcinoma (PDC). Since animal models can be sampled under controlled conditions, better
standardization is possible compared with heterogeneous human studies. Transgenic rats
with conditional activation of oncogenic RAS in pancreatic tissue develop PDC that closely
resembles the biological and histopathological features of human PDC. Using this model, we
evaluated the usefulness of leucine-rich α2-glycoprotein-1 (LRG-1) as a serum marker. In
this study, we found that LRG-1 was overexpressed in rat PDC compared with normal pancreas
tissue of the control rats. Serum levels of LRG-1 were also significantly higher in rats
bearing PDC than in controls. Importantly, chronic pancreatitis in male Wistar Bonn/Kobori
rats, which is a widely accepted as a model of chronic pancreatitis, did not cause serum
levels of LRG-1 to become elevated. These results strongly support serum LRG-1 as a
candidate biomarker for noninvasive diagnosis of PDC. Our models of pancreas cancer
provide a useful strategy for evaluation of candidate markers applicable to human
cancer.
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Affiliation(s)
- Katsumi Fukamachi
- Department of Molecular Toxicology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8601, Japan
| | - Yoshiaki Hagiwara
- Immuno-Biological Laboratories, 1091-1 Naka, Fujioka-shi, Gunma 375-0005, Japan
| | - Mitsuru Futakuchi
- Department of Molecular Toxicology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8601, Japan
| | - David B Alexander
- Nanotoxicology Project, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Hiroyuki Tsuda
- Nanotoxicology Project, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Masumi Suzui
- Department of Molecular Toxicology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, Aichi 467-8601, Japan
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10
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McGovern SP, Purfield DC, Ring SC, Carthy TR, Graham DA, Berry DP. Candidate genes associated with the heritable humoral response to Mycobacterium avium ssp. paratuberculosis in dairy cows have factors in common with gastrointestinal diseases in humans. J Dairy Sci 2019; 102:4249-4263. [PMID: 30852025 DOI: 10.3168/jds.2018-15906] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/20/2019] [Indexed: 01/09/2023]
Abstract
Infection of cattle with bovine paratuberculosis (i.e., Johne's disease) is caused by Mycobacterium avium ssp. paratuberculosis (MAP) and results in a chronic incurable gastroenteritis. This disease, which has economic ramifications for the cattle industry, is increasing in detected prevalence globally; subclinically infected animals can silently shed the bacterium into the environment for years, exposing contemporaries and hampering disease-control programs. The objective of the present study was to first quantify the genetic parameters for humoral response to MAP in dairy cattle. This was followed by a genome-based association analysis and subsequent downstream bioinformatic analyses from imputed whole genome sequence SNP data. After edits, ELISA test records were available on 136,767 cows; analyses were also undertaken on a subset of 33,818 of these animals from herds with at least 5 MAP ELISA-positive cows, with at least 1 of those positive cows being homebred. Variance components were estimated using univariate animal and sire linear mixed models. The heritability calculated from the animal model for humoral response to MAP using alternative phenotype definitions varied from 0.02 (standard error = 0.003) to 0.05 (standard error = 0.008). The genome-based associations were undertaken within a mixed model framework using weighted deregressed estimated breeding values as a dependent variable on 1,883 phenotyped animals that were ≥87.5% Holstein-Friesian. Putative susceptibility quantitative trait loci (QTL) were identified on Bos taurus autosome 1, 3, 5, 6, 8, 9, 10, 11, 13, 14, 18, 21, 23, 25, 26, 27, and 29; mapping the most significant SNP to genes within and overlapping these QTL revealed that the most significant associations were with the 10 functional candidate genes KALRN, ZBTB20, LPP, SLA2, FI3A1, LRCH3, DNAJC6, ZDHHC14, SNX1, and HAS2. Pathway analysis failed to reveal significantly enriched biological pathways, when both bovine-specific pathway data and human ortholog data were taken into account. The existence of genetic variation for MAP susceptibility in a large data set of dairy cows signifies the potential of breeding programs for reducing MAP susceptibility. Furthermore, the identification of susceptible QTL facilitates greater biological understanding of bovine paratuberculosis and potential therapeutic targets for future investigation. The novel molecular similarities identified between bovine paratuberculosis and human inflammatory bowel disease suggest potential for human therapeutic interventions to be translated to veterinary medicine and vice versa.
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Affiliation(s)
- S P McGovern
- Department of Microbiology, University College Cork, Coláiste na hOllscoile Corcaigh, College Road, Cork City, Co. Cork, Ireland T12 CY82
| | - D C Purfield
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - S C Ring
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co. Cork, Ireland P72 X050
| | - T R Carthy
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996
| | - D A Graham
- Animal Health Ireland, 4-5 The Archways, Carrick-on-Shannon, Co. Leitrim, Ireland N41 WN27
| | - D P Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland P61 C996.
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11
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Sabrkhany S, Kuijpers MJE, Knol JC, Olde Damink SWM, Dingemans AMC, Verheul HM, Piersma SR, Pham TV, Griffioen AW, Oude Egbrink MGA, Jimenez CR. Exploration of the platelet proteome in patients with early-stage cancer. J Proteomics 2018; 177:65-74. [PMID: 29432918 DOI: 10.1016/j.jprot.2018.02.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/29/2017] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
Abstract
Platelets play an important role in tumor growth and, at the same time, platelet characteristics are affected by cancer presence. Therefore, we investigated whether the platelet proteome harbors differentially expressed proteins associated with early-stage cancer. For this proof-of-concept study, patients with early-stage lung (n = 8) or head of pancreas cancer (n = 4) were included, as were healthy sex- and age-matched controls for both subgroups. Blood samples were collected from controls and from patients before surgery. Furthermore, from six of the patients, a second sample was collected two months after surgery. NanoLC-MS/MS-based proteomics of gel-fractionated platelet proteins was used for comparative spectral count analyses of patients to controls and before to after surgery samples. The total platelet proteome dataset included 4384 unique proteins of which 85 were significantly (criteria Fc > 1.5 and p < 0.05) changed in early-stage cancer compared to controls. In addition, the levels of 81 platelet proteins normalized after tumor resection. When filtering for the most discriminatory proteins, we identified seven promising platelet proteins associated with early-stage cancer. In conclusion, this pioneering study on the platelet proteome in cancer patients clearly identifies platelets as a new source of candidate protein biomarkers of early-stage cancer. BIOLOGICAL SIGNIFICANCE Currently, most blood-based diagnostics/biomarker research is performed in serum or plasma, while the content of blood cells is usually neglected. It is known that especially blood platelets, which are the main circulating pool of many bioactive proteins, such as growth factors, chemokines, and cytokines, are a potentially rich source of biomarkers. The current study is the first to measure the effect of early-stage cancer on the platelet proteome of patients. Our study demonstrates that the platelet proteome of patients with early-stage lung or head of pancreas cancer differs considerably compared to that of healthy individuals of matched sex and age. In addition, the platelet proteome of cancer patients normalized after surgical resection of the tumor. Exploiting platelet proteome differences linked to both tumor presence and disease status, we were able to demonstrate that the platelet proteome can be mined for potential biomarkers of cancer.
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Affiliation(s)
- Siamack Sabrkhany
- Cardiovascular Research Institute Maastricht, Department of Physiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marijke J E Kuijpers
- Cardiovascular Research Institute Maastricht, Department of Biochemistry, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jaco C Knol
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Steven W M Olde Damink
- Cardiovascular Research Institute Maastricht, Department of Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Anne-Marie C Dingemans
- Cardiovascular Research Institute Maastricht, Department of Pulmonology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Henk M Verheul
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | - Mirjam G A Oude Egbrink
- Cardiovascular Research Institute Maastricht, Department of Physiology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands.
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12
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Mazzoccoli G, Colangelo T, Panza A, Rubino R, Tiberio C, Palumbo O, Carella M, Trombetta D, Gentile A, Tavano F, Valvano MR, Storlazzi CT, Macchia G, De Cata A, Bisceglia G, Capocefalo D, Colantuoni V, Sabatino L, Piepoli A, Mazza T. Analysis of clock gene-miRNA correlation networks reveals candidate drivers in colorectal cancer. Oncotarget 2018; 7:45444-45461. [PMID: 27323779 PMCID: PMC5216733 DOI: 10.18632/oncotarget.9989] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/29/2016] [Indexed: 12/20/2022] Open
Abstract
Altered functioning of the biological clock is involved in cancer onset and progression. MicroRNAs (miRNAs) interact with the clock genes modulating the function of genetically encoded molecular clockworks. Collaborative interactions may take place within the coding-noncoding RNA regulatory networks. We aimed to evaluate the cross-talk among miRNAs and clock genes in colorectal cancer (CRC). We performed an integrative analysis of miRNA-miRNA and miRNA-mRNA interactions on high-throughput molecular profiling of matched human CRC tissue and non-tumor mucosa, pinpointing core clock genes and their targeting miRNAs. Data obtained in silico were validated in CRC patients and human colon cancer cell lines. In silico we found severe alterations of clock gene–related coding-noncoding RNA regulatory networks in tumor tissues, which were later corroborated by the analysis of human CRC specimens and experiments performed in vitro. In conclusion, specific miRNAs target and regulate the transcription/translation of clock genes and clock gene-related miRNA-miRNA as well as mRNA-miRNA interactions are altered in colorectal cancer. Exploration of the interplay between specific miRNAs and genes, which are critically involved in the functioning of the biological clock, provides a better understanding of the importance of the miRNA-clock genes axis and its derangement in colorectal cancer.
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Affiliation(s)
- Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Tommaso Colangelo
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Anna Panza
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Rosa Rubino
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Cristiana Tiberio
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Orazio Palumbo
- Medical Genetics Service, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Medical Genetics Service, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Domenico Trombetta
- Oncology-Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Annamaria Gentile
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Maria Rosa Valvano
- Division of Gastroenterology and Research Laboratory, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | | | - Gemma Macchia
- Department of Biology, University of Bari, Bari, Italy
| | - Angelo De Cata
- Division of Internal Medicine and Chronobiology Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Giovanni Bisceglia
- Department of Surgical Sciences, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Vittorio Colantuoni
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Lina Sabatino
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Ada Piepoli
- Division of Epidemiology and Health Statistics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo (FG), Italy
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13
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Shi Q, Xiong B, Zhong J, Wang H, Ma D, Miao C. MFHAS1 suppresses TLR4 signaling pathway via induction of PP2A C subunit cytoplasm translocation and inhibition of c-Jun dephosphorylation at Thr239. Mol Immunol 2017; 88:79-88. [PMID: 28609714 DOI: 10.1016/j.molimm.2017.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/30/2017] [Accepted: 06/02/2017] [Indexed: 11/20/2022]
Abstract
TLR4, an important Toll-like receptor in innate immunity, can be activated by LPS and induce proinflammatory cytokines to resist invasion of pathogenic microorganism, but excessive inflammation can trigger tissue injury. Many genes negatively regulate TLR4 signaling pathway. Recent studies found that malignant fibrous histiocytoma amplified sequence 1 (MFHAS1) suppressed the expression of cytokine IL6 in Raw264.7 cells stimulated by LPS, but the mechanisms remained unclear. This study investigated the role of MFHAS1 in TLR4 signaling pathway and the possible mechanisms implicated. The results indicated that the expression of MFHAS1 was significantly increased in cells stimulated with LPS. Up-regulation of MFHAS1 effectively suppressed inflammatory cytokine expression in cells exposed to LPS, whereas down-regulation of MFHAS1 markedly increased inflammatory cytokines expression. Co-immunoprecipitation, pull-down and immunofluorescence tests demonstrated that MFHAS1 combined with the B and C subunits of PP2A and induced cytoplasm translocation of the C subunit, leading to decrease dephosphorylation of c-Jun at Thr239 and increase degradation of c-Jun. Reduction of c-Jun protein results in decreased AP-1 activity, which is independent of inhibition of JNK or p38MAPK phosphorylation. Taken together, these results indicate that MFHAS1 suppresses TLR4 signaling pathway through induction of PP2A C subunit cytoplasm translocation and subsequent c-Jun degradation, leading finally to decrease AP-1 activity and cytokines expression.
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Affiliation(s)
- Qiqing Shi
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Anesthesiology, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Bo Xiong
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jing Zhong
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Huihui Wang
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China; Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Changhong Miao
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
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14
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Mazza T, Mazzoccoli G, Fusilli C, Capocefalo D, Panza A, Biagini T, Castellana S, Gentile A, De Cata A, Palumbo O, Stallone R, Rubino R, Carella M, Piepoli A. Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer. Nucleic Acids Res 2016; 44:4025-36. [PMID: 27067546 PMCID: PMC4872111 DOI: 10.1093/nar/gkw245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/24/2016] [Indexed: 12/16/2022] Open
Abstract
Alterations in the balance of mRNA and microRNA (miRNA) expression profiles contribute to the onset and development of colorectal cancer. The regulatory functions of individual miRNA-gene pairs are widely acknowledged, but group effects are largely unexplored. We performed an integrative analysis of mRNA–miRNA and miRNA–miRNA interactions using high-throughput mRNA and miRNA expression profiles obtained from matched specimens of human colorectal cancer tissue and adjacent non-tumorous mucosa. This investigation resulted in a hypernetwork-based model, whose functional backbone was fulfilled by tight micro-societies of miRNAs. These proved to modulate several genes that are known to control a set of significantly enriched cancer-enhancer and cancer-protection biological processes, and that an array of upstream regulatory analyses demonstrated to be dependent on miR-145, a cell cycle and MAPK signaling cascade master regulator. In conclusion, we reveal miRNA-gene clusters and gene families with close functional relationships and highlight the role of miR-145 as potent upstream regulator of a complex RNA–RNA crosstalk, which mechanistically modulates several signaling pathways and regulatory circuits that when deranged are relevant to the changes occurring in colorectal carcinogenesis.
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Affiliation(s)
- Tommaso Mazza
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Anna Panza
- Department of Medical Sciences, Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Annamaria Gentile
- Department of Medical Sciences, Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Angelo De Cata
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Orazio Palumbo
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Raffaella Stallone
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Rosa Rubino
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Ada Piepoli
- Division of Epidemiology and Health Statistics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
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15
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Wang Z, Hu J, Li G, Qu L, He Q, Lou Y, Song Q, Ma D, Chen Y. PHF23 (plant homeodomain finger protein 23) negatively regulates cell autophagy by promoting ubiquitination and degradation of E3 ligase LRSAM1. Autophagy 2015; 10:2158-70. [PMID: 25484098 DOI: 10.4161/auto.36439] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Autophagy is a multistep process that involves the degradation and digestion of intracellular components by the lysosome. It has been proved that many core autophagy-related molecules participate in this event. However, new component proteins that regulate autophagy are still being discovered. At present, we report PHF23 (PHD finger protein 23) with a PHD-like zinc finger domain that can negatively regulate autophagy. Data from experiments indicated that the overexpression of PHF23 impaired autophagy, as characterized by decreased levels of LC3B-II and weakened degradation of endogenous and exogenous autophagic substrates. Conversely, knockdown of PHF23 resulted in opposite effects. Molecular mechanism studies suggested that PHF23 interacts with LRSAM1, which is an E3 ligase key for ubiquitin-dependent autophagy against invading bacteria. PHF23 promotes the ubiquitination and proteasome degradation of LRSAM1. We also show that the PHD finger of PHF23 is a functional domain needed for the interaction with LRSAM1. Altogether, our results indicate that PHF23 is a negative regulator associated in autophagy via the LRSAM1 signaling pathway. The physical and functional connection between the PHF23 and LRSAM1 needs further investigation.
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Key Words
- AML, acute myeloid leukemia
- ATG, autophagy-related
- BafA1, bafilomycin A1
- CALCOCO2, calcium binding and coiled-coil domain 2
- CQ, chloroquine
- EBSS, Earle's balanced salt solution
- FBS, fetal bovine serum
- GFP, green fluorescent protein
- GST, glutathione S-transferase
- IP, immunoprecipitation
- LRSAM1
- LRSAM1, leucine rich repeat and sterile α motif containing 1
- MAP1LC3B/LC3B
- PHD domain
- PHD, plant homeodomain
- PHF23
- PHF23, PHD finger protein 23
- PIK3C3, phosphatidylinositol 3-kinase, catalytic subunit type 3
- SQSTM1, sequestosome 1
- Three-MA, 3-methyladenine
- autophagy
- microtubule-associated protein 1 light chain 3 β
- ubiquitination
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Affiliation(s)
- Zhenda Wang
- a Key Laboratory of Medical Immunology; Ministry of Health ; Peking University Health Science Center ; Beijing , China
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16
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Integrated exon level expression analysis of driver genes explain their role in colorectal cancer. PLoS One 2014; 9:e110134. [PMID: 25335079 PMCID: PMC4204855 DOI: 10.1371/journal.pone.0110134] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 09/16/2014] [Indexed: 12/14/2022] Open
Abstract
Integrated analysis of genomic and transcriptomic level changes holds promise for a better understanding of colorectal cancer (CRC) biology. There is a pertinent need to explain the functional effect of genome level changes by integrating the information at the transcript level. Using high resolution cytogenetics array, we had earlier identified driver genes by ‘Genomic Identification of Significant Targets In Cancer (GISTIC)’ analysis of paired tumour-normal samples from colorectal cancer patients. In this study, we analyze these driver genes at three levels using exon array data – gene, exon and network. Gene level analysis revealed a small subset to experience differential expression. These results were reinforced by carrying out separate differential expression analyses (SAM and LIMMA). ATP8B1 was found to be the novel gene associated with CRC that shows changes at cytogenetic, gene and exon levels. Splice index of 29 exons corresponding to 13 genes was found to be significantly altered in tumour samples. Driver genes were used to construct regulatory networks for tumour and normal groups. There were rearrangements in transcription factor genes suggesting the presence of regulatory switching. The regulatory pattern of AHR gene was found to have the most significant alteration. Our results integrate data with focus on driver genes resulting in highly enriched novel molecules that need further studies to establish their role in CRC.
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