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Rizzi G, Digiovanni S, Degani G, Barbiroli A, Di Pisa F, Popolo L, Visentin C, Vanoni MA, Ricagno S. Site-directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus. Protein Sci 2024; 33:e5036. [PMID: 38801230 PMCID: PMC11129622 DOI: 10.1002/pro.5036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Reactive intermediate deaminase A (RidA) is a highly conserved enzyme that catalyzes the hydrolysis of 2-imino acids to the corresponding 2-keto acids and ammonia. RidA thus prevents the accumulation of such potentially harmful compounds in the cell, as exemplified by its role in the degradation of 2-aminoacrylate, formed during the metabolism of cysteine and serine, catalyzing the conversion of its stable 2-iminopyruvate tautomer into pyruvate. Capra hircus (goat) RidA (ChRidA) was the first mammalian RidA to be isolated and described. It has the typical homotrimeric fold of the Rid superfamily, characterized by remarkably high thermal stability, with three active sites located at the interface between adjacent subunits. ChRidA exhibits a broad substrate specificity with a preference for 2-iminopyruvate and other 2-imino acids derived from amino acids with non-polar non-bulky side chains. Here we report a biophysical and biochemical characterization of eight ChRidA variants obtained by site-directed mutagenesis to gain insight into the role of specific residues in protein stability and catalytic activity. Each mutant was produced in Escherichia coli cells, purified and characterized in terms of quaternary structure, thermal stability and substrate specificity. The results are rationalized in the context of the high-resolution structures obtained by x-ray crystallography.
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Affiliation(s)
- Giulia Rizzi
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | | | - Genny Degani
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'AmbienteUniversità degli Studi di MilanoMilanItaly
| | - Flavio Di Pisa
- Istituto di BiofisicaConsiglio Nazionale delle RicercheMilanItaly
| | - Laura Popolo
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | - Cristina Visentin
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | | | - Stefano Ricagno
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
- Institute of Molecular and Translational CardiologyI.R.C.C.S. Policlinico San DonatoSan Donato MilaneseItaly
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He J, Chen Z, Jing C, Zhang W, Peng H, Zhou H, Hu F. Behavioral and biochemical responses of the marine polychaete Perinereis aibuhitensis to 2-ethylhexyl-4-methoxycinnamate (EHMC) exposure. Comp Biochem Physiol C Toxicol Pharmacol 2024; 279:109868. [PMID: 38423197 DOI: 10.1016/j.cbpc.2024.109868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/02/2024] [Accepted: 02/24/2024] [Indexed: 03/02/2024]
Abstract
2-ethylhexyl-4-methoxycinnamate (EHMC) is a commonly used UV filter, and is receiving increasing concerns due to its ubiquitous occurrence in a variety of environmental media and potential adverse effects. This study was aimed to assess the ecotoxicological potentials of EHMC on the marine polychaete Perinereis aibuhitensis. To this end, ragworms were exposed to 2, 20, 200 μg/L EHMC for 14 days and multiple toxicological endpoints were investigated. The results showed that EHMC significantly reduced burrowing rate, but did not affect AChE activity. Exposure to EHMC significantly elevated the activities of SOD and CAT and decreased the levels of lipid peroxidation. Besides, the induction of AKP activity indicated a stimulated immune response in the ragworms when exposed to high concentration of EHMC. Furthermore, the upregulated expression of caspase-8 suggested that EHMC might induce apoptosis in ragworms via the death receptor-mediated extrinsic pathway. Our findings highlight the potential environmental risks of EHMC to marine ecosystems.
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Affiliation(s)
- Jiabo He
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhi Chen
- Freshwater Fisheries Research Institute of Fujian, Fuzhou 350002, China
| | - Chen Jing
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiwei Zhang
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangke Peng
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Honglei Zhou
- Fujian Yangze Marine Biotechnology Co., Ltd, Fuzhou 350600, China.
| | - Fengxiao Hu
- Key Laboratory of Marine Biotechnology of Fujian Province, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Technology Innovation Center for Monitoring and Restoration Engineering of Ecological Fragile Zone in Southeast China, Ministry of Natural Resources, Fuzhou 350001, China.
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3
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Rezaee A, Ahmadpour S, Jafari A, Aghili S, Zadeh SST, Rajabi A, Raisi A, Hamblin MR, Mahjoubin-Tehran M, Derakhshan M. MicroRNAs, long non-coding RNAs, and circular RNAs and gynecological cancers: focus on metastasis. Front Oncol 2023; 13:1215194. [PMID: 37854681 PMCID: PMC10580988 DOI: 10.3389/fonc.2023.1215194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/28/2023] [Indexed: 10/20/2023] Open
Abstract
Gynecologic cancer is a significant cause of death in women worldwide, with cervical cancer, ovarian cancer, and endometrial cancer being among the most well-known types. The initiation and progression of gynecologic cancers involve a variety of biological functions, including angiogenesis and metastasis-given that death mostly occurs from metastatic tumors that have invaded the surrounding tissues. Therefore, understanding the molecular pathways underlying gynecologic cancer metastasis is critical for enhancing patient survival and outcomes. Recent research has revealed the contribution of numerous non-coding RNAs (ncRNAs) to metastasis and invasion of gynecologic cancer by affecting specific cellular pathways. This review focuses on three types of gynecologic cancer (ovarian, endometrial, and cervical) and three kinds of ncRNAs (long non-coding RNAs, microRNAs, and circular RNAs). We summarize the detailed role of non-coding RNAs in the different pathways and molecular interactions involved in the invasion and metastasis of these cancers.
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Affiliation(s)
- Aryan Rezaee
- Student Research Committee, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Ahmadpour
- Biotechnology Department, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Ameneh Jafari
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sarehnaz Aghili
- Department of Gynecology and Obstetrics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Ali Rajabi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Arash Raisi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marzieh Derakhshan
- Shahid Beheshti Fertility Clinic, Department of Gynecology and Obsteterics, Isfahan University of Medical Sciences, Isfahan, Iran
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4
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Scimone C, Alibrandi S, Donato L, De Gaetano GV, Fusco C, Nardella G, Castori M, Rinaldi C, Alafaci C, Germanò A, D'Angelo R, Sidoti A. Amplification of protease-activated receptors signaling in sporadic cerebral cavernous malformation endothelial cells. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119474. [PMID: 37030452 DOI: 10.1016/j.bbamcr.2023.119474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/13/2023] [Accepted: 03/30/2023] [Indexed: 04/10/2023]
Abstract
In the central nervous system, thrombin-mediated activation of protease-activated receptors (PARs) results in neuroinflammation and increased vascular permeability. These events have been linked to cancer and neurodegeneration. Endothelial cells (ECs) isolated from sporadic cerebral cavernous malformation (CCM) specimens showed dysregulation of genes involved in "thrombin-mediated PAR-1 activation" signaling. CCM is a vascular disease involving brain capillaries. In CCM, ECs show defective cell junctions. Oxidative stress and neuroinflammation play a key role in disease onset and progression. In order to confirm the possible role of thrombin pathway in sporadic CCM pathogenesis, we evaluated PARs expression in CCM-ECs. We found that sporadic CCM-ECs overexpress PAR1, PAR3 and PAR4, together with other coagulation factor encoding genes. Moreover, we investigated about expression of the three familial CCM genes (KRIT1, CCM2 and PDCD10) in human cerebral microvascular ECs, following thrombin exposure, as well as protein level. Thrombin exposure affects EC viability and results in dysregulation of CCM gene expression and, then, in decreased protein level. Our results confirm amplification of PAR pathway in CCM suggesting, for the first time, the possible role of PAR1-mediated thrombin signaling in sporadic CCM. Thrombin-mediated PARs over activation results in increased blood-brain barrier permeability due to loss of cell junction integrity and, in this context, also the three familial CCM genes may be involved.
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Affiliation(s)
- Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy; Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., via Michele Miraglia 20, Palermo 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy; Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., via Michele Miraglia 20, Palermo 90139, Italy; Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, C.da Papardo-Sperone 31, 98100 Messina, Italy
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy; Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., via Michele Miraglia 20, Palermo 90139, Italy
| | | | - Carmela Fusco
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Grazia Nardella
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy.
| | - Concetta Alafaci
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy
| | - Antonino Germanò
- Neurosurgery Unit, Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy; Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., via Michele Miraglia 20, Palermo 90139, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, via Consolare Valeria 1, 98125 Messina, Italy; Department of Biomolecular Strategies, Genetics, Cutting-edge Therapies, I.E.ME.S.T., via Michele Miraglia 20, Palermo 90139, Italy
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Rashmi R, Majumdar S. Pan-Cancer Analysis Reveals the Prognostic Potential of the THAP9/THAP9-AS1 Sense-Antisense Gene Pair in Human Cancers. Noncoding RNA 2022; 8:ncrna8040051. [PMID: 35893234 PMCID: PMC9326536 DOI: 10.3390/ncrna8040051] [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: 04/05/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Human THAP9, which encodes a domesticated transposase of unknown function, and lncRNA THAP9-AS1 (THAP9-antisense1) are arranged head-to-head on opposite DNA strands, forming a sense and antisense gene pair. We predict that there is a bidirectional promoter that potentially regulates the expression of THAP9 and THAP9-AS1. Although both THAP9 and THAP9-AS1 are reported to be involved in various cancers, their correlative roles on each other’s expression has not been explored. We analyzed the expression levels, prognosis, and predicted biological functions of the two genes across different cancer datasets (TCGA, GTEx). We observed that although the expression levels of the two genes, THAP9 and THAP9-AS1, varied in different tumors, the expression of the gene pair was strongly correlated with patient prognosis; higher expression of the gene pair was usually linked to poor overall and disease-free survival. Thus, THAP9 and THAP9-AS1 may serve as potential clinical biomarkers of tumor prognosis. Further, we performed a gene co-expression analysis (using WGCNA) followed by a differential gene correlation analysis (DGCA) across 22 cancers to identify genes that share the expression pattern of THAP9 and THAP9-AS1. Interestingly, in both normal and cancer samples, THAP9 and THAP9-AS1 often co-express; moreover, their expression is positively correlated in each cancer type, suggesting the coordinated regulation of this H2H gene pair.
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Valentino M, Dejana E, Malinverno M. The multifaceted PDCD10/CCM3 gene. Genes Dis 2021; 8:798-813. [PMID: 34522709 PMCID: PMC8427250 DOI: 10.1016/j.gendis.2020.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/10/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
The programmed cell death 10 (PDCD10) gene was originally identified as an apoptosis-related gene, although it is now usually known as CCM3, as the third causative gene of cerebral cavernous malformation (CCM). CCM is a neurovascular disease that is characterized by vascular malformations and is associated with headaches, seizures, focal neurological deficits, and cerebral hemorrhage. The PDCD10/CCM3 protein has multiple subcellular localizations and interacts with several multi-protein complexes and signaling pathways. Thus PDCD10/CCM3 governs many cellular functions, which include cell-to-cell junctions and cytoskeleton organization, cell proliferation and apoptosis, and exocytosis and angiogenesis. Given its central role in the maintenance of homeostasis of the cell, dysregulation of PDCD10/CCM3 can result in a wide range of altered cell functions. This can lead to severe diseases, including CCM, cognitive disability, and several types of cancers. Here, we review the multifaceted roles of PDCD10/CCM3 in physiology and pathology, with a focus on its functions beyond CCM.
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Affiliation(s)
| | - Elisabetta Dejana
- The FIRC Institute of Molecular Oncology (IFOM), Milan, 16 20139, Italy.,Department of Oncology and Haemato-Oncology, University of Milan, Milan, 7 20122, Italy.,Vascular Biology, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, SE-751 05, Sweden
| | - Matteo Malinverno
- The FIRC Institute of Molecular Oncology (IFOM), Milan, 16 20139, Italy
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Qu C, Dai C, Guo Y, Qin R, Liu J. Long non-coding RNA PVT1-mediated miR-543/SERPINI1 axis plays a key role in the regulatory mechanism of ovarian cancer. Biosci Rep 2020; 40:BSR20200800. [PMID: 32441301 PMCID: PMC7295634 DOI: 10.1042/bsr20200800] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
PURPOSE To investigate the regulation mechanism of long non-coding RNA (lncRNA) plasmocytoma variant translocation 1 (PVT1) in ovarian cancer (OC). METHODS The levels of PVT1, microRNA (miR)-543, serpin peptidase inhibitor-clade I (neuroserpin)-member 1 (SERPINI1) in OC tissues and OVCAR-3, A2780, TOV-112D of OC cell lines were detected by quantitative real-time PCR (qRT-PCR) and Western Blot (WB). Cell proliferation, migration, invasion, apoptosis and the regulatory relationship between genes and target genes were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), Transwell, flow cytometry and dual luciferase reporter (DLR). The OC patients were followed up for 5 years to analyze the relationship between PVT1 and 5-year overall survival (OS). RESULTS In contrast with miR-543, PVT1 and SERPINI1 were highly expressed in OC tissues and cell lines, and high levels of PVT1 were significantly associated with lower 5-year OS of patients. Down-regulating PVT1 not only inhibited the malignant proliferation, migration and invasion of OC cells, but promoted cell apoptosis. PVT1 regulated miR-543 in a targeted manner, and its overexpression could attenuate the anticancer effect of miR-543 on OC cells. In addition, miR-543 also directly targeted SERPINI1, and miR-543 knockdown weakened the inhibitory effect of down-regulated SERPINI1 on OC progression. Furthermore, we found that PVT1 acted as a competitive endogenous RNA to sponge miR-543, thereby regulating the expression of SERPINI1. CONCLUSION PVT1 can mediate the molecular mechanism of OC by miR-543/SERPINI1 axis regulatory network, which is a new therapeutic direction for OC.
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Affiliation(s)
- Chong Qu
- Department of Neurosurgery, China-Japan Union Hopsital of Jilin University, Changchun City, Jilin Province, China
| | - Chunmei Dai
- School Hospital, Changchun University of Chinese Medicine, Changchun City, Jilin Province, China
| | - Yahua Guo
- Department of Obstetrics and Gynaecology of the China-Japan Union Hospital of Jilin University, Changchun City, Jilin Province, China
| | - Rui Qin
- Department of Obstetrics and Gynaecology of the China-Japan Union Hospital of Jilin University, Changchun City, Jilin Province, China
| | - Junbao Liu
- Department of Obstetrics and Gynaecology of the China-Japan Union Hospital of Jilin University, Changchun City, Jilin Province, China
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Fan L, Lei H, Zhang S, Peng Y, Fu C, Shu G, Yin G. Non-canonical signaling pathway of SNAI2 induces EMT in ovarian cancer cells by suppressing miR-222-3p transcription and upregulating PDCD10. Theranostics 2020; 10:5895-5913. [PMID: 32483426 PMCID: PMC7254989 DOI: 10.7150/thno.43198] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background: Epithelial ovarian cancer (EOC) is one of the most lethal malignancies in women worldwide. Many studies showed the transcription factor SNAI2-induced Epithelial-Mesenchymal Transition (EMT) through inhibiting E-cadherin (E-cad) expression. Our previous study reported that miR-222-3p was an important tumor-suppressive miRNA for EOC development and dissemination. The present study aimed to acquire a deeper mechanistic understanding of the role of miR-222-3p regulation that might contribute to improving current anti-metastasis strategies in EOC. Methods: A variety of techniques were used to measure mRNA and protein expression levels, including quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, immunohistochemical (IHC) staining, and immunofluorescence (IF). Four different microRNA (miRNA) target prediction databases were used to predict the target genes of miR-222. Luciferase assay was performed to determine the direct binding of miR-222-3p to the untranslated region (3'-UTR) of PDCD10. The biological effects of PDCD10 and miR-222-3p were also investigated in vitro by Transwell and wound healing assays, as well as in vivo by a xenograft mice model. Combining UCSC and JASPAR, as well as ENCODE public databases, we predicted that the transcription factor SNAI2 could affect miR-222-3p expression. Luciferase assay was utilized to examine the validity of putative SNAI2 binding sites for miR-222-3p regulation. Chromatin immunoprecipitation (ChIP) was used to explore the SNAI2's occupancy on the miR-222-3p promoter. Results: We observed the inhibitory effect of SNAI2 on miR-222-3p transcription and confirmed the tumor-suppressive function of miR-222-3p both in EOC cells and tissues. PDCD10 was upregulated and inversely correlated with miR-222-3p, both in vitro and in vivo, which was consistent with the information in bioinformatics databases. Furthermore, We observed direct binding of miR-222-3p to the 3'-UTR of PDCD10 and inhibition of PDCD10 translation, which, in turn, inhibited EOC cell migration in vitro and repressed EOC xenografted tumor metastasis in vivo. We found that genetic overexpression of PDCD10 (OE-PDCD10) increased cancer metastasis by down-regulating E-cad and enhancing Vimentin (VIM) thereby inducing EMT and promoting β-catenin/Wnt-mediated cell migration.
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Affiliation(s)
- Lili Fan
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Han Lei
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Sai Zhang
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Yulong Peng
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Chunyan Fu
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
| | - Guang Shu
- School of Basic Medical Sciences, Central South University, Changsha, Hunan Province
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
- China-Africa Research Center of Infectious Diseases, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, China
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9
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Nuamtanong S, Reamtong O, Phuphisut O, Chotsiri P, Malaithong P, Dekumyoy P, Adisakwattana P. Transcriptome and excretory-secretory proteome of infective-stage larvae of the nematode Gnathostoma spinigerum reveal potential immunodiagnostic targets for development. ACTA ACUST UNITED AC 2019; 26:34. [PMID: 31166909 PMCID: PMC6550564 DOI: 10.1051/parasite/2019033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/16/2019] [Indexed: 01/02/2023]
Abstract
Background: Gnathostoma spinigerum is a harmful parasitic nematode that causes severe morbidity and mortality in humans and animals. Effective drugs and vaccines and reliable diagnostic methods are needed to prevent and control the associated diseases; however, the lack of genome, transcriptome, and proteome databases remains a major limitation. In this study, transcriptomic and secretomic analyses of advanced third-stage larvae of G. spinigerum (aL3Gs) were performed using next-generation sequencing, bioinformatics, and proteomics. Results: An analysis that incorporated transcriptome and bioinformatics data to predict excretory–secretory proteins (ESPs) classified 171 and 292 proteins into classical and non-classical secretory groups, respectively. Proteins with proteolytic (metalloprotease), cell signaling regulatory (i.e., kinases and phosphatase), and metabolic regulatory function (i.e., glucose and lipid metabolism) were significantly upregulated in the transcriptome and secretome. A two-dimensional (2D) immunomic analysis of aL3Gs-ESPs with G. spinigerum-infected human sera and related helminthiases suggested that the serine protease inhibitor (serpin) was a promising antigenic target for the further development of gnathostomiasis immunodiagnostic methods. Conclusions: The transcriptome and excretory–secretory proteome of aL3Gs can facilitate an understanding of the basic molecular biology of the parasite and identifying multiple associated factors, possibly promoting the discovery of novel drugs and vaccines. The 2D-immunomic analysis identified serpin, a protein secreted from aL3Gs, as an interesting candidate for immunodiagnosis that warrants immediate evaluation and validation.
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Affiliation(s)
- Supaporn Nuamtanong
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Orawan Phuphisut
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Palang Chotsiri
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand
| | - Preeyarat Malaithong
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Paron Dekumyoy
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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10
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Moretti AIS, Pavanelli JC, Nolasco P, Leisegang MS, Tanaka LY, Fernandes CG, Wosniak J, Kajihara D, Dias MH, Fernandes DC, Jo H, Tran NV, Ebersberger I, Brandes RP, Bonatto D, Laurindo FRM. Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. Sci Rep 2017; 7:17262. [PMID: 29222525 PMCID: PMC5722932 DOI: 10.1038/s41598-017-16947-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/21/2017] [Indexed: 02/07/2023] Open
Abstract
Protein disulfide isomerases (PDIs) support endoplasmic reticulum redox protein folding and cell-surface thiol-redox control of thrombosis and vascular remodeling. The family prototype PDIA1 regulates NADPH oxidase signaling and cytoskeleton organization, however the related underlying mechanisms are unclear. Here we show that genes encoding human PDIA1 and its two paralogs PDIA8 and PDIA2 are each flanked by genes encoding Rho guanine-dissociation inhibitors (GDI), known regulators of RhoGTPases/cytoskeleton. Evolutionary histories of these three microsyntenic regions reveal their emergence by two successive duplication events of a primordial gene pair in the last common vertebrate ancestor. The arrangement, however, is substantially older, detectable in echinoderms, nematodes, and cnidarians. Thus, PDI/RhoGDI pairing in the same transcription orientation emerged early in animal evolution and has been largely maintained. PDI/RhoGDI pairs are embedded into conserved genomic regions displaying common cis-regulatory elements. Analysis of gene expression datasets supports evidence for PDI/RhoGDI coexpression in developmental/inflammatory contexts. PDIA1/RhoGDIα were co-induced in endothelial cells upon CRISP-R-promoted transcription activation of each pair component, and also in mouse arterial intima during flow-induced remodeling. We provide evidence for physical interaction between both proteins. These data support strong functional links between PDI and RhoGDI families, which likely maintained PDI/RhoGDI microsynteny along > 800-million years of evolution.
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Affiliation(s)
- Ana I S Moretti
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Jessyca C Pavanelli
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Patrícia Nolasco
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | | | - Leonardo Y Tanaka
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Carolina G Fernandes
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - João Wosniak
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Daniela Kajihara
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Matheus H Dias
- Special Laboratory for Cell Cycle, Center of Toxins, Immune-Response and Cell Signaling - CeTICS-Cepid, Butantan Institute, São Paulo, Brazil
| | - Denise C Fernandes
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil
| | - Hanjoong Jo
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA
| | - Ngoc-Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology & Neuroscience, Goethe University, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology & Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Center (BiK-F), Frankfurt, Germany
| | - Ralf P Brandes
- Institut für Kardiovaskuläre Physiologie, Goethe University, Frankfurt, Germany
| | - Diego Bonatto
- Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Francisco R M Laurindo
- Vascular Biology Laboratory, Heart Institute (Incor), University of São Paulo School of Medicine, São Paulo, Brazil.
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Catsper1 promoter is bidirectional and regulates the expression of a novel lncRNA. Sci Rep 2017; 7:13351. [PMID: 29042633 PMCID: PMC5645346 DOI: 10.1038/s41598-017-13867-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/03/2017] [Indexed: 11/10/2022] Open
Abstract
The Catsper1 gene, whose expression is restricted to male germ cells, has great importance in reproductive biology because of its function in sperm motility and fertilization. We previously reported that the promoter of this gene has transcriptional activity in either direction in a heterologous system. In the present study, we found that the Catsper1 promoter has in vitro transcriptional activity in either orientation in GC-1 spg mouse spermatogonial cells. The results also showed that this promoter regulates the expression of a new divergent Catsper1 gene named Catsper1au (Catsper1 antisense upstream transcript). Catsper1au is expressed in adult male mouse testis and liver tissues but not in female mouse liver or ovary tissues. In the testis, Catsper1au is expressed in embryos at 11.5 days post-coitum and from newborns to adults. This gene is also expressed in 1- to 3-week postnatal hearts and in 1-week to adult stage livers. The analysis of the 1402 bp whole genome sequence revealed that Catsper1au is an intronless and polyadenylated lncRNA, located in the nuclei of Sertoli and spermatogenic cells from adult testis. These data indicate that Catsper1au is divergently expressed from the Catsper1 promoter and could regulate gene expression during spermatogenesis.
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Rath M, Jenssen SE, Schwefel K, Spiegler S, Kleimeier D, Sperling C, Kaderali L, Felbor U. High-throughput sequencing of the entire genomic regions of CCM1/KRIT1 , CCM2 and CCM3/PDCD10 to search for pathogenic deep-intronic splice mutations in cerebral cavernous malformations. Eur J Med Genet 2017. [DOI: 10.1016/j.ejmg.2017.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Scimone C, Bramanti P, Ruggeri A, Donato L, Alafaci C, Crisafulli C, Mucciardi M, Rinaldi C, Sidoti A, D’Angelo R. CCM3/SERPINI1 bidirectional promoter variants in patients with cerebral cavernous malformations: a molecular and functional study. BMC MEDICAL GENETICS 2016; 17:74. [PMID: 27737651 PMCID: PMC5064884 DOI: 10.1186/s12881-016-0332-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/29/2016] [Indexed: 01/24/2023]
Abstract
BACKGROUND Cerebral cavernous malformations (CCMs) are vascular anomalies of the nervous system mostly located in the brain presenting sporadically or familial. Causes of familial forms are mutations in CCM1 (Krit1), CCM2 (MGC4607) and CCM3 (PDCD10) genes. Sporadic forms with no affected relative most often have only one lesion and no germ line mutations. However, a number of sporadic cases with multiple lesions have been reported and are indeed genetic cases with a de novo mutation or a mutation inherited from an asymptomatic parent. METHODS Here, we performed an analysis of regulatory region of CCM genes in 60 sporadic patients, negative for mutations in coding region and intron-exon boundaries and large deletion/duplications in CCM genes by direct sequencing and MLPA. Among 5 variants identified in 851-bp region shared by CCM3 and SERPINI1 genes and acting as asymmetric bidirectional promoter, two polymorphisms c.-639 T > C/rs9853967 and c.-591 T > C/rs11714980 were selected. A case-control study was performed to analyze their possible relationships with sporadic CCMs. Promoter haplotypes activities on CCM3/SERPINI1 genes expression were tested by dual-luciferase assay. RESULTS No variants were identified in CCM1 and CCM2 regulatory regions. In CCM3/SERPINI1 asymmetric bidirectional promoter 5 variants, 2 of them unknown and 3 corresponding to polymorphisms c.-639 T > C/rs9853967, c.-591 T > C/rs11714980 and c.-359G > A/rs9834676 were detected. While rs9853967 and rs11714980 polymorphisms fall in a critical regulatory fragment outside the minimal promoter in intergenic region, other variants had no effects on transcription factor binding according to RegRNA tool. Case-control study performed on 60 patients and 350 healthy controls showed frequencies of the mutated alleles significantly higher in the control group than in patients. Furthermore, the functional assay showed a significant reduction of CCM3 expression for C-C haplotype even more than for T-C and C-T haplotypes. In SERPINI1 direction, the reduction was not statistically significant. CONCLUSIONS Our data indicated that rs9853967 and rs11714980 polymorphisms could be associated with a protective role in CCM disease.
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Affiliation(s)
- Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
- Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies And Neuroscience, Section of Neuroscience-applied, Molecular Genetics and Predictive Medicine, I.E.ME.S.T, Palermo, Italy
| | | | - Alessia Ruggeri
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
| | - Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
- Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies And Neuroscience, Section of Neuroscience-applied, Molecular Genetics and Predictive Medicine, I.E.ME.S.T, Palermo, Italy
| | - Concetta Alafaci
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
| | - Concetta Crisafulli
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
| | | | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
- Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies And Neuroscience, Section of Neuroscience-applied, Molecular Genetics and Predictive Medicine, I.E.ME.S.T, Palermo, Italy
| | - Rosalia D’Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, via C. Valeria 1, 98125 Messina, Italy
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Kim JW, Jeong JM, Bae JS, Cho DH, Jung SH, Hwang JY, Kwon MG, Seo JS, Baeck GW, Park CI. First description of programmed cell death10 (PDCD10) in rock bream (Oplegnathus fasciatus): Potential relations to the regulation of apoptosis by several pathogens. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 55:51-55. [PMID: 26472617 DOI: 10.1016/j.dci.2015.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
In this study, we isolated and characterized programmed cell death10 (PDCD10), which is known to be related to apoptosis, from rock bream (Oplegnathus fasciatus). The full-length rock bream PDCD10 (RbPDCD10) cDNA (1459 bp) contains an open reading frame of 633 bp that encodes 210 amino acids. Furthermore, multiple alignments revealed that the six of the α-helix bundles were well conserved among the other PDCD10 sequences tested. RbPDCD10 was significantly expressed in the liver, RBC (red blood cell), gill, intestine, trunk kidney and spleen. RbPDCD10 gene expression was also examined in several tissues, including the kidney, spleen, liver, and gill, under bacterial and viral challenges. Generally, all of the examined tissues from the fish that were infected with Edwardsiella tarda and the red sea bream iridovirus (RSIV) exhibited significant up-regulations of RbPDCD10 expression compared to the controls. However, RbPDCD10 expression exhibited dramatic down-regulations in all of the examined tissues following injections of Streptococcus iniae, which is major bacterial pathogen that is responsible for mass mortality in rock bream. Our results revealed that rock bream PDCD10 may be involved in the apoptotic regulation of rock bream immune responses.
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Affiliation(s)
- Ju-Won Kim
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 38 Cheondaegukchi-Gil, Tongyeong, Gyeongnam 650-160, Republic of Korea
| | - Ji-Min Jeong
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 38 Cheondaegukchi-Gil, Tongyeong, Gyeongnam 650-160, Republic of Korea
| | - Jin-Sol Bae
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 38 Cheondaegukchi-Gil, Tongyeong, Gyeongnam 650-160, Republic of Korea
| | - Dong-Hee Cho
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 38 Cheondaegukchi-Gil, Tongyeong, Gyeongnam 650-160, Republic of Korea
| | - Sung Hee Jung
- Pathology Division, National Fisheries Research and Development Institute, Busan 619-900, Republic of Korea
| | - Jee-Youn Hwang
- Pathology Division, National Fisheries Research and Development Institute, Busan 619-900, Republic of Korea
| | - Mun-Gyeong Kwon
- Pathology Division, National Fisheries Research and Development Institute, Busan 619-900, Republic of Korea
| | - Jung Soo Seo
- Pathology Division, National Fisheries Research and Development Institute, Busan 619-900, Republic of Korea
| | - Gun-Wook Baeck
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 38 Cheondaegukchi-Gil, Tongyeong, Gyeongnam 650-160, Republic of Korea
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, College of Marine Science, Gyeongsang National University, 38 Cheondaegukchi-Gil, Tongyeong, Gyeongnam 650-160, Republic of Korea.
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Lambertz N, El Hindy N, Kreitschmann-Andermahr I, Stein KP, Dammann P, Oezkan N, Mueller O, Sure U, Zhu Y. Downregulation of programmed cell death 10 is associated with tumor cell proliferation, hyperangiogenesis and peritumoral edema in human glioblastoma. BMC Cancer 2015; 15:759. [PMID: 26490252 PMCID: PMC4618952 DOI: 10.1186/s12885-015-1709-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/08/2015] [Indexed: 11/22/2022] Open
Abstract
Background Neovascularization and peritumoral edema are hallmarks of glioblastoma (GBM). Programmed cell death 10 (PDCD10) plays a pivotal role in regulating apoptosis, neoangiogenesis and vessel permeability and is implicated in certain tumor signaling pathways. However, little is known about PDCD10 in GBM. We aimed to investigate the expression pattern of PDCD10 and to identify the association of its expression with some molecular and clinical parameters in human GBM. Methods mRNA and protein expression of PDCD10 were examined respectively by real-time RT-PCR and Western blotting in GBM (n = 27), astrocytoma grade II (n = 13) and control (n = 11). The protein level of p-Akt and GFAP was detected by Western blot. Double-imunofluorecent staining was performed to reveal the cellular expression profile of PDCD10. Brain edema and microvascular density (MVD) were respectively analyzed based on pre-operative MRI and after laminin immnostaining. MGMT promoter methylation was detected by methylation specific PCR. Results mRNA and protein levels of PDCD10 were significantly downregulated in GBM, concomitantly accompanied by the activation of Akt. PDCD10 immunoreactivity was absent in proliferating tumor cells, endothelial cells and GFAP-positive cells, but exclusively present in the hypoxic pseudopalisading cells which underwent apoptosis. Moreover, loss of PDCD10 was associated with a higher MVD and a more severe peritumoral edema but not with MGMT promoter methylation in GBM. Conclusion We report for the first time that PDCD10 expression is downregulated in GBM, which is associated with the activation of Akt signaling protein. PDCD10 is potentially implicated in tumor proliferation and apoptosis, hyperangiogenesis and peritumoral edema in GBM.
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Affiliation(s)
- Nicole Lambertz
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Nicolai El Hindy
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | | | - Klaus Peter Stein
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany. .,Present Address: Department of Neurosurgery, KRH Klinikum Nordstadt, Haltenhoffstr. 41, 30167, Hannover, Germany.
| | - Philipp Dammann
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Neriman Oezkan
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Oliver Mueller
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Ulrich Sure
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Yuan Zhu
- Department of Neurosurgery, Medical Faculty, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
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Wang Y, Zhang Y, Zhang C, Weng H, Li Y, Cai W, Xie M, Long Y, Ai Q, Liu Z, Du G, Wang S, Niu Y, Song F, Ozaki T, Bu Y. The gene pair PRR11 and SKA2 shares a NF-Y-regulated bidirectional promoter and contributes to lung cancer development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1133-44. [PMID: 26162986 DOI: 10.1016/j.bbagrm.2015.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022]
Abstract
Head-to-head gene pairs represent a unique feature of gene organization in eukaryotes, accounting for >10% of genes in the human genome. Identification and functional analysis of such gene pairs is only in its infancy. Recently, we identified PRR11 as a novel cancer-related gene that is implicated in cell cycle and lung cancer. Here we demonstrate that PRR11 is oriented in a head-to-head configuration with its neighboring gene, SKA2. 5'-RACE assay revealed that the intergenic spacer region between the two genes is <500 bp. Serial luciferase reporter assays demonstrated that a minimal 80-bp intergenic region functions as a core bidirectional promoter to drive basal transcription in both the PRR11 and SKA2 orientations. EMSA and ChIP assays demonstrated that NF-Y binds to and directly transactivates the PRR11-SKA2 bidirectional promoter. SiRNA-mediated NF-Y depletion significantly downregulated PRR11 and SKA2 expression. Expression of both PRR11 and SKA2 was significantly upregulated in lung cancer. Expression of the two genes was highly correlated with each other and with NF-Y expression. Remarkably, high expression of both PRR11 and SKA2 was associated with poorer prognosis in lung cancer patients compared with high expression of one gene or low expression of both genes. Knockdown of PRR11 and/or SKA2 remarkably reduced cell proliferation, migration, and invasion in lung cancer cells. Thus, the PRR11-SKA2 bidirectional transcription unit, which is a novel direct target of NF-Y, is essential for the accelerated proliferation and motility of lung cancer cells and may represent a potential target in the diagnosis and/or treatment of human lung cancer.
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Affiliation(s)
- Yitao Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Chundong Zhang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Huali Weng
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yi Li
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Mengyu Xie
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yinjiang Long
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Qing Ai
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Zhu Liu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Gang Du
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Sen Wang
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Yulong Niu
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Fangzhou Song
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Toshinori Ozaki
- Laboratory of DNA Damage Signaling, Chiba Cancer Center Research Institute, 666-2 Nitona, Chuohku, Chiba 260-8717, Japan
| | - Youquan Bu
- Department of Biochemistry and Molecular Biology, Chongqing Medical University, Chongqing 400016, China; Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, China.
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Kumar A. Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY. PeerJ 2015; 3:e1026. [PMID: 26157611 PMCID: PMC4476131 DOI: 10.7717/peerj.1026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 05/26/2015] [Indexed: 11/20/2022] Open
Abstract
The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1-V6), based on three independent biological features-genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α 2-AP/SERPINF2) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. Additionally in this study, details of the phylogenetic history and genomic characteristics of vertebrate serpins are revisited.
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Affiliation(s)
- Abhishek Kumar
- Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
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Caccia S, Ricagno S, Bolognesi M. Molecular bases of neuroserpin function and pathology. Biomol Concepts 2015; 1:117-30. [PMID: 25961991 DOI: 10.1515/bmc.2010.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Serpins build a large and evolutionary widespread protein superfamily, hosting members that are mainly Ser-protease inhibitors. Typically, serpins display a conserved core domain composed of three main β-sheets and 9-10 α-helices, for a total of approximately 350 amino acids. Neuroserpin (NS) is mostly expressed in neurons and in the central and peripheral nervous systems, where it targets tissue-type plasminogen activator. NS activity is relevant for axogenesis, synaptogenesis and synaptic plasticity. Five (single amino acid) NS mutations are associated with severe neurodegenerative disease in man, leading to early onset dementia, epilepsy and neuronal death. The functional aspects of NS protease inhibition are linked to the presence of a long exposed loop (reactive center loop, RCL) that acts as bait for the incoming partner protease. Large NS conformational changes, associated with the cleavage of the RCL, trap the protease in an acyl-enzyme complex. Contrary to other serpins, this complex has a half-life of approximately 10 min. Conformational flexibility is held to be at the bases of NS polymerization leading to Collins bodies intracellular deposition and neuronal damage in the pathological NS variants. Two main general mechanisms of serpin polymerization are currently discussed. Both models require the swapping of the RCL among neighboring serpin molecules. Specific differences in the size of swapped regions, as well as differences in the folding stage at which polymerization can occur, distinguish the two models. The results provided by recent crystallographic and biophysical studies allow rationalization of the functional and pathological roles played by NS based on the analysis of four three-dimensional structures.
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Baxter SS, Dibble CF, Byrd WC, Carlson J, Mack CR, Saldarriaga I, Bencharit S. Role of cytoskeletal proteins in cerebral cavernous malformation signaling pathways: a proteomic analysis. MOLECULAR BIOSYSTEMS 2015; 10:1881-9. [PMID: 24770493 PMCID: PMC4043921 DOI: 10.1039/c3mb70199a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three genetic mutations were found to cause cerebral cavernous malformation (CCM), a vascular anomaly predisposing affected individuals to hemorrhagic stroke. These CCM proteins function together as a protein complex in the cell. Loss of expression of each CCM gene results in loss of in vitro endothelial tube formation. Label-free differential protein expression analysis using multidimensional liquid chromatography/tandem mass spectrometry (2D-LC-MS/MS) was applied to explore the proteomic profile for loss of each CCM gene expression in mouse endothelial stem cells (MEES) compared to mock shRNA and no shRNA control cell-lines. Differentially expressed proteins were identified (p < 0.05). 120 proteins were differentially expressed among the cell-lines. Principal component analysis and cluster analysis show the effects of individual knockdown. In all knockdown cell-lines, altered expression of cytoskeletal proteins is the most common. While all CCM mutations result in similar pathology, different CCM mutations have their own distinct pathogenesis in cell signaling.
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Affiliation(s)
- Sarah Schwartz Baxter
- David H. Murdock Research Institute, North Carolina Research Campus, Kannapolis, NC 28081, USA
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Dutta UR, Hansmann I, Schlote D. Molecular cytogenetic characterization of a familial pericentric inversion 3 associated with short stature. Eur J Med Genet 2015; 58:154-9. [PMID: 25595572 DOI: 10.1016/j.ejmg.2015.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/05/2015] [Indexed: 12/21/2022]
Abstract
Short stature refers to the height of an individual which is below expected. The causes are heterogenous and influenced by several genetic and environmental factors. Chromosomal abnormalities are a major cause of diseases and cytogenetic mapping is one of the powerful tools for the identification of novel disease genes. Here we report a three generation family with a heterozygous pericentric inversion of 46, XX, inv(3) (p24.1q26.1) associated with Short stature. Positional cloning strategy was used to physically map the breakpoint regions by Fluorescence in situ hybridization (FISH). Fine mapping was performed with Bacterial Artificial Chromosome (BAC) clones spanning the breakpoint regions. In order to further characterize the breakpoint regions extensive molecular mapping was carried out with the breakpoint spanning BACs which narrowed down the breakpoint region to 2.9 kb and 5.3 kb regions on p and q arm respectively. Although these breakpoints did not disrupt any validated genes, we had identified a novel putative gene in the vicinity of 3q26.1 breakpoint region by in silico analysis. Trying to find the presence of any transcripts of this putative gene we analyzed human total RNA by RT-PCR and identified transcripts containing three new exons confirming the existence of a so far unknown gene close to the 3q breakpoint.
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Affiliation(s)
- Usha R Dutta
- Institut fuer Humangenetik, Martin Luther University, Halle-Wittenberg, Halle (Saale) 06097, Germany; Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500 001, India.
| | - Ingo Hansmann
- Institut fuer Humangenetik, Martin Luther University, Halle-Wittenberg, Halle (Saale) 06097, Germany
| | - Dietmar Schlote
- Institut fuer Humangenetik, Martin Luther University, Halle-Wittenberg, Halle (Saale) 06097, Germany
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Yang YJ, Liu ZS, Lu SY, Li C, Hu P, Li YS, Liu NN, Tang F, Xu YM, Zhang JH, Li ZH, Feng XL, Zhou Y, Ren HL. Molecular cloning, expression and characterization of programmed cell death 10 from sheep (Ovis aries). Gene 2014; 558:65-74. [PMID: 25541025 DOI: 10.1016/j.gene.2014.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 11/27/2014] [Accepted: 12/19/2014] [Indexed: 11/30/2022]
Abstract
Programmed cell death 10 (PDCD10) is a highly conserved adaptor protein. Its mutations result in cerebral cavernous malformations (CCMs). In this study, PDCD10 cDNA from the buffy coat of Small Tail Han sheep (Ovis aries) was cloned from a suppression subtractive hybridization cDNA library, named OaPDCD10. The full-length cDNA of OaPDCD10 was 1343bp with a 639bp open reading frame (ORF) encoding 212 amino acid residues. Tissue distribution of OaPDCD10 mRNA determined that it was ubiquitously expressed in all tested tissue samples, and the highest expression was observed in the heart. The differential expression of OaPDCD10 between infected sheep (challenged with Brucella melitensis) and vaccinated sheep (vaccinated with Brucella suis S2) was also investigated. The results revealed that, compared to the control group, the expression of OaPDCD10 from infected and vaccinated sheep was both significantly up-regulated (p<0.05). Moreover, the expression levels of OaPDCD10 from the vaccinated sheep were significantly higher than the infected sheep (p<0.05) after 30days post-inoculation. The recombinant OaPDCD10 (rOaPDCD10) protein was expressed in Escherichia coli BL21 (DE3), and then purified by affinity chromatography. The rOaPDCD10 protein was demonstrated to induce apoptosis and promote cell proliferation. Our studies are intended to discover potential diagnostic biomarkers of brucellosis to discern infected sheep from vaccinated sheep, and OaPDCD10 could be considered as a potential diagnostic biomarker of brucellosis.
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Affiliation(s)
- Yong-Jie Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Department of Food Science, College of Agriculture, Yanbian University, Yanji 133002, China
| | - Zeng-Shan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Shi-Ying Lu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Chuang Li
- Department of Food Science, College of Agriculture, Yanbian University, Yanji 133002, China
| | - Pan Hu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yan-Song Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Nan-Nan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Feng Tang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; College of Animal Husbandry and Veterinary, Liaoning Medical University, Jinzhou 121001, China
| | - Yun-Ming Xu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; Department of Husbandry and Veterinary Medicine, Jiangsu Polytechnic College of Agriculture and Forestry, Jurong 212400, China
| | - Jun-Hui Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhao-Hui Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiao-Li Feng
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Yu Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Hong-Lin Ren
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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22
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Mangiola A, Saulnier N, De Bonis P, Orteschi D, Sica G, Lama G, Pettorini BL, Sabatino G, Zollino M, Lauriola L, Colabianchi A, Proietti G, Kovacs G, Maira G, Anile C. Gene expression profile of glioblastoma peritumoral tissue: an ex vivo study. PLoS One 2013; 8:e57145. [PMID: 23472076 PMCID: PMC3589444 DOI: 10.1371/journal.pone.0057145] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/18/2013] [Indexed: 01/01/2023] Open
Abstract
The gene expression pattern of glioblastoma (GBM) is well documented but the expression profile of brain adjacent to tumor is not yet analysed. This may help to understand the oncogenic pathway of GBM development. We have established the genome-wide expression profiles of samples isolated from GBM tumor mass, white matter adjacent to tumor (apparently free of tumor cells), and white matter controls by using the Affymetrix HG-U133 arrays. Array-CGH (aCGH) was also performed to detect genomic alterations. Among genes dysregulated in peritumoral white matter, 15 were over-expressed, while 42 were down-regulated when compared to white matter controls. A similar expression profile was detected in GBM cells. Growth, proliferation and cell motility/adhesion-associated genes were up-regulated while genes involved in neurogenesis were down-regulated. Furthermore, several tumor suppressor genes along with the KLRC1 (a member of natural killer receptor) were also down-regulated in the peritumoral brain tissue. Several mosaic genomic lesions were detected by aCGH, mostly in tumor samples and several GBM-associated mosaic genomic lesions were also present in the peritumoral brain tissue, with a similar mosaicism pattern. Our data could be explained by a dilution of genes expressed from tumor cells infiltrating the peritumour tissue. Alternatively, these findings could be substained by a relevant amount of “apparently normal” cells presenting a gene profile compatible with a precancerous state or even “quiescent” cancer cells. Otherwise, the recurrent tumor may arise from both infiltrating tumor cells and from an interaction and recruitment of apparently normal cells in the peritumor tissue by infiltrating tumor cells.
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Affiliation(s)
- Annunziato Mangiola
- Institute of Neurosurgery, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Nathalie Saulnier
- Institute of Human Anatomy, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Pasquale De Bonis
- Institute of Neurosurgery, Faculty of Medicine, Catholic University of Rome, Rome, Italy
- * E-mail:
| | - Daniela Orteschi
- Institute of Genetics, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Gigliola Sica
- Institute of Histology and Embryology, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Gina Lama
- Institute of Histology and Embryology, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | | | - Giovanni Sabatino
- Institute of Neurosurgery, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Marcella Zollino
- Institute of Genetics, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Libero Lauriola
- Institute of Pathology, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Anna Colabianchi
- Institute of Histology and Embryology, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Gabriella Proietti
- Institute of Histology and Embryology, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Gyula Kovacs
- Medical Faculty, Ruprecht Karls University, Heidelberg, Germany
| | - Giulio Maira
- Institute of Neurosurgery, Faculty of Medicine, Catholic University of Rome, Rome, Italy
| | - Carmelo Anile
- Institute of Neurosurgery, Faculty of Medicine, Catholic University of Rome, Rome, Italy
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23
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Didych DA, Shamsutdinov MF, Smirnov NA, Akopov SB, Monastyrskaya GS, Uspenskaya NY, Nikolaev LG, Sverdlov ED. Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter. Gene 2012; 515:34-41. [PMID: 23246698 DOI: 10.1016/j.gene.2012.11.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 10/31/2012] [Accepted: 11/29/2012] [Indexed: 11/16/2022]
Abstract
Head-to-head genes with a short distance between their transcription start sites may constitute up to 10% of all genes in the genomes of various species. It was hypothesized that this intergenic space may represent bidirectional promoters which are able to initiate transcription of both genes, but the true bidirectionality was proved only for a few of them. We present experimental evidence that, according to several criteria, a 269 bp region located between the PSENEN and U2AF1L4 human genes is a genuine bidirectional promoter regulating a concerted divergent transcription of these genes. Concerted transcription of PSENEN and U2AF1L4 can be necessary for regulation of T-cell activity.
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Affiliation(s)
- D A Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
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24
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Liu B, Chen J, Shen B. Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 1:S2. [PMID: 21689477 PMCID: PMC3121118 DOI: 10.1186/1752-0509-5-s1-s2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study the inner properties of this gene organization and the difference between bi- and uni-directional genes, we conducted a genome-wide investigation in terms of their sequence composition, functional association and regulatory motif discovery. Results We identified 1210 bi-directional gene pairs based on the GRCh37 assembly data, accounting for 11.6% of all the human genes owning RNAs. CpG islands were detected in 98.42% of bi-directional promoters and 61.07% of unidirectional promoters. Functional enrichment analysis in GO and GeneGO both revealed that bi-directional genes tend to be associated with housekeeping functions in metabolism pathways and nuclear processes, and 46.84% of the pair members are involved in the same biological function. By fold-enrichment analysis, we characterized 73 and 43 putative transcription factor binding sites(TFBS) that preferentially occur in bi-directional promoters from TRANSFAC and JASPAR database respectively. By text mining, some of them were verified by individual experiments and several novel binding motifs were also identified. Conclusions Bi-directional promoters feature a significant enrichment of CpG-islands as well as a high GC content. We provided insight into the function constraints of bi-directional genes and found that paired genes are biased toward functional similarities. We hypothesized that the functional association underlies the co-expression of bi-directional genes. Furthermore, we proposed a set of putative regulatory motifs in the bi-directional promoters for further experimental studies to investigate transcriptional regulation of bi-directional genes.
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Affiliation(s)
- Bingchuan Liu
- Center for Systems Biology, Soochow University, Suzhou, China
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25
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Garcia SAB, Nagai MA. Transcriptional regulation of bidirectional gene pairs by 17-β-estradiol in MCF-7 breast cancer cells. Braz J Med Biol Res 2010; 44:112-22. [PMID: 21180879 DOI: 10.1590/s0100-879x2010007500149] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 12/08/2010] [Indexed: 11/22/2022] Open
Abstract
Using cDNA microarray analysis, we previously identified a set of differentially expressed genes in primary breast tumors based on the status of estrogen and progesterone receptors. In the present study, we performed an integrated computer-assisted and manual search of potential estrogen response element (ERE) binding sites in the promoter region of these genes to characterize their potential to be regulated by estrogen receptors (ER). Publicly available databases were used to annotate the position of these genes in the genome and to extract a 5'flanking region 2 kb upstream to 2 kb downstream of the transcription start site for transcription binding site analysis. The search for EREs and other binding sites was performed using several publicly available programs. Overall, approximately 40% of the genes analyzed were potentially able to be regulated by estrogen via ER. In addition, 17% of these genes are located very close to other genes organized in a head-to-head orientation with less than 1.0 kb between their transcript units, sharing a bidirectional promoter, and could be classified as bidirectional gene pairs. Using quantitative real-time PCR, we further investigated the effects of 17β-estradiol and antiestrogens on the expression of the bidirectional gene pairs in MCF-7 breast cancer cells. Our results showed that some of these gene pairs, such as TXNDC9/EIF5B, GALNS/TRAPPC2L, and SERINC1/PKIB, are modulated by 17β-estradiol via ER in MCF-7 breast cancer cells. Here, we also characterize the promoter region of potential ER-regulated genes and provide new information on the transcriptional regulation of bidirectional gene pairs.
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Affiliation(s)
- S A B Garcia
- Disciplina de Oncologia, Departamento de Radiologia, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, SP, Brazil
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26
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Dibble CF, Horst JA, Malone MH, Park K, Temple B, Cheeseman H, Barbaro JR, Johnson GL, Bencharit S. Defining the functional domain of programmed cell death 10 through its interactions with phosphatidylinositol-3,4,5-trisphosphate. PLoS One 2010; 5:e11740. [PMID: 20668527 PMCID: PMC2909203 DOI: 10.1371/journal.pone.0011740] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/01/2010] [Indexed: 11/25/2022] Open
Abstract
Cerebral cavernous malformations (CCM) are vascular abnormalities of the central nervous system predisposing blood vessels to leakage, leading to hemorrhagic stroke. Three genes, Krit1 (CCM1), OSM (CCM2), and PDCD10 (CCM3) are involved in CCM development. PDCD10 binds specifically to PtdIns(3,4,5)P3 and OSM. Using threading analysis and multi-template modeling, we constructed a three-dimensional model of PDCD10. PDCD10 appears to be a six-helical-bundle protein formed by two heptad-repeat-hairpin structures (α1–3 and α4–6) sharing the closest 3D homology with the bacterial phosphate transporter, PhoU. We identified a stretch of five lysines forming an amphipathic helix, a potential PtdIns(3,4,5)P3 binding site, in the α5 helix. We generated a recombinant wild-type (WT) and three PDCD10 mutants that have two (Δ2KA), three (Δ3KA), and five (Δ5KA) K to A mutations. Δ2KA and Δ3KA mutants hypothetically lack binding residues to PtdIns(3,4,5)P3 at the beginning and the end of predicted helix, while Δ5KA completely lacks all predicted binding residues. The WT, Δ2KA, and Δ3KA mutants maintain their binding to PtdIns(3,4,5)P3. Only the Δ5KA abolishes binding to PtdIns(3,4,5)P3. Both Δ5KA and WT show similar secondary and tertiary structures; however, Δ5KA does not bind to OSM. When WT and Δ5KA are co-expressed with membrane-bound constitutively-active PI3 kinase (p110-CAAX), the majority of the WT is co-localized with p110-CAAX at the plasma membrane where PtdIns(3,4,5)P3 is presumably abundant. In contrast, the Δ5KA remains in the cytoplasm and is not present in the plasma membrane. Combining computational modeling and biological data, we propose that the CCM protein complex functions in the PI3K signaling pathway through the interaction between PDCD10 and PtdIns(3,4,5)P3.
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Affiliation(s)
- Christopher F. Dibble
- Department of Pharmacology, School of Medicine, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeremy A. Horst
- Department of Microbiology, School of Medicine, and Department of Oral Biology, School of Dentistry, University of Washington, Seattle, Washington, United States of America
| | - Michael H. Malone
- Department of Pharmacology, School of Medicine, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kun Park
- Department of Prosthodontics and the Dental Research Center, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Brenda Temple
- Department of Pharmacology, School of Medicine, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Holly Cheeseman
- Department of Prosthodontics and the Dental Research Center, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Justin R. Barbaro
- Department of Prosthodontics and the Dental Research Center, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Gary L. Johnson
- Department of Pharmacology, School of Medicine, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sompop Bencharit
- Department of Pharmacology, School of Medicine, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Prosthodontics and the Dental Research Center, School of Dentistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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27
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Chen PY, Chang WSW, Lai YK, Wu CW. c-Myc regulates the coordinated transcription of brain disease-related PDCD10-SERPINI1 bidirectional gene pair. Mol Cell Neurosci 2009; 42:23-32. [PMID: 19442737 DOI: 10.1016/j.mcn.2009.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 04/05/2009] [Accepted: 05/04/2009] [Indexed: 10/20/2022] Open
Abstract
Two brain disease-related genes, one coding for the protease inhibitor SERPINI1 which is down-regulated in brain tumors, and the other for the PDCD10 programmed cell death gene which is often mutated in cerebral cavernous malformation, are closely adjacent in a head-to-head configuration and separated by only 851 bp on human chromosome 3q26. The 851-bp intergenic region contains a GC-rich 175-bp minimal bidirectional promoter which is essential for transcriptional activation of the two flanking genes. The oncogenic c-Myc transcription factor was identified to bind to a non-canonical E-box element (5'-CATGCG-3') of the minimal bidirectional promoter to drive both gene expressions. Methylation at the specific C nucleotide within the E-box sequence (5'-CATG(m)CG-3'), however, would severely interfere with the binding of c-Myc to the E-box. These results suggest that c-Myc plays an important role in regulating the coordinated transcription of the PDCD10-SERPINI1 bidirectional gene pair, and is possibly involved in differential expressions of these two neighboring genes in central nervous system diseases such as brain cancer.
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Affiliation(s)
- Ping-Yen Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan, ROC
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28
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Huang CC, Chang WSW. Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair. BMC Mol Biol 2009; 10:67. [PMID: 19575798 PMCID: PMC2713978 DOI: 10.1186/1471-2199-10-67] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 07/03/2009] [Indexed: 11/11/2022] Open
Abstract
Background Many mammalian genes are organized as bidirectional (head-to-head) gene pairs with the two genes separated only by less than 1 kb. The transcriptional regulation of these bidirectional gene pairs remains largely unclear, but a few studies have suggested that the two closely adjacent genes in divergent orientation can be co-regulated by a single transcription factor binding to a specific regulatory fragment. Here we report an evolutionarily conserved bidirectional gene pair, known as the PREPL-C2ORF34 gene pair, whose transcription relies on the synergic cooperation of two transcription factors binding to an intergenic bidirectional minimal promoter. Results While PREPL is present primarily in brain and heart, C2ORF34 is ubiquitously and abundantly expressed in almost all tissues. Genomic analyses revealed that these two non-homologous genes are adjacent in a head-to-head configuration on human chromosome 2p21 and separated by only 405 bp. Within this short intergenic region, a 243-bp GC-rich segment was demonstrated to function as a bidirectional minimal promoter to initiate the transcription of both flanking genes. Two key transcription factors, NRF-2 and YY-1, were further identified to coordinately participate in driving both gene expressions in an additive manner. The functional cooperation between these two transcription factors, along with their genomic binding sites and some cis-acting repressive elements, are essential for the transcriptional activation and tissue distribution of the PREPL-C2ORF34 bidirectional gene pair. Conclusion This study provides new insights into the complex transcriptional mechanism of a mammalian head-to-head gene pair which requires cooperative binding of multiple transcription factors to a bidirectional minimal promoter of the shared intergenic region.
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Affiliation(s)
- Chien-Chang Huang
- 1Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan.
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29
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Co-regulated expression of HAND2 and DEIN by a bidirectional promoter with asymmetrical activity in neuroblastoma. BMC Mol Biol 2009; 10:28. [PMID: 19348682 PMCID: PMC2670301 DOI: 10.1186/1471-2199-10-28] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 04/06/2009] [Indexed: 12/29/2022] Open
Abstract
Background HAND2, a key regulator for the development of the sympathetic nervous system, is located on chromosome 4q33 in a head-to-head orientation with DEIN, a recently identified novel gene with stage specific expression in primary neuroblastoma (NB). Both genes are expressed in primary NB as well as most NB cell lines and are separated by a genomic sequence of 228 bp. The similar expression profile of both genes suggests a common transcriptional regulation mediated by a bidirectional promoter. Results Northern Blot analysis of DEIN and HAND2 in 20 primary NBs indicated concurrent expression levels of the two genes, which was confirmed by microarray analysis of 236 primary NBs (Pearson's correlation coefficient r = 0.65). While DEIN expression in the latter cohort was associated with stage 4S (p = 0.02), HAND2 expression was not associated with tumor stage. In contrast, both HAND2 and DEIN transcript levels were highly associated with age at diagnosis <12 months (p = 0.001). The intergenic region shows substantial homology in different species (89%, 72% and 53% identity between human and mouse, chicken and zebrafish, respectively) and contains many highly conserved putative transcription factor binding sites. Using luciferase reporter gene constructs, asymmetrical bidirectional promoter activity was found in four NB cell lines: In DEIN orientation, an average 3.4 fold increase in activity was observed as compared to the promoterless vector, whereas an average 15.4 fold activation was detected in HAND2 orientation. The presence of two highly conserved putative regulatory elements, one of which was shown to enhance HAND2 expression in branchial arches previously, displayed weak repressor activity for both genes. Conclusion HAND2 and DEIN represent a gene pair that is tightly linked by a bidirectional promoter in an evolutionary highly conserved manner. Expression of both genes in NB is co-regulated by asymmetrical activity of this promoter and modulated by the activity of two cis-regulatory elements acting as weak repressors. The concurrent quantitative and tissue specific expression of HAND2 and DEIN suggests a functional link between both genes.
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30
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Lebeurrier N, Launay S, Macrez R, Maubert E, Legros H, Leclerc A, Jamin SP, Picard JY, Marret S, Laudenbach V, Berger P, Sonderegger P, Ali C, di Clemente N, Vivien D. Anti-Mullerian-hormone-dependent regulation of the brain serine-protease inhibitor neuroserpin. J Cell Sci 2008; 121:3357-65. [PMID: 18796535 DOI: 10.1242/jcs.031872] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
The balance between tissue-type plasminogen activator (tPA) and one of its inhibitors, neuroserpin, has crucial roles in the central nervous system, including the control of neuronal migration, neuronal plasticity and neuronal death. In the present study, we demonstrate that the activation of the transforming growth factor-beta (TGFbeta)-related BMPR-IB (also known as BMPR1B and Alk6)- and Smad5-dependent signalling pathways controls neuroserpin transcription. Accordingly, we demonstrate for the first time that anti-Mullerian hormone (AMH), a member of the TGFbeta family, promotes the expression of neuroserpin in cultured neurons but not in astrocytes. The relevance of these findings is confirmed by the presence of both AMH and AMH type-II receptor (AMHR-II) in brain tissues, and is supported by the observation of reduced levels of neuroserpin in the brain of AMHR-II-deficient mice. Interestingly, as previously demonstrated for neuroserpin, AMH protects neurons against N-methyl-D-aspartate (NMDA)-mediated excitotoxicity both in vitro and in vivo. This study demonstrates the existence of an AMH-dependent signalling pathway in the brain leading to an overexpression of the serine-protease inhibitor, neuroserpin, and neuronal survival.
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Affiliation(s)
- Nathalie Lebeurrier
- INSERM, INSERM U919, Serine Proteases and Pathophysiology of the neurovascular Unit (SP2U), Cyceron, F-14074 France
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31
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Kumar A, Ragg H. Ancestry and evolution of a secretory pathway serpin. BMC Evol Biol 2008; 8:250. [PMID: 18793432 PMCID: PMC2556349 DOI: 10.1186/1471-2148-8-250] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 09/15/2008] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The serpin (serine protease inhibitor) superfamily constitutes a class of functionally highly diverse proteins usually encompassing several dozens of paralogs in mammals. Though phylogenetic classification of vertebrate serpins into six groups based on gene organisation is well established, the evolutionary roots beyond the fish/tetrapod split are unresolved. The aim of this study was to elucidate the phylogenetic relationships of serpins involved in surveying the secretory pathway routes against uncontrolled proteolytic activity. RESULTS Here, rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group 3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait, though subtle functional and compartmental specialisations have developed during their evolution. The results also suggest that massive changes in the exon-intron organisation of serpin genes have occurred along the lineage leading to vertebrate neuroserpin, in contrast with the immediately adjacent PDCD10 gene that is linked to its neighbour at least since divergence of echinoderms. The intron distribution pattern of closely adjacent and co-regulated genes thus may experience quite different fates during evolution of metazoans. CONCLUSION This study demonstrates that the analysis of microsynteny and other rare characters can provide insight into the intricate family history of metazoan serpins. Serpins with the capacity to defend the main cellular export/import routes against uncontrolled endogenous and/or foreign proteolytic activity represent an ancient trait in eukaryotes that has been maintained continuously in metazoans though subtle changes affecting function and subcellular location have evolved. It is shown that the intron distribution pattern of neuroserpin gene orthologs has undergone substantial rearrangements during metazoan evolution.
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Affiliation(s)
- Abhishek Kumar
- Department of Biotechnology, Faculty of Technology and Center for Biotechnology, University of Bielefeld, D-33501 Bielefeld, Germany
| | - Hermann Ragg
- Department of Biotechnology, Faculty of Technology and Center for Biotechnology, University of Bielefeld, D-33501 Bielefeld, Germany
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32
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Liu B, Paton JF, Kasparov S. Viral vectors based on bidirectional cell-specific mammalian promoters and transcriptional amplification strategy for use in vitro and in vivo. BMC Biotechnol 2008; 8:49. [PMID: 18485188 PMCID: PMC2396617 DOI: 10.1186/1472-6750-8-49] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 05/16/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Using cell-type-specific promoters to restrict gene expression to particular cells is an attractive approach for gene therapy, but often hampered by insufficient transcriptional activity of these promoters. Previous studies have shown that transcriptional amplification strategy (TAS) can be used to enhance the activity of such promoters without loss of cell type specificity. Originally TAS involved the use of two copies of a cell-specific promoter leading to generation of large expression cassettes, which can be hard to use given the space limitations of the conventional viral gene expression vectors. RESULTS We have now developed a new bidirectional lentiviral vector system, based on TAS that can enhance the transcriptional activity of human synapsin-1 (SYN) promoter and the compact glial fibrillary acidic protein (GfaABC1D) promoter. In the opposite orientation, a minimal core promoter (65 bp) derived from the human cytomegalovirus (CMV) was joined upstream of the SYN promoter or GfaABC1D promoter. This led to the formation of synthetic bidirectional promoters which were flanked with two gene expression cassettes. The 5' cassette transcribed the artificial transcriptional activator. The downstream cassette drove the synthesis of the gene of interest. Studies in both cell cultures and in vivo showed that the new bidirectional promoters greatly increased the expression level of the reporter gene. In vivo studies also showed that transgene expression was enhanced without loss of cell specificity of both SYN and GfaABC1D promoters. CONCLUSION This work establishes a novel approach for creating compact TAS-amplified cell-specific promoters, a feature important for their use in viral backbones. This improved approach should prove useful for the development of powerful gene expression systems based on weak cell-specific promoters.
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Affiliation(s)
- Beihui Liu
- Department of Physiology and Pharmacology, Bristol Heart Institute, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK.
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Nakagawa H, Tategu M, Yamauchi R, Sasaki K, Sekimachi S, Yoshida K. Transcriptional regulation of an evolutionary conserved intergenic region of CDT2-INTS7. PLoS One 2008; 3:e1484. [PMID: 18213392 PMCID: PMC2194621 DOI: 10.1371/journal.pone.0001484] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Accepted: 12/18/2007] [Indexed: 11/24/2022] Open
Abstract
Background In the mammalian genome, a substantial number of gene pairs (approximately 10%) are arranged head-to-head on opposite strands within 1,000 base pairs, and separated by a bidirectional promoter(s) that generally drives the co-expression of both genes and results in functional coupling. The significance of unique genomic configuration remains elusive. Methodology/Principal Findings Here we report on the identification of an intergenic region of non-homologous genes, CDT2, a regulator of DNA replication, and an integrator complex subunit 7 (INTS7), an interactor of the largest subunit of RNA polymerase II. The CDT2-INTS7 intergenic region is 246 and 245 base pairs long in human and mouse respectively and is evolutionary well-conserved among several mammalian species. By measuring the luciferase activity in A549 cells, the intergenic human sequence was shown to be able to drive the reporter gene expression in either direction and notably, among transcription factors E2F, E2F1∼E2F4, but not E2F5 and E2F6, this sequence clearly up-regulated the reporter gene expression exclusively in the direction of the CDT2 gene. In contrast, B-Myb, c-Myb, and p53 down-regulated the reporter gene expression in the transcriptional direction of the INTS7 gene. Overexpression of E2F1 by adenoviral-mediated gene transfer resulted in an increased CDT2, but not INTS7, mRNA level. Real-time polymerase transcription (RT-PCR) analyses of the expression pattern for CDT2 and INTS7 mRNA in human adult and fetal tissues and cell lines revealed that transcription of these two genes are asymmetrically regulated. Moreover, the abundance of mRNA between mouse and rat tissues was similar, but these patterns were quite different from the results obtained from human tissues. Conclusions/Significance These findings add a unique example and help to understand the mechanistic insights into the regulation of gene expression through an evolutionary conserved intergenic region of the mammalian genome.
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Affiliation(s)
- Hiroki Nakagawa
- Department of Life Sciences, Meiji University School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Moe Tategu
- Department of Life Sciences, Meiji University School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Rieko Yamauchi
- Department of Life Sciences, Meiji University School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Kaori Sasaki
- Department of Life Sciences, Meiji University School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Sota Sekimachi
- Department of Life Sciences, Meiji University School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Kenichi Yoshida
- Department of Life Sciences, Meiji University School of Agriculture, Kawasaki, Kanagawa, Japan
- * To whom correspondence should be addressed. E-mail:
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Spitz F, Duboule D. Global control regions and regulatory landscapes in vertebrate development and evolution. ADVANCES IN GENETICS 2008; 61:175-205. [PMID: 18282506 DOI: 10.1016/s0065-2660(07)00006-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the course of evolution, many genes that control the development of metazoan body plans were co-opted to exert novel functions, along with the emergence or modification of structures. Gene amplification and/or changes in the cis-regulatory modules responsible for the transcriptional activity of these genes have certainly contributed in a major way to evolution of gene functions. In some cases, these processes led to the formation of groups of adjacent genes that appear to be controlled by both global and shared mechanisms.
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Affiliation(s)
- Francois Spitz
- Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany
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