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Ludhiadch A, Sulena, Singh S, Chakraborty S, Sharma D, Kulharia M, Singh P, Munshi A. Genomic Variation Affecting MPV and PLT Count in Association with Development of Ischemic Stroke and Its Subtypes. Mol Neurobiol 2023; 60:6424-6440. [PMID: 37453995 DOI: 10.1007/s12035-023-03460-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
Platelets play a significant role in the pathophysiology of ischemic stroke since they are involved in the formation of intravascular thrombus after erosion or rupture of the atherosclerotic plaques. Platelet (PLT) count and mean platelet volume (MPV) are the two significant parameters that affect the functions of platelets. In the current study, MPV and PLT count was evaluated using flow cytometry and a cell counter. SonoClot analysis was carried out to evaluate activated clot timing (ACT), clot rate (CR), and platelet function (PF). Genotyping was carried out using GSA and Sanger sequencing, and expression analysis was performed using RT-PCR. In silico analysis was carried out using the GROMACS tool and UNAFold. The interaction of significant proteins with other proteins was predicted using the STRING database. Ninety-six genes were analyzed, and a significant association of THPO (rs6141) and ARHGEF3 (rs1354034) was observed with the disease and its subtypes. Altered genotypes were associated significantly with increased MPV, decreased PLT count, and CR. Expression analysis revealed a higher expression in patients bearing the variant genotypes of both genes. In silico analysis revealed that mutation in the THPO gene leads to the reduced compactness of protein structure. mRNA encoded by mutated ARHGEF3 gene increases the half-life of mRNA. The two significant proteins interact with many other proteins, especially the ones involved in platelet activation, aggregation, erythropoiesis, megakaryocyte maturation, and cytoskeleton rearrangements, suggesting that they could be important players in the determination of MPV values. In conclusion, the current study demonstrated the role of higher MPV affected by genetic variation in the development of IS and its subtypes. The results of the current study also indicate that higher MPV can be used as a biomarker for the disease and altered genotypes, and higher MPV can be targeted for better therapeutic outcomes.
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Affiliation(s)
- Abhilash Ludhiadch
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Sulena
- Department of Neurology, Guru Gobind Singh Medical College and Hospital, Sadiq Road, Faridkot, Punjab, 151203, India
| | | | - Sudip Chakraborty
- Department of Computational Sciences, School of Basic and Applied Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Dixit Sharma
- Department of Animal Sciences, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| | - Mahesh Kulharia
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, 176206, India
| | - Paramdeep Singh
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Bathinda, Punjab, 151001, India
| | - Anjana Munshi
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India.
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Bamford CGG, Aranday-Cortes E, Sanchez-Velazquez R, Mullan C, Kohl A, Patel AH, Wilson SJ, McLauchlan J. A Human and Rhesus Macaque Interferon-Stimulated Gene Screen Shows That Over-Expression of ARHGEF3/XPLN Inhibits Replication of Hepatitis C Virus and Other Flavivirids. Viruses 2022; 14:v14081655. [PMID: 36016278 PMCID: PMC9414520 DOI: 10.3390/v14081655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/11/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
Natural hepatitis C virus (HCV) infection is restricted to humans, whereas other primates such as rhesus macaques are non-permissive for infection. To identify human and rhesus macaque genes that differ or share the ability to inhibit HCV replication, we conducted a medium-throughput screen of lentivirus-expressed host genes that disrupt replication of HCV subgenomic replicon RNA expressing secreted Gaussia luciferase. A combined total of >800 interferon-stimulated genes (ISGs) were screened. Our findings confirmed established anti-HCV ISGs, such as IRF1, PKR and DDX60. Novel species−specific inhibitors were also identified and independently validated. Using a cell-based system that recapitulates productive HCV infection, we identified that over-expression of the ‘Rho Guanine Nucleotide Exchange Factor 3’ gene (ARHGEF3) from both species inhibits full-length virus replication. Additionally, replication of two mosquito-borne flaviviruses, yellow fever virus (YFV) and Zika virus (ZIKV), were also reduced in cell lines over-expressing ARHGEF3 compared to controls. In conclusion, we ascribe novel antiviral activity to the cellular gene ARHGEF3 that inhibits replication of HCV and other important human viral pathogens belonging to the Flaviviridae, and which is conserved between humans and rhesus macaques.
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Affiliation(s)
- Connor G. G. Bamford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT7 1NN, UK
| | - Elihu Aranday-Cortes
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
| | - Ricardo Sanchez-Velazquez
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
- BioNTech SE, 55131 Mainz, Germany
| | - Catrina Mullan
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK; (C.G.G.B.); (E.A.-C.); (R.S.-V.); (C.M.); (A.K.); (A.H.P.); (S.J.W.)
- Correspondence:
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Khaliq SA, Umair Z, Yoon MS. Role of ARHGEF3 as a GEF and mTORC2 Regulator. Front Cell Dev Biol 2022; 9:806258. [PMID: 35174167 PMCID: PMC8841341 DOI: 10.3389/fcell.2021.806258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
Guanine nucleotide exchange factors (GEFs) activate GTPases by stimulating the release of guanosine diphosphate to permit the binding of guanosine triphosphate. ARHGEF3 or XPLN (exchange factor found in platelets, leukemic, and neuronal tissues) is a selective guanine nucleotide exchange factor for Rho GTPases (RhoGEFs) that activates RhoA and RhoB but not RhoC, RhoG, Rac1, or Cdc42. ARHGEF3 contains the diffuse B-cell lymphoma homology and pleckstrin homology domains but lacks similarity with other known functional domains. ARHGEF3 also binds the mammalian target of rapamycin complex 2 (mTORC2) and subsequently inhibits mTORC2 and Akt. In vivo investigation has also indicated the communication between ARHGEF3 and autophagy-related muscle pathologies. Moreover, studies on genetic variation in ARHGEF3 and genome-wide association studies have predicted exciting novel roles of ARHGEF3 in controlling bone mineral density, platelet formation and differentiation, and Hirschsprung disease. In conclusion, we hypothesized that additional biochemical and functional studies are required to elucidate the detailed mechanism of ARHGEF3-related pathologies and therapeutics.
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Affiliation(s)
- Sana Abdul Khaliq
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
| | - Zobia Umair
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- *Correspondence: Zobia Umair, ; Mee-Sup Yoon,
| | - Mee-Sup Yoon
- Department of Molecular Medicine, Gachon University College of Medicine, Incheon, South Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, South Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, South Korea
- *Correspondence: Zobia Umair, ; Mee-Sup Yoon,
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Panagopoulos I, Gorunova L, Andersen K, Lobmaier I, Heim S. Several Fusion Genes Identified in a Spermatic Cord Leiomyoma With Rearrangements of Chromosome Arms 3p and 21q. Cancer Genomics Proteomics 2021; 18:531-542. [PMID: 34183386 DOI: 10.21873/cgp.20278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Benign smooth-muscle tumors, leiomyomas, occur in nearly every organ but are most common in the uterus. Whereas much is known about the genetics of uterine leiomyomas, little genetic information exists about leiomyomas of other organs. Here, we report and discuss the genetic findings in a para-testicular leiomyoma. MATERIALS AND METHODS Cytogenetic, array comparative genomic hybridization (aCGH) RNA sequencing, reverse-transcription polymerase chain reaction (RT- PCR), and Sanger sequencing analyses were performed on a leiomyoma of the spermatic cord removed from a 61-year-old man. RESULTS The karyotype was 48~50,XY,add(3) (p21),+4,+7,+8,+9,add(21)(q22)[cp9]/46,XY[2]. aCGH confirmed the trisomies and also detected multiple gains and losses from 3p and 21q. RNA sequencing detected the chimeras ARHGEF3-CACNA2D2, TRAK1-TIMP4, ITPR1- DT-NR2C2, CLASP2-IL17RD, ZNF621-LARS2, CNTN4- RHOA, and NR2C2-CFAP410. All chimeras were confirmed by RT-PCR and Sanger sequencing. CONCLUSION Our data, together with those previously published, indicate that a group of leiomyomas may be cytogenetically characterized by aberrations of 3p and the formation of fusion genes.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ingvild Lobmaier
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Huang Y, Li Y, Wang X, Yu J, Cai Y, Zheng Z, Li R, Zhang S, Chen N, Asadollahpour Nanaei H, Hanif Q, Chen Q, Fu W, Li C, Cao X, Zhou G, Liu S, He S, Li W, Chen Y, Chen H, Lei C, Liu M, Jiang Y. An atlas of CNV maps in cattle, goat and sheep. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1747-1764. [PMID: 33486588 DOI: 10.1007/s11427-020-1850-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/16/2020] [Indexed: 11/26/2022]
Abstract
Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P<0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms (SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.
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Affiliation(s)
- Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yunjia Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiantao Yu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shunjin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | | | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, 577, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, 45650, Islamabad, Pakistan
| | - Qiuming Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Weiwei Fu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiukai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shudong Liu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Sangang He
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Wenrong Li
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Mingjun Liu
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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Yoo KS, Lee K, Lee YS, Oh WJ, Kim HK. Rho Guanine Nucleotide Exchange Factor 4 (Arhgef4) Deficiency Enhances Spatial and Object Recognition Memory. Exp Neurobiol 2020; 29:334-343. [PMID: 33154196 PMCID: PMC7649087 DOI: 10.5607/en20049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 01/03/2023] Open
Abstract
Guanine nucleotide exchange factors (GEFs) play multiple functional roles in neurons. In a previous study, we reported that Arhgef4 (Rho guanine nucleotide exchange factor 4) functioned as a negative regulator of the excitatory synaptic function by sequestering postsynaptic density protein 95 (PSD-95). However, the role of Arhgef4 in behavior has not been examined. We performed comprehensive behavioral tests in knockout (KO) mice to investigate of the effects of Arhgef4 deficiency. We found that the expressed PSD-95 particle size was significantly increased in hippocampal neuronal cultures from Arhgef4 KO mice, which is consistent with the previous in vitro findings. Arhgef4 KO mice exhibited general motor activity and anxiety-like behavior comparable to those of the wild type littermates. However, spatial memory and object recognition memory were significantly enhanced in the Arhgef4 KO mice. Taken together, these data confirm the role of Arhgef4 as a negative synaptic regulator at the behavioral level.
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Affiliation(s)
- Ki-Seo Yoo
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Kina Lee
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Korea
| | - Yong-Seok Lee
- Department of Physiology, Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Won-Jong Oh
- Neurovascular Unit Research Group, Korea Brain Research Institute, Daegu 41062, Korea
| | - Hyong Kyu Kim
- Department of Medicine and Microbiology, Graduate Program in Neuroscience, College of Medicine, Chungbuk National University, Cheongju 28644, Korea
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Harlid S, Xu Z, Kirk E, Wilson LE, Troester MA, Taylor JA. Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study. Epigenetics 2019; 14:146-157. [PMID: 30821641 PMCID: PMC6557608 DOI: 10.1080/15592294.2019.1580111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Hormone therapy (HT) is associated with increased risk of breast cancer, strongly dependent on type, duration, and recency of use. HT use could affect cancer risk by changing breast tissue transcriptional programs. We hypothesize that these changes are preceded by changes in DNA methylation. To explore this hypothesis we used histologically normal-appearing breast tissue from the Normal Breast Study (NBS). DNA methylation β-values were obtained using the Illumina HumanMethylation 450 BeadChips for 90 samples including all NBS-participants who used HT within 5 y before surgery. Data were analyzed using the reference-free cell mixture method. Cancer Genome Atlas (TCGA) mRNA-Seq data were used to assess correlation between DNA methylation and gene expression. We identified 527 CpG sites in 403 genes that were associated with ever using HT at genome wide significance (FDR q < 0.05), of these, 68 sites were also significantly associated with duration of use or recency of use. Twelve sites reached significance in all analyses one of which was cg01382688 in ARHGEF4 (p < 1.2x10−7). Mutations in ARHGEF4 have been reported in breast tumors, but this is the first report of possible breast cancer-related DNA methylation changes. In addition, 22 genes included more than one significant CpG site and a majority of these sites were significantly correlated with gene expression. Although based on small numbers, these findings support the hypothesis that HT is associated with epigenetic alterations in breast tissue, and identifies genes with altered DNA methylation states which could be linked to breast cancer development.
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Affiliation(s)
- Sophia Harlid
- a Epigenetics & Stem Cell Biology Laboratory , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA.,b Department of Radiation Sciences, Oncology , Umeå University , Umeå , Sweden
| | - Zongli Xu
- c Epidemiology Branch , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA
| | - Erin Kirk
- d Department of Epidemiology , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Lauren E Wilson
- c Epidemiology Branch , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA.,e Department of Population Health Sciences , Duke University School of Medicine , Durham , NC , USA
| | - Melissa A Troester
- d Department of Epidemiology , University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Jack A Taylor
- a Epigenetics & Stem Cell Biology Laboratory , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA.,c Epidemiology Branch , National Institute of Environmental Health Sciences, NIH , Research Triangle Park , NC , USA
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Vasudeva K, Munshi A. Genetics of platelet traits in ischaemic stroke: focus on mean platelet volume and platelet count. Int J Neurosci 2018; 129:511-522. [PMID: 30371123 DOI: 10.1080/00207454.2018.1538991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Purpose/Aim of the study: The aim of this review is to summarize the role of genetic variants affecting mean platelet volume (MPV) and platelet count (PLT) leading to higher platelet reactivity and in turn to thrombotic events like stroke and cardiovascular diseases. MATERIALS AND METHODS A search was conducted in PUBMED, MEDLINE, EMBASE, PROQUEST, Science Direct, Cochrane Library, and Google Scholar related to the studies focussing on genome-wide association studies (GWAS), whole exome sequencing (WES), whole genome sequencing (WGS), phenome-wide association studies (PheWAS) and multi-omic analysis that have been employed to identify the genetic variants influencing MPV and PLT. RESULTS Antiplatelet agents underscore the crucial role of platelets in the pathogenesis of stroke. Higher platelet reactivity in terms of mean platelet volume (MPV) and platelet count (PLT) contributes significantly to the interindividual variation in platelet reaction at the site of vessel wall injury. Some individuals encounter thrombotic events as platelets get occluded at the site of vessel wall injury whereas others heal the injury without occluding the circulation. Evidence suggests that MPV and PLT have a strong genetic component. High throughput techniques including genome-wide association studies (GWAS), whole exome sequencing (WES), whole genome sequencing (WGS), phenome-wide association studies (PheWAS) and multi-omic analysis have identified different genetic variants influencing MPV and PLT. CONCLUSIONS Identification of complex genetic cross talks affecting PLT and MPV might help to develop novel treatment strategies in treating neurovascular diseases like stroke.
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Affiliation(s)
- Kanika Vasudeva
- a Department of Human Genetics and Molecular Medicine , Central University of Punjab Bathinda , Punjab , India
| | - Anjana Munshi
- a Department of Human Genetics and Molecular Medicine , Central University of Punjab Bathinda , Punjab , India
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Taniuchi K, Furihata M, Naganuma S, Saibara T. ARHGEF4 predicts poor prognosis and promotes cell invasion by influencing ERK1/2 and GSK-3α/β signaling in pancreatic cancer. Int J Oncol 2018; 53:2224-2240. [PMID: 30226582 DOI: 10.3892/ijo.2018.4549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/05/2018] [Indexed: 11/06/2022] Open
Abstract
Rho guanine nucleotide exchange factor 4 (ARHGEF4) is a guanine nucleotide exchange factor that is specific for Rac1 and Cdc42. The aim of the present study was to investigate the role of ARHGEF4 in the motility and invasiveness of pancreatic cancer cells. Evaluation of an immunohistochemical staining of 102 resected pancreatic cancer samples demonstrated that high ARHGEF4 expression was correlated with an independent predictor of worse overall survival in univariate and multivariate analyses. Immunofluorescence analyses and Matrigel invasion assays demonstrated that suppression of ARHGEF4 inhibited the formation of membrane protrusions, and in turn inhibited cell motility and invasion. A phosphoprotein array analysis demonstrated that knockdown of ARHGEF4 decreased phosphorylated extracellular signal-regulated kinase (ERK)1/2 and glycogen synthase kinase-3 (GSK-3)α/β in pancreatic cancer cells, and ERK1/2 and GSK-3α/β were associated with ARHGEF4-related motility and invasiveness through an increase in cell protrusions. These results suggested that ARHGEF4 stimulates ERK1/2 and GSK-3α/β, and provided evidence that ARHGEF4 promotes cell motility and invasiveness. Inhibition of ARHGEF4 may be a novel approach to a targeted molecular therapy, as any such therapy would limit the motility and invasiveness of pancreatic cancer cells.
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Affiliation(s)
- Keisuke Taniuchi
- Departments of Endoscopic Diagnostics and Therapeutics, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Mutsuo Furihata
- Departments of Pathology, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Seiji Naganuma
- Departments of Pathology, Kochi University, Nankoku, Kochi 783-8505, Japan
| | - Toshiji Saibara
- Departments of Endoscopic Diagnostics and Therapeutics, Kochi University, Nankoku, Kochi 783-8505, Japan
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Liu TH, Zheng F, Cai MY, Guo L, Lin HX, Chen JW, Liao YJ, Kung HF, Zeng YX, Xie D. The putative tumor activator ARHGEF3 promotes nasopharyngeal carcinoma cell pathogenesis by inhibiting cellular apoptosis. Oncotarget 2017; 7:25836-48. [PMID: 27028992 PMCID: PMC5041948 DOI: 10.18632/oncotarget.8283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 03/06/2016] [Indexed: 11/28/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is one of the most prevalent forms of highly invasive malignancy in Southern China and Southeast Asia. The pathogenesis of NPC is a multistep process driven by the acquisition of numerous genetic abnormalities. We investigated the potential oncogenic role of the Rho-guanine nucleotide exchange factor 3 gene, ARHGEF3, in NPC pathogenesis. Expression levels of ARHGEF3 were frequently up-regulated in NPC cell lines and tissues. In a large cohort of clinical NPC tissues high expression of ARHGEF3 was positively associated with an increased T status, distant metastasis, and a more advanced clinical stage (P < 0.05). Survival analysis revealed that ARHGEF3 expression was a significant and independent prognosis factor for NPC patients. In NPC cell lines, knockdown of ARHGEF3 was sufficient to inhibit cell growth, motility, and invasion in vitro, whereas ectopic overexpression of ARHGEF3 substantially enhanced NPC cells tumorigenesis and metastasis in vivo. Depletion of ARHGEF3 in NPC cells dramatically promoted caspase-3 induced apoptosis and an anti-apoptosis factor, BIRC8, was identified as a critical downstream target of the ARHGEF3. Our findings suggest that increased expression of ARHGEF3 plays a critical oncogenic role in NPC pathogenesis by preventing cell apoptosis through the up-regulation of BIRC8, and ARHGEF3 might be employed as a novel prognostic marker and effective therapeutic target for human NPC.
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Affiliation(s)
- Tian-Hao Liu
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Fang Zheng
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Medical Research Center, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mu-Yan Cai
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Lin Guo
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Nasopharyngeal Cancer, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Huan-Xin Lin
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jie-Wei Chen
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yi-Ji Liao
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hsiang-Fu Kung
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yi-Xin Zeng
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dan Xie
- Sun Yat-Sen University Cancer Center, The State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
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11
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Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2432957. [PMID: 28428959 PMCID: PMC5385910 DOI: 10.1155/2017/2432957] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/26/2017] [Accepted: 02/06/2017] [Indexed: 01/11/2023]
Abstract
Introduction. Increase in body weight is a gradual process that usually begins in childhood and in adolescence as a result of multiple interactions among environmental and genetic factors. This study aimed to analyze the relationship between copy number variants (CNVs) in five genes and four intergenic regions with obesity in Mexican children. Methods. We studied 1423 children aged 6–12 years. Anthropometric measurements and blood levels of biochemical parameters were obtained. Identification of CNVs was performed by real-time PCR. The effect of CNVs on obesity or body composition was assessed using regression models adjusted for age, gender, and family history of obesity. Results. Gains in copy numbers of LEPR and NEGR1 were associated with decreased body mass index (BMI), waist circumference (WC), and risk of abdominal obesity, whereas gain in ARHGEF4 and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d and losses in INS were associated with increased BMI and WC. Conclusion. Our results indicate a possible contribution of CNVs in LEPR, NEGR1, ARHGEF4, and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d to the development of obesity, particularly abdominal obesity in Mexican children.
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12
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Bracken CP, Li X, Wright JA, Lawrence DM, Pillman KA, Salmanidis M, Anderson MA, Dredge BK, Gregory PA, Tsykin A, Neilsen C, Thomson DW, Bert AG, Leerberg JM, Yap AS, Jensen KB, Khew-Goodall Y, Goodall GJ. Genome-wide identification of miR-200 targets reveals a regulatory network controlling cell invasion. EMBO J 2014; 33:2040-56. [PMID: 25069772 DOI: 10.15252/embj.201488641] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The microRNAs of the miR-200 family maintain the central characteristics of epithelia and inhibit tumor cell motility and invasiveness. Using the Ago-HITS-CLIP technology for transcriptome-wide identification of direct microRNA targets in living cells, along with extensive validation to verify the reliability of the approach, we have identified hundreds of miR-200a and miR-200b targets, providing insights into general features of miRNA target site selection. Gene ontology analysis revealed a predominant effect of miR-200 targets in widespread coordinate control of actin cytoskeleton dynamics. Functional characterization of the miR-200 targets indicates that they constitute subnetworks that underlie the ability of cancer cells to migrate and invade, including coordinate effects on Rho-ROCK signaling, invadopodia formation, MMP activity, and focal adhesions. Thus, the miR-200 family maintains the central characteristics of the epithelial phenotype by acting on numerous targets at multiple levels, encompassing both cytoskeletal effectors that control actin filament organization and dynamics, and upstream signals that locally regulate the cytoskeleton to maintain cell morphology and prevent cell migration.
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Affiliation(s)
- Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Xiaochun Li
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Josephine A Wright
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - David M Lawrence
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Marika Salmanidis
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Matthew A Anderson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - B Kate Dredge
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Anna Tsykin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Corine Neilsen
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Daniel W Thomson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Joanne M Leerberg
- Division of Molecular Cell Biology, Institute for Molecular Bioscience University of Queensland, St Lucia, Brisbane, Qld, Australia
| | - Alpha S Yap
- Division of Molecular Cell Biology, Institute for Molecular Bioscience University of Queensland, St Lucia, Brisbane, Qld, Australia
| | - Kirk B Jensen
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Yeesim Khew-Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, Australia Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia
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13
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Gimelli S, Stathaki E, Béna F, Leoni M, Di Rocco M, Cuoco C, Tassano E. Recurrent microdeletion 2q21.1: report on a new patient with neurological disorders. Am J Med Genet A 2013; 164A:801-5. [PMID: 24591035 DOI: 10.1002/ajmg.a.36357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/09/2013] [Indexed: 11/07/2022]
Abstract
Whole genome profiling such as array comparative genomic hybridization has identified novel genomic imbalances. Copy number studies led to an explosion of the discoveries of new segmental duplication-mediated deletions and duplications. These rearrangements are mostly the result of non-allelic homologous recombination (NAHR) between low-copy repeats or segmental duplications. We have identified an individual with a small, rare deletion on chromosome 2q21.1 with psychomotor delay, hyperactivity, and aggressive behavior. The rearranged region is flanked by large complex low-copy repeats and includes only five genes: GPR148, FAM123C (AMER3), ARHGEF4, FAM168B, and PLEKHB2. The comparison between our patient and the cases previously reported in the literature contributes to a better definition of genotype-phenotype correlation of 2q21.1 microdeletions.
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Affiliation(s)
- Stefania Gimelli
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
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14
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Dharmadhikari AV, Kang SHL, Szafranski P, Person RE, Sampath S, Prakash SK, Bader PI, Phillips JA, Hannig V, Williams M, Vinson SS, Wilfong AA, Reimschisel TE, Craigen WJ, Patel A, Bi W, Lupski JR, Belmont J, Cheung SW, Stankiewicz P. Small rare recurrent deletions and reciprocal duplications in 2q21.1, including brain-specific ARHGEF4 and GPR148. Hum Mol Genet 2012; 21:3345-55. [PMID: 22543972 DOI: 10.1093/hmg/dds166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We have identified a rare small (~450 kb unique sequence) recurrent deletion in a previously linked attention-deficit hyperactivity disorder (ADHD) locus at 2q21.1 in five unrelated families with developmental delay (DD)/intellectual disability (ID), ADHD, epilepsy and other neurobehavioral abnormalities from 17 035 samples referred for clinical chromosomal microarray analysis. Additionally, a DECIPHER (http://decipher.sanger.ac.uk) patient 2311 was found to have the same deletion and presented with aggressive behavior. The deletion was not found in either six control groups consisting of 13 999 healthy individuals or in the DGV database. We have also identified reciprocal duplications in five unrelated families with autism, developmental delay (DD), seizures and ADHD. This genomic region is flanked by large, complex low-copy repeats (LCRs) with directly oriented subunits of ~109 kb in size that have 97.7% DNA sequence identity. We sequenced the deletion breakpoints within the directly oriented paralogous subunits of the flanking LCR clusters, demonstrating non-allelic homologous recombination as a mechanism of formation. The rearranged segment harbors five genes: GPR148, FAM123C, ARHGEF4, FAM168B and PLEKHB2. Expression of ARHGEF4 (Rho guanine nucleotide exchange factor 4) is restricted to the brain and may regulate the actin cytoskeletal network, cell morphology and migration, and neuronal function. GPR148 encodes a G-protein-coupled receptor protein expressed in the brain and testes. We suggest that small rare recurrent deletion of 2q21.1 is pathogenic for DD/ID, ADHD, epilepsy and other neurobehavioral abnormalities and, because of its small size, low frequency and more severe phenotype might have been missed in other previous genome-wide screening studies using single-nucleotide polymorphism analyses.
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Affiliation(s)
- Avinash V Dharmadhikari
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room R809, Houston, TX 77030, USA
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15
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Zhang Z, Chen L, Gao L, Lin K, Zhu L, Lu Y, Shi X, Gao Y, Zhou J, Xu P, Zhang J, Wu G. Structural basis for the recognition of Asef by adenomatous polyposis coli. Cell Res 2011; 22:372-86. [PMID: 21788986 DOI: 10.1038/cr.2011.119] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Adenomatous polyposis coli (APC) regulates cell-cell adhesion and cell migration through activating the APC-stimulated guanine nucleotide-exchange factor (GEF; Asef), which is usually autoinhibited through the binding between its Src homology 3 (SH3) and Dbl homology (DH) domains. The APC-activated Asef stimulates the small GTPase Cdc42, which leads to decreased cell-cell adherence and enhanced cell migration. In colorectal cancers, truncated APC constitutively activates Asef and promotes cancer cell migration and angiogenesis. Here, we report crystal structures of the human APC/Asef complex. We find that the armadillo repeat domain of APC uses a highly conserved surface groove to recognize the APC-binding region (ABR) of Asef, conformation of which changes dramatically upon binding to APC. Key residues on APC and Asef for the complex formation were mutated and their importance was demonstrated by binding and activity assays. Structural superimposition of the APC/Asef complex with autoinhibited Asef suggests that the binding between APC and Asef might create a steric clash between Asef-DH domain and APC, which possibly leads to a conformational change in Asef that stimulates its GEF activity. Our structures thus elucidate the molecular mechanism of Asef recognition by APC, as well as provide a potential target for pharmaceutical intervention against cancers.
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Affiliation(s)
- Zhenyi Zhang
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
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16
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Varkonyi T, Nagy B, Fule T, Tarca AL, Karaszi K, Schonleber J, Hupuczi P, Mihalik N, Kovalszky I, Rigo J, Meiri H, Papp Z, Romero R, Than NG. Microarray profiling reveals that placental transcriptomes of early-onset HELLP syndrome and preeclampsia are similar. Placenta 2011; 32 Suppl:S21-9. [PMID: 20541258 PMCID: PMC3917714 DOI: 10.1016/j.placenta.2010.04.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 04/23/2010] [Accepted: 04/29/2010] [Indexed: 02/05/2023]
Abstract
BACKGROUND The involvement of the placenta in the pathogenesis of preeclampsia and HELLP syndrome is well established, and placental lesions are also similar in these two syndromes. Here we aimed to examine the placental transcriptome and to identify candidate biomarkers in early-onset preeclampsia and HELLP syndrome. METHODS Placental specimens were obtained at C-sections from women with early-onset preeclampsia and HELLP syndrome, and from controls who delivered preterm or at term. After histopathological examination, fresh-frozen placental specimens were used for microarray profiling and validation by qRT-PCR. Differential expression was analysed using log-linear models while adjusting for gestational age. Gene ontology and pathway analyses were used to interpret gene expression changes. Tissue microarrays were constructed from paraffin-embedded placental specimens and immunostained. RESULTS Placental gene expression was gestational age-dependent among preterm and term controls. Out of the 350 differentially expressed genes in preeclampsia and 554 genes in HELLP syndrome, 224 genes (including LEP, CGB, LHB, INHA, SIGLEC6, PAPPA2, TREM1, and FLT1) changed in the same direction (elevated or reduced) in both syndromes. Many of these encode proteins that have been implicated as biomarkers for preeclampsia. Enrichment analyses revealed similar biological processes, cellular compartments and biological pathways enriched in early-onset preeclampsia and HELLP syndrome; however, some processes and pathways (e.g., cytokine-cytokine receptor interaction) were over-represented only in HELLP syndrome. CONCLUSION High-throughput transcriptional and tissue microarray expression profiling revealed that placental transcriptomes of early-onset preeclampsia and HELLP syndrome largely overlap, underlying a potential common cause and pathophysiologic processes in these syndromes. However, gene expression changes may also suggest a more severe placental pathology and pronounced inflammatory response in HELLP syndrome than in preeclampsia.
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Affiliation(s)
- T Varkonyi
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - B Nagy
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - T Fule
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - AL Tarca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - K Karaszi
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - J Schonleber
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - P Hupuczi
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - N Mihalik
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - I Kovalszky
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - J Rigo
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - H Meiri
- Diagnostic Technologies, Yokneam, Israel
| | - Z Papp
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
| | - R Romero
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - NG Than
- First Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary
- Wayne State University, Detroit, MI, USA
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17
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Abstract
Genetic and environmental factors contribute to a substantial variation in platelet function seen among normal persons. Candidate gene association studies represent a valiant effort to define the genetic component in an era where genetic tools were limited, but the single nucleotide polymorphisms identified in those studies need to be validated by more objective, comprehensive approaches, such as genome-wide association studies (GWASs) of quantitative functional traits in much larger cohorts of more carefully selected normal subjects. During the past year, platelet count and mean platelet volume, which indirectly affect platelet function, were the subjects of GWAS. The majority of the GWAS signals were located to noncoding regions, a consistent outcome of all GWAS to date, suggesting a major role for mechanisms that alter phenotype at the level of transcription or posttranscriptional modifications. Of 15 quantitative trait loci associated with mean platelet volume and platelet count, one located at 12q24 is also a risk locus for coronary artery disease. In most cases, the effect sizes of individual quantitative trait loci are admittedly small, but the results of these studies have led to new insight into regulators of hematopoiesis and megakaryopoiesis that would otherwise be unapparent and difficult to define.
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18
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Lyons R, Williams O, Morrow M, Sebire N, Hubank M, Anderson J. The RAC specific guanine nucleotide exchange factor Asef functions downstream from TEL-AML1 to promote leukaemic transformation. Leuk Res 2010; 34:109-15. [DOI: 10.1016/j.leukres.2009.06.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/13/2009] [Accepted: 06/26/2009] [Indexed: 10/20/2022]
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19
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Meisinger C, Prokisch H, Gieger C, Soranzo N, Mehta D, Rosskopf D, Lichtner P, Klopp N, Stephens J, Watkins NA, Deloukas P, Greinacher A, Koenig W, Nauck M, Rimmbach C, Völzke H, Peters A, Illig T, Ouwehand WH, Meitinger T, Wichmann HE, Döring A. A genome-wide association study identifies three loci associated with mean platelet volume. Am J Hum Genet 2009; 84:66-71. [PMID: 19110211 DOI: 10.1016/j.ajhg.2008.11.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 11/14/2008] [Accepted: 11/21/2008] [Indexed: 01/30/2023] Open
Abstract
Mean platelet volume (MPV) is increased in myocardial and cerebral infarction and is an independent and strong predictor for postevent morbidity and mortality. We conducted a genome-wide association study (GWAS), the KORA (Kooperative Gesundheitsforschung in der Region Augsburg) F3 500K study, and found MPV to be strongly associated with three common single-nucleotide polymorphisms (SNPs): rs7961894 located within intron 3 of WDR66 on chromosome 12q24.31, rs12485738 upstream of the ARHGEF3 on chromosome 3p13-p21, and rs2138852 located upstream of TAOK1 on chromosome 17q11.2. We replicated all three SNPs in another GWAS from the UK and in two population-based samples from Germany. In a combined analysis including 10,048 subjects, the SNPs had p values of 7.24 x 10(-48) for rs7961894, 3.81 x 10(-27) for rs12485738, and 7.19 x 10(-28) for rs2138852. These three quantitative trait loci together accounted for 4%-5% of the variance in MPV. In-depth sequence analysis of WDR66 in 382 samples from the extremes revealed 20 new variants and a haplotype with three coding SNPs and one SNP at the transcription start site associated with MPV (p = 6.8 x 10(-5)). In addition, expression analysis indicated a direct correlation of WDR66 transcripts and MPV. These findings may not only enhance our understanding of platelet activation and function, but may also provide a focus for several novel research avenues.
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Affiliation(s)
- Christa Meisinger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
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20
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Mitin N, Betts L, Yohe ME, Der CJ, Sondek J, Rossman KL. Release of autoinhibition of ASEF by APC leads to CDC42 activation and tumor suppression. Nat Struct Mol Biol 2007; 14:814-23. [PMID: 17704816 PMCID: PMC2716141 DOI: 10.1038/nsmb1290] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 07/13/2007] [Indexed: 12/19/2022]
Abstract
Autoinhibition of the Rho guanine nucleotide exchange factor ASEF is relieved by interaction with the APC tumor suppressor. Here we show that binding of the armadillo repeats of APC to a 'core APC-binding' (CAB) motif within ASEF, or truncation of the SH3 domain of ASEF, relieves autoinhibition, allowing the specific activation of CDC42. Structural determination of autoinhibited ASEF reveals that the SH3 domain forms an extensive interface with the catalytic DH and PH domains to obstruct binding and activation of CDC42, and the CAB motif is positioned adjacent to the SH3 domain to facilitate activation by APC. In colorectal cancer cell lines, full-length, but not truncated, APC activates CDC42 in an ASEF-dependent manner to suppress anchorage-independent growth. We therefore propose a model in which ASEF acts as a tumor suppressor when activated by APC and inactivation of ASEF by mutation or APC truncation promotes tumorigenesis.
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Affiliation(s)
- Natalia Mitin
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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21
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Papadopoulos T, Korte M, Eulenburg V, Kubota H, Retiounskaia M, Harvey RJ, Harvey K, O'Sullivan GA, Laube B, Hülsmann S, Geiger JRP, Betz H. Impaired GABAergic transmission and altered hippocampal synaptic plasticity in collybistin-deficient mice. EMBO J 2007; 26:3888-99. [PMID: 17690689 PMCID: PMC1994120 DOI: 10.1038/sj.emboj.7601819] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Accepted: 07/19/2007] [Indexed: 11/09/2022] Open
Abstract
Collybistin (Cb) is a brain-specific guanine nucleotide exchange factor that has been implicated in plasma membrane targeting of the postsynaptic scaffolding protein gephyrin found at glycinergic and GABAergic synapses. Here we show that Cb-deficient mice display a region-specific loss of postsynaptic gephyrin and GABA(A) receptor clusters in the hippocampus and the basolateral amygdala. Cb deficiency is accompanied by significant changes in hippocampal synaptic plasticity, due to reduced dendritic GABAergic inhibition. Long-term potentiation is enhanced, and long-term depression reduced, in Cb-deficient hippocampal slices. Consistent with the anatomical and electrophysiological findings, the animals show increased levels of anxiety and impaired spatial learning. Together, our data indicate that Cb is essential for gephyrin-dependent clustering of a specific set of GABA(A) receptors, but not required for glycine receptor postsynaptic localization.
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Affiliation(s)
- Theofilos Papadopoulos
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Martin Korte
- Zoological Institute, Technical University Braunschweig, Braunschweig, Germany
| | - Volker Eulenburg
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Hisahiko Kubota
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
- Independent Hertie Research Group, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Marina Retiounskaia
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Robert J Harvey
- Department of Pharmacology, The School of Pharmacy, London, UK
| | - Kirsten Harvey
- Department of Pharmacology, The School of Pharmacy, London, UK
| | - Gregory A O'Sullivan
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Bodo Laube
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Swen Hülsmann
- Department of Neuro- and Sensory Physiology, University of Göttingen, Göttingen, Germany
| | - Jörg R P Geiger
- Independent Hertie Research Group, Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Heinrich Betz
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Frankfurt, Germany
- Department of Neurochemistry, Max-Planck-Institute for Brain Research, Deutschordenstrassee 46, 60528 Frankfurt am Main, Germany. Tel.: +49 69 96769 220; Fax: +49 69 96769 441; E-mail:
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22
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Lockyer AE, Spinks JN, Walker AJ, Kane RA, Noble LR, Rollinson D, Dias-Neto E, Jones CS. Biomphalaria glabrata transcriptome: identification of cell-signalling, transcriptional control and immune-related genes from open reading frame expressed sequence tags (ORESTES). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2007; 31:763-82. [PMID: 17208299 PMCID: PMC1871615 DOI: 10.1016/j.dci.2006.11.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/06/2006] [Accepted: 11/08/2006] [Indexed: 05/13/2023]
Abstract
Biomphalaria glabrata is the major intermediate snail host for Schistosoma mansoni, one of the important schistosomes infecting man. Much remains to be discovered concerning specific molecules mediating the defence events in these intermediate hosts, triggered by invading schistosomes. An expressed sequence tag (EST) gene discovery strategy known as ORESTES has been employed to identify transcripts that might be involved in snail-schistosome interactions in order to examine gene expression patterns in infected B. glabrata. Over 3930 ESTs were sequenced from cDNA libraries made from both schistosome-exposed and unexposed snails using different tissue types, producing a database of 1843 non-redundant clones. The non-redundant set has been assessed for gene ontology and KEGG pathway assignments. This approach has revealed a number of signalling, antioxidant and immune-related gene homologues that, based on current understanding of molluscan and other comparative systems, might play an important role in the molluscan defence response towards infection.
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Affiliation(s)
- Anne E Lockyer
- Wolfson Wellcome Biomedical Laboratory, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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23
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Hilgers RHP, Webb RC. Molecular aspects of arterial smooth muscle contraction: focus on Rho. Exp Biol Med (Maywood) 2006; 230:829-35. [PMID: 16339747 DOI: 10.1177/153537020523001107] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The vascular smooth muscle cell is a highly specialized cell whose primary function is contraction and relaxation. It expresses a variety of contractile proteins, ion channels, and signalling molecules that regulate contraction. Upon contraction, vascular smooth muscle cells shorten, thereby decreasing the diameter of a blood vessel to regulate the blood flow and pressure. Contractile activity in vascular smooth muscle cells is initiated by a Ca(2+)-calmodulin interaction to stimulate phosphorylation of the light chain of myosin. Ca(2+)-sensitization of the contractile proteins is signaled by the RhoA/Rho-kinase pathway to inhibit the dephosphorylation of the light chain by myosin phosphatase, thereby maintaining force. Removal of Ca(2+) from the cytosol and stimulation of myoson phosphatase initiate the relaxation of vascular smooth muscle.
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Affiliation(s)
- Rob H P Hilgers
- Department of Physiology, Medical College of Georgia, Augusta, GA 30912-3000, USA.
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Yoshizawa M, Sone M, Matsuo N, Nagase T, Ohara O, Nabeshima YI, Hoshino M. Dynamic and coordinated expression profile of dbl-family guanine nucleotide exchange factors in the developing mouse brain. Gene Expr Patterns 2003; 3:375-81. [PMID: 12799088 DOI: 10.1016/s1567-133x(03)00002-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dbl-family guanine nucleotide exchange factors (Dbl-GEFs) act as activators of Rho-like small G proteins such as Rac1, Cdc42 and RhoA. Recently, some GEFs have been suggested to play important roles in the development of the nervous system. Here, we report a comprehensive expression profile analysis of 20 Dbl-GEFs that have yet to be well investigated. Northern analyses of murine mRNAs from brains of E13, E17, P7 and adult mice revealed expression of 18 out of 20 GEFs in some or all stages. In addition, we found that three human GEFs were highly expressed in the brain. Examination of the spatial expression patterns of five GEFs in embryos or neonatal brain by in situ hybridization revealed distinct patterns for each GEF. Our study reveals the dynamic and coordinated expression profiles of the Dbl-GEFs and provides a basic framework for understanding the function of GEFs in neural development.
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Affiliation(s)
- Masato Yoshizawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, 606-8501 Kyoto, Japan
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Arthur WT, Ellerbroek SM, Der CJ, Burridge K, Wennerberg K. XPLN, a guanine nucleotide exchange factor for RhoA and RhoB, but not RhoC. J Biol Chem 2002; 277:42964-72. [PMID: 12221096 DOI: 10.1074/jbc.m207401200] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rho proteins cycle between an inactive, GDP-bound state and an active, GTP-bound state. Activation of these GTPases is mediated by guanine nucleotide exchange factors (GEFs), which promote GDP to GTP exchange. In this study we have characterized XPLN, a Rho family GEF. Like other Rho GEFs, XPLN contains a tandem Dbl homology and pleckstrin homology domain topography, but lacks homology with other known functional domains or motifs. XPLN protein is expressed in the brain, skeletal muscle, heart, kidney, platelets, and macrophage and neuronal cell lines. In vitro, XPLN stimulates guanine nucleotide exchange on RhoA and RhoB, but not RhoC, RhoG, Rac1, or Cdc42. Consistent with these data, XPLN preferentially associates with RhoA and RhoB. The specificity of XPLN for RhoA and RhoB, but not RhoC, is surprising given that they share over 85% sequence identity. We determined that the inability of XPLN to exchange RhoC is mediated by isoleucine 43 in RhoC, a position occupied by valine in RhoA and RhoB. When expressed in cells, XPLN activates RhoA and RhoB, but not RhoC, and stimulates the assembly of stress fibers and focal adhesions in a Rho kinase-dependent manner. We also found that XPLN possesses transforming activity, as determined by focus formation assays. In conclusion, here we describe a Rho family GEF that can discriminate between the closely related RhoA, RhoB, and RhoC, possibly giving insight to the divergent functions of these three proteins.
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Affiliation(s)
- William T Arthur
- Department of Cell and Developmental Biology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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