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Ma Y, Li Y, Sun J, Liang Q, Wu R, Ding Q, Dai J. Complete F9 Gene Deletion, Duplication, and Triplication Rearrangements: Implications for Factor IX Expression and Clinical Phenotypes. Thromb Haemost 2024; 124:374-385. [PMID: 38011862 DOI: 10.1055/a-2217-9837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
BACKGROUND Factor IX (FIX) plays a critical role in blood coagulation. Complete deletion of F9 results in severe hemophilia B, whereas the clinical implications of complete F9 duplication and triplication remain understudied. OBJECTIVE To investigate the rearrangement mechanisms underlying complete F9 deletion (cases 1 and 2), duplication (cases 3 and 4), and triplication (case 5), and to explore their association with FIX expression levels and clinical impacts. METHODS Plasma FIX levels were detected using antigen and activity assays. CNVplex technology, optical genome mapping, and long-distance polymerase chain reaction were employed to characterize the breakpoints of the chromosomal rearrangements. RESULTS Cases 1 and 2 exhibited FIX activities below 1%. Case 3 displayed FIX activities within the reference range. However, cases 4 and 5 showed a significant increase in FIX activities. Alu-mediated nonallelic homologous recombination was identified as the cause of F9 deletion in case 1; FoSTeS/MMBIR (Fork Stalling and Template Switching/microhomology-mediated break-induced replication) contributed to both F9 deletion and tandem duplication observed in cases 2 and 3; BIR/MMBIR (break-induced replication/microhomology-mediated break-induced replication) mediated by the same pair of low-copy repeats results in similar duplication-triplication/inversion-duplication (DUP-TRP/INV-DUP) rearrangements in cases 4 and 5, leading to complete F9 duplication and triplication, respectively. CONCLUSION Large deletions involving the F9 gene exhibit no apparent pattern, and the extra-hematologic clinical phenotypes require careful analysis of other genes within the deletion. The impact of complete F9 duplication and triplication on FIX expression might depend on the integrity of the F9 upstream sequence and the specific rearrangement mechanisms. Notably, DUP-TRP/INV-DUP rearrangements significantly elevate FIX activity and are closely associated with thrombotic phenotypes.
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Affiliation(s)
- YuXin Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
| | - Yang Li
- Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
| | - Jie Sun
- Haemophilia Comprehensive Care Center, Capital Medical University, Beijing Children's Hospital, Beijing, China
| | - Qian Liang
- Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
| | - Runhui Wu
- Haemophilia Comprehensive Care Center, Capital Medical University, Beijing Children's Hospital, Beijing, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jing Dai
- Department of Laboratory Medicine, Shanghai Jiaotong University School of Medicine, Ruijin Hospital, Shanghai, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Alhenc-Gelas M, Plu-Bureau G, Mauge L, Gandrille S, Présot I. Genotype-Phenotype Relationships in a Large French Cohort of Subjects with Inherited Protein C Deficiency. Thromb Haemost 2020; 120:1270-1281. [PMID: 32717757 DOI: 10.1055/s-0040-1714100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Inherited protein C (PC) deficiency caused by mutations in the PROC gene is a well-known risk factor for venous thromboembolism. Few studies have investigated the relationship between PROC genotype and plasma or clinical phenotypes. We addressed this issue in a large retrospective cohort of 1,115 heterozygous carriers of 226 PROC pathogenic or likely pathogenic mutations. Mutations were classified in three categories according to their observed or presumed association with type I, type IIa, or type IIb PC deficiency. The study population comprised 876 carriers of type I category mutations, 55 carriers of type IIa category mutations, and 184 carriers of type IIb category mutations. PC anticoagulant activity significantly influenced risk of first venous thrombosis (p trend < 10-4). No influence of mutation category on risk of whole or unprovoked thrombotic events was observed. Both PC anticoagulant activity and genotype significantly influenced risk of venous thrombosis. Effect of detrimental mutations on plasma phenotype was ambiguous in several carriers, whatever the mutation category. Altogether, our findings confirm that diagnosing PC inherited deficiency based on plasma measurement may be difficult but show that diagnosis can be improved by PROC genotyping.
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Affiliation(s)
- Martine Alhenc-Gelas
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France
| | - Geneviève Plu-Bureau
- Unité d'hémostase, Unité de Gynécologie Endocrinienne, AP-HP, Hôpital Cochin, QUP Centre Université de Paris, Paris, France
| | - Laetitia Mauge
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France
| | - Sophie Gandrille
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France.,Innovative Therapies in Haemostasis, Université de Paris, Paris, France
| | - Isabelle Présot
- Hématologie Biologique, AP-HP Hôpital Européen G Pompidou, QUP Centre Université de Paris, Paris, France
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Protein C deficiency (a novel mutation: ala291Thr) with systemic lupus erythematosus leads to the deep vein thrombosis. Blood Coagul Fibrinolysis 2019; 29:714-719. [PMID: 30439769 DOI: 10.1097/mbc.0000000000000778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
: The current study aims to explore the phenotype and genotype of a mutation Ala291Thr, which responsible for type I protein C (PC) deficiency in a Chinese woman. The PROC antigen was tested with chromogenic substrate method. PROC gene were amplified by PCR with direct sequencing. Bioinformatics and model analysis were used to study the harm of the mutation. PC activity (PC: A) levels of three members were reduced to 39, 57 and 56%, respectively, PC: antigen was decreased parallelly same as PC: A. Sequencing analysis showed proband with a novel heterozygous c.997G>A point mutation in exon 9 of PROC gene resulting in Ala291Thr. The Ala291Thr mutation is responsible for the decrease of PC: A, which is cross-reacting material negative deficiency and the first reported in the world. This mutation alone may not have significant clinical symptoms, whereas it will cause deep vein thrombosis when combined with systemic lupus erythematosus.
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Xie W, Liu Z, Chen B. Protein C deficiency resulting from two mutations in PROC presenting with recurrent venous thromboembolism. JOURNAL OF VASCULAR SURGERY CASES INNOVATIONS AND TECHNIQUES 2018; 3:254-256. [PMID: 29349439 PMCID: PMC5765183 DOI: 10.1016/j.jvscit.2017.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/01/2017] [Indexed: 11/28/2022]
Abstract
Hereditary protein C (PC) deficiency is an autosomal dominant disorder associated with a high risk of venous thromboembolism (VTE). Here we report a case of inherited PC deficiency associated with recurrent deep venous thrombosis. Two mutations were revealed in PROC (c.1152C>G, p.N384K and c.1207G>T, p.G403W) by genetic testing. Results from this case suggest that the inherited PC deficiency due to the PROC mutations may cause recurrent VTE. Long-term anticoagulant therapy may be appropriate for these patients with recurrent VTE and hereditary PC deficiency.
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Affiliation(s)
- Weijia Xie
- Department of General Surgery, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhenjie Liu
- Department of Vascular Surgery, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Bing Chen
- Department of Vascular Surgery, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Branchini A, Baroni M, Burini F, Puzzo F, Nicolosi F, Mari R, Gemmati D, Bernardi F, Pinotti M. The carboxyl-terminal region is NOT essential for secreted and functional levels of coagulation factor X. J Thromb Haemost 2015; 13:1468-74. [PMID: 26083275 DOI: 10.1111/jth.13034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/10/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND The homologous coagulation factor X (FX), VII (FVII), IX (FIX) and protein C (PC) display striking differences in the carboxyl-terminus, with that of FX being the most extended. This region is essential for FVII, FIX and PC secretion. OBJECTIVES To provide experimental evidence for the role of the FX carboxyl-terminus. METHODS Recombinant FX (rFX) variants were expressed in multiple eukaryotic cell systems. Protein and activity levels were evaluated by ELISA, coagulant and amidolytic assays. RESULTS AND DISCUSSION Expression of a panel of progressively truncated rFX variants in HEK293 cells revealed that the deletion of up to 21 residues in the carboxyl-terminus did not significantly affect secreted protein levels, as confirmed in HepG2 and BHK21 cells. In contrast, chimeric rFX-FVII variants with swapped terminal residues showed severely reduced levels. The truncated rFX variants revealed normal amidolytic activity, suggesting an intact active site. Intriguingly, these variants, which included that resembling the activated FXβ form once cleaved, also displayed remarkable or normal pro-coagulant capacity in PT- and aPTT-based assays. This supports the hypothesis that subjects with nonsense mutations in the FX carboxyl-terminus, so far never identified, would be asymptomatic. CONCLUSIONS For the first time we demonstrate that the FX carboxyl-terminal region downstream of residue K467 is not essential for secretion and provides a modest contribution to pro-coagulant properties. These findings, which might suggest an involvement of the carboxyl-terminal region in the divergence of the homologous FX, FVII, FIX and PC, help to interpret the mutational pattern of FX deficiency.
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Affiliation(s)
- A Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- LTTA Centre, University of Ferrara, Ferrara, Italy
| | - M Baroni
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- LTTA Centre, University of Ferrara, Ferrara, Italy
| | - F Burini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - F Puzzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - F Nicolosi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - R Mari
- Centre for Haemostasis and Thrombosis, Haematology Section, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - D Gemmati
- Centre for Haemostasis and Thrombosis, Haematology Section, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - F Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- LTTA Centre, University of Ferrara, Ferrara, Italy
| | - M Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- LTTA Centre, University of Ferrara, Ferrara, Italy
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Kovács KB, Pataki I, Bárdos H, Fekete A, Pfliegler G, Haramura G, Gindele R, Komáromi I, Balla G, Ádány R, Muszbek L, Bereczky Z. Molecular characterization of p.Asp77Gly and the novel p.Ala163Val and p.Ala163Glu mutations causing protein C deficiency. Thromb Res 2015; 135:718-26. [DOI: 10.1016/j.thromres.2015.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 12/17/2014] [Accepted: 01/11/2015] [Indexed: 11/29/2022]
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Liu H, Wang HF, Tang L, Yang Y, Wang QY, Zeng W, Wu YY, Cheng ZP, Hu B, Guo T, Hu Y. Compound heterozygous protein C deficiency in a family with venous thrombosis: Identification and in vitro study of p.Asp297His and p.Val420Leu mutations. Gene 2015; 563:35-40. [PMID: 25748729 DOI: 10.1016/j.gene.2015.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 02/05/2015] [Accepted: 03/02/2015] [Indexed: 10/23/2022]
Abstract
Hereditary protein C deficiency (PCD) is an autosomal inherited disorder associated with high risk for venous thromboembolism (VTE). This study aimed to explore the functional consequences of two missense mutations, p.Asp297His and p.Val420Ile, responsible for type I/II PCD and recurrent deep vein thrombosis (DVT) in a Chinese family. The plasma protein C activities (PC:A) of the proband and his sister were reduced to 4% and 5% of normal activity. However, protein C antigen (PC:Ag) concentrations were not equally decreased, with levels of 90.5% and 88.7%, respectively. Two missense mutations p.Asp297His and p.Val420Leu were identified in the protein C gene (PROC). The PC:A and PC:Ag levels in heterozygous state for p.Asp297His were 66% and 64.8%, whereas in heterozygous state for p.Val420Leu, these levels were 67% and 145%, respectively. Wild type (WT) and two mutant PROC cDNA expression plasmids were constructed and transfected into HEK 293T cells. Western blot analysis revealed that both p.Asp297His and p.Val420Leu showed a normal intracellular protein level. The extracellular protein level and specific activity of p.Asp297His were equally reduced to 37.7 ± 4.3% and 22.1 ± 2.5%, respectively. Mutant p.Val420Leu showed a relatively higher PC:Ag level and undetectable PC:A. Immunofluorescence staining revealed that WT and p.Val420Leu proteins were largely co-localized with both the protein disulfide isomerase (PDI) and cis-Golgi Marker (GM130), while the PC p.Asp297His mutant protein was mainly co-localized with PDI and much less co-localized with GM130. The thrombosis symptom in this family was associated with the two missense mutations in the PROC gene.
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Affiliation(s)
- Hui Liu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Hua-Fang Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Liang Tang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China.
| | - Yan Yang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Qing-Yun Wang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Wei Zeng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Ying-Ying Wu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Zhi-Peng Cheng
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Bei Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Tao Guo
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China
| | - Yu Hu
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Collaborative Innovation Center of Hematology, Huazhong University of Science and Technology, China.
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Luan CJ, Shen W, Yu Z, Chen L, Gu Y, Tang LY, Wang ZG, Dai L, Gu MM. Two nonsense mutations cause protein C deficiency by nonsense-mediated mRNA decay. Thromb Res 2015; 135:733-8. [PMID: 25648792 DOI: 10.1016/j.thromres.2015.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/22/2014] [Accepted: 01/19/2015] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Protein C deficiency is a genetic disorder caused by mutations in the protein C gene (PROC). More than 10% of nonsense and frameshift mutations carrying premature termination codons have been identified in PROC, but the exact molecular mechanisms of these mutations on the pathogenesis of protein C deficiency remain unclear. OBJECTIVE The aim of this study is to investigate whether nonsense-mediated mRNA decay (NMD) can be a mechanism accounting for protein C deficiency. METHODS PROC of genomic DNA was amplified and sequenced. Recombinant plasmids expressing wild-type (wt) and mutant EGFP-protein C (EGFP-PC) cDNA were constructed and transiently transfected into human embryonic kidney cells using lipofectamine. Expression of mRNAs and proteins of EGFP-PC and NMD factor UPF1 were analyzed by qPCR and Western blot. RESULTS DNA sequencing revealed a novel heterozygous nonsense mutation (p.Trp247*) in patient 1 and two compound heterozygous mutations (p.Phe181Val and p.Arg199*) in patient 2. Expression studies showed that cells transfected with the mutant plasmids expressed significantly lower levels of EGFP-PC mRNAs and proteins compared to cells transfected with the wt plasmid. A translation inhibitor cycloheximide and UPF1 small interfering RNA (UPF1 siRNA) significantly increased mRNA or protein expression of EGFP-PC in cells transfected with the mutant plasmids. CONCLUSION Two PROC nonsense mutations (p.Trp247* and p.Arg199*) trigger NMD, resulting in protein C deficiency.
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Affiliation(s)
- Chun-jie Luan
- Department of Medical Genetics, E-Institutes of Shanghai Universities, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Shen
- Department of Laboratory Medicine, Renji Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Zhen Yu
- Department of Medical Genetics, E-Institutes of Shanghai Universities, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Chen
- Department of Medical Genetics, E-Institutes of Shanghai Universities, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi Gu
- Department of Laboratory Medicine, Renji Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Lin-yun Tang
- State Key Laboratory of Medical Genomics, Research Centre for Experimental Medicine, Ruijin Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu-gang Wang
- Department of Medical Genetics, E-Institutes of Shanghai Universities, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Medical Genomics, Research Centre for Experimental Medicine, Ruijin Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Letian Dai
- Centre for Haemostasis and Thrombosis, Haemophilia Reference Centre, St Thomas Hospital, London SE1 7EH, UK
| | - Ming-min Gu
- Department of Medical Genetics, E-Institutes of Shanghai Universities, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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D’Ursi P, Orro A, Morra G, Moscatelli M, Trombetti G, Milanesi L, Rovida E. Molecular dynamics and docking simulation of a natural variant of Activated Protein C with impaired protease activity: implications for integrin-mediated antiseptic function. J Biomol Struct Dyn 2013; 33:85-92. [DOI: 10.1080/07391102.2013.851033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Protein C anticoagulant and cytoprotective pathways. Int J Hematol 2012; 95:333-45. [PMID: 22477541 DOI: 10.1007/s12185-012-1059-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 03/09/2012] [Accepted: 03/14/2012] [Indexed: 12/11/2022]
Abstract
Plasma protein C is a serine protease zymogen that is transformed into the active, trypsin-like protease, activated protein C (APC), which can exert multiple activities. For its anticoagulant action, APC causes inactivation of the procoagulant cofactors, factors Va and VIIIa, by limited proteolysis, and APC's anticoagulant activity is promoted by protein S, various lipids, high-density lipoprotein, and factor V. Hereditary heterozygous deficiency of protein C or protein S is linked to moderately increased risk for venous thrombosis, while a severe or total deficiency of either protein is linked to neonatal purpura fulminans. In recent years, the beneficial direct effects of APC on cells which are mediated by several specific receptors have become the focus of much attention. APC-induced signaling can promote multiple cytoprotective actions which can minimize injuries in various preclinical animal injury models. Remarkably, pharmacologic therapy using APC demonstrates substantial neuroprotective effects in various murine injury models, including ischemic stroke. This review summarizes the molecules that are central to the protein C pathways, the relationship of pathway deficiencies to venous thrombosis risk, and mechanisms for the beneficial effects of APC.
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COOPER PC, HILL M, MACLEAN RM. The phenotypic and genetic assessment of protein C deficiency. Int J Lab Hematol 2012; 34:336-46. [DOI: 10.1111/j.1751-553x.2012.01401.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Genetic defects in Portuguese families with inherited protein C deficiency. Thromb Res 2011; 128:299-302. [DOI: 10.1016/j.thromres.2011.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 04/28/2011] [Accepted: 05/02/2011] [Indexed: 11/18/2022]
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Facchiano A, Marabotti A. Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach. Protein Eng Des Sel 2009; 23:103-13. [PMID: 20008339 DOI: 10.1093/protein/gzp076] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe the prediction of the structural and functional effects of mutations on the enzyme galactose-1-phosphate uridyltransferase related to the genetic disease galactosemia, using a fully computational approach. One hundred and seven single-point mutants were simulated starting from the structural model of the enzyme obtained by homology modeling methods. Several bioinformatics programs were then applied to each resulting mutant protein to analyze the effect of the mutations. The mutations have a direct effect on the active site, or on the dimer assembly and stability, or on the monomer stability. We describe how mutations may exert their effect at a molecular level by altering H-bonds, salt bridges, secondary structure or surface features. The alteration of protein stability, at level of monomer and/or dimer, is the main effect observed. We found an agreement between our results and the functional experimental data available in literature for some mutants. The data and analyses for all the mutants are fully available in the web-accessible database hosted at http://bioinformatica.isa.cnr.it/GALT.
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Affiliation(s)
- A Facchiano
- Institute of Food Science, CNR, Via Roma, 64, 83100 Avellino, Italy
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D'Ursi P, Marino F, Caprera A, Milanesi L, Faioni EM, Rovida E. ProCMD: a database and 3D web resource for protein C mutants. BMC Bioinformatics 2007; 8 Suppl 1:S11. [PMID: 17430555 PMCID: PMC1885840 DOI: 10.1186/1471-2105-8-s1-s11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Activated Protein C (ProC) is an anticoagulant plasma serine protease which also plays an important role in controlling inflammation and cell proliferation. Several mutations of the gene are associated with phenotypic functional deficiency of protein C, and with the risk of developing venous thrombosis. Structure prediction and computational analysis of the mutants have proven to be a valuable aid in understanding the molecular aspects of clinical thrombophilia. RESULTS We have built a specialized relational database and a search tool for natural mutants of protein C. It contains 195 entries that include 182 missense and 13 stop mutations. A menu driven search engine allows the user to retrieve stored information for each variant, that include genetic as well as structural data and a multiple alignment highlighting the substituted position. Molecular models of variants can be visualized with interactive tools; PDB coordinates of the models are also available for further analysis. Furthermore, an automatic modelling interface allows the user to generate multiple alignments and 3D models of new variants. CONCLUSION ProCMD is an up-to-date interactive mutant database that integrates phenotypical descriptions with functional and structural data obtained by computational approaches. It will be useful in the research and clinical fields to help elucidate the chain of events leading from a molecular defect to the related disease. It is available for academics at the URL http://www.itb.cnr.it/procmd/.
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Affiliation(s)
- Pasqualina D'Ursi
- Department of Science and Biomedical Technologies, University of Milano, Italy
| | - Francesca Marino
- Institute of Biomedical Technologies, National Research Council, Segrate (Mi), Italy
| | - Andrea Caprera
- Institute of Biomedical Technologies, National Research Council, Segrate (Mi), Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Segrate (Mi), Italy
| | - Elena M Faioni
- Hematology and Thrombosis Unit, DMCO- University of Milano and Az. Ospedaliera San Paolo, Italy
| | - Ermanna Rovida
- Institute of Biomedical Technologies, National Research Council, Segrate (Mi), Italy
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