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Shotgun Immunoproteomics for Identification of Nonhuman Leukocyte Antigens Associated With Cellular Dysfunction in Heart Transplant Rejection. Transplantation 2021; 106:1376-1389. [PMID: 34923540 DOI: 10.1097/tp.0000000000004012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The International Society for Heart and Lung Transplant consensus panel notes that too little data exist regarding the role of non-HLA in allograft rejection. We developed a novel shotgun immunoproteomic approach to determine the identities and potential roles non-HLA play in antibody-mediated rejection (AMR) in heart transplant recipients. METHODS Serum was collected longitudinally from heart transplant recipients experiencing AMR in the absence of donor-specific anti-HLA antibodies (n = 6) and matched no rejection controls (n = 7). Antidonor heart affinity chromatography columns were formed by recipient immunoglobulin G immobilization at transplantation, acute rejection, and chronic postrejection time points. Affinity chromatography columns were used to capture antigens from individual patient's donor heart biopsies collected at transplantation. Captured proteins were subjected to quantitative proteomic analysis and the longitudinal response was calculated. RESULTS Overlap in antigen-specific response between AMR and non-AMR patients was only 8.3%. In AMR patients, a total of 155 non-HLAs were identified, with responses toward 43 high prevalence antigens found in ≥50% of patients. Immunofluorescence staining for representative high prevalence antigens demonstrated that their abundance increased at acute rejection, correlating with their respective non-HLA antibody response. Physiological changes in cardiomyocyte and endothelial cell function, following in vitro culture with patient immunoglobulin G, correlated with response toward several high prevalence antigens. CONCLUSIONS This work demonstrates a novel high-throughput strategy to identify clinically relevant non-HLA from donor endomyocardial biopsy. Such a technique has the potential to improve understanding of longitudinal timing of antigen-specific responses and their cause and effect relationship in graft rejection.
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Genetic Dissection of Hypertrophic Cardiomyopathy with Myocardial RNA-Seq. Int J Mol Sci 2020; 21:ijms21093040. [PMID: 32344918 PMCID: PMC7246737 DOI: 10.3390/ijms21093040] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is an inherited disorder of the myocardium, and pathogenic mutations in the sarcomere genes myosin heavy chain 7 (MYH7) and myosin-binding protein C (MYBPC3) explain 60%–70% of observed clinical cases. The heterogeneity of phenotypes observed in HCM patients, however, suggests that novel causative genes or genetic modifiers likely exist. Here, we systemically evaluated RNA-seq data from 28 HCM patients and 9 healthy controls with pathogenic variant identification, differential expression analysis, and gene co-expression and protein–protein interaction network analyses. We identified 43 potential pathogenic variants in 19 genes in 24 HCM patients. Genes with more than one variant included the following: MYBPC3, TTN, MYH7, PSEN2, and LDB3. A total of 2538 protein-coding genes, six microRNAs (miRNAs), and 1617 long noncoding RNAs (lncRNAs) were identified differentially expressed between the groups, including several well-characterized cardiomyopathy-related genes (ANKRD1, FHL2, TGFB3, miR-30d, and miR-154). Gene enrichment analysis revealed that those genes are significantly involved in heart development and physiology. Furthermore, we highlighted four subnetworks: mtDNA-subnetwork, DSP-subnetwork, MYH7-subnetwork, and MYBPC3-subnetwork, which could play significant roles in the progression of HCM. Our findings further illustrate that HCM is a complex disease, which results from mutations in multiple protein-coding genes, modulation by non-coding RNAs and perturbations in gene networks.
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Li W, Li L, Zhang S, Zhang C, Huang H, Li Y, Hu E, Deng G, Guo S, Wang Y, Li W, Chen L. Identification of potential genes for human ischemic cardiomyopathy based on RNA-Seq data. Oncotarget 2018; 7:82063-82073. [PMID: 27852050 PMCID: PMC5347674 DOI: 10.18632/oncotarget.13331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/07/2016] [Indexed: 12/30/2022] Open
Abstract
Ischemic cardiomyopathy (ICM) is an important cause of heart failure, yet no ICM disease genes were stored in any public databases. Mutations of genes provided by RNA-Seq data could set a foundation for a variety of biological processes. This also made it possible to elucidate the mechanism and identify potential genes for ICM. In this paper, an integrated co-expression network was constructed using univariate and bivariate canonical correlation analysis for RNA-Seq data of human ICM samples. Three ICM-related modules were recognized after comparing between Pearson correlation coefficients of ICM samples and normal controls. Furthermore, 32 ICM potential genes were identified from ICM-related modules considering protein-protein interactions. Most of these genes were verified to be involved in ICM and diseases caused it by OMIM and literature. Our study could provide a novel perspective for potential gene identification and the pathogenesis for ICM and other complex diseases.
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Affiliation(s)
- Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Liansheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shiying Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Ce Zhang
- Department of internal medicine, Heilongjiang Commercial Hospital, Harbin, Heilongjiang, China
| | - Hao Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yiran Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Erqiang Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Gui Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shanshan Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yahui Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Weimin Li
- Department of Cardiology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
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Colak D, Alaiya AA, Kaya N, Muiya NP, AlHarazi O, Shinwari Z, Andres E, Dzimiri N. Integrated Left Ventricular Global Transcriptome and Proteome Profiling in Human End-Stage Dilated Cardiomyopathy. PLoS One 2016; 11:e0162669. [PMID: 27711126 PMCID: PMC5053516 DOI: 10.1371/journal.pone.0162669] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 08/28/2016] [Indexed: 01/30/2023] Open
Abstract
Aims The disease pathways leading to idiopathic dilated cardiomyopathy (DCM) are still elusive. The present study investigated integrated global transcriptional and translational changes in human DCM for disease biomarker discovery. Methods We used identical myocardial tissues from five DCM hearts compared to five non-failing (NF) donor hearts for both transcriptome profiling using the ABI high-density oligonucleotide microarrays and proteome expression with One-Dimensional Nano Acquity liquid chromatography coupled with tandem mass spectrometry on the Synapt G2 system. Results We identified 1262 differentially expressed genes (DEGs) and 269 proteins (DEPs) between DCM cases and healthy controls. Among the most significantly upregulated (>5-fold) proteins were GRK5, APOA2, IGHG3, ANXA6, HSP90AA1, and ATP5C1 (p< 0.01). On the other hand, the most significantly downregulated proteins were GSTM5, COX17, CAV1 and ANXA3. At least ten entities were concomitantly upregulated on the two analysis platforms: GOT1, ALDH4A1, PDHB, BDH1, SLC2A11, HSP90AA1, HSP90AB1, H2AFV, HSPA5 and NDUFV1. Gene ontology analyses of DEGs and DEPs revealed significant overlap with enrichment of genes/proteins related to metabolic process, biosynthetic process, cellular component organization, oxidative phosphorylation, alterations in glycolysis and ATP synthesis, Alzheimer’s disease, chemokine-mediated inflammation and cytokine signalling pathways. Conclusion The concomitant use of transcriptome and proteome expression to evaluate global changes in DCM has led to the identification of sixteen commonly altered entities as well as novel genes, proteins and pathways whose cardiac functions have yet to be deciphered. This data should contribute towards better management of the disease.
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Affiliation(s)
- Dilek Colak
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Ayodele A. Alaiya
- Proteomics Unit, Stem Cell Tissue Re-Engineering Program, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Namik Kaya
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nzioka P. Muiya
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Olfat AlHarazi
- Biostatistics, Epidemiology and Scientific Computing Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Zakia Shinwari
- Proteomics Unit, Stem Cell Tissue Re-Engineering Program, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Editha Andres
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
| | - Nduna Dzimiri
- Genetics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Saudi Arabia
- * E-mail:
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Abstract
Mitochondrial dynamics, fission and fusion, were first identified in yeast with investigation in heart cells beginning only in the last 5 to 7 years. In the ensuing time, it has become evident that these processes are not only required for healthy mitochondria, but also, that derangement of these processes contributes to disease. The fission and fusion proteins have a number of functions beyond the mitochondrial dynamics. Many of these functions are related to their membrane activities, such as apoptosis. However, other functions involve other areas of the mitochondria, such as OPA1's role in maintaining cristae structure and preventing cytochrome c leak, and its essential (at least a 10 kDa fragment of OPA1) role in mtDNA replication. In heart disease, changes in expression of these important proteins can have detrimental effects on mitochondrial and cellular function.
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Affiliation(s)
- A A Knowlton
- Molecular & Cellular Cardiology, Division of Cardiovascular Medicine and Pharmacology Department, University of California, Davis, and The Department of Veteran's Affairs, Northern California VA, Sacramento, California, USA
| | - T T Liu
- Molecular & Cellular Cardiology, Division of Cardiovascular Medicine and Pharmacology Department, University of California, Davis, and The Department of Veteran's Affairs, Northern California VA, Sacramento, California, USA
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Du Y, Meng Y, Zhu J, Kang L, Jia X, Guo L, Zhang L, Ye M, Hu L, Zhao X, Gu J, Yang B, Zou H. Quantitative proteomic study of myocardial mitochondria in urea transporter B knockout mice. Proteomics 2014; 14:2072-83. [PMID: 25044461 DOI: 10.1002/pmic.201400123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/26/2014] [Accepted: 07/04/2014] [Indexed: 11/08/2022]
Abstract
In previous research, we showed that 16-week-old urea transporter B (UT-B) null mice have an atrial-ventricular conduction block, and hypothesized myocardial mitochondrial dysfunction. To investigate the mechanism of this block, we examined the proteomic differences in the myocardial mitochondria of UT-B null and wild-type mice with nanoscale LC-MS/MS. Of 26 proteins clearly downregulated in the UT-B null mice, 15 are involved in complexes I, III, IV, and V of the respiratory chain, which would strongly reduce the activity of the electron transport chain. Excess electrons from complexes I and III pass directly to O2 to generate ROS and deplete ROS-scavenging enzymes. Myocardial intracellular ROS were significantly higher in UT-B null mice than in wild-type mice (p < 0.01), constituting an important cause of oxidative stress injury in the myocardia of UT-B null mice. The mitochondrial membrane potential (ΔΨm) was also lower in UT-B null mice than in wild-type mice (p < 0.05), causing oxidative phosphorylation dysfunction of complex V and insufficient ATP in the myocardial cells of UT-B null mice. HADHA (a trifunctional protein) and HSP60 were also downregulated in the UT-B null myocardial mitochondria. These results confirm that mitochondrial dysfunction underlies the pathogenesis of the atrial-ventricular conduction block in UT-B null mice.
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Affiliation(s)
- Yanwei Du
- Key Laboratory of Pathobiology, Department of Pathophysiology, Ministry of Education, College of Basic Medicine, Jilin University, Changchun, P. R. China
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Marecki JC, Parajuli N, Crow JP, MacMillan-Crow LA. The use of the Cre/loxP system to study oxidative stress in tissue-specific manganese superoxide dismutase knockout models. Antioxid Redox Signal 2014; 20:1655-70. [PMID: 23641945 PMCID: PMC3942694 DOI: 10.1089/ars.2013.5293] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE Respiring mitochondria are a significant site for reactions involving reactive oxygen and nitrogen species that contribute to irreversible cellular, structural, and functional damage leading to multiple pathological conditions. Manganese superoxide dismutase (MnSOD) is a critical component of the antioxidant system tasked with protecting the oxidant-sensitive mitochondrial compartment from oxidative stress. Since global knockout of MnSOD results in significant cardiac and neuronal damage leading to early postnatal lethality, this approach has limited use for studying the mechanisms of oxidant stress and the development of disease in specific tissues lacking MnSOD. To circumvent this problem, a number of investigators have employed the Cre/loxP system to precisely knockout MnSOD in individual tissues. RECENT ADVANCES Multiple tissue and organ-specific Cre-expressing mice have been generated, which greatly enhance the specificity of MnSOD knockout in tissues and organ systems that were once difficult, if not impossible to study. CRITICAL ISSUES Evaluating the contribution of MnSOD deficiency to oxidant-mediated mitochondrial damage requires careful consideration of the promoter system used for creating the tissue-specific knockout animal, in addition to the collection and interpretation of multiple indices of oxidative stress and damage. FUTURE DIRECTIONS Expanded use of well-characterized tissue-specific promoter elements and inducible systems to drive the Cre/loxP recombinational events will lead to a spectrum of MnSOD tissue knockout models, and a clearer understanding of the role of MnSOD in preventing mitochondrial dysfunction in human disease.
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Affiliation(s)
- John C Marecki
- 1 Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences , Little Rock, Arkansas
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Liu T, Chen L, Kim E, Tran D, Phinney BS, Knowlton AA. Mitochondrial proteome remodeling in ischemic heart failure. Life Sci 2014; 101:27-36. [PMID: 24548633 DOI: 10.1016/j.lfs.2014.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 01/24/2014] [Accepted: 02/07/2014] [Indexed: 01/05/2023]
Abstract
AIMS Mitochondrial dysfunction is an important part of the decline in cardiac function in heart failure. We hypothesized for hypothesized that there would be specific abnormalities in mitochondrial function and proteome with the progression of ischemic heart failure (HF). MAIN METHODS We used a high left anterior descending artery (LAD) ligation in 3-4month old male rats to generate HF. Rats were studied 9weeks post-ligation. KEY FINDINGS Electron microscopy of left ventricle samples showed mitochondrial changes including decreased size, increased number, abnormal distribution, and cristae loss. Mitochondria in ischemic HF exhibited decreased total ATP, impaired mitochondrial respiration, as well as reduced complex I activity. Analysis of LV mitochondrial proteins by mass spectrometry was performed, and 31 differentially expressed proteins (p<0.05) of more than 500 total proteins were identified. Of these proteins, 15 were up-regulated and 16 were down-regulated in the failing heart. A set of complex I proteins was significantly decreased, consistent with the impairment of complex I activity. There were distinct changes in mitochondrial function and proteome in ischemic HF. Although there were similarities, the distinction between the reported proteomic changed with TAC pressure overload induced HF and ischemic HF in the current study suggested different pathological mechanisms. SIGNIFICANCE Specific changes in mitochondrial protein expression, which correlate with changes in mitochondrial function, have been identified in ischemic HF for the first time.
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Affiliation(s)
- Tingting Liu
- Molecular & Cellular Cardiology, Cardiovascular Division, University of California - Davis, Davis, CA, USA
| | - Le Chen
- Molecular & Cellular Cardiology, Cardiovascular Division, University of California - Davis, Davis, CA, USA
| | - Eunjung Kim
- Clinical Research, St. Mary's Hospital of Daejeon Catholic University, Daejeon, Republic of Korea
| | - Diana Tran
- Proteomics Core Facility, University of California - Davis, Davis, CA, USA
| | - Brett S Phinney
- Proteomics Core Facility, University of California - Davis, Davis, CA, USA
| | - Anne A Knowlton
- Molecular & Cellular Cardiology, Cardiovascular Division, University of California - Davis, Davis, CA, USA; Pharmacology Department, University of California - Davis, Davis, CA, USA; VA Medical Center Sacramento, CA, USA.
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Analysis of beat fluctuations and oxygen consumption in cardiomyocytes by scanning electrochemical microscopy. Anal Biochem 2014; 447:39-42. [DOI: 10.1016/j.ab.2013.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/18/2013] [Accepted: 11/07/2013] [Indexed: 11/19/2022]
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NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels. Adv Bioinformatics 2011; 2011:657341. [PMID: 22110502 PMCID: PMC3206323 DOI: 10.1155/2011/657341] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 08/11/2011] [Indexed: 02/06/2023] Open
Abstract
Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software
tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents a known variant or a previously unknown variant. In a second step, each variant is classified into one of 15 SNP classes or 19 InDel classes. Beside the classes used by Ensembl, we introduce POTENTIAL_START_GAINED and START_LOST as new functional classes and present a classification scheme for InDels. NovelSNPer is based upon the gene structure information stored in Ensembl. It processes two million SNPs in six hours. The tool can be used online or downloaded.
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