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Hinton AO, N'jai AU, Vue Z, Wanjalla C. Connection Between HIV and Mitochondria in Cardiovascular Disease and Implications for Treatments. Circ Res 2024; 134:1581-1606. [PMID: 38781302 PMCID: PMC11122810 DOI: 10.1161/circresaha.124.324296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
HIV infection and antiretroviral therapy alter mitochondrial function, which can progressively lead to mitochondrial damage and accelerated aging. The interaction between persistent HIV reservoirs and mitochondria may provide insight into the relatively high rates of cardiovascular disease and mortality in persons living with HIV. In this review, we explore the intricate relationship between HIV and mitochondrial function, highlighting the potential for novel therapeutic strategies in the context of cardiovascular diseases. We reflect on mitochondrial dynamics, mitochondrial DNA, and mitochondrial antiviral signaling protein in the context of HIV. Furthermore, we summarize how toxicities related to early antiretroviral therapy and current highly active antiretroviral therapy can contribute to mitochondrial dysregulation, chronic inflammation, and poor clinical outcomes. There is a need to understand the mechanisms and develop new targeted therapies. We further consider current and potential future therapies for HIV and their interplay with mitochondria. We reflect on the next-generation antiretroviral therapies and HIV cure due to the direct and indirect effects of HIV persistence, associated comorbidities, coinfections, and the advancement of interdisciplinary research fields. This includes exploring novel and creative approaches to target mitochondria for therapeutic intervention.
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Affiliation(s)
- Antentor O Hinton
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN (A.O.H., Z.V.)
| | - Alhaji U N'jai
- Biological Sciences, Fourah Bay College and College of Medicine and Allied Health Sciences (COMAHS), University of Sierra Leone, Freetown, Sierra Leone and Koinadugu College, Kabala (A.U.N.)
| | - Zer Vue
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN (A.O.H., Z.V.)
| | - Celestine Wanjalla
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN (C.W.)
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2
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Purandare N, Ghosalkar E, Grossman LI, Aras S. Mitochondrial Oxidative Phosphorylation in Viral Infections. Viruses 2023; 15:2380. [PMID: 38140621 PMCID: PMC10747082 DOI: 10.3390/v15122380] [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: 10/25/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Mitochondria have been identified as the "powerhouse" of the cell, generating the cellular energy, ATP, for almost seven decades. Research over time has uncovered a multifaceted role of the mitochondrion in processes such as cellular stress signaling, generating precursor molecules, immune response, and apoptosis to name a few. Dysfunctional mitochondria resulting from a departure in homeostasis results in cellular degeneration. Viruses hijack host cell machinery to facilitate their own replication in the absence of a bonafide replication machinery. Replication being an energy intensive process necessitates regulation of the host cell oxidative phosphorylation occurring at the electron transport chain in the mitochondria to generate energy. Mitochondria, therefore, can be an attractive therapeutic target by limiting energy for viral replication. In this review we focus on the physiology of oxidative phosphorylation and on the limited studies highlighting the regulatory effects viruses induce on the electron transport chain.
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Affiliation(s)
- Neeraja Purandare
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
| | - Esha Ghosalkar
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
| | - Siddhesh Aras
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (N.P.); (E.G.); (L.I.G.)
- Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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3
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Lu H, Chen W, Peng K, Huang M, Zhao J, Chen X, Sun Y, Ruan Z, Li C, Liu D, Liu Z, Li H, Zhang Y, Huang W. Rapid adaptive and acute stimulatory responses to low salinity stress in Pacific white shrimp (Litopenaeus vannamei): Insights from integrative transcriptomic and proteomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101149. [PMID: 37883838 DOI: 10.1016/j.cbd.2023.101149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023]
Abstract
The Pacific white shrimp (Litopenaeus vannamei) is a euryhaline crustacean capable of tolerating a wide range of ambient salinity, but the strategies of hepatopancreas to rapid adaptive or acute stimulatory responses to extremely low salinity fluctuations remains unclear. In this study, we integrated transcriptomic and proteomic analyses on the hepatopancreas derived from rapid adaptative (RA) and acute stimulatory (AS) responses to extremely low salinity stress (0.3 ppt) to unveil specific regulatory mechanisms. The RA group displayed normal epithelial cells and tubule structures, while the AS group showed histological changes and lesions. A total of 754 and 649 differentially expressed genes (DEGs) were identified in RA and AS treatments, respectively. For proteome, a total of 206 and 66 differentially expressed proteins (DEPs) were obtained in the RA/CT and AS/CT comparison groups, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted among the DEGs and DEPs, revealing that metabolic related pathways were significantly enriched pathways in both comparison groups. In addition, correlation analysis of transcriptomic and proteomic results showed that 20 and 3 pairs of DEGs/DEPs were identified in RA vs. CT and AS vs. CT comparison groups, respectively. This study is the first report on the rapid adaptive and acute stimulatory transcriptomic and proteomic responses of L. vannamei to extremely low salinity, shedding light on the mechanisms underlying osmoregulation in euryhaline crustaceans.
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Affiliation(s)
- Huijie Lu
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Wenchun Chen
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Kai Peng
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Minwei Huang
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jichen Zhao
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoying Chen
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuping Sun
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhuohao Ruan
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chaozheng Li
- Maoming Branch Center of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Maoming 525099, China; State Key Laboratory of Biocontrol and School of Life Sciences, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ding Liu
- Guangdong Provincial Engineering Research Center of Prawn Culture, Guangdong Havwii Agricultural Group Co., Ltd., Zhanjiang 524000, China
| | - Zhenxing Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Huo Li
- Guangdong Provincial Engineering and Technology Research Center, Guangdong Jinyang Biotechnology Co., Ltd., Maoming 525027, China
| | - Yong Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen Huang
- Collaborative Innovation Center of Aquatic Sciences, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; Maoming Branch Center of Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Maoming 525099, China; Guangdong Provincial Engineering Research Center of Prawn Culture, Guangdong Havwii Agricultural Group Co., Ltd., Zhanjiang 524000, China; Guangdong Provincial Engineering and Technology Research Center, Guangdong Jinyang Biotechnology Co., Ltd., Maoming 525027, China.
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The Dynamic Linkage between Provirus Integration Sites and the Host Functional Genome Property Alongside HIV-1 Infections Associated with Antiretroviral Therapy. Vaccines (Basel) 2023; 11:vaccines11020402. [PMID: 36851277 PMCID: PMC9963931 DOI: 10.3390/vaccines11020402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
(1) Background: The HIV-1 latent reservoir harboring replication-competent proviruses is the major barrier in the quest for an HIV-1 infection cure. HIV-1 infection at all stages of disease progression is associated with immune activation and dysfunctional production of proinflammatory soluble factors (cytokines and chemokines), and it is expected that during HIV-1 infection, different immune components and immune cells, in turn, participate in immune responses, subsequently activating downstream biological pathways. However, the functional interaction between HIV-1 integration and the activation of host biological pathways is presently not fully understood. (2) Methods: In this work, I used genes targeted by proviruses from published datasets to seek enriched immunologic signatures and host biological pathways alongside HIV-1 infections based on MSigDb and KEGG over-representation analysis. (3) Results: I observed that different combinations of immunologic signatures of immune cell types and proinflammatory soluble factors appeared alongside HIV-1 infections associated with antiretroviral therapy. Moreover, enriched KEGG pathways were often related to "cancer specific types", "immune system", "infectious disease viral", and "signal transduction". (4) Conclusions: The observations in this work suggest that the gene sets harboring provirus integration sites may define specific immune cells and proinflammatory soluble factors during HIV-1 infections associated with antiretroviral therapy.
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Zhang Y, Wen R, Bao J, Gong Y, Wang X. Mancozeb induces nephrotoxicity by impairing the oxidative phosphorylation pathway: A transcriptome study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114471. [PMID: 38321686 DOI: 10.1016/j.ecoenv.2022.114471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 02/08/2024]
Abstract
This study analyzed the mechanism underlying mancozeb (MCZ)-induced kidney injury by detecting kidney function indicators, combined with transcriptome and metabolome sequencing. Twenty mice were randomly assigned into two groups (control and MCZ groups) to explore the MCZ-induced kidney toxicity. The control group was gavaged with 0.2 mL of deionized water, and the MCZ group with 0.2 mL of 100 mg/kg MCZ for 30 days. The kidney structure of the MCZ group was damaged, with slight hyaline degeneration in the kidney tubular epithelial envelope. The creatinine (CRE) and uric acid (UA) were significantly increased in the MCZ group than in the control group. Moreover, the reactive oxygen species (ROS) significantly accumulated in the MCZ group kidneys. Compared to the control group, superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) were significantly decreased in the MCZ group, while the MDA content was substantially increased. The differentially expressed genes (DEGs) in the MCZ group were mainly enriched in the oxidative phosphorylation pathway. Besides, in the MCZ group, ndufs1 and ndufab1 genes were significantly up-regulated, while cox5b, ndufa5, and ndufa6 genes were significantly down-regulated, consistent with the PCR verification results. The metabolomic analysis identified cGMP-PKG signaling pathway of MCZ-induced nephrotoxicity, with Guanosine monophosphate and Adenosine 5'-monophosphate as the main altered metabolites. These results indicated that MCZ impairs the mice kidneys by obstructing the oxidative phosphorylation pathway, which increases oxidative stress in the kidneys, resulting in kidney injury.
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Affiliation(s)
- Yan Zhang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Ran Wen
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Jialu Bao
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Yinglan Gong
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China
| | - Xiaodan Wang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding 071001, China.
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T-cell evasion and invasion during HIV-1 infection: The role of HIV-1 Tat protein. Cell Immunol 2022; 377:104554. [DOI: 10.1016/j.cellimm.2022.104554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 12/22/2022]
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Costa TJ, Potje SR, Fraga-Silva TFC, da Silva-Neto JA, Barros PR, Rodrigues D, Machado MR, Martins RB, Santos-Eichler RA, Benatti MN, de Sá KSG, Almado CEL, Castro ÍA, Pontelli MC, Serra LL, Carneiro FS, Becari C, Louzada-Junior P, Oliveira RDR, Zamboni DS, Arruda E, Auxiliadora-Martins M, Giachini FRC, Bonato VLD, Zachara NE, Bomfim GF, Tostes RC. Mitochondrial DNA and TLR9 activation contribute to SARS-CoV-2-induced endothelial cell damage. Vascul Pharmacol 2021; 142:106946. [PMID: 34838735 PMCID: PMC8612754 DOI: 10.1016/j.vph.2021.106946] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/15/2021] [Indexed: 12/11/2022]
Abstract
Background and purpose Mitochondria play a central role in the host response to viral infection and immunity, being key to antiviral signaling and exacerbating inflammatory processes. Mitochondria and Toll-like receptor (TLR) have been suggested as potential targets in SARS-CoV-2 infection. However, the involvement of TLR9 in SARS-Cov-2-induced endothelial dysfunction and potential contribution to cardiovascular complications in COVID-19 have not been demonstrated. This study determined whether infection of endothelial cells by SARS-CoV-2 affects mitochondrial function and induces mitochondrial DNA (mtDNA) release. We also questioned whether TLR9 signaling mediates the inflammatory responses induced by SARS-CoV-2 in endothelial cells. Experimental approach Human umbilical vein endothelial cells (HUVECs) were infected by SARS-CoV-2 and immunofluorescence was used to confirm the infection. Mitochondrial function was analyzed by specific probes and mtDNA levels by real-time polymerase chain reaction (RT-PCR). Inflammatory markers were measured by ELISA, protein expression by western blot, intracellular calcium (Ca2+) by FLUOR-4, and vascular reactivity with a myography. Key results SARS-CoV-2 infected HUVECs, which express ACE2 and TMPRSS2 proteins, and promoted mitochondrial dysfunction, i.e. it increased mitochondria-derived superoxide anion, mitochondrial membrane potential, and mtDNA release, leading to activation of TLR9 and NF-kB, and release of cytokines. SARS-CoV-2 also decreased nitric oxide synthase (eNOS) expression and inhibited Ca2+ responses in endothelial cells. TLR9 blockade reduced SARS-CoV-2-induced IL-6 release and prevented decreased eNOS expression. mtDNA increased vascular reactivity to endothelin-1 (ET-1) in arteries from wild type, but not TLR9 knockout mice. These events were recapitulated in serum samples from COVID-19 patients, that exhibited increased levels of mtDNA compared to sex- and age-matched healthy subjects and patients with comorbidities. Conclusion and applications SARS-CoV-2 infection impairs mitochondrial function and activates TLR9 signaling in endothelial cells. TLR9 triggers inflammatory responses that lead to endothelial cell dysfunction, potentially contributing to the severity of symptoms in COVID-19. Targeting mitochondrial metabolic pathways may help to define novel therapeutic strategies for COVID-19.
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Affiliation(s)
- Tiago J Costa
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil; Department of Biological Chemistry, The Johns Hopkins University School of Medicine, USA.
| | - Simone R Potje
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil; Minas Gerais State University - UEMG, Brazil
| | - Thais F C Fraga-Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Júlio A da Silva-Neto
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Paula R Barros
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Daniel Rodrigues
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Mirele R Machado
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Ronaldo B Martins
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | | | - Maira N Benatti
- Department of Clinical Medicine, Division of Internal Medicine, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Keyla S G de Sá
- Department of Cell and Molecular Biology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Carlos Eduardo L Almado
- Institute of Biological and Health Sciences, Federal University of Mato Grosso - UFMT, Brazil
| | - Ítalo A Castro
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Marjorie C Pontelli
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Leonardo La Serra
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Fernando S Carneiro
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Christiane Becari
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Paulo Louzada-Junior
- Department of Clinical Medicine, Division of Internal Medicine, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Rene D R Oliveira
- Department of Clinical Medicine, Division of Internal Medicine, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Dario S Zamboni
- Department of Cell and Molecular Biology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Eurico Arruda
- Virology Research Center, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Maria Auxiliadora-Martins
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Fernanda R C Giachini
- Institute of Biological and Health Sciences, Federal University of Mato Grosso - UFMT, Brazil
| | - Vânia L D Bonato
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil
| | - Natasha E Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, USA
| | - Gisele F Bomfim
- Institute of Health Sciences, Federal University of Mato Grosso - UFMT, Brazil
| | - Rita C Tostes
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo - USP, Brazil.
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Zhao Y, Wang Y, Guo F, Lu B, Sun J, Wang J, Ren Z. iTRAQ-based proteomic analysis of sperm reveals candidate proteins that affect the quality of spermatozoa from boars on plateaus. Proteome Sci 2021; 19:9. [PMID: 34330296 PMCID: PMC8323236 DOI: 10.1186/s12953-021-00177-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/09/2021] [Indexed: 01/19/2023] Open
Abstract
Background Tibetan pigs (TP) exhibit heritable adaptations to their hypoxic environments as a result of natural selection. However, candidate proteins that affect the sperm quality of boars on plateaus have not yet been clearly investigated. Methods In this study, to reveal the candidate proteins that affect the quality of spermatozoa of boars on plateaus, we analyzed the sperm quality using computer-assisted semen analysis (CASA) system and reactive oxygen species (ROS) levels. We also compared the proteomes of sperm proteomes between TP and Yorkshire pigs (YP) raised at high altitudes using the isobaric tags for relative and absolute quantitation (iTRAQ) in combination with the liquid chromatography-tandem mass spectrometry (LC–MS/MS) proteomic method, and confirmed the relative expression levels of the four proteins by western blotting. Results The sperm quality of the TP was superior to that of the YP on plateaus. Of the 1,555 quantified proteins, 318 differentially expressed proteins (DEPs) were identified. Gene ontology (GO) analysis revealed that the DEPs were predominantly associated with the sorbitol metabolic process, removal of superoxide radicals, cellular response to superoxide, response to superoxide and regulation of the mitotic spindle assembly. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were mainly enriched in pathways involved in the regulation of the actin cytoskeleton, glutathione metabolism, oxidative phosphorylation, and estrogen signaling. Based on the protein–protein interaction (PPI) network analysis, we identified 8 candidate proteins (FN1, EGF, HSP90B1, CFL1, GPX4, NDUFA6, VDAC2, and CP) that might play important roles and affect the sperm quality of boars on plateaus. Moreover, the relative expression levels of four proteins (CFL1, EGF, FN1, and GPX4) were confirmed by western blot analysis. Conclusions Our study revealed 8 candidate proteins (FN1, EGF, HSP90B1, CFL1, GPX4, NDUFA6, VDAC2, and CP) that affect the sperm quality of boar on plateaus and provide a reference for further studies on improving sperm quality and the molecular breeding of boars on plateaus. Supplementary Information The online version contains supplementary material available at 10.1186/s12953-021-00177-9.
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Affiliation(s)
- Yanling Zhao
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Yaomei Wang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Feipeng Guo
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Bo Lu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Jiale Sun
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Jianzhou Wang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China
| | - Zili Ren
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, 860000, P.R. China.
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Jao J, Jacobson DL, Russell JS, Wang J, Yu W, Gojanovich GS, Siminski S, Hyzy L, Geffner ME, Gerschenson M. Perinatally acquired HIV infection is associated with abnormal blood mitochondrial function during childhood/adolescence. AIDS 2021; 35:1385-1394. [PMID: 33730749 PMCID: PMC8243810 DOI: 10.1097/qad.0000000000002884] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVE We assessed differences in mitochondrial function between youth living with perinatal HIV (YPHIV) and youth perinatally HIV-exposed but uninfected (YPHEU). DESIGN Cross-sectional analysis. METHODS We measured lactate and pyruvate values, as well as mitochondrial Complex I and Complex IV activity in peripheral blood mononuclear cells. Logistic or linear regression models were fit, as appropriate, to assess the association between PHIV status and each mitochondrial parameter, adjusted for confounders. We introduced interaction terms to assess effect modification of PHIV status on the relationship between anthropometric factors and each mitochondrial parameter. Among YPHIV, similar regression models were fit to assess the relationship between HIV-associated factors and each mitochondrial outcome. RESULTS A total of 243 YPHIV and 118 YPHEU were compared. On average, YPHIV had higher lactate/pyruvate ratio (β: 7.511, 95% confidence interval [95% CI]: 0.402, 14.620) and Complex IV activity (β: 0.037, 95% CI: 0.002, 0.072) compared to YPHEU, adjusted for confounders. Among YPHIV, body mass index Z score (BMIZ) and Complex I activity were inversely associated, whereas, among YPHEU, there was a positive association (β for interaction: -0.048, P = 0.003). Among YPHIV, current (β: -0.789, 95% CI: -1.174, -0.404) and nadir CD4+% (β: -0.605, 95% CI: -1.086, -0.125) were inversely associated with lactate/pyruvate ratio; higher current (4.491, 95% CI: 0.754, 8.229) and peak (7.978, 95% CI: 1.499, 14.457) HIV RNA levels were positively associated with lactate/pyruvate ratio in adjusted models. CONCLUSIONS Mitochondrial function and substrate utilization appear perturbed in YPHIV compared to YPHEU. Increasing immunosuppression and viremia are associated with mitochondrial dysfunction among YPHIV.
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Affiliation(s)
- Jennifer Jao
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Department of Medicine, Division of Adult Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Denise L Jacobson
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Jonathan S Russell
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY
| | - Jiajia Wang
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Wendy Yu
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Greg S Gojanovich
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI
| | - Sue Siminski
- Frontier Science and Technology Research Foundation, Amherst Office, NY
| | - Laurie Hyzy
- Frontier Science and Technology Research Foundation, Amherst Office, NY
| | - Mitchell E Geffner
- The Saban Research Institute of Children's Hospital Los Angeles, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Mariana Gerschenson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI
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10
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Biswas B, Goswami R. Differential gene expression analysis in 1,25(OH)2D3 treated human monocytes establishes link between AIDS progression, neurodegenerative disorders, and aging. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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11
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Shui JE, Wang W, Liu H, Stepanova A, Liao G, Qian J, Ai X, Ten V, Lu J, Cardoso WV. Prematurity alters the progenitor cell program of the upper respiratory tract of neonates. Sci Rep 2021; 11:10799. [PMID: 34031475 PMCID: PMC8144386 DOI: 10.1038/s41598-021-90093-x] [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: 01/06/2021] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
The impact of prematurity on human development and neonatal diseases, such as bronchopulmonary dysplasia, has been widely reported. However, little is known about the effects of prematurity on the programs of stem cell self-renewal and differentiation of the upper respiratory epithelium, which is key for adaptation to neonatal life. We developed a minimally invasive methodology for isolation of neonatal basal cells from nasopharyngeal (NP) aspirates and performed functional analysis in organotypic cultures to address this issue. We show that preterm NP progenitors have a markedly distinct molecular signature of abnormal proliferation and mitochondria quality control compared to term progenitors. Preterm progenitors had lower oxygen consumption at baseline and were unable to ramp up consumption to the levels of term cells when challenged. Although they formed a mucociliary epithelium, ciliary function tended to decline in premature cells as they differentiated, compared to term cells. Together, these differences suggested increased sensitivity of preterm progenitors to environmental stressors under non-homeostatic conditions.
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Affiliation(s)
- Jessica E Shui
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Wang
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Helu Liu
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Anna Stepanova
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Grace Liao
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jun Qian
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA
| | - Xingbin Ai
- Division of Neonatology and Newborn Medicine, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Vadim Ten
- Division of Neonatology, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jining Lu
- Division of Lung Diseases, NHLBI, NIH, Bethesda, MD, USA
| | - Wellington V Cardoso
- Columbia Center for Human Development, Pulmonary Allergy & Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, 650 West 168th Street, BB 8-812, New York, NY, 10032, USA.
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12
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Ramdas P, Sahu AK, Mishra T, Bhardwaj V, Chande A. From Entry to Egress: Strategic Exploitation of the Cellular Processes by HIV-1. Front Microbiol 2020; 11:559792. [PMID: 33343516 PMCID: PMC7746852 DOI: 10.3389/fmicb.2020.559792] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/05/2020] [Indexed: 01/23/2023] Open
Abstract
HIV-1 employs a rich arsenal of viral factors throughout its life cycle and co-opts intracellular trafficking pathways. This exquisitely coordinated process requires precise manipulation of the host microenvironment, most often within defined subcellular compartments. The virus capitalizes on the host by modulating cell-surface proteins and cleverly exploiting nuclear import pathways for post entry events, among other key processes. Successful virus–cell interactions are indeed crucial in determining the extent of infection. By evolving defenses against host restriction factors, while simultaneously exploiting host dependency factors, the life cycle of HIV-1 presents a fascinating montage of an ongoing host–virus arms race. Herein, we provide an overview of how HIV-1 exploits native functions of the host cell and discuss recent findings that fundamentally change our understanding of the post-entry replication events.
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Affiliation(s)
- Pavitra Ramdas
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Amit Kumar Sahu
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Tarun Mishra
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Vipin Bhardwaj
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
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13
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Tao S, Zhou T, Saelao P, Wang Y, Zhu Y, Li T, Zhou H, Wang J. Intrauterine Growth Restriction Alters the Genome-Wide DNA Methylation Profiles in Small Intestine, Liver and Longissimus Dorsi Muscle of Newborn Piglets. Curr Protein Pept Sci 2019; 20:713-726. [PMID: 30678618 DOI: 10.2174/1389203720666190124165243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 01/20/2023]
Abstract
Intrauterine growth restriction (IUGR) remains a major problem in swine production since the associated low birth weight leads to high rates of pre-weaning morbidity and mortality, and permanent retardation of growth and development. The underlying regulatory mechanisms from the aspects of epigenetic modification has received widespread attention. Studies explore the changes in genome wide methylation in small intestine (SI), liver and longissimus dorsi muscle (LDM) between IUGR and normal birth weight (NBW) newborn piglets using a methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) approach. The data demonstrated that methylated peaks were prominently distributed in distal intergenic regions and the quantities of peaks in IUGR piglets were more than that of NBW piglets. IUGR piglets had relatively high methylated level in promoters, introns and coding exons in all the three tissues. Through KEGG pathway analysis of differentially methylated genes found that 33, 54 and 5 differentially methylated genes in small intestine, liver and longissimus dorsi muscle between NBW and IUGR piglets, respectively, which are related to development and differentiation, carbohydrate and energy metabolism, lipid metabolism, protein turnover, immune response, detoxification, oxidative stress and apoptosis pathway. The objective of this review is to assess the impact of differentially methylation status on developmental delay, metabolic disorders and immune deficiency of IUGR piglets.
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Affiliation(s)
- Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianjiao Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Yuhua Zhu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tiantian Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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14
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Lei Z, JunHui L, PeiFeng L. Candidate genes mediated by estrogen-related receptor γ in pancreatic β cells. J Biochem Mol Toxicol 2019; 33:e22390. [PMID: 31478280 DOI: 10.1002/jbt.22390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/22/2019] [Indexed: 12/25/2022]
Abstract
Recent studies have established the importance of estrogen-related receptor γ (ERRγ) as a required participant for insulin secretion in pancreatic β cells. Key downstream genes of ERRγ remain unclear in the pancreatic β cell. To understand the molecular role of ERRγ and elucidate potential key candidate genes involved in pancreatic β cells, the eukaryotic expression plasmid containing mouse ERRγ was constructed and transfected into NIT-1 pancreatic β cells. Overexpression of ERRγ was confirmed by quantitative real-time reverse-transcription polymerase chain reaction and Western blot analyses. RNA-seq was conducted to get the gene expression profiling between the overexpression group cells and control cells. Differentially expressed genes (DEGs) were identified by edgR and subsequently analyzed by gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. We found that overexpression of ERRγ in pancreatic β cells enables regulation of the expression of certain genes involved in cell apoptosis and mitochondrial function, such as TFPT, Bcl7c, Dap, Thoc6, Ube2d3, ATP5H, MPV17, and NDUFA6. GO analysis revealed that the DEGs were mainly enriched in apoptotic process, cytoplasm, and protein binding. KEGG pathway analysis demonstrated that downregulated DEGs were mainly enriched in protein processing in endoplasmic reticulum, estrogen signaling pathway, and metabolic pathways. This study helps to further understand and reposition the molecular mechanisms of ERRγ in β cells.
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Affiliation(s)
- Zhou Lei
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China.,College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, China
| | - Lv JunHui
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China.,College of Urban and Environmental Sciences, MOE Laboratory for Earth Surface Process, Peking University, Beijing, China
| | - Li PeiFeng
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, China
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15
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Masud AJ, Kastaniotis AJ, Rahman MT, Autio KJ, Hiltunen JK. Mitochondrial acyl carrier protein (ACP) at the interface of metabolic state sensing and mitochondrial function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118540. [PMID: 31473256 DOI: 10.1016/j.bbamcr.2019.118540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022]
Abstract
Acyl carrier protein (ACP) is a principal partner in the cytosolic and mitochondrial fatty acid synthesis (FAS) pathways. The active form holo-ACP serves as FAS platform, using its 4'-phosphopantetheine group to present covalently attached FAS intermediates to the enzymes responsible for the acyl chain elongation process. Mitochondrial unacylated holo-ACP is a component of mammalian mitoribosomes, and acylated ACP species participate as interaction partners in several ACP-LYRM (leucine-tyrosine-arginine motif)-protein heterodimers that act either as assembly factors or subunits of the electron transport chain and Fe-S cluster assembly complexes. Moreover, octanoyl-ACP provides the C8 backbone for endogenous lipoic acid synthesis. Accumulating evidence suggests that mtFAS-generated acyl-ACPs act as signaling molecules in an intramitochondrial metabolic state sensing circuit, coordinating mitochondrial acetyl-CoA levels with mitochondrial respiration, Fe-S cluster biogenesis and protein lipoylation.
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Affiliation(s)
- Ali J Masud
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - M Tanvir Rahman
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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16
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Huang Q, Chen Z, Cheng P, Jiang Z, Wang Z, Huang Y, Yang C, Pan J, Qiu F, Huang J. LYRM2 directly regulates complex I activity to support tumor growth in colorectal cancer by oxidative phosphorylation. Cancer Lett 2019; 455:36-47. [DOI: 10.1016/j.canlet.2019.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/31/2019] [Accepted: 04/15/2019] [Indexed: 01/24/2023]
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17
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Song JH, Ahn JH, Kim SR, Cho S, Hong EH, Kwon BE, Kim DE, Choi M, Choi HJ, Cha Y, Chang SY, Ko HJ. Manassantin B shows antiviral activity against coxsackievirus B3 infection by activation of the STING/TBK-1/IRF3 signalling pathway. Sci Rep 2019; 9:9413. [PMID: 31253850 PMCID: PMC6599049 DOI: 10.1038/s41598-019-45868-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/04/2019] [Indexed: 11/27/2022] Open
Abstract
Coxsackievirus B3 (CVB3) is an important human pathogen associated with the development of acute pancreatitis, myocarditis, and type 1 diabetes. Currently, no vaccines or antiviral therapeutics are approved for the prevention and treatment of CVB3 infection. We found that Saururus chinensis Baill extract showed critical antiviral activity against CVB3 infection in vitro. Further, manassantin B inhibited replication of CVB3 and suppressed CVB3 VP1 protein expression in vitro. Additionally, oral administration of manassantin B in mice attenuated CVB3 infection-associated symptoms by reducing systemic production of inflammatory cytokines and chemokines including TNF-α, IL-6, IFN-γ, CCL2, and CXCL-1. We found that the antiviral activity of manassantin B is associated with increased levels of mitochondrial ROS (mROS). Inhibition of mROS generation attenuated the antiviral activity of manassantin B in vitro. Interestingly, we found that manassantin B also induced cytosolic release of mitochondrial DNA based on cytochrome C oxidase DNA levels. We further confirmed that STING and IRF-3 expression and STING and TBK-1 phosphorylation were increased by manassantin B treatment in CVB3-infected cells. Collectively, these results suggest that manassantin B exerts antiviral activity against CVB3 through activation of the STING/TKB-1/IRF3 antiviral pathway and increased production of mROS.
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Affiliation(s)
- Jae-Hyoung Song
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Jae-Hee Ahn
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Seong-Ryeol Kim
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Sungchan Cho
- Anticancer Agent Research Center, Korea Research Institute of Bioscience & Biotechnology, Ochang, South Korea
| | - Eun-Hye Hong
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Bo-Eun Kwon
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Dong-Eun Kim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience & Biotechnology, Ochang, South Korea
| | - Miri Choi
- Anticancer Agent Research Center, Korea Research Institute of Bioscience & Biotechnology, Ochang, South Korea
| | - Hwa-Jung Choi
- Department of Beauty Science, Kwangju Women's University, Gwangju, South Korea
| | - Younggil Cha
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea
| | - Sun-Young Chang
- Research Institute of Pharmaceutical Science and Technology (RIPST), College of Pharmacy, Ajou University, Suwon, South Korea.
| | - Hyun-Jeong Ko
- College of Pharmacy, Kangwon National University, Chuncheon, South Korea.
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18
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Rathore A, Chu Q, Tan D, Martinez TF, Donaldson CJ, Diedrich JK, Yates JR, Saghatelian A. MIEF1 Microprotein Regulates Mitochondrial Translation. Biochemistry 2018; 57:5564-5575. [PMID: 30215512 DOI: 10.1021/acs.biochem.8b00726] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent technological advances led to the discovery of hundreds to thousands of peptides and small proteins (microproteins) encoded by small open reading frames (smORFs). Characterization of new microproteins demonstrates their role in fundamental biological processes and highlights the value in discovering and characterizing more microproteins. The elucidation of microprotein-protein interactions (MPIs) is useful for determining the biochemical and cellular roles of microproteins. In this study, we characterize the protein interaction partners of mitochondrial elongation factor 1 microprotein (MIEF1-MP) using a proximity labeling strategy that relies on APEX2. MIEF1-MP localizes to the mitochondrial matrix where it interacts with the mitochondrial ribosome (mitoribosome). Functional studies demonstrate that MIEF1-MP regulates mitochondrial translation via its binding to the mitoribosome. Loss of MIEF1-MP decreases the mitochondrial translation rate, while an elevated level of MIEF1-MP increases the translation rate. The identification of MIEF1-MP reveals a new gene involved in this process.
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Affiliation(s)
- Annie Rathore
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States.,Division of Biological Sciences , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Cynthia J Donaldson
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Jolene K Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States.,Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - John R Yates
- Department of Molecular Medicine , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology , The Salk Institute for Biological Studies , 10010 North Torrey Pines Road , La Jolla , California 92037 , United States
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19
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Song S, Gong S, Singh P, Lyu J, Bai Y. The interaction between mitochondria and oncoviruses. Biochim Biophys Acta Mol Basis Dis 2018; 1864:481-487. [PMID: 28962899 PMCID: PMC8895674 DOI: 10.1016/j.bbadis.2017.09.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022]
Abstract
Mitochondria play important roles in multiple aspects of viral tumorigenesis. Mitochondrial genomes contribute to the host's genetic background. After viruses enter the cell, they modulate mitochondrial function and thus alter bioenergetics and retrograde signaling pathways. At the same time, mitochondria also regulate and mediate viral oncogenesis. In this context, oncogenesis by oncoviruses like Hepatitis B virus (HBV), Hepatitis C virus (HCV), Human papilloma virus (HPV), Human Immunodeficiency virus (HIV) and Epstein-Barr virus (EBV) will be discussed.
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Affiliation(s)
- Shujie Song
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shasha Gong
- School of Medicine, Taizhou College, Taizhou, Zhejiang, China
| | - Pragya Singh
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China,Corresponding author: Wenzhou Medical University, Chashan, Wenzhou 325035, China. (J. Lyu); (Y. Bai). Fax: 86-577-86689771; Tel: 86-577-86689805
| | - Yidong Bai
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas, USA,Corresponding author: Wenzhou Medical University, Chashan, Wenzhou 325035, China. (J. Lyu); (Y. Bai). Fax: 86-577-86689771; Tel: 86-577-86689805
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20
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Abstract
HIV infection and antiretroviral therapy (ART) treatment exert diverse effects on adipocytes and stromal-vascular fraction cells, leading to changes in adipose tissue quantity, distribution, and energy storage. A HIV-associated lipodystrophic condition was recognized early in the epidemic, characterized by clinically apparent changes in subcutaneous, visceral, and dorsocervical adipose depots. Underlying these changes is altered adipose tissue morphology and expression of genes central to adipocyte maturation, regulation, metabolism, and cytokine signaling. HIV viral proteins persist in circulation and locally within adipose tissue despite suppression of plasma viremia on ART, and exposure to these proteins impairs preadipocyte maturation and reduces adipocyte expression of peroxisome proliferator-activated receptor gamma (PPAR-γ) and other genes involved in cell regulation. Several early nucleoside reverse transcriptase inhibitor and protease inhibitor antiretroviral drugs demonstrated substantial adipocyte toxicity, including reduced mitochondrial DNA content and respiratory chain enzymes, reduced PPAR-γ and other regulatory gene expression, and increased proinflammatory cytokine production. Newer-generation agents, such as integrase inhibitors, appear to have fewer adverse effects. HIV infection also alters the balance of CD4+ and CD8+ T cells in adipose tissue, with effects on macrophage activation and local inflammation, while the presence of latently infected CD4+ T cells in adipose tissue may constitute a protected viral reservoir. This review provides a synthesis of the literature on how HIV virus, ART treatment, and host characteristics interact to affect adipose tissue distribution, immunology, and contribution to metabolic health, and adipocyte maturation, cellular regulation, and energy storage. © 2017 American Physiological Society. Compr Physiol 7:1339-1357, 2017.
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Affiliation(s)
- John R Koethe
- Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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21
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Li H, Wei S, Fang Y, Li M, Li X, Li Z, Zhang J, Zhu G, Li C, Bi L, Zhang G, Wang D, Zhang XE. Quantitative proteomic analysis of host responses triggered by Mycobacterium tuberculosis infection in human macrophage cells. Acta Biochim Biophys Sin (Shanghai) 2017; 49:835-844. [PMID: 28910983 DOI: 10.1093/abbs/gmx080] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 02/03/2023] Open
Abstract
Macrophages are primary host of Mycobacterium tuberculosis (M.tb) and the central effector of in vivo innate immune responses against bacteria. Though the interaction between macrophages and mycobacteria has been widely investigated, the molecular mechanisms of M.tb pathogenesis in macrophages are still not clear. In this work, we investigated the altered protein expression profiles of macrophages after virulent H37Rv strain and avirulent H37Ra strain infection by tandem mass tag-based quantitative proteomics. Among 6762 identified proteins of macrophages, the expression levels of 235 proteins were significantly altered, which is supposed to be related to the infection of different strains. By bioinformatics analysis at systems level, we found that these proteins are mainly involved in the biological process of apoptosis, blood coagulation, oxidative phosphorylation, and others. The enormous variation in protein profiles between macrophages infected with H37Ra and H37Rv suggests the existence of four different immunity mechanisms that decide the fates of macrophages and M.tb. These data may provide a better understanding of M.tb pathogenesis within the host, which contributes to the prevention and clinical treatment of tuberculosis.
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Abstract
: The increased prevalence of age-related comorbidities and mortality is worrisome in ageing HIV-infected patients. Here, we aim to analyse the different ageing mechanisms with regard to HIV infection. Ageing results from the time-dependent accumulation of random cellular damage. Epigenetic modifications and mitochondrial DNA haplogroups modulate ageing. In antiretroviral treatment-controlled patients, epigenetic clock appears to be advanced, and some haplogroups are associated with HIV infection severity. Telomere shortening is enhanced in HIV-infected patients because of HIV and some nucleoside analogue reverse transcriptase inhibitors. Mitochondria-related oxidative stress and mitochondrial DNA mutations are increased during ageing and also by some nucleoside analogue reverse transcriptase inhibitors. Overall, increased inflammation or 'inflammageing' is a major driver of ageing and could result from cell senescence with secreted proinflammatory mediators, altered gut microbiota, and coinfections. In HIV-infected patients, the level of inflammation and innate immunity activation is enhanced and related to most comorbidities and to mortality. This status could result, in addition to age, from the virus itself or viral protein released from reservoirs, from HIV-enhanced gut permeability and dysbiosis, from antiretroviral treatment, from frequent cytomegalovirus and hepatitis C virus coinfections, and also from personal and environmental factors, as central fat accumulation or smoking. Adaptive immune activation and immunosenescence are associated with comorbidities and mortality in the general population but are less predictive in HIV-infected patients. Biomarkers to evaluate ageing in HIV-infected patients are required. Numerous systemic or cellular inflammatory, immune activation, oxidative stress, or senescence markers can be tested in serum or peripheral blood mononuclear cells. The novel European Study to Establish Biomarkers of Human Ageing MARK-AGE algorithm, evaluating the biological age, is currently assessed in HIV-infected patients and reveals an advanced biological age. Some enhanced inflammatory or innate immune activation markers are interesting but still not validated for the patient's follow-up. To be able to assess patients' biological age is an important objective to improve their healthspan.
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23
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Willig AL, Kramer PA, Chacko BK, Darley-Usmar VM, Heath SL, Overton ET. Monocyte bioenergetic function is associated with body composition in virologically suppressed HIV-infected women. Redox Biol 2017; 12:648-656. [PMID: 28395172 PMCID: PMC5388916 DOI: 10.1016/j.redox.2017.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/28/2017] [Accepted: 04/01/2017] [Indexed: 12/20/2022] Open
Abstract
Women living with HIV may present with high levels of body fat that are associated with altered bioenergetic function. Excess body fat may therefore exacerbate the bioenergetic dysfunction observed with HIV infection. To determine if body fat is associated with bioenergetic function in HIV, we conducted a cross-sectional study of 42 women with HIV who were virologically suppressed on antiretroviral therapy. Body composition was determined via dual-energy x-ray absorptiometry. Oxygen consumption rate (OCR) of monocytes was sorted from peripheral blood mononuclear cells obtained from participants in the fasting state. Differences in bioenergetic function, as measured by OCR, was assessed using Kruskal-Wallis tests and Spearman correlations adjusted for age, race, and smoking status. Participants were 86% Black, 45.5 years old, 48% current smokers, and 57% were obese (body mass index ≥30). Nearly all women (93%) had >30% total fat mass, while 12% had >50% total fat mass. Elevated levels of total fat mass, trunk fat, and leg fat were inversely correlated with measures of bioenergetic health as evidenced by lower maximal and reserve capacity OCR, and Bioenergetic Health Index. Measures of extracellular acidification (ECAR) in the absence (basal) or maximal (with oligomycin) were positively correlated with measures of bioenergetics, except proton leak, and were negatively correlated with fat mass. Despite virological suppression, women with HIV present with extremely high levels of adiposity that correlate with impaired bioenergetic health. Without effective interventions, this syndemic of HIV infection and obesity will likely have devastating consequences for our patients, potentially mediated through altered mitochondrial and glycolytic function.
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Affiliation(s)
- Amanda L Willig
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - Philip A Kramer
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - Balu K Chacko
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - Victor M Darley-Usmar
- Mitochondrial Medicine Laboratory, University of Alabama at Birmingham, Birmingham, AL 35294, United States; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - Sonya L Heath
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
| | - E Turner Overton
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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Frezza C, Grelli S, Federico M, Marino-Merlo F, Mastino A, Macchi B. Testing anti-HIV activity of antiretroviral agents in vitro using flow cytometry analysis of CEM-GFP cells infected with transfection-derived HIV-1 NL4-3. J Med Virol 2015; 88:979-86. [PMID: 26519867 DOI: 10.1002/jmv.24418] [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] [Accepted: 10/29/2015] [Indexed: 11/09/2022]
Abstract
An assay, specifically optimized to evaluate the anti-HIV activity of antiretrovirals by flow cytometry analysis, is described. As widely used anti-HIV agents, zidovudine (AZT), abacavir (ABC), 2',3'-dideoxyinosine (DDI), lamivudine (3TC), nevirapine (NVP), and efavirenz (EFV), and as drugs of recent approval raltegravir (RAL), etravirine (ETR), and rilpivirine (RPV), were utilized as reference drugs. HIV-1 NL4-3 virus was prepared by transfection of HEK293T cells with purified plasmid DNA and quantified by p24 antigen-capture assay. For infection, CEM-GFP cells were exposed to vehicle or to several concentrations of the drugs for 2 hr at 37 °C before HIV-1 NL4-3 was added to each sample. The adsorption was prolonged for 3 hr at 37 °C. After 72 hr of incubation, HIV-induced GFP expression in infected CEM-GFP cells was assessed by flow cytometry analysis and expressed as % positive cells. For comparison, p24 production in supernatants was assessed by a commercial ELISA kit. On the basis of IC50 values, the anti-HIV activity, as assayed by this method, was EFV > 3TC > AZT > NVP > DDI > ABC and ETR > RPV > RAL. The comparison between the IC50 values calculated through flow cytometry and p24 production revealed overlapping results, showing that the optimized protocol of CEM-GFP infection with HIV NL4-3 is a suitable method to perform quantitative, rapid and low-expensive screening tests to evaluate the in vitro effect of new candidate anti-HIV drugs.
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Affiliation(s)
- Caterina Frezza
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Maurizio Federico
- Division of Pathogenesis of Retroviruses, National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Francesca Marino-Merlo
- Department of Biological and Environmental Sciences, University of Messina, Messina, Italy
| | - Antonio Mastino
- Department of Biological and Environmental Sciences, University of Messina, Messina, Italy.,Institute of Translational Pharmacology, CNR, Rome, Italy
| | - Beatrice Macchi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
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Rodríguez-Mora S, Mateos E, Moran M, Martín MÁ, López JA, Calvo E, Terrón MC, Luque D, Muriaux D, Alcamí J, Coiras M, López-Huertas MR. Intracellular expression of Tat alters mitochondrial functions in T cells: a potential mechanism to understand mitochondrial damage during HIV-1 replication. Retrovirology 2015; 12:78. [PMID: 26376973 PMCID: PMC4571071 DOI: 10.1186/s12977-015-0203-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 08/26/2015] [Indexed: 01/22/2023] Open
Abstract
Background HIV-1 replication results in mitochondrial damage that is enhanced during antiretroviral therapy (ART). The onset of HIV-1 replication is regulated by viral protein Tat, a 101-residue protein codified by two exons that elongates viral transcripts. Although the first exon of Tat (aa 1–72) forms itself an active protein, the presence of the second exon (aa 73–101) results in a more competent transcriptional protein with additional functions. Results Mitochondrial overall functions were analyzed in Jurkat cells stably expressing full-length Tat (Tat101) or one-exon Tat (Tat72). Representative results were confirmed in PBLs transiently expressing Tat101 and in HIV-infected Jurkat cells. The intracellular expression of Tat101 induced the deregulation of metabolism and cytoskeletal proteins which remodeled the function and distribution of mitochondria. Tat101 reduced the transcription of the mtDNA, resulting in low
ATP production. The total amount of mitochondria increased likely to counteract their functional impairment. These effects were enhanced when Tat second exon was expressed. Conclusions Intracellular Tat altered mtDNA transcription, mitochondrial content and distribution in CD4+ T cells. The importance of Tat second exon in non-transcriptional functions was confirmed. Tat101 may be responsible for mitochondrial dysfunctions found in HIV-1 infected patients. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0203-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Rodríguez-Mora
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Elena Mateos
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - María Moran
- Laboratorio de Enfermedades Raras: mitocondriales y neuromusculares, Instituto de Investigación Hospital 12 de Octubre, "i + 12", Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U723, Madrid, Spain.
| | - Miguel Ángel Martín
- Laboratorio de Enfermedades Raras: mitocondriales y neuromusculares, Instituto de Investigación Hospital 12 de Octubre, "i + 12", Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U723, Madrid, Spain.
| | - Juan Antonio López
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.
| | - Enrique Calvo
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.
| | - María Carmen Terrón
- Unidad de Microscopía Electrónica y Confocal, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Daniel Luque
- Unidad de Microscopía Electrónica y Confocal, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Delphine Muriaux
- Unité de Virologie Humaine - INSERM U758/École Normale Supérieure, Lyon, France. .,Laboratoire de Domaines Membranaires et Assemblage Viral, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, Montpellier, France.
| | - José Alcamí
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Mayte Coiras
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - María Rosa López-Huertas
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. .,Unité de Virologie Humaine - INSERM U758/École Normale Supérieure, Lyon, France.
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Song G, Nesil T, Cao J, Yang Z, Chang SL, Li MD. Nicotine mediates expression of genes related to antioxidant capacity and oxidative stress response in HIV-1 transgenic rat brain. J Neurovirol 2015; 22:114-24. [PMID: 26306689 DOI: 10.1007/s13365-015-0375-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/18/2015] [Accepted: 08/10/2015] [Indexed: 12/25/2022]
Abstract
Oxidative stress plays an important role in the progression of HIV-1 infection. Nicotine can either protect neurons from neurodegeneration or induce oxidative stress, depending on its dose and degree of oxidative stress impairment. However, the relationship between nicotine and oxidative stress in the HIV-1-infected individuals remains largely unknown. The purpose of this study was to determine the effect of nicotine on expression of genes related to the glutathione (GSH)-centered antioxidant system and oxidative stress in the nucleus accumbens (NAc) and ventral tegmental area (VTA) of HIV-1 transgenic (HIV-1Tg) and F344 control rats. Adult HIV-1Tg and F344 rats received nicotine (0.4 mg/kg, base, s.c.) or saline injections once per day for 27 days. At the end of treatment, various brain regions including the NAc and VTA were collected from each rat. Following total RNA extraction and complementary DNA (cDNA) synthesis of each sample, quantitative reverse transcription PCR (RT-PCR) analysis was performed for 43 oxidative-stress-related genes. Compared with F344 control rats, HIV-1Tg rats showed a significant downregulation of genes involved in ATPase and cyctochrome oxidase at the messenger RNA (mRNA) level in both regions. Further, we found a significant downregulation of Gstm5 in the NAc and upregulation of Cox1, Cox3, and Gsta6 in the VTA of HIV-1Tg rats. HIV-1Tg rats showed brain-region-specific responses to chronic nicotine treatment. This response resulted in a change in the expression of genes involved in antioxidant mechanisms including the downregulation of genes such as Atp5h, Calml1, Gpx7, Gstm5, Gsr, and Gsta6 and upregulation of Sod1 in the NAc, as well as downregulation of genes like Cox5a, Gpx4, Gpx6, Gpx7, Gstm5, and Sod1 in the VTA of HIV-1Tg rats. Together, we conclude that chronic nicotine treatment has a dual effect on the antioxidant defense system and oxidative-stress-induced apoptosis signaling in HIV-1Tg rats. These findings suggest that nicotine has a negative effect on response to oxidative stress and antioxidant processes in HIV-1 Tg rat brain, especially in the VTA.
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Affiliation(s)
- Guohua Song
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, 450 Ray C Hunt Drive, Suite G-170, Charlottesville, VA, 22903, USA.,Shanxi Key Laboratory of Experimental Animal Science and Animal Model of Human Disease, Shanxi Medical University, Taiyuan, China
| | - Tanseli Nesil
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, 450 Ray C Hunt Drive, Suite G-170, Charlottesville, VA, 22903, USA
| | - Junran Cao
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, 450 Ray C Hunt Drive, Suite G-170, Charlottesville, VA, 22903, USA
| | - Zhongli Yang
- Institute of NeuroImmune Pharmacology, Seton Hall University, South Orange, NJ, USA
| | - Sulie L Chang
- Institute of NeuroImmune Pharmacology, Seton Hall University, South Orange, NJ, USA.,Department of Biological Sciences, Seton Hall University, South Orange, NJ, USA
| | - Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, 450 Ray C Hunt Drive, Suite G-170, Charlottesville, VA, 22903, USA.
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Yadav SK, Batra JK. Ribotoxin restrictocin manifests anti-HIV-1 activity through its specific ribonuclease activity. Int J Biol Macromol 2015; 76:58-62. [PMID: 25709025 DOI: 10.1016/j.ijbiomac.2015.01.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/23/2015] [Accepted: 01/27/2015] [Indexed: 01/18/2023]
Abstract
Restrictocin, a highly specific ribonuclease produced by Aspergillus restrictus, cleaves a single phosphodiester bond in a universally conserved stem and loop structure termed sarcin/ricin loop within the large ribosomal RNA of all organisms. In the current study, we demonstrate restrictocin to manifest anti-HIV-1 activity in two model cell systems. Using two mutants of restrictocin, we further show that the anti-HIV-1 activity of restrictocin is due to its specific ribonucleolytic activity. The study suggests that restrictocin is able to recognize region(s) within HIV-1 genome as its target. Restrictocin appears to have potential as a therapeutic antiviral agent against HIV-1.
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Affiliation(s)
- Santosh K Yadav
- Immunochemistry Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Janendra K Batra
- Immunochemistry Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India; Centre for Molecular Medicine, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Angerer H. Eukaryotic LYR Proteins Interact with Mitochondrial Protein Complexes. BIOLOGY 2015; 4:133-50. [PMID: 25686363 PMCID: PMC4381221 DOI: 10.3390/biology4010133] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/04/2015] [Indexed: 01/18/2023]
Abstract
In eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. LYR (leucine/tyrosine/arginine) motif proteins (LYRMs) of the Complex1_LYR-like superfamily interact with protein complexes of bacterial origin. Many LYR proteins function as extra subunits (LYRM3 and LYRM6) or novel assembly factors (LYRM7, LYRM8, ACN9 and FMC1) of the oxidative phosphorylation (OXPHOS) core complexes. Structural insights into complex I accessory subunits LYRM6 and LYRM3 have been provided by analyses of EM and X-ray structures of complex I from bovine and the yeast Yarrowia lipolytica, respectively. Combined structural and biochemical studies revealed that LYRM6 resides at the matrix arm close to the ubiquinone reduction site. For LYRM3, a position at the distal proton-pumping membrane arm facing the matrix space is suggested. Both LYRMs are supposed to anchor an acyl-carrier protein (ACPM) independently to complex I. The function of this duplicated protein interaction of ACPM with respiratory complex I is still unknown. Analysis of protein-protein interaction screens, genetic analyses and predicted multi-domain LYRMs offer further clues on an interaction network and adaptor-like function of LYR proteins in mitochondria.
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Affiliation(s)
- Heike Angerer
- Goethe University Frankfurt, Medical School, Institute of Biochemistry II, Structural Bioenergetics Group, Max-von-Laue Street 9, Frankfurt am Main 60438, Germany.
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Talla V, Koilkonda R, Porciatti V, Chiodo V, Boye SL, Hauswirth WW, Guy J. Complex I subunit gene therapy with NDUFA6 ameliorates neurodegeneration in EAE. Invest Ophthalmol Vis Sci 2015; 56:1129-40. [PMID: 25613946 DOI: 10.1167/iovs.14-15950] [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] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To address the permanent disability induced by mitochondrial dysfunction in experimental autoimmune encephalomyelitis (EAE). METHODS Mice sensitized for EAE were rescued by intravitreal injection of adeno-associated viral vector serotype 2 with the complex I subunit gene scAAV-NDUFA6Flag. Controls were injected with a mitochondrially targeted red fluorescent protein (scAAV-COX8-cherry). Another group received scAAV-COX8-cherry, but was not sensitized for EAE. Serial pattern electroretinograms (PERGs) and optical coherent tomography (OCT) evaluated visual function and structure of the retina at 1, 3, and 6 months post injection (MPI). Treated mice were killed 6 MPI for histopathology. Immunodetection of cleaved caspase 3 gauged apoptosis. Complex I activity was assessed spectrophotometrically. Expression of NDUFA6Flag in the retina and optic nerve were evaluated between 1 week to 1 month post injection by RT-PCR, immunofluorescence and immunoblotting. RESULTS Reverse transcription-PCR and immunoblotting confirmed NDUFA6Flag overexpression with immunoprecipitation and blue native PAGE showing integration into murine complex I. Overexpression of NDUFA6Flag in the visual system of EAE mice rescued retinal complex I activity completely, axonal loss by 73%, and retinal ganglion cell (RGC) loss by 88%, RGC apoptosis by 66%, and restored the 33% loss of complex I activity in EAE to normal levels; thereby, preventing loss of vision indicated by the 43% reduction in the PERG amplitudes of EAE mice. CONCLUSIONS NDUFA6 gene therapy provided long-term suppression of neurodegeneration in the EAE animal model suggesting that it may also ameliorate the mitochondrial dysfunction associated with permanent disability in optic neuritis and MS patients.
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Affiliation(s)
- Venu Talla
- Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida, United States
| | - Rajeshwari Koilkonda
- Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida, United States
| | - Vittorio Porciatti
- Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida, United States
| | - Vince Chiodo
- Departments of Ophthalmology, University of Florida, College of Medicine, Gainesville, Florida, United States
| | - Sanford L Boye
- Departments of Ophthalmology, University of Florida, College of Medicine, Gainesville, Florida, United States
| | - William W Hauswirth
- Departments of Ophthalmology, University of Florida, College of Medicine, Gainesville, Florida, United States
| | - John Guy
- Bascom Palmer Eye Institute, University of Miami, Miller School of Medicine, Miami, Florida, United States
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Dhamija N, Choudhary D, Ladha JS, Pillai B, Mitra D. Tat predominantly associates with host promoter elements in HIV-1-infected T-cells - regulatory basis of transcriptional repression of c-Rel. FEBS J 2014; 282:595-610. [PMID: 25472883 DOI: 10.1111/febs.13168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/19/2014] [Accepted: 12/02/2014] [Indexed: 11/28/2022]
Abstract
HIV-1 Tat is a multifunctional regulatory protein that, in addition to its primary function of transactivating viral transcription, also tends to modulate cellular gene expression, for which the molecular mechanism remains to be clarified. We have reported earlier nuclear factor kappa B (NFκB) enhancer binding activity of Tat and proposed this DNA binding activity as a possible molecular basis for Tat-mediated regulation of cellular gene expression in infected cells. In the present study, we analyzed the genome-wide occupancy of Tat protein on host cell chromatin in HIV-1-infected T-cells to investigate a potential role of Tat on cellular gene expression. The results obtained identify a spectrum of binding sites of Tat protein on the chromatin and reveal that Tat is also recruited on a number of cellular gene promoters in HIV-1-infected T-cells, indicating its possible involvement in the regulation of gene expression of such cellular genes. Tat was identified as a repressor of one such validated gene, c-Rel, because it downregulates the expression of c-Rel in both Tat expressing and HIV-1-infected T-cells. The results also show that Tat downregulates c-Rel promoter activity by interacting with specific NFκB sites on the c-Rel promoter, thus providing a molecular basis of Tat-mediated regulation of cellular gene expression. Thus, in the present study, we have not only identified recruitment sites of Tat on the chromatin in HIV-1-infected T-cells, but also report for the first time that c-Rel is downregulated in HIV-1-infected cells specifically by interaction of Tat with NFκB binding sites on the promoter.
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The LYR protein subunit NB4M/NDUFA6 of mitochondrial complex I anchors an acyl carrier protein and is essential for catalytic activity. Proc Natl Acad Sci U S A 2014; 111:5207-12. [PMID: 24706851 DOI: 10.1073/pnas.1322438111] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial complex I is the largest and most complicated enzyme of the oxidative phosphorylation system. It comprises a number of so-called accessory subunits of largely unknown structure and function. Here we studied subunit NB4M [NDUFA6, LYR motif containing protein 6 (LYRM6)], a member of the LYRM family of proteins. Chromosomal deletion of the corresponding gene in the yeast Yarrowia lipolytica caused concomitant loss of the mitochondrial acyl carrier protein subunit ACPM1 from the enzyme complex and paralyzed ubiquinone reductase activity. Exchanging the LYR motif and an associated conserved phenylalanine by alanines in subunit NB4M also abolished the activity and binding of subunit ACPM1. We show, by single-particle electron microscopy and structural modeling, that subunits NB4M and ACPM1 form a subdomain that protrudes from the peripheral arm in the vicinity of central subunit domains known to be involved in controlling the catalytic activity of complex I.
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Ahmed N, Brahmbhatt KG, Khan SI, Jacob M, Tekwani BL, Sabde S, Mitra D, Singh IP, Khan IA, Bhutani KK. Synthesis and biological evaluation of tricyclic guanidine analogues of batzelladine K for antimalarial, antileishmanial, antibacterial, antifungal, and anti-HIV activities. Chem Biol Drug Des 2013; 81:491-8. [PMID: 23534411 DOI: 10.1111/cbdd.1427] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Fifty analogues of batzelladine K were synthesized and evaluated for in vitro antimalarial (Plasmodium falciparum), antileishmanial (Leishmania donovani), antimicrobial (panel of bacteria and fungi), antiviral (HIV-1) activities. Analogues 14h and 20l exhibited potential antimalarial activity against chloroquine-sensitive D6 strain with IC(50) 1.25 and 0.88 μM and chloroquine-resistant W2 strain with IC(50) 1.64 and 1.07 μM, respectively. Analogues 12c and 14c having nonyl substitution showed the most potent antileishmanial activity with IC(50) 2.39 and 2.78 μM and IC(90) 11.27 and 12.76 μM, respectively. Three analogues 12c, 14c, and 14i were the most active against various pathogenic bacteria and fungi with IC(50) < 3.02 μM and MIC/MBC/MFC <6 μM. Analogue 20l having pentyl and methyl substituents on tricycle showed promising activities against all pathogens. However, none was found active against HIV-1. Our study demonstrated that the tricyclic guanidine compounds provide new structural class for broad spectrum activity.
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Affiliation(s)
- Nafees Ahmed
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
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Abstract
Mitochondrial complex I has a molecular mass of almost 1 MDa and comprises more than 40 polypeptides. Fourteen central subunits harbour the bioenergetic core functions. We are only beginning to understand the significance of the numerous accessory subunits. The present review addresses the role of accessory subunits for assembly, stability and regulation of complex I and for cellular functions not directly associated with redox-linked proton translocation.
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The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins. Biochem Soc Trans 2013; 41:1335-41. [DOI: 10.1042/bst20130116] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial LYRM (leucine/tyrosine/arginine motif) proteins are members of the Complex1_LYR-like superfamily. Individual LYRM proteins have been identified as accessory subunits or assembly factors of mitochondrial OXPHOS (oxidative phosphorylation) complexes I, II, III and V respectively, and they play particular roles in the essential Fe–S cluster biogenesis and in acetate metabolism. LYRM proteins have been implicated in mitochondrial dysfunction, e.g. in the context of insulin resistance. However, the functional significance of the common LYRM is still unknown. Analysis of protein–protein interaction screens suggests that LYRM proteins form protein complexes with phylogenetically ancient proteins of bacterial origin. Interestingly, the mitochondrial FAS (fatty acid synthesis) type II acyl-carrier protein ACPM associates with some of the LYRM protein-containing complexes. Eukaryotic LYRM proteins interfere with mitochondrial homoeostasis and might function as adaptor-like ‘accessory factors’.
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Massanella M, Singhania A, Beliakova-Bethell N, Pier R, Lada SM, White CH, Pérez-Santiago J, Blanco J, Richman DD, Little SJ, Woelk CH. Differential gene expression in HIV-infected individuals following ART. Antiviral Res 2013; 100:420-8. [PMID: 23933117 DOI: 10.1016/j.antiviral.2013.07.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/23/2013] [Accepted: 07/25/2013] [Indexed: 01/13/2023]
Abstract
Previous studies of the effect of ART on gene expression in HIV-infected individuals have identified small numbers of modulated genes. Since these studies were underpowered or cross-sectional in design, a paired analysis of peripheral blood mononuclear cells (PBMCs), isolated before and after ART, from a robust number of HIV-infected patients (N=32) was performed. Gene expression was assayed by microarray and 4157 differentially expressed genes (DEGs) were identified following ART using multivariate permutation tests. Pathways and gene ontology (GO) terms over-represented for DEGs reflected the transition from a period of active virus replication before ART to one of viral suppression (e.g., repression of JAK-STAT signaling) and possible prolonged drug exposure (e.g., oxidative phosphorylation pathway) following ART. CMYC was the DEG whose product made the greatest number of interactions at the protein level in protein interaction networks (PINs), which has implications for the increased incidence of Hodgkin's lymphoma (HL) in HIV-infected patients. The differential expression of multiple genes was confirmed by RT-qPCR including well-known drug metabolism genes (e.g., ALOX12 and CYP2S1). Targets not confirmed by RT-qPCR (i.e., GSTM2 and RPL5) were significantly confirmed by droplet digital (ddPCR), which may represent a superior method when confirming DEGs with low fold changes. In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized.
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Affiliation(s)
- Marta Massanella
- Fundació irsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
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McComsey GA, Daar ES, O'Riordan M, Collier AC, Kosmiski L, Santana JL, Fichtenbaum CJ, Fink H, Sax PE, Libutti DE, Gerschenson M. Changes in fat mitochondrial DNA and function in subjects randomized to abacavir-lamivudine or tenofovir DF-emtricitabine with atazanavir-ritonavir or efavirenz: AIDS Clinical Trials Group study A5224s, substudy of A5202. J Infect Dis 2013; 207:604-11. [PMID: 23204164 PMCID: PMC3549598 DOI: 10.1093/infdis/jis720] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/05/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The effect of nonthymidine nucleoside reverse-transcriptase inhibitors (NRTIs) on fat mitochondrial DNA (mtDNA) content and function is unclear. METHODS A5202 randomized antiretroviral therapy-naive human immunodeficiency virus-infected subjects to abacavir-lamivudine (ABC/3TC) versus tenofovir DF-emtricitabine (TDF/FTC) with efavirenz (EFV) or atazanavir-ritonavir (ATV/r). A5224s, substudy of A5202, enrolled 269 subjects with fat measurements by dual-energy x-ray absorptiometry and computed tomography. A subset of subjects underwent fat biopsies at baseline and week 96 for mtDNA content (real-time polymerase chain reaction) and oxidative phosphorylation nicotinamide adenine dinucleotide (reduced) dehydrogenase (complex I) and cytochrome c oxidase (complex IV) activity levels (immunoassays). Intent-to-treat analyses were performed using analysis of variance and paired t tests. RESULTS Fifty-six subjects (87% male; median age, 39 years) were included; their median body mass index, CD4 cell count, and fat mtDNA level were 26 kg/m(2), 227 cells/μL, and 1197 copies/cell, respectively. Fat mtDNA content decreased within the ABC/3TC and TDF/FTC groups (combining EFV and ATV/r arms; median change, -341 [interquartile range, -848 to 190; P = .03] and -400 [-661 to -221; P < .001] copies/cell, respectively), but these changes did not differ significantly between the 2 groups (P = .57). Complex I and IV activity decreased significantly in the TDF/FTC group (median change, -12.45 [interquartile range, -24.70 to 2.90; P = .003] and -8.25 [-13.90 to -1.30; P < .001], optical density × 10(3)/µg, respectively) but not the ABC/3TC group. Differences between the ABC/3TC and TDF/FTC groups were significant for complex I (P = .03). CONCLUSIONS ABC/3TC and TDF/FTC significantly and similarly decreased fat mtDNA content, but only TDF/FTC decreased complex I and complex IV activity levels. CLINICAL TRIALS REGISTRATION NCT00118898.
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Sitole LJ, Williams AA, Meyer D. Metabonomic analysis of HIV-infected biofluids. MOLECULAR BIOSYSTEMS 2012; 9:18-28. [PMID: 23114495 DOI: 10.1039/c2mb25318f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monitoring the progression of HIV infection to full-blown acquired immune deficiency syndrome (AIDS) and assessing responses to treatment will benefit greatly from the identification of novel biological markers especially since existing clinical indicators of disease are not infallible. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are powerful methodologies used in metabonomic analyses for an approximation of HIV-induced changes to the phenotype of an infected individual. Although early in its application to HIV/AIDS, (biofluid) metabonomics has already identified metabolic pathways influenced by both HIV and/or its treatment. To date, biofluid NMR and MS data show that the virus and highly active antiretroviral treatment (HAART) mainly influence carbohydrate and lipid metabolism, suggesting that infected individuals are susceptible to very specific metabolic complications. A number of well-defined biofluid metabonomic studies clearly distinguished HIV negative, positive and treatment experienced patient profiles from one another. While many of the virus or treatment affected metabolites have been identified, the metabonomics measurements were mostly qualitative. The identities of the molecules were not always validated neither were the statistical models used to distinguish between groups. Assigning particular metabolic changes to specific drug regimens using metabonomics also remains to be done. Studies exist where identified metabolites have been linked to various disease states suggesting great potential for the use of metabonomics in disease prognostics. This review therefore examines the field of metabonomics in the context of HIV/AIDS, comments on metabolites routinely detected as being affected by the pathogen or treatment, explains what existing data suggest and makes recommendations on future research.
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Affiliation(s)
- Lungile J Sitole
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa
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Roy S, Short MK, Stanley ER, Jubinsky PT. Essential role of Drosophila black-pearl is mediated by its effects on mitochondrial respiration. FASEB J 2012; 26:3822-33. [PMID: 22700875 DOI: 10.1096/fj.11-193540] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Black-pearl (Blp) is a highly conserved, essential inner-mitochondrial membrane protein. The yeast Blp homologue, Magmas/Pam16, is required for mitochondrial protein transport, growth, and survival. Our purpose was to determine the role of Drosophila Blp in mitochondrial function, cell survival, and proliferation. To this end, we performed mitotic recombination in Drosophila melanogaster, RNAi-mediated knockdown, MitoTracker staining, measurement of reactive oxygen species (ROS), flow cytometry, electron transport chain complex assays, and hemocyte isolation from Drosophila larvae. Proliferation-defective, Blp-deficient Drosophila Schneider cells exhibited mitochondrial membrane depolarization, a 60% decrease in ATP levels, increased amounts of ROS (3.5-fold), cell cycle arrest, and activation of autophagy that were associated with a selective 65% reduction of cytochrome c oxidase activity. N-acetyl cysteine (NAC) rescued Blp-RNAi-treated cells from cell cycle arrest, indicating that increased production of ROS is the primary cause of the proliferation and survival defects in Blp-depleted cells. blp hypomorph larvae had a 35% decreased number of plasmatocytes with a 45% reduced active mitochondrial staining and their viability was increased 2-fold by administration of NAC, which blocked melanotic lesions. Loss of Blp decreases cytochrome c oxidase activity and uncouples oxidative phosphorylation, causing ROS production, which selectively affects mitochondria-rich plasmatocyte survival and function, leading to melanotic lesions in Blp-deficient flies.
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Affiliation(s)
- Soumit Roy
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Li Y, Zhong XB. Epigenetic regulation of developmental expression of Cyp2d genes in mouse liver. Acta Pharm Sin B 2012. [DOI: 10.1016/j.apsb.2012.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Bull VH, Rajalingam K, Thiede B. Sorafenib-induced mitochondrial complex I inactivation and cell death in human neuroblastoma cells. J Proteome Res 2012; 11:1609-20. [PMID: 22268697 DOI: 10.1021/pr200790e] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sorafenib is a multikinase inhibitor that is approved for use against renal cell and hepatocellular carcinoma. We found that sorafenib potently induced cell death in human neuroblastoma cells. To understand the molecular basis of sorafenib-mediated cell death in human SH-SY5Y cells, we performed a temporal quantitative proteome analysis. The results showed significant quantitative changes of 193 unique proteins. Bioinformatics-assisted pathway analysis of the regulated proteins revealed that mitochondrial proteins, especially components of the electron transport chain and the mitochondrial ribosomes, were significantly affected upon exposure to sorafenib. The observed down-regulation of the respiratory chain complex I (NADH dehydrogenase) was accompanied with loss of mitochondrial transmembrane potential (Δψm) and complete impairment of complex I enzyme activity. The destabilization of complex I subunits was consistent, rapid, and independent of caspase activation as well as Bcl-2 overexpression. This study provides an overview of the molecular machinery driving sorafenib-mediated cell death in neuroblastoma cells and suggests that sorafenib could be a potential therapeutic drug for the treatment of neuroblastoma.
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Affiliation(s)
- Vibeke Hervik Bull
- The Biotechnology Centre of Oslo, University of Oslo , P.O. Box 1125 Blindern, 0317 Oslo, Norway
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Murali TM, Dyer MD, Badger D, Tyler BM, Katze MG. Network-based prediction and analysis of HIV dependency factors. PLoS Comput Biol 2011; 7:e1002164. [PMID: 21966263 PMCID: PMC3178628 DOI: 10.1371/journal.pcbi.1002164] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 06/30/2011] [Indexed: 01/27/2023] Open
Abstract
HIV Dependency Factors (HDFs) are a class of human proteins that are essential for HIV replication, but are not lethal to the host cell when silenced. Three previous genome-wide RNAi experiments identified HDF sets with little overlap. We combine data from these three studies with a human protein interaction network to predict new HDFs, using an intuitive algorithm called SinkSource and four other algorithms published in the literature. Our algorithm achieves high precision and recall upon cross validation, as do the other methods. A number of HDFs that we predict are known to interact with HIV proteins. They belong to multiple protein complexes and biological processes that are known to be manipulated by HIV. We also demonstrate that many predicted HDF genes show significantly different programs of expression in early response to SIV infection in two non-human primate species that differ in AIDS progression. Our results suggest that many HDFs are yet to be discovered and that they have potential value as prognostic markers to determine pathological outcome and the likelihood of AIDS development. More generally, if multiple genome-wide gene-level studies have been performed at independent labs to study the same biological system or phenomenon, our methodology is applicable to interpret these studies simultaneously in the context of molecular interaction networks and to ask if they reinforce or contradict each other. Medicines to cure infectious diseases usually target proteins in the pathogens. Since pathogens have short life cycles, the targeted proteins can rapidly evolve and make the medicines ineffective, especially in viruses such as HIV. However, since viruses have very small genomes, they must exploit the cellular machinery of the host to propagate. Therefore, disrupting the activity of selected host proteins may impede viruses. Three recent experiments have discovered hundreds of such proteins in human cells that HIV depends upon. Surprisingly, these three sets have very little overlap. In this work, we demonstrate that this discrepancy can be explained by considering physical interactions between the human proteins in these studies. Moreover, we exploit these interactions to predict new dependency factors for HIV. Our predictions show very significant overlaps with human proteins that are known to interact with HIV proteins and with human cellular processes that are known to be subverted by the virus. Most importantly, we show that proteins predicted by us may play a prominent role in affecting HIV-related disease progression in lymph nodes. Therefore, our predictions constitute a powerful resource for experimentalists who desire to discover new human proteins that can control the spread of HIV.
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Affiliation(s)
- T. M. Murali
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail: (TMM) (TM); (MGK) (MK)
| | - Matthew D. Dyer
- Applied Biosystems, Foster City, California, United States of America
| | - David Badger
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Michael G. Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (TMM) (TM); (MGK) (MK)
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Bodiwala HS, Sabde S, Mitra D, Bhutani KK, Singh IP. Synthesis of 9-substituted derivatives of berberine as anti-HIV agents. Eur J Med Chem 2011; 46:1045-9. [DOI: 10.1016/j.ejmech.2011.01.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 01/06/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
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Danielson SR, Held JM, Oo M, Riley R, Gibson BW, Andersen JK. Quantitative mapping of reversible mitochondrial Complex I cysteine oxidation in a Parkinson disease mouse model. J Biol Chem 2011; 286:7601-8. [PMID: 21196577 PMCID: PMC3045014 DOI: 10.1074/jbc.m110.190108] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/15/2010] [Indexed: 11/06/2022] Open
Abstract
Differential cysteine oxidation within mitochondrial Complex I has been quantified in an in vivo oxidative stress model of Parkinson disease. We developed a strategy that incorporates rapid and efficient immunoaffinity purification of Complex I followed by differential alkylation and quantitative detection using sensitive mass spectrometry techniques. This method allowed us to quantify the reversible cysteine oxidation status of 34 distinct cysteine residues out of a total 130 present in murine Complex I. Six Complex I cysteine residues were found to display an increase in oxidation relative to controls in brains from mice undergoing in vivo glutathione depletion. Three of these residues were found to reside within iron-sulfur clusters of Complex I, suggesting that their redox state may affect electron transport function.
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Affiliation(s)
| | - Jason M. Held
- From the Buck Institute for Age Research, Novato, California 94945
| | - May Oo
- From the Buck Institute for Age Research, Novato, California 94945
| | - Rebeccah Riley
- From the Buck Institute for Age Research, Novato, California 94945
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Bodiwala HS, Sabde S, Gupta P, Mukherjee R, Kumar R, Garg P, Bhutani KK, Mitra D, Singh IP. Design and synthesis of caffeoyl-anilides as portmanteau inhibitors of HIV-1 integrase and CCR5. Bioorg Med Chem 2011; 19:1256-63. [DOI: 10.1016/j.bmc.2010.12.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/26/2010] [Accepted: 12/13/2010] [Indexed: 11/28/2022]
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46
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Brahmbhatt KG, Ahmed N, Sabde S, Mitra D, Singh IP, Bhutani KK. Synthesis and evaluation of β-carboline derivatives as inhibitors of human immunodeficiency virus. Bioorg Med Chem Lett 2010; 20:4416-9. [DOI: 10.1016/j.bmcl.2010.06.052] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/08/2010] [Accepted: 06/09/2010] [Indexed: 10/19/2022]
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Tripathy MK, Ahmed Z, Ladha JS, Mitra D. The cell death regulator GRIM-19 is involved in HIV-1 induced T-cell apoptosis. Apoptosis 2010; 15:1453-60. [DOI: 10.1007/s10495-010-0527-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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Zhou L, Diefenbach E, Crossett B, Tran SL, Ng T, Rizos H, Rua R, Wang B, Kapur A, Gandhi K, Brew BJ, Saksena NK. First evidence of overlaps between HIV-Associated Dementia (HAD) and non-viral neurodegenerative diseases: proteomic analysis of the frontal cortex from HIV+ patients with and without dementia. Mol Neurodegener 2010; 5:27. [PMID: 20573273 PMCID: PMC2904315 DOI: 10.1186/1750-1326-5-27] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 06/24/2010] [Indexed: 12/12/2022] Open
Abstract
Background The pathogenesis of HIV-associated dementia (HAD) is poorly understood. To date, detailed proteomic fingerprinting directly from autopsied brain tissues of HAD and HIV non-dementia patients has not been performed. Result Here, we have analyzed total proteins from the frontal cortex of 9 HAD and 5 HIV non-dementia patients. Using 2-Dimensional differential in-gel electrophoresis (2-DIGE) to analyze the brain tissue proteome, 76 differentially expressed proteins (p < 0.05; fold change>1.25) were identified between HAD and HIV non-dementia patients, of which 36 protein spots (based on 3D appearance of spots on the images) were chosen for the mass spectrometry analysis. The large majority of identified proteins were represented in the energy metabolic (mitochondria) and signal transduction pathways. Furthermore, over 90% of the protein candidates are common to both HAD and other non-viral neurodegenerative disease, such as Alzheimer's disease. The data was further validated using specific antibodies to 4 proteins (CA2, GS, CKMT and CRMP2) by western blot (WB) in the same samples used for 2D-DIGE, with additional confirmation by immunohistochemitsry (IHC) using frontal lobe tissue from different HAD and HIV+ non-dementia patients. The validation for all 4 antibodies by WB and IHC was in concordance with the DIGE results, lending further credence to the current findings. Conclusion These results suggest not only convergent pathogenetic pathways for the two diseases but also the possibility of increased Alzheimer's disease (AD) susceptibility in HAD patients whose life expectancy has been significantly increased by highly active antiretroviral therapy.
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Affiliation(s)
- Li Zhou
- Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead, NSW 2145, Sydney, Australia.
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Xiao S, Wang Q, Jia J, Cong P, Mo D, Yu X, Qin L, Li A, Niu Y, Zhu K, Wang X, Liu X, Chen Y. Proteome changes of lungs artificially infected with H-PRRSV and N-PRRSV by two-dimensional fluorescence difference gel electrophoresis. Virol J 2010; 7:107. [PMID: 20504321 PMCID: PMC2887434 DOI: 10.1186/1743-422x-7-107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2010] [Accepted: 05/26/2010] [Indexed: 02/07/2023] Open
Abstract
Background Porcine reproductive and respiratory syndrome with PRRS virus (PRRSV) infection, which causes significant economic losses annually, is one of the most economically important diseases affecting swine industry worldwide. In 2006 and 2007, a large-scale outbreak of highly pathogenic porcine reproductive and respiratory syndrome (PRRS) happened in China and Vietnam. However little data is available on global host response to PRRSV infection at the protein level, and similar approaches looking at mRNA is problematic since mRNA levels do not necessarily predict protein levels. In order to improve the knowledge of host response and viral pathogenesis of highly virulent Chinese-type PRRSV (H-PRRSV) and Non-high-pathogenic North American-type PRRSV strains (N-PRRSV), we analyzed the protein expression changes of H-PRRSV and N-PRRSV infected lungs compared with those of uninfected negative control, and identified a series of proteins related to host response and viral pathogenesis. Results According to differential proteomes of porcine lungs infected with H-PRRSV, N-PRRSV and uninfected negative control at different time points using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry identification, 45 differentially expressed proteins (DEPs) were identified. These proteins were mostly related to cytoskeleton, stress response and oxidation reduction or metabolism. In the protein interaction network constructed based on DEPs from lungs infected with H-PRRSV, HSPA8, ARHGAP29 and NDUFS1 belonged to the most central proteins, whereas DDAH2, HSPB1 and FLNA corresponded to the most central proteins in those of N-PRRSV infected. Conclusions Our study is the first attempt to provide the complex picture of pulmonary protein expression during H-PRRSV and N-PRRSV infection under the in vivo environment using 2D-DIGE technology and bioinformatics tools, provides large scale valuable information for better understanding host proteins-virus interactions of these two PRRSV strains.
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Affiliation(s)
- Shuqi Xiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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