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Li S, He RC, Wu SG, Song Y, Zhang KL, Tang ML, Bei YR, Zhang T, Lu JB, Ma X, Jiang M, Qin LJ, Xu Y, Dong XH, Wu J, Dai X, Hu YW. LncRNA PSMB8-AS1 Instigates Vascular Inflammation to Aggravate Atherosclerosis. Circ Res 2024; 134:60-80. [PMID: 38084631 DOI: 10.1161/circresaha.122.322360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 11/20/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Increasing evidence suggests that long noncoding RNAs play significant roles in vascular biology and disease development. One such long noncoding RNA, PSMB8-AS1, has been implicated in the development of tumors. Nevertheless, the precise role of PSMB8-AS1 in cardiovascular diseases, particularly atherosclerosis, has not been thoroughly elucidated. Thus, the primary aim of this investigation is to assess the influence of PSMB8-AS1 on vascular inflammation and the initiation of atherosclerosis. METHODS We generated PSMB8-AS1 knockin and Apoe (Apolipoprotein E) knockout mice (Apoe-/-PSMB8-AS1KI) and global Apoe and proteasome subunit-β type-9 (Psmb9) double knockout mice (Apoe-/-Psmb9-/-). To explore the roles of PSMB8-AS1 and Psmb9 in atherosclerosis, we fed the mice with a Western diet for 12 weeks. RESULTS Long noncoding RNA PSMB8-AS1 is significantly elevated in human atherosclerotic plaques. Strikingly, Apoe-/-PSMB8-AS1KI mice exhibited increased atherosclerosis development, plaque vulnerability, and vascular inflammation compared with Apoe-/- mice. Moreover, the levels of VCAM1 (vascular adhesion molecule 1) and ICAM1 (intracellular adhesion molecule 1) were significantly upregulated in atherosclerotic lesions and serum of Apoe-/-PSMB8-AS1KI mice. Consistently, in vitro gain- and loss-of-function studies demonstrated that PSMB8-AS1 induced monocyte/macrophage adhesion to endothelial cells and increased VCAM1 and ICAM1 levels in a PSMB9-dependent manner. Mechanistic studies revealed that PSMB8-AS1 induced PSMB9 transcription by recruiting the transcription factor NONO (non-POU domain-containing octamer-binding protein) and binding to the PSMB9 promoter. PSMB9 (proteasome subunit-β type-9) elevated VCAM1 and ICAM1 expression via the upregulation of ZEB1 (zinc finger E-box-binding homeobox 1). Psmb9 deficiency decreased atherosclerotic lesion size, plaque vulnerability, and vascular inflammation in Apoe-/- mice in vivo. Importantly, endothelial overexpression of PSMB8-AS1-increased atherosclerosis and vascular inflammation were attenuated by Psmb9 knockout. CONCLUSIONS PSMB8-AS1 promotes vascular inflammation and atherosclerosis via the NONO/PSMB9/ZEB1 axis. Our findings support the development of new long noncoding RNA-based strategies to counteract atherosclerotic cardiovascular disease.
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Affiliation(s)
- Shu Li
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Run-Chao He
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Shao-Guo Wu
- Department of Clinical Laboratory, Guangzhou Twelfth People's Hospital, Guangdong, China (S.-G.W.)
| | - Yu Song
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Ke-Lan Zhang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Mao-Lin Tang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Yan-Rou Bei
- Laboratory Medicine Center (Y.-R.B.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ting Zhang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Jin-Bo Lu
- Department of Peripheral Vascular Surgery, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen (J.-B.L.)
| | - Xin Ma
- Department of Anesthesiology (X.M.), Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Min Jiang
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Liang-Jun Qin
- Department of Pathology, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (L.J.Q.)
| | - Yudan Xu
- Laboratory Medicine Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China (Y.X.)
| | - Xian-Hui Dong
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Jia Wu
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
| | - Xiaoyan Dai
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangdong, China (X.D.)
- Clinical Research Institute, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hunan, China (X.D.)
| | - Yan-Wei Hu
- Department of Clinical Laboratory, Guangzhou Women & Children Medical Center, Guangzhou Medical University, Guangdong, China (S.L., R.-C.H., Y.S., K.-L.Z., M.-L.T., T.Z., M.J., X.-H.D., J.W., Y.-W.H.)
- Department of Laboratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China (Y.-W.H.)
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Wang S, Ding X, Li Z, Rao F, Xu H, Lu J, Ma X, Zhang M, Xie Z. Comprehensive analyses identify potential biomarkers for encephalitis in HIV infection. Sci Rep 2023; 13:18418. [PMID: 37891420 PMCID: PMC10611703 DOI: 10.1038/s41598-023-45922-6] [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] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023] Open
Abstract
Human immunodeficiency virus encephalitis (HIVE) is a severe neurological complication after HIV infection. Evidence shows that genetic factors play an important role in HIVE. The aim of the present study was to identify new potential therapeutic targets for HIVE. Differentially expressed gene (DEG), functional annotation and pathway, and protein-protein interaction analyses were performed to identify the hub genes associated with HIVE. Gene co-expression analysis was carried out to confirm the association between the hub genes and HIVE. Finally, the role of the hub genes in HIVE therapy was evaluated by conducting drug-gene interaction analysis. A total of 20 overlapping DEGs closely related to HIVE were identified. Functional annotation and pathway enrichment analysis indicated that the markedly enriched DEG terms included ion transport, type II interferon signaling, and synaptic signaling. Moreover, protein-protein interaction analysis revealed that 10 key HIVE-related genes were hub genes, including SCN8A, CDK5R2, GRM5, SCN2B, IFI44L, STAT1, SLC17A7, ISG15, FGF12, and FGF13. Furthermore, six hub genes were co-expressed with HIVE-associated host genes in human brain tissue. Finally, three hub genes (STAT1, ISG15, and SCN2B) interacted with several inflammation-associated drugs. These findings suggested that SCN8A, CDK5R2, GRM5, SCN2B, IFI44L, STAT1, SLC17A7, ISG15, FGF12, and FGF13 may be new targets for diagnosis and therapy of HIVE.
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Affiliation(s)
- Shitao Wang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China.
| | - Xiangqian Ding
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Zongyou Li
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China
| | - Feng Rao
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China
| | - Hui Xu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China
| | - Jinghong Lu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China
| | - Xuelu Ma
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China
| | - Mengen Zhang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, China
| | - Zhenrong Xie
- The Medical Biobank, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
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Borrajo A, Pérez-Rodríguez D, Fernández-Pereira C, Prieto-González JM, Agís-Balboa RC. Genomic Factors and Therapeutic Approaches in HIV-Associated Neurocognitive Disorders: A Comprehensive Review. Int J Mol Sci 2023; 24:14364. [PMID: 37762667 PMCID: PMC10531836 DOI: 10.3390/ijms241814364] [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: 07/18/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
HIV-associated neurocognitive disorders (HANDs) still persist despite improved life expectancy, reduced viral loads, and decreased infection severity. The number of patients affected by HANDs ranges from (30 to 50) % of HIV-infected individuals. The pathological mechanisms contributing to HANDs and the most serious manifestation of the disease, HIV-associated dementia (HAD), are not yet well understood. Evidence suggests that these mechanisms are likely multifactorial, producing neurocognitive complications involving disorders such as neurogenesis, autophagy, neuroinflammation, and mitochondrial dysfunction. Over the years, multiple pharmacological approaches with specific mechanisms of action acting upon distinct targets have been approved. Although these therapies are effective in reducing viral loading to undetectable levels, they also present some disadvantages such as common side effects, the need for administration with a very high frequency, and the possibility of drug resistance. Genetic studies on HANDs provide insights into the biological pathways and mechanisms that contribute to cognitive impairment in people living with HIV-1. Furthermore, they also help identify genetic variants that increase susceptibility to HANDs and can be used to tailor treatment approaches for HIV-1 patients. Identification of the genetic markers associated with disease progression can help clinicians predict which individuals require more aggressive management and by understanding the genetic basis of the disorder, it will be possible to develop targeted therapies to mitigate cognitive impairment. The main goal of this review is to provide details on the epidemiological data currently available and to summarise the genetic (specifically, the genetic makeup of the immune system), transcriptomic, and epigenetic studies available on HANDs to date. In addition, we address the potential pharmacological therapeutic strategies currently being investigated. This will provide valuable information that can guide clinical care, drug development, and our overall understanding of these diseases.
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Affiliation(s)
- Ana Borrajo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, 00133 Roma, Italy
| | - Daniel Pérez-Rodríguez
- NeuroEpigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain; (D.P.-R.); (C.F.-P.); (J.M.P.-G.)
- Facultade de Bioloxía, Universidade de Vigo (UVigo), Campus Universitario Lagoas-Marcosende, s/n, 36310 Vigo, Spain
| | - Carlos Fernández-Pereira
- NeuroEpigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain; (D.P.-R.); (C.F.-P.); (J.M.P.-G.)
- Translational Neuroscience Group, Galicia Sur Health Research Institute (IIS Galicia Sur), Area Sanitaria de Vigo-Hospital Álvaro Cunqueiro, SERGAS-UVIGO, CIBERSAM-ISCIII, 36213 Vigo, Spain
- Rare Disease and Pediatric Medicine Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36312 Vigo, Spain
| | - José María Prieto-González
- NeuroEpigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain; (D.P.-R.); (C.F.-P.); (J.M.P.-G.)
- Translational Research in Neurological Diseases (ITEN), Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
| | - Roberto Carlos Agís-Balboa
- NeuroEpigenetics Lab, Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain; (D.P.-R.); (C.F.-P.); (J.M.P.-G.)
- Translational Research in Neurological Diseases (ITEN), Health Research Institute of Santiago de Compostela (IDIS), Santiago University Hospital Complex, 15706 Santiago de Compostela, Spain
- Servicio de Neurología, Hospital Clínico Universitario de Santiago, 15706 Santiago de Compostela, Spain
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Gene Self-Expressive Networks as a Generalization-Aware Tool to Model Gene Regulatory Networks. Biomolecules 2023; 13:biom13030526. [PMID: 36979461 PMCID: PMC10046116 DOI: 10.3390/biom13030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
Self-expressiveness is a mathematical property that aims at characterizing the relationship between instances in a dataset. This property has been applied widely and successfully in computer-vision tasks, time-series analysis, and to infer underlying network structures in domains including protein signaling interactions and social-networks activity. Nevertheless, despite its potential, self-expressiveness has not been explicitly used to infer gene networks. In this article, we present Generalizable Gene Self-Expressive Networks, a new, interpretable, and generalization-aware formalism to model gene networks, and we propose two methods: GXN•EN and GXN•OMP, based respectively on ElasticNet and OMP (Orthogonal Matching Pursuit), to infer and assess Generalizable Gene Self-Expressive Networks. We evaluate these methods on four Microarray datasets from the DREAM5 benchmark, using both internal and external metrics. The results obtained by both methods are comparable to those obtained by state-of-the-art tools, but are fast to train and exhibit high levels of sparsity, which make them easier to interpret. Moreover we applied these methods to three complex datasets containing RNA-seq informations from different mammalian tissues/cell-types. Lastly, we applied our methodology to compare a normal vs. a disease condition (Alzheimer), which allowed us to detect differential expression of genes’ sub-networks between these two biological conditions. Globally, the gene networks obtained exhibit a sparse and modular structure, with inner communities of genes presenting statistically significant over/under-expression on specific cell types, as well as significant enrichment for some anatomical GO terms, suggesting that such communities may also drive important functional roles.
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5
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Mass spectrometry analysis of gut tissue in acute SIV-infection in rhesus macaques identifies early proteome alterations preceding the interferon inflammatory response. Sci Rep 2023; 13:690. [PMID: 36639424 PMCID: PMC9839751 DOI: 10.1038/s41598-022-27112-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/26/2022] [Indexed: 01/15/2023] Open
Abstract
HIV infection damages the gut mucosa leading to chronic immune activation, increased morbidities and mortality, and antiretroviral therapies, do not completely ameliorate mucosal dysfunction. Understanding early molecular changes in acute infection may identify new biomarkers underlying gut dysfunction. Here we utilized a proteomics approach, coupled with flow cytometry, to characterize early molecular and immunological alterations during acute SIV infection in gut tissue of rhesus macaques. Gut tissue biopsies were obtained at 2 times pre-infection and 4 times post-infection from 6 macaques. The tissue proteome was analyzed by mass spectrometry, and immune cell populations in tissue and blood by flow cytometry. Significant proteome changes (p < 0.05) occurred at 3 days post-infection (dpi) (13.0%), 14 dpi (13.7%), 28 dpi (16.9%) and 63 dpi (14.8%). At 3 dpi, proteome changes included cellular structural activity, barrier integrity, and activation of epithelial to mesenchymal transition (EMT) (FDR < 0.0001) prior to the antiviral response at 14 dpi (IFNa/g pathways, p < 0.001). Novel EMT proteomic biomarkers (keratins 2, 6A and 20, collagen 12A1, desmoplakin) and inflammatory biomarkers (PSMB9, FGL2) were associated with early infection and barrier dysfunction. These findings identify new biomarkers preceding inflammation in SIV infection involved with EMT activation. This warrants further investigation of the role of these biomarkers in chronic infection, mucosal inflammation, and disease pathogenesis of HIV.
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Vaganova AN, Murtazina RZ, Shemyakova TS, Prjibelski AD, Katolikova NV, Gainetdinov RR. Pattern of TAAR5 Expression in the Human Brain Based on Transcriptome Datasets Analysis. Int J Mol Sci 2021; 22:ijms22168802. [PMID: 34445502 PMCID: PMC8395715 DOI: 10.3390/ijms22168802] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Trace amine-associated receptors (TAAR) recognize organic compounds, including primary, secondary, and tertiary amines. The TAAR5 receptor is known to be involved in the olfactory sensing of innate socially relevant odors encoded by volatile amines. However, emerging data point to the involvement of TAAR5 in brain functions, particularly in the emotional behaviors mediated by the limbic system which suggests its potential contribution to the pathogenesis of neuropsychiatric diseases. TAAR5 expression was explored in datasets available in the Gene Expression Omnibus, Allen Brain Atlas, and Human Protein Atlas databases. Transcriptomic data demonstrate ubiquitous low TAAR5 expression in the cortical and limbic brain areas, the amygdala and the hippocampus, the nucleus accumbens, the thalamus, the hypothalamus, the basal ganglia, the cerebellum, the substantia nigra, and the white matter. Altered TAAR5 expression is identified in Down syndrome, major depressive disorder, or HIV-associated encephalitis. Taken together, these data indicate that TAAR5 in humans is expressed not only in the olfactory system but also in certain brain structures, including the limbic regions receiving olfactory input and involved in critical brain functions. Thus, TAAR5 can potentially be involved in the pathogenesis of brain disorders and represents a valuable novel target for neuropsychopharmacology.
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Affiliation(s)
- Anastasia N. Vaganova
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (R.Z.M.); (T.S.S.); (A.D.P.); (N.V.K.)
| | - Ramilya Z. Murtazina
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (R.Z.M.); (T.S.S.); (A.D.P.); (N.V.K.)
| | - Taisiia S. Shemyakova
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (R.Z.M.); (T.S.S.); (A.D.P.); (N.V.K.)
| | - Andrey D. Prjibelski
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (R.Z.M.); (T.S.S.); (A.D.P.); (N.V.K.)
| | - Nataliia V. Katolikova
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (R.Z.M.); (T.S.S.); (A.D.P.); (N.V.K.)
| | - Raul R. Gainetdinov
- Institute of Translational Biomedicine, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia; (A.N.V.); (R.Z.M.); (T.S.S.); (A.D.P.); (N.V.K.)
- St. Petersburg University Hospital, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 St. Petersburg, Russia
- Correspondence:
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7
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Central nervous system (CNS) transcriptomic correlates of human immunodeficiency virus (HIV) brain RNA load in HIV-infected individuals. Sci Rep 2021; 11:12176. [PMID: 34108514 PMCID: PMC8190104 DOI: 10.1038/s41598-021-88052-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/26/2021] [Indexed: 11/08/2022] Open
Abstract
To generate new mechanistic hypotheses on the pathogenesis and disease progression of neuroHIV and identify novel therapeutic targets to improve neuropsychological function in people with HIV, we investigated host genes and pathway dysregulations associated with brain HIV RNA load in gene expression profiles of the frontal cortex, basal ganglia, and white matter of HIV+ patients. Pathway analyses showed that host genes correlated with HIV expression in all three brain regions were predominantly related to inflammation, neurodegeneration, and bioenergetics. HIV RNA load directly correlated particularly with inflammation genesets representative of cytokine signaling, and this was more prominent in white matter and the basal ganglia. Increases in interferon signaling were correlated with high brain HIV RNA load in the basal ganglia and the white matter although not in the frontal cortex. Brain HIV RNA load was inversely correlated with genesets that are indicative of neuronal and synaptic genes, particularly in the cortex, indicative of synaptic injury and neurodegeneration. Brain HIV RNA load was inversely correlated with genesets that are representative of oxidative phosphorylation, electron transfer, and the tricarboxylic acid cycle in all three brain regions. Mitochondrial dysfunction has been implicated in the toxicity of some antiretrovirals, and these results indicate that mitochondrial dysfunction is also associated with productive HIV infection. Genes and pathways correlated with brain HIV RNA load suggest potential therapeutic targets to ameliorate neuropsychological functioning in people living with HIV.
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Pays E. The function of apolipoproteins L (APOLs): relevance for kidney disease, neurotransmission disorders, cancer and viral infection. FEBS J 2021; 288:360-381. [PMID: 32530132 PMCID: PMC7891394 DOI: 10.1111/febs.15444] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/24/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
The discovery that apolipoprotein L1 (APOL1) is the trypanolytic factor of human serum raised interest about the function of APOLs, especially following the unexpected finding that in addition to their protective action against sleeping sickness, APOL1 C-terminal variants also cause kidney disease. Based on the analysis of the structure and trypanolytic activity of APOL1, it was proposed that APOLs could function as ion channels of intracellular membranes and be involved in mechanisms triggering programmed cell death. In this review, the recent finding that APOL1 and APOL3 inversely control the synthesis of phosphatidylinositol-4-phosphate (PI(4)P) by the Golgi PI(4)-kinase IIIB (PI4KB) is commented. APOL3 promotes Ca2+ -dependent activation of PI4KB, but due to their increased interaction with APOL3, APOL1 C-terminal variants can inactivate APOL3, leading to reduction of Golgi PI(4)P synthesis. The impact of APOLs on several pathological processes that depend on Golgi PI(4)P levels is discussed. I propose that through their effect on PI4KB activity, APOLs control not only actomyosin activities related to vesicular trafficking, but also the generation and elongation of autophagosomes induced by inflammation.
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Affiliation(s)
- Etienne Pays
- Laboratory of Molecular ParasitologyIBMMUniversité Libre de BruxellesGosseliesBelgium
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9
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Zeng X, Tsui JCC, Shi M, Peng J, Cao CY, Kan LLY, Lau CPY, Liang Y, Wang L, Liu L, Chen Z, Tsui SKW. Genome-Wide Characterization of Host Transcriptional and Epigenetic Alterations During HIV Infection of T Lymphocytes. Front Immunol 2020; 11:2131. [PMID: 33013899 PMCID: PMC7511662 DOI: 10.3389/fimmu.2020.02131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Background and methods: Host genomic alterations are closely related to dysfunction of CD4+ T lymphocytes in the HIV–host interplay. However, the roles of aberrant DNA methylation and gene expression in the response to HIV infection are not fully understood. We investigated the genome-wide DNA methylation and transcriptomic profiles in two HIV-infected T lymphocyte cell lines using high-throughput sequencing. Results: Based on DNA methylation data, we identified 3,060 hypomethylated differentially methylated regions (DMRs) and 2,659 hypermethylated DMRs in HIV-infected cells. Transcription-factor-binding motifs were significantly associated with methylation alterations, suggesting that DNA methylation modulates gene expression by affecting the binding to transcription factors during HIV infection. In support of this hypothesis, genes with promoters overlapping with DMRs were enriched in the biological function related to transcription factor activities. Furthermore, the analysis of gene expression data identified 1,633 upregulated genes and 2,142 downregulated genes on average in HIV-infected cells. These differentially expressed genes (DEGs) were significantly enriched in apoptosis-related pathways. Our results suggest alternative splicing as an additional mechanism that may contribute to T-cell apoptosis during HIV infection. We also demonstrated a genome-scale correlation between DNA methylation and gene expression in HIV-infected cells. We identified 831 genes with alterations in both DNA methylation and gene expression, which were enriched in apoptosis. Our results were validated using various experimental methods. In addition, consistent with our in silico results, a luciferase assay showed that the activity of the PDX1 and SMAD3 promoters was significantly decreased in the presence of HIV proteins, indicating the potential of these genes as genetic markers of HIV infection. Conclusions: Our results suggest important roles for DNA methylation and gene expression regulation in T-cell apoptosis during HIV infection. We propose a list of novel genes related to these processes for further investigation. This study also provides a comprehensive characterization of changes occurring at the transcriptional and epigenetic levels in T cells in response to HIV infection.
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Affiliation(s)
- Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Chi-Ching Tsui
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Mai Shi
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jie Peng
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Cyanne Ye Cao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lea Ling-Yu Kan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Carol Po-Ying Lau
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yonghao Liang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lingyi Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Li Liu
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Zhiwei Chen
- Acquired Immunodeficiency Syndrome (AIDS) Institute, The University of Hong Kong, Hong Kong, China
| | - Stephen Kwok-Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China.,Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong, Hong Kong, China
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10
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Canchi S, Swinton MK, Rissman RA, Fields JA. Transcriptomic analysis of brain tissues identifies a role for CCAAT enhancer binding protein β in HIV-associated neurocognitive disorder. J Neuroinflammation 2020; 17:112. [PMID: 32276639 PMCID: PMC7149918 DOI: 10.1186/s12974-020-01781-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-associated neurocognitive disorders (HAND) persist in the era of combined antiretroviral therapy (ART) despite reductions in viral load (VL) and overall disease severity. The mechanisms underlying HAND in the ART era are not well understood but are likely multifactorial, involving alterations in common pathways such as inflammation, autophagy, neurogenesis, and mitochondrial function. Newly developed omics approaches hold potential to identify mechanisms driving neuropathogenesis of HIV in the ART era. METHODS In this study, using 33 postmortem frontal cortex (FC) tissues, neuropathological, molecular, and biochemical analyses were used to determine cellular localization and validate expression levels of the prolific transcription factor (TF), CCAAT enhancer binding protein (C/EBP) β, in brain tissues from HIV+ cognitively normal and HAND cases. RNA sequencing (seq) and transcriptomic analyses were performed on FC tissues including 24 specimens from well-characterized people with HIV that had undergone neurocognitive assessments. In vitro models for brain cells were used to investigate the role of C/EBPβ in mediating gene expression. RESULTS The most robust signal for TF dysregulation was observed in cases diagnosed with minor neurocognitive disorder (MND) compared to cognitive normal (CN) cases. Of particular interest, due to its role in inflammation, autophagy and neurogenesis, C/EBPβ was significantly upregulated in MND compared to CN brains. C/EBPβ was increased at the protein level in HAND brains. C/EBPβ levels were significantly reduced in neurons and increased in astroglia in HAND brains compared to CN. Transfection of human astroglial cells with a plasmid expressing C/EBPβ induced expression of multiple targets identified in the transcriptomic analysis of HAND brains, including dynamin-1-like protein (DNM1L) and interleukin-1 receptor-associated kinase 1. Recombinant HIV-Tat reduced and increased C/EBPβ levels in neuronal and astroglial cells, respectively. CONCLUSIONS These findings are the first to present RNAseq-based transcriptomic analyses of HIV+ brain tissues, providing further evidence of altered neuroinflammation, neurogenesis, mitochondrial function, and autophagy in HAND. Interestingly, these studies confirm a role for CEBPβ in regulating inflammation, metabolism, and autophagy in astroglia. Therapeutic strategies aimed at transcriptional regulation of astroglia or downstream pathways may provide relief to HIV+ patients at risk for HAND and other neurological disorders.
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Affiliation(s)
- Saranya Canchi
- Veterans Affairs San Diego Healthcare System, San Diego, CA USA
- Department of Neurosciences, University of California San Diego, San Diego, La Jolla, CA USA
| | - Mary K. Swinton
- Department of Psychiatry, School of Medicine, University of California San Diego, 9500 Gilman Dr., BSB 3009, San Diego, La Jolla, CA 92093-0603 USA
| | - Robert A. Rissman
- Veterans Affairs San Diego Healthcare System, San Diego, CA USA
- Department of Neurosciences, University of California San Diego, San Diego, La Jolla, CA USA
| | - Jerel Adam Fields
- Department of Psychiatry, School of Medicine, University of California San Diego, 9500 Gilman Dr., BSB 3009, San Diego, La Jolla, CA 92093-0603 USA
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11
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Sarma A, Das MK. Nose to brain delivery of antiretroviral drugs in the treatment of neuroAIDS. MOLECULAR BIOMEDICINE 2020; 1:15. [PMID: 34765998 PMCID: PMC7725542 DOI: 10.1186/s43556-020-00019-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
NeuroAIDS (Neuro Acquired Immunodeficiency Syndrome) or HIV (Human Immunodeficiency Virus) associated neuronal abnormality is continuing to be a significant health issue among AIDS patients even under the treatment of combined antiretroviral therapy (cART). Injury and damage to neurons of the brain are the prime causes of neuroAIDS, which happens due to the ingress of HIV by direct permeation across the blood-brain barrier (BBB) or else via peripherally infected macrophage into the central nervous system (CNS). The BBB performs as a stringent barricade for the delivery of therapeutics drugs. The intranasal route of drug administration exhibits as a non-invasive technique to bypass the BBB for the delivery of antiretroviral drugs and other active pharmaceutical ingredients inside the brain and CNS. This method is fruitful for the drugs that are unable to invade the BBB to show its action in the CNS and thus erase the demand of systemic delivery and thereby shrink systemic side effects. Drug delivery from the nose to the brain/CNS takes very less time through both olfactory and trigeminal nerves. Intranasal delivery does not require the involvement of any receptor as it occurs by an extracellular route. Nose to brain delivery also involves nasal associated lymphatic tissues (NALT) and deep cervical lymph nodes. However, very little research has been done to explore the utility of nose to brain delivery of antiretroviral drugs in the treatment of neuroAIDS. This review focuses on the potential of nasal route for the effective delivery of antiretroviral nanoformulations directly from nose to the brain.
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Affiliation(s)
- Anupam Sarma
- Drug Delivery Research Laboratory, Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India.,Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam 781026 India
| | - Malay K Das
- Drug Delivery Research Laboratory, Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh, Assam 786004 India
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12
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Solomon IH, Chettimada S, Misra V, Lorenz DR, Gorelick RJ, Gelman BB, Morgello S, Gabuzda D. White Matter Abnormalities Linked to Interferon, Stress Response, and Energy Metabolism Gene Expression Changes in Older HIV-Positive Patients on Antiretroviral Therapy. Mol Neurobiol 2019; 57:1115-1130. [PMID: 31691183 DOI: 10.1007/s12035-019-01795-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/22/2019] [Indexed: 12/11/2022]
Abstract
Neurocognitive impairment (NCI) remains a significant cause of morbidity in human immunodeficiency virus (HIV)-positive individuals despite highly active antiretroviral therapy (HAART). White matter abnormalities have emerged as a key component of age-related neurodegeneration, and accumulating evidence suggests they play a role in HIV-associated neurocognitive disorders. Viral persistence in the brain induces chronic inflammation associated with lymphocytic infiltration, microglial proliferation, myelin loss, and cerebrovascular lesions. In this study, gene expression profiling was performed on frontal white matter from 34 older HIV+ individuals on HAART (18 with NCI) and 24 HIV-negative controls. We used the NanoString nCounter platform to evaluate 933 probes targeting inflammation, interferon and stress responses, energy metabolism, and central nervous system-related genes. Viral loads were measured using single-copy assays. Compared to HIV- controls, HIV+ individuals exhibited increased expression of genes related to interferon, MHC-1, and stress responses, myeloid cells, and T cells and decreased expression of genes associated with oligodendrocytes and energy metabolism in white matter. These findings correlated with increased white matter inflammation and myelin pallor, suggesting interferon (IRFs, IFITM1, ISG15, MX1, OAS3) and stress response (ATF4, XBP1, CHOP, CASP1, WARS) gene expression changes are associated with decreased energy metabolism (SREBF1, SREBF2, PARK2, TXNIP) and oligodendrocyte myelin production (MAG, MOG), leading to white matter dysfunction. Machine learning identified a 15-gene signature predictive of HIV status that was validated in an independent cohort. No specific gene expression patterns were associated with NCI. These findings suggest therapies that decrease chronic inflammation while protecting mitochondrial function may help to preserve white matter integrity in older HIV+ individuals.
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Affiliation(s)
- Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Sukrutha Chettimada
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Vikas Misra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Benjamin B Gelman
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Susan Morgello
- Department of Neurology, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, CLS 1010, 450 Brookline Ave, Boston, MA, 02215, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, USA.
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13
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Mathews S, Branch Woods A, Katano I, Makarov E, Thomas MB, Gendelman HE, Poluektova LY, Ito M, Gorantla S. Human Interleukin-34 facilitates microglia-like cell differentiation and persistent HIV-1 infection in humanized mice. Mol Neurodegener 2019; 14:12. [PMID: 30832693 PMCID: PMC6399898 DOI: 10.1186/s13024-019-0311-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
Background Microglia are the principal innate immune defense cells of the centeral nervous system (CNS) and the target of the human immunodeficiency virus type one (HIV-1). A complete understanding of human microglial biology and function requires the cell’s presence in a brain microenvironment. Lack of relevant animal models thus far has also precluded studies of HIV-1 infection. Productive viral infection in brain occurs only in human myeloid linage microglia and perivascular macrophages and requires cells present throughout the brain. Once infected, however, microglia become immune competent serving as sources of cellular neurotoxic factors leading to disrupted brain homeostasis and neurodegeneration. Methods Herein, we created a humanized bone-marrow chimera producing human “microglia like” cells in NOD.Cg-PrkdcscidIl2rgtm1SugTg(CMV-IL34)1/Jic mice. Newborn mice were engrafted intrahepatically with umbilical cord blood derived CD34+ hematopoietic stem progenitor cells (HSPC). After 3 months of stable engraftment, animals were infected with HIV-1ADA, a myeloid-specific tropic viral isolate. Virologic, immune and brain immunohistology were performed on blood, peripheral lymphoid tissues, and brain. Results Human interleukin-34 under the control of the cytomegalovirus promoter inserted in NSG mouse strain drove brain reconstitution of HSPC derived peripheral macrophages into microglial-like cells. These human cells expressed canonical human microglial cell markers that included CD14, CD68, CD163, CD11b, ITGB2, CX3CR1, CSFR1, TREM2 and P2RY12. Prior restriction to HIV-1 infection in the rodent brain rested on an inability to reconstitute human microglia. Thus, the natural emergence of these cells from ingressed peripheral macrophages to the brain could allow, for the first time, the study of a CNS viral reservoir. To this end we monitored HIV-1 infection in a rodent brain. Viral RNA and HIV-1p24 antigens were readily observed in infected brain tissues. Deep RNA sequencing of these infected mice and differential expression analysis revealed human-specific molecular signatures representative of antiviral and neuroinflammatory responses. Conclusions This humanized microglia mouse reflected human HIV-1 infection in its known principal reservoir and showed the development of disease-specific innate immune inflammatory and neurotoxic responses mirroring what can occur in an infected human brain. Electronic supplementary material The online version of this article (10.1186/s13024-019-0311-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saumi Mathews
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Amanda Branch Woods
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Ikumi Katano
- Central Institute for Experimental Animals, Kawasaki-ku, Kawasaki, Japan
| | - Edward Makarov
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Midhun B Thomas
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Larisa Y Poluektova
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Mamoru Ito
- Central Institute for Experimental Animals, Kawasaki-ku, Kawasaki, Japan
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985880 Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
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14
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Siangphoe U, Archer KJ, Mukhopadhyay ND. Classical and Bayesian random-effects meta-analysis models with sample quality weights in gene expression studies. BMC Bioinformatics 2019; 20:18. [PMID: 30626315 PMCID: PMC6327440 DOI: 10.1186/s12859-018-2491-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Random-effects (RE) models are commonly applied to account for heterogeneity in effect sizes in gene expression meta-analysis. The degree of heterogeneity may differ due to inconsistencies in sample quality. High heterogeneity can arise in meta-analyses containing poor quality samples. We applied sample-quality weights to adjust the study heterogeneity in the DerSimonian and Laird (DSL) and two-step DSL (DSLR2) RE models and the Bayesian random-effects (BRE) models with unweighted and weighted data, Gibbs and Metropolis-Hasting (MH) sampling algorithms, weighted common effect, and weighted between-study variance. We evaluated the performance of the models through simulations and illustrated application of the methods using Alzheimer's gene expression datasets. RESULTS Sample quality adjusting within study variance (wP6) models provided an appropriate reduction of differentially expressed (DE) genes compared to other weighted functions in classical RE models. The BRE model with a uniform(0,1) prior was appropriate for detecting DE genes as compared to the models with other prior distributions. The precision of DE gene detection in the heterogeneous data was increased with the DSLR2wP6 weighted model compared to the DSLwP6 weighted model. Among the BRE weighted models, the wP6weighted- and unweighted-data models and both Gibbs- and MH-based models performed similarly. The wP6 weighted common-effect model performed similarly to the unweighted model in the homogeneous data, but performed worse in the heterogeneous data. The wP6weighted data were appropriate for detecting DE genes with high precision, while the wP6weighted between-study variance models were appropriate for detecting DE genes with high overall accuracy. Without the weight, when the number of genes in microarray increased, the DSLR2 performed stably, while the overall accuracy of the BRE model was reduced. When applying the weighted models in the Alzheimer's gene expression data, the number of DE genes decreased in all metadata sets with the DSLR2wP6weighted and the wP6weighted between study variance models. Four hundred and forty-six DE genes identified by the wP6weighted between study variance model could be potentially down-regulated genes that may contribute to good classification of Alzheimer's samples. CONCLUSIONS The application of sample quality weights can increase precision and accuracy of the classical RE and BRE models; however, the performance of the models varied depending on data features, levels of sample quality, and adjustment of parameter estimates.
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Affiliation(s)
- Uma Siangphoe
- Office of Biostatistics, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland USA
| | - Kellie J. Archer
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio USA
| | - Nitai D. Mukhopadhyay
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia USA
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15
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Risk Factors and Pathogenesis of HIV-Associated Neurocognitive Disorder: The Role of Host Genetics. Int J Mol Sci 2018; 19:ijms19113594. [PMID: 30441796 PMCID: PMC6274730 DOI: 10.3390/ijms19113594] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023] Open
Abstract
Neurocognitive impairments associated with human immunodeficiency virus (HIV) infection remain a considerable health issue for almost half the people living with HIV, despite progress in HIV treatment through combination antiretroviral therapy (cART). The pathogenesis and risk factors of HIV-associated neurocognitive disorder (HAND) are still incompletely understood. This is partly due to the complexity of HAND diagnostics, as phenotypes present with high variability and change over time. Our current understanding is that HIV enters the central nervous system (CNS) during infection, persisting and replicating in resident immune and supporting cells, with the subsequent host immune response and inflammation likely adding to the development of HAND. Differences in host (human) genetics determine, in part, the effectiveness of the immune response and other factors that increase the vulnerability to HAND. This review describes findings from studies investigating the role of human host genetics in the pathogenesis of HAND, including potential risk factors for developing HAND. The similarities and differences between HAND and Alzheimer's disease are also discussed. While some specific variations in host genes regulating immune responses and neurotransmission have been associated with protection or risk of HAND development, the effects are generally small and findings poorly replicated. Nevertheless, a few specific gene variants appear to affect the risk for developing HAND and aid our understanding of HAND pathogenesis.
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16
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Zhang X, Hu Y, Justice AC, Li B, Wang Z, Zhao H, Krystal JH, Xu K. DNA methylation signatures of illicit drug injection and hepatitis C are associated with HIV frailty. Nat Commun 2017; 8:2243. [PMID: 29269866 PMCID: PMC5740109 DOI: 10.1038/s41467-017-02326-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/20/2017] [Indexed: 01/13/2023] Open
Abstract
Intravenous illicit drug use (IDU) and hepatitis C infection (HCV) commonly co-occur among HIV-infected individuals. These co-occurring conditions may produce interacting epigenetic effects in white blood cells that influence immune function and health outcomes. Here, we report an epigenome-wide association analysis comparing IDU+/ HCV+ and IDU-/HCV- in 386 HIV-infected individuals as a discovery sample and in 412 individuals as a replication sample. We observe 6 significant CpGs in the promoters of 4 genes, NLRC5, TRIM69, CX3CR1, and BCL9, in the discovery sample and in meta-analysis. We identify 19 differentially methylated regions on chromosome 6 harboring MHC gene clusters. Importantly, a panel of IDU+/HCV+-associated CpGs discriminated HIV frailty based upon a validated index with an area under the curve of 79.3% for high frailty and 82.3% for low frailty. These findings suggest that IDU and HCV involve epigenetic programming and that their associated methylation signatures discriminate HIV pathophysiologic frailty.
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Affiliation(s)
- Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Ying Hu
- National Cancer Institute Center for Biomedical Information & Information Technology, 9609 Medical Center Drive, Bethesda, MD, 20850, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
- Yale University School of Medicine, New Haven Veterans Affairs Connecticut Healthcare System, New Haven, CT, 06516, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA.
- VA Connecticut Healthcare System, 950 Campbell Avenue, West Haven, CT, 06516, USA.
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17
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Li W, Gorantla S, Gendelman HE, Poluektova LY. Systemic HIV-1 infection produces a unique glial footprint in humanized mouse brains. Dis Model Mech 2017; 10:1489-1502. [PMID: 29084769 PMCID: PMC5769612 DOI: 10.1242/dmm.031773] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/17/2017] [Indexed: 01/22/2023] Open
Abstract
Studies of innate glial cell responses for progressive human immunodeficiency virus type one (HIV-1) infection are limited by a dearth of human disease-relevant small-animal models. To overcome this obstacle, newborn NOD/SCID/IL2Rγc−/− (NSG) mice were reconstituted with a humanized brain and immune system. NSG animals of both sexes were transplanted with human neuroglial progenitor cells (NPCs) and hematopoietic stem cells. Intraventricular injection of NPCs symmetrically repopulated the mouse brain parenchyma with human astrocytes and oligodendrocytes. Human glia were in periventricular areas, white matter tracts, the olfactory bulb and the brain stem. HIV-1 infection led to meningeal and perivascular human leukocyte infiltration into the brain. Species-specific viral-neuroimmune interactions were identified by deep RNA sequencing. In the corpus callosum and hippocampus of infected animals, overlapping human-specific transcriptional alterations for interferon type 1 and 2 signaling pathways (STAT1, STAT2, IRF9, ISG15, IFI6) and a range of host antiviral responses (MX1, OAS1, RSAD2, BST2, SAMHD1) were observed. Glial cytoskeleton reorganization, oligodendrocyte differentiation and myelin ensheathment (MBP, MOBP, PLP1, MAG, ZNF488) were downregulated. The data sets were confirmed by real-time PCR. These viral defense-signaling patterns paralleled neuroimmune communication networks seen in HIV-1-infected human brains. In this manner, this new mouse model of neuroAIDS can facilitate diagnostic, therapeutic and viral eradication strategies for an infected nervous system. Summary: In mice with a humanized brain and immune system, systemic infection led to human-specific transcriptional induction of glial interferon antiviral innate immune pathways and alteration of neuronal progenitor differentiation and myelination.
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Affiliation(s)
- Weizhe Li
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198-5880, USA
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198-5880, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198-5880, USA
| | - Larisa Y Poluektova
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198-5880, USA
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18
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Fang G, Zhang QH, Tang Q, Jiang Z, Xing S, Li J, Pang Y. Comprehensive analysis of gene expression and DNA methylation datasets identify valuable biomarkers for rheumatoid arthritis progression. Oncotarget 2017; 9:2977-2983. [PMID: 29423022 PMCID: PMC5790439 DOI: 10.18632/oncotarget.22918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/03/2017] [Indexed: 11/29/2022] Open
Abstract
Rheumatoid arthritis (RA) represents a common systemic autoimmune disease which lays chronic and persistent pain on patients. The purpose of our study is to identify novel RA-related genes and biological processes/pathways. All the datasets of this study, including gene expression and DNA methylation datasets of RA and OA samples, were obtained from the free available database, i.e. Gene Expression Omnibus (GEO). We firstly identified the differentially expressed genes (DEGs) between RA and OA samples through the limma package of R programming software followed by the functional enrichment analysis in the Database for Annotation, Visualization and Integrated Discovery (DAVID) for the exploring of potential involved biological processes/pathways of DEGs. For DNA methylation datasets, we used the IMA package for their normalization and identification of differential methylation genes (DMGs) in RA compared with OA samples. Comprehensive analysis of DEGs and DMGs was also conducted for the identification of valuable RA-related biomarkers. As a result, we obtained 394 DEGs and 363 DMGs in RA samples with the thresholds of |log2fold change|> 1 and p-value < 0.05, and |delta beta|> 0.2 and p-value < 0.05 respectively. Functional analysis of DEGs obtained immune and inflammation associated biological processes/pathways. Besides, several valuable biomarkers of RA, including BCL11B, CCDC88C, FCRLA and APOL6, were identified through the integrated analysis of gene expression and DNA methylation datasets. Our study should be helpful for the development of novel drugs and therapeutic methods for RA.
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Affiliation(s)
- Gang Fang
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
| | - Qing Huai Zhang
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
| | - Qianqian Tang
- Department of Rheumatism, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Zuling Jiang
- Department of Zhuang Medicine, The First Affiliated of Guangxi University of Chinese Medicine, Nanning, China
| | - Shasha Xing
- Department of Rheumatism, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Jianying Li
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
| | - Yuzhou Pang
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
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19
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He P, Xia W, Wang L, Wu J, Guo YF, Zeng KQ, Wang MJ, Bing PF, Xie FF, Lu X, Zhang YH, Lei SF, Deng FY. Identification of expression quantitative trait loci (eQTLs) in human peripheral blood mononuclear cells (PBMCs) and shared with liver and brain. J Cell Biochem 2017; 119:1659-1669. [PMID: 28792098 DOI: 10.1002/jcb.26325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 08/02/2017] [Indexed: 12/21/2022]
Abstract
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified. We identified 443 cis- and 2386 trans-eSNPs (FDR <0.05), which regulated 128 and 635 target genes, respectively. A transcriptome-wide expression regulation network was constructed, highlighting the importance of 28 pleiotropic eSNPs and 18 dually (cis- and trans-) regulated genes. Three genes, that is, TIPRL, HSPB8, and EGLN3, were commonly regulated by hundreds of eSNPs and constituted a very complex interaction network. Strikingly, the missense SNP rs371513 trans- regulated 25 target genes, which were functionally related to poly(A) RNA binding. Among 8904 eQTLs (P < 0.001) identified herein in PBMCs, a minority (163) was overlapped with lymphoblastoid, monocytes, liver, and/or brain. Besides, two cis-eSNPs in PBMC were confirmed by AEI. The present results demonstrated a comprehensive expression regulation network for human PBMCs and may provide novel insights into the pathogenesis of immunological diseases related to PBMCs.
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Affiliation(s)
- Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Wei Xia
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Lan Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Jian Wu
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yu-Fan Guo
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ke-Qin Zeng
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ming-Jun Wang
- Department of Rheumatology, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, P. R. China
| | - Peng-Fei Bing
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fang-Fei Xie
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
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20
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Shetty GA, Hattiangady B, Upadhya D, Bates A, Attaluri S, Shuai B, Kodali M, Shetty AK. Chronic Oxidative Stress, Mitochondrial Dysfunction, Nrf2 Activation and Inflammation in the Hippocampus Accompany Heightened Systemic Inflammation and Oxidative Stress in an Animal Model of Gulf War Illness. Front Mol Neurosci 2017; 10:182. [PMID: 28659758 PMCID: PMC5469946 DOI: 10.3389/fnmol.2017.00182] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/26/2017] [Indexed: 01/21/2023] Open
Abstract
Memory and mood dysfunction are the key symptoms of Gulf war illness (GWI), a lingering multi-symptom ailment afflicting >200,000 veterans who served in the Persian Gulf War-1. Research probing the source of the disease has demonstrated that concomitant exposures to anti-nerve gas agent pyridostigmine bromide (PB), pesticides, and war-related stress are among the chief causes of GWI. Indeed, exposures to GWI-related chemicals (GWIR-Cs) and mild stress in animal models cause memory and mood impairments alongside reduced neurogenesis and chronic low-level inflammation in the hippocampus. In the current study, we examined whether exposure to GWIR-Cs and stress causes chronic changes in the expression of genes related to increased oxidative stress, mitochondrial dysfunction, and inflammation in the hippocampus. We also investigated whether GWI is linked with chronically increased activation of Nrf2 (a master regulator of antioxidant response) in the hippocampus, and inflammation and enhanced oxidative stress at the systemic level. Adult male rats were exposed daily to low-doses of PB and pesticides (DEET and permethrin), in combination with 5 min of restraint stress for 4 weeks. Analysis of the hippocampus performed 6 months after the exposure revealed increased expression of many genes related to oxidative stress response and/or antioxidant activity (Hmox1, Sepp1, and Srxn1), reactive oxygen species metabolism (Fmo2, Sod2, and Ucp2) and oxygen transport (Ift172 and Slc38a1). Furthermore, multiple genes relevant to mitochondrial respiration (Atp6a1, Cox6a1, Cox7a2L, Ndufs7, Ndufv1, Lhpp, Slc25a10, and Ucp1) and neuroinflammation (Nfkb1, Bcl6, Csf2, IL6, Mapk1, Mapk3, Ngf, N-pac, and Prkaca) were up-regulated, alongside 73–88% reduction in the expression of anti-inflammatory genes IL4 and IL10, and nuclear translocation and increased expression of Nrf2 protein. These hippocampal changes were associated with elevated levels of pro-inflammatory cytokines and chemokines (Tnfa, IL1b, IL1a, Tgfb, and Fgf2) and lipid peroxidation byproduct malondialdehyde in the serum, suggesting the presence of an incessant systemic inflammation and elevated oxidative stress. These results imply that chronic oxidative stress, inflammation, and mitochondrial dysfunction in the hippocampus, and heightened systemic inflammation and oxidative stress likely underlie the persistent memory and mood dysfunction observed in GWI.
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Affiliation(s)
- Geetha A Shetty
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Bharathi Hattiangady
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Dinesh Upadhya
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Adrian Bates
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Sahithi Attaluri
- Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Bing Shuai
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Maheedhar Kodali
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
| | - Ashok K Shetty
- Research Service, Olin E. Teague Veterans' Medical Center, Central Texas Veterans Health Care System, TempleTX, United States.,Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple and College StationTX, United States.,Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College StationTX, United States
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21
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Wong YY, Johnson B, Friedrich TC, Trepanier LA. Hepatic expression profiles in retroviral infection: relevance to drug hypersensitivity risk. Pharmacol Res Perspect 2017; 5:e00312. [PMID: 28603631 PMCID: PMC5464341 DOI: 10.1002/prp2.312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/11/2022] Open
Abstract
HIV‐infected patients show a markedly increased risk of delayed hypersensitivity (HS) reactions to potentiated sulfonamide antibiotics (trimethoprim/sulfamethoxazole or TMP/SMX). Some studies have suggested altered SMX biotransformation in HIV infection, but hepatic biotransformation pathways have not been evaluated directly. Systemic lupus erythematosus (SLE) is another chronic inflammatory disease with a higher incidence of sulfonamide HS, but it is unclear whether retroviral infection and SLE share risk factors for drug HS. We hypothesized that retroviral infection would lead to dysregulation of hepatic pathways of SMX biotransformation, as well as pathway alterations in common with SLE that could contribute to drug HS risk. We characterized hepatic expression profiles and enzymatic activities in an SIV‐infected macaque model of retroviral infection, and found no evidence for dysregulation of sulfonamide drug biotransformation pathways. Specifically, NAT1,NAT2,CYP2C8,CYP2C9,CYB5R3,MARC1/2, and glutathione‐related genes (GCLC,GCLM,GSS,GSTM1, and GSTP1) were not differentially expressed in drug naïve SIVmac239‐infected male macaques compared to age‐matched controls, and activities for SMX N‐acetylation and SMX hydroxylamine reduction were not different. However, multiple genes that are reportedly over‐expressed in SLE patients were also up‐regulated in retroviral infection, to include enhanced immunoproteasomal processing and presentation of antigens as well as up‐regulation of gene clusters that may be permissive to autoimmunity. These findings support the hypothesis that pathways downstream from drug biotransformation may be primarily important in drug HS risk in HIV infection.
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Affiliation(s)
- Yat Yee Wong
- Department of Medical Sciences School of Veterinary Medicine Madison Wisconsin
| | - Brian Johnson
- Molecular and Environmental Toxicology Center School of Medicine and Public Health University of Wisconsin-Madison Madison Wisconsin
| | - Thomas C Friedrich
- Department of Pathobiological Sciences School of Veterinary Medicine Madison Wisconsin.,AIDS Vaccine Research Laboratory Wisconsin National Primate Research Center Madison Wisconsin
| | - Lauren A Trepanier
- Department of Medical Sciences School of Veterinary Medicine Madison Wisconsin
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22
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Corley MJ, Dye C, D'Antoni ML, Byron MM, Yo KLA, Lum-Jones A, Nakamoto B, Valcour V, SahBandar I, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment. Sci Rep 2016; 6:33310. [PMID: 27629381 PMCID: PMC5024304 DOI: 10.1038/srep33310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 08/24/2016] [Indexed: 11/20/2022] Open
Abstract
Monocytes/macrophages contribute to the neuropathogenesis of HIV-related cognitive impairment (CI); however, considerable gaps in our understanding of the precise mechanisms driving this relationship remain. Furthermore, whether a distinct biological profile associated with HIV-related CI resides in immune cell populations remains unknown. Here, we profiled DNA methylomes and transcriptomes of monocytes derived from HIV-infected individuals with and without CI using genome-wide DNA methylation and gene expression profiling. We identified 1,032 CI-associated differentially methylated loci in monocytes. These loci related to gene networks linked to the central nervous system (CNS) and interactions with HIV. Most (70.6%) of these loci exhibited higher DNA methylation states in the CI group and were preferentially distributed over gene bodies and intergenic regions of the genome. CI-associated DNA methylation states at 12 CpG sites associated with neuropsychological testing performance scores. CI-associated DNA methylation also associated with gene expression differences including CNS genes CSRNP1 (P = 0.017), DISC1 (P = 0.012), and NR4A2 (P = 0.005); and a gene known to relate to HIV viremia, THBS1 (P = 0.003). This discovery cohort data unveils cell type-specific DNA methylation patterns related to HIV-associated CI and provide an immunoepigenetic DNA methylation “signature” potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against CI.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Christian Dye
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Michelle L D'Antoni
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Mary Margaret Byron
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Kaahukane Leite-Ah Yo
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Beau Nakamoto
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ivo SahBandar
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Cecilia M Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA.,Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
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23
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Mariani E, Frabetti F, Tarozzi A, Pelleri MC, Pizzetti F, Casadei R. Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PLoS One 2016; 11:e0161567. [PMID: 27611585 PMCID: PMC5017670 DOI: 10.1371/journal.pone.0161567] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023] Open
Abstract
The understanding of the genetic basis of the Parkinson's disease (PD) and the correlation between genotype and phenotype has revolutionized our knowledge about the pathogenetic mechanisms of neurodegeneration, opening up exciting new therapeutic and neuroprotective perspectives. Genomic knowledge of PD is still in its early stages and can provide a good start for studies of the molecular mechanisms that underlie the gene expression variations and the epigenetic mechanisms that may contribute to the complex and characteristic phenotype of PD. In this study we used the software TRAM (Transcriptome Mapper) to analyse publicly available microarray data of a total of 151 PD patients and 130 healthy controls substantia nigra (SN) samples, to identify chromosomal segments and gene loci differential expression. In particular, we separately analyzed PD patients and controls data from post-mortem snap-frozen SN whole tissue and from laser microdissected midbrain dopamine (DA) neurons, to better characterize the specific DA neuronal expression profile associated with the late-stage Parkinson's condition. The default "Map" mode analysis resulted in 10 significantly over/under-expressed segments, mapping on 8 different chromosomes for SN whole tissue and in 4 segments mapping on 4 different chromosomes for DA neurons. In conclusion, TRAM software allowed us to confirm the deregulation of some genomic regions and loci involved in key molecular pathways related to neurodegeneration, as well as to provide new insights about genes and non-coding RNA transcripts not yet associated with the disease.
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Affiliation(s)
- Elisa Mariani
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Flavia Frabetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Andrea Tarozzi
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
| | - Maria Chiara Pelleri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Fabrizio Pizzetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Raffaella Casadei
- Department for Life Quality Studies, University of Bologna, Rimini, Italy
- * E-mail:
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