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Xie Q, Dasari R, Namba MD, Buck LA, Side CM, Park K, Jackson JG, Barker JM. Astrocytic regulation of cocaine locomotor sensitization in EcoHIV infected mice. Neuropharmacology 2024; 265:110245. [PMID: 39631679 DOI: 10.1016/j.neuropharm.2024.110245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 10/30/2024] [Accepted: 11/30/2024] [Indexed: 12/07/2024]
Abstract
Cocaine use disorder (CUD) is highly comorbid with HIV infection and worsens HIV outcomes. Preclinical research on the outcomes of HIV infection may yield crucial information on neurobehavioral changes resulting from chronic drug exposure in people living with HIV (PLWH). Repeated exposure to cocaine alters behavioral responses to cocaine. This includes development of cocaine locomotor sensitization - or increased locomotor responses to the same doses of cocaine - which depends on nucleus accumbens (NAc) neural plasticity. NAc astrocytes are key regulators of neural activity and plasticity, and their function can be impaired by cocaine exposure and HIV infection, thus implicating them as potential regulators of HIV-induced changes in behavioral response to cocaine. To characterize the effects of HIV infection on cocaine locomotor sensitization, we employed the EcoHIV mouse model in male and female mice to assess changes in locomotor responses after repeated cocaine (10 mg/kg) exposure and challenge. EcoHIV infection potentiated expression of cocaine sensitization. We also identified EcoHIV-induced increases in expression of the astrocytic nuclear marker Sox9 selectively in the NAc core. To investigate whether modulation of NAc astrocytes could reverse EcoHIV-induced deficits, we employed a chemogenetic approach. We found that chemogenetic activation of NAc astrocyte Gq signaling attenuated EcoHIV-enhanced cocaine sensitization. We propose that HIV infection contributes to cocaine behavioral sensitization and induces adaptations in NAc astrocytes, while promoting NAc astrocytic Gq-signaling can recover EcoHIV-induced behavioral changes. These findings identify potential cellular substrates of disordered cocaine-driven behavior in the context of HIV infection and point toward strategies to reduce cocaine-related behavior in PLWH.
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Affiliation(s)
- Qiaowei Xie
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA; Graduate Program in Pharmacology and Physiology, Drexel University College of Medicine, USA
| | - Rohan Dasari
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA
| | - Mark D Namba
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA
| | - Lauren A Buck
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA
| | - Christine M Side
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA
| | - Kyewon Park
- University of Pennsylvania Center for AIDS Research, USA
| | - Joshua G Jackson
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA
| | - Jacqueline M Barker
- Department of Pharmacology and Physiology, Drexel University College of Medicine, USA.
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Xie Q, Dasari R, Namba MD, Buck LA, Side CM, Park K, Jackson JG, Barker JM. Astrocytic Regulation of Cocaine Locomotor Sensitization in EcoHIV Infected Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611213. [PMID: 39282274 PMCID: PMC11398419 DOI: 10.1101/2024.09.04.611213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
Abstract
Cocaine use disorder (CUD) is highly comorbid with HIV infection and worsens HIV outcomes. Preclinical research on the outcomes of HIV infection may yield crucial information on neurobehavioral changes resulting from chronic drug exposure in people living with HIV (PLWH). Repeated exposure to cocaine alters behavioral responses to cocaine. This includes development of cocaine locomotor sensitization - or increased locomotor responses to the same doses of cocaine - which depends on nucleus accumbens (NAc) neural plasticity. NAc astrocytes are key regulators of neural activity and plasticity, and their function can be impaired by cocaine exposure and HIV infection, thus implicating them as potential regulators of HIV-induced changes in behavioral response to cocaine. To characterize the effects of HIV infection on cocaine locomotor sensitization, we employed the EcoHIV mouse model to assess changes in locomotor responses after repeated cocaine (10mg/kg) exposure and challenge. EcoHIV infection potentiated expression of cocaine sensitization. We also identified EcoHIV-induced increases in expression of the astrocytic nuclear marker Sox9 selectively in the NAc core. To investigate whether modulation of NAc astrocytes could reverse EcoHIV-induced deficits, we employed a chemogenetic approach. We found that chemogenetic activation of NAc astrocyte Gq signaling attenuated EcoHIV-enhanced cocaine sensitization. We propose that HIV infection contributes to cocaine behavioral sensitization and induces adaptations in NAc astrocytes, while promoting NAc astrocytic Gq-signaling can recover EcoHIV-induced behavioral changes. These findings identify potential cellular substrates of disordered cocaine-driven behavior in the context of HIV infection and point toward strategies to reduce cocaine-related behavior in PLWH.
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Van Duyne R, Irollo E, Lin A, Johnson JA, Guillem AM, O’Brien EV, Merja L, Nash B, Jackson JG, Sarkar A, Klase ZA, Meucci O. Adult Human Brain Tissue Cultures to Study NeuroHIV. Cells 2024; 13:1127. [PMID: 38994979 PMCID: PMC11240386 DOI: 10.3390/cells13131127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/11/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
HIV-associated neurocognitive disorders (HAND) persist under antiretroviral therapy as a complex pathology that has been difficult to study in cellular and animal models. Therefore, we generated an ex vivo human brain slice model of HIV-1 infection from surgically resected adult brain tissue. Brain slice cultures processed for flow cytometry showed >90% viability of dissociated cells within the first three weeks in vitro, with parallel detection of astrocyte, myeloid, and neuronal populations. Neurons within brain slices showed stable dendritic spine density and mature spine morphologies in the first weeks in culture, and they generated detectable activity in multi-electrode arrays. We infected cultured brain slices using patient-matched CD4+ T-cells or monocyte-derived macrophages (MDMs) that were exposed to a GFP-expressing R5-tropic HIV-1 in vitro. Infected slice cultures expressed viral RNA and developed a spreading infection up to 9 days post-infection, which were significantly decreased by antiretrovirals. We also detected infected myeloid cells and astrocytes within slices and observed minimal effect on cellular viability over time. Overall, this human-centered model offers a promising resource to study the cellular mechanisms contributing to HAND (including antiretroviral toxicity, substance use, and aging), infection of resident brain cells, and new neuroprotective therapeutics.
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Affiliation(s)
- Rachel Van Duyne
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Elena Irollo
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Angel Lin
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - James A. Johnson
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Alain M. Guillem
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Erick V. O’Brien
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Laura Merja
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Bradley Nash
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Joshua G. Jackson
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Atom Sarkar
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Neurosurgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Global Neurosciences Institute, LLC, Philadelphia, PA 19107, USA
| | - Zachary A. Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Neuroimmunology and CNS Therapeutics, Institute for Molecular Medicine and Infectious Diseases, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Olimpia Meucci
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Center for Neuroimmunology and CNS Therapeutics, Institute for Molecular Medicine and Infectious Diseases, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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Bransfield RC, Goud Gadila SK, Kursawe LJ, Dwork AJ, Rosoklija G, Horn EJ, Cook MJ, Embers ME. Late-stage borreliosis and substance abuse. Heliyon 2024; 10:e31159. [PMID: 38779029 PMCID: PMC11108998 DOI: 10.1016/j.heliyon.2024.e31159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Background Infectious diseases can contribute to substance abuse. Here, a fatal case of borreliosis and substance abuse is reported. This patient had a history of multiple tick bites and increasing multisystem symptoms, yet diagnosis and treatment were delayed. He experimented with multiple substances including phencyclidine (PCP), an N-methyl-d-aspartate (NMDA) receptor antagonist that opposes NMDA agonism caused by Borrelia infection. During PCP withdrawal, he committed one homicide, two assaults, and suicide. Methods Brain tissue was obtained from autopsy and stained for microglial activation and quinolinic acid (QA). Immunoflouresence (IFA) and fluorescence in situ hybridization (FISH) were used to identify the presence of pathogens in autopsy tissue. Results Autopsy tissue evaluation demonstrated Borrelia in the pancreas by IFA and heart by IFA and FISH. Activated microglia and QA were found in the brain, indicating neuroinflammation. It is postulated that PCP withdrawal may exacerbate symptoms produced by Borrelia-induced biochemical imbalances in the brain. This combination may have greatly increased his acute homicidal and suicidal risk. Patient databases also demonstrated the risk of homicide or suicide in patients diagnosed with borreliosis and confirmed multiple symptoms in these patients, including chronic pain, anxiety, and anhedonia. Conclusions Late-stage borreliosis is associated with multiple symptoms that may contribute to an increased risk of substance abuse and addictive disorders. More effective diagnosis and treatment of borreliosis, and attention to substance abuse potential may help reduce associated morbidity and mortality in patients with borreliosis, particularly in endemic areas.
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Affiliation(s)
- Robert C. Bransfield
- Rutgers-RWJ Medical School, Piscataway, NJ, USA. Hackensack Meridian Health-School of Medicine, Nutley, NJ, USA
| | - Shiva Kumar Goud Gadila
- Division of Immunology, Tulane National Primate Research Center, Tulane University Health Sciences, Covington, LA, USA
| | - Laura J. Kursawe
- Charité – Universitatsmedizin Berlin, Corporate Member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Andrew J. Dwork
- Department of Psychiatry, Columbia University, New York, NY, United States. Division of Molecular Imaging and Neuropathology, New York, USA
- State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Gorazd Rosoklija
- State Psychiatric Institute, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | | | | | - Monica E. Embers
- Division of Immunology, Tulane National Primate Research Center, Tulane University Health Sciences, Covington, LA, USA
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Xie Q, Namba MD, Buck LA, Park K, Jackson JG, Barker JM. Effects of Antiretroviral Treatment on Central and Peripheral Immune Response in Mice with EcoHIV Infection. Cells 2024; 13:882. [PMID: 38786105 PMCID: PMC11120433 DOI: 10.3390/cells13100882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
HIV infection is an ongoing global health issue, despite increased access to antiretroviral therapy (ART). People living with HIV (PLWH) who are virally suppressed through ART still experience negative health outcomes, including neurocognitive impairment. It is increasingly evident that ART may act independently or in combination with HIV infection to alter the immune state, though this is difficult to disentangle in the clinical population. Thus, these experiments used multiplexed chemokine/cytokine arrays to assess peripheral (plasma) and brain (nucleus accumbens; NAc) expression of immune targets in the presence and absence of ART treatment in the EcoHIV mouse model. The findings identify the effects of EcoHIV infection and of treatment with bictegravir (B), emtricitabine (F), and tenofovir alafenamide (TAF) on the expression of numerous immune targets. In the NAc, this included EcoHIV-induced increases in IL-1α and IL-13 expression and B/F/TAF-induced reductions in KC/CXCL1. In the periphery, EcoHIV suppressed IL-6 and LIF expression, while B/F/TAF reduced IL-12p40 expression. In the absence of ART, IBA-1 expression was negatively correlated with CX3CL1 expression in the NAc of EcoHIV-infected mice. These findings identify distinct effects of ART and EcoHIV infection on peripheral and central immune factors and emphasize the need to consider ART effects on neural and immune outcomes.
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Affiliation(s)
- Qiaowei Xie
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA; (Q.X.); (M.D.N.); (L.A.B.); (J.G.J.)
- Graduate Program in Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Mark D. Namba
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA; (Q.X.); (M.D.N.); (L.A.B.); (J.G.J.)
| | - Lauren A. Buck
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA; (Q.X.); (M.D.N.); (L.A.B.); (J.G.J.)
| | - Kyewon Park
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Joshua G. Jackson
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA; (Q.X.); (M.D.N.); (L.A.B.); (J.G.J.)
| | - Jacqueline M. Barker
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19102, USA; (Q.X.); (M.D.N.); (L.A.B.); (J.G.J.)
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Namba MD, Xie Q, Park K, Jackson JG, Barker JM. EcoHIV Infection Modulates the Effects of Cocaine Exposure Pattern and Abstinence on Cocaine Seeking and Neuroimmune Protein Expression in Male Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589615. [PMID: 38659915 PMCID: PMC11042347 DOI: 10.1101/2024.04.15.589615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cocaine use disorders (CUDs) and human immunodeficiency virus (HIV) remain persistent public health dilemmas throughout the world. One major hurdle for treating CUD is the increase in cocaine craving and seeking behavior that occurs over a protracted period of abstinence, an effect known as the incubation of craving. Little is known about how HIV may modulate this process. Thus, we sought to examine the impact of chronic HIV infection on the incubation of cocaine craving and associated changes in the central and peripheral immune systems. Here, mice were inoculated with EcoHIV, which is a chimeric HIV-1 construct that produces chronic HIV infection in mice. EcoHIV- and sham-infected mice were conditioned with cocaine daily or intermittently in a conditioned place preference (CPP) paradigm, followed by 1 or 21 days of forced abstinence prior to assessing preference for the cocaine-paired chamber. Under both conditioning regimens, sham mice exhibited incubation of cocaine CPP after 21 days of abstinence. EcoHIV-infected mice conditioned daily with cocaine showed enhanced cocaine seeking at both abstinence timepoints, whereas infected mice conditioned intermittently showed a reversal of the incubation effect, with higher cocaine seeking after 1 day of abstinence compared to 21 days. Analysis of corticolimbic CX3CL1-CX3CR1 and glutamate receptor expression revealed alterations in medial prefrontal cortex (mPFC) CX3CL1 and nucleus accumbens (NAc) GluN2A receptors that correlated with cocaine seeking following daily cocaine exposure. Moreover, examination of peripheral immune markers showed that the effect of abstinence and EcoHIV infection on these measures depended on the cocaine exposure regimen. Altogether, these results highlight the importance of cocaine abstinence and exposure pattern as critical variables that modulate HIV-associated neuroimmune outcomes and relapse vulnerability.
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Affiliation(s)
- Mark D. Namba
- Department of Pharmacology & Physiology, College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Qiaowei Xie
- Department of Pharmacology & Physiology, College of Medicine, Drexel University, Philadelphia, PA, USA
- Graduate Program in Pharmacology and Physiology, College of Medicine, Drexel University
| | - Kyewon Park
- Center for AIDS Research (CFAR), University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua G. Jackson
- Department of Pharmacology & Physiology, College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Jacqueline M. Barker
- Department of Pharmacology & Physiology, College of Medicine, Drexel University, Philadelphia, PA, USA
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Xie Q, Namba MD, Buck LA, Park K, Jackson JG, Barker JM. Effects of antiretroviral treatment on central and peripheral immune response in mice with EcoHIV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.589109. [PMID: 38645059 PMCID: PMC11030421 DOI: 10.1101/2024.04.11.589109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
HIV infection is an ongoing global health issue despite increased access to antiretroviral therapy (ART). People living with HIV (PLWH) who are virally suppressed through ART still experience negative health outcomes, including neurocognitive impairment. It is increasingly evident that ART may act independently or in combination with HIV infection to alter immune state, though this is difficult to disentangle in the clinical population. Thus, these experiments used multiplexed chemokine/cytokine arrays to assess peripheral (plasma) and brain (nucleus accumbens; NAc) expression of immune targets in the presence and absence of ART treatment in the EcoHIV mouse model. The findings identify effects of EcoHIV infection and of treatment with bictegravir (B), emtricitabine (F) and tenofovir alafenamide (TAF) on expression of numerous immune targets. In the NAc, this included EcoHIV-induced increases in IL-1α and IL-13 expression and B/F/TAF-induced reductions in KC/CXCL1. In the periphery, EcoHIV suppressed IL-6 and LIF expression, while B/F/TAF reduced IL-12p40 expression. In absence of ART, IBA-1 expression was negatively correlated with CX3CL1 expression in the NAc of EcoHIV-infected mice. These findings identify distinct effects of ART and EcoHIV infection on peripheral and central immune factors and emphasize the need to consider ART effects on neural and immune outcomes.
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Buck LA, Xie Q, Willis M, Side CM, Giacometti LL, Gaskill PJ, Park K, Shaheen F, Guo L, Gorantla S, Barker JM. Impaired extinction of cocaine seeking in HIV-infected mice is accompanied by peripheral and central immune dysregulation. Commun Biol 2024; 7:387. [PMID: 38553542 PMCID: PMC10980811 DOI: 10.1038/s42003-024-06079-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/20/2024] [Indexed: 04/01/2024] Open
Abstract
Substance use disorders (SUDs) are highly comorbid with HIV infection, necessitating an understanding of the interactive effects of drug exposure and HIV. The relationship between HIV infection and cocaine use disorder is likely bidirectional, with cocaine use directly impacting immune function while HIV infection alters addiction-related behavior. To better characterize the neurobehavioral and immune consequences of HIV infection and cocaine exposure, this study utilizes a humanized mouse model to investigate the outcomes of HIV-1 infection on cocaine-related behaviors in a conditioned place preference (CPP) model, and the interactive effects of cocaine and HIV infection on peripheral and central nervous system inflammation. HIV infection selectively impairs cocaine CPP extinction without effecting reinstatement or cocaine seeking under conflict. Behavioral alterations are accompanied by immune changes in HIV infected mice, including increased prefrontal cortex astrocyte immunoreactivity and brain-region specific effects on microglia number and reactivity. Peripheral immune system changes are observed in human cytokines, including HIV-induced reductions in human TNFα, and cocaine and HIV interactions on GM-CSF levels. Together these data provide new insights into the unique neurobehavioral outcomes of HIV infection and cocaine exposure and how they interact to effect immune responses.
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Affiliation(s)
- Lauren A Buck
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Qiaowei Xie
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
- Graduate Program in Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michelle Willis
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Christine M Side
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Laura L Giacometti
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Peter J Gaskill
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Kyewon Park
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Farida Shaheen
- Center for AIDS Research, University of Pennsylvania, Philadelphia, PA, USA
| | - Lili Guo
- Medical Center, University of Nebraska, Omaha, NE, USA
| | | | - Jacqueline M Barker
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, USA.
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Li X, Qian Y, Hu Y, Chen J, Yue H, Deng L. MSF-PFP: A Novel Multisource Feature Fusion Model for Protein Function Prediction. J Chem Inf Model 2024; 64:1502-1511. [PMID: 38413369 DOI: 10.1021/acs.jcim.3c01794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Protein function prediction is essential for disease treatment and drug development; yet, traditional biological experimental methods are less efficient in annotating protein function, and existing automated methods fail to fully leverage protein multisource data. Here, we present MSF-PFP, a computational framework that fuses multisource data features to predict protein function with high accuracy. Our framework designs specific models for feature extraction based on the characteristics of various data sources, including a global-local-individual strategy for local location features. MSF-PFP then integrates extracted features through a multisource feature fusion model, ultimately categorizing protein functions. Experimental results demonstrate that MSF-PFP outperforms eight state-of-the-art models, achieving FMax scores of 0.542, 0.675, and 0.624 for the biological process (BP), molecular function (MF), and cellular component (CC), respectively. The source code and data set for MSF-PFP are available at https://swanhub.co/TianGua/MSF-PFP, facilitating further exploration and validation of the proposed framework. This study highlights the potential of multisource data fusion in enhancing protein function prediction, contributing to improved disease therapy and medication discovery strategies.
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Affiliation(s)
- Xinhui Li
- School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Signal Detection and Processing in Xinjiang Uygur Autonomous Region, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Yurong Qian
- School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Signal Detection and Processing in Xinjiang Uygur Autonomous Region, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Yue Hu
- School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Signal Detection and Processing in Xinjiang Uygur Autonomous Region, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Jiaying Chen
- School of Software, Xinjiang University, Urumqi 830091, China
- Key Laboratory of Signal Detection and Processing in Xinjiang Uygur Autonomous Region, Xinjiang University, Urumqi 830046, China
- Key Laboratory of Software Engineering, Xinjiang University, Urumqi 830091, China
| | - Haitao Yue
- School of Future Technology, Xinjiang University, Urumqi 830017, China
- Laboratory of Synthetic Biology, School of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Lei Deng
- School of Software, Xinjiang University, Urumqi 830091, China
- School of Computer Science and Engineering, Central South University, Changsha 410083, China
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