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Raines SLM, Falcinelli SD, Peterson JJ, Van Gulck E, Allard B, Kirchherr J, Vega J, Najera I, Boden D, Archin NM, Margolis DM. Nanoparticle delivery of Tat synergizes with classical latency reversal agents to express HIV antigen targets. Antimicrob Agents Chemother 2024; 68:e0020124. [PMID: 38829049 PMCID: PMC11232404 DOI: 10.1128/aac.00201-24] [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: 02/05/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Limited cellular levels of the HIV transcriptional activator Tat are one contributor to proviral latency that might be targeted in HIV cure strategies. We recently demonstrated that lipid nanoparticles containing HIV tat mRNA induce HIV expression in primary CD4 T cells. Here, we sought to further characterize tat mRNA in the context of several benchmark latency reversal agents (LRAs), including inhibitor of apoptosis protein antagonists (IAPi), bromodomain and extra-Terminal motif inhibitors (BETi), and histone deacetylase inhibitors (HDACi). tat mRNA reversed latency across several different cell line models of HIV latency, an effect dependent on the TAR hairpin loop. Synergistic enhancement of tat mRNA activity was observed with IAPi, HDACi, and BETi, albeit to variable degrees. In primary CD4 T cells from durably suppressed people with HIV, tat mRNA profoundly increased the frequencies of elongated, multiply-spliced, and polyadenylated HIV transcripts, while having a lesser impact on TAR transcript frequencies. tat mRNAs alone resulted in variable HIV p24 protein induction across donors. However, tat mRNA in combination with IAPi, BETi, or HDACi markedly enhanced HIV RNA and protein expression without overt cytotoxicity or cellular activation. Notably, combination regimens approached or in some cases exceeded the latency reversal activity of maximal mitogenic T cell stimulation. Higher levels of tat mRNA-driven HIV p24 induction were observed in donors with larger mitogen-inducible HIV reservoirs, and expression increased with prolonged exposure time. Combination LRA strategies employing both small molecule inhibitors and Tat delivered to CD4 T cells are a promising approach to effectively target the HIV reservoir.
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Affiliation(s)
- Samuel L. M. Raines
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shane D. Falcinelli
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jackson J. Peterson
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ellen Van Gulck
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Brigitte Allard
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jerel Vega
- Arcturus Therapeutics, Science Center Drive, San Diego, California, USA
| | - Isabel Najera
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Daniel Boden
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Nancie M. Archin
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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2
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Levinger C, Natalie Howard J, Bosque A. An Ultrasensitive p24 Assay to Measure HIV-1 in Diverse Biological Matrixes. Methods Mol Biol 2024; 2807:343-354. [PMID: 38743239 DOI: 10.1007/978-1-0716-3862-0_23] [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] [Indexed: 05/16/2024]
Abstract
Assays to study HIV persistence are crucial to evaluate therapeutic strategies aimed toward an HIV cure. Several assays have been developed to date that rely on the measurement of nucleic acids. In recent years, the advancement of ultrasensitive technologies for the detection of proteins has improved our understanding of the role of translation-competent reservoirs in HIV persistence. In this chapter, we describe the development of an ultrasensitive p24 ELISA that uses planar array technology. This assay allows for the detection of HIV-1 p24 in the low fg/ml range in different biological matrixes, including cell lysates. This assay can be used to investigate the efficacy of latency reversing agents to reactivate HIV or to evaluate the persistence of translation-competent reservoirs in people living with HIV (PWH) in cells or diverse biological fluids.
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Affiliation(s)
- Callie Levinger
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, USA
| | - J Natalie Howard
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Alberto Bosque
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington, DC, USA.
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3
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Kuzmichev YV, Lackman-Smith C, Bakkour S, Wiegand A, Bale MJ, Musick A, Bernstein W, Aronson N, Ake J, Tovanabutra S, Stone M, Ptak RG, Kearney MF, Busch MP, Wonderlich ER, Kulpa DA. Application of ultrasensitive digital ELISA for p24 enables improved evaluation of HIV-1 reservoir diversity and growth kinetics in viral outgrowth assays. Sci Rep 2023; 13:10958. [PMID: 37414788 PMCID: PMC10326067 DOI: 10.1038/s41598-023-37223-9] [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: 08/22/2022] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
The advent of combined antiretroviral therapy (cART) has been instrumental in controlling HIV-1 replication and transmission and decreasing associated morbidity and mortality. However, cART alone is not able to cure HIV-1 due to the presence of long-lived, latently infected immune cells, which re-seed plasma viremia when cART is interrupted. Assessment of HIV-cure strategies using ex vivo culture methods for further understanding of the diversity of reactivated HIV, viral outgrowth, and replication dynamics are enhanced using ultrasensitive digital ELISA based on single-molecule array (Simoa) technology to increase the sensitivity of endpoint detection. In viral outgrowth assays (VOA), exponential HIV-1 outgrowth has been shown to be dependent upon initial virus burst size surpassing a critical growth threshold of 5100 HIV-1 RNA copies. Here, we show an association between ultrasensitive HIV-1 Gag p24 concentrations and HIV-1 RNA copy number that characterize viral dynamics below the exponential replication threshold. Single-genome sequencing (SGS) revealed the presence of multiple identical HIV-1 sequences, indicative of low-level replication occurring below the threshold of exponential outgrowth early during a VOA. However, SGS further revealed diverse related HIV variants detectable by ultrasensitive methods that failed to establish exponential outgrowth. Overall, our data suggest that viral outgrowth occurring below the threshold necessary for establishing exponential growth in culture does not preclude replication competence of reactivated HIV, and ultrasensitive detection of HIV-1 p24 may provide a method to detect previously unquantifiable variants. These data strongly support the use of the Simoa platform in a multi-prong approach to measuring latent viral burden and efficacy of therapeutic interventions aimed at an HIV-1 cure.
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Affiliation(s)
- Yury V Kuzmichev
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA.
| | - Carol Lackman-Smith
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Sonia Bakkour
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael J Bale
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew Musick
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Wendy Bernstein
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Naomi Aronson
- Uniformed Services University, Bethesda, MD, USA
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Julie Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Roger G Ptak
- Department of Infectious Disease Research, Southern Research, Frederick, MD, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, NCI at Frederick, NIH, Frederick, MD, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Deanna A Kulpa
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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4
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Wu Y, Fu Y, Guo J, Guo J. Single-molecule immunoassay technology: Recent advances. Talanta 2023; 265:124903. [PMID: 37418954 DOI: 10.1016/j.talanta.2023.124903] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/09/2023]
Abstract
Detecting diseases at the molecular level aids in early diagnosis and treatment. However, traditional immunological detection techniques, such as enzyme-linked immunosorbent assay (ELISA) and chemiluminescence, have detection sensitivities between 10-16 and 10-12 mol/L, which are inadequate for early diagnosis. Single-molecule immunoassays can reach detection sensitivities of 10-18 mol/L and can detect biomarkers that are difficult to measure using conventional detection techniques. It can confine molecules to be detected in a small spatial area and provide absolute counting of the detected signal, offering the advantage of high efficiency and accuracy. Herein, we demonstrate the principles and equipment of two single-molecule immunoassay techniques and discuss their applications. It is shown that the detection sensitivity can be improved by 2-3 orders of magnitude compared to common chemiluminescence or ELISA assays. The microarray-based single-molecule immunoassay technique can test 66 samples in 1 h, which is more efficient than conventional immunological detection techniques. In contrast, microdroplet-based single-molecule immunoassay techniques can generate 107 droplets in 10 min, which is more than 100 times faster than a single droplet generator. By comparing the two single-molecule immunoassay techniques, we highlight our personal perspectives on the current limitations of point-of-care applications and future development trends.
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Affiliation(s)
- Yi Wu
- University of Electronic Science and Technology of China, Chengdu, China
| | - Yusheng Fu
- University of Electronic Science and Technology of China, Chengdu, China
| | - Jiuchuan Guo
- University of Electronic Science and Technology of China, Chengdu, China.
| | - Jinhong Guo
- School of Sensing Science and Engineering, Shanghai Jiao Tong University, Shanghai, China; The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, #1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, China.
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5
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Tang Y, Chaillon A, Gianella S, Wong LM, Li D, Simermeyer TL, Porrachia M, Ignacio C, Woodworth B, Zhong D, Du J, de la Parra Polina E, Kirchherr J, Allard B, Clohosey ML, Moeser M, Sondgeroth AL, Whitehill GD, Singh V, Dashti A, Smith DM, Eron JJ, Bar KJ, Chahroudi A, Joseph SB, Archin NM, Margolis DM, Jiang G. Brain microglia serve as a persistent HIV reservoir despite durable antiretroviral therapy. J Clin Invest 2023; 133:e167417. [PMID: 37317962 PMCID: PMC10266791 DOI: 10.1172/jci167417] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/25/2023] [Indexed: 06/16/2023] Open
Abstract
Brain microglia (MG) may serve as a human immunodeficiency virus 1 (HIV) reservoir and ignite rebound viremia following cessation of antiretroviral therapy (ART), but they have yet to be proven to harbor replication-competent HIV. Here, we isolated brain myeloid cells (BrMCs) from nonhuman primates and rapid autopsy of people with HIV (PWH) on ART and sought evidence of persistent viral infection. BrMCs predominantly displayed microglial markers, in which up to 99.9% of the BrMCs were TMEM119+ MG. Total and integrated SIV or HIV DNA was detectable in the MG, with low levels of cell-associated viral RNA. Provirus in MG was highly sensitive to epigenetic inhibition. Outgrowth virus from parietal cortex MG in an individual with HIV productively infected both MG and PBMCs. This inducible, replication-competent virus and virus from basal ganglia proviral DNA were closely related but highly divergent from variants in peripheral compartments. Phenotyping studies characterized brain-derived virus as macrophage tropic based on the ability of the virus to infect cells expressing low levels of CD4. The lack of genetic diversity in virus from the brain suggests that this macrophage-tropic lineage quickly colonized brain regions. These data demonstrate that MG harbor replication-competent HIV and serve as a persistent reservoir in the brain.
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Affiliation(s)
- Yuyang Tang
- University of North Carolina (UNC) HIV Cure Center, and
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Sara Gianella
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Lilly M. Wong
- University of North Carolina (UNC) HIV Cure Center, and
| | - Dajiang Li
- University of North Carolina (UNC) HIV Cure Center, and
| | | | | | | | | | - Daniel Zhong
- University of North Carolina (UNC) HIV Cure Center, and
| | - Jiayi Du
- University of North Carolina (UNC) HIV Cure Center, and
| | | | | | | | | | - Matt Moeser
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amy L. Sondgeroth
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gregory D. Whitehill
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vidisha Singh
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amir Dashti
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Joseph J. Eron
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Katherine J. Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta and Emory University, Atlanta, Georgia, USA
| | - Sarah B. Joseph
- University of North Carolina (UNC) HIV Cure Center, and
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie M. Archin
- University of North Carolina (UNC) HIV Cure Center, and
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- University of North Carolina (UNC) HIV Cure Center, and
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Guochun Jiang
- University of North Carolina (UNC) HIV Cure Center, and
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, North Carolina, USA
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6
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Zhang X, Chen J. HIV Reservoir: How to Measure It? Curr HIV/AIDS Rep 2023; 20:29-41. [PMID: 37004676 DOI: 10.1007/s11904-023-00653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 04/04/2023]
Abstract
PURPOSEOF REVIEW In the current quest for a complete cure for HIV/AIDS, the persistence of a long-lived reservoir of cells carrying replication-competent proviruses is the major challenge. Here, we describe the main elements and characteristics of several widely used assays of HIV latent reservoir detection. RECENT FINDINGS To date, researchers have developed several different HIV latent reservoir detection assays. Among them, the in vitro quantitative viral outgrowth assay (QVOA) has been the gold standard for assessing latent HIV-1 viral load. The intact proviral DNA assay (IPDA) based on PCR also demonstrated the predominance of defective viruses. However, these assays all have some drawbacks and may still be inadequate in detecting the presence of ultralow levels of latent virus in many patients who were initially thought to have been cured, but eventually showed viral rebound. An accurate and precise measurement of the HIV reservoir is therefore needed to evaluate curative strategies, aimed to functional cure or sterilizing cure.
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Affiliation(s)
- Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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Ta TM, Malik S, Anderson EM, Jones AD, Perchik J, Freylikh M, Sardo L, Klase ZA, Izumi T. Insights Into Persistent HIV-1 Infection and Functional Cure: Novel Capabilities and Strategies. Front Microbiol 2022; 13:862270. [PMID: 35572626 PMCID: PMC9093714 DOI: 10.3389/fmicb.2022.862270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/23/2022] Open
Abstract
Although HIV-1 replication can be efficiently suppressed to undetectable levels in peripheral blood by combination antiretroviral therapy (cART), lifelong medication is still required in people living with HIV (PLWH). Life expectancies have been extended by cART, but age-related comorbidities have increased which are associated with heavy physiological and economic burdens on PLWH. The obstacle to a functional HIV cure can be ascribed to the formation of latent reservoir establishment at the time of acute infection that persists during cART. Recent studies suggest that some HIV reservoirs are established in the early acute stages of HIV infection within multiple immune cells that are gradually shaped by various host and viral mechanisms and may undergo clonal expansion. Early cART initiation has been shown to reduce the reservoir size in HIV-infected individuals. Memory CD4+ T cell subsets are regarded as the predominant cellular compartment of the HIV reservoir, but monocytes and derivative macrophages or dendritic cells also play a role in the persistent virus infection. HIV latency is regulated at multiple molecular levels in transcriptional and post-transcriptional processes. Epigenetic regulation of the proviral promoter can profoundly regulate the viral transcription. In addition, transcriptional elongation, RNA splicing, and nuclear export pathways are also involved in maintaining HIV latency. Although most proviruses contain large internal deletions, some defective proviruses may induce immune activation by expressing viral proteins or producing replication-defective viral-like particles. In this review article, we discuss the state of the art on mechanisms of virus persistence in the periphery and tissue and summarize interdisciplinary approaches toward a functional HIV cure, including novel capabilities and strategies to measure and eliminate the infected reservoirs and induce immune control.
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Affiliation(s)
- Tram M. Ta
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Sajjaf Malik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Elizabeth M. Anderson
- Office of the Assistant Secretary for Health, Region 3, U.S. Department of Health and Human Services, Washington, DC, United States
| | - Amber D. Jones
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jocelyn Perchik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Maryann Freylikh
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Luca Sardo
- Department of Infectious Disease and Vaccines, Merck & Co., Inc., Kenilworth, NJ, United States
| | - Zackary A. Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University of Medicine, Philadelphia, PA, United States
| | - Taisuke Izumi
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,*Correspondence: Taisuke Izumi,
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8
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Molecular epidemiology and clinical characterization of human rhinoviruses circulating in Shanghai, 2012-2020. Arch Virol 2022; 167:1111-1123. [PMID: 35303167 PMCID: PMC8931777 DOI: 10.1007/s00705-022-05405-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/22/2022] [Indexed: 12/30/2022]
Abstract
Human rhinoviruses (HRVs) cause acute upper and lower respiratory tract infections and aggravation of asthma and chronic obstructive pulmonary disease. The 5’ untranslated region (5' UTR) and the VP4/VP2 region are widely used for genotyping of HRVs. Members of the species Rhinovirus A and Rhinovirus C have been reported to be more frequently associated with severe disease than members of the species Rhinovirus B. We report the clinical and molecular epidemiological characteristics of HRVs circulating from 2012 to 2020 in Shanghai. A total of 5832 nasopharyngeal swabs from patients with acute respiratory infections were collected. A real-time reverse transcription polymerase chain reaction assay was used for virus detection. The 5' untranslated region and VP4/VP2 region were amplified and sequenced for genotyping and phylogenetic analysis. The overall rate of rhinovirus detection was 2.74% (160/5832), with members of species A, B, and C accounting for 68.13% (109/160), 20.00% (32/160), and 11.88% (19/160) of the total, respectively. A peak of HRV infection was observed in autumn (5.34%, 58/1087). Patients in the 3- to 14-year-old age group were the most susceptible to HRV infection (χ2 = 23.88, P = 0.017). Influenza virus and Streptococcus pneumoniae were detected more frequently than other pathogens in cases of coinfection. Recombination events were identified in 10 strains, which were successfully genotyped by phylogenetic analysis based on the 5’ UTR-VP4/VP2 region but not the 5’ UTR region alone. We observed a high degree of variability in the relative distribution of HRV genotypes and the prevalence of HRV infection in Shanghai and found evidence of recombination events in the portion of the genome containing the 5’ UTR and the VP4/VP2 region between HRV-C strains and HRV-A-like strains. This study is important for surveillance of the spread of HRVs and the emergence of new variants.
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Ge C, Feng J, Zhang J, Hu K, Wang D, Zha L, Hu X, Li R. Aptamer/antibody sandwich method for digital detection of SARS-CoV2 nucleocapsid protein. Talanta 2022; 236:122847. [PMID: 34635237 PMCID: PMC8421254 DOI: 10.1016/j.talanta.2021.122847] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022]
Abstract
Nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV2 and is highly conserved, and there are no homologous proteins in the human body, making it an ideal biomarker for the early diagnosis of SARS-CoV2. However, early detection of clinical specimens for SARS-CoV2 remains a challenge due to false-negative results with viral RNA and host antibodies based testing. In this manuscript, a microfluidic chip with femtoliter-sized wells was fabricated for the sensitive digital detection of N protein. Briefly, β-galactosidase (β-Gal)-linked antibody/N protein/aptamer immunocomplexes were formed on magnetic beads (MBs). Afterwards, the MBs and β-Gal substrate fluorescein-di-β-d-galactopyranoside (FDG) were injected into the chip together. Each well of the chip would only hold one MB as confined by the diameter of the wells. The MBs in the wells were sealed by fluorocarbon oil, which confines the fluorescent (FL) product generated from the reaction between β-Gal and FDG in the individual femtoliter-sized well and creates a locally high concentration of the FL product. The FL images of the wells were acquired using a conventional inverted FL microscope. The number of FL wells with MBs (FL wells number) and the number of wells with MBs (MBs wells number) were counted, respectively. The percentage of FL wells was calculated by dividing (FL wells number) by (MBs wells number). The higher the percentage of FL wells, the higher the N protein concentration. The detection limit of this digital method for N protein was 33.28 pg/mL, which was 300 times lower than traditional double-antibody sandwich based enzyme-linked immunosorbent assay (ELISA).
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Affiliation(s)
- Chenchen Ge
- College of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China
| | - Juan Feng
- College of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China
| | - Jiaming Zhang
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China
| | - Kai Hu
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China
| | - Dou Wang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong, 518055, PR China.
| | - Ling Zha
- College of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China
| | - Xuejuan Hu
- Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China.
| | - Rongsong Li
- College of Health Science and Environmental Engineering, Shenzhen Technology University, 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong, 518118, PR China.
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10
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An ultrasensitive planar array p24 Gag ELISA to detect HIV-1 in diverse biological matrixes. Sci Rep 2021; 11:23682. [PMID: 34880361 PMCID: PMC8654962 DOI: 10.1038/s41598-021-03072-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/25/2021] [Indexed: 11/25/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) persistence in the presence of antiretroviral therapy (ART) has halted the development of curative strategies. Measuring HIV persistence is complex due to the low frequency of cells containing virus in vivo. Most of the commercially available assays to date measure nucleic acid. These assays have the advantage of being highly sensitive and allow for the analysis of sequence diversity, intactness of the HIV genome or evaluation of diverse RNA species. However, these assays are limited in evaluating translational competent viral reservoirs. In here, we developed an ultrasensitive p24 ELISA that uses the Simoa planar array technology that can detect HIV-1 virions and HIV-1 infected cells with limit of detection similar to nucleic acid assays. Furthermore, the assay is optimized to measure very low levels of p24 in different biological fluids without a major loss of sensitivity or reproducibility. Our results demonstrate that the ‘homebrew’ planar p24 ELISA immunoassay is a broadly applicable new tool to evaluate HIV persistence in diverse biological fluids and cells.
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Tsurusawa N, Chang J, Namba M, Makioka D, Yamura S, Iha K, Kyosei Y, Watabe S, Yoshimura T, Ito E. Modified ELISA for Ultrasensitive Diagnosis. J Clin Med 2021; 10:5197. [PMID: 34768717 PMCID: PMC8585087 DOI: 10.3390/jcm10215197] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/11/2022] Open
Abstract
An enzyme-linked immunosorbent assay (ELISA) can be used for quantitative measurement of proteins, and improving the detection sensitivity to the ultrasensitive level would facilitate the diagnosis of various diseases. In the present review article, we first define the term 'ultrasensitive'. We follow this with a survey and discussion of the current literature regarding modified ELISA methods with ultrasensitive detection and their application for diagnosis. Finally, we introduce our own newly devised system for ultrasensitive ELISA combined with thionicotinamide adenine dinucleotide cycling and its application for the diagnosis of infectious diseases and lifestyle-related diseases. The aim of the present article is to expand the application of ultrasensitive ELISAs in the medical and biological fields.
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Affiliation(s)
- Naoko Tsurusawa
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Jyunhao Chang
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Mayuri Namba
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Daiki Makioka
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Sou Yamura
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Kanako Iha
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Yuta Kyosei
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
| | - Satoshi Watabe
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan;
| | - Teruki Yoshimura
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu 061-0293, Hokkaido, Japan;
| | - Etsuro Ito
- Department of Biology, Waseda University, Tokyo 162-8480, Japan; (N.T.); (J.C.); (M.N.); (D.M.); (S.Y.); (K.I.); (Y.K.)
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan;
- Graduate Institute of Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
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Momenbeitollahi N, Cloet T, Li H. Pushing the detection limits: strategies towards highly sensitive optical-based protein detection. Anal Bioanal Chem 2021; 413:5995-6011. [PMID: 34363087 PMCID: PMC8346249 DOI: 10.1007/s00216-021-03566-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 01/07/2023]
Abstract
Proteins are one of the main constituents of living cells. Studying the quantities of proteins under physiological and pathological conditions can give valuable insights into health status, since proteins are the functional molecules of life. To be able to detect and quantify low-abundance proteins in biofluids for applications such as early disease diagnostics, sensitive analytical techniques are desired. An example of this application is using proteins as biomarkers for detecting cancer or neurological diseases, which can provide early, lifesaving diagnoses. However, conventional methods for protein detection such as ELISA, mass spectrometry, and western blotting cannot offer enough sensitivity for certain applications. Recent advances in optical-based micro- and nano-biosensors have demonstrated promising results to detect proteins at low quantities down to the single-molecule level, shining lights on their capacities for ultrasensitive disease diagnosis and rare protein detection. However, to date, there is a lack of review articles synthesizing and comparing various optical micro- and nano-sensing methods of enhancing the limits of detections of the antibody-based protein assays. The purpose of this article is to critically review different strategies of improving assay sensitivity using miniaturized biosensors, such as assay miniaturization, improving antibody binding capacity, sample purification, and signal amplification. The pros and cons of different methods are compared, and the future perspectives of this research field are discussed.
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Affiliation(s)
| | - Teran Cloet
- School of Engineering, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Huiyan Li
- School of Engineering, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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VIP-SPOT: an Innovative Assay To Quantify the Productive HIV-1 Reservoir in the Monitoring of Cure Strategies. mBio 2021; 12:e0056021. [PMID: 34154408 PMCID: PMC8262951 DOI: 10.1128/mbio.00560-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Improved assays are critical to the successful implementation of novel HIV-1 cure strategies, given the limited ability of currently available assays to quantify true effects on the viral reservoir. As interventions based on immune clearance target infected cells producing viral antigens, irrespective of whether the viruses generated are infectious or not, we developed a novel assay to identify viral protein production at the single-cell level. The novel viral protein spot (VIP-SPOT) assay, based on the enzyme-linked ImmunoSpot (ELISpot) approach, quantifies the frequency of CD4+ T cells that produce HIV antigen upon stimulation. The performance of the VIP-SPOT assay was validated in samples from viremic (n = 18) and antiretroviral therapy (ART)-treated subjects (n = 35), and the results were compared with total and intact proviral DNA and plasma viremia. The size of the functional reservoir, measured by VIP-SPOT, correlates with total HIV-1 DNA and, more strongly, with intact proviruses. However, the frequency of HIV antigen-producing cells is 100-fold lower than that of intact proviruses, thus suggesting that most latently infected cells harboring full-length proviruses are not prone to reactivation. Furthermore, VIP-SPOT was useful for evaluating the efficacy of latency reversing agents (LRAs) in primary cells. VIP-SPOT is a novel tool for measuring the size of the functional HIV-1 reservoir in a rapid, sensitive, and precise manner. It might benefit the evaluation of cure strategies based on immune clearance, as these will specifically target this minor fraction of the viral reservoir, and might assist in the identification of novel therapeutic candidates that modulate viral latency.
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Lungu C, Banga R, Gruters RA, Procopio FA. Inducible HIV-1 Reservoir Quantification: Clinical Relevance, Applications and Advancements of TILDA. Front Microbiol 2021; 12:686690. [PMID: 34211450 PMCID: PMC8239294 DOI: 10.3389/fmicb.2021.686690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/21/2021] [Indexed: 01/07/2023] Open
Abstract
The presence of a stable HIV-1 reservoir persisting over time despite effective antiretroviral suppression therapy precludes a cure for HIV-1. Characterizing and quantifying this residual reservoir is considered an essential prerequisite to develop and validate curative strategies. However, a sensitive, reproducible, cost-effective, and easily executable test is still needed. The quantitative viral outgrowth assay is considered the gold standard approach to quantify the reservoir in HIV-1-infected patients on suppressive ART, but it has several limitations. An alternative method to quantify the viral reservoir following the reactivation of latent HIV-1 provirus detects multiply-spliced tat/rev RNA (msRNA) molecules by real-time PCR [tat/rev induced limiting dilution assay (TILDA)]. This article provides a perspective overview of the clinical relevance, various applications, recent advancements of TILDA, and how the assay has contributed to our understanding of the HIV-1 reservoir.
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Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Riddhima Banga
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A. Procopio
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland,*Correspondence: Francesco A. Procopio,
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Wu G, Cheney C, Huang Q, Hazuda DJ, Howell BJ, Zuck P. Improved Detection of HIV Gag p24 Protein Using a Combined Immunoprecipitation and Digital ELISA Method. Front Microbiol 2021; 12:636703. [PMID: 33796087 PMCID: PMC8007784 DOI: 10.3389/fmicb.2021.636703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Greater than 90% of HIV-1 proviruses are thought to be defective and incapable of viral replication. While replication competent proviruses are of primary concern with respect to disease progression or transmission, studies have shown that even defective proviruses are not silent and can produce viral proteins, which may contribute to inflammation and immune responses. Viral protein expression also has implications for immune-based HIV-1 clearance strategies, which rely on antigen recognition. Thus, sensitive assays aimed at quantifying both replication-competent proviruses and defective, yet translationally competent proviruses are needed to understand the contribution of viral protein to HIV-1 pathogenesis and determine the effectiveness of HIV-1 cure interventions. Previously, we reported a modified HIV-1 gag p24 digital enzyme-linked immunosorbent assay with single molecule array (Simoa) detection of cell-associated viral protein. Here we report a novel p24 protein enrichment method coupled with the digital immunoassay to further extend the sensitivity and specificity of viral protein detection. Immunocapture of HIV gag p24 followed by elution in a Simoa-compatible format resulted in higher protein recovery and lower background from various biological matrices and sample volumes. Quantification of as little as 1 fg of p24 protein from cell lysates from cells isolated from peripheral blood or tissues from ART-suppressed HIV participants, as well as simian-human immunodeficiency virus-infected non-human primates (NHPs), with high recovery and reproducibility is demonstrated here. The application of these enhanced methods to patient-derived samples has potential to further the study of the persistent HIV state and examine in vitro response to therapies, as well as ex vivo study of translationally competent cells from a variety of donors.
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Affiliation(s)
| | | | | | | | | | - Paul Zuck
- Department of Infectious Disease and Vaccines, Merck & Co. Inc., Kenilworth, NJ, United States
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