1
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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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2
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Kulkarni S, Endsley JJ, Lai Z, Bradley T, Sharan R. Single-Cell Transcriptomics of Mtb/HIV Co-Infection. Cells 2023; 12:2295. [PMID: 37759517 PMCID: PMC10529032 DOI: 10.3390/cells12182295] [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: 05/31/2023] [Revised: 08/17/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Tuberculosis (TB) and Human Immunodeficiency Virus (HIV) co-infection continues to pose a significant healthcare burden. HIV co-infection during TB predisposes the host to the reactivation of latent TB infection (LTBI), worsening disease conditions and mortality. There is a lack of biomarkers of LTBI reactivation and/or immune-related transcriptional signatures to distinguish active TB from LTBI and predict TB reactivation upon HIV co-infection. Characterizing individual cells using next-generation sequencing-based technologies has facilitated novel biological discoveries about infectious diseases, including TB and HIV pathogenesis. Compared to the more conventional sequencing techniques that provide a bulk assessment, single-cell RNA sequencing (scRNA-seq) can reveal complex and new cell types and identify more high-resolution cellular heterogeneity. This review will summarize the progress made in defining the immune atlas of TB and HIV infections using scRNA-seq, including host-pathogen interactions, heterogeneity in HIV pathogenesis, and the animal models employed to model disease. This review will also address the tools needed to bridge the gap between disease outcomes in single infection vs. co-infection. Finally, it will elaborate on the translational benefits of single-cell sequencing in TB/HIV diagnosis in humans.
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Affiliation(s)
- Smita Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Janice J. Endsley
- Departments of Microbiology & Immunology and Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Zhao Lai
- Greehey Children’s Cancer Research Institute, The University of Texas Health San Antonio, San Antonio, TX 78229, USA;
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA;
- Departments of Pediatrics and Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, MO 66160, USA
- Department of Pediatrics, UMKC School of Medicine, Kansas City, MO 64108, USA
| | - Riti Sharan
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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3
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Porto PS, Rivera A, Moonrinta R, Wobus CE. Entry and egress of human astroviruses. Adv Virus Res 2023; 117:81-119. [PMID: 37832992 DOI: 10.1016/bs.aivir.2023.08.001] [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] [Indexed: 10/15/2023]
Abstract
Astroviruses encapsidate a positive-sense, single-stranded RNA genome into ∼30nm icosahedral particles that infect a wide range of mammalian and avian species, but their biology is not well understood. Human astroviruses (HAstV) are divided into three clades: classical HAstV serotypes 1-8, and novel or non-classical HAstV of the MLB and VA clades. These viruses are part of two genogroups and phylogenetically cluster with other mammalian astroviruses, highlighting their zoonotic potential. HAstV are a highly prevalent cause of nonbacterial gastroenteritis, primarily in children, the elderly and immunocompromised. Additionally, asymptomatic infections and extraintestinal disease (e.g., encephalitis), are also observed, mostly in immunocompetent or immunocompromised individuals, respectively. While these viruses are highly prevalent, no approved vaccines or antivirals are available to prevent or treat infections. This is in large part due to their understudied nature and the limited understanding of even very basic features of their life cycle and pathogenesis at the cellular and organismal level. This review will summarize molecular features of human astrovirus biology, pathogenesis, and tropism, and then focus on two stages of the viral life cycle, namely entry and egress, since these are proven targets for therapeutic interventions. We will further highlight gaps in knowledge in hopes of stimulating future research into these understudied viruses.
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Affiliation(s)
- Pedro Soares Porto
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United states
| | - Andres Rivera
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United states
| | - Rootjikarn Moonrinta
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United states
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United states.
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4
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Ruggiero E, Frasson I, Tosoni E, Scalabrin M, Perrone R, Marušič M, Plavec J, Richter SN. Fused in Liposarcoma Protein, a New Player in the Regulation of HIV-1 Transcription, Binds to Known and Newly Identified LTR G-Quadruplexes. ACS Infect Dis 2022; 8:958-968. [PMID: 35502456 PMCID: PMC9112328 DOI: 10.1021/acsinfecdis.1c00508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Indexed: 11/29/2022]
Abstract
HIV-1 integrated long terminal repeat (LTR) promoter activity is modulated by folding of its G-rich region into non-canonical nucleic acids structures, such as G-quadruplexes (G4s), and their interaction with cellular proteins. Here, by a combined pull-down/mass spectrometry/Western-blot approach, we identified the fused in liposarcoma (FUS) protein and found it to preferentially bind and stabilize the least stable and bulged LTR G4, especially in the cell environment. The outcome of this interaction is the down-regulation of viral transcription, as assessed in a reporter assay with LTR G4 mutants in FUS-silencing conditions. These data indicate that the complexity and dynamics of HIV-1 LTR G4s are much greater than previously envisaged. The G-rich LTR region, with its diverse G4 landscape and multiple cell protein interactions, stands out as prime sensing center for the fine regulation of viral transcription. This region thus represents a rational antiviral target for inhibiting both the actively transcribing and latent viruses.
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Affiliation(s)
- Emanuela Ruggiero
- Department
of Molecular Medicine, University of Padua, via Aristide Gabelli 63, Padua 35121, Italy
| | - Ilaria Frasson
- Department
of Molecular Medicine, University of Padua, via Aristide Gabelli 63, Padua 35121, Italy
| | - Elena Tosoni
- Department
of Molecular Medicine, University of Padua, via Aristide Gabelli 63, Padua 35121, Italy
| | - Matteo Scalabrin
- Department
of Molecular Medicine, University of Padua, via Aristide Gabelli 63, Padua 35121, Italy
| | - Rosalba Perrone
- Buck
Institute for Research on Aging, 8001 Redwood Boulevard, Novato, California 94945, United States
| | - Maja Marušič
- Slovenian
NMR Center, National Institute of Chemistry, Hajdrihova, 19, Ljubljana SI-1000, Slovenia
| | - Janez Plavec
- Slovenian
NMR Center, National Institute of Chemistry, Hajdrihova, 19, Ljubljana SI-1000, Slovenia
| | - Sara N. Richter
- Department
of Molecular Medicine, University of Padua, via Aristide Gabelli 63, Padua 35121, Italy
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5
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Abstract
Chimaeric antigen receptor (CAR) T cells can generate durable clinical responses in B-cell haematologic malignancies. The manufacturing of these T cells typically involves their activation, followed by viral transduction and expansion ex vivo for at least 6 days. However, the activation and expansion of CAR T cells leads to their progressive differentiation and the associated loss of anti-leukaemic activity. Here we show that functional CAR T cells can be generated within 24 hours from T cells derived from peripheral blood without the need for T-cell activation or ex vivo expansion, and that the efficiency of viral transduction in this process is substantially influenced by the formulation of the medium and the surface area-to-volume ratio of the culture vessel. In mouse xenograft models of human leukaemias, the rapidly generated non-activated CAR T cells exhibited higher anti-leukaemic in vivo activity per cell than the corresponding activated CAR T cells produced using the standard protocol. The rapid manufacturing of CAR T cells may reduce production costs and broaden their applicability.
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Bhat T, Cao A, Yin J. Virus-like Particles: Measures and Biological Functions. Viruses 2022; 14:383. [PMID: 35215979 PMCID: PMC8877645 DOI: 10.3390/v14020383] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/25/2022] Open
Abstract
Virus-like particles resemble infectious virus particles in size, shape, and molecular composition; however, they fail to productively infect host cells. Historically, the presence of virus-like particles has been inferred from total particle counts by microscopy, and infectious particle counts or plaque-forming-units (PFUs) by plaque assay; the resulting ratio of particles-to-PFUs is often greater than one, easily 10 or 100, indicating that most particles are non-infectious. Despite their inability to hijack cells for their reproduction, virus-like particles and the defective genomes they carry can exhibit a broad range of behaviors: interference with normal virus growth during co-infections, cell killing, and activation or inhibition of innate immune signaling. In addition, some virus-like particles become productive as their multiplicities of infection increase, a sign of cooperation between particles. Here, we review established and emerging methods to count virus-like particles and characterize their biological functions. We take a critical look at evidence for defective interfering virus genomes in natural and clinical isolates, and we review their potential as antiviral therapeutics. In short, we highlight an urgent need to better understand how virus-like genomes and particles interact with intact functional viruses during co-infection of their hosts, and their impacts on the transmission, severity, and persistence of virus-associated diseases.
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Affiliation(s)
| | | | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI 53715, USA; (T.B.); (A.C.)
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Davids BO, Balasubramaniam M, Sapp N, Prakash P, Ingram S, Li M, Craigie R, Hollis T, Pandhare J, Dash C. Human Three Prime Repair Exonuclease 1 Promotes HIV-1 Integration by Preferentially Degrading Unprocessed Viral DNA. J Virol 2021; 95:e0055521. [PMID: 34105995 PMCID: PMC8354242 DOI: 10.1128/jvi.00555-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/20/2022] Open
Abstract
Three prime repair exonuclease 1 (TREX1) is the most abundant 3'→5' exonuclease in mammalian cells. It has been suggested that TREX1 degrades HIV-1 DNA to enable the virus to evade the innate immune system. However, the exact role of TREX1 during early steps of HIV-1 infection is not clearly understood. In this study, we report that HIV-1 infection is associated with upregulation, perinuclear accumulation, and nuclear localization of TREX1. However, TREX1 overexpression did not affect reverse transcription or nuclear entry of the virus. Surprisingly, HIV-1 DNA integration was increased in TREX1-overexpressing cells, suggesting a role of the exonuclease in the post-nuclear entry step of infection. Accordingly, preintegration complexes (PICs) extracted from TREX1-overexpressing cells retained higher levels of DNA integration activity. TREX1 depletion resulted in reduced levels of proviral integration, and PICs formed in TREX1-depleted cells retained lower DNA integration activity. Addition of purified TREX1 to PICs also enhanced DNA integration activity, suggesting that TREX1 promotes HIV-1 integration by stimulating PIC activity. To understand the mechanism, we measured TREX1 exonuclease activity on substrates containing viral DNA ends. These studies revealed that TREX1 preferentially degrades the unprocessed viral DNA, but the integration-competent 3'-processed viral DNA remains resistant to degradation. Finally, we observed that TREX1 addition stimulates the activity of HIV-1 intasomes assembled with the unprocessed viral DNA but not that of intasomes containing the 3'-processed viral DNA. These biochemical analyses provide a mechanism by which TREX1 directly promotes HIV-1 integration. Collectively, our study demonstrates that HIV-1 infection upregulates TREX1 to facilitate viral DNA integration. IMPORTANCE Productive HIV-1 infection is dependent on a number of cellular factors. Therefore, a clear understanding of how the virus exploits the cellular machinery will identify new targets for inhibiting HIV-1 infection. The three prime repair exonuclease 1 (TREX1) is the most active cellular exonuclease in mammalian cells. It has been reported that TREX1 prevents accumulation of HIV-1 DNA and enables the virus to evade the host innate immune response. Here, we show that HIV-1 infection results in the upregulation, perinuclear accumulation, and nuclear localization of TREX1. We also provide evidence that TREX1 promotes HIV-1 integration by preferentially degrading viral DNAs that are incompatible with chromosomal insertion. These observations identify a novel role of TREX1 in a post-nuclear entry step of HIV-1 infection.
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Affiliation(s)
- Benem-Orom Davids
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Nicklas Sapp
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Shalonda Ingram
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
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8
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Bulcha JT, Wang Y, Ma H, Tai PWL, Gao G. Viral vector platforms within the gene therapy landscape. Signal Transduct Target Ther 2021; 6:53. [PMID: 33558455 PMCID: PMC7868676 DOI: 10.1038/s41392-021-00487-6] [Citation(s) in RCA: 497] [Impact Index Per Article: 165.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/05/2020] [Accepted: 10/23/2020] [Indexed: 01/30/2023] Open
Abstract
Throughout its 40-year history, the field of gene therapy has been marked by many transitions. It has seen great strides in combating human disease, has given hope to patients and families with limited treatment options, but has also been subject to many setbacks. Treatment of patients with this class of investigational drugs has resulted in severe adverse effects and, even in rare cases, death. At the heart of this dichotomous field are the viral-based vectors, the delivery vehicles that have allowed researchers and clinicians to develop powerful drug platforms, and have radically changed the face of medicine. Within the past 5 years, the gene therapy field has seen a wave of drugs based on viral vectors that have gained regulatory approval that come in a variety of designs and purposes. These modalities range from vector-based cancer therapies, to treating monogenic diseases with life-altering outcomes. At present, the three key vector strategies are based on adenoviruses, adeno-associated viruses, and lentiviruses. They have led the way in preclinical and clinical successes in the past two decades. However, despite these successes, many challenges still limit these approaches from attaining their full potential. To review the viral vector-based gene therapy landscape, we focus on these three highly regarded vector platforms and describe mechanisms of action and their roles in treating human disease.
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Affiliation(s)
- Jote T Bulcha
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic medical sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hong Ma
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
- VIDE Program, University of Massachusetts Medical School, Worcester, MA, USA.
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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9
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Tsang JOL, Zhou J, Zhao X, Li C, Zou Z, Yin F, Yuan S, Yeung ML, Chu H, Chan JFW. Development of Three-Dimensional Human Intestinal Organoids as a Physiologically Relevant Model for Characterizing the Viral Replication Kinetics and Antiviral Susceptibility of Enteroviruses. Biomedicines 2021; 9:88. [PMID: 33477611 PMCID: PMC7831294 DOI: 10.3390/biomedicines9010088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/16/2022] Open
Abstract
Enteroviruses are important causes of hand, foot, and mouth disease, respiratory infections, and neurological infections in human. A major hurdle for the development of anti-enterovirus agents is the lack of physiologically relevant evaluation platforms that closely correlate with the in vivo state. We established the human small intestinal organoids as a novel platform for characterizing the viral replication kinetics and evaluating candidate antivirals for enteroviruses. The organoids supported productive replication of enterovirus (EV)-A71, coxsackievirus B2, and poliovirus type 3, as evidenced by increasing viral loads, infectious virus titers, and the presence of cytopathic effects. In contrast, EV-D68, which mainly causes respiratory tract infection in humans, did not replicate significantly in the organoids. The differential expression profiles of the receptors for these enteroviruses correlated with their replication kinetics. Using itraconazole as control, we showed that the results of various antiviral assays, including viral load reduction, plaque reduction, and cytopathic effect inhibition assays, were highly reproducible in the organoids. Moreover, itraconazole attenuated virus-induced inflammatory response in the organoids, which helped to explain its antiviral effects and mechanism. Collectively, these data showed that the human small intestinal organoids may serve as a robust platform for investigating the pathogenesis and evaluating antivirals for enteroviruses.
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Affiliation(s)
- Jessica Oi-Ling Tsang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Xiaoyu Zhao
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Cun Li
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Zijiao Zou
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Feifei Yin
- Hainan-Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Man-Lung Yeung
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (J.O.-L.T.); (J.Z.); (X.Z.); (C.L.); (Z.Z.); (S.Y.); (M.-L.Y.); (H.C.)
- Hainan-Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China;
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10
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Kleinpenning F, Steigenberger B, Wu W, Heck AJR. Fishing for newly synthesized proteins with phosphonate-handles. Nat Commun 2020; 11:3244. [PMID: 32591520 PMCID: PMC7320153 DOI: 10.1038/s41467-020-17010-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term PhosID. In this approach, click-able phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets. Here the authors describe PhosID, an enrichment strategy using phosphonate-handles, that combines click chemistry and IMAC-based phospho-enrichment for quantitative proteomics analysis of newly synthesized proteins.
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Affiliation(s)
- Fleur Kleinpenning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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Cassotta M, Forbes-Hernández TY, Calderón Iglesias R, Ruiz R, Elexpuru Zabaleta M, Giampieri F, Battino M. Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research. Nutrients 2020; 12:E1827. [PMID: 32575399 PMCID: PMC7353391 DOI: 10.3390/nu12061827] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
The interaction between nutrition and human infectious diseases has always been recognized. With the emergence of molecular tools and post-genomics, high-resolution sequencing technologies, the gut microbiota has been emerging as a key moderator in the complex interplay between nutrients, human body, and infections. Much of the host-microbial and nutrition research is currently based on animals or simplistic in vitro models. Although traditional in vivo and in vitro models have helped to develop mechanistic hypotheses and assess the causality of the host-microbiota interactions, they often fail to faithfully recapitulate the complexity of the human nutrient-microbiome axis in gastrointestinal homeostasis and infections. Over the last decade, remarkable progress in tissue engineering, stem cell biology, microfluidics, sequencing technologies, and computing power has taken place, which has produced a new generation of human-focused, relevant, and predictive tools. These tools, which include patient-derived organoids, organs-on-a-chip, computational analyses, and models, together with multi-omics readouts, represent novel and exciting equipment to advance the research into microbiota, infectious diseases, and nutrition from a human-biology-based perspective. After considering some limitations of the conventional in vivo and in vitro approaches, in this review, we present the main novel available and emerging tools that are suitable for designing human-oriented research.
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Affiliation(s)
- Manuela Cassotta
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Tamara Yuliett Forbes-Hernández
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
| | - Ruben Calderón Iglesias
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Roberto Ruiz
- Centre for Nutrition and Health, Universidad Europea del Atlántico (UEA), 39001 Santander, Spain; (M.C.); (R.C.I.); (R.R.)
| | - Maria Elexpuru Zabaleta
- Dipartimento di Scienze Cliniche e Molecolari, Facoltà di Medicina, Università Politecnica delle Marche, 60131 Ancona, Italy;
| | - Francesca Giampieri
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy
- College of Food Science and Technology, Northwest University, Xi’an 710069, China
| | - Maurizio Battino
- Department of Analytical and Food Chemistry, Nutrition and Food Science Group, CITACA, CACTI, University of Vigo, 36310 Vigo, Spain;
- Department of Clinical Sciences, Faculty of Medicine, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
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12
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Pinzone MR, Bertuccio MP, VanBelzen DJ, Zurakowski R, O'Doherty U. Next-Generation Sequencing in a Direct Model of HIV Infection Reveals Important Parallels to and Differences from In Vivo Reservoir Dynamics. J Virol 2020; 94:e01900-19. [PMID: 32051279 PMCID: PMC7163122 DOI: 10.1128/jvi.01900-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) represents a powerful tool to unravel the genetic make-up of the HIV reservoir, but limited data exist on its use in vitro Moreover, most NGS studies do not separate integrated from unintegrated DNA, even though selection pressures on these two forms should be distinct. We reasoned we could use NGS to compare the infection of resting and activated CD4 T cells in vitro to address how the metabolic state affects reservoir formation and dynamics. To address these questions, we obtained HIV sequences 2, 4, and 8 days after NL4-3 infection of metabolically activated and quiescent CD4 T cells (cultured with 2 ng/ml interleukin-7). We compared the composition of integrated and total HIV DNA by isolating integrated HIV DNA using pulsed-field electrophoresis before performing sequencing. After a single-round infection, the majority of integrated HIV DNA was intact in both resting and activated T cells. The decay of integrated intact proviruses was rapid and similar in both quiescent and activated T cells. Defective forms accumulated relative to intact ones analogously to what is observed in vivo Massively deleted viral sequences formed more frequently in resting cells, likely due to lower deoxynucleoside triphosphate (dNTP) levels and the presence of multiple restriction factors. To our surprise, the majority of these deleted sequences did not integrate into the human genome. The use of NGS to study reservoir dynamics in vitro provides a model that recapitulates important aspects of reservoir dynamics. Moreover, separating integrated from unintegrated HIV DNA is important in some clinical settings to properly study selection pressures.IMPORTANCE The major implication of our work is that the decay of intact proviruses in vitro is extremely rapid, perhaps as a result of enhanced expression. Gaining a better understanding of why intact proviruses decay faster in vitro might help the field identify strategies to purge the reservoir in vivo When used wisely, in vitro models are a powerful tool to study the selective pressures shaping the viral landscape. Our finding that massively deleted sequences rarely succeed in integrating has several ramifications. It demonstrates that the total HIV DNA can differ substantially in character from the integrated HIV DNA under certain circumstances. The presence of unintegrated HIV DNA has the potential to obscure selection pressures and confound the interpretation of clinical studies, especially in the case of trials involving treatment interruptions.
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Affiliation(s)
- Marilia Rita Pinzone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Maria Paola Bertuccio
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - D Jake VanBelzen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Ryan Zurakowski
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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13
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Affiliation(s)
- Abimbola O. Kolawole
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Kim Y, Cameron PU, Lewin SR, Anderson JL. Limitations of dual-fluorescent HIV reporter viruses in a model of pre-activation latency. J Int AIDS Soc 2019; 22:e25425. [PMID: 31855322 PMCID: PMC6922067 DOI: 10.1002/jia2.25425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION HIV latency can be established in vitro following direct infection of a resting CD4+ T cell (pre-activation latency) or infection of an activated CD4+ T cell which then returns to a resting state (post-activation latency). We modified a previously published dual-fluorescent reporter virus seeking to track the establishment and reactivation of pre-activation latency in primary CD4+ T cells. METHODS A previously published dual-fluorescent reporter virus was modified so that expression of enhanced green fluorescent protein (GFP) was under control of the elongation factor 1 alpha (EF1α) promoter to detect latent infection, and E2 crimson (E2CRM) was under control of the nef promoter to detect productive infection. NL4.3 that expressed GFP in place of nef was used as a positive control. We infected the Jurkat T-cell line and primary CD4+ T cells that were either unstimulated or stimulated with either the chemokine CCL19 or phytohaemagglutinin (PHA)/IL-2 and quantified the expression of both fluorescent proteins by flow cytometry. The study was carried out over a period of two years from September 2016 to October 2018. RESULTS AND DISCUSSION Expression of both fluorophores was detected following infection of the Jurkat T-cell line while only low levels of the latent reporter were observed following infection of primary CD4+ T cells. In unstimulated and CCL19-treated CD4+ T cells, expression of the GFP latent reporter, increased after further activation of the cells with PHA/phorbol 12-myristate 13-acetate (PMA). CONCLUSIONS Our findings demonstrate that the EF1α promoter has poor constitutive expression in resting CD4+ T cells. Therefore, dual-fluorescent reporter viruses with the EF1α promoter may underestimate the frequency of latent infection in resting CD4+ T cells.
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Affiliation(s)
- Youry Kim
- Department of Microbiology and ImmunologyThe University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneVictoriaAustralia
- The Peter Doherty Institute for Infection and ImmunityThe University of Melbourne and Royal Melbourne HospitalMelbourneVictoriaAustralia
| | - Paul U Cameron
- The Peter Doherty Institute for Infection and ImmunityThe University of Melbourne and Royal Melbourne HospitalMelbourneVictoriaAustralia
- Department of Infectious DiseasesAlfred Hospital and Monash UniversityMelbourneVictoriaAustralia
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and ImmunityThe University of Melbourne and Royal Melbourne HospitalMelbourneVictoriaAustralia
- Department of Infectious DiseasesAlfred Hospital and Monash UniversityMelbourneVictoriaAustralia
| | - Jenny L Anderson
- The Peter Doherty Institute for Infection and ImmunityThe University of Melbourne and Royal Melbourne HospitalMelbourneVictoriaAustralia
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Abstract
Viral vectors provide an efficient means for modification of eukaryotic cells, and their use is now commonplace in academic laboratories and industry for both research and clinical gene therapy applications. Lentiviral vectors, derived from the human immunodeficiency virus, have been extensively investigated and optimized over the past two decades. Third-generation, self-inactivating lentiviral vectors have recently been used in multiple clinical trials to introduce genes into hematopoietic stem cells to correct primary immunodeficiencies and hemoglobinopathies. These vectors have also been used to introduce genes into mature T cells to generate immunity to cancer through the delivery of chimeric antigen receptors (CARs) or cloned T-cell receptors. CAR T-cell therapies engineered using lentiviral vectors have demonstrated noteworthy clinical success in patients with B-cell malignancies leading to regulatory approval of the first genetically engineered cellular therapy using lentiviral vectors. In this review, we discuss several aspects of lentiviral vectors that will be of interest to clinicians, including an overview of lentiviral vector development, the current uses of viral vectors as therapy for primary immunodeficiencies and cancers, large-scale manufacturing of lentiviral vectors, and long-term follow-up of patients treated with gene therapy products.
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Single-cell analysis identifies cellular markers of the HIV permissive cell. PLoS Pathog 2017; 13:e1006678. [PMID: 29073251 PMCID: PMC5658171 DOI: 10.1371/journal.ppat.1006678] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
Cellular permissiveness to HIV infection is highly heterogeneous across individuals. Heterogeneity is also found across CD4+ T cells from the same individual, where only a fraction of cells gets infected. To explore the basis of permissiveness, we performed single-cell RNA-seq analysis of non-infected CD4+ T cells from high and low permissive individuals. Transcriptional heterogeneity translated in a continuum of cell states, driven by T-cell receptor-mediated cell activation and was strongly linked to permissiveness. Proteins expressed at the cell surface and displaying the highest correlation with T cell activation were tested as biomarkers of cellular permissiveness to HIV. FACS sorting using antibodies against several biomarkers of permissiveness led to an increase of HIV cellular infection rates. Top candidate biomarkers included CD25, a canonical activation marker. The combination of CD25 high expression with other candidate biomarkers led to the identification of CD298, CD63 and CD317 as the best biomarkers for permissiveness. CD25highCD298highCD63highCD317high cell population showed an enrichment of HIV-infection of up to 28 fold as compared to the unsorted cell population. The purified hyper-permissive cell subpopulation was characterized by a downregulation of interferon-induced genes and several known restriction factors. Single-cell RNA-seq analysis coupled with functional characterization of cell biomarkers provides signatures of the "HIV-permissive cell".
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Exploring viral infection using single-cell sequencing. Virus Res 2016; 239:55-68. [PMID: 27816430 DOI: 10.1016/j.virusres.2016.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/31/2022]
Abstract
Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication.
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