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Domingues W, Folgosi VÂ, Sanabani SS, Leite Junior PD, Assone T, Casseb J. Novel approaches for HTLV-1 therapy: innovative applications of CRISPR-Cas9. Rev Inst Med Trop Sao Paulo 2024; 66:e48. [PMID: 39194140 DOI: 10.1590/s1678-9946202466048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/07/2024] [Indexed: 08/29/2024] Open
Abstract
The human T-cell lymphotropic virus type 1 (HTLV-1) is a single-stranded positive-sense RNA virus that belongs to the Retroviridae family, genus Deltaretro, and infects approximately five to 10 million people worldwide. Although a significant number of individuals living with HTLV-1 remain asymptomatic throughout their lives, some develop one or more severe clinical conditions, such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a progressive and debilitating disease, and/or a subtype of non-Hodgkin's lymphoma with a more threatening course known as adult T-cell leukemia/lymphoma (ATLL). Moreover, current therapeutic options are limited and focus primarily on treating symptoms and controlling viral latency. CRISPR-Cas9 gene editing is proposed as a promising tool to address the intricate links associated with HTLV-1. By targeting or silencing key genes during initial infection and dysregulating immune signaling pathways, CRISPR-Cas9 offers potential intervention opportunities. In this review, we address the therapeutic potential of CRISPR-Cas9 gene editing, as well as examine the primary mechanisms involved in editing potential target genes and discuss the existing evidence in the current scientific literature.
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Affiliation(s)
- Wilson Domingues
- Universidade de São Paulo, Faculdade de Medicina, Divisão de Dermatologia, Laboratório de Investigação Médica LIM-56, São Paulo, São Paulo, Brazil
| | - Victor Ângelo Folgosi
- Universidade de São Paulo, Faculdade de Medicina, Divisão de Dermatologia, Laboratório de Investigação Médica LIM-56, São Paulo, São Paulo, Brazil
| | - Sabri Saeed Sanabani
- Universidade de São Paulo, Faculdade de Medicina, Divisão de Dermatologia, Laboratório de Investigação Médica LIM-56, São Paulo, São Paulo, Brazil
| | - Pedro Domingos Leite Junior
- Universidade de São Paulo, Faculdade de Medicina, Divisão de Dermatologia, Laboratório de Investigação Médica LIM-56, São Paulo, São Paulo, Brazil
| | - Tatiane Assone
- Universidade de São Paulo, Faculdade de Medicina, Divisão de Dermatologia, Laboratório de Investigação Médica LIM-56, São Paulo, São Paulo, Brazil
| | - Jorge Casseb
- Universidade de São Paulo, Faculdade de Medicina, Divisão de Dermatologia, Laboratório de Investigação Médica LIM-56, São Paulo, São Paulo, Brazil
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Mariano A, Ammendola S, Migliorini A, Leopizzi M, Raimondo D, Scotto d'Abusco A. Intron retention in PI-PLC γ1 mRNA as a key mechanism affecting MMP expression in human primary fibroblast-like synovial cells. Cell Biochem Funct 2024; 42:e4091. [PMID: 38973151 DOI: 10.1002/cbf.4091] [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: 03/27/2024] [Revised: 06/26/2024] [Accepted: 06/30/2024] [Indexed: 07/09/2024]
Abstract
The intron retention (IR) is a phenomenon utilized by cells to allow diverse fates at the same mRNA, leading to a different pattern of synthesis of the same protein. In this study, we analyzed the modulation of phosphoinositide-specific phospholipase C (PI-PLC) enzymes by Harpagophytum procumbens extract (HPE) in synoviocytes from joins of osteoarthritis (OA) patients. In some samples, the PI-PLC γ1 isoform mature mRNA showed the IR and, in these synoviocytes, the HPE treatment increased the phenomenon. Moreover, we highlighted that as a consequence of IR, a lower amount of PI-PLC γ1 was produced. The decrease of PI-PLC γ1 was associated with the decrease of metalloprotease-3 (MMP-3), and MMP-13, and ADAMTS-5 after HPE treatment. The altered expression of MMPs is a hallmark of the onset and progression of OA, thus substances able to decrease their expression are very desirable. The interesting outcomes of this study are that 35% of analyzed synovial tissues showed the IR phenomenon in the PI-PLC γ1 mRNA and that the HPE treatment increased this phenomenon. For the first time, we found that the decrease of PI-PLC γ1 protein in synoviocytes interferes with MMP production, thus affecting the pathways involved in the MMP expression. This finding was validated by the silencing of PI-PLC γ1 in synoviocytes where the IR phenomenon was not present. Our results shed new light on the biochemical mechanisms involved in the degrading enzyme production in the joint of OA patients, suggesting a new therapeutic target and highlighting the importance of personalized medicine.
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Affiliation(s)
- Alessia Mariano
- Department of Biochemical Sciences, Sapienza University of Rome, Roma, Italy
| | | | - Arianna Migliorini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Martina Leopizzi
- Department of Medico-Surgical Sciences and Biotechnologies, Polo Pontino-Sapienza University, Latina, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Letafati A, Bahavar A, Tabarraei A, Norouzi M, Amiri A, Mozhgani SH. Human T-cell lymphotropic virus type 1 (HTLV-1) grip on T-cells: investigating the viral tapestry of activation. Infect Agent Cancer 2024; 19:23. [PMID: 38734673 PMCID: PMC11088018 DOI: 10.1186/s13027-024-00584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
INTRODUCTION Human T-cell Lymphotropic virus type 1 (HTLV-1) belongs to retroviridae which is connected to two major diseases, including HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and Adult T-cell leukemia/lymphoma (ATLL). This study aims to investigate the mRNA expressions of key proteins correlated to T-cell activation in asymptomatic carriers (ACs) HTLV-1 infected patients, shedding light on early molecular events and T-cell activation following HTLV-1 infection. MATERIAL AND METHODS The study involved 40 participants, including 20 ACs and 20 healthy subjects. Blood samples were collected, ELISA assessment for screening and confirmation with PCR for Trans-activating transcriptional regulatory protein (Tax) and HTLV-1 basic leucine zipper factor (HBZ) of the HTLV-1 were done. mRNA expressions of C-terminal Src kinase (CSK), Glycogen Synthase Kinase-3 Beta (GSK3β), Mitogen-Activated Protein Kinase 14 (MAP3K14 or NIK), Phospholipase C Gamma-1 (PLCG1), Protein Tyrosine Phosphatase non-Receptor Type 6 (PTPN6) and Mitogen-Activated Protein Kinase Kinase Kinase-7 (SLP-76) and Mitogen-Activated Protein Kinase14 (MAP3K7 or TAK1) were assayed using RT-qPCR. Statistical analyses were performed using PRISM and SPSS software. RESULTS While there were no significant upregulation in CSK and PTPN6 in ACs compared to healthy individuals, expression levels of GSK3β, MAP3K14, PLCG1, SLP-76, and TAK1 were significantly higher in ACs compared to healthy subjects which directly contributes to T-cell activation in the HTLV-1 ACs. CONCLUSION HTLV-1 infection induces differential mRNA expressions in key proteins associated with T-cell activation. mRNAs related to T-cell activation showed significant upregulation compared to PTPN6 and CSK which contributed to T-cell regulation. Understanding these early molecular events in ACs may provide potential markers for disease progression and identify therapeutic targets for controlling viral replication and mitigating associated diseases. The study contributes novel insights to the limited literature on T-cell activation and HTLV-1 pathogenesis.
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Affiliation(s)
- Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Atefeh Bahavar
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabarraei
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Norouzi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran.
| | - Abdollah Amiri
- Department of Microbiology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sayed-Hamidreza Mozhgani
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran.
- Department of Microbiology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
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Visvanathan R, Utsuki T, Beck DE, Clayton WB, Lendy E, Sun KL, Liu Y, Hering KW, Mesecar A, Zhang ZY, Putt KS. A novel micellular fluorogenic substrate for quantitating the activity of 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma (PLCγ) enzymes. PLoS One 2024; 19:e0299541. [PMID: 38551930 PMCID: PMC10980208 DOI: 10.1371/journal.pone.0299541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/12/2024] [Indexed: 04/01/2024] Open
Abstract
The activities of the phospholipase C gamma (PLCγ) 1 and 2 enzymes are essential for numerous cellular processes. Unsurprisingly, dysregulation of PLCγ1 or PLCγ2 activity is associated with multiple maladies including immune disorders, cancers, and neurodegenerative diseases. Therefore, the modulation of either of these two enzymes has been suggested as a therapeutic strategy to combat these diseases. To aid in the discovery of PLCγ family enzyme modulators that could be developed into therapeutic agents, we have synthesized a high-throughput screening-amenable micellular fluorogenic substrate called C16CF3-coumarin. Herein, the ability of PLCγ1 and PLCγ2 to enzymatically process C16CF3-coumarin was confirmed, the micellular assay conditions were optimized, and the kinetics of the reaction were determined. A proof-of-principle pilot screen of the Library of Pharmacologically Active Compounds 1280 (LOPAC1280) was performed. This new substrate allows for an additional screening methodology to identify modulators of the PLCγ family of enzymes.
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Affiliation(s)
- Ramya Visvanathan
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States of America
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States of America
| | - Tadanobu Utsuki
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States of America
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
| | - Daniel E. Beck
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States of America
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
| | - W. Brent Clayton
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Emma Lendy
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States of America
| | - Kuai-lin Sun
- Cayman Chemical Company, Ann Arbor, MI, United States of America
| | - Yinghui Liu
- Cayman Chemical Company, Ann Arbor, MI, United States of America
| | - Kirk W. Hering
- Cayman Chemical Company, Ann Arbor, MI, United States of America
| | - Andrew Mesecar
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States of America
| | - Zhong-Yin Zhang
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States of America
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States of America
| | - Karson S. Putt
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States of America
- IUSM-Purdue TREAT-AD Center, West Lafayette, IN, United States of America
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Schmidt R, Ward CC, Dajani R, Armour-Garb Z, Ota M, Allain V, Hernandez R, Layeghi M, Xing G, Goudy L, Dorovskyi D, Wang C, Chen YY, Ye CJ, Shy BR, Gilbert LA, Eyquem J, Pritchard JK, Dodgson SE, Marson A. Base-editing mutagenesis maps alleles to tune human T cell functions. Nature 2024; 625:805-812. [PMID: 38093011 PMCID: PMC11065414 DOI: 10.1038/s41586-023-06835-6] [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: 05/12/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.
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Affiliation(s)
- Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
| | - Rama Dajani
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Zev Armour-Garb
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Mineto Ota
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent Allain
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Université Paris Cité, INSERM UMR976, Hôpital Saint-Louis, Paris, France
| | - Rosmely Hernandez
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Madeline Layeghi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Galen Xing
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Dmytro Dorovskyi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte Wang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Yan Yi Chen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, USA
- Arc Institute, Palo Alto, CA, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Stacie E Dodgson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics (IHG), University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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