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Dampier W, Berman R, Nonnemacher MR, Wigdahl B. Computational analysis of cas proteins unlocks new potential in HIV-1 targeted gene therapy. Front Genome Ed 2024; 5:1248982. [PMID: 38239625 PMCID: PMC10794619 DOI: 10.3389/fgeed.2023.1248982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction: The human immunodeficiency virus type 1 (HIV-1) pandemic has been slowed with the advent of anti-retroviral therapy (ART). However, ART is not a cure and as such has pushed the disease into a chronic infection. One potential cure strategy that has shown promise is the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas gene editing system. It has recently been shown to successfully edit and/or excise the integrated provirus from infected cells and inhibit HIV-1 in vitro, ex vivo, and in vivo. These studies have primarily been conducted with SpCas9 or SaCas9. However, additional Cas proteins are discovered regularly and modifications to these known proteins are being engineered. The alternative Cas molecules have different requirements for protospacer adjacent motifs (PAMs) which impact the possible targetable regions of HIV-1. Other modifications to the Cas protein or gRNA handle impact the tolerance for mismatches between gRNA and the target. While reducing off-target risk, this impacts the ability to fully account for HIV-1 genetic variability. Methods: This manuscript strives to examine these parameter choices using a computational approach for surveying the suitability of a Cas editor for HIV-1 gene editing. The Nominate, Diversify, Narrow, Filter (NDNF) pipeline measures the safety, broadness, and effectiveness of a pool of potential gRNAs for any PAM. This technique was used to evaluate 46 different potential Cas editors for their HIV therapeutic potential. Results: Our examination revealed that broader PAMs that improve the targeting potential of editors like SaCas9 and LbCas12a have larger pools of useful gRNAs, while broader PAMs reduced the pool of useful SpCas9 gRNAs yet increased the breadth of targetable locations. Investigation of the mismatch tolerance of Cas editors indicates a 2-missmatch tolerance is an ideal balance between on-target sensitivity and off-target specificity. Of all of the Cas editors examined, SpCas-NG and SPRY-Cas9 had the highest number of overall safe, broad, and effective gRNAs against HIV. Discussion: Currently, larger proteins and wider PAMs lead to better targeting capacity. This implies that research should either be targeted towards delivering longer payloads or towards increasing the breadth of currently available small Cas editors. With the discovery and adoption of additional Cas editors, it is important for researchers in the HIV-1 gene editing field to explore the wider world of Cas editors.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States
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Khan A, Paneerselvam N, Lawson BR. Antiretrovirals to CCR5 CRISPR/Cas9 gene editing - A paradigm shift chasing an HIV cure. Clin Immunol 2023; 255:109741. [PMID: 37611838 PMCID: PMC10631514 DOI: 10.1016/j.clim.2023.109741] [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: 07/18/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
The evolution of drug-resistant viral strains and anatomical and cellular reservoirs of HIV pose significant clinical challenges to antiretroviral therapy. CCR5 is a coreceptor critical for HIV host cell fusion, and a homozygous 32-bp gene deletion (∆32) leads to its loss of function. Interestingly, an allogeneic HSCT from an HIV-negative ∆32 donor to an HIV-1-infected recipient demonstrated a curative approach by rendering the recipient's blood cells resistant to viral entry. Ex vivo gene editing tools, such as CRISPR/Cas9, hold tremendous promise in generating allogeneic HSC grafts that can potentially replace allogeneic ∆32 HSCTs. Here, we review antiretroviral therapeutic challenges, clinical successes, and failures of allogeneic and allogeneic ∆32 HSCTs, and newer exciting developments within CCR5 editing using CRISPR/Cas9 in the search to cure HIV.
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Affiliation(s)
- Amber Khan
- The Scintillon Research Institute, 6868 Nancy Ridge Drive, San Diego, CA 92121, USA
| | | | - Brian R Lawson
- The Scintillon Research Institute, 6868 Nancy Ridge Drive, San Diego, CA 92121, USA.
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Xu H, Lin S, Zhou Z, Li D, Zhang X, Yu M, Zhao R, Wang Y, Qian J, Li X, Li B, Wei C, Chen K, Yoshimura T, Wang JM, Huang J. New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine. Cell Mol Immunol 2023:10.1038/s41423-023-01032-x. [PMID: 37198402 DOI: 10.1038/s41423-023-01032-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Over the past thirty years, the importance of chemokines and their seven-transmembrane G protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine interactions with receptors trigger signaling pathway activity to form a network fundamental to diverse immune processes, including host homeostasis and responses to disease. Genetic and nongenetic regulation of both the expression and structure of chemokines and receptors conveys chemokine functional heterogeneity. Imbalances and defects in the system contribute to the pathogenesis of a variety of diseases, including cancer, immune and inflammatory diseases, and metabolic and neurological disorders, which render the system a focus of studies aiming to discover therapies and important biomarkers. The integrated view of chemokine biology underpinning divergence and plasticity has provided insights into immune dysfunction in disease states, including, among others, coronavirus disease 2019 (COVID-19). In this review, by reporting the latest advances in chemokine biology and results from analyses of a plethora of sequencing-based datasets, we outline recent advances in the understanding of the genetic variations and nongenetic heterogeneity of chemokines and receptors and provide an updated view of their contribution to the pathophysiological network, focusing on chemokine-mediated inflammation and cancer. Clarification of the molecular basis of dynamic chemokine-receptor interactions will help advance the understanding of chemokine biology to achieve precision medicine application in the clinic.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China
| | - Ziyun Zhou
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Duoduo Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xiting Zhang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Muhan Yu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Ruoyi Zhao
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Yiheng Wang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Junru Qian
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xinyi Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Bohan Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Chuhan Wei
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China.
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China.
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
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Wan S, Zhou T, Che R, Li Y, Peng J, Wu Y, Gu S, Cheng J, Hua X. CT-based machine learning radiomics predicts CCR5 expression level and survival in ovarian cancer. J Ovarian Res 2023; 16:1. [PMID: 36597144 PMCID: PMC9809527 DOI: 10.1186/s13048-022-01089-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE We aimed to evaluate the prognostic value of C-C motif chemokine receptor type 5 (CCR5) expression level for patients with ovarian cancer and to establish a radiomics model that can predict CCR5 expression level using The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA) database. METHODS A total of 343 cases of ovarian cancer from the TCGA were used for the gene-based prognostic analysis. Fifty seven cases had preoperative computed tomography (CT) images stored in TCIA with genomic data in TCGA were used for radiomics feature extraction and model construction. 89 cases with both TCGA and TCIA clinical data were used for radiomics model evaluation. After feature extraction, a radiomics signature was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis. A prognostic scoring system incorporating radiomics signature based on CCR5 expression level and clinicopathologic risk factors was proposed for survival prediction. RESULTS CCR5 was identified as a differentially expressed prognosis-related gene in tumor and normal sample, which were involved in the regulation of immune response and tumor invasion and metastasis. Four optimal radiomics features were selected to predict overall survival. The performance of the radiomics model for predicting the CCR5 expression level with 10-fold cross- validation achieved Area Under Curve (AUCs) of 0.770 and of 0.726, respectively, in the training and validation sets. A predictive nomogram was generated based on the total risk score of each patient, the AUCs of the time-dependent receiver operating characteristic (ROC) curve of the model was 0.8, 0.673 and 0.792 for 1-year, 3-year and 5-year, respectively. Along with clinical features, important imaging biomarkers could improve the overall survival accuracy of the prediction model. CONCLUSION The expression levels of CCR5 can affect the prognosis of patients with ovarian cancer. CT-based radiomics could serve as a new tool for prognosis prediction.
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Affiliation(s)
- Sheng Wan
- grid.24516.340000000123704535Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China
| | - Tianfan Zhou
- grid.24516.340000000123704535Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China
| | - Ronghua Che
- grid.24516.340000000123704535Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China
| | - Ying Li
- grid.412793.a0000 0004 1799 5032Reproductive Medicine Center, Tongji Hospital Affiliated to Tongji University, Shanghai, China
| | - Jing Peng
- grid.24516.340000000123704535Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China
| | - Yuelin Wu
- grid.24516.340000000123704535Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China
| | - Shengyi Gu
- grid.24516.340000000123704535Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China
| | - Jiejun Cheng
- grid.24516.340000000123704535Department of Radiology, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China ,grid.24516.340000000123704535Department of Radiology, Shanghai First Maternity and infant hospital, Shanghai Tongji University School of Medicine, 2699 West Gaoke Road, Shanghai, 201204 China
| | - Xiaolin Hua
- grid.24516.340000000123704535Department of Gynecology and Obstetrics, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China ,grid.24516.340000000123704535Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092 China ,grid.24516.340000000123704535Department of Obstetrics, Shanghai First Maternity and infant hospital, Shanghai Tongji University School of Medicine, 2699 West Gaoke Road, Shanghai, 201204 China
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Closing the Door with CRISPR: Genome Editing of CCR5 and CXCR4 as a Potential Curative Solution for HIV. BIOTECH 2022; 11:biotech11030025. [PMID: 35892930 PMCID: PMC9326690 DOI: 10.3390/biotech11030025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection can be controlled by anti-retroviral therapy. Suppressing viral replication relies on life-long medication, but anti-retroviral therapy is not without risks to the patient. Therefore, it is important that permanent cures for HIV infection are developed. Three patients have been described to be completely cured from HIV infection in recent years. In all cases, patients received a hematopoietic stem cell (HSC) transplantation due to a hematological malignancy. The HSCs were sourced from autologous donors that expressed a homozygous mutation in the CCR5 gene. This mutation results in a non-functional receptor, and confers resistance to CCR5-tropic HIV strains that rely on CCR5 to enter host cells. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system is one of the methods of choice for gene editing, and the CRISPR/Cas system has been employed to target loci of interest in the context of HIV. Here, the current literature regarding CRISPR-mediated genome editing to render cells resistant to HIV (re)-infection by knocking out the co-receptors CCR5 and CXCR4 is summarized, and an outlook is provided regarding future (research) directions.
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Hawsawi YM, Shams A, Theyab A, Siddiqui J, Barnawee M, Abdali WA, Marghalani NA, Alshelali NH, Al-Sayed R, Alzahrani O, Alqahtani A, Alsulaiman AM. The State-of-the-Art of Gene Editing and its Application to Viral Infections and Diseases Including COVID-19. Front Cell Infect Microbiol 2022; 12:869889. [PMID: 35782122 PMCID: PMC9241565 DOI: 10.3389/fcimb.2022.869889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/09/2022] [Indexed: 11/26/2022] Open
Abstract
Gene therapy delivers a promising hope to cure many diseases and defects. The discovery of gene-editing technology fueled the world with valuable tools that have been employed in various domains of science, medicine, and biotechnology. Multiple means of gene editing have been established, including CRISPR/Cas, ZFNs, and TALENs. These strategies are believed to help understand the biological mechanisms of disease progression. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been designated the causative virus for coronavirus disease 2019 (COVID-19) that emerged at the end of 2019. This viral infection is a highly pathogenic and transmissible disease that caused a public health pandemic. As gene editing tools have shown great success in multiple scientific and medical areas, they could eventually contribute to discovering novel therapeutic and diagnostic strategies to battle the COVID-19 pandemic disease. This review aims to briefly highlight the history and some of the recent advancements of gene editing technologies. After that, we will describe various biological features of the CRISPR-Cas9 system and its diverse implications in treating different infectious diseases, both viral and non-viral. Finally, we will present current and future advancements in combating COVID-19 with a potential contribution of the CRISPR system as an antiviral modality in this battle.
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Affiliation(s)
- Yousef M. Hawsawi
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- *Correspondence: Yousef M. Hawsawi, ; Anwar Shams, ;
| | - Anwar Shams
- Department of Pharmacology, College of Medicine, Taif University, Mecca, Saudi Arabia
- *Correspondence: Yousef M. Hawsawi, ; Anwar Shams, ;
| | - Abdulrahman Theyab
- College of Medicine, Al-Faisal University, Riyadh, Saudi Arabia
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia
| | - Jumana Siddiqui
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mawada Barnawee
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Wed A. Abdali
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Nada A. Marghalani
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Nada H. Alshelali
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Rawan Al-Sayed
- Research Center, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Othman Alzahrani
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
- Genome and Biotechnology Unit, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Alanoud Alqahtani
- Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
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