1
|
Zaongo SD, Chen Y. Metformin may be a viable adjunctive therapeutic option to potentially enhance immune reconstitution in HIV-positive immunological non-responders. Chin Med J (Engl) 2023; 136:2147-2155. [PMID: 37247620 PMCID: PMC10508460 DOI: 10.1097/cm9.0000000000002493] [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] [Received: 12/08/2022] [Indexed: 05/31/2023] Open
Abstract
ABSTRACT Incomplete immune reconstitution remains a global challenge for human immunodeficiency virus (HIV) treatment in the present era of potent antiretroviral therapy (ART), especially for those individuals referred to as immunological non-responders (INRs), who exhibit dramatically low CD4 + T-cell counts despite the use of effective antiretroviral therapy, with long-term inhibition of viral replication. In this review, we provide a critical overview of the concept of ART-treated HIV-positive immunological non-response, and also explain the known mechanisms which could potentially account for the emergence of immunological non-response in some HIV-infected individuals treated with appropriate and effective ART. We found that immune cell exhaustion, combined with chronic inflammation and the HIV-associated dysbiosis syndrome, may represent strategic aspects of the immune response that may be fundamental to incomplete immune recovery. Interestingly, we noted from the literature that metformin exhibits properties and characteristics that may potentially be useful to specifically target immune cell exhaustion, chronic inflammation, and HIV-associated gut dysbiosis syndrome, mechanisms which are now recognized for their critically important complicity in HIV disease-related incomplete immune recovery. In light of evidence discussed in this review, it can be seen that metformin may be of particularly favorable use if utilized as adjunctive treatment in INRs to potentially enhance immune reconstitution. The approach described herein may represent a promising area of therapeutic intervention, aiding in significantly reducing the risk of HIV disease progression and mortality in a particularly vulnerable subgroup of HIV-positive individuals.
Collapse
Affiliation(s)
| | - Yaokai Chen
- Division of Infectious diseases, Chongqing Public Health Medical Center, Chongqing 400036, China
| |
Collapse
|
2
|
Pan Y, Landis JT, Moorad R, Wu D, Marron JS, Dittmer DP. The Poisson distribution model fits UMI-based single-cell RNA-sequencing data. BMC Bioinformatics 2023; 24:256. [PMID: 37330471 PMCID: PMC10276395 DOI: 10.1186/s12859-023-05349-2] [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: 01/26/2023] [Accepted: 05/24/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Modeling of single cell RNA-sequencing (scRNA-seq) data remains challenging due to a high percentage of zeros and data heterogeneity, so improved modeling has strong potential to benefit many downstream data analyses. The existing zero-inflated or over-dispersed models are based on aggregations at either the gene or the cell level. However, they typically lose accuracy due to a too crude aggregation at those two levels. RESULTS We avoid the crude approximations entailed by such aggregation through proposing an independent Poisson distribution (IPD) particularly at each individual entry in the scRNA-seq data matrix. This approach naturally and intuitively models the large number of zeros as matrix entries with a very small Poisson parameter. The critical challenge of cell clustering is approached via a novel data representation as Departures from a simple homogeneous IPD (DIPD) to capture the per-gene-per-cell intrinsic heterogeneity generated by cell clusters. Our experiments using real data and crafted experiments show that using DIPD as a data representation for scRNA-seq data can uncover novel cell subtypes that are missed or can only be found by careful parameter tuning using conventional methods. CONCLUSIONS This new method has multiple advantages, including (1) no need for prior feature selection or manual optimization of hyperparameters; (2) flexibility to combine with and improve upon other methods, such as Seurat. Another novel contribution is the use of crafted experiments as part of the validation of our newly developed DIPD-based clustering pipeline. This new clustering pipeline is implemented in the R (CRAN) package scpoisson.
Collapse
Affiliation(s)
- Yue Pan
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Justin T Landis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Razia Moorad
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Adam School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - J S Marron
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, USA
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, USA.
| |
Collapse
|
3
|
Baroncini L, Bredl S, Nicole KP, Speck RF. The Humanized Mouse Model: What Added Value Does It Offer for HIV Research? Pathogens 2023; 12:pathogens12040608. [PMID: 37111494 PMCID: PMC10142098 DOI: 10.3390/pathogens12040608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
In the early 2000s, novel humanized mouse models based on the transplantation of human hematopoietic stem and progenitor cells (HSPCs) into immunocompromised mice were introduced (hu mice). The human HSPCs gave rise to a lymphoid system of human origin. The HIV research community has greatly benefitted from these hu mice. Since human immunodeficiency virus (HIV) type 1 infection results in a high-titer disseminated HIV infection, hu mice have been of great value for all types of HIV research from pathogenesis to novel therapies. Since the first description of this new generation of hu mice, great efforts have been expended to improve humanization by creating other immunodeficient mouse models or supplementing mice with human transgenes to improve human engraftment. Many labs have their own customized hu mouse models, making comparisons quite difficult. Here, we discuss the different hu mouse models in the context of specific research questions in order to define which characteristics should be considered when determining which hu mouse model is appropriate for the question posed. We strongly believe that researchers must first define their research question and then determine whether a hu mouse model exists, allowing the research question to be studied.
Collapse
Affiliation(s)
- Luca Baroncini
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Simon Bredl
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Kadzioch P Nicole
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Roberto F Speck
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091 Zurich, Switzerland
| |
Collapse
|
4
|
Zaongo SD, Harypursat V, Chen Y. Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature. Front Immunol 2022; 13:828860. [PMID: 35185920 PMCID: PMC8850777 DOI: 10.3389/fimmu.2022.828860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
Abstract
Knowledge gaps remain in the understanding of HIV disease establishment and progression. Scientists continue to strive in their endeavor to elucidate the precise underlying immunopathogenic mechanisms of HIV-related disease, in order to identify possible preventive and therapeutic targets. A useful tool in the quest to reveal some of the enigmas related to HIV infection and disease is the single-cell sequencing (scRNA-seq) technique. With its proven capacity to elucidate critical processes in cell formation and differentiation, to decipher critical hematopoietic pathways, and to understand the regulatory gene networks that predict immune function, scRNA-seq is further considered to be a potentially useful tool to explore HIV immunopathogenesis. In this article, we provide an overview of single-cell sequencing platforms, before delving into research findings gleaned from the use of single cell sequencing in HIV research, as published in recent literature. Finally, we describe two important avenues of research that we believe should be further investigated using the single-cell sequencing technique.
Collapse
Affiliation(s)
- Silvere D Zaongo
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| |
Collapse
|
5
|
Gillgrass A, Wessels JM, Yang JX, Kaushic C. Advances in Humanized Mouse Models to Improve Understanding of HIV-1 Pathogenesis and Immune Responses. Front Immunol 2021; 11:617516. [PMID: 33746940 PMCID: PMC7973037 DOI: 10.3389/fimmu.2020.617516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Although antiretroviral therapy has transformed human immunodeficiency virus-type 1 (HIV-1) from a deadly infection into a chronic disease, it does not clear the viral reservoir, leaving HIV-1 as an uncurable infection. Currently, 1.2 million new HIV-1 infections occur globally each year, with little decrease over many years. Therefore, additional research is required to advance the current state of HIV management, find potential therapeutic strategies, and further understand the mechanisms of HIV pathogenesis and prevention strategies. Non-human primates (NHP) have been used extensively in HIV research and have provided critical advances within the field, but there are several issues that limit their use. Humanized mouse (Hu-mouse) models, or immunodeficient mice engrafted with human immune cells and/or tissues, provide a cost-effective and practical approach to create models for HIV research. Hu-mice closely parallel multiple aspects of human HIV infection and disease progression. Here, we highlight how innovations in Hu-mouse models have advanced HIV-1 research in the past decade. We discuss the effect of different background strains of mice, of modifications on the reconstitution of the immune cells, and the pros and cons of different human cells and/or tissue engraftment methods, on the ability to examine HIV-1 infection and immune response. Finally, we consider the newest advances in the Hu-mouse models and their potential to advance research in emerging areas of mucosal infections, understand the role of microbiota and the complex issues in HIV-TB co-infection. These innovations in Hu-mouse models hold the potential to significantly enhance mechanistic research to develop novel strategies for HIV prevention and therapeutics.
Collapse
Affiliation(s)
- Amy Gillgrass
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Jocelyn M. Wessels
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada
| | - Jack X. Yang
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Charu Kaushic
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| |
Collapse
|
6
|
Guo R, Lü M, Cao F, Wu G, Gao F, Pang H, Li Y, Zhang Y, Xing H, Liang C, Lyu T, Du C, Li Y, Guo R, Xie X, Li W, Liu D, Song Y, Jiang Z. Single-cell map of diverse immune phenotypes in the acute myeloid leukemia microenvironment. Biomark Res 2021; 9:15. [PMID: 33648605 PMCID: PMC7919996 DOI: 10.1186/s40364-021-00265-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Knowledge of immune cell phenotypes, function, and developmental trajectory in acute myeloid leukemia (AML) microenvironment is essential for understanding mechanisms of evading immune surveillance and immunotherapy response of targeting special microenvironment components. METHODS Using a single-cell RNA sequencing (scRNA-seq) dataset, we analyzed the immune cell phenotypes, function, and developmental trajectory of bone marrow (BM) samples from 16 AML patients and 4 healthy donors, but not AML blasts. RESULTS We observed a significant difference between normal and AML BM immune cells. Here, we defined the diversity of dendritic cells (DC) and macrophages in different AML patients. We also identified several unique immune cell types including T helper cell 17 (TH17)-like intermediate population, cytotoxic CD4+ T subset, T cell: erythrocyte complexes, activated regulatory T cells (Treg), and CD8+ memory-like subset. Emerging AML cells remodels the BM immune microenvironment powerfully, leads to immunosuppression by accumulating exhausted/dysfunctional immune effectors, expending immune-activated types, and promoting the formation of suppressive subsets. CONCLUSION Our results provide a comprehensive AML BM immune cell census, which can help to select pinpoint targeted drug and predict efficacy of immunotherapy.
Collapse
Affiliation(s)
- Rongqun Guo
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mengdie Lü
- Joint National Laboratory for Antibody Drug Engineering, Key Laboratory of Cellular and Molecular Immunology of Henan Province, Institute of Translational Medicine, School of Basic Medicine, Henan University, Kaifeng, Henan, China
| | - Fujiao Cao
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Guanghua Wu
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan, China
| | - Fengcai Gao
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haili Pang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yadan Li
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan, China
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Yinyin Zhang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haizhou Xing
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chunyan Liang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Tianxin Lyu
- The Academy of Medical Science, College of Medical, Zhengzhou University, Zhengzhou, Henan, China
- The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Chunyan Du
- Laboratory Animal Center, School of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yingmei Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Rong Guo
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinsheng Xie
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wei Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Delong Liu
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Yongping Song
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Zhongxing Jiang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|