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Tiwari R, Singh VK, Rajneesh, Kumar A, Gautam V, Kumar R. MHC tetramer technology: Exploring T cell biology in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:327-345. [PMID: 38762273 DOI: 10.1016/bs.apcsb.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Major histocompatibility complex (MHC) tetramers stand as formidable tools within T cell biology, facilitating the exploration and comprehension of immune responses. These artificial molecules, comprising four bound MHC molecules, typically with a specified peptide and a fluorescent label, play a pivotal role in characterizing T cell subsets, monitoring clonal expansion, and unraveling T cell dynamics during responses to infections or immunotherapies. Beyond their applications in T cell biology, MHC tetramers prove valuable in investigating a spectrum of diseases such as infectious diseases, autoimmune disorders, and cancers. Their instrumental role extends to vaccine research and development. Notably, when appropriately configured, tetramers transcend T cell biology research and find utility in exploring natural killer T cells and contributing to specific T cell clonal deletions.
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Affiliation(s)
- Rahul Tiwari
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vishal Kumar Singh
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajneesh
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Awnish Kumar
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vibhav Gautam
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajiv Kumar
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
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Omotoso MO, Lanis MR, Schneck JP. Artificial Antigen-Presenting Cell Fabrication for Murine T Cell Expansion. Curr Protoc 2024; 4:e976. [PMID: 38400601 PMCID: PMC11062398 DOI: 10.1002/cpz1.976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Antigen-presenting cells (APCs), such as dendritic cells and macrophages, have a unique ability to survey the body and present information to T cells via peptide-loaded major histocompatibility complexes (signal 1). This presentation, along with a co-stimulatory signal (signal 2), leads to activation and subsequent expansion of T cells. This process can be harnessed and utilized for therapeutic applications, but the use of patient-derived APCs can be complex and inefficient. Alternatively, artificial APCs (aAPCs) provide a simplified method to achieve T cell activation by presenting the two necessary stimulatory signals. This protocol describes the utilization of magnetic nanoparticles and stimulatory proteins to create aAPCs that can be employed for activating and expanding antigen-specific T cells for both basic and translational immunology and immunotherapy studies. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Protein and particle modification for aAPC fabrication Basic Protocol 2: aAPC validation by immunolabeling of conjugated protein Support Protocol 1: Quantification of aAPC stock concentration Basic Protocol 3: Determination of aAPC usage for murine CD8+ T cell activation Support Protocol 2: Isolation of murine CD8+ T cells.
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Affiliation(s)
- Mary O. Omotoso
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD
- Departments of Pathology and Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mara R. Lanis
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD
- Departments of Pathology and Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jonathan P. Schneck
- Departments of Pathology and Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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Lin Y, Chen CY, Ku YC, Wang LC, Hung CC, Lin ZQ, Chen BH, Hung JT, Sun YC, Hung KF. A modified SELEX approach to identify DNA aptamers with binding specificity to the major histocompatibility complex presenting ovalbumin model antigen. RSC Adv 2023; 13:32681-32693. [PMID: 37936644 PMCID: PMC10626974 DOI: 10.1039/d3ra04686a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
Aptamers have sparked significant interest in cell recognition because of their superior binding specificity and biocompatibility. Cell recognition can be mediated by targeting the major histocompatibility complex (MHC) that presents short peptides derived from intracellular antigens. Although numerous antibodies have demonstrated a specific affinity for the peptide-MHC complex, the number of aptamers that exhibit comparable characteristics is limited. Aptamers are usually selected from large libraries via the Systemic Evolution of Ligands by Exponential Enrichment (SELEX), an iterative process of selection and PCR amplification to enrich a pool of aptamers with high affinity. However, the success rate of aptamer identification is low, possibly due to the presence of complementary sequences or sequences rich in guanine and cytosine that are less accessible for primers. Here, we modified SELEX by employing systemic consecutive selections with minimal PCR amplification. We also modified the analysis by selecting aptamers that were identified in multiple selection rounds rather than those that are highly enriched. Using this approach, we were able to identify two aptamers with binding specificity to cells expressing the ovalbumin alloantigen as a proof of concept. These two aptamers were also discovered among the top 150 abundant candidates, despite not being highly enriched, by performing conventional SELEX. Additionally, we found that highly enriched aptamers tend to contain fractions of the primer sequence and have minimal target affinity. Candidate aptamers are easily missed in the conventional SELEX process. Therefore, our modification for SELEX may facilitate the identification of aptamers for more application in diverse biomedical fields. Significance: we modify the conventional method to improve the efficiency in the identification of the aptamer, a single strand of nucleic acid with binding specificity to the target molecule, showing as a proof of concept that this approach is particularly useful to select aptamers that can selectively bind to cells presenting a particular peptide by the major histocompatibility complex (MHC) on the cell surface. Given that cancer cells may express mutant peptide-MHC complexes that are distinct from those expressed by normal cells, this study sheds light on the potential application of aptamers to cancer cell targeting.
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Affiliation(s)
- Yang Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Yu-Chia Ku
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Li-Chin Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University Taipei Taiwan
| | - Chia-Chien Hung
- School of Computer Science, Georgia Institute of Technology Atlanta GA USA
| | - Zhi-Qian Lin
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | - Bing-Hong Chen
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
| | | | - Yi-Chen Sun
- School of Medicine, Tzu-Chi University Hualien Taiwan
- Department of Ophthalmology, Taipei Tzu Chi Hospital, The Buddhist Tzu Chi Medical Foundation New Taipei City Taiwan
| | - Kai-Feng Hung
- Department of Medical Research, Taipei Veterans General Hospital 201, Section 2, Shi-Pai Road Taipei 112 Taiwan +886-2-28712121-7382
- Department of Dentistry, School of Dentistry, National Yang Ming Chiao Tung University Taipei Taiwan
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Bolivar AM, Duzagac F, Sinha KM, Vilar E. Advances in vaccine development for cancer prevention and treatment in Lynch Syndrome. Mol Aspects Med 2023; 93:101204. [PMID: 37478804 PMCID: PMC10528439 DOI: 10.1016/j.mam.2023.101204] [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: 04/13/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Lynch Syndrome (LS) is one of the most common hereditary cancer syndromes, and is caused by mutations in one of the four DNA mismatch repair (MMR) genes, namely MLH1, MSH2, MSH6 and PMS2. Tumors developed by LS carriers display high levels of microsatellite instability, which leads to the accumulation of large numbers of mutations, among which frameshift insertion/deletions (indels) within microsatellite (MS) loci are the most common. As a result, MMR-deficient (MMRd) cells generate increased rates of tumor-specific neoantigens (neoAgs) that can be recognized by the immune system to activate cancer cell killing. In this context, LS is an ideal disease to leverage immune-interception strategies. Therefore, the identification of these neoAgs is an ongoing effort for the development of LS cancer preventive vaccines. In this review, we summarize the computational methods used for in silico neoAg prediction, including their challenges, and the experimental techniques used for in vitro validation of their immunogenicity. In addition, we outline results from past and on-going vaccine clinical trials and highlight avenues for improvement and future directions.
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Affiliation(s)
- Ana M Bolivar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fahriye Duzagac
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna M Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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Szittner Z, Péter B, Kurunczi S, Székács I, Horváth R. Functional blood cell analysis by label-free biosensors and single-cell technologies. Adv Colloid Interface Sci 2022; 308:102727. [DOI: 10.1016/j.cis.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
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Kudlay D, Kofiadi I, Khaitov M. Peculiarities of the T Cell Immune Response in COVID-19. Vaccines (Basel) 2022; 10:242. [PMID: 35214700 PMCID: PMC8877307 DOI: 10.3390/vaccines10020242] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/11/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Understanding the T cell response to SARS-CoV-2 is critical to vaccine development, epidemiological surveillance, and control strategies for this disease. This review provides data from studies of the immune response in coronavirus infections. It describes general mechanisms of immunity, its T cell components, and presents a detailed scheme of the T cell response in SARS-CoV-2 infection, including from the standpoint of determining the most promising targets for assessing its level. In addition, we reviewed studies investigating post-vaccination immunity in the development of vaccines against COVID-19. This review also includes the peculiarities of immunity in different age and gender groups, and in the presence of a number of factors, for example, comorbidity or disease severity. This study summarizes the most informative methods for assessing the immune response to SARS-CoV-2 infection.
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Affiliation(s)
- Dmitry Kudlay
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Ilya Kofiadi
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Immunology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Musa Khaitov
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Immunology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Baek KY, Kim S, Koh HR. Molecular Tension Probes to Quantify Cell-Generated Mechanical Forces. Mol Cells 2022; 45:26-32. [PMID: 35114645 PMCID: PMC8819489 DOI: 10.14348/molcells.2022.2049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 11/27/2022] Open
Abstract
Living cells generate, sense, and respond to mechanical forces through their interaction with neighboring cells or extracellular matrix, thereby regulating diverse cellular processes such as growth, motility, differentiation, and immune responses. Dysregulation of mechanosensitive signaling pathways is found associated with the development and progression of various diseases such as cancer. Yet, little is known about the mechanisms behind mechano-regulation, largely due to the limited availability of tools to study it at the molecular level. The recent development of molecular tension probes allows measurement of cellular forces exerted by single ligandreceptor interaction, which has helped in revealing the hitherto unknown mechanistic details of various mechanosensitive processes in living cells. Here, we provide an introductory overview of two methods based on molecular tension probes, tension gauge tether (TGT), and molecular tension fluorescence microscopy (MTFM). TGT utilizes the irreversible rupture of double-stranded DNA tether upon application of force in the piconewton (pN) range, whereas MTFM utilizes the reversible extension of molecular springs such as polymer or single-stranded DNA hairpin under applied pN forces. Specifically, the underlying principle of how molecular tension probes measure cell-generated mechanical forces and their applications to mechanosensitive biological processes are described.
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Affiliation(s)
- Kyung Yup Baek
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Seohyun Kim
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Hye Ran Koh
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
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