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Alves E, Chopra A, Ram R, Currenti J, Kalams SA, Mallal SA, Phillips EJ, Gaudieri S. Underrepresentation of activating KIR gene expression in single-cell RNA-seq data is due to KIR gene misassignment. Eur J Immunol 2024; 54:e2350590. [PMID: 37944995 DOI: 10.1002/eji.202350590] [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: 06/05/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023]
Abstract
Standard single-cell RNA-sequencing alignment pipelines exhibit a propensity for misassigning killer immunoglobulin-like receptor (KIR) transcripts, thereby giving rise to inaccuracies in quantifying KIR expression. Alves et al. elucidated that these default workflows frequently misclassify activating KIR transcripts as inhibitory KIR expression, resulting in a skewed representation of the KIR repertoire.
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Affiliation(s)
- Eric Alves
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Ramesh Ram
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Jennifer Currenti
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- School of Medicine, Curtin University, Bentley, Western Australia, Australia
| | - Spyros A Kalams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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Graham LV, Fisher JG, Khakoo SI, Blunt MD. Targeting KIR as a novel approach to improve CAR-NK cell function. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2023; 7:230-235. [PMID: 38229912 PMCID: PMC7615527 DOI: 10.20517/jtgg.2023.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Chimeric antigen receptor (CAR) NK cells are demonstrating promising activity in clinical trials and possess a favorable safety profile compared to CAR-T cells. The Killer cell Immunoglobulin-like Receptors (KIR) have a critical role in the control of NK cell function, and recently, this family of activating and inhibitory receptors have been targeted to improve CAR-NK function. These strategies include the utilisation of inhibitory KIR to reduce trogocytosis-associated NK cell fratricide, the downregulation of inhibitory KIR on CAR-NK cells to alleviate HLA mediated suppression, the selection of CAR-NK cell donors enriched for activating KIR, and the use of activating KIR intracellular domains within novel CAR constructs. These pre-clinical studies demonstrate the potential utility of targeting the KIR to improve CAR-NK cell efficacy and patient outcomes.
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Affiliation(s)
- Lara V Graham
- School of Clinical and Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Jack G Fisher
- School of Clinical and Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Salim I Khakoo
- School of Clinical and Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Matthew D Blunt
- School of Clinical and Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
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Zhang M, Lam KP, Xu S. Natural Killer Cell Engagers (NKCEs): a new frontier in cancer immunotherapy. Front Immunol 2023; 14:1207276. [PMID: 37638058 PMCID: PMC10450036 DOI: 10.3389/fimmu.2023.1207276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/03/2023] [Indexed: 08/29/2023] Open
Abstract
Natural Killer (NK) cells are a type of innate lymphoid cells that play a crucial role in immunity by killing virally infected or tumor cells and secreting cytokines and chemokines. NK cell-mediated immunotherapy has emerged as a promising approach for cancer treatment due to its safety and effectiveness. NK cell engagers (NKCEs), such as BiKE (bispecific killer cell engager) or TriKE (trispecific killer cell engager), are a novel class of antibody-based therapeutics that exhibit several advantages over other cancer immunotherapies harnessing NK cells. By bridging NK and tumor cells, NKCEs activate NK cells and lead to tumor cell lysis. A growing number of NKCEs are currently undergoing development, with some already in clinical trials. However, there is a need for more comprehensive studies to determine how the molecular design of NKCEs affects their functionality and manufacturability, which are crucial for their development as off-the-shelf drugs for cancer treatment. In this review, we summarize current knowledge on NKCE development and discuss critical factors required for the production of effective NKCEs.
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Affiliation(s)
- Minchuan Zhang
- Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Kong-Peng Lam
- Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore, Singapore
| | - Shengli Xu
- Singapore Immunology Network, Agency for Science, Technology, and Research, Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Perce-da-Silva DDS, Joaquim TE, Aleixo ALQDC, Motta JPR, Lima-Junior JDC, Ribeiro-Alves M, de Oliveira-Ferreira J, Porto LCDMS, Banic DM, Amendoeira MRR. Influence of killer immunoglobulin-like receptors genes on the recurrence rate of ocular toxoplasmosis in Brazil. Mem Inst Oswaldo Cruz 2023; 118:e220203. [PMID: 37018796 PMCID: PMC10065411 DOI: 10.1590/0074-02760220203] [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: 08/31/2022] [Accepted: 02/14/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Recurrence is a hallmark of ocular toxoplasmosis (OT), and conditions that influence its occurrence remain a challenge. Natural killer cells (NK) are effectors cells whose primary is cytotoxic function against many parasites, including Toxoplasma gondii. Among the NK cell receptors, immunoglobulin-like receptors (KIR) deserve attention due to their high polymorphism. OBJECTIVES This study aimed to analyse the influence of KIR gene polymorphism in the course of OT infection and its association with recurrences after an active episode. METHODS Ninety-six patients from the Ophthalmologic Clinic of the National Institute of Infectology Evandro Chagas were followed for up to five years. After DNA extraction, genotyping of the patients was performed by polymerase chain reaction sequence-specific oligonucleotide (PCR-SSO) utilising Luminex equipment for reading. During follow-up, 60.4% had a recurrence. FINDINGS We identified 25 KIR genotypes and found a higher frequency of genotype 1 (31.7%) with worldwide distribution. We note that the KIR2DL2 inhibitor gene and the gene activator KIR2DS2 were more frequent in patients without recurrence. Additionally, we observed that individuals who carry these genes progressed recurrence episodes slowly compared to individuals who do not carry these genes. MAIN CONCLUSIONS The KIR2DL2 and KIR2DS2 are associated as possible protection markers against ocular toxoplasmosis recurrence (OTR).
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Affiliation(s)
- Daiana de Souza Perce-da-Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunologia Clínica, Rio de Janeiro, RJ, Brasil
- Centro Universitário Arthur Sá Earp Neto, Faculdade de Medicina de Petrópolis, Laboratório de Imunologia Básica e Aplicada, Petrópolis, RJ, Brasil
- + Corresponding authors: /
| | - Thays Euzebio Joaquim
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Toxoplasmose e outras Protozooses, Rio de Janeiro, RJ, Brasil
| | - Ana Luisa Quintella do Couto Aleixo
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Laboratório de Pesquisa Clínica em Oftalmologia Infecciosa, Rio de Janeiro, RJ, Brasil
| | | | - Josué da Costa Lima-Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunoparasitologia, Rio de Janeiro, RJ, Brasil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Centro de Pesquisa Clínica HIV/AIDS, Rio de Janeiro, RJ, Brasil
| | - Joseli de Oliveira-Ferreira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunoparasitologia, Rio de Janeiro, RJ, Brasil
| | | | - Dalma Maria Banic
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Imunologia Clínica, Rio de Janeiro, RJ, Brasil
| | - Maria Regina Reis Amendoeira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Toxoplasmose e outras Protozooses, Rio de Janeiro, RJ, Brasil
- + Corresponding authors: /
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Scott MA, Woolums AR, Karisch BB, Harvey KM, Capik SF. Impact of preweaning vaccination on host gene expression and antibody titers in healthy beef calves. Front Vet Sci 2022; 9:1010039. [PMID: 36225796 PMCID: PMC9549141 DOI: 10.3389/fvets.2022.1010039] [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: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The impact of preweaning vaccination for bovine respiratory viruses on cattle health and subsequent bovine respiratory disease morbidity has been widely studied yet questions remain regarding the impact of these vaccines on host response and gene expression. Six randomly selected calves were vaccinated twice preweaning (T1 and T3) with a modified live vaccine for respiratory pathogens and 6 randomly selected calves were left unvaccinated. Whole blood samples were taken at first vaccination (T1), seven days later (T2), at revaccination and castration (T3), and at weaning (T4), and utilized for RNA isolation and sequencing. Serum from T3 and T4 was analyzed for antibodies to BRSV, BVDV1a, and BHV1. Sequenced RNA for all 48 samples was bioinformatically processed with a HISAT2/StringTie pipeline, utilizing reference guided assembly with the ARS-UCD1.2 bovine genome. Differentially expressed genes were identified through analyzing the impact of time across all calves, influence of vaccination across treatment groups at each timepoint, and the interaction of time and vaccination. Calves, regardless of vaccine administration, demonstrated an increase in gene expression over time related to specialized proresolving mediator production, lipid metabolism, and stimulation of immunoregulatory T-cells. Vaccination was associated with gene expression related to natural killer cell activity and helper T-cell differentiation, enriching for an upregulation in Th17-related gene expression, and downregulated genes involved in complement system activity and coagulation mechanisms. Type-1 interferon production was unaffected by the influence of vaccination nor time. To our knowledge, this is the first study to evaluate mechanisms of vaccination and development in healthy calves through RNA sequencing analysis.
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Affiliation(s)
- Matthew A. Scott
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, United States
- *Correspondence: Matthew A. Scott
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Brandi B. Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Kelsey M. Harvey
- Prairie Research Unit, Mississippi State University, Prairie, MS, United States
| | - Sarah F. Capik
- Texas A&M AgriLife Research, Texas A&M University System, Amarillo, TX, United States
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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