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Ertosun MG, Özkan Ö, Darbaş Ş, Özel D, BİLGE U, Sayin Ekinci N, Yilmaz VT, Uçar F, Koçak H, Özkan Ö. The relationship between COVID-19 and HLA in kidney transplant recipients, an evaluation of predictive and prognostic factors. Clin Transplant 2022; 36:e14525. [PMID: 34726292 PMCID: PMC8646315 DOI: 10.1111/ctr.14525] [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: 06/09/2021] [Revised: 10/14/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Abstract
INTRODUCTION The purpose of this study was to determine the predictive and prognostic factors for COVID-19 infection and its relationship with human leukocyte antigen (HLA) in kidney transplant recipients. MATERIAL AND METHOD Three hundred fifty kidney transplant recipients were included in the study. Recipients were divided into two groups: COVID-19(+) (n = 100) and control (n = 250). The relationships between HLA frequencies, COVID-19 infection, and prognostic factors (age, donor type, immunosuppression protocol, etc.) were then evaluated. Logistic regression analysis, heatmap, and decision tree methods were used to determine predictive and prognostic factors. The study was performed retrospectively. RESULTS Advanced age and deceased transplantation emerged as predictive of SARS-CoV-2 infection, while the presence of HLA-A*11, the HLA match ratio, and high-dose tacrolimus were identified as prognostic factors in kidney transplant recipients. HLA-A10, HLA-B*13, HLA-B22, and HLA-B*55 were shown to be associated with SARS-CoV-2 infection at univariate analysis, and HLA-B*57, HLA-DRB1*11, and HLA-DRB1*13 at logistic regression analysis. CONCLUSION HLA-A10, HLA-B*13, HLA-B*55, HLA-B*57, HLA-DRB1*11, and HLA-DRB1*13 were identified for the first time in the literature associated with SARS-CoV-2 infection in kidney transplant recipients.
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Affiliation(s)
- Mustafa Gökhan Ertosun
- Department of Plastic, Reconstructive, and Aesthetic SurgeryAkdeniz University School of MedicineAntalyaTurkey
- Tissue Typing and Transplantation LaboratoryAkdeniz University HospitalAntalyaTurkey
| | - Özlenen Özkan
- Department of Plastic, Reconstructive, and Aesthetic SurgeryAkdeniz University School of MedicineAntalyaTurkey
| | - Şule Darbaş
- Tissue Typing and Transplantation LaboratoryAkdeniz University HospitalAntalyaTurkey
| | - Deniz Özel
- Statistical ConsultingApplication and Research CenterAkdeniz UniversityAntalyaTurkey
| | - Uğur BİLGE
- Department of Biostatistics and Medical InformaticsFaculty of MedicineAkdeniz UniversityAntalyaTurkey
| | - Nurten Sayin Ekinci
- Tissue Typing and Transplantation LaboratoryAkdeniz University HospitalAntalyaTurkey
| | - Vural Taner Yilmaz
- Department of Internal Medicine Division of NephrologyAkdeniz University School of MedicineAntalyaTurkey
| | - Fahri Uçar
- Tissue Typing and Transplantation LaboratoryAkdeniz University HospitalAntalyaTurkey
- Department of Medical Biology and GeneticsAkdeniz University School of MedicineAntalyaTurkey
| | - Hüseyin Koçak
- Department of Internal Medicine Division of NephrologyAkdeniz University School of MedicineAntalyaTurkey
| | - Ömer Özkan
- Department of Plastic, Reconstructive, and Aesthetic SurgeryAkdeniz University School of MedicineAntalyaTurkey
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Koufaris C, Nicolaidou V. Glutamine addiction in virus-infected mammalian cells: A target of the innate immune system? Med Hypotheses 2021; 153:110620. [PMID: 34130112 DOI: 10.1016/j.mehy.2021.110620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/30/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022]
Abstract
Control of core cell metabolism is a key aspect of the evolutionary conflict between viruses and the host's defence mechanisms. From their side, the invading viruses press the accelerator on their host cell's glycolysis, fatty acid, and glutaminolytic metabolic processes among others. It is also well established that activation of innate immune system responses modulates facets of metabolism such as that of polyamine, cholesterol, tryptophan and many more. But what about glutamine, a proteogenic amino acid that is a crucial nutrient for multiple cellular biosynthetic processes? Although mammalian cells can normally synthesize glutamine de novo, it has been noted that infections with genetically and phylogenetically diverse viruses are followed by the acquisition of a dependency on supplies of exogenous glutamine i.e. "glutamine addiction". Here we present our novel hypothesis that glutamine metabolism is also a target of the innate immune system, possibly through the action of interferons, as part of the evolutionary conserved antiviral metabolic reprogramming.
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Affiliation(s)
- C Koufaris
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - V Nicolaidou
- Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus.
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McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA. No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. BMC Biol 2021; 19:10. [PMID: 33472616 PMCID: PMC7816397 DOI: 10.1186/s12915-020-00941-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/13/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) provides high-dimensional measurements of transcript counts in individual cells. However, high assay costs and artifacts associated with analyzing samples across multiple sequencing runs limit the study of large numbers of samples. Sample multiplexing technologies such as MULTI-seq and antibody hashing using single-cell multiplexing kit (SCMK) reagents (BD Biosciences) use sample-specific sequence tags to enable individual samples to be sequenced in a pooled format, markedly lowering per-sample processing and sequencing costs while minimizing technical artifacts. Critically, however, pooling samples could introduce new artifacts, partially negating the benefits of sample multiplexing. In particular, no study to date has evaluated whether pooling peripheral blood mononuclear cells (PBMCs) from unrelated donors under standard scRNA-seq sample preparation conditions (e.g., 30 min co-incubation at 4 °C) results in significant changes in gene expression resulting from alloreactivity (i.e., response to non-self). The ability to demonstrate minimal to no alloreactivity is crucial to avoid confounded data analyses, particularly for cross-sectional studies evaluating changes in immunologic gene signatures. RESULTS Here, we applied the 10x Genomics scRNA-seq platform to MULTI-seq and/or SCMK-labeled PBMCs from a single donor with and without pooling with PBMCs from unrelated donors for 30 min at 4 °C. We did not detect any alloreactivity signal between mixed and unmixed PBMCs across a variety of metrics, including alloreactivity marker gene expression in CD4+ T cells, cell type proportion shifts, and global gene expression profile comparisons using Gene Set Enrichment Analysis and Jensen-Shannon Divergence. These results were additionally mirrored in publicly-available scRNA-seq data generated using a similar experimental design. Moreover, we identified confounding gene expression signatures linked to PBMC preparation method (e.g., Trima apheresis), as well as SCMK sample classification biases against activated CD4+ T cells which were recapitulated in two other SCMK-incorporating scRNA-seq datasets. CONCLUSIONS We demonstrate that (i) mixing PBMCs from unrelated donors under standard scRNA-seq sample preparation conditions (e.g., 30 min co-incubation at 4 °C) does not cause an allogeneic response, and (ii) that Trima apheresis and PBMC sample multiplexing using SCMK reagents can introduce undesirable technical artifacts into scRNA-seq data. Collectively, these observations establish important benchmarks for future cross-sectional immunological scRNA-seq experiments.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Siegel
- Department of Medicine, Division of HIV/AIDS, UCSF, San Francisco, CA, USA
| | - Guorui Xie
- Gladstone Institute of Virology, San Francisco, CA, USA
- Department of Urology, UCSF, San Francisco, CA, USA
| | - George Hartoularos
- Institute for Human Genetics, UCSF, San Francisco, CA, USA
- Graduate Program in Biological and Medical Informatics, UCSF, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, UCSF, San Francisco, CA, USA
- Vitalant Research Institute, UCSF, San Francisco, CA, USA
| | - Chun J Ye
- Institute for Human Genetics, UCSF, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg BioHub, UCSF, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg BioHub, UCSF, San Francisco, CA, USA
- Center for Cellular Construction, UCSF, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Nadia R Roan
- Gladstone Institute of Virology, San Francisco, CA, USA.
- Department of Urology, UCSF, San Francisco, CA, USA.
| | - Sulggi A Lee
- Department of Medicine, Division of HIV/AIDS, UCSF, San Francisco, CA, USA.
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Peltier D, Reddy P. Non-Coding RNA Mediated Regulation of Allogeneic T Cell Responses After Hematopoietic Transplantation. Front Immunol 2018; 9:1110. [PMID: 29963039 PMCID: PMC6013767 DOI: 10.3389/fimmu.2018.01110] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/03/2018] [Indexed: 12/21/2022] Open
Abstract
Allogeneic bone marrow transplantation (BMT) is an effective therapy for several malignant and non-malignant disorders. The precise control of allogeneic T cells is critical for successful outcomes after BMT. The mechanisms governing desirable (graft-versus-leukemia) versus undesirable (graft-versus-host disease) allogeneic responses remain incompletely understood. Non-coding RNAs (ncRNA) are controllers of gene expression that fine-tune cellular responses. Multiple microRNAs (miRNAs), a type of ncRNA, have recently been shown to influence allogeneic T cell responses in both murine models and clinically. Here, we review the role of various miRNAs that regulate T cell responses, either positively or negatively, to allo-stimulation and highlight their potential relevance as biomarkers and as therapeutic targets for improving outcomes after allogeneic BMT.
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Affiliation(s)
- Daniel Peltier
- Division of Hematology and Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, United States
| | - Pavan Reddy
- Division of Hematology and Oncology, Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, United States
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