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Ding XH, Xiao Y, Chen F, Liu CL, Fu T, Shao ZM, Jiang YZ. The HLA-I landscape confers prognosis and antitumor immunity in breast cancer. Brief Bioinform 2024; 25:bbae151. [PMID: 38602320 PMCID: PMC11007120 DOI: 10.1093/bib/bbae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/12/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Breast cancer is a highly heterogeneous disease with varied subtypes, prognoses and therapeutic responsiveness. Human leukocyte antigen class I (HLA-I) shapes the immunity and thereby influences the outcome of breast cancer. However, the implications of HLA-I variations in breast cancer remain poorly understood. In this study, we established a multiomics cohort of 1156 Chinese breast cancer patients for HLA-I investigation. We calculated four important HLA-I indicators in each individual, including HLA-I expression level, somatic HLA-I loss of heterozygosity (LOH), HLA-I evolutionary divergence (HED) and peptide-binding promiscuity (Pr). Then, we evaluated their distribution and prognostic significance in breast cancer subtypes. We found that the four breast cancer subtypes had distinct features of HLA-I indicators. Increased expression of HLA-I and LOH were enriched in triple-negative breast cancer (TNBC), while Pr was relatively higher in hot tumors within TNBCs. In particular, a higher Pr indicated a better prognosis in TNBCs by regulating the infiltration of immune cells and the expression of immune molecules. Using the matched genomic and transcriptomic data, we found that mismatch repair deficiency-related mutational signature and pathways were enriched in low-Pr TNBCs, suggesting that targeting mismatch repair deficiency for synthetic lethality might be promising therapy for these patients. In conclusion, we presented an overview of HLA-I indicators in breast cancer and provided hints for precision treatment for low-Pr TNBCs.
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Affiliation(s)
- Xiao-Hong Ding
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Yi Xiao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Fenfang Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
| | - Cheng-Lin Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
| | - Tong Fu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center; Fudan University, Shanghai, 200032, P.R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P.R. China
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Saigí M, Mate JL, Carcereny E, Martínez-Cardús A, Esteve A, Andreo F, Centeno C, Cucurull M, Mesia R, Pros E, Sanchez-Cespedes M. HLA-I levels correlate with survival outcomes in response to immune checkpoint inhibitors in non-small cell lung cancer. Lung Cancer 2024; 189:107502. [PMID: 38359742 DOI: 10.1016/j.lungcan.2024.107502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/16/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
OBJECTIVES Immune checkpoint inhibitors (ICIs) have provided a breakthrough in the treatment of non-small cell lung cancer (NSCLC) patients, but only some patients benefit substantively. Identifying definitive predictive biomarkers could overcome this limitation. MATERIALS AND METHODS We selected 146 metastatic NSCLC patients treated with anti-PD-(L)1. Immunohistochemistry of HLA-I, PD-L1 and CD73 was performed in 122 tumor biopsies at diagnosis. The association with patients, tumor parameters, and the predictive value to ICI treatment were determined. RESULTS In our cohort, 42 %, 25 %, and 21 % of the tumors exhibited high levels of HLA-I, PD-L1, and CD73, respectively. Lung adenocarcinomas displayed elevated CD73 levels, compared with lung squamous cell carcinomas (P = 0.026). High PD-L1 was significantly correlated with high levels of HLA-I (P = 0.005) and of CD73 (P = 0.025). Patients with high-level HLA-I tumors exhibited more favorable clinical outcomes following ICI, with a median overall survival of 30.7 months (95 % confidence interval [CI]: 18.3 months-not reached), compared with 18.2 months (95 % CI: 12.4-25.2 months) in patients with low-level HLA-I tumors (P = 0.016). The median progression-free survival (PFS) for patients with high-level HLA-I tumors was 18.5 months (95 % CI: 11.1-57.1 months), longer than patients with low-level HLA-I tumors, whose median PFS was 9.2 months (95 % CI: 7.2-11.9 months) (P = 0.006). In a multivariable analysis, high-level HLA-I was independently associated with lower risk of progression to ICI (HR = 0.46, 95 % CI 0.24-0.87; P = 0.018). CONCLUSIONS High-level HLA-I were associated with better clinical outcomes to ICI in our cohort of NSCLC patients. Therefore, further investigations are warranted to refine this biomarker and validate its efficacy in prospective and larger set of patients.
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Affiliation(s)
- Maria Saigí
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.
| | - Jose L Mate
- Department of Pathology, Germans Trias i Pujol University Hospital, Badalona, Barcelona, Spain
| | - Enric Carcereny
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Anna Martínez-Cardús
- Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Anna Esteve
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Statistics Department, Catalan Institute of Oncology (ICO)-Badalona, Badalona, Barcelona, Spain
| | - Felipe Andreo
- Pulmonology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Carmen Centeno
- Pulmonology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Marc Cucurull
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Ricard Mesia
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), Badalona, Barcelona, Spain; Badalona·Applied Research Group in Oncology (B·ARGO), Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain
| | - Eva Pros
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Montse Sanchez-Cespedes
- Cancer Genetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.
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3
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Pulliam T, Jani S, Jing L, Ryu H, Jojic A, Shasha C, Zhang J, Kulikauskas R, Church C, Garnett-Benson C, Gooley T, Chapuis A, Paulson K, Smith KN, Pardoll DM, Newell EW, Koelle DM, Topalian SL, Nghiem P. Circulating cancer-specific CD8 T cell frequency is associated with response to PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101412. [PMID: 38340723 PMCID: PMC10897614 DOI: 10.1016/j.xcrm.2024.101412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Understanding cancer immunobiology has been hampered by difficulty identifying cancer-specific T cells. Merkel cell polyomavirus (MCPyV) causes most Merkel cell carcinomas (MCCs). All patients with virus-driven MCC express MCPyV oncoproteins, facilitating identification of virus (cancer)-specific T cells. We studied MCPyV-specific T cells from 27 patients with MCC using MCPyV peptide-HLA-I multimers, 26-color flow cytometry, single-cell transcriptomics, and T cell receptor (TCR) sequencing. In a prospective clinical trial, higher circulating MCPyV-specific CD8 T cell frequency before anti-PD-1 treatment was strongly associated with 2-year recurrence-free survival (75% if detectable, 0% if undetectable, p = 0.0018; ClinicalTrial.gov: NCT02488759). Intratumorally, such T cells were typically present, but their frequency did not significantly associate with response. Circulating MCPyV-specific CD8 T cells had increased stem/memory and decreased exhaustion signatures relative to their intratumoral counterparts. These results suggest that cancer-specific CD8 T cells in the blood may play a role in anti-PD-1 responses. Thus, strategies that augment their number or mobilize them into tumors could improve outcomes.
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Affiliation(s)
- Thomas Pulliam
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Saumya Jani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ana Jojic
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn Shasha
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jiajia Zhang
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rima Kulikauskas
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Ted Gooley
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aude Chapuis
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Paulson
- Paul G. Allen Research Center, Providence-Swedish Cancer Institute, Seattle, WA 98104, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Kellie N Smith
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Evan W Newell
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Suzanne L Topalian
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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4
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Lerner A, Benzvi C, Vojdani A. HLA-DQ2/8 and COVID-19 in Celiac Disease: Boon or Bane. Microorganisms 2023; 11:2977. [PMID: 38138121 PMCID: PMC10745744 DOI: 10.3390/microorganisms11122977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The SARS-CoV-2 pandemic continues to pose a global threat. While its virulence has subsided, it has persisted due to the continual emergence of new mutations. Although many high-risk conditions related to COVID-19 have been identified, the understanding of protective factors remains limited. Intriguingly, epidemiological evidence suggests a low incidence of COVID-19-infected CD patients. The present study explores whether their genetic background, namely, the associated HLA-DQs, offers protection against severe COVID-19 outcomes. We hypothesize that the HLA-DQ2/8 alleles may shield CD patients from SARS-CoV-2 and its subsequent effects, possibly due to memory CD4 T cells primed by previous exposure to human-associated common cold coronaviruses (CCC) and higher affinity to those allele's groove. In this context, we examined potential cross-reactivity between SARS-CoV-2 epitopes and human-associated CCC and assessed the binding affinity (BA) of these epitopes to HLA-DQ2/8. Using computational methods, we analyzed sequence similarity between SARS-CoV-2 and four distinct CCC. Of 924 unique immunodominant 15-mer epitopes with at least 67% identity, 37 exhibited significant BA to HLA-DQ2/8, suggesting a protective effect. We present various mechanisms that might explain the protective role of HLA-DQ2/8 in COVID-19-afflicted CD patients. If substantiated, these insights could enhance our understanding of the gene-environment enigma and viral-host relationship, guiding potential therapeutic innovations against the ongoing SARS-CoV-2 pandemic.
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Affiliation(s)
- Aaron Lerner
- The Zabludowicz Center for Autoimmune Diseases, Chaim Sheba Medical Center, Ramat Gan 5262160, Israel;
- Research Department, Ariel University, Ariel 4077625, Israel
| | - Carina Benzvi
- The Zabludowicz Center for Autoimmune Diseases, Chaim Sheba Medical Center, Ramat Gan 5262160, Israel;
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5
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Wang Y, Fenyö D. Proteogenomics Reveal the Overexpression of HLA-I in Cancer. J Proteome Res 2023; 22:3625-3639. [PMID: 37857377 PMCID: PMC10629274 DOI: 10.1021/acs.jproteome.3c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Indexed: 10/21/2023]
Abstract
An accurate quantification of HLA class I gene expression is important in understanding the interplay with the tumor microenvironment of antitumor cytotoxic T cell activities. Because HLA-I sequences are highly variable, standard RNAseq and mass spectrometry-based quantification workflows using common genome and protein sequence references do not provide HLA-I allele specific quantifications. Here, we used personalized HLA-I nucleotide and protein reference sequences based on the subjects' HLA-I genotypes and surveyed tumor and adjacent normal samples from patients across nine cancer types. Mass spectrometry using data dependent acquisition data was validated to be sufficient to estimate HLA-A protein expression at the allele level. We found that HLA-I proteins were present in significantly higher levels in tumors compared to adjacent normal tissues from 41 to 63% of head and neck squamous cell carcinoma, uterine corpus endometrial carcinoma, and clear cell renal cell carcinoma patients, and this was driven by increased levels of HLA-I gene transcripts. Most immune cell types are universally enriched in HLA-I high tumors, while endothelial and neuronal cells showed divergent relationships with HLA-I. Pathway analysis revealed that tumor senescence and autophagy activity influence the level of HLA-I proteins in glioblastoma. Genes correlated to HLA-I protein expression are mostly the ones directly involved in HLA-I function in immune response and cell death, while glycosylation genes are exclusively co-expressed with HLA-I at the protein level.
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Affiliation(s)
- Ying Wang
- Institute
for Systems Genetics, NYU Grossman School
of Medicine, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - David Fenyö
- Institute
for Systems Genetics, NYU Grossman School
of Medicine, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
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6
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Yin S, Klaeger S, Chea VA, Carulli IP, Rachimi S, Black KE, Filbin M, Hariri LP, Knipe RS, Padera RF, Stevens JD, Lane WJ, Carr SA, Wu CJ, Kim EY, Keskin DB. Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies. Front Immunol 2023; 14:1269335. [PMID: 37942334 PMCID: PMC10628763 DOI: 10.3389/fimmu.2023.1269335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction Severe respiratory illness is the most prominent manifestation of patients infected with SARS-CoV-2, and yet the molecular mechanisms underlying severe lung disease in COVID-19 affected patients still require elucidation. Human leukocyte antigen class I (HLA-I) expression is crucial for antigen presentation and the host's response to SARS-CoV-2. Methods To gain insights into the immune response and molecular pathways involved in severe lung disease, we performed immunopeptidomic and proteomic analyses of lung tissues recovered at four COVID-19 autopsy and six non-COVID-19 transplants. Results We found signals of tissue injury and regeneration in lung fibroblast and alveolar type I/II cells, resulting in the production of highly immunogenic self-antigens within the lungs of COVID-19 patients. We also identified immune activation of the M2c macrophage as the primary source of HLA-I presentation and immunogenicity in this context. Additionally, we identified 28 lung signatures that can serve as early plasma markers for predicting infection and severe COVID-19 disease. These protein signatures were predominantly expressed in macrophages and epithelial cells and were associated with complement and coagulation cascades. Discussion Our findings emphasize the significant role of macrophage-mediated immunity in the development of severe lung disease in COVID-19 patients.
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Affiliation(s)
- Shanye Yin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Vipheaviny A. Chea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Isabel P. Carulli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Suzanna Rachimi
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Katharine E. Black
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Michael Filbin
- Harvard Medical School, Boston, MA, United States
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Lida P. Hariri
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
| | - Rachel S. Knipe
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Robert F. Padera
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jonathan D. Stevens
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - William J. Lane
- Harvard Medical School, Boston, MA, United States
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, United States
| | - Steven A. Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Edy Yong Kim
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Derin B. Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, United States
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, United States
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7
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Russell MA, Richardson SJ, Morgan NG. The role of the interferon/JAK-STAT axis in driving islet HLA-I hyperexpression in type 1 diabetes. Front Endocrinol (Lausanne) 2023; 14:1270325. [PMID: 37867531 PMCID: PMC10588626 DOI: 10.3389/fendo.2023.1270325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/06/2023] [Indexed: 10/24/2023] Open
Abstract
The hyperexpression of human leukocyte antigen class I (HLA-I) molecules on pancreatic beta-cells is widely accepted as a hallmark feature of type 1 diabetes pathogenesis. This response is important clinically since it may increase the visibility of beta-cells to autoreactive CD8+ T-cells, thereby accelerating disease progression. In this review, key factors which drive HLA-I hyperexpression will be explored, and their clinical significance examined. It is established that the presence of residual beta-cells is essential for HLA-I hyperexpression by islet cells at all stages of the disease. We suggest that the most likely drivers of this process are interferons released from beta-cells (type I or III interferon; possibly in response to viral infection) or those elaborated from influent, autoreactive immune cells (type II interferon). In both cases, Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) pathways will be activated to induce the downstream expression of interferon stimulated genes. A variety of models have highlighted that HLA-I expression is enhanced in beta-cells in response to interferons, and that STAT1, STAT2 and interferon regulatory factor 9 (IRF9) play key roles in mediating these effects (depending on the species of interferon involved). Importantly, STAT1 expression is elevated in the beta-cells of donors with recent-onset type I diabetes, and this correlates with HLA-I hyperexpression on an islet-by-islet basis. These responses can be replicated in vitro, and we consider that chronically elevated STAT1 may have a role in maintaining HLA-I hyperexpression. However, other data have highlighted that STAT2-IRF9 may also be critical to this process. Thus, a better understanding of how these factors regulate HLA-I under chronically stimulated conditions needs to be gathered. Finally, JAK inhibitors can target interferon signaling pathways to diminish HLA-I expression in mouse models. It seems probable that these agents may also be effective in patients; diminishing HLA-I hyperexpression on islets, reducing the visibility of beta-cells to the immune system and ultimately slowing disease progression. The first clinical trials of selective JAK inhibitors are underway, and the outcomes should have important implications for type 1 diabetes clinical management.
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Affiliation(s)
- Mark A. Russell
- Department of Clinical and Biomedical Sciences, University of Exeter, Exeter, United Kingdom
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8
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Rachdi L, Zhou Z, Berthault C, Lourenço C, Fouque A, Domet T, Armanet M, You S, Peakman M, Mallone R, Scharfmann R. Tryptophan metabolism promotes immune evasion in human pancreatic β cells. EBioMedicine 2023; 95:104740. [PMID: 37536063 PMCID: PMC10412781 DOI: 10.1016/j.ebiom.2023.104740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND To resist the autoimmune attack characteristic of type 1 diabetes, insulin producing pancreatic β cells need to evade T-cell recognition. Such escape mechanisms may be conferred by low HLA class I (HLA-I) expression and upregulation of immune inhibitory molecules such as Programmed cell Death Ligand 1 (PD-L1). METHODS The expression of PD-L1, HLA-I and CXCL10 was evaluated in the human β cell line, ECN90, and in primary human and mouse pancreatic islets. Most genes were determined by real-time RT-PCR, flow cytometry and Western blot. Activator and inhibitor of the AKT signaling were used to modulate PD-L1 induction. Key results were validated by monitoring activity of CD8+ Jurkat T cells presenting β cell specific T-cell receptor and transduced with reporter genes in contact culture with the human β cell line, ECN90. FINDINGS In this study, we identify tryptophan (TRP) as an agonist of PD-L1 induction through the AKT signaling pathway. TRP also synergistically enhanced PD-L1 expression on β cells exposed to interferon-γ. Conversely, interferon-γ-mediated induction of HLA-I and CXCL10 genes was down-regulated upon TRP treatment. Finally, TRP and its derivatives inhibited the activation of islet-reactive CD8+ T cells by β cells. INTERPRETATION Collectively, our findings indicate that TRP could induce immune tolerance to β cells by promoting their immune evasion through HLA-I downregulation and PD-L1 upregulation. FUNDING Dutch Diabetes Research Foundation, DON Foundation, the Laboratoire d'Excellence consortium Revive (ANR-10-LABX-0073), Agence Nationale de la Recherche (ANR-19-CE15-0014-01), Fondation pour la Recherche Médicale (EQ U201903007793-EQU20193007831), Innovative Medicines InitiativeINNODIA and INNODIA HARVEST, Aides aux Jeunes Diabetiques (AJD) and Juvenile Diabetes Research Foundation Ltd (JDRF).
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Affiliation(s)
- Latif Rachdi
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France.
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France
| | - Claire Berthault
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France
| | - Chloe Lourenço
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France
| | - Alexis Fouque
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France
| | - Thomas Domet
- Assistance Publique Hôpitaux de Paris, Cell Therapy Unit, Saint Louis Hospital, Paris 75010, France
| | - Mathieu Armanet
- Assistance Publique Hôpitaux de Paris, Cell Therapy Unit, Saint Louis Hospital, Paris 75010, France
| | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France
| | - Mark Peakman
- Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France; Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris 75014, France
| | - Raphael Scharfmann
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris 75014, France
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9
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Härkönen J, Pölönen P, Deen AJ, Selvarajan I, Teppo HR, Dimova EY, Kietzmann T, Ahtiainen M, Väyrynen JP, Väyrynen SA, Elomaa H, Tynkkynen N, Eklund T, Kuopio T, Talvitie EM, Taimen P, Kallajoki M, Kaikkonen MU, Heinäniemi M, Levonen AL. A pan-cancer analysis shows immunoevasive characteristics in NRF2 hyperactive squamous malignancies. Redox Biol 2023; 61:102644. [PMID: 36867945 PMCID: PMC10011429 DOI: 10.1016/j.redox.2023.102644] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a NRF2 activity metric and utilized it to conduct a pan-cancer analysis of oncogenic NRF2 signaling. We identified an immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFNγ), HLA-I expression and T cell and macrophage infiltration in squamous malignancies of the lung, head and neck area, cervix and esophagus. Squamous NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11, SLC2A1 and PD-L1. Based on our functional genomics analyses, these genes represent candidate NRF2 targets, suggesting direct modulation of the tumor immune milieu. Single-cell mRNA data shows that cancer cells of this subtype exhibit decreased expression of IFNγ responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. In addition, we discovered that the negative relationship of NRF2 and immune cells are explained by stromal populations of lung squamous cell carcinoma, and this effect spans multiple squamous malignancies based on our molecular subtyping and deconvolution data.
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Affiliation(s)
- Jouni Härkönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland; Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Petri Pölönen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland; Faculty of Health Sciences, Institute of Biomedicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Ashik Jawahar Deen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland
| | - Ilakya Selvarajan
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland
| | - Hanna-Riikka Teppo
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, 90220, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, 90570, Finland; Department of Pathology, Oulu University Hospital, Oulu, 90220, Finland
| | - Elitsa Y Dimova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu and Biocenter Oulu, Oulu, 90570, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu and Biocenter Oulu, Oulu, 90570, Finland
| | - Maarit Ahtiainen
- Department of Education and Research, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland
| | - Juha P Väyrynen
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, 90220, Finland; Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, 90570, Finland; Department of Pathology, Oulu University Hospital, Oulu, 90220, Finland
| | - Sara A Väyrynen
- Department of Internal Medicine, Oulu University Hospital, Oulu, 90220, Finland
| | - Hanna Elomaa
- Department of Education and Research, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland; Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40100, Finland
| | - Niko Tynkkynen
- Gerontology Research Center (GEREC), Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Tiia Eklund
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40100, Finland
| | - Teijo Kuopio
- Department of Pathology, Hospital Nova of Central Finland, Jyväskylä, 40620, Finland; Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, 40100, Finland
| | - Eva-Maria Talvitie
- Department of Genomics, Turku University Hospital and University of Turku, Turku, 20520, Finland
| | - Pekka Taimen
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, 20520, Finland; Department of Pathology, Turku University Hospital, Turku, 20521, Finland
| | - Markku Kallajoki
- Department of Pathology, Turku University Hospital, Turku, 20521, Finland
| | - Minna U Kaikkonen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland
| | - Merja Heinäniemi
- Faculty of Health Sciences, Institute of Biomedicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Anna-Liisa Levonen
- Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70210, Finland.
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10
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Bogomiakova ME, Sekretova EK, Anufrieva KS, Khabarova PO, Kazakova AN, Bobrovsky PA, Grigoryeva TV, Eremeev AV, Lebedeva OS, Bogomazova AN, Lagarkova MA. iPSC-derived cells lack immune tolerance to autologous NK-cells due to imbalance in ligands for activating and inhibitory NK-cell receptors. Stem Cell Res Ther 2023; 14:77. [PMID: 37038186 PMCID: PMC10088155 DOI: 10.1186/s13287-023-03308-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/28/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Dozens of transplants generated from pluripotent stem cells are currently in clinical trials. The creation of patient-specific iPSCs makes personalized therapy possible due to their main advantage of immunotolerance. However, some reports have claimed recently that aberrant gene expression followed by proteome alterations and neoantigen formation can result in iPSCs recognition by autologous T-cells. Meanwhile, the possibility of NK-cell activation has not been previously considered. This study focused on the comparison of autologous and allogeneic immune response to iPSC-derived cells and isogeneic parental somatic cells used for reprogramming. METHODS We established an isogeneic cell model consisting of parental dermal fibroblasts, fibroblast-like iPSC-derivatives (iPS-fibro) and iPS-fibro lacking beta-2-microglobulin (B2M). Using the cells obtained from two patients, we analyzed the activation of autologous and allogeneic T-lymphocytes and NK-cells co-cultured with target cells. RESULTS Here we report that cells differentiated from iPSCs can be recognized by NK-cells rather than by autologous T-cells. We observed that iPS-fibro elicited a high level of NK-cell degranulation and cytotoxicity, while isogeneic parental skin fibroblasts used to obtain iPSCs barely triggered an NK-cell response. iPSC-derivatives with B2M knockout did not cause an additional increase in NK-cell activation, although they were devoid of HLA-I, the major inhibitory molecules for NK-cells. Transcriptome analysis revealed a significant imbalance of ligands for activating and inhibitory NK-cell receptors in iPS-fibro. Compared to parental fibroblasts, iPSC-derivatives had a reduced expression of HLA-I simultaneously with an increased gene expression of major activating ligands, such as MICA, NECTIN2, and PVR. The lack of inhibitory signals might be due to insufficient maturity of cells differentiated from iPSCs. In addition, we showed that pretreatment of iPS-fibro with proinflammatory cytokine IFNγ restored the ligand imbalance, thereby reducing the degranulation and cytotoxicity of NK-cells. CONCLUSION In summary, we showed that iPSC-derived cells can be sensitive to the cytotoxic potential of autologous NK-cells regardless of HLA-I status. Thus, the balance of ligands for NK-cell receptors should be considered prior to iPSC-based cell therapies. Trial registration Not applicable.
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Affiliation(s)
- Margarita E Bogomiakova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435.
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russia, 119991.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435.
| | - Elizaveta K Sekretova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russia, 119991
| | - Ksenia S Anufrieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
| | - Polina O Khabarova
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russia, 119991
| | - Anastasia N Kazakova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
| | - Pavel A Bobrovsky
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
| | | | - Artem V Eremeev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
| | - Olga S Lebedeva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
| | - Alexandra N Bogomazova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya, Moscow, Russia, 119435
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, Moscow, Russia, 119991
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11
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Abd El-Baky N, Amara AA, Redwan EM. HLA-I and HLA-II Peptidomes of SARS-CoV-2: A Review. Vaccines (Basel) 2023; 11:548. [PMID: 36992131 PMCID: PMC10058130 DOI: 10.3390/vaccines11030548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
The adaptive (T-cell-mediated) immune response is a key player in determining the clinical outcome, in addition to neutralizing antibodies, after SARS-CoV-2 infection, as well as supporting the efficacy of vaccines. T cells recognize viral-derived peptides bound to major histocompatibility complexes (MHCs) so that they initiate cell-mediated immunity against SARS-CoV-2 infection or can support developing a high-affinity antibody response. SARS-CoV-2-derived peptides bound to MHCs are characterized via bioinformatics or mass spectrometry on the whole proteome scale, named immunopeptidomics. They can identify potential vaccine targets or therapeutic approaches for SARS-CoV-2 or else may reveal the heterogeneity of clinical outcomes. SARS-CoV-2 epitopes that are naturally processed and presented on the human leukocyte antigen class I (HLA-I) and class II (HLA-II) were identified for immunopeptidomics. Most of the identified SARS-CoV-2 epitopes were canonical and out-of-frame peptides derived from spike and nucleocapsid proteins, followed by membrane proteins, whereby many of which are not caught by existing vaccines and could elicit effective responses of T cells in vivo. This review addresses the detection of SARS-CoV-2 viral epitopes on HLA-I and HLA-II using bioinformatics prediction and mass spectrometry (HLA peptidomics). Profiling the HLA-I and HLA-II peptidomes of SARS-CoV-2 is also detailed.
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Affiliation(s)
- Nawal Abd El-Baky
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Amro A. Amara
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria P.O. Box 21934, Egypt
| | - Elrashdy M. Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah P.O. Box 80203, Saudi Arabia
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12
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Sankaranarayanan S, Mohkhedkar M, Janakiraman V. Mutations in spike protein T cell epitopes of SARS-COV-2 variants: Plausible influence on vaccine efficacy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166432. [PMID: 35568352 PMCID: PMC9109158 DOI: 10.1016/j.bbadis.2022.166432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 01/25/2023]
Abstract
With emerging SARS-CoV-2 variants, vaccines approved so far are under scrutiny for long term effectiveness against the circulating strains. There is a prevalent obsession with humoral immunity as in vitro studies have indicated diminished effects of vaccine-induced neutralizing antibodies. However, this need not clinically translate to vaccine resistance as immune response against all forms of present vaccine preparations is T dependent unlike that against native viral particles which can induce T independent immune responses. Thus, we focused on this major correlate of protection against infections, T cell response. Using bioinformatics tools, we analyzed SARS-CoV-2 Spike protein T cell epitopes and their diversity across Delta plus/B.1.617.2.1, Gamma/P.1 (variant of concern), B.1.1.429, Zeta/P.2 and Mink cluster 5/B.1.1.298 variants as well as Omicron/B.1.1.529 (variant of concern). We also compared HLA restriction profiles of the mutant epitopes with that of the native epitopes (from Wuhan_hu_1 strain, used in vaccine formulations). Our observations show ~90% conservation of CD4+ and CD8+ epitopes across Delta plus/B.1.617.2.1, Gamma/P.1 (variant of concern), B.1.1.429, Zeta/P.2 and Mink cluster 5/B.1.1.298. For the Omicron/B.1.1.529 variant, ~75% of CD4+ and ~ 87% CD8+ epitopes were conserved. Majority of the mutated CD4+ and CD8+ epitopes of this variant were predicted to retain the HLA restriction pattern as their native epitopes. The results of our bioinformatics analysis suggest largely conserved T cell responses across the studied variants, ability of T cells to tackle new SARS-CoV-2 variants and aid in protection from COVID-19 post vaccination. In conclusion, the results suggest that current vaccines may not be rendered completely ineffective against new variants.
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Affiliation(s)
| | | | - Vani Janakiraman
- Corresponding author at: Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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13
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Bonté PE, Arribas YA, Merlotti A, Carrascal M, Zhang JV, Zueva E, Binder ZA, Alanio C, Goudot C, Amigorena S. Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides. Cell Rep 2022; 39:110916. [PMID: 35675780 DOI: 10.1016/j.celrep.2022.110916] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/22/2022] [Accepted: 05/12/2022] [Indexed: 11/03/2022] Open
Abstract
We analyze transposable elements (TEs) in glioblastoma (GBM) patients using a proteogenomic pipeline that combines single-cell transcriptomics, bulk RNA sequencing (RNA-seq) samples from tumors and healthy-tissue cohorts, and immunopeptidomic samples. We thus identify 370 human leukocyte antigen (HLA)-I-bound peptides encoded by TEs differentially expressed in GBM. Some of the peptides are encoded by repeat sequences from intact open reading frames (ORFs) present in up to several hundred TEs from recent long interspersed nuclear element (LINE)-1, long terminal repeat (LTR), and SVA subfamilies. Other HLA-I-bound peptides are encoded by single copies of TEs from old subfamilies that are expressed recurrently in GBM tumors and not expressed, or very infrequently and at low levels, in healthy tissues (including brain). These peptide-coding, GBM-specific, highly recurrent TEs represent potential tumor-specific targets for cancer immunotherapies.
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Affiliation(s)
- Pierre-Emmanuel Bonté
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Jiasi Vicky Zhang
- GBM Translational Center of Excellence, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elina Zueva
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Zev A Binder
- GBM Translational Center of Excellence, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cécile Alanio
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, Paris 75005, France; Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Christel Goudot
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
| | - Sebastian Amigorena
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
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14
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Xiong X, Tian S, Yang P, Lebreton F, Bao H, Sheng K, Yin L, Chen P, Zhang J, Qi W, Ruan J, Wu H, Chen H, Breault DT, Wu H, Earl AM, Gilmore MS, Abraham J, Dong M. Emerging enterococcus pore-forming toxins with MHC/ HLA-I as receptors. Cell 2022; 185:1157-1171.e22. [PMID: 35259335 PMCID: PMC8978092 DOI: 10.1016/j.cell.2022.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/15/2021] [Accepted: 02/01/2022] [Indexed: 01/12/2023]
Abstract
Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, and E. hirae strains isolated across the globe. Structural studies reveal that Epxs form a branch of β-barrel pore-forming toxins with a β-barrel protrusion (designated the top domain) sitting atop the cap domain. Through a genome-wide CRISPR-Cas9 screen, we identify human leukocyte antigen class I (HLA-I) complex as a receptor for two members (Epx2 and Epx3), which preferentially recognize human HLA-I and homologous MHC-I of equine, bovine, and porcine, but not murine, origin. Interferon exposure, which stimulates MHC-I expression, sensitizes human cells and intestinal organoids to Epx2 and Epx3 toxicity. Co-culture with Epx2-harboring E. faecium damages human peripheral blood mononuclear cells and intestinal organoids, and this toxicity is neutralized by an Epx2 antibody, demonstrating the toxin-mediated virulence of Epx-carrying Enterococcus.
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Affiliation(s)
- Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pan Yang
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Francois Lebreton
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Linxiang Yin
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Zhang
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Wanshu Qi
- Division of Endocrinology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jianbin Ruan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology, University of Connecticut Health School of Medicine, Farmington, CT 06030, USA
| | - Hao Wu
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hong Chen
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Gilmore
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jonathan Abraham
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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15
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Abstract
Peptide ligands presented by human leukocyte antigen (HLA) molecules on the cell surface represent the immunopeptidome that could be utilized for identification of antigenic peptides for immunotherapy and prevention of autoimmune diseases. Although T-cells are well-known key players in the destruction of pancreatic beta-cells in type 1 diabetes (T1D), increasing evidence points toward a role for B-cells in disease pathogenesis. However, as antigen presenting cells, little is known about the comprehensive immunopeptidome of B cells and their changes in the context of T1D. We performed HLA allele-specific quantitative immunopeptidomics using B lymphocytes derived from T1D patients and healthy controls. Hundreds of HLA-I and HLA-II immunopeptides were identified as differentially regulated in T1D per HLA allele for B cells sharing identical HLA alleles. The results were further validated using additional T1D and healthy B cells with partially overlapped HLA alleles. Differentially expressed immunopeptides were confirmed with targeted proteomics and for reactivity using known T-cell assays in the immune epitope database. Considering samples with identical HLA alleles are difficult to obtain for T1D and other similar HLA-restricted diseases, our work represents a viable approach to better understand HLA allele-specific antigen presentation and may facilitate identification of immunopeptides for therapeutic applications in autoimmune diseases. Data are available via ProteomeXchange with identifier PXD026184.
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Affiliation(s)
- Putty-Reddy Sudhir
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Tai-Du Lin
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA,Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA,Corresponding author: Qibin Zhang ()
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16
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Kaaijk P, Emmelot ME, Kerkhof J, van Els CACM, Meiring HD, de Wit J, Bodewes R. Genetic Analysis Reveals Differences in CD8 + T Cell Epitope Regions That May Impact Cross-Reactivity of Vaccine-Induced T Cells against Wild-Type Mumps Viruses. Vaccines (Basel) 2021; 9:699. [PMID: 34202193 DOI: 10.3390/vaccines9070699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
Nowadays, mumps is re-emerging in highly vaccinated populations. Waning of vaccine-induced immunity plays a role, but antigenic differences between vaccine and mumps outbreak strains could also contribute to reduced vaccine effectiveness. CD8+ T cells play a critical role in immunity to viruses. However, limited data are available about sequence variability in CD8+ T cell epitope regions of mumps virus (MuV) proteins. Recently, the first set of naturally presented human leukocyte antigen Class I (HLA-I) epitopes of MuV was identified by us. In the present study, sequences of 40 CD8+ T cell epitope candidates, including previously and newly identified, obtained from Jeryl–Lynn mumps vaccine strains were compared with genomes from 462 circulating MuV strains. In 31 epitope candidates (78%) amino acid differences were detected, and in 17 (43%) of the epitope candidates the corresponding sequences in wild-type strains had reduced predicted HLA-I-binding compared to the vaccine strains. These findings suggest that vaccinated persons may have reduced T cell immunity to circulating mumps viruses due to antigenic differences.
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Wang S, Fang Y, Jiang N, Xing S, Li Q, Chen R, Yi X, Zhang Z, Li N. Comprehensive Genomic Profiling of Rare Tumors in China: Routes to Immunotherapy. Front Immunol 2021; 12:631483. [PMID: 33732253 PMCID: PMC7959707 DOI: 10.3389/fimmu.2021.631483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/18/2021] [Indexed: 01/10/2023] Open
Abstract
Treatment options for rare tumors are limited, and comprehensive genomic profiling may provide useful information for novel treatment strategies and improving outcomes. The aim of this study is to explore the treatment opportunities of patients with rare tumors using immune checkpoint inhibitors (ICIs) that have already been approved for routine treatment of common tumors. We collected immunotherapy-related indicators data from a total of 852 rare tumor patients from across China, including 136 programmed cell death ligand-1 (PD-L1) expression, 821 tumors mutational burden (TMB), 705 microsatellite instability (MSI) and 355 human leukocyte antigen class I (HLA-I) heterozygosity reports. We calculated the positive rates of these indicators and analyzed the consistency relationship between TMB and PD-L1, TMB and MSI, and HLA-I and PD-L1. The prevalence of PD-L1 positive, TMB-H, MSI-, and HLA-I -heterozygous was 47.8%, 15.5%, 7.4%, and 78.9%, respectively. The consistency ratio of TMB and PD-L1, TMB and MSI, and HLA-I and PD-L1 was 54.8% (78/135), 87.3% (598/685), and 47.4% (54/114), respectively. The prevalence of the four indicators varied widely across tumors systems and subtypes. The probability that neuroendocrine tumors (NETs) and biliary tumors may benefit from immunotherapy is high, since the proportion of TMB-H is as high as 50% and 25.4% respectively. The rates of PD-L1 positivity, TMB-H and MSI-H in carcinoma of unknown primary (CUP) were relatively high, while the rates of TMB-H and MSI-H in soft tissue tumors were both relatively low. Our study revealed the distribution of immunotherapeutic indicators in patients with rare tumors in China. Comprehensive genomic profiling may offer novel therapeutic modalities for patients with rare tumors to solve the dilemma of limited treatment options.
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Affiliation(s)
- Shuhang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cell Biology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yuan Fang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Jiang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shujun Xing
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qin Li
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Rongrong Chen
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Xin Yi
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Zhiqian Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cell Biology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ning Li
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Abella JR, Antunes DA, Clementi C, Kavraki LE. Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests. Front Immunol 2020; 11:1583. [PMID: 32793224 PMCID: PMC7387700 DOI: 10.3389/fimmu.2020.01583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/15/2020] [Indexed: 01/13/2023] Open
Abstract
Prediction of stable peptide binding to Class I HLAs is an important component for designing immunotherapies. While the best performing predictors are based on machine learning algorithms trained on peptide-HLA (pHLA) sequences, the use of structure for training predictors deserves further exploration. Given enough pHLA structures, a predictor based on the residue-residue interactions found in these structures has the potential to generalize for alleles with little or no experimental data. We have previously developed APE-Gen, a modeling approach able to produce pHLA structures in a scalable manner. In this work we use APE-Gen to model over 150,000 pHLA structures, the largest dataset of its kind, which were used to train a structure-based pan-allele model. We extract simple, homogenous features based on residue-residue distances between peptide and HLA, and build a random forest model for predicting stable pHLA binding. Our model achieves competitive AUROC values on leave-one-allele-out validation tests using significantly less data when compared to popular sequence-based methods. Additionally, our model offers an interpretation analysis that can reveal how the model composes the features to arrive at any given prediction. This interpretation analysis can be used to check if the model is in line with chemical intuition, and we showcase particular examples. Our work is a significant step toward using structure to achieve generalizable and more interpretable prediction for stable pHLA binding.
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Affiliation(s)
- Jayvee R. Abella
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Dinler A. Antunes
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Cecilia Clementi
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, Houston, TX, United States
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Owoicho O, Olwal CO, Quaye O. Commentary: An enzymatic pathway in the human gut microbiome that converts A to universal O type blood. Front Immunol 2020; 11:772. [PMID: 32411149 PMCID: PMC7198812 DOI: 10.3389/fimmu.2020.00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/06/2020] [Indexed: 11/27/2022] Open
Affiliation(s)
| | | | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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20
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Grant EJ, Nguyen AT, Lobos CA, Szeto C, Chatzileontiadou DSM, Gras S. The unconventional role of HLA-E: The road less traveled. Mol Immunol 2020; 120:101-112. [PMID: 32113130 DOI: 10.1016/j.molimm.2020.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/16/2020] [Accepted: 02/18/2020] [Indexed: 12/14/2022]
Abstract
Histocompatibility Leukocyte Antigens, or HLAs, are one of the most polymorphic molecules in humans. This high degree of polymorphism endows HLA molecules with the ability to present a vast array of peptides, an essential trait for responding to ever-evolving pathogens. Unlike classical HLA molecules (HLA-Ia), some non-classical HLA-Ib molecules, including HLA-E, are almost monomorphic. Several studies show HLA-E can present self-peptides originating from the leader sequence of other HLA molecules, which signals to our immune system that the cell is healthy. Therefore, it was traditionally thought that the chief role of HLA-E in the body was in immune surveillance. However, there is emerging evidence that HLA-E is also able to present pathogen-derived peptides to the adaptive immune system, namely T cells, in a manner that is similar to classical HLA-Ia molecules. Here we describe the early findings of this less conventional role of HLA-E in the adaptive immune system and its importance for immunity.
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Affiliation(s)
- Emma J Grant
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Andrea T Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Christian A Lobos
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
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Abstract
PURPOSE OF REVIEW Hyperexpression of classical HLA class I (HLA-I) molecules in insulin-containing islets has become a widely accepted hallmark of type 1 diabetes pathology. In comparison, relatively little is known about the expression, function and role of non-classical subtypes of HLA-I. This review focuses on the current understanding of the non-classical HLA-I subtypes: HLA-E, HLA-F and HLA-G, within and outside the field of type 1 diabetes, and considers the possible impacts of these molecules on disease etiology. RECENT FINDINGS Evidence is growing to suggest that non-classical HLA-I proteins are upregulated, both at the RNA and protein levels in the pancreas of individuals with recent-onset type 1 diabetes. Moreover, associations between non-classical HLA-I genotypes and age at onset of type 1 diabetes have been reported in some studies. As with classical HLA-I, it is likely that hyperexpression of non-classical HLA-I is driven by the release of diffusible interferons by stressed β cells (potentially driven by viral infection) and exacerbated by release of cytokines from infiltrating immune cells. Non-classical HLA-I proteins predominantly (but not exclusively) transduce negative signals to immune cells infiltrating at the site of injury/inflammation. We propose a model in which the islet endocrine cells, through expression of non-classical HLA-I are fighting back against the infiltrating immune cells. By inhibiting the activity and function on NK, B and select T cells, the non-classical HLA-I, proteins will reduce the non-specific bystander effects of inflammation, while at the same time still allowing the targeted destruction of β cells by specific islet-reactive CD8+ T cells.
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Affiliation(s)
- Rebecca C. Wyatt
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW UK
| | - Giacomo Lanzoni
- Diabetes Research Institute, University of Miami – Miller School of Medicine, 1450 NW 10th Avenue, Miami, FL 33136 USA
- Department of Biochemistry and Molecular Biology, University of Miami – Miller School of Medicine, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Mark A. Russell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW UK
| | - Ivan Gerling
- Department of Medicine University of Tennessee Health Science Center and VA Medical Center Research Service, 1030 Jefferson Avenue, Memphis, TN 38128 USA
| | - Sarah J. Richardson
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Barrack Road, Exeter, EX2 5DW UK
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Boppana S, Sterrett S, Files J, Qin K, Fiore-Gartland A, Cohen KW, De Rosa SC, Bansal A, Goepfert PA. HLA-I Associated Adaptation Dampens CD8 T-Cell Responses in HIV Ad5-Vectored Vaccine Recipients. J Infect Dis 2019; 220:1620-1628. [PMID: 31301135 PMCID: PMC6782105 DOI: 10.1093/infdis/jiz368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/10/2019] [Indexed: 01/08/2023] Open
Abstract
HLA-I-associated human immunodeficiency virus (HIV) adaptation is known to negatively affect disease progression and CD8 T-cell responses. We aimed to assess how HLA-I-associated adaptation affects HIV vaccine-induced CD8 T-cell responses in 2 past vaccine efficacy trials. We found that vaccine-encoded adapted epitopes were less immunogenic than vaccine-encoded nonadapted epitopes, and adapted epitope-specific responses were less polyfunctional than nonadapted epitope-specific responses. Along those lines, vaccine recipients with higher HLA-I adaptation to the Gag vaccine insert mounted less polyfunctional CD8 T-cell responses at the protein level. Breadth of response, which correlated with viral control in recipients who became infected, is also dampened by HLA-I adaptation. These findings suggest that HLA-I-associated adaptation is an important consideration for strategies aiming to induce robust CD8 T-cell responses.
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Affiliation(s)
- Sushma Boppana
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Sarah Sterrett
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Jacob Files
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Kai Qin
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kristen W Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen C De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Anju Bansal
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
| | - Paul A Goepfert
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham
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Angénieux C, Dupuis A, Gachet C, de la Salle H, Maître B. Cell surface expression of HLA I molecules as a marker of young platelets. J Thromb Haemost 2019; 17:1511-1521. [PMID: 31207003 DOI: 10.1111/jth.14537] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Accurate identification of the proportion of young platelets is important to distinguish peripheral thrombocytopenia from a deficit in platelet production. Young platelets are defined by their higher RNA content and are often assessed as thiazole orange bright (TObright ) by flow cytometry. In clinical practice, their proportion is estimated by automatic blood counter according to their greater RNA content, which identifies a so-called immature platelet fraction (IPF). However, the detected IPFs are not strictly identical to the young TObright platelet population observed by flow cytometry. OBJECTIVES The aim of this study was to assess the reliability of HLA I/major histocompatibility I (MHC I) cell surface expression as a marker of young platelets. METHODS The HLA I/MHC I expression was evaluated by flow cytometry after costaining blood with TO and antibodies directed against HLA I/MHC I molecules. RESULTS We found that platelets with a higher expression of plasma membrane-localized MHC I molecules displayed an increased TO staining and a higher content in ribosomal P-antigen. Transfusion experiments in mice showed that the number of MHC I molecules expressed on the cell surface of young murine platelets decreased during platelet aging, reaching basal levels within 24 h. Finally, we demonstrated that for patients with thrombocytopenias, the identification of young platelets is better assessed by the flow cytometric determination of the level of HLA I expression than by TO staining or the use of hematological blood counter. CONCLUSION Overall, our results highlight the relevance of MHC I/HLA I expression as a valuable parameter to identify young platelets.
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Affiliation(s)
- Catherine Angénieux
- UMR_S1255, INSERM, Strasbourg, France
- Etablissement Français du Sang-Grand Est, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Arnaud Dupuis
- UMR_S1255, INSERM, Strasbourg, France
- Etablissement Français du Sang-Grand Est, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Christian Gachet
- UMR_S1255, INSERM, Strasbourg, France
- Etablissement Français du Sang-Grand Est, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Henri de la Salle
- UMR_S1255, INSERM, Strasbourg, France
- Etablissement Français du Sang-Grand Est, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Blandine Maître
- UMR_S1255, INSERM, Strasbourg, France
- Etablissement Français du Sang-Grand Est, Strasbourg, France
- Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
- Université de Strasbourg, Strasbourg, France
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Akya A, Farasat A, Ghadiri K, Rostamian M. Identification of HLA-I restricted epitopes in six vaccine candidates of Leishmania tropica using immunoinformatics and molecular dynamics simulation approaches. Infect Genet Evol 2019; 75:103953. [PMID: 31284043 DOI: 10.1016/j.meegid.2019.103953] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/12/2022]
Abstract
In spite of numerous studies on vaccination for various species of Leishmania, research on the development of an effective vaccine for L. tropica is very scarce. In silico epitope prediction is a new way to survey the best vaccine candidates. Here, we predicted the best epitopes of six L. tropica antigens with vaccine capability against this pathogen, using highly frequent HLA-I alleles. Based on the frequent HLA alleles, the protein sequences were screened individually using four different MHC prediction applications, namely SYFPEITHI, ProPredI, BIMAS, and IEDB. Several in silico assays including clustering, human similarity exclusion, epitope conservancy prediction, investigating in experimental records, immunogenicity prediction, and prediction of population coverage were performed to narrow the results and to find the best epitopes. The selected epitopes and their restricted HLA-I alleles were docked and the final epitopes with the lowest binding energy (the highest binding affinity) were chosen. Finally, the stability and the binding properties of the best epitope-HLA-I combinations were analyzed using molecular dynamics simulation studies. We found ten potential peptides with strong binding affinity to highly frequent HLA-I alleles that can be further evaluated as vaccine targets against L. tropica.
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Affiliation(s)
- Alisha Akya
- Infectious Diseases Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Alireza Farasat
- Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Keyghobad Ghadiri
- Infectious Diseases Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Wiener HW, Shrestha S, Lu H, Karita E, Kilembe W, Allen S, Hunter E, Goepfert PA, Tang J. Immunogenetic factors in early immune control of human immunodeficiency virus type 1 (HIV-1) infection: Evaluation of HLA class I amino acid variants in two African populations. Hum Immunol 2017; 79:166-171. [PMID: 29289742 DOI: 10.1016/j.humimm.2017.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 01/07/2023]
Abstract
Immune control of HIV-1 infection depends heavily on cytotoxic T-lymphocyte responses restricted by diverse HLA class I molecules. Recent work has uncovered specific amino acid residues (AARs) that seem to dictate the extent of immune control in African Americans, which prompted us to test these emerging hypotheses in seroconverters (SCs) from southern and eastern Africa. Based on data from 196 Zambians and 76 Rwandans with fully resolved HLA alleles and pre-therapy HIV-1 viral loads (VL) in the first 3- to 36-month of infection (>2300 person-visits), four AARs of primary interest (positions 63, 97, 116 and 245 in the mature HLA-B protein) were found to explain 8.1% and 15.8% of variance in set-point VL for these cohorts (P = .024 and 7.5 × 10-6, respectively). Two AARs not reported previously (167S in HLA-B and 116F in HLA-C) also showed relatively consistent associations with VL (adjusted P = .009-.069), while many population-specific associations were also noted (false discovery rate <0.05). Extensive and often strong linkage disequilibrium among neighboring AAR variants called for more extensive analyses of AAR haplotypes in diverse cohorts before the structural basis of antigen presentation can be fully comprehended.
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Affiliation(s)
- Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hailin Lu
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Susan Allen
- Zambia-Emory HIV Research Project, Lusaka, Zambia; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Eric Hunter
- Vaccine Research Center, Emory University, Atlanta, GA, USA
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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Chandra H, Yadav JS. Human leukocyte antigen (HLA)-binding epitopes dataset for the newly identified T-cell antigens of Mycobacterium immunogenum. Data Brief 2016; 8:1069-71. [PMID: 27508266 PMCID: PMC4969084 DOI: 10.1016/j.dib.2016.06.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/17/2016] [Accepted: 06/24/2016] [Indexed: 11/04/2022] Open
Abstract
The dataset described herein is related to our article entitled “T-cell antigens of Mycobacterium immunogenum (MI), an etiological agent of occupational hypersensitivity pneumonitis’’ (Chandra and Yadav, 2016) [1]. The data include in silico-predicted T-cell epitopes of the T-cell antigens AgA and AgD of MI predicted to bind to HLA-I or HLA-II alleles. Data on two reference T-cell antigens ESAT-6 and CFP-10 of Mycobacterium tuberculosis H37Rv are included for comparison. The data for each antigen include the predicted epitope׳s amino acid sequence, its first amino acid position, and its ability to bind HLA-I or HLA-II allele(s).
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Affiliation(s)
- Harish Chandra
- Microbial Pathogenesis and Toxicogenomics Laboratory, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, United States of America
| | - Jagjit S Yadav
- Microbial Pathogenesis and Toxicogenomics Laboratory, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, United States of America
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27
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Martínez-Sánchez MV, Periago A, Legaz I, Gimeno L, Mrowiec A, Montes-Barqueros NR, Campillo JA, Bolarin JM, Bernardo MV, López-Álvarez MR, González C, García-Garay MC, Muro M, Cabañas-Perianes V, Fuster JL, García-Alonso AM, Moraleda JM, Álvarez-Lopez MR, Minguela A. Overexpression of KIR inhibitory ligands ( HLA-I) determines that immunosurveillance of myeloma depends on diverse and strong NK cell licensing. Oncoimmunology 2015; 5:e1093721. [PMID: 27141379 DOI: 10.1080/2162402x.2015.1093721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/08/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2022] Open
Abstract
Missing self recognition makes cancer sensitive to natural killer cell (NKc) reactivity. However, this model disregards the NKc licensing effect, which highly increases NKc reactivity through interactions of inhibitory killer cell immunoglobulin-like receptors (iKIR) with their cognate HLA-I ligands. The influence of iKIR/HLA-ligand (HLA-C1/C2) licensing interactions on the susceptibility to and progression of plasma cell (PC) dyscrasias was evaluated in 164 Caucasian patients and 286 controls. Compared to controls, myeloma accumulates KIR2DL1-L2+L3- genotypes (2.8% vs. 13.2%, p < 0.01, OR = 5.29) and less diverse peripheral repertoires of NKc clones. Less diverse and weaker-affinity repertoires of iKIR2D/HLA-C licensing interactions increased myeloma susceptibility. Thus, the complete absence of conventional iKIR2D/HLA-C licensing interactions (KIR2DL1-L2+L3-/C2C2, 2.56% vs. 0.35%; p < 0.05; OR = 15.014), single-KIR2DL3+/C1+ (20.51% vs. 10.84%; p < 0.05; OR = 2.795) and single-KIR2DL2+/C1+ (12.82% vs. 4.9%; p < 0.01; OR = 5.18) interactions were over-represented in myeloma, compared to controls. Additionally, KIR2DL1-L2+L3- (20% vs. 83%, p < 0.00001) as well as KIR3DL1- (23% vs. 82%, p < 0.00001) genotypes had a dramatic negative impact on the 3-y progression-free survival (PFS), particularly in patients with low-tumor burden. Remarkably, myeloma-PCs, compared to K562 and other hematological cancers, showed substantial over-expression of HLA-I ("increasing-self" instead of missing-self), including HLA-C, and mild expression of ligands for NKc activating receptors (aRec) CD112, CD155, ULBP-1 and MICA/B, which apparently renders myeloma-PCs susceptible to lysis mainly by licensed NKc. KIR2DL1-L2+L3-/C2C2 patients (with no conventional iKIR2D/HLA-C licensing interactions) lyse K562 but barely lyse myeloma-PCs (4% vs. 15%; p < 0.05, compared to controls). These results support a model where immunosurveillance of no-missing-self cancers, e.g., myeloma, mainly depends on NKc licensing.
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Affiliation(s)
- María V Martínez-Sánchez
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - Adela Periago
- Hematology Service, Hospital Rafael Méndez , Lorca, Murcia, Spain
| | - Isabel Legaz
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - Lourdes Gimeno
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - Anna Mrowiec
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - Natividad R Montes-Barqueros
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - José A Campillo
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - José M Bolarin
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - María V Bernardo
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - María R López-Álvarez
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | | | | | - Manuel Muro
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | | | - Jose L Fuster
- Hematology Service, Hospital General Universitario Santa Lucía , Cartagena, Murcia, Spain
| | - Ana M García-Alonso
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | | | - María R Álvarez-Lopez
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
| | - Alfredo Minguela
- Immunology Service, Instituto Murciano de investigación biosanitaria (IMIB) and Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), El Palmar , Murcia, Spain
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Pratheek BM, Suryawanshi AR, Chattopadhyay S, Chattopadhyay S. In silico analysis of MHC-I restricted epitopes of Chikungunya virus proteins: Implication in understanding anti-CHIKV CD8(+) T cell response and advancement of epitope based immunotherapy for CHIKV infection. Infect Genet Evol 2015; 31:118-26. [PMID: 25643869 DOI: 10.1016/j.meegid.2015.01.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 11/27/2022]
Abstract
Chikungunya virus (CHIKV) is a mosquito-borne Alphavirus, responsible for acute febrile infection. The high morbidity and socio-economic loss associated with the recent CHIKV epidemics worldwide have raised a great public health concern and emphasize the need to study the immunological basis of CHIKV infection to control the disease. MHC-I restricted CD8(+) T cell response represent one of the major anti-viral immune responses. Accordingly, it is essential to have a detailed understanding towards CHIKV specific MHC-I restricted immunogenic epitopes for anti-viral CD8(+) CTL immunogenicity. In the present study, a computational approach was used to predict the conserved MHC-I epitopes for mouse haplotypes (H2-Db and H2-Dd) and some alleles of the major HLA-I supertypes (HLA-A2, -A3, -A24, -B7, -B15) of all CHIKV proteins. Further, an in-depth computational analysis was carried out to validate the selected epitopes for their nature of conservation in different global CHIKV isolates to assess their binding affinities to the appropriate site of respective MHC-I molecules and to predict anti-CHIKV CD8(+) CTL immunogenicity. Our analyses resulted in fifteen highly conserved epitopes for H2-Db and H2-Dd and fifty epitopes for different HLA-I supertypes. Out of these, the MHC-I epitopes VLLPNVHTL and MTPERVTRL were found to have highest predictable CTL immunogenicities and least binding energies for H2-Db and H2-Dd, whereas, for HLA-I, the epitope FLTLFVNTL was with the highest population coverage, CTL immunogenicity and least binding energy. Hence, our study has identified MHC-I restricted epitopes that may help in the advancement of MHC-I restricted epitope based anti-CHIKV immune responses against this infection and this will be useful towards the development of epitope based anti-CHIKV immunotherapy in the future. However, further experimental investigations for cross validation and evaluation are warranted to establish the ability of epitopes to induce CD8(+) T cell mediated immune responses.
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Affiliation(s)
- B M Pratheek
- School of Biological Sciences, National Institute of Science Education & Research, Bhubaneswar 751005, Odisha, India
| | - Amol R Suryawanshi
- Infectious Disease Biology, Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Soma Chattopadhyay
- Infectious Disease Biology, Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
| | - Subhasis Chattopadhyay
- School of Biological Sciences, National Institute of Science Education & Research, Bhubaneswar 751005, Odisha, India.
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Chen XH, Liu ZC, Zhang G, Wei W, Wang XX, Wang H, Ke HP, Zhang F, Wang HS, Cai SH, Du J. TGF-β and EGF induced HLA-I downregulation is associated with epithelial-mesenchymal transition (EMT) through upregulation of snail in prostate cancer cells. Mol Immunol 2015; 65:34-42. [PMID: 25618241 DOI: 10.1016/j.molimm.2014.12.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/21/2014] [Accepted: 12/26/2014] [Indexed: 01/05/2023]
Abstract
Human leukocyte antigen class I antigens (HLA-I) is essential in immune response by presenting antigenic peptides to cytotoxic T lymphocytes. Downregulation of HLA-I is observed in primary and metastatic prostate cancers, which facilitates them escape from immune surveillance, thereby promotes prostate cancer progression. In addition, elevated level of growth factors like TGF-β or EGF in microenvironment is related to the prostate cancer deterioration. Thus, we wondered whether TGF-β or EGF was involved in the regulation of HLA-I during the development of prostate cancer cells. In this study, we demonstrated that TGF-β and EGF both downregulated the expression of HLA-I, thereby attenuated the cytotoxic T cell mediated lysis of prostate cancer cells. Next, we revealed that TGF-β and EGF induced downregulation of HLA-I is associated with classical epithelial-mesenchymal transition (EMT) morphological changes and expression profiles. We further illustrated that overexpression of Snail is crucial for HLA-I downregulation and its association with EMT. At last, we discussed that NF-κB/p65 is the plausible target for Snail to induce HLA-I downregulation. Taken together, this is the first evidence to reveal that both TGF-β and EGF can induce HLA-I downregulation which is then proven to be associated with EMT in prostate cancer cells. These discoveries provide a deeper understanding of growth factors induced immune escape and introduce potential therapeutic targets for prostate cancers.
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Affiliation(s)
- Xiao-Hui Chen
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Zong-Cai Liu
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Ge Zhang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Wei Wei
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Xiao-Xiong Wang
- Department of Pharmacology, School of Pharmaceutical Sciences, Jinan University, Guangzhou 510632, PR China
| | - Hao Wang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Hong-Peng Ke
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Fan Zhang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China
| | - Hong-Sheng Wang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China.
| | - Shao-Hui Cai
- Department of Pharmacology, School of Pharmaceutical Sciences, Jinan University, Guangzhou 510632, PR China.
| | - Jun Du
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou 510006, China.
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30
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Fernández L, Portugal R, Valentín J, Martín R, Maxwell H, González-Vicent M, Díaz MÁ, de Prada I, Pérez-Martínez A. In vitro Natural Killer Cell Immunotherapy for Medulloblastoma. Front Oncol 2013; 3:94. [PMID: 23626949 PMCID: PMC3630393 DOI: 10.3389/fonc.2013.00094] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 04/05/2013] [Indexed: 11/17/2022] Open
Abstract
How the immune system attacks medulloblastoma (MB) tumors effectively is unclear, although natural killer (NK) cells play an important role in immune defense against tumor cells. Interactions between receptors on NK cells and ligands expressed by tumor cells are critical for tumor control by immunotherapy. In this study, we analyzed tumor samples from 54 MB patients for expression of major histocompatibility complex class I-related chains A (MICA) and UL16 binding protein (ULPB-2), which are ligands for the NK group 2 member D activatory receptor (NKG2D). The percentage of MICA and ULBP-2 positive cells was higher than 25% in 68% and 6% of MB patients, respectively. A moderate-high intensity of MICA cytoplasmic staining was observed in 46% MB patients and weak ULBP-2 staining was observed in 8% MB patients. No correlation between MICA/ULBP-2 expression and patient outcome was found. We observed that HTB-186, a MB cell line, was moderately resistant to NK cell cytotoxicity in vitro. Blocking MICA/ULBP-2 on HTB-186, and NKG2D receptor on NK cells increased resistance to NK cell lysis in vitro. However, HLA class I blocking on HTB-186 and overnight incubation with IL-15 stimulated NK cells efficiently killed tumor cells in vitro. We conclude that although NKG2D/MICA-ULBP-2 interactions have a role in NK cell cytotoxicity against MB, high expression of HLA class I can protect MB from NK cell cytotoxicity. Even so, our in vitro data indicate that if NK cells are appropriately stimulated, they may have the potential to target MB in vivo.
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Affiliation(s)
- Lucia Fernández
- Department of Hemato-Oncology and Stem Cell Transplantation, Hospital Infantil Universitario Niño Jesús Madrid, Spain
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