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Jing Y, Zhang S, Wang H. DapNet-HLA: Adaptive dual-attention mechanism network based on deep learning to predict non-classical HLA binding sites. Anal Biochem 2023; 666:115075. [PMID: 36740003 DOI: 10.1016/j.ab.2023.115075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
Human leukocyte antigen (HLA) plays a vital role in immunomodulatory function. Studies have shown that immunotherapy based on non-classical HLA has essential applications in cancer, COVID-19, and allergic diseases. However, there are few deep learning methods to predict non-classical HLA alleles. In this work, an adaptive dual-attention network named DapNet-HLA is established based on existing datasets. Firstly, amino acid sequences are transformed into digital vectors by looking up the table. To overcome the feature sparsity problem caused by unique one-hot encoding, the fused word embedding method is used to map each amino acid to a low-dimensional word vector optimized with the training of the classifier. Then, we use the GCB (group convolution block), SENet attention (squeeze-and-excitation networks), BiLSTM (bidirectional long short-term memory network), and Bahdanau attention mechanism to construct the classifier. The use of SENet can make the weight of the effective feature map high, so that the model can be trained to achieve better results. Attention mechanism is an Encoder-Decoder model used to improve the effectiveness of RNN, LSTM or GRU (gated recurrent neural network). The ablation experiment shows that DapNet-HLA has the best adaptability for five datasets. On the five test datasets, the ACC index and MCC index of DapNet-HLA are 4.89% and 0.0933 higher than the comparison method, respectively. According to the ROC curve and PR curve verified by the 5-fold cross-validation, the AUC value of each fold has a slight fluctuation, which proves the robustness of the DapNet-HLA. The codes and datasets are accessible at https://github.com/JYY625/DapNet-HLA.
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Affiliation(s)
- Yuanyuan Jing
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China
| | - Shengli Zhang
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China.
| | - Houqiang Wang
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China
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Peripheral HLA-G/ILT-2 immune checkpoint axis in acute and convalescent COVID-19 patients. Hum Immunol 2023:S0198-8859(23)00043-5. [PMID: 36925435 PMCID: PMC10011044 DOI: 10.1016/j.humimm.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023]
Abstract
The immunosuppressive non-classical human leukocyte antigen-G (HLA-G) can elicits pro-viral activities by down-modulating immune responses. We analysed soluble forms of HLA-G, IL-6 and IL-10 as well as on immune effector cell expression of HLA-G and its cognate ILT-2 receptor in peripheral blood obtained from hospitalised and convalescent COVID-19 patients. Compared with convalescents (N = 202), circulating soluble HLA-G levels (total and vesicular-bound molecules) were significantly increased in hospitalised patients (N = 93) irrespective of the disease severity. During COVID-19, IL-6 and IL-10 levels were also elevated. Regarding the immune checkpoint expression of HLA-G/ILT-2 on peripheral immune effector cells, the frequencies of membrane-bound HLA-G on CD3+ and CD14+ cells were almost identical in patients during and post COVID-19, while the frequency of ILT-2 receptor on CD3+ and CD14+ cells was increased during acute infection. A multi-parametric correlation analysis of soluble HLA-G forms with IL-6, IL-10, activation markers CD25 and CD154, HLA-G, and ILT-2 expression on immune cells revealed a strong positive correlation of soluble HLA-G forms with membrane-bound HLA-G molecules on CD3+/CD14+ cells only in convalescents. During COVID-19, only vesicular-bound HLA-G were positively correlated with the activation marker CD25 on T cells. Thus, our data suggest that the elevated levels of soluble HLA-G in COVID-19 are due to increased expression in organ tissues other than circulating immune effector cells. The concomitant increased expression of soluble HLA-G and ILT-2 receptor frequencies supports the concept that the immune checkpoint HLA-G/ILT-2 plays a role in the immune-pathogenesis of COVID-19.
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Beltrami S, Rizzo S, Strazzabosco G, Gentili V, Alogna A, Narducci M, Bortolotti D, Schiuma G, Rizzo R. Non-classical HLA class I molecules and their potential role in viral infections. Hum Immunol 2023:S0198-8859(23)00061-7. [PMID: 37005169 DOI: 10.1016/j.humimm.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/14/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Human Leukocyte Antigens (HLA) are classified in three different classes I, II and III, and represent the key mediators of immune responses, self-tolerance development and pathogen recognition. Among them, non-classical subtypes (HLA-Ib), e.g. HLA-E and HLA-G, are characterize by tolerogenic functions that are often exploited by viruses to evade the host immune responses. In this perspective, we will review the main current data referred to HLA-G and HLA-E and viral infections, as well as the impact on immune response. Data were selected following eligibility criteria accordingly to the reviewed topic. We used a set of electronic databases (Medline/PubMed, Scopus, Web of Sciences (WOS), Cochrane library) for a systematic search until November 2022 using MeSH keywords/terms (i.e. HLA, HLA-G, HLA-E, viral infection, SARS-CoV-2, etc.…). Recent studies support the involvement of non-classical molecules, such as HLA-E and HLA-G, in the control of viral infection. On one side, viruses exploit HLA-G and HLA-E molecule to control host immune activation. On the other side, the expression of these molecules might control the inflammatory condition generated by viral infections. Hence, this review has the aim to summarize the state of art of literature about the modulation of these non-classical HLA-I molecules, to provide a general overview of the new strategies of viral immune system regulation to counteract immune defenses.
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Affiliation(s)
- Silvia Beltrami
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Sabrina Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Giovanni Strazzabosco
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Andrea Alogna
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Marco Narducci
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy; Temple University, Japan Campus, 1 Chome-14-29 Taishido, Setagaya City, Tokyo 154-0004, Italy
| | - Daria Bortolotti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Giovanna Schiuma
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy - Via Luigi Borsari, 46, 44121 Ferrara, Italy; LTTA, University of Ferrara, Via Luigi Borsari, 46, 44121 Ferrara, Italy.
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Traina L, Mucignat M, Rizzo R, Gafà R, Bortolotti D, Passaro A, Zamboni P. COVID-19 induced aorto duodenal fistula following evar in the so called "negative" patient. Vascular 2023; 31:189-195. [PMID: 34919005 DOI: 10.1177/17085381211053695] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Since October 2019, SARS-CoV-2 pandemic represents a challenge for the international healthcare system and for the treatment and survival of patients. We normally focus on symptomatic patients, and symptoms can range from the respiratory to the gastrointestinal system. In addition, we consider patients without fever and respiratory symptoms, with both a negative RT nasopharyngeal swab and lung CT, as a "Covid-19 negative patient." In this article, we present a so called Covid-19 "negative" patient, with an unsuspected vascular clinical onset of the viral infection. METHODS An 80 y.o. man, who previously underwent endovascular aortic repair for an infrarenal abdominal aortic aneurysm, presented to our department with an atypical presentation of an aorto-enteric fistula during the pandemic. While in hospital, weekly nasopharyngeal swab tests were always negative for SARS-CoV-2. However, the absence of aortic endograft complications, the gross anatomy of duodenal ischemic injury, and the recent history of the patient who lived the last months in Bergamo, the Italian city with the highest number of COVID-19 deaths, lead the senior Author to suspect an occult SARS-CoV-2 infection. The patient underwent to resection of the fourth portion of the duodenum and the first jejunal loop, with subsequent duodenum-jejunal latero-lateral anastomosis and the direct suture of the aortic wall. The intestinal specimen was investigated as suspected SARS-CoV-2 bowel infection by the means of immune-histochemistry (IHC). An ileum sample obtained in the pre-COVID-19 era was used as a control tissue. RESULTS The histological analysis of the bowel revealed sustained wall ischemia and liponecrosis of the duodenal wall, with intramural blood vessels thrombosis. Blood vessel endotheliitis and neo-angiogenesis were also observed. Finally, the IHC was strongly positive for SARS-CoV-2 RNA and for HLA-G presence, with a particular concentration both in blood vessels and in the intestinal villi. The control tissue sample was not positive for both SARS-CoV-2 and HLA-G. CONCLUSIONS Coronavirus pandemic continues to be an international challenge and more studies and trials must be done to learn its pathogenesis and its complications. As for thromboembolic events caused by SARS-COV-2, vascular surgeons are involved in treatment and prevention of the complications of this syndrome and must be ready with general surgeons to investigate atypical and particular cases such as the one discussed in this article.
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Affiliation(s)
- Luca Traina
- Unit of Vascular and Endovascular Surgery, 18560Azienda Ospedaliero Universitaria di Ferrara - Arcispedale S.Anna, Ferrara, Italy
| | - Marianna Mucignat
- Unit of Vascular and Endovascular Surgery, 18560Azienda Ospedaliero Universitaria di Ferrara - Arcispedale S.Anna, Ferrara, Italy.,Department of Translational Medicine for Romagna, and Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Roberta Rizzo
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Roberta Gafà
- Department of Translational Medicine for Romagna, and Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Daria Bortolotti
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Angelina Passaro
- Department of Translational Medicine for Romagna, and Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Paolo Zamboni
- Department of Translational Medicine for Romagna, and Vascular Diseases Center, University of Ferrara, Ferrara, Italy
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Amodio G, Capogrosso P, Pontillo M, Tassara M, Boeri L, Carenzi C, Cignoli D, Ferrara AM, Ramirez GA, Tresoldi C, Locatelli M, Santoleri L, Castagna A, Zangrillo A, De Cobelli F, Tresoldi M, Landoni G, Rovere‐Querini P, Ciceri F, Montorsi F, Salonia A, Gregori S. Combined plasma levels of IL-10 and testosterone, but not soluble HLA-G5, predict the risk of death in COVID-19 patients. Andrology 2023; 11:32-44. [PMID: 36323494 PMCID: PMC9877736 DOI: 10.1111/andr.13334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND The identification of biomarkers correlated with coronavirus disease 2019 (COVID-19) outcomes is a relevant need for clinical management. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is characterized by elevated interleukin (IL)-6, IL-10, HLA-G, and impaired testosterone production. OBJECTIVES We aimed at defining the combined impact of sex hormones, interleukin-10, and HLA-G on COVID-19 pathophysiology and their relationship in male patients. MATERIALS AND METHODS We measured by chemiluminescence immunoassay, electrochemiluminescent assays, and enzyme-linked immunosorbent assay circulating total testosterone, 17β-estradiol (E2 ), IL-10, and -HLAG5 as well as SARS-CoV-2 S1/S2 Immunoglobulin G from 292 healthy controls and 111 COVID-19 patients with different disease severity at hospital admission, and in 53 COVID-19 patients at 7-month follow-up. RESULTS AND DISCUSSION We found significantly higher levels of IL-10, HLA-G, and E2 in COVID-19 patients compared to healthy controls and an inverse correlation between IL-10 and testosterone, with IL-10, progressively increasing and testosterone progressively decreasing with disease severity. This correlation was lost at the 7-month follow-up. The risk of death in COVID-19 patients with low testosterone increased in the presence of high IL-10. A negative correlation between SARS-CoV-2 Immunoglobulin G and HLA-G or IL-10 at hospitalization was observed. At the 7-month follow-up, IL-10 and testosterone normalized, and HLA-G decreased. CONCLUSION Our findings indicate that combined evaluation of IL-10 and testosterone predicts the risk of death in men with COVID-19 and support the hypothesis that IL-10 fails to suppress excessive inflammation by promoting viral spreading.
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Affiliation(s)
- Giada Amodio
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS Ospedale San RaffaeleMilanItaly
| | - Paolo Capogrosso
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly,Department of Urology and AndrologyOspedale di Circolo and Macchi FoundationVareseItaly
| | - Marina Pontillo
- Laboratory Medicine ServiceIRCCS Ospedale San RaffaeleMilanItaly
| | - Michela Tassara
- Laboratory Medicine ServiceIRCCS Ospedale San RaffaeleMilanItaly
| | - Luca Boeri
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly,IRCCS Foundation Ca’ Granda, Maggiore Policlinico Hospital, Department of UrologyUniversity of MilanMilanItaly
| | - Cristina Carenzi
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly
| | - Daniele Cignoli
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly,University Vita‐Salute San RaffaeleMilanItaly
| | - Anna Maria Ferrara
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly
| | - Giuseppe A. Ramirez
- University Vita‐Salute San RaffaeleMilanItaly,Immunology, Rheumatology, Allergology and Rare Diseases UnitIRCCS Ospedale San RaffaeleMilanItaly
| | | | | | - Luca Santoleri
- Immunohematology and Transfusion MedicineIRRCS Ospedale San RaffaeleMilanItaly
| | - Antonella Castagna
- University Vita‐Salute San RaffaeleMilanItaly,Department of Infectious DiseasesIRCCS Ospedale San RaffaeleMilanItaly
| | - Alberto Zangrillo
- University Vita‐Salute San RaffaeleMilanItaly,Anesthesia and Intensive Care DepartmentIRCCS Ospedale San RaffaeleMilanItaly
| | - Francesco De Cobelli
- University Vita‐Salute San RaffaeleMilanItaly,Department of RadiologyIRCCS Ospedale San RaffaeleMilanItaly
| | - Moreno Tresoldi
- General Medicine and Advanced Care UnitIRCCS Ospedale San RaffaeleMilanItaly
| | - Giovanni Landoni
- University Vita‐Salute San RaffaeleMilanItaly,Anesthesia and Intensive Care DepartmentIRCCS Ospedale San RaffaeleMilanItaly
| | - Patrizia Rovere‐Querini
- University Vita‐Salute San RaffaeleMilanItaly,Internal Medicine, Diabetes, and Endocrinology UnitIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Fabio Ciceri
- University Vita‐Salute San RaffaeleMilanItaly,Hematology and Bone Marrow Transplant UnitIRCCS Ospedale San RaffaeleMilanItaly
| | - Francesco Montorsi
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly,University Vita‐Salute San RaffaeleMilanItaly
| | - Andrea Salonia
- Division of Experimental Oncology/Unit of UrologyURI, IRCCS Ospedale San RaffaeleMilanItaly,University Vita‐Salute San RaffaeleMilanItaly
| | - Silvia Gregori
- San Raffaele Telethon Institute for Gene Therapy (SR‐TIGET)IRCCS Ospedale San RaffaeleMilanItaly
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Wang X, Xiong H, Ning Z. Implications of NKG2A in immunity and immune-mediated diseases. Front Immunol 2022; 13:960852. [PMID: 36032104 PMCID: PMC9399941 DOI: 10.3389/fimmu.2022.960852] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022] Open
Abstract
In recent studies, NKG2A is revealed to be a key immune checkpoint for both natural killer (NK) cells and CD8+ T cells. It form heterodimer receptors with CD94, and targets the peptide-presenting human leukocyte antigen-E (HLA-E) molecules. Upon crosslinking, NKG2A/CD94 delivers inhibitory signals for NK cells and CD8+ T cells, while blocking NKG2A can effectively unleash functions of these cytotoxic lymphocytes. The interaction between NKG2A and HLA-E contributes to tumor immune escape, and NKG2A-mediated mechanisms are currently being exploited to develop potential antitumor therapeutic strategies. In addition, growing evidence shows that NKG2A also plays important roles in other immune-related diseases including viral infections, autoimmune diseases, inflammatory diseases, parasite infections and transplant rejection. Therefore, the current work focuses on describing the effect of NKG2A on immune regulation and exploring its potential role in immune-mediated disorders.
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Affiliation(s)
- Xiaotong Wang
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
- Jining Key Laboratory of Immunology, Jining Medical University, Jining, China
| | - Huabao Xiong
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
- Jining Key Laboratory of Immunology, Jining Medical University, Jining, China
- *Correspondence: Zhaochen Ning, ; Huabao Xiong,
| | - Zhaochen Ning
- Institute of Immunology and Molecular Medicine, Jining Medical University, Jining, China
- Jining Key Laboratory of Immunology, Jining Medical University, Jining, China
- *Correspondence: Zhaochen Ning, ; Huabao Xiong,
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Ramzannezhad S, Tarighi M, Mohammadnia-Afrouzi M, Aghapour S, Bagherzadeh M, Ahmadnia Z, Hosseini A, Javanian M, Ghorbani H, Shahbazi M. The association of decreased HLA-G + immune cell frequencies with critical COVID-19 patients. Microb Pathog 2022; 167:105550. [PMID: 35584714 PMCID: PMC9107627 DOI: 10.1016/j.micpath.2022.105550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 01/31/2023]
Abstract
INTRODUCTION COVID-19 (coronavirus disease-2019) is an infectious disease caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Immune dysregulation causes inflammation and massive production of inflammatory mediators that worsen the patients' status. Here, regulatory immune cells may ameliorate inflammation and improve the severity of the disease. MATERIALS AND METHODS A total of 76 participants were enrolled in this study and divided into 3 groups as follows: patients with moderate/severe COVID-19 (n = 25), patients with critical COVID-19 (n = 26), and healthy controls (n = 25). After blood collection, peripheral blood mononuclear cells (PBMCs) were isolated and stained by FITC-conjugated anti-CD4 monoclonal antibodies (mABs), PE-conjugated anti-HLA-G mABs, PerCPCy5.5-conjugated anti-CD14 mABs, and APC-conjugated anti-CD8 mABs. RESULTS Critical COVID-19 patients had a significantly lower frequency of CD4+ HLA-G+ T lymphocytes compared with moderate/severe COVID-19 patients (p value < 0.001; SMD, -1.27; 95% CI [-1.86, -0.66]) and healthy controls (p value < 0.05; SMD, -0.69; 95% CI [-1.25, -0.12]). Critical COVID-19 patients had a significantly lower frequency of CD14+ HLA-G+ monocytes compared with moderate/severe COVID-19 patients (p value < 0.001; SMD, -2.09; 95% CI [-2.77, -1.41]) and healthy controls (p value < 0.05; SMD, -0.83; 95% CI [-1.40, -0.25]). However, there was no difference between the groups regarding the frequency of CD8+ HLA-G+ T lymphocytes. CONCLUSION The increased amount of immunomodulatory HLA-G+ cells may reduce the severity of the disease in moderate/severe COVID-19 patients compared with critical COVID-19 patients.
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Affiliation(s)
- Somayeh Ramzannezhad
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Pathology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mona Tarighi
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Immunology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mousa Mohammadnia-Afrouzi
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Immunology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Soudabeh Aghapour
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Immunology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mojgan Bagherzadeh
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Immunology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Zahra Ahmadnia
- Department of Pathology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Akramossadat Hosseini
- Department of Pathology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Mostafa Javanian
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Housein Ghorbani
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Pathology, School of Medicine, Babol University of Medical Sciences, Babol, Iran,Corresponding author. Department of Pathology, School of Medicine, Babol University of Medical Sciences, Ganj Afrooz Avenue, Babol, Mazandaran, Iran
| | - Mehdi Shahbazi
- Immunoregulation Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran,Department of Immunology, School of Medicine, Babol University of Medical Sciences, Babol, Iran,Corresponding author. Department of Immunology, School of Medicine, Babol University of Medical Sciences, Ganj Afrooz Avenue, Babol, Mazandaran, Iran
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Dhall A, Patiyal S, Raghava GPS. HLAncPred: a method for predicting promiscuous non-classical HLA binding sites. Brief Bioinform 2022; 23:6587168. [PMID: 35580839 DOI: 10.1093/bib/bbac192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022] Open
Abstract
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional HLA-based immunotherapy, particularly against cancer and COVID-19 infection. In the last two decades, several methods have been developed to predict the binders of classical HLA alleles. In contrast, limited attempts have been made to develop methods for predicting non-classical HLA binding peptides, due to the scarcity of sufficient experimental data. Of note, in order to facilitate the scientific community, we have developed an artificial intelligence-based method for predicting binders of class-Ib HLA alleles. All the models were trained and tested on experimentally validated data obtained from the recent release of IEDB. The machine learning models achieved more than 0.98 AUC for HLA-G alleles on validation dataset. Similarly, our models achieved the highest AUC of 0.96 and 0.94 on the validation dataset for HLA-E*01:01 and HLA-E*01:03, respectively. We have summarized the models developed in the past for non-classical HLA and validated the performance with the models developed in this study. Moreover, to facilitate the community, we have utilized our tool for predicting the potential non-classical HLA binding peptides in the spike protein of different variants of virus causing COVID-19, including Omicron (B.1.1.529). One of the major challenges in the field of immunotherapy is to identify the promiscuous binders or antigenic regions that can bind to a large number of HLA alleles. To predict the promiscuous binders for the non-classical HLA alleles, we developed a web server HLAncPred (https://webs.iiitd.edu.in/raghava/hlancpred) and standalone package.
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Affiliation(s)
- Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
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Ad'hiah AH, Al-Bayatee NT. HLA-G 14-bp insertion/deletion polymorphism and risk of coronavirus disease 2019 (COVID-19) among Iraqi patients. Hum Immunol 2022; 83:521-527. [PMID: 35305830 PMCID: PMC8920981 DOI: 10.1016/j.humimm.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 12/24/2022]
Abstract
Human leukocyte antigen (HLA)-G molecules are proposed to influence susceptibility to coronavirus disease 2019 (COVID-19). A case-control study was conducted on 209 patients with COVID-19 and198 controls to assess soluble HLA-G (sHLA-G) levels and HLA-G 14-bp insertion [Ins]/deletion [Del] polymorphism. Results revealed that median levels of sHLA-G were significantly higher in serum of COVID-19 patients than in controls (17.92 [interquartile range: 14.86–21.15] vs. 13.42 [9.95–17.38] ng/mL; probability <0.001). sHLA-G levels showed no significant differences between patients with moderate, severe or critical disease. Del allele was significantly associated with the risk of COVID-19 (odds ratio = 1.89; 95% confidence interval = 1.44–2.48; corrected probability = 0.001), while a higher risk was associated with Del/Del genotype (odds ratio = 2.39; 95% confidence interval = 1.25–4.58; corrected probability = 0.048). Allele and genotype frequencies of HLA-G 14-bp Ins/Del polymorphism stratified by gender or disease severity showed no significant differences in each stratum. Further, there was no significant impact of genotypes on sHLA-G levels. In conclusion, sHLA-G levels were up-regulated in COVID-19 patients regardless of disease severity. Further, it is suggested that HLA-G 14-bp Ins/Del polymorphism is associated with COVID-19 risk.
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Immunomodulatory Potential of Non-Classical HLA-G in Infections including COVID-19 and Parasitic Diseases. Biomolecules 2022; 12:biom12020257. [PMID: 35204759 PMCID: PMC8961671 DOI: 10.3390/biom12020257] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/23/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023] Open
Abstract
Human Leukocyte Antigen-G (HLA-G), a polymorphic non-classical HLA (HLA-Ib) with immune-regulatory properties in cancers and infectious diseases, presents both membrane-bound and soluble (sHLA-G) isoforms. Polymorphism has implications in host responses to pathogen infections and in pathogenesis. Differential expression patterns of HLA-G/sHLA-G or its polymorphism seem to be related to different pathological conditions, potentially acting as a disease progression biomarker. Pathogen antigens might be involved in the regulation of both membrane-bound and sHLA-G levels and impact immune responses during co-infections. The upregulation of HLA-G in viral and bacterial infections induce tolerance to infection. Recently, sHLA-G was found useful to identify the prognosis of Coronavirus disease 2019 (COVID-19) among patients and it was observed that the high levels of sHLA-G are associated with worse prognosis. The use of pathogens, such as Plasmodium falciparum, as immune modulators for other infections could be extended for the modulation of membrane-bound HLA-G in COVID-19-infected tissues. Overall, such information might open new avenues concerning the effect of some pathogens such as parasites in decreasing the expression level of HLA-G to restrict pathogenesis in some infections or to influence the immune responses after vaccination among others.
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11
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Zepeda-Cervantes J, Martínez-Flores D, Ramírez-Jarquín JO, Tecalco-Cruz ÁC, Alavez-Pérez NS, Vaca L, Sarmiento-Silva RE. Implications of the Immune Polymorphisms of the Host and the Genetic Variability of SARS-CoV-2 in the Development of COVID-19. Viruses 2022; 14:94. [PMID: 35062298 PMCID: PMC8778858 DOI: 10.3390/v14010094] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current pandemic affecting almost all countries in the world. SARS-CoV-2 is the agent responsible for coronavirus disease 19 (COVID-19), which has claimed millions of lives around the world. In most patients, SARS-CoV-2 infection does not cause clinical signs. However, some infected people develop symptoms, which include loss of smell or taste, fever, dry cough, headache, severe pneumonia, as well as coagulation disorders. The aim of this work is to report genetic factors of SARS-CoV-2 and host-associated to severe COVID-19, placing special emphasis on the viral entry and molecules of the immune system involved with viral infection. Besides this, we analyze SARS-CoV-2 variants and their structural characteristics related to the binding to polymorphic angiotensin-converting enzyme type 2 (ACE2). Additionally, we also review other polymorphisms as well as some epigenetic factors involved in the immunopathogenesis of COVID-19. These factors and viral variability could explain the increment of infection rate and/or in the development of severe COVID-19.
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Affiliation(s)
- Jesús Zepeda-Cervantes
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Daniel Martínez-Flores
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Josué Orlando Ramírez-Jarquín
- Departamento de Neuropatología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Ángeles C. Tecalco-Cruz
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico City 06720, Mexico;
| | - Noé Santiago Alavez-Pérez
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Luis Vaca
- Departamento de Biología Celular y del Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Rosa Elena Sarmiento-Silva
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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12
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Yiğenoğlu TN, Başcı S, Şahin D, Ulaş T, Dal MS, Korkmaz S, Hacıbekiroğlu T, Namdaroğlu S, Erkurt MA, Turgut B, Altuntaş F. Mesenchymal stem cell transfusion: Possible beneficial effects in COVID-19 patients. Transfus Apher Sci 2021; 60:103237. [PMID: 34419356 PMCID: PMC8372452 DOI: 10.1016/j.transci.2021.103237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/15/2021] [Accepted: 08/08/2021] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 attaches to the angiotensin-converting enzyme 2 (ACE-2) receptor on human cells. The virus causes hypercytokinemia, capillary leak, pulmonary edema, acute respiratory distress syndrome, acute cardiac injury, and leads to death. Mesenchymal stem cells (MSCs) are ACE-2 negative cells; therefore, can escape from SARS-CoV-2. MSCs prevent hypercytokinemia and help the resolution of the pulmonary edema and other damages occurred during the course of COVID-19. In addition, MSCs enhance the regeneration of the lung and other tissues affected by SARS-CoV-2. The case series reported beneficial effect of MSCs in COVID-19 treatment. However, there are some concerns about the safety of MSCs, particularly referring to the increased risk of disseminated intravascular coagulation, and thromboembolism due to the expression of TF/CD142. Prospective, randomized, large scale studies are needed to reveal the optimum dose, administration way, time, efficacy, and safety of MSCs in the COVID-19 treatment.
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Affiliation(s)
- Tuğçe Nur Yiğenoğlu
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Ankara, Turkey
| | - Semih Başcı
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Ankara, Turkey,Corresponding author
| | - Derya Şahin
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Ankara, Turkey
| | - Turgay Ulaş
- Near East University, School of Medicine, Department of Internal Medicine, Department of Hematology, Cyprus
| | - Mehmet Sinan Dal
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Ankara, Turkey
| | - Serdal Korkmaz
- University of Health Sciences, Kayseri Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Kayseri, Turkey
| | - Tuba Hacıbekiroğlu
- Sakarya University, School of Medicine, Department of Internal Medicine, Division of Hematology, Sakarya, Turkey
| | - Sinem Namdaroğlu
- University of Health Sciences, Bozyaka Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Izmir, Turkey
| | - Mehmet Ali Erkurt
- Inonu University, School of Medicine, Department of Internal Medicine, Division of Hematology and Bone Marrow Transplantation Center, Malatya, Turkey
| | - Burhan Turgut
- Namık Kemal University, School of Medicine, Department of Internal Medicine, Division of Hematology and Bone Marrow Transplantation Center, Tekirdağ, Turkey
| | - Fevzi Altuntaş
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Hematology and Bone Marrow Transplantation Center, Ankara, Turkey,Ankara Yıldırım Beyazıt University, School of Medicine, Department of Internal Medicine, Division of Hematology, Ankara, Turkey
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13
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Su T, Wang H, Yao Y. Novel nucleic acid aptamer gold (Au)-nanoparticles (AuNPs-AptHLA-G5-1 and AuNPs-AptHLA-G5-2) to detect the soluble human leukocyte antigen G5 subtype (HLA-G5) in liquid samples. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1416. [PMID: 34733968 PMCID: PMC8506699 DOI: 10.21037/atm-21-3334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022]
Abstract
Background The human leukocyte antigen G5 subtype (HLA-G5) is a major histocompatibility complex (MHC) molecule that is selectively expressed at the maternal-foetal tissue interface and is required for the successful implantation of the in vitro fertilized embryo. It is critical to detect HLA-G5, especially HLA-G5 expression in embryo fluid, during in vitro embryo incubation and culture. However, the specificity and sensitivity of traditional ELISA methods to detect sHLA-G5 are insufficient. This work aimed to explore novel nucleic acid aptamer gold (Au)-nanoparticles to detect soluble HLA-G5 in liquid samples. Methods Soluble HLA-G5 was obtained using a prokaryotic expression system, and two novel aptamers (HLA-G5-Apt1 and HLA-G5-Apt2) detecting HLA-G5 were screened by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. Small (10 nm) gold nanoparticles (AuNPs) were incubated with AptHLAs to form two novel nucleic acid aptamers: Au-nanoparticles (AuNPs-AptHLA-G5-1 and AuNPs-AptHLA-G5-2). Results The results showed that AptHLA-G5-1 and AptHLA-G5-2 have a high affinity for HLA-G5 and can detect its presence in liquid samples. Using the colorimetric sensing method, AuNPs-AptHLA-G1 had a detection limit as low as 20 ng/mL (recovery range between 98.7% to 102.0%), while AuNPs-AptHLA-G2 had a detection limit as low as 20 ng/mL (recovery range between 98.9% to 103.6%). Conclusions Our work demonstrates that novel AuNPs are efficient detectors for HLA-G5 and are useful for diagnosis and treatment in the field of obstetrics-gynaecology.
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Affiliation(s)
- Tao Su
- Medical School of Chinese PLA & Reproductive Center, the First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hui Wang
- Medical School of Chinese PLA & Reproductive Center, the First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuanqing Yao
- Medical School of Chinese PLA & Reproductive Center, the First Medical Center of Chinese PLA General Hospital, Beijing, China
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14
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Bortolotti D, Gentili V, Rizzo S, Schiuma G, Beltrami S, Spadaro S, Strazzabosco G, Campo G, Carosella ED, Papi A, Rizzo R, Contoli M. Increased sHLA-G Is Associated with Improved COVID-19 Outcome and Reduced Neutrophil Adhesion. Viruses 2021; 13:v13091855. [PMID: 34578436 PMCID: PMC8473385 DOI: 10.3390/v13091855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022] Open
Abstract
Human leukocyte antigen (HLA) is a group of molecules involved in inflammatory and infective responses. We evaluated blood sHLA-E and sHLA-G levels in hospitalized COVID-19 patients with respiratory failure and their relationship with clinical evolution, changes in endothelial activation biomarker profile, and neutrophil adhesion. sHLA-E, sHLA-G, and endothelial activation biomarkers were quantified by ELISA assay in plasma samples. Neutrophil adhesion to endothelium was assessed in the presence/absence of patients’ plasma samples. At admission, plasma levels of sHLA-G and sHLA-E were significantly higher in COVID-19 patients with respiratory failure compared to controls. COVID-19 clinical improvement was associated with increased sHLA-G plasma levels. In COVID-19, but not in control patients, an inverse correlation was found between serum sICAM-1 and E-selectin levels and plasma sHLA-G values. The in vitro analysis of activated endothelial cells confirmed the ability of HLA-G molecules to control sICAM-1 and sE-selectin expression via CD160 interaction and FGF2 induction and consequently neutrophil adhesion. We suggest a potential role for sHLA-G in improving COVID-19 patients’ clinical condition related to the control of neutrophil adhesion to activated endothelium.
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Affiliation(s)
- Daria Bortolotti
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
| | - Valentina Gentili
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
| | - Sabrina Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
| | - Giovanna Schiuma
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
| | - Silvia Beltrami
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
| | - Savino Spadaro
- Intensive Care Unit, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy;
| | - Giovanni Strazzabosco
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
| | - Gianluca Campo
- Cardiology Unit, Azienda Ospedaliero Universitaria di Ferrara, Cona, 44124 Ferrara, Italy;
| | - Edgardo D. Carosella
- CEA, Institute of Emerging Diseases and Innovative Therapies (iMETI), Research Division in Hematology and Immunology (SRHI), Saint-Louis Hospital, 75001 Paris, France;
| | - Alberto Papi
- Respiratory Section, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (A.P.); (M.C.)
- Respiratory Unit, Azienda Ospedaliera Universitaria Ferrara, Cona, 44124 Ferrara, Italy
| | - Roberta Rizzo
- Department of Chemical, Pharmaceutical and Agricultural Science, University of Ferrara, 44121 Ferrara, Italy; (D.B.); (V.G.); (S.R.); (G.S.); (S.B.); (G.S.)
- Industrial Research and Technology Transfer Laboratory (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-0532455382
| | - Marco Contoli
- Respiratory Section, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (A.P.); (M.C.)
- Respiratory Unit, Azienda Ospedaliera Universitaria Ferrara, Cona, 44124 Ferrara, Italy
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15
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Deng W, Zeng J, Lu S, Li C. Comprehensive investigation of RNA-sequencing dataset reveals the hub genes and molecular mechanisms of coronavirus disease 2019 acute respiratory distress syndrome. IET Syst Biol 2021; 15:205-218. [PMID: 34350693 PMCID: PMC8441671 DOI: 10.1049/syb2.12034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 01/08/2023] Open
Abstract
The goal of this study is to reveal the hub genes and molecular mechanisms of the coronavirus disease 2019 (COVID‐19) acute respiratory distress syndrome (ARDS) based on the genome‐wide RNA sequencing dataset. The RNA sequencing dataset of COVID‐19 ARDS was obtained from GSE163426. A total of 270 differentially expressed genes (DEGs) were identified between COVID‐19 ARDS and control group patients. Functional enrichment analysis of DEGs suggests that these DEGs may be involved in the following biological processes: response to cytokine, G‐protein coupled receptor activity, ionotropic glutamate receptor signalling pathway and G‐protein coupled receptor signalling pathway. By using the weighted correlation network analysis approach to analyse these DEGs, 10 hub DEGs that may play an important role in COVID‐19 ARDS were identified. A total of 67 potential COVID‐19 ARDS targetted drugs were identified by a complement map analysis. Immune cell infiltration analysis revealed that the levels of T cells CD4 naive, T cells follicular helper, macrophages M1 and eosinophils in COVID‐19 ARDS patients were significantly different from those in control group patients. In conclusion, this study identified 10 COVID‐19 ARDS‐related hub DEGs and numerous potential molecular mechanisms through a comprehensive analysis of the RNA sequencing dataset and also revealed the difference in immune cell infiltration of COVID‐19 ARDS.
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Affiliation(s)
- Wangsheng Deng
- Emergency Department, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Jiaxing Zeng
- Emergency Department, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, China
| | - Shunyu Lu
- Department of Pharmacy, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Chaoqian Li
- Emergency Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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16
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Saulle I, Vicentini C, Clerici M, Biasin M. Antigen presentation in SARS-CoV-2 infection: the role of class I HLA and ERAP polymorphisms. Hum Immunol 2021; 82:551-560. [PMID: 34116863 PMCID: PMC8108382 DOI: 10.1016/j.humimm.2021.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022]
Abstract
Given the highly polymorphic nature of Human Leukocyte Antigen (HLA) molecules, it is not surprising that they function as key regulators of the host immune response to almost all invading pathogens, including SARS-CoV-2, the etiological agent responsible for the recent COVID-19 pandemic. Several correlations have already been established between the expression of a specific HLA allele/haplotype and susceptibility/progression of SARS-CoV-2 infection and new ones are continuously emerging. Protective and harmful HLA variants have been described in both mild and severe forms of the disease, but considering the huge amount of existing variants, the data gathered in such a brief span of time are to some extent confusing and contradictory. The aim of this mini-review is to provide a snap-shot of the main findings so far collected on the HLA-SARS-CoV-2 interaction, so as to partially untangle this intricate yarn. As key factors in the generation of antigenic peptides to be presented by HLA molecules, ERAP1 and ERAP2 role in SARS-CoV-2 infection will be revised as well.
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Affiliation(s)
- Irma Saulle
- Department of Biomedical and Clinical Sciences- L. Sacco, University of Milan, Italy; Department of Pathophysiology and Transplantation, Milan, Italy.
| | - Chiara Vicentini
- Department of Biomedical and Clinical Sciences- L. Sacco, University of Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, Milan, Italy; SM Nascente Scientific Institute, IRCCS, Don C Gnocchi Foundation, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences- L. Sacco, University of Milan, Italy
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17
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Al-Bayatee NT, Ad'hiah AH. Soluble HLA-G is upregulated in serum of patients with severe COVID-19. Hum Immunol 2021; 82:726-732. [PMID: 34304938 PMCID: PMC8282477 DOI: 10.1016/j.humimm.2021.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 02/06/2023]
Abstract
Soluble HLA-G (sHLA-G) molecules are considered potent immunomodulators, and their dysregulated expression has been implicated in several pathological conditions, including coronavirus disease 19 (COVID-19). Therefore, a case-control study (103 COVID-19 patients and 105 controls) was performed to determine sHLA-G role in severity of COVID-19. Results revealed that median levels of sHLA-G were significantly increased in serum of patients compared to controls (19.3 vs. 12.7 ng/mL; p <0.001). When patients and controls were stratified by age group, gender, body mass index, chronic disease, or ABO and Rh blood groups, the sHLA-G level did not show a significant difference in each stratum. Logistic regression analysis demonstrated that the up-regulated expression of sHLA-G was associated with an elevated risk of developing COVID-19. Receiver operating characteristic curve analysis showed that sHLA-G was a very good predictor of COVID-19, and at a cut-off value of 15.4 ng/mL, the sensitivity and specificity of sHLA-G were 79.6 and 79.0%, respectively. Spearman rank correlation analysis revealed that sHLA-G was positively correlated with age, erythrocyte sedimentation rate, white blood cell count, and random blood glucose, while a negative correlation was recorded with vitamin D. In conclusion, up-regulated expression of sHLA-G was indicated in patients with severe COVID-19.
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Affiliation(s)
- Noor T Al-Bayatee
- Biotechnology Department, College of Science, University of Baghdad, Baghdad, Iraq
| | - Ali H Ad'hiah
- Tropical-Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.
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18
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Fraga-Silva TFDC, Maruyama SR, Sorgi CA, Russo EMDS, Fernandes APM, de Barros Cardoso CR, Faccioli LH, Dias-Baruffi M, Bonato VLD. COVID-19: Integrating the Complexity of Systemic and Pulmonary Immunopathology to Identify Biomarkers for Different Outcomes. Front Immunol 2021; 11:599736. [PMID: 33584667 PMCID: PMC7878380 DOI: 10.3389/fimmu.2020.599736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022] Open
Abstract
In the last few months, the coronavirus disease 2019 (COVID-19) pandemic has affected millions of people worldwide and has provoked an exceptional effort from the scientific community to understand the disease. Clinical evidence suggests that severe COVID-19 is associated with both dysregulation of damage tolerance caused by pulmonary immunopathology and high viral load. In this review article, we describe and discuss clinical studies that show advances in the understanding of mild and severe illness and we highlight major points that are critical for improving the comprehension of different clinical outcomes. The understanding of pulmonary immunopathology will contribute to the identification of biomarkers in an attempt to classify mild, moderate, severe and critical COVID-19 illness. The interface of pulmonary immunopathology and the identification of biomarkers are critical for the development of new therapeutic strategies aimed to reduce the systemic and pulmonary hyperinflammation in severe COVID-19.
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Affiliation(s)
- Thais Fernanda de Campos Fraga-Silva
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Sandra Regina Maruyama
- Department of Genetics and Evolution, Federal University of Sao Carlos, Sao Carlos, Brazil
| | - Carlos Arterio Sorgi
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Elisa Maria de Sousa Russo
- Department of Clinical Analysis, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Ana Paula Morais Fernandes
- Department of General and Specialized Nursing, School of Nursing of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Cristina Ribeiro de Barros Cardoso
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- Department of Clinical Analysis, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Lucia Helena Faccioli
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- Department of Clinical Analysis, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Marcelo Dias-Baruffi
- Department of Clinical Analysis, Toxicological and Food Science Analysis, School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Vânia Luiza Deperon Bonato
- Basic and Applied Immunology Program, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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