Oxford open immunology最新文献_第4页

Correction to: Molecular mimicry among human proteinase 3 and bacterial antigens: implications for development of c-ANCA associated vasculitis. 更正:人蛋白酶3和细菌抗原之间的分子模拟:c-ANCA相关血管炎发展的意义。

Oxford open immunology Pub Date : 2022-01-01 DOI: 10.1093/oxfimm/iqac011

引用次数: 0

Isolation of single cells from human uterus in the third trimester of pregnancy: myometrium, decidua, amnion and chorion. 妊娠晚期人子宫单细胞的分离:子宫肌层、蜕膜、羊膜和绒毛膜。

Oxford open immunology Pub Date : 2022-01-01 DOI: 10.1093/oxfimm/iqac010

Alexander T H Cocker, Emily M Whettlock, Brendan Browne, Pei F Lai, Jonathan K H Li, Sivatharjini P Sivarajasingam, Nesrina Imami, Mark R Johnson, Victoria Male

{"title":"Isolation of single cells from human uterus in the third trimester of pregnancy: myometrium, decidua, amnion and chorion.","authors":"Alexander T H Cocker, Emily M Whettlock, Brendan Browne, Pei F Lai, Jonathan K H Li, Sivatharjini P Sivarajasingam, Nesrina Imami, Mark R Johnson, Victoria Male","doi":"10.1093/oxfimm/iqac010","DOIUrl":"https://doi.org/10.1093/oxfimm/iqac010","url":null,"abstract":"During pregnancy, interactions between uterine immune cells and cells of the surrounding reproductive tissues are thought to be vital for regulating labour. The mechanism that specifically initiates spontaneous labour has not been determined, but distinct changes in uterine immune cell populations and their activation status have been observed during labour at term gestation. To understand the regulation of human labour by the immune system, the ability to isolate both immune cells and non-immune cells from the uterus is required. Here, we describe protocols developed in our laboratory to isolate single cells from uterine tissues, which preserve both immune and non-immune cell populations for further analysis. We provide detailed methods for isolating immune and non-immune cells from human myometrium, chorion, amnion and decidua, together with representative flow cytometry analysis of isolated cell populations present. The protocols can be completed in tandem and take approximately 4-5 h, resulting in single-cell suspensions that contain viable leucocytes, and non-immune cells in sufficient numbers for single-cell analysis approaches such as flow cytometry and single cell RNA sequencing (scRNAseq).","PeriodicalId":74384,"journal":{"name":"Oxford open immunology","volume":"3 1","pages":"iqac010"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9914580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9342394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

COP27 Climate Change Conference: urgent action needed for Africa and the world: Wealthy nations must step up support for Africa and vulnerable countries in addressing past, present and future impacts of climate change. COP27气候变化会议:非洲和世界需要采取紧急行动:富裕国家必须加强对非洲和脆弱国家的支持，以应对气候变化过去、现在和未来的影响。

Oxford open immunology Pub Date : 2022-01-01 DOI: 10.1093/oxfimm/iqac008

Lukoye Atwoli, Gregory E Erhabor, Aiah A Gbakima, Abraham Haileamlak, Jean-Marie Kayembe Ntumba, James Kigera, Laurie Laybourn-Langton, Bob Mash, Joy Muhia, Fhumulani Mavis Mulaudzi, David Ofori-Adjei, Friday Okonofua, Arash Rashidian, Maha El-Adawy, Siaka Sidibé, Abdelmadjid Snouber, James Tumwine, Mohammad Sahar Yassien, Paul Yonga, Lilia Zakhama, Chris Zielinski

引用次数: 2

Naive and memory T cells TCR-HLA-binding prediction. 幼稚T细胞和记忆T细胞tcr - hla结合预测。

Oxford open immunology Pub Date : 2022-01-01 DOI: 10.1093/oxfimm/iqac001

Neta Glazer, Ofek Akerman, Yoram Louzoun

{"title":"Naive and memory T cells TCR-HLA-binding prediction.","authors":"Neta Glazer, Ofek Akerman, Yoram Louzoun","doi":"10.1093/oxfimm/iqac001","DOIUrl":"https://doi.org/10.1093/oxfimm/iqac001","url":null,"abstract":"T cells recognize antigens through the interaction of their T cell receptor (TCR) with a peptide-major histocompatibility complex (pMHC) molecule. Following thymic-positive selection, TCRs in peripheral naive T cells are expected to bind MHC alleles of the host. Peripheral clonal selection is expected to further increase the frequency of antigen-specific TCRs that bind to the host MHC alleles. To check for a systematic preference for MHC-binding T cells in TCR repertoires, we developed Natural Language Processing-based methods to predict TCR-MHC binding independently of the peptide presented for Class I MHC alleles. We trained a classifier on published TCR-pMHC binding pairs and obtained a high area under curve (AUC) of over 0.90 on the test set. However, when applied to TCR repertoires, the accuracy of the classifier dropped. We thus developed a two-stage prediction model, based on large-scale naive and memory TCR repertoires, denoted TCR HLA-binding predictor (CLAIRE). Since each host carries multiple human leukocyte antigen (HLA) alleles, we first computed whether a TCR on a CD8 T cell binds an MHC from any of the host Class-I HLA alleles. We then performed an iteration, where we predict the binding with the most probable allele from the first round. We show that this classifier is more precise for memory than for naïve cells. Moreover, it can be transferred between datasets. Finally, we developed a CD4-CD8 T cell classifier to apply CLAIRE to unsorted bulk sequencing datasets and showed a high AUC of 0.96 and 0.90 on large datasets. CLAIRE is available through a GitHub at: https://github.com/louzounlab/CLAIRE, and as a server at: https://claire.math.biu.ac.il/Home.","PeriodicalId":74384,"journal":{"name":"Oxford open immunology","volume":"3 1","pages":"iqac001"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9914496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10851758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Molecular mimicry among human proteinase 3 and bacterial antigens: implications for development of c-ANCA associated vasculitis. 人蛋白酶3和细菌抗原之间的分子模拟:c-ANCA相关血管炎发展的意义

Oxford open immunology Pub Date : 2022-01-01 DOI: 10.1093/oxfimm/iqac009

Y Chavez, J Garces, R Díaz, M Escobar, A Sanchez, E Buendía, M Múnera

{"title":"Molecular mimicry among human proteinase 3 and bacterial antigens: implications for development of c-ANCA associated vasculitis.","authors":"Y Chavez, J Garces, R Díaz, M Escobar, A Sanchez, E Buendía, M Múnera","doi":"10.1093/oxfimm/iqac009","DOIUrl":"https://doi.org/10.1093/oxfimm/iqac009","url":null,"abstract":"Wegener's granulomatosis is an autoimmune disease where autoantibodies target human autoantigen PR3, a serine protease locates on the neutrophil membrane. This disease affects blood small vessels and could be deadly. The origin of these autoantibodies is unknown, but infections have been implicated with autoimmune disease. In this study, we explored potential molecular mimicry between human PR3 and homologous pathogens through in silico analysis. Thirteen serine proteases from human pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Salmonella sp., Streptococcus suis, Vibrio parahaemolyticus, Bacteroides fragilis, Enterobacter ludwigii, Vibrio alginolyticus, Staphylococcus haemolyticus, Enterobacter cloacae, Escherichia coli and Pseudomonas aeruginosa) shared structural homology and amino acid sequence identity with human PR3. Epitope prediction found an only conserved epitope IVGG, located between residues 59-74. However, multiple alignments showed conserved regions that could be involved in cross-reactivity between human and pathogens serine proteases (90-98, 101-108, 162-169, 267 and 262 residues positions). In conclusion, this is the first report providing in silico evidence about the existence of molecular mimicry between human and pathogens serine proteases, that could explain the origins of autoantibodies found in patients suffering from Wegener's granulomatosis.","PeriodicalId":74384,"journal":{"name":"Oxford open immunology","volume":"3 1","pages":"iqac009"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9914470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10851756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Neutrophilia, lymphopenia and myeloid dysfunction: a living review of the quantitative changes to innate and adaptive immune cells which define COVID-19 pathology. 中性粒细胞增多症、淋巴细胞减少症和骨髓功能障碍：先天性和适应性免疫细胞定量变化的生动回顾，COVID-19病理学的定义。

Oxford open immunology Pub Date : 2021-07-15 eCollection Date: 2021-01-01 DOI: 10.1093/oxfimm/iqab016

Amy S Codd, Stephanie J Hanna, Ewoud B Compeer, Felix C Richter, Eleanor J Pring, Ester Gea-Mallorquí, Mariana Borsa, Owen R Moon, D Oliver Scourfield, Awen M Gallimore, Anita Milicic

{"title":"Neutrophilia, lymphopenia and myeloid dysfunction: a living review of the quantitative changes to innate and adaptive immune cells which define COVID-19 pathology.","authors":"Amy S Codd, Stephanie J Hanna, Ewoud B Compeer, Felix C Richter, Eleanor J Pring, Ester Gea-Mallorquí, Mariana Borsa, Owen R Moon, D Oliver Scourfield, Awen M Gallimore, Anita Milicic","doi":"10.1093/oxfimm/iqab016","DOIUrl":"10.1093/oxfimm/iqab016","url":null,"abstract":"Destabilization of balanced immune cell numbers and frequencies is a common feature of viral infections. This occurs due to, and further enhances, viral immune evasion and survival. Since the discovery of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), which manifests in coronavirus disease 2019 (COVID-19), a great number of studies have described the association between this virus and pathologically increased or decreased immune cell counts. In this review, we consider the absolute and relative changes to innate and adaptive immune cell numbers, in COVID-19. In severe disease particularly, neutrophils are increased, which can lead to inflammation and tissue damage. Dysregulation of other granulocytes, basophils and eosinophils represents an unusual COVID-19 phenomenon. Contrastingly, the impact on the different types of monocytes leans more strongly to an altered phenotype, e.g. HLA-DR expression, rather than numerical changes. However, it is the adaptive immune response that bears the most profound impact of SARS-CoV-2 infection. T cell lymphopenia correlates with increased risk of intensive care unit admission and death; therefore, this parameter is particularly important for clinical decision-making. Mild and severe diseases differ in the rate of immune cell counts returning to normal levels post disease. Tracking the recovery trajectories of various immune cell counts may also have implications for long-term COVID-19 monitoring. This review represents a snapshot of our current knowledge, showing that much has been achieved in a short period of time. Alterations in counts of distinct immune cells represent an accessible metric to inform patient care decisions or predict disease outcomes.","PeriodicalId":74384,"journal":{"name":"Oxford open immunology","volume":"2 1","pages":"iqab016"},"PeriodicalIF":0.0,"publicationDate":"2021-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371938/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9180794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Protease inhibitor plasma concentrations associate with COVID-19 infection. 蛋白酶抑制剂血浆浓度与新冠肺炎感染相关。

Oxford open immunology Pub Date : 2021-07-07 eCollection Date: 2021-01-01 DOI: 10.1093/oxfimm/iqab014

Nicholas R Medjeral-Thomas, Anne Troldborg, Annette G Hansen, Rasmus Pihl, Candice L Clarke, James E Peters, David C Thomas, Michelle Willicombe, Yaseelan Palarasah, Marina Botto, Matthew C Pickering, Steffen Thiel

{"title":"Protease inhibitor plasma concentrations associate with COVID-19 infection.","authors":"Nicholas R Medjeral-Thomas, Anne Troldborg, Annette G Hansen, Rasmus Pihl, Candice L Clarke, James E Peters, David C Thomas, Michelle Willicombe, Yaseelan Palarasah, Marina Botto, Matthew C Pickering, Steffen Thiel","doi":"10.1093/oxfimm/iqab014","DOIUrl":"10.1093/oxfimm/iqab014","url":null,"abstract":"Protease inhibitors influence a range of innate immunity and inflammatory pathways. We quantified plasma concentrations of key anti-inflammatory protease inhibitors in chronic haemodialysis patients with coronavirus disease 2019 (COVID-19). The samples were collected early in the disease course to determine whether plasma protease inhibitor levels associated with the presence and severity of COVID-19. We used antibody-based immunoassays to measure plasma concentrations of C1 esterase inhibitor, alpha2-macroglobulin, antithrombin and inter-alpha-inhibitor heavy chain 4 (ITIH4) in 100 serial samples from 27 haemodialysis patients with COVID-19. ITIH4 was tested in two assays, one measuring intact ITIH4 and another also detecting any fragmented ITIH4 (total ITIH4). Control cohorts were 32 haemodialysis patients without COVID-19 and 32 healthy controls. We compared protease inhibitor concentration based on current and future COVID-19 severity and with C-reactive protein. Results were adjusted for repeated measures and multiple comparisons. Analysis of all available samples demonstrated lower plasma C1 esterase inhibitor and α2M and higher total ITIH4 in COVID-19 compared with dialysis controls. These differences were also seen in the first sample collected after COVID-19 diagnosis, a median of 4 days from diagnostic swab. Plasma ITIH4 levels were higher in severe than the non-severe COVID-19. Serum C-reactive protein correlated positively with plasma levels of antithrombin, intact ITIH4 and total ITIH4. In conclusion, plasma protease inhibitor concentrations are altered in COVID-19.","PeriodicalId":74384,"journal":{"name":"Oxford open immunology","volume":"2 1","pages":"iqab014"},"PeriodicalIF":0.0,"publicationDate":"2021-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9150082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Overview of approved and upcoming vaccines for SARS-CoV-2: a living review. 已批准和即将推出的严重急性呼吸系统综合征冠状病毒2型疫苗概述：活的综述。

Oxford open immunology Pub Date : 2021-05-22 eCollection Date: 2021-01-01 DOI: 10.1093/oxfimm/iqab010

Jennifer Alderson, Vicky Batchelor, Miriam O'Hanlon, Liliana Cifuentes, Felix Clemens Richter, Jakub Kopycinski

引用次数: 0

The emerging role of group 3 innate lymphoid cells in the neonate: interaction with the maternal and neonatal microbiome. 第3组先天淋巴样细胞在新生儿中的新作用:与母体和新生儿微生物组的相互作用。

Oxford open immunology Pub Date : 2021-05-12 eCollection Date: 2021-01-01 DOI: 10.1093/oxfimm/iqab009

Julie Mirpuri

引用次数: 5

The T-cell response to SARS-CoV-2: kinetic and quantitative aspects and the case for their protective role. t细胞对SARS-CoV-2的反应:动力学和定量方面及其保护作用的案例

Oxford open immunology Pub Date : 2021-02-23 eCollection Date: 2021-01-01 DOI: 10.1093/oxfimm/iqab006

Antonio Bertoletti, Anthony T Tan, Nina Le Bert

引用次数: 0