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Solh M, Aubrey MT, Zhang X, Bashey A, Freed BM, Roark CL, Bachier-Rdriguez L, Morris LE, Kent Holland H, Solomon SR. HLA evolutionary divergence (HED) informs the effect of HLA-B mismatch on outcomes after haploidentical transplantation. Bone Marrow Transplant 2024; 59:1433-1439. [PMID: 39085372 DOI: 10.1038/s41409-024-02341-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/20/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024]
Abstract
Graft versus tumor relies on tumor-associated antigens (TAAs) that are presented to donor T cells via human leukocyte antigens (HLAs). The HLA evolutionary divergence (HED) between alleles of a single individual can dictate the ability to present TAAs. The impact of HED in haploidentical donor transplantation (HIDT) has not been studied. We studied the effect of HED on transplant outcomes following HIDT. We analyzed 322 consecutive recipient/donor pairs with a median follow-up of 57.2 months. Pairwise divergence of HLA class I and II showed that HLA-B, -DRB1, and -DQB1 contributing most to mean HED. The mean HED was class I 6.85 (HLA-A 7.08, -B 8.24, and -C 5.07), class II 8.58 (HLA-DRB1 10.97, -DQB1 10.06 and -DPB1 4.06). A high HED in class I mismatched recipient/donor haplotype (RD MM) was significant for worse DFS (HR 1.11, p = 0.020), and relapse (HR 1.11, p = 0.02). Also, a high HED in RD MM HLA-B haplotype had worse OS (HR 1.07, p = 0.02), DFS (HR 1.09, p = 0.002), higher relapse (HR 1.10, p = 0.003), and similar NRM to low HED. The multivariate analysis showed that high HED in RD MM HLA-B (≥7.8 vs <7.8) had worse DFS (HR 1.53, p = 0.01), higher relapse (HR 1.61, p = 0.024), and similar NRM and OS.
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Affiliation(s)
- Melhem Solh
- The Blood and Marrow Transplant Program at Northside Hospital, Atlanta, GA, USA.
| | - Michael T Aubrey
- University of Colorado Blood Bank and Clinimmune Laboratory, Aurora, CO, USA
| | - Xu Zhang
- School of Public Health, University of Texas, Houston, TX, USA
| | - Asad Bashey
- The Blood and Marrow Transplant Program at Northside Hospital, Atlanta, GA, USA
| | - Brian M Freed
- University of Colorado Blood Bank and Clinimmune Laboratory, Aurora, CO, USA
| | - Christina L Roark
- University of Colorado Blood Bank and Clinimmune Laboratory, Aurora, CO, USA
| | | | - Lawrence E Morris
- The Blood and Marrow Transplant Program at Northside Hospital, Atlanta, GA, USA
| | - H Kent Holland
- The Blood and Marrow Transplant Program at Northside Hospital, Atlanta, GA, USA
| | - Scott R Solomon
- The Blood and Marrow Transplant Program at Northside Hospital, Atlanta, GA, USA
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2
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Ahuja S, Lazar IM. Proteomic insights into breast cancer response to brain cell-secreted factors. Sci Rep 2024; 14:19351. [PMID: 39169222 PMCID: PMC11339284 DOI: 10.1038/s41598-024-70386-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 08/16/2024] [Indexed: 08/23/2024] Open
Abstract
The most devastating feature of cancer cells is their ability to metastasize to distant sites in the body. HER2 + and TN breast cancers frequently metastasize to the brain and stay potentially dormant for years until favorable conditions support their proliferation. The sheltered and delicate nature of the brain prevents, however, early disease detection and effective delivery of therapeutic drugs. Moreover, the challenges associated with the acquisition of brain biopsies add compounding difficulties to exploring the mechanistic aspects of tumor development. To provide insights into the determinants of cancer cell behavior at the brain metastatic site, this study was aimed at exploring the early response of HER2 + breast cancer cells (SKBR3) to factors present in the brain perivascular niche. The neural microenvironment was simulated by using the secretome of a set of brain cells that come first in contact with the cancer cells upon crossing the blood brain barrier, i.e., endothelial cells, astrocytes, and microglia. Cytokine microarrays were used to investigate the secretome mediators of intercellular communication, and proteomic technologies for assessing the changes in the behavior of cancer cells upon exposure to the brain cell-secreted factors. The cytokines detected in the brain secretomes were supportive of inflammatory conditions, while the SKBR3 cells secreted numerous cancer-promoting growth factors that were either absent or present in lower abundance in the brain cell cultures, indicating that upon exposure the SKBR3 cells may have been deprived of favorable conditions for optimal growth. Altogether, the results suggest that the exposure of SKBR3 cells to the brain cell-secreted factors altered their growth potential and drove them toward a state of quiescence, with broader overall outcomes that affected cellular metabolism, adhesion and immune response processes. The findings of this study underscore the key role played by the neural niche in shaping the behavior of metastasized cancer cells, provide insights into the cellular cross-talk that may lead cancer cells into dormancy, and highlight novel opportunities for the development of metastatic breast cancer therapeutic strategies.
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Affiliation(s)
- Shreya Ahuja
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
- Fralin Life Sciences Institute, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
- Carilion School of Medicine, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
- Division of Systems Biology/AIS, Virginia Tech, 1981 Kraft Drive, Blacksburg, VA, 24061, USA.
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3
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Szukiewicz D. Reproductive Immunology and Pregnancy 2.0. Int J Mol Sci 2024; 25:5132. [PMID: 38791171 PMCID: PMC11121238 DOI: 10.3390/ijms25105132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
This Special Issue comprises original articles in the field of clinical studies whose major topics concern the genetic and immunological aspects of miscarriage and pre-eclampsia, the isolation of decidua macrophages and Hofbauer cells in the placenta for diagnostic purposes, and epigenetic mechanisms that trigger labor [...].
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Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
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4
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Naidoo L, Arumugam T, Ramsuran V. HLA-B and C Expression Contributes to COVID-19 Disease Severity within a South African Cohort. Genes (Basel) 2024; 15:522. [PMID: 38674456 PMCID: PMC11050528 DOI: 10.3390/genes15040522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Globally, SARS-CoV-2 has negatively impacted many lives and industries due to its rapid spread, severe outcomes, and the need for the implementation of lockdown strategies across the world. SARS-CoV-2 disease severity varies among different populations. Host genetics have been associated with various diseases, and their ability to alter disease susceptibility and severity. In addition, Human Leukocyte Antigen (HLA) expression levels and alleles vary significantly among ethnic groups, which might impact the host's response to SARS-CoV-2. Our previous study highlighted that HLA-A might have an effect on COVID-19 disease severity across ethnicities. Therefore, in this study, we aim to examine the effect of HLA-B and C expression levels on COVID-19 disease severity. To achieve this, we used real-time PCR to measure the HLA mRNA expression levels of SARS-CoV-2-infected individuals from a South African cohort and compared them across ethnic groups, disease outcomes, gender, comorbidities, and age. Our results show (1) that the effect of HLA-B mRNA expression levels was associated with differences in disease severity when we compare symptomatic vs. asymptomatic (p < 0.0001). While HLA-C mRNA expression levels were not associated with COVID-19 disease severity. (2) In addition, we observed that HLA-B and HLA-C mRNA expression levels were significantly different between South African Black individuals and South African Indian individuals (p < 0.0001, p < 0.0001). HLA-B mRNA expression levels among symptomatic South African Black individuals were significantly higher than symptomatic South African Indian individuals (p < 0.0001). In addition, the HLA-B mRNA expression levels of symptomatic South African Black individuals were significantly higher than asymptomatic South African Black individuals (p > 0.0001). HLA-C mRNA expression levels among symptomatic South African Black individuals were significantly higher than among symptomatic South African Indian individuals (p = 0.0217). (3) HLA-C expression levels were significantly different between males and females (p = 0.0052). In addition, the HLA-C expression levels of asymptomatic males are higher than asymptomatic females (p = 0.0375). (4) HLA-B expression levels were significantly different between individuals with and without comorbidities (p = 0.0009). In addition, we observed a significant difference between individuals with no comorbidities and non-communicable diseases (p = 0.0034), in particular, hypertension (p = 0.0487). (5) HLA-B expression levels were significantly different between individuals between 26-35 and 56-65 years (p = 0.0380). Our work is expected to strengthen the understanding of the relationship between HLA and COVID-19 by providing insights into HLA-B and C expression levels across ethnic populations in South Africa among COVID-19-symptomatic and asymptomatic individuals. Our results highlight that HLA-B mRNA expression levels contribute to COVID-19 severity as well as variation in ethnicities associated with COVID-19. Further studies are needed to examine the effect of HLA expression levels across various ethnic groups with contributing factors.
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Affiliation(s)
- Lisa Naidoo
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; (L.N.); (T.A.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4041, South Africa
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5
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Apoorva E, Jacob R, Rao DN, Kumar S. Helicobacter pylori enhances HLA-C expression in the human gastric adenocarcinoma cells AGS and can protect them from the cytotoxicity of natural killer cells. Helicobacter 2024; 29:e13069. [PMID: 38516860 DOI: 10.1111/hel.13069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024]
Abstract
Helicobacter pylori (H. pylori) seems to play causative roles in gastric cancers. H. pylori has also been detected in established gastric cancers. How the presence of H. pylori modulates immune response to the cancer is unclear. The cytotoxicity of natural killer (NK) cells, toward infected or malignant cells, is controlled by the repertoire of activating and inhibitory receptors expressed on their surface. Here, we studied H. pylori-induced changes in the expression of ligands, of activating and inhibitory receptors of NK cells, in the gastric adenocarcinoma AGS cells, and their impacts on NK cell responses. AGS cells lacked or had low surface expression of the class I major histocompatibility complex (MHC-I) molecules HLA-E and HLA-C-ligands of the major NK cell inhibitory receptors NKG2A and killer-cell Ig-like receptor (KIR), respectively. However, AGS cells had high surface expression of ligands of activating receptors DNAM-1 and CD2, and of the adhesion molecules LFA-1. Consistently, AGS cells were sensitive to killing by NK cells despite the expression of inhibitory KIR on NK cells. Furthermore, H. pylori enhanced HLA-C surface expression on AGS cells. H. pylori infection enhanced HLA-C protein synthesis, which could explain H. pylori-induced HLA-C surface expression. H. pylori infection enhanced HLA-C surface expression also in the hepatoma Huh7 and HepG2 cells. Furthermore, H. pylori-induced HLA-C surface expression on AGS cells promoted inhibition of NK cells by KIR, and thereby protected AGS cells from NK cell cytotoxicity. These results suggest that H. pylori enhances HLA-C expression in host cells and protects them from the cytotoxic attack of NK cells expressing HLA-C-specific inhibitory receptors.
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Affiliation(s)
- Etikala Apoorva
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rini Jacob
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
| | - Desirazu N Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Santosh Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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6
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Bar J, Leibowitz R, Reinmuth N, Ammendola A, Jacob E, Moskovitz M, Levy-Barda A, Lotem M, Katsenelson R, Agbarya A, Abu-Amna M, Gottfried M, Harkovsky T, Wolf I, Tepper E, Loewenthal G, Yellin B, Brody Y, Dahan N, Yanko M, Lahav C, Harel M, Raveh Shoval S, Elon Y, Sela I, Dicker AP, Shaked Y. Biological insights from plasma proteomics of non-small cell lung cancer patients treated with immunotherapy. Front Immunol 2024; 15:1364473. [PMID: 38487531 PMCID: PMC10937428 DOI: 10.3389/fimmu.2024.1364473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/02/2024] [Indexed: 03/17/2024] Open
Abstract
Introduction Immune checkpoint inhibitors have made a paradigm shift in the treatment of non-small cell lung cancer (NSCLC). However, clinical response varies widely and robust predictive biomarkers for patient stratification are lacking. Here, we characterize early on-treatment proteomic changes in blood plasma to gain a better understanding of treatment response and resistance. Methods Pre-treatment (T0) and on-treatment (T1) plasma samples were collected from 225 NSCLC patients receiving PD-1/PD-L1 inhibitor-based regimens. Plasma was profiled using aptamer-based technology to quantify approximately 7000 plasma proteins per sample. Proteins displaying significant fold changes (T1:T0) were analyzed further to identify associations with clinical outcomes using clinical benefit and overall survival as endpoints. Bioinformatic analyses of upregulated proteins were performed to determine potential cell origins and enriched biological processes. Results The levels of 142 proteins were significantly increased in the plasma of NSCLC patients following ICI-based treatments. Soluble PD-1 exhibited the highest increase, with a positive correlation to tumor PD-L1 status, and, in the ICI monotherapy dataset, an association with improved overall survival. Bioinformatic analysis of the ICI monotherapy dataset revealed a set of 30 upregulated proteins that formed a single, highly interconnected network, including CD8A connected to ten other proteins, suggestive of T cell activation during ICI treatment. Notably, the T cell-related network was detected regardless of clinical benefit. Lastly, circulating proteins of alveolar origin were identified as potential biomarkers of limited clinical benefit, possibly due to a link with cellular stress and lung damage. Conclusions Our study provides insights into the biological processes activated during ICI-based therapy, highlighting the potential of plasma proteomics to identify mechanisms of therapy resistance and biomarkers for outcome.
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Affiliation(s)
- Jair Bar
- Institute of Oncology, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Raya Leibowitz
- Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
- Shamir Medical Center, Oncology Institute, Zerifin, Israel
| | - Niels Reinmuth
- German Center for Lung Research (DZL), Munich-Gauting, Germany
- Biobank of lung disease, Asklepios Klinik Gauting GmbH, Gauting, Germany
| | - Astrid Ammendola
- Biobank of lung disease, Asklepios Klinik Gauting GmbH, Gauting, Germany
| | | | - Mor Moskovitz
- Thoracic oncology service, Davidoff Cancer Center, Rabin Medical Center, Petah Tikva, Israel
| | - Adva Levy-Barda
- Biobank, Department of Pathology, Rabin Medical Center, Petah Tikva, Israel
| | - Michal Lotem
- Center for Melanoma and Cancer Immunotherapy, Hadassah Hebrew University Medical Center, Sharett Institute of Oncology, Jerusalem, Israel
| | | | - Abed Agbarya
- Institute of Oncology, Bnai Zion Medical Center, Haifa, Israel
| | - Mahmoud Abu-Amna
- Oncology & Hematology Division, Cancer Center, Emek Medical Center, Afula, Israel
| | - Maya Gottfried
- Department of Oncology, Meir Medical Center, Kfar-Saba, Israel
| | - Tatiana Harkovsky
- Barzilai Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Ashkelon, Israel
| | - Ido Wolf
- Division of Oncology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ella Tepper
- Department of Oncology, Assuta Hospital, Tel Aviv, Israel
| | | | | | | | | | | | | | | | | | | | | | - Adam P. Dicker
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Yuval Shaked
- Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
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7
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Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
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8
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Anand S, Littler DR, Mobbs JI, Braun A, Baker DG, Tennant L, Purcell AW, Vivian JP, Rossjohn J. Complimentary electrostatics dominate T Cell Receptor binding to a psoriasis-associated-peptide-antigen presented by Human Leukocyte Antigen (HLA) C*06:02. J Biol Chem 2023:104930. [PMID: 37330172 PMCID: PMC10371836 DOI: 10.1016/j.jbc.2023.104930] [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: 04/20/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Psoriasis is a chronic skin disease characterised by hyperproliferative epidermal lesions infiltrated by autoreactive T cells. Individuals expressing the Human Leukocyte antigen (HLA) C*06:02 allele are at highest risk for developing psoriasis. An autoreactive T cell clone (termed Vα3S1/Vβ13S1) isolated from psoriatic plaques is selective for HLA-C*06:02-presenting a peptide derived from the melanocyte-specific auto-antigen ADAMTSL5 (VRSRRCLRL). Here we determine the crystal structure of this psoriatic TCR-HLA-C*06:02- ADAMTSL5 complex with a stabilised peptide. Docking of the TCR involves an extensive complementary charge network formed between negatively charged TCR residues interleaving with exposed arginine residues from the self-peptide and the HLA-C*06:02 α1 helix. We probed these interactions through mutagenesis and activation assays. The charged interface spans the polymorphic region of the C1/C2 HLA group. Notably the peptide binding groove of HLA C*06:02 appears exquisitely suited for presenting highly charged Arg-rich epitopes recognised by this acidic psoriatic TCR. Overall, we provide a structural basis for understanding engagement of melanocyte antigen-presenting cells by a TCR implicated in psoriasis, while simultaneously expanding our knowledge of how TCRs engage HLA-C.
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Affiliation(s)
- Sushma Anand
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Jesse I Mobbs
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Asolina Braun
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania, USA
| | - Luke Tennant
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff, UK.
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Martínez-Jiménez F, Priestley P, Shale C, Baber J, Rozemuller E, Cuppen E. Genetic immune escape landscape in primary and metastatic cancer. Nat Genet 2023; 55:820-831. [PMID: 37165135 PMCID: PMC10181939 DOI: 10.1038/s41588-023-01367-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/10/2023] [Indexed: 05/12/2023]
Abstract
Studies have characterized the immune escape landscape across primary tumors. However, whether late-stage metastatic tumors present differences in genetic immune escape (GIE) prevalence and dynamics remains unclear. We performed a pan-cancer characterization of GIE prevalence across six immune escape pathways in 6,319 uniformly processed tumor samples. To address the complexity of the HLA-I locus in the germline and in tumors, we developed LILAC, an open-source integrative framework. One in four tumors harbors GIE alterations, with high mechanistic and frequency variability across cancer types. GIE prevalence is generally consistent between primary and metastatic tumors. We reveal that GIE alterations are selected for in tumor evolution and focal loss of heterozygosity of HLA-I tends to eliminate the HLA allele, presenting the largest neoepitope repertoire. Finally, high mutational burden tumors showed a tendency toward focal loss of heterozygosity of HLA-I as the immune evasion mechanism, whereas, in hypermutated tumors, other immune evasion strategies prevail.
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Affiliation(s)
- Francisco Martínez-Jiménez
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands.
- Hartwig Medical Foundation, Amsterdam, the Netherlands.
- Vall d'Hebron Institute of Oncology, Barcelona, Spain.
| | - Peter Priestley
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Charles Shale
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | - Jonathan Baber
- Hartwig Medical Foundation Australia, Sydney, New South Wales, Australia
| | | | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands.
- Hartwig Medical Foundation, Amsterdam, the Netherlands.
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10
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Park JS, Kim K. Antigen Coverage Presented by MHC Class I Has a Negative Correlation with SARS-CoV-2-Induced Mortality. Vaccines (Basel) 2022; 10:1917. [PMID: 36423013 PMCID: PMC9698063 DOI: 10.3390/vaccines10111917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/29/2022] [Accepted: 11/09/2022] [Indexed: 11/11/2023] Open
Abstract
The COVID-19 pandemic has caused a health crisis worldwide; therefore, it is necessary to understand the factors related to its prognosis. In this study, we hypothesized that SARS-CoV-2-derived antigens presented by MHC class I may correlate with mortality in COVID-19 because they induce adaptive immune responses. Antigen coverage at the national level was inferred using country-specific HLA allele frequencies and relative predictions of binding antigens. We performed regression analysis between antigen coverage and the death rate due to COVID-19 across countries and found a negative correlation, although it was statistically significant only in HLA-B. This negative correlation was corroborated in multiple regression analysis with known risk factors, such as the prevalence of underlying disease. Furthermore, we analyzed antigen coverage in accordance with SARS-CoV-2 domains and identified a significant negative correlation when it was derived from the spike domain, which is reported to be favorable for COVID-19 prognosis. Taken together, the results indicate that the antigen coverage of SARS-CoV-2 specifically presented by HLA-B may act as a favorable factor when explaining COVID-19-induced mortality.
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Affiliation(s)
- Ji Soo Park
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Kwoneel Kim
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
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11
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Hu X, Li Z, Ji M, Lin Y, Chen Y, Lu J. Identification of cellular heterogeneity and immunogenicity of chondrocytes via single-cell RNA sequencing technique in human osteoarthritis. Front Pharmacol 2022; 13:1004766. [PMID: 36249797 PMCID: PMC9562112 DOI: 10.3389/fphar.2022.1004766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Osteoarthritis (OA) has placed a heavy burden to the economy and humanistics. To explore the biological functions and markers of chondrocytes contributes significantly to the accurate diagnosis and targeted treatment of OA. Methods: We systematically analyzed the immunogenicity and biological function of varied chondrocytes at single cell resolution, and identified the chondrocyte subtypes and biomarkers involved in the development of OA, which are verified in the bulk sequencing cohort. Results: Based on previous study, we defined eight subtypes of chondrocytes with different biological functions, finding out that effector chondrocytes (ECs) and fibrocartilage chondrocytes (FCs) may promote the development of OA. Compared with other chondrocytes, ECs and FCs show stronger immunogenicity. FCs mainly affects the degeneration of cartilage caused by fibrous degeneration, while ECs mainly exerts immune function and causes tissues inflammation. In addition, the canonical gene markers of EC and FC assist with the prediction of OA, which has been verified in Bulk RNA sequencing data from two GEO datasets. Conclusion: In summary, this study provides a new perspective for the exploration of cellular heterogeneity and pathophysiology in OA and will make contribution to the accurate diagnosis and targeted treatment of OA.
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Affiliation(s)
- Xinyue Hu
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Zhuang Li
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Mingliang Ji
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Yucheng Lin
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Yuzhi Chen
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Jun Lu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
- *Correspondence: Jun Lu,
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12
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Kitano Y, Nishimura S, Kato TM, Ueda A, Takigawa K, Umekage M, Nomura M, Kawakami A, Ogawa H, Xu H, Hotta A, Takasu N, Tsukahara M. Generation of hypoimmunogenic induced pluripotent stem cells by CRISPR-Cas9 system and detailed evaluation for clinical application. Mol Ther Methods Clin Dev 2022; 26:15-25. [PMID: 35755947 PMCID: PMC9198376 DOI: 10.1016/j.omtm.2022.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/25/2022] [Indexed: 11/06/2022]
Abstract
In order to expand the promise of regenerative medicine using allogeneic induced pluripotent stem cells (iPSCs), precise and efficient genome editing of human leukocyte antigen (HLA) genes would be advantageous to minimize the immune rejection caused by mismatches of HLA type. However, clinical-grade genome editing of multiple HLA genes in human iPSC lines remains unexplored. Here, we optimized the protocol for good manufacturing practice (GMP)-compatible CRISPR-Cas9 genome editing to deplete the three gene locus (HLA-A, HLA-B, and CIITA genes) simultaneously in HLA homozygous iPSCs. The use of HLA homozygous iPSCs has one main advantage over heterozygous iPSCs for inducing biallelic knockout by a single gRNA. RNA-seq and flow cytometry analyses confirmed the successful depletion of HLAs, and lineage-specific differentiation into cardiomyocytes was verified. We also confirmed that the pluripotency of genome-edited iPSCs was successfully maintained by the three germ layers of differentiation. Moreover, whole-genome sequencing, karyotyping, and optical genome mapping analyses revealed no evident genomic abnormalities detected in some clones, whereas unexpected copy number losses, chromosomal translocations, and complex genomic rearrangements were observed in other clones. Our results indicate the importance of multidimensional analyses to ensure the safety and quality of the genome-edited cells. The manufacturing and assessment pipelines presented here will be the basis for clinical-grade genome editing of iPSCs.
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Affiliation(s)
- Yuko Kitano
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Sayaka Nishimura
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Tomoaki M Kato
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Anna Ueda
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Kaho Takigawa
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Masafumi Umekage
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Masaki Nomura
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Ayane Kawakami
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Haruna Ogawa
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Huaigeng Xu
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoko Takasu
- CiRA Foundation, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
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13
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Vigón L, Galán M, Torres M, Martín-Galiano AJ, Rodríguez-Mora S, Mateos E, Corona M, Malo R, Navarro C, Murciano-Antón MA, García-Gutiérrez V, Planelles V, Martínez-Laso J, López-Huertas MR, Coiras M. Association between HLA-C alleles and COVID-19 severity in a pilot study with a Spanish Mediterranean Caucasian cohort. PLoS One 2022; 17:e0272867. [PMID: 35960731 PMCID: PMC9374209 DOI: 10.1371/journal.pone.0272867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/27/2022] [Indexed: 12/15/2022] Open
Abstract
The clinical presentations of COVID-19 may range from an asymptomatic or mild infection to a critical or fatal disease. Several host factors such as elderly age, male gender, and previous comorbidities seem to be involved in the most severe outcomes, but also an impaired immune response that causes a hyperinflammatory state but is unable to clear the infection. In order to get further understanding about this impaired immune response, we aimed to determine the association of specific HLA alleles with different clinical presentations of COVID-19. Therefore, we analyzed HLA Class I and II, as well as KIR gene sequences, in 72 individuals with Spanish Mediterranean Caucasian ethnicity who presented mild, severe, or critical COVID-19, according to their clinical characteristics and management. This cohort was recruited in Madrid (Spain) during the first and second pandemic waves between April and October 2020. There were no significant differences in HLA-A or HLA-B alleles among groups. However, despite the small sample size, we found that HLA-C alleles from group C1 HLA-C*08:02, -C*12:03, or -C*16:01 were more frequently associated in individuals with mild COVID-19 (43.8%) than in individuals with severe (8.3%; p = 0.0030; pc = 0.033) and critical (16.1%; p = 0.0014; pc = 0.0154) disease. C1 alleles are supposed to be highly efficient to present peptides to T cells, and HLA-C*12:03 may present a high number of verified epitopes from abundant SARS-CoV-2 proteins M, N, and S, thereby being allegedly able to trigger an efficient antiviral response. On the contrary, C2 alleles are usually poorly expressed on the cell surface due to low association with β2-microglobulin (β2M) and peptides, which may impede the adequate formation of stable HLA-C/β2M/peptide heterotrimers. Consequently, this pilot study described significant differences in the presence of specific HLA-C1 alleles in individuals with different clinical presentations of COVID-19, thereby suggesting that HLA haplotyping could be valuable to get further understanding in the underlying mechanisms of the impaired immune response during critical COVID-19.
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Affiliation(s)
- Lorena Vigón
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Galán
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Montserrat Torres
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio J. Martín-Galiano
- Intrahospital Infections Laboratory, National Centre of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Rodríguez-Mora
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research Center Network in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Elena Mateos
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research Center Network in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Magdalena Corona
- Hematology Service, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Rosa Malo
- Neumology Service, Hospital Universitario Puerta de Hierro, Majadahonda, Spain
| | | | | | | | - Vicente Planelles
- Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jorge Martínez-Laso
- Immunogenetic Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - María Rosa López-Huertas
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research Center Network in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Mayte Coiras
- Immunopathology Unit, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Biomedical Research Center Network in Infectious Diseases (CIBERINFEC), Madrid, Spain
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14
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Clay SM, Schoettler N, Goldstein AM, Carbonetto P, Dapas M, Altman MC, Rosasco MG, Gern JE, Jackson DJ, Im HK, Stephens M, Nicolae DL, Ober C. Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region. Genome Med 2022; 14:55. [PMID: 35606880 PMCID: PMC9128203 DOI: 10.1186/s13073-022-01058-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/12/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Genome-wide association studies of asthma have revealed robust associations with variation across the human leukocyte antigen (HLA) complex with independent associations in the HLA class I and class II regions for both childhood-onset asthma (COA) and adult-onset asthma (AOA). However, the specific variants and genes contributing to risk are unknown. METHODS We used Bayesian approaches to perform genetic fine-mapping for COA and AOA (n=9432 and 21,556, respectively; n=318,167 shared controls) in White British individuals from the UK Biobank and to perform expression quantitative trait locus (eQTL) fine-mapping in immune (lymphoblastoid cell lines, n=398; peripheral blood mononuclear cells, n=132) and airway (nasal epithelial cells, n=188) cells from ethnically diverse individuals. We also examined putatively causal protein coding variation from protein crystal structures and conducted replication studies in independent multi-ethnic cohorts from the UK Biobank (COA n=1686; AOA n=3666; controls n=56,063). RESULTS Genetic fine-mapping revealed both shared and distinct causal variation between COA and AOA in the class I region but only distinct causal variation in the class II region. Both gene expression levels and amino acid variation contributed to risk. Our results from eQTL fine-mapping and amino acid visualization suggested that the HLA-DQA1*03:01 allele and variation associated with expression of the nonclassical HLA-DQA2 and HLA-DQB2 genes accounted entirely for the most significant association with AOA in GWAS. Our studies also suggested a potentially prominent role for HLA-C protein coding variation in the class I region in COA. We replicated putatively causal variant associations in a multi-ethnic cohort. CONCLUSIONS We highlight roles for both gene expression and protein coding variation in asthma risk and identified putatively causal variation and genes in the HLA region. A convergence of genomic, transcriptional, and protein coding evidence implicates the HLA-DQA2 and HLA-DQB2 genes and HLA-DQA1*03:01 allele in AOA.
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Affiliation(s)
- Selene M Clay
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Nathan Schoettler
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Andrew M Goldstein
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, 98101, USA
| | - Mario G Rosasco
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, 98101, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew Stephens
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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15
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Bernard NF, Kant S, Kiani Z, Tremblay C, Dupuy FP. Natural Killer Cells in Antibody Independent and Antibody Dependent HIV Control. Front Immunol 2022; 13:879124. [PMID: 35720328 PMCID: PMC9205404 DOI: 10.3389/fimmu.2022.879124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/21/2022] [Indexed: 11/15/2022] Open
Abstract
Infection with the human immunodeficiency virus (HIV), when left untreated, typically leads to disease progression towards acquired immunodeficiency syndrome. Some people living with HIV (PLWH) control their virus to levels below the limit of detection of standard viral load assays, without treatment. As such, they represent examples of a functional HIV cure. These individuals, called Elite Controllers (ECs), are rare, making up <1% of PLWH. Genome wide association studies mapped genes in the major histocompatibility complex (MHC) class I region as important in HIV control. ECs have potent virus specific CD8+ T cell responses often restricted by protective MHC class I antigens. Natural Killer (NK) cells are innate immune cells whose activation state depends on the integration of activating and inhibitory signals arising from cell surface receptors interacting with their ligands on neighboring cells. Inhibitory NK cell receptors also use a subset of MHC class I antigens as ligands. This interaction educates NK cells, priming them to respond to HIV infected cell with reduced MHC class I antigen expression levels. NK cells can also be activated through the crosslinking of the activating NK cell receptor, CD16, which binds the fragment crystallizable portion of immunoglobulin G. This mode of activation confers NK cells with specificity to HIV infected cells when the antigen binding portion of CD16 bound immunoglobulin G recognizes HIV Envelope on infected cells. Here, we review the role of NK cells in antibody independent and antibody dependent HIV control.
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Affiliation(s)
- Nicole F. Bernard
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Clinical Immunology, McGill University Health Centre, Montreal, QC, Canada
- *Correspondence: Nicole F. Bernard,
| | - Sanket Kant
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Zahra Kiani
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Cécile Tremblay
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Microbiology Infectiology and Immunology, University of Montreal, Montreal, QC, Canada
| | - Franck P. Dupuy
- Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Infectious Diseases, Immunology and Global Health Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
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16
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Badr H, Blutrich R, Chan K, Tong J, Taylor P, Zhang W, Kafri R, Röst HL, Tsao MS, Moran MF. Proteomic characterization of a candidate polygenic driver of metabolism in non-small cell lung cancer. J Mol Biol 2022; 434:167636. [PMID: 35595168 DOI: 10.1016/j.jmb.2022.167636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 11/18/2022]
Abstract
Proteome analysis revealed signatures of co-expressed upregulated metabolism proteins highly conserved between primary and non-small cell lung cancer (NSCLC) patient-derived xenograft tumors (Li et al. 2014, Nat. Communications 5:5469). The C10 signature is encoded by seven genes (ADSS, ATP2A2, CTPS1, IMPDH2, PKM2, PTGES3, SGPL1) and DNA alterations in C10-encoding genes are associated with longer survival in a subset of NSCLC. To explore the C10 signature as an oncogenic driver and address potential mechanisms of action, C10 protein expression and protein-protein interactions were determined. In independent NSCLC cohorts, the coordinated expression of C10 proteins was significant and mutations in C10 genes were associated with better outcome. Affinity purification-mass spectrometry and in vivo proximity-based biotin identification defined a C10 interactome involving 667 proteins including candidate drug targets and clusters associated with glycolysis, calcium homeostasis, and nucleotide and sphingolipid metabolism. DNA alterations in genes encoding C10 interactome components were also found to be associated with better survival. These data support the notion that the coordinated upregulation of the C10 signature impinges metabolic processes that collectively function as an oncogenic driver in NSCLC.
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Affiliation(s)
- Heba Badr
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ron Blutrich
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kaitlin Chan
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jiefei Tong
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Paul Taylor
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; SPARC BioCentre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wen Zhang
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ran Kafri
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hannes L Röst
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; Departments of Medical Biophysics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Michael F Moran
- Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada; SPARC BioCentre, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada.
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17
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Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Rep Med 2022; 3:100522. [PMID: 35233546 PMCID: PMC8784611 DOI: 10.1016/j.xcrm.2022.100522] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/22/2021] [Accepted: 01/16/2022] [Indexed: 01/07/2023]
Abstract
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.
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Affiliation(s)
- Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Foox
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - David C. Danko
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | - Youngmi Kim
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Daniel J. Butler
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Evan E. Afshin
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - André F. Rendeiro
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Saravia-Butler
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Logyx, LLC, Mountain View, CA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Jonathan Schisler
- McAllister Heart Institute at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, and Department of Pathology and Lab Medicine at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | - Steven Salvatore
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas P. Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison J. Kriegel
- Department of Physiology, Cardiovascular Center, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Olivier Elemento
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert E. Schwartz
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E. Mason
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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18
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Hovhannisyan A, Madelian V, Avagyan S, Nazaretyan M, Hyussyan A, Sirunyan A, Arakelyan R, Manukyan Z, Yepiskoposyan L, Mayilyan KR, Jordan F. HLA-C*04:01 Affects HLA Class I Heterozygosity and Predicted Affinity to SARS-CoV-2 Peptides, and in Combination With Age and Sex of Armenian Patients Contributes to COVID-19 Severity. Front Immunol 2022; 13:769900. [PMID: 35185875 PMCID: PMC8850920 DOI: 10.3389/fimmu.2022.769900] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
The novel SARS-CoV-2 coronavirus infection has become a global health concern, causing the COVID-19 pandemic. The disease symptoms and outcomes depend on the host immunity, in which the human leukocyte antigen (HLA) molecules play a distinct role. The HLA alleles have an inter-population variability, and understanding their link to the COVID-19 in an ethnically distinct population may contribute to personalized medicine. The present study aimed at detecting associations between common HLA alleles and COVID-19 susceptibility and severity in Armenians. In 299 COVID-19 patients (75 asymptomatic, 102 mild/moderate, 122 severe), the association between disease severity and classic HLA-I and II loci was examined. We found that the advanced age, male sex of patients, and sex and age interaction significantly contributed to the severity of the disease. We observed that an age-dependent effect of HLA-B*51:01 carriage [odds ratio (OR)=0.48 (0.28-0.80), Pbonf <0.036] is protective against severe COVID-19. Contrary, the HLA-C*04:01 allele, in a dose-dependent manner, was associated with a significant increase in the disease severity [OR (95% CI) =1.73 (1.20-2.49), Pbonf <0.021] and an advancing age (P<0.013). The link between HLA-C*04:01 and age was secondary to a stronger association between HLA-C*04:01 and disease severity. However, HLA-C*04:01 exerted a sex-dependent differential distribution between clinical subgroups [females: P<0.0012; males: P=0.48]. The comparison of HLA-C*04:01 frequency between subgroups and 2,781 Armenian controls revealed a significant incidence of HLA-C*04:01 deficiency in asymptomatic COVID-19. HLA-C*04:01 homozygous genotype in patients blueprinted a decrease in heterozygosity of HLA-B and HLA class-I loci. In HLA-C*04:01 carriers, these changes translated to the SARS-CoV-2 peptide presentation predicted inefficacy by HLA-C and HLA class-I molecules, simultaneously enhancing the appropriate HLA-B potency. In patients with clinical manifestation, due to the high prevalence of HLA-C*04:01, these effects provided a decrease of the HLA class-I heterozygosity and an ability to recognize SARS-CoV-2 peptides. Based on our observations, we developed a prediction model involving demographic variables and HLA-C*04:01 allele for the identification of potential cases with the risk of hospitalization (the area under the curve (AUC) = 86.2%) or severe COVID-19 (AUC =71%).
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Affiliation(s)
- Anahit Hovhannisyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
- Russian-Armenian University, Yerevan, Armenia
| | - Vergine Madelian
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Sevak Avagyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Mihran Nazaretyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Armine Hyussyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | - Alina Sirunyan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
| | | | | | | | - Karine R. Mayilyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | - Frieda Jordan
- Armenian Bone Marrow Donor Registry Charitable Trust, Yerevan, Armenia
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19
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Zeng H, Wang L, Li J, Luo S, Han Q, Su F, Wei J, Wei X, Wu J, Li B, Huang J, Tang P, Cao C, Zhou Y, Yang Q. Single-cell RNA-sequencing reveals distinct immune cell subsets and signaling pathways in IgA nephropathy. Cell Biosci 2021; 11:203. [PMID: 34895340 PMCID: PMC8665497 DOI: 10.1186/s13578-021-00706-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/31/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND IgA nephropathy (IgAN) is the most common primary glomerulonephritis globally. Increasing evidence suggests the importance of host immunity in the development of IgAN, but its dynamics during the early stage of IgAN are still largely unclear. RESULTS Here we successfully resolved the early transcriptomic changes in immune cells of IgAN by conducting single-cell RNA-sequencing (scRNA-seq) with peripheral blood mononuclear cells. The differentially expressed genes (DEGs) between control and IgAN were predominantly enriched in NK cell-mediated cytotoxicity and cell killing pathways. Interestingly, we discovered that the number and cytotoxicity of NK cells are significantly reduced in IgAN patients, where both the number and marker genes of NK cells were negatively associated with the clinical parameters, including the levels of urine protein creatinine ratio (UPCR), serum galactose-deficient IgA1 and IgA. A distinctive B cell subset, which had suppressed NFκB signaling was predominantly in IgAN and positively associated with disease progression. Moreover, the DEGs of B cells were enriched in different viral infection pathways. Classical monocytes also significantly changed in IgAN and a monocyte subset expressing interferon-induced genes was positively associated with the clinical severity of IgAN. Finally, we identified vast dynamics in intercellular communications in IgAN. CONCLUSIONS We dissected the immune landscape of IgAN at the single-cell resolution, which provides new insights in developing novel biomarkers and immunotherapy against glomerulonephritis.
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Affiliation(s)
- Honghui Zeng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Le Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jiajia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Siweier Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Qianqian Han
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Fang Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jing Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Xiaona Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jianping Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Bin Li
- Clinical Trials Unit, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Jingang Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Patrick Tang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Chunwei Cao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Yiming Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
| | - Qiongqiong Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
- Department of Nephrology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China.
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20
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Schwartz JC, Maccari G, Heimeier D, Hammond JA. Highly-contiguous bovine genomes underpin accurate functional analyses and updated nomenclature of MHC class I. HLA 2021; 99:167-182. [PMID: 34802191 DOI: 10.1111/tan.14494] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022]
Abstract
The major histocompatibility complex (MHC) class I region of cattle is both highly polymorphic and, unlike many species, highly variable in gene content between haplotypes. Cattle MHC class I alleles were historically grouped by sequence similarity in the more conserved 3' end of the coding sequence to form phylogenetic allele groups. This has formed the basis of current cattle MHC class I nomenclature. We presently describe and compare five fully assembled MHC class I haplotypes using the latest cattle and yak genome assemblies. Of the five previously described "pseudogenes" in the cattle MHC class I region, Pseudogene 3 is putatively functional in all haplotypes and Pseudogene 6 and Pseudogene 7 are putatively functional in some haplotypes. This was reinforced by evidence of transcription. Based on full gene sequences as well as 3' coding sequence, we identified distinct subgroups of BoLA-3 and BoLA-6 that represent distinct genetic loci. We further examined allele-specific expression using transcriptomic data revealing that certain alleles are consistently weakly expressed compared to others. These observations will help to inform further studies into how MHC class I region variability influences T cell and natural killer cell functions in cattle.
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Affiliation(s)
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, UK.,Anthony Nolan Research Institute, London, UK
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21
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Hellesen A, Aslaksen S, Breivik L, Røyrvik EC, Bruserud Ø, Edvardsen K, Brokstad KA, Wolff ASB, Husebye ES, Bratland E. 21-Hydroxylase-Specific CD8+ T Cells in Autoimmune Addison's Disease Are Restricted by HLA-A2 and HLA-C7 Molecules. Front Immunol 2021; 12:742848. [PMID: 34721410 PMCID: PMC8551825 DOI: 10.3389/fimmu.2021.742848] [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: 07/16/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
Objectives CD8+ T cells targeting 21-hydroxylase (21OH) are presumed to play a central role in the destruction of adrenocortical cells in autoimmune Addison’s disease (AAD). Earlier reports have suggested two immunodominant CD8+ T cell epitopes within 21OH: LLNATIAEV (21OH342-350), restricted by HLA-A2, and EPLARLEL (21OH431-438), restricted by HLA-B8. We aimed to characterize polyclonal CD8+ T cell responses to the proposed epitopes in a larger patient cohort with AAD. Methods Recombinant fluorescent HLA-peptide multimer reagents were used to quantify antigen-specific CD8+ T cells by flow cytometry. Interferon-gamma (IFNγ) Elispot and biochemical assays were used to functionally investigate the 21OH-specific T cells, and to map the exactly defined epitopes of 21OH. Results We found a significantly higher frequency of HLA-A2 restricted LLNATIAEV-specific cells in patients with AAD than in controls. These cells could also be expanded in vitro in an antigen specific manner and displayed a robust antigen-specific IFNγ production. In contrast, only negligible frequencies of EPLARLEL-specific T cells were detected in both patients and controls with limited IFNγ response. However, significant IFNγ production was observed in response to a longer peptide encompassing EPLARLEL, 21OH430-447, suggesting alternative dominant epitopes. Accordingly, we discovered that the slightly offset ARLELFVVL (21OH434-442) peptide is a novel dominant epitope restricted by HLA-C7 and not by HLA-B8 as initially postulated. Conclusion We have identified two dominant 21OH epitopes targeted by CD8+ T cells in AAD, restricted by HLA-A2 and HLA-C7, respectively. To our knowledge, this is the first HLA-C7 restricted epitope described for an autoimmune disease.
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Affiliation(s)
- Alexander Hellesen
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Sigrid Aslaksen
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Lars Breivik
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ellen Christine Røyrvik
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Øyvind Bruserud
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Kine Edvardsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Karl Albert Brokstad
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Broegelmann Research Laboratory, University of Bergen, Bergen, Norway
| | - Anette Susanne Bøe Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Eystein Sverre Husebye
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Eirik Bratland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,KG Jebsen Centre for Autoimmune Diseases, University of Bergen, Bergen, Norway.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
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22
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Hoek M, Demmers LC, Wu W, Heck AJR. Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins. J Proteome Res 2021; 20:4518-4528. [PMID: 34415762 PMCID: PMC8419865 DOI: 10.1021/acs.jproteome.1c00466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Presentation of antigens
by human leukocyte antigen (HLA) complexes
at the cell surface is a key process in the immune response. The α-chain,
containing the peptide-binding groove, is one of the most polymorphic
proteins in the proteome. All HLA class I α-chains carry a conserved
N-glycosylation site, but little is known about its nature and function.
Here, we report an in-depth characterization of N-glycosylation features
of HLA class I molecules. We observe that different HLA-A α-chains
carry similar glycosylation, distinctly different from the HLA-B,
HLA-C, and HLA-F α-chains. Although HLA-A displays the broadest
variety of glycan characteristics, HLA-B α-chains carry mostly
mature glycans, and HLA-C and HLA-F α-chains carry predominantly
high-mannose glycans. We expected these glycosylation features to
be directly linked to cellular localization of the HLA complexes.
Indeed, analyzing HLA class I complexes from crude plasma and inner
membrane-enriched fractions confirmed that most HLA-B complexes can
be found at the plasma membrane, while most HLA-C and HLA-F molecules
reside in the endoplasmic reticulum and Golgi membrane, and HLA-A
molecules are more equally distributed over these cellular compartments.
This allotype-specific cellular distribution of HLA molecules should
be taken into account when analyzing peptide antigen presentation
by immunopeptidomics.
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Affiliation(s)
- Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
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23
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Burns TC, Quinones-Hinojosa A. Regenerative medicine for neurological diseases-will regenerative neurosurgery deliver? BMJ 2021; 373:n955. [PMID: 34162530 DOI: 10.1136/bmj.n955] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Regenerative medicine aspires to transform the future practice of medicine by providing curative, rather than palliative, treatments. Healing the central nervous system (CNS) remains among regenerative medicine's most highly prized but formidable challenges. "Regenerative neurosurgery" provides access to the CNS or its surrounding structures to preserve or restore neurological function. Pioneering efforts over the past three decades have introduced cells, neurotrophins, and genes with putative regenerative capacity into the CNS to combat neurodegenerative, ischemic, and traumatic diseases. In this review we critically evaluate the rationale, paradigms, and translational progress of regenerative neurosurgery, harnessing access to the CNS to protect, rejuvenate, or replace cell types otherwise irreversibly compromised by neurological disease. We discuss the evidence surrounding fetal, somatic, and pluripotent stem cell derived implants to replace endogenous neuronal and glial cell types and provide trophic support. Neurotrophin based strategies via infusions and gene therapy highlight the motivation to preserve neuronal circuits, the complex fidelity of which cannot be readily recreated. We specifically highlight ongoing translational efforts in Parkinson's disease, amyotrophic lateral sclerosis, stroke, and spinal cord injury, using these to illustrate the principles, challenges, and opportunities of regenerative neurosurgery. Risks of associated procedures and novel neurosurgical trials are discussed, together with the ethical challenges they pose. After decades of efforts to develop and refine necessary tools and methodologies, regenerative neurosurgery is well positioned to advance treatments for refractory neurological diseases. Strategic multidisciplinary efforts will be critical to harness complementary technologies and maximize mechanistic feedback, accelerating iterative progress toward cures for neurological diseases.
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Affiliation(s)
- Terry C Burns
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, USA
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24
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Truong HV, Sgourakis NG. Dynamics of MHC-I molecules in the antigen processing and presentation pathway. Curr Opin Immunol 2021; 70:122-128. [PMID: 34153556 PMCID: PMC8622473 DOI: 10.1016/j.coi.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 01/07/2023]
Abstract
The endogenous antigen processing and presentation (APP) is a fundamental pathway found in jawed vertebrates, which allows for a set of epitope peptides sampled from the intracellular proteome to be assembled and displayed on class I proteins of the major histocompatibility complex (MHC-I). Peptide/MHC-I antigens enable different aspects of adaptive immunity to emerge, by providing a basis for recognition of self vs. non-self by T cells and Natural Killer (NK) cells. Pioneering studies of pMHC-I molecules and their higher-order protein complexes with molecular chaperones and membrane receptors have gleaned important insights into the peptide loading and antigen recognition mechanisms. While X-ray and cryoEM structures have provided us with static snapshots of different MHC-I assembly stages, complementary biophysical techniques have revealed that MHC-I molecules are highly mobile on a range of biologically relevant timescales, which bears importance for their assembly, peptide repertoire selection, membrane display and turnover. This review summarizes insights gained from experimental and simulation studies aimed at investigating MHC-I dynamics, and their functional implications.
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Affiliation(s)
- Hau V Truong
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA.
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25
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Cuspoca AF, Díaz LL, Acosta AF, Peñaloza MK, Méndez YR, Clavijo DC, Yosa Reyes J. An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population. Vaccines (Basel) 2021; 9:vaccines9060581. [PMID: 34205992 PMCID: PMC8228945 DOI: 10.3390/vaccines9060581] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022] Open
Abstract
The coronavirus pandemic is a major public health crisis affecting global health systems with dire socioeconomic consequences, especially in vulnerable regions such as Latin America (LATAM). There is an urgent need for a vaccine to help control contagion, reduce mortality and alleviate social costs. In this study, we propose a rational multi-epitope candidate vaccine against SARS-CoV-2. Using bioinformatics, we constructed a library of potential vaccine peptides, based on the affinity of the most common major human histocompatibility complex (HLA) I and II molecules in the LATAM population to predict immunological complexes among antigenic, non-toxic and non-allergenic peptides extracted from the conserved regions of 92 proteomes. Although HLA-C, had the greatest antigenic peptide capacity from SARS-CoV-2, HLA-B and HLA-A, could be more relevant based on COVID-19 risk of infection in LATAM countries. We also used three-dimensional structures of SARS-CoV-2 proteins to identify potential regions for antibody production. The best HLA-I and II predictions (with increased coverage in common alleles and regions evoking B lymphocyte responses) were grouped into an optimized final multi-epitope construct containing the adjuvants Beta defensin-3, TpD, and PADRE, which are recognized for invoking a safe and specific immune response. Finally, we used Molecular Dynamics to identify the multi-epitope construct which may be a stable target for TLR-4/MD-2. This would prove to be safe and provide the physicochemical requirements for conducting experimental tests around the world.
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Affiliation(s)
- Andrés Felipe Cuspoca
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Laura Lorena Díaz
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Alvaro Fernando Acosta
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Marcela Katherine Peñaloza
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Yardany Rafael Méndez
- Grupo de Investigación en Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia; (A.F.C.); (L.L.D.); (A.F.A.); (M.K.P.); (Y.R.M.)
| | - Diana Carolina Clavijo
- Facultad de Ingeniería y Ciencias, Pontificia Universidad Javeriana Cali, Santiago de Cali 760031, Colombia;
| | - Juvenal Yosa Reyes
- Laboratorio de Simulación Molecular, Facultad de Ciencias Básicas y Biomédicas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
- Correspondence:
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26
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Park J, Foox J, Hether T, Danko D, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti N, Shapira S, Salvatore M, Loda M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Borczuk AC, Meydan C, Schwartz RE, Mason CE. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33758858 DOI: 10.1101/2021.03.08.434433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.
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Kedzierska K, Koutsakos M. The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease. Viral Immunol 2021; 33:160-178. [PMID: 32286182 PMCID: PMC7185345 DOI: 10.1089/vim.2019.0184] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.
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Affiliation(s)
- Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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28
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Pretti MAM, Galvani RG, Vieira GF, Bonomo A, Bonamino MH, Boroni M. Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19. Front Immunol 2020; 11:565730. [PMID: 33391255 PMCID: PMC7772148 DOI: 10.3389/fimmu.2020.565730] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
The world is dealing with one of the worst pandemics ever. SARS-CoV-2 is the etiological agent of COVID-19 that has already spread to more than 200 countries. However, infectivity, severity, and mortality rates do not affect all countries equally. Here we consider 140 HLA alleles and extensively investigate the landscape of 3,723 potential HLA-I A and B restricted SARS-CoV-2-derived antigens and how 37 countries in the world are predicted to respond to those peptides considering their HLA-I distribution frequencies. The clustering of HLA-A and HLA-B allele frequencies partially separates most countries with the lowest number of deaths per million inhabitants from the other countries. We further correlated the patterns of in silico predicted population coverage and epidemiological data. The number of deaths per million inhabitants correlates to the predicted antigen coverage of S and N derived peptides and its module is influenced if a given set of frequent or rare HLA alleles are analyzed in a given population. Moreover, we highlighted a potential risk group carrying HLAs associated with an elevated number of deaths per million inhabitants. In addition, we identified three potential antigens bearing at least one amino acid of the four-length insertion that differentiates SARS-CoV-2 from previous coronavirus strains. We believe these data can contribute to the search for peptides with the potential to be used in vaccine strategies considering the role of herd immunity to hamper the spread of the disease. Importantly, to the best of our knowledge, this work is the first to use a populational approach in association with COVID-19 outcome.
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Affiliation(s)
- Marco Antônio M. Pretti
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
- Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Rômulo G. Galvani
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
- Faculdade de Biomedicina, Universidade Veiga de Almeida, Rio de Janeiro, Brazil
- Laboratory for Thymus Research (LPT), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Gustavo Fioravanti Vieira
- Laboratory of Immunoinformatics (NBLI), Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Laboratory of In Silico Human Health, Post Graduate Program in Health and Human Development, La Salle University, Canoas, Brazil
| | - Adriana Bonomo
- Laboratory for Thymus Research (LPT), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
- Vice-Presidency of Research and Biological Collections (VPPCB), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Martín H. Bonamino
- Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
- Vice-Presidency of Research and Biological Collections (VPPCB), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Mariana Boroni
- Laboratory of Bioinformatics and Computational Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
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29
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Kaufman J. From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles. Front Immunol 2020; 11:601089. [PMID: 33381122 PMCID: PMC7767893 DOI: 10.3389/fimmu.2020.601089] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
In humans, killer immunoglobulin-like receptors (KIRs), expressed on natural killer (NK) and thymus-derived (T) cells, and their ligands, primarily the classical class I molecules of the major histocompatibility complex (MHC) expressed on nearly all cells, are both polymorphic. The variation of this receptor-ligand interaction, based on which alleles have been inherited, is known to play crucial roles in resistance to infectious disease, autoimmunity, and reproduction in humans. However, not all the variation in response is inherited, since KIR binding can be affected by a portion of the peptide bound to the class I molecules, with the particular peptide presented affecting the NK response. The extent to which the large multigene family of chicken immunoglobulin-like receptors (ChIRs) is involved in functions similar to KIRs is suspected but not proven. However, much is understood about the two MHC-I molecules encoded in the chicken MHC. The BF2 molecule is expressed at a high level and is thought to be the predominant ligand of cytotoxic T lymphocytes (CTLs), while the BF1 molecule is expressed at a much lower level if at all and is thought to be primarily a ligand for NK cells. Recently, a hierarchy of BF2 alleles with a suite of correlated properties has been defined, from those expressed at a high level on the cell surface but with a narrow range of bound peptides to those expressed at a lower level on the cell surface but with a very wide repertoire of bound peptides. Interestingly, there is a similar hierarchy for human class I alleles, although the hierarchy is not as wide. It is a question whether KIRs and ChIRs recognize class I molecules with bound peptide in a similar way, and whether fastidious to promiscuous hierarchy of class I molecules affect both T and NK cell function. Such effects might be different from those predicted by the similarities of peptide-binding based on peptide motifs, as enshrined in the idea of supertypes. Since the size of peptide repertoire can be very different for alleles with similar peptide motifs from the same supertype, the relative importance of these two properties may be testable.
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Affiliation(s)
- Jim Kaufman
- School of Biological Sciences, Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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30
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Hosseini-Moghaddam SM, Xu Q, Jevnikar AM, House AA, Luke P, Campigotto A, Kum JJY, Singh G, Alharbi H, Speechley MR. The effect of human leukocyte antigen A1 and B35-Cw4 on sustained BK polyomavirus DNAemia after renal transplantation. Clin Transplant 2020; 34:e14110. [PMID: 33053214 DOI: 10.1111/ctr.14110] [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: 07/02/2020] [Revised: 10/01/2020] [Accepted: 10/03/2020] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA) class I presentation pathway plays a central role in natural killer (NK) cell and cytotoxic T-cell activities against BK polyomavirus (BKPyV) DNAemia. We determined the risk of sustained BKPyV DNAemia in 175 consecutive renal transplant recipients considering the simultaneous effect of donor/recipient HLA class I antigens and pre- or post-transplant variables. Median (IQR) age was 53 (44-64) years, and 37% of patients were female. 40 patients (22.9%) developed sustained BKPyV DNAemia [median (IQR) viral load: 9740 (4350-17 125) copies/ml]. In the Cox proportional hazard analysis, HLA-A1 (HR: 3.06, 95% CI: 1.51-6.17) and HLA-B35-Cw4 (HR: 4.63, 95% CI: 2.12-10.14) significantly increased the risk of sustained BKPyV DNAemia, while 2 HLA-C mismatches provided a marginally protective effect (HR: 0.32, 95% CI: 0.10-0.98). HLA-Cw4 is a ligand for NK cell inhibitory receptor, and HLA-B35 is in strong linkage disequilibrium with the HLA-Cw4 allele. The association between HLA-B35-Cw4 expression and sustained BKPyV DNAemia supports the important role of cytotoxic T cells and NK cells that would normally control BKPyV activation through engagement with immunoglobulin-like killer receptors (KIRs). Further studies are required to investigate the effect of HLA-C alleles along with NK cell activity against BKPyV DNAemia.
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Affiliation(s)
- Seyed M Hosseini-Moghaddam
- Division of Infectious Diseases, Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada.,Department of Epidemiology and Biostatistics, Western University, London, ON, Canada.,Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada
| | - Qingyong Xu
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada.,Histocompatibility Laboratory, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Anthony M Jevnikar
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada
| | - Andrew A House
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada
| | - Patrick Luke
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada
| | - Aaron Campigotto
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jina J Y Kum
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada.,Department of Pathology and Laboratory Medicine, London Health Sciences Centre, Western University, London, ON, Canada
| | - Gagandeep Singh
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada
| | - Hajed Alharbi
- Multiorgan Transplant Program, London Health Sciences Centre, Western University, London, ON, Canada
| | - Mark R Speechley
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
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31
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Ivanchenko M, Thorlacius GE, Hedlund M, Ottosson V, Meneghel L, Björkander S, Ossoinak A, Tingström J, Bremme K, Sverremark-Ekström E, Gemzell-Danielsson K, Sonesson SE, Chemin K, Wahren-Herlenius M. Natural killer cells and type II interferon in Ro/SSA and La/SSB autoantibody-exposed newborns at risk of congenital heart block. Ann Rheum Dis 2020; 80:194-202. [PMID: 33004330 DOI: 10.1136/annrheumdis-2019-216786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Congenital heart block (CHB) with immune cell infiltration develops in the fetus after exposure to maternal Ro/La autoantibodies. CHB-related serology has been extensively studied, but reports on immune-cell profiles of anti-Ro/La-exposed neonates are lacking. In the current study, we characterised circulating immune-cell populations in anti-Ro/La+mothers and newborns, and explored potential downstream effects of skewed neonatal cell populations. METHODS In total, blood from mothers (n=43) and neonates (n=66) was sampled at birth from anti-Ro/La+ (n=36) and control (n=30) pregnancies with or without rheumatic disease and CHB. Flow cytometry, microarrays and ELISA were used for characterising cells and plasma. RESULTS Similar to non-pregnant systemic lupus erythematosus and Sjögren-patients, anti-Ro/La+mothers had altered B-cell subset frequencies, relative T-cell lymphopenia and lower natural killer (NK)-cell frequencies. Surprisingly, their anti-Ro/La exposed neonates presented higher frequencies of CD56dimCD16hi NK cells (p<0.01), but no other cell frequency differences compared with controls. Type I and II interferon (IFN) gene-signatures were revealed in neonates of anti-Ro/La+ pregnancy, and exposure of fetal cardiomyocytes to type I IFN induced upregulation of several NK-cell chemoattractants and activating ligands. Intracellular flow cytometry revealed IFNγ production by NK cells, CD8+ and CD4+ T cells in anti-Ro/La exposed neonates. IFNγ was also detectable in their plasma. CONCLUSION Our study demonstrates an increased frequency of NK cells in anti-Ro/La exposed neonates, footprints of type I and II IFN and an upregulation of ligands activating NK cells in fetal cardiac cells after type I IFN exposure. These novel observations demonstrate innate immune activation in neonates of anti-Ro/La+pregnancy, which could contribute to the risk of CHB.
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Affiliation(s)
- Margarita Ivanchenko
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gudny Ella Thorlacius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Hedlund
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vijole Ottosson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lauro Meneghel
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sophia Björkander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Amina Ossoinak
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Joanna Tingström
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Katarina Bremme
- Division of Obstetrics and Gynecology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Sverremark-Ekström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kristina Gemzell-Danielsson
- Division of Obstetrics and Gynecology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sven-Erik Sonesson
- Division of Pediatric Cardiology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Karine Chemin
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden .,Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Hordaland, Norway
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32
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Souza AS, Sonon P, Paz MA, Tokplonou L, Lima THA, Porto IOP, Andrade HS, Silva NDSB, Veiga-Castelli LC, Oliveira MLG, Sadissou IA, Massaro JD, Moutairou KA, Donadi EA, Massougbodji A, Garcia A, Ibikounlé M, Meyer D, Sabbagh A, Mendes-Junior CT, Courtin D, Castelli EC. Hla-C genetic diversity and evolutionary insights in two samples from Brazil and Benin. HLA 2020; 96:468-486. [PMID: 32662221 DOI: 10.1111/tan.13996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen-C (HLA-C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA-C has a dual function because it also interacts with Killer-cell immunoglobulin-like receptors (KIR) receptors expressed in natural killer and T cells, modulating their activity. The structure and diversity of the HLA-C regulatory regions, as well as the relationship among variants along the HLA-C locus, are poorly addressed, and few population-based studies explored the HLA-C variability in the entire gene in different population samples. Here we present a molecular and bioinformatics method to evaluate the entire HLA-C diversity, including regulatory sequences. Then, we applied this method to survey the HLA-C diversity in two population samples with different demographic histories, one highly admixed from Brazil with major European contribution, and one from Benin with major African contribution. The HLA-C promoter and 3'UTR were very polymorphic with the presence of few, but highly divergent haplotypes. These segments also present conserved sequences that are shared among different primate species. Nucleotide diversity was higher in other segments rather than exons 2 and 3, particularly around exon 5 and the second half of the 3'UTR region. We detected evidence of balancing selection on the entire HLA-C locus and positive selection in the HLA-C leader peptide, for both populations. HLA-C motifs previously associated with KIR interaction and expression regulation are similar between both populations. Each allele group is associated with specific regulatory sequences, reflecting the high linkage disequilibrium along the entire HLA-C locus in both populations.
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Affiliation(s)
- Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paulin Sonon
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Léonidas Tokplonou
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France.,Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin.,Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Nayane Dos S B Silva
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ibrahim Abiodoun Sadissou
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin
| | - André Garcia
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo (USP), São Paulo, Brazil
| | - Audrey Sabbagh
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - David Courtin
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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33
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Chou YC, Chen CH, Chen MJ, Chang CW, Chen PH, Yu MH, Chen YJ, Tsai EM, Yang PS, Lin SY, Tzeng CR. Killer cell immunoglobulin-like receptors (KIR) and human leukocyte antigen-C (HLA-C) allorecognition patterns in women with endometriosis. Sci Rep 2020; 10:4897. [PMID: 32184413 PMCID: PMC7078270 DOI: 10.1038/s41598-020-61702-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
Endometriosis shares similarities with several autoimmune diseases. The human leukocyte antigen (HLA)-C genotype is associated with several human autoimmune diseases. HLA-C is a ligand of killer cell immunoglobulin receptors (KIRs) and is an essential regulator of natural killer cell activity, which is associated with endometriosis progression. Polymorphisms in HLA-C and KIR affect the activity of NK cells and susceptibility to several diseases. Therefore, we attempted to investigate an association between HLA-C genotype and KIR polymorphism and the occurrence of endometriosis. We tested the association of certain KIR and HLA-C combinations and the development of endometriosis by characterizing both KIR and HLA-C genes in 147 women with endometriosis and 117 controls. The HLA-C genotypes and KIR polymorphisms were analyzed via DNA-based method for higher-resolution genotyping. We found that the occurrence of HLA-C*03:03*01 was increased in endometriosis than in control groups. Analysis of various KIR haplotypes revealed differences between the endometriosis and control cohorts. The number of KIR centromeric A/A haplotypes was increased in the endometriosis group than controls. Moreover, the endometriosis cohort was characterized by reduced number of KIR2DS2-positive individuals in the Han Chinese population. Our current findings suggest that the KIR and HLA-C genotypes are associated with the pathogenesis of endometriosis.
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Affiliation(s)
- Ya-Ching Chou
- Center for Reproductive Medicine & Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, Taiwan
| | - Chi-Huang Chen
- Center for Reproductive Medicine & Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ming-Jer Chen
- Department of Obstetrics and Gynecology and Women's Health, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ching-Wen Chang
- Center for Reproductive Medicine & Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Pi-Hua Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Obstetrics and Gynecology, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Mu-Hsien Yu
- Department of Obstetrics & Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Jen Chen
- Department of Obstetrics and Gynecology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Eing-Mei Tsai
- General Research Centers of R&D office, Kaohsiung Medical University, Kaohsiung, Taiwan.,Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Peng-Sheng Yang
- Center for Reproductive Medicine & Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan
| | - Shyr-Yeu Lin
- Center for Reproductive Medicine & Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chii-Ruey Tzeng
- Center for Reproductive Medicine & Sciences, Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei, Taiwan. .,Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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Siegel RJ, Bridges SL, Ahmed S. HLA-C: An Accomplice in Rheumatic Diseases. ACR Open Rheumatol 2019; 1:571-579. [PMID: 31777841 PMCID: PMC6858028 DOI: 10.1002/acr2.11065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
Human leukocyte antigen c (HLA-C) is a polymorphic membrane protein encoded by the HLA-C gene in the class I major histocompatibility complex. HLA-C plays an essential role in protection against cancer and viruses but has also been implicated in allograft rejection, preeclampsia, and autoimmune disease. This review summarizes reports and proposed mechanisms for the accessory role of HLA-C in rheumatic diseases. Historically, contributions of HLA-C to rheumatic diseases were eclipsed by the stronger association with HLA-DRB1 alleles containing the "shared epitope" with rheumatoid arthritis. Larger genetic association studies and more powerful analytical approaches have revealed independent associations of HLA-C with rheumatic disease-associated phenotypes, including development of anticitrullinated peptide antibodies. HLA-C functions by presenting antigens to T cells and by binding activatory and inhibitory receptors on natural killer (NK) cells, but the exact mechanisms by which the HLA-C locus contributes to autoimmunity are largely undefined. Studies have suggested that HLA-C and NK cell receptor polymorphisms may predict responsiveness to pharmacotherapy. Understanding the mechanisms of the role of HLA-C in rheumatic disease could uncover therapeutic targets or guide precision pharmacologic treatments.
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Affiliation(s)
- Ruby J. Siegel
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
| | - S. Louis Bridges
- Division of Clinical Immunology and RheumatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Salahuddin Ahmed
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
- Division of RheumatologyUniversity of Washington School of MedicineSeattleWashington
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Gao K, Chen L, Zhang Y, Zhao Y, Wan Z, Wu J, Lin L, Kuang Y, Lu J, Zhang X, Tian L, Liu X, Qiu X. Germline-Encoded TCR-MHC Contacts Promote TCR V Gene Bias in Umbilical Cord Blood T Cell Repertoire. Front Immunol 2019; 10:2064. [PMID: 31543879 PMCID: PMC6730489 DOI: 10.3389/fimmu.2019.02064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
T cells recognize antigens as peptides bound to major histocompatibility complex (MHC) proteins through T cell receptors (TCRs) on their surface. To recognize a wide range of pathogens, each individual possesses a substantial number of TCRs with an extremely high degree of variability. It remains controversial whether germline-encoded TCR repertoire is shaped by MHC polymorphism and, if so, what is the preference between MHC genetic variants and TCR V gene compatibility. To investigate the "net" genetic association between MHC variations and TRBV genes, we applied quantitative trait locus (QTL) mapping to test the associations between MHC polymorphism and TCR β chain V (TRBV) genes usage using umbilical cord blood (UCB) samples of 201 Chinese newborns. We found TRBV gene and MHC loci that are predisposed to interact with one another differ from previous conclusions. The majority of MHC amino acid residues associated with the TRBV gene usage show spatial proximities in known structures of TCR-pMHC complexes. These results show for the first time that MHC variants bias TRBV gene usage in UCB of Chinese ancestry and indicate that germline-encoded contacts influence TCR-MHC interactions in intact T cell repertoires.
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Affiliation(s)
- Kai Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | | | | | - Yi Zhao
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | | | | | - Yashu Kuang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinhua Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Women and Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Xiao Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Women and Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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36
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Souri Z, Wierenga APA, Mulder A, Jochemsen AG, Jager MJ. HLA Expression in Uveal Melanoma: An Indicator of Malignancy and a Modifiable Immunological Target. Cancers (Basel) 2019; 11:cancers11081132. [PMID: 31394860 PMCID: PMC6721545 DOI: 10.3390/cancers11081132] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/17/2019] [Accepted: 08/01/2019] [Indexed: 12/23/2022] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, and gives rise to metastases in 50% of cases. The presence of an inflammatory phenotype is a well-known risk factor for the development of metastases. This inflammatory phenotype is characterized by the presence of high numbers of lymphocytes and macrophages, and a high expression of the HLA Class I and II antigens. An abnormal expression of HLA Class I may influence cytotoxic T lymphocyte (CTL) as well as Natural Killer (NK) cell responses. We provide a comprehensive review regarding the inflammatory phenotype in UM and the expression of locus- and allele-specific HLA Class I and of Class II antigens in primary UM and its metastases. Furthermore, we describe the known regulators and the role of genetics (especially chromosome 3 and BRCA-Associated Protein 1 (BAP1 status)), and, last but not least, the effect of putative therapeutic treatments on HLA expression.
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Affiliation(s)
- Zahra Souri
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Annemijn P A Wierenga
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Arend Mulder
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Aart G Jochemsen
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands.
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37
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Zhu M, Xu K, Chen Y, Gu Y, Zhang M, Luo F, Liu Y, Gu W, Hu J, Xu H, Xie Z, Sun C, Li Y, Sun M, Xu X, Hsu HT, Chen H, Fu Q, Shi Y, Xu J, Ji L, Liu J, Bian L, Zhu J, Chen S, Xiao L, Li X, Jiang H, Shen M, Huang Q, Fang C, Li X, Huang G, Fan J, Jiang Z, Jiang Y, Dai J, Ma H, Zheng S, Cai Y, Dai H, Zheng X, Zhou H, Ni S, Jin G, She JX, Yu L, Polychronakos C, Hu Z, Zhou Z, Weng J, Shen H, Yang T. Identification of Novel T1D Risk Loci and Their Association With Age and Islet Function at Diagnosis in Autoantibody-Positive T1D Individuals: Based on a Two-Stage Genome-Wide Association Study. Diabetes Care 2019; 42:1414-1421. [PMID: 31152121 DOI: 10.2337/dc18-2023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 05/03/2019] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Type 1 diabetes (T1D) is a highly heritable disease with much lower incidence but more adult-onset cases in the Chinese population. Although genome-wide association studies (GWAS) have identified >60 T1D loci in Caucasians, less is known in Asians. RESEARCH DESIGN AND METHODS We performed the first two-stage GWAS of T1D using 2,596 autoantibody-positive T1D case subjects and 5,082 control subjects in a Chinese Han population and evaluated the associations between the identified T1D risk loci and age and fasting C-peptide levels at T1D diagnosis. RESULTS We observed a high genetic correlation between children/adolescents and adult T1D case subjects (r g = 0.87), as well as subgroups of autoantibody status (r g ≥ 0.90). We identified four T1D risk loci reaching genome-wide significance in the Chinese Han population, including two novel loci, rs4320356 near BTN3A1 (odds ratio [OR] 1.26, P = 2.70 × 10-8) and rs3802604 in GATA3 (OR 1.24, P = 2.06 × 10-8), and two previously reported loci, rs1770 in MHC (OR 4.28, P = 2.25 × 10-232) and rs705699 in SUOX (OR 1.46, P = 7.48 × 10-20). Further fine mapping in the MHC region revealed five independent variants, including another novel locus, HLA-C position 275 (omnibus P = 9.78 × 10-12), specific to the Chinese population. Based on the identified eight variants, we achieved an area under the curve value of 0.86 (95% CI 0.85-0.88). By building a genetic risk score (GRS) with these variants, we observed that the higher GRS were associated with an earlier age of T1D diagnosis (P = 9.08 × 10-11) and lower fasting C-peptide levels (P = 7.19 × 10-3) in individuals newly diagnosed with T1D. CONCLUSIONS Our results extend current knowledge on genetic contributions to T1D risk. Further investigations in different populations are needed for genetic heterogeneity and subsequent precision medicine.
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Affiliation(s)
- Meng Zhu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Kuanfeng Xu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yang Chen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yong Gu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mei Zhang
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feihong Luo
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yu Liu
- Department of Endocrinology and Metabolism, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Wei Gu
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Ji Hu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Haixia Xu
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhiguo Xie
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Chengjun Sun
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yuxiu Li
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Min Sun
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xinyu Xu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hsiang-Ting Hsu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Heng Chen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qi Fu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Shi
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingjing Xu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Li Ji
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin Liu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lingling Bian
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Zhu
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuang Chen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Xiao
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Li
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hemin Jiang
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Min Shen
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianwen Huang
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chen Fang
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xia Li
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Gan Huang
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Jingyi Fan
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Zhu Jiang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Shuai Zheng
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yun Cai
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Dai
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xuqin Zheng
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongwen Zhou
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shining Ni
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA
| | - Liping Yu
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Constantin Polychronakos
- The Endocrine Genetics Laboratory, Child Health and Human Development Program and Department of Pediatrics, McGill University Health Centre Research Institute, Montreal, Canada
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China .,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiguang Zhou
- Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, China .,National Clinical Research Center for Metabolic Diseases, Changsha, China.,Key Laboratory of Diabetes Immunology, Central South University, Ministry of Education, Changsha, China
| | - Jianping Weng
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, China .,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tao Yang
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China .,Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, China
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Würfel FM, Winterhalter C, Trenkwalder P, Wirtz RM, Würfel W. European Patent in Immunoncology: From Immunological Principles of Implantation to Cancer Treatment. Int J Mol Sci 2019; 20:ijms20081830. [PMID: 31013867 PMCID: PMC6514949 DOI: 10.3390/ijms20081830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
The granted European patent EP 2 561 890 describes a procedure for an immunological treatment of cancer. It is based on the principles of the HLA-supported communication of implantation and pregnancy. These principles ensure that the embryo is not rejected by the mother. In pregnancy, the placenta, more specifically the trophoblast, creates an “interface” between the embryo/fetus and the maternal immune system. Trophoblasts do not express the “original” HLA identification of the embryo/fetus (HLA-A to -DQ), but instead show the non-classical HLA groups E, F, and G. During interaction with specific receptors of NK cells (e.g., killer-immunoglobulin-like receptors (KIR)) and lymphocytes (lymphocyte-immunoglobulin-like receptors (LIL-R)), the non-classical HLA groups inhibit these immunocompetent cells outside pregnancy. However, tumors are known to be able to express these non-classical HLA groups and thus make use of an immuno-communication as in pregnancies. If this occurs, the prognosis usually worsens. This patent describes, in a first step, the profiling of the non-classical HLA groups in primary tumor tissue as well as metastases and recurrent tumors. The second step comprises tailored antibody therapies, which is the subject of this patent. In this review, we analyze the underlying mechanisms and describe the currently known differences between HLA-supported communication of implantation and that of tumors.
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Affiliation(s)
- Franziska M Würfel
- STRATIFYER Molecular Pathology GmbH, D-50935 Cologne, Werthmannstrasse 1c, 50935 Cologne, Germany.
| | | | | | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, D-50935 Cologne, Werthmannstrasse 1c, 50935 Cologne, Germany.
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Tonarelli L. Discover the Potential: Exploring New Frontiers of IL-23 Inhibitors. EUROPEAN MEDICAL JOURNAL 2019. [DOI: 10.33590/emj/10310287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Affecting up to 11.4% of the population worldwide,1 psoriasis is one of the most common chronic autoinflammatory diseases. It is associated with multiple comorbidities and can have profound negative effects on physical and emotional wellbeing and overall quality of life, making it a serious public health concern. A primary objective of this symposium was to explain the pathogenesis of psoriasis and its relation to the development of novel targeted immune therapies. Psoriasis is characterised by skin and systemic damage consequent to pathogenic cytokine production under the influence of both environmental and genetic factors. Differentiation of Th17 cells from naïve T cells is central to the development of psoriasis, and recently pathogenic models have identified IL-23 as the pathogenic cytokine responsible for promoting Th17 cell proliferation and IL-17 production. Therefore, selective blockade of IL-23 may be instrumental in controlling Th17-mediated inflammation in psoriasis. Another key objective of the symposium was to evaluate key learnings from the latest available clinical trial data on agents targeting the IL-23/Th17 signalling pathway and how these learnings can be harnessed to improve the management of patients with psoriasis. Both IL-17 inhibitors (e.g., ixekizumab and secukinumab) and IL-23 inhibitors (e.g., guselkumab and risankizumab) have demonstrated high efficacy and a good safety profile. Anti-IL-17 agents have faster onset of action and allow the achievement of good response rates very rapidly. Efficacy is better maintained over time with anti-IL-23 agents, including in patients who have stopped and those that then restarted anti-IL-23 therapy after a withdrawal period. Despite the availability of effective treatments, undertreatment in psoriasis is common. This can be attributed to factors such as the heterogeneous nature of psoriasis and relatively large prevalence of addictive behaviours in patients with the condition. When making treatment decisions, it is important to consider these factors as well as patient preferences and expectations, so that treatment can be individualised as much as possible. The symposium concluded with an interactive session, which offered the audience the opportunity to ask questions and discuss relevant issues of interest.
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Faden DL, Concha-Benavente F, Chakka AB, McMichael EL, Chandran U, Ferris RL. Immunogenomic correlates of response to cetuximab monotherapy in head and neck squamous cell carcinoma. Head Neck 2019; 41:2591-2601. [PMID: 30828910 DOI: 10.1002/hed.25726] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/16/2019] [Accepted: 02/19/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mechanisms of resistance to immune-modulating cancer treatments are poorly understood. Using a novel cohort of patients with head and neck squamous cell carcinoma (HNSCC), we investigated mechanisms of immune escape from epidermal growth factor receptor-specific monoclonal antibody (mAb) therapy. METHODS HNSCC tumors (n = 20) from a prospective trial of neoadjuvant cetuximab monotherapy underwent whole-exome sequencing. Expression of killer-cell immunoglobulin-like receptor (KIR) and human leukocyte antigen-C (HLA-C) and the effect of KIR blockade were assessed in HNSCC cell lines. RESULTS Nonresponders to cetuximab had an increased rate of mutations in HLA-C compared to responders and HNSCC tumors (n = 528) in The Cancer Genome Atlas (P < 0.00001). In vitro, cetuximab-activated natural killer (NK) cells induced upregulation of HLA-C on HNSCC cells (P < 0.01) via interferon gamma. Treatment of NK cells with the anti-KIR mAb lirilumab increased killing of HNSCC cells (P < 0.001). CONCLUSIONS Alterations in HLA-C may provide a mechanism of immune evasion through disruption of NK activation.
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Affiliation(s)
- Daniel L Faden
- Department of Otolaryngology, Division of Head and Neck Surgical Oncology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Fernando Concha-Benavente
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Anish B Chakka
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert L Ferris
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.,Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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Li L, Liu Y, Gorny MK. Association of Diverse Genotypes and Phenotypes of Immune Cells and Immunoglobulins With the Course of HIV-1 Infection. Front Immunol 2018; 9:2735. [PMID: 30534128 PMCID: PMC6275200 DOI: 10.3389/fimmu.2018.02735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/06/2018] [Indexed: 12/19/2022] Open
Abstract
Disease progression among HIV-1-infected individuals varies widely, but the mechanisms underlying this variability remains unknown. Distinct disease outcomes are the consequences of many factors working in concert, including innate and adaptive immune responses, cell-mediated and humoral immunity, and both genetic and phenotypic factors. Current data suggest that these multifaceted aspects in infected individuals should be considered as a whole, rather than as separate unique elements, and that analyses must be performed in greater detail in order to meet the requirements of personalized medicine and guide optimal vaccine design. However, the wide adoption of antiretroviral therapy (ART) influences the implementation of systematic analyses of the HIV-1-infected population. Consequently, fewer data will be available for acquisition in the future, preventing the comprehensive investigations required to elucidate the underpinnings of variability in disease outcome. This review seeks to recapitulate the distinct genotypic and phenotypic features of the immune system, focusing in particular on comparing the surface proteins of immune cells among individuals with different HIV infection outcomes.
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Affiliation(s)
- Liuzhe Li
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Yan Liu
- Institute of Pathogenic Biology, Medical College, University of South China, Hengyang, China
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
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42
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Genomic alterations driving psoriasis pathogenesis. Gene 2018; 683:61-71. [PMID: 30287254 DOI: 10.1016/j.gene.2018.09.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/22/2018] [Accepted: 09/22/2018] [Indexed: 11/23/2022]
Abstract
Psoriasis is an immune mediated inflammatory skin disease with complex etiology involving interplay between environmental and genetic risk factors as disease initiating event. Enhanced understanding on genetic risk factors, differentially expressed genes, deregulated proteins and pathway-targeted therapeutics have established multiple axis of psoriasis pathogenesis. So far, loci in 424 genes are reported to be associated with psoriasis alongside copy number variations and epigenetic alterations. From clinical perspective, presence of specific genetic trigger(s) in individual psoriasis patient could aid in devising a personalized therapeutic strategy. Therefore, the review presents an updates on reported genomic alterations and their subsequent course of cutaneous inflammations that potentially drive to psoriasis.
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Kyriakidis NC, Kockum I, Julkunen H, Hoxha A, Salomonsson S, Meneghel L, Ebbing C, Dilthey A, Eronen M, Carolis SD, Kiserud T, Ruffatti A, Kere J, Meisgen S, Wahren-Herlenius M. European families reveal MHC class I and II associations with autoimmune-mediated congenital heart block. Ann Rheum Dis 2018; 77:1381-1382. [DOI: 10.1136/annrheumdis-2018-212953] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 11/03/2022]
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44
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Kaufman J. Generalists and Specialists: A New View of How MHC Class I Molecules Fight Infectious Pathogens. Trends Immunol 2018; 39:367-379. [PMID: 29396014 PMCID: PMC5929564 DOI: 10.1016/j.it.2018.01.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/24/2022]
Abstract
In comparison with the major histocompatibility complexes (MHCs) of typical mammals, the chicken MHC is simple and compact with a single dominantly expressed class I molecule that can determine the immune response. In addition to providing useful information for the poultry industry and allowing insights into the evolution of the adaptive immune system, the simplicity of the chicken MHC has allowed the discovery of phenomena that are more difficult to discern in the more complicated mammalian systems. This review discusses the new concept that poorly expressed promiscuous class I alleles act as generalists to protect against a wide variety of infectious pathogens, while highly expressed fastidious class I alleles can act as specialists to protect against new and dangerous pathogens. A broad overview of classical MHC I expression and bound peptides reveals an inverse correlation between repertoire breadth and cell-surface expression in some chicken and human alleles. Several chicken class I alleles with wide peptide-binding repertoires (promiscuity) are associated with resistance to a variety of common diseases. Conversely, a narrow peptide-binding repertoire (fastidiousness) in some human HLA-B alleles is associated with resistance to HIV progression. Cell-surface expression of some classical class I alleles depends on the regulation of translocation to the cell surface rather than of transcription or translation. MHC translocation is influenced by peptide translocation in chickens and by tapasin interaction in humans.
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Affiliation(s)
- Jim Kaufman
- University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK; University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge CB2 0ES, UK.
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45
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Hosie L, Pachnio A, Zuo J, Pearce H, Riddell S, Moss P. Cytomegalovirus-Specific T Cells Restricted by HLA-Cw*0702 Increase Markedly with Age and Dominate the CD8 + T-Cell Repertoire in Older People. Front Immunol 2017; 8:1776. [PMID: 29312307 PMCID: PMC5732243 DOI: 10.3389/fimmu.2017.01776] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
Cytomegalovirus (CMV) infection elicits a strong T-cell immune response, which increases further during aging in a process termed "memory inflation." CMV downregulates the expression of HLA-A and HLA-B on the surface of infected cells to limit presentation of viral peptides to T-cells although HLA-C is relatively spared as it also engages with inhibitory killer immunoglobulin receptor receptors and therefore reduces lysis by natural killer cells. We investigated the magnitude and functional properties of CMV-specific CD8+ T-cells specific for 10 peptides restricted by HLA-C in a cohort of 53 donors between the age of 23 and 91 years. This was achieved via peptide stimulation of PBMCs followed by multicolor flow cytometry. Three peptides, derived from proteins generated in the immediate-early period of viral replication and restricted by HLA-Cw*0702, elicited strong immune responses, which increased substantially with age such that the average aggregate response represented 37% of the CD8+ T-cell pool within donors above 70 years of age. Remarkably, a single response represented 70% of the total CD8+ T-cell pool within a 91-year-old donor. HLA-Cw*0702-restricted CD8+ T-cell responses were immunodominant over HLA-A and HLA-B-restricted CMV-specific responses and did not show features of exhaustion such as PD-1 or CD39 expression. Indeed, such CTL exhibit a polyfunctional cytokine profile with co-expression of IFN-γ and TNF-α and a strong cytotoxic phenotype with intracellular expression of perforin and granzymeB. Functionally, HLA-Cw*0702-restricted CTL show exceptionally high avidity for cognate peptide-HLA and demonstrate very early and efficient recognition of virally infected cells. These observations indicate that CD8+ T-cells restricted by HLA-C play an important role in the control of persistent CMV infection and could represent a novel opportunity for CD8+ T-cell therapy of viral infection within immunosuppressed patients. In addition, the findings provide further evidence for the importance of HLA-C-restricted T-cells in the control of chronic viral infection.
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Affiliation(s)
- Louise Hosie
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Annette Pachnio
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Jianmin Zuo
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Hayden Pearce
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
| | - Stanley Riddell
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Paul Moss
- College of Medical and Dental Sciences, Institute of Immunology and Immunotherapy, Birmingham Health Partners, University of Birmingham, Birmingham, United Kingdom
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46
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Hyun SJ, Sohn HJ, Lee HJ, Lee SD, Kim S, Sohn DH, Hong CH, Choi H, Cho HI, Kim TG. Comprehensive Analysis of Cytomegalovirus pp65 Antigen-Specific CD8 + T Cell Responses According to Human Leukocyte Antigen Class I Allotypes and Intraindividual Dominance. Front Immunol 2017; 8:1591. [PMID: 29209324 PMCID: PMC5702484 DOI: 10.3389/fimmu.2017.01591] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/06/2017] [Indexed: 11/24/2022] Open
Abstract
To define whether individual human leukocyte antigen (HLA) class I allotypes are used preferentially in human cytomegalovirus (CMV)-specific cytotoxic T lymphocyte responses, CD8+ T cell responses restricted by up to six HLA class I allotypes in an individual were measured in parallel using K562-based artificial antigen-presenting cells expressing both CMV pp65 antigen and one of 32 HLA class I allotypes (7 HLA-A, 14 HLA-B, and 11 HLA-C) present in 50 healthy Korean donors. The CD8+ T cell responses to pp65 in the HLA-C allotypes were lower than responses to those in HLA-A and -B allotypes and there was no difference between the HLA-A and HLA-B loci. HLA-A*02:01, -B*07:02, and -C*08:01 showed the highest magnitude and frequency of immune responses to pp65 at each HLA class I locus. However, HLA-A*02:07, -B*59:01, -B*58:01, -B*15:11, -C*03:02, and -C*02:02 did not show any immune responses. Although each individual has up to six different HLA allotypes, 46% of the donors showed one allotype, 24% showed two allotypes, and 2% showed three allotypes that responded to pp65. Interestingly, the frequencies of HLA-A alleles were significantly correlated with the positivity of specific allotypes. Our results demonstrate that specific HLA class I allotypes are preferentially used in the CD8+ T cell immune response to pp65 and that a hierarchy among HLA class I allotypes is present in an individual.
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Affiliation(s)
- Seung-Joo Hyun
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Jung Sohn
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Joo Lee
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Seon-Duk Lee
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sueon Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Dae-Hee Sohn
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Cheol-Hwa Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Haeyoun Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hyun-Il Cho
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,College of Medicine, Cancer Research Institute, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,College of Medicine, Cancer Research Institute, The Catholic University of Korea, Seoul, South Korea
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47
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Di Marco M, Schuster H, Backert L, Ghosh M, Rammensee HG, Stevanović S. Unveiling the Peptide Motifs of HLA-C and HLA-G from Naturally Presented Peptides and Generation of Binding Prediction Matrices. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:2639-2651. [PMID: 28904123 DOI: 10.4049/jimmunol.1700938] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2023]
Abstract
The classical HLA-C and the nonclassical HLA-E and HLA-G molecules play important roles both in the innate and adaptive immune system. Starting already during embryogenesis and continuing throughout our lives, these three Ags exert major functions in immune tolerance, defense against infections, and anticancer immune responses. Despite these important roles, identification and characterization of the peptides presented by these molecules has been lacking behind the more abundant HLA-A and HLA-B gene products. In this study, we elucidated the peptide specificities of these HLA molecules using a comprehensive analysis of naturally presented peptides. To that end, the 15 most frequently expressed HLA-C alleles as well as HLA-E*01:01 and HLA-G*01:01 were transfected into lymphoblastoid C1R cells expressing low endogenous HLA. Identification of naturally presented peptides was performed by immunoprecipitation of HLA and subsequent analysis of HLA-bound peptides by liquid chromatographic tandem mass spectrometry. Peptide motifs of HLA-C unveil anchors in position 2 or 3 with high variances between allotypes, and a less variable anchor at the C-terminal end. The previously reported small ligand repertoire of HLA-E was confirmed within our analysis, and we could show that HLA-G combines a large ligand repertoire with distinct features anchoring peptides at positions 3 and 9, supported by an auxiliary anchor in position 1 and preferred residues in positions 2 and 7. The wealth of HLA ligands resulted in prediction matrices for octa-, nona-, and decamers. Matrices were validated in terms of their binding prediction and compared with the latest NetMHC prediction algorithm NetMHCpan-3.0, which demonstrated their predictive power.
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Affiliation(s)
- Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Heiko Schuster
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Immatics Biotechnologies GmbH, 72076 Tübingen, Germany; and
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany;
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48
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Powell RM, Lissauer D, Tamblyn J, Beggs A, Cox P, Moss P, Kilby MD. Decidual T Cells Exhibit a Highly Differentiated Phenotype and Demonstrate Potential Fetal Specificity and a Strong Transcriptional Response to IFN. THE JOURNAL OF IMMUNOLOGY 2017; 199:3406-3417. [PMID: 28986438 DOI: 10.4049/jimmunol.1700114] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/30/2017] [Indexed: 01/16/2023]
Abstract
Immune tolerance during human pregnancy is maintained by a range of modifications to the local and systemic maternal immune system. Lymphoid infiltration is seen at the implantation site of the fetal-maternal interface, and decidual NK cells have been demonstrated to facilitate extravillous trophoblast invasion into maternal decidua during the first trimester, optimizing hemochorial placentation. However, although there is considerable T cell infiltration of the maternal decidua, the functional properties of this T cell response remain poorly defined. We investigated the specificity and regulation of CD4+ and CD8+ T cells obtained from human third trimester decidua and demonstrated that decidual CD4+ and CD8+ T cells exhibit a highly differentiated effector memory phenotype in comparison with peripheral blood and display increased production of IFN-γ and IL-4. Moreover, decidual T cells proliferated in response to fetal tissue, and depletion of T regulatory cells led to an increase in fetal-specific proliferation. HY-specific T cells were detectable in the decidua of women with male pregnancies and were shown to be highly differentiated. Transcriptional analysis of decidual T cells revealed a unique gene profile characterized by elevated expression of proteins associated with the response to IFN signaling. These data have considerable importance both for the study of healthy placentation and for the investigation of the potential importance of fetal-specific alloreactive immune responses within disorders of pregnancy.
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Affiliation(s)
- Richard M Powell
- Institute of Immunology and Immunotherapy, Birmingham Health Partners, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom;
| | - David Lissauer
- Centre for Women's and Newborn Health, Birmingham Health Partners, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jennifer Tamblyn
- Centre for Women's and Newborn Health, Birmingham Health Partners, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.,Centre of Endocrinology, Diabetes and Metabolism, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Andrew Beggs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; and
| | - Philip Cox
- Department of Perinatal Pathology, Centre of Women's and Children's Health, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Paul Moss
- Institute of Immunology and Immunotherapy, Birmingham Health Partners, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mark D Kilby
- Centre for Women's and Newborn Health, Birmingham Health Partners, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.,Centre of Endocrinology, Diabetes and Metabolism, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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49
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Perez-Martinez AP, Ong E, Zhang L, Marrs CF, He Y, Yang Z. Conservation in gene encoding Mycobacterium tuberculosis antigen Rv2660 and a high predicted population coverage of H56 multistage vaccine in South Africa. INFECTION GENETICS AND EVOLUTION 2017; 55:244-250. [PMID: 28941991 DOI: 10.1016/j.meegid.2017.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 09/11/2017] [Accepted: 09/19/2017] [Indexed: 01/26/2023]
Abstract
H56/AERAS-456+IC31 (H56), composed of two early secretion proteins, Ag85B and ESAT-6, and a latency associated protein, Rv2660, and the IC31 Intercell adjuvant, is a new fusion subunit vaccine candidate designed to induce immunity against both new infection and reactivation of latent tuberculosis infection. Efficacy of subunit vaccines may be affected by the diversity of vaccine antigens among clinical strains and the extent of recognition by the diverse HLA molecules in the recipient population. Although a previous study showed the conservative nature of Ag85B- and ESAT-6-encoding genes, genetic diversity of Rv2660c that encodes RV2660 is largely unknown. The population coverage of H56 as a whole yet remains to be assessed. The present study was conducted to address these important knowledge gaps. DNA sequence analysis of Rv2660c found no variation among 83 of the 84 investigated clinical strains belonging to four genetic lineages. H56 was predicted to have as high as 99.6% population coverage in the South Africa population using the Immune Epitope Database (IEDB) Population Coverage Tool. Further comparison of H56 population coverage between South African Blacks and Caucasians based on the phenotypic frequencies of binding MHC Class I and Class II supertype alleles found that all of the nine MHC-I and six of eight MHC-II human leukocyte antigen (HLA) supertype alleles analyzed were significantly differentially expressed between the two subpopulations. This finding suggests the presence of race-specific functional binding motifs of MHC-I and MHC-II HLA alleles, which, in turn, highlights the importance of including diverse populations in vaccine clinical evaluation. In conclusion, H56 vaccine is predicted to have a promising population coverage in South Africa; this study demonstrates the utility of integrating comparative genomics and bioinformatics in bridging animal and clinical studies of novel TB vaccines.
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Affiliation(s)
- Angy P Perez-Martinez
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Lixin Zhang
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Carl F Marrs
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States; Department of Microbiology and Immunology Department, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States; Center of Computational Medicine and Bioinformatics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
| | - Zhenhua Yang
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, United States.
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50
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Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP. The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. J Biol Chem 2017; 292:17203-17215. [PMID: 28855257 DOI: 10.1074/jbc.m117.806976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.
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Affiliation(s)
- Jesse I Mobbs
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Patricia T Illing
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Nadine L Dudek
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania 19044
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia,
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and.,the Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Julian P Vivian
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and
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