1
|
Barquera R, Del Castillo-Chávez O, Nägele K, Pérez-Ramallo P, Hernández-Zaragoza DI, Szolek A, Rohrlach AB, Librado P, Childebayeva A, Bianco RA, Penman BS, Acuña-Alonzo V, Lucas M, Lara-Riegos JC, Moo-Mezeta ME, Torres-Romero JC, Roberts P, Kohlbacher O, Warinner C, Krause J. Ancient genomes reveal insights into ritual life at Chichén Itzá. Nature 2024; 630:912-919. [PMID: 38867041 DOI: 10.1038/s41586-024-07509-7] [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: 03/30/2023] [Accepted: 05/02/2024] [Indexed: 06/14/2024]
Abstract
The ancient city of Chichén Itzá in Yucatán, Mexico, was one of the largest and most influential Maya settlements during the Late and Terminal Classic periods (AD 600-1000) and it remains one of the most intensively studied archaeological sites in Mesoamerica1-4. However, many questions about the social and cultural use of its ceremonial spaces, as well as its population's genetic ties to other Mesoamerican groups, remain unanswered2. Here we present genome-wide data obtained from 64 subadult individuals dating to around AD 500-900 that were found in a subterranean mass burial near the Sacred Cenote (sinkhole) in the ceremonial centre of Chichén Itzá. Genetic analyses showed that all analysed individuals were male and several individuals were closely related, including two pairs of monozygotic twins. Twins feature prominently in Mayan and broader Mesoamerican mythology, where they embody qualities of duality among deities and heroes5, but until now they had not been identified in ancient Mayan mortuary contexts. Genetic comparison to present-day people in the region shows genetic continuity with the ancient inhabitants of Chichén Itzá, except at certain genetic loci related to human immunity, including the human leukocyte antigen complex, suggesting signals of adaptation due to infectious diseases introduced to the region during the colonial period.
Collapse
Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Oana Del Castillo-Chávez
- Centro INAH Yucatán, Instituto Nacional de Antropología e Historia (INAH), Mérida, Yucatán, Mexico.
| | - Kathrin Nägele
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- University of the Basque Country (EHU), San Sebastián-Donostia, Spain
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology and Cultural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Diana Iraíz Hernández-Zaragoza
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Pablo Librado
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, University of Texas at Austin, Austin, TX, USA
| | - Raffaela Angelina Bianco
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
| | - Bridget S Penman
- The Zeeman Institute and the School of Life Sciences, University of Warwick, Coventry, UK
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mary Lucas
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | | | | | | | - Patrick Roberts
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center, University of Tübingen, Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max-Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany.
| |
Collapse
|
2
|
Slieker RC, Warmerdam DO, Vermeer MH, van Doorn R, Heemskerk MHM, Scheeren FA. Reassessing human MHC-I genetic diversity in T cell studies. Sci Rep 2024; 14:7966. [PMID: 38575727 PMCID: PMC10995142 DOI: 10.1038/s41598-024-58777-2] [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: 11/01/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analysed (pre)clinical publications focusing on COVID-19 studies and T cell receptor (TCR)-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian, and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
Collapse
Affiliation(s)
- Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël O Warmerdam
- Centre for Future Affordable & Sustainable Therapy Development (FAST), The Hague, The Netherlands
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Dermatology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands.
| |
Collapse
|
3
|
Kim D, Song J, Mancuso N, Mangul S, Jung J, Jang W. Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis. Arthritis Res Ther 2024; 26:47. [PMID: 38336809 PMCID: PMC10858498 DOI: 10.1186/s13075-024-03280-2] [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: 09/29/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Juvenile idiopathic arthritis (JIA) is one of the most prevalent rheumatic disorders in children and is classified as an autoimmune disease (AID). While a robust genetic contribution to JIA etiology has been established, the exact pathogenesis remains unclear. METHODS To prioritize biologically interpretable susceptibility genes and proteins for JIA, we conducted transcriptome-wide and proteome-wide association studies (TWAS/PWAS). Then, to understand the genetic architecture of JIA, we systematically analyzed single-nucleotide polymorphism (SNP)-based heritability, a signature of natural selection, and polygenicity. Next, we conducted HLA typing using multi-ethnicity RNA sequencing data. Additionally, we examined the T cell receptor (TCR) repertoire at a single-cell level to explore the potential links between immunity and JIA risk. RESULTS We have identified 19 TWAS genes and two PWAS proteins associated with JIA risks. Furthermore, we observe that the heritability and cell type enrichment analysis of JIA are enriched in T lymphocytes and HLA regions and that JIA shows higher polygenicity compared to other AIDs. In multi-ancestry HLA typing, B*45:01 is more prevalent in African JIA patients than in European JIA patients, whereas DQA1*01:01, DQA1*03:01, and DRB1*04:01 exhibit a higher frequency in European JIA patients. Using single-cell immune repertoire analysis, we identify clonally expanded T cell subpopulations in JIA patients, including CXCL13+BHLHE40+ TH cells which are significantly associated with JIA risks. CONCLUSION Our findings shed new light on the pathogenesis of JIA and provide a strong foundation for future mechanistic studies aimed at uncovering the molecular drivers of JIA.
Collapse
Affiliation(s)
- Daeun Kim
- Department of Life Sciences, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Jaeseung Song
- Department of Life Sciences, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Serghei Mangul
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Junghyun Jung
- Department of Life Sciences, Dongguk University-Seoul, Seoul, 04620, Republic of Korea.
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Hollywood, CA, USA.
| | - Wonhee Jang
- Department of Life Sciences, Dongguk University-Seoul, Seoul, 04620, Republic of Korea.
| |
Collapse
|
4
|
Marzouka NAD, Alnaqbi H, Al-Aamri A, Tay G, Alsafar H. Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing. Sci Rep 2024; 14:3392. [PMID: 38337023 PMCID: PMC10858242 DOI: 10.1038/s41598-024-53986-1] [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: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population's unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.
Collapse
Affiliation(s)
- Nour Al Dain Marzouka
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amira Al-Aamri
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan Tay
- Division of Psychiatry, Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
5
|
Afolabi H, Zhang BM, O'Shaughnessy M, Chertow GM, Lafayette R, Charu V. The Association of Class I and II Human Leukocyte Antigen Serotypes With End-Stage Kidney Disease Due to Membranoproliferative Glomerulonephritis and Dense Deposit Disease. Am J Kidney Dis 2024; 83:79-89. [PMID: 37739026 DOI: 10.1053/j.ajkd.2023.06.005] [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: 11/27/2022] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 09/24/2023]
Abstract
RATIONALE & OBJECTIVE Membranoproliferative glomerulonephritis (MPGN), encompassing several distinct diseases, is a rare but significant cause of kidney failure in the United States. The potential etiologies of MPGN are unclear, but prior studies have suggested dysregulation of the alternative complement pathway and, recently, autoimmunity as potential mechanisms driving MPGN pathogenesis. In this study, we examined HLA associations with end-stage kidney disease (ESKD) due to MPGN and dense deposit disease (DDD) in a large racially and ethnically diverse US-based cohort. STUDY DESIGN Case-control study. SETTING & PARTICIPANTS Using US Renal Data System (USRDS) and United Network for Organ Sharing (UNOS) data, we identified 3,424 patients with kidney failure due to MPGN and 263 due to DDD. We matched patients to kidney donor controls on designated race and ethnicity in a 1:15 ratio. EXPOSURE 58 class I and II HLA serotypes. OUTCOME Case-control status. ANALYTICAL APPROACH For each disease cohort, univariable and multivariable logistic regression analyses were used to investigate associations between the disease and 58 HLA serotypes. In subgroup analyses, we investigated HLA associations in White and Black patients. We also studied antiglomerular basement membrane (anti-GBM) nephritis as a positive-control outcome. We applied a Bonferroni correction to account for multiple comparisons. RESULTS Eighteen serotypes were significantly associated with the odds of having MPGN in univariable analyses, with DR17 having the strongest association (odds ratio [OR], 1.55 [95% CI, 1.44-1.68], P=4.33e-28). No significant associations were found between any HLA serotype and DDD. Designated race-specific analyses showed comparable findings. We recapitulated known HLA associations in anti-GBM nephritis. LIMITATIONS Reliance on HLA serotypes (rather than genotype), lack of biopsy-confirmed diagnoses. CONCLUSIONS HLA-DR17 is associated with ESKD due to MPGN in a racially and ethnically diverse cohort. The strength of association was similar in White and Black patients, suggesting a role in the pathogenesis of MPGN. No HLA associations were observed in patients with DDD. PLAIN-LANGUAGE SUMMARY Prior studies have suggested dysregulation of the alternative complement pathway as a potential etiology of membranoproliferative glomerulonephritis (MPGN), but recent evidence from a British White population has implicated an autoimmune mechanism in MPGN pathogenesis. We investigated HLA associations between MPGN and dense deposit disease (DDD) in a large racially and ethnically diverse cohort of patients. We found that HLA-DR17 is associated with end-stage kidney disease (ESKD) due to MPGN in both White and Black patients. By contrast, no significant HLA associations with ESKD due to DDD were identified. These results suggest a role for autoimmunity in some cases of MPGN and highlight differences in the disease etiology of MPGN compared with DDD.
Collapse
Affiliation(s)
- Halimat Afolabi
- Department of Pathology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | | | - Glenn M Chertow
- Division of Nephrology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | - Richard Lafayette
- Division of Nephrology, Department of Medicine, School of Medicine, Stanford University, Stanford, California
| | - Vivek Charu
- Department of Pathology, Department of Medicine, School of Medicine, Stanford University, Stanford, California; Department of Medicine and Quantitative Sciences Unit, Department of Medicine, School of Medicine, Stanford University, Stanford, California.
| |
Collapse
|
6
|
Huang X, Hu B, Ye L, Li T, He L, Tan W, Yang G, Liu JP, Guo C. Pharmacogenomics and adverse effects of anti-infective drugs in children. Clin Exp Pharmacol Physiol 2024; 51:3-9. [PMID: 37840030 DOI: 10.1111/1440-1681.13830] [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: 02/21/2023] [Revised: 08/23/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
Children, as a special group, have their own peculiarities in terms of individualized medication use compared to adults. Adverse drug reactions have been an important issue that needs to be addressed in the hope of safe medication use in children, and the occurrence of adverse drug reactions is partly due to genetic factors. Anti-infective drugs are widely used in children, and they have always been an important cause of the occurrence of adverse reactions in children. Pharmacogenomic technologies are becoming increasingly sophisticated, and there are now many guidelines describing the pharmacogenomics of anti-infective drugs. However, data from paediatric-based studies are scarce. This review provides a systematic review of the pharmacogenomics of anti-infective drugs recommended for gene-guided use in CPIC guidelines by exploring the relationship between pharmacogenetic frequencies and the incidence of adverse reactions, which will help inform future studies of individualized medication use in children.
Collapse
Affiliation(s)
- Xin Huang
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Biwen Hu
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ling Ye
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Tong Li
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Li He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Wei Tan
- Department of Neonatology, Maternal & Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Guoping Yang
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Jun-Ping Liu
- Institute of Aging Research, Hangzhou Normal University School of Medicine, Zhejiang, China
- Department of Immunology, Monash University Faculty of Medicine, Prahran, Victoria, Australia
| | - Chengxian Guo
- Center of Clinical Pharmacology, The Third Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
7
|
Julve M, Kennedy O, Frampton AE, Bagwan I, Lythgoe MP. Gene of the month: cancer testis antigen gene 1b (NY-ESO-1). J Clin Pathol 2023; 77:1-7. [PMID: 37857483 DOI: 10.1136/jcp-2023-209053] [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] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Cancer testis antigen gene 1B (CTAG1B) and its associated gene product; New York oesophageal squamous carcinoma 1 (NY-ESO-1), represent a unique and promising target for cancer immunotherapy. As a member of the cancer testis antigen family (CTA), the protein's restricted expression pattern and ability to elicit spontaneous humoural and cellular immune responses has resulted in a plethora of novel modalities and approaches attempting to harness its immunotherapeutic anti-cancer potential. Here, we discuss the structure and function of CTAG1B/NY-ESO-1 in both health and disease, immunohistochemical detection, as well as the most promising advances in the development of associated anti-cancer therapies. From cancer vaccines to engineered cellular therapy approaches, a multitude of immunotherapies targeting CTA's are coming to the forefront of oncology. Although the efficacy of such approaches have yet to provide convincing evidence of durable response, early phase clinical trial data has resulted in some exciting findings which will have significant potential to act as a platform for future practice changing technologies.
Collapse
Affiliation(s)
- Max Julve
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Oliver Kennedy
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Adam Enver Frampton
- Department of Surgery and Cancer, Imperial College London, London, UK
- Section of Oncology, Deptartment of Clinical and Experimental Medicine, FHMS, University of Surrey, Guildford, UK
| | - Izhar Bagwan
- Department of Cellular Pathology, Royal Surrey Hospital, Guildford, UK
| | - Mark P Lythgoe
- Department of Surgery and Cancer, Imperial College London, London, UK
| |
Collapse
|
8
|
Björnsson HK, Björnsson ES. Review of human risk factors for idiosyncratic drug-induced liver injury: latest advances and future goals. Expert Opin Drug Metab Toxicol 2023; 19:969-977. [PMID: 37997265 DOI: 10.1080/17425255.2023.2288260] [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: 10/02/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023]
Abstract
INTRODUCTION Idiosyncratic drug-induced liver injury (DILI) is a common cause of acute liver injury and can lead to death from acute liver failure or require liver transplantation. Although the total burden of liver injury is high, the frequency of DILI caused by specific agents is often low. As the liver injury is by per definition idiosyncratic, the prediction of which patients will develop liver injury from specific drugs is currently a very difficult challenge. AREAS COVERED The current paper highlights the most important studies on prediction of DILI published in 2019-2023, including studies on genetic, metabolomic, and demographic risk factors, concomitant medication, and the role of comorbid liver diseases. Risk stratification using demographic, metabolomic, and multigenetic risk factors is discussed. EXPERT OPINION Great advances have been made in identifying genetic risk factors for DILI. Combining these risk factors with demographic information and other biomarkers into multigenetic risk models might become highly useful in risk stratifying patients exposed to DILI. However, a more detailed mapping of genetic risk factors is needed. Results of these studies need to be validated in the selected ethnic groups before applicability and cost-effectiveness can be determined.
Collapse
Affiliation(s)
- Helgi Kristinn Björnsson
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Einar Stefan Björnsson
- Division of Gastroenterology and Hepatology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| |
Collapse
|
9
|
Schendel DJ. Evolution by innovation as a driving force to improve TCR-T therapies. Front Oncol 2023; 13:1216829. [PMID: 37810959 PMCID: PMC10552759 DOI: 10.3389/fonc.2023.1216829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
Adoptive cell therapies continually evolve through science-based innovation. Specialized innovations for TCR-T therapies are described here that are embedded in an End-to-End Platform for TCR-T Therapy Development which aims to provide solutions for key unmet patient needs by addressing challenges of TCR-T therapy, including selection of target antigens and suitable T cell receptors, generation of TCR-T therapies that provide long term, durable efficacy and safety and development of efficient and scalable production of patient-specific (personalized) TCR-T therapy for solid tumors. Multiple, combinable, innovative technologies are used in a systematic and sequential manner in the development of TCR-T therapies. One group of technologies encompasses product enhancements that enable TCR-T therapies to be safer, more specific and more effective. The second group of technologies addresses development optimization that supports discovery and development processes for TCR-T therapies to be performed more quickly, with higher quality and greater efficiency. Each module incorporates innovations layered onto basic technologies common to the field of immunology. An active approach of "evolution by innovation" supports the overall goal to develop best-in-class TCR-T therapies for treatment of patients with solid cancer.
Collapse
Affiliation(s)
- Dolores J. Schendel
- Medigene Immunotherapies GmbH, Planegg, Germany
- Medigene AG, Planegg, Germany
| |
Collapse
|
10
|
Khalil R, Petrushkin H, Rees A, Westcott M. The incidence, presenting clinical findings and treatment patterns of Birdshot Retinochoroiditis in a high-prevalence region: findings from Northern Ireland, England and Wales. Eye (Lond) 2023; 37:2817-2825. [PMID: 36765269 PMCID: PMC10482920 DOI: 10.1038/s41433-023-02425-y] [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: 06/20/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Birdshot Retinochoroiditis (BSRC) is a rare, chronic posterior uveitis that is strongly associated with HLA-A*29.2 positivity. To date, no robust incidence studies of BSRC have been undertaken. We present the first epidemiological study of BSRC in a high-prevalence region. METHODS In collaboration with the British Ophthalmological Surveillance Unit, all new cases of BSRC between May 2017 and June 2019 were prospectively collected. Presenting demographics, symptoms, signs and treatment modalities were collected. A follow-up questionnaire twelve months later was also sent. RESULTS Thirty-seven confirmed cases meeting the reporting criteria were identified. Twenty-three cases had both baseline and follow-up data. The total population incidence of BSRC was 0.035 cases per 100,000 person-years [95% CI 0.025-0.048 cases per 100 000 people]. 97.3% were HLA-A*29 positive. The median age was 46 years, with females making up 78% of patients. There were no significant differences in the latitudinal incidence of BSRC. At presentation, floaters were the most common symptom. Optic disc swelling was the most common sign. Mean presenting visual acuity was independent of symptom duration. Combined systemic corticosteroids and immunomodulatory therapy were the most common treatments at baseline and follow-up. Intravitreal steroids were equally popular at follow-up. CONCLUSIONS This study provides the first nationwide estimate of the incidence of BSRC in a high-prevalence region. Cases were more common in females, with a broad range of presentation ages. No significant latitudinal effect of incidence was identified. Systemic therapy with steroids and IMT remain the most common treatments.
Collapse
Affiliation(s)
- Rana Khalil
- Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin, D02 YN77, Republic of Ireland.
| | - Harry Petrushkin
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, United Kingdom
- Great Ormond Street Hospital for Children, Great Ormond Street, London, WC1N 3JH, United Kingdom
- UCL Institute of Ophthalmology, 11-43 Bath St, London, EC1V 9EL, United Kingdom
| | - Angela Rees
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, United Kingdom
| | - Mark Westcott
- Moorfields Eye Hospital NHS Foundation Trust, 162 City Road, London, EC1V 2PD, United Kingdom
- Queen Mary University of London, Mile End Rd, Bethnal Green, London, E1 4NS, United Kingdom
| |
Collapse
|
11
|
Tansir G, Rastogi S, Kumar A, Barwad A, Mridha AR, Dhamija E, Shamim SA, Bhatnagar S, Bhoriwal S. A phase II study of gemcitabine and docetaxel combination in relapsed metastatic or unresectable locally advanced synovial sarcoma. BMC Cancer 2023; 23:639. [PMID: 37422615 DOI: 10.1186/s12885-023-11099-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 06/21/2023] [Indexed: 07/10/2023] Open
Abstract
Synovial sarcoma (SS) is one of the commonest non-rhabdomyosarcoma soft tissue sarcoma with limited treatment options in the relapsed and advanced settings. The combination of gemcitabine and docetaxel has demonstrated its role predominantly in leiomyosarcoma and pleomorphic sarcomas but has not been prospectively studied in SS. This trial assesses the efficacy, tolerability and quality of life (QoL) with this regimen in metastatic/unresectable locally advanced relapsed SS.Patients and methods This was a single-arm, two-stage, phase II, investigator-initiated interventional study among patients with metastatic or unresectable locally advanced SS who had progressed after at least one line of chemotherapy. Gemcitabine 900 mg/m2 on days 1 and 8 and docetaxel 75 mg/m2 on day 8 were administered intravenously every 21 days. The primary endpoint was 3-month progression-free rate (PFR); overall survival (OS), progression-free survival (PFS), overall response rate (ORR), safety and quality of life (QoL) constituted the secondary endpoints.Results Twenty-two patients were enrolled between March 2020 and September 2021 and the study had to be closed early due to slow accrual. The study population comprised of 18 (81.8%) patients with metastatic disease and 4 (18.2%) patients with locally advanced, unresectable disease. The most common primary sites of disease were extremity in 15 (68%) and the median number of lines of prior therapies received was 1 (range 1-4). 3-month PFR was 45.4% (95% CI 24.8-66.1) and ORR was 4.5%. Median progression-free survival (PFS) was 3 months (95% CI 2.3-3.6) and median OS was 14 months (95% CI 8.9-19.0). 7 (31.8%) patients experienced grade 3 or worse toxicities, including anemia (18%), neutropenia (9%) and mucositis (9%). QoL analysis demonstrated significant decline in certain functional and symptom scales, while financial and global health scales remained stable.Conclusion This is the first prospective study on the combination of gemcitabine and docetaxel performed specifically in patients with advanced, relapsed SS. Although the accrual of patients could not be completed as planned, the therapy did produce clinically meaningful outcomes and met its primary endpoint of 3-month PFR. This result, along with the manageable toxicity profile and stable global health status on QoL analysis, should encourage further studies.Trial registration This trial was prospectively registered under the Clinical Trials Registry of India on 26/02/2020 (Registration number: CTRI/2020/02/023612).
Collapse
Affiliation(s)
- Ghazal Tansir
- Department of Medical Oncology, Dr. BRAIRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Sameer Rastogi
- Department of Medical Oncology, Dr. BRAIRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
| | - Akash Kumar
- Department of Medical Oncology, National Cancer Institute, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Adarsh Barwad
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Asit R Mridha
- Department of Pathology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Ekta Dhamija
- Department of Radiodiagnosis, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India, 110029
| | - Shamim A Shamim
- Department of Nuclear Medicine, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India, 110029
| | - Sushma Bhatnagar
- Department of Oncoanesthesia and Palliative Medicine, Dr. BRAIRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India, 110029
| | - Sandeep Bhoriwal
- Department of Surgical Oncology, Dr. BRAIRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| |
Collapse
|
12
|
Begg TJA, Schmidt A, Kocher A, Larmuseau MHD, Runfeldt G, Maier PA, Wilson JD, Barquera R, Maj C, Szolek A, Sager M, Clayton S, Peltzer A, Hui R, Ronge J, Reiter E, Freund C, Burri M, Aron F, Tiliakou A, Osborn J, Behar DM, Boecker M, Brandt G, Cleynen I, Strassburg C, Prüfer K, Kühnert D, Meredith WR, Nöthen MM, Attenborough RD, Kivisild T, Krause J. Genomic analyses of hair from Ludwig van Beethoven. Curr Biol 2023; 33:1431-1447.e22. [PMID: 36958333 DOI: 10.1016/j.cub.2023.02.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/11/2022] [Accepted: 02/13/2023] [Indexed: 03/25/2023]
Abstract
Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.
Collapse
Affiliation(s)
- Tristan James Alexander Begg
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
| | - Axel Schmidt
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Arthur Kocher
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Maarten H D Larmuseau
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Laboratory of Human Genetic Genealogy, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; ARCHES - Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, 2000 Antwerp, Belgium; Histories vzw, 9000 Gent, Belgium
| | | | | | - John D Wilson
- Austrian Academy of Sciences, 1030 Vienna, Austria; University of Vienna, 1010 Vienna, Austria
| | - Rodrigo Barquera
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Carlo Maj
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany; Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany; Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | | | - Stephen Clayton
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Alexander Peltzer
- Quantitative Biology Center (QBiC) University of Tübingen, Tübingen, Germany
| | - Ruoyun Hui
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; Alan Turing Institute, 2QR, John Dodson House, London NW1 2DB, UK
| | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Marta Burri
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Franziska Aron
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Anthi Tiliakou
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Joanna Osborn
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK
| | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Guido Brandt
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Isabelle Cleynen
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Strassburg
- Department of Internal Medicine I, University Hospital Bonn, 53127 Bonn, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - William Rhea Meredith
- American Beethoven Society, San Jose State University, San Jose, CA 95192, USA; Ira F. Brilliant Center for Beethoven Studies, San Jose State University, San Jose, CA 95192, USA; School of Music and Dance, San Jose State University, San Jose, CA 95192, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital of Bonn, Bonn 53127, Germany
| | - Robert David Attenborough
- MacDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK; School of Archaeology & Anthropology, Australian National University, Canberra, ACT 0200, Australia
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, CB2 3ER Cambridge, UK; Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany.
| |
Collapse
|
13
|
Fuchs JR, Schulte BC, Fuchs JW, Agulnik M. Emerging targeted and cellular therapies in the treatment of advanced and metastatic synovial sarcoma. Front Oncol 2023; 13:1123464. [PMID: 36761952 PMCID: PMC9905840 DOI: 10.3389/fonc.2023.1123464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Synovial sarcoma is a soft tissue sarcoma accounting for approximately 1,000 cases per year in the United States. Currently, standard treatment of advanced and metastatic synovial sarcoma is anthracycline-based chemotherapy. While advanced synovial sarcoma is more responsive to chemotherapy compared to other soft tissue sarcomas, survival rates are poor, with a median survival time of less than 18 months. Enhanced understanding of tumor antigen expression and molecular mechanisms behind synovial sarcoma provide potential targets for treatment. Adoptive Cell Transfer using engineered T-cell receptors is in clinical trials for treatment of synovial sarcoma, specifically targeting New York esophageal squamous cell carcinoma-1 (NY-ESO-1), preferentially expressed antigen in melanoma (PRAME), and melanoma antigen-A4 (MAGE-A4). In this review, we explore the opportunities and challenges of these treatments. We also describe artificial adjuvant vector cells (aAVCs) and BRD9 inhibitors, two additional potential targets for treatment of advanced synovial sarcoma. This review demonstrates the progress that has been made in treatment of synovial sarcoma and highlights the future study and qualification needed to implement these technologies as standard of care.
Collapse
Affiliation(s)
- Joseph R. Fuchs
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, United States
| | - Brian C. Schulte
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jeffrey W. Fuchs
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, United States
| | - Mark Agulnik
- Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, United States,*Correspondence: Mark Agulnik,
| |
Collapse
|
14
|
Kapp KL, Arul AB, Zhang KC, Du L, Yende S, Kellum JA, Angus DC, Peck-Palmer OM, Robinson RAS. Proteomic changes associated with racial background and sepsis survival outcomes. Mol Omics 2022; 18:923-937. [PMID: 36097965 DOI: 10.1039/d2mo00171c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Intra-abdominal infection is a common cause of sepsis, and intra-abdominal sepsis leads to ∼156 000 U.S. deaths annually. African American/Black adults have higher incidence and mortality rates from sepsis compared to Non-Hispanic White adults. A limited number of studies have traced survival outcomes to molecular changes; however, these studies primarily only included Non-Hispanic White adults. Our goal is to better understand molecular changes that may contribute to differences in sepsis survival in African American/Black and Non-Hispanic White adults with primary intra-abdominal infection. We employed discovery-based plasma proteomics of patient samples from the Protocolized Care for Early Septic Shock (ProCESS) cohort (N = 107). We identified 49 proteins involved in the acute phase response and complement system whose expression levels are associated with both survival outcome and racial background. Additionally, 82 proteins differentially-expressed in survivors were specific to African American/Black or Non-Hispanic White patients, suggesting molecular-level heterogeneity in sepsis patients in key inflammatory pathways. A smaller, robust set of 19 proteins were in common in African American/Black and Non-Hispanic White survivors and may represent potential universal molecular changes in sepsis. Overall, this study identifies molecular factors that may contribute to differences in survival outcomes in African American/Black patients that are not fully explained by socioeconomic or other non-biological factors.
Collapse
Affiliation(s)
- Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA.,The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA.
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA
| | - Kevin C Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA
| | - Liping Du
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37203, USA.,Vanderbilt Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sachin Yende
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - John A Kellum
- Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Derek C Angus
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA
| | - Octavia M Peck-Palmer
- The Clinical Research, Investigation, and Systems Modeling of Acute Illnesses (CRISMA) Center, University of Pittsburgh, Pittsburgh, PA, 15213, USA.,Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.,Department of Clinical and Translational Science, University of Pittsburgh, PA, 15261, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, 5423 Stevenson Center, Nashville, TN, 37235, USA.,The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 32732, USA.
| |
Collapse
|
15
|
Vij S, Thakur R, Rishi P. Reverse engineering approach: a step towards a new era of vaccinology with special reference to Salmonella. Expert Rev Vaccines 2022; 21:1763-1785. [PMID: 36408592 DOI: 10.1080/14760584.2022.2148661] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Salmonella is responsible for causing enteric fever, septicemia, and gastroenteritis in humans. Due to high disease burden and emergence of multi- and extensively drug-resistant Salmonella strains, it is becoming difficult to treat the infection with existing battery of antibiotics as we are not able to discover newer antibiotics at the same pace at which the pathogens are acquiring resistance. Though vaccines against Salmonella are available commercially, they have limited efficacy. Advancements in genome sequencing technologies and immunoinformatics approaches have solved the problem significantly by giving rise to a new era of vaccine designing, i.e. 'Reverse engineering.' Reverse engineering/vaccinology has expedited the vaccine identification process. Using this approach, multiple potential proteins/epitopes can be identified and constructed as a single entity to tackle enteric fever. AREAS COVERED This review provides details of reverse engineering approach and discusses various protein and epitope-based vaccine candidates identified using this approach against typhoidal Salmonella. EXPERT OPINION Reverse engineering approach holds great promise for developing strategies to tackle the pathogen(s) by overcoming the limitations posed by existing vaccines. Progressive advancements in the arena of reverse vaccinology, structural biology, and systems biology combined with an improved understanding of host-pathogen interactions are essential components to design new-generation vaccines.
Collapse
Affiliation(s)
- Shania Vij
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Reena Thakur
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Praveen Rishi
- Department of Microbiology, Panjab University, Chandigarh, India
| |
Collapse
|
16
|
Immunological Control of HIV-1 Disease Progression by Rare Protective HLA Allele. J Virol 2022; 96:e0124822. [DOI: 10.1128/jvi.01248-22] [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
HLA-B57 is a relatively rare allele around world and the strongest protective HLA allele in Caucasians and African black individuals infected with HIV-1. Previous studies suggested that the advantage of this allele in HIV-1 disease progression is due to a strong functional ability of HLA-B57-restricted Gag-specific T cells and lower fitness of mutant viruses selected by the T cells.
Collapse
|
17
|
Birdshot Chorioretinopathy: A Review. J Clin Med 2022; 11:jcm11164772. [PMID: 36013011 PMCID: PMC9410532 DOI: 10.3390/jcm11164772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 01/26/2023] Open
Abstract
Birdshot chorioretinopathy (BSCR) is a bilateral chronic inflammation of the eye with no extraocular manifestations. BSCR affects middle-aged individuals from European descent and is strongly associated with the human leucocyte antigen (HLA)-A29 allele. The immune mechanisms involved are not fully understood, but recent advances have shown the role of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in disease pathogenesis. Multimodal imaging, including fluorescein angiography, indocyanine angiography, fundus autofluorescence, and optical coherence tomography, are useful in confirming the diagnosis and monitoring disease activity. Visual field testing is also important to assess the disease progression. To date, there is no consensus for optimal treatment regimen and duration. Local and systemic corticosteroids can be used for short periods, but immunosuppressive or biological therapies are usually needed for the long-term management of the disease. Here, we will review publications focused on birdshot chorioretinopathy to give an update on the pathophysiology, the multimodal imaging, and the treatment of the disease.
Collapse
|
18
|
Physical and in silico immunopeptidomic profiling of a cancer antigen prostatic acid phosphatase reveals targets enabling TCR isolation. Proc Natl Acad Sci U S A 2022; 119:e2203410119. [PMID: 35878026 PMCID: PMC9351518 DOI: 10.1073/pnas.2203410119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tissue-specific antigens can serve as targets for adoptive T cell transfer-based cancer immunotherapy. Recognition of tumor by T cells is mediated by interaction between peptide-major histocompatibility complexes (pMHCs) and T cell receptors (TCRs). Revealing the identity of peptides bound to MHC is critical in discovering cognate TCRs and predicting potential toxicity. We performed multimodal immunopeptidomic analyses for human prostatic acid phosphatase (PAP), a well-recognized tissue antigen. Three physical methods, including mild acid elution, coimmunoprecipitation, and secreted MHC precipitation, were used to capture a thorough signature of PAP on HLA-A*02:01. Eleven PAP peptides that are potentially A*02:01-restricted were identified, including five predicted strong binders by NetMHCpan 4.0. Peripheral blood mononuclear cells (PBMCs) from more than 20 healthy donors were screened with the PAP peptides. Seven cognate TCRs were isolated which can recognize three distinct epitopes when expressed in PBMCs. One TCR shows reactivity toward cell lines expressing both full-length PAP and HLA-A*02:01. Our results show that a combined multimodal immunopeptidomic approach is productive in revealing target peptides and defining the cloned TCR sequences reactive with prostatic acid phosphatase epitopes.
Collapse
|
19
|
Abstract
PURPOSE OF REVIEW To summarize the development of modified T-cell therapies in sarcomas and discuss relevant published and ongoing clinical trials to date. RECENT FINDINGS Numerous clinical trials are underway evaluating tumor-specific chimeric antigen receptor T cells and high affinity T-cell receptor (TCR)-transduced T cells in sarcomas. Notably, translocation-dependent synovial sarcoma and myxoid/round cell liposarcoma are the subject of several phase II trials evaluating TCRs targeting cancer testis antigens New York esophageal squamous cell carcinoma-1 (NY-ESO-1) and melanoma antigen-A4 (MAGE A4), and response rates of up to 60% have been observed for NY-ESO-1 directed, modified T cells in synovial sarcoma. Challenges posed by modified T-cell therapy include limitations conferred by HLA-restriction, non-immunogenic tumor microenvironments (TME), aggressive lymphodepletion and immune-mediated toxicities restricting coinfusion of cytokines. SUMMARY Cellular therapy to augment the adaptive immune response through delivery of modified T cells is an area of novel therapeutic development in sarcomas where a reliably expressed, ubiquitous target antigen can be identified. Therapeutic tools to improve the specificity, signaling, proliferation and persistence of modified TCRs and augment clinical responses through safe manipulation of the sarcoma TME will be necessary to harness the full potential of this approach.
Collapse
|
20
|
Maruthamuthu S, Rajalingam K, Kaur N, Morvan MG, Soto J, Lee N, Kong D, Hu Z, Reyes K, Ng D, Butte AJ, Chiu C, Rajalingam R. Individualized Constellation of Killer Cell Immunoglobulin-Like Receptors and Cognate HLA Class I Ligands that Controls Natural Killer Cell Antiviral Immunity Predisposes COVID-19. Front Genet 2022; 13:845474. [PMID: 35273641 PMCID: PMC8902362 DOI: 10.3389/fgene.2022.845474] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causes coronavirus disease-2019 (COVID-19) in some individuals, while the majority remain asymptomatic. Natural killer (NK) cells play an essential role in antiviral defense. NK cell maturation and function are regulated mainly by highly polymorphic killer cell immunoglobulin-like receptors (KIR) and cognate HLA class I ligands. Herein, we tested our hypothesis that the individualized KIR and HLA class I ligand combinations that control NK cell function determine the outcome of SARS-CoV-2 infection. Methods: We characterized KIR and HLA genes in 200 patients hospitalized for COVID-19 and 195 healthy general population controls. Results: The KIR3DL1+HLA-Bw4+ [Odds ratio (OR) = 0.65, p = 0.03] and KIR3DL2+HLA-A3/11+ (OR = 0.6, p = 0.02) combinations were encountered at significantly lower frequency in COVID-19 patients than in the controls. Notably, 40% of the patients lacked both of these KIR+HLA+ combinations compared to 24.6% of the controls (OR = 2.04, p = 0.001). Additionally, activating receptors KIR2DS1+KIR2DS5+ are more frequent in patients with severe COVID-19 than patients with mild disease (OR = 1.8, p = 0.05). Individuals carrying KIR2DS1+KIR2DS5+ genes but missing either KIR3DL1+HLA-Bw4+ combination (OR = 1.73, p = 0.04) or KIR3DL2+HLA-A3/11+ combination (OR = 1.75, p = 0.02) or both KIR3DL1+HLA-Bw4+ and KIR2DL2+HLA-A3/11+ combinations (OR = 1.63, p = 0.03) were more frequent in the COVID-19 cohort compared to controls. Conclusions: The absence of KIR3DL1+HLA-Bw4+ and KIR3DL2+HLA-A3/11+ combinations presumably yields inadequate NK cell maturation and reduces anti-SARS-CoV-2 defense, causing COVID-19. An increased frequency of KIR2DS1+KIR2DS5+ in severe COVID-19 patients suggests vigorous NK cell response triggered via these activating receptors and subsequent production of exuberant inflammatory cytokines responsible for severe COVID-19. Our results demonstrate that specific KIR-HLA combinations that control NK cell maturation and function are underlying immunogenetic variables that determine the dual role of NK cells in mediating beneficial antiviral and detrimental pathologic action. These findings offer a framework for developing potential host genetic biomarkers to distinguish individuals prone to COVID-19.
Collapse
Affiliation(s)
- Stalinraja Maruthamuthu
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Karan Rajalingam
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, United States
| | - Navchetan Kaur
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Maelig G Morvan
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Jair Soto
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Nancy Lee
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Denice Kong
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Zicheng Hu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Kevin Reyes
- UCSF-Abbott Viral Diagnostics and Discovery Center, Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States.,Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Dianna Ng
- Department of Pathology, University of California, San Francisco, San Francisco, CA, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States.,Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Charles Chiu
- UCSF-Abbott Viral Diagnostics and Discovery Center, Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States.,Department of Pathology, University of California, San Francisco, San Francisco, CA, United States.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| |
Collapse
|
21
|
Stasiak M, Zawadzka-Starczewska K, Lewiński A. Significance of HLA Haplotypes in Two Patients with Subacute Thyroiditis Triggered by mRNA-Based COVID-19 Vaccine. Vaccines (Basel) 2022; 10:280. [PMID: 35214738 PMCID: PMC8879821 DOI: 10.3390/vaccines10020280] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
Subacute thyroiditis (SAT) can be triggered by several viral factors in genetically predisposed individuals. In the case of COVID-19, SAT can be induced by SARS-CoV-2 infection as well as COVID-19 vaccination. The aim of this study was to present two cases of SAT triggered by mRNA-based COVID-19 vaccines, with special attention paid to the possible significance of HLA-related SAT susceptibility. In our patients, a strong similarity of HLA profiles with regard not only to SAT high-risk alleles but also to other SAT-unrelated ones was observed. The rare phenomenon of SAT occurrence after COVID-19 vaccination can be HLA-dependent and related to a co-presence of HLA-B*35:03 and -C*04:01. Taking into account the similarity of HLA profiles in both our patients, the co-presence of other alleles, such as HLA-A*03:01, -DQA1:01, DQB1*05:01 as well as some of HLA-DRB1, can also play a role. This hypothesis is strongly consistent with autoimmune/inflammatory syndrome induced by adjuvants (ASIA) being the postulated mechanism of this post-vaccine reaction, as ASIA-related immune reactions are directly associated with HLA-based genetic susceptibility. Further research is necessary to confirm these findings.
Collapse
Affiliation(s)
- Magdalena Stasiak
- Department of Endocrinology and Metabolic Diseases, Polish Mother’s Memorial Hospital—Research Institute, 281/289 Rzgowska St., 93-338 Lodz, Poland; (M.S.); (K.Z.-S.)
| | - Katarzyna Zawadzka-Starczewska
- Department of Endocrinology and Metabolic Diseases, Polish Mother’s Memorial Hospital—Research Institute, 281/289 Rzgowska St., 93-338 Lodz, Poland; (M.S.); (K.Z.-S.)
| | - Andrzej Lewiński
- Department of Endocrinology and Metabolic Diseases, Polish Mother’s Memorial Hospital—Research Institute, 281/289 Rzgowska St., 93-338 Lodz, Poland; (M.S.); (K.Z.-S.)
- Department of Endocrinology and Metabolic Diseases, Medical University of Lodz, 281/289 Rzgowska St., 93-338 Lodz, Poland
| |
Collapse
|
22
|
Turner TR, Hayward DR, Gymer AW, Barker DJ, Leen G, Cambridge CA, Macpherson HL, Georgiou X, Cooper MA, Lucas JAM, Nadeem D, Robinson J, Mayor NP, Marsh SGE. Widespread non‐coding polymorphism in
HLA
class
II
genes of International
HLA
and Immunogenetics Workshop cell lines. HLA 2022; 99:328-356. [DOI: 10.1111/tan.14571] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Thomas R. Turner
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | - Arthur W. Gymer
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | - Gayle Leen
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | | | | | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | | | | | - Daud Nadeem
- Anthony Nolan Research Institute, Royal Free Hospital London UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Neema P. Mayor
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| | - Steven G. E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital London UK
- UCL Cancer Institute, Royal Free Campus London UK
| |
Collapse
|
23
|
van Bentem K, Bos M, van der Keur C, Kapsenberg H, Lashley E, Eikmans M, van der Hoorn ML. Different immunoregulatory components at the decidua basalis of oocyte donation pregnancies. Hum Immunol 2021; 83:319-327. [PMID: 34785097 DOI: 10.1016/j.humimm.2021.10.008] [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: 08/05/2021] [Revised: 10/08/2021] [Accepted: 10/31/2021] [Indexed: 11/04/2022]
Abstract
Oocyte donation (OD) pregnancies are characterized by more fetal-maternal human leukocyte antigen (HLA) mismatches compared with naturally conceived (NC) and in vitro fertilization (IVF) pregnancies. The maternal immune system has to cope with greater immunogenetic dissimilarity, but involved immunoregulation remains poorly understood. We examined whether the amount of regulatory T cells (Tregs) and immunoregulatory cytokines in decidua basalis of OD pregnancies differs from NC and IVF pregnancies. The cohort included 25 OD, 11 IVF and 16 NC placentas, maternal peripheral blood, and umbilical cord blood of uncomplicated pregnancies. Placenta slides were stained for FOXP3, IL-10, IL-6, gal-1, TGF-β and Flt-1. Semi-quantitative (FOXP3+ Tregs) and computerized analysis (cytokines) were executed. The blood samples were typed for HLA class I and II to calculate fetal-maternal HLA mismatches. The percentage of Tregs was significantly higher in pregnancies with 4-6 HLA class I mismatches (n = 17), compared to 0-3 mismatches (n = 35; p = 0.04). Cytokine analysis showed significant differences between OD, IVF and NC pregnancies. Flt-1 was significantly lower in pregnancies with 4-6 HLA class I mismatches (p = 0.004), and in pregnancies with 6-10 HLA mismatches in total (p = 0.024). This study suggests that immunoregulation at the fetal-maternal interface in OD pregnancies with more fetal-maternal HLA mismatches is altered.
Collapse
Affiliation(s)
- Kim van Bentem
- Department of Obstetrics and Gynecology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
| | - Manon Bos
- Department of Obstetrics and Gynecology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands; Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Carin van der Keur
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Hanneke Kapsenberg
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Eileen Lashley
- Department of Obstetrics and Gynecology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Michael Eikmans
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Marie-Louise van der Hoorn
- Department of Obstetrics and Gynecology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| |
Collapse
|
24
|
Kloypan C, Koomdee N, Satapornpong P, Tempark T, Biswas M, Sukasem C. A Comprehensive Review of HLA and Severe Cutaneous Adverse Drug Reactions: Implication for Clinical Pharmacogenomics and Precision Medicine. Pharmaceuticals (Basel) 2021; 14:1077. [PMID: 34832859 PMCID: PMC8622011 DOI: 10.3390/ph14111077] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) encoded by the HLA gene is an important modulator for immune responses and drug hypersensitivity reactions as well. Genetic polymorphisms of HLA vary widely at population level and are responsible for developing severe cutaneous adverse drug reactions (SCARs) such as Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), drug reaction with eosinophilia and systemic symptoms (DRESS), maculopapular exanthema (MPE). The associations of different HLA alleles with the risk of drug induced SJS/TEN, DRESS and MPE are strongly supportive for clinical considerations. Prescribing guidelines generated by different national and international working groups for translation of HLA pharmacogenetics into clinical practice are underway and functional in many countries, including Thailand. Cutting edge genomic technologies may accelerate wider adoption of HLA screening in routine clinical settings. There are great opportunities and several challenges as well for effective implementation of HLA genotyping globally in routine clinical practice for the prevention of drug induced SCARs substantially, enforcing precision medicine initiatives.
Collapse
Affiliation(s)
- Chiraphat Kloypan
- Unit of Excellence in Integrative Molecular Biomedicine, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand;
- Division of Clinical Immunology and Transfusion Science, Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
| | - Patompong Satapornpong
- Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand;
- Excellence Pharmacogenomics and Precision Medicine Centre, College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand
| | - Therdpong Tempark
- Division of Dermatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Mohitosh Biswas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
- Department of Pharmacy, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
- The Thai Severe Cutaneous Adverse Drug Reaction THAI-SCAR Research-Genomics Thailand, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- The Preventive Genomics & Family Check-Up Services Center, Bumrungrad International Hospital, Pharmacogenomics and Precision Medicine Clinic, Bangkok 10110, Thailand
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3GL, UK
| |
Collapse
|
25
|
Chawla S, Chawla S. Comparative Analysis of Susceptibility and Severity of COVID-19 in Countries from the Eastern and the Western World Till March '21. Microbiol Insights 2021; 14:11786361211041367. [PMID: 34483666 PMCID: PMC8411631 DOI: 10.1177/11786361211041367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 07/27/2021] [Indexed: 11/24/2022] Open
Abstract
Majority of the world’s human population today is affected by Covid-19. The
disease has not only exhibited differences in susceptibility among people of
different countries, but also the mortality rate. In general, Western world has
been reporting a greater number of infected cases than eastern countries. Even
the mortality rates are quite high there. The aim of this study was to analyse
the data available on the infectivity and mortality rates of Covid-19 in
different countries till March’21 and then reviewed the literature to find
reasons for the differences in susceptibility and severity in eastern and
western countries. The reasons for the observed differences may be: (i) Eastern
countries followed stricter modalities and got grace period to create better
healthcare facilities to tackle COVID-19. This probably also slowed the
transmission of virus and its evolution, (ii) Vaccination policies in the east
may have provided some immunity due to cross reactivity, (iii) Frequent exposure
to infections at young age in eastern countries might be helping in better
immunity, (iv) Mutations in viral genome may be geography based and (v) Genetic
differences in the immune system of the hosts with respect to ACE receptors and
MHC may be playing an important role. In this article, an attempt has been made
to put forth and discuss these plausible reasons along with suitable evidences.
These findings may help in future research on the diagnosis, treatment and
prevention of Covid-19.
Collapse
Affiliation(s)
- Shashi Chawla
- Department of Microbiology, Gargi College, New Delhi, India
| | | |
Collapse
|
26
|
Kyobe S, Mwesigwa S, Kisitu GP, Farirai J, Katagirya E, Mirembe AN, Ketumile L, Wayengera M, Katabazi FA, Kigozi E, Wampande EM, Retshabile G, Mlotshwa BC, Williams L, Morapedi K, Kasvosve I, Kyosiimire-Lugemwa J, Nsangi B, Tsimako-Johnstone M, Brown CW, Joloba M, Anabwani G, Bhekumusa L, Mpoloka SW, Mardon G, Matshaba M, Kekitiinwa A, Hanchard NA. Exome Sequencing Reveals a Putative Role for HLA-C*03:02 in Control of HIV-1 in African Pediatric Populations. Front Genet 2021; 12:720213. [PMID: 34512729 PMCID: PMC8428176 DOI: 10.3389/fgene.2021.720213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022] Open
Abstract
Human leucocyte antigen (HLA) class I molecules present endogenously processed antigens to T-cells and have been linked to differences in HIV-1 disease progression. HLA allelotypes show considerable geographical and inter-individual variation, as does the rate of progression of HIV-1 disease, with long-term non-progression (LTNP) of disease having most evidence of an underlying genetic contribution. However, most genetic analyses of LTNP have occurred in adults of European ancestry, limiting the potential transferability of observed associations to diverse populations who carry the burden of disease. This is particularly true of HIV-1 infected children. Here, using exome sequencing (ES) to infer HLA allelotypes, we determine associations with HIV-1 LTNP in two diverse African pediatric populations. We performed a case-control association study of 394 LTNPs and 420 rapid progressors retrospectively identified from electronic medical records of pediatric HIV-1 populations in Uganda and Botswana. We utilized high-depth ES to perform high-resolution HLA allelotyping and assessed evidence of association between HLA class I alleles and LTNP. Sixteen HLA alleles and haplotypes had significantly different frequencies between Uganda and Botswana, with allelic differences being more prominent in HLA-A compared to HLA-B and C allelotypes. Three HLA allelotypes showed association with LTNP, including a novel association in HLA-C (HLA-B∗57:03, aOR 3.21, Pc = 0.0259; B∗58:01, aOR 1.89, Pc = 0.033; C∗03:02, aOR 4.74, Pc = 0.033). Together, these alleles convey an estimated population attributable risk (PAR) of non-progression of 16.5%. We also observed novel haplotype associations with HLA-B∗57:03-C∗07:01 (aOR 5.40, Pc = 0.025) and HLA-B∗58:01-C∗03:02 (aOR 4.88, Pc = 0.011) with a PAR of 9.8%, as well as a previously unreported independent additive effect and heterozygote advantage of HLA-C∗03:02 with B∗58:01 (aOR 4.15, Pc = 0.005) that appears to limit disease progression, despite weak LD (r 2 = 0.18) between these alleles. These associations remained irrespective of gender or country. In one of the largest studies of HIV in Africa, we find evidence of a protective effect of canonical HLA-B alleles and a novel HLA-C association that appears to augment existing HIV-1 control alleles in pediatric populations. Our findings outline the value of using multi-ethnic populations in genetic studies and offer a novel HIV-1 association of relevance to ongoing vaccine studies.
Collapse
Affiliation(s)
- Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Grace P. Kisitu
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | - John Farirai
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Lesego Ketumile
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Edward M. Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C. Mlotshwa
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Morapedi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Betty Nsangi
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
| | | | - Chester W. Brown
- University of Tennessee Health Science Center, Memphis, TN, United States
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
| | - Lukhele Bhekumusa
- Eswatini - Baylor College of Medicine Children’s Foundation, Mbabane, Eswatini
| | - Sununguko W. Mpoloka
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Centre of Excellence, Gaborone, Botswana
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Adeodata Kekitiinwa
- Baylor College of Medicine Children’s Foundation, Kampala, Uganda
- Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
27
|
Immunoinformatics aided design of peptide-based vaccines against ebolaviruses. VITAMINS AND HORMONES 2021; 117:157-187. [PMID: 34420579 DOI: 10.1016/bs.vh.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ebolaviruses are at the forefront of emerging viruses and present a very perceptible threat to global peace and harmony. In the last decade, Ebola virus disease has claimed more than 90% of total lives since its inception in 1976. Owing to multiple host immune evasion methods employed by the virus and the limitations of traditional vaccine development approaches, finding a globally effective and reliable counter measure against Ebola virus remains a challenge. Highly conserved peptide fragments belonging to critical viral proteins and containing multiple epitopes which have the capacity to interact with a wide array of HLA molecules present a viable solution. Immunoinformatics or computational immunology enables rapid screening and shortlisting of plausible epitopes with a high immunogenic potential, thus, supporting expeditious elucidation of efficacious vaccine candidates. In light of above facts, we describe a computational methodology in this chapter for identification of potent peptide vaccine candidates against human infecting viruses. By applying this stringent methodology, we were able to identify multiple, immunogenic ebolavirus peptide fragments which, after verification in animal models, might be considered as part of future synthetic Ebola vaccine.
Collapse
|
28
|
Hernández-Doño S, Jakez-Ocampo J, Márquez-García JE, Ruiz D, Acuña-Alonzo V, Lima G, Llorente L, Tovar-Méndez VH, García-Silva R, Granados J, Zúñiga J, Vargas-Alarcón G. Heterogeneity of Genetic Admixture Determines SLE Susceptibility in Mexican. Front Genet 2021; 12:701373. [PMID: 34413879 PMCID: PMC8369992 DOI: 10.3389/fgene.2021.701373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune inflammatory disorder for which Major Histocompatibility Complex (MHC) genes are well identified as risk factors. SLE patients present different clinical phenotypes, which are partly explained by admixture patterns variation among Mexicans. Population genetic has insight into the high genetic variability of Mexicans, mainly described through HLA gene studies with anthropological and biomedical importance. A prospective, case-control study was performed. In this study, we recruited 146 SLE patients, and 234 healthy individuals were included as a control group; both groups were admixed Mexicans from Mexico City. The HLA typing methods were based on Next Generation Sequencing and Sequence-Based Typing (SBT). The data analysis was performed with population genetic programs and statistical packages. The admixture estimations based on HLA-B and -DRB1 revealed that SLE patients have a higher Southwestern European ancestry proportion (48 ± 8%) than healthy individuals (30 ± 7%). In contrast, Mexican Native American components are diminished in SLE patients (44 ± 1%) and augmented in Healthy individuals (63 ± 4%). HLA alleles and haplotypes' frequency analysis found variants previously described in SLE patients from Mexico City. Moreover, a conserved extended haplotype that confers risk to develop SLE was found, the HLA-A∗29:02∼C∗16:01∼B∗44:03∼DRB1∗07:01∼DQB1∗02:02, pC = 0.02, OR = 1.41. Consistent with the admixture estimations, the origin of all risk alleles and haplotypes found in this study are European, while the protection alleles are Mexican Native American. The analysis of genetic distances supported that the SLE patient group is closer to the Southwestern European parental populace and farthest from Mexican Native Americans than healthy individuals. Heterogeneity of genetic admixture determines SLE susceptibility and protection in Mexicans. HLA sequencing is helpful to determine susceptibility alleles and haplotypes restricted to some populations.
Collapse
Affiliation(s)
- Susana Hernández-Doño
- Immunogenetics Division, Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Juan Jakez-Ocampo
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Eduardo Márquez-García
- Molecular Biology Core Facility, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Daniela Ruiz
- Department of Dermatology, Hospital General Dr. Manuel Gea González, Mexico City, Mexico
| | - Víctor Acuña-Alonzo
- Laboratory of Physiology, Biochemistry, and Genetics, Escuela Nacional de Antropología e Historia, Mexico City, Mexico
| | - Guadalupe Lima
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Luis Llorente
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Víctor Hugo Tovar-Méndez
- Department of Endocrinology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Rafael García-Silva
- Department of Internal Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julio Granados
- Immunogenetics Division, Department of Transplant, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | | |
Collapse
|
29
|
Ishii M, Ando J, Yamazaki S, Toyota T, Ohara K, Furukawa Y, Suehara Y, Nakanishi M, Nakashima K, Ohshima K, Nakauchi H, Ando M. iPSC-Derived Neoantigen-Specific CTL Therapy for Ewing Sarcoma. Cancer Immunol Res 2021; 9:1175-1186. [PMID: 34385178 DOI: 10.1158/2326-6066.cir-21-0193] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/22/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022]
Abstract
The prognosis of Ewing sarcoma caused by EWS/FLI1 fusion is poor, especially after metastasis. Although therapy with CTLs targeted against altered EWS/FLI1 sequences at the gene break/fusion site may be effective, CTLs generated from peripheral blood are often exhausted because of continuous exposure to tumor antigens. We addressed this by generating induced pluripotent stem cell (iPSC)-derived functionally rejuvenated CTLs (rejT) directed against the neoantigen encoded by the EWS/FLI1 fusion gene. In this study, we examined the antitumor effects of EWS/FLI1-rejTs against Ewing sarcoma. The altered amino acid sequence at the break/fusion point of EWS/FLI1, when presented as a neoantigen, evokes an immune response that targets EWS/FLI1 + sarcoma. Although the frequency of generated EWS/FLI1-specific CTLs was only 0.003%, we successfully established CTL clones from a healthy donor. We established iPSCs from a EWS/FLI1-specific CTL clone and redifferentiated them into EWS/FLI1-specific rejTs. To evaluate cytotoxicity, we cocultured EWS/FLI1-rejTs with Ewing sarcoma cell lines. EWS/FLI1-rejTs rapidly and continuously suppressed the proliferation of Ewing sarcoma for >40 hours. Using a Ewing sarcoma xenograft mouse model, we verified the antitumor effect of EWS/FLI1-rejTs via imaging, and EWS/FLI1-rejTs conferred a statistically significant survival advantage. "Off-the-shelf" therapy is less destructive and disruptive than chemotherapy, and radiation is always desirable, particularly in adolescents, whom Ewing sarcoma most often affects. Thus, EWS/FLI1-rejTs targeting a Ewing sarcoma neoantigen could be a promising new therapeutic tool.
Collapse
Affiliation(s)
- Midori Ishii
- Department of Hematology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Orthopaedic Surgery, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Jun Ando
- Department of Hematology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
- Department of Blood Transfusion Medicine and Stem Cell Regulation, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Satoshi Yamazaki
- Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
- Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tokuko Toyota
- Department of Hematology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Kazuo Ohara
- Department of Hematology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Yoshiki Furukawa
- Department of Hematology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Yoshiyuki Suehara
- Department of Orthopaedic Surgery, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Mahito Nakanishi
- TOKIWA-Bio, Inc., Tsukuba Center Inc. (TCI), Tsukuba, Ibaraki, Japan
| | - Kazutaka Nakashima
- Department of Pathology, School of Medicine, Kurume University, Kurume City, Fukuoka, Japan
| | - Koichi Ohshima
- Department of Pathology, School of Medicine, Kurume University, Kurume City, Fukuoka, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, School of Medicine, Stanford, California
| | - Miki Ando
- Department of Hematology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan.
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| |
Collapse
|
30
|
Kolou M, Poda A, Diallo Z, Konou E, Dokpomiwa T, Zoungrana J, Salou M, Mba-Tchounga L, Bigot A, Ouedraogo AS, Bouyout-Akoutet M, Ekouevi DK, Eholie SP. Prevalence of human leukocyte antigen HLA-B*57:01 in individuals with HIV in West and Central Africa. BMC Immunol 2021; 22:48. [PMID: 34294032 PMCID: PMC8299582 DOI: 10.1186/s12865-021-00427-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 05/11/2021] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The presence of the human leukocyte antigen HLA-B*57:01 is associated with the development of a hypersensitivity reaction to abacavir (ABC). Limited data exist on HLA-B*57:01 prevalence in individuals with HIV-1 in Africa. This study aimed to estimate HLA-B*57:01 prevalence in individuals with HIV-1 in West and Central Africa. METHODS A cross-sectional study was conducted in four countries in West and central Africa (Burkina-Faso, Côte d'Ivoire, Gabon, and Togo) from January 2016 to February 2020 to determine the status of HLA-B*57:01 in adults with HIV-1. The presence of HLA-B*57:01 was determined by using Single Specific Primer-Polymerase Chain Reaction (SSP-PCR) in blood samples. Prevalence rates were stratified based on country. RESULTS A total of 4016 (69.8% women) individuals with HIV were enrolled. Their median age was 45, and the interquartile range was 38-52. We included 500 (12.4%) patients in Burkina-Faso, 1453 (36.2%) in Côte d'Ivoire, 951 (23.7%) in Gabon, and 1112 (27.7%) in Togo. The overall HLA-B*57:01 prevalence was 0.1% [95% CI: 0.0-0.2%]. The prevalence of HLA-B*57:01 was similar according to the four countries. Only one case was reported in each country except Togo, with no cases. CONCLUSIONS HLA-B*57:01 prevalence is low in individuals with HIV in West and central Africa, and there is no difference among countries. This study does not confirm the utility of HLA-B*57:01 allele testing for abacavir use in this region.
Collapse
Affiliation(s)
- Malewe Kolou
- Laboratoire de Biologie Moléculaire et d'Immunologie (BIOLIM), Université de Lomé, Faculté des Sciences de la santé, Lomé, Togo
| | - Armel Poda
- Department of Infectious Diseases, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Zelica Diallo
- Département de Dermatologie et Maladies Infectieuses, Université Félix Houphouët-Boigny, UFR des Sciences Médicales, Abidjan, Côte d'Ivoire
| | - Esther Konou
- Laboratoire de Biologie Moléculaire et d'Immunologie (BIOLIM), Université de Lomé, Faculté des Sciences de la santé, Lomé, Togo
| | - Tatiana Dokpomiwa
- Department of Pharmacy, Faculty of Health Science, University of Abomey-Calavi, Cotonou, Benin
| | - Jacques Zoungrana
- Department of Infectious Diseases, Université Nazi Boni, Bobo-Dioulasso, Burkina Faso
| | - Mounerou Salou
- Laboratoire de Biologie Moléculaire et d'Immunologie (BIOLIM), Université de Lomé, Faculté des Sciences de la santé, Lomé, Togo
| | - Lionèle Mba-Tchounga
- Programme PACCI, Site de recherche ANRS de Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - André Bigot
- Department of Pharmacy, Faculty of Health Science, University of Abomey-Calavi, Cotonou, Benin
| | - Abdoul-Salam Ouedraogo
- Department of Medical Bacteriology and Virology, Université Nazi BONI, CHU Souro Sanou, Bobo-Dioulasso, Burkina Faso
| | - Marielle Bouyout-Akoutet
- Department of Parasitology, Mycology and Tropical Medicine, Université des Sciences de la Santé, Libreville, Gabon
| | - Didier K Ekouevi
- Département de santé Publique, Université de Lomé, Faculté des Sciences de la santé, Lomé, Togo.
- Centre Inserm 1219 & Institut de Santé Publique d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.
| | - Serge P Eholie
- Département de Dermatologie et Maladies Infectieuses, Université Félix Houphouët-Boigny, UFR des Sciences Médicales, Abidjan, Côte d'Ivoire
| |
Collapse
|
31
|
CONNOLLY S, CARLSON JM, SCHAEFER M, BERE A, KILEMBE W, ALLEN S, HUNTER E. HLA-associated preadaptation in HIV Vif is associated with higher set point viral load and faster CD4+ decline in Zambian transmission pairs. AIDS 2021; 35:1157-1165. [PMID: 33710015 PMCID: PMC8546905 DOI: 10.1097/qad.0000000000002868] [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] [Indexed: 11/27/2022]
Abstract
OBJECTIVE S We investigated the relationship between human leukocyte antigen (HLA)-associated preadaptation for the entire subtype C HIV-1 proteome of the transmitted founder virus and subsequent HIV-1 disease progression in a cohort of heterosexual linked transmission pairs in Zambia. DESIGN An adaptation model was used to calculate an adaptation score for each virus-HLA combination in order to quantify the degree of preadaptation of the transmitted virus to the linked recipient's HLA alleles. These scores were then assessed for their relationship to viral load and longitudinal CD4+ decline in the recipient. METHODS Viral RNA was extracted from the plasma of the donor partner and the linked recipient near the time of transmission, as well as longitudinally from the linked recipient. Viral adaptation scores were calculated for each individual and each protein in the subtype C HIV-1 proteome. RESULTS The majority of HLA-associated sites were located in Gag, Pol and Nef; however, proportional to protein length, the accessory and regulatory proteins contained a relatively high proportion of HLA-associated sites. Over the course of infection, HLA-mediated immune adaptation increased for all proteins except Vpu and gp120. Preadaptation was positively associated with higher early set point viral load and faster CD4+ decline. When examined by protein, preadaptation in Pol and Vif were statistically significantly associated with these markers of disease progression. CONCLUSION Adaptation in Pol had the greatest impact on viral control. Despite containing a large proportion of HLA-associated sites, Vif was the only regulatory or accessory protein for which preadaptation significantly correlated with disease progression.
Collapse
Affiliation(s)
- Sarah CONNOLLY
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
| | | | - Malinda SCHAEFER
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
| | - Alfred BERE
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
| | | | - Susan ALLEN
- Zambia–Emory HIV Research Project, Lusaka, Zambia
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
| | - Eric HUNTER
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329
- Zambia–Emory HIV Research Project, Lusaka, Zambia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
| |
Collapse
|
32
|
Sukasem C, Sririttha S, Chaichan C, Nakkrut T, Satapornpong P, Jaruthamsophon K, Jantararoungtong T, Koomdee N, Medhasi S, Oo-Puthinan S, Rerkpattanapipat T, Klaewsongkram J, Rerknimitr P, Tuchinda P, Chularojanamontri L, Tovanabutra N, Suvannang N, Rungrotmongkol T, Saokaew S, Aekplakorn W, Puangpetch A. Spectrum of cutaneous adverse reactions to aromatic antiepileptic drugs and human leukocyte antigen genotypes in Thai patients and meta-analysis. THE PHARMACOGENOMICS JOURNAL 2021; 21:682-690. [PMID: 34175889 PMCID: PMC8602035 DOI: 10.1038/s41397-021-00247-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/23/2021] [Accepted: 06/14/2021] [Indexed: 11/09/2022]
Abstract
Aromatic antiepileptic drugs (AEDs)-induced cutaneous adverse drug reactions (cADRs) add up to the limited use of the AEDs in the treatment and prevention of seizures. Human leukocyte antigen-B (HLA-B) alleles have been linked to AEDs-induced cADRs. We investigated the association between cADRs (including Stevens-Johnson syndrome; SJS/toxic epidermal necrolysis; TEN, drug reaction with eosinophilia and systemic symptoms; DRESS, and Maculopapular eruption; MPE) caused by AEDs (phenytoin, carbamazepine, lamotrigine, phenobarbital and oxcarbazepine) and HLA-B alleles in Thai population. Through the case-control study, 166 patients with AEDs-induced cADRs, 426 AEDs-tolerant patients (AEDs-tolerant controls), and 470 healthy subjects (Thai population) were collected. The HLA genotypes were detected using the polymerase chain reaction-sequence specific oligonucleotide probe (PCR-SSOP) method. We also performed a meta-analysis with these data and other populations. The carrier rate of HLA-B*15:02 was significantly different between AEDs-induced cADRs group and AEDs-tolerant group (Odds ratio; OR 4.28, 95% Confidence interval; CI 2.64-6.95, p < 0.001), AEDs-induced cADRs group and Thai population (OR 2.15, 95%CI 1.41-3.29, p < 0.001). In meta-analysis showed the strong association HLA-B*15:02 with AEDs-induced cADRs (OR 4.77, 95%CI 1.79-12.73, p < 0.001). Furthermore, HLA-B*15:02 was associated with SJS/TEN induced by AEDs (OR 10.28, 95%CI 6.50-16.28, p < 0.001) Phenytoin (OR 4.12, 95%CI 1.77-9.59, p = 0.001) and carbamazepine (OR 137.69, 95%CI 50.97-371.98, p < 0.001). This study demonstrated that genetic association for AEDs-induced cADRs was phenotype-specific. A strong association between HLA-B*15:02 and AEDs-induced SJS/TEN was demonstrated with an OR of 10.79 (95%CI 5.50-21.16, p < 0.001) when compared with AEDs-tolerant group. On the other hand, the carrier rates of HLA-B*08:01, HLA-B*13:01, and HLA-B*56:02 were significantly higher in the DRESS group compared with the AEDs-tolerant group (p = 0.029, 0.007, and 0.017, respectively). The HLA-B*15:02 allele may represent a risk factor for AEDs-induced cADRs.
Collapse
Affiliation(s)
- Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand. .,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand. .,The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand. .,Pharmacogenomics and Precision Medicine, The Preventive Genomics & Family Check-up Services Center, Bumrungrad International Hospital, Bangkok, Thailand.
| | - Suthida Sririttha
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Department of Clinical Pharmacy Practice, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Chonlawat Chaichan
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Department of Pathology, School of medicine, University of Phayao, Phayao, Thailand
| | - Thapanat Nakkrut
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand.,Department of Pharmacy, Neurological Institute of Thailand, Bangkok, Thailand
| | - Patompong Satapornpong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani, Thailand
| | - Kanoot Jaruthamsophon
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkla, Thailand
| | - Thawinee Jantararoungtong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Sadeep Medhasi
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sarawut Oo-Puthinan
- Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand
| | - Ticha Rerkpattanapipat
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand.,Division of Allergy Immunology and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Jettanong Klaewsongkram
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand.,Skin and Allergy Research Unit, Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pawinee Rerknimitr
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand.,Division of Dermatology, Department of Medicine, Faculty of Medicine, Skin and Allergy Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Papapit Tuchinda
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand.,Department of Dermatology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Leena Chularojanamontri
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand.,Department of Dermatology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Napatra Tovanabutra
- The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) research group, Bangkok, Thailand.,Division of Dermatology, Department of Internal Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science and Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Surasak Saokaew
- Division of Pharmacy Practice, Department of Pharmaceutical Care, School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand.,Center of Health Outcomes Research and Therapeutic Safety (Cohorts), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand.,Unit of Excellence on Clinical Outcomes Research and IntegratioN (UNICORN), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Wichai Aekplakorn
- Department of Community Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Apichaya Puangpetch
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| |
Collapse
|
33
|
Mitchell G, Pollack SM, Wagner MJ. Targeting cancer testis antigens in synovial sarcoma. J Immunother Cancer 2021; 9:jitc-2020-002072. [PMID: 34083416 PMCID: PMC8183285 DOI: 10.1136/jitc-2020-002072] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 02/02/2023] Open
Abstract
Synovial sarcoma (SS) is a rare cancer that disproportionately affects children and young adults. Cancer testis antigens (CTAs) are proteins that are expressed early in embryonic development, but generally not expressed in normal tissue. They are aberrantly expressed in many different cancer types and are an attractive therapeutic target for immunotherapies. CTAs are expressed at high levels in SS. This high level of CTA expression makes SS an ideal cancer for treatment strategies aimed at harnessing the immune system to recognize aberrant CTA expression and fight against the cancer. Pivotal clinical trials are now underway, with the potential to dramatically alter the landscape of SS management and treatment from current standards of care. In this review, we describe the rationale for targeting CTAs in SS with a focus on NY-ESO-1 and MAGE-A4, the current state of vaccine and T-cell receptor-based therapies, and consider emerging opportunities for future development.
Collapse
Affiliation(s)
| | - Seth M Pollack
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Oncology, University of Washington, Seattle, Washington, USA.,Lurie Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Michael J Wagner
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA .,Oncology, University of Washington, Seattle, Washington, USA
| |
Collapse
|
34
|
Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
Collapse
Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| |
Collapse
|
35
|
Kouo T, Chaisawangwong W. SARS-CoV-2 as a superantigen in multisystem inflammatory syndrome in children. J Clin Invest 2021; 131:149327. [PMID: 33844652 DOI: 10.1172/jci149327] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a rare but deadly new disease in children that rapidly progresses to hyperinflammation and shock, and can lead to multiple organ failure if unrecognized. It has been found to be temporally associated with the COVID-19 pandemic and is often associated with SARS-CoV-2 exposure in children. In this issue of the JCI, Porritt, Paschold, et al. identify restricted T cell receptor (TCR) β-chain variable domain (Vβ) usage in patients with severe MIS-C, indicating a potential role for SARS-CoV-2 as a superantigen. These findings suggest that a blood test that determines the presence of specific TCRβ variable gene (TRBV) segments may identify patients at risk for severe MIS-C.
Collapse
Affiliation(s)
- Theodore Kouo
- Department of Pediatrics, Division of Pediatric Emergency Medicine, and
| | - Worarat Chaisawangwong
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
36
|
Immel A, Key FM, Szolek A, Barquera R, Robinson MK, Harrison GF, Palmer WH, Spyrou MA, Susat J, Krause-Kyora B, Bos KI, Forrest S, Hernández-Zaragoza DI, Sauter J, Solloch U, Schmidt AH, Schuenemann VJ, Reiter E, Kairies MS, Weiß R, Arnold S, Wahl J, Hollenbach JA, Kohlbacher O, Herbig A, Norman PJ, Krause J. Analysis of genomic DNA from medieval plague victims suggests long-term effect of Yersinia pestis on human immunity genes. Mol Biol Evol 2021; 38:4059-4076. [PMID: 34002224 PMCID: PMC8476174 DOI: 10.1093/molbev/msab147] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggests that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.
Collapse
Affiliation(s)
- Alexander Immel
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - András Szolek
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Rodrigo Barquera
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Madeline K Robinson
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Genelle F Harrison
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - William H Palmer
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Maria A Spyrou
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105 Kiel, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Stephen Forrest
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Diana I Hernández-Zaragoza
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | | | | | | | - Verena J Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Madita S Kairies
- Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Rainer Weiß
- State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Susanne Arnold
- State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Joachim Wahl
- Institute for Archaeological Sciences, WG Palaeoanthropology, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,State Office for Cultural Heritage Management, Stuttgart Regional Council, Berliner Strasse 12, 73728 Esslingen, Germany
| | - Jill A Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, USA
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. for Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany.,Translational Bioinformatics, University Hospital Tübingen, Sand 14, 72076 Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology & Microbiology, University of Colorado, CO 80045, USA
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany.,Institute of Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany.,Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| |
Collapse
|
37
|
Lemin AJ, Foster L. HLA-DPB1 allele frequencies in the West Midlands region of the United Kingdom: A critical evaluation against the common, intermediate and well-documented allele catalogues CWD 2.0.0, EFI CWD and CIWD 3.0.0. HLA 2021; 98:5-13. [PMID: 33934529 DOI: 10.1111/tan.14291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/27/2021] [Indexed: 01/08/2023]
Abstract
The Birmingham H&I laboratory performed HLA typing on 456 potential deceased solid organ donors in the UK between 2014 and 2016. Accurate DPB1 typing is essential for determining HLA compatibility in transplantation, thus we report HLA-DPB1 for potential deceased solid organ donors. To correctly interpret HLA typing data, laboratories must understand both international and local HLA allele frequencies. In this analysis, we determined HLA-DPB1 allele and genotype frequencies for these 456 donors. HLA-DPB1 diversity was evaluated against the common and well-documented (CWD) alleles 2.0.0 catalogue, the European Federation for Immunogenetics (EFI) CWD catalogue and the common, intermediate and well-documented (CIWD) 3.0.0 catalogue. Additionally, we determined which alleles are common in our local deceased donor population. We observed 27 HLA-DPB1 alleles with DPB1*04:01 being the most frequently observed (allele frequency = 0.4342). All alleles detected locally were present in CIWD 3.0.0, however, DPB1*124:01 and *135:01 were not present in CWD 2.0.0 and DPB1*104:01 and *135:01 were not present in EFI CWD. Twenty of 27 DPB1 alleles identified were defined as locally common and also listed as common in CIWD 3.0.0 representing 62.5% of common alleles in the subset of CIWD 3.0.0 from individuals of a European geographic, ancestral or ethnic background. The alleles HLA-DPB1*16:01 and *20:01 are locally common but not listed as common in EFI CWD and DPB1*104:01 is not listed as common in CWD 2.0.0 catalogue. Our analysis showed that the detected alleles and locally common alleles within our population were aligned with the CIWD 3.0.0 catalogue.
Collapse
Affiliation(s)
- Andrew James Lemin
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, Birmingham, UK
| | - Luke Foster
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, Birmingham, UK
| |
Collapse
|
38
|
Satapornpong P, Pratoomwun J, Rerknimitr P, Klaewsongkram J, Nakkam N, Rungrotmongkol T, Konyoung P, Saksit N, Mahakkanukrauh A, Amornpinyo W, Khunarkornsiri U, Tempark T, Wantavornprasert K, Jinda P, Koomdee N, Jantararoungtong T, Rerkpattanapipat T, Wang CW, Naisbitt D, Tassaneeyakul W, Ariyachaipanich M, Roonghiranwat T, Pirmohamed M, Chung WH, Sukasem C. HLA-B*13 :01 Is a Predictive Marker of Dapsone-Induced Severe Cutaneous Adverse Reactions in Thai Patients. Front Immunol 2021; 12:661135. [PMID: 34017337 PMCID: PMC8130671 DOI: 10.3389/fimmu.2021.661135] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/13/2021] [Indexed: 01/25/2023] Open
Abstract
HLA-B*13:01 allele has been identified as the genetic determinant of dapsone hypersensitivity syndrome (DHS) among leprosy and non-leprosy patients in several studies. Dapsone hydroxylamine (DDS-NHOH), an active metabolite of dapsone, has been believed to be responsible for DHS. However, studies have not highlighted the importance of other genetic polymorphisms in dapsone-induced severe cutaneous adverse reactions (SCAR). We investigated the association of HLA alleles and cytochrome P450 (CYP) alleles with dapsone-induced SCAR in Thai non-leprosy patients. A prospective cohort study, 16 Thai patients of dapsone-induced SCARs (5 SJS-TEN and 11 DRESS) and 9 Taiwanese patients of dapsone-induced SCARs (2 SJS-TEN and 7 DRESS), 40 dapsone-tolerant controls, and 470 general Thai population were enrolled. HLA class I and II alleles were genotyped using polymerase chain reaction-sequence specific oligonucleotides (PCR-SSOs). CYP2C9, CYP2C19, and CYP3A4 genotypes were determined by the TaqMan real-time PCR assay. We performed computational analyses of dapsone and DDS-NHOH interacting with HLA-B*13:01 and HLA-B*13:02 alleles by the molecular docking approach. Among all the HLA alleles, only HLA-B*13:01 allele was found to be significantly associated with dapsone-induced SCARs (OR = 39.00, 95% CI = 7.67–198.21, p = 5.3447 × 10−7), SJS-TEN (OR = 36.00, 95% CI = 3.19–405.89, p = 2.1657 × 10−3), and DRESS (OR = 40.50, 95% CI = 6.38–257.03, p = 1.0784 × 10−5) as compared to dapsone-tolerant controls. Also, HLA-B*13:01 allele was strongly associated with dapsone-induced SCARs in Asians (OR = 36.00, 95% CI = 8.67–149.52, p = 2.8068 × 10−7) and Taiwanese (OR = 31.50, 95% CI = 4.80–206.56, p = 2.5519 × 10−3). Furthermore, dapsone and DDS-NHOH fit within the extra-deep sub pocket of the antigen-binding site of the HLA-B*13:01 allele and change the antigen-recognition site. However, there was no significant association between genetic polymorphism of cytochrome P450 (CYP2C9, CYP2C19, and CYP3A4) and dapsone-induced SCARs (SJS-TEN and DRESS). The results of this study support the specific genotyping of the HLA-B*13:01 allele to avoid dapsone-induced SCARs including SJS-TEN and DRESS before initiating dapsone therapy in the Asian population.
Collapse
Affiliation(s)
- Patompong Satapornpong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani, Thailand
| | - Jirawat Pratoomwun
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,Department of Clinical Chemistry, Faculty of Medical Technology, Huachiew Chalermprakiet University, Samut Prakan, Thailand
| | - Pawinee Rerknimitr
- The Skin and Allergy Research Unit, Chulalongkorn University, Bangkok, Thailand.,Division of Dermatology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jettanong Klaewsongkram
- The Skin and Allergy Research Unit, Chulalongkorn University, Bangkok, Thailand.,Division of Allergy and Clinical Immunology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Nontaya Nakkam
- Department of Pharmacology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Program in Bioinformatics and Computational Biology, Graduated School, Chulalongkorn University, Bangkok, Thailand
| | | | - Niwat Saksit
- Unit of Excellence on Pharmacogenomic Pharmacokinetic and Pharmacotherapeutic Researches (UPPER), School of Pharmaceutical Sciences, University of Phayao, Phayao, Thailand
| | - Ajanee Mahakkanukrauh
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Warayuwadee Amornpinyo
- Division of Dermatology, Department of Internal Medicine, Khon Kaen Hospital, Khon Kaen, Thailand
| | | | - Therdpong Tempark
- Division of Dermatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Pimonpan Jinda
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Thawinee Jantararoungtong
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Ticha Rerkpattanapipat
- Division of Allergy Immunology and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chuang-Wei Wang
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital (CGMH), Taipei, Taiwan.,Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China
| | - Dean Naisbitt
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | | | | | | | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, United Kingdom
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital (CGMH), Taipei, Taiwan.,Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen, China.,Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.,The Thai Severe Cutaneous Adverse Drug Reaction (THAI-SCAR) Research Group, Bangkok, Thailand
| |
Collapse
|
39
|
Abacavir adverse reactions related with HLA-B*57: 01 haplotype in a large cohort of patients infected with HIV. Pharmacogenet Genomics 2021; 30:167-174. [PMID: 32453265 DOI: 10.1097/fpc.0000000000000409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Carriage of human leukocyte antigen (HLA)-B*57:01 allele increases the risk of abacavir hypersensitivity reaction. Therefore, since 2008 HIV treatment guidelines recommend HLA-B*57:01 screening before abacavir administration, greatly reducing hypersensitivity reaction rate. However, clinically suspected abacavir-related hypersensitivity reactions are described in allele non-carriers. Major aim of this study was to evaluate the relationship between HLA-B*57:01 pattern and abacavir-related hypersensitivity reaction, focusing on hypersensitivity reaction prevalence in allele non-carriers. METHODS We included all outpatients aged >18 years old with HIV infection and known HLA-B*57:01 pattern, followed at our Department from January 2000 until December 2017. Patients were divided according to HLA-B*57:01 pattern and first antiretroviral treatment prescribed (containing or not abacavir) as follows: HLA-B*57:01 allele carriers treated with abacavir and HLA-B*57:01 allele non-carriers treated with abacavir. We considered all adverse events reported during first abacavir administration, differentiating between confirmed hypersensitivity reactions and non-hypersensitivity reactions, according to abacavir hypersensitivity reaction definition included in the abacavir EU Summary of Product Characteristics and the US Prescribing Information. RESULTS A total of 3144 patients had a known HLA-B*57:01 pattern. About 5.4% of them showed allele polymorphism; Caucasian ethnicity was the most represented. In this cohort, 1801 patients were treated with a first abacavir-containing regimen (98.2% of them was represented by allele non-carriers). 191 out of 1801 patients discontinued abacavir because of toxicity/intolerance; among them 107 described adverse events fulfilled the criteria of confirmed abacavir hypersensitivity reaction (22/32 allele-positive patients and 85/1769 allele-negative patients). After having experienced a confirmed abacavir hypersensitivity reaction, abacavir was re-administered to eight HLA-B*57:01 negative patients. Seven of them re-experienced a syndrome consistent with hypersensitivity reaction, finally leading to drug discontinuation. Overall, no fatal reactions were described. CONCLUSION Not all abacavir-related side effects occur as a result of classic HLA-B*57:01-mediated hypersensitivity reaction, as they can develop irrespective of HLA-B*57:01 status. Clinical vigilance must be an essential part of the management of individuals starting abacavir, at any time during treatment. In a 'real-life' setting, clinical diagnosis of suspected abacavir hypersensitivity reaction in allele non-carriers remains crucial for further clinical decision making.
Collapse
|
40
|
Oyarzun P, Kashyap M, Fica V, Salas-Burgos A, Gonzalez-Galarza FF, McCabe A, Jones AR, Middleton D, Kobe B. A Proteome-Wide Immunoinformatics Tool to Accelerate T-Cell Epitope Discovery and Vaccine Design in the Context of Emerging Infectious Diseases: An Ethnicity-Oriented Approach. Front Immunol 2021; 12:598778. [PMID: 33717077 PMCID: PMC7952308 DOI: 10.3389/fimmu.2021.598778] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/11/2021] [Indexed: 01/06/2023] Open
Abstract
Emerging infectious diseases (EIDs) caused by viruses are increasing in frequency, causing a high disease burden and mortality world-wide. The COVID-19 pandemic caused by the novel SARS-like coronavirus (SARS-CoV-2) underscores the need to innovate and accelerate the development of effective vaccination strategies against EIDs. Human leukocyte antigen (HLA) molecules play a central role in the immune system by determining the peptide repertoire displayed to the T-cell compartment. Genetic polymorphisms of the HLA system thus confer a strong variability in vaccine-induced immune responses and may complicate the selection of vaccine candidates, because the distribution and frequencies of HLA alleles are highly variable among different ethnic groups. Herein, we build on the emerging paradigm of rational epitope-based vaccine design, by describing an immunoinformatics tool (Predivac-3.0) for proteome-wide T-cell epitope discovery that accounts for ethnic-level variations in immune responsiveness. Predivac-3.0 implements both CD8+ and CD4+ T-cell epitope predictions based on HLA allele frequencies retrieved from the Allele Frequency Net Database. The tool was thoroughly assessed, proving comparable performances (AUC ~0.9) against four state-of-the-art pan-specific immunoinformatics methods capable of population-level analysis (NetMHCPan-4.0, Pickpocket, PSSMHCPan and SMM), as well as a strong accuracy on proteome-wide T-cell epitope predictions for HIV-specific immune responses in the Japanese population. The utility of the method was investigated for the COVID-19 pandemic, by performing in silico T-cell epitope mapping of the SARS-CoV-2 spike glycoprotein according to the ethnic context of the countries where the ChAdOx1 vaccine is currently initiating phase III clinical trials. Potentially immunodominant CD8+ and CD4+ T-cell epitopes and population coverages were predicted for each population (the Epitope Discovery mode), along with optimized sets of broadly recognized (promiscuous) T-cell epitopes maximizing coverage in the target populations (the Epitope Optimization mode). Population-specific epitope-rich regions (T-cell epitope clusters) were further predicted in protein antigens based on combined criteria of epitope density and population coverage. Overall, we conclude that Predivac-3.0 holds potential to contribute in the understanding of ethnic-level variations of vaccine-induced immune responsiveness and to guide the development of epitope-based next-generation vaccines against emerging pathogens, whose geographic distributions and populations in need of vaccinations are often well-defined for regional epidemics.
Collapse
Affiliation(s)
- Patricio Oyarzun
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Manju Kashyap
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | - Victor Fica
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Sede Concepción, Concepción, Chile
| | | | - Faviel F Gonzalez-Galarza
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Antony McCabe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Derek Middleton
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
41
|
Haizel-Cobbina J, Spector LG, Moertel C, Parsons HM. Racial and ethnic disparities in survival of children with brain and central nervous tumors in the United States. Pediatr Blood Cancer 2021; 68:e28738. [PMID: 32970937 DOI: 10.1002/pbc.28738] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Despite improvements in overall survival for pediatric cancers, treatment disparities remain for racial/ethnic minorities compared to non-Hispanic Whites; however, the impact of race on treatment outcomes for pediatric brain and central nervous system (CNS) tumors in the United States is not well known. METHODS We included 8713 children aged 0-19 years with newly diagnosed primary brain and CNS tumors between 2000 and 2015 from the Census Tract-level SES and Rurality Database developed by Surveillance, Epidemiology, and End Results (SEER) Program. We used chi-square tests to assess differences in sociodemographic, cancer, and treatment characteristics by race/ethnicity and Kaplan-Meier curves and Cox proportional hazards models to examine differences in 10-year survival, adjusting for these characteristics. RESULTS Among 8713 patients, 56.75% were non-Hispanic White, 9.59% non-Hispanic Black, 25.46% Hispanic, and 8.19% from "other" racial/ethnic groups. Median unadjusted survival for all pediatric brain tumors was 53 months, but varied significantly by race/ethnicity with a median survival of 62 months for non-Hispanic Whites, 41 months for non-Hispanic Blacks, and 40 months for Hispanic and other. Multivariable analyses demonstrated minority racial groups still had significantly higher hazard of death than non-Hispanic Whites; Hispanic (adjusted hazard ratio [aHR] 1.25 [1.18-1.31]); non-Hispanic Black (aHR 1.12 [1.04-1.21]); other (aHR 1.22 [1.12-1.32]). Results were consistent when stratified by tumor histology. CONCLUSION We identified disparities in survival among racial/ethnic minorities with pediatric brain and CNS tumors, with Hispanic patients having the highest risk of mortality. Eliminating these disparities requires commitment toward promoting heath equity and personalized cancer treatment.
Collapse
Affiliation(s)
| | - Logan G Spector
- Division of Pediatric Epidemiology and Clinical Research, University of Minnesota, Minneapolis, Minnesota
| | - Christopher Moertel
- Division of Pediatric Hematology and Oncology, University of Minnesota, Minneapolis, Minnesota
| | - Helen M Parsons
- Division of Health Policy and Management, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
42
|
Devi YD, Devi A, Gogoi H, Dehingia B, Doley R, Buragohain AK, Singh CS, Borah PP, Rao CD, Ray P, Varghese GM, Kumar S, Namsa ND. Exploring rotavirus proteome to identify potential B- and T-cell epitope using computational immunoinformatics. Heliyon 2020; 6:e05760. [PMID: 33426322 PMCID: PMC7779714 DOI: 10.1016/j.heliyon.2020.e05760] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/02/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
Rotavirus is the most common cause of acute gastroenteritis in infants and children worldwide. The functional correlation of B- and T-cells to long-lasting immunity against rotavirus infection in the literature is limited. In this work, a series of computational immuno-informatics approaches were applied and identified 28 linear B-cells, 26 conformational B-cell, 44 TC cell and 40 TH cell binding epitopes for structural and non-structural proteins of rotavirus. Further selection of putative B and T cell epitopes in the multi-epitope vaccine construct was carried out based on immunogenicity, conservancy, allergenicity and the helical content of predicted epitopes. An in-silico vaccine constructs was developed using an N-terminal adjuvant (RGD motif) followed by TC and TH cell epitopes and B-cell epitope with an appropriate linker. Multi-threading models of multi-epitope vaccine construct with B- and T-cell epitopes were generated and molecular dynamics simulation was performed to determine the stability of designed vaccine. Codon optimized multi-epitope vaccine antigens was expressed and affinity purified using the E. coli expression system. Further the T cell epitope presentation assay using the recombinant multi-epitope constructs and the T cell epitope predicted and identified in this study have not been investigated. Multi-epitope vaccine construct encompassing predicted B- and T-cell epitopes may help to generate long-term immune responses against rotavirus. The computational findings reported in this study may provide information in developing epitope-based vaccine and diagnostic assay for rotavirus-led diarrhea in children's.
Collapse
Affiliation(s)
- Yengkhom Damayanti Devi
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, Assam, India
| | - Arpita Devi
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, Assam, India
| | - Hemanga Gogoi
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, Assam, India
| | - Bondita Dehingia
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, Assam, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, Assam, India
| | | | - Ch Shyamsunder Singh
- Department of Paediatrics, Regional Institute of Medical Sciences, Imphal, India
| | - Partha Pratim Borah
- Department of Paediatrics and Neonatology, Pratiksha Hospital, Guwahati, India
| | - C Durga Rao
- School of Liberal Arts and Basic Sciences, SRM University AP, Amaravati, India
| | - Pratima Ray
- Department of Biotechnology, Jamia Hamdard, Delhi, India
| | - George M Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | - Nima D Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam 784 028, Assam, India
| |
Collapse
|
43
|
An R, Jiao S, Chi X, Pang S. Genomic full-length sequence of the HLA-A*26:89 allele was identified by full-length group-specific sequencing. HLA 2020; 97:222-224. [PMID: 33184999 DOI: 10.1111/tan.14136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 01/10/2023]
Abstract
Genomic full-length sequence of HLA-A*26:89 was identified by group-specific sequencing in a Chinese individual.
Collapse
Affiliation(s)
- Run An
- HLA Typing Lab, Institute of Transfusion Medicine, Qingdao Blood Center, Qingdao, Shandong, China
| | - Shuxian Jiao
- HLA Typing Lab, Institute of Transfusion Medicine, Qingdao Blood Center, Qingdao, Shandong, China
| | - Xiaoyun Chi
- HLA Typing Lab, Institute of Transfusion Medicine, Qingdao Blood Center, Qingdao, Shandong, China
| | - Shutao Pang
- HLA Typing Lab, Institute of Transfusion Medicine, Qingdao Blood Center, Qingdao, Shandong, China
| |
Collapse
|
44
|
Wang H, Nakajima T, Ito Y, Naito H, Zhao N, Li H, Qiu X, Xia L, Chen J, Wu Q, Li L, Huang H, Yanagiba Y, Qu H, Yatsuya H, Kamijima M. Increased risk of occupational trichloroethylene hypersensitivity syndrome at exposure levels higher than 15 mg/L of urinary trichloroacetic acid, regardless of whether the patients had the HLA-B*13:01 allele. ENVIRONMENTAL RESEARCH 2020; 191:109972. [PMID: 32758551 DOI: 10.1016/j.envres.2020.109972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/18/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
Occupational trichloroethylene (TCE) exposure can cause hypersensitivity syndrome (TCE-HS). The human leukocyte antigen (HLA)-B*13:01 is reportedly an important allele involved in TCE-HS onset. However, the threshold exposure level causing TCE-HS in relation to HLA-B*13:01 remains unknown. We conducted a case-control study comprising 37 TCE-HS patients and 97 age- and sex-matched TCE-tolerant controls from the Han Chinese population. Urine and blood of patients were collected on the first day of hospitalization, and those of controls were collected at the end of their shifts. Urinary trichloroacetic acid (TCA) was measured as an exposure marker, and end-of-shift levels in the patients were estimated using the biological half-life of 83.7 h. HLA-B genotype was identified using DNA from blood. Crude odds ratios (ORs) for TCE-HS in the groups with urinary TCA concentration >15 mg/L to ≤50 mg/L and of >50 mg/L were 21.9 [95% confidence interval (CI) 4.2-114.1] and 27.6 (6.1-125.8), respectively, when the group with urinary TCA ≤15 mg/L was used as a reference. The frequency of HLA-B*13:01, the most common allele in the patients, was 62.2% (23/37), which was significantly higher than 17.5% (17/97) in the TCE-tolerant controls, with a crude OR of 8.4 (3.1-22.6). The mutually-adjusted ORs for urinary TCA >15 to ≤50 mg/L, >50 mg/L, and for HLA-B*13:01 were 33.4 (4.1-270.8), 34.0 (5.3-217.1), and 11.0 (2.4-50.7), respectively. In conclusion, reduction of TCE exposure to ≤15 mg/L is required for TCE-HS prevention because urinary TCA concentration >15 mg/L showed increased risk of TCE-HS, regardless of whether the patients had the HLA-B*13:01 allele.
Collapse
Affiliation(s)
- Hailan Wang
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Tamie Nakajima
- Department of Life and Health Sciences, Chubu University, 487-8501, Kasugai, Japan.
| | - Yuki Ito
- Department of Occupational and Environmental Health, Nagoya City University Graduate School of Medical Sciences, 467-8601, Nagoya, Japan.
| | - Hisao Naito
- Department of Public Health, Fujita Health University School of Medicine, 470-1192, Toyoake, Japan.
| | - Na Zhao
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Hongling Li
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Xinxiang Qiu
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Lihua Xia
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Jiabin Chen
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Qifeng Wu
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Laiyu Li
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Hanlin Huang
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Yukie Yanagiba
- National Institute of Occupational Safety and Health, 214-8585, Kawasaki, Japan.
| | - Hongyung Qu
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, 510300, Guangzhou, PR China.
| | - Hiroshi Yatsuya
- Department of Public Health, Fujita Health University School of Medicine, 470-1192, Toyoake, Japan.
| | - Michihiro Kamijima
- Department of Occupational and Environmental Health, Nagoya City University Graduate School of Medical Sciences, 467-8601, Nagoya, Japan.
| |
Collapse
|
45
|
Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL. Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 2020; 117:23835-23846. [PMID: 32900948 PMCID: PMC7519347 DOI: 10.1073/pnas.2008615117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.
Collapse
Affiliation(s)
- Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | | | - Madeline S Merlino
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew W Robertson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Megan R McLeod
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Lyanne Gomez-Rodriguez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Kirsten A Garcia
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jolie A Leonard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Kay E Leopold
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Eli Olson
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109
| |
Collapse
|
46
|
Dimou A, Grewe P, Sidney J, Sette A, Norman PJ, Doebele RC. HLA Class I Binding of Mutant EGFR Peptides in NSCLC Is Associated With Improved Survival. J Thorac Oncol 2020; 16:104-112. [PMID: 32927123 DOI: 10.1016/j.jtho.2020.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 07/11/2020] [Accepted: 08/30/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Cancer-associated mutations have the potential to generate neoantigens and elicit CD8-positive T-cell-dependent adaptive immune responses. There are currently no reports of CD8-positive T-cells with specificity for neoepitopes generated by EGFR mutations, which are driver oncogenes in a subset of patients with lung cancer. METHODS We used NETMHCpan 4.0 to identify putative protective human leukocyte antigen (HLA) class I allotypes that are predicted in silico to bind and present mutant EGFR-generated peptides on the basis of predefined criteria. We associated the presence or absence of these alleles with clinical outcomes in patients from The Cancer Genome Atlas with lung adenocarcinoma. RESULTS We identified 12 HLA class I alleles that fulfilled the predefined criteria for being protective for EGFR p.L858R and six for EGFR p.E746_A750del, the two most common EGFR mutations in lung cancer. We validated the in silico predictions for peptide-HLA allele binding in vitro. A third (12 of 36) of patients with mostly early stage lung adenocarcinoma in The Cancer Genome Atlas with either EGFR p.L858R or EGFR p.E746_A750del had at least one protective allele in their host genomes. More importantly, patients with protective alleles exhibited better disease-free (hazard ratio: 0.20, 95% confidence interval: 0.05-0.78) and overall survival (hazard ratio: 0.13, 95% confidence interval: 0.02-0.64), and this effect was independent of the EGFR mutation type, stage, age, and sex. CONCLUSIONS Our data revealed that clinical outcomes were improved in patients with EGFR mutation-positive lung adenocarcinoma who harbored protective HLA class I alleles. Thus, immunity with specificity for mutant EGFR is possible in a subset of patients with early stage lung cancer and portends a better prognosis.
Collapse
Affiliation(s)
- Anastasios Dimou
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado; Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota.
| | - Paul Grewe
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado
| | - John Sidney
- La Jolla Institute for Immunology, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, California; Department of Medicine, University of California in San Diego, La Jolla, California
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Aurora, Colorado; Department of Microbiology and Immunology, School of Medicine, University of Colorado, Aurora, Colorado
| | - Robert C Doebele
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado
| |
Collapse
|
47
|
Hayes E, Derrick C, Smalls D, Smith H, Kremer N, Weissman S. Short-term Adverse Events With BIC/FTC/TAF: Postmarketing Study. Open Forum Infect Dis 2020; 7:ofaa285. [PMID: 32908943 PMCID: PMC7470466 DOI: 10.1093/ofid/ofaa285] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/21/2020] [Indexed: 11/17/2022] Open
Abstract
Bictegravir (BIC)/emtricitabine (FTC)/tenofovir alafenamide (TAF) was Food and Drug Administration approved in February 2018. The paucity of real-world data prompted this retrospective, observational evaluation of discontinuation rates, adverse effects, and virologic control. In a Southern US, predominantly African American overweight population, we found optimal virologic control and low discontinuation rates, with 4% discontinuing BIC/FTC/TAF due to rash, low platelets, loss of appetite, and insomnia.
Collapse
Affiliation(s)
- Edwin Hayes
- Palmetto Health - University of South Carolina Immunology Center, Prisma Health, Columbia, South Carolina
| | - Caroline Derrick
- University of South Carolina College of Pharmacy, Prisma Health, Columbia, South Carolina
| | - Danielle Smalls
- University of South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina
| | - Hilary Smith
- University of South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina
| | - Nicole Kremer
- University of South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina
| | - Sharon Weissman
- Palmetto Health - University of South Carolina Immunology Center, Prisma Health, Columbia, South Carolina
| |
Collapse
|
48
|
Barquera R, Hernández-Zaragoza DI, Bravo-Acevedo A, Arrieta-Bolaños E, Clayton S, Acuña-Alonzo V, Martínez-Álvarez JC, López-Gil C, Adalid-Sáinz C, Vega-Martínez MDR, Escobedo-Ruíz A, Juárez-Cortés ED, Immel A, Pacheco-Ubaldo H, González-Medina L, Lona-Sánchez A, Lara-Riegos J, Sánchez-Fernández MGDJ, Díaz-López R, Guizar-López GU, Medina-Escobedo CE, Arrazola-García MA, Montiel-Hernández GD, Hernández-Hernández O, Ramos-de la Cruz FDR, Juárez-Nicolás F, Pantoja-Torres JA, Rodríguez-Munguía TJ, Juárez-Barreto V, Delgado-Aguirre H, Escutia-González AB, Goné-Vázquez I, Benítez-Arvizu G, Arellano-Prado FP, García-Arias VE, Rodríguez-López ME, Méndez-Mani P, García-Álvarez R, González-Martínez MDR, Aquino-Rubio G, Escareño-Montiel N, Vázquez-Castillo TV, Uribe-Duarte MG, Ruíz-Corral MDJ, Ortega-Yáñez A, Bernal-Felipe N, Gómez-Navarro B, Arriaga-Perea AJ, Martínez-Bezies V, Macías-Medrano RM, Aguilar-Campos JA, Solís-Martínez R, Serrano-Osuna R, Sandoval-Sandoval MJ, Jaramillo-Rodríguez Y, Salgado-Adame A, Juárez-de la Cruz F, Novelo-Garza B, Pavón-Vargas MDLÁ, Salgado-Galicia N, Bortolini MC, Gallo C, Bedoya G, Rothhammer F, González-José R, Ruiz-Linares A, Canizales-Quinteros S, Romero-Hidalgo S, Krause J, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure. Hum Immunol 2020; 81:461-474. [PMID: 32651014 DOI: 10.1016/j.humimm.2020.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022]
Abstract
We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.
Collapse
Affiliation(s)
- Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany; Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.
| | - Diana Iraíz Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico; Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Alicia Bravo-Acevedo
- Blood Bank, UMAE Hospital de Gineco Obstetricia No. 4 "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
| | - Víctor Acuña-Alonzo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Julio César Martínez-Álvarez
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Concepción López-Gil
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Carmen Adalid-Sáinz
- Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - María Del Rosario Vega-Martínez
- Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
| | - Araceli Escobedo-Ruíz
- Histocompatibility Laboratory, Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Eva Dolores Juárez-Cortés
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Alexander Immel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany; Institute of Clinical Molecular Biology (IKMB), Kiel University, University Hospital, Schleswig-Holstein, Germany
| | - Hanna Pacheco-Ubaldo
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Liliana González-Medina
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Abraham Lona-Sánchez
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Julio Lara-Riegos
- Chemistry Faculty, Universidad Autónoma de Yucatán (UADY), Mérida, Yucatán, Mexico
| | - María Guadalupe de Jesús Sánchez-Fernández
- Department of Nephrology and Transplantation Unit, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Rosario Díaz-López
- Molecular Biology Laboratory, Hospital Central Militar, Secretaría de la Defensa Nacional (SEDENA), Mexico City, Mexico
| | - Gregorio Ulises Guizar-López
- Molecular Biology Laboratory, Hospital Central Militar, Secretaría de la Defensa Nacional (SEDENA), Mexico City, Mexico
| | - Carolina Elizabeth Medina-Escobedo
- Unit of Research and Education in Health, Unidad Médica de Alta Especialidad (UMAE) # 10, Instituto Mexicano del Seguro Social (IMSS), Mérida, Yucatán, Mexico
| | - María Araceli Arrazola-García
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | | | - Flor Del Rocío Ramos-de la Cruz
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | | | - Jorge Arturo Pantoja-Torres
- Immunology Division, Unidad Médica de Alta Especialidad (UMAE) # 1, Instituto Mexicano del Seguro Social (IMSS), León, Guanajuato, Mexico
| | - Tirzo Jesús Rodríguez-Munguía
- Molecular Biology Laboratory, Hospital General "Norberto Treviño Zapata", Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico
| | | | - Héctor Delgado-Aguirre
- Laboratory of Histocompatibility, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | | | - Isis Goné-Vázquez
- Histocompatibility Laboratory, Hospital de Especialidades, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Gamaliel Benítez-Arvizu
- HLA Laboratory, Central Blood Bank, Hospital de Especialidades, Unidad Médica de Alta Especialidad (UMAE), Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Francia Paulina Arellano-Prado
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Víctor Eduardo García-Arias
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Marla Estefanía Rodríguez-López
- Pediatrics Hospital, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Patricia Méndez-Mani
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Raquel García-Álvarez
- Pharmacology Laboratory, Research Unit, Instituto Nacional de Pediatría (INP), Mexico City, Mexico
| | | | - Guadalupe Aquino-Rubio
- Molecular Biology Laboratory, Hospital General "Norberto Treviño Zapata", Dirección de Servicios de Salud de Tamaulipas, Ciudad Victoria, Tamaulipas, Mexico
| | - Néstor Escareño-Montiel
- Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | | | - María Guadalupe Uribe-Duarte
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - María de Jesús Ruíz-Corral
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Andrea Ortega-Yáñez
- Department of Development Genetics and Molecular Physiology, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | | | - Benjamín Gómez-Navarro
- Central Office of Nephrology, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico
| | - Agustín Jericó Arriaga-Perea
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | | | - Rosa María Macías-Medrano
- Histocompatibility Laboratory, Central Blood Bank, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jesús Abraham Aguilar-Campos
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Raúl Solís-Martínez
- Department of Molecular Biology, Laboratorios Diagnóstica, Villahermosa, Tabasco, Mexico
| | - Ricardo Serrano-Osuna
- Clinical Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 2, Instituto Mexicano del Seguro Social (IMSS), Ciudad Obregón, Sonora, Mexico
| | - Mario J Sandoval-Sandoval
- Central Office of Transplantation, Centro Médico Nacional de Occidente (CMNO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, Mexico; Health Research Division, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Yolanda Jaramillo-Rodríguez
- Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Antonio Salgado-Adame
- Direction of Health Education and Research, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Federico Juárez-de la Cruz
- Department of Transplantation, Unidad Médica de Alta Especialidad (UMAE) # 71, Instituto Mexicano del Seguro Social (IMSS), Torreón, Coahuila, Mexico
| | - Bárbara Novelo-Garza
- Medical Infrastructure Planning Committee, Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - María de Los Ángeles Pavón-Vargas
- Histocompatibility Laboratory, Unidad Médica de Alta Especialidad (UMAE) # 6, Instituto Mexicano del Seguro Social (IMSS), Puebla, Puebla, Mexico
| | - Norma Salgado-Galicia
- Molecular Biology and Histocompatibility Laboratory, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos (PEMEX), Mexico City, Mexico
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gabriel Bedoya
- Genética Molecular (GENMOL, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Rothhammer
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile; Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas-Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China; Aix-Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Samuel Canizales-Quinteros
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, Universidad Nacional Autónoma de México e Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sandra Romero-Hidalgo
- Department of Computational Genomics, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena, Germany
| | - Joaquín Zúñiga
- Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico; Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico City, Mexico
| | - Edmond J Yunis
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carolina Bekker-Méndez
- Immunology and Infectology Research Unit, Infectology Hospital, Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" (INCMNSZ), Mexico City, Mexico.
| |
Collapse
|
49
|
Oppermans N, Kueberuwa G, Hawkins RE, Bridgeman JS. Transgenic T-cell receptor immunotherapy for cancer: building on clinical success. Ther Adv Vaccines Immunother 2020; 8:2515135520933509. [PMID: 32613155 PMCID: PMC7309387 DOI: 10.1177/2515135520933509] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/18/2020] [Indexed: 12/30/2022] Open
Abstract
With the advent of immunotherapy as a realistic and promising option for cancer treatment, adoptive cellular therapies are gaining significant interest in the clinic. Whilst the recent successes of chimeric antigen receptor T-cell therapies for haematological malignancies are widely known, they have yet to show great success in solid cancers. However, immune cells transduced with T-cell receptors have been shown to traffic to and exert anti-cancer effects on solid tumour cells with some great successes. In this review, we explore the field of transgenic T-cell receptor immunotherapy, highlighting some of the key clinical trials which have paved the way for this type of cellular immunotherapy. Some trials have shown amazing clinical results, including long-term remissions and minimal toxicity, and can be looked at as an exemplar for this adoptive cell therapy. There have also been key trials where unexpected, fatal, off-tumour toxicity has occurred, and these trials have also been instrumental in shaping safer clinical trials, particularly regarding preclinical testing. In addition to previous trials, we analysed the current clinical trial space for T-cell receptor T-cell therapy, showing which trials are dominating in the clinic and which targets are being prioritised by researchers around the world. By looking at both past and current trials, we have been able to identify key drivers in developing transgenic T-cell receptor immunotherapy for the future.
Collapse
Affiliation(s)
| | - Gray Kueberuwa
- Immetacyte Ltd., University of Manchester, Manchester, Greater Manchester, UK
| | | | - John S Bridgeman
- Immetacyte Ltd., University of Manchester, Manchester, Greater Manchester, UK
| |
Collapse
|
50
|
Factors associated with psoriasis in a French Nationwide HIV cohort: the independent role of HLA-B*57:01. AIDS 2020; 34:1057-1063. [PMID: 32167971 DOI: 10.1097/qad.0000000000002519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Psoriasis is a T-cell-mediated inflammatory disease with genetic factors involved in its etiopathogenesis. In non-HIV populations, HLA-B57:01 has been associated with a higher risk of psoriasis. The aim of this study was to investigate demographic and immunovirological characteristics associated with psoriasis, and to assess whether HLA-B57:01 is associated with psoriasis among people living with HIV (PLHIV) followed in a large French multicenter Dat'AIDS cohort. METHODS All PLHIV followed up from January 2000 to December 2018 with an available result for HLA-B57:01 were included. Logistic regression models were used to identify associations between psoriasis (outcome variable) and explanatory variables. RESULTS Among 31 076 PLHIV, the overall prevalence of psoriasis and HLA-B57:01 were 2.25 and 4.73%, respectively and varied according to ethnicity. By multivariate analysis, male gender [OR 1.81 (95% CI 1.46-2.24), P < 10], positive HLA-B57:01 [OR 2.66 (95% CI 2.12-3.33), P < 10], nadir CD4 cell count less than 200 cells/μl [OR 1.41 (95% CI 1.19-1.67), P < 10] and positive HCV serology [OR 1.45 (95% CI 1.20-1.76), P < 10] were significantly associated with a higher risk of psoriasis. Being born in West and Central Africa [OR 0.15 (95% CI 0.10-0.25), P < 10], the Caribbean islands [OR 0.14 (95% CI 0.05-0.45), P = 0.0008] or Latin America [OR 0.31 (95% CI 0.14-0.69), P = 0.004] was associated with a lower risk of psoriasis compared with patients born in mainland France. CONCLUSION PLHIV carrying HLA-B57:01 have around a three-fold increased risk of psoriasis. This association might provide a possible explanation for the observed differences in psoriasis prevalence between ethnic groups.
Collapse
|