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Samudrala M, Dhaveji S, Savsani K, Dakshanamurthy S. AutoEpiCollect, a Novel Machine Learning-Based GUI Software for Vaccine Design: Application to Pan-Cancer Vaccine Design Targeting PIK3CA Neoantigens. Bioengineering (Basel) 2024; 11:322. [PMID: 38671743 PMCID: PMC11048108 DOI: 10.3390/bioengineering11040322] [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: 02/27/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Previous epitope-based cancer vaccines have focused on analyzing a limited number of mutated epitopes and clinical variables preliminarily to experimental trials. As a result, relatively few positive clinical outcomes have been observed in epitope-based cancer vaccines. Further efforts are required to diversify the selection of mutated epitopes tailored to cancers with different genetic signatures. To address this, we developed the first version of AutoEpiCollect, a user-friendly GUI software, capable of generating safe and immunogenic epitopes from missense mutations in any oncogene of interest. This software incorporates a novel, machine learning-driven epitope ranking method, leveraging a probabilistic logistic regression model that is trained on experimental T-cell assay data. Users can freely download AutoEpiCollectGUI with its user guide for installing and running the software on GitHub. We used AutoEpiCollect to design a pan-cancer vaccine targeting missense mutations found in the proto-oncogene PIK3CA, which encodes the p110ɑ catalytic subunit of the PI3K kinase protein. We selected PIK3CA as our gene target due to its widespread prevalence as an oncokinase across various cancer types and its lack of presence as a gene target in clinical trials. After entering 49 distinct point mutations into AutoEpiCollect, we acquired 361 MHC Class I epitope/HLA pairs and 219 MHC Class II epitope/HLA pairs. From the 49 input point mutations, we identified MHC Class I epitopes targeting 34 of these mutations and MHC Class II epitopes targeting 11 mutations. Furthermore, to assess the potential impact of our pan-cancer vaccine, we employed PCOptim and PCOptim-CD to streamline our epitope list and attain optimized vaccine population coverage. We achieved a world population coverage of 98.09% for MHC Class I data and 81.81% for MHC Class II data. We used three of our predicted immunogenic epitopes to further construct 3D models of peptide-HLA and peptide-HLA-TCR complexes to analyze the epitope binding potential and TCR interactions. Future studies could aim to validate AutoEpiCollect's vaccine design in murine models affected by PIK3CA-mutated or other mutated tumor cells located in various tissue types. AutoEpiCollect streamlines the preclinical vaccine development process, saving time for thorough testing of vaccinations in experimental trials.
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Affiliation(s)
- Madhav Samudrala
- College of Arts and Sciences, The University of Virginia, Charlottesville, VA 22903, USA
| | | | - Kush Savsani
- College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA 22043, USA
| | - Sivanesan Dakshanamurthy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Sharma N, Chopra A, Kandalkar Y, Choudhary A, Magotra A. Population-wide genetic analysis of Ovar-DQA1 and DQA2 loci across sheep breeds in India revealed their evolutionary importance and fitness of sheep in a tropical climate. Anim Biotechnol 2023; 34:4645-4657. [PMID: 36847639 DOI: 10.1080/10495398.2023.2180010] [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] [Indexed: 03/01/2023]
Abstract
Genetic variability at the major histocompatibility complex (MHC) is important in any species due to significant role played by MHC for antigen presentation. DQA locus has not been studied for its genetic variability across sheep population in India. In the present study, MHC of sheep at DQA1 and DQA2 loci were evaluated across 17 Indian sheep breeds. Results revealed high degree of heterozygosity (10.34% to 100% for DQA1 and 37.39 to 100% for DQA2). 18 DQA1 alleles and 22 DQA2 alleles were isolated in different breeds. Nucleotide content for DQA region revealed richness of AT content (54.85% for DQA1 and 53.89% for DQA2). DQA1 and DQA2 sequences clustered independently. We could see evidence of divergence of DQA as DQA1 and DQA2 across sheep breeds. Wu-Kabat variability index revealed vast genetic variation across DQA1 and DQA2, specifically at peptide binding sites (PBS) that consisted 21 residues for DQA1 and 17 residues for DQA2. Evolutionary analysis revealed the presence of positive and balancing selection for DQA1 locus, however DQA2 was under purifying selection across sheep breeds. Higher heterozygosity and large diversity at both loci especially at PBS indicated the fitness of the sheep population for evading pathogens and adapt to the harsh tropical climate.
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Affiliation(s)
- G R Gowane
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - S S Misra
- Animal Genetics and Breeding Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar
| | - Rani Alex
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Nikita Sharma
- Animal Health Section, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics and Breeding Division, ICAR-Arid Region Campus, Central Sheep and Wool Research Institute, Bikaner, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | | | - Ankit Magotra
- Animal Genetics and Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
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Gowane GR, Sharma P, Kumar R, Misra SS, Alex R, Vohra V, Chhotaray S, Dass G, Chopra A, Kandalkar Y, Vijay V, Choudhary A, Magotra A, Rajendran R. Cross-population genetic analysis revealed genetic variation and selection in the Ovar-DRB1 gene of Indian sheep breeds. Anim Biotechnol 2023; 34:2928-2939. [PMID: 36153754 DOI: 10.1080/10495398.2022.2125404] [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] [Indexed: 11/01/2022]
Abstract
In sheep, MHC variability is studied widely to explore disease association. The aim of the current study was to explore the genetic diversity of Ovar-DRB diversity across sheep breeds of India. Here, Ovar-DRB1 locus was studied across 20 sheep breeds. DRB1 was amplified (301 bp) and sequenced using a PCR-sequence-based typing approach. Results revealed a high degree of heterozygosity across breeds (mean: 73.99%). Overall mean distance for DRB1 was highest in Sangamneri (0.18) and lowest in Madgyal sheep (0.10). There was a higher rate of transition, across breeds. Further, 39 alleles were isolated in different breeds, out of which 10 were new. To allow easy access and use of the immune-polymorphic database, an online database management system was launched (http://www.mhcdbms.in/). Nucleotide content across breeds for the DRB1 region revealed the richness of GC content (59.26%). Wu-Kabat index revealed vast genetic variation across peptide binding sites (PBS) of DRB1. Residues 6, 66, 69, 52, and 81, were polymorphic showing utility for antigen presentation. All breeds were under positive selection for DRB1 locus (dN > dS). Study revealed the importance of DRB locus diversity for beta chain specifically at PBS across sheep breeds of the Indian subcontinent and presented evidence of positive selection for DRB owing to its evolutionary significance.
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Affiliation(s)
- G R Gowane
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Priya Sharma
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Rajiv Kumar
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - S S Misra
- Animal Genetics & Breeding Division, ICAR-Central Sheep & Wool Research Institute, Avikanagar, India
| | - Rani Alex
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - V Vohra
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - S Chhotaray
- Animal Genetics & Breeding Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Gopal Dass
- Animal Genetics & Breeding Division, ICAR-Central Institute for Research on Goats, Makhdoom, India
| | - Ashish Chopra
- Animal Genetics & Breeding Division, ICAR-Arid Region Campus, Central Sheep & Wool Research Institute Bikaner, Avikanagar, India
| | - Yogesh Kandalkar
- Deccani Sheep Breeding Unit, NWPSI at Mahatma Phule Krishi Vidyapith, Rahuri, India
| | - V Vijay
- Sonadi Seep Breeding Unit, NWPSI at Navaniya Maharana Pratap University of Agriculture and Technology, Udaipur, India
| | | | - Ankit Magotra
- Animal Genetics & Breeding Division, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - R Rajendran
- Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Theni, India
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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Cao Y, Shao L, Wang L, Su K, Zhang D, Xie Y, Zheng Q, Xu Y, Lu H, Xin M, Qiao Z, Guo Y. Heat shock cognate 70 protein like-2 protein in camphor pollen is one of the major culprits of asthma. Mol Immunol 2023; 156:170-176. [PMID: 36933345 DOI: 10.1016/j.molimm.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/08/2023] [Accepted: 01/13/2023] [Indexed: 03/18/2023]
Abstract
AIMS In recent decades, Cinnamomum camphora have gradually become the main street trees in Shanghai. This study aims to investigate the allergenicity of camphor pollen. MAIN METHODS A total of 194 serum samples from patients with respiratory allergy were collected and analyzed. Through protein profile identification and bioinformatics analysis, we hypothesized that heat shock cognate protein 2-like protein (HSC70L2) is the major potential allergenic protein in camphor pollen. Recombinant HSC70L2 (rHSC70L2) was expressed and purified, and a mouse model of camphor pollen allergy was established by subcutaneous injection of total camphor pollen protein extract (CPPE) and rHSC70L2. KEY FINDINGS Specific IgE was found in the serum of 5 patients in response to camphor pollen and three positive bands were identified by Western blotting. Enzyme-linked immunosorbent assay (ELISA), Immune dot blot and Western blot experiments confirmed that CPPE and rHSC70L2 can cause allergies in mice. Moreover, rHSC70L2 induces polarization of peripheral blood CD4+ T cells to Th2 cells in patients with respiratory allergies and mice with camphor pollen allergy. Finally, we predicted the T cell epitope of the HSC70L2 protein, and through the mouse spleen T cell stimulation experiment, we found that the 295EGIDFYSTITRARFE309 peptide induced T cells differentiation to Th2 and macrophages differentiation to the alternatively activated (M2) state. Moreover, 295EGIDFYSTITRARFE309 peptide increased the serum IgE levels in mice. SIGNIFICANCE The identification of HSC70L2 protein can provide novel diagnostic and therapeutic targets for allergies caused by camphor pollen.
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Affiliation(s)
- Yong Cao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Shao
- Department of Allergy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lianyun Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Allergy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Su
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yilin Xie
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Zheng
- Department of Allergy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanhua Xu
- Department of Allergy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Lu
- Department of Allergy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mei Xin
- Department of Nuclear Medicine, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Zhongdong Qiao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Yinshi Guo
- Department of Allergy, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Non-random Codon Usage of Synonymous and Non-synonymous Mutations in the Human HLA-A Gene. J Mol Evol 2023; 91:169-191. [PMID: 36809491 DOI: 10.1007/s00239-023-10093-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/13/2023] [Indexed: 02/23/2023]
Abstract
The structure and function of human leucocyte antigen (HLA-A) is well known and is an extremely variable protein. From the public HLA-A database, we chose 26 high frequency HLA-A alleles (45% of sequenced alleles). Using five arbitrary references from these alleles, we analyzed synonymous mutations at the third codon position (sSNP3) and non-synonymous mutations (NSM). Both mutation types showed non-random locations of 29 sSNP3 codons and 71 NSM codons in the five reference lists. Most sSNP3 codons show identical mutation types with many mutations resulting from cytosine deamination. We proposed 23 ancestral parents of sSNP3 in five reference sequences using conserved parents in five unidirectional codons and 18 majority parents in reciprocal codons. These 23 proposed ancestral parents show exclusive codon usage of G3 or C3 parents located on both DNA strands that mutate to A3 or T3 variants mostly (76%) by cytosine deamination The sSNP3 and NSM show clear separation of the two variant types with most sSNP3 located in conserved areas in exons 2, 3 and 4, compared to most NSM appearing in two Variable Areas with no sSNP3 in the latter parts of exons 2 (α1) and 3 (α2). The Variable Areas contain NSM (polymorphic) residues at the center of the groove that bind the foreign peptide. We find distinctly different mutation patterns in NSM codons from those of sSNP3. Namely, G-C to A-T mutation frequency was much smaller, suggesting that evolutional pressures of deamination and other mechanisms applied to the two areas are significantly different.
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Papadaki GF, Ani O, Florio TJ, Young MC, Danon JN, Sun Y, Dersh D, Sgourakis NG. Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front Immunol 2023; 14:1116906. [PMID: 36761745 PMCID: PMC9905809 DOI: 10.3389/fimmu.2023.1116906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Major Histocompatibility Complex class I (MHC-I) molecules display self, viral or aberrant epitopic peptides to T cell receptors (TCRs), which employ interactions between complementarity-determining regions with both peptide and MHC-I heavy chain 'framework' residues to recognize specific Human Leucocyte Antigens (HLAs). The highly polymorphic nature of the HLA peptide-binding groove suggests a malleability of interactions within a common structural scaffold. Here, using structural data from peptide:MHC-I and pMHC:TCR structures, we first identify residues important for peptide and/or TCR binding. We then outline a fixed-backbone computational design approach for engineering synthetic molecules that combine peptide binding and TCR recognition surfaces from existing HLA allotypes. X-ray crystallography demonstrates that chimeric molecules bridging divergent HLA alleles can bind selected peptide antigens in a specified backbone conformation. Finally, in vitro tetramer staining and biophysical binding experiments using chimeric pMHC-I molecules presenting established antigens further demonstrate the requirement of TCR recognition on interactions with HLA framework residues, as opposed to interactions with peptide-centric Chimeric Antigen Receptors (CARs). Our results underscore a novel, structure-guided platform for developing synthetic HLA molecules with desired properties as screening probes for peptide-centric interactions with TCRs and other therapeutic modalities.
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Affiliation(s)
- Georgia F. Papadaki
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Omar Ani
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Tyler J. Florio
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael C. Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Julia N. Danon
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Devin Dersh
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh SGE. The IPD-IMGT/HLA Database. Nucleic Acids Res 2022; 51:D1053-D1060. [PMID: 36350643 PMCID: PMC9825470 DOI: 10.1093/nar/gkac1011] [Citation(s) in RCA: 358] [Impact Index Per Article: 179.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.
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Affiliation(s)
- Dominic J Barker
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK,UCL Cancer Institute, University College London (UCL), Royal Free Campus, Pond Street, London, NW3 2QG, UK
| | - Giuseppe Maccari
- Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Xenia Georgiou
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Michael A Cooper
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London, NW3 2QG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - James Robinson
- To whom correspondence should be addressed. Tel: +44 20 7284 8307;
| | - Steven G E Marsh
- Correspondence may also be addressed to Steven G.E. Marsh. Tel: +44 20 7284 8321;
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Peel E, Silver L, Brandies P, Zhu Y, Cheng Y, Hogg CJ, Belov K. Best genome sequencing strategies for annotation of complex immune gene families in wildlife. Gigascience 2022; 11:6780307. [PMID: 36310247 PMCID: PMC9618407 DOI: 10.1093/gigascience/giac100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The biodiversity crisis and increasing impact of wildlife disease on animal and human health provides impetus for studying immune genes in wildlife. Despite the recent boom in genomes for wildlife species, immune genes are poorly annotated in nonmodel species owing to their high level of polymorphism and complex genomic organisation. Our research over the past decade and a half on Tasmanian devils and koalas highlights the importance of genomics and accurate immune annotations to investigate disease in wildlife. Given this, we have increasingly been asked the minimum levels of genome quality required to effectively annotate immune genes in order to study immunogenetic diversity. Here we set out to answer this question by manually annotating immune genes in 5 marsupial genomes and 1 monotreme genome to determine the impact of sequencing data type, assembly quality, and automated annotation on accurate immune annotation. RESULTS Genome quality is directly linked to our ability to annotate complex immune gene families, with long reads and scaffolding technologies required to reassemble immune gene clusters and elucidate evolution, organisation, and true gene content of the immune repertoire. Draft-quality genomes generated from short reads with HiC or 10× Chromium linked reads were unable to achieve this. Despite mammalian BUSCOv5 scores of up to 94.1% amongst the 6 genomes, automated annotation pipelines incorrectly annotated up to 59% of manually annotated immune genes regardless of assembly quality or method of automated annotation. CONCLUSIONS Our results demonstrate that long reads and scaffolding technologies, alongside manual annotation, are required to accurately study the immune gene repertoire of wildlife species.
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Affiliation(s)
- Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Luke Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ying Zhu
- Sichuan Provincial Academy of Natural Resource Sciences, Chengdu, Sichuan 610000, China
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, University of Sydney, Sydney NSW 2006, Australia
| | - Katherine Belov
- Correspondence address. Katherine Belov, School of Life and Environmental Sciences, Rm 206, RMC Gunn Building (B19), The University of Sydney, Sydney, NSW 2006, Australia. E-mail:
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10
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Olafsdottir TA, Bjarnadottir K, Norddahl GL, Halldorsson GH, Melsted P, Gunnarsdottir K, Ivarsdottir E, Olafsdottir T, Arnthorsson AO, Theodors F, Eythorsson E, Helgason D, Eggertsson HP, Masson G, Bjarnadottir S, Saevarsdottir S, Runolfsdottir HL, Olafsson I, Saemundsdottir J, Sigurdsson MI, Ingvarsson RF, Palsson R, Thorgeirsson G, Halldorsson BV, Holm H, Kristjansson M, Sulem P, Thorsteinsdottir U, Jonsdottir I, Gudbjartsson DF, Stefansson K. HLA alleles, disease severity, and age associate with T-cell responses following infection with SARS-CoV-2. Commun Biol 2022; 5:914. [PMID: 36068292 PMCID: PMC9446630 DOI: 10.1038/s42003-022-03893-w] [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: 12/06/2021] [Accepted: 08/25/2022] [Indexed: 12/12/2022] Open
Abstract
Memory T-cell responses following SARS-CoV-2 infection have been extensively investigated but many studies have been small with a limited range of disease severity. Here we analyze SARS-CoV-2 reactive T-cell responses in 768 convalescent SARS-CoV-2-infected (cases) and 500 uninfected (controls) Icelanders. The T-cell responses are stable three to eight months after SARS-CoV-2 infection, irrespective of disease severity and even those with the mildest symptoms induce broad and persistent T-cell responses. Robust CD4+ T-cell responses are detected against all measured proteins (M, N, S and S1) while the N protein induces strongest CD8+ T-cell responses. CD4+ T-cell responses correlate with disease severity, humoral responses and age, whereas CD8+ T-cell responses correlate with age and functional antibodies. Further, CD8+ T-cell responses associate with several class I HLA alleles. Our results, provide new insight into HLA restriction of CD8+ T-cell immunity and other factors contributing to heterogeneity of T-cell responses following SARS-CoV-2 infection. A study of 768 convalescent SARS CoV-2-infected and 500 uninfected Icelanders reveals broad and stable T-cell responses 3-8 months from infection. HLA alleles, disease severity, and age contribute to the heterogeneity of cellular immunity.
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Affiliation(s)
| | | | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Elias Eythorsson
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Dadi Helgason
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | - Sólveig Bjarnadottir
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Hrafnhildur L Runolfsdottir
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Isleifur Olafsson
- Clinical Laboratory Services, Diagnostics and Blood Bank, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Martin I Sigurdsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Perioperative Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Ragnar F Ingvarsson
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Runolfur Palsson
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Science and Engineering, Reykjavik University, Reykjavík, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Mar Kristjansson
- Internal Medicine and Emergency Services, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland. .,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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11
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Vijayakumar S. Harnessing Fuzzy Rule Based System for Screening Major Histocompatibility Complex Class I Peptide Epitopes from the Whole Proteome: An Implementation on the Proteome of Leishmania donovani. J Comput Biol 2022; 29:1045-1058. [PMID: 35404099 DOI: 10.1089/cmb.2021.0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of peptide-based vaccines is enhanced by immunoinformatics, which predicts the patterns that B cells and T cells recognize. Although several tools are available for predicting the Major histocompatibility complex (MHC-I) binding peptides, the wide variants of human leucocyte antigen allele make it challenging to choose a peptide that will induce an immune response in a majority of people. In addition, for a peptide to be considered a potential vaccine candidate, factors such as T cell affinity, proteasome cleavage, and similarity to human proteins also play a major role. Identifying peptides that satisfy the earlier cited measures across the entire proteome is, therefore, challenging. Hence, the fuzzy inference system (FIS) is proposed to detect each peptide's potential as a vaccine candidate and assign it either a very high, high, moderate, or low ranking. The FIS includes input features from 6 modules (binding of 27 major alleles, T cell propensity, pro-inflammatory response, proteasome cleavage, transporter associated with antigen processing, and similarity with human peptide) and rules derived from an observation of features on positive samples. On validation of experimentally verified peptides, a balanced accuracy of ∼80% was achieved, with a Mathew's correlation coefficient score of 0.67 and an F-1 score of 0.74. In addition, the method was implemented on complete proteome of Leishmania donovani, which contains ∼4,800,000 peptides. Lastly, a searchable database of the ranked results of the L. donovani proteome was made and is available online (MHC-FIS-LdDB). It is hoped that this method will simplify the identification of potential MHC-I binding candidates from a large proteome.
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Affiliation(s)
- Saravanan Vijayakumar
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
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12
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Abdelhafiz AS, Ali A, Fouda MA, Sayed DM, Kamel MM, Kamal LM, Khalil MA, Bakry RM. HLA-B*15 predicts survival in Egyptian patients with COVID-19. Hum Immunol 2022; 83:10-16. [PMID: 34607724 PMCID: PMC8485223 DOI: 10.1016/j.humimm.2021.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/30/2021] [Accepted: 09/23/2021] [Indexed: 01/08/2023]
Abstract
Genetic differences among individuals could affect the clinical presentations and outcomes of COVID-19. Human Leukocyte Antigens are associated with COVID-19 susceptibility, severity, and prognosis. This study aimed to identify HLA-B and -C genotypes among 69 Egyptian patients with COVID-19 and correlate them with disease outcomes and other clinical and laboratory data. HLA-B and -C typing was performed using Luminex-based HLA typing kits. Forty patients (58%) had severe COVID-19; 55% of these patients died, without reported mortality in the moderate group. The alleles associated with severe COVID-19 were HLA-B*41, -B*42, -C*16, and -C*17, whereas HLA-B*15, -C*7, and -C*12 were significantly associated with protection against mortality. Regression analysis showed that HLA-B*15 was the only allele associated with predicted protection against mortality, where the likelihood of survival increased with HLA-B*15 (P < 0.001). Patient survival was less likely to occur with higher total leukocytic count, ferritin, and creatinine levels. This study provides interesting insights into the association between HLA class I alleles and protection from or severity of COVID-19 through immune response modulation. This is the first study to investigate this relationship in Egyptian patients. More studies are needed to understand how HLA class I alleles interact and affect Cytotoxic T lymphocytes and natural killer cell function.
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Affiliation(s)
- Ahmed Samir Abdelhafiz
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Asmaa Ali
- Department of Pulmonary Medicine, Abbassia Chest Hospital, MOH, Cairo, Egypt
| | - Merhan A Fouda
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Douaa M Sayed
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
| | - Mahmoud M Kamel
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Lamyaa Mohamed Kamal
- Department of Clinical and Chemical Pathology, Elsahel Teaching Hospital, MOH, Cairo, Egypt
| | - Mahmoud Ali Khalil
- Department of Tropical Medicine and Infectious Disease, Imbaba Fever Hospital, MOH, Cairo, Egypt
| | - Rania M Bakry
- Department of Clinical Pathology, South Egypt Cancer Institute, Assiut University, Assiut, Egypt
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13
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Soto C, Bombardi RG, Kozhevnikov M, Sinkovits RS, Chen EC, Branchizio A, Kose N, Day SB, Pilkinton M, Gujral M, Mallal S, Crowe JE. High Frequency of Shared Clonotypes in Human T Cell Receptor Repertoires. Cell Rep 2021; 32:107882. [PMID: 32668251 PMCID: PMC7433715 DOI: 10.1016/j.celrep.2020.107882] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/18/2020] [Accepted: 06/16/2020] [Indexed: 01/30/2023] Open
Abstract
The collection of T cell receptors (TCRs) generated by somatic recombination is large but unknown. We generate large TCR repertoire datasets as a resource to facilitate detailed studies of the role of TCR clonotypes and repertoires in health and disease. We estimate the size of individual human recombined and expressed TCRs by sequence analysis and determine the extent of sharing between individual repertoires. Our experiments reveal that each blood sample contains between 5 million and 21 million TCR clonotypes. Three individuals share 8% of TCRβ- or 11% of TCRα-chain clonotypes. Sorting by T cell phenotypes in four individuals shows that 5% of naive CD4+ and 3.5% of naive CD8+ subsets share their TCRβ clonotypes, whereas memory CD4+ and CD8+ subsets share 2.3% and 0.4% of their clonotypes, respectively. We identify the sequences of these shared TCR clonotypes that are of interest for studies of human T cell biology. Soto et al. examine the extent to which five healthy adults share their T cell receptor (TCR) repertoire. Using sequencing and bioinformatics, they show a high prevalence of shared clonotypes even considering different T cell phenotypes. Possible functions for some clonotypes are inferred based on homology with TCRs in GenBank.
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Affiliation(s)
- Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin G Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Morgan Kozhevnikov
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert S Sinkovits
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Elaine C Chen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Andre Branchizio
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Samuel B Day
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark Pilkinton
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madhusudan Gujral
- San Diego Supercomputer Center, University of California, San Diego, San Diego, CA 92093, USA
| | - Simon Mallal
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
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14
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Karami E, Sabatier JM, Behdani M, Irani S, Kazemi-Lomedasht F. A nanobody-derived mimotope against VEGF inhibits cancer angiogenesis. J Enzyme Inhib Med Chem 2021; 35:1233-1239. [PMID: 32441172 PMCID: PMC7717616 DOI: 10.1080/14756366.2020.1758690] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vascular Endothelial Growth Factor (VEGF) promotes angiogenesis in tumours of various cancers. Monoclonal antibodies and nanobodies are one of the potent agents in the treatment of cancer. Due to their high costs, researchers are considering to design and produce peptides as a substitute approach in recent years. The aim of the current study was designing a mimotope against VEGF and evaluate its effects on cell proliferation and tube formation in the HUVEC cell line. For this, a peptide was designed against VEGF and chemically produced. The effects of synthetic peptide and nanobody on the inhibition of proliferation of HUVEC cells were examined using MTT and tube formation assays. The data indicate that the peptide was able to significantly inhibit both HUVEC cell proliferation and tube formation through inhibition of VEGF, highlighting the potential of peptides as a ‘novel’ class of candidate drugs to inhibit angiogenesis.
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Affiliation(s)
- Elmira Karami
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Jean-Marc Sabatier
- Aix-Marseille Université, Institut de Neurophysiopathologie (INP) UMR 7051, 27 boulevard Jean Moulin, Faculté de Médecine, 13385 - Marseille Cédex 5, France
| | - Mahdi Behdani
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Kazemi-Lomedasht
- Venom and Biotherapeutics Molecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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15
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Han XJ, Ma XL, Yang L, Wei YQ, Peng Y, Wei XW. Progress in Neoantigen Targeted Cancer Immunotherapies. Front Cell Dev Biol 2020; 8:728. [PMID: 32850843 PMCID: PMC7406675 DOI: 10.3389/fcell.2020.00728] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 02/05/2023] Open
Abstract
Immunotherapies that harness the immune system to kill cancer cells have showed significant therapeutic efficacy in many human malignancies. A growing number of studies have highlighted the relevance of neoantigens in recognizing cancer cells by intrinsic T cells. Cancer neoantigens are a direct consequence of somatic mutations presenting on the surface of individual cancer cells. Neoantigens are fully cancer-specific and exempt from central tolerance. In addition, neoantigens are important targets for checkpoint blockade therapy. Recently, technological innovations have made neoantigen discovery possible in a variety of malignancies, thus providing an impetus to develop novel immunotherapies that selectively enhance T cell reactivity for the destruction of cancer cells while leaving normal tissues unharmed. In this review, we aim to introduce the methods of the identification of neoantigens, the mutational patterns of human cancers, related clinical trials, neoantigen burden and sensitivity to immune checkpoint blockade. Moreover, we focus on relevant challenges of targeting neoantigens for cancer treatment.
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16
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Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. IPD-IMGT/HLA Database. Nucleic Acids Res 2020; 48:D948-D955. [PMID: 31667505 PMCID: PMC7145640 DOI: 10.1093/nar/gkz950] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/03/2019] [Accepted: 10/29/2019] [Indexed: 11/14/2022] Open
Abstract
The IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, currently contains over 25 000 allele sequence for 45 genes, which are located within the Major Histocompatibility Complex (MHC) of the human genome. This region is the most polymorphic region of the human genome, and the levels of polymorphism seen exceed most other genes. Some of the genes have several thousand variants and are now termed hyperpolymorphic, rather than just simply polymorphic. The IPD-IMGT/HLA Database has provided a stable, highly accessible, user-friendly repository for this information, providing the scientific and medical community access to the many variant sequences of this gene system, that are critical for the successful outcome of transplantation. The number of currently known variants, and dramatic increase in the number of new variants being identified has necessitated a dedicated resource with custom tools for curation and publication. The challenge for the database is to continue to provide a highly curated database of sequence variants, while supporting the increased number of submissions and complexity of sequences. In order to do this, traditional methods of accessing and presenting data will be challenged, and new methods will need to be utilized to keep pace with new discoveries.
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Affiliation(s)
- James Robinson
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, University College London (UCL), London, UK
| | | | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, University College London (UCL), London, UK
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17
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Maccari G, Robinson J, Hammond JA, Marsh SGE. The IPD Project: a centralised resource for the study of polymorphism in genes of the immune system. Immunogenetics 2020; 72:49-55. [PMID: 31641782 PMCID: PMC6970959 DOI: 10.1007/s00251-019-01133-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/20/2019] [Indexed: 01/30/2023]
Abstract
The Immuno Polymorphism Database (IPD), https://www.ebi.ac.uk/ipd/, is a set of specialist databases that enable the study of polymorphic genes which function as part of the vertebrate immune system. The major focus is on the hyperpolymorphic major histocompatibility complex (MHC) genes and the killer-cell immunoglobulin-like receptor (KIR) genes, by providing the official repository and primary source of sequence data. Databases are centred around humans as well as animals important for food security, for companionship and as disease models. The IPD project works with specialist groups or nomenclature committees who provide and manually curate individual sections before they are submitted for online publication. To reflect the recent advance of allele sequencing technologies and the increasing demands of novel tools for the analysis of genomic variation, the IPD project is undergoing a progressive redesign and reorganisation. In this review, recent updates and future developments are discussed, with a focus on the core concepts to better future-proof the project.
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Affiliation(s)
- Giuseppe Maccari
- The Pirbright Institute, Pirbright, Woking, Surrey, UK
- 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
| | | | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
- UCL Cancer Institute, Royal Free Campus, London, UK.
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18
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Papúchová H, Meissner TB, Li Q, Strominger JL, Tilburgs T. The Dual Role of HLA-C in Tolerance and Immunity at the Maternal-Fetal Interface. Front Immunol 2019; 10:2730. [PMID: 31921098 PMCID: PMC6913657 DOI: 10.3389/fimmu.2019.02730] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
To establish a healthy pregnancy, maternal immune cells must tolerate fetal allo-antigens and remain competent to respond to infections both systemically and in placental tissues. Extravillous trophoblasts (EVT) are the most invasive cells of extra-embryonic origin to invade uterine tissues and express polymorphic Human Leucocyte Antigen-C (HLA-C) of both maternal and paternal origin. Thus, HLA-C is a key molecule that can elicit allogeneic immune responses by maternal T and NK cells and for which maternal-fetal immune tolerance needs to be established. HLA-C is also the only classical MHC molecule expressed by EVT that can present a wide variety of peptides to maternal memory T cells and establish protective immunity. The expression of paternal HLA-C by EVT provides a target for maternal NK and T cells, whereas HLA-C expression levels may influence how this response is shaped. This dual function of HLA-C requires tight transcriptional regulation of its expression to balance induction of tolerance and immunity. Here, we critically review new insights into: (i) the mechanisms controlling expression of HLA-C by EVT, (ii) the mechanisms by which decidual NK cells, effector T cells and regulatory T cells recognize HLA-C allo-antigens, and (iii) immune recognition of pathogen derived antigens in context of HLA-C.
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Affiliation(s)
- Henrieta Papúchová
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Torsten B Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Qin Li
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Jack L Strominger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
| | - Tamara Tilburgs
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States.,Division of Immunobiology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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19
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Stürner KH, Siembab I, Schön G, Stellmann JP, Heidari N, Fehse B, Heesen C, Eiermann TH, Martin R, Binder TM. Is multiple sclerosis progression associated with the HLA-DR15 haplotype? Mult Scler J Exp Transl Clin 2019; 5:2055217319894615. [PMID: 31839982 PMCID: PMC6902395 DOI: 10.1177/2055217319894615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/04/2019] [Accepted: 11/09/2019] [Indexed: 11/17/2022] Open
Abstract
Background The prevalence of multiple sclerosis is associated with the major histocompatibility complex class II DR15 haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Objective To assess whether multiple sclerosis progression is associated with the main susceptibility haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Methods Patients (n = 1230) and healthy controls (n = 2110) were genotyped for HLA-DRB1 and HLA-DRB5. The baseline Expanded Disability Status Scale (EDSS) score was determined and patients were followed for at least 3 years. Results After follow-up of the consecutive cohort 349 patients were classified as having clinical isolated syndrome and 881 patients as having multiple sclerosis. The susceptibility allele HLA-DRB1*15:01 was more frequent in clinical isolated syndrome (odds ratio 1.56) and multiple sclerosis (odds ratio 3.17) compared to controls. HLA- DRB1*15:01 was the only enriched HLA-DRB1 allele in multiple sclerosis patients. Comparison of clinical characteristics between HLA-DRB1*15:01∼HLA-DRB5*01:01 negative and positive patients with multiple sclerosis showed that baseline EDSS score, disease duration and frequency of the category secondary progressive multiple sclerosis with relapse were increased in the HLA-DRB1*15:01∼HLA-DRB5*01:01 positive group. Conclusion The study confirmed HLA-DRB1*15:01 and HLA-DRB5*01:01 as the main susceptibility alleles and showed weak indirect evidence for a role in progression of the disease.
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Affiliation(s)
- Klarissa Hanja Stürner
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Inessa Siembab
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Gerhard Schön
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Germany
| | - Jan-Patrick Stellmann
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Nika Heidari
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Germany
| | - Christoph Heesen
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas H Eiermann
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
| | - Roland Martin
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas Mc Binder
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
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20
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Nomenclature report 2019: major histocompatibility complex genes and alleles of Great and Small Ape and Old and New World monkey species. Immunogenetics 2019; 72:25-36. [PMID: 31624862 DOI: 10.1007/s00251-019-01132-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/27/2022]
Abstract
The major histocompatibility complex (MHC) is central to the innate and adaptive immune responses of jawed vertebrates. Characteristic of the MHC are high gene density, gene copy number variation, and allelic polymorphism. Because apes and monkeys are the closest living relatives of humans, the MHCs of these non-human primates (NHP) are studied in depth in the context of evolution, biomedicine, and conservation biology. The Immuno Polymorphism Database (IPD)-MHC NHP Database (IPD-MHC NHP), which curates MHC data of great and small apes, as well as Old and New World monkeys, has been upgraded. The curators of the database are responsible for providing official designations for newly discovered alleles. This nomenclature report updates the 2012 report, and summarizes important nomenclature issues and relevant novel features of the IPD-MHC NHP Database.
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21
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Yogurtcu ON, Sauna ZE, McGill JR, Tegenge MA, Yang H. TCPro: an In Silico Risk Assessment Tool for Biotherapeutic Protein Immunogenicity. AAPS JOURNAL 2019; 21:96. [PMID: 31376048 DOI: 10.1208/s12248-019-0368-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022]
Abstract
Most immune responses to biotherapeutic proteins involve the development of anti-drug antibodies (ADAs). New drugs must undergo immunogenicity assessments to identify potential risks at early stages in the drug development process. This immune response is T cell-dependent. Ex vivo assays that monitor T cell proliferation often are used to assess immunogenicity risk. Such assays can be expensive and time-consuming to carry out. Furthermore, T cell proliferation requires presentation of the immunogenic epitope by major histocompatibility complex class II (MHCII) proteins on antigen-presenting cells. The MHC proteins are the most diverse in the human genome. Thus, obtaining cells from subjects that reflect the distribution of the different MHCII proteins in the human population can be challenging. The allelic frequencies of MHCII proteins differ among subpopulations, and understanding the potential immunogenicity risks would thus require generation of datasets for specific subpopulations involving complex subject recruitment. We developed TCPro, a computational tool that predicts the temporal dynamics of T cell counts in common ex vivo assays for drug immunogenicity. Using TCPro, we can test virtual pools of subjects based on MHCII frequencies and estimate immunogenicity risks for different populations. It also provides rapid and inexpensive initial screens for new biotherapeutics and can be used to determine the potential immunogenicity risk of new sequences introduced while bioengineering proteins. We validated TCPro using an experimental immunogenicity dataset, making predictions on the population-based immunogenicity risk of 15 protein-based biotherapeutics. Immunogenicity rankings generated using TCPro are consistent with the reported clinical experience with these therapeutics.
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Affiliation(s)
- Osman N Yogurtcu
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US FDA, 10903 New Hampshire Ave, Silver Spring, 20993, Maryland, USA
| | - Zuben E Sauna
- Office of Tissues and Advanced Therapy, Center for Biologics Evaluation and Research, US FDA, 10903 New Hampshire Ave, Silver Spring, 20993, Maryland, USA
| | - Joseph R McGill
- Office of Tissues and Advanced Therapy, Center for Biologics Evaluation and Research, US FDA, 10903 New Hampshire Ave, Silver Spring, 20993, Maryland, USA
| | - Million A Tegenge
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US FDA, 10903 New Hampshire Ave, Silver Spring, 20993, Maryland, USA
| | - Hong Yang
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US FDA, 10903 New Hampshire Ave, Silver Spring, 20993, Maryland, USA.
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22
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Kamyshova ES, Bobkova IN, Gorelova IA, Каkhsurueva PA, Filatova EE. Genetic determinants of the development and course of membranous nephropathy. TERAPEVT ARKH 2019; 90:105-111. [PMID: 30701913 DOI: 10.26442/terarkh2018906105-111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Membranous nephropathy (MN) is one of the most common causes of nephrotic syndrome in adults and is classified as either primary (idiopatic) or secondary MN according to underlying etiology (the later result from some known disease such as systemic autoimmune diseases, infections, malignancies, drugs, etc). In recent years, phospholipase A2 receptor 1 (PLA2R) and thrombospondin type-1 domain-containing 7A (THSD7A) were identified as two major podocytic antigens involved in the pathogenesis of idiopatic MN (IMN). And the discovery of circulating antibodies specific for these target antigens has transformed the diagnostic workup and significally improved management of IMN. However why do such antibodies develop is not conclusively established. The role of underlying genetic factors is discussed. The review presents the results of recent studies, that have shown significant associations of specific genetic factors (particularly human leucocyte antigen class II and PLA2R1 genes) with IMN.
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Affiliation(s)
- E S Kamyshova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - I N Bobkova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - I A Gorelova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - P A Каkhsurueva
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - E E Filatova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
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23
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Slade JWG, Watson MJ, MacDougall‐Shackleton EA. "Balancing" balancing selection? Assortative mating at the major histocompatibility complex despite molecular signatures of balancing selection. Ecol Evol 2019; 9:5146-5157. [PMID: 31110668 PMCID: PMC6509439 DOI: 10.1002/ece3.5087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 12/20/2022] Open
Abstract
In vertebrate animals, genes of the major histocompatibility complex (MHC) determine the set of pathogens to which an individual's adaptive immune system can respond. MHC genes are extraordinarily polymorphic, often showing elevated nonsynonymous relative to synonymous sequence variation and sharing presumably ancient polymorphisms between lineages. These patterns likely reflect pathogen-mediated balancing selection, for example, rare-allele or heterozygote advantage. Such selection is often reinforced by disassortative mating at MHC. We characterized exon 2 of MHC class II, corresponding to the hypervariable peptide-binding region, in song sparrows (Melospiza melodia). We compared nonsynonymous to synonymous sequence variation in order to identify positively selected sites; assessed evidence for trans-species polymorphisms indicating ancient balancing selection; and compared MHC similarity of socially mated pairs to expectations under random mating. Six codons showed elevated ratios of nonsynonymous to synonymous variation, consistent with balancing selection, and we characterized several alleles similar to those occurring in at least four other avian families. Despite this evidence for historical balancing selection, mated pairs were significantly more similar at MHC than were randomly generated pairings. Nonrandom mating at MHC thus appears to partially counteract, not reinforce, pathogen-mediated balancing selection in this system. We suggest that in systems where individual fitness does not increase monotonically with MHC diversity, assortative mating may help to avoid excessive offspring heterozygosity that could otherwise arise from long-standing balancing selection.
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Affiliation(s)
- Joel W. G. Slade
- Department of BiologyUniversity of Western OntarioLondonOntarioCanada
| | - Matthew J. Watson
- Department of BiologyUniversity of Western OntarioLondonOntarioCanada
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24
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Ch'ng ACW, Chan SK, Ignatius J, Lim TS. Human T-cell receptor V gene segment of alpha and beta families: A revised primer design strategy. Eur J Immunol 2019; 49:1186-1199. [PMID: 30919413 DOI: 10.1002/eji.201747328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 02/28/2019] [Accepted: 03/25/2019] [Indexed: 11/11/2022]
Abstract
The application of human TCR in cancer immunotherapy has gained momentum with developments in tumor killing strategies using endogenous adaptive immune responses. The successful coverage of a diverse TCR repertoire is mainly attributed to the primer design of the human TCR V genes. Here, we present a refined primer design strategy of the human TCR V gene by clustering V gene sequence homolog for degenerate primer design based on the data from IMGT. The primers designed were analyzed and the PCR efficiency of each primer set was optimized. A total of 112 alpha and 160 beta sequences were aligned and clustered using a phylogram yielding 32 and 27 V gene primers for the alpha and beta family. The new primer set was able to provide 93.75% and 95.63% coverage for the alpha and beta family, respectively. A semi-qualitative approach using the designed primer set was able to provide a relative view of the TCR V gene diversity in different populations. Taken together, the new primers provide a more comprehensive coverage of the TCR gene diversity for improved TCR library generation and TCR V gene analysis studies.
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Affiliation(s)
- Angela Chiew Wen Ch'ng
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Joshua Ignatius
- Warwick Manufacturing Group, University of Warwick, Coventry, United Kingdom
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.,Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia
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25
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Abstract
The IMGT/HLA Database has provided a repository for information regarding polymorphism in the genes of the immune system since 1998. In 2003, it was absorbed into the Immuno Polymorphism Database (IPD). The IPD project has enabled us to create and maintain a platform for curating and publishing locus-specific databases which are either involved directly with, or relate to, the function of the Major Histocompatibility Complex across a number of species. In collaboration with specialist groups and nomenclature committees individual sections have been curated prior to their submission to the IPD for online publication. The IPD consists of five core databases, with the primary database being the IMGT/HLA Database. With the work of various nomenclature committees, the HLA Informatics Group, and alongside the European Bioinformatics Institute, we provide access to this data through the website ( http://www.ebi.ac.uk/ipd/ ) to the public domain. The IPD project continually develops new tools in conjunction with on-going scientific developments-such as Next-Generation Sequencing-to maintain efficiency and usability in response to user feedback and requests. The website is updated on a regular basis to ensure that new and confirmatory sequences are distributed to the immunogenetics community, as well as the wider research and clinical communities.
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26
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Xiang SD, Wilson KL, Goubier A, Heyerick A, Plebanski M. Design of Peptide-Based Nanovaccines Targeting Leading Antigens From Gynecological Cancers to Induce HLA-A2.1 Restricted CD8 + T Cell Responses. Front Immunol 2018; 9:2968. [PMID: 30631324 PMCID: PMC6315164 DOI: 10.3389/fimmu.2018.02968] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/03/2018] [Indexed: 01/02/2023] Open
Abstract
Gynecological cancers are a leading cause of mortality in women. CD8+ T cell immunity largely correlates with enhanced survival, whereas inflammation is associated with poor prognosis. Previous studies have shown polystyrene nanoparticles (PSNPs) are biocompatible, do not induce inflammation and when used as vaccine carriers for model peptides induce CD8+ T cell responses. Herein we test the immunogenicity of 24 different peptides, from three leading vaccine target proteins in gynecological cancers: the E7 protein of human papilloma virus (HPV); Wilms Tumor antigen 1 (WT1) and survivin (SV), in PSNP conjugate vaccines. Of relevance to vaccine development was the finding that a minimal CD8+ T cell peptide epitope from HPV was not able to induce HLA-A2.1 specific CD8+ T cell responses in transgenic humanized mice using conventional adjuvants such as CpG, but was nevertheless able to generate strong immunity when delivered as part of a specific longer peptide conjugated to PSNPs vaccines. Conversely, in most cases, when the minimal CD8+ T cell epitopes were able to induce immune responses (with WT1 or SV super agonists) in CpG, they also induced responses when conjugated to PSNPs. In this case, extending the sequence around the CD8+ T cell epitope, using the natural protein context, or engineering linker sequences proposed to enhance antigen processing, had minimal effects in enhancing or changing the cross-reactivity pattern induced by the super agonists. Nanoparticle approaches, such as PSNPs, therefore may offer an alternative vaccination strategy when conventional adjuvants are unable to elicit the desired CD8+ T cell specificity. The findings herein also offer sequence specific insights into peptide vaccine design for nanoparticle-based vaccine carriers.
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Affiliation(s)
- Sue D Xiang
- Department of Immunology, Faculty of Medicine, Nursing and Health Sciences, Central Clinical School, Monash University, Melbourne, VIC, Australia.,PX Biosolutions Pty Ltd., South Melbourne, VIC, Australia.,Ovarian Cancer Biomarker Laboratory, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Kirsty L Wilson
- Department of Immunology, Faculty of Medicine, Nursing and Health Sciences, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Anne Goubier
- PX Biosolutions Pty Ltd., South Melbourne, VIC, Australia
| | - Arne Heyerick
- PX Biosolutions Pty Ltd., South Melbourne, VIC, Australia
| | - Magdalena Plebanski
- Department of Immunology, Faculty of Medicine, Nursing and Health Sciences, Central Clinical School, Monash University, Melbourne, VIC, Australia.,PX Biosolutions Pty Ltd., South Melbourne, VIC, Australia.,School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
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27
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Shen WJ, Zhang X, Zhang S, Liu C, Cui W. The Utility of Supertype Clustering in Prediction for Class II MHC-Peptide Binding. Molecules 2018; 23:molecules23113034. [PMID: 30463372 PMCID: PMC6278554 DOI: 10.3390/molecules23113034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 02/05/2023] Open
Abstract
MOTIVATION Extensive efforts have been devoted to understanding the antigenic peptides binding to MHC class I and II molecules since they play a fundamental role in controlling immune responses and due their involvement in vaccination, transplantation, and autoimmunity. The genes coding for the MHC molecules are highly polymorphic, and it is difficult to build computational models for MHC molecules with few know binders. On the other hand, previous studies demonstrated that some MHC molecules share overlapping peptide binding repertoires and attempted to group them into supertypes. Herein, we present a framework of the utility of supertype clustering to gain more information about the data to improve the prediction accuracy of class II MHC-peptide binding. RESULTS We developed a new method, called superMHC, for class II MHC-peptide binding prediction, including three MHC isotypes of HLA-DR, HLA-DP, and HLA-DQ, by using supertype clustering in conjunction with RLS regression. The supertypes were identified by using a novel repertoire dissimilarity index to quantify the difference in MHC binding specificities. The superMHC method achieves the state-of-the-art performance and is demonstrated to predict binding affinities to a series of MHC molecules with few binders accurately. These results have implications for understanding receptor-ligand interactions involved in MHC-peptide binding.
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Affiliation(s)
- Wen-Jun Shen
- Department of Bioinformatics, Shantou University Medical College, Shantou 515000, China.
| | - Xun Zhang
- Department of Bioinformatics, Shantou University Medical College, Shantou 515000, China.
| | - Shaohong Zhang
- Department of Computer Science, Guangzhou University, Guangzhou 510000, China.
| | - Cheng Liu
- Department of Bioinformatics, Shantou University Medical College, Shantou 515000, China.
| | - Wenjuan Cui
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China.
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28
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Koşaloğlu-Yalçın Z, Lanka M, Frentzen A, Logandha Ramamoorthy Premlal A, Sidney J, Vaughan K, Greenbaum J, Robbins P, Gartner J, Sette A, Peters B. Predicting T cell recognition of MHC class I restricted neoepitopes. Oncoimmunology 2018; 7:e1492508. [PMID: 30377561 PMCID: PMC6204999 DOI: 10.1080/2162402x.2018.1492508] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/31/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
Epitopes that arise from a somatic mutation, also called neoepitopes, are now known to play a key role in cancer immunology and immunotherapy. Recent advances in high-throughput sequencing have made it possible to identify all mutations and thereby all potential neoepitope candidates in an individual cancer. However, most of these neoepitope candidates are not recognized by T cells of cancer patients when tested in vivo or in vitro, meaning they are not immunogenic. Especially in patients with a high mutational load, usually hundreds of potential neoepitopes are detected, highlighting the need to further narrow down this candidate list. In our study, we assembled a dataset of known, naturally processed, immunogenic neoepitopes to dissect the properties that make these neoepitopes immunogenic. The tools to use and thresholds to apply for prioritizing neoepitopes have so far been largely based on experience with epitope identification in other settings such as infectious disease and allergy. Here, we performed a detailed analysis on our dataset of curated immunogenic neoepitopes to establish the appropriate tools and thresholds in the cancer setting. To this end, we evaluated different predictors for parameters that play a role in a neoepitope's immunogenicity and suggest that using binding predictions and length-rescaling yields the best performance in discriminating immunogenic neoepitopes from a background set of mutated peptides. We furthermore show that almost all neoepitopes had strong predicted binding affinities (as expected), but more surprisingly, the corresponding non-mutated peptides had nearly as high affinities. Our results provide a rational basis for parameters in neoepitope filtering approaches that are being commonly used. Abbreviations: SNV: single nucleotide variant; nsSNV: nonsynonymous single nucleotide variant; ROC: receiver operating characteristic; AUC: area under ROC curve; HLA: human leukocyte antigen; MHC: major histocompatibility complex; PD-1: Programmed cell death protein 1; PD-L1 or CTLA-4: cytotoxic T-lymphocyte associated protein 4.
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Affiliation(s)
- Zeynep Koşaloğlu-Yalçın
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Manasa Lanka
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Angela Frentzen
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | | | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Kerrie Vaughan
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Jason Greenbaum
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Paul Robbins
- Surgery Branch, National Cancer Institute, Bethesda, MD, USA
| | - Jared Gartner
- Surgery Branch, National Cancer Institute, Bethesda, MD, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, La Jolla, CA, USA
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29
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Hu S, Yuan F, Feng L, Zheng F, Gong F, Huang H, Sun B. KIR2DL2/C1 is a Risk Factor for Chronic Infection and Associated with Non-response to PEG-IFN and RBV Combination Therapy in Hepatitis C Virus Genotype 1b Patients in China. Virol Sin 2018; 33:369-372. [PMID: 30039498 DOI: 10.1007/s12250-018-0042-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022] Open
Affiliation(s)
- Song Hu
- Medical College, Jianghan University, Wuhan, 430056, China
| | - Fahu Yuan
- Medical College, Jianghan University, Wuhan, 430056, China
| | - Lingyan Feng
- Medical College, Jianghan University, Wuhan, 430056, China
| | - Fang Zheng
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Feili Gong
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hanju Huang
- Department of Pathogen Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Binlian Sun
- Medical College, Jianghan University, Wuhan, 430056, China.
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30
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Maccari G, Robinson J, Bontrop RE, Otting N, de Groot NG, Ho CS, Ballingall KT, Marsh SGE, Hammond JA. IPD-MHC: nomenclature requirements for the non-human major histocompatibility complex in the next-generation sequencing era. Immunogenetics 2018; 70:619-623. [PMID: 30027299 PMCID: PMC6182402 DOI: 10.1007/s00251-018-1072-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/03/2018] [Indexed: 12/25/2022]
Abstract
The IPD-MHC Database is the official repository for non-human MHC sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. To address the increasing amount and complexity of data being submitted, an entirely upgraded version of the IPD-MHC Database was recently released to maintain IPD-MHC as the central platform for the comparison of curated MHC data. As a consequence, a new level of nomenclature standardisation is required between the different species to enable data submission and to allow the unambiguous inter- and intra-species comparison of alleles. However, any changes must retain the flexibility demanded by the unique biology of different taxonomic groups. Here, we describe the rationale for a standardised nomenclature system and summarise the changes that have been driven by the requirements of implementing the IPD-MHC database. This modified nomenclature system is essential to maintain the current functionality of IPD-MHC and provide a scalable future-proof database organisation to fully exploit the bioinformatic tools used for analysis.
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Affiliation(s)
- Giuseppe Maccari
- The Pirbright Institute, Woking, Surrey, UK.,Anthony Nolan Research Institute, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | | | - Nel Otting
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | | | | | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
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31
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Khan N, Kumar R, Chauhan S, Farooq U. An immunoinformatics approach to promiscuous peptide design for the Plasmodium falciparum erythrocyte membrane protein-1. MOLECULAR BIOSYSTEMS 2018; 13:2160-2167. [PMID: 28856362 DOI: 10.1039/c7mb00332c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Plasmodium falciparum erythrocyte membrane protein-1 (Pfemp-1), a variant adhesion molecule, can act as a key component of immunity against malaria. In the current selection of malaria vaccines, no efficient vaccines are available that can be employed for its proper treatment. Unfortunately, resistance to post-infection treatments is increasing and therefore there is a pressing need to develop an efficient vaccine. Peptide-based vaccines can be effective tools against malaria but HLA restriction is a major hindrance which can be conquered by using promiscuous peptides. In this work, we employed a combined in silico and experimental approach to identify promiscuous peptides for the treatment of malaria. At first, using the immunoinformatics approach, promiscuous peptides were predicted from two conserved domains, CIDR-1 and DBL-3γ, of the Pfemp-1 antigen. These peptides were selected on the basis of their predicted binding affinity with different HLA class-I & class-II alleles. A total of 13 peptides were selected based on their predicted IFN-γ and IL-4 induction ability as well as their hydrophobicity. Out of these 13, the peptide C6 was synthesised and experimentally evaluated for further rationalization, HLA-peptide complex modelling and binding interaction analysis. Interestingly, the peptide C6 (SFIHIYLYRNIRIQL) showed an encouraging immunological response and T-cell proliferation in the immunological assay. This valuable content can aid the better design of more potent and selective vaccine candidates against infectious diseases.
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Affiliation(s)
- Nazam Khan
- Department of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, HP, India.
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32
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Angelone S, Jowers MJ, Molinar Min AR, Fandos P, Prieto P, Pasquetti M, Cano-Manuel FJ, Mentaberre G, Olvera JRL, Ráez-Bravo A, Espinosa J, Pérez JM, Soriguer RC, Rossi L, Granados JE. Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica). BMC Genet 2018; 19:28. [PMID: 29739323 PMCID: PMC5941765 DOI: 10.1186/s12863-018-0616-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/30/2018] [Indexed: 01/09/2023] Open
Abstract
Background Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is that isolated (and eventually small) wild animal populations hide unexpected genetic diversity due to their maintenance of ancient polymorphisms or introgressions. Results We tested this hypothesis using the Iberian ibex (Capra pyrenaica) as an example. Previous studies based on large sample sizes taken from its principal populations have revealed that the Iberian ibex has a remarkably small MHC DRB1 diversity (only six remnant alleles) as a result of recent population bottlenecks and a marked demographic decline that has led to the extinction of two recognized subspecies. Extending on the geographic range to include non-studied isolated Iberian ibex populations, we sequenced a new MHC DRB1 in what seemed three small isolated populations in Southern Spain (n = 132). The findings indicate a higher genetic diversity than previously reported in this important gene. The newly discovered allele, MHC DRB1*7, is identical to one reported in the domestic goat C. aegagrus hircus. Whether or not this is the result of ancient polymorphisms maintained by balancing selection or, alternatively, introgressions from domestic goats through hybridization needs to be clarified in future studies. However, hybridization between Iberian ibex and domestic goats has been reported in Spain and the fact that the newly discovered allele is only present in one of the small isolated populations and not in the others suggests introgression. The new discovered allele is not expected to increase fitness in C. pyrenaica since it generates the same protein as the existing MHC DRB1*6. Analysis of a microsatellite locus (OLADRB1) near the new MHC DRB1*7 gene reveals a linkage disequilibrium between these two loci. The allele OLADRB1, 187 bp in length, was unambiguously linked to the MHC DRB1*7 allele. This enabled us to perform a DRB-STR matching method for the recently discovered MHC allele. Conclusions This finding is critical for the conservation of the Iberian ibex since it directly affects the identification of the units of this species that should be managed and conserved separately (Evolutionarily Significant Units). Electronic supplementary material The online version of this article (10.1186/s12863-018-0616-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samer Angelone
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio s/n, 41092, Sevilla, Spain. .,Institute of Evolutionary Biology and Environmental Studies (IEU), University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.
| | - Michael J Jowers
- CIBIO/ InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Universidade do Porto, Campus Agrario De Vairão, 4485-661, Vairão, Portugal
| | - Anna Rita Molinar Min
- Dipartimento di Scienze Veterinarie, Universita` degli Studi di Torino, Grugliasco, Italy
| | - Paulino Fandos
- Agencia de Medio Ambiente y Agua, E-41092, Sevilla, Isla de la Cartuja, Spain
| | - Paloma Prieto
- Parque Natural Sierras de Cazorla, Segura y Las Villas, Martínez Falero11, E-23470, Cazorla, Jaén, Spain
| | - Mario Pasquetti
- Dipartimento di Scienze Veterinarie, Universita` degli Studi di Torino, Grugliasco, Italy
| | | | - Gregorio Mentaberre
- Servei d'Ecopatologia de Fauna Salvatge (SEFAS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), E-08193 Bellaterra, Barcelona, Spain
| | - Jorge Ramón López Olvera
- Servei d'Ecopatologia de Fauna Salvatge (SEFAS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), E-08193 Bellaterra, Barcelona, Spain
| | - Arián Ráez-Bravo
- Servei d'Ecopatologia de Fauna Salvatge (SEFAS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), E-08193 Bellaterra, Barcelona, Spain
| | - José Espinosa
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus Las Lagunillas, s.n., E-23071, Jaén, Spain
| | - Jesús M Pérez
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus Las Lagunillas, s.n., E-23071, Jaén, Spain
| | - Ramón C Soriguer
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio s/n, 41092, Sevilla, Spain
| | - Luca Rossi
- Dipartimento di Scienze Veterinarie, Universita` degli Studi di Torino, Grugliasco, Italy
| | - José Enrique Granados
- Espacio Natural Sierra Nevada, Carretera Antigua de Sierra Nevada, Km 7, E-18071, Pinos Genil, Granada, Spain
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Zingsem J, Hauck-Dlimi B, Dullinger K, Weisbach V, Strobel J. Identification of the novel allele, HLA-C*01:136 in a German cord blood donor originating from Azerbaijan. HLA 2018; 91:305-306. [DOI: 10.1111/tan.13233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 11/30/2022]
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Strobel J, Hauck-Dlimi B, Dullinger K, Weisbach V, Zingsem J. Identification of the novel allele, HLA-A*01:234, in the mother of a German cord blood donor. HLA 2018; 91:530-531. [PMID: 29469182 DOI: 10.1111/tan.13241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 02/17/2018] [Indexed: 10/18/2022]
Abstract
HLA-A*01:234 was identified by next-generation sequencing and confirmed by Sanger sequencing.
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Affiliation(s)
- J Strobel
- Department of Transfusion Medicine and Haemostaseology, University Hospital Erlangen-Nuremberg, Erlangen, Germany
| | - B Hauck-Dlimi
- Department of Transfusion Medicine and Haemostaseology, University Hospital Erlangen-Nuremberg, Erlangen, Germany
| | - K Dullinger
- Department of Transfusion Medicine and Haemostaseology, University Hospital Erlangen-Nuremberg, Erlangen, Germany
| | - V Weisbach
- Department of Transfusion Medicine and Haemostaseology, University Hospital Erlangen-Nuremberg, Erlangen, Germany
| | - J Zingsem
- Department of Transfusion Medicine and Haemostaseology, University Hospital Erlangen-Nuremberg, Erlangen, Germany
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35
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Althaf MM, El Kossi M, Jin JK, Sharma A, Halawa AM. Human leukocyte antigen typing and crossmatch: A comprehensive review. World J Transplant 2017; 7:339-348. [PMID: 29312863 PMCID: PMC5743871 DOI: 10.5500/wjt.v7.i6.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/22/2017] [Accepted: 10/17/2017] [Indexed: 02/05/2023] Open
Abstract
Renal transplantation remains the best option for patients suffering from end stage renal disease (ESRD). Given the worldwide shortage of organs and growing population of patients with ESRD, those waitlisted for a transplant is ever expanding. Contemporary crossmatch methods and human leukocyte antigen (HLA) typing play a pivotal role in improving organ allocation and afford better matches to recipients. Understanding crossmatch as well as HLA typing for renal transplantation and applying it in clinical practice is the key step to achieve a successful outcome. Interpretation of crossmatch results can be quite challenging where clinicians have not had formal training in applied transplant immunology. This review aims to provide a worked example using a clinical vignette. Furthermore, each technique is discussed in detail with its pros and cons. The index case is that of a young male with ESRD secondary to Lupus nephritis. He is offered a deceased donor kidney with a 1-0-0 mismatch. His complement dependent cytotoxicity (CDC) crossmatch reported positive for B lymphocyte, but flow cytometry crossmatch (FCXM) was reported negative for both B and T lymphocytes. Luminex-SAB (single antigen bead) did not identify any donor specific antibodies (DSA). He never had a blood transfusion. The positive CDC-crossmatch result is not concordant with DSA status. These implausible results are due to underlying lupus erythematosus, leading to false-positive B-lymphocyte crossmatch as a result of binding immune complexes to Fc-receptors. False positive report of CDC crossmatch can be caused by the underlying autoimmune diseases such as lupus erythematosus, that may lead to inadvertent refusal of adequate kidney grafts. Detailed study of DSA by molecular technique would prevent wrong exclusion of such donors. Based on these investigations this patient is deemed to have "standard immunological risk" for renal transplantation.
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Affiliation(s)
- Mohammed Mahdi Althaf
- Jack Pryor Renal Unit, Norfolk and Norwich University Hospital - NHS Foundation Trust, Norwich NR4 7UY, United Kingdom
- Faculty of Health and Science, University of Liverpool, Institute of Learning and Teaching, School of Medicine, Liverpool L69 3GB, United Kingdom
| | - Mohsen El Kossi
- Faculty of Health and Science, University of Liverpool, Institute of Learning and Teaching, School of Medicine, Liverpool L69 3GB, United Kingdom
- Doncaster Royal Infirmary, Doncaster DN2 5LT, United Kingdom
| | - Jon Kim Jin
- Faculty of Health and Science, University of Liverpool, Institute of Learning and Teaching, School of Medicine, Liverpool L69 3GB, United Kingdom
- Nottingham Children Hospital, Nottingham NG7 2UH, United Kingdom
| | - Ajay Sharma
- Faculty of Health and Science, University of Liverpool, Institute of Learning and Teaching, School of Medicine, Liverpool L69 3GB, United Kingdom
- Royal Liverpool University Hospitals, Liverpool L7 8XP, United Kingdom
| | - Ahmed Mostafa Halawa
- Faculty of Health and Science, University of Liverpool, Institute of Learning and Teaching, School of Medicine, Liverpool L69 3GB, United Kingdom
- Department of Transplantation Surgery, Sheffield Teaching Hospitals, Sheffield S5 7AU, United Kingdom
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36
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Dhanda SK, Usmani SS, Agrawal P, Nagpal G, Gautam A, Raghava GPS. Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics. Brief Bioinform 2017; 18:467-478. [PMID: 27016393 DOI: 10.1093/bib/bbw025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 12/19/2022] Open
Abstract
The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using the whole pathogen responsible for the disease. In the post-genomic era, a major challenge is to identify antigenic regions or epitopes that can stimulate different arms of the immune system. In the past two decades, numerous methods and databases have been developed for designing vaccine or immunotherapy against various pathogen-causing diseases. This review describes various computational resources important for designing subunit vaccines or epitope-based immunotherapy. First, different immunological databases are described that maintain epitopes, antigens and vaccine targets. This is followed by in silico tools used for predicting linear and conformational B-cell epitopes required for activating humoral immunity. Finally, information on T-cell epitope prediction methods is provided that includes indirect methods like prediction of Major Histocompatibility Complex and transporter-associated protein binders. Different studies for validating the predicted epitopes are also examined critically. This review enlists novel in silico resources and tools available for predicting humoral and cell-mediated immune potential. These predicted epitopes could be used for designing epitope-based vaccines or immunotherapy as they may activate the adaptive immunity. Authors emphasized the need to develop tools for the prediction of adjuvants to activate innate and adaptive immune system simultaneously. In addition, attention has also been given to novel prediction methods to predict general therapeutic properties of peptides like half-life, cytotoxicity and immune toxicity.
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37
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Terao C, Okada Y, Ikari K, Kochi Y, Suzuki A, Ohmura K, Matsuo K, Taniguchi A, Kubo M, Raychaudhuri S, Yamamoto K, Yamanaka H, Kamatani Y, Mimori T, Matsuda F. Genetic landscape of interactive effects of HLA-DRB1 alleles on susceptibility to ACPA(+) rheumatoid arthritis and ACPA levels in Japanese population. J Med Genet 2017; 54:853-858. [PMID: 29025870 DOI: 10.1136/jmedgenet-2017-104779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/28/2017] [Accepted: 09/18/2017] [Indexed: 11/04/2022]
Abstract
BACKGROUND HLA-DRB1 is the strongest susceptibility gene to rheumatoid arthritis (RA). HLA-DRB1 alleles showed significant non-additive and interactive effects on susceptibility to RA in the European population, but these effects on RA susceptibility should vary between populations due to the difference in allelic distribution. Furthermore, non-additive or interactive effects on the phenotypes of RA are not fully known. We evaluated the non-additive and interactive effects of HLA-DRB1 alleles on RA susceptibility and anticitrullinated protein/peptide antibody (ACPA) levels in Japanese patients. METHODS A total of 5581 ACPA(+) RA and 19 170 controls were genotyped or imputed for HLA-DRB1 alleles. Logistic regression analysis was performed for both allelic non-additive effects and interactive effects of allelic combinations. The significant levels were set by Bonferroni's correction. A total of 4371 ACPA(+) RA were analysed for ACPA levels. RESULTS We obtained evidence of non-additive and interactive effects of HLA-DRB1 on ACPA(+) RA susceptibility (p=2.5×10-5 and 1.5×10-17, respectively). Multiple HLA-DRB1 alleles including HLA-DRB1*04:05, the most common susceptibility allele in the Japanese, showed significant non-additive effects (p≤0.0043). We identified multiple allelic combinations with significant interactive effects including a common combination with the European population as well as novel combinations. Additional variance of ACPA(+) RA susceptibility could be explained substantially by heterozygote dominance or interactive effects. We did not find evidence of non-additive and interactive effects on levels of ACPA. CONCLUSION HLA allelic non-additive and interactive effects on ACPA(+) RA susceptibility were observed in the Japanese population. The allelic non-additive and interactive effects depend on allelic distribution in populations.
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Affiliation(s)
- Chikashi Terao
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan.,Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory of Statistical Immunology, Immunology, Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Atsuo Taniguchi
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hisashi Yamanaka
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Distribution of HLA-A, -B and -DRB1 antigenic groups and haplotypes from the Brazilian bone marrow donor registry (REDOME). Hum Immunol 2017; 78:602-609. [DOI: 10.1016/j.humimm.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 07/08/2017] [Accepted: 08/08/2017] [Indexed: 11/19/2022]
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39
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Chen X, Poncette L, Blankenstein T. Human TCR-MHC coevolution after divergence from mice includes increased nontemplate-encoded CDR3 diversity. J Exp Med 2017; 214:3417-3433. [PMID: 28835417 PMCID: PMC5679170 DOI: 10.1084/jem.20161784] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 06/19/2017] [Accepted: 07/19/2017] [Indexed: 12/14/2022] Open
Abstract
Chen et al. demonstrate that human MHC selects a larger human TCR repertoire than mouse MHC. They show how humans optimized TCR diversity and suggest that CDR3 length adjusts for different V segment–MHC affinity. For thymic selection and responses to pathogens, T cells interact through their αβ T cell receptor (TCR) with peptide–major histocompatibility complex (MHC) molecules on antigen-presenting cells. How the diverse TCRs interact with a multitude of MHC molecules is unresolved. It is also unclear how humans generate larger TCR repertoires than mice do. We compared the TCR repertoire of CD4 T cells selected from a single mouse or human MHC class II (MHC II) in mice containing the human TCR gene loci. Human MHC II yielded greater thymic output and a more diverse TCR repertoire. The complementarity determining region 3 (CDR3) length adjusted for different inherent V-segment affinities to MHC II. Humans evolved with greater nontemplate-encoded CDR3 diversity than did mice. Our data, which demonstrate human TCR–MHC coevolution after divergence from rodents, explain the greater T cell diversity in humans and suggest a mechanism for ensuring that any V–J gene combination can be selected by a single MHC II.
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Affiliation(s)
- Xiaojing Chen
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Charité Campus Buch, Institute of Immunology, Berlin, Germany
| | - Lucia Poncette
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Thomas Blankenstein
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany .,Charité Campus Buch, Institute of Immunology, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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40
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Mumtaz S, Nabney IT, Flower DR. Scrutinizing human MHC polymorphism: Supertype analysis using Poisson-Boltzmann electrostatics and clustering. J Mol Graph Model 2017; 77:130-136. [PMID: 28850895 DOI: 10.1016/j.jmgm.2017.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/25/2017] [Indexed: 11/26/2022]
Abstract
Peptide-binding MHC proteins are thought the most variable across the human population; the extreme MHC polymorphism observed is functionally important and results from constrained divergent evolution. MHCs have vital functions in immunology and homeostasis: cell surface MHC class I molecules report cell status to CD8+ T cells, NKT cells and NK cells, thus playing key roles in pathogen defence, as well as mediating smell recognition, mate choice, Adverse Drug Reactions, and transplantation rejection. MHC peptide specificity falls into several supertypes exhibiting commonality of binding. It seems likely that other supertypes exist relevant to other functions. Since comprehensive experimental characterization is intractable, structure-based bioinformatics is the only viable solution. We modelled functional MHC proteins by homology and used calculated Poisson-Boltzmann electrostatics projected from the top surface of the MHC as multi-dimensional descriptors, analysing them using state-of-the-art dimensionality reduction techniques and clustering algorithms. We were able to recover the 3 MHC loci as separate clusters and identify clear sub-groups within them, vindicating unequivocally our choice of both data representation and clustering strategy. We expect this approach to make a profound contribution to the study of MHC polymorphism and its functional consequences, and, by extension, other burgeoning structural systems, such as GPCRs.
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Affiliation(s)
- Shahzad Mumtaz
- School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom; Department of Computer Science, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Ian T Nabney
- School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom
| | - Darren R Flower
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom.
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41
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Sullivan HC, Gebel HM, Bray RA. Understanding solid-phase HLA antibody assays and the value of MFI. Hum Immunol 2017; 78:471-480. [DOI: 10.1016/j.humimm.2017.05.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 05/26/2017] [Accepted: 05/29/2017] [Indexed: 01/10/2023]
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42
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Liu XS, Mardis ER. Applications of Immunogenomics to Cancer. Cell 2017; 168:600-612. [PMID: 28187283 DOI: 10.1016/j.cell.2017.01.014] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 01/05/2023]
Abstract
Cancer immunogenomics originally was framed by research supporting the hypothesis that cancer mutations generated novel peptides seen as "non-self" by the immune system. The search for these "neoantigens" has been facilitated by the combination of new sequencing technologies, specialized computational analyses, and HLA binding predictions that evaluate somatic alterations in a cancer genome and interpret their ability to produce an immune-stimulatory peptide. The resulting information can characterize a tumor's neoantigen load, its cadre of infiltrating immune cell types, the T or B cell receptor repertoire, and direct the design of a personalized therapeutic.
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Affiliation(s)
- X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, 450 Brookline Ave, Boston MA 02215, USA.
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, and The Ohio State University College of Medicine, 575 Children's Crossroad, Columbus OH 43205, USA.
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43
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Understanding CD8 + T-cell responses toward the native and alternate HLA-A*02:01-restricted WT1 epitope. Clin Transl Immunology 2017; 6:e134. [PMID: 28435676 PMCID: PMC5382434 DOI: 10.1038/cti.2017.4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 01/09/2023] Open
Abstract
The Wilms' tumor 1 (WT1) antigen is expressed in solid and hematological malignancies, but not healthy tissues, making it a promising target for cancer immunotherapies. Immunodominant WT1 epitopes, the native HLA-A2/WT1126-134 (RMFPNAPYL) (HLA-A2/RMFPNAPYL epitope (WT1A)) and its modified variant YMFPNAPYL (HLA-A2/YMFPNAPYL epitope (WT1B)), can induce WT1-specific CD8+ T cells, although WT1B is more stably bound to HLA-A*02:01. Here, to further determine the benefits of those two targets, we assessed the naive precursor frequencies; immunogenicity and cross-reactivity of CD8+ T cells directed toward these two WT1 epitopes. Ex vivo naive WT1A- and WT1B-specific CD8+ T cells were detected in healthy HLA-A*02:01+ individuals with comparable precursor frequencies (1 in 105–106) to other naive CD8+ T-cell pools (for example, A2/HIV-Gag77-85), but as expected, ~100 × lower than those found in memory populations (influenza, A2/M158-66; EBV, A2/BMLF1280-288). Importantly, only WT1A-specific naive precursors were detected in HLA-A2.1 mice. To further assess the immunogenicity and recruitment of CD8+ T cells responding to WT1A and WT1B, we immunized HLA-A2.1 mice with either peptide. WT1A immunization elicited numerically higher CD8+ T-cell responses to the native tumor epitope following re-stimulation, although both regimens produced functionally similar responses toward WT1A via cytokine analysis and CD107a expression. Interestingly, however, WT1B immunization generated cross-reactive CD8+ T-cell responses to WT1A and could be further expanded by WT1A peptide revealing two distinct populations of single- and cross-reactive WT1A+CD8+ T cells with unique T-cell receptor-αβ gene signatures. Therefore, although both epitopes are immunogenic, the clinical benefits of WT1B vaccination remains debatable and perhaps both peptides may have separate clinical benefits as treatment targets.
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Pourhashem Z, Mehrpouya M, Yardehnavi N, Eslamparast A, Kazemi-Lomedasht F. An in-silico approach to find a peptidomimetic targeting extracellular domain of HER3 from a HER3 Nanobody. Comput Biol Chem 2017; 68:39-42. [PMID: 28235665 DOI: 10.1016/j.compbiolchem.2017.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 01/01/2017] [Accepted: 02/02/2017] [Indexed: 12/11/2022]
Abstract
HER3 is an important therapeutic target in cancer treatments. HER3 Nanobodies (Nbs) are a novel class of antibodies with several competitive advantages over conventional antibodies. A peptidomimetic derived from these Nbs can be considered to be a small peptide mimicking some of the molecular recognition interactions of a natural peptide or protein in a three-dimensional (3D) space, with a receptor that has improved properties. In this study, we introduce a new approach to design a peptidomimetic derived from HER3 Nb through an in silico analysis. We propose that the complementarity determining region (CDR3) of HER3 Nb is large enough to effectively interact with HER3 antigen as well as with the entire Nb. A computational analysis has been performed using Nb models retrieved from SWISS-pdb Viewer 4.1.0 (spdbv) as a target spot and HER3 extracellular domain as its antigenic target to identify the interactions between them by the protein-protein docking method. Detailed analysis of selected models with docked complex help us to identify the interacting amino acid residues between the two molecules. The results of in silico analysis show that the CDR3 of HER3 Nb might be used by itself as a peptidomimetic drug instead of the full Nb. HER3 peptidomimetic-derived HER3 Nb may reduce Nb production costs and be used as a substitute for HER3 Nb after further experimental work. The paper demonstrates the feasibility of peptidomimetics designs using bioinformatic tools.
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Affiliation(s)
- Z Pourhashem
- School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - M Mehrpouya
- School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - N Yardehnavi
- Laboratory Science Research Center, Golestan University of Medical Sciences, Gorgan, Iran; School of Advanced Technologies in Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
| | - A Eslamparast
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - F Kazemi-Lomedasht
- Biotechnology Research Center, Venom & Biotherapeutics Molecules Lab., Pasteur Institute of Iran, Tehran, Iran
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45
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de Groot N, Stanbury K, de Vos-Rouweler AJM, de Groot NG, Poirier N, Blancho G, de Luna C, Doxiadis GGM, Bontrop RE. A quick and robust MHC typing method for free-ranging and captive primate species. Immunogenetics 2017; 69:231-240. [PMID: 28084496 PMCID: PMC5350218 DOI: 10.1007/s00251-016-0968-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) of human and non-human primates play a crucial role in adaptive immunity, and most of the relevant genes not only show a high degree of variability (polymorphism) but also copy number variation (CNV) is observed. Due to this diversity, MHC proteins influence the capability of individuals to cope with various pathogens. MHC and/or MHC-linked gene products such as odorant receptor genes are thought to influence mate choice and reproductive success. Therefore, MHC typing of wild and captive primate populations is considered to be useful in conservation biology, which is, however, often hampered by the need of invasive and time-consuming methods. All intact Mhc-DRB genes in primates appear to possess a complex and highly divergent microsatellite, DRB-STR. A panel of 154 pedigreed olive baboons (Papio anubis) was examined for their DRB content by DRB-STR analysis of genomic DNA. Using the same methodology on DNA of feces samples, DRB variability of a silvery gibbon population (Hylobates moloch) (N = 24), an endangered species, could successfully be studied. In both species, length determination of the DRB-STR resulted in the definition of unique genotyping patterns that appeared to be specific for a certain chromosome. Moreover, the different STR lengths were shown to segregate with the allelic variation of the respective gene. The results obtained expand data gained previously on DRB-STR typing in macaques, great apes, and humans and strengthen the conclusion that this protocol is applicable in molecular ecology, conservation biology, and colony management, especially of endangered primate species.
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Affiliation(s)
- N de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - K Stanbury
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - A J M de Vos-Rouweler
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N Poirier
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - G Blancho
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - C de Luna
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - G G M Doxiadis
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - R E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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46
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Carapito R, Radosavljevic M, Bahram S. Next-Generation Sequencing of the HLA locus: Methods and impacts on HLA typing, population genetics and disease association studies. Hum Immunol 2016; 77:1016-1023. [DOI: 10.1016/j.humimm.2016.04.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/15/2016] [Accepted: 04/04/2016] [Indexed: 12/30/2022]
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Wu JD, Zhang WJ, Zhang L, Zuo WZ, Lu LJ, Ding YL, Yang DL. A novel HLA-DRB1 allele, DRB1*16:36 identified in a Chinese individual from the Xinjiang region. ACTA ACUST UNITED AC 2016; 86:389-90. [PMID: 26467900 DOI: 10.1111/tan.12677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/05/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022]
Abstract
A novel class II human leukocyte antigen allele HLA-DRB1*16:36 is described.
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Affiliation(s)
- J-D Wu
- Department of Infectious Diseases, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - W-J Zhang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - L Zhang
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - W-Z Zuo
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - L-J Lu
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Y-L Ding
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - D-L Yang
- Department of Infectious Diseases, Union Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Abbas M, Berka N, Khraiwesh M, Ramadan A, Apprey V, Furbert-Harris P, Quinn T, Brim H, Dunston G. Genetic Polymorphisms of TLR4 and MICA are Associated with Severity of Trachoma Disease in Tanzania. ACTA ACUST UNITED AC 2016; 2. [PMID: 27559544 PMCID: PMC4993598 DOI: 10.16966/2470-1025.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aim To examine the association of TLR4 Asp299Gly and MICA exon 5 microsatellites polymorphisms with severity of trachoma in a sub-Saharan East Africa population of Tanzanian villagers. Methods The samples were genotyped for MICA exon 5 microsatellites and the TLR4 299 A/G polymorphism by Restriction Fragment Length Polymorphism (RFLP), and GeneScan®, respectively. The association of TLR4 Asp299Gly and MICA exon 5 microsatellites with inflammatory trachoma (TI) and trichiasis (TI) were examined. Results The results showed an association between TLR4 and MICA polymorphisms and trachoma disease severity, as well as with protection. TLR4 an allele was significantly associated with inflammatory trachoma (p=0.0410), while the G allele (p=0.0410) was associated with protection. Conclusion TLR4 and MICA may modulate the risk of severity to trachoma disease by modulating the immune response to Ct. In addition; the increased frequency of MICA-A9 heterozygote in controls may suggest a positive selection of these alleles in adaptation to environments where Ct is endemic.
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Affiliation(s)
- Muneer Abbas
- Department of Microbiology, Howard University, Washington, DC, USA
| | | | - Mozna Khraiwesh
- Division of Experimental Therapeutics, Department of Drug Discovery, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Ali Ramadan
- Department of Pathology, Howard University Hospital, Washington, DC, USA
| | - Victor Apprey
- Department of Microbiology, Howard University, Washington, DC, USA; Department of Community Health and Family Medicine, Howard University, Washington DC, USA
| | | | - Thomas Quinn
- International Health, School of Medicine, Johns Hopkins University, Baltimore Maryland, USA
| | - Hassan Brim
- Department of Pathology, Howard University Hospital, Washington, DC, USA
| | - Georgia Dunston
- Department of Microbiology, Howard University, Washington, DC, USA
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Grogan KE, McGinnis GJ, Sauther ML, Cuozzo FP, Drea CM. Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications. BMC Genomics 2016; 17:204. [PMID: 26957424 PMCID: PMC4782575 DOI: 10.1186/s12864-016-2503-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/18/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Across species, diversity at the Major Histocompatibility Complex (MHC) is critical to disease resistance and population health; however, use of MHC diversity to quantify the genetic health of populations has been hampered by the extreme variation found in MHC genes. Next generation sequencing (NGS) technology generates sufficient data to genotype even the most diverse species, but workflows for distinguishing artifacts from alleles are still under development. We used NGS to evaluate the MHC diversity of over 300 captive and wild ring-tailed lemurs (Lemur catta: Primates: Mammalia). We modified a published workflow to address errors that arise from deep sequencing individuals and tested for evidence of selection at the most diverse MHC genes. RESULTS In addition to evaluating the accuracy of 454 Titanium and Ion Torrent PGM for genotyping large populations at hypervariable genes, we suggested modifications to improve current methods of allele calling. Using these modifications, we genotyped 302 out of 319 individuals, obtaining an average sequencing depth of over 1000 reads per amplicon. We identified 55 MHC-DRB alleles, 51 of which were previously undescribed, and provide the first sequences of five additional MHC genes: DOA, DOB, DPA, DQA, and DRA. The additional five MHC genes had one or two alleles each with little sequence variation; however, the 55 MHC-DRB alleles showed a high dN/dS ratio and trans-species polymorphism, indicating a history of positive selection. Because each individual possessed 1-7 MHC-DRB alleles, we suggest that ring-tailed lemurs have four, putatively functional, MHC-DRB copies. CONCLUSIONS In the future, accurate genotyping methods for NGS data will be critical to assessing genetic variation in non-model species. We recommend that future NGS studies increase the proportion of replicated samples, both within and across platforms, particularly for hypervariable genes like the MHC. Quantifying MHC diversity within non-model species is the first step to assessing the relationship of genetic diversity at functional loci to individual fitness and population viability. Owing to MHC-DRB diversity and copy number, ring-tailed lemurs may serve as an ideal model for estimating the interaction between genetic diversity, fitness, and environment, especially regarding endangered species.
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Affiliation(s)
- Kathleen E Grogan
- University Program in Ecology, Duke University, Durham, NC, USA.
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.
- Emory University, Room 2006 O. Wayne Rollins Research Center, 1510 Clifton Rd NE, Atlanta, GA, 30322, USA.
| | | | - Michelle L Sauther
- Department of Anthropology, University of Colorado-Boulder, Boulder, CO, USA
| | - Frank P Cuozzo
- Department of Anthropology, University of North Dakota, Grand Forks, ND, USA
| | - Christine M Drea
- University Program in Ecology, Duke University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biology, Duke University, Durham, USA
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Jin SZ, Li Z, Zou HY. Identification of a novelHLA-A*02 allele,HLA-A*02:432, in a Chinese individual. HLA 2015; 87:37-8. [DOI: 10.1111/tan.12718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/02/2015] [Accepted: 11/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- S.-Z. Jin
- Immunogenetic Laboratory; Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center; Shenzhen Guangdong China
| | - Z. Li
- Immunogenetic Laboratory; Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center; Shenzhen Guangdong China
| | - H.-Y. Zou
- Immunogenetic Laboratory; Shenzhen Institute of Transfusion Medicine, Shenzhen Blood Center; Shenzhen Guangdong China
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