1
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Zou DD, Sun YZ, Li XJ, Wu WJ, Xu D, He YT, Qi J, Tu Y, Tang Y, Tu YH, Wang XL, Li X, Lu FY, Huang L, Long H, He L, Li X. Single-cell sequencing highlights heterogeneity and malignant progression in actinic keratosis and cutaneous squamous cell carcinoma. eLife 2023; 12:e85270. [PMID: 38099574 PMCID: PMC10783873 DOI: 10.7554/elife.85270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as a precancerous lesion. To comprehensively delineate the underlying mechanisms for the whole progression from normal skin to AK to invasive cSCC, we performed single-cell RNA sequencing (scRNA-seq) to acquire the transcriptomes of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC, and their matched normal tissues, covering comprehensive clinical courses of cSCC. We identified diverse cell types, including important subtypes with different gene expression profiles and functions in major keratinocytes. In SCCIS, we discovered the malignant subtypes of basal cells with differential proliferative and migration potential. Differentially expressed genes (DEGs) analysis screened out multiple key driver genes including transcription factors along AK to cSCC progression. Immunohistochemistry (IHC)/immunofluorescence (IF) experiments and single-cell ATAC sequencing (scATAC-seq) data verified the expression changes of these genes. The functional experiments confirmed the important roles of these genes in regulating cell proliferation, apoptosis, migration, and invasion in cSCC tumor. Furthermore, we comprehensively described the tumor microenvironment (TME) landscape and potential keratinocyte-TME crosstalk in cSCC providing theoretical basis for immunotherapy. Together, our findings provide a valuable resource for deciphering the progression from AK to cSCC and identifying potential targets for anticancer treatment of cSCC.
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Affiliation(s)
- Dan-Dan Zou
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
- Department of Dermatology, The Affiliated Hospital of Kunming University of Science and Technology, The First People's Hospital of Yunnan Province, KunmingYunnanChina
| | - Ya-Zhou Sun
- Clinical Big Data Research Center, The Seventh Affiliated Hospital of Sun Yat-sen UniversityShenzhen, GuangdongChina
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
| | - Xin-Jie Li
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
| | - Wen-Juan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Dan Xu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Yu-Tong He
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
| | - Jue Qi
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Ying Tu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Yang Tang
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Yun-Hua Tu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Xiao-Li Wang
- Department of Dermatology, Changzheng Hospital, Naval Medical UniversityShanghaiChina
| | - Xing Li
- Department of Dermatology, People's Hospital of Chuxiong Yi Autonomous Prefecture, ChuxiongYunnanChina
| | - Feng-Yan Lu
- Department of Dermatology, Qujing Affiliated Hospital of Kunming Medical University, The First People’s Hospital of QujingYunnanChina
| | - Ling Huang
- Department of Dermatology, First Affiliated Hospital of Dali University, DaliYunnanChina
| | - Heng Long
- Wenshan Zhuang and Miao Autonomous Prefecture Dermatology Clinic, Wenshan Zhuang and Miao Autonomous Prefecture Specialist Hospital of Dermatology, WenshanYunnanChina
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical UniversityYunnanChina
| | - Xin Li
- School of Medical, Shenzhen Campus of Sun Yat-sen UniversityShenzhen, GuangdongChina
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen UniversityGuangdongChina
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2
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Mittra S, Harding SM, Kaech SM. Memory T Cells in the Immunoprevention of Cancer: A Switch from Therapeutic to Prophylactic Approaches. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:907-916. [PMID: 37669503 PMCID: PMC10491418 DOI: 10.4049/jimmunol.2300049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/24/2023] [Indexed: 09/07/2023]
Abstract
Cancer immunoprevention, the engagement of the immune system to prevent cancer, is largely overshadowed by therapeutic approaches to treating cancer after detection. Vaccines or, alternatively, the utilization of genetically engineered memory T cells could be methods of engaging and creating cancer-specific T cells with superb memory, lenient activation requirements, potent antitumor cytotoxicity, tumor surveillance, and resilience against immunosuppressive factors in the tumor microenvironment. In this review we analyze memory T cell subtypes based on their potential utility in cancer immunoprevention with regard to longevity, localization, activation requirements, and efficacy in fighting cancers. A particular focus is on how both tissue-resident memory T cells and stem memory T cells could be promising subtypes for engaging in immunoprevention.
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Affiliation(s)
- Siddhesh Mittra
- University of Toronto Schools, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shane M. Harding
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Departments of Radiation Oncology and Immunology, University of Toronto; Toronto, Canada
| | - Susan M. Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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3
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Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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4
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Nuñez-Corona D, Contreras-Sanzón E, Puente-Rivera J, Arreola R, Camacho-Nuez M, Cruz Santiago J, Estrella-Parra EA, Torres-Romero JC, López-Camarillo C, Alvarez-Sánchez ME. Epigenetic Factors and ncRNAs in Testicular Cancer. Int J Mol Sci 2023; 24:12194. [PMID: 37569569 PMCID: PMC10418327 DOI: 10.3390/ijms241512194] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Testicular cancer is the most prevalent tumor among males aged 15 to 35, resulting in a significant number of newly diagnosed cases and fatalities annually. Non-coding RNAs (ncRNAs) have emerged as key regulators in various cellular processes and pathologies, including testicular cancer. Their involvement in gene regulation, coding, decoding, and overall gene expression control suggests their potential as targets for alternative treatment approaches for this type of cancer. Furthermore, epigenetic modifications, such as histone modifications, DNA methylation, and the regulation by microRNA (miRNA), have been implicated in testicular tumor progression and treatment response. Epigenetics may also offer critical insights for prognostic evaluation and targeted therapies in patients with testicular germ cell tumors (TGCT). This comprehensive review aims to present the latest discoveries regarding the involvement of some proteins and ncRNAs, mainly miRNAs and lncRNA, in the epigenetic aspect of testicular cancer, emphasizing their relevance in pathogenesis and their potential, given the fact that their specific expression holds promise for prognostic evaluation and targeted therapies.
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Affiliation(s)
- David Nuñez-Corona
- Posgrado en Ciencias Genómicas, Universidad Autónoma De México (UACM), San Lorenzo 290, Col. Del Valle, México City 03100, Mexico
| | - Estefania Contreras-Sanzón
- Posgrado en Ciencias Genómicas, Universidad Autónoma De México (UACM), San Lorenzo 290, Col. Del Valle, México City 03100, Mexico
| | | | - Rodrigo Arreola
- Departamento De Genética, Instituto Nacional De Psiquiatría “Ramón De la Fuente Muñiz”, Calz. Mexico, Xochimilco 101, Col. Huipulco, Tlalpan, México City 14370, Mexico
| | - Minerva Camacho-Nuez
- Posgrado en Ciencias Genómicas, Universidad Autónoma De México (UACM), San Lorenzo 290, Col. Del Valle, México City 03100, Mexico
| | - José Cruz Santiago
- Hospital De Especialidades Centro Médico Nacional La Raza, IMSS, México City 02990, Mexico
| | - Edgar Antonio Estrella-Parra
- Laboratorio De Fitoquímica, UBIPRO, FES-Iztacala, Unidad Nacional Autónoma de México, Av. De los Barrios No.1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico
| | - Julio César Torres-Romero
- Laboratorio De Bioquímica y Genética Molecular, Facultad De Química, Universidad Autónoma De Yucatán, Calle 43 s/n x Calle 96, Paseo De las Fuentes y 40, Col. Inalambrica, Yucatán 97069, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma De México (UACM), San Lorenzo 290, Col. Del Valle, México City 03100, Mexico
| | - María Elizbeth Alvarez-Sánchez
- Posgrado en Ciencias Genómicas, Universidad Autónoma De México (UACM), San Lorenzo 290, Col. Del Valle, México City 03100, Mexico
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Saotome K, Dudgeon D, Colotti K, Moore MJ, Jones J, Zhou Y, Rafique A, Yancopoulos GD, Murphy AJ, Lin JC, Olson WC, Franklin MC. Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Nat Commun 2023; 14:2401. [PMID: 37100770 PMCID: PMC10132440 DOI: 10.1038/s41467-023-37532-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023] Open
Abstract
The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length α/β TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.
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Affiliation(s)
- Kei Saotome
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
| | - Drew Dudgeon
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Jennifer Jones
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Zhou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | | | - John C Lin
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
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6
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Gerber HP, Presta LG. TCR mimic compounds for pHLA targeting with high potency modalities in oncology. Front Oncol 2022; 12:1027548. [PMID: 36338746 PMCID: PMC9635445 DOI: 10.3389/fonc.2022.1027548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/29/2022] [Indexed: 12/02/2022] Open
Abstract
pHLA complexes represent the largest class of cell surface markers on cancer cells, making them attractive for targeted cancer therapies. Adoptive cell therapies expressing TCRs that recognize tumor specific pHLAs take advantage of the unique selectivity and avidity of TCR: pHLA interactions. More recently, additional protein binding domains binding to pHLAs, known as TCR mimics (TCRm), were developed for tumor targeting of high potency therapeutic modalities, including bispecifics, ADCs, CAR T and -NK cells. TCRm compounds take advantage of the exquisite tumor specificity of certain pHLA targets, including cell lineage commitment markers and cancer testis antigens (CTAs). To achieve meaningful anti-tumor responses, it is critical that TCRm compounds integrate both, high target binding affinities and a high degree of target specificity. In this review, we describe the most advanced approaches to achieve both criteria, including affinity- and specificity engineering of TCRs, antibodies and alternative protein scaffolds. We also discuss the status of current TCRm based therapeutics developed in the clinic, key challenges, and emerging trends to improve treatment options for cancer patients treated with TCRm based therapeutics in Oncology.
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7
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Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen. Nat Commun 2022; 13:5333. [PMID: 36088370 PMCID: PMC9464187 DOI: 10.1038/s41467-022-32811-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Neoantigens derived from somatic mutations are specific to cancer cells and are ideal targets for cancer immunotherapy. KRAS is the most frequently mutated oncogene and drives the pathogenesis of several cancers. Here we show the identification and development of an affinity-enhanced T cell receptor (TCR) that recognizes a peptide derived from the most common KRAS mutant, KRASG12D, presented in the context of HLA-A*11:01. The affinity of the engineered TCR is increased by over one million-fold yet fully able to distinguish KRASG12D over KRASWT. While crystal structures reveal few discernible differences in TCR interactions with KRASWT versus KRASG12D, thermodynamic analysis and molecular dynamics simulations reveal that TCR specificity is driven by differences in indirect electrostatic interactions. The affinity enhanced TCR, fused to a humanized anti-CD3 scFv, enables selective killing of cancer cells expressing KRASG12D. Our work thus reveals a molecular mechanism that drives TCR selectivity and describes a soluble bispecific molecule with therapeutic potential against cancers harboring a common shared neoantigen. Cancers often harbor mutations in genes encoding important regulatory proteins, but therapeutic targeting of these molecules proves difficult due to their high structural similarity to their non-mutated counterpart. Here authors show the engineering of T cell engaging bispecific protein able to selectively target cancer cells with a high-frequency mutation in the KRAS oncogene.
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8
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Simister PC, Border EC, Vieira JF, Pumphrey NJ. Structural insights into engineering a T-cell receptor targeting MAGE-A10 with higher affinity and specificity for cancer immunotherapy. J Immunother Cancer 2022; 10:jitc-2022-004600. [PMID: 35851311 PMCID: PMC9295655 DOI: 10.1136/jitc-2022-004600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND T-cell receptor (TCR) immunotherapy is becoming a viable modality in cancer treatment with efficacy in clinical trials. The safety of patients is paramount, so innovative cell engineering methods are being employed to exploit adaptive immunity while controlling the factors governing antigen receptor (ie, TCR) specificity and cross-reactivity. We recently reported a TCR engineering campaign and selectivity profiling assay (X-scan) targeting a melanoma antigen gene (MAGE)-A10 peptide. This helped to distinguish between two well-performing TCRs based on cross-reactivity potential during preclinical drug evaluation, allowing one to be advanced to T-cell immunotherapeutic clinical trials. Here, we present three-dimensional structural information on those TCRs, highlighting engineering improvements and molecular mechanisms likely underpinning differential selectivity. METHODS Parental and engineered TCRs were purified and crystallized either alone or complexed to human leucocyte antigen (HLA)-A*02:01 presenting the MAGE-A10 9-mer peptide, GLYDGMEHL (pHLA/MAGE-A10-9). Using X-ray diffraction, we solved four high-resolution crystal structures and evaluated them relative to previously reported functional results. RESULTS The unligated parental TCR displayed similar complementarity-determining region (CDR) loop conformations when bound to pHLA/MAGE-A10-9; a rigid-body movement of TCR beta chain variable domain (TRBV) relative to TCR alpha chain variable domain helped optimal pHLA engagement. This first view of an HLA-bound MAGE-A10 peptide revealed an intrachain non-covalent 'staple' between peptide Tyr3 and Glu7. A subtle Glu31-Asp mutation in βCDR1 of the parental TCR generated a high-affinity derivative. Its pHLA-complexed structure shows that the shorter Asp leans toward the pHLA with resulting rigid-body TRBV shift, creating localized changes around the peptide's C-terminus. Structural comparison with a less selective TCR indicated that differential cross-reactivity to MAGE-A10 peptide variants is most readily explained by alterations in surface electrostatics, and the size and geometry of TCR-peptide interfacial cavities. CONCLUSIONS Modest changes in engineered TCRs targeting MAGE-A10 produced significantly different properties. Conformational invariance of TCR and antigen peptide plus more space-filling CDR loop sequences may be desirable properties for clinically relevant TCR-pHLA systems to reduce the likelihood of structurally similar peptide mimics being tolerated by a TCR. Such properties may partially explain why the affinity-enhanced, in vitro-selected TCR has been generally well tolerated in patients.
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9
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Panhuber A, Lamorte G, Bruno V, Cetin H, Bauer W, Höftberger R, Erber AC, Frommlet F, Koneczny I. A systematic review and meta-analysis of HLA class II associations in patients with IgG4 autoimmunity. Sci Rep 2022; 12:9229. [PMID: 35654912 PMCID: PMC9163138 DOI: 10.1038/s41598-022-13042-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/13/2022] [Indexed: 11/22/2022] Open
Abstract
Autoimmune diseases caused by pathogenic IgG4 subclass autoantibodies (IgG4-AID) include diseases like MuSK myasthenia gravis, pemphigus vulgaris or thrombotic thrombocytopenic purpura. Their etiology is still unknown. Polymorphisms in the human leukocyte antigen (HLA) gene locus, particularly in HLA-DRB1, are known genetic susceptibility factors for autoimmune diseases. We hypothesized a similar role for HLA polymorphisms in IgG4-AID and conducted a systematic review and meta-analysis with case-control studies on IgG4-AID based on MOOSE/ HuGENet guidelines. Genotype (G) and allele (A) frequencies of HLA-DQB1*05 (G: OR 3.8; 95% CI 2.44-5.9; p < 0.00001; A: OR 2.54; 95% CI 1.82-3.55; p < 0.00001) and HLA-DRB1*14 (G: OR 4.31; 95% CI 2.82-6.59; p < 0.00001; A: OR 4.78; 95% CI 3.52-6.49; p < 0.00001) and the HLA-DRB1*14-DQB1*05 haplotype (OR 6.3; 95% CI 3.28-12.09; p < 0.00001/OR 4.98; 95% CI 3.8-6.53; p < 0.00001) were increased while HLA-DRB1*13 (G: OR 0.48; 95% CI 0.34-0.68; p < 0.0001; A: OR 0.46; 95% CI 0.34-0.62; p < 0.00001) was decreased in IgG4-AID patients. In conclusion, the HLA-DQB1*05, HLA-DRB1*14 alleles and the HLA-DQB1*05-DRB1*14 haplotype could be genetic risk factors that predispose for the production of pathogenic IgG4 autoantibodies and the HLA-DRB1*13 allele may protect from IgG4 autoimmunity.
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Affiliation(s)
- Anja Panhuber
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Giovanni Lamorte
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Veronica Bruno
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Bauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Astrid C Erber
- Department of Epidemiology, Center for Public Health, Medical University of Vienna, Vienna, Austria
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Florian Frommlet
- Center for Medical Statistics Informatics and Intelligent Systems, Section for Medical Statistics, Medical University of Vienna, Vienna, Austria
| | - Inga Koneczny
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria.
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10
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Hopkins JR, MacLachlan BJ, Harper S, Sewell AK, Cole DK. Unconventional modes of peptide-HLA-I presentation change the rules of TCR engagement. DISCOVERY IMMUNOLOGY 2022; 1:kyac001. [PMID: 38566908 PMCID: PMC10917088 DOI: 10.1093/discim/kyac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 04/04/2024]
Abstract
The intracellular proteome of virtually every nucleated cell in the body is continuously presented at the cell surface via the human leukocyte antigen class I (HLA-I) antigen processing pathway. This pathway classically involves proteasomal degradation of intracellular proteins into short peptides that can be presented by HLA-I molecules for interrogation by T-cell receptors (TCRs) expressed on the surface of CD8+ T cells. During the initiation of a T-cell immune response, the TCR acts as the T cell's primary sensor, using flexible loops to mould around the surface of the pHLA-I molecule to identify foreign or dysregulated antigens. Recent findings demonstrate that pHLA-I molecules can also be highly flexible and dynamic, altering their shape according to minor polymorphisms between different HLA-I alleles, or interactions with different peptides. These flexible presentation modes have important biological consequences that can, for example, explain why some HLA-I alleles offer greater protection against HIV, or why some cancer vaccine approaches have been ineffective. This review explores how these recent findings redefine the rules for peptide presentation by HLA-I molecules and extend our understanding of the molecular mechanisms that govern TCR-mediated antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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11
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Xiao K, Ma X, Wang Y, Zhu C, Guo L, Lu R. Diagnostic value of serum tumor-associated autoantibodies in esophageal cancer. Biomark Med 2021; 15:1333-1343. [PMID: 34541870 DOI: 10.2217/bmm-2021-0351] [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: 11/21/2022] Open
Abstract
Aim: To explore the application value of serum autoantibodies in the early diagnosis of esophageal cancer. Materials & methods: A total of 130 patients with esophageal cancer and 110 controls were included and tested by ELISA. Results: According to the receiver operating characteristic curve, total sensitivity is 83.08%, total specificity is 72.73%. A nomogram was established based on the positive judgment standard, the area under the receiver operating characteristic curve was calculated to be 0.880 after verification with the calibration curve. A 2-week follow-up analysis found compared with the preoperative control, the postoperative model integral value will significantly decrease. Conclusion: The combination of serum autoantibody groups has certain clinical application value in the early diagnosis of esophageal cancer and can be used as an auxiliary index for early diagnosis.
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Affiliation(s)
- Kangjia Xiao
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
| | - Xiaolu Ma
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
| | - Yanchun Wang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
| | - Cheng Zhu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
| | - Lin Guo
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai, 200032, China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'an Road, Shanghai, 200032, China
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12
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Zhu Y, Huang C, Su M, Ge Z, Gao L, Shi Y, Wang X, Chen J. Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:495. [PMID: 33850892 PMCID: PMC8039679 DOI: 10.21037/atm-21-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The present study aimed to explore residues’ properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy. Methods We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex’s molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution. Results The main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB. Conclusions The findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.
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Affiliation(s)
- Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Meng Su
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Zuanmin Ge
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Lanlan Gao
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Yanfei Shi
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Xuechun Wang
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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13
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Venema WJ, Hiddingh S, de Boer JH, Claas FHJ, Mulder A, den Hollander AI, Stratikos E, Sarkizova S, van der Veken LT, Janssen GMC, van Veelen PA, Kuiper JJW. ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29. Front Immunol 2021; 12:634441. [PMID: 33717175 PMCID: PMC7950316 DOI: 10.3389/fimmu.2021.634441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labeled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Greece
| | - Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lars T van der Veken
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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14
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TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers. Int J Mol Sci 2020; 22:ijms22010068. [PMID: 33374673 PMCID: PMC7793522 DOI: 10.3390/ijms22010068] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR-pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR-pMHC-I structures and their impact on T cell activation.
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15
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Kuiper JJW, Venema WJ. HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole. Front Immunol 2020; 11:599558. [PMID: 33262772 PMCID: PMC7687429 DOI: 10.3389/fimmu.2020.599558] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
HLA class I alleles constitute established risk factors for non-infectious uveitis and preemptive genotyping of HLA class I alleles is standard practice in the diagnostic work-up. The HLA-A29 serotype is indispensable to Birdshot Uveitis (BU) and renders this enigmatic eye condition a unique model to better understand how the antigen processing and presentation machinery contributes to non-infectious uveitis or chronic inflammatory conditions in general. This review will discuss salient points regarding the protein structure of HLA-A29 and how key amino acid positions impact the peptide binding preference and interaction with T cells. We discuss to what extent the risk genes ERAP1 and ERAP2 uniquely affect HLA-A29 and how the discovery of a HLA-A29-specific submotif may impact autoantigen discovery. We further provide a compelling argument to solve the long-standing question why BU only affects HLA-A29-positive individuals from Western-European ancestry by exploiting data from the 1000 Genomes Project. We combine novel insights from structural and immunopeptidomic studies and discuss the functional implications of genetic associations across the HLA class I antigen presentation pathway to refine the etiological basis of Birdshot Uveitis.
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Affiliation(s)
- Jonas J. W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Wouter J. Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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