Kacen, A. et al. Publish-translational modifications reshape the antigenic panorama of the MHC I immunopeptidome in tumors. Nat. Biotechnol. 41, 239–251 (2023).
Google Scholar
Kelly, S. D., Allas, M. J., Goodridge, L. D., Lowary, T. L. & Whitfield, C. Construction, biosynthesis and regulation of the T1 antigen, a phase-variable floor polysaccharide conserved in lots of Salmonella serovars. Nat. Commun. 15, 6504 (2024).
Google Scholar
Teplensky, M. H. et al. Multi-antigen spherical nucleic acid most cancers vaccines. Nat. Biomed. Eng. 7, 911–927 (2023).
Google Scholar
Ando, Y. et al. Utilizing tumor marker gene variants to enhance the diagnostic accuracy of DUPAN-2 and carbohydrate antigen 19-9 for pancreatic most cancers. J. Clin. Oncol. 42, 2196–2206 (2024).
Google Scholar
Liang, X., Cheng, H., Liu, C. & Liu, G. Antigen self-presenting nanovaccine for most cancers immunotherapy. Sci. Bull. 67, 1611–1613 (2022).
Google Scholar
Yang, J., Chen, Y., Jing, Y., Inexperienced, M. R. & Han, L. Advancing CAR T cell remedy by way of the usage of multidimensional omics information. Nat. Rev. Clin. Oncol. 20, 211–228 (2023).
Google Scholar
Xie, N. et al. Neoantigens: promising targets for most cancers remedy. Sign Transduct. Goal. Ther. 8, 9 (2023).
Google Scholar
Ding, Q. et al. Signaling pathways in rheumatoid arthritis: implications for focused remedy. Sign Transduct. Goal. Ther. 8, 68 (2023).
Google Scholar
Zhong, Q. et al. Protein posttranslational modifications in well being and illnesses: features, regulatory mechanisms, and therapeutic implications. MedComm 4, e261 (2023).
Google Scholar
Curran, A. M. et al. Citrullination modulates antigen processing and presentation by revealing cryptic epitopes in rheumatoid arthritis. Nat. Commun. 14, 1061 (2023).
Google Scholar
Alivernini, S., Firestein, G. S. & McInnes, I. B. The pathogenesis of rheumatoid arthritis. Immunity 55, 2255–2270 (2022).
Google Scholar
Maggi, J. et al. Isolation of HLA-DR-naturally offered peptides identifies T-cell epitopes for rheumatoid arthritis. Ann. Rheum. Dis. 81, 1096–1105 (2022).
Google Scholar
Toes, R. & Pisetsky, D. S. Pathogenic effector features of ACPA: the place will we stand? Ann. Rheum. Dis. 78, 716–721 (2019).
Google Scholar
Ge, C. et al. Structural foundation of cross-reactivity of anti-citrullinated protein antibodies. Arthritis Rheumatol. 71, 210–221 (2019).
Google Scholar
Steen, J. et al. Recognition of amino acid motifs, slightly than particular proteins, by human plasma cell-derived monoclonal antibodies to posttranslationally modified proteins in rheumatoid arthritis. Arthritis Rheumatol. 71, 196–209 (2019).
Google Scholar
Lewallen, D. M. et al. Chemical proteomic platform to determine citrullinated proteins. ACS Chem. Biol. 10, 2520–2528 (2015).
Google Scholar
Tilvawala, R. et al. The rheumatoid arthritis-associated citrullinome. Cell Chem. Biol. 25, 691–704.e696 (2018).
Google Scholar
Juarez, M. et al. Identification of novel antiacetylated vimentin antibodies in sufferers with early inflammatory arthritis. Ann. Rheum. Dis. 75, 1099–1107 (2016).
Google Scholar
Scherer, H. U., van der Woude, D. & Toes, R. E. M. From threat to chronicity: evolution of autoreactive B cell and antibody responses in rheumatoid arthritis. Nat. Rev. Rheumatol. 18, 371–383 (2022).
Google Scholar
Suwannalai, P. et al. Low-avidity anticitrullinated protein antibodies (ACPA) are related to the next charge of joint destruction in rheumatoid arthritis. Ann. Rheum. Dis. 73, 270–276 (2014).
Google Scholar
Bondt, A. et al. ACPA IgG galactosylation associates with illness exercise in pregnant sufferers with rheumatoid arthritis. Ann. Rheum. Dis. 77, 1130–1136 (2018).
Google Scholar
Willemze, A., Trouw, L. A., Toes, R. E. & Huizinga, T. W. The affect of ACPA standing and traits on the course of RA. Nat. Rev. Rheumatol. 8, 144–152 (2012).
Google Scholar
van der Woude, D. & Toes, R. E. M. Immune response to post-translationally modified proteins in rheumatoid arthritis: what makes it particular?. Ann. Rheum. Dis. 83, 838–846 (2024).
Google Scholar
Gerlag, D. M. et al. EULAR suggestions for terminology and analysis in people liable to rheumatoid arthritis: report from the research group for threat elements for rheumatoid arthritis. Ann. Rheum. Dis. 71, 638–641 (2012).
Google Scholar
He, S. et al. A longitudinal cohort research uncovers plasma protein biomarkers predating scientific onset and therapy response of rheumatoid arthritis. Nat. Commun. 16, 6692 (2025).
Google Scholar
Mondal, S. & Thompson, P. R. Protein arginine deiminases (PADs): biochemistry and chemical biology of protein citrullination. Acc. Chem. Res. 52, 818–832 (2019).
Google Scholar
Assohou-Luty, C. et al. The human peptidylarginine deiminases sort 2 and sort 4 have distinct substrate specificities. Biochim. Biophys. Acta. 1844, 829–836 (2014).
Google Scholar
Gong, Y. et al. Acetylation profiling by Iseq-Kac reveals insights into HSC getting older and lineage resolution. Nat. Chem. Biol. 21, 1675–1687 (2025).
Google Scholar
Rebak, A. S. et al. A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates. Nat. Struct. Mol. Biol. 31, 977–995 (2024).
Google Scholar
Clancy, Okay. W., Weerapana, E. & Thompson, P. R. Detection and identification of protein citrullination in complicated organic programs. Curr. Opin. Chem. Biol. 30, 1–6 (2016).
Google Scholar
Lee, C. Y. et al. Mining the human tissue proteome for protein citrullination. Mol. Cell. Proteom. 17, 1378–1391 (2018).
Google Scholar
Hensen, S. M. & Pruijn, G. J. Strategies for the detection of peptidylarginine deiminase (PAD) exercise and protein citrullination. Mol. Cell. Proteom. 13, 388–396 (2014).
Google Scholar
Buda, M., Maki, A. & Mazurowski, M. A. A scientific research of the category imbalance downside in convolutional neural networks. Neural Netw. 106, 249–259 (2018).
Google Scholar
Murata, Okay. et al. Hypoxia-sensitive COMMD1 integrates signaling and mobile metabolism in human macrophages and suppresses osteoclastogenesis. Immunity 47, 66–79.e65 (2017).
Google Scholar
Lee, S. et al. Identification of MYH9 as a key regulator for synoviocyte migration and invasion by way of secretome profiling. Ann. Rheum. Dis. 82, 1035–1048 (2023).
Google Scholar
Zhao, X. et al. Circulating immune complexes include citrullinated fibrinogen in rheumatoid arthritis. Arthritis Res. Ther. 10, R94 (2008).
Google Scholar
Iwamoto, N. et al. Osteogenic differentiation of fibroblast-like synovial cells in rheumatoid arthritis is induced by microRNA-218 by way of a ROBO/Slit pathway. Arthritis Res. Ther. 20, 189 (2018).
Google Scholar
Muller, S. & Radic, M. Citrullinated autoantigens: from diagnostic markers to pathogenetic mechanisms. Clin. Rev. Allergy Immunol. 49, 232–239 (2015).
Google Scholar
Sturfelt, G. & Truedsson, L. Complement within the immunopathogenesis of rheumatic illness. Nat. Rev. Rheumatol. 8, 458–468 (2012).
Google Scholar
Tran, L. S. et al. ER O-glycosylation in synovial fibroblasts drives cartilage degradation. Nat. Commun. 16, 2535 (2025).
Google Scholar
Olumuyiwa-Akeredolu, O. O., Web page, M. J., Soma, P. & Pretorius, E. Platelets: rising facilitators of mobile crosstalk in rheumatoid arthritis. Nat. Rev. Rheumatol. 15, 237–248 (2019).
Google Scholar
Niehaus, J. Okay., Taylor-Blake, B., Bathroom, L., Simon, J. M. & Zylka, M. J. Spinal macrophages resolve nociceptive hypersensitivity after peripheral harm. Neuron 109, 1274–1282.e1276 (2021).
Google Scholar
Ummarino, D. Rheumatoid arthritis: ACPA standing influences RA growth. Nat. Rev. Rheumatol. 13, 450 (2017).
Google Scholar
Pertsinidou, E. et al. In early rheumatoid arthritis, anticitrullinated peptide antibodies affiliate with low variety of affected joints and rheumatoid issue associates with systemic irritation. Ann. Rheum. Dis. 83, 277–287 (2024).
Google Scholar
Kastbom, A. et al. Adjustments in anti-citrullinated protein antibody isotype ranges in relation to illness exercise and response to therapy in early rheumatoid arthritis. Clin. Exp. Immunol. 194, 391–399 (2018).
Google Scholar
Takeuchi, T. et al. Excessive titers of each rheumatoid issue and anti-CCP antibodies at baseline in sufferers with rheumatoid arthritis are related to elevated circulating baseline TNF stage, low drug ranges, and diminished scientific responses: a submit hoc evaluation of the RISING research. Arthritis Res. Ther. 19, 194 (2017).
Google Scholar
Wells, G. et al. Validation of the 28-joint illness exercise rating (DAS28) and European league towards rheumatism response standards primarily based on C-reactive protein towards illness development in sufferers with rheumatoid arthritis, and comparability with the DAS28 primarily based on erythrocyte sedimentation charge. Ann. Rheum. Dis. 68, 954–960 (2009).
Google Scholar
Smolen, J. S. et al. EULAR suggestions for the administration of rheumatoid arthritis with artificial and organic disease-modifying antirheumatic medication. Ann. Rheum. Dis. 69, 964–975 (2010).
Google Scholar
Megahed, F. M. et al. The category imbalance downside. Nat. Strategies 18, 1270–1272 (2021).
Google Scholar
Muthukrishnan, R. & Rohini, R. in 2016 IEEE Worldwide Convention on Advances in Laptop Functions (ICACA) 18–20 (IEEE, 2016).
Zhu, X. W., Xin, Y. J. & Ge, H. L. Recursive random forests allow higher predictive efficiency and mannequin interpretation than variable choice by LASSO. J. Chem. Inf. Mannequin. 55, 736–746 (2015).
Google Scholar
Shieh, M.-D. & Yang, C.-C. Multiclass SVM-RFE for product kind function choice. Knowledgeable Syst. Appl. 35, 531–541 (2008).
Google Scholar
Guan, S. et al. Figuring out potential targets for stopping most cancers development by way of the PLA2G1B recombinant protein utilizing bioinformatics and machine studying strategies. Int. J. Biol. Macromol. 276, 133918 (2024).
Google Scholar
Efthimiou, O. et al. Growing scientific prediction fashions: a step-by-step information. BMJ 386, e078276 (2024).
Google Scholar
Sahlström, P. et al. Completely different hierarchies of anti-modified protein autoantibody reactivities in rheumatoid arthritis. Arthritis Rheumatol. 72, 1643–1657 (2020).
Google Scholar
Zheng, Z. et al. Disordered antigens and epitope overlap between anti-citrullinated protein antibodies and rheumatoid consider rheumatoid arthritis. Arthritis Rheumatol. 72, 262–272 (2020).
Google Scholar
Lo, Okay. C. et al. Complete profiling of the rheumatoid arthritis antibody repertoire. Arthritis Rheumatol. 72, 242–250 (2020).
Google Scholar
Thandapani, P., O’Connor, T. R., Bailey, T. L. & Richard, S. Defining the RGG/RG motif. Mol. Cell 50, 613–623 (2013).
Google Scholar
Ali, S. M. et al. Baseline serum NTx ranges are prognostic in metastatic breast most cancers sufferers with bone-only metastasis. Ann. Oncol. 15, 455–459 (2004).
Google Scholar
Fert-Bober, J., Darrah, E. & Andrade, F. Insights into the research and origin of the citrullinome in rheumatoid arthritis. Immunol. Rev. 294, 133–147 (2020).
Google Scholar
Kokkonen, H. et al. Antibodies of IgG, IgA and IgM isotypes towards cyclic citrullinated peptide precede the event of rheumatoid arthritis. Arthritis Res. Ther. 13, R13 (2011).
Google Scholar
Ten Brinck, R. M., Toes, R. E. M. & van der Helm-van Mil, A. H. M. Irritation features as a key mediator within the hyperlink between ACPA and erosion growth: an affiliation research in clinically suspect arthralgia. Arthritis Res. Ther. 20, 89 (2018).
Google Scholar
van Delft, M. A. M. & Huizinga, T. W. J. An summary of autoantibodies in rheumatoid arthritis. J. Autoimmun. 110, 102392 (2020).
Google Scholar
Yu, Okay. & Proost, P. Insights into peptidylarginine deiminase expression and citrullination pathways. Developments Cell Biol. 32, 746–761 (2022).
Google Scholar
Wouters, F. et al. Figuring out by which pre-arthritis stage HLA-shared epitope alleles and smoking exert their impact on the event of rheumatoid arthritis. Ann. Rheum. Dis. 81, 48–55 (2022).
Google Scholar
Di Matteo, A., Bathon, J. M. & Emery, P. Rheumatoid arthritis. Lancet 402, 2019–2033 (2023).
Google Scholar
Sparks, J. A. & Costenbader, Okay. H. Rheumatoid arthritis in 2017: protecting dietary and hormonal elements delivered to mild. Nat. Rev. Rheumatol. 14, 71–72 (2018).
Google Scholar
Smolen, J. S., Aletaha, D. & McInnes, I. B. Rheumatoid arthritis. Lancet 388, 2023–2038 (2016).
Google Scholar
Jiang, L. et al. A high-fiber weight loss program synergizes with Prevotella copri and exacerbates rheumatoid arthritis. Cell. Mol. Immunol. 19, 1414–1424 (2022).
Google Scholar
Trocmé, C. et al. Apolipoprotein A-I and platelet issue 4 are biomarkers for infliximab response in rheumatoid arthritis. Ann. Rheum. Dis. 68, 1328–1333 (2009).
Google Scholar
Cho, A. et al. A multi-biomarker panel for predicting tocilizumab response in rheumatoid arthritis sufferers. Transl. Res. 273, 23–31 (2024).
Google Scholar
Smolen, J. S. et al. EULAR suggestions for the administration of rheumatoid arthritis with artificial and organic disease-modifying antirheumatic medication: 2019 replace. Ann. Rheum. Dis. 79, 685–699 (2020).
Google Scholar
Zhang, T. et al. Serum proteomics evaluation of biomarkers for evaluating scientific response to MTX/IGU remedy in early rheumatoid arthritis. Mol. Immunol. 153, 119–125 (2023).
Google Scholar
Ponchel, F. et al. An immunological biomarker to foretell MTX response in early RA. Ann. Rheum. Dis. 73, 2047–2053 (2014).
Google Scholar
Maciejewski, M. et al. Prediction of response of methotrexate in sufferers with rheumatoid arthritis utilizing serum lipidomics. Sci. Rep. 11, 7266 (2021).
Google Scholar
Owen, S. A. et al. Genetic polymorphisms in key methotrexate pathway genes are related to response to therapy in rheumatoid arthritis sufferers. Pharmacogenomics J. 13, 227–234 (2013).
Google Scholar
Liu, T., Shi, Okay. & Li, W. Deep studying strategies enhance linear B-cell epitope prediction. BioData Min. 13, 1 (2020).
Google Scholar
Shashkova, T. I. et al. SEMA: antigen B-cell conformational epitope prediction utilizing deep switch studying. Entrance. Immunol. 13, 960985 (2022).
Google Scholar
Ju, Z. & Wang, S. Y. Prediction of citrullination websites by incorporating k-spaced amino acid pairs into Chou’s normal pseudo amino acid composition. Gene 664, 78–83 (2018).
Google Scholar
Liu, Y., Li, A., Zhao, X. M. & Wang, M. DeepTL-Ubi: a novel deep switch studying methodology for successfully predicting ubiquitination websites of a number of species. Strategies 192, 103–111 (2021).
Google Scholar
Yang, H., Wang, M., Liu, X., Zhao, X. M. & Li, A. PhosIDN: an built-in deep neural community for bettering protein phosphorylation web site prediction by combining sequence and protein-protein interplay data. Bioinformatics 37, 4668–4676 (2021).
Google Scholar
Wang, H., Zhao, H., Yan, Z., Zhao, J. & Han, J. MDCAN-Lys: a mannequin for predicting succinylation websites primarily based on multilane dense convolutional consideration community. Biomolecules 11, 872 (2021).
Google Scholar
Meng, L. et al. TransPTM: a transformer-based mannequin for non-histone acetylation web site prediction. Temporary. Bioinform. 25, 3 (2024).
Google Scholar
Luo, F., Wang, M., Liu, Y., Zhao, X. M. & Li, A. DeepPhos: prediction of protein phosphorylation websites with deep studying. Bioinformatics 35, 2766–2773 (2019).
Google Scholar
Deznabi, I., Arabaci, B., Koyutürk, M. & Tastan, O. DeepKinZero: zero-shot studying for predicting kinase-phosphosite associations involving understudied kinases. Bioinformatics 36, 3652–3661 (2020).
Google Scholar
Parvez, A., Ali, S. D., Tayara, H. & Chong, Okay. T. Stacking primarily based ensemble studying framework for identification of nitrotyrosine websites. Comput. Biol. Med. 183, 109200 (2024).
Google Scholar
Anashkina, A. A. et al. A novel strategy for predicting protein S-glutathionylation. BMC Bioinform. 21, 282 (2020).
Google Scholar
Guo, Y. et al. GPS-PBS: a deep studying framework to foretell phosphorylation websites that particularly work together with phosphoprotein-binding domains. Cells 9, 1266 (2020).
Google Scholar
Ahmed, S., Kabir, M., Arif, M., Khan, Z. U. & Yu, D. J. DeepPPSite: a deep learning-based mannequin for evaluation and prediction of phosphorylation websites utilizing environment friendly sequence data. Anal. Biochem. 612, 113955 (2021).
Google Scholar
Tilvawala, R. et al. The position of SERPIN citrullination in thrombosis. Cell Chem. Biol. 28, 1728–1739.e1725 (2021).
Google Scholar
Solar, L. et al. A brand new unconventional HLA-A2-restricted epitope from HBV core protein elicits antiviral cytotoxic T lymphocytes. Protein Cell 5, 317–327 (2014).
Google Scholar
Lagattuta, Okay. A. et al. Repertoire analyses reveal T cell antigen receptor sequence options that affect T cell destiny. Nat. Immunol. 23, 446–457 (2022).
Google Scholar
Sakuma, S. et al. FK506 potently inhibits T cell activation induced TNF-alpha and IL-1beta manufacturing in vitro by human peripheral blood mononuclear cells. Br. J. Pharmacol. 130, 1655–1663 (2000).
Google Scholar
Sanchez-Trincado, J. L., Gomez-Perosanz, M. & Reche, P. A. Fundamentals and strategies for T- and B-cell epitope prediction. J. Immunol. Res. 2017, 2680160 (2017).
Google Scholar
Hao, G. et al. Impartial lack of isocyanic acid in peptide CID spectra: a novel diagnostic marker for mass spectrometric identification of protein citrullination. J. Am. Soc. Mass Spectrom. 20, 723–727 (2009).
Google Scholar
Chaerkady, R. et al. Characterization of citrullination websites in neutrophils and mast cells activated by ionomycin through integration of mass spectrometry and machine studying. J. Proteome Res. 20, 3150–3164 (2021).
Google Scholar
Sonnett, M., Yeung, E. & Wühr, M. Correct, delicate, and exact multiplexed proteomics utilizing the complement reporter ion cluster. Anal. Chem. 90, 5032–5039 (2018).
Google Scholar
Hu, M. et al. Low-input, deep studying platform for citrullinated peptide identification, autoantigen discovery, and rheumatoid arthritis therapy stratification. iProX (2025).
He, S. et al. A longitudinal cohort research uncovers plasma protein biomarkers predating scientific onset and therapy response of rheumatoid arthritis. iProX (2025).



