Ajalla Aleixo, M. A., Rangel, V. L., Rustiguel, J. K., de Pádua, R. A., & Nonato, M. C. (2019). Structural, biochemical and biophysical characterization of recombinant human fumarate hydratase. The FEBS Journal, 286(10), 1925–1940.
https://doi.org/10.1111/febs.14782
Akdis, C. A. (2021). Does the epithelial barrier hypothesis explain the increase in allergy, autoimmunity and other chronic conditions? Nature Reviews Immunology, 21(11), 739–751.
https://doi.org/10.1038/s41577-021-00538-7
Anderson, D. D., Quintero, C. M., & Stover, P. J. (2011). Identification of a de novo thymidylate biosynthesis pathway in mammalian mitochondria. Proceedings of the National Academy of Sciences, 108(37), 15163–15168.
https://doi.org/10.1073/pnas.1103623108
Antunes, L. C., Visca, P., & Towner, K. J. (2014). Acinetobacter baumannii: Evolution of a global pathogen. Pathogens and Disease, 71(3), 292–301.
https://doi.org/10.1111/2049-632X.12125
Apweiler, R., Martin, M. J., O'Donovan, C., Magrane, M., Alam-Faruque, Y., Antunes, R., et al. (2010). The universal protein resource (UniProt) in 2010. Nucleic Acids Research, 38, D142–D148.
https://doi.org/10.1093/nar/gkp846
Axelrod, M. L., Cook, R. S., Johnson, D. B., & Balko, J. M. (2019). Biological consequences of MHC-II expression by tumor cells in cancer. Clinical Cancer Research, 25(8), 2392–2402.
https://doi.org/10.1158/1078-0432.CCR-18-3200
Bai, J. A., Jie, H., Wei, S., Wang, S., Guo, H., & Tang, Q. (2016). GART mediates the renewal of intestinal epithelial barrier via p38/p53/PUMA cascade in colitis. Apoptosis, 21, 1386–1397.
https://doi.org/10.1007/s10495-016-1301-y
Berkun, Y., Zandman-Goddard, G., Barzilai, O., Boaz, M., Sherer, Y., Larida, B., et al. (2009). Infectious antibodies in systemic lupus erythematosus patients. Lupus, 18(13), 1129–1135.
https://doi.org/10.1177/0961203309345729
Bhasin, M., Garg, A., & Raghava, G. P. S. (2005). PSLpred: Prediction of subcellular localization of bacterial proteins. Bioinformatics, 21(10), 2522–2524.
https://doi.org/10.1093/bioinformatics/bti309
Blum, J. S., Wearsch, P. A., & Cresswell, P. (2013). Pathways of antigen processing. Annual Review of Immunology, 31(1), 443–473.
https://doi.org/10.1146/annurev-immunol-032712-095910
Bullock, J., Rizvi, S. A., Saleh, A. M., Ahmed, S. S., Do, D. P., Ansari, R. A., et al. (2019). Rheumatoid arthritis: A brief overview of the treatment. Medical Principles and Practice, 27(6), 501–507.
https://doi.org/10.1159/000493390
Cabreiro, F., Picot, C. R., Perichon, M., Castel, J., Friguet, B., & Petropoulos, I. (2008). Overexpression of mitochondrial methionine sulfoxide reductase B2 protects leukemia cells from oxidative stress-induced cell death and protein damage. Journal of Biological Chemistry, 283(24), 16673–16681.
https://doi.org/10.1074/jbc.M708580200
Chen, M., Peng, B., Zhang, Y., & Lu, C. (2024). CELLO: Causal Evaluation of Large Vision-Language Models. arXiv preprint arXiv:2406.19131.
https://doi.org/10.48550/arXiv.2406.19131
Christen, U. (2018). Pathogen infection and autoimmune disease. Clinical and Experimental Immunology, 195(1), 10–14.
https://doi.org/10.1111/cei.13239
Chu, C. H., & Cheng, D. (2007). Expression, purification, characterization of human 3-methylcrotonyl-CoA carboxylase (MCCC). Protein Expression and Purification, 53(2), 421–427.
https://doi.org/10.1016/j.pep.2007.01.012
Clayton, S. A., MacDonald, L., Kurowska-Stolarska, M., & Clark, A. R. (2021). Mitochondria as key players in the pathogenesis and treatment of rheumatoid arthritis. Frontiers in Immunology, 12, 673916.
https://doi.org/10.3389/fimmu.2021.673916
Coppo, R., & Robert, T. (2020). IgA nephropathy in children and in adults: Two separate entities or the same disease? Journal of Nephrology, 33, 1219–1229.
https://doi.org/10.1007/s40620-020-00725-0
Crotzer, V. L., & Blum, J. S. (2009). Autophagy and its role in MHC-mediated antigen presentation. The Journal of Immunology, 182(6), 3335–3341.
https://doi.org/10.4049/jimmunol.0803458
Cunningham, M. W. (2019). Molecular mimicry, autoimmunity, and infection: The cross-reactive antigens of group A streptococci and their sequelae. Microbiology Spectrum, 7(4), e0045-18.
https://doi.org/10.1128/microbiolspec.gpp3-0045-2018
Davis, K. A., Moran, K. A., McAllister, C. K., & Gray, P. J. (2005). Multidrug-resistant Acinetobacter extremity infections in soldiers. Emerg. Infect. Dis., 11(8), 1218–1224.
https://doi.org/10.3201/1108.050103
De Virgilio, A., Greco, A., Fabbrini, G., Inghilleri, M., Rizzo, M. I., Gallo, A., et al. (2016). Parkinson's disease: Autoimmunity and neuroinflammation. Autoimmunity Reviews, 15(10), 1005–1011.
https://doi.org/10.1016/j.autrev.2016.07.022
Delogu, L. G., Deidda, S., Delitala, G., & Manetti, R. (2011). Infectious diseases and autoimmunity. The Journal of Infection in Developing Countries, 5(10), 679–687.
https://doi.org/10.3855/jidc.2061
Dendrou, C. A., Petersen, J., Rossjohn, J., & Fugger, L. (2018). HLA variation and disease. Nature Reviews Immunology, 18(5), 325–339.
https://doi.org/10.1038/nri.2017.143
Dobson, R., & Giovannoni, G. (2019). Multiple sclerosis–a review. European Journal of Neurology, 26(1), 27–40. https://doi.org/10.1111/ene.13819
Duan, X., Yang, L., & Xia, P. (2010). Septic arthritis of the knee caused by antibiotic-resistant Acinetobacter baumannii in a gout patient: A rare case report. Archives of Orthopaedic and Trauma Surgery, 130, 381–384.
https://doi.org/10.1007/s00402-009-0958-x
Ebringer, A., Rashid, T., & Wilson, C. (2012). The role of Acinetobacter in the pathogenesis of multiple sclerosis examined by using Popper sequences. Medical Hypotheses, 78(6), 763–769.
https://doi.org/10.1016/j.mehy.2012.02.026
Finlay, B. B., & McFadden, G. (2006). Anti-immunology: Evasion of the host immune system by bacterial and viral pathogens. Cell, 124(4), 767–782.
https://doi.org/10.1016/j.cell.2006.01.034
Freire, M., de Oliveira Garcia, D., Garcia, C., Bueno, M. C., Camargo, C., Magri, A. K., et al. (2016). Bloodstream infection caused by extensively drug-resistant Acinetobacter baumannii in cancer patients: High mortality associated with delayed treatment rather than with the degree of neutropenia. Clinical Microbiology and Infection, 22(4), 352–358.
https://doi.org/10.1016/j.cmi.2015.12.010
Garcia, D., & Erkan, D. (2018). Diagnosis and management of the antiphospholipid syndrome. New England Journal of Medicine, 378(21), 2010–2021.
https://doi.org/10.1056/NEJMra1705454
Garretti, F., Agalliu, D., Lindestam Arlehamn, C. S., Sette, A., & Sulzer, D. (2019). Autoimmunity in Parkinson's disease: The role of α-synuclein-specific T cells. Frontiers in Immunology, 10, 303.
https://doi.org/10.3389/fimmu.2019.00303
Glover, J., Sullivan, K., Browning, B., Ticer, T., Dooley, S., DiGrazia, J., et al. (2024). Acinetobacter species secrete compounds that promote intestinal inflammation. Physiology, 39(S1), 1549.
https://doi.org/10.1152/physiol.2024.39.S1.1549
Glover, J. S. (2024). Gut Check: Exploring the Role of Acinetobacter in Intestinal Inflammation (Thesis No. 862). MUSC Theses and Dissertations.
https://medica-musc.researchcommons.org/theses/862
Guerrero, D. M., Perez, F., Conger, N. G., Solomkin, J. S., Adams, M. D., Rather, P. N., et al. (2010). Acinetobacter baumannii-associated skin and soft tissue infections: Recognizing a broadening spectrum of disease. Surgical Infections, 11(1), 49–57.
https://doi.org/10.1089/sur.2009.022
Hughes, L., Smith, P., Bonell, S., Natt, R., Wilson, C., Rashid, T., et al. (2003). Cross-reactivity between related sequences found in Acinetobacter sp., Pseudomonas aeruginosa, myelin basic protein and myelin oligodendrocyte glycoprotein in multiple sclerosis. Journal of Neuroimmunology, 144(1-2), 105–115.
https://doi.org/10.1016/s0165-5728(03)00274-1
Jo, J., Kwon, K. T., & Ko, K. S. (2023). Multiple heteroresistance to tigecycline and colistin in Acinetobacter baumannii isolates and its implications for combined antibiotic treatment. Journal of Biomedical Science, 30(1), 37.
https://doi.org/10.1186/s12929-023-00914-6
Johnson, D., & Jiang, W. (2023). Infectious diseases, autoantibodies, and autoimmunity. Journal of Autoimmunity, 137, 102962.
https://doi.org/10.1016/j.jaut.2022.102962
Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan-4.0: Improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. The Journal of Immunology, 199(9), 3360–3368.
https://doi.org/10.4049/jimmunol.1700893
Kadono, J., Inoue, M., Taki, C., Ishizaki, N., Osako, M., Ishibe, R., et al. (2015). A case of superior mesenteric artery thrombosis associated with transient elevation of antiphospholipid antibodies. International Surgery, 100(9-10), 1346–1350.
https://doi.org/10.9738/INTSURG-D-15-00054.1
Kaushik, H., Kumar, V., & Parsad, D. (2023). Mitochondria–Melanocyte cellular interactions: An emerging mechanism of vitiligo pathogenesis. Journal of the European Academy of Dermatology and Venereology, 37(11), 2196–2207.
https://doi.org/10.1111/jdv.19019
Kern, F., LiPira, G., Gratama, J. W., Manca, F., & Roederer, M. (2005). Measuring Ag-specific immune responses: Understanding immunopathogenesis and improving diagnostics in infectious disease, autoimmunity and cancer. Trends in Immunology, 26(9), 477–484.
https://doi.org/10.1016/j.it.2005.07.005
Kiuru, M., & Launonen, V. (2004). Hereditary leiomyomatosis and renal cell cancer (HLRCC). Current Molecular Medicine, 4(8), 869–875.
https://doi.org/10.1007/s10689-014-9735-2
Kivity, S., Agmon-Levin, N., Blank, M., & Shoenfeld, Y. (2009). Infections and autoimmunity–friends or foes? Trends in Immunology, 30(8), 409–414.
https://doi.org/10.1016/j.it.2009.05.005
Lam, S., & Huang, T. (1997). Acinetobacter pericarditis with tamponade in a patient with systemic lupus erythematosus. Lupus, 6(5), 480–483.
https://doi.org/10.1177/096120339700600513
Li, G., Liu, X., & Zhao, J. (2025). Clinical characteristics, microbiological and risk factors of infections in patients with systemic lupus erythematosus. Journal of Community Hospital Internal Medicine Perspectives, 15(1), 36–41.
https://doi.org/10.55729/2000-9666.1447
Li, N., Tan, E., Chang, X., Mao, X., Zhao, D., Zhang, J., et al. (2013). MCCC1/LAMP3 reduces risk of sporadic Parkinson's disease in Han Chinese. Acta Neurologica Scandinavica, 128(2), 136–139.
https://doi.org/10.1111/ane.12108
Liang, K., Li, N., Wang, X., Dai, J., Liu, P., Wang, C., et al. (2018). Cryo-EM structure of human mitochondrial trifunctional protein. Proceedings of the National Academy of Sciences, 115(27), 7039–7044.
https://doi.org/10.1073/pnas.1801252115
Lima, A., Seabra, V., Bernardes, M., Azevedo, R., Sousa, H., & Medeiros, R. (2014). Role of key TYMS polymorphisms on methotrexate therapeutic outcome in portuguese rheumatoid arthritis patients. PLOS ONE, 9(10), e108165.
https://doi.org/10.1371/journal.pone.0108165
Lu, G., Hao, X., Chen, W. H., & Mu, S. (2018). GAAD: A gene and autoimmune disease association database. Genomics, Proteomics & Bioinformatics, 16(4), 252–261.
https://doi.org/10.1016/j.gpb.2018.05.001
Lv, S., Fan, H., Li, J., Yang, H., Huang, J., Shu, X., et al. (2018). Genetic polymorphisms of TYMS, MTHFR, ATIC, MTR, and MTRR are related to the outcome of methotrexate therapy for rheumatoid arthritis in a Chinese population. Frontiers in Pharmacology, 9, 1390.
https://doi.org/10.3389/fphar.2018.01390
Mahram, A., & Herbordt, M. C. (2015). NCBI BLASTP on high-performance reconfigurable computing systems. ACM Transactions on Reconfigurable Technology and Systems (TRETS), 7(4), 1–20.
https://doi.org/10.1145/2629691
Muralidharan, N., Misra, D. P., Jain, V. K., & Negi, V. S. (2017). Effect of thymidylate synthase (TYMS) gene polymorphisms with methotrexate treatment outcome in south Indian Tamil patients with rheumatoid arthritis. Clinical Rheumatology, 36, 1253–1259.
https://doi.org/10.1007/s10067-017-3608-7
Pan, Q., Liu, Z., Liao, S., Ye, L., Lu, X., Chen, X., et al. (2019). Current mechanistic insights into the role of infection in systemic lupus erythematosus. Biomedicine & Pharmacotherapy, 117, 109122.
https://doi.org/10.1016/j.biopha.2019.109122
Peace, C. G., O’Carroll, S. M., & O’Neill, L. A. (2024). Fumarate hydratase as a metabolic regulator of immunity. Trends in Cell Biology, 34(6), 442–450.
https://doi.org/10.1016/j.tcb.2023.10.005
Peleg, A. Y., Seifert, H., & Paterson, D. L. (2008). Acinetobacter baumannii: Emergence of a successful pathogen. Clinical Microbiology Reviews, 21(3), 538–582.
https://doi.org/10.1128/CMR.00058-07
Pires, S., & Parker, D. (2019). Innate immune responses to Acinetobacter baumannii in the airway. Journal of Interferon & Cytokine Research, 39(8), 441–449.
https://doi.org/10.1089/jir.2019.0008
Ramos, G. P., & Papadakis, K. A. (2019). Mechanisms of disease: Inflammatory bowel diseases. Mayo Clinic Proceedings, 94(1), 155–165.
https://doi.org/10.1016/j.mayocp.2018.09.013
Raro, O. H. F., Gallo, S. W., Ferreira, C. A. S., & Oliveira, S. D. (2017). Carbapenem-resistant Acinetobacter baumannii contamination in an intensive care unit. Revista da Sociedade Brasileira de Medicina Tropical, 50(2), 167–172.
https://doi.org/10.1590/0037-8682-0329-2016
Reynisson, B., Alvarez, B., Paul, S., Peters, B., & Nielsen, M. (2020). NetMHCpan-4.1 and NetMHCIIpan-4.0: Improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Research, 48(W1), W449–W454.
https://doi.org/10.1093/nar/gkaa379
Rojas, M., Restrepo-Jiménez, P., Monsalve, D. M., Pacheco, Y., Acosta-Ampudia, Y., Ramírez-Santana, C., et al. (2018). Molecular mimicry and autoimmunity. Journal of Autoimmunity, 95, 100–123.
https://doi.org/10.1016/j.jaut.2018.10.012
Rupasree, Y., Naushad, S. M., Rajasekhar, L., & Kutala, V. K. (2014). Epigenetic modulation of RFC1, MHC2TA and HLA-DR in systemic lupus erythematosus: Association with serological markers and six functional polymorphisms of one-carbon metabolic pathway. Gene, 536(1), 45–52.
https://doi.org/10.1016/j.gene.2013.11.094
Sanchez-Trincado, J. L., Gomez-Perosanz, M., & Reche, P. A. (2017). Fundamentals and methods for T-and B-cell epitope prediction. Journal of Immunology Research, 2017(1), 2680160.
https://doi.org/10.1155/2017/2680160
Sarkar, P., Redondo, J., Hares, K., Bailey, S., Georgievskaya, A., Heesom, K., et al. (2022). Reduced expression of mitochondrial fumarate hydratase in progressive multiple sclerosis contributes to impaired in vitro mesenchymal stromal cell-mediated neuroprotection. Multiple Sclerosis Journal, 28(8), 1179–1188.
https://doi.org/10.1177/13524585211048651
Sato, Y., Tsukaguchi, H., Higasa, K., Kawata, N., Inui, K., Linh, T. N. T., et al. (2021). Positive renal familial history in IgA nephropathy is associated with worse renal outcomes: A single-center longitudinal study. BMC Nephrology, 22(1), 230.
https://doi.org/10.1186/s12882-021-02425-8
Schallreuter, K. U., Rübsam, K., Gibbons, N. C., Maitland, D. J., Chavan, B., Zothner, C., et al. (2008). Methionine sulfoxide reductases A and B are deactivated by hydrogen peroxide (H2O2) in the epidermis of patients with vitiligo. Journal of Investigative Dermatology, 128(4), 808–815.
https://doi.org/10.1038/sj.jid.5701100
Senapati, S., Singh, S., Das, M., Kumar, A., Gupta, R., Kumar, U., et al. (2014). Genome-wide analysis of methotrexate pharmacogenomics in rheumatoid arthritis shows multiple novel risk variants and leads for TYMS regulation. Pharmacogenetics and Genomics, 24(4), 211–219.
https://doi.org/10.1097/FPC.0000000000000036
Shakhshir, A., Mo’tasem, Z., Awashra, A., & Al-ali, K. (2024). Dramatic devastative complications in a patient with catastrophic antiphospholipid syndrome: A case report and literature. SAGE Open Medical Case Reports, 12, 2050313X241272678.
https://doi.org/10.1177/2050313X241272678
Shedlock, D. J., & Shen, H. (2003). Requirement for CD4 T cell help in generating functional CD8 T cell memory. Science, 300(5617), 337–339.
https://doi.org/10.1126/science.1082305
Smith, D. A., & Germolec, D. R. (1999). Introduction to immunology and autoimmunity. Environmental Health Perspectives, 107(Suppl 5), 661–665.
https://doi.org/10.1289/ehp.99107s5661
Tai, Y., Wang, Q., Korner, H., Zhang, L., & Wei, W. (2018). Molecular mechanisms of T cells activation by dendritic cells in autoimmune diseases. Frontiers in Pharmacology, 9, 642.
https://doi.org/10.3389/fphar.2018.00642
Taungjaruwinai, W. M., Bhawan, J., Keady, M., & Thiele, J. J. (2009). Differential expression of the antioxidant repair enzyme methionine sulfoxide reductase (MSRA and MSRB) in human skin. The American Journal of Dermatopathology, 31(5), 427–431.
https://doi.org/10.1097/DAD.0b013e3181882c21
Thapa, P., & Farber, D. L. (2019). The role of the thymus in the immune response. Thoracic Surgery Clinics, 29(2), 123–131.
https://doi.org/10.1016/j.thorsurg.2018.12.001
Tsokos, G. C. (2020). Autoimmunity and organ damage in systemic lupus erythematosus. Nature Immunology, 21(6), 605–614.
https://doi.org/10.1038/s41590-020-0677-6
Turturici, G., Tinnirello, R., Sconzo, G., Asea, A., Savettieri, G., Ragonese, P., et al. (2014). Positive or negative involvement of heat shock proteins in multiple sclerosis pathogenesis: An overview. Journal of Neuropathology & Experimental Neurology, 73(12), 1092–1106.
https://doi.org/10.1097/NEN.0000000000000136
Vita, R., Mahajan, S., Overton, J. A., Dhanda, S. K., Martini, S., Cantrell, J. R., et al. (2019). The immune epitope database (IEDB): 2018 update. Nucleic Acids Research, 47(D1), D339–D343.
https://doi.org/10.1093/nar/gky1006
Wang, Y. Q., Tang, B. S., Yu, R. L., Li, K., Liu, Z. H., Xu, Q., et al. (2014). Association analysis of STK39, MCCC1/LAMP3 and sporadic PD in the Chinese Han population. Neuroscience Letters, 566, 206–209.
https://doi.org/10.1016/j.neulet.2014.03.007
Welin, M., Grossmann, J. G., Flodin, S., Nyman, T., Stenmark, P., Tresaugues, L., et al. (2010). Structural studies of tri-functional human GART. Nucleic Acids Research, 38(20), 7308–7319.
https://doi.org/10.1093/nar/gkq595
Wierczeiko, A., Linke, M., Friedrich, J. P., Koch, J., Schwarting, A., Krause, A., et al. (2024). A call for gene expression analysis in whole blood of patients with rheumatoid arthritis (RA) as a biomarker for RA-associated interstitial lung disease. The Journal of Rheumatology, 51(2), 130–133.
https://doi.org/10.3899/jrheum.2023-0588
Yang, X. Y., Zheng, K. D., Lin, K., Zheng, G., Zou, H., Wang, J. M., et al. (2015). Energy metabolism disorder as a contributing factor of rheumatoid arthritis: a comparative proteomic and metabolomic study. PLOS ONE, 10(7), e0132695.
https://doi.org/10.1371/journal.pone.0132695
Yu, N. Y., Wagner, J. R., Laird, M. R., Melli, G., Rey, S., Lo, R., & Foster, L. J. (2010). PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26(13), 1608–1615.
https://doi.org/10.1093/bioinformatics/btq249
Zhan, Z., Lao, M., Su, F., Chen, D., Liang, L., & Yang, X. (2018). Hospital-acquired infection in patients with systemic lupus erythematosus: a case-control study in a southern Chinese population. Clinical Rheumatology, 37, 709–717.
https://doi.org/10.1007/s10067-017-3919-8
Zhang, Y., Zhang, J., Yang, J., Wang, Y., Zhang, L., Zuo, X., & Wang, T. (2015). Meta-analysis of GWAS on two Chinese populations followed by replication identifies novel genetic variants on the X chromosome associated with systemic lupus erythematosus. Human Molecular Genetics, 24(1), 274–284.
https://doi.org/10.1093/hmg/ddu429
