In silico selection of damage-associated molecular patterns (DAMPS) and their receptors in humans
DOI:
https://doi.org/10.33448/rsd-v11i10.32838Keywords:
Bioinformatics; Immune system; Innate Immunity; mRNA; Molecular Biology.Abstract
Damage-associated molecular patterns (DAMPs) are intracellular molecules released into the extracellular environment after injury. These are recognized by pattern recognition receptors (PRRs) and activate the innate immune system, triggering an inflammatory response. The most commonly studied DAMPs are S100 proteins, Thermal Shock Proteins (HSPs) and High Mobility Box Group 1 (HMGB1). Among the PRRs are the Toll-like Receptor (TLRs), the Receptor for Advanced Glycation End Products (RAGEs), Nod-like Receptor (NLRs) and the Absent Receptor in Melanoma 2 (AIM-2). DAMPs are intimately involved in the etiopathogenesis of chronic diseases such as cancer, diabetes, liver disease, heart disease and neurodegenerative diseases. It is very important to select molecular markers that enable the assembly of biological assays, with a view to elucidating the evaluation of the immune response. The present study evaluated different human DAMPs and their receptors in order to find molecular markers associated with diseases using bioinformatics tools. The screening of messenger RNA (mRNA) amino acid sequences was performed on the NCBI database using the nucleotide tool. Secondary mRNA prediction using RNAStructure and RNA foldWebServer software, epitope antigenicity prediction using the Immune Epitope Database Analysis Resource software and primer design using the Primer-BLAST Platform were evaluated. Considering the best predictions of secondary mRNA from receptors and DAMPs, 104 epitopes and 83 molecular marker candidates were predicted. The results presented are promising and could be used as immunomodulators or as diagnostic and prognostic platforms in various diseases.
References
Ahmad, S., Khan, H., Siddiqui, Z., Khan, M. Y., Rehman, S., Shahab, U., et al. (2018). AGEs, RAGEs and s-RAGE; friend or foe for cancer. Paper presented at the Seminars in cancer biology.
Anttila, J. E., Whitaker, K. W., Wires, E. S., Harvey, B. K., & Airavaara, M. (2017). Role of microglia in ischemic focal stroke and recovery: focus on Toll-like receptors. Progress in Neuro-Psychopharmacology and Biological Psychiatry, 79, 3-14.
Bauer, A. K., Upham, B. L., Rondini, E. A., Tennis, M. A., Velmuragan, K., & Wiese, D. (2017). Toll-like receptor expression in human non-small cell lung carcinoma: Potential prognostic indicators of disease. Oncotarget, 8(54), 91860.
Bergman, P., Esfahani, S. S., & Engström, Y. (2017). Drosophila as a model for human diseases—focus on innate immunity in barrier epithelia. Current topics in developmental biology, 121, 29-81.
Carra, S., Alberti, S., Benesch, J. L., Boelens, W., Buchner, J., Carver, J. A., et al. (2019). Small heat shock proteins: multifaceted proteins with important implications for life. Cell Stress and Chaperones, 24(2), 295-308.
Chen, J.-Q., Szodoray, P., & Zeher, M. (2016). Toll-like receptor pathways in autoimmune diseases. Clinical reviews in allergy & immunology, 50(1), 1-17.
Drouin-Ouellet, J., St-Amour, I., Saint-Pierre, M., Lamontagne-Proulx, J., Kriz, J., Barker, R. A., et al. (2015). Toll-like receptor expression in the blood and brain of patients and a mouse model of Parkinson’s disease. International Journal of Neuropsychopharmacology, 18(6).
Feng, A., Tu, Z., & Yin, B. (2016). The effect of HMGB1 on the clinicopathological and prognostic features of non-small cell lung cancer. Oncotarget, 7(15), 20507.
Ferrara-Bowens, T. M., Chandler, J. K., Guignet, M. A., Irwin, J. F., Laitipaya, K., Palmer, D. D., et al. (2017). Neuropathological and behavioral sequelae in IL-1R1 and IL-1Ra gene knockout mice after soman (GD) exposure. Neurotoxicology, 63, 43-56.
Gao, L., Dong, Q., Song, Z., Shen, F., Shi, J., & Li, Y. (2017). NLRP3 inflammasome: a promising target in ischemic stroke. Inflammation Research, 66(1), 17-24.
Gehrke, N., Hövelmeyer, N., Waisman, A., Straub, B. K., Weinmann-Menke, J., Wörns, M. A., et al. (2018). Hepatocyte-specific deletion of IL1-RI attenuates liver injury by blocking IL-1 driven autoinflammation. Journal of hepatology, 68(5), 986-995.
Gülke, E., Gelderblom, M., & Magnus, T. (2018). Danger signals in stroke and their role on microglia activation after ischemia. Therapeutic advances in neurological disorders, 11, 1756286418774254.
Hulina‐Tomašković, A., Rajković, M. G., Somborac‐Bačura, A., Čeri, A., Dabelić, S., & Rumora, L. (2018). Extracellular Hsp70 modulates the inflammatory response of cigarette smoke extract in NCI‐H292 cells. Experimental Physiology, 103(12), 1704-1716.
Ivády, G., Madar, L., Dzsudzsák, E., Koczok, K., Kappelmayer, J., Krulisova, V., et al. (2018). Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system. BMC genomics, 19(1), 1-8.
Kang, R., Chen, R., Zhang, Q., Hou, W., Wu, S., Cao, L., et al. (2014). HMGB1 in health and disease. Molecular aspects of medicine, 40, 1-116.
Khan, M. I., Su, Y.-K., Zou, J., Yang, L.-W., Chou, R.-H., & Yu, C. (2018). S100B as an antagonist to block the interaction between S100A1 and the RAGE V domain. PLoS One, 13(2), e0190545.
Kim, C., Spencer, B., Rockenstein, E., Yamakado, H., Mante, M., Adame, A., et al. (2018). Immunotherapy targeting toll-like receptor 2 alleviates neurodegeneration in models of synucleinopathy by modulating α-synuclein transmission and neuroinflammation. Molecular neurodegeneration, 13(1), 1-18.
Kolaskar, A. S., & Tongaonkar, P. C. (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS letters, 276(1-2), 172-174.
Kuramochi, M., Izawa, T., Pervin, M., Bondoc, A., Kuwamura, M., & Yamate, J. (2016). The kinetics of damage-associated molecular patterns (DAMPs) and toll-like receptors during thioacetamide-induced acute liver injury in rats. Experimental and Toxicologic Pathology, 68(8), 471-477.
Leclerc, E., & Vetter, S. W. (2015). The role of S100 proteins and their receptor RAGE in pancreatic cancer. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 1852(12), 2706-2711.
Liu, J., Li, R., Liu, T., Rausch-Fan, X., & Wang, M. (2017). High mobility group box 1 protein level as a novel biomarker for the development of peri-implant disease. Scientific Reports, 7(1), 1-7.
Mou, K., Liu, W., Han, D., & Li, P. (2017). HMGB1/RAGE axis promotes autophagy and protects keratinocytes from ultraviolet radiation-induced cell death. Journal of dermatological science, 85(3), 162-169.
Mymrikov, E. V., Daake, M., Richter, B., Haslbeck, M., & Buchner, J. (2017). The chaperone activity and substrate spectrum of human small heat shock proteins. Journal of Biological Chemistry, 292(2), 672-684.
Nakahira, K., Hisata, S., & Choi, A. M. (2015). The roles of mitochondrial damage-associated molecular patterns in diseases. Antioxidants & redox signaling, 23(17), 1329-1350.
Oh, S., Son, M., Choi, J., Lee, S., & Byun, K. (2018). sRAGE prolonged stem cell survival and suppressed RAGE-related inflammatory cell and T lymphocyte accumulations in an Alzheimer's disease model. Biochemical and biophysical research communications, 495(1), 807-813.
Ozturk, A. R., & Can, T. (2017). A multiplex primer design algorithm for target amplification of continuous genomic regions. BMC bioinformatics, 18(1), 1-9.
Patidar, A., Selvaraj, S., Sarode, A., Chauhan, P., Chattopadhyay, D., & Saha, B. (2018). DAMP-TLR-cytokine axis dictates the fate of tumor. Cytokine, 104, 114-123.
Paul, S., & Mahanta, S. (2014). Association of heat-shock proteins in various neurodegenerative disorders: is it a master key to open the therapeutic door? Molecular and cellular biochemistry, 386(1), 45-61.
Paul, S., Sidney, J., Sette, A., & Peters, B. (2016). TepiTool: a pipeline for computational prediction of T cell epitope candidates. Current protocols in immunology, 114(1), 18.19. 11-18.19. 24.
Pennisi, R., Ascenzi, P., & Di Masi, A. (2015). Hsp90: a new player in DNA repair? Biomolecules, 5(4), 2589-2618.
Pradillo, J. M., Murray, K. N., Coutts, G. A., Moraga, A., Oroz-Gonjar, F., Boutin, H., et al. (2017). Reparative effects of interleukin-1 receptor antagonist in young and aged/co-morbid rodents after cerebral ischemia. Brain, behavior, and immunity, 61, 117-126.
Rani, M., Nicholson, S. E., Zhang, Q., & Schwacha, M. G. (2017). Damage-associated molecular patterns (DAMPs) released after burn are associated with inflammation and monocyte activation. Burns, 43(2), 297-303.
Riera Romo, M., Pérez‐Martínez, D., & Castillo Ferrer, C. (2016). Innate immunity in vertebrates: an overview. Immunology, 148(2), 125-139.
Sanajou, D., Haghjo, A. G., Argani, H., & Aslani, S. (2018). AGE-RAGE axis blockade in diabetic nephropathy: current status and future directions. European journal of pharmacology, 833, 158-164.
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.
Shao, Y., Nanayakkara, G., Cheng, J., Cueto, R., Yang, W. Y., Park, J.-Y., et al. (2018). Lysophospholipids and their receptors serve as conditional DAMPs and DAMP receptors in tissue oxidative and inflammatory injury. Antioxidants & Redox Signaling, 28(10), 973-986.
Shi, X., Li, M., Huang, K., Zhou, S., Hu, Y., Pan, S., et al. (2017). HMGB1 binding heptamer peptide improves survival and ameliorates brain injury in rats after cardiac arrest and cardiopulmonary resuscitation. Neuroscience, 360, 128-138.
Shin, J. J., Lee, E. K., Park, T. J., & Kim, W. (2015). Damage-associated molecular patterns and their pathological relevance in diabetes mellitus. Ageing Research Reviews, 24, 66-76.
Srikrishna, G., & Freeze, H. H. (2009). Endogenous damage-associated molecular pattern molecules at the crossroads of inflammation and cancer. Neoplasia, 11(7), 615-628.
Tai, N., Wong, F. S., & Wen, L. (2016). The role of the innate immune system in destruction of pancreatic beta cells in NOD mice and humans with type I diabetes. Journal of autoimmunity, 71, 26-34.
Tomasini, M. D., Wang, Y., Karamafrooz, A., Li, G., Beuming, T., Gao, J., et al. (2018). Conformational landscape of the PRKACA-DNAJB1 chimeric kinase, the driver for fibrolamellar hepatocellular carcinoma. Scientific reports, 8(1), 1-11.
Turner, N. A. (2016). Inflammatory and fibrotic responses of cardiac fibroblasts to myocardial damage associated molecular patterns (DAMPs). Journal of Molecular and Cellular Cardiology, 94, 189-200.
Turnier, J. L., Fall, N., Thornton, S., Witte, D., Bennett, M. R., Appenzeller, S., et al. (2017). Urine S100 proteins as potential biomarkers of lupus nephritis activity. Arthritis research & therapy, 19(1), 1-11.
Van Linthout, S., & Tschöpe, C. (2017). Inflammation–cause or consequence of heart failure or both? Current heart failure reports, 14(4), 251-265.
Wang, F., Zou, Z.-R., Yuan, D., Gong, Y., Zhang, L., Chen, X., et al. (2017). Correlation between serum S100β protein levels and cognitive dysfunction in patients with cerebral small vessel disease: a case–control study. Bioscience Reports, 37(2).
Wautier, M.-P., Guillausseau, P.-J., & Wautier, J.-L. (2017). Activation of the receptor for advanced glycation end products and consequences on health. Diabetes & Metabolic Syndrome: Clinical Research & Reviews, 11(4), 305-309.
Wu, X., Valli, A., García, J. A., Zhou, X., & Cheng, X. (2019). The tug-of-war between plants and viruses: great progress and many remaining questions. Viruses, 11(3), 203.
Wu, Y., Shi, B., Ding, X., Liu, T., Hu, X., Yip, K. Y., et al. (2015). Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic acids research, 43(15), 7247-7259.
Xia, C., Braunstein, Z., Toomey, A. C., Zhong, J., & Rao, X. (2018). S100 proteins as an important regulator of macrophage inflammation. Frontiers in immunology, 8, 1908.
Xu, Z. Z., & Mathews, D. H. (2016). Secondary structure prediction of single sequences using RNAstructure RNA Structure Determination (pp. 15-34): Springer.
Yang, R., Zou, X., Tenhunen, J., & Tønnessen, T. I. (2017). HMGB1 and extracellular histones significantly contribute to systemic inflammation and multiple organ failure in acute liver failure. Mediators of Inflammation, 2017.
Yu, Y., Wang, L., Delguste, F., Durand, A., Guilbaud, A., Rousselin, C., et al. (2017). Advanced glycation end products receptor RAGE controls myocardial dysfunction and oxidative stress in high-fat fed mice by sustaining mitochondrial dynamics and autophagy-lysosome pathway. Free Radical Biology and Medicine, 112, 397-410.
Zhang, J., Zhang, L., Zhang, S., Yu, Q., Xiong, F., Huang, K., et al. (2017). HMGB1, an innate alarmin, plays a critical role in chronic inflammation of adipose tissue in obesity. Molecular and cellular endocrinology, 454, 103-111.
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