Allergy, asthma, and proteomics: opportunities with immediate impact
Main Article Content
Keywords
Allergy, atopic diseases, bioinformatics, mass spectrometry, peptidomics
Abstract
Allergy is widely discussed by researchers due to its complex mechanism that leads to disorders and injuries, but the reason behind the allergic status remains unclear. Current treatments are insufficient to improve the patient’s quality of life significantly. New technologies in scientific and technological development are emerging. For instance, the union between allergy and peptidomics and bioinformatics tools may help fill the gaps in this field, diagnosis, and treatment. In this review, we look at peptidomics and address some findings, such as target proteins or biomarkers that help better understand mechanisms that lead to inflammation, organ damage, and, consequently, poor quality of life or even death.
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2. Cooke A, Zaccone P, Raine T, Phillips JM, Dunne DW. Infection and autoimmunity: are we winning the war, only to lose the peace? Trends Parasitol.2004; 20(7): 316–21. 10.1016/j.pt.2004.04.010
3. Palomares O, Akdis M, Martín-Fontecha M, Akdis CA. Mechanisms of immune regulation in allergic diseases: the role of regulatory T and B cells. Immunol Rev. 2017;278(1): 219–36. 10.1111/imr.12555
4. Valenta R, Karaulov A, Niederberger V, Gattinger P, van Hage M, Flicker S, et al. Molecular Aspects of allergens and allergy. In Advances in Immunology. 1st ed, vol. 138. Elsevier Inc; 2018.
5. Thomsen SF. Epidemiology and natural history of atopic diseases. Eur Clin Respir J. 2015; 1: 279–341. 10.3402/ecrj.v2.24642
6. Joan O, Stephan A. Recent advances in experimental allergy. Int Arch Allergy Immunol.2018; 177(4):281–89. 10.1159/000494440
7. Verschoor D, Gunten S Von. Allergyand atopic diseases: an update on experimental evidence. Int Arch Allergy Immunol. 2019; 180(4): 235–43. 10.1159/000504439
8. Macchiaverni P, Arslanian C, Frazão JB, Palmeira P, Russo M, Verhasselt V, Condino-Neto A. Mother to child transfer of IgG and IgA antibodies against dermatophagoides pteronyssinus. Scand J Immunol.2011; 74(6): 619–27. 10.1111/j.1365-3083.2011.02615.x
9. Holgate ST, Polosa R. Treatment strategies for allergy and asthma. Nat RevImmunol.2008; 8(3): 218–30. 10.1038/nri2262
10. Galli SJ, Tsai M, Piliponsky AM. The development of allergic inflammation. Nature. 2013;454: 445–54. 10.1038/nature07204
11. Yoo Y, Perzanowski MS. Allergic sensitization and the environment: latest update. Curr Allergy Asthma Rep. 2014;14(1): 465. 10.1007/s11882-014-0465-1
12. Gaurav R, Agrawal DK, Science T. Clinical view on the importance of the dendritic cells in asthma. Expert Rev Clin Immunol. 2015; 9(10): 899–919. 10.1586/1744666X.2013.837260
13. Humeniuk P, Dubiela P, Hoffmann-Sommergruber K. Dendritic cells and their role in allergy: uptake, proteolytic processing and presentation of allergens. Int JMolSci. 2017;18(7): 1491. 10.3390/ijms18071491
14. Hill DA, Spergel J. The atopic march: critical evidence and clinical relevance. Ann Allergy Asthma Immunol.2019;120(2): 131–37. 10.1016/j.anai.2017.10.037
15. Lowe AJ, Leung DYM, Tang MLK., Su JC, Allen KJ. The skin as a target for prevention of the atopic march. Ann Allergy Asthma Immunol. 2018;120(2): 145–51. 10.1016/j.anai.2017.11.023
16. Spergel JM. Epidemiology of atopic dermatitis and atopic march in children. Immunol Allergy Clin North Am. 2010;30(3): 269–80. 10.1016/j.iac.2010.06.003
17. Boonpiyathad T, Sözener ZC, Satitsuksanoa P, Akdis CA. Immunologic mechanisms in asthma. Semin Immunol. 2019; 46: 101333. 10.1016/j.smim.2019.101333
18. Holgate ST. The epidemic of allergy and asthma. Nature. 1999; 402(6760): 2–4. 10.1038/35037000
19. Shea KM, Truckner RT, Weber RW, Peden DB. Climate change and allergic disease. J Allergy Clin Immunol.2008;122(3): 443–53. 10.1016/j.jaci.2008.06.032
20. Pawankar R. Allergic diseases and asthma: a global public health concern and a call to action. World Allergy Organ J. 2014; 7(1):1–3. 10.1186/1939-4551-7-12
21. Pawankar R, Canonica GW, ST Holgate ST, Lockey RF, Blaiss M. White Book on Allergy. World Allergy Organization; 2013.
22. Ebert CS, Pillsbury HC. Epidemiology of allergy. Otolaryngol Clin North Am. 2011; 44(3): 537–48. 10.1016/j.otc.2011.03.001
23. Simon D. Recent advances in clinical allergy and immunology. Int Arch Allergy Immunol. 2018; 177(4): 324–33. 10.1159/000494931
24. Camelo-Nunes, IC, Solé D. Allergic rhinitis: indicators of quality of life. J Bras Pneumol. 2010;36(1): 124–33. 10.1590/s1806-37132010000100017
25. Wangberg H, Woessner K. Choice of biologics in asthma endotypes. Curr Opin Allergy Clin Immunol. 2021; 21(1): 79–85. 10.1097/ACI.0000000000000708
26. Doroudchi A, Pathria M, Modena BD. Asthma biologics: comparing trial designs, patient cohort and study results. Ann Allergy Asthma Immunol. 2020; 124: 44–56. 10.1016/j.anai.2019.10.016
27. Fitzpatrick AM, Chipps BE, Holguin F, Woodruff PG. T-2 ‘Low’ asthma: overview and management strategies. J Allergy Clin Immunol Pract. 2020; 8: 452–63. 10.1016/j.jaip.2019.11.006
28. Fahy JV. Type 2 inflammation in asthma–present in most, absent in many. Nat Rev Immunol. 2015; 15(1): 57–65. 10.1038/nri3786
29. Kuruvilla ME, Lee FE, Lee GB. Understanding asthma phenotypes, endotypes, and mechanisms of disease. Clin Rev Allergy Immunol. 2019; 56: 219–33. 10.1007/s12016-018-8712-1
30. Principe S, Porsbjerg C, Ditlev SB, Klein DK, Golebski K, Dyhre-Petersen N, et al. Treating severe asthma: targeting the IL-5 pathway. Clin Exp Allergy. 2021; 51: 992–1005. 10.1111/cea.13885
31. Pelaia C, Crimi C, Vatrella A, Tinello C, Terracciano R, Pelaia G. Molecular targets for biological therapies of severe asthma. Front Immunol. 2020; 11(603312): 1–11. 10.3389/fimmu.2020.603312
32. Kocher T, Superti-Furga G. Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods. 2007; 4(10): 807–15. 10.1038/nmeth1093
33. McDonald WH, Yates III JR. Shotgun proteomics and biomarker discovery. Dis Markers. 2002; 18(2): 99–105. 10.1155/2002/505397
34. Eng JK, McCormack AL, Yates I JR. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J Am Soc of Mass Spectrom. 1994; 5: 976–89. 10.1016/1044-0305(94)80016-2
35. Han X, Aslanian A, Yates III JR. Mass spectrometry for proteomics. Curr Opin Chem Biol. 2008; 12(5): 483–90. 10.1016/j.cbpa.2008.07.024
36. MacCoss MJ, Yates III JR. Proteomics: analytical tools a technique. Curr Opin Clin Nutr Metab Care. 2001; 4: 369–75. 10.1097/00075197-200109000-00006
37. Tabb DL, Fernando CG, Chambers MC. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J Proteome Res. 2007; 6(2): 654–61. 10.1021/pr0604054
38. Tabb DL, Narasimhan C, Strader MB, Hettich RL. DBDigger: reorganized proteomic database identification that improves flexibility and speed. Anal Chem. 2005; 77(8): 2464–474. 10.1021/ac0487000
39. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis. 1999; 20(18): 3551–567. 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2
40. Liu K, Zhang J, Wang J, Zhao L, Peng X, Jia W, et al Relationship between sample loading amount and peptide identification and its effects on quantitative proteomics. Anal Chem. 2009; 81(4): 1307–14. 10.1021/ac801466k
41. Moberg M, Bergquist J, Bylund D. A generic stepwise optimization strategy for liquid chromatography electrospray ionization tandem mass spectrometry methods. J Mass Spectrom. 2006; 41(10): 1334–345. 10.1002/jms.1108
42. Venable JD, Yates I JR. Impact of ion trap tandem mass spectra variability on the identification of peptides. Anal Chem. 2004; 76: 2928–937. 10.1021/ac0348219
43. Wenner BR, Lynn BC. Factors that affect ion trap data-dependent MS/MS in proteomics. J Am Soc Mass Spectrom. 2004; 15: 150–57. 10.1016/j.jasms.2003.10.006
44. Riter LS, Vitek O, Gooding KM, Hodge BD, Julian-Jr RK. Statistical design of experiments as a tool in mass spectrometry. J Mass Spectrom. 2005; 40(5): 565–79. 10.1002/jms.871
45. Jiang X, Jiang X, Han G, Ye M, Zou H. Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics. BMC Bioinformatics. 2007; 8(323): 1–12. 10.1186/1471-2105-8-323
46. Subramanian I, Verma S, Kumar S, Jere A, Anamika K. Multi-omics data integration, interpretation, and its application. Bioinform Biol Insights. 2020; 14: 7–9. 10.1177/1177932219899051
47. Whitley KV, Tueller JA, Weber KS. Genomics education in the era of personal genomics: academic, professional, and public considerations. Int J Mol Sci. 2020; 21(3): 1–19. 10.3390/ijms21030768
48. Suhre K, McCarthy MI, Schwenk JM. Genetics meets proteomics: perspectives for large population-based studies. Nat Rev Genet. 2021;22(1): 19–37. 10.1038/s41576-020-0268-2
49. Hedl TJ, Gil RS, Cheng F, Rayner SL, Davidson JM, Luca A De, Lee A. Proteomics approaches for biomarker and drug target discovery in als and ftd.Front Neurosci. 2019;13: 1–25. 10.3389/fnins.2019.00548
50. Vitorino R, Guedes S, da Costa JP, Kašička V. Microfluidics for peptidomics, proteomics, and cell analysis. Nanomaterials. 2021;11(5): 1–33. 10.3390/nano11051118
51. Bush A. Cytokines and chemokines as biomarkers of future asthma. Front Pediatr. 2019;7: 72. 10.3389/fped.2019.00072
52. Sun X, Hou T, Cheung E, Lu TNT, Tam VWH, Chu IMT, Wong CK. Anti-inflammatory mechanisms of the novel cytokine interleukin-38 in allergic asthma. Cell Mol Immunol.2020; 17(6): 631–46. 10.1038/s41423-019-0300-7
53. Varricchi G, Rossi FW, Galdiero MR, Granata F, Criscuolo G, Spadaro G, Marone G. Physiological roles of mast cells: collegium internationale allergologicum update 2019. Int Arch Allergy Immunol. 2019; 179(4): 247–61. 10.1159/000500088
54. MacMullan MA, Dunn ZS, Graham N, Yang L, Wang P. Quantitative proteomics and metabolomics reveal biomarkers of disease as potential immunotherapy targets and indicators of therapeutic efficacy. Theranostics. 2019;9(25): 7872–888. 10.7150/thno.37373
55. López-Pedrouso M, Lorenzo JM, Gagaoua M, Franco D. Current trends in proteomic advances for food allergen analysis. Biology. 2020;9(9): 247. 10.3390/biology9090247
56. Pilolli R, Gadaleta A, di Stasio L, Lamonaca A, de Angelis E, Nigro D, Monaci L. A comprehensive peptidomic approach to characterize the protein profile of selected durum wheat genotypes: implication for celiac disease and wheat allergy. Nutrients. 2019; 11(10): 2321. 10.3390/nu11102321
57. Aquino A, Conte-Junior CA. A systematic review of food allergy: nanobiosensor and food allergen detection. Biosensors. 2020; 10(12): 194. 10.3390/bios10120194
58. Schrader M, Schulz-Knappe P, Fricker LD. Historical perspective of peptidomics. EuPA Open Proteom. 2014;3: 171–82. 10.1016/j.euprot.2014.02.014
59. Vitorino R. Digging deep into peptidomics applied to body fluids. Proteomics. 2018; 18(2): 1–15. 10.1002/pmic.201700401
60. Bassani-Sternberg M, Pletscher-Frankild S, Jensen LJ, Mann M. Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation. Mol Cell Proteomics. 2015; 14(3): 658–73. 10.1074/mcp.M114.042812
61. Mamone G, Picariello G, Addeo F, Ferranti P. Proteomic analysis in allergy and intolerance to wheat products. Expert Rev Proteomics. 2011; 8(1): 95–115. 10.1586/epr.10.98
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