Proteomic patterns in glomerular research, a laser capture microdissection and liquid chromatography-tandem mass spectrometry approach

1 Mariani LH, Kretzler M. Pro: “The usefulness of biomarkers in glomerular diseases”. The problem: moving from syndrome to mechanism-individual patient variability in disease presentation, course and response to therapy. Nephrol Dial Transplant. 2015 Jun;30(6):892-8. DOI: 10.1093/ndt/gfv108 Search in Google Scholar

2 Kerlin BA, Ayoob R, Smoyer WE. Epidemiology and Pathophysiology of Nephrotic Syndrome-Associated Thromboembolic Disease. Clin J Am Soc Nephrol. 2012 Mar;7(3):513-20. DOI: 10.2215/CJN.10131011 Search in Google Scholar

3 Caster DJ, Hobeika L, Klein JB, Powell DW, McLeish KR. Changing the concepts of immune-mediated glomerular diseases through proteomics. PROTEOMICS - Clin Appl. 2015 Dec;9(11-12):967-71 DOI: 10.1002/prca.201400159 Search in Google Scholar

4 Cavanaugh C, Okusa MD. The Evolving Role of Novel Biomarkers in Glomerular Disease: A Review. Am J Kidney Dis. 2021 Jan;77(1):122-31. DOI: 10.1053/j.ajkd.2020.06.016 Search in Google Scholar

5 Waldman M, Crew RJ, Valeri A, Busch J, Stokes B, Markowitz G, et al. Adult Minimal-Change Disease. Clin J Am Soc Nephrol. 2007 May;2(3):445-53. DOI: 10.2215/CJN.03531006 Search in Google Scholar

6 Pérez V, López D, Boixadera E, Ibernón M, Espinal A, Bonet J, et al. Comparative differential proteomic analysis of minimal change disease and focal segmental glomerulosclerosis. BMC Nephrol. 2017 Feb;18:49-58. DOI: 10.1186/s12882-017-0452-6 Search in Google Scholar

7 Datta S, Malhotra L, Dickerson R, Chaffee S, Sen CK, Roy S. Laser capture microdissection: Big data from small samples. Histol Histopathol. 2015 Nov;30(11):1255-69. DOI: 10.14670/HH-11-622 Search in Google Scholar

8 Yoshida Y, Miyamoto M, Taguchi I, Xu B, Zhang Y, Yaoita E, et al. Human kidney glomerulus proteome and biomarker discovery of kidney diseases. PROTEOMICS - Clin Appl. 2008 Mar;2(3):420-7. DOI: 10.1002/prca.200780016 Search in Google Scholar

9 Kawata N, Kang D, Aiuchi T, Obama T, Yoshitake O, Shibata T, et al. Proteomics of human glomerulonephritis by laser microdissection and liquid chromatography-tandem mass spectrometry. Nephrology. 2020 Apr;25(4):351-9. DOI: 10.1111/nep.13676 Search in Google Scholar

10 Guo T, Kouvonen P, Koh CC, Gillet LC, Wolski WE, Röst HL, et al. Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps. Nat Med. 2015 Apr;21(4):407-13. DOI: 10.1038/nm.3807 Search in Google Scholar

11 Hughes CS, Moggridge S, Müller T, Sorensen PH, Morin GB, Krijgsveld J. Single-pot, solid-phase-enhanced sample preparation for proteomics experiments. Nat Protoc. 2019 Jan;14(1):68-85. DOI: 10.1038/s41596-018-0082-x Search in Google Scholar

12 Distler U, Kuharev J, Navarro P, Tenzer S. Label-free quantification in ion mobility-enhanced data-independent acquisition proteomics. Nat Protoc. 2016 Apr;11(4):795-812. DOI: 10.1038/nprot.2016.042 Search in Google Scholar

13 Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009 Apr;25(8):1091-3. DOI: 10.1093/bioinformatics/btp101 Search in Google Scholar

14 Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, et al. Proteomics. Tissue-based map of the human proteome. Science. 2015 Jan;347(6220):1260419-30. DOI: 10.1126/science.1260419 Search in Google Scholar

15 Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, et al. A subcellular map of the human proteome. Science. 2017 May;356(6340):eaal3321-35. DOI: 10.1126/science.aal3321 Search in Google Scholar

16 Haas M. Glomerular Disease Pathology in the Era of Proteomics: From Pattern to Pathogenesis. J Am Soc Nephrol. 2018 Jan;29(1):2-4. DOI: 10.1681/ASN.2017080881 Search in Google Scholar

17 Madhavan SM, Almaani S, Shapiro JP, Satoskar AA, Ayoub I, Rovin BH, et al. Differentiating steroid-sensitive minimal change disease and primary and secondary focal segmental glomerulosclerosis: A proteomics-based approach. In: Glomerular Diseases: Antibodies, Complement, and Inflammatory Mediators. J Am Soc Nephrol- Kidney week 2021. Nov, 2021; Simulive, Virtual Only. https://www.asn-online.org/education/kidneyweek/2021/program-abstract.aspx?controlId=3612125 Search in Google Scholar

18 Brinkkoetter PT, Ising C, Benzing T. The role of the podocyte in albumin filtration. Nat Rev Nephrol. 2013 Jun;9(6):328-36. DOI: 10.1038/nrneph.2013.78 Search in Google Scholar

19 Yu SM-W, Nissaisorakarn P, Husain I, Jim B. Proteinuric Kidney Diseases: A Podocyte’s Slit Diaphragm and Cytoskeleton Approach. Front Med. 2018 Sep;5: 394585-600. DOI: 10.3389/fmed.2018.00221 Search in Google Scholar

20 Finne K, Marti H-P, Leh S, Skogstrand T, Vethe H, Tenstad O, et al. Proteomic Analysis of Minimally Damaged Renal Tubular Tissue from Two-Kidney-One-Clip Hypertensive Rats Demonstrates Extensive Changes Compared to Tissue from Controls. Nephron. 2016 Jan;132(1):70-80. DOI: 10.1159/000442825 Search in Google Scholar

21 Finne K, Vethe H, Skogstrand T, Leh S, Dahl TD, Tenstad O, et al. Proteomic analysis of formalin-fixed paraffin-embedded glomeruli suggests depletion of glomerular filtration barrier proteins in two-kidney, one-clip hypertensive rats. Nephrol Dial Transplant. 2014 Dec;29(12):2217-27. DOI: 10.1093/ndt/gfu268 Search in Google Scholar

22 Sethi S, Vrana JA, Theis JD, Leung N, Sethi A, Nasr SH, et al. Laser microdissection and mass spectrometry-based proteomics aids the diagnosis and typing of renal amyloidosis. Kidney Int. 2012 Jul;82(2):226-34. DOI: 10.1038/ki.2012.108 Search in Google Scholar

23 Ning X, Yin Z, Li Z, Xu J, Wang L, Shen W, et al. Comparative proteomic analysis of urine and laser microdissected glomeruli in IgA nephropathy. Clin Exp Pharmacol Physiol. 2017 May;44(5):576-85. DOI: 10.1111/1440-1681.12733 Search in Google Scholar

24 Kim AD, Lake BB, Chen S, Wu Y, Guo J, Parvez RK, et al. Cellular Recruitment by Podocyte-Derived Pro-migratory Factors in Assembly of the Human Renal Filter. iScience. 2019 Oct;20:402-14. DOI: 10.1016/j.isci.2019.09.029 Search in Google Scholar

25 Klein J, Caubet C, Camus M, Makridakis M, Denis C, Gilet M, et al. Connectivity mapping of glomerular proteins identifies dimethylaminoparthenolide as a new inhibitor of diabetic kidney disease. Sci Rep. 2020 Sep;10(1):1-12. DOI: 10.1038/s41598-020-71950-7 Search in Google Scholar

26 Bukosza EN, Kornauth C, Hummel K, Schachner H, Huttary N, Krieger S, et al. ECM Characterization Reveals a Massive Activation of Acute Phase Response during FSGS. Int J Mol Sci. 2020 Mar;21(6):2095-108. DOI: 10.3390/ijms21062095 Search in Google Scholar

27 Martin CE, Jones N. Nephrin Signaling in the Podocyte: An Updated View of Signal Regulation at the Slit Diaphragm and Beyond. Front Endocrinol (Lausanne). 2018 Jun;9:384121-33. DOI: 10.3389/fendo.2018.00302 Search in Google Scholar

28 Solanki AK, Widmeier E, Arif E, Sharma S, Daga A, Srivastava P, et al. Mutations in KIRREL1, a slit diaphragm component, cause steroid-resistant nephrotic syndrome. Kidney Int. 2019 Oct;96(4):883-9. DOI: 10.1016/j.kint.2019.06.016 Search in Google Scholar

29 Fuiano G, Comi N, Magri P, Sepe V, Balletta MM, Esposito C, et al. Serial morphometric analysis of sclerotic lesions in primary “focal” segmental glomerulosclerosis. J Am Soc Nephrol. 1996 Jan;7(1):49-55. DOI: 10.1681/ASN.V7149 Search in Google Scholar

30 McGrogan A, Franssen CFM, de Vries CS. The incidence of primary glomerulonephritis worldwide: a systematic review of the literature. Nephrol Dial Transplant. 2011 Feb;26(2):414-30. DOI: 10.1093/ndt/gfq665 Search in Google Scholar