LABORATORY OF PROTEOMICS RESEARCH
A HUN-REN BRC & HCEMM Research and Resource Facility

Proteomics has become one of the most exciting and dynamic research areas. Since the genomes sequenced failed to answer several questions, systems biology research started to target other biomolecules. Proteomic studies aim to decipher structural changes of proteins and protein complexes, their role in different interactions, biological functions and processes by characterizing the qualitative and quantitative changes in protein mixtures of varied complexity: up to cellular organelles, cell lines, tissues, or even individuals. Mass spectrometry has become the method of choice for such research. It is equally well suited for protein identification, de novo sequencing, for the characterization of post-translational modifications, or other covalent labeling. It can also be used for probing the 3D structure of proteins, the spatial organization of protein complexes, or studying intact protein populations. Last but not least, mass spectrometry can also deliver quantitative results.

We have extensive collaborations within the HUN-REN BRC and with academic organizations in Hungary and abroad. Biological samples are provided by our partners. Our tasks are the analytical sample preparation, chromatographic fractionation if necessary, mass spectrometry analysis as well as data interpretation. However, an ideal collaboration starts at the planning stage, designing the experiments together. Obviously our goal is to assure that the samples will be compatible with the following analyses, but the number of biological and technical replicates or the selection of proper controls is also discussed whenever it is necessary. We developed and routinely use a reliable protocol for the isolation of protein complexes. We also regularly perform the qualitative and (semi)quantitative characterization of the resulting mixtures, as well as other protein samples of different complexity. Such analysis may include the characterization of certain posttranslational modifications. We are experienced in the characterization of disulfide-bridges, proteolytic cleavage sites, ubiquitination, phosphorylation and glycosylation. For about a decade we have been successfully developing new methods for the characterization of mucin-type O-glycosylation.

Selected Publications

1. Tukacs V, Mittli D, Hunyadi-Gulyás É, Hlatky D, Medzihradszky KF, Darula Z, Nyitrai G, Czurkó A, Juhász G, Kardos J, Kékesi KA. Chronic Cerebral Hypoperfusion-Induced Disturbed Proteostasis of Mitochondria and MAM Is Reflected in the CSF of Rats by Proteomic Analysis. Mol. Neurobiol. (2023) doi: 10.1007/s12035-023-03215-z.

2. Zhang S, Wang T, Lima RM, Pettkó-Szandtner A, Kereszt A, Downie JA, Kondorosi E. Widely conserved AHL transcription factors are essential for NCR gene expression and nodule development in Medicago. Nat. Plants (2023) 9(2):280-288.

3. Mihailova, G, Solti Á, Sárvári É, Hunyadi-Gulyás É, Georgieva K. Protein Changes in Shade and Sun Haberlea rhodopensis Leaves during Dehydration at Optimal and Low Temperatures. Plants (2023) 12, 401.

4. Ughy B, Nagyapati S, Lajko DB, Letoha T, Prohaszka A, Deeb D, Der A, Pettko-Szandtner A, Szilak L. Reconsidering Dogmas about the Growth of Bacterial Populations. Cells (2023) 19;12(10):1430.

5. Bartha A, Darula Z, Munkacsy G, Klement E, Nyirady P, Gyorffy B. Proteotranscriptomic Discrimination of Tumor and Normal Tissues in Renal Cell Carcinoma Int. J. Mol. Sci.(2023) 24(5), 4488.

6. Verster KI, Cinege G, Lipinszki Z, Magyar LB, Kurucz É, Tarnopol RL, Ábrahám E, Darula Z, Karageorgi M, Tamsil JA, Akalu SM, Andó I, Whiteman NK. Evolution of insect innate immunity through domestication of bacterial toxins. Proc Natl Acad Sci U S A. (2023) 120(16):e2218334120.

7. Pap A, Kiraly IE, Medzihradszky KF, Darula Z. Multiple Layers of Complexity in O-Glycosylation Illustrated With the Urinary Glycoproteome. Mol. Cell. Proteomics (2022) 21(12):100439.

8. Rethi-Nagy Z, Abraham E, Udvardy K, Klement E, Darula Z, Pal M, Katona RL, Tubak V, Pali T, Kota Z, Sinka R, Udvardy A, Lipinszki Z. STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins. Int. J. Mol. Sci. (2022) 23(15):8168.

9. Birinyi Z, Réder D, Dios A, Korponay-Szabo IR, Hunyadi-Gulyas E, Florides CG, Juhasz A, Gell G. Immunoanalytic Investigation of Grain Proteins Antigenic for Celiac Disease Patients in an Einkorn Collection. Food Chemistry (2022) doi:10.1016/j.foodchem.2021.131148.

10. Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M. Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis. Nat. Methods (2021) 18(11):1304-1316.

11. Viczián, A., Ádám, É., Staudt, A. M., Lambert, D., Klement, E., Romero Montepaone, S., Hiltbrunner, A., Casal, J., Schäfer, E., Nagy, F., & Klose, C. Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling. The New phytologist (2020) 225(4): 1635–1650.

12. Lokdarshi, A., Papdi, C., Pettkó-Szandtner, A., Dorokhov, S., Scheres, B., Magyar, Z., von Arnim, A. G., Bögre, L., & Horváth, B. M. ErbB-3 binding protein 1 Regulates Translation and Counteracts Retinoblastoma Related to Maintain the Root Meristem. Plant Physiology (2020) 182(2):919–932.

13. Lin King, J. V., Emrick, J. J., Kelly, M., Herzig, V., King, G. F., Medzihradszky, K. F., & Julius, D. A Cell-Penetrating Scorpion Toxin Enables Mode-Specific Modulation of TRPA1 and Pain. Cell (2019) 178(6):1362–1374.e16.

14. Andrási N, Rigó G, Zsigmond L, Pérez-Salamó I, Papdi C, Klement E, Pettkó-Szandtner A, Baba AI, Ayaydin F, Dasari R, Cséplő Á, Szabados L. The mitogen-activated protein kinase 4-phosphorylated heat shock factor A4A regulates responses to combined salt and heat stresses. Exp. Bot. (2019) 70(18):4903-4918.

15. Letoha, T., Hudák, A., Kusz, E., Pettkó-Szandtner, A., Domonkos, I., Jósvay, K., Hofmann-Apitius, M., & Szilák, L. Contribution of syndecans to cellular internalization and fibrillation of amyloid-β(1-42). Scientific reports (2019) 9(1):1393.

16. Szél, E., Bozó, R., Hunyadi-Gulyás, É., Manczinger, M., Szabó, K., Kemény, L., Bata-Csörgő, Z., & Groma, G. Comprehensive Proteomic Analysis Reveals Intermediate Stage of Non-Lesional Psoriatic Skin and Points out the Importance of Proteins Outside this Trend. Scientific reports (2019) 9(1), 11382.

17. Gyukity-Sebestyén E, Harmati M, Dobra G, Németh IB, Mihály J, Zvara Á, Hunyadi-Gulyás É, Katona R, Nagy I, Horváth P, Bálind Á, Szkalisity Á, Kovács M, Pankotai T, Borsos B, Erdélyi M, Szegletes Z, Veréb ZJ, Buzás EI, Kemény L, Bíró T, Buzás K. Melanoma-Derived Exosomes Induce PD-1 Overexpression and Tumor Progression via Mesenchymal Stem Cell Oncogenic Reprogramming. Front. Immunol. (2019) 10:2459.

18. Schmitt LR, Henderson R, Barrett A, Darula Z, Issaian A, D'Alessandro A, Clendenen N, Hansen KC. Mass spectrometry-based molecular mapping of native FXIIIa cross-links in insoluble fibrin clots. J Biol Chem. (2019) 294(22):8773-8778.

19. Darula Z, Pap Á, Medzihradszky KF. Extended Sialylated O-Glycan Repertoire of Human Urinary Glycoproteins Discovered and Characterized Using Electron-Transfer/Higher-Energy Collision Dissociation. J. Proteome Res. (2019) 18(1):280-291.

20. Darula Z, Medzihradszky KF. Analysis of Mammalian O-Glycopeptides-We Have Made a Good Start, but There is a Long Way to Go. Mol. Cell Proteomics. (2018) 17(1):2-17.