@article{MTMT:34790193,
	title = {Lectin-Based Immunophenotyping and Whole Proteomic Profiling of CT-26 Colon Carcinoma Murine Model.},
	url = {https://m2.mtmt.hu/api/publication/34790193},
	author = {Faragó, Anna and Zvara, Ágnes and Tiszlavicz, László and Hunyadi-Gulyás Éva, Csilla and Darula, Zsuzsanna and Hegedűs, Zoltán and Szabó, Enikő and Surguta, Sára Eszter and Tóvári, József and Puskás, László and Szebeni, Gábor},
	doi = {10.3390/ijms25074022},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {25},
	unique-id = {34790193},
	issn = {1661-6596},
	abstract = {A murine colorectal carcinoma (CRC) model was established. CT26 colon carcinoma cells were injected into BALB/c mice's spleen to study the primary tumor and the mechanisms of cell spread of colon cancer to the liver. The CRC was verified by the immunohistochemistry of Pan Cytokeratin and Vimentin expression. Immunophenotyping of leukocytes isolated from CRC-bearing BALB/c mice or healthy controls, such as CD19+ B cells, CD11+ myeloid cells, and CD3+ T cells, was carried out using fluorochrome-labeled lectins. The binding of six lectins to white blood cells, such as galectin-1 (Gal1), siglec-1 (Sig1), Sambucus nigra lectin (SNA), Aleuria aurantia lectin (AAL), Phytolacca americana lectin (PWM), and galectin-3 (Gal3), was assayed. Flow cytometric analysis of the splenocytes revealed the increased binding of SNA, and AAL to CD3 + T cells and CD11b myeloid cells; and increased siglec-1 and AAL binding to CD19 B cells of the tumor-bearing mice. The whole proteomic analysis of the established CRC-bearing liver and spleen versus healthy tissues identified differentially expressed proteins, characteristic of the primary or secondary CRC tissues. KEGG Gene Ontology bioinformatic analysis delineated the established murine CRC characteristic protein interaction networks, biological pathways, and cellular processes involved in CRC. Galectin-1 and S100A4 were identified as upregulated proteins in the primary and secondary CT26 tumor tissues, and these were previously reported to contribute to the poor prognosis of CRC patients. Modelling the development of liver colonization of CRC by the injection of CT26 cells into the spleen may facilitate the understanding of carcinogenesis in human CRC and contribute to the development of novel therapeutic strategies.},
	keywords = {colorectal carcinoma; lectin binding sugar code; proteomic analysis of murine CRC},
	year = {2024},
	eissn = {1422-0067},
	orcid-numbers = {Tóvári, József/0000-0002-5543-3204; Szebeni, Gábor/0000-0002-6998-5632}
}

@article{MTMT:34497633,
	title = {Comparative analysis of hippocampal extracellular space uncovers widely altered peptidome upon epileptic seizure in urethane-anaesthetized rats},
	url = {https://m2.mtmt.hu/api/publication/34497633},
	author = {Tukacs, Vanda and Mittli, Dániel Árpád and Hunyadi-Gulyás Éva, Csilla and Darula, Zsuzsanna and Juhász, Gábor Dénes and Kardos, József and Kékesi, Adrienna Katalin},
	doi = {10.1186/s12987-024-00508-w},
	journal-iso = {FLUIDS BARRIERS CNS},
	journal = {FLUIDS AND BARRIERS OF THE CNS},
	volume = {21},
	unique-id = {34497633},
	issn = {2045-8118},
	abstract = {Background: The brain extracellular fluid (ECF), composed of secreted neurotransmitters, metabolites, peptides, and proteins, may reflect brain processes. Analysis of brain ECF may provide new potential markers for synaptic activity or brain damage and reveal additional information on pathological alterations. Epileptic seizure induction is an acute and harsh intervention in brain functions, and it can activate extra- and intracellular proteases, which implies an altered brain secretome. Thus, we applied a 4-aminopyridine (4-AP) epilepsy model to study the hippocampal ECF peptidome alterations upon treatment in rats. Methods: We performed in vivo microdialysis in the hippocampus for 3–3 h of control and 4-AP treatment phase in parallel with electrophysiology measurement. Then, we analyzed the microdialysate peptidome of control and treated samples from the same subject by liquid chromatography-coupled tandem mass spectrometry. We analyzed electrophysiological and peptidomic alterations upon epileptic seizure induction by two-tailed, paired t-test. Results: We detected 2540 peptides in microdialysate samples by mass spectrometry analysis; and 866 peptides—derived from 229 proteins—were found in more than half of the samples. In addition, the abundance of 322 peptides significantly altered upon epileptic seizure induction. Several proteins of significantly altered peptides are neuropeptides (Chgb) or have synapse- or brain-related functions such as the regulation of synaptic vesicle cycle (Atp6v1a, Napa), astrocyte morphology (Vim), and glutamate homeostasis (Slc3a2). Conclusions: We have detected several consequences of epileptic seizures at the peptidomic level, as altered peptide abundances of proteins that regulate epilepsy-related cellular processes. Thus, our results indicate that analyzing brain ECF by in vivo microdialysis and omics techniques is useful for monitoring brain processes, and it can be an alternative method in the discovery and analysis of CNS disease markers besides peripheral fluid analysis. © 2024, The Author(s).},
	keywords = {Animals; Male; PEPTIDES; metabolism; PEPTIDE; SEIZURES; comparative study; amino acid sequence; Extracellular Space; nonhuman; animal model; animal experiment; pathology; slow brain wave; Electroencephalogram; urethan; glial fibrillary acidic protein; area under the curve; in vivo study; seizure; AMIDES; AMIDE; upregulation; brain function; neuropeptide Y; ASTROCYTE; tandem mass spectrometry; Temporal lobe epilepsy; Urethane; MICRODIALYSIS; synapse vesicle; FAMPRIDINE; peptidomics; Gene set enrichment analysis; rat; secretoneurin; Chromogranin B},
	year = {2024},
	eissn = {2045-8118},
	orcid-numbers = {Juhász, Gábor Dénes/0000-0002-0849-6931; Kardos, József/0000-0002-2135-2932; Kékesi, Adrienna Katalin/0000-0003-3042-4878}
}

@article{MTMT:34334193,
	title = {Biofilm formation initiating rotifer-specific biopolymer and its predicted components},
	url = {https://m2.mtmt.hu/api/publication/34334193},
	author = {Datki, Zsolt László and Darula, Zsuzsanna and Vedelek, Viktor and Hunyadi-Gulyás Éva, Csilla and Dingmann, Brian J. and Vedelek, Balázs and Kalman, Janos and Urban, Peter and Gyenesei, Attila and Galik-Olah, Zita and Gálik, Bence and Sinka, Rita},
	doi = {10.1016/j.ijbiomac.2023.127157},
	journal-iso = {INT J BIOL MACROMOL},
	journal = {INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES},
	volume = {253},
	unique-id = {34334193},
	issn = {0141-8130},
	abstract = {The rotifer-specific biopolymer, namely Rotimer, is a recently discovered group of the biomolecule family. Rotimer has an active role in the biofilm formation initiated by rotifers (e.g., Euchlanis dilatata or Adineta vaga) or in the female-male sexual interaction of monogononts. To understand the Ca2+- and polarity-dependent formation of this multifunctional viscoelastic material, it is essential to explore its molecular composition. The investigation of the rotifer-enhanced biofilm and Rotimer-inductor conglomerate (RIC) formation yielded several protein candidates to predict the Rotimer-specific main components. The exudate of E. dilatata males was primarily applied from different biopolimer-containing samples (biofilm or RIC). The advantage of males over females lies in their degenerated digestive system and simple anatomy. Thus, their exudate is less contaminated with food and endosymbiont elements. The sequenced and annotated genome and transcriptome of this species opened the way for identifying Rotimer proteins by mass spectrometry. The predicted rotifer-biopolymer forming components are SCO-spondins and 14-3-3 protein. The characteristics of Rotimer are similar to Reissner's fiber, which is found in the central nervous system of vertebrates and is mainly formed from SCO-spondins. This molecular information serves as a starting point for its interdisciplinary investigation and application in biotechnology, biomedicine, or neurodegeneration-related drug development.},
	keywords = {IN-VIVO; PROTEINS; 14-3-3 PROTEIN; ANTIBODY; Biofilm; Ecotoxicology; Clearance; Chemistry, Applied; Biochemistry & Molecular Biology; Rotimer; SCO-spondin},
	year = {2023},
	eissn = {1879-0003},
	orcid-numbers = {Datki, Zsolt László/0000-0002-2537-4741; Vedelek, Balázs/0000-0001-6981-0026; Sinka, Rita/0000-0003-4040-4184}
}

@article{MTMT:33744872,
	title = {Evolution of insect innate immunity through domestication of bacterial toxins},
	url = {https://m2.mtmt.hu/api/publication/33744872},
	author = {Verster, Kirsten I. and Cinege, Gyöngyi Ilona and Lipinszki, Zoltán and Magyar, Lilla Brigitta and Kurucz, Judit Éva and Tarnopol, Rebecca L. and Ábrahám, Edit and Darula, Zsuzsanna and Karageorgi, Marianthi and Tamsil, Josephine A. and Akalu, Saron M. and Andó, István and Whiteman, Noah K.},
	doi = {10.1073/pnas.2218334120},
	journal-iso = {P NATL ACAD SCI USA},
	journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
	volume = {120},
	unique-id = {33744872},
	issn = {0027-8424},
	abstract = {Toxin cargo genes are often horizontally transferred by phages between bacterial species and are known to play an important role in the evolution of bacterial pathogenesis. Here, we show how these same genes have been horizontally transferred from phage or bacteria to animals and have resulted in novel adaptations. We discovered that two widespread bacterial genes encoding toxins of animal cells, cytolethal distending toxin subunit B ( cdtB ) and apoptosis-inducing protein of 56 kDa ( aip56) , were captured by insect genomes through horizontal gene transfer from bacteria or phages. To study the function of these genes in insects, we focused on Drosophila ananassae as a model. In the D. ananassae subgroup species, cdtB and aip56 are present as singular ( cdtB ) or fused copies ( cdtB::aip56 ) on the second chromosome. We found that cdtB and aip56 genes and encoded proteins were expressed by immune cells, some proteins were localized to the wasp embryo’s serosa, and their expression increased following parasitoid wasp infection. Species of the ananassae subgroup are highly resistant to parasitoid wasps, and we observed that D. ananassae lines carrying null mutations in cdtB and aip56 toxin genes were more susceptible to parasitoids than the wild type. We conclude that toxin cargo genes were captured by these insects millions of years ago and integrated as novel modules into their innate immune system. These modules now represent components of a heretofore undescribed defense response and are important for resistance to parasitoid wasps. Phage or bacterially derived eukaryotic toxin genes serve as macromutations that can spur the instantaneous evolution of novelty in animals.},
	year = {2023},
	eissn = {1091-6490},
	orcid-numbers = {Lipinszki, Zoltán/0000-0002-2067-0832; Tarnopol, Rebecca L./0000-0001-5675-8513; Karageorgi, Marianthi/0000-0003-2934-7019; Tamsil, Josephine A./0000-0002-3173-1848; Andó, István/0000-0002-4648-9396; Whiteman, Noah K./0000-0003-1448-4678}
}

@article{MTMT:33697350,
	title = {Proteotranscriptomic Discrimination of Tumor and Normal Tissues in Renal Cell Carcinoma},
	url = {https://m2.mtmt.hu/api/publication/33697350},
	author = {Bartha, Áron and Darula, Zsuzsanna and Munkácsy, Gyöngyi and Klement, Éva and Nyirády, Péter and Győrffy, Balázs},
	doi = {10.3390/ijms24054488},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {33697350},
	issn = {1661-6596},
	abstract = {Clear cell renal carcinoma is the most frequent type of kidney cancer, with an increasing incidence rate worldwide. In this research, we used a proteotranscriptomic approach to differentiate normal and tumor tissues in clear cell renal cell carcinoma (ccRCC). Using transcriptomic data of patients with malignant and paired normal tissue samples from gene array cohorts, we identified the top genes over-expressed in ccRCC. We collected surgically resected ccRCC specimens to further investigate the transcriptomic results on the proteome level. The differential protein abundance was evaluated using targeted mass spectrometry (MS). We assembled a database of 558 renal tissue samples from NCBI GEO and used these to uncover the top genes with higher expression in ccRCC. For protein level analysis 162 malignant and normal kidney tissue samples were acquired. The most consistently upregulated genes were IGFBP3, PLIN2, PLOD2, PFKP, VEGFA, and CCND1 (p < 10−5 for each gene). Mass spectrometry further validated the differential protein abundance of these genes (IGFBP3, p = 7.53 × 10−18; PLIN2, p = 3.9 × 10−39; PLOD2, p = 6.51 × 10−36; PFKP, p = 1.01 × 10−47; VEGFA, p = 1.40 × 10−22; CCND1, p = 1.04 × 10−24). We also identified those proteins which correlate with overall survival. Finally, a support vector machine-based classification algorithm using the protein-level data was set up. We used transcriptomic and proteomic data to identify a minimal panel of proteins highly specific for clear cell renal carcinoma tissues. The introduced gene panel could be used as a promising tool in the clinical setting.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Munkácsy, Gyöngyi/0000-0001-9124-4788; Nyirády, Péter/0000-0002-7037-4919; Győrffy, Balázs/0000-0002-5772-3766}
}

@article{MTMT:33657316,
	title = {Chronic Cerebral Hypoperfusion-Induced Disturbed Proteostasis of Mitochondria and MAM Is Reflected in the CSF of Rats by Proteomic Analysis},
	url = {https://m2.mtmt.hu/api/publication/33657316},
	author = {Tukacs, Vanda and Mittli, Dániel Árpád and Hunyadi-Gulyás Éva, Csilla and Hlatky, Dávid and Medzihradszky F., Katalin and Darula, Zsuzsanna and Nyitrai, Gabriella and Czurkó, András and Juhász, Gábor Dénes and Kardos, József and Kékesi, Adrienna Katalin},
	doi = {10.1007/s12035-023-03215-z},
	journal-iso = {MOL NEUROBIOL},
	journal = {MOLECULAR NEUROBIOLOGY},
	volume = {60},
	unique-id = {33657316},
	issn = {0893-7648},
	abstract = {Declining cerebral blood flow leads to chronic cerebral hypoperfusion which can induce neurodegenerative disorders, such as vascular dementia. The reduced energy supply of the brain impairs mitochondrial functions that could trigger further damaging cellular processes. We carried out stepwise bilateral common carotid occlusions on rats and investigated long-term mitochondrial, mitochondria-associated membrane (MAM), and cerebrospinal fluid (CSF) proteome changes. Samples were studied by gel-based and mass spectrometry-based proteomic analyses. We found 19, 35, and 12 significantly altered proteins in the mitochondria, MAM, and CSF, respectively. Most of the changed proteins were involved in protein turnover and import in all three sample types. We confirmed decreased levels of proteins involved in protein folding and amino acid catabolism, such as P4hb and Hibadh in the mitochondria by western blot. We detected reduced levels of several components of protein synthesis and degradation in the CSF as well as in the subcellular fractions, implying that hypoperfusion-induced altered protein turnover of brain tissue can be detected in the CSF by proteomic analysis.},
	year = {2023},
	eissn = {1559-1182},
	pages = {3158-3174},
	orcid-numbers = {Czurkó, András/0000-0002-1985-7296; Juhász, Gábor Dénes/0000-0002-0849-6931; Kardos, József/0000-0002-2135-2932; Kékesi, Adrienna Katalin/0000-0003-3042-4878}
}

@article{MTMT:33554742,
	title = {Impact of Experimental Conditions on Extracellular Vesicles’ Proteome: A Comparative Study},
	url = {https://m2.mtmt.hu/api/publication/33554742},
	author = {Böröczky, Timea and Dobra, Gabriella and Bukva, Mátyás and Gyukity-Sebestyén, Edina and Hunyadi-Gulyás Éva, Csilla and Darula, Zsuzsanna and Horváth, Péter and Buzás, Krisztina and Harmati, Mária},
	doi = {10.3390/life13010206},
	journal-iso = {LIFE-BASEL},
	journal = {LIFE-BASEL},
	volume = {13},
	unique-id = {33554742},
	abstract = {Extracellular vesicle (EV) research is a rapidly developing field, mainly due to the key role of EVs in intercellular communication and pathophysiological processes. However, the heterogeneity of EVs challenges their exploration and the establishment of gold-standard methods. Here, we aimed to reveal the influence of technical changes on EV biology and the reliability of experimental data. We used B16F1 melanoma cells as a model and applied nanoparticle tracking analysis, mass spectrometry (LC-MS/MS) and pathway enrichment analysis to analyze the quantity, size distribution, proteome and function of their small EVs (sEVs) produced in sEV-depleted fetal bovine serum (FBS)-containing medium or serum-free medium. Additionally, we investigated the effects of minor technical variances on the quality of sEV preparations. We found that storage of the isolates at −80 °C has no adverse effect on LC-MS/MS analysis, and an additional washing step after differential ultracentrifugation has a minor influence on the sEV proteome. In contrast, FBS starvation affects the production and proteome of sEVs; moreover, these vesicles may have a greater impact on protein metabolism, but a smaller impact on cell adhesion and membrane raft assembly, than the control sEVs. As we demonstrated that FBS starvation has a strong influence on sEV biology, applying serum-free conditions might be considered in in vitro sEV studies.},
	year = {2023},
	eissn = {2075-1729},
	orcid-numbers = {Böröczky, Timea/0009-0009-3390-7809; Dobra, Gabriella/0000-0002-2814-7720; Bukva, Mátyás/0000-0002-5225-0285; Gyukity-Sebestyén, Edina/0000-0003-1383-6301; Buzás, Krisztina/0000-0001-8933-2033; Harmati, Mária/0000-0002-4875-5723}
}

@article{MTMT:33548024,
	title = {Multiple Layers of Complexity in O-Glycosylation Illustrated With the Urinary Glycoproteome},
	url = {https://m2.mtmt.hu/api/publication/33548024},
	author = {Pap, Ádám and Kiraly, Istvan Elod and Medzihradszky F., Katalin and Darula, Zsuzsanna},
	doi = {10.1016/j.mcpro.2022.100439},
	journal-iso = {MOL CELL PROTEOMICS},
	journal = {MOLECULAR & CELLULAR PROTEOMICS},
	volume = {21},
	unique-id = {33548024},
	issn = {1535-9476},
	abstract = {While N-glycopeptides are relatively easy to characterize, O-glycosylation analysis is more complex. In this article, we illustrate the multiple layers of O-glycopeptide char-acterization that make this task so challenging. We believe our carefully curated dataset represents perhaps the largest intact human glycopeptide mixture derived from individuals, not from cell lines. The samples were collected from healthy individuals, patients with superficial or advanced bladder cancer (three of each group), and a single bladder inflammation patient. The data were scru-tinized manually and interpreted using three different search engines: Byonic, Protein Prospector, and O-Pair, and the tool MS-Filter. Despite all the recent advances, reliable automatic O-glycopeptide assignment has not been solved yet. Our data reveal such diversity of site -specific O-glycosylation that has not been presented before. In addition to the potential biological implications, this dataset should be a valuable resource for software developers in the same way as some of our previously released data has been used in the development of O-Pair and O-Glycoproteome Analyzer. Based on the manual evaluation of the performance of the existing tools with our data, we lined up a series of recommendations that if implemented could significantly improve the reliability of glycopeptide assignments.},
	keywords = {SITES; IDENTIFICATION; PERFORMANCE; Carbohydrate; Antigens; GLYCOPEPTIDES; LC-MS/MS},
	year = {2022},
	eissn = {1535-9484}
}

@article{MTMT:33063331,
	title = {STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins},
	url = {https://m2.mtmt.hu/api/publication/33063331},
	author = {Réthi-Nagy, Zsuzsánna and Ábrahám, Edit and Udvardy, Katalin and Klement, Éva and Darula, Zsuzsanna and Pál, Margit and Katona, Robert L. and Tubak, Vilmos and Páli, Tibor and Kóta, Zoltán and Sinka, Rita and Udvardy, Andor and Lipinszki, Zoltán},
	doi = {10.3390/ijms23158168},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {23},
	unique-id = {33063331},
	issn = {1661-6596},
	abstract = {The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is very limited. We have identified and characterized a conserved 13-mer protein segment derived from the p54/Rpn10 ubiquitin receptor subunit of the Drosophila 26S proteasome, which fulfills all the characteristics of a protein stabilization motif (STABILON). Attachment of STABILON to various intracellular as well as medically relevant secreted model proteins resulted in a significant increase in their cellular or extracellular concentration in mammalian cells. We demonstrate that STABILON acts as a universal and dual function motif that, on the one hand, increases the concentration of the corresponding mRNAs and, on the other hand, prevents the degradation of short-lived fusion proteins. Therefore, STABILON may lead to a breakthrough in biomedical recombinant protein production.},
	keywords = {SYSTEM; SUBUNIT; DROSOPHILA; Protein Stability; ENHANCER; proteasome; protein degradation; SECRETED PROTEINS; Biochemistry & Molecular Biology; Protein production; mRNA stability; stabilization motif},
	year = {2022},
	eissn = {1422-0067},
	orcid-numbers = {Páli, Tibor/0000-0003-1649-1097; Kóta, Zoltán/0000-0003-2420-8773; Sinka, Rita/0000-0003-4040-4184; Lipinszki, Zoltán/0000-0002-2067-0832}
}

@article{MTMT:32148359,
	title = {Stellaria media tea protects against diabetes-induced cardiac dysfunction in rats without affecting glucose tolerance},
	url = {https://m2.mtmt.hu/api/publication/32148359},
	author = {Demján, Virág and Apjok-Sója, Andrea and Kiss, Tivadar and Fejes, Alexandra and Gausz, Flóra Diána and Szűcs, Gergő and Siska, Andrea and Földesi, Imre and Tengölics, Roland and Darula, Zsuzsanna and Csupor, Dezső and Pipicz, Márton and Csont, Tamás Bálint},
	doi = {10.1016/j.jtcme.2021.08.003},
	journal-iso = {J TRADITIONAL COMP MED},
	journal = {JOURNAL OF TRADITIONAL AND COMPLEMENTARY MEDICINE},
	volume = {12},
	unique-id = {32148359},
	issn = {2225-4110},
	year = {2022},
	eissn = {2225-4110},
	pages = {250-259},
	orcid-numbers = {Demján, Virág/0000-0002-6792-3024; Apjok-Sója, Andrea/0000-0003-3691-5889; Kiss, Tivadar/0000-0003-3538-377X; Fejes, Alexandra/0000-0002-2905-709X; Szűcs, Gergő/0000-0003-1874-2718; Földesi, Imre/0000-0002-3329-8136; Csupor, Dezső/0000-0002-4088-3333; Pipicz, Márton/0000-0002-0944-1684; Csont, Tamás Bálint/0000-0001-5792-2768}
}