@article{MTMT:34812598, title = {Editorial: Functions, working mechanisms, and regulation of rotary ATPases and Ductin proteins}, url = {https://m2.mtmt.hu/api/publication/34812598}, author = {Páli, Tibor and Feniouk, Boris and Wilkens, Stephan}, doi = {10.3389/fmolb.2024.1399421}, journal-iso = {FRONT MOL BIOSCI}, journal = {FRONTIERS IN MOLECULAR BIOSCIENCES}, volume = {11}, unique-id = {34812598}, year = {2024}, eissn = {2296-889X}, orcid-numbers = {Páli, Tibor/0000-0003-1649-1097} } @article{MTMT:34804520, title = {Cellular Immunity of Drosophila willistoni Reveals Novel Complexity in Insect Anti-Parasitoid Defense}, url = {https://m2.mtmt.hu/api/publication/34804520}, author = {Cinege, Gyöngyi Ilona and Fodor, K. and Magyar, Lilla Brigitta and Lipinszki, Zoltán and Hultmark, D. and Andó, István}, doi = {10.3390/cells13070593}, journal-iso = {CELLS-BASEL}, journal = {CELLS}, volume = {13}, unique-id = {34804520}, year = {2024}, eissn = {2073-4409}, orcid-numbers = {Lipinszki, Zoltán/0000-0002-2067-0832; Andó, István/0000-0002-4648-9396} } @article{MTMT:34797924, title = {Transient Receptor Potential Ankyrin 1 Ion Channel Is Expressed in Osteosarcoma and Its Activation Reduces Viability}, url = {https://m2.mtmt.hu/api/publication/34797924}, author = {Hudhud, Lina and Rozmer, Katalin and Kecskés, Angéla and Pohóczky, Krisztina and Bencze, Noémi and Buzás, Krisztina and Szőke, Éva and Helyes, Zsuzsanna}, doi = {10.3390/ijms25073760}, journal-iso = {INT J MOL SCI}, journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, volume = {25}, unique-id = {34797924}, issn = {1661-6596}, abstract = {Osteosarcoma is a highly malignant, painful cancer with poor treatment opportunities and a bad prognosis. Transient receptor potential ankyrin 1 (TRPA1) and vanilloid 1 (TRPV1) receptors are non-selective cation channels that have been of great interest in cancer, as their expression is increased in some malignancies. In our study we aim to characterize the expression and functionality of the TRPA1 and TRPV1 channels in human and mouse osteosarcoma tissues and in a mouse cell line. TRPA1/Trpa1 and TRPV1/Trpv1 mRNA expressions were demonstrated by PCR gel electrophoresis and RNAscope in situ hybridization. The function of these channels was confirmed by their radioactive 45Ca2+ uptake in response to the TRPA1 agonist, Allyl-isothiocyanate (AITC), and TRPV1 agonist, capsaicin, in K7M2 cells. An ATP-based K2M7 cell viability luminescence assay was used to determine cell viability after AITC or capsaicin treatments. Both TRPA1/Trpa1 and TRPV1/Trpv1 were expressed similarly in human and mouse osteosarcoma tissues, while Trpa1 transcripts were more abundantly present in K7M2 cells. TRPA1 activation with 200 µM AITC induced a significant 45Ca2+ influx into K7M2 cells, and the antagonist attenuated this effect. In accordance with the lower Trpv1 expression, capsaicin induced a moderate 45Ca2+ uptake, which did not reach the level of statistical significance. Both AITC and capsaicin significantly reduced K7M2 cell viability, demonstrating EC50 values of 22 µM and 74 µM. The viability-decreasing effect of AITC was significantly but only partially antagonized by HC-030031, but the action of capsaicin was not affected by the TRPV1 antagonist capsazepine. We provide here the first data on the functional expression of the TRPA1 and TRPV1 ion channels in osteosarcoma, suggesting novel diagnostic and/or therapeutic perspectives.}, keywords = {CAPSAICIN; TRPV1; Cell viability; mustard oil; TRPA1; Osteosarcoma; RNAscope in situ hybridization; radioactive 45Ca2+ uptake}, year = {2024}, eissn = {1422-0067}, orcid-numbers = {Pohóczky, Krisztina/0000-0003-0385-5162; Buzás, Krisztina/0000-0001-8933-2033} } @article{MTMT:34797803, title = {Effects of lipids on the rate-limiting steps in the dark-to-light transition of Photosystem II core complex of Thermostichus vulcanus}, url = {https://m2.mtmt.hu/api/publication/34797803}, author = {Magyar, Melinda and Akhtar, Parveen and Sipka, Gábor and Racskóné Domonkos, Ildikó and Han, W. and Li, X. and Han, G. and Shen, J.-R. and Lambrev, Petar and Garab, Győző}, doi = {10.3389/fpls.2024.1381040}, journal-iso = {FRONT PLANT SCI}, journal = {FRONTIERS IN PLANT SCIENCE}, volume = {15}, unique-id = {34797803}, issn = {1664-462X}, abstract = {In our earlier works, we have shown that the rate-limiting steps, associated with the dark-to-light transition of Photosystem II (PSII), reflecting the photochemical activity and structural dynamics of the reaction center complex, depend largely on the lipidic environment of the protein matrix. Using chlorophyll-a fluorescence transients (ChlF) elicited by single-turnover saturating flashes, it was shown that the half-waiting time (Δτ1/2) between consecutive excitations, at which 50% of the fluorescence increment was reached, was considerably larger in isolated PSII complexes of Thermostichus (T.) vulcanus than in the native thylakoid membrane (TM). Further, it was shown that the addition of a TM lipid extract shortened Δτ1/2 of isolated PSII, indicating that at least a fraction of the ‘missing’ lipid molecules, replaced by detergent molecules, caused the elongation of Δτ1/2. Here, we performed systematic experiments to obtain information on the nature of TM lipids that are capable of decreasing Δτ1/2. Our data show that while all lipid species shorten Δτ1/2, the negatively charged lipid phosphatidylglycerol appears to be the most efficient species – suggesting its prominent role in determining the structural dynamics of PSII reaction center. Copyright © 2024 Magyar, Akhtar, Sipka, Domonkos, Han, Li, Han, Shen, Lambrev and Garab.}, keywords = {STRUCTURAL DYNAMICS; CHLOROPHYLL-A FLUORESCENCE; Waiting time; Thylakoid lipids; Rate-limiting step; core complex of photosystem II}, year = {2024}, eissn = {1664-462X}, orcid-numbers = {Magyar, Melinda/0000-0002-1144-4657; Akhtar, Parveen/0000-0002-3264-7154; Sipka, Gábor/0000-0002-8553-4890} } @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:34786803, title = {SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy}, url = {https://m2.mtmt.hu/api/publication/34786803}, author = {Grexa, István and Iván, Zsanett Zsófia and Migh, Ede and Kovács, Ferenc and Bolck, Hella A and Zheng, Xiang and Mund, Andreas and Moshkov, Nikita and Csapóné Miczán, Vivien and Koós, Krisztián and Horváth, Péter}, doi = {10.1093/bib/bbae029}, journal-iso = {BRIEF BIOINFORM}, journal = {BRIEFINGS IN BIOINFORMATICS}, volume = {25}, unique-id = {34786803}, issn = {1467-5463}, abstract = {Numerous imaging techniques are available for observing and interrogating biological samples, and several of them can be used consecutively to enable correlative analysis of different image modalities with varying resolutions and the inclusion of structural or molecular information. Achieving accurate registration of multimodal images is essential for the correlative analysis process, but it remains a challenging computer vision task with no widely accepted solution. Moreover, supervised registration methods require annotated data produced by experts, which is limited. To address this challenge, we propose a general unsupervised pipeline for multimodal image registration using deep learning. We provide a comprehensive evaluation of the proposed pipeline versus the current state-of-the-art image registration and style transfer methods on four types of biological problems utilizing different microscopy modalities. We found that style transfer of modality domains paired with fully unsupervised training leads to comparable image registration accuracy to supervised methods and, most importantly, does not require human intervention.}, year = {2024}, eissn = {1477-4054}, orcid-numbers = {Mund, Andreas/0000-0002-7843-5341} } @article{MTMT:34782533, title = {A new family of bacterial ribosome hibernation factors}, url = {https://m2.mtmt.hu/api/publication/34782533}, author = {Helena-Bueno, Karla and Rybak, Mariia Yu. and Ekemezie, Chinenye L. and Sullivan, Rudi and Brown, Charlotte R. and Dingwall, Charlotte and Basle, Arnaud and Schneider, Claudia and Connolly, James P. R. and Blaza, James N. and Csörgő, Bálint and Moynihan, Patrick J. and Gagnon, Matthieu G. and Hill, Chris H. and Melnikov, Sergey V.}, doi = {10.1038/s41586-024-07041-8}, journal-iso = {NATURE}, journal = {NATURE}, volume = {626}, unique-id = {34782533}, issn = {0028-0836}, abstract = {To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3-6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation. A study identifies a new bacterial ribosome hibernation factor, Balon, and describes its association with EF-Tu and its initiation of mRNA-independent hibernation during protein synthesis.}, keywords = {MECHANISM; PROTEIN; ESCHERICHIA-COLI; STRUCTURAL BASIS; CRYSTAL-STRUCTURE; ELONGATION; TERMINATION; EF1-alpha; PEPTIDE-BOND FORMATION}, year = {2024}, eissn = {1476-4687}, pages = {1125-1132}, orcid-numbers = {Rybak, Mariia Yu./0000-0002-0478-0222; Blaza, James N./0000-0001-5420-2116; Csörgő, Bálint/0000-0003-0397-6845; Moynihan, Patrick J./0000-0003-4182-6223} } @article{MTMT:34782532, title = {Learning representations for image-based profiling of perturbations}, url = {https://m2.mtmt.hu/api/publication/34782532}, author = {Moshkov, Nikita and Bornholdt, Michael and Benoit, Santiago and Smith, Matthew and Mcquin, Claire and Goodman, Allen and Senft, Rebecca A. and Han, Yu and Babadi, Mehrtash and Horváth, Péter and Cimini, Beth A. and Carpenter, Anne E. and Singh, Shantanu and Caicedo, Juan C.}, doi = {10.1038/s41467-024-45999-1}, journal-iso = {NAT COMMUN}, journal = {NATURE COMMUNICATIONS}, volume = {15}, unique-id = {34782532}, issn = {2041-1723}, abstract = {Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient and powerful way of studying cell biology, and requires computational methods for transforming images into quantitative data. Here, we present an improved strategy for learning representations of treatment effects from high-throughput imaging, following a causal interpretation. We use weakly supervised learning for modeling associations between images and treatments, and show that it encodes both confounding factors and phenotypic features in the learned representation. To facilitate their separation, we constructed a large training dataset with images from five different studies to maximize experimental diversity, following insights from our causal analysis. Training a model with this dataset successfully improves downstream performance, and produces a reusable convolutional network for image-based profiling, which we call Cell Painting CNN. We evaluated our strategy on three publicly available Cell Painting datasets, and observed that the Cell Painting CNN improves performance in downstream analysis up to 30% with respect to classical features, while also being more computationally efficient. Assessing cell phenotypes in image-based assays requires solid computational methods for transforming images into quantitative data. Here, the authors present a strategy for learning representations of treatment effects from high-throughput imaging, following a causal interpretation.}, year = {2024}, eissn = {2041-1723} } @article{MTMT:34772438, title = {Mitochondrial Differentiation during Spermatogenesis: Lessons from Drosophila melanogaster}, url = {https://m2.mtmt.hu/api/publication/34772438}, author = {Vedelek, Viktor and Jankovics, Ferenc and Zádori, János and Sinka, Rita}, doi = {10.3390/ijms25073980}, journal-iso = {INT J MOL SCI}, journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, volume = {25}, unique-id = {34772438}, issn = {1661-6596}, abstract = {Numerous diseases can arise as a consequence of mitochondrial malfunction. Hence, there is a significant focus on studying the role of mitochondria in cancer, ageing, neurodegenerative diseases, and the field of developmental biology. Mitochondria could exist as discrete organelles in the cell; however, they have the ability to fuse, resulting in the formation of interconnected reticular structures. The dynamic changes between these forms correlate with mitochondrial function and mitochondrial health, and consequently, there is a significant scientific interest in uncovering the specific molecular constituents that govern these transitions. Moreover, the specialized mitochondria display a wide array of variable morphologies in their cristae formations. These inner mitochondrial structures are closely associated with the specific functions performed by the mitochondria. In multiple cases, the presence of mitochondrial dysfunction has been linked to male sterility, as it has been observed to cause a range of abnormal spermatogenesis and sperm phenotypes in different species. This review aims to elucidate the dynamic alterations and functions of mitochondria in germ cell development during the spermatogenesis of Drosophila melanogaster.}, year = {2024}, eissn = {1422-0067}, orcid-numbers = {Vedelek, Viktor/0000-0002-0420-8226; Sinka, Rita/0000-0003-4040-4184} } @article{MTMT:34770405, title = {International consensus guidelines for the definition, detection, and interpretation of autophagy-dependent ferroptosis}, url = {https://m2.mtmt.hu/api/publication/34770405}, author = {Chen, Xin and Tsvetkov, Andrey S. and Shen, Han-Ming and Isidoro, Ciro and Ktistakis, Nicholas T. and Linkermann, Andreas and Koopman, Werner J. H. and Simon, Hans-Uwe and Galluzzi, Lorenzo and Luo, Shouqing and Xu, Daqian and Gu, Wei and Peulen, Olivier and Cai, Qian and Rubinsztein, David C. and Chi, Jen-Tsan and Zhang, Donna D. and Li, Changfeng and Toyokuni, Shinya and Liu, Jinbao and Roh, Jong-Lyel and Dai, Enyong and Juhász, Gábor and Liu, Wei and Zhang, Jianhua and Yang, Minghua and Liu, Jiao and Zhu, Ling-Qiang and Zou, Weiping and Piacentini, Mauro and Ding, Wen-Xing and Yue, Zhenyu and Xie, Yangchun and Petersen, Morten and Gewirtz, David A. and Mandell, Michael A. and Chu, Charleen T. and Sinha, Debasish and Eftekharpour, Eftekhar and Zhivotovsky, Boris and Besteiro, Sebastien and Gabrilovich, Dmitry I. and Kim, Do-Hyung and Kagan, Valerian E. and Bayir, Hulya and Chen, Guang-Chao and Ayton, Scott and Luenemann, Jan D. and Komatsu, Masaaki and Krautwald, Stefan and Loos, Ben and Baehrecke, Eric H. and Wang, Jiayi and Lane, Jon D. and Sadoshima, Junichi and Yang, Wan Seok and Gao, Minghui and Munz, Christian and Thumm, Michael and Kampmann, Martin and Yu, Di and Lipinski, Marta M. and Jones, Jace W. and Jiang, Xuejun and Zeh, Herbert J. and Kang, Rui and Klionsky, Daniel J. and Kroemer, Guido and Tang, Daolin}, doi = {10.1080/15548627.2024.2319901}, journal-iso = {AUTOPHAGY}, journal = {AUTOPHAGY}, unique-id = {34770405}, issn = {1554-8627}, abstract = {Macroautophagy/autophagy is a complex degradation process with a dual role in cell death that is influenced by the cell types that are involved and the stressors they are exposed to. Ferroptosis is an iron-dependent oxidative form of cell death characterized by unrestricted lipid peroxidation in the context of heterogeneous and plastic mechanisms. Recent studies have shed light on the involvement of specific types of autophagy (e.g. ferritinophagy, lipophagy, and clockophagy) in initiating or executing ferroptotic cell death through the selective degradation of anti-injury proteins or organelles. Conversely, other forms of selective autophagy (e.g. reticulophagy and lysophagy) enhance the cellular defense against ferroptotic damage. Dysregulated autophagy-dependent ferroptosis has implications for a diverse range of pathological conditions. This review aims to present an updated definition of autophagy-dependent ferroptosis, discuss influential substrates and receptors, outline experimental methods, and propose guidelines for interpreting the results.Abbreviation: 3-MA:3-methyladenine; 4HNE: 4-hydroxynonenal; ACD: accidentalcell death; ADF: autophagy-dependentferroptosis; ARE: antioxidant response element; BH2:dihydrobiopterin; BH4: tetrahydrobiopterin; BMDMs: bonemarrow-derived macrophages; CMA: chaperone-mediated autophagy; CQ:chloroquine; DAMPs: danger/damage-associated molecular patterns; EMT,epithelial-mesenchymal transition; EPR: electronparamagnetic resonance; ER, endoplasmic reticulum; FRET: Forsterresonance energy transfer; GFP: green fluorescent protein;GSH: glutathione;IF: immunofluorescence; IHC: immunohistochemistry; IOP, intraocularpressure; IRI: ischemia-reperfusion injury; LAA: linoleamide alkyne;MDA: malondialdehyde; PGSK: Phen Green (TM) SK;RCD: regulatedcell death; PUFAs: polyunsaturated fatty acids; RFP: red fluorescentprotein;ROS: reactive oxygen species; TBA: thiobarbituricacid; TBARS: thiobarbituric acid reactive substances; TEM:transmission electron microscopy.}, keywords = {LIPID-PEROXIDATION; MASS-SPECTROMETRY; PROTEIN; CANCER-CELLS; Lipid Peroxidation; IRON; Cell Death; acute kidney injury; transcription factor Nrf2; Lipophagy; ferritinophagy; ferritinophagy; ERASTIN-INDUCED FERROPTOSIS; NONAPOPTOTIC CELL-DEATH}, year = {2024}, eissn = {1554-8635}, orcid-numbers = {Simon, Hans-Uwe/0000-0002-9404-7736; Juhász, Gábor/0000-0001-8548-8874; Ayton, Scott/0000-0002-3479-2427; Lane, Jon D./0000-0002-6828-5888} }