@article{MTMT:34850804,
	title = {T-reg transcriptomic signatures identify response to check-point inhibitors},
	url = {https://m2.mtmt.hu/api/publication/34850804},
	author = {Noblejas-López, M.D.M. and García-Gil, E. and Pérez-Segura, P. and Pandiella, A. and Győrffy, Balázs and Ocaña, A.},
	doi = {10.1038/s41598-024-60819-8},
	journal-iso = {SCI REP},
	journal = {SCIENTIFIC REPORTS},
	volume = {14},
	unique-id = {34850804},
	issn = {2045-2322},
	year = {2024},
	eissn = {2045-2322},
	orcid-numbers = {Győrffy, Balázs/0000-0002-5772-3766}
}

@article{MTMT:34836109,
	title = {Normal transferrin glycosylation does not rule out severe ALG1 deficiency},
	url = {https://m2.mtmt.hu/api/publication/34836109},
	author = {Bosnyák, Inez and Sadek, Mustafa and Ranatunga, Wasantha and Kozicz, Tamás and Morava-Kozicz, Éva},
	doi = {10.1002/jmd2.12415},
	journal-iso = {JIMDS REPORTS},
	journal = {JOURNAL OF INHERITED METABOLIC DISEASE REPORTS},
	unique-id = {34836109},
	issn = {2192-8304},
	abstract = {ALG1‐CDG is a rare, clinically variable metabolic disease, caused by the defect of adding the first mannose (Man) to N‐acetylglucosamine (GlcNAc 2 )‐pyrophosphate (PP)‐dolichol to the growing oligosaccharide chain, resulting in impaired N‐glycosylation of proteins. N‐glycosylation has a key role in functionality, stability, and half‐life of most proteins. Therefore, congenital defects of glycosylation typically are multisystem disorders. Here we report a 3‐year‐old patient with severe neurological, cardiovascular, respiratory, musculoskeletal and gastrointestinal symptoms. ALG1‐CDG was suggested based on exome sequencing and Western blot analysis. Despite her severe clinical manifestations and genetic diagnosis, serum transferrin glycoform analysis was normal. Western blot analysis of highly glycosylated proteins in fibroblasts revealed decreased intercellular adhesion molecule 1 (ICAM1), but normal lysosomal associated membrane protein 1 and 2 (LAMP1 and LAMP2) expression levels. Glycoproteomics in fibroblasts showed the presence of the abnormal tetrasacharide. Reviewing the literature, we found 86 reported ALG1‐CDG patients, but only one with normal transferrin analysis. Based on our results we would like to highlight the importance of multiple approaches in diagnosing ALG1‐CDG, as normal serum transferrin glycosylation or other biomarkers with normal expression levels can occur.},
	year = {2024},
	eissn = {2192-8312}
}

@article{MTMT:34831592,
	title = {Integrated analysis of public datasets for the discovery and validation of survival-associated genes in solid tumors},
	url = {https://m2.mtmt.hu/api/publication/34831592},
	author = {Győrffy, Balázs},
	doi = {10.1016/j.xinn.2024.100625},
	journal-iso = {INNOVATION(UNITED STATES)},
	journal = {INNOVATION(UNITED STATES)},
	volume = {5},
	unique-id = {34831592},
	year = {2024},
	eissn = {2666-6758},
	orcid-numbers = {Győrffy, Balázs/0000-0002-5772-3766}
}

@article{MTMT:34825015,
	title = {Prognostic significance of a signature based on senescence-related genes in colorectal cancer},
	url = {https://m2.mtmt.hu/api/publication/34825015},
	author = {Ungvári, Zoltán István and Ungvári, Anna Sára and Bianchini, Giampaolo and Győrffy, Balázs},
	doi = {10.1007/s11357-024-01164-6},
	journal-iso = {GEROSCIENCE},
	journal = {GEROSCIENCE: OFFICIAL JOURNAL OF THE AMERICAN AGING ASSOCIATION (AGE)},
	unique-id = {34825015},
	issn = {2509-2715},
	abstract = {Colorectal cancer, recognized as a quintessential age-related disease, underscores the intricate interplay between aging mechanisms and disease pathogenesis. Cellular senescence, a DNA damage-induced cellular stress response, is characterized by cell cycle arrest, the expression of an inflammatory senescence-associated secretory phenotype, and alterations in extracellular matrix metabolism. It is widely recognized as a fundamental and evolutionarily conserved mechanism of aging. Guided by geroscience principles, which assert that the pathogenesis of age-related diseases involves cellular mechanisms of aging, this study delves into the role of senescence-related genes in colon cancer progression. Leveraging a gene set reflective of senescence-associated pathways, we employed uni- and multivariate Cox proportional hazards survival analysis combined with the determination of the false discovery rate to analyze correlations between gene expression and survival. The integrated database of 1130 colon cancer specimens with available relapse-free survival time and relapse event data from ten independent cohorts provided a robust platform for survival analyses. We identified senescence-related genes associated with differential expression levels linked to shorter survival. Our findings unveil a prognostic signature utilizing cellular senescence-related genes (hazard ratio: 2.73, 95% CI 2.12-3.52, p = 6.4E - 16), offering valuable insights into survival prediction in colon cancer. Multivariate analysis underscored the independence of the senescence-related signature from available epidemiological and pathological variables. This study highlights the potential of senescence-related genes as prognostic biomarkers. Overall, our results underscore the pivotal role of cellular senescence, a fundamental mechanism of aging, in colon cancer progression.},
	keywords = {CANCER; Aging; colorectal cancer; senescence; Gerooncology},
	year = {2024},
	eissn = {2509-2723},
	orcid-numbers = {Ungvári, Zoltán István/0000-0002-6035-6039; Győrffy, Balázs/0000-0002-5772-3766}
}

@article{MTMT:34825014,
	title = {Transient loss of Polycomb components induces an epigenetic cancer fate},
	url = {https://m2.mtmt.hu/api/publication/34825014},
	author = {Parreno, V and Loubiere, V and Schuettengruber, B and Fritsch, L and Rawal, C C and Erokhin, M and Győrffy, Balázs and Normanno, D and Di Stefano, M and Moreaux, J and Butova, N L and Chiolo, I and Chetverina, D and Martinez, A-M and Cavalli, G},
	doi = {10.1038/s41586-024-07328-w},
	journal-iso = {NATURE},
	journal = {NATURE},
	unique-id = {34825014},
	issn = {0028-0836},
	abstract = {Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.},
	year = {2024},
	eissn = {1476-4687},
	orcid-numbers = {Győrffy, Balázs/0000-0002-5772-3766}
}

@article{MTMT:34797930,
	title = {Motor properties of Myosin 5c are modulated by tropomyosin isoforms and inhibited by pentabromopseudilin},
	url = {https://m2.mtmt.hu/api/publication/34797930},
	author = {Kengyel, András Miklós and Palarz, Philip M and Krohn, Jacqueline and Marquardt, Anja and Greve, Johannes N and Heiringhoff, Robin and Jörns, Anne and Manstein, Dietmar J},
	doi = {10.3389/fphys.2024.1394040},
	journal-iso = {FRONT PHYSIOL},
	journal = {FRONTIERS IN PHYSIOLOGY},
	volume = {15},
	unique-id = {34797930},
	abstract = {Myosin 5c (Myo5c) is a motor protein that is produced in epithelial and glandular tissues, where it plays an important role in secretory processes. Myo5c is composed of two heavy chains, each containing a generic motor domain, an elongated neck domain consisting of a single α-helix with six IQ motifs, each of which binds to a calmodulin (CaM) or a myosin light chain from the EF-hand protein family, a coiled-coil dimer-forming region and a carboxyl-terminal globular tail domain. Although Myo5c is a low duty cycle motor, when two or more Myo5c-heavy meromyosin (HMM) molecules are linked together, they move processively along actin filaments. We describe the purification and functional characterization of human Myo5c-HMM co-produced either with CaM alone or with CaM and the essential and regulatory light chains Myl6 and Myl12b. We describe the extent to which cofilaments of actin and Tpm1.6, Tpm1.8 or Tpm3.1 alter the maximum actin-activated ATPase and motile activity of the recombinant Myo5c constructs. The small allosteric effector pentabromopseudilin (PBP), which is predicted to bind in a groove close to the actin and nucleotide binding site with a calculated ΔG of -18.44 kcal/mol, inhibits the motor function of Myo5c with a half-maximal concentration of 280 nM. Using immunohistochemical staining, we determined the distribution and exact localization of Myo5c in endothelial and endocrine cells from rat and human tissue. Particular high levels of Myo5c were observed in insulin-producing β-cells located within the pancreatic islets of Langerhans.},
	keywords = {immunohistochemistry; Molecular docking; tropomyosin; pentabromopseudilin; Myosin 5c},
	year = {2024},
	eissn = {1664-042X}
}

@article{MTMT:34777718,
	title = {Cooperation of Various Cytoskeletal Components Orchestrates Intercellular Spread of Mitochondria between B-Lymphoma Cells through Tunnelling Nanotubes},
	url = {https://m2.mtmt.hu/api/publication/34777718},
	author = {Halász, Henriett and Tárnai, Viktória and Matkó, J and Nyitrai, Miklós and Szabó-Meleg, Edina},
	doi = {10.3390/cells13070607},
	journal-iso = {CELLS-BASEL},
	journal = {CELLS},
	volume = {13},
	unique-id = {34777718},
	abstract = {Membrane nanotubes (NTs) are dynamic communication channels connecting spatially separated cells even over long distances and promoting the transport of different cellular cargos. NTs are also involved in the intercellular spread of different pathogens and the deterioration of some neurological disorders. Transport processes via NTs may be controlled by cytoskeletal elements. NTs are frequently observed membrane projections in numerous mammalian cell lines, including various immune cells, but their functional significance in the ‘antibody factory’ B cells is poorly elucidated. Here, we report that as active channels, NTs of B-lymphoma cells can mediate bidirectional mitochondrial transport, promoted by the cooperation of two different cytoskeletal motor proteins, kinesin along microtubules and myosin VI along actin, and bidirectional transport processes are also supported by the heterogeneous arrangement of the main cytoskeletal filament systems of the NTs. We revealed that despite NTs and axons being different cell extensions, the mitochondrial transport they mediate may exhibit significant similarities. Furthermore, we found that microtubules may improve the stability and lifespan of B-lymphoma-cell NTs, while F-actin strengthens NTs by providing a structural framework for them. Our results may contribute to a better understanding of the regulation of the major cells of humoral immune response to infections.},
	year = {2024},
	eissn = {2073-4409},
	orcid-numbers = {Halász, Henriett/0009-0003-7132-634X; Nyitrai, Miklós/0000-0002-6229-4337}
}

@article{MTMT:34763944,
	title = {Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells},
	url = {https://m2.mtmt.hu/api/publication/34763944},
	author = {Rosano, Dalia and Sofyali, Emre and Dhiman, Heena and Ghirardi, Chiara and Ivanoiu, Diana and Heide, Timon and Vingiani, Andrea and Bertolotti, Alessia and Pruneri, Giancarlo and Canale, Eleonora and Dewhurst, Hannah F and Saha, Debjani and Slaven, Neil and Barozzi, Iros and Li, Tong and Zemlyanskiy, Grigory and Phillips, Henry and James, Chela and Győrffy, Balázs and Lynn, Claire and Cresswell, George D and Rehman, Farah and Noberini, Roberta and Bonaldi, Tiziana and Sottoriva, Andrea and Magnani, Luca},
	doi = {10.1158/2159-8290.CD-23-1161},
	journal-iso = {CANCER DISCOV},
	journal = {CANCER DISCOVERY},
	volume = {14},
	unique-id = {34763944},
	issn = {2159-8274},
	abstract = {Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs.This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs.},
	year = {2024},
	eissn = {2159-8290},
	pages = {866-889},
	orcid-numbers = {Győrffy, Balázs/0000-0002-5772-3766}
}

@book{MTMT:34742597,
	title = {BioX: Math in the Lab},
	url = {https://m2.mtmt.hu/api/publication/34742597},
	isbn = {9789636262419},
	author = {Bugyi, Beáta and Gaszler, Péter and Rauan, Sakenov and Szütsné Tóth, Mónika Ágnes and Leipold Vig, Andrea},
	publisher = {University of Pécs Medical School Department of Medical Biology},
	unique-id = {34742597},
	year = {2024}
}

@article{MTMT:34729568,
	title = {Neural and metabolic dysregulation in PMM2-deficient human in vitro neural models.},
	url = {https://m2.mtmt.hu/api/publication/34729568},
	author = {Radenkovic, Silvia and Budhraja, Rohit and Klein-Gunnewiek, Teun and King, Alexia Tyler and Bhatia, Tarun N and Ligezka, Anna N and Driesen, Karen and Shah, Rameen and Ghesquière, Bart and Pandey, Akhilesh and Kasri, Nael Nadif and Sloan, Steven A and Morava-Kozicz, Éva and Kozicz, Tamás},
	doi = {10.1016/j.celrep.2024.113883},
	journal-iso = {CELL REP},
	journal = {CELL REPORTS},
	volume = {43},
	unique-id = {34729568},
	issn = {2211-1247},
	abstract = {Phosphomannomutase 2-congenital disorder of glycosylation (PMM2-CDG) is a rare inborn error of metabolism caused by deficiency of the PMM2 enzyme, which leads to impaired protein glycosylation. While the disorder presents with primarily neurological symptoms, there is limited knowledge about the specific brain-related changes caused by PMM2 deficiency. Here, we demonstrate aberrant neural activity in 2D neuronal networks from PMM2-CDG individuals. Utilizing multi-omics datasets from 3D human cortical organoids (hCOs) derived from PMM2-CDG individuals, we identify widespread decreases in protein glycosylation, highlighting impaired glycosylation as a key pathological feature of PMM2-CDG, as well as impaired mitochondrial structure and abnormal glucose metabolism in PMM2-deficient hCOs, indicating disturbances in energy metabolism. Correlation between PMM2 enzymatic activity in hCOs and symptom severity suggests that the level of PMM2 enzyme function directly influences neurological manifestations. These findings enhance our understanding of specific brain-related perturbations associated with PMM2-CDG, offering insights into the underlying mechanisms and potential directions for therapeutic interventions.},
	keywords = {disease model; neurodevelopmental disorder; congenital disorder of glycosylation; phosphomannomutase 2; CP: Neuroscience; hiPSC-derived cortical organoids; hiPSC-derived iNeuronal networks},
	year = {2024},
	eissn = {2211-1247}
}