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001-es BibID:	BIBFORM115627
035-os BibID:	(wos)001103294600001 (scopus)85176506719
Első szerző:	Csoma Szilvia Lilla (Klinikai laboratóriumi kutató)
Cím:	Correlation Analyses between Histological Staging and Molecular Alterations in Tumor-Derived and Cell-Free DNA of Early-Stage Primary Cutaneous Melanoma / Csoma Szilvia Lilla, Madarász Kristóf, Chang Chien Yi Che, Emri Gabriella, Bedekovics Judit, Méhes Gábor, Mokánszki Attila
Dátum:	2023
ISSN:	2072-6694
Megjegyzések:	Primary cutaneous melanoma (PCM) is a highly aggressive and potentially lethal form of skin neoplasm with a rapidly increasing incidence rate worldwide. The most common genetic aberration in PCM is the BRAF gene p.V600E pathogenic variant. The use of liquid biopsy (LB), which is a non-invasive, low-risk procedure that can be repeated multiple times, is becoming increasingly important in precision oncology. Because of the limited information about the applicability of LB in melanoma, here we investigate the correlation analyses and statistical significance between histopathological staging and molecular alterations in tumor-derived and cell-free DNA. The Breslow depth (BD) and Clark level were applied to categorize the study population. A positive correlation was proven between the tumor depth and peripheral blood plasma cfDNA yield in all mutant and negative cases. This observation is also supported by the fact that a statistically significantly higher concentration of cfDNA can be isolated from Clark V category cases compared to the others. Here, we investigate the correlation and statistical analyses between histological staging and molecular alterations in tumor-derived (tdDNA) and cell-free DNA (cfDNA) obtained from early-stage primary cutaneous melanoma (PCM) patients using digital PCR (dPCR) for the detection of the BRAF p.V600E somatic pathogenic variant. In the prospective study, a total of 68 plasma and paired tdDNA samples, and in the retrospective cohort, a total of 100 tdDNA samples were analyzed using dPCR and reverse hybridization StripAssay. The Breslow depth (BD) and Clark level were applied to categorize the study population. Our results demonstrate that dPCR is a highly sensitive and specific method for the detection of BRAF p.V600E somatic variants in cfDNA samples from PCM patients. A strong correlation was detected between BD and cfDNA concentration in all mutant and negative cases, between the tdDNA concentration and the tumor-derived variant allele frequency (VAF) of BRAF p.V600E, between the tdVAF and the cfVAF in all cases, and between the cfDNA and cfVAF in mutant cases. The tdVAF and cfVAF of BRAF p.V600E and cfDNA concentration were the highest in Clark's V category. The cfDNA concentration was statistically significantly higher in Clark's III, IV, and V groups compared to cases with a better prognosis. It can also be explained by the fact that cases with a more advanced stage classification release more cfDNA into the peripheral circulation.
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Cancers. - 15 : 21 (2023), p. 1-13. -
További szerzők:	Madarász Kristóf (1996-) (biológus) Chang Chien, Yi-Che (1975-) (pathológus) Emri Gabriella (1972-) (bőrgyógyász, allergológus, onkológus) Bedekovics Judit (1986-) (orvos) Méhes Gábor (1966-) (patológus) Mokánszki Attila (1983-) (molekuláris biológus Ph.D hallgató)
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001-es BibID:	BIBFORM129427
035-os BibID:	(scopus)105002288198
Első szerző:	Madarász Kristóf (biológus)
Cím:	BCOR-rearranged sarcomas : In silico insights into altered domains and BCOR interactions / Madarász Kristóf, Mótyán János András, Chang Chien Yi-Che, Bedekovics Judit, Csoma Szilvia Lilla, Méhes Gábor, Mokánszki Attila
Dátum:	2025
ISSN:	0010-4825
Megjegyzések:	BCOR (BCL-6 corepressor) rearranged small round cell sarcoma (BRS) represents an uncommon soft tissue malignancy, frequently characterized by the BCOR::CCNB3 fusion. Other noteworthy fusions include BCOR::MAML3, BCOR::CLGN, BCOR::MAML1, ZC3H7B::BCOR, KMT2D::BCOR, CIITA::BCOR, RTL9::BCOR, and AHR::BCOR. The BCOR gene plays a pivotal role in the Polycomb Repressive Complex 1 (PRC1), essential for histone modification and gene silencing. It interfaces with the Polycomb group RING finger homolog (PCGF1). This study employed comprehensive in silico methodologies to investigate the structural and functional effects of BCOR fusion events in BRS. The analysis revealed significant alterations in the domain architecture of BCOR, which resulted in the loss of BCL6-regulated transcriptional repression. Furthermore, IUPred3 prediction indicated a significant increase in disorder in the C-terminal regions of the BCOR in the fusion proteins. A detailed analysis of the physicochemical properties by ProtParam revealed a decrease in isoelectric point, stability, and hydrophobicity. The analysis of protein structures predicted by AlphaFold3 using the PRODIGY algorithm revealed statistically significant deviations in binding affinities for BCOR-PCGF1 dimers and a non-canonical PRC1 variant tetramer compared to the wild-type BCOR. The findings provide a comprehensive summary and elucidation of the fusion proteome associated with BRS, suggesting a substantial impact on the stability and functionality of the fusion proteins, thereby contributing to the oncogenic mechanisms underlying BRS. In this study, we provide the first compilation and comparative analysis of the known BCOR fusions of BRS and introduce a new in silico approach to enhance a better understanding of the molecular basis of BRS.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk BRS BCOR AlphaFold3 Szarkóma Bioinformatika
Megjelenés:	Computers in Biology and Medicine. - 191 (2025), p. 1-22. -
További szerzők:	Mótyán János András (1981-) (biokémikus, molekuláris biológus) Chang Chien, Yi-Che (1975-) (pathológus) Bedekovics Judit (1986-) (orvos) Csoma Szilvia Lilla (1994-) (Klinikai laboratóriumi kutató) Méhes Gábor (1966-) (patológus) Mokánszki Attila (1983-) (molekuláris biológus Ph.D hallgató)
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001-es BibID:	BIBFORM135671
Első szerző:	Méhes Gábor (patológus)
Cím:	One-Day FISH Procedure / Gábor Méhes, Péter Juhász, Chang Chien Yi-che, Anikó Ujfalusi, Judit Bedekovics
Dátum:	2026
ISBN:	978-1-0716-5149-0
Tárgyszavak:	Orvostudományok Klinikai orvostudományok könyvfejezet könyvrészlet
Megjelenés:	Fluorescence In Situ Hybridization (FISH) : Application Guide / Ed. Thomas Liehr. - p. 145-153. -
További szerzők:	Juhász Péter (1987-) Chang Chien, Yi-Che (1975-) (pathológus) Ujfalusi Anikó (1968-) (gyermekorvos, laboratóriumi szakorvos) Bedekovics Judit (1986-) (orvos)
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