We have collaborated on the following publications
2022
4.
Soltész, B.; Pös, O.; Wlachovska, Z.; Budis, J.; Hekel, R.; Strieskova, L.; Liptak, J. B.; Krampl, W.; Styk, J.; Németh, N.; Keserű, J. S.; Jenei, A.; Buglyó, G.; Klekner, Á.; Nagy, B.; Szemes, T.
Mitochondrial DNA copy number changes, heteroplasmy, and mutations in plasma-derived exosomes and brain tissue of glioblastoma patients Journal Article
In: Molecular and Cellular Probes, 66 , 2022, ISSN: 08908508.
Abstract | Links | BibTeX | Tags: Copy number variation, Mitochondria, Oncology
@article{Soltész2022b,
title = {Mitochondrial DNA copy number changes, heteroplasmy, and mutations in plasma-derived exosomes and brain tissue of glioblastoma patients},
author = {B. Soltész and O. Pös and Z. Wlachovska and J. Budis and R. Hekel and L. Strieskova and J. B. Liptak and W. Krampl and J. Styk and N. Németh and J. S. Keserű and A. Jenei and G. Buglyó and Á. Klekner and B. Nagy and T. Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85142723801&doi=10.1016%2fj.mcp.2022.101875&partnerID=40&md5=cfe8239029a20ab89e08e1321a98c75e},
doi = {10.1016/j.mcp.2022.101875},
issn = {08908508},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Molecular and Cellular Probes},
volume = {66},
publisher = {Academic Press},
abstract = {Glioblastoma is the most common malignant tumor of the central nervous system (CNS) in adults. Glioblastoma cells show increased glucose consumption associated with poor prognosis. Since mitochondria play a crucial role in energy metabolism, mutations and copy number changes of mitochondrial DNA may serve as biomarkers. As the brain is difficult to access, analysis of mitochondria directly from the brain tissue represents a challenge. Exosome analysis is an alternative (still poorly explored) approach to investigate molecular changes in CNS tumors. We analyzed brain tissue DNA and plasma-derived exosomal DNA (exoDNA) of 44 glioblastoma patients and 40 control individuals. Quantitative real-time PCR was performed to determine mtDNA copy numbers and the Kruskal-Wallis and Mann-Whitney U test were used for statistical analysis of data. Subsequently, sequencing libraries were prepared and sequenced on the MiSeq platform to identify mtDNA point mutations. Tissue mtDNA copy number was different among controls and patients in multiple comparisons. A similar tendency was detected in exosomes. Based on NGS analysis, several mtDNA point mutations showed slightly different frequencies between cases and controls, but the clinical relevance of these observations is difficult to assess and likely less than that of overall mtDNA copy number changes. Allele frequencies of variants were used to determine the level of heteroplasmy (found to be higher in exo-mtDNA of control individuals). Despite the suggested potential, the use of such biomarkers for the screening and/or diagnosis of glioblastomas is still limited, thus further studies are needed. © 2022},
keywords = {Copy number variation, Mitochondria, Oncology},
pubstate = {published},
tppubtype = {article}
}
Glioblastoma is the most common malignant tumor of the central nervous system (CNS) in adults. Glioblastoma cells show increased glucose consumption associated with poor prognosis. Since mitochondria play a crucial role in energy metabolism, mutations and copy number changes of mitochondrial DNA may serve as biomarkers. As the brain is difficult to access, analysis of mitochondria directly from the brain tissue represents a challenge. Exosome analysis is an alternative (still poorly explored) approach to investigate molecular changes in CNS tumors. We analyzed brain tissue DNA and plasma-derived exosomal DNA (exoDNA) of 44 glioblastoma patients and 40 control individuals. Quantitative real-time PCR was performed to determine mtDNA copy numbers and the Kruskal-Wallis and Mann-Whitney U test were used for statistical analysis of data. Subsequently, sequencing libraries were prepared and sequenced on the MiSeq platform to identify mtDNA point mutations. Tissue mtDNA copy number was different among controls and patients in multiple comparisons. A similar tendency was detected in exosomes. Based on NGS analysis, several mtDNA point mutations showed slightly different frequencies between cases and controls, but the clinical relevance of these observations is difficult to assess and likely less than that of overall mtDNA copy number changes. Allele frequencies of variants were used to determine the level of heteroplasmy (found to be higher in exo-mtDNA of control individuals). Despite the suggested potential, the use of such biomarkers for the screening and/or diagnosis of glioblastomas is still limited, thus further studies are needed. © 2022
2021
3.
Poláková, S Bágeľová; Lichtner, Ž; Szemes, T; Smolejová, M; Sulo, P
Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization Journal Article
In: Scientific Reports, 11 (1), 2021, ISSN: 20452322.
Abstract | Links | BibTeX | Tags: Fungi, Mitochondria
@article{BágeľováPoláková2021,
title = {Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization},
author = {S Bágeľová Poláková and Ž Lichtner and T Szemes and M Smolejová and P Sulo},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108161297&doi=10.1038%2fs41598-021-92125-y&partnerID=40&md5=6bc31d15f4fb89003df9c7623ab3db19},
doi = {10.1038/s41598-021-92125-y},
issn = {20452322},
year = {2021},
date = {2021-01-01},
journal = {Scientific Reports},
volume = {11},
number = {1},
publisher = {Nature Research},
abstract = {mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes. © 2021, The Author(s).},
keywords = {Fungi, Mitochondria},
pubstate = {published},
tppubtype = {article}
}
mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes. © 2021, The Author(s).
2019
2.
Strieskova, L; Gazdaricova, I; Kajsik, M; Soltys, K; Budis, J; Pos, O; Lickova, M; Klempa, B; Szemes, T
Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome Journal Article
In: Journal of Biotechnology, 299 , pp. 8-12, 2019, ISSN: 01681656.
Abstract | Links | BibTeX | Tags: Assembly, Mitochondria, Single nucleotide variants, Transcriptomics
@article{Strieskova20198,
title = {Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome},
author = {L Strieskova and I Gazdaricova and M Kajsik and K Soltys and J Budis and O Pos and M Lickova and B Klempa and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064954323&doi=10.1016%2fj.jbiotec.2019.04.019&partnerID=40&md5=90856f6a0fd40fd7eeaf877edfdbdeb3},
doi = {10.1016/j.jbiotec.2019.04.019},
issn = {01681656},
year = {2019},
date = {2019-01-01},
journal = {Journal of Biotechnology},
volume = {299},
pages = {8-12},
publisher = {Elsevier B.V.},
abstract = {The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. © 2019 Elsevier B.V.},
keywords = {Assembly, Mitochondria, Single nucleotide variants, Transcriptomics},
pubstate = {published},
tppubtype = {article}
}
The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. © 2019 Elsevier B.V.
2017
1.
Sulo, P; Szabóová, D; Bielik, P; Poláková, S; Soltys, K; Jatzová, K; Szemes, T
In: DNA Research, 24 (6), pp. 571-583, 2017, ISSN: 13402838.
Abstract | Links | BibTeX | Tags: Assembly, Fungi, Mitochondria, Phylogeny
@article{Sulo2017571,
title = {The evolutionary history of Saccharomyces species inferred fromcompleted mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'},
author = {P Sulo and D Szabóová and P Bielik and S Poláková and K Soltys and K Jatzová and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043997344&doi=10.1093%2fdnares%2fdsx026&partnerID=40&md5=06765f8bce0a85c0d5b881f73efb11f8},
doi = {10.1093/dnares/dsx026},
issn = {13402838},
year = {2017},
date = {2017-01-01},
journal = {DNA Research},
volume = {24},
number = {6},
pages = {571-583},
publisher = {Oxford University Press},
abstract = {The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species. © The Author 2017.},
keywords = {Assembly, Fungi, Mitochondria, Phylogeny},
pubstate = {published},
tppubtype = {article}
}
The yeast Saccharomyces are widely used to test ecological and evolutionary hypotheses. A large number of nuclear genomic DNA sequences are available, but mitochondrial genomic data are insufficient. We completed mitochondrial DNA (mtDNA) sequencing from Illumina MiSeq reads for all Saccharomyces species. All are circularly mapped molecules decreasing in size with phylogenetic distance from Saccharomyces cerevisiae but with similar gene content including regulatory and selfish elements like origins of replication, introns, free-standing open reading frames or GC clusters. Their most profound feature is species-specific alteration in gene order. The genetic code slightly differs from well-established yeast mitochondrial code as GUG is used rarely as the translation start and CGA and CGC code for arginine. The multilocus phylogeny, inferred from mtDNA, does not correlate with the trees derived from nuclear genes. mtDNA data demonstrate that Saccharomyces cariocanus should be assigned as a separate species and Saccharomyces bayanus CBS 380T should not be considered as a distinct species due to mtDNA nearly identical to Saccharomyces uvarum mtDNA. Apparently, comparison of mtDNAs should not be neglected in genomic studies as it is an important tool to understand the origin and evolutionary history of some yeast species. © The Author 2017.