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Article ; Online: Schmidtea mediterranea

Rabiasz, Alicja / Ziętkiewicz, Ewa

International journal of molecular sciences

2023 Volume 24, Issue 5

Abstract: Cilia and flagella are evolutionarily conserved organelles that form protrusions on the surface of many growth-arrested or differentiated eukaryotic cells. Due to the structural and functional differences, cilia can be roughly classified as motile and ... ...

Abstract	Cilia and flagella are evolutionarily conserved organelles that form protrusions on the surface of many growth-arrested or differentiated eukaryotic cells. Due to the structural and functional differences, cilia can be roughly classified as motile and non-motile (primary). Genetically determined dysfunction of motile cilia is the basis of primary ciliary dyskinesia (PCD), a heterogeneous ciliopathy affecting respiratory airways, fertility, and laterality. In the face of the still incomplete knowledge of PCD genetics and phenotype-genotype relations in PCD and the spectrum of PCD-like diseases, a continuous search for new causative genes is required. The use of model organisms has been a great part of the advances in understanding molecular mechanisms and the genetic basis of human diseases; the PCD spectrum is not different in this respect. The planarian model (
MeSH term(s)	Animals ; Humans ; Mediterranea ; Ciliopathies ; Flagella ; Cilia/physiology ; Planarians/genetics ; Mutation
Language	English
Publishing date	2023-02-24
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24054472
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Article ; Online: Perspectives for Primary Ciliary Dyskinesia.

Bukowy-Bieryllo, Zuzanna / Witt, Michal / Zietkiewicz, Ewa

International journal of molecular sciences

2022 Volume 23, Issue 8

Abstract: Primary ciliary dyskinesia (PCD) is a ciliopathy caused by genetically determined impairment of motile cilia-organelles present on the surface of many types of cells [ ... ]. ...

Abstract	Primary ciliary dyskinesia (PCD) is a ciliopathy caused by genetically determined impairment of motile cilia-organelles present on the surface of many types of cells [...].
MeSH term(s)	Cilia ; Ciliary Motility Disorders/genetics ; Humans ; Mutation
Language	English
Publishing date	2022-04-08
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23084122
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Article ; Online: Correction to: The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems.

Daca-Roszak, Patrycja / Fiedorowicz, Joanna / Jankowski, Maciej / Ciesielka, Marzanna / Teresiński, Grzegorz / Lipska-Ziętkiewicz, Beata / Ziętkiewicz, Ewa / Grzybowski, Tomasz / Skonieczna, Katarzyna

Journal of applied genetics

2024

Language	English
Publishing date	2024-04-13
Publishing country	England
Document type	Published Erratum
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-024-00864-1
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Article ; Online: Properties of Non-Aminoglycoside Compounds Used to Stimulate Translational Readthrough of PTC Mutations in Primary Ciliary Dyskinesia.

Dabrowski, Maciej / Bukowy-Bieryllo, Zuzanna / Jackson, Claire L / Zietkiewicz, Ewa

International journal of molecular sciences

2021 Volume 22, Issue 9

Abstract: Primary ciliary dyskinesia (PCD) is a rare disease with autosomal recessive inheritance, caused mostly by bi-allelic gene mutations that impair motile cilia structure and function. Currently, there are no causal treatments for PCD. In many disease models, ...

Abstract	Primary ciliary dyskinesia (PCD) is a rare disease with autosomal recessive inheritance, caused mostly by bi-allelic gene mutations that impair motile cilia structure and function. Currently, there are no causal treatments for PCD. In many disease models, translational readthrough of premature termination codons (PTC-readthrough) induced by aminoglycosides has been proposed as an effective way of restoring functional protein expression and reducing disease symptoms. However, variable outcomes of pre-clinical trials and toxicity associated with long-term use of aminoglycosides prompt the search for other compounds that might overcome these problems. Because a high proportion of PCD-causing variants are nonsense mutations, readthrough therapies are an attractive option. We tested a group of chemical compounds with known PTC-readthrough potential (ataluren, azithromycin, tylosin, amlexanox, and the experimental compound TC007), collectively referred to as non-aminoglycosides (NAGs). We investigated their PTC-readthrough efficiency in six PTC mutations found in Polish PCD patients, in the context of cell and cilia health, and in comparison to the previously tested aminoglycosides. The NAGs did not compromise the viability of the primary nasal respiratory epithelial cells, and the ciliary beat frequency was retained, similar to what was observed for gentamicin. In HEK293 cells transfected with six PTC-containing inserts, the tested compounds stimulated PTC-readthrough but with lower efficiency than aminoglycosides. The study allowed us to select compounds with minimal negative impact on cell viability and function but still the potential to induce PTC-readthrough.
MeSH term(s)	Aminoglycosides/pharmacology ; Cell Death/drug effects ; Cells, Cultured ; Cilia/drug effects ; Cilia/metabolism ; Ciliary Motility Disorders/genetics ; Codon, Nonsense/genetics ; Epithelial Cells/drug effects ; Epithelial Cells/metabolism ; HEK293 Cells ; Humans ; Mutation/genetics ; Nose/pathology ; Protein Biosynthesis/drug effects ; Protein Biosynthesis/genetics
Chemical Substances	Aminoglycosides ; Codon, Nonsense
Language	English
Publishing date	2021-05-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22094923
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Article ; Online: The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems.

Daca-Roszak, Patrycja / Fiedorowicz, Joanna / Jankowski, Maciej / Ciesielka, Marzanna / Teresiński, Grzegorz / Lipska-Zietkiewicz, Beata / Zietkiewicz, Ewa / Grzybowski, Tomasz / Skonieczna, Katarzyna

Journal of applied genetics

2023

Abstract: Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and ... ...

Abstract	Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (Nextera XT DNA Library Preparation Kit and Nextera DNA Flex Library Preparation Kit) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.
Language	English
Publishing date	2023-12-19
Publishing country	England
Document type	Journal Article
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-023-00821-4
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Article ; Online: Advances in therapeutic use of a drug-stimulated translational readthrough of premature termination codons.

Dabrowski, Maciej / Bukowy-Bieryllo, Zuzanna / Zietkiewicz, Ewa

Molecular medicine (Cambridge, Mass.)

2018 Volume 24, Issue 1, Page(s) 25

Abstract: Premature termination codons (PTCs) in the coding regions of mRNA lead to the incorrect termination of translation and generation of non-functional, truncated proteins. Translational readthrough of PTCs induced by pharmaceutical compounds is a promising ... ...

Abstract	Premature termination codons (PTCs) in the coding regions of mRNA lead to the incorrect termination of translation and generation of non-functional, truncated proteins. Translational readthrough of PTCs induced by pharmaceutical compounds is a promising way of restoring functional protein expression and reducing disease symptoms, without affecting the genome or transcriptome of the patient. While in some cases proven effective, the clinical use of readthrough-inducing compounds is still associated with many risks and difficulties. This review focuses on problems directly associated with compounds used to stimulate PTC readthrough, such as their interactions with the cell and organism, their toxicity and bioavailability (cell permeability; tissue deposition etc.). Various strategies designed to overcome these problems are presented.
MeSH term(s)	Animals ; Codon, Nonsense ; Drug Therapy ; Humans ; Protein Biosynthesis
Chemical Substances	Codon, Nonsense
Language	English
Publishing date	2018-05-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1283676-x
ISSN	1528-3658 ; 1076-1551
ISSN (online)	1528-3658
ISSN	1076-1551
DOI	10.1186/s10020-018-0024-7
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Article ; Online: Genetic diversity in Kashubs: the regional increase in the frequency of several disease-causing variants.

Jankowski, Maciej / Daca-Roszak, Patrycja / Obracht-Prondzyński, Cezary / Płoski, Rafał / Lipska-Ziętkiewicz, Beata S / Ziętkiewicz, Ewa

Journal of applied genetics

2022 Volume 63, Issue 4, Page(s) 691–701

Abstract: Differential distribution of genetic variants' frequency among human populations is caused by the genetic drift in isolated populations, historical migrations, and demography. Some of these variants are identical by descent and represent founder ... ...

Abstract	Differential distribution of genetic variants' frequency among human populations is caused by the genetic drift in isolated populations, historical migrations, and demography. Some of these variants are identical by descent and represent founder mutations, which - if pathogenic in nature - lead to the increased frequency of otherwise rare diseases. The detection of the increased regional prevalence of pathogenic variants may shed light on the historical processes that affected studied populations and can help to develop effective screening and diagnostic strategies as a part of personalized medicine. Here, we discuss the specific genetic diversity in Kashubs, the minority group living in northern Poland, reflected in the biased distribution of some of the repetitively found disease-causing variants. These include the following: (1) c.662A > G (p.Asp221Gly) in LDLR, causing heterozygous familial hypercholesterolemia; (2) c.3700_3704del in BRCA1, associated with hereditary breast and ovarian cancer syndrome; (3) c.1528G > C (p.Glu510Gln) in HADHA, seen in long-chain 3-hydroxy acyl-CoA dehydrogenase (LCHAD) deficiency, and (4) c.1032delT in NPHS2, associated with steroid-resistant nephrotic syndrome.
MeSH term(s)	Humans ; Genetic Predisposition to Disease ; Mitochondrial Myopathies ; Lipid Metabolism, Inborn Errors ; Genetic Variation ; Mutation
Language	English
Publishing date	2022-08-15
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-022-00713-z
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Article: European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients

Hryhorowicz, Szymon / Ustaszewski, Adam / Kaczmarek-Ryś, Marta / Lis, Emilia / Witt, Michał / Pławski, Andrzej / Ziętkiewicz, Ewa

Journal of applied genetics. 2021 May, v. 62, no. 2

2021

Abstract: To provide a comprehensive analysis of the SARS-CoV-2 sequence diversity in Poland in the European context. All publicly available (n = 115; GISAID database) whole-genome SARS-Cov-2 sequences from Polish samples, including those obtained during ... ...

Abstract	To provide a comprehensive analysis of the SARS-CoV-2 sequence diversity in Poland in the European context. All publicly available (n = 115; GISAID database) whole-genome SARS-Cov-2 sequences from Polish samples, including those obtained during coronavirus testing performed in our COVID-19 Lab, were examined. Multiple sequence alignment of Polish isolates, phylogenetic analysis (ML tree), and multidimensional scaling (based on the pairwise DNA distances) were complemented by the comparison of the coronavirus clades frequency and diversity in the subset of over 5000 European GISAID sequences. Approximately seventy-seven percent of isolates in the European dataset carried frequent and ubiquitously found haplotypes; the remaining haplotype diversity was population-specific and resulted from population-specific mutations, homoplasies, and recombinations. Coronavirus strains circulating in Poland represented the variability found in other European countries. The prevalence of clades circulating in Poland was shifted in favor of GR, both in terms of the diversity (number of distinct haplotypes) and the frequency (number of isolates) of the clade. Polish-specific haplotypes were rare and could be explained by changes affecting common European strains. The analysis of the whole viral genomes allowed detection of several tight clusters of isolates, presumably reflecting local outbreaks. New mutations, homoplasies, and, to a smaller extent, recombinations increase SARS-CoV-2 haplotype diversity, but the majority of these variants do not increase in frequency and remains rare and population-specific. The spectrum of SARS-CoV-2 haplotypes in the Polish dataset reflects many independent transfers from a variety of sources, followed by many local outbreaks. The prevalence of the sequences belonging to the GR clade among Polish isolates is consistent with the European trend of the GR clade frequency increase.
Keywords	COVID-19 infection ; DNA ; Severe acute respiratory syndrome coronavirus 2 ; data collection ; databases ; haplotypes ; phylogeny ; sequence alignment ; sequence diversity ; viral genome ; Poland
Language	English
Dates of publication	2021-05
Size	p. 327-337.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-020-00603-2
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin.

Daca-Roszak, Patrycja / Jaksik, Roman / Paczkowska, Julia / Witt, Michał / Ziętkiewicz, Ewa

BMC genomics

2020 Volume 21, Issue 1, Page(s) 706

Abstract: Background: Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the ... ...

Abstract	Background: Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines. Results: The goal of our study was to identify a set of CpG sites sufficient to discriminate between populations of European and Chinese ancestry based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of 10 pop-CpGs characterized by the best differentiating criteria (\|Mdiff\| > 1, q < 0.05; lack of the confounding genomic features), and 10 additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as "composite pop (CEU-CHB)-CpG marker"), three classification methods were applied. The predictive ability of the composite 8-site pop (CEU-CHB)-CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples. Conclusions: Our results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender.
MeSH term(s)	Adult ; Cell Line ; China ; CpG Islands ; DNA Methylation ; Europe ; Female ; Genetics, Population/methods ; Humans ; Leukocytes, Mononuclear ; Male
Language	English
Publishing date	2020-10-12
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-020-07092-x
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Article ; Online: In vitro differentiation of ciliated cells in ALI-cultured human airway epithelium - The framework for functional studies on airway differentiation in ciliopathies.

Bukowy-Bieryłło, Zuzanna / Daca-Roszak, Patrycja / Jurczak, Joanna / Przystałowska-Macioła, Hanna / Jaksik, Roman / Witt, Michał / Ziętkiewicz, Ewa

European journal of cell biology

2021 Volume 101, Issue 1, Page(s) 151189

Abstract: Primary cultures of the human airway epithelium (AE) cells are an indispensable tool in studies of pathophysiology of genetic and environmental pulmonary diseases, including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and chronic obstructive ... ...

Abstract	Primary cultures of the human airway epithelium (AE) cells are an indispensable tool in studies of pathophysiology of genetic and environmental pulmonary diseases, including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and chronic obstructive pulmonary disease (COPD). Air-liquid interface (ALI) culture is the best method to follow the differentiation of ciliated cells, whose dysfunction forms the basis of PCD. Here, we used custom-designed Taqman Low Density Array (TLDA), qRT-PCR-based assay, to analyze expression of 14 AE genes in cells from healthy donors, cultured in ALI settings using Pneumacult medium, with the focus on genes involved in cilia differentiation and in PCD pathogenesis. The results of TLDA assay were compared with the bulk RNAseq analysis, and placed in the cellular context using immunofluorescent staining (IF) of ALI cultured cells. Expression analysis revealed culture time-related upregulation of the majority of cilia-related genes, followed by the appearance of respective protein signals visualized by IF. Strong correlation of TLDA with RNAseq results indicated that TLDA assay is a reliable and scalable approach to analyze expression of selected genes specific for different AE cell types. Characterization of temporal and inter-donor changes in the expression of these genes, performed in healthy donors and in well-defined ALI/Pnemacult culture conditions, provides a useful reference relevant for a broad spectrum of functional studies where the in vitro AE differentiation is in focus.
MeSH term(s)	Cell Differentiation ; Cells, Cultured ; Cilia ; Ciliopathies ; Epithelial Cells ; Epithelium ; Humans
Language	English
Publishing date	2021-12-02
Publishing country	Germany
Document type	Journal Article
ZDB-ID	391967-5
ISSN	1618-1298 ; 0070-2463 ; 0171-9335
ISSN (online)	1618-1298
ISSN	0070-2463 ; 0171-9335
DOI	10.1016/j.ejcb.2021.151189
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