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Article ; Online: Perspectives for Primary Ciliary Dyskinesia

Zuzanna Bukowy-Bieryllo / Michal Witt / Ewa Zietkiewicz

International Journal of Molecular Sciences, Vol 23, Iss 4122, p

2022 Volume 4122

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 [.]
Keywords	n/a ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genetic testing—whether to allow complete freedom? Direct to consumer tests versus genetic tests for medical purposes

Malgorzata, Madej / Maria, Sąsiadek / Michał, Witt

Journal of applied genetics. 2022 Feb., v. 63, no. 1

2022

Abstract: Direct-to-consumer tests opened the opportunity of genetic testing without medical supervision, e.g., without medical referral and medical interpretation of the results. Thus, these approaches allow for free access to information concerning individual ... ...

Abstract	Direct-to-consumer tests opened the opportunity of genetic testing without medical supervision, e.g., without medical referral and medical interpretation of the results. Thus, these approaches allow for free access to information concerning individual genetic profile increasing the area of personal freedom, but also posing the risk of false (positive and negative) or misinterpreted results along with health and psychological negative consequences. The paper discusses medical and non-medical applications of DTC, exploring also the legal framework implemented by European states and organizations. These legal acts strive to control the developing DTC market through such basic principles as patient protection, informed consent, medical information confidentiality, and the rights to know and to refuse knowledge about one’s genetic predispositions.
Keywords	genetic profile ; markets ; patients ; risk
Language	English
Dates of publication	2022-02
Size	p. 119-126.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	Review
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-021-00670-z
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic testing-whether to allow complete freedom? Direct to consumer tests versus genetic tests for medical purposes.

Malgorzata, Madej / Maria, Sąsiadek / Michał, Witt

Journal of applied genetics

2021 Volume 63, Issue 1, Page(s) 119–126

Abstract	Direct-to-consumer tests opened the opportunity of genetic testing without medical supervision, e.g., without medical referral and medical interpretation of the results. Thus, these approaches allow for free access to information concerning individual genetic profile increasing the area of personal freedom, but also posing the risk of false (positive and negative) or misinterpreted results along with health and psychological negative consequences. The paper discusses medical and non-medical applications of DTC, exploring also the legal framework implemented by European states and organizations. These legal acts strive to control the developing DTC market through such basic principles as patient protection, informed consent, medical information confidentiality, and the rights to know and to refuse knowledge about one's genetic predispositions.
MeSH term(s)	Confidentiality ; Freedom ; Genetic Predisposition to Disease ; Genetic Testing ; Humans ; Informed Consent
Language	English
Publishing date	2021-11-26
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/s13353-021-00670-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: DNA Methylation in T-Cell Acute Lymphoblastic Leukemia

Natalia Maćkowska / Monika Drobna-Śledzińska / Michał Witt / Małgorzata Dawidowska

International Journal of Molecular Sciences, Vol 22, Iss 3, p

In Search for Clinical and Biological Meaning

2021 Volume 1388

Abstract: Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes ...

Abstract	Distinct DNA methylation signatures, related to different prognosis, have been observed across many cancers, including T-cell acute lymphoblastic leukemia (T-ALL), an aggressive hematological neoplasm. By global methylation analysis, two major phenotypes might be observed in T-ALL: hypermethylation related to better outcome and hypomethylation, which is a candidate marker of poor prognosis. Moreover, DNA methylation holds more than a clinical meaning. It reflects the replicative history of leukemic cells and most likely different mechanisms underlying leukemia development in these T-ALL subtypes. The elucidation of the mechanisms and aberrations specific to (epi-)genomic subtypes might pave the way towards predictive diagnostics and precision medicine in T-ALL. We present the current state of knowledge on the role of DNA methylation in T-ALL. We describe the involvement of DNA methylation in normal hematopoiesis and T-cell development, focusing on epigenetic aberrations contributing to this leukemia. We further review the research investigating distinct methylation phenotypes in T-ALL, related to different outcomes, pointing to the most recent research aimed to unravel the biological mechanisms behind differential methylation. We highlight how technological advancements facilitated broadening the perspective of the investigation into DNA methylation and how this has changed our understanding of the roles of this epigenetic modification in T-ALL.
Keywords	T-cell acute lymphoblastic leukemia ; T-ALL ; DNA methylation ; epigenetic aberrations ; epigenetic prognostic markers ; methylation phenotypes in cancer ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	612
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology

Monika Drobna-Śledzińska / Natalia Maćkowska-Maślak / Roman Jaksik / Paulina Dąbek / Michał Witt / Małgorzata Dawidowska

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 11

Abstract: Abstract miRNAs form a class of noncoding RNAs, involved in post-transcriptional regulation of gene expression, broadly studied for their involvement in physiological and pathological context. Inhibition of mature miRNA transcripts, commonly used in ... ...

Abstract	Abstract miRNAs form a class of noncoding RNAs, involved in post-transcriptional regulation of gene expression, broadly studied for their involvement in physiological and pathological context. Inhibition of mature miRNA transcripts, commonly used in miRNA loss-of-function experiments, may not be specific in case of miRNAs with high sequence homology, e.g. miRNAs from the same seed family. Phenotypic effects of miRNA repression might be biased by the repression of highly similar miRNAs. Another challenge is simultaneous inhibition of multiple miRNAs encoded within policistronic clusters, potentially co-regulating common biological processes. To elucidate roles of miRNA clusters and miRNAs with high sequence homology, it is of key importance to selectively repress only the miRNAs of interest. Targeting miRNAs on genomic level with CRISPR/dCas9-based methods is an attractive alternative to blocking mature miRNAs. Yet, so far no clear guidelines on the design of CRISPR inhibition (CRISPRi) experiments, specifically for miRNA repression, have been proposed. To address this need, here we propose a strategy for effective inhibition of miRNAs and miRNA clusters using CRISPRi. We provide clues on how to approach the challenges in using CRISPR/dCas in miRNA studies, which include prediction of miRNA transcription start sites (TSSs) and the design of single guide RNAs (sgRNAs). The strategy implements three TSS prediction online tools, dedicated specifically for miRNAs: miRStart, FANTOM 5 miRNA atlas, DIANA-miRGen, and CRISPOR tool for sgRNAs design; it includes testing and selection of optimal sgRNAs. We demonstrate that compared to siRNA/shRNA-based miRNA silencing, CRISPRi improves the repression specificity for miRNAs with highly similar sequence and contribute to higher uniformity of the effects of silencing the whole miRNA clusters. This strategy may be adapted for CRISPR-mediated activation (CRISPRa) of miRNA expression.
Keywords	Medicine ; R ; Science ; Q
Subject code	500
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia

Małgorzata Dawidowska / Natalia Maćkowska-Maślak / Monika Drobna-Śledzińska / Maria Kosmalska / Roman Jaksik / Donata Szymczak / Małgorzata Jarmuż-Szymczak / Alicja Sadowska-Klasa / Marzena Wojtaszewska / Łukasz Sędek / Tomasz Wróbel / Jan Maciej Zaucha / Tomasz Szczepański / Krzysztof Lewandowski / Sebastian Giebel / Michał Witt

International Journal of Molecular Sciences, Vol 23, Iss 10117, p

2022 Volume 10117

Abstract: We aimed to identify miRNAs and pathways specifically deregulated in adolescent and young adult (AYA) T-ALL patients. Small RNA-seq showed no major differences between AYA and pediatric T-ALL, but it revealed downregulation of miR-143-3p in T-ALL ... ...

Abstract	We aimed to identify miRNAs and pathways specifically deregulated in adolescent and young adult (AYA) T-ALL patients. Small RNA-seq showed no major differences between AYA and pediatric T-ALL, but it revealed downregulation of miR-143-3p in T-ALL patients. Prediction algorithms identified several known and putative oncogenes targeted by this miRNA, including KRAS , FGF1 , and FGF9 . Pathway analysis indicated signaling pathways related to cell growth and proliferation, including FGFR signaling and PI3K-AKT signaling, with the majority of genes overrepresented in these pathways being predicted targets of hsa-miR-143-3p. By luciferase reporter assays, we validated direct interactions of this miRNA with KRAS , FGF1 and FGF9 . In cell proliferation assays, we showed reduction of cell growth upon miR-143-3p overexpression in two T-ALL cell lines. Our study is the first description of the miRNA transcriptome in AYA T-ALL patients and the first report on tumor suppressor potential of miR-143-3p in T-ALL. Downregulation of this miRNA in T-ALL patients might contribute to enhanced growth and viability of leukemic cells. We also discuss the potential role of miR-143-3p in FGFR signaling. Although this requires more extensive validation, it might be an interesting direction, since FGFR inhibition proved promising in preclinical studies in various cancers.
Keywords	T-cell acute lymphoblastic leukemia (T-ALL) ; adolescents and young adults (AYA) ; miR-143-3p ; tumor suppressor miRNA ; targeting FGFR signaling ; miRNA-seq ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	500
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: ZMYND10--Mutation Analysis in Slavic Patients with Primary Ciliary Dyskinesia.

Małgorzata Kurkowiak / Ewa Ziętkiewicz / Agnieszka Greber / Katarzyna Voelkel / Alina Wojda / Andrzej Pogorzelski / Michał Witt

PLoS ONE, Vol 11, Iss 1, p e

2016 Volume 0148067

Abstract: Primary ciliary dyskinesia (PCD) is a rare recessive disease with a prevalence of 1/10,000; its symptoms are caused by a kinetic dysfunction of motile cilia in the respiratory epithelium, flagella in spermatozoids, and primary cilia in the embryonic node. ...

Abstract	Primary ciliary dyskinesia (PCD) is a rare recessive disease with a prevalence of 1/10,000; its symptoms are caused by a kinetic dysfunction of motile cilia in the respiratory epithelium, flagella in spermatozoids, and primary cilia in the embryonic node. PCD is genetically heterogeneous: genotyping the already known PCD-related genes explains the genetic basis in 60-65% of the cases, depending on the population. While identification of new genes involved in PCD pathogenesis remains crucial, the search for new, population-specific mutations causative for PCD is equally important. The Slavs remain far less characterized in this respect compared to West European populations, which significantly limits diagnostic capability. The main goal of this study was to characterize the profile of causative genetic defects in one of the PCD-causing genes, ZMYND10, in the cohort of PCD patients of Slavic origin. The study was carried out using biological material from 172 unrelated PCD individuals of Polish origin, with no causative mutation found in nine major PCD genes. While none of the previously described mutations was found using the HRM-based screening, a novel frameshift mutation (c.367delC) in ZMYND10, unique for Slavic PCD population, was found in homozygous state in two unrelated PCD patients. Immunofluorescence analysis confirmed the absence of outer and inner dynein arms from the ciliary axoneme, consistent with the already published ZMYND10-mutated phenotype; cDNA analysis revealed the lack of ZMYND10 mRNA, indicating nonsense-mediated decay of the truncated transcript.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of Endogenous Control miRNAs for RT-qPCR in T-Cell Acute Lymphoblastic Leukemia

Monika Drobna / Bronisława Szarzyńska-Zawadzka / Patrycja Daca-Roszak / Maria Kosmalska / Roman Jaksik / Michał Witt / Małgorzata Dawidowska

International Journal of Molecular Sciences, Vol 19, Iss 10, p

2018 Volume 2858

Abstract: Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. ... ...

Abstract	Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. Universal endogenous controls are lacking, thus candidate normalizers must be evaluated individually for each experiment. Here we present a strategy that we applied to the identification of optimal control miRNAs for RT-qPCR profiling of miRNA expression in T-cell acute lymphoblastic leukemia (T-ALL) and in normal cells of T-lineage. First, using NormFinder for an iterative analysis of miRNA stability in our miRNA-seq data, we established the number of control miRNAs to be used in RT-qPCR. Then, we identified optimal control miRNAs by a comprehensive analysis of miRNA stability in miRNA-seq data and in RT-qPCR by analysis of RT-qPCR amplification efficiency and expression across a variety of T-lineage samples and T-ALL cell line culture conditions. We then showed the utility of the combination of three miRNAs as endogenous normalizers (hsa-miR-16-5p, hsa-miR-25-3p, and hsa-let-7a-5p). These miRNAs might serve as first-line candidate endogenous controls for RT-qPCR analysis of miRNAs in different types of T-lineage samples: T-ALL patient samples, T-ALL cell lines, normal immature thymocytes, and mature T-lymphocytes. The strategy we present is universal and can be transferred to other RT-qPCR experiments.
Keywords	miRNA (microRNA) ; T-cell acute lymphoblastic leukemia (T-ALL) ; normalization of miRNA expression in RT-qPCR ; endogenous controls ; reference genes ; tissue analysis ; cell lines ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	500
Language	English
Publishing date	2018-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: hsa-miR-20b-5p and hsa-miR-363-3p Affect Expression of PTEN and BIM Tumor Suppressor Genes and Modulate Survival of T-ALL Cells In Vitro

Monika Drobna / Bronisława Szarzyńska / Roman Jaksik / Łukasz Sędek / Anna Kuchmiy / Tom Taghon / Pieter Van Vlierberghe / Tomasz Szczepański / Michał Witt / Małgorzata Dawidowska

Cells, Vol 9, Iss 1137, p

2020 Volume 1137

Abstract: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy arising from T lymphocyte precursors. We have previously shown by miRNA-seq, that miRNAs from the mir-106a-363 cluster are overexpressed in pediatric T-ALL. In silico analysis ... ...

Abstract	T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy arising from T lymphocyte precursors. We have previously shown by miRNA-seq, that miRNAs from the mir-106a-363 cluster are overexpressed in pediatric T-ALL. In silico analysis indicated their potential involvement in the regulation of apoptosis. Here, we aimed to test the hypothesis on the pro-tumorigenic roles of these miRNAs in T-ALL cells in vitro. We demonstrate, for the first time, that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster, when upregulated in T-ALL cells in vitro, protect leukemic cells from apoptosis, enhance proliferation, and contribute to growth advantage. We show, using dual luciferase reporter assays, Ago2-RNA immunoprecipitation, RT-qPCR, and Western blots, that the oncogenic effects of these upregulated miRNAs might, at least in part, be mediated by the downregulation of two important tumor suppressor genes, PTEN and BIM , targeted by both miRNAs. Additionally, we demonstrate the cooperative effects of these two miRNAs by simultaneous inhibition of both miRNAs as compared to the inhibition of single miRNAs. We postulate that hsa-miR-20b-5p and hsa-miR-363-3p from the mir-106a-363 cluster might serve as oncomiRs in T-ALL, by contributing to post-transcriptional repression of key tumor suppressors, PTEN and BIM .
Keywords	oncogenic miRNAs ; acute lymphoblastic leukemia ; silencing tumor suppressor genes ; miRNA cluster ; noncoding RNAs in cancer ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Ciliary genes are down-regulated in bronchial tissue of primary ciliary dyskinesia patients.

Maciej Geremek / Ewa Ziętkiewicz / Marcel Bruinenberg / Lude Franke / Andrzej Pogorzelski / Cisca Wijmenga / Michał Witt

PLoS ONE, Vol 9, Iss 2, p e

2014 Volume 88216

Abstract: Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous disease characterized by recurrent respiratory tract infections, sinusitis, bronchiectasis and male infertility. The pulmonary phenotype in PCD is caused by the impaired motility of ... ...

Abstract	Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous disease characterized by recurrent respiratory tract infections, sinusitis, bronchiectasis and male infertility. The pulmonary phenotype in PCD is caused by the impaired motility of cilia in the respiratory epithelium, due to ultrastructural defects of these organelles. We hypothesized that defects of multi-protein ciliary complexes should be reflected by gene expression changes in the respiratory epithelium. We have previously found that large group of genes functionally related to cilia share highly correlated expression pattern in PCD bronchial tissue. Here we performed an explorative analysis of differential gene expression in the bronchial tissue from six PCD patients and nine non-PCD controls, using Illumina HumanRef-12 Whole Genome BeadChips. We observed 1323 genes with at least 2-fold difference in the mean expression level between the two groups (t-test p-value <0.05). Annotation analysis showed that the genes down-regulated in PCD biopsies (602) were significantly enriched for terms related to cilia, whereas the up-regulated genes (721) were significantly enriched for terms related to cell cycle and mitosis. We assembled a list of human genes predicted to encode ciliary proteins, components of outer dynein arms, inner dynein arms, radial spokes, and intraflagellar transport proteins. A significant down-regulation of the expression of genes from all the four groups was observed in PCD, compared to non-PCD biopsies. Our data suggest that a coordinated down-regulation of the ciliome genes plays an important role in the molecular pathomechanism of PCD.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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