1
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Kostecka A, Nowikiewicz T, Olszewski P, Koczkowska M, Horbacz M, Heinzl M, Andreou M, Salazar R, Mair T, Madanecki P, Gucwa M, Davies H, Skokowski J, Buckley PG, Pęksa R, Śrutek E, Szylberg Ł, Hartman J, Jankowski M, Zegarski W, Tiemann-Boege I, Dumanski JP, Piotrowski A. High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing. NPJ Breast Cancer 2022; 8:76. [PMID: 35768433 PMCID: PMC9243094 DOI: 10.1038/s41523-022-00443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.
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Affiliation(s)
- Anna Kostecka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
| | - Tomasz Nowikiewicz
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland.
- Department of Breast Cancer and Reconstructive Surgery, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland.
| | - Paweł Olszewski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Koczkowska
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Horbacz
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Maria Andreou
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Patomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Śrutek
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Perinatology, Gynaecology and Gynaecologic, Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
- MedTech Labs, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Michał Jankowski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | | | - Jan P Dumanski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arkadiusz Piotrowski
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
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2
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Gebert M, Sobolewska A, Bartoszewska S, Cabaj A, Crossman DK, Króliczewski J, Madanecki P, Dąbrowski M, Collawn JF, Bartoszewski R. Genome-wide mRNA profiling identifies X-box-binding protein 1 (XBP1) as an IRE1 and PUMA repressor. Cell Mol Life Sci 2021; 78:7061-7080. [PMID: 34636989 PMCID: PMC8558229 DOI: 10.1007/s00018-021-03952-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023]
Abstract
Accumulation of misfolded proteins in ER activates the unfolded protein response (UPR), a multifunctional signaling pathway that is important for cell survival. The UPR is regulated by three ER transmembrane sensors, one of which is inositol-requiring protein 1 (IRE1). IRE1 activates a transcription factor, X-box-binding protein 1 (XBP1), by removing a 26-base intron from XBP1 mRNA that generates spliced XBP1 mRNA (XBP1s). To search for XBP1 transcriptional targets, we utilized an XBP1s-inducible human cell line to limit XBP1 expression in a controlled manner. We also verified the identified XBP1-dependent genes with specific silencing of this transcription factor during pharmacological ER stress induction with both an N-linked glycosylation inhibitor (tunicamycin) and a non-competitive inhibitor of the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) (thapsigargin). We then compared those results to the XBP1s-induced cell line without pharmacological ER stress induction. Using next‐generation sequencing followed by bioinformatic analysis of XBP1-binding motifs, we defined an XBP1 regulatory network and identified XBP1 as a repressor of PUMA (a proapoptotic gene) and IRE1 mRNA expression during the UPR. Our results indicate impairing IRE1 activity during ER stress conditions accelerates cell death in ER-stressed cells, whereas elevating XBP1 expression during ER stress using an inducible cell line correlated with a clear prosurvival effect and reduced PUMA protein expression. Although further studies will be required to test the underlying molecular mechanisms involved in the relationship between these genes with XBP1, these studies identify a novel repressive role of XBP1 during the UPR.
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Affiliation(s)
- Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416, Gdansk, Poland
| | - Aleksandra Sobolewska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416, Gdansk, Poland
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Aleksandra Cabaj
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - David K Crossman
- Department of Genetics, Heflin Center for Genomic Science, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Jarosław Króliczewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416, Gdansk, Poland
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416, Gdansk, Poland
| | - Michał Dąbrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Hallera 107, 80-416, Gdansk, Poland.
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3
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Mioduchowska M, Nitkiewicz B, Roszkowska M, Kačarević U, Madanecki P, Pinceel T, Namiotko T, Gołdyn B, Kaczmarek Ł. Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades? Genome 2021; 64:951-958. [PMID: 34015229 DOI: 10.1139/gen-2020-0036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e., a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in previous studies on the microbial community of tardigrades, and Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.
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Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.,Department of Marine Plankton Research, Institute of Oceanography, University of Gdansk, Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland; Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Bartosz Nitkiewicz
- Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury, M. Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Milena Roszkowska
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.,Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Uroš Kačarević
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdansk, J. Hallera 107, 80-416 Gdansk, Poland
| | - Tom Pinceel
- Animal Ecology, Global Change and Sustainable Development, KU Leuven, Charles Deberiotstraat 32, 3000 Leuven, Belgium.,Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Tadeusz Namiotko
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Bartłomiej Gołdyn
- Department of General Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
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4
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Mioduchowska M, Zając K, Bartoszek K, Madanecki P, Kur J, Zając T. 16S rRNA
gene‐based metagenomic analysis of the gut microbial community associated with the DUI species
Unio crassus
(Bivalvia: Unionidae). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Monika Mioduchowska
- Department of Genetics and Biosystematics Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Katarzyna Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
| | - Krzysztof Bartoszek
- Department of Computer and Information Science Division of Statistics and Machine Learning Linköping University Linköping Sweden
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany Faculty of Pharmacy Medical University of Gdańsk Gdańsk Poland
| | | | - Tadeusz Zając
- Institute of Nature Conservation Polish Academy of Sciences Kraków Poland
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5
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Gebert M, Bartoszewska S, Janaszak-Jasiecka A, Moszyńska A, Cabaj A, Króliczewski J, Madanecki P, Ochocka RJ, Crossman DK, Collawn JF, Bartoszewski R. PIWI proteins contribute to apoptosis during the UPR in human airway epithelial cells. Sci Rep 2018; 8:16431. [PMID: 30401887 PMCID: PMC6219583 DOI: 10.1038/s41598-018-34861-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/27/2018] [Indexed: 01/13/2023] Open
Abstract
Small noncoding microRNAs (miRNAs) post-transcriptionally regulate a large portion of the human transcriptome. miRNAs have been shown to play an important role in the unfolded protein response (UPR), a cellular adaptive mechanism that is important in alleviating endoplasmic reticulum (ER) stress and promoting cell recovery. Another class of small noncoding RNAs, the Piwi-interacting RNAs (piRNAs) together with PIWI proteins, was originally shown to play a role as repressors of germline transposable elements. More recent studies, however, indicate that P-element induced WImpy proteins (PIWI proteins) and piRNAs also regulate mRNA levels in somatic tissues. Using genome-wide small RNA next generation sequencing, cell viability assays, and caspase activity assays in human airway epithelial cells, we demonstrate that ER stress specifically up-regulates total piRNA expression profiles, and these changes correlate with UPR-induced apoptosis as shown by up-regulation of two pro-apoptotic factor mRNAs, CHOP and NOXA. Furthermore, siRNA knockdown of PIWIL2 and PIWIL4, two proteins involved in piRNA function, attenuates UPR-related cell death, inhibits piRNA expression, and inhibits the up-regulation of CHOP and NOXA mRNA expression. Hence, we provide evidence that PIWIL2 and PIWIL4 proteins, and potentially the up-regulated piRNAs, constitute a novel epigenetic mechanism that control cellular fate during the UPR.
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Affiliation(s)
- Magdalena Gebert
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Anna Janaszak-Jasiecka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Adrianna Moszyńska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Aleksandra Cabaj
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Króliczewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Renata J Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - David K Crossman
- Department of Genetics, Heflin Center for Genomic Science, University of Alabama at Birmingham, Birmingham, USA
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland.
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6
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Mieczkowska A, Schumacher A, Filipowicz N, Wardowska A, Zieliński M, Madanecki P, Nowicka E, Langa P, Deptuła M, Zieliński J, Kondej K, Renkielska A, Buckley PG, Crossman DK, Crowley MR, Czupryn A, Mucha P, Sachadyn P, Janus Ł, Skowron P, Rodziewicz-Motowidło S, Cichorek M, Pikuła M, Piotrowski A. Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells. Sci Rep 2018; 8:11339. [PMID: 30054533 PMCID: PMC6063933 DOI: 10.1038/s41598-018-29477-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Adipose-derived stem cells (ASCs) have become an important research model in regenerative medicine. However, there are controversies regarding the impact of prolonged cell culture on the ASCs phenotype and their differentiation potential. Hence, we studied 10 clinical ASCs replicates from plastic and oncological surgery patients, in six-passage FBS supplemented cultures. We quantified basic mesenchymal cell surface marker transcripts and the encoded proteins after each passage. In parallel, we investigated the differentiation potential of ASCs into chondrocytes, osteocytes and adipocytes. We further determined the effects of FBS supplementation and subsequent deprivation on the whole transcriptome by comprehensive mRNA and miRNA sequencing. Our results show that ASCs maintain differentiation potential and consistent profile of key mesenchymal markers, with apparent expression of distinct isoforms, in long-term cultures. No significant differences were observed between plastic and oncological surgery cohorts. ASCs in FBS supplemented primary cultures are almost committed to mesenchymal lineages as they express key epithelial-mesenchymal transition genes including early mesenchymal markers. Furthermore, combined mRNA/miRNA expression profiling strongly supports a modulatory role for the miR-30 family in the commitment process to mesenchymal lineages. Finally, we propose improvements to existing qPCR based assays that address alternative isoform expression of mesenchymal markers.
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Affiliation(s)
| | - Adriana Schumacher
- Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | | | - Anna Wardowska
- Department of Clinical Immunology and Transplantology, Medical University of Gdansk, Gdansk, Poland
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Zieliński
- Department of Clinical Immunology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Nowicka
- Department of Clinical Anatomy, Medical University of Gdansk, Gdansk, Poland
| | - Paulina Langa
- Department of Clinical Immunology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Milena Deptuła
- Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Zieliński
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Karolina Kondej
- Department of Plastic Surgery, Medical University of Gdansk, Gdansk, Poland
| | - Alicja Renkielska
- Department of Plastic Surgery, Medical University of Gdansk, Gdansk, Poland
| | | | - David K Crossman
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael R Crowley
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Artur Czupryn
- Laboratory of Neurobiology, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Piotr Mucha
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Gdansk University of Technology, Gdansk, Poland
| | | | - Piotr Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | | | - Mirosława Cichorek
- Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Michał Pikuła
- Department of Clinical Immunology and Transplantology, Medical University of Gdansk, Gdansk, Poland.
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland.
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7
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Madanecki P, Bałut M, Buckley PG, Ochocka JR, Bartoszewski R, Crossman DK, Messiaen LM, Piotrowski A. High-Throughput Tabular Data Processor - Platform independent graphical tool for processing large data sets. PLoS One 2018; 13:e0192858. [PMID: 29432475 PMCID: PMC5809091 DOI: 10.1371/journal.pone.0192858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks. The program is intended to aid global, real-time processing of large data sets using a graphical user interface (GUI). Therefore, no prior expertise in programming, regular expression, or command line usage is required of the user. Additionally, no a priori assumptions are imposed on the internal file composition. We demonstrate the flexibility and potential of HTDP in real-life research tasks including microarray and massively parallel sequencing, i.e. identification of disease predisposing variants in the next generation sequencing data as well as comprehensive concurrent analysis of microarray and sequencing results. We also show the utility of HTDP in technical tasks including data merge, reduction and filtering with external criteria files. HTDP was developed to address functionality that is missing or rudimentary in other GUI software for processing character-delimited column data from high-throughput technologies. Flexibility, in terms of input file handling, provides long term potential functionality in high-throughput analysis pipelines, as the program is not limited by the currently existing applications and data formats. HTDP is available as the Open Source software (https://github.com/pmadanecki/htdp).
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Affiliation(s)
- Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
- * E-mail: (PM); (AP)
| | - Magdalena Bałut
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | | | - J. Renata Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - David K. Crossman
- Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ludwine M. Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
- * E-mail: (PM); (AP)
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8
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Górnikiewicz B, Ronowicz A, Madanecki P, Sachadyn P. Genome-wide DNA methylation profiling of the regenerative MRL/MpJ mouse and two normal strains. Epigenomics 2017; 9:1105-1122. [DOI: 10.2217/epi-2017-0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: We aimed to identify the pivotal differences in the DNA methylation profiles between the regeneration capable MRL/MpJ mouse and reference mouse strains. Materials & methods: Global DNA methylation profiling was performed in ear pinnae, bone marrow, spleen, liver and heart from uninjured adult females of the MRL/MpJ and C57BL/6J and BALB/c. Results & conclusion: A number of differentially methylated regions (DMRs) distinguishing between the MRL/MpJ mouse and both references were identified. In the ear pinnae, the DMRs were enriched in genes associated with development, inflammation and apoptosis, and in binding sites of transcriptional modulator Smad1. Several DMRs overlapped previously mapped quantitative trait loci of regenerative capability. The results suggest potential epigenetic determinants of regenerative phenomenon.
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Affiliation(s)
- Bartosz Górnikiewicz
- Department of Molecular Biotechnology & Microbiology, Gdańsk University of Technology, Gdańsk, Poland
| | - Anna Ronowicz
- Department of Biology & Pharmaceutical Botany of Medical University of Gdańsk, Gdańsk, Poland
| | - Piotr Madanecki
- Department of Biology & Pharmaceutical Botany of Medical University of Gdańsk, Gdańsk, Poland
| | - Paweł Sachadyn
- Department of Molecular Biotechnology & Microbiology, Gdańsk University of Technology, Gdańsk, Poland
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9
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Ronowicz A, Janaszak-Jasiecka A, Skokowski J, Madanecki P, Bartoszewski R, Bałut M, Seroczyńska B, Kochan K, Bogdan A, Butkus M, Pęksa R, Ratajska M, Kuźniacka A, Wasąg B, Gucwa M, Krzyżanowski M, Jaśkiewicz J, Jankowski Z, Forsberg L, Ochocka JR, Limon J, Crowley MR, Buckley PG, Messiaen L, Dumanski JP, Piotrowski A. Concurrent DNA Copy-Number Alterations and Mutations in Genes Related to Maintenance of Genome Stability in Uninvolved Mammary Glandular Tissue from Breast Cancer Patients. Hum Mutat 2015. [PMID: 26219265 DOI: 10.1002/humu.22845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Somatic mosaicism for DNA copy-number alterations (SMC-CNAs) is defined as gain or loss of chromosomal segments in somatic cells within a single organism. As cells harboring SMC-CNAs can undergo clonal expansion, it has been proposed that SMC-CNAs may contribute to the predisposition of these cells to genetic disease including cancer. Herein, the gross genomic alterations (>500 kbp) were characterized in uninvolved mammary glandular tissue from 59 breast cancer patients and matched samples of primary tumors and lymph node metastases. Array-based comparative genomic hybridization showed 10% (6/59) of patients harbored one to 359 large SMC-CNAs (mean: 1,328 kbp; median: 961 kbp) in a substantial portion of glandular tissue cells, distal from the primary tumor site. SMC-CNAs were partially recurrent in tumors, albeit with considerable contribution of stochastic SMC-CNAs indicating genomic destabilization. Targeted resequencing of 301 known predisposition and somatic driver loci revealed mutations and rare variants in genes related to maintenance of genomic integrity: BRCA1 (p.Gln1756Profs*74, p.Arg504Cys), BRCA2 (p.Asn3124Ile), NCOR1 (p.Pro1570Glnfs*45), PALB2 (p.Ser500Pro), and TP53 (p.Arg306*). Co-occurrence of gross SMC-CNAs along with point mutations or rare variants in genes responsible for safeguarding genomic integrity highlights the temporal and spatial neoplastic potential of uninvolved glandular tissue in breast cancer patients.
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Affiliation(s)
- Anna Ronowicz
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | | | - Jarosław Skokowski
- The Central Bank of Tissues and Genetic Specimens, Medical University of Gdansk, Gdansk, Poland.,Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | | | - Magdalena Bałut
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Barbara Seroczyńska
- The Central Bank of Tissues and Genetic Specimens, Medical University of Gdansk, Gdansk, Poland
| | - Kinga Kochan
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Adam Bogdan
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasąg
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Krzyżanowski
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Janusz Jaśkiewicz
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Zbigniew Jankowski
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Lars Forsberg
- Department of Immunology, Genetics and Pathology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - J Renata Ochocka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Crowley
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology and SciLifeLab, Uppsala University, Uppsala, Sweden
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Madanecki P, Nozell S, Ochocka R, Collawn JF, Bartoszewski R. RNAdigest: a web-based tool for the analysis and prediction of structure-specific RNAse digestion results. PLoS One 2014; 9:e96759. [PMID: 24801507 PMCID: PMC4011862 DOI: 10.1371/journal.pone.0096759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/10/2014] [Indexed: 11/19/2022] Open
Abstract
Despite recent developments in analyzing RNA secondary structures, relatively few RNA structures have been determined. To date, many investigators have relied on the traditional method of using structure-specific RNAse enzymes to probe RNA secondary structures. However, if these data were combined with novel computational approaches, investigators would have an informative and valuable tool for RNA structural analysis. To this end, we created the web server “RNAdigest.” RNAdigest uses mfold RNA structural models in order to predict the results of RNAse digestion experiments. Furthermore, RNAdigest also utilizes both RNA sequence and the experimental digestion patterns to formulate the constraints for predicting secondary structures of the RNA. Thus, RNAdigest allows for the structural interpretation of RNAse digestion experiments. Overall, RNAdigest simplifies RNAse digestion result analyses while allowing for the identification of unique fragments. These unique fragments can then be used for testing predicted mfold structures and for designing structural-specific DNA/RNA probes.
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Affiliation(s)
- Piotr Madanecki
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Susan Nozell
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Renata Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - James F. Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
- * E-mail:
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11
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Piotrowski A, Xie J, Liu YF, Poplawski AB, Gomes AR, Madanecki P, Fu C, Crowley MR, Crossman DK, Armstrong L, Babovic-Vuksanovic D, Bergner A, Blakeley JO, Blumenthal AL, Daniels MS, Feit H, Gardner K, Hurst S, Kobelka C, Lee C, Nagy R, Rauen KA, Slopis JM, Suwannarat P, Westman JA, Zanko A, Korf BR, Messiaen LM. Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas. Nat Genet 2013; 46:182-7. [PMID: 24362817 DOI: 10.1038/ng.2855] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 12/02/2013] [Indexed: 12/18/2022]
Abstract
Constitutional SMARCB1 mutations at 22q11.23 have been found in ∼50% of familial and <10% of sporadic schwannomatosis cases. We sequenced highly conserved regions along 22q from eight individuals with schwannomatosis whose schwannomas involved somatic loss of one copy of 22q, encompassing SMARCB1 and NF2, with a different somatic mutation of the other NF2 allele in every schwannoma but no mutation of the remaining SMARCB1 allele in blood and tumor samples. LZTR1 germline mutations were identified in seven of the eight cases. LZTR1 sequencing in 12 further cases with the same molecular signature identified 9 additional germline mutations. Loss of heterozygosity with retention of an LZTR1 mutation was present in all 25 schwannomas studied. Mutations segregated with disease in all available affected first-degree relatives, although four asymptomatic parents also carried an LZTR1 mutation. Our findings identify LZTR1 as a gene predisposing to an autosomal dominant inherited disorder of multiple schwannomas in ∼80% of 22q-related schwannomatosis cases lacking mutation in SMARCB1.
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Affiliation(s)
- Arkadiusz Piotrowski
- 1] Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA. [2] Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland. [3]
| | - Jing Xie
- 1] Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA. [2]
| | - Ying F Liu
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrzej B Poplawski
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alicia R Gomes
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Chuanhua Fu
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael R Crowley
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David K Crossman
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Linlea Armstrong
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Amanda Bergner
- Johns Hopkins Comprehensive Neurofibromatosis Center, Baltimore, Maryland, USA
| | - Jaishri O Blakeley
- Johns Hopkins Comprehensive Neurofibromatosis Center, Baltimore, Maryland, USA
| | | | - Molly S Daniels
- Clinical Cancer Genetics Program, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Howard Feit
- Department of Neurology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Kathy Gardner
- Department of Neurology, Veterans Administration Hospital of Pittsburgh and University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Christine Kobelka
- Kaiser Permanente Genetics Northern California, San Francisco, California, USA
| | - Chung Lee
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Rebecca Nagy
- Department of Internal Medicine, Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Katherine A Rauen
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, San Francisco, California, USA
| | - John M Slopis
- Department of Neuro-Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Pim Suwannarat
- Kaiser Permanente Genetics Northern California, San Francisco, California, USA
| | - Judith A Westman
- Department of Internal Medicine, Division of Human Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Andrea Zanko
- Department of Pediatrics, Division of Medical Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Bruce R Korf
- 1] Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA. [2] Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ludwine M Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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12
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Górnikiewicz B, Ronowicz A, Podolak J, Madanecki P, Stanisławska-Sachadyn A, Sachadyn P. Epigenetic basis of regeneration: analysis of genomic DNA methylation profiles in the MRL/MpJ mouse. DNA Res 2013; 20:605-21. [PMID: 23929942 PMCID: PMC3859327 DOI: 10.1093/dnares/dst034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Epigenetic regulation plays essential role in cell differentiation and dedifferentiation, which are the intrinsic processes involved in regeneration. To investigate the epigenetic basis of regeneration capacity, we choose DNA methylation as one of the most important epigenetic mechanisms and the MRL/MpJ mouse as a model of mammalian regeneration known to exhibit enhanced regeneration response in different organs. We report the comparative analysis of genomic DNA methylation profiles of the MRL/MpJ and the control C57BL/6J mouse. Methylated DNA immunoprecipitation followed by microarray analysis using the Nimblegen '3 × 720 K CpG Island Plus RefSeq Promoter' platform was applied in order to carry out genome-wide DNA methylation profiling covering 20 404 promoter regions. We identified hundreds of hypo- and hypermethylated genes and CpG islands in the heart, liver, and spleen, and 37 of them in the three tissues. Decreased inter-tissue diversification and the shift of DNA methylation balance upstream the genes distinguish the genomic methylation patterns of the MRL/MpJ mouse from the C57BL/6J. Homeobox genes and a number of other genes involved in embryonic morphogenesis are significantly overrepresented among the genes hypomethylated in the MRL/MpJ mouse. These findings indicate that epigenetic patterning might be a likely molecular basis of regeneration capability in the MRL/MpJ mouse.
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13
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Filipowicz N, Madanecki P, Gołebiowski M, Stepnowski P, Ochocka JR. HS-SPME/GC analysis reveals the population variability of terpene contents in Juniperus communis needles. Chem Biodivers 2010; 6:2290-301. [PMID: 20020463 DOI: 10.1002/cbdv.200900070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Juniperus communis var. communis L. is an aromatic plant - typical boreal element of flora. In the extensive literature concerning J. communis, there is much data on the composition and the content of essential oil of needles and coneberries, but a detailed analysis of terpene distribution within and between populations is missing. A representative pool of 74 J. communis individuals originating from ten populations of Northern Poland was investigated in order to evaluate the intra- and interpopulational variability of the terpene pattern. Headspace solid-phase microextraction (HS-SPME) coupled with GC/MS and GC/FID was applied in achiral and enantioselective analysis. The majority of the samples (85%), despite different origin, were similar in the terpene pattern. High diversity of terpenes was observed within the populations and low diversity between them. High variation of enantiomeric composition was in accordance with large variation of individual compounds in general (achiral analysis). J. communis samples from Northern Poland could be distinguished by the alpha-pinene/sabinene ratio, and they were divided into three chemical races.
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Affiliation(s)
- Natalia Filipowicz
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, PL-80416 Gdańsk, Poland.
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