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Stachowiak M, Nowacka-Woszuk J, Szabelska-Beresewicz A, Zyprych-Walczak J, Krzeminska P, Sosinski O, Nowak T, Switonski M. A massive alteration of gene expression in undescended testicles of dogs and the association of KAT6A variants with cryptorchidism. Proc Natl Acad Sci U S A 2024; 121:e2312724121. [PMID: 38315849 PMCID: PMC10873591 DOI: 10.1073/pnas.2312724121] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
Cryptorchidism is the most common form of disorder of sex development in male dogs, but its hereditary predisposition is poorly elucidated. The gonadal transcriptome of nine unilaterally cryptorchid dogs and seven control dogs was analyzed using RNA-seq. Comparison between the scrotal and inguinal gonads of unilateral cryptorchid dogs revealed 8,028 differentially expressed genes (DEGs) (3,377 up-regulated and 4,651 down-regulated). A similar number of DEGs (7,619) was found by comparing the undescended testicles with the descended testicles of the control dogs. The methylation status of the selected DEGs was also analyzed, with three out of nine studied DEGs showing altered patterns. Bioinformatic analysis of the cDNA sequences revealed 20,366 SNP variants, six of which showed significant differences in allelic counts between cryptorchid and control dogs. Validation studies in larger cohorts of cryptorchid (n = 122) and control (n = 173) dogs showed that the TT genotype (rs850666472, p.Ala1230Val) and the AA genotype in 3'UTR (16:23716202G>A) in KATA6, responsible for acetylation of lysine 9 in histone H3, are associated with cryptorchidism (P = 0.0383). Both the transcript level of KAT6A and H3K9 acetylation were lower in undescended testes, and additionally, the acetylation depended on the genotypes in exon 17 and the 3'UTR. Our study showed that the massive alteration of the transcriptome in undescended testicles is not caused by germinal DNA variants in DEG regulatory sequences but is partly associated with an aberrant DNA methylation and H3K9 acetylation patterns. Moreover, variants of KAT6A can be considered markers associated with the risk of this disorder.
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Affiliation(s)
- Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Paulina Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704Poznan, Poland
| | - Oskar Sosinski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Tomasz Nowak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637Poznan, Poland
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2
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Szabelska-Beresewicz A, Zyprych-Walczak J, Siatkowski I, Okoniewski M. Ambiguous genes due to aligners and their impact on RNA-seq data analysis. Sci Rep 2023; 13:21770. [PMID: 38066001 PMCID: PMC10709571 DOI: 10.1038/s41598-023-41085-6] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/22/2023] [Indexed: 12/18/2023] Open
Abstract
The main scope of the study is ambiguous genes, i.e. genes whose expression is difficult to estimate from the data produced by next-generation sequencing technologies. We focused on the RNA sequencing (RNA-Seq) type of experiment performed on the Illumina platform. It is crucial to identify such genes and understand the cause of their difficulty, as these genes may be involved in some diseases. By giving misleading results, they could contribute to a misunderstanding of the cause of certain diseases, which could lead to inappropriate treatment. We thought that the ambiguous genes would be difficult to map because of their complex structure. So we looked at RNA-seq analysis using different mappers to find genes that would have different measurements from the aligners. We were able to identify such genes using a generalized linear model with two factors: mappers and groups introduced by the experiment. A large proportion of ambiguous genes are pseudogenes. High sequence similarity of pseudogenes to functional genes may indicate problems in alignment procedures. In addition, predictive analysis verified the performance of difficult genes in classification. The effectiveness of classifying samples into specific groups was compared, including the expression of difficult and not difficult genes as covariates. In almost all cases considered, ambiguous genes have less predictive power.
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Affiliation(s)
- Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637, Poznan, Poland
| | - Michał Okoniewski
- Scientific IT Services, ETH Zurich, Weinbergstrasse 11, 8092, Zurich, Switzerland
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Gawlik-Dziki U, Wrzesińska-Krupa B, Nowak R, Pietrzak W, Zyprych-Walczak J, Obrępalska-Stęplowska A. Herbicide resistance status impacts the profile of non-anthocyanin polyphenolics and some phytomedical properties of edible cornflower (Centaurea cyanus L.) flowers. Sci Rep 2023; 13:11538. [PMID: 37460793 DOI: 10.1038/s41598-023-38520-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
To ensure sufficient food supply worldwide, plants are treated with pesticides to provide protection against pathogens and pests. Herbicides are the most commonly utilised pesticides, used to reduce the growth of weeds. However, their long-term use has resulted in the emergence of herbicide-resistant biotypes in many weed species. Cornflower (Centaurea cyanus L., Asteraceae) is one of these plants, whose biotypes resistant to herbicides from the group of acetolactate synthase (ALS) inhibitors have begun to emerge in recent years. Some plants, although undesirable in crops and considered as weeds, are of great importance in phytomedicine and food production, and characterised by a high content of health-promoting substances, including antioxidants. Our study aimed to investigate how the acquisition of herbicide resistance affects the health-promoting properties of plants on the example of cornflower, as well as how they are affected by herbicide treatment. To this end, we analysed non-anthocyanin polyphenols and antioxidant capacity in flowers of C. cyanus from herbicide-resistant and susceptible biotypes. Our results indicated significant compositional changes associated with an increase in the content of substances and activities that have health-promoting properties. High antioxidant activity and higher total phenolic and flavonoid compounds as well as reducing power were observed in resistant biotypes. The latter one increased additionally after herbicide treatment which might also suggest their role in the resistance acquisition mechanism. Overall, these results show that the herbicide resistance development, although unfavourable to crop production, may paradoxically have very positive effects for medicinal plants such as cornflower.
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Affiliation(s)
- Urszula Gawlik-Dziki
- Department of Biochemistry and Food Chemistry, University of Life Sciences, 8 Skromna St, 20-704, Lublin, Poland.
| | - Barbara Wrzesińska-Krupa
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection - National Research Institute, 20 Wegorka St, 60-318, Poznań, Poland
| | - Renata Nowak
- Department of Pharmaceutical Botany, Medical University of Lublin, Chodźki 1 Str., 20-093, Lublin, Poland
| | - Wioletta Pietrzak
- Department of Pharmaceutical Botany, Medical University of Lublin, Chodźki 1 Str., 20-093, Lublin, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, 28 Wojska Polskiego St, 60-637, Poznań, Poland
| | - Aleksandra Obrępalska-Stęplowska
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection - National Research Institute, 20 Wegorka St, 60-318, Poznań, Poland.
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Wertheim-Tysarowska K, Osipowicz K, Gielniewski B, Wojtaś B, Szabelska-Beręsewicz A, Zyprych-Walczak J, Mika A, Tysarowski A, Duk K, Rygiel AM, Niepokój K, Woźniak K, Kowalewski C, Wierzba J, Jezela-Stanek A. The Epidermal Transcriptome Analysis of a Novel c.639_642dup LORICRIN Variant-Delineation of the Loricrin Keratoderma Pathology. Int J Mol Sci 2023; 24:ijms24119459. [PMID: 37298411 DOI: 10.3390/ijms24119459] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Loricrin keratoderma (LK) is a rare autosomal dominant genodermatosis caused by LORICRIN gene mutations. The pathogenesis of the disease is not yet fully understood. So far, only 10 pathogenic variants in LORICRIN have been described, with all of them but one being deletions or insertions. The significance of rare nonsense variants remains unclear. Furthermore, no data regarding the RNA expression in affected patients are available. The aim of this study is to describe the two variants in the LORICRIN gene found in two distinct families: the novel pathogenic variant c.639_642dup and a rare c.10C > T (p.Gln4Ter) of unknown significance. We also present the results of the transcriptome analysis of the lesional loricrin keratoderma epidermis of a patient with c.639_642dup. We show that in the LK lesion, the genes associated with epidermis development and keratocyte differentiation are upregulated, while genes engaged in cell adhesion, differentiation developmental processes, ion homeostasis and transport, signaling and cell communication are downregulated. In the context of the p.Gln4Ter clinical significance evaluation, we provide data indicating that LORICRIN haploinsufficiency has no skin consequences. Our results give further insight into the pathogenesis of LK, which may have therapeutic implications in the future and important significance in the context of genetic counseling.
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Affiliation(s)
| | - Katarzyna Osipowicz
- Department of Dermatology, Immunodermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland
| | - Bartłomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Bartosz Wojtaś
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Alicja Szabelska-Beręsewicz
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Adriana Mika
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Andrzej Tysarowski
- Molecular and Translational Oncology Department and Cancer Molecular and Genetic Diagnostics Department, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Katarzyna Duk
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | | | - Katarzyna Niepokój
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Katarzyna Woźniak
- Department of Dermatology, Immunodermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland
| | - Cezary Kowalewski
- Department of Dermatology, Immunodermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland
| | - Jolanta Wierzba
- Department of Paediatrics, Haematology and Oncology, Department of General Nursery, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Aleksandra Jezela-Stanek
- Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland
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5
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Nowacka-Woszuk J, Stachowiak M, Szczerbal I, Szydlowski M, Szabelska-Beresewicz A, Zyprych-Walczak J, Krzeminska P, Nowak T, Lukomska A, Ligocka Z, Biezynski J, Dzimira S, Nizanski W, Switonski M. Whole genome sequencing identifies a missense polymorphism in PADI6 associated with testicular/ovotesticular XX disorder of sex development in dogs. Genomics 2022; 114:110389. [PMID: 35597501 DOI: 10.1016/j.ygeno.2022.110389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/07/2022] [Accepted: 05/11/2022] [Indexed: 12/17/2022]
Abstract
Disorders of sex development (DSDs) are congenital malformations defined as discrepancies between sex chromosomes and phenotypical sex. Testicular or ovotesticular XX DSDs are frequently observed in female dogs, while monogenic XY DSDs are less frequent. Here, we applied whole genome sequencing (WGS) to search for causative mutations in XX DSD females in French Bulldogs (FB) and American Staffordshire Terries (AST) and in XY DSD Yorkshire Terries (YT). The WGS results were validated by Sanger sequencing and ddPCR. It was shown that a missense SNP of the PADI6 gene, is significantly associated with the XX DSD (SRY-negative) phenotype in AST (P = 0.0051) and FB (P = 0.0306). On the contrary, we did not find any associated variant with XY DSD in YTs. Our study suggests that the genetic background of the XX DSD may be more complex and breed-specific.
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Affiliation(s)
- Joanna Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Maciej Szydlowski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Alicja Szabelska-Beresewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznan, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Wojska Polskiego 28, 60-637 Poznan, Poland
| | - Paulina Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Tomasz Nowak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Anna Lukomska
- Department of Preclinical Sciences and Infectious Diseases, Poznan University of Life Sciences, Wolynska 35, 60-637 Poznan, Poland
| | - Zuzanna Ligocka
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 49, 50-366 Wroclaw, Poland
| | - Janusz Biezynski
- Department of Surgery, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 51, 50-366 Wroclaw, Poland
| | - Stanislaw Dzimira
- Department of Pathology, Wroclaw University of Environmental and Life Sciences, C. K. Norwida 31, 50-375 Wroclaw, Poland
| | - Wojciech Nizanski
- Department of Reproduction and Clinic of Farm Animals, Wroclaw University of Environmental and Life Sciences, Pl. Grunwaldzki 49, 50-366 Wroclaw, Poland
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland.
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Lütge A, Zyprych-Walczak J, Brykczynska Kunzmann U, Crowell HL, Calini D, Malhotra D, Soneson C, Robinson MD. CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data. Life Sci Alliance 2021; 4:e202001004. [PMID: 33758076 PMCID: PMC7994321 DOI: 10.26508/lsa.202001004] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 12/05/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
A key challenge in single-cell RNA-sequencing (scRNA-seq) data analysis is batch effects that can obscure the biological signal of interest. Although there are various tools and methods to correct for batch effects, their performance can vary. Therefore, it is important to understand how batch effects manifest to adjust for them. Here, we systematically explore batch effects across various scRNA-seq datasets according to magnitude, cell type specificity, and complexity. We developed a cell-specific mixing score (cms) that quantifies mixing of cells from multiple batches. By considering distance distributions, the score is able to detect local batch bias as well as differentiate between unbalanced batches and systematic differences between cells of the same cell type. We compare metrics in scRNA-seq data using real and synthetic datasets and whereas these metrics target the same question and are used interchangeably, we find differences in scalability, sensitivity, and ability to handle differentially abundant cell types. We find that cell-specific metrics outperform cell type-specific and global metrics and recommend them for both method benchmarks and batch exploration.
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Affiliation(s)
- Almut Lütge
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Poznań, Poland
| | | | - Helena L Crowell
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Daniela Calini
- F. Hoffmann-LaRoche Ltd, Pharma Research and Early Development, Neuroscience, Ophthalmologyand Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Dheeraj Malhotra
- F. Hoffmann-LaRoche Ltd, Pharma Research and Early Development, Neuroscience, Ophthalmologyand Rare Diseases, Roche Innovation Center Basel, Basel, Switzerland
| | - Charlotte Soneson
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
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Szenajch J, Szabelska-Beręsewicz A, Świercz A, Zyprych-Walczak J, Siatkowski I, Góralski M, Synowiec A, Handschuh L. Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. Int J Mol Sci 2020; 21:E9218. [PMID: 33287223 PMCID: PMC7730278 DOI: 10.3390/ijms21239218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
Resistance to anti-cancer drugs is the main challenge in oncology. In pre-clinical studies, established cancer cell lines are primary tools in deciphering molecular mechanisms of this phenomenon. In this study, we proposed a new, transcriptome-focused approach, utilizing a model of isogenic cancer cell lines with gradually changing resistance. We analyzed trends in gene expression in the aim to find out a scaffold of resistance development process. The ovarian cancer cell line A2780 was treated with stepwise increased concentrations of paclitaxel (PTX) to generate a series of drug resistant sublines. To monitor transcriptome changes we submitted them to mRNA-sequencing, followed by the identification of differentially expressed genes (DEGs), principal component analysis (PCA), and hierarchical clustering. Functional interactions of proteins, encoded by DEGs, were analyzed by building protein-protein interaction (PPI) networks. We obtained human ovarian cancer cell lines with gradually developed resistance to PTX and collateral sensitivity to cisplatin (CDDP) (inverse resistance). In their transcriptomes, we identified two groups of DEGs: (1) With fluctuations in expression in the course of resistance acquiring; and (2) with a consistently changed expression at each stage of resistance development, constituting a scaffold of the process. In the scaffold PPI network, the cell cycle regulator-polo-like kinase 2 (PLK2); proteins belonging to the tumor necrosis factor (TNF) ligand and receptor family, as well as to the ephrin receptor family were found, and moreover, proteins linked to osteo- and chondrogenesis and the nervous system development. Our cellular model of drug resistance allowed for keeping track of trends in gene expression and studying this phenomenon as a process of evolution, reflected by global transcriptome remodeling. This approach enabled us to explore novel candidate genes and surmise that abrogation of the osteomimic phenotype in ovarian cancer cells might occur during the development of inverse resistance between PTX and CDDP.
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Affiliation(s)
- Jolanta Szenajch
- Laboratory for Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland;
| | - Alicja Szabelska-Beręsewicz
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland; (A.S.-B.); (J.Z.-W.); (I.S.)
| | - Aleksandra Świercz
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, 61-704 Poznań, Poland; (A.Ś.); (M.G.); (L.H.)
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznań, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland; (A.S.-B.); (J.Z.-W.); (I.S.)
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland; (A.S.-B.); (J.Z.-W.); (I.S.)
| | - Michał Góralski
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, 61-704 Poznań, Poland; (A.Ś.); (M.G.); (L.H.)
| | - Agnieszka Synowiec
- Laboratory for Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland;
| | - Luiza Handschuh
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Science, 61-704 Poznań, Poland; (A.Ś.); (M.G.); (L.H.)
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8
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Weigt D, Niemann J, Siatkowski I, Zyprych-Walczak J, Olejnik P, Kurasiak-Popowska D. Effect of Zearalenone and Hormone Regulators on Microspore Embryogenesis in Anther Culture of Wheat. Plants (Basel) 2019; 8:plants8110487. [PMID: 31717618 PMCID: PMC6918171 DOI: 10.3390/plants8110487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/02/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022]
Abstract
The purpose of this work was to assess the impact of zearalenone (ZEN) and selected hormone regulators on the effectiveness of microspore embryogenesis in anther culture of wheat. The plant material comprised F1 hybrids of winter and spring wheat. Six combinations of media inducing microspore proliferation and formation of embryogenic structures were investigated: two combinations of growth regulators (D - 2,4-D + dicamba, K - 2,4-D + kinetin), each with three ZEN concentrations (0 mL/L, 0.1 mL/L, 0.2 mL/L). A significant increase in microspore embryogenesis effectiveness on media with the addition of ZEN was observed both at the stages of its induction and the formation of green plants in some genotypes. In case of both combinations of growth regulators, an increased concentration of ZEN resulted in more effective induction of microspore embryogenesis. The most effective induction medium was the D medium supplemented with 0.2 mL/L ZEN. As a result of the use of zearalenone together with two combinations of growth regulators, all genotypes tested produced androgenic structures, which indicates the breakdown of genotypic recalcitrant in the analysed hybrids. In addition, green plants were obtained from 18 out of 19 tested hybrids. The addition of ZEN to the medium did not affect the number of regenerated albino plants nor the number of spontaneous genome doublings proportion.
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Affiliation(s)
- Dorota Weigt
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, 11 Dojazd St., 60–632 Poznań, Poland
| | - Janetta Niemann
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, 11 Dojazd St., 60–632 Poznań, Poland
- Correspondence:
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 28 Wojska Polskiego St., 60–637 Poznań, Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 28 Wojska Polskiego St., 60–637 Poznań, Poland
| | - Przemysław Olejnik
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, 11 Dojazd St., 60–632 Poznań, Poland
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, 11 Dojazd St., 60–632 Poznań, Poland
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9
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Obrępalska-Stęplowska A, Zmienko A, Wrzesińska B, Goralski M, Figlerowicz M, Zyprych-Walczak J, Siatkowski I, Pospieszny H. The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA. Viruses 2018; 10:E449. [PMID: 30142955 PMCID: PMC6165542 DOI: 10.3390/v10090449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 01/22/2023] Open
Abstract
Peanut stunt virus (PSV) is a widespread disease infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.
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Affiliation(s)
- Aleksandra Obrępalska-Stęplowska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Barbara Wrzesińska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Michal Goralski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Henryk Pospieszny
- Department of Virology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
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10
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Leśniewska A, Zyprych-Walczak J, Szabelska-Beręsewicz A, Okoniewski MJ. Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures. Biol Direct 2018; 13:3. [PMID: 29467011 PMCID: PMC5822623 DOI: 10.1186/s13062-018-0205-x] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis and selection of genes used for classification. This paper aims in pointing out several factors that may influence the downstream machine learning analysis. In particular those factors are: type of the primary analysis, type of the classifier and increased correlation between the genes sharing a protein domain. They influence the analysis directly, but also interplay between them may be important. We have compiled the gene-domain database and used it for analysis to see the differences between the genes that share a domain versus the rest of the genes in the datasets. RESULTS The major findings are: pairs of genes that share a domain have an increased Spearman's correlation coefficients of counts; genes sharing a domain are expected to have a lower predictive power due to increased correlation. For most of the cases it can be seen with the higher number of misclassified samples; classifiers performance may vary depending on a method, still in most cases using genes sharing a domain in the training set results in a higher misclassification rate; increased correlation in genes sharing a domain results most often in worse performance of the classifiers regardless of the primary analysis tools used, even if the primary analysis alignment yield varies. CONCLUSIONS The effect of sharing a domain is likely more a results of real biological co-expression than just sequence similarity and artifacts of mapping and counting. Still, this is more difficult to conclude and needs further research. The effect is interesting itself, but we also point out some practical aspects in which it may influence the RNA sequencing analysis and RNA biomarker use. In particular it means that a gene signature biomarker set build out of RNA-sequencing results should be depleted for genes sharing common domains. It may cause to perform better when applying classification. REVIEWERS This article was reviewed by Dimitar Vassiliev and Susmita Datta.
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Affiliation(s)
- Anna Leśniewska
- Department of Computer Science, Poznan University of Technology, Piotrowo 2, Poznan, 60-965 Poland
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Poznan, 60-637 Poland
| | - Alicja Szabelska-Beręsewicz
- Department of Mathematical and Statistical Methods, Poznan University of Life Sciences, Poznan, 60-637 Poland
| | - Michal J. Okoniewski
- Scientific IT Services, ETH Zurich, Weinbergstrasse 11, Zürich, 8092 Switzerland
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11
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Różańska-Zawieja J, Szabelska-Beręsewicz A, Sobek Z, Nienartowicz-Zdrojewska A, Zyprych-Walczak J, Siatkowski I. The effect of population size of paternal
groups and herds on optimal estimation of the
heritability index for gestation length in cattle. Roczniki Naukowe Polskiego Towarzystwa Zootechnicznego 2017. [DOI: 10.5604/01.3001.0013.5268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Estimation of genetic parameters is a crucial element in the process of population improvement. In
the case of farm animals this process is based on a sample which is a subset of the whole population.
For this reason it is important to know the effect of the size of paternal groups and of the herd on the
accuracy of estimations of these parameters, particularly heritability. The aim of this study was to
show the effect of the population size of paternal groups and herds on the accuracy of estimation of
the heritability index (h2). The material for the analyses comprised data of Holstein-Friesian cattle
born in 2005-2010 and subject to use value assessment in Poland. The trait analysed was gestation
length. Calculations using a linear mixed model were performed using the R 3.1.3 platform. The
analyses showed that calculations concerning daughters in paternal groups are more accurate when
the daughters are in a smaller number of herds, but of greater size. An increase in the size of paternal
groups at the expense of their number does not have such a negative effect on the accuracy of the
estimate as in the case of a reduced number of small herds. Limiting the estimate to only the largest
herds reduces its accuracy.
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Affiliation(s)
- Jolanta Różańska-Zawieja
- Poznan University of Life Sciences Faculty of Veterinary Medicine and Animal Science Department of Genetics and Animal Breeding
| | | | - Zbigniew Sobek
- Poznan University of Life Sciences Department of Genetics and Animal Breeding
| | | | | | - Idzi Siatkowski
- Poznan University of Life Sciences Department of Mathematical and Statistical Methods
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12
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Uszczyńska B, Zyprych-Walczak J, Handschuh L, Szabelska A, Kaźmierczak M, Woronowicz W, Kozłowski P, Sikorski MM, Komarnicki M, Siatkowski I, Figlerowicz M. Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure. Int J Mol Med 2013; 32:668-84. [PMID: 23857190 DOI: 10.3892/ijmm.2013.1443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/28/2013] [Indexed: 11/06/2022] Open
Abstract
DNA microarrays, which are among the most popular genomic tools, are widely applied in biology and medicine. Boutique arrays, which are small, spotted, dedicated microarrays, constitute an inexpensive alternative to whole-genome screening methods. The data extracted from each microarray-based experiment must be transformed and processed prior to further analysis to eliminate any technical bias. The normalization of the data is the most crucial step of microarray data pre-processing and this process must be carefully considered as it has a profound effect on the results of the analysis. Several normalization algorithms have been developed and implemented in data analysis software packages. However, most of these methods were designed for whole-genome analysis. In this study, we tested 13 normalization strategies (ten for double-channel data and three for single-channel data) available on R Bioconductor and compared their effectiveness in the normalization of four boutique array datasets. The results revealed that boutique arrays can be successfully normalized using standard methods, but not every method is suitable for each dataset. We also suggest a universal seven-step workflow that can be applied for the selection of the optimal normalization procedure for any boutique array dataset. The described workflow enables the evaluation of the investigated normalization methods based on the bias and variance values for the control probes, a differential expression analysis and a receiver operating characteristic curve analysis. The analysis of each component results in a separate ranking of the normalization methods. A combination of the ranks obtained from all the normalization procedures facilitates the selection of the most appropriate normalization method for the studied dataset and determines which methods can be used interchangeably.
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Affiliation(s)
- Barbara Uszczyńska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
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Okoniewski MJ, Leśniewska A, Szabelska A, Zyprych-Walczak J, Ryan M, Wachtel M, Morzy T, Schäfer B, Schlapbach R. Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage. Nucleic Acids Res 2011; 40:e63. [PMID: 22210855 PMCID: PMC3351146 DOI: 10.1093/nar/gkr1249] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The informational content of RNA sequencing is currently far from being completely explored. Most of the analyses focus on processing tables of counts or finding isoform deconvolution via exon junctions. This article presents a comparison of several techniques that can be used to estimate differential expression of exons or small genomic regions of expression, based on their coverage function shapes. The problem is defined as finding the differentially expressed exons between two samples using local expression profile normalization and statistical measures to spot the differences between two profile shapes. Initial experiments have been done using synthetic data, and real data modified with synthetically created differential patterns. Then, 160 pipelines (5 types of generator × 4 normalizations × 8 difference measures) are compared. As a result, the best analysis pipelines are selected based on linearity of the differential expression estimation and the area under the ROC curve. These platform-independent techniques have been implemented in the Bioconductor package rnaSeqMap. They point out the exons with differential expression or internal splicing, even if the counts of reads may not show this. The areas of application include significant difference searches, splicing identification algorithms and finding suitable regions for QPCR primers.
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Affiliation(s)
- Michal J Okoniewski
- Functional Genomics Center Zurich, UNI ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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