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Dyńka D, Kowalcze K, Charuta A, Paziewska A. Reply to Najjar, R.S. Comment on "Dyńka et al. The Ketogenic Diet and Cardiovascular Diseases. Nutrients 2023, 15, 3368". Nutrients 2023; 15:4312. [PMID: 37892389 PMCID: PMC10609625 DOI: 10.3390/nu15204312] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/18/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
We thank Dr. Najjar for his interest [...].
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Affiliation(s)
| | | | | | - Agnieszka Paziewska
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland; (D.D.); (K.K.); (A.C.)
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Charuta A, Wegner R, Charuta KM, Hanusek K, Paziewska A. Types of colourants used in tattoo and permanent make-up techniques, legal regulations, health, and psychological aspects of tattooing. Health Sci Rep 2023; 6:e1360. [PMID: 37692794 PMCID: PMC10485912 DOI: 10.1002/hsr2.1360] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/09/2023] [Accepted: 06/08/2023] [Indexed: 09/12/2023] Open
Abstract
Background It is estimated that more than 60 million people in Europe, that is, around 12% of the European population, have at least one tattoo. However, there is still little information on the long-term effects of tattoos. Inks used for tattooing are a mixture of chemicals, with pigments being the main components responsible for the visual effect. The pigments used are not produced specifically as ingredients for tattooing, but mainly/primarily for the needs of industry, where lower purity requirements and quality standards are acceptable. It is therefore necessary to understand the risks associated with tattoos, but also to implement appropriate legal regulations. The aim of this article was to collect and summarise the results of research conducted so far on the type of colourants used in tattoo ink and to analyze the impact of these on human health. In addition, as part of this work, the current legal acts regulating the concentration limits and composition of inks used in tattooing as well as the psychological aspects of tattooing were collected and presented. Methods Scientific reports and articles from renowned journals from 1994 to 2022, relevant review and research publications in PubMed, and Google Scholar were analyzed. To analyze the available research literature, the Web of Science, Scopus, PubMed databases were used. The following keywords were used to search for publications: tattoos, colourants used in tattoos, side effects of tattoos, legal acts, psychological aspects of tattoos. Results The result of the literature analysis indicates a risk to health and side effects associated with tattooing the body. There are still no standardised test methods to analyze tattoo inks and assess their safety. Although the art of tattooing has been known for millennia, European legal authorities have not yet implemented effective regulations. Currently, tattoo products in Europe are covered by the general REACH regulation (Resolution ResAP, 2008; EU regulation 2020/2081, 2020). on product safety. The new amendment in force since January 4, 2022 introduces concentration limits for certain substances used in tattoo and permanent makeup inks. However, these provisions do not sufficiently protect either the consumer or the tattoo industry. Conclusions The results of the research indicate a potentially harmful effect on skin health. A more stringent safety assessment of the colourants used for tattooing is recommended, supported by studies and applicable legislation.
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Affiliation(s)
- Anna Charuta
- Institute of Health, Faculty of Medical and Health SciencesSiedlce University of Natural Sciences and HumanitiesSiedlcePoland
| | - Robert Wegner
- Institute of Health, Faculty of Medical and Health SciencesSiedlce University of Natural Sciences and HumanitiesSiedlcePoland
| | | | | | - Agnieszka Paziewska
- Institute of Health, Faculty of Medical and Health SciencesSiedlce University of Natural Sciences and HumanitiesSiedlcePoland
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Dyńka D, Paziewska A, Kowalcze K. Keto Menu-Effect of Ketogenic Menu and Intermittent Fasting on the Biochemical Markers and Body Composition in a Physically Active Man-A Controlled Case Study. Foods 2023; 12:3219. [PMID: 37685152 PMCID: PMC10486763 DOI: 10.3390/foods12173219] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
The combination of ketogenic diet (KD) with intermittent fasting (IF) has, for years, aroused a great interest in the scientific world and among healthy lifestyle enthusiasts. Its importance is even greater when the study subjects are physically active individuals. The aim of the study was a determination of the effect of strict calculated ketogenic menu combined with IF and with caloric deficit on the selected biochemical markers and body composition in a 23-year-old man performing strength training. At the same time, we decided to conduct the first so-deeply investigated and controlled case study in this respect. The study protocol included a 13-week-long ketogenic diet with intermittent fasting (of delayed time-restricted eating 16:8 type) and caloric deficit. A detailed menu was designed and was used by the man throughout the whole study duration. A number of blood tests were performed before and after the implemented dietary intervention. Additionally, body composition was determined weekly and the concentrations of glucose and ketone bodies, as well as pulse rate and arterial pressure, were measured daily. The most important changes noted included a significant increase in testosterone and vitamin D concentrations and significant reduction in the HOMA-IR index and concentrations of hepatic enzymes, insulin, glucose, iron, urea, and free triiodothyronine (FT3). Moreover, a significant improvement of body composition occurred (the ratio of total body mass to the adipose and muscular tissue and water mass improved). Favourable changes were also noted in heart rate and arterial pressure values. In view of that, the KD with IF and caloric deficit exerted favourable effects on most biochemical parameters and on body composition and caused an almost twofold increase in serum testosterone concentration.
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Affiliation(s)
| | | | - Katarzyna Kowalcze
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland; (D.D.); (A.P.)
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Dyńka D, Kowalcze K, Charuta A, Paziewska A. The Ketogenic Diet and Cardiovascular Diseases. Nutrients 2023; 15:3368. [PMID: 37571305 PMCID: PMC10421332 DOI: 10.3390/nu15153368] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 07/10/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
The most common and increasing causes of death worldwide are cardiovascular diseases (CVD). Taking into account the fact that diet is a key factor, it is worth exploring this aspect of CVD prevention and therapy. The aim of this article is to assess the potential of the ketogenic diet in the prevention and treatment of CVD. The article is a comprehensive, meticulous analysis of the literature in this area, taking into account the most recent studies currently available. The ketogenic diet has been shown to have a multifaceted effect on the prevention and treatment of CVD. Among other aspects, it has a beneficial effect on the blood lipid profile, even compared to other diets. It shows strong anti-inflammatory and cardioprotective potential, which is due, among other factors, to the anti-inflammatory properties of the state of ketosis, the elimination of simple sugars, the restriction of total carbohydrates and the supply of omega-3 fatty acids. In addition, ketone bodies provide "rescue fuel" for the diseased heart by affecting its metabolism. They also have a beneficial effect on the function of the vascular endothelium, including improving its function and inhibiting premature ageing. The ketogenic diet has a beneficial effect on blood pressure and other CVD risk factors through, among other aspects, weight loss. The evidence cited is often superior to that for standard diets, making it likely that the ketogenic diet shows advantages over other dietary models in the prevention and treatment of cardiovascular diseases. There is a legitimate need for further research in this area.
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Affiliation(s)
| | | | | | - Agnieszka Paziewska
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland; (D.D.); (K.K.); (A.C.)
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Skubisz K, Dąbkowski K, Samborowska E, Starzyńska T, Deskur A, Ambrozkiewicz F, Karczmarski J, Radkiewicz M, Kusnierz K, Kos-Kudła B, Sulikowski T, Cybula P, Paziewska A. Serum Metabolite Biomarkers for Pancreatic Tumors: Neuroendocrine and Pancreatic Ductal Adenocarcinomas-A Preliminary Study. Cancers (Basel) 2023; 15:3242. [PMID: 37370852 DOI: 10.3390/cancers15123242] [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: 04/14/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Pancreatic cancer is the most common pancreatic solid malignancy with an aggressive clinical course and low survival rate. There are a limited number of reliable prognostic biomarkers and a need to understand the pathogenesis of pancreatic tumors; neuroendocrine (PNET) and pancreatic ductal adenocarcinomas (PDAC) encouraged us to analyze the serum metabolome of pancreatic tumors and disturbances in the metabolism of PDAC and PNET. METHODS Using the AbsoluteIDQ® p180 kit (Biocrates Life Sciences AG, Innsbruck, Austria) with liquid chromatography-mass spectrometry (LC-MS), we identified changes in metabolite profiles and disrupted metabolic pathways serum of NET and PDAC patients. RESULTS The concentration of six metabolites showed statistically significant differences between the control group and PDAC patients (p.adj < 0.05). Glutamine (Gln), acetylcarnitine (C2), and citrulline (Cit) presented a lower concentration in the serum of PDAC patients, while phosphatidylcholine aa C32:0 (PC aa C32:0), sphingomyelin C26:1 (SM C26:1), and glutamic acid (Glu) achieved higher concentrations compared to serum samples from healthy individuals. Five of the tested metabolites: C2 (FC = 8.67), and serotonin (FC = 2.68) reached higher concentration values in the PNET serum samples compared to PDAC, while phosphatidylcholine aa C34:1 (PC aa C34:1) (FC = -1.46 (0.68)) had a higher concentration in the PDAC samples. The area under the curves (AUC) of the receiver operating characteristic (ROC) curves presented diagnostic power to discriminate pancreatic tumor patients, which were highest for acylcarnitines: C2 with AUC = 0.93, serotonin with AUC = 0.85, and PC aa C34:1 with AUC = 0.86. CONCLUSIONS The observations presented provide better insight into the metabolism of pancreatic tumors, and improve the diagnosis and classification of tumors. Serum-circulating metabolites can be easily monitored without invasive procedures and show the present clinical patients' condition, helping with pharmacological treatment or dietary strategies.
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Affiliation(s)
- Karolina Skubisz
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Pediatric Hospital of Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Krzysztof Dąbkowski
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Emilia Samborowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Teresa Starzyńska
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Anna Deskur
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, 32300 Pilsen, Czech Republic
| | - Jakub Karczmarski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Mariusz Radkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Katarzyna Kusnierz
- The Department of Gastrointestinal Surgery, Medical University of Silesia, 40-752 Katowice, Poland
| | - Beata Kos-Kudła
- Department of Endocrinology and Neuroendocrine Tumours, Department of Pathophysiology and Endocrinology, Medical University of Silesia, 40-752 Katowice, Poland
| | - Tadeusz Sulikowski
- Department of General, Minimally Invasive and Gastroenterological Surgery, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland
| | - Patrycja Cybula
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
- Molecular Biology Laboratory, Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, 02-776 Warsaw, Poland
| | - Agnieszka Paziewska
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
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Charuta A, Smuniewska M, Woźniak Z, Paziewska A. Effect of COVID-19 on Pregnancy and Neonate's Vital Parameters: A Systematic Review. J Pregnancy 2023; 2023:3015072. [PMID: 37215313 PMCID: PMC10199793 DOI: 10.1155/2023/3015072] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/19/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
Background COVID-19 is a new pandemic, which was declared by the World Health Organization in 2019 as a threat to public health. According to numerous reports, it can have negative consequences for pregnant women, labour, and neonates born to infected mothers. The aim of this paper was to gather the evidence and to present a summary of the results of studies concerning COVID-19 in pregnant women and their neonates. Methods Articles from prestigious journals covering the period from 2020 to February 2023, relevant review papers, and original research articles from PubMed were analysed. In order to analyse the available research literature, the Web of Science, Scopus, and PubMed databases were used, in which the search for articles was conducted using terms ("pregnancy," "coronavirus," "SARS-CoV-2," and "newborn") and using PRISMA (Preferred Reporting Items for Systemic Reviews and Meta-Analysis) guidelines for clinical trials. Meta-analyses and systematic reviews (2022-2023) on symptoms, neonatal course, and risk of COVID-19 infection have been summarized. Summary of meta-analyses and systematic reviews (2022-2023) on the effect and adverse reaction of the COVID-19 vaccination is presented. Results As a result of the research conducted, it was confirmed that in most pregnant women, no serious signs of the infection were observed, although isolated cases of death related to COVID-19 in pregnant women were reported. Several authors called attention to the more severe course of the infection in pregnant women with obesity. It seemed that no vertical transmission from mother to child was occurring. Nevertheless, the information was not clinching. The condition of the neonates born to mothers with COVID-19 was in most cases described as normal; however, some papers reported deaths of infected neonates. Conclusions Due to insufficient data, further research is necessary. Further studies and follow-up are recommended, which would make possible an assessment of remote effects of COVID-19 on pregnancy and vital parameters of the newborn.
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Affiliation(s)
- Anna Charuta
- Siedlce University of Natural Sciences and Humanities, Institute of Health, Faculty of Medical and Health Sciences, Poland
| | - Monika Smuniewska
- Siedlce University of Natural Sciences and Humanities, Institute of Health, Faculty of Medical and Health Sciences, Mazowiecki Provincial Hospital in Siedlce Named after Saint John Paul II in Siedlce, Poland
| | - Zofia Woźniak
- Siedlce University of Natural Sciences and Humanities, Institute of Health, Faculty of Medical and Health Sciences, Independent Public Health Care Center in Sokołów Podlaski, Poland
| | - Agnieszka Paziewska
- Siedlce University of Natural Sciences and Humanities, Institute of Health, Faculty of Medical and Health Sciences, Poland
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Olszewska J, Charuta A, Paziewska A, Wawrzyniak A, Baj J, Teresiński G, Buszewicz G, Kryska M. The relation between the depth of pigment disposition and men's skin thickness, the age and tattoo locations on the body. Histol Histopathol 2023; 38:503-511. [PMID: 36468542 DOI: 10.14670/hh-18-559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The most important function of the skin is to protect the body against harmful mechanical, physical and chemical factors. Its regenerative capacity is sufficient for self-repair in the event of damage, for example, during tattooing, which can be treated as an invasive procedure introducing pigment molecules into skin layers. In the present research on tattoo pigment deposition, the structure of the dermis and epidermis was evaluated using the standard histological technique with hematoxylin and eosin staining. In addition, statistically significant differences between the depth of pigment deposition on the one hand and age, dermis and epidermis thickness and tattoo location on the other were demonstrated.
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Affiliation(s)
- Justyna Olszewska
- Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
| | - Anna Charuta
- Siedlce University of Natural Sciences and Humanities, Siedlce, Poland.
| | | | | | - Jacek Baj
- Medical University of Lublin, Lublin, Poland
| | | | | | - Magdalena Kryska
- Siedlce University of Natural Sciences and Humanities, Siedlce, Poland
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Hanusek K, Karczmarski J, Litwiniuk A, Urbańska K, Ambrozkiewicz F, Kwiatkowski A, Martyńska L, Domańska A, Bik W, Paziewska A. Obesity as a Risk Factor for Breast Cancer-The Role of miRNA. Int J Mol Sci 2022; 23:ijms232415683. [PMID: 36555323 PMCID: PMC9779381 DOI: 10.3390/ijms232415683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/15/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) is the most common cancer diagnosed among women in the world, with an ever-increasing incidence rate. Due to the dynamic increase in the occurrence of risk factors, including obesity and related metabolic disorders, the search for new regulatory mechanisms is necessary. This will help a complete understanding of the pathogenesis of breast cancer. The review presents the mechanisms of obesity as a factor that increases the risk of developing breast cancer and that even initiates the cancer process in the female population. The mechanisms presented in the paper relate to the inflammatory process resulting from current or progressive obesity leading to cell metabolism disorders and disturbed hormonal metabolism. All these processes are widely regulated by the action of microRNAs (miRNAs), which may constitute potential biomarkers influencing the pathogenesis of breast cancer and may be a promising target of anti-cancer therapies.
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Affiliation(s)
- Karolina Hanusek
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Jakub Karczmarski
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Anna Litwiniuk
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Katarzyna Urbańska
- Department of General, Oncological, Metabolic and Thoracic Surgery, Military Institute of Medicine, 128 Szaserów St, 04-141 Warsaw, Poland
| | - Filip Ambrozkiewicz
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1665/76, 32300 Pilsen, Czech Republic
| | - Andrzej Kwiatkowski
- Department of General, Oncological, Metabolic and Thoracic Surgery, Military Institute of Medicine, 128 Szaserów St, 04-141 Warsaw, Poland
| | - Lidia Martyńska
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Anita Domańska
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Wojciech Bik
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
- Faculty of Medical and Health Sciences, Institute of Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
- Correspondence:
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Dyńka D, Kowalcze K, Paziewska A. The Role of Ketogenic Diet in the Treatment of Neurological Diseases. Nutrients 2022; 14:5003. [PMID: 36501033 PMCID: PMC9739023 DOI: 10.3390/nu14235003] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022] Open
Abstract
Over a hundred years of study on the favourable effect of ketogenic diets in the treatment of epilepsy have contributed to a long-lasting discussion on its potential influence on other neurological diseases. A significant increase in the number of scientific studies in that field has been currently observed. The aim of this paper is a widespread, thorough analysis of the available scientific evidence in respect of the role of the ketogenic diet in the therapy of neurological diseases such as: epilepsy, Alzheimer's disease (AD), Parkinson's disease (PD), multiple sclerosis (MS) and migraine. A wide range of the mechanisms of action of the ketogenic diet has been demonstrated in neurological diseases, including, among other effects, its influence on the reduction in inflammatory conditions and the amount of reactive oxygen species (ROS), the restoration of the myelin sheath of the neurons, the formation and regeneration of mitochondria, neuronal metabolism, the provision of an alternative source of energy for neurons (ketone bodies), the reduction in glucose and insulin concentrations, the reduction in amyloid plaques, the induction of autophagy, the alleviation of microglia activation, the reduction in excessive neuronal activation, the modulation of intestinal microbiota, the expression of genes, dopamine production and the increase in glutamine conversion into GABA. The studies discussed (including randomised controlled studies), conducted in neurological patients, have stressed the effectiveness of the ketogenic diet in the treatment of epilepsy and have demonstrated its promising therapeutic potential in Alzheimer's disease (AD), Parkinson's disease (PD), multiple sclerosis (MS) and migraine. A frequent advantage of the diet was demonstrated over non-ketogenic diets (in the control groups) in the therapy of neurological diseases, with simultaneous safety and feasibility when conducting the nutritional model.
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Affiliation(s)
- Damian Dyńka
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
| | - Katarzyna Kowalcze
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
| | - Agnieszka Paziewska
- Institute of Health Sciences, Faculty of Medical and Health Sciences, Siedlce University of Natural Sciences and Humanities, 08-110 Siedlce, Poland
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland
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Zeber-Lubecka N, Kulecka M, Lindner B, Krynicki R, Paziewska A, Nowakowski A, Bidzinski M, Ostrowski J. Increased diversity of a cervical microbiome associates with cervical cancer. Front Oncol 2022; 12:1005537. [PMID: 36249017 PMCID: PMC9562559 DOI: 10.3389/fonc.2022.1005537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 12/02/2022] Open
Abstract
The cervical microbiome (CM) is a complex ecosystem that can change in response to gynecological cancers. We aimed to evaluate changes in the CM of patients who underwent chemoradiation (CRT) therapy for locally advanced cervical cancer. Before and after CRT, cervical swab samples were collected from 16 patients with squamous cell carcinoma of the cervix, and 30 healthy women. All samples were subjected to 16s rRNA-Seq analysis. In healthy premenopausal women the CM comprised mostly Lactobacillus (>90%); the CM community in samples from both pre- and postmenopausal pre-treatment cancer patients was heterogeneous, with a low proportion of Lactobacillus in younger cases. On the genus level, 27 and 11 taxa differentiated healthy controls from cancer patients in pre- and postmenopausal age groups, while 31 and 2 genera differentiated pre- and post-radiation samples and pre-radiation and the follow-up samples, respectively. Microbiome diversity was significantly higher in pre-treatment patients than in healthy controls. The results reveal significant alterations in the CM of cervical cancer patients relative to that in healthy controls; these changes were more striking after CRT. However, further research is needed to determine whether alteration of the CM offers new therapeutic options.
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Affiliation(s)
- Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Bogusław Lindner
- Department of Gynaecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Ryszard Krynicki
- Department of Gynaecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Andrzej Nowakowski
- Department of Cancer Prevention, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Mariusz Bidzinski
- Department of Gynaecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- *Correspondence: Jerzy Ostrowski,
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Paszkiewicz-Kozik E, Kluska A, Piątkowska M, Bałabas A, Żeber-Lubecka N, Karczmarski J, Goryca K, Kulecka M, Wojciechowska-Lampka E, Osiadacz W, Romejko-Jarosińska J, Świerkowska M, Paziewska A, Ambrożkiewicz F, Walewski J, Mikula M, Ostrowski J. Genetic associations with lymphomas in Polish patients: A pooled-DNA genome-wide association analysis. Int J Immunogenet 2022; 49:353-363. [PMID: 36036752 DOI: 10.1111/iji.12596] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Abstract
Several single nucleotide polymorphisms (SNPs) associated with susceptibility to Hodgkin lymphoma (HL) and diffuse large B-cell lymphoma (DLBCL) have been identified. The aim of this study was to identify susceptibility loci for HL and DLBCL in Polish patients. Altogether, DLBCL (n = 218 and HL patients (n = 224) and healthy individuals (n = 1181) were recruited. Lymphoma diagnosis was based on standard criteria. Genome-wide association study (GWAS) was performed using pooled-DNA samples on llumina Infinium Omni2.5 Exome-8 v1.3, and selected loci were replicated by TaqMan SNP genotyping of individuals. GWAS detected thirteen and seven SNPs associated with DLBCL and HL, respectively. In the replication study, six and seven SNPs reached significance after correction for multiple testing in the DLBCL and HL cohorts, respectively. One and four SNPs associated with DLBCL and HL, respectively, were localized within, and two SNPs-near the major histocompatibility complex (MHC) region. In conclusion, the majority of loci associated with HL and DLBCL aetiology in previous studies have potential roles in immune function. Our pooled-DNA GWAS enabled the identification of several susceptibility loci for DLBCL and HL in the Polish population; some of them were mapped within or adjacent to the MHC, and other associated SNPs were located outside the MHC.
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Affiliation(s)
- Ewa Paszkiewicz-Kozik
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Aneta Bałabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Krzysztof Goryca
- Genomics Core Facility, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Elżbieta Wojciechowska-Lampka
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Włodzimierz Osiadacz
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Joanna Romejko-Jarosińska
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Monika Świerkowska
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
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12
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Wróbel M, Cendrowski J, Szymańska E, Grębowicz-Maciukiewicz M, Budick-Harmelin N, Macias M, Szybińska A, Mazur M, Kolmus K, Goryca K, Dąbrowska M, Paziewska A, Mikula M, Miączyńska M. Correction: ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway. Life Sci Alliance 2022; 5:5/10/e202201537. [PMID: 35672146 PMCID: PMC9175455 DOI: 10.26508/lsa.202201537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Marta Wróbel
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Jarosław Cendrowski
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ewelina Szymańska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Noga Budick-Harmelin
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Matylda Macias
- Microscopy and Cytometry Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Aleksandra Szybińska
- Microscopy and Cytometry Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Mazur
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Kolmus
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marta Miączyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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13
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Wróbel M, Cendrowski J, Szymańska E, Grębowicz-Maciukiewicz M, Budick-Harmelin N, Macias M, Szybińska A, Mazur M, Kolmus K, Goryca K, Dąbrowska M, Paziewska A, Mikula M, Miączyńska M. ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway. Life Sci Alliance 2022; 5:5/7/e202101239. [PMID: 35354596 PMCID: PMC8967991 DOI: 10.26508/lsa.202101239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/13/2022] Open
Abstract
ESCRT-I deficiency impairs lysosome membrane turnover and induces homeostatic responses to lysosomal nutrient starvation including activation of MiT-TFE signaling caused by inhibition of the substrate-specific mTORC1 pathway. Within the endolysosomal pathway in mammalian cells, ESCRT complexes facilitate degradation of proteins residing in endosomal membranes. Here, we show that mammalian ESCRT-I restricts the size of lysosomes and promotes degradation of proteins from lysosomal membranes, including MCOLN1, a Ca2+ channel protein. The altered lysosome morphology upon ESCRT-I depletion coincided with elevated expression of genes annotated to biogenesis of lysosomes due to prolonged activation of TFEB/TFE3 transcription factors. Lack of ESCRT-I also induced transcription of cholesterol biosynthesis genes, in response to inefficient delivery of cholesterol from endolysosomal compartments. Among factors that could possibly activate TFEB/TFE3 signaling upon ESCRT-I deficiency, we excluded lysosomal cholesterol accumulation and Ca2+-mediated dephosphorylation of TFEB/TFE3. However, we discovered that this activation occurs due to the inhibition of Rag GTPase–dependent mTORC1 pathway that specifically reduced phosphorylation of TFEB at S122. Constitutive activation of the Rag GTPase complex in cells lacking ESCRT-I restored S122 phosphorylation and prevented TFEB/TFE3 activation. Our results indicate that ESCRT-I deficiency evokes a homeostatic response to counteract lysosomal nutrient starvation, that is, improper supply of nutrients derived from lysosomal degradation.
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Affiliation(s)
- Marta Wróbel
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Jarosław Cendrowski
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ewelina Szymańska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | | - Noga Budick-Harmelin
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Matylda Macias
- Microscopy and Cytometry Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Aleksandra Szybińska
- Microscopy and Cytometry Facility, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Michał Mazur
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Kolmus
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marta Miączyńska
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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14
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Ostrowski J, Kulecka M, Zawada I, Żeber-Lubecka N, Paziewska A, Graca-Pakulska K, Dąbkowski K, Skubisz K, Cybula P, Ambrożkiewicz F, Urasińska E, Mikula M, Starzyńska T. The gastric microbiota in patients with Crohn's disease; a preliminary study. Sci Rep 2021; 11:17866. [PMID: 34504159 PMCID: PMC8429686 DOI: 10.1038/s41598-021-97261-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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 08/23/2021] [Indexed: 11/09/2022] Open
Abstract
The gastric microbiota in Crohn's disease (CD) has not been studied. The purpose of the study was to evaluate differences of stomach microbiota between CD patients and controls. DNA was extracted from gastric mucosal and fluid samples, from 24 CD patients and 19 controls. 16S rRNA gene sequencing identified 1511 operational taxonomic units (OTUs), of which 239 passed the low abundance and low variance filters. All but one CD patients were HP negative. Fifteen bacterial phyla were identified in at least one mucosal or fluid site. Of these, Bacteroidota and Firmicutes accounted for 70% of all phyla. Proteobacteria, Actinobacteriota, and Fusobacteriota combined accounted for 27%. There was significant difference in the relative abundance of Bacteroidota, Proteobacteria, Fusobacteriota, and Campilobacterota between CD patients and controls only in gastric corpus samples. In gastric liquid, there was a significant difference only in Actinobacteriota. Pairwise comparison identified 67 differentially abundant OTUs in at least one site. Of these, 13 were present in more than one comparison, and four differentiating OTUs (Neisseriaceae, Neisseria, Absconditabacteriales, and Microbacteriaceae) were identified at all tested sites. The results reveal significant changes in gastric microbial profiles (beta diversity, phylum, and individual taxa levels) between H. pylori-negative CD patients and controls.
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Affiliation(s)
- Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland.
| | - Maria Kulecka
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Iwona Zawada
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.,Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Katarzyna Graca-Pakulska
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Krzysztof Dąbkowski
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Elżbieta Urasińska
- Department of Pathology, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Teresa Starzyńska
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland.
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15
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Gaweł AM, Ratajczak M, Gajda E, Grzanka M, Paziewska A, Cieślicka M, Kulecka M, Oczko-Wojciechowska M, Godlewska M. Analysis of the Role of FRMD5 in the Biology of Papillary Thyroid Carcinoma. Int J Mol Sci 2021; 22:6726. [PMID: 34201607 PMCID: PMC8268710 DOI: 10.3390/ijms22136726] [Citation(s) in RCA: 4] [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: 05/21/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Thyroid carcinoma (TC) is the most common endocrine system malignancy, and papillary thyroid carcinoma (PTC) accounts for >80% of all TC cases. Nevertheless, PTC pathogenesis is still not fully understood. The aim of the study was to elucidate the role of the FRMD5 protein in the regulation of biological pathways associated with the development of PTC. We imply that the presence of certain genetic aberrations (e.g., BRAF V600E mutation) is associated with the activity of FRMD5. METHODS The studies were conducted on TPC1 and BCPAP (BRAF V600E) model PTC-derived cells. Transfection with siRNA was used to deplete the expression of FRMD5. The mRNA expression and protein yield were evaluated using RT-qPCR and Western blot techniques. Proliferation, migration, invasiveness, adhesion, spheroid formation, and survival tests were performed. RNA sequencing and phospho-kinase proteome profiling were used to assess signaling pathways associated with the FRMD5 expressional status. RESULTS The obtained data indicate that the expression of FRMD5 is significantly enhanced in BRAF V600E tumor specimens and cells. It was observed that a drop in intracellular yield of FRMD5 results in significant alternations in the migration, invasiveness, adhesion, and spheroid formation potential of PTC-derived cells. Importantly, significant divergences in the effect of FRMD5 depletion in both BRAF-wt and BRAF-mutated PTC cells were observed. It was also found that knockdown of FRMD5 significantly alters the expression of multidrug resistant genes. CONCLUSIONS This is the first report highlighting the importance of the FRMD5 protein in the biology of PTCs. The results suggest that the FRMD5 protein can play an important role in controlling the metastatic potential and multidrug resistance of thyroid tumor cells.
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Affiliation(s)
- Agata M. Gaweł
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Marymoncka 99/103, 01-813 Warsaw, Poland; (A.M.G.); (M.G.)
- Faculty of Medicine, Medical University of Warsaw, Histology and Embryology Students’ Science Association HESA, Chałubinskiego 5, 02-004 Warsaw, Poland
| | - Maciej Ratajczak
- Centre of Postgraduate Medical Education, Department of Endocrinology, Marymoncka 99/103, 01-813 Warsaw, Poland;
| | - Ewa Gajda
- Centre of Postgraduate Medical Education, Department of Immunohematology, Marymoncka 99/103, 01-813 Warsaw, Poland;
| | - Małgorzata Grzanka
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Marymoncka 99/103, 01-813 Warsaw, Poland; (A.M.G.); (M.G.)
| | - Agnieszka Paziewska
- Centre of Postgraduate Medical Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Marymoncka 99/103, 01-813 Warsaw, Poland; (A.P.); (M.K.)
- Centre of Postgraduate Medical Education, Department of Neuroendocrinology, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Marta Cieślicka
- Department of Genetic and Molecular Diagnostics of Cancer, M. Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland; (M.C.); (M.O.-W.)
| | - Maria Kulecka
- Centre of Postgraduate Medical Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Marymoncka 99/103, 01-813 Warsaw, Poland; (A.P.); (M.K.)
| | - Małgorzata Oczko-Wojciechowska
- Department of Genetic and Molecular Diagnostics of Cancer, M. Sklodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland; (M.C.); (M.O.-W.)
| | - Marlena Godlewska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Marymoncka 99/103, 01-813 Warsaw, Poland; (A.M.G.); (M.G.)
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16
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Kulecka M, Waker E, Ambrozkiewicz F, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. BMC Microbiol 2021; 21:36. [PMID: 33509087 PMCID: PMC7842062 DOI: 10.1186/s12866-021-02090-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/15/2020] [Accepted: 01/08/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Clostridium difficile (C. difficile) is a major source of healthcare-associated infection with a high risk of recurrence, attributable to many factors such as usage of antibiotics, older age and immunocompromised status of the patients. C. difficile has also a highly diverse genome, which may contribute to its high virulence. Herein we examined whether the genome conservation, measured as non-synonymous to synonymous mutations ratio (dN/dS) in core genes, presence of single genes, plasmids and prophages increased the risk of reinfection in a subset of 134 C. difficile isolates from our previous study in a singly hemato-oncology ward. METHODS C. difficile isolates were subjected to whole-genome sequencing (WGS) on Ion Torrent PGM sequencer. Genomes were assembled with MIRA5 and annotated with prokka and VRprofile. Logistic regression was used to asses the relationship between single gene presence and the odds of infection recurrence. DN/dS ratios were computed with codeml. Functional annotation was conducted with eggNOG-Mapper. RESULTS We have found that the presence of certain genes, associated with carbon metabolism and oxidative phosphorylation, increased the odds of infection recurrence. More core genes were under positive selective pressure in recurrent disease isolates - they were mostly associated with the metabolism of aminoacids. Finally, prophage elements were more prevalent in single infection isolates and plasmids did not influence the odds of recurrence. CONCLUSIONS Our findings suggest higher genetic plasticity in isolates causing recurrent infection, associated mainly with metabolism. On the other hand, the presence of prophages seems to reduce the isolates' virulence.
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Affiliation(s)
- Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Edyta Waker
- Department of Clinical Microbiology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 02-781, Warsaw, Poland.
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Kulecka M, Fraczek B, Mikula M, Zeber-Lubecka N, Karczmarski J, Paziewska A, Ambrozkiewicz F, Jagusztyn-Krynicka K, Cieszczyk P, Ostrowski J. The composition and richness of the gut microbiota differentiate the top Polish endurance athletes from sedentary controls. Gut Microbes 2020; 11:1374-1384. [PMID: 32401138 PMCID: PMC7524299 DOI: 10.1080/19490976.2020.1758009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Little data are available on the subject of gut microbiota composition in endurance athletes as well as connections between diet and specific bacteria abundance. However, most studies suggest that athletes' microbiota undergoes major alterations, which may contribute to increased physical performance. Therefore, we decided to investigate differences in gut microbiota between healthy controls and endurance athletes. MATERIALS AND METHODS Stools samples were collected from 14 marathon runners, 11 cross-country skiers and 46 sedentary healthy controls. The athletes' diet evaluation was performed with 24-h diet recall, using the Aliant programme. The 16S gene sequencing was performed using the Ion 16S Metagenomics Kit on Ion Torrent PGM sequencer. Taxonomic classification and diversity indices computation was performed with Mothur. RESULTS 20 and 5 taxa differentiated healthy controls from marathon runners and cross-country skiers, respectively. Both groups presented a lowered abundance of major gut microbiota genus, Bacteroidetes and higher abundance of Prevotella. The athletes' microbiome was also more diverse in cross-country skiers than the one of sedentary controls (Simpson index p-value at 0.025). Thirty-one strong correlations (Spearman's coefficient > 0.6) were uncovered between bacteria abundance and diet, including inverse correlation of Prevotella with sucrose intake, Phascolarctobacterium with polyunsaturated fatty acids as well as positive correlation of Christensenellaceae with folic acid intake and Agathobacter with fiber amount in diet. CONCLUSIONS The excessive training associates with both differences in composition and promotion of higher bacterial diversity. Taxons enriched in athletes are known to participate in fiber fermentation.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland,Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Barbara Fraczek
- Department of Sports Medicine and Human Nutrition, Institute of Biomedical Sciences, Faculty of Physical Education and Sport, University of Physical Education in Krakow, Krakow, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland,Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Katarzyna Jagusztyn-Krynicka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Cieszczyk
- Department of Molecular Biology, Faculty of Physical Education, Gdansk University of Physical Education and Sport, Gdansk, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland,Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland,CONTACT Jerzy Ostrowski Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena 5, Warsaw02-781, Poland
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Paziewska A, Polkowski M, Goryca K, Karczmarski J, Wiechowska-Kozlowska A, Dabrowska M, Mikula M, Ostrowski J. Mutational Mosaics of Cell-Free DNA from Pancreatic Cyst Fluids. Dig Dis Sci 2020; 65:2294-2301. [PMID: 31925676 DOI: 10.1007/s10620-019-06043-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/31/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Pancreatic cyst fluids (PCFs) enriched in tumor-derived DNA are a potential source of new biomarkers. The study aimed to analyze germinal variants and mutational profiles of cell-free (cf)DNA shed into the cavity of pancreatic cysts. METHODS The study cohort consisted of 71 patients who underwent endoscopic ultrasound fine-needle aspiration of PCF. Five malignant cysts, 19 intraductal papillary mucinous neoplasms (IPMNs), 11 mucinous cystic neoplasms (MCNs), eight serous cystic neoplasms (SCNs), and 28 pseudocysts were identified. The sequencing of 409 genes included in Comprehensive Cancer Panel was performed using Ion Proton System. The mutation rate of the KRAS and GNAS canonical loci was additionally determined using digital PCR. RESULTS The number of mutations detected with NGS varied from 0 to 22 per gene, and genes with the most mutations were: TP53, KRAS, PIK3CA, GNAS, ADGRA2, and APC. The frequencies of the majority of mutations did not differ between non-malignant cystic neoplasms and pseudocysts. NGS detected KRAS mutations in malignant cysts (60%), IPMNs (32%), MCNs (64%), SCNs (13%), and pseudocysts (14%), with GNAS mutations in 20%, 26%, 27%, 13%, and 21% of samples, respectively. Digital PCR-based testing increased KRAS (68%) and GNAS (52%) mutations detection level in IPMNs, but not other cyst types. CONCLUSIONS We demonstrate relatively high rates of somatic mutations of cancer-related genes, including KRAS and GNAS, in cfDNA isolated from PCFs irrespectively of the pancreatic cyst type. Further studies on molecular mechanisms of pancreatic cysts malignant transformation in relation to their mutational profiles are required.
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Affiliation(s)
- Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781, Warsaw, Poland.,Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | - Marcin Polkowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland.,Next Generation Sequencing Core Facility, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | | | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland.
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Starzyńska T, Karczmarski J, Paziewska A, Kulecka M, Kuśnierz K, Żeber-Lubecka N, Ambrożkiewicz F, Mikula M, Kos-Kudła B, Ostrowski J. Differences between Well-Differentiated Neuroendocrine Tumors and Ductal Adenocarcinomas of the Pancreas Assessed by Multi-Omics Profiling. Int J Mol Sci 2020; 21:E4470. [PMID: 32586046 PMCID: PMC7352720 DOI: 10.3390/ijms21124470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/18/2020] [Revised: 06/12/2020] [Accepted: 06/18/2020] [Indexed: 02/07/2023] Open
Abstract
Most pancreatic neuroendocrine tumors (PNETs) are indolent, while pancreatic ductal adenocarcinomas (PDACs) are particularly aggressive. To elucidate the basis for this difference and to establish the biomarkers, by using the deep sequencing, we analyzed somatic variants across coding regions of 409 cancer genes and measured mRNA/miRNA expression in nine PNETs, eight PDACs, and four intestinal neuroendocrine tumors (INETs). There were 153 unique somatic variants considered pathogenic or likely pathogenic, found in 50, 57, and 24 genes in PDACs, PNETs, and INETs, respectively. Ten and 11 genes contained a pathogenic mutation in at least one sample of all tumor types and in PDACs and PNETs, respectively, while 28, 34, and 11 genes were found to be mutated exclusively in PDACs, PNETs, and INETs, respectively. The mRNA and miRNA transcriptomes of PDACs and NETs were distinct: from 54 to 1659 differentially expressed mRNAs and from 117 to 250 differentially expressed miRNAs exhibited high discrimination ability and resulted in models with an area under the receiver operating characteristics curve (AUC-ROC) >0.9 for both miRNA and mRNA. Given the miRNAs high stability, we proposed exploring that class of RNA as new pancreatic tumor biomarkers.
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Affiliation(s)
- Teresa Starzyńska
- Department of Gastroenterology, Pomeranian Medical University in Szczecin, 70-204 Szczecin, Poland;
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (A.P.); (M.K.); (F.A.); (M.M.)
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (A.P.); (M.K.); (F.A.); (M.M.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland;
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (A.P.); (M.K.); (F.A.); (M.M.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland;
| | - Katarzyna Kuśnierz
- Department of Gastrointestinal Surgery, Medical University of Silesia, 40-514 Katowice, Poland;
| | - Natalia Żeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland;
| | - Filip Ambrożkiewicz
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (A.P.); (M.K.); (F.A.); (M.M.)
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (A.P.); (M.K.); (F.A.); (M.M.)
| | - Beata Kos-Kudła
- Department of Endocrinology and Neuroendocrine Tumors, ENETS Center of Excelence, Department of Pathophysiology and Endocrinology, Medical University of Silesia, 40-514 Katowice, Poland;
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (A.P.); (M.K.); (F.A.); (M.M.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland;
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20
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Boresowicz J, Kober P, Rusetska N, Maksymowicz M, Paziewska A, Dąbrowska M, Zeber-Lubecka N, Kunicki J, Bonicki W, Ostrowski J, Siedlecki JA, Bujko M. DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors. Life (Basel) 2020; 10:E59. [PMID: 32413978 PMCID: PMC7281098 DOI: 10.3390/life10050059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/31/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022] Open
Abstract
microRNAs are involved in pathogenesis of cancer. DNA methylation plays a role in transcription of miRNA-encoding genes and may contribute to changed miRNA expression in tumors. This issue was not investigated in pituitary neuroendocrine tumors (PitNETs) previously. DNA methylation patterns, assessed with HumanMethylation450K arrays in 34 PitNETs and five normal pituitaries, were used to determine differentially methylated CpGs located at miRNA genes. It showed aberrant methylation in regions encoding for 131 miRNAs. DNA methylation data and matched miRNA expression profiles, determined with next-generation sequencing (NGS) of small RNAs, were correlated in 15 PitNETs. This showed relationship between methylation and expression levels for 12 miRNAs. DNA methylation and expression levels of three of them (MIR145, MIR21, and MIR184) were determined in the independent group of 80 tumors with pyrosequencing and qRT-PCR and results confirmed both aberrant methylation in PitNETs and correlation between methylation and expression. Additionally, in silico target prediction was combined with analysis of established miRNA profiles and matched mRNA expression pattern, assessed with amplicon-based NGS to indicate putative target genes of epigenetically deregulated miRNAs. This study reveals aberrant DNA methylation in miRNA-encoding genes in gonadotroph PitNETs. Methylation changes affect expression level of miRNAs that regulate putative target genes with tumorigenesis-relevant functions.
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Affiliation(s)
- Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Natalia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland;
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland;
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland;
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (W.B.)
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (W.B.)
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland;
| | - Janusz A. Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
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21
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Waker E, Ambrozkiewicz F, Kulecka M, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years. Front Microbiol 2020; 11:1618. [PMID: 32793147 PMCID: PMC7384382 DOI: 10.3389/fmicb.2020.01618] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
Aims: Clostridium difficile (C. difficile) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008-2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile, the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.
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Affiliation(s)
- Edyta Waker
- Department of Clinical Microbiology, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
- *Correspondence: Jerzy Ostrowski,
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22
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Kosela-Paterczyk H, Paziewska A, Kulecka M, Balabas A, Kluska A, Dabrowska M, Piatkowska M, Zeber-Lubecka N, Ambrozkiewicz F, Karczmarski J, Mikula M, Rutkowski P, Ostrowski J. Signatures of circulating microRNA in four sarcoma subtypes. J Cancer 2020; 11:874-882. [PMID: 31949491 PMCID: PMC6959019 DOI: 10.7150/jca.34723] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/08/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Sarcomas are rare malignant tumors of mesenchymal origin. The discovery of circulating biomarkers with high diagnostic value could supplement diagnosis of this heterogenous group of tumors. The aim of this study was to identify the profiles of circulating miRNA (c-miRNAs) in four groups of common bone and soft tissue sarcomas. Methods: At the time of diagnosis, blood samples were collected from 86 patients: 36 with locally advanced/unresectable/metastatic gastrointestinal stromal tumor (GIST) who received first-line treatment with imatinib; 16 with locally advanced osteosarcoma (OS); 26 with locally advanced synovial sarcoma (SS); and eight with locally advanced Ewing sarcoma (ES). In addition, samples were collected from 30 healthy controls. C-miRNAs were isolated using a miRCURY RNA Isolation Kit, followed by preparation of cDNA libraries and sequencing on the Ion Proton platform. Results: Pair-wise comparisons identified 156 unique c-miRNAs (adjusted P-value < 0.05) showing significant dysregulation between controls and patients; of these, 24, 36, 42, and 99 differentiated controls from pretherapeutic OS, SS, ES, and GIST, respectively. Ten c-miRNAs were commonly altered in at least three sarcoma types. Receiver operating characteristic curves and area under the curve (ROC-AUC) analyses revealed that a four-miRNA diagnostic classifier was able to differentiate controls from ES, GIST, OS, and SS, with AUC-ROC values of 1, 0.97, 0.95, and 0.94, respectively. Conclusions: Aberrant miRNA expression signatures were identified in serum from patients with four different sarcoma subtypes. Differences in miRNA expression profiles between sarcoma patients and healthy volunteers suggest that miRNAs may play a role in sarcoma development.
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Affiliation(s)
- Hanna Kosela-Paterczyk
- Department of Soft Tissue, Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute - Oncology Centre, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland.,Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland.,Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue, Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute - Oncology Centre, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland.,Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Centre; 02-781 Warsaw, Poland
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23
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Boresowicz J, Kober P, Rusetska N, Maksymowicz M, Paziewska A, Dąbrowska M, Zeber-Lubecka N, Kunicki J, Bonicki W, Ostrowski J, Siedlecki JA, Bujko M. The Search of miRNA Related to Invasive Growth of Nonfunctioning Gonadotropic Pituitary Tumors. Int J Endocrinol 2020; 2020:3730657. [PMID: 33354213 PMCID: PMC7737439 DOI: 10.1155/2020/3730657] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/31/2020] [Accepted: 11/19/2020] [Indexed: 01/06/2023] Open
Abstract
PURPOSE Nonfunctioning gonadotropic pituitary neuroendocrine tumors (PitNETs) are among the most frequent neoplasms of pituitary gland. Although PitNETs are commonly considered benign, a notable part of patients suffer from tumor recurrence after treatment. Invasive growth of pituitary tumor is among the most important prognostic factors. Since molecular features of invasiveness are of potential clinical usefulness, this study was aimed to verify whether invasive and noninvasive nonfunctioning gonadotropic PitNETs differ in the miRNA expression profile and whether the differences could provide a possible molecular classifier. METHODS miRNA profiles were determined in 20 patients (11 invasive and 9 noninvasive tumors) using next-generation sequencing. The expression of selected miRNAs was assessed in the independent cohort of 80 patients with qRT-PCR. RESULTS When miRNA profiles of invasive and noninvasive tumors were compared, 29 miRNAs were found differentially expressed. Hsa-miR-184, hsa-miR-181a-2-3p, hsa-miR-93-3p, hsa-miR-574-5p, hsa-miR-185-5p, and hsa-miR-3200-5p showed a potential clinical value according to ROC curve analysis. Unfortunately, differential expression of only hsa-miR-185-5p was confirmed in the validation cohort, with AUG at 0.654. CONCLUSION Differences in miRNAs expression profiles in invasive and noninvasive gonadotropic PitNETs are slight and the level of miRNA expression seems not to be applicable as useful classifier of tumor invasiveness.
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Affiliation(s)
- Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Janusz A. Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
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24
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Bujko M, Kober P, Boresowicz J, Rusetska N, Paziewska A, Dąbrowska M, Piaścik A, Pękul M, Zieliński G, Kunicki J, Bonicki W, Ostrowski J, Siedlecki JA, Maksymowicz M. USP8 mutations in corticotroph adenomas determine a distinct gene expression profile irrespective of functional tumour status. Eur J Endocrinol 2019; 181:615-627. [PMID: 31581124 DOI: 10.1530/eje-19-0194] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 10/02/2019] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Pituitary corticotroph adenomas commonly cause Cushing's disease (CD) but part of these tumours are hormonally inactive (silent corticotroph adenomas, SCA). USP8 mutations are well-known driver mutations in corticotrophinomas. Differences in transcriptomic profiles between functioning and silent tumours or tumours with different USP8 status have not been investigated. DESIGN AND METHODS Forty-eight patients (28 CD, 20 SCA) were screened for USP8 mutations with Sanger sequencing. Twenty-four patients were included in transcriptomic profiling with Ampliseq Transcriptome Human Gene Expression Core Panel. The entire patients group was included in qRT-PCR analysis of selected genes expression. Immunohistochemistry was used for visualization of selected protein. RESULTS We found USP8 mutation in 15 patients with CD and 4 SCAs. USP8 mutations determine molecular profile of the tumours as showed by hierarchical clustering and identification of 1648 genes differentially expressed in USP8-mutated and USP8-wild-type tumours. Mutations affect many molecular pathways as observed in Gene Set Enrichment analysis. USP8-mutated adenomas showed higher level of POMC, CDC25A, MAPK4 but lower level of CCND2, CDK6, CDKN1B than USP8-wt tumours. Eighty-seven genes differentially expressed between CD-related adenomas and SCAs were found, including those involved in cell signalling (GLI2, DLC1, TBX2, RASSF6), cell adhesion (GJA1, CDH6), ion transport (KCNN4, KCNJ5) and GABA signalling (GABBR2, GABRD). CONCLUSION USP8 mutations occur in functioning and silent corticotrophinomas. They have pleiotropic effect, not limited to EGFR signalling, and affect expression levels of many genes involved in different pathways. Expression of GABA-related genes GABBR2, GNAL, GABARD and KCNJ5 correspond to functional status of the tumours.
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Affiliation(s)
- Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Natalia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Agata Piaścik
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Monika Pękul
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Grzegorz Zieliński
- Department of Neurosurgery, Military Institute of Medicine, Warsaw, Poland
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
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Konieczny P, Lichawska-Cieslar A, Kwiecinska P, Cichy J, Pietrzycka R, Szukala W, Declercq W, Devos M, Paziewska A, Rumienczyk I, Kulecka M, Mikula M, Fu M, Borowczyk J, Santamaria-Babí LF, Jura J. Keratinocyte-specific ablation of Mcpip1 impairs skin integrity and promotes local and systemic inflammation. J Mol Med (Berl) 2019; 97:1669-1684. [PMID: 31786670 DOI: 10.1007/s00109-019-01853-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/21/2019] [Revised: 10/08/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
MCPIP1 (Regnase-1, encoded by the ZC3H12A gene) regulates the mRNA stability of several inflammatory cytokines. Due to the critical role of this RNA endonuclease in the suppression of inflammation, Mcpip1 deficiency in mice leads to the development of postnatal multiorgan inflammation and premature death. Here, we generated mice with conditional deletion of Mcpip1 in the epidermis (Mcpip1EKO). Mcpip1 loss in keratinocytes resulted in the upregulated expression of transcripts encoding factors related to inflammation and keratinocyte differentiation, such as IL-36α/γ cytokines, S100a8/a9 antibacterial peptides, and Sprr2d/2h proteins. Upon aging, the Mcpip1EKO mice showed impaired skin integrity that led to the progressive development of spontaneous skin pathology and systemic inflammation. Furthermore, we found that the lack of epidermal Mcpip1 expression impaired the balance of keratinocyte proliferation and differentiation. Overall, we provide evidence that keratinocyte-specific Mcpip1 activity is crucial for the maintenance of skin integrity as well as for the prevention of excessive local and systemic inflammation. KEY MESSAGES: Loss of murine epidermal Mcpip1 upregulates transcripts related to inflammation and keratinocyte differentiation. Keratinocyte Mcpip1 function is essential to maintain the integrity of skin in adult mice. Ablation of Mcpip1 in mouse epidermis leads to the development of local and systemic inflammation.
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Affiliation(s)
- Piotr Konieczny
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Agata Lichawska-Cieslar
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Patrycja Kwiecinska
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Joanna Cichy
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Roza Pietrzycka
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Weronika Szukala
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Michael Devos
- Molecular Signaling and Cell Death Unit, VIB Center for Inflammation Research Center, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Izabela Rumienczyk
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Marymoncka 99/103, 01-813, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Mingui Fu
- Department of Biomedical Science and Shock/Trauma Research Center, School of Medicine, University of Missouri-Kansas City, 5100 Rockhill Rd, Kansas City, MO, 64110, USA
| | - Julia Borowczyk
- Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.,Current address: Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Rue Gabrielle Perret-Gentil 4, 1211, Geneva, Switzerland
| | - Luis F Santamaria-Babí
- Translational Immunology, Department of Cellular Biology, Physiology and Immunology, Faculty of Biology, University de Barcelona, Gran Via de les Corts Catalanes 585, 08007, Barcelona, Spain
| | - Jolanta Jura
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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Kober P, Boresowicz J, Rusetska N, Maksymowicz M, Paziewska A, Dąbrowska M, Kunicki J, Bonicki W, Ostrowski J, Siedlecki JA, Bujko M. The Role of Aberrant DNA Methylation in Misregulation of Gene Expression in Gonadotroph Nonfunctioning Pituitary Tumors. Cancers (Basel) 2019; 11:E1650. [PMID: 31731486 PMCID: PMC6895980 DOI: 10.3390/cancers11111650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 09/05/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/21/2022] Open
Abstract
Gonadotroph nonfunctioning pituitary adenomas (NFPAs) are common intracranial tumors, but the role of aberrant epigenetic regulation in their development remains poorly understood. In this study, we investigated the effect of impaired CpG methylation in NFPAs. We determined DNA methylation and transcriptomic profiles in 32 NFPAs and normal pituitary sections using methylation arrays and sequencing, respectively. Ten percent of differentially methylated CpGs were correlated with gene expression, and the affected genes are involved in a variety of tumorigenesis-related pathways. Different proportions of gene body and promoter region localization were observed in CpGs with negative and positive correlations between methylation and gene expression, and different proportions of CpGs were located in 'open sea' and 'shelf/shore' regions. The expression of ~8% of genes differentially expressed in NFPAs was related to aberrant methylation. Methylation levels of seven CpGs located in the regulatory regions of FAM163A, HIF3A and PRSS8 were determined by pyrosequencing, and gene expression was measured by qRT-PCR and immunohistochemistry in 83 independent NFPAs. The results clearly confirmed the negative correlation between methylation and gene expression for these genes. By identifying which aberrantly methylated CpGs affect gene expression in gonadotrophinomas, our data confirm the role of aberrant methylation in pathogenesis of gonadotroph NFPAs.
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Affiliation(s)
- Paulina Kober
- Department of Molecular and Translational Oncology, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (P.K.); (J.B.); (N.R.); (J.A.S.)
| | - Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (P.K.); (J.B.); (N.R.); (J.A.S.)
| | - Natalia Rusetska
- Department of Molecular and Translational Oncology, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (P.K.); (J.B.); (N.R.); (J.A.S.)
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland;
| | - Agnieszka Paziewska
- Department of Genetics, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (J.K.); (W.B.)
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (J.K.); (W.B.)
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland
| | - Janusz A. Siedlecki
- Department of Molecular and Translational Oncology, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (P.K.); (J.B.); (N.R.); (J.A.S.)
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Skłodowska-Curie Institute—Oncology Center, 02-034 Warsaw, Poland; (P.K.); (J.B.); (N.R.); (J.A.S.)
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27
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Hennig EE, Piątkowska M, Goryca K, Pośpiech E, Paziewska A, Karczmarski J, Kluska A, Brewczyńska E, Ostrowski J. Non- CYP2D6 Variants Selected by a GWAS Improve the Prediction of Impaired Tamoxifen Metabolism in Patients with Breast Cancer. J Clin Med 2019; 8:jcm8081087. [PMID: 31344832 PMCID: PMC6722498 DOI: 10.3390/jcm8081087] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/28/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
A certain minimum plasma concentration of (Z)-endoxifen is presumably required for breast cancer patients to benefit from tamoxifen therapy. In this study, we searched for DNA variants that could aid in the prediction of risk for insufficient (Z)-endoxifen exposure. A metabolic ratio (MR) corresponding to the (Z)-endoxifen efficacy threshold level was adopted as a cutoff value for a genome-wide association study comprised of 287 breast cancer patients. Multivariate regression was used to preselect variables exhibiting an independent impact on the MR and develop models to predict below-threshold MR values. In total, 15 single-nucleotide polymorphisms (SNPs) were significantly associated with below-threshold MR values. The strongest association was with rs8138080 (WBP2NL). Two alternative models for MR prediction were developed. The predictive accuracy of Model 1, including rs7245, rs6950784, rs1320308, and the CYP2D6 genotype, was considerably higher than that of the CYP2D6 genotype alone (AUC 0.879 vs 0.758). Model 2, which was developed using the same three SNPs as for Model 1 plus rs8138080, appeared as an interesting alternative to the full CYP2D6 genotype testing. In conclusion, the four novel SNPs, tested alone or in combination with the CYP2D6 genotype, improved the prediction of impaired tamoxifen-to-endoxifen metabolism, potentially allowing for treatment optimization.
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Affiliation(s)
- Ewa E Hennig
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland.
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Elżbieta Brewczyńska
- Department of Breast Cancer and Reconstructive Surgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
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Mazan M, Majewska E, Mikula M, Wiklik K, Combik M, Golas A, Masiejczyk M, Fiedor E, Polak A, Cybulska M, Grochowska A, Kopczynski M, Kuklinska U, Sandowska-Markiewicz Z, Statkiewicz M, Paziewska A, Dabrowska M, Bialas A, Mikulski M, Windak R, Ostrowski J, Juszczynski P, Brzozka K, Rzymski T. Abstract 1306: SEL120, a potent and specific inhibitor of CDK8 induces complete remission in human patient derived xenograft models of acute myeloid leukemia. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1306] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cyclin-dependent kinase 8 inhibitors (CDK8i) have anti-cancer activity in human acute myeloid leukaemia (AML) cell lines both in vitro and in vivo. Activity of CDK8i often involves deregulation of super-enhancer-associated genes in AML cell lines. Previous studies established SEL120 as a specific CDK8 inhibitor active in AML cells with increased STAT1/5 signalling pathways. Differential gene expression analysis demonstrated high enrichment of leukaemia stem cell (LSC) signatures in responding cells, linked to resistance to standard therapies and relapsed disease. Cells sensitive to SEL120 treatment were positive for CD34 and negative for lineage commitment surface markers. SEL120 markedly reduced STAT5 phosphorylation on serine 726 (STAT5 pS726) in sensitive cell lines. Prolonged SEL120 treatment led to significant downregulation of CD34 and induction of lineage commitment markers. Transcriptomic analysis revealed that SEL120 regulated many genes involved in differentiation and apoptosis. We observed synergistic effects of SEL120 with standard of care cytotoxic drugs such as cytarabine. Treatment of AML cells with cytarabine spared many CD34+ cells, which could be effectively eradicated by subsequent treatment with SEL120. Many cell lines which were resistant to SEL120 treatment could be sensitized by concomitant treatment with BH3 mimetic agent ABT-199. Combination of both compounds resulted in potent induction of apoptosis in AML cells in vitro and in vivo. Treatment of mice bearing subcutaneously implanted human leukaemia cell lines resulted in significant tumour growth inhibition, whereas cotreatment with ABT-199 led to complete regressions at doses which were vey well tolerated by animals. Next we have selected patient derived primary AML cells using gene expression signatures identifying SEL120 -responder cell lines. In these cells SEL120 significantly reduced viability, induced apoptosis and lineage commitment. Further, the same cells were implanted into NOD scid gamma mice. Animals succumbed to AML, diagnosed by a significant presence of human CD45/CD34 positive leukaemia cells in a peripheral blood and splenomegaly. Stand-alone treatment with SEL120 resulted in the complete remission of AML cells in a peripheral blood and bone marrow, and reduced spleen weight, without symptoms of compound-related toxicity. These results validate SEL120 as a promising agent in the treatment of AML.
Citation Format: Milena Mazan, Eliza Majewska, Michal Mikula, Katarzyna Wiklik, Michal Combik, Aniela Golas, Magdalena Masiejczyk, Elzbieta Fiedor, Anna Polak, Magdalena Cybulska, Aleksandra Grochowska, Michal Kopczynski, Urszula Kuklinska, Zuzanna Sandowska-Markiewicz, Malgorzata Statkiewicz, Agnieszka Paziewska, Michalina Dabrowska, Arkadiusz Bialas, Maciej Mikulski, Renata Windak, Jerzy Ostrowski, Przemyslaw Juszczynski, Krzysztof Brzozka, Tomasz Rzymski. SEL120, a potent and specific inhibitor of CDK8 induces complete remission in human patient derived xenograft models of acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1306.
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Affiliation(s)
| | | | - Michal Mikula
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | | | | | | | | | | | - Anna Polak
- 3Institute of Hematology and Transfusion Medicine, Poland
| | - Magdalena Cybulska
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | - Aleksandra Grochowska
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | - Michal Kopczynski
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | - Urszula Kuklinska
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | | | - Malgorzata Statkiewicz
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | - Agnieszka Paziewska
- 4Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Poland
| | - Michalina Dabrowska
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
| | | | | | | | - Jerzy Ostrowski
- 2Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Poland
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Rudzińska M, Grzanka M, Stachurska A, Mikula M, Paczkowska K, Stępień T, Paziewska A, Ostrowski J, Czarnocka B. Molecular Signature of Prospero Homeobox 1 (PROX1) in Follicular Thyroid Carcinoma Cells. Int J Mol Sci 2019; 20:ijms20092212. [PMID: 31060342 PMCID: PMC6539481 DOI: 10.3390/ijms20092212] [Citation(s) in RCA: 6] [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: 03/13/2019] [Revised: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 01/15/2023] Open
Abstract
The prospero homeobox 1 (PROX1) transcription factor is a product of one of the lymphangiogenesis master genes. It has also been suggested to play a role in carcinogenesis, although its precise role in tumour development and metastasis remains unclear. The aim of this study was to gain more knowledge on the PROX1 function in thyroid tumorigenesis. Follicular thyroid cancer-derived cells—CGTH-W-1—were transfected with PROX1-siRNA (small interfering RNA) and their proliferation, cell cycle, apoptosis and motility were then analysed. The transcriptional signature of PROX1 depletion was determined using RNA-Sequencing (RNA-Seq) and the expression of relevant genes was further validated using reverse transcriptase quantitative PCR (RT-qPCR), Western blot and immunocytochemistry. PROX1 depletion resulted in a decreased cell motility, with both migratory and invasive potential being significantly reduced. The cell morphology was also affected, while the other studied cancer-related cell characteristics were not significantly altered. RNA-seq analysis revealed significant changes in the expression of transcripts encoding genes involved in both motility and cytoskeleton organization. Our transcriptional analysis of PROX1-depleted follicular thyroid carcinoma cells followed by functional and phenotypical analyses provide, for the first time, evidence that PROX1 plays an important role in the metastasis of thyroid cancer cells by regulating genes involved in focal adhesion and cytoskeleton organization in tumour cells.
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Affiliation(s)
- Magdalena Rudzińska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Małgorzata Grzanka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Anna Stachurska
- Department of Immunohematology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Michał Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland.
| | - Katarzyna Paczkowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland.
| | - Tomasz Stępień
- Clinic of Endocrinological and General Surgery, Medical University of Lodz, 93-513 Lodz, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland.
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
| | - Barbara Czarnocka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
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30
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Ostrowski J, Dabrowska M, Lazowska I, Paziewska A, Balabas A, Kluska A, Kulecka M, Karczmarski J, Ambrozkiewicz F, Piatkowska M, Goryca K, Zeber-Lubecka N, Kierkus J, Socha P, Lodyga M, Klopocka M, Iwanczak B, Bak-Drabik K, Walkowiak J, Radwan P, Grzybowska-Chlebowczyk U, Korczowski B, Starzynska T, Mikula M. Redefining the Practical Utility of Blood Transcriptome Biomarkers in Inflammatory Bowel Diseases. J Crohns Colitis 2019; 13:626-633. [PMID: 30541017 PMCID: PMC6486489 DOI: 10.1093/ecco-jcc/jjy205] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS The study investigates the practical utility of whole-blood gene expression profiling to diagnose inflammatory bowel diseases [IBDs]. METHODS The discovery cohorts included 102 and 51 paediatric IBD patients and controls, and 95 and 46 adult IBD patients and controls, respectively. The replication cohorts included 447 and 76 paediatric IBD patients and controls, and 271 and 108 adult IBD patients and controls, respectively. In the discovery phase, RNA samples extracted from whole peripheral blood were analysed using RNA-Seq, and the predictive values of selected biomarkers were validated using quantitative polymerase chain reaction [qPCR]. RESULTS In all, 15 differentially expressed transcripts [adjusted p ≤0.05] were selected from the discovery sequencing datasets. The receiver operating characteristic curves and area under the curve [ROC-AUC] in replication analyses showed high discriminative power [AUC range, 0.91-0.98] for 11 mRNAs in paediatric patients with active IBD. By contrast, the AUC-ROC values ranged from 0.63 to 0.75 in comparison among inactive paediatric IBDs and active/inactive adult IBDs, indicating a lack of discriminative power. The best multi-mRNA diagnostic classifier showed moderate discriminative power [AUC = 0.81] for paediatric inactive IBD, but was not able to discriminate active or inactive adult IBD patients from controls. The AUC-ROC values did not confirm an ability of the mRNAs abundances to discriminate between active ulcerative colitis and active Crohn's disease in paediatric or adult populations. CONCLUSIONS This study identifies and validates blood transcriptional biomarkers that could be used in clinical settings as diagnostic predictors of IBD clinical activity in paediatric, but not adult, IBD patients.
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Affiliation(s)
- Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland,Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland,Corresponding author: Jerzy Ostrowski, MD, PhD; Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland. Tel.: +48 225462575; e-mail:
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Izabella Lazowska
- Department of Pediatric Gastroenterology and Nutrition, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Jaroslaw Kierkus
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children’s Memorial Health Institute, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children’s Memorial Health Institute, Warsaw, Poland
| | - Michal Lodyga
- Department of Internal Medicine and Gastroenterology with IBD Subdivision, Central Clinical Hospital of the Ministry of the Interior, Warsaw, Poland
| | - Maria Klopocka
- Vascular Diseases and Internal Medicine, Nicolaus Copernicus University in Torun, Collegium Medicum, Bydgoszcz, Poland
| | - Barbara Iwanczak
- Department of Pediatrics, Gastroenterology and Nutrition, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Bak-Drabik
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia, Katowice, Poland
| | - Jaroslaw Walkowiak
- Department of Pediatric Gastroenterology & Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Piotr Radwan
- Department of Gastroenterology, Medical University of Lublin, Lublin, Poland
| | | | | | - Teresa Starzynska
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Institute – Oncology Centre, Warsaw, Poland
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Kluska A, Kulecka M, Litwin T, Dziezyc K, Balabas A, Piatkowska M, Paziewska A, Dabrowska M, Mikula M, Kaminska D, Wiernicka A, Socha P, Czlonkowska A, Ostrowski J. Whole-exome sequencing identifies novel pathogenic variants across the ATP7B gene and some modifiers of Wilson's disease phenotype. Liver Int 2019; 39:177-186. [PMID: 30230192 DOI: 10.1111/liv.13967] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/05/2018] [Accepted: 09/09/2018] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Wilson's disease (WD) is an autosomal recessive disorder associated with disease-causing alterations across the ATP7B gene, with highly variable symptoms and age of onset. We aimed to assess whether the clinical variability of WD relates to modifier genes. METHODS A total of 248 WD patients were included, of whom 148 were diagnosed after age of 17. Human exome libraries were constructed using AmpliSeq technology and sequenced using the IonProton platform. RESULTS ATP7B p.His1069Gln mutation was present in 215 patients, with 112 homozygotes and 103 heterozygotes. Three other mutations: p.Gln1351Ter, p.Trp779Ter and c.3402delC were identified in >10 patients. Among patients, 117 had a homozygous mutation, 101 were compound heterozygotes, 27 had one heterozygous mutation, and 3 other patients had no identifiable pathogenic variant of ATP7B. Sixteen mutations were novel, found as part of a compound mutation or as a sole, homozygous mutation. For disease phenotype prediction, age at diagnosis was a deciding factor, while frameshift allelic variants of ATP7B and being male increased the odds of developing a neurological phenotype. Rare allelic variants in ESD and INO80 increased and decreased chances for the neurological phenotype, respectively, while rare variants in APOE and MBD6 decreased the chances of WD early manifestation. Compound mutations contributed to earlier age of onset. CONCLUSIONS In a Polish population, genetic screening for WD may help genotype for four variants (p.His1069Gln, p.Gln1351Ter, p.Trp779Ter and c.3402delC), with direct sequencing of all ATP7B amplicons as a second diagnostic step. We also identified some allelic variants that may modify a WD phenotype.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology and Hepatology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Tomasz Litwin
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Karolina Dziezyc
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland
| | | | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | | | - Michal Mikula
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland
| | - Diana Kaminska
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Wiernicka
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology, Nutritional Disorders and Pediatrics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Anna Czlonkowska
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Cancer Center-Institute, Warsaw, Poland.,Department of Gastroenterology and Hepatology, Centre of Postgraduate Medical Education, Warsaw, Poland
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Goryca K, Kulecka M, Paziewska A, Dabrowska M, Grzelak M, Skrzypczak M, Ginalski K, Mroz A, Rutkowski A, Paczkowska K, Mikula M, Ostrowski J. Exome scale map of genetic alterations promoting metastasis in colorectal cancer. BMC Genet 2018; 19:85. [PMID: 30231850 PMCID: PMC6146521 DOI: 10.1186/s12863-018-0673-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 11/14/2017] [Accepted: 09/12/2018] [Indexed: 12/19/2022] Open
Abstract
Background Approximately 90% of colorectal cancer (CRC) deaths are caused by tumors ability to migrate into the adjacent tissues and metastase into distant organs. More than 40 genes have been causally linked to the development of CRC but no mutations have been associated with metastasis yet. To identify molecular basis of CRC metastasis we performed whole-exome and genome-scale transcriptome sequencing of 7 liver metastases along with their matched primary tumours and normal tissue. Multiple, spatially separated fragments of primary tumours were analyzed in each case. Uniformly malignant tissue specimen were selected with macrodissection, for three samples followed with laser microdissection. Results > 100 sequencing coverage allowed for detection of genetic alterations in subpopulation of tumour cells. Mutations in KRAS, APC, POLE, and PTPRT, previously associated with CRC development, were detected in most patients. Several new associations were identified, including PLXND1, CELSR3, BAHD1 and PNPLA6. Conclusions We confirm the essential role of inflammation in CRC progression but question the mechanism of matrix metalloproteinases activation described in other work. Comprehensive sequencing data made it possible to associate genome-scale mutation distribution with gene expression patterns. To our knowledge, this is the first work to report such link in CRC metastasis context. Electronic supplementary material The online version of this article (10.1186/s12863-018-0673-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Krzysztof Goryca
- Depatment of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michalina Dabrowska
- Depatment of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Marta Grzelak
- Laboratory of Bioinformatics and Systems Biology, Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Center of New Technologies, University of Warsaw, Warsaw, Poland
| | - Andrzej Mroz
- Department of Patomorphology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Andrzej Rutkowski
- Department of Oncological Gastroenterology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Katarzyna Paczkowska
- Depatment of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Michal Mikula
- Depatment of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Depatment of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
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Zagajewska K, Piątkowska M, Goryca K, Bałabas A, Kluska A, Paziewska A, Pośpiech E, Grabska-Liberek I, Hennig EE. GWAS links variants in neuronal development and actin remodeling related loci with pseudoexfoliation syndrome without glaucoma. Exp Eye Res 2018; 168:138-148. [DOI: 10.1016/j.exer.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 01/13/2023]
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Lichawska-Cieslar A, Pietrzycka R, Ligeza J, Kulecka M, Paziewska A, Kalita A, Dolicka DD, Wilamowski M, Miekus K, Ostrowski J, Mikula M, Jura J. RNA sequencing reveals widespread transcriptome changes in a renal carcinoma cell line. Oncotarget 2018; 9:8597-8613. [PMID: 29492220 PMCID: PMC5823589 DOI: 10.18632/oncotarget.24269] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/24/2017] [Accepted: 12/30/2017] [Indexed: 12/12/2022] Open
Abstract
We used RNA sequencing (RNA-Seq) technology to investigate changes in the transcriptome profile in the Caki-1 clear cell renal cell carcinoma (ccRCC) cells, which overexpress monocyte chemoattractant protein-induced protein 1 (MCPIP1). RNA-Seq data showed changes in 11.6% and 41.8% of the global transcriptome of Caki-1 cells overexpressing wild-type MCPIP1 or its D141N mutant, respectively. Gene ontology and KEGG pathway functional analyses showed that these transcripts encoded proteins involved in cell cycle progression, protein folding in the endoplasmic reticulum, hypoxia response and cell signalling. We identified 219 downregulated transcripts in MCPIP1-expressing cells that were either unchanged or upregulated in D141N-expressing cells. We validated downregulation of 15 transcripts belonging to different functional pathways by qRT-PCR. The growth and viability of MCPIP1-expressing cells was reduced because of elevated p21Cip1 levels. MCPIP1-expressing cells also showed reduced levels of DDB1 transcript that encodes component of the E3 ubiquitin ligase that degrades p21Cip1. These results demonstrate that MCPIP1 influences the growth and viability of ccRCC cells by increasing or decreasing the transcript levels for proteins involved in cell cycle progression, protein folding, hypoxia response, and cell signaling.
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Affiliation(s)
- Agata Lichawska-Cieslar
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Roza Pietrzycka
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Janusz Ligeza
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Maria Kulecka
- Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Agata Kalita
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dobrochna D. Dolicka
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Mateusz Wilamowski
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Katarzyna Miekus
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jerzy Ostrowski
- Departments of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland
| | - Jolanta Jura
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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Paziewska A, Mikula M, Dabrowska M, Kulecka M, Goryca K, Antoniewicz A, Dobruch J, Borowka A, Rutkowski P, Ostrowski J. Candidate diagnostic miRNAs that can detect cancer in prostate biopsy. Prostate 2018; 78:178-185. [PMID: 29226351 DOI: 10.1002/pros.23427] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/30/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND While histopathological evaluation remains the gold standard for diagnosis of prostate cancer (PCa), sampling errors remain a frequent problem; therefore, use of tissue biomarkers that can distinguish between benign and malignant prostate disease is a potentially beneficial diagnostic strategy. METHODS Deep sequencing of the miRNA transcriptome of 14 benign prostatic hyperplasia (BPH) and 60 cancerous and non-cancerous prostate samples extracted from 34 cancer-bearing prostates removed by prostatectomy was performed; of the latter 60 samples, 16, 21, and 23 samples contained <10%, >30%, and no dysplastic cells, respectively. The predictive value of selected miRNAs was then tested by quantitative reverse-transcribed PCR (qRT-PCR), using two separate chemistries, Exiqon and Taqman, to evaluate the tissue samples obtained by prostatectomy. Validation experiments were also performed for a subset of miRNAs by qRT-PCR of 87 prostate core biopsies. RESULTS We identified 123 miRNAs significantly dysregulated in PCa (adjusted P-values <0.05); 110 and 13 miRNAs were dysregulated only in cancerous samples and non-cancerous samples extracted from cancer-bearing prostates, respectively, while 31 were dysregulated regardless of the dysplastic cell content of the studied specimens. The clinical utility of eight selected miRNAs was analyzed using the same sample set with two qRT-PCR chemistries. Measurable qRT-PCR signals were obtained for seven and six miRNAs using the Exiqon and Taqman chemistries, respectively, and expression levels of six and four of these miRNAs differed significantly between BPH and PCa samples, regardless of dysplastic cell content. Validation experiments on core biopsies using qRT-PCR confirmed differential expression between BPH and PCa of four miRNAs (miR-187-3p, miR-183-5p, miR-32-5p, and miR-141-5p) using the Exiqon and one miRNA (miR-187-3p) with the Taqman chemistry. CONCLUSIONS Our sequencing analyses identified several candidate diagnostic miRNAs and confirmed some which have previously been reported as diagnostic in prostate malignancy. The results of this study suggest also that some of selected miRNAs can differentiate between non-malignant and malignant prostates even when neoplastic cells are missing from the studied specimen.
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Affiliation(s)
- Agnieszka Paziewska
- Departmentof Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Departmentof Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Artur Antoniewicz
- Department of Urology, Multidisciplinary Hospital Warsaw-Miedzylesie, Warsaw, Poland
| | - Jakub Dobruch
- Clinical Department of Urology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Andrzej Borowka
- Clinical Department of Urology, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue, Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Departmentof Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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Kosela Paterczyk H, Mikula M, Paziewska A, Kulecka M, Kaczmarski J, Dabrowska M, Kluska A, Balabas A, Piatkowska M, Rutkowski P, Ostrowski J. Serum miRNA discriminates treatment-naive localized synovial sarcoma patients from those in follow-up after radical combined therapy. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx675.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Kulecka M, Wierzbicka A, Paziewska A, Mikula M, Habior A, Janczyk W, Dabrowska M, Karczmarski J, Lazniewski M, Ginalski K, Czlonkowska A, Socha P, Ostrowski J. A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase. J Hepatol 2017; 67:1026-1030. [PMID: 28716744 DOI: 10.1016/j.jhep.2017.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/16/2017] [Accepted: 07/01/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Macro-aspartate aminotransferase (macro-AST) manifests as a persistent elevation of AST levels, because of association of the protein with immunoglobulins in the circulation. Macro-AST is a rare, benign condition without a previously confirmed genetic basis. METHODS Whole exome sequencing (WES)-based screening was performed on 32 participants with suspected familial macro-AST, while validation of variants was performed on an extended cohort of 92 probands and 1,644 healthy controls using Taqman genotyping. RESULTS A missense variant (p.Gln208Glu, rs374966349) in glutamate oxaloacetate transaminase 1 (GOT1) was found, as a putative causal variant predisposing to familial macro-AST. The GOT1 p.Gln208Glu mutation was detected in 50 (54.3%) of 92 probands from 20 of 29 (69%) families, while its prevalence in healthy controls was only 0.18%. In silico analysis demonstrated that the amino acid at this position is not conserved among different species and that, functionally, a negatively charged glutamate on the GOT1 surface could strongly anchor serum immunoglobulins. CONCLUSIONS Our data highlight that testing for the p.Gln208Glu genetic variant may be useful in diagnosis of macro-AST. LAY SUMMARY Higher than normal levels of aspartate aminotransferase (AST) in the bloodstream may be a sign of a health problem. Individuals with macro-AST have elevated blood AST levels, without ongoing disease and often undergo unnecessary medical tests before the diagnosis of macro-AST is established. We found a genetic variant in the GOT1 gene associated with macro-AST. Genetic testing for this variant may aid diagnosis of macro-AST.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw 01-813, Poland
| | - Aldona Wierzbicka
- Department of Biochemistry, Radioimmunology and Experimental Medicine, Children's Memorial Health Institute, Warsaw 04-730, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw 01-813, Poland
| | - Michal Mikula
- Department of Genetics, Cancer Center-Institute, Warsaw 02-781, Poland
| | - Andrzej Habior
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw 01-813, Poland
| | - Wojciech Janczyk
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children's Memorial Health Institute, Warsaw 04-730, Poland
| | | | - Jakub Karczmarski
- Department of Genetics, Cancer Center-Institute, Warsaw 02-781, Poland
| | - Michal Lazniewski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw 02-089, Poland; Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw 02-097, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw 02-089, Poland
| | - Anna Czlonkowska
- Department of Neurology, Institute of Psychiatry and Neurology, Warsaw, Poland
| | - Piotr Socha
- Department of Gastroenterology, Hepatology and Feeding Disorders, Children's Memorial Health Institute, Warsaw 04-730, Poland.
| | - Jerzy Ostrowski
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw 01-813, Poland; Department of Genetics, Cancer Center-Institute, Warsaw 02-781, Poland.
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Losko M, Lichawska-Cieslar A, Kulecka M, Paziewska A, Rumienczyk I, Mikula M, Jura J. Ectopic overexpression of MCPIP1 impairs adipogenesis by modulating microRNAs. Biochim Biophys Acta Mol Cell Res 2017; 1865:186-195. [PMID: 28939056 DOI: 10.1016/j.bbamcr.2017.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 01/12/2023]
Abstract
Adipogenesis is a process of preadipocyte differentiation that requires action of numerous factors. Monocyte chemoattractant protein-1-induced protein 1 (MCPIP1) possesses the N-terminus of the PilT protein (PilT N-terminus or PIN domain) that has RNase properties. This protein degrades transcripts coding for inflammation and differentiation - related proteins. Moreover, MCPIP1 is a broad suppressor of the miRNA biogenesis. We previously found that MCPIP1 degrades transcript encoding CCAAT/Enhancer Binding Protein Beta (C/EBPβ) and influences adipogenesis. Subsequently, we aimed to determine adipocyte miRNA expression profile in differentiating mouse preadipocytes, 3T3-L1, by overexpressing MCPIP1. Using Next-Generation Sequencing (NSG) we showed that MCPIP1 overexpression results in modulated levels of 58 miRNAs in adipocytes on day 2 of differentiation. Among them, 30 miRNAs showed significantly reduced levels and 28 showed increased levels in comparison to control. Approximately one third of the modulated miRNAs were not previously reported to be involved in adipocytes differentiation. Our analysis revealed that 24 down-regulated and 23 up-regulated miRNAs (at least 1.5-fold) influence 19 signaling pathways that are important for adipogenesis. Furthermore, reduced miRNA levels result in the up-regulation of their targets. By using luciferase reporter assay, we demonstrated that miR-32-5p and miR-9-3p directly target the 3'UTR region of Mapk8 and Tiam1, respectively. In addition, activation of MAP kinases pathway (JNK and p38), proposed as being regulated by down-regulated miRNAs, was higher in WTMCPIP1 than in D141NMCPIP1 or control 3T3-L1 adipocytes. Our results indicate a considerable impact of MCPIP1 on miRNAs levels and its significance in adipogenesis.
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Affiliation(s)
- Magdalena Losko
- Department of General Biochemistry, Jagiellonian University, Krakow, Poland
| | | | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Izabela Rumienczyk
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jolanta Jura
- Department of General Biochemistry, Jagiellonian University, Krakow, Poland.
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Kosela Paterczyk H, Paziewska A, Kulecka M, Karczmarski J, Dabrowska M, Kluska A, Balabas A, Piatkowska M, Mikula M, Rutkowski P, Ostrowski J. Serum miRNA abundances discriminate imatinib-naive patients with advanced gastrointestinal stromal tumors (GIST) from those in remission on Imatinib therapy. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx387.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Rzymski T, Wrobel A, Mikula M, Pyziak K, Bartosik A, Sroka A, Paziewska A, Grochowska A, Statkiewicz M, Paczkowska K, Dabrowska M, Ostrowski J, Brzozka K. Abstract 5063: Epigenetic modulators show differential activity on lung adenocarcinoma cells with loss-of-function mutations of SWI/SNF protein SMARCA4. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5063] [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: 11/16/2022]
Abstract
Abstract
SWI/SNF is a multiprotein chromatin remodeler with ATP-dependent activities leading to selective gene expression, DNA repair, recombination and replication. Various sequencing efforts indicated that nearly 20% of cancers bear mutations in at least one subunit of the complex. One of the crucial regulators of the complex is SMARCA4, a member of SWI/SNF family of helicases with ATPase activities, which are thought to regulate transcription of certain genes by altering the chromatin structure. SMARCA4 is mutated in virtually all cases of small cell carcinoma of the ovary and SMARCA4 is fourth the most frequently mutated gene in lung adenocarcinoma. High occurrence of inactivating mutations prompted several screenings projects focused on synthetic lethality interactions with other proteins, which led to the identification of SMARCA2 as an essential gene in SMARCA4 mutated cancers. This vulnerability could be potentially exploited therapeutically and several groups managed to identify potent ligands of SMARCA2 bromodomain. Surprisingly these molecules were inactive in SMARCA4 mutant cells, however additional studies indicated that ATPase rather than bromodomain is a target for novel compounds with anticancer activities. Overall, these results revealed functional complexity of SMARCA2 and SMARCA4 in cancer cells. In order to characterize molecular consequences of SMARCA2 silencing in SMARCA4 mutant lung adenocarcinoma cells, we have carried out a series of gene knockdown experiments, followed by transcriptional profiling by RNAseq and analysis of posttranslational histone modifications. These studies indicated rapid and irreversible loss of viability in SMARCA4 mutant cells after SMARCA2 gene silencing. Interestingly double SMARCA2/SMARCA4 knockdown in SMARCA4 WT cells has not resulted in lowered viability. Transcriptional profiling of SMARCA2 knockdown in SMARCA4 mutated cells revealed broad, predominantly repressory effects on gene expression levels. Gene set enrichment analysis showed significant inhibitory effects of SMARCA2 knockdown, particularly on transcripts which could be induced after reintroduction of SMARCA4. Furthermore MS/MS analysis indicated global rearrangements in histone epigenetic marks. These results prompted us to test activity of small-molecule epigenetic modulators, including DNA Methyltransferases (DNMTs), Histone Acetyltransferases (HATs), Histone Deacetylases (HDACs), Histone Methyltransferases (HMTs), Histone Demethylases (HDMs) and a distinct set of chromatin readers, bromodomains. Differential activity of these compounds provides a strong basis for novel strategies for the treatment of cancers with loss-of-function mutations of SMARCA4.
Citation Format: Tomasz Rzymski, Anna Wrobel, Michal Mikula, Karolina Pyziak, Anna Bartosik, Agnieszka Sroka, Agnieszka Paziewska, Aleksandra Grochowska, Malgorzata Statkiewicz, Katarzyna Paczkowska, Michalina Dabrowska, Jerzy Ostrowski, Krzysztof Brzozka. Epigenetic modulators show differential activity on lung adenocarcinoma cells with loss-of-function mutations of SWI/SNF protein SMARCA4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5063. doi:10.1158/1538-7445.AM2017-5063
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Affiliation(s)
| | | | - Michal Mikula
- 2Maria Sklodowska-Curie Memorial Cancer Center, Warsaw, Poland
| | | | | | | | | | | | | | | | | | - Jerzy Ostrowski
- 2Maria Sklodowska-Curie Memorial Cancer Center, Warsaw, Poland
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Kulecka M, Habior A, Paziewska A, Goryca K, Dąbrowska M, Ambrozkiewicz F, Walewska-Zielecka B, Gabriel A, Mikula M, Ostrowski J. Clinical Applicability of Whole-Exome Sequencing Exemplified by a Study in Young Adults with the Advanced Cryptogenic Cholestatic Liver Diseases. Gastroenterol Res Pract 2017; 2017:4761962. [PMID: 28626473 PMCID: PMC5463139 DOI: 10.1155/2017/4761962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The proper use of new medical tests in clinical practice requires the establishment of their value and range of diagnostic usefulness. While whole-exome sequencing (WES) has already entered the medical practice, recognizing its diagnostic usefulness in multifactorial diseases has not yet been achieved. AIMS The objective of this study was to establish usability of WES in determining genetic background of chronic cholestatic liver disease (CLD) in young patients. METHODS WES was performed on six young patients (between 17 and 22 years old) with advanced fibrosis or cirrhosis due to CLD and their immediate families. Sequencing was performed on an Ion Proton sequencer. RESULTS On average, 19,673 variants were identified, of which from 7 to 14 variants of an individual were nonsynonymous, homozygous, recessively inherited, and considered in silico as pathogenic. Although monogenic cause of CLD has not been determined, several heterozygous rare variants and polymorphisms were uncovered in genes previously known to be associated with CLD, including ATP8B1, ABCB11, RXRA, and ABCC4, indicative of multifactorial genetic background. CONCLUSIONS WES is a potentially useful diagnostic tool in determining genetic background of multifactorial diseases, but its main limitation results from the lack of opportunities for direct linkage between the uncovered genetic variants and molecular mechanisms of disease.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
| | - Andrzej Habior
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland
| | - Michalina Dąbrowska
- Department of Genetics, Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
| | - Bożena Walewska-Zielecka
- Department of Public Health, Faculty of Health Sciences, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Andrzej Gabriel
- Department of Pathomorphology, Medical University of Silesia, Medyków 18, 40-752 Katowice, Poland
| | - Michal Mikula
- Department of Genetics, Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781 Warsaw, Poland
- Department of Genetics, Cancer Center-Institute, Roentgena 5, 02-781 Warsaw, Poland
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Paziewska A, Habior A, Rogowska A, Zych W, Goryca K, Karczmarski J, Dabrowska M, Ambrozkiewicz F, Walewska-Zielecka B, Krawczyk M, Cichoz-Lach H, Milkiewicz P, Kowalik A, Mucha K, Raczynska J, Musialik J, Boryczka G, Wasilewicz M, Ciecko-Michalska I, Ferenc M, Janiak M, Kanikowska A, Stankiewicz R, Hartleb M, Mach T, Grzymislawski M, Raszeja-Wyszomirska J, Wunsch E, Bobinski T, Mikula M, Ostrowski J. A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients. BMC Med Genomics 2017; 10:2. [PMID: 28056976 PMCID: PMC5217265 DOI: 10.1186/s12920-016-0239-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 12/15/2016] [Indexed: 01/28/2023] Open
Abstract
Background Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are forms of hepatic autoimmunity, and risk for both diseases has a strong genetic component. This study aimed to define the genetic architecture of PBC and PSC within the Polish population. Methods Subjects were 443 women with PBC, 120 patients with PSC, and 934 healthy controls recruited from Gastroenterology Departments in various Polish hospitals. Allelotyping employed a pooled-DNA sample-based genome-wide association study (GWAS) approach, using Illumina Human Omni2.5-Exome BeadChips and the following novel selection criteria for risk loci: blocks of at least 10 single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium, where the distance between each adjacent SNP pair in the block was less than 30 kb, and each SNP was associated with disease at a significance level of P < 0.005. A selected index SNP from each block was validated using TaqMan SNP genotyping assays. Results Nineteen and twenty-one SNPs were verified as associated with PBC and PSC, respectively, by individual genotyping; 19 (10/9, PBC/PSC) SNPs reached a stringent (corrected) significance threshold and a further 21 (9/12, PBC/PSC) reached a nominal level of significance (P < 0.05 with odds ratio (OR) > 1.2 or < 0.83), providing suggestive evidence of association. The SNPs mapped to seven (1p31.3, 3q13, 6p21, 7q32.1, 11q23.3, 17q12, 19q13.33) and one (6p21) chromosome region previously associated with PBC and PSC, respectively. The SNP, rs35730843, mapping to the POLR2G gene promoter (P = 1.2 × 10-5, OR = 0.39) demonstrated the highest effect size, and was protective for PBC, whereas for PSC respective SNPs were: rs13191240 in the intron of ADGRB3 gene (P = 0.0095, OR = 0.2) and rs3822659 (P = 0.0051, OR = 0.236) along with rs9686714 (P = 0.00077, OR = 0.2), both located in the WWC1 gene. Conclusions Our cost-effective GWAS approach followed by individual genotyping confirmed several previously identified associations and discovered new susceptibility loci associated with PBC and/or PSC in Polish patients. However, further functional studies are warranted to understand the roles of these newly identified variants in the development of the two disorders. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0239-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Andrzej Habior
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Rogowska
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Włodzimierz Zych
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Bozena Walewska-Zielecka
- Department of Public Health, Faculty of Health Sciences, Medical University of Warsaw, Warsaw, Poland
| | - Marek Krawczyk
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | | | - Piotr Milkiewicz
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland.,Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Raczynska
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Musialik
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Grzegorz Boryczka
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Michal Wasilewicz
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Irena Ciecko-Michalska
- Department of Gastroenterology and Infectious Diseases, Collegium Medicum Jagiellonian University, Krakow, Poland
| | - Malgorzata Ferenc
- Department of Gastroenterology, Provincial Hospital, Olsztyn, Poland
| | - Maria Janiak
- Department of Gastroenterology and Hepatology, Medical University of Gdansk, Gdansk, Poland
| | - Alina Kanikowska
- Department of Internal and Metabolic Diseases and Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Rafal Stankiewicz
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Marek Hartleb
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Tomasz Mach
- Department of Gastroenterology and Infectious Diseases, Collegium Medicum Jagiellonian University, Krakow, Poland
| | - Marian Grzymislawski
- Department of Internal and Metabolic Diseases and Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Raszeja-Wyszomirska
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Wunsch
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Bobinski
- Department of Gastroenterology, Provincial Hospital, Ostroleka, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
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Kistowski M, Dębski J, Karczmarski J, Paziewska A, Olędzki J, Mikula M, Ostrowski J, Dadlez M. A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome. Mol Cell Proteomics 2016; 16:213-227. [PMID: 27927741 DOI: 10.1074/mcp.m116.058818] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 11/12/2016] [Indexed: 12/18/2022] Open
Abstract
Proteolytic cascades are deeply involved in critical stages of cancer progression. During the course of peptide-wise analysis of shotgun proteomic data sets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed of a set of numerous protein fragments cleaved C-terminally to V, I, A, T, or C residues, significantly overrepresented in AC. A peptide set linked by a common VIATC cleavage consensus was the only prominent cancer-specific proteolytic fingerprint detected. This sequence consensus indicated neutrophil elastase as a source of the fingerprint. We also found that a large fraction of affected proteins are RNA processing proteins associated with the nuclear fraction and mostly cleaved within their functionally important RNA-binding domains. Thus, we detected a new class of cancer-specific peptides that are possible markers of tumor-infiltrating neutrophil activity, which often correlates with the clinical outcome. Data are available via ProteomeXchange with identifiers: PXD005274 (Data set 1) and PXD004249 (Data set 2). Our results indicate the value of peptide-wise analysis of large global proteomic analysis data sets as opposed to protein-wise analysis, in which outlier differential peptides are usually neglected.
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Affiliation(s)
- Michał Kistowski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Janusz Dębski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Jakub Karczmarski
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Agnieszka Paziewska
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jacek Olędzki
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Michał Mikula
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- ¶Department of Gastroenterology Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Dadlez
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw;
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Kulecka M, Paziewska A, Zeber-Lubecka N, Ambrozkiewicz F, Kopczynski M, Kuklinska U, Pysniak K, Gajewska M, Mikula M, Ostrowski J. Prolonged transfer of feces from the lean mice modulates gut microbiota in obese mice. Nutr Metab (Lond) 2016; 13:57. [PMID: 27559357 PMCID: PMC4995824 DOI: 10.1186/s12986-016-0116-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [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: 06/13/2016] [Accepted: 08/16/2016] [Indexed: 12/31/2022] Open
Abstract
Background Transplanting a fecal sample from lean, healthy donors to obese recipients has been shown to improve metabolic syndrome symptoms. We therefore examined the gut microbiota in mice after administering a long-term, high-fat diet (HFD) supplemented with feces from lean mice through the fecal-oral route. Methods C57BL6/W mice were allowed to adapt to a non-specific pathogen free (SFP) environment for 2 weeks before being divided into three groups of 16 animals. Animals were fed for 28 weeks with a normal diet (ND), HFD or HFD supplemented with feces from ND-fed mice (HFDS). The composition of colonizing bacteria was evaluated in droppings collected under SPF conditions at the beginning of the study and at 12 and 28 weeks using an 16S Metagenomics Kit on Ion PGM sequencer. Results HFD and HFDS-fed mice attained (p < 0.05) greater body weights by weeks 6 and 5, respectively. HFDS-fed mice gained more weight than HFD-fed mice by week 25. Both species diversity and richness indices increased with time in HFDS mice only. Conclusions Prolonged HFD-fed mice supplementation with feces from lean mice altered bacteria species diversity and richness, accelerated the onset of obesity, and caused increased weight gain in the later weeks of the HFD regimen. Electronic supplementary material The online version of this article (doi:10.1186/s12986-016-0116-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michal Kopczynski
- Department of Genetics, Maria Sklodowska-Curie Memorial, Cancer Center and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - Urszula Kuklinska
- Department of Genetics, Maria Sklodowska-Curie Memorial, Cancer Center and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - Kazimiera Pysniak
- Department of Genetics, Maria Sklodowska-Curie Memorial, Cancer Center and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - Marta Gajewska
- Department of Genetics, Maria Sklodowska-Curie Memorial, Cancer Center and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial, Cancer Center and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland ; Department of Genetics, Maria Sklodowska-Curie Memorial, Cancer Center and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
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Zeber-Lubecka N, Kulecka M, Ambrozkiewicz F, Paziewska A, Goryca K, Karczmarski J, Rubel T, Wojtowicz W, Mlynarz P, Marczak L, Tomecki R, Mikula M, Ostrowski J. Limited prolonged effects of rifaximin treatment on irritable bowel syndrome-related differences in the fecal microbiome and metabolome. Gut Microbes 2016; 7:397-413. [PMID: 27662586 PMCID: PMC5046165 DOI: 10.1080/19490976.2016.1215805] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a chronic functional disorder and its development may be linked, directly and indirectly, to intestinal dysbiosis. Here we investigated the interactions between IBS symptoms and the gut microbiome, including the relation to rifaximin (1200 mg daily; 11.2 g per a treatment). We recruited 72 patients, including 31 with IBS-D (diarrhea), 11 with IBS-C (constipation), and 30 with IBS-M (mixed constipation and diarrhea) and 30 healthy controls (HCs). Of them, 68%, 64%, and 53% patients with IBS-D, IBS-C, and IBS-M, respectively, achieved 10-12 week-term improvement after the rifaximin treatment. Stool samples were collected before and after the treatment, and fecal microbiotic profiles were analyzed by deep sequencing of 16S rRNA, while stool metabolic profiles were studied by hydrogen 1-nuclear magnetic resonance ((1)H-NMR) and gas chromatography-mass spectrometry (GC-MS). Of 26 identified phyla, only Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria were consistently found in all samples. Bacteroidetes was predominant in fecal samples from HCs and IBS-D and IBS-M subjects, whereas Firmicutes was predominant in samples from IBS-C subjects. Species richness, but not community diversity, differentiated all IBS patients from HCs. Metabolic fingerprinting, using NMR spectra, distinguished HCs from all IBS patients. Thirteen metabolites identified by GC-MS differed HCs and IBS patients. However, neither metagenomics nor metabolomics analyses identified significant differences between patients with and without improvement after treatment.
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Affiliation(s)
- Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Tymon Rubel
- Institute of Radioelectronics, Warsaw University of Technology, Warsaw, Poland
| | - Wojciech Wojtowicz
- Department of Bioorganic Chemistry Wroclaw University of Technology, Wroclaw, Poland
| | - Piotr Mlynarz
- Department of Bioorganic Chemistry Wroclaw University of Technology, Wroclaw, Poland
| | - Lukasz Marczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
| | - Roman Tomecki
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland,Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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Zeber-Lubecka N, Kulecka M, Ambrozkiewicz F, Paziewska A, Lechowicz M, Konopka E, Majewska U, Borszewska-Kornacka M, Mikula M, Cukrowska B, Ostrowski J. Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants. PLoS One 2016; 11:e0150306. [PMID: 26918330 PMCID: PMC4769247 DOI: 10.1371/journal.pone.0150306] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/11/2016] [Indexed: 12/14/2022] Open
Abstract
Background Recent advances in culture-independent approaches have enabled insights into the diversity, complexity, and individual variability of gut microbial communities. Objectives To examine the effect of oral administration of Saccharomyces (S.) boulardii and mode of delivery on the intestinal microbial community in preterm infants. Study Design Stool samples were collected from preterm newborns randomly divided into two groups: a probiotic-receiving group (n = 18) or a placebo group (n = 21). Samples were collected before probiotic intake (day 0), and after 2 and 6 weeks of supplementation. The composition of colonizing bacteria was assessed by 16S ribosomal RNA (rRNA) gene sequencing of fecal samples using the Ion 16S Metagenomics Kit and the Ion Torrent Personal Genome Machine platform. Results A total of 11932257 reads were generated, and were clustered into 459, 187, and 176 operational taxonomic units at 0 days, 2 weeks, and 6 weeks, respectively. Of the 17 identified phyla, Firmicutes Actinobacteria, Proteobacteria, and Bacteroidetes were universal. The microbial community differed at day 0 compared with at 2 weeks and 6 weeks. There was a tendency for increased bacterial diversity at 2 weeks and 6 weeks compared with day 0, and infants with a gestational age of 31 weeks or higher presented increased bacterial diversity prior to S. boulardii administration. Firmicutes and Proteobacteria remained stable during the observation period, whereas Actinobacteria and Bacteroidetes increased in abundance, the latter particularly more sharply in vaginally delivered infants. Conclusion While the mode of delivery may influence the development of a microbial community, this study had not enough power to detect statistical differences between cohorts supplemented with probiotics, and in a consequence, to speculate on S. boulardii effect on gut microbiome composition in preterm newborns.
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MESH Headings
- Administration, Oral
- Bacteria/isolation & purification
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Delivery, Obstetric
- Double-Blind Method
- Feces/microbiology
- Female
- Gastrointestinal Microbiome
- Humans
- Infant, Newborn
- Infant, Premature
- Male
- Metagenome
- Probiotics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Reagent Kits, Diagnostic
- Ribotyping
- Saccharomyces
- Symbiosis
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Affiliation(s)
- Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Milosz Lechowicz
- Neonatal and Intensive Care Department, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Konopka
- Department of Pathology, The Children’s Memorial Health Institute, Warsaw, Poland
| | - Urszula Majewska
- Neonatal and Intensive Care Department, Medical University of Warsaw, Warsaw, Poland
| | | | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Bozena Cukrowska
- Department of Pathology, The Children’s Memorial Health Institute, Warsaw, Poland
- * E-mail: (JO); (BC)
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
- * E-mail: (JO); (BC)
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Hennig EE, Piatkowska M, Karczmarski J, Goryca K, Brewczynska E, Jazwiec R, Kluska A, Omiotek R, Paziewska A, Dadlez M, Ostrowski J. Limited predictive value of achieving beneficial plasma (Z)-endoxifen threshold level by CYP2D6 genotyping in tamoxifen-treated Polish women with breast cancer. BMC Cancer 2015; 15:570. [PMID: 26232141 PMCID: PMC4522133 DOI: 10.1186/s12885-015-1575-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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] [Received: 05/29/2015] [Accepted: 07/27/2015] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Tamoxifen, the most frequently used drug for treating estrogen receptor-positive breast cancer, must be converted into active metabolites to exert its therapeutic efficacy, mainly through CYP2D6 enzymes. The objective of this study was to investigate the impact of CYP2D6 polymorphisms on (Z)-endoxifen-directed tamoxifen metabolism and to assess the usefulness of CYP2D6 genotyping for identifying patients who are likely to have insufficient (Z)-endoxifen concentrations to benefit from standard therapy. METHODS Blood samples from 279 Polish women with breast cancer receiving tamoxifen 20 mg daily were analyzed for CYP2D6 genotype and drug metabolite concentration. Steady-state plasma levels of tamoxifen and its 14 metabolites were measured by using the ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method. RESULTS In nearly 60 % of patients, including over 30 % of patients with fully functional CYP2D6, (Z)-endoxifen concentration was below the predefined threshold of therapeutic efficacy. The most frequently observed CYP2D6 genotype was EM/PM (34.8 %), among which 83.5 % of patients had a combination of wild-type and *4 alleles. Plasma concentration of five metabolites was significantly correlated with CYP2D6 genotype. For the first time, we identified an association between decreased (E/Z)-4-OH-N-desmethyl-tamoxifen-β-D-glucuronide levels (r (2) = 0.23; p < 10(-16)) and increased CYP2D6 functional impairment. The strongest correlation was observed for (Z)-endoxifen, whose concentration was significantly lower in groups of patients carrying at least one CYP2D6 null allele, compared with EM/EM patients. The CYP2D6 genotype accounted for plasma level variability of (Z)-endoxifen by 27 % (p < 10(-16)) and for the variability of metabolic ratio indicating (Z)-endoxifen-directed metabolism of tamoxifen by 51 % (p < 10(-43)). CONCLUSIONS The majority of breast cancer patients in Poland may not achieve a therapeutic level of (Z)-endoxifen upon receiving a standard dose of tamoxifen. This finding emphasizes the limited value of CYP2D6 genotyping in routine clinical practice for identifying patients who might not benefit from the therapy. In its place, direct monitoring of plasma steady-state (Z)-endoxifen concentration should be performed to personalize and optimize the treatment.
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Affiliation(s)
- Ewa E Hennig
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland. .,Cancer Center-Institute, Roentgena 5, 02-781, Warsaw, Poland.
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
| | - Elzbieta Brewczynska
- Department of Breast Cancer and Reconstructive Surgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
| | - Radoslaw Jazwiec
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
| | - Robert Omiotek
- Department of Internal Medicine and Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland.
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
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Kluska A, Balabas A, Paziewska A, Kulecka M, Nowakowska D, Mikula M, Ostrowski J. New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. BMC Med Genomics 2015; 8:19. [PMID: 25948282 PMCID: PMC4429836 DOI: 10.1186/s12920-015-0092-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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] [Received: 02/14/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the present study, we report the utility of next generation sequencing (NGS) to identify new pathogenic variants of BRCA1/2. Methods BRCA1 and BRCA2 exons were amplified using the Ion AmpliSeq BRCA1/2 Panel and sequenced on the Ion Torrent PGM sequencer in 512 women with familial and/or only early onset breast and/or ovarian cancers who were negative for selected BRCA1/2 mutations. Results 146 single nucleotide variants (SNVs) and 32 indels were identified. Of them, 14 SNVs and 17 indels were considered as pathogenic or likely pathogenic. One and 18 pathogenic mutations had been detected previously in the Polish and other populations, respectively, and 12 deleterious mutations were previously unknown. Eight mutations were recurrent; Q563X (BRCA1), N3124I (BRCA2) and c.4516delG (BRCA1) were found in eight, six and four patients, respectively, and two other mutations (c.9118-2A > G and c.7249delCA in BRCA2) were detected in three patients each. Altogether, BRCA1/2 pathogenic mutations were identified in 52 out of 512 (10%) patients. Conclusions NGS substantially improved the detection rates of a wide spectrum of mutations in Polish patients with familial breast and/or ovarian cancer. Although targeted screening for specific BRCA1 mutations can be offered to all Polish breast or ovarian cancer patients, NGS-based testing is justified in patients with breast or ovarian cancer likely related to BRCA1/2 who test negative for the selected BRCA1/2 pathogenic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0092-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Dorota Nowakowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
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Maryan N, Statkiewicz M, Mikula M, Goryca K, Paziewska A, Strzałkowska A, Dabrowska M, Bujko M, Ostrowski J. Regulation of the expression of claudin 23 by the enhancer of zeste 2 polycomb group protein in colorectal cancer. Mol Med Rep 2015; 12:728-36. [PMID: 25695204 DOI: 10.3892/mmr.2015.3378] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 01/21/2015] [Indexed: 11/05/2022] Open
Abstract
Altered epigenetic mechanisms, similar to gene mutations, contribute to the pathogenesis and molecular heterogeneity of neoplasms, including colorectal cancer (CRC). Enhancer of zeste 2 (EZH2) is a histone methyltransferase, which is involved in epigenetic gene silencing and is aberrantly expressed in CRC. Therefore, the identification of the genes regulated by EZH2 in CRC is important to improve current understanding of its role in cancer epigenetics. The present study used chromatin immunoprecipitation (ChIP) followed by deep sequencing to assess genome-wide EZH2‑DNA interactions in healthy or CRC mucosa samples. In total, 86.9/61.6 and 92.5/62.6 million tags were sequenced/mapped in healthy and CRC mucosa samples, respectively. The EZH2-binding densities were correlated with transcriptomic datasets and this demonstrated that the claudin-23 (CLDN23) gene, which encodes a component of cell-cell adhesion structures, was occupied by EZH2 and significantly silenced in CRC tissue. The measurement of DNA methylation at the CLDN23 promoter using pyrosequencing excluded the possibility that silencing of this gene in CRC patient samples was a result of DNA hypermethylation. Following treatment of the Colo205 and HT-29 CRC cell lines, with the EZH2 inhibitor, GSK126, the level of histone H3 lysine 27 trimethylation (H3K27me3) was reduced and the mRNA and protein expression levels of CLDN23 were increased. ChIP analysis confirmed that the level of H3K27m3 along the CLDN23 gene was decreased in the GSK126-treated cell lines. Furthermore, ChIP analysis of these samples detected histone H3 lysine 4 trimethylation (H3K4me3) at the CLDN23 promoter, demonstrating that the balance between H3K27me3 and H3K4me3 may underlie the regulation of the expression of CLDN23. The present study demonstrated an epigenetic link between the activity of the EZH2 methyltransferase at the CLDN23 locus and the expression of CLDN23 in CRC tissue.
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Affiliation(s)
- Natalia Maryan
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Malgorzata Statkiewicz
- Department of Genetics, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Adriana Strzałkowska
- Department of Genetics, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Maria Sklodowska‑Curie Memorial Cancer Center and Institute of Oncology, Warsaw 02‑781, Poland
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Paziewska A, Horbacka K, Goryca K, Mikula M, Jarosz D, Dabrowska M, Krokowicz P, Karon J, Ostrowski J. Transcriptional changes between uninflamed ulcerative colitis and familial adenomatous polyposis pouch mucosa can be attributed to an altered immune response. Acta Biochim Pol 2015; 62:69-75. [PMID: 25654358 DOI: 10.18388/abp.2014_778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 11/04/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022]
Abstract
A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and some patients with ulcerative colitis (UC). However, this surgical treatment is often associated with pouchitis, a long-term complication that occurs mostly in UC patients. The purpose of this study was to better define the molecular background of pouchitis. A microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients undergoing surgery for UC and FAP, respectively. There were 4,770 genes that significantly differentiated uninflamed from inflamed mucosal samples, and their functional features were represented mostly by metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed genes between UC and FAP samples, irrespective of mucosal inflammation status, revealed multiple pathways and terms that were linked to changes in immune response. Interestingly, the comparison of uninflamed UC and FAP samples identified a set of 29 altered probe sets, including an inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most distinct changes in gene expression profiles differentiating uninflamed UC and FAP pouch mucosal samples were attributed to the Gene Ontology category innate immune response. Our study confirmed that alterations in immune responses can be found between patients who underwent surgery for UC and FAP, independent of the pouch inflammation status. This observation may be important when managing IPAA patients.
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Affiliation(s)
- Agnieszka Paziewska
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Karolina Horbacka
- Department of General and Colorectal Surgery, Poznan University of Medical Sciences, Poznań, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Dorota Jarosz
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education and Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Piotr Krokowicz
- Department of General and Colorectal Surgery, Poznan University of Medical Sciences, Poznań, Poland
| | - Jacek Karon
- Department of General and Colorectal Surgery, Poznan University of Medical Sciences, Poznań, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology and Hepatology, Medical Center for Postgraduate Education and Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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