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1. NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies

Author

Szymon Grabia, Urszula Smyczynska, Konrad Pagacz, and Wojciech Fendler

Subjects
GPU acceleration, CUDA, Reference genes, qPRC, miRNA, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it removes unwanted, non-biological variability from data. In targeted qPCR assays it is typically performed with respect to prespecified reference genes, but the lack of robust strategy of their selection is reported in literature, especially in studies concerning circulating microRNAs (miRNA). Unfortunately, this problem impedes translation of scientific discoveries on miRNA biomarkers into widely available laboratory assays. Previous studies concluded that averaged expressions of multi-miRNA combinations are more stable references than single genes. However, due to the number of such combinations the computational load is considerable and may be hindering for objective reference selection in large datasets. Existing implementations of normalization algorithms (geNorm, NormFinder and BestKeeper) have poor performance and may require days to compute stability values for all potential reference as the evaluation is performed sequentially. Results We designed NormiRazor - an integrative tool which implements those methods in a parallel manner on a graphics processing unit (GPU) using CUDA platform. We tested our approach on publicly available miRNA expression datasets. As a result, the times of executions on 8 datasets containing from 50 to 400 miRNAs (subsets of GSE68314) decreased 18.7 ±0.6 (mean ±SD), 104.7 ±4.2 and 76.5 ±2.2 times for geNorm, BestKeeper and NormFinder with respect to previous Python implementation. To allow for easy access to normalization pipeline for biomedical researchers we implemented NormiRazor as an online platform where a user could normalize their datasets based on the automatically selected references. It is available at norm.btm.umed.pl, together with instruction manual and exemplary datasets. Conclusions NormiRazor allows for an easy, informed choice of reference genes for qPCR transcriptomic studies. As such it can improve comparability and repeatability of experiments and in longer perspective help translate newly discovered biomarkers into readily available assays.

Published
2020
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2. A systemic approach to screening high-throughput RT-qPCR data for a suitable set of reference circulating miRNAs

Author

Konrad Pagacz, Przemyslaw Kucharski, Urszula Smyczynska, Szymon Grabia, Dipanjan Chowdhury, and Wojciech Fendler

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The consensus on how to choose a reference gene for serum or plasma miRNA expression qPCR studies has not been reached and none of the potential candidates have yet been convincingly validated. We proposed a new in silico approach of finding a suitable reference for human, circulating miRNAs and identified a new set of endogenous reference miRNA based on miRNA profiling experiments from Gene Expression Omnibus. We used 3 known normalization algorithms (NormFinder, BestKeeper, GeNorm) to calculate a new normalization score. We searched for a universal set of endogenous miRNAs and validated our findings on 2 new datasets using our approach. Results We discovered and validated a set of 13 miRNAs (miR-222, miR-92a, miR-27a, miR-17, miR-24, miR-320a, miR-25, miR-126, miR-19b, miR-199a-3p, miR-30b, miR-30c, miR-374a) that can be used to create a reliable reference combination of 3 miRNAs. We showed that on average the mean of 3 miRNAs (p = 0.0002) and 2 miRNAs (p = 0.0031) were a better reference than single miRNA. The arithmetic means of 3 miRNAs: miR-24, miR-222 and miR-27a was shown to be the most stable combination of 3 miRNAs in validation sets. Conclusions No single miRNA was suitable as a universal reference in serum miRNA qPCR profiling, but it was possible to designate a set of miRNAs, which consistently contributed to most stable combinations.

Published
2020
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4. mTOR Inhibitor Treatment in Patients with Tuberous Sclerosis Complex Is Associated with Specific Changes in microRNA Serum Profile

Author

Bartłomiej Pawlik, Urszula Smyczyńska, Szymon Grabia, Wojciech Fendler, Izabela Dróżdż, Katarzyna Bąbol-Pokora, Katarzyna Kotulska, Sergiusz Jóźwiak, Julita Borkowska, Wojciech Młynarski, and Joanna Trelińska

Subjects
General Medicine, tuberous sclerosis, mTOR inhibitor, sirolimus, microRNA
Abstract

The aim of this study was to determine the serum profiles of miRNAs in patients with tuberous sclerosis (TSC) upon sirolimus treatment and compare them with those previously treated with everolimus in a similarly designed experiment. Serum microRNA profiling was performed in ten TSC patients before sirolimus therapy and again after 3–6 months using qPCR panels (Exiqon). Of 752 tested miRNAs, 28 showed significant differences in expression between TSC patients before and after sirolimus treatment. Of these, 11 miRNAs were dysregulated in the same directions as in the sirolimus groupcompared with the previously described everolimus group, miR-142-3p, miR-29c-3p, miR-150-5p, miR-425-5p, miR-376a-3p, miR-376a-3p, miR-532-3p, and miR-136-5p were upregulated, while miR-15b-3p, miR-100-5p, and miR-185-5p were downregulated. The most significant changes of expression, with fold changes exceeding 1.25 for both treatments, were noted for miR-136-5p, miR-376a-3p, and miR-150-5p. The results of a pathway analysis of the possible target genes for these miRNAs indicated the involvement of the Ras and MAPK signaling pathway. Upregulation of miR-136, miR-376a-3p, and miR-150-5p was noted in TSC patients treated with mTOR inhibitors, indicating a role in the downregulation of the mTOR pathway. Further studies are needed to determine the relationship between upregulated microRNAs and treatment efficacy.

Published
2022
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5. Prediction of radiation-induced hypothyroidism using radiomic data analysis does not show superiority over standard normal tissue complication models

Author

Zuzanna Nowicka, Jacek Fijuth, Wojciech Fendler, Bartłomiej Tomasik, Anna Papis-Ubych, Robert Bibik, Urszula Smyczynska, Tomasz Rutkowski, Szymon Grabia, and Tomasz Latusek

Subjects
medicine.medical_specialty, Imrt plan, business.industry, medicine.medical_treatment, Radiation induced, Radiation therapy, Radiomics, Total dose, medicine, Radiology, Radiation treatment planning, Head and neck, business, Complication
Abstract

State-of-art normal tissue complication probability (NTCP) models do not take into account more complex individual anatomical variations, which can be objectively quantitated and compared in radiomic analysis. The goal of this project was development of radiomic NTCP model for radiation-induced hypothyroidism (RIHT) using imaging biomarkers (radiomics). We gathered CT images and clinical data from 98 patients, who underwent intensity-modulated radiation therapy (IMRT) for head and neck cancers with a planned total dose of 70.0 Gy (33–35 fractions). During the 28-month (median) follow-up 27 patients (28%) developed RIHT. For each patient, we extracted 1316 radiomic features from original and transformed images using manually contoured thyroid masks. Creating models based on clinical, radiomic features or a combination thereof, we considered 3 variants of data preprocessing. Based on their performance metrics (sensitivity, specificity), we picked best models for each variant ((0.8, 0.96), (0.9, 0.93), (0.9, 0.89) variant-wise) and compared them with external NTCP models ((0.82, 0.88), (0.82, 0.88), (0.76, 0.91)). Our models reach accuracy comparable with or better than previously presented non-radiomic NTCP models. The benefit of our approach is obtaining the RIHT predictions before treatment planning to adjust IMRT plan to avoid the thyroid region in most susceptible patients.

Published
2021
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6. MicroRNA Expression Profile in TSC Cell Lines and the Impact of mTOR Inhibitor

Author

Bartłomiej Pawlik, Szymon Grabia, Urszula Smyczyńska, Wojciech Fendler, Izabela Dróżdż, Ewa Liszewska, Jacek Jaworski, Katarzyna Kotulska, Sergiusz Jóźwiak, Wojciech Młynarski, and Joanna Trelińska

Subjects
Sirolimus, microRNA, mTOR inhibitor, rapamycin, tuberous sclerosis, shTSC1 and shTSC2 cells, TOR Serine-Threonine Kinases, Organic Chemistry, MTOR Inhibitors, General Medicine, Catalysis, Cell Line, Computer Science Applications, Inorganic Chemistry, MicroRNAs, Tuberous Sclerosis, Humans, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy
Abstract

The aim of this study was to assess the potential implication of microRNA on tuberous sclerosis (TSC) pathogenesis by performing microRNA profiling on cell lines silencing TSC1 or TSC2 genes using qPCR panels, before and after incubation with rapamycin. (Qiagen). Significant differences in expression were observed between samples before and after rapamycin treatment in 19 miRNAs in TSC1, five miRNAs in TSC2 and seven miRNAs in controls. Of six miRNAs dysregulated before rapamycin treatment in the TSC1 group, three normalized after treatment (miR-21-3p, miR-433-3p, let-7g-3p). Of three miRNAs dysregulated before rapamycin incubation in TSC2 group, one normalized after treatment (miR-1224-3p). Of the miRNAs dysregulated before rapamycin treatment in TSC1 and TSC2 group, two did not normalize after treatment (miR-33a-3p, miR-29a-3p). The results of the possible targets indicated that there are four common genes with seed regions susceptible to the regulation by those miRNAs: ZBTB20, PHACTR2, PLXNC1 and ATP1B4. Our data show no changes in mRNA expression of these targets before rapamycin treatment. These data suggest that miRNA may play a pivotal role in TSC pathogenesis. Some may serve as biomarkers of treatment efficacy. The variability of miR-29a-3p and miR-33a-3p after rapamycin treatment and the lack of changes in their downstream regulatory targets suggests that they might be mTOR independent.

Published
2022
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7. A systemic approach to screening high-throughput RT-qPCR data for a suitable set of reference circulating miRNAs

Author

Urszula Smyczynska, Dipanjan Chowdhury, Szymon Grabia, Wojciech Fendler, Konrad Pagacz, and Przemysław Kucharski

Subjects
Circulating mirnas, lcsh:QH426-470, lcsh:Biotechnology, In silico, Computational biology, Biology, Proteomics, Real-Time Polymerase Chain Reaction, 03 medical and health sciences, 0302 clinical medicine, lcsh:TP248.13-248.65, microRNA, Databases, Genetic, Genetics, Reference gene, Mirna profiling, Humans, Computer Simulation, Systemic approach, Circulating MicroRNA, 030304 developmental biology, 0303 health sciences, Gene Expression Profiling, Methodology Article, Computational Biology, Reference Standards, lcsh:Genetics, 030220 oncology & carcinogenesis, DNA microarray, Algorithms, Biotechnology
Abstract

BackgroundThe consensus on how to choose a reference gene for serum or plasma miRNA expression qPCR studies has not been reached and none of the potential candidates have yet been convincingly validated. We proposed a new in silico approach of finding a suitable reference for human, circulating miRNAs and identified a new set of endogenous reference miRNA based on miRNA profiling experiments from Gene Expression Omnibus. We used 3 known normalization algorithms (NormFinder, BestKeeper, GeNorm) to calculate a new normalization score. We searched for a universal set of endogenous miRNAs and validated our findings on 2 new datasets using our approach.ResultsWe discovered and validated a set of 13 miRNAs (miR-222, miR-92a, miR-27a, miR-17, miR-24, miR-320a, miR-25, miR-126, miR-19b, miR-199a-3p, miR-30b, miR-30c, miR-374a) that can be used to create a reliable reference combination of 3 miRNAs. We showed that on average the mean of 3 miRNAs (p = 0.0002) and 2 miRNAs (p = 0.0031) were a better reference than single miRNA. The arithmetic means of 3 miRNAs: miR-24, miR-222 and miR-27a was shown to be the most stable combination of 3 miRNAs in validation sets.ConclusionsNo single miRNA was suitable as a universal reference in serum miRNA qPCR profiling, but it was possible to designate a set of miRNAs, which consistently contributed to most stable combinations.

Published
2019

8. Kongres 'Zdrowie Polaków 2021' : raport

Author

Małgorzata Andryszczyk, Piotr Andziak, Adam Antczak, Marek Balicki, Katarzyna Barna, Joanna Basiaga-Pasternak, Jerzy Bertrandt, Dariusz Białoszewski, Agnieszka Bielska-Brodziak, Marzanna Bieńkowska, Justyna Bloda, Paweł Bogdański, Janusz Bohosiewicz, Borawska, Maria H., Leszek Borkowski, Agnieszka Borowiec, Joanna Bugajska, Elżbieta Brzozowska, Małgorzata Buksińska, Adrian Chabowski, Dariusz Chajewski, Bartłomiej Chmielowiec, Alicja Chybicka, Agnieszka Chyrc, Krzysztof Czajkowski, Dariusz Czaprowski, Anna Czarnecka, Piotr Czauderna, Marcin Czech, Roman Czejarek, Anna Członkowska, Czuczwar, Stanisław J., Leszek Czupryniak, Andrzej Czyżewski, Roman Danielewicz, Justyna Dąbrowska-Bień, Anna Dembińska, Bożenna Dembowska-Bagińska, Agnieszka Dobrzyń, Izabela Domagała, Joanna Domienik-Andrzejewska, Zuzanna Donath-Kasiura, Marta Dora, Mariola Drozd, Wojciech Drygas, Sławomira Drzymała-Czyż, Władysław Duda, Dominika Dudek, Mirosława Dulat, Magdalena Durlik, Jarosław Dziadek, Daniel Dziekoński, Stanisław Dziekoński, Paweł Elbanowski, Jarosław Fedorowski, Wojciech Fendler, Anna Fijałkowska, Jarosław Filipczak, Filipiak, Krzysztof J., Urszula Fiszer, Robert Flisiak, Edward Franek, Mariusz Frączek, Adam Fronczak, Renata Furman, Małgorzata Gałązka-Sobotka, Aneta Gawlik, Ryszard Gellert, Kalina Gierblińska, Adam Giza, Jolanta Gładczuk, Mariola Głowacka, Wojciech Golusiński, Agnieszka Gonczaryk, Małgorzata Gosiewska, Renata Górska, Jarosław Górski, Szymon Grabia, Andrzej Grabowski, Iwona Grabska-Liberek, Bartosz Grabski, Beata Graff, Małgorzata Grembecka, Anna Gręziak, Radosław Grochal, Tomasz Grodzicki, Tomasz Grodzki, Monika Guszkowska, Wojciech Hanke, Dawid Harasim, Emilia Harasim-Piszczatowska, Janusz Heitzman, Ewa Helwich, Marcin Iżycki, Ewa Jabłońska, Renata Jachowicz, Marta Jakubiak, Witold Jamróz, Małgorzata Janas-Kozik, Mariusz Janikowski, Beata Jankowska-Polanska, Monika Jarzębska, Anna Jasińska, Urszula Jaworska, Jędrzejczak, Wiesław W., Michał Jędrzejek, Arleta Beata Jurczykowska, Joanna Jurewicz, Grzegorz Juszczyk, Bolesław Kalicki, KRZYSZTOF KALWAK, Wit Kania, Beata Karakiewicz, Alicja Karney, Beata Kawala, Andrzej Kawecki, Renata Kaznowska, Agnieszka Kędra, Kornelia Kędziora-Kornatowska, Michał Kleiber, Ewa Kleszczewska, Jan Klinkowski, Krzysztof Klukowski, Teresa Kłys, Brygida Knysz, Wojciech Koch, Krzysztof Kochanek, Elżbieta Kois-Żurek, Aleksandra Kolwicz-Gańko, Sylwia Kołtan, Iwona Konarska, Małgorzata Konaszczuk, Tomasz Konopka, Krzysztof Kopeć, Danuta Koradecka, Dorota Korycińska, Barbara Korzeniowska, Kosior, Dariusz A., Andrzej Kosmol, Dariusz Kossakowski, Bożena Kostek, Anna Kostera-Pruszczyk, Joanna Kostka, Tomasz Kostka, Dariusz Kostrzewa, Jerzy Kotowicz, Tomasz Kotwicki, Paweł Kowal, Anna Kowalczuk, Karolina Kowalska, Mateusz Kozinoga, Katarzyna Kozińska, Witold Kozłowski, Paulina Krasnodębska, Krawczyński, Maciej R., Marcin Kruk, Andrzej Krupienicz, Grażyna Kruszniewska, Paweł Kruś, Maciej Krzakowski, Paweł Krzesiński, Tomasz Książczyk, Brygida Kwiatkowska, Jolanta Kujawa, Paweł Kukołowicz, Iwona Kurkowska-Jastrzębska, Adam Kurowski, Magdalena Kwaśniewska, Bartosz Kwiatek, Adrian Kwiecień, Elżbieta Lanc, Tomasz Latos, Ewa Lech-Marańda, Jacek Lewandowski, Adam Liebert, Monika Lipińska, Jan Łaszczyk, Mariola Łodzińska, Bogusław Machaliński, Piotr Maciejak, Agnieszka Maciejewska-Skrendo, Tomasz Mikołaj Maciejewski, Katarzyna Madziarska, Piotr Majcher, Andrzej Malinowski, Beata Małecka-Libera, Beata Mańkowska, Barbara Marcinkowska, Leszek Markuszewski, Wojciech Marlicz, Marek Maruszyński, Andrzej Mastalerz, Andrzej Matyja, Artur Mazur, Justyna Mazurek, Maria Mazurkiewicz-Bełdzińska, Janusz Meder, Piotr Merks, Beata Miaśkiewicz, Arkadiusz Michalak, Janusz Michalak, Piotr Mierzejewski, Marek Migdał, Magdalena Mijas, Maciej Miłkowski, Dagmara Mirowska-Guzel, Barbara Misiewicz-Jagielak, Tomasz Młynarski, Wojciech Młynarski, Hanna Mojska, Bartosz Molik, Kamal Morshed, Wojciech Moskal, Marzena Mrozek, Piotr Murawski, Marcin Mycko, Małgorzata Myśliwiec, Michał Myśliwiec, Piotr Myśliwiec, Krzysztof Narkiewicz, Dawid Nidzworski, Ewelina Nojszewska, Nowak, Alojzy Z., Joanna Nyczak, Piotr Odya, Dominik Olejniczak, Regina Olędzka, Jurek Olszewski, Monika Ołdak, Włodzimierz Opoka, Przemysław Oszukowski, Jan Pachocki, Małgorzata Pacholec, Krzysztof Paśnik, Mikołaj Pawlak, Bolesław Piecha, Mariusz Piechota, Anna Piekarska, Barbara Piekarska, Katarzyna Pietrasik, Radosław Pietrzak, Ewa Pilarska, Olga Pilarska-Siennicka, Jarosław Pinkas, Katarzyna Pinkosz, Ryszard Piotrowicz, Paweł Piwoński, Elżbieta Anna, Joanna Popławska, Róża Poźniak-Balicka, Artur Prusaczyk, Piotr Pruszczyk, Krzysztof Przybył, Krzysztof Puchalski, Paweł Rabiej, Konstanty Radziwiłł, Leszek Rafalski, Danuta Raj-Koziak, Magda Rakita, Anna Ratuszniak, Tomasz Rechberger, Adam Reich, Barbara Remberk, Sylwia Rembiszewska-Piątek, Edyta Reszka, Radosław Rola, Dorota Romanowska, Tomasz Rosłonek, Iga Rudawska, Aleksandra Rudnicka, Anna Rulkiewicz, Piotr Rutkowski, Filip Rybakowski, Łukasz Salwarowski, Jerzy Samochowiec, Bolesław Samoliński, Iwona Sarzyńska-Długosz, Małgorzata Schlegel-Zawadzka, Andrzej Sęk, Halina Sienkiewicz-Jarosz, Piotr Sieroszewski, Krzysztof Simon, Skarżyński, Piotr H., Karolina Skonieczna-Żydecka, Agnieszka Skowron, Maciej Słodki, Zofia Słońska, Agnieszka Słopień, Urszula Smyczyńska, Jolanta Sobierańska-Grenda, Katarzyna Socha, Andrzej Sochal, Andrzej Sroczyński, Anna Staniszewska, Jerzy Starzyk, Bożena Stasiak, Rafał Stec, Agnieszka Stępień, Paulina Stochniałek, Łukasz Stoliński, Krystyna Strzała, Jan Styczyński, Edyta, Michał Sutkowski, Piotr Suwalski, Jolanta Sykut-Cegielska, Malgorzata Synowiec-Pilat, Jerzy Szaflik, Dominika Szalewska, Tomasz Szczapa, Dariusz Szczepanek, Joanna Szczepańska-Gieracha, Tomasz Szczepański, Wojciech Szczerba, Małgorzata Szczudłowska, Leszek Szenborn, Agata Szkiełkowska, Henryk Szrubarz, Urszula Szybowicz, Joanna Szyman, Anna Śliwińska, Tomasz Śmiałkowski, Grażyna Tacikowska, Ryszard Tadeusiewicz, Wiesław Tarnowski, Piotr Tederko, Krzysztof Tomasiewicz, Tomasz Trojanowski, Krzysztof Turlejski, Marcin Tyrakowski, Kamila Urbańczyk, Gertruda Uścińska, Piotr Wachowiak, Mieczysław Walczak, Jolanta Walusiak-Skorupa, Anna Warczyńska, Bożena Werner, Stefan Wesołowski, Marcin Wiącek, Adam Wichniak, Magdalena Wieczorkowska, Anna Wiela-Hojeńska, Andrzej Więcek, Maria Wilińska, Anna Wilmowska-Pietruszyńska, Piotr Artur Winciunas, Marta Wiszniewska, Cezary Włodarczyk, Marek Wojtukiewicz, Andrzej Wojtyła, Bogdan Wojtyniak, Tomasz Wolańczyk, Mariusz Wyleżoł, Romuald Zabielski, Wojciech Załuska, Krzysztof Zaremba, Danuta Zarzycka, Tomasz Zatonski, Marta Zawadzka, Tomasz Zdrojewski, Wojciech Zegarski, Wojciech Zgliczyński, Piotr Zgorzelski, Hanna Zielińska-Bliźniewska, Andrzej Ziemba, Krzysztof Zieniewicz, Mariusz Zimmer, Agnieszka Zimmerman, Dorota Żołnierczyk-Zreda, Żuber Zbigniew, and Henryk Skarżyński

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