Review
Virology
Jacek Furmaga, Marek Kowalczyk, Tomasz Zapolski, Olga Furmaga, Leszek Krakowski, Grzegorz Rudzki, Andrzej Jaroszynski, Andrzej Jakubczak
Summary: BK polyomavirus is a widespread virus in human population, which is activated in cases of immune deficiency. It is particularly important for kidney or HSC transplant recipients, as it can lead to kidney loss or hemorrhagic cystitis. The virus has four main genotypes based on molecular differentiation, with varying distributions in different regions. The development of molecular methods has significantly improved diagnostics and treatment monitoring for BK polyomavirus.
Article
Virology
Wei Zou, Gau Shoua Vue, Benedetta Assetta, Heather Manza, Walter J. Atwood, Michael J. Imperiale
Summary: BK polyomavirus is a common human pathogen that can cause complications in the kidneys and bladder. The viral intron may be spliced out from primary RNA transcripts that circulate multiple times, providing a mechanism for expressing viral miRNA.
JOURNAL OF VIROLOGY
(2021)
Article
Urology & Nephrology
Tobias F. Koyro, Emma Kraus, Sebastian Lunemann, Angelique Hoelzemer, Sonia Wulf, Johannes Jung, Pia Fittje, Florian Henseling, Christian Koerner, Tobias B. Huber, Adam Grundhoff, Thorsten Wiech, Ulf Panzer, Nicole Fischer, Marcus Altfeld
Summary: A recent study found that the activating natural killer cell receptor KIR3DS1 plays a protective role in controlling BK polyomavirus infection in the kidney, by regulating the interaction between HLA-F and KIR3DS1 to control disease progression, providing a rationale for exploring immunotherapeutic approaches for BK polyomavirus-associated nephropathy.
KIDNEY INTERNATIONAL
(2021)
Article
Immunology
Jian Zhang, Hao Qin, Mingyu Chang, Yang Yang, Jun Lin
Summary: This study aimed to characterize the gut microbiota in BK polyomavirus-infected renal transplant recipients and establish a prediction model for posttransplant BK polyomavirus infection based on the gut microbiota. The results showed that BK polyomavirus-infected patients had gut microbiota dysbiosis with an increased Firmicutes/Bacteroidetes ratio. Nine distinguishing bacterial taxa were identified as potential biomarkers of BK polyomavirus infection. The random forest model achieved a high accuracy in predicting the infectious status.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Immunology
Yu Fan, Duan Guo, Shangping Zhao, Qiang Wei, Yi Li, Tao Lin
Summary: This study aimed to explore the potential involvement of human genes with codon usage bias (CUB) similar to human polyomaviruses (HPyVs) genes in the pathogenesis of polyomavirus nephropathy (PVAN). The analysis revealed a significant correlation between HPyV genes and human genes, with a strong protein-protein interaction network. Gene expression analysis identified differentially expressed genes between normal kidney tissues and PVAN patients, which were involved in transcription, protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation, and immune system. These findings may have implications for the diagnosis and treatment of HPyV-associated diseases, particularly PVAN.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Linbo Zhao, Michael J. Imperiale
Summary: BK polyomavirus (BKPyV) is a widespread virus infecting a large portion of the global population, with the potential to cause severe disease in immunosuppressed individuals. Researchers have successfully established an in vitro model of BKPyV persistence, showing that the virus can persist for varying periods before undergoing random genome recombination which enhances its replication ability.
Article
Virology
Dorian McIlroy, Cecile Peltier, My-Linh Nguyen, Louise Manceau, Lenha Mobuchon, Nicolas Le Baut, Ngoc-Khanh Nguyen, Minh-Chau Tran, The-Cuong Nguyen, Celine Bressollette-Bodin
Summary: Mutations in the BKPyV capsid accumulate in kidney transplant recipients, and are associated with neutralization escape. The mutations are mainly caused by cytosine deamination by APOBEC3A/B enzymes.
Article
Virology
Nannan Liu, Chenjian Gu, Yang Yang, Zixiang Gao, Ning Kang, Jing Liu, Youhua Xie
Summary: This study reports a method for the generation of circular viral genomes through DNA recombination in cells. It allows for simpler manipulation of the BKV genome and results in higher virus yield.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Medicine, General & Internal
Haris Omic, Johannes Phillip Klaeger, Harald Herkner, Stephan W. Aberle, Heinz Regele, Lukas Weseslindtner, Tarek Arno Schrag, Gregor Bond, Katharina Hohenstein, Bruno Watschinger, Johannes Werzowa, Robert Strassl, Michael Eder, Zeljko Kikic
Summary: This study shows that the decrease in absolute BK viral load is an independent risk factor for graft loss, indicating its importance in predicting short-term graft survival.
FRONTIERS IN MEDICINE
(2022)
Article
Immunology
Yiling Fang, Chengfeng Zhang, Yuchen Wang, Zhiyin Yu, Zhouting Wu, Yi Zhou, Ziyan Yan, Jia Luo, Renfei Xia, Wenli Zeng, Wenfeng Deng, Jian Xu, Zheng Chen, Yun Miao
Summary: Dynamic Cox regression based on the landmarking method is effective in assessing the risk of BKV reactivation in the early period after renal transplantation and serves as a guide for clinical intervention.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Virology
Yi-Jung Li, Hsin-Hsu Wu, Cheng-Hsu Chen, Hsu-Han Wang, Yang-Jen Chiang, Hsiang-Hao Hsu, See-Tong Pang, Robert Y. L. Wang, Ya-Chung Tian
Summary: The study demonstrates that BKPyVAN patients have increased risk of allograft losses, higher incidence of UTC, lower cancer-free survival rate, and earlier onset of UTC compared to non-BKPyVAN patients.
Article
Multidisciplinary Sciences
Steven D. Forsythe, Richard A. Erali, Preston Laney, Hemamylammal Sivakumar, Wencheng Li, Aleksander Skardal, Shay Soker, Konstantinos Votanopoulos
Summary: This study explores the application of patient tumor organoids (PTOs) in modeling personalized research in Merkel cell carcinoma (MCC). PTOs and immune enhanced organoids (iPTOs) were established from surgical specimens and treated with chemotherapy or immunotherapy agents. Results showed chemotherapy efficacy in some specimens while immunotherapy was not effective. Resistance to pembrolizumab correlated with the corresponding patient's treatment response. The study demonstrates the feasibility of establishing and immune enhancing MCC PTOs for personalized research and exploration of treatment regimens in the preclinical setting.
SCIENTIFIC REPORTS
(2022)
Article
Urology & Nephrology
Evert Cleenders, Priyanka Koshy, Elisabet Van Loon, Katrien Lagrou, Kurt Beuselinck, Graciela Andrei, Marta Crespo, Katrien De Vusser, Dirk Kuypers, Evelyne Lerut, Kris Mertens, Olga Mineeva-Sangwo, Parmjeet Randhawa, Aleksandar Senev, Robert Snoeck, Ben Sprangers, Claire Tinel, Amaryllis Van Craenenbroeck, Jan van den Brand, Marc Van Ranst, Geert Verbeke, Maarten Coemans, Maarten Naesens
Summary: This study aimed to investigate the value of performing a biopsy at the time of BKPyV-DNAemia in distinguishing presumptive and proven PyVAN. The results showed that plasma viral load had good predictive value for SV40 positivity, while the dichotomy of SV40 immunohistochemistry did not predict viral clearance. Therefore, the distinction between presumptive and proven PyVAN based on SV40 immunohistochemistry has limited clinical value.
KIDNEY INTERNATIONAL
(2023)
Review
Urology & Nephrology
Waseem Albasha, Golnaz Vahdani, Ankita Ashoka, Erika Bracamonte, Amy A. Yau
Summary: BK virus nephropathy, classically described in renal allografts, is increasingly recognized in native kidneys of non-renal solid organ transplants. This article discusses a 68-year-old woman with a history of bilateral lung transplant who was diagnosed with BK virus nephropathy. Despite treatment with reduced immunosuppression and intravenous cidofovir, the patient's clinical parameters did not improve. The challenges of screening and management in lung transplant recipients with polyoma virus nephropathy are also reviewed.
CLINICAL KIDNEY JOURNAL
(2022)
Review
Virology
Suwasin Udomkarnjananun, J. Stephen Kerr, I. Marith Francke, Yingyos Avihingsanon, M. Nicole van Besouw, C. Carla Baan, A. Dennis Hesselink
Summary: The ELISPOT assay has been shown to be a valuable tool in monitoring the recipient's anti-BKV immune response post-transplantation, aiding in BKV risk assessment and guiding immunosuppressive therapy.
JOURNAL OF CLINICAL VIROLOGY
(2021)
Article
Environmental Sciences
Martina Hyzdalova, Jirina Prochazkova, Simona Strapacova, Lucie Svrzkova, Ondrej Vacek, Radek Fedr, Zdenek Andrysik, Eva Hruba, Helena Libalova, Jiri Klema, Jan Topinka, Josef Masek, Karel Soucek, Jan Vondracek, Miroslav Machala
Summary: Studying the role of AhR in lung cancer cells can provide insights into the impact of toxic AhR ligands on lung carcinogenesis. Exposure of lung carcinoma cells to genotoxic and non-genotoxic AhR agonists resulted in different effects on cell proliferation and phenotype, highlighting the complex mechanisms involved in lung cancer progression.
Article
Biochemistry & Molecular Biology
Tereza Cervena, Michal Vojtisek-Lom, Kristyna Vrbova, Antonin Ambroz, Zuzana Novakova, Fatima Elzeinova, Michal Sima, Vit Beranek, Martin Pechout, David Macoun, Jiri Klema, Andrea Rossnerova, Miroslav Ciganek, Jan Topinka, Pavel Rossner
Summary: Ordinary gasoline engine emissions have been classified as a potential carcinogen to humans and pose a significant health risk. This study showed that exposure to gasoline exhaust impacted the integrity of the 3D airway model and caused leakage of LDH and AK, while also affecting gene expression in BEAS-2B cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Vladimir Kunc, Jiri Klema
Summary: The NIH LINCS program has made gene expression profiling more cost-effective by profiling about 1,000 selected landmark genes. The D-GEX method uses neural networks to infer the entire profile, but can be further improved. The proposed transformative adaptive activation function significantly improves gene expression inference accuracy with only a small increase in model complexity and training procedure.
Letter
Surgery
Ivan Zahradka, Vojtech Petr, Maria Magicova, Ondrej Viklicky
AMERICAN JOURNAL OF TRANSPLANTATION
(2022)
Article
Oncology
Michaela Dostalova Merkerova, Jiri Klema, David Kundrat, Katarina Szikszai, Zdenek Krejcik, Andrea Hrustincova, Iva Trsova, Anh Vu Le, Jaroslav Cermak, Anna Jonasova, Monika Belickova
Summary: This study reveals that lncRNAs have the strongest predictive potential for AZA treatment. Through RNA sequencing analysis, a set of 14 lncRNAs and a few other genes and RNAs were identified as biomarkers for predicting the effectiveness of AZA treatment. The study also suggests the importance of epigenetic regulation and recombinational repair in AZA response.
CANCER GENOMICS & PROTEOMICS
(2022)
Article
Medicine, General & Internal
Ivan Zahradka, Vojtech Petr, Istvan Modos, Maria Magicova, Ladislav Dusek, Ondrej Viklicky
Summary: This retrospective observational cohort study examined the association between mRNA vaccination and SARS-CoV-2 infection rate in kidney transplant recipients (KTRs). The study found that vaccination of KTRs is associated with a lower risk for SARS-CoV-2 infection.
ANNALS OF INTERNAL MEDICINE
(2022)
Article
Gastroenterology & Hepatology
Veronika Iatsiuk, Frantisek Malinka, Marketa Pickova, Jolana Tureckova, Jiri Klema, Frantisek Spoutil, Vendula Novosadova, Jan Prochazka, Radislav Sedlacek
Summary: In this study, a semantic biclustering technique was used to analyze the expression profiling of Ub-ligases and ubiquitination-related genes in the murine gastrointestinal tract (GIT). The clustering protocol revealed gene clusters with potentially redundant features and demonstrated their complementary role during tissue regeneration. This optimized semantic clustering protocol provides a new method for the functional classification of Ub-ligases and ubiquitination-related genes.
BMC GASTROENTEROLOGY
(2022)
Article
Oncology
Monika Kaisrlikova, Jitka Vesela, David Kundrat, Hana Votavova, Michaela Dostalova Merkerova, Zdenek Krejcik, Vladimir Divoky, Marek Jedlicka, Jan Fric, Jiri Klema, Dana Mikulenkova, Marketa Stastna Markova, Marie Lauermannova, Jolana Mertova, Jacqueline Soukupova Maaloufova, Anna Jonasova, Jaroslav Cermak, Monika Belickova
Summary: This study found that the RUNX1 mutation is the main predictor of rapid progression in LR-MDS patients. Comparison of gene expression profiles between patients with and without RUNX1 mutations suggests that RUNX1 mutations may trigger malignant transformation. Dysregulation of DDR and cellular senescence was also observed. Additionally, the expression profiles of RUNX1-mutated LR-MDS resemble those of higher-risk MDS.
Article
Toxicology
Michal Sima, Tereza Cervena, Fatima Elzeinova, Antonin Ambroz, Vit Beranek, Michal Vojtisek-Lom, Jiri Klema, Miroslav Ciganek, Pavel Rossner
Summary: Air pollution from road traffic has adverse effects on the environment and human health. This study found that extractable organic matter (EOM) from gasoline emissions had toxic effects on cell models of the human airways. Longer exposure had a more pronounced impact on cytotoxicity and mucin production, while the effects on ROS generation and DNA integrity were limited. The ethanol content in fuels did not significantly affect the toxicity of EOM. Biological effects were primarily related to xenobiotic metabolism and inflammatory response, with BEAS-2B cells being more sensitive to the treatment.
TOXICOLOGY IN VITRO
(2022)
Article
Environmental Sciences
Antonin Ambroz, Pavel Rossner, Andrea Rossnerova, Katerina Honkova, Alena Milcova, Anna Pastorkova, Jiri Klema, Jana Pulkrabova, Ondrej Parizek, Veronika Vondraskova, Jaroslav Zelenka, Nikola Vrzackova, Jana Schmuczerova, Jan Topinka, Radim J. Sram
Summary: The study found that oxidative damage was mainly influenced by different locations and levels of inflammatory mediators, while the impact of other variables, including environmental pollutants, was minimal.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Biochemical Research Methods
Petr Rysavy, Jiri Klema, Michaela Dostalova Merkerova
Summary: Recent research has shown that circRNAs play a role in gene expression regulation and disease, and this paper proposes an efficient method of predicting circRNA annotations based on their interaction with miRNAs.
BMC BIOINFORMATICS
(2022)
Article
Transplantation
Kamila Bednarova, Geir Mjoen, Petra Hruba, Istvan Modos, Ludek Voska, Marek Kollar, Ondrej Viklicky
Summary: This study developed a multivariable Cox model based on clinical data and a web-based nomogram to predict the recurrence and graft loss in kidney transplant recipients with IgA nephropathy (IgAN). The nomogram was externally validated and identified age, gender, retransplantation status, proteinuria, and C4d positivity as independent risk factors. The nomogram showed good predictive performance in identifying IgAN patients at risk for premature graft loss.
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2023)
Article
Biochemistry & Molecular Biology
Anh Vu Le, Tomas Vetrovsky, Denis Barucic, Joao Pedro Saraiva, Priscila Thiago Dobbler, Petr Kohout, Martin Pospisek, Ulisses Nunes da Rocha, Jiri Klema, Petr Baldrian
Summary: Metagenomics is a useful tool for assessing the functional potential of microbiomes, but gene prediction is limited for eukaryotic organisms, resulting in underrepresentation of eukaryotic genes in metagenomics datasets. This study developed an algorithm that predicts fungal introns in environmental DNA and improves the annotation of metagenomes. The proportion of newly predicted genes increased with the share of eukaryotic genes and the number of introns per gene. The approach provides a tool for improved annotation of microbiomes with a high proportion of eukaryotes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Oncology
Iva Trsova, Andrea Hrustincova, Zdenek Krejcik, David Kundrat, Ales Holoubek, Karolina Staflova, Lucie Janstova, Sarka Vanikova, Katarina Szikszai, Jiri Klema, Petr Rysavy, Monika Belickova, Monika Kaisrlikova, Jitka Vesela, Jaroslav Cermak, Anna Jonasova, Jiri Dostal, Jan Fric, Jan Musil, Michaela Dostalova Merkerova
Summary: SF3B1 mutations in MDS patients can cause abnormal expression of certain circRNAs, especially upregulation of ZEB1-circRNA. This upregulation is specific to SF3B1-mutated patients and is not related to mutations in other splicing factors or other recurrently mutated genes or clinical variables.
MOLECULAR ONCOLOGY
(2023)
Article
Urology & Nephrology
Michal Schmalz, Hana Vankova, Silvie Rajnochova-Bloudickova, Petra Hruba, Martina Fialova, Jiri Gurka, Maria Magicova, Ilja Striz, Ivan Zahradka, Ondrej Viklicky
Summary: Frailty syndrome assessment may determine the most vulnerable population for an impaired humoral immune response to SARS-CoV-2 mRNA vaccination in kidney transplant recipients.
INTERNATIONAL UROLOGY AND NEPHROLOGY
(2023)
