Article
Multidisciplinary Sciences
Yasaman KalantarMotamedi, Ran Joo Choi, Siang-Boon Koh, Jo L. Bramhall, Tai-Ping Fan, Andreas Bender
Summary: Resistance to current therapies is common in pancreatic cancer, necessitating novel treatment options. A computational method was developed to select synergistic compound combinations based on transcriptomic profiles and pathway scoring system, successfully identifying effective compound combinations against pancreatic cancer cells.
Article
Biochemistry & Molecular Biology
Xiaoping Pan, Xiaolv Hong, Sumei Li, Ping Meng, Feng Xiao
Summary: This study identified the METTL3/miR-221-3p/HIPK2/Che-1 axis as a potential mechanism for breast cancer cell resistance to adriamycin. Knockdown of METTL3 resulted in reduced expression of miR-221-3p, leading to decreased drug resistance and increased apoptosis in ADR-resistant MCF-7 cells.These findings suggest that targeting the METTL3/miR-221-3p/HIPK2/Che-1 axis may improve chemotherapy efficacy in breast cancer.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biology
Alvaro Molina-Cruz, Nadia Raytselis, Roxanne Withers, Ankit Dwivedi, Peter D. Crompton, Boubacar Traore, Giovanna Carpi, Joana C. Silva, Carolina Barillas-Mury
Summary: The study analyzed the Plasmodium falciparum Pfs47 gene sequences and identified two SNP loci that can determine the likely continent of origin of P. falciparum isolates. Sequences from Africa, Asia, and the New World showed over 99% frequency of unique combinations of the SNPs 707 and 725 genotypes, while Papua New Guinea sequences exhibited the highest diversity in these SNPs. Development of accurate High-Resolution Melting assays for genotyping these SNPs can help assess the geographic origin and transmission risk of imported P. falciparum malaria cases.
COMMUNICATIONS BIOLOGY
(2021)
Article
Neurosciences
Shitao Wang, Xuemei Cai, Shiyong Liu, Qixin Zhou, Ting Wang, Sunbing Du, Dan Wang, Fei Yang, Qian Wu, Yanbing Han
Summary: This study found that the BCL11A gene is associated with the susceptibility to develop epileptic seizures and drug resistance. The rs2556375 variant increases the risk for both epileptic seizures and drug resistance. Furthermore, it was found that rs2556375 regulates the expression of the BCL11A gene in human brain tissues, potentially impacting the development and treatment outcomes of epilepsy.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Luca Freschi, Roger Vargas, Ashaque Husain, S. M. Mostofa Kamal, Alena Skrahina, Sabira Tahseen, Nazir Ismail, Anna Barbova, Stefan Niemann, Daniela Maria Cirillo, Anna S. Dean, Matteo Zignol, Maha Reda Farhat
Summary: Mycobacterium tuberculosis, a clonal pathogen that has co-evolved with humans for millennia, is reevaluated in terms of population structure. Ancient Indo-Oceanic Lineage 1 and modern Central Asian Lineage 3 are analyzed in depth, expanding understanding of Lineages 2 and 4.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Agata Zieba, Dariusz Matosiuk, Agnieszka A. A. Kaczor
Summary: Complex disorders like depression are still a puzzle for scientists. Genetic factors are important for predicting vulnerability, but it is difficult to estimate the risk for depression based on just one category of vulnerability criteria. Genetic factors also influence drug metabolism and can lead to increased drug resistance. Understanding the genetic basis of depression is crucial for developing new medications and effective management strategies. This review analyzes recent literature on the correlation between specific genes and depression, highlights high drug resistance in patients with major depressive disorder, and discusses future directions for drug discovery.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Hematology
Richard J. Marrero, Xueyuan Cao, Huiyun Wu, Abdelrahman H. Elsayed, Jeffery M. Klco, Raul C. Ribeiro, Jeffrey E. Rubnitz, Xiaotu Ma, Soheil Meshinchi, Richard Aplenc, E. Anders Kolb, Rhonda E. Ries, Todd A. Alonzo, Stanley B. Pounds, Jatinder K. Lamba
Summary: Cytarabine arabinoside (Ara-C) is an important drug in acute myeloid leukemia (AML) chemotherapy. The SAMHD1 gene, which is involved in Ara-C metabolism, has been found to affect the response to this drug. In this study, we investigated the association between genetic variations in SAMHD1 and clinical outcome in pediatric AML patients. The results demonstrate the relevance of SAMHD1 pharmacogenomics in the context of Ara-C response and suggest the need for further validation in larger patient cohorts.
Article
Biochemistry & Molecular Biology
Ahmad Nasimian, Lina Al Ashiri, Mehreen Ahmed, Hongzhi Duan, Xiaoyue Zhang, Lars Roennstrand, Julhash U. Kazi
Summary: Despite progress in cancer treatment, therapy resistance remains a major obstacle for long-term survival. By using highly variable genes and pharmacogenomic data, a drug sensitivity prediction model for the tyrosine kinase inhibitor sorafenib was developed with over 80% accuracy. AXL was identified as an important feature for drug resistance and PKC signaling was found to be enriched in drug-resistant patient samples. Inhibition of tyrosine kinase activity enhanced AXL expression and phosphorylation of the PKC-substrate CREB protein, showing synergy with AXL and PKC inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pharmacology & Pharmacy
Kai Zhao, Yujia Shi, Hon-Cheong So
Summary: This article presents a novel computational approach for drug target discovery based on machine learning models. The approach integrates expression profiles from drug-induced gene perturbations and predicts targets for specific diseases. The method was validated and showed promising results in identifying known drug targets.
Article
Biochemistry & Molecular Biology
Yunxiao Ren, Trinad Chakraborty, Swapnil Doijad, Linda Falgenhauer, Jane Falgenhauer, Alexander Goesmann, Oliver Schwengers, Dominik Heider
Summary: Multi-drug resistance (MDR) is a significant public health problem, and our study demonstrates that multi-label classification methods can accurately predict MDR in pathogens.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Microbiology
M. Claassens, V Dreyer, E. Nepolo, Q. Mokomele, G. van Rooyen, N. Ruswa, G. Guenther, S. Niemann
Summary: Namibia, a country with a high burden of tuberculosis, lacks comprehensive data on the transmission and evolution of drug-resistant Mycobacterium tuberculosis complex (Mtbc) strains. In this study, whole-genome sequencing was conducted on a population of rifampicin-resistant Mtbc strains from Namibia. The findings revealed a significant proportion of multidrug-resistant (MDR) and pre-extensively drug resistant (pre-XDR) strains, as well as the presence of borderline resistance-conferring mutations. These results highlight the urgent need for interventions to break the transmission of MDR tuberculosis in Namibia.
MICROBIOLOGY SPECTRUM
(2022)
Article
Genetics & Heredity
Hui Zhao, Liang Pi, Luyi Zhao, Yucheng Qin, Weilin Zeng, Zheng Xiang, Qi Yang, Maohua Pan, Xinxin Li, Chunyan Zou, Xi Chen, Wei Zhao, Yuxin Lu, Yanrui Wu, Mengxi Duan, Xun Wang, Xiaosong Li, Dominique Mazier, Yaming Huang, Zhaoqing Yang
Summary: This study analyzed mutations in drug resistance genes in imported malaria patients from Africa in Guangxi, China, and identified new potential drug resistance-associated molecular markers. The study provides the latest data for molecular marker surveillance related to antimalarial drug resistance genes imported from Africa in Chinese migrant workers in Guangxi.
FRONTIERS IN GENETICS
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Ye Li, Zexuan Xu, Xinna Lv, Chenghai Li, Wei He, Yan Lv, Dailun Hou
Summary: This study aimed to develop a radiomics model based on the tree-in-bud (TIB) sign and nodules and validate its predictive performance for multidrug-resistant TB (MDR-TB). The results showed that the radiomics models had good performance in predicting MDR-TB. Therefore, CT-based radiomics models hold promise as a non-invasive tool for predicting MDR-TB.
EUROPEAN RADIOLOGY
(2023)
Article
Infectious Diseases
Xiaocui Wu, Guangkun Tan, Jinghui Yang, Yinjuan Guo, Chengchen Huang, Wei Sha, Fangyou Yu
Summary: This study evaluated the performance of nucleotide matrix-assisted laser desorption/ionization time-offlight mass spectrometry (MALDI-TOF-MS) in predicting drug resistance in Mycobacterium tuberculosis. The results showed that nucleotide MALDI-TOF-MS had high sensitivities and specificities in predicting drug resistance to multiple drugs in Mycobacterium tuberculosis. The study suggests that nucleotide MALDI-TOF-MS could be a promising tool for rapid detection of drug sensitivity in Mycobacterium tuberculosis.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Biochemical Research Methods
Narmada Sambaturu, Vaidehi Pusadkar, Sridhar Hannenhalli, Nagasuma Chandra
Summary: PathExt is a computational tool that can identify differentially active paths with a control, or most active paths without one, in an omics-integrated biological network. It can extract characteristic genes and pathways for studying systems effectively.
Review
Pharmacology & Pharmacy
Alzbeta Kloudova-Spalenkova, Petr Holy, Pavel Soucek
Summary: Oxysterols play a significant role in cancer therapy by modulating estrogen receptor activity, affecting the efficacy of chemotherapy, and showing selective cytotoxic properties. They also have the potential to serve as biomarkers for cancer management and patient stratification.
BRITISH JOURNAL OF PHARMACOLOGY
(2021)
Article
Oncology
Petra Bendova, Barbara Pardini, Simona Susova, Jachym Rosendorf, Miloslav Levy, Pavel Skrobanek, Tomas Buchler, Jan Kral, Vaclav Liska, Ludmila Vodickova, Stefano Landi, Pavel Soucek, Alessio Naccarati, Pavel Vodicka, Veronika Vymetalkova
Summary: miRSNPs may impact patient's survival in colorectal cancer by altering miRNA binding to SLC transporter genes, but no significant association was observed with CRC risk. This study is the first to investigate the potential effects of miRSNPs on CRC susceptibility and prognosis.
Article
Genetics & Heredity
Viktor Hlavac, Radka Vaclavikova, Veronika Brynychova, Pavel Dvorak, Katerina Elsnerova, Renata Kozevnikovova, Karel Raus, Katerina Kopeckova, Sona Mestakova, David Vrana, Jiri Gatek, Pavel Soucek
Summary: This study revealed the prognostic value of gene expression and genetic variability of SLC46A1 and SLCO1A2 in breast cancer, identifying pathogenic variants in both genes and a significant association between a SLC46A1 haplotype block and ERBB2/HER2 status and disease-free survival in hormonally treated patients that should be further studied.
MOLECULAR DIAGNOSIS & THERAPY
(2021)
Article
Biochemistry & Molecular Biology
Viktor Hlavac, Radka Vaclavikova, Veronika Brynychova, Pavel Ostasov, Renata Kozevnikovova, Katerina Kopeckova, David Vrana, Jiri Gatek, Pavel Soucek
Summary: This study found that germline variants in certain CYP genes are associated with the response of breast cancer patients to neoadjuvant cytotoxic chemotherapy, with the variant rs17102977 in the CYP4X1 gene showing clinical and statistical validation. However, other variants related to disease-free survival in breast cancer patients require further research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Karolina Seborova, Alzbeta Kloudova-Spalenkova, Kamila Koucka, Petr Holy, Marie Ehrlichova, Changwei Wang, Iwao Ojima, Iveta Voleska, Petr Daniel, Kamila Balusikova, Michael Jelinek, Jan Kovar, Lukas Rob, Martin Hruda, Marcela Mrhalova, Pavel Soucek, Radka Vaclavikova
Summary: This study investigated the gene expression changes of ABCC3, CPS1, and TRIP6 in highly resistant ovarian carcinoma cells, revealing that combining Stony Brook taxanes with paclitaxel led to downregulation of CPS1. The overexpression of CPS1 may serve as a prognostic biomarker for poor survival in epithelial ovarian carcinoma patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Food Science & Technology
Petr Pavek, Jan Dusek, Tomas Smutny, Lukas Lochman, Radim Kucera, Josef Skoda, Lucie Smutna, Rajamanikkam Kamaraj, Pavel Soucek, Radim Vrzal, Zdenek Dvorak
Summary: This study suggests that VDR or vitamin D supplementation is unlikely to significantly influence liver detoxification enzymes apart from CYP3A4.
MOLECULAR NUTRITION & FOOD RESEARCH
(2022)
Article
Chemistry, Physical
Jaroslav Zenisek, Pavel Ondracka, Jan Cencnal, Pavel Soucek, David Holec, Petr Vasina
Summary: This paper critically evaluates the applicability of a procedure proposed by Mirzaei et al. (Surf. Coat. Technol. 358, 2019) for fitting the XPS spectrum of amorphous W-B-C material. The authors show that W-W bonds significantly influence the positions of peak components, which has implications for the correct interpretation of measured XPS spectra. Their analysis confirms expected chemical shifts caused by W-B and W-C bonds and reveals the same directional shift of W-W bonds and W-B bonds in the W 4f electronic states.
APPLIED SURFACE SCIENCE
(2022)
Article
Materials Science, Coatings & Films
Michael Kroker, Pavel Soucek, Marta Slapanska, Vjaceslav Sochora, Mojmir Jilek, Petr Vasina
Summary: Computational methods have gained attention in industrial magnetron sputtering for their ability to predict coating composition and deposition rates. This study used SDTrimSP and SiMTra to simulate the deposition process of industrially sputtered W-B-C coatings. The research discovered a correlation between the chemical composition and target segment placement, as well as the impact of substrate movement on composition. Simulations revealed different particle trajectories and explained the nanolayering observed in the non-reactively deposited coatings.
SURFACE & COATINGS TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Petr Holy, Viktor Hlavac, Pavel Ostasov, Veronika Brynychova, Renata Kozevnikovova, Marketa Trnkova, Katorina Kopeckova, Sona Mestakova, Marcela Mrhalova, Pavel Soucek
Summary: This study investigates the association between oxysterol-related genes and breast cancer patients. Germline variants in certain genes were found to be associated with the survival of patients, while somatic variants in other genes were associated with a poor prognosis. However, these associations did not remain significant after correction for multiple tests. The study suggests further exploration of these genes in combination with gene expression and epigenomic data.
Article
Oncology
Veronika Skarkova, Barbora Vitovcova, Petra Matouskova, Monika Manethova, Petra Kazimirova, Adam Skarka, Veronika Brynychova, Pavel Soucek, Hana Vosmikova, Emil Rudolf
Summary: The role of N-cadherin expression in epithelial-to-mesenchymal transition (EMT) and aggressive tumor colon cancer cell phenotype was investigated. It was found that artificially increased N-cadherin expression has limited reprogramming potential, while naturally elevated N-cadherin expression in colon cancer cells leads to an aggressive and chemoresistant phenotype.
Article
Biology
Viktor Hlavac, Petr Holy, Radka Vaclavikova, Lukas Rob, Martin Hruda, Marcela Mrhalova, Petr Cernaj, Jiri Bouda, Pavel Soucek
Summary: This study highlights the importance of somatic mutations in TP53 and Hippo pathway genes in predicting platinum resistance and prognosis in patients with epithelial ovarian carcinoma (EOC). Understanding the genetic landscape of EOC subgroups can provide valuable insights for precision oncology.
LIFE SCIENCE ALLIANCE
(2022)
Article
Oncology
Matteo Giaccherini, Riccardo Farinella, Manuel Gentiluomo, Beatrice Mohelnikova-Duchonova, Emanuele Federico Kauffmann, Matteo Palmeri, Faik Uzunoglu, Pavel Soucek, Dalius Petrauskas, Giulia Martina Cavestro, Romanas Zykus, Silvia Carrara, Raffaele Pezzilli, Marta Puzzono, Andrea Szentesi, John Neoptolemos, Livia Archibugi, Orazio Palmieri, Anna Caterina Milanetto, Gabriele Capurso, Casper H. J. van Eijck, Hannah Stocker, Rita T. Lawlor, Pavel Vodicka, Martin Lovecek, Jakob R. Izbicki, Francesco Perri, Rita Kupcinskaite-Noreikiene, Mara Gotz, Juozas Kupcinskas, Tamas Hussein, Peter Hegyi, Olivier R. Busch, Thilo Hackert, Andrea Mambrini, Hermann Brenner, Maurizio Lucchesi, Daniela Basso, Francesca Tavano, Ben Schottker, Giuseppe Vanella, Stefania Bunduc, Agota Petranyi, Stefano Landi, Luca Morelli, Federico Canzian, Daniele Campa
Summary: This study analyzed the common genetic variability of PDAC familial genes and found that the CDKN2B-AS1/ANRIL gene located in the 9p21.3 region plays an important role in the development of PDAC. The results strongly support the association between genetic variability in the 9p21.3 region and PDAC pathogenesis.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Dominika Flasarova, Katerina Urban, Ondrej Strouhal, Dusan Klos, Radmila Lemstrova, Pavel Dvorak, Pavel Soucek, Beatrice Mohelnikova-Duchonova
Summary: DNA repair pathways are crucial for maintaining genome stability and understanding their regulation can contribute to the development of new treatment strategies, prevention of chemoresistance, and enhancement of patient survival in ovarian cancer. The study aimed to compare the expression levels of 84 genes involved in DNA repair pathways in tumors and peritoneal metastatic tissue of ovarian cancer patients treated with cytoreductive surgery and platinum-based HIPEC, in relation to patient survival, peritoneal carcinomatosis, treatment response, and alterations in BRCA1 and BRCA2 genes. The findings revealed significant gene interactions and correlations between gene expression and overall survival.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Pharmacology & Pharmacy
Viktor Hlavac, Petr Holy, Pavel Soucek
Summary: Sequencing exomes of synchronous and metachronous liver metastases of colorectal cancer has the potential to improve treatment outcomes by identifying distinct molecular profiles from primary tumors.
Review
Biochemistry & Molecular Biology
Bhavana Hemantha Rao, Pavel Soucek, Viktor Hlavac
Summary: The heterogeneity of pancreatic cancer complicates cancer research, and traditional tissue analysis methods are no longer sufficient. The application of single-cell separation techniques helps researchers better understand specific cell populations in pancreatic cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
