Article
Multidisciplinary Sciences
Juan Zhang, Ying Ma, Daojun Xie, Yuancheng Bao, Wenming Yang, Han Wang, Huaizhou Jiang, Hui Han, Ting Dong
Summary: This study investigated the lncRNA-mRNA regulation network in a TX WD mouse model, identifying differentially expressed lncRNAs and mRNAs associated with WD liver injury. Functional and pathway analyses revealed enrichment in key processes such as apoptosis and pathways including drug metabolism and signaling pathways. The differential lncRNAs identified may play a role in the pathogenesis and development of WD liver injury.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Changsheng Guo, Yuanqing Hua, Zuanhao Qian
Summary: This study identified differentially expressed lncRNAs and genes in Kawasaki disease (KD), as well as constructed ceRNA networks involving miRNAs and mRNAs. The study found specific lncRNAs (PSORS1C3, LINC00999, SNHG5) and genes (GATA3, SOD2, MAPK14, PPARG) that may play a key role in the pathogenesis and development of KD. Validation in a separate dataset showed that intravenous immunoglobulin treatment alleviated the deregulated RNA profiles in KD patients.
Article
Multidisciplinary Sciences
Junwei Zhao, ShuHui Gao, Chunguang Chen, Hui Li, Shaohua Wang, Yongmin Yu, Liang Ming
Summary: Efforts to eradicate MDR-TB are hindered by drug resistance. This study identifies differentially expressed lncRNAs and mRNAs in MDR-TB patients and reveals potential biomarkers such as lncRNA n335659. GO and KEGG analyses provide insights into the biological functions and signaling pathways associated with MDR-TB.
Article
Oncology
Lu Yin, Yi Zhang, Leizhen Zheng
Summary: Cervical cancer is a major threat to women's health and the role of long non-coding RNAs (lncRNAs) in this cancer type is largely unknown. In this study, researchers analyzed the expression of different lncRNAs in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tissues and found that MIR205HG was overexpressed in CESC tissues. Further analysis revealed that genes related to MIR205HG were enriched in cancer-related pathways. Knockdown of MIR205HG significantly reduced the proliferation and migratory and invasive abilities of CESC cells. These findings identify potential lncRNA candidates for cervical cancer research and suggest a pro-tumor role of MIR205HG in CESC.
MOLECULAR MEDICINE REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Mina Baek, Jin Choul Chai, Hae In Choi, Eunyoung Yoo, Bert Binas, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Summary: In this study, the researchers identified inflammation-related lncRNAs and correlated mRNAs in a human microglial cell line treated with LPS. They used bioinformatics tools such as GO, KEGG, and WGCNA to explore the potential roles and interactions of these RNAs. The results provide insight into the regulation of neuroinflammation and suggest that small-molecule BET inhibitors may be a potential therapy.
Article
Biology
Job van Riet, Chinmoy Saha, Nikolaos Strepis, Rutger W. W. Brouwer, Elena S. Martens-Uzunova, Wesley S. van de Geer, Sigrid M. A. Swagemakers, Andrew Stubbs, Yassir Halimi, Sanne Voogd, Arif Mohammad Tanmoy, Malgorzata A. Komor, Youri Hoogstrate, Bart Janssen, Remond J. A. Fijneman, Yashar S. Niknafs, Arul M. Chinnaiyan, Wilfred F. J. van IJcken, Peter J. van der Spek, Guido Jenster, Rogier Louwen
Summary: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) have been discovered in the human genome, termed hCRISPRs, which are expressed as small non-coding RNAs (sncRNAs) and can distinguish normal from malignant tissues. These findings suggest the potential use of hCRISPRs as diagnostic biomarkers for cancer and the development of point-of-care tests based on their differential expression.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Ruijuan Guan, Suonan Angxiu, Ling Li, Zefeng Kang, Xin Yan
Summary: This study identified differentially expressed circRNAs (DEcircRNAs) in peripheral blood samples from patients with glaucoma through transcriptome sequencing, suggesting that DEcircRNAs are involved in the pathogenesis of glaucoma and may serve as potential biomarkers and therapeutic targets.
SCIENTIFIC REPORTS
(2023)
Article
Cell Biology
Mohd Shuaib, Kumari Sunita Prajapati, Atul Kumar Singh, Shashank Kumar
Summary: In this study, novel miRNAs were identified in breast normal cells treated with Withaferin A and their expression patterns were studied in breast cancer cells. Bioinformatics tools and molecular dynamics simulations were used to analyze the secondary/tertiary structure of the identified miRNAs, target gene enrichment, miRNA-mRNA interaction, and stability. Hsa-miR-N88585 and hsa-miR-N461089 were identified as novel miRNAs in breast normal cells, showing overexpression in breast cancer cells and interaction with genes involved in important signaling pathways and GO terms. Molecular dynamics simulations indicated stable complex formation between hsa-miR-N88585/hsa-miR-N461089 and AGO protein. These findings suggest the potential role of these novel miRNAs in breast cancer pathophysiology.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Oncology
Samarth Kansara, Agrata Singh, Abhishesh Kumar Badal, Reshma Rani, Prakash Baligar, Manoj Garg, Amit Kumar Pandey
Summary: Altered energy metabolism is a key characteristic of tumorigenesis, and non-coding RNAs (ncRNAs) play a significant role in regulating glucose metabolism in human cancers. In this review, the aberrant expression of glucose metabolic pathways in breast cancer is outlined, and the potential applications of ncRNAs in regulating energy pathways, as well as their importance in prognosis, diagnosis, and future therapeutics for breast carcinoma, are discussed.
SEMINARS IN CANCER BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lulu Chen, Yingzhou Lu, Chiung-Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Summary: The study introduces a new method for detecting SDEGs, which was applied to gene expression datasets and demonstrated superior performance in improving deconvolution accuracy.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Yufang Liu, Guiling Cao, Yujing Xie, Mingxing Chu
Summary: The study aimed to identify genes related to precocious puberty in goats by SSH, using pituitary tissues from goats at different growth stages. DEGs were annotated and enriched in GO terms related to ribosome structure, translation, and GTP binding, as well as in KEGG pathways related to Jak-STAT signaling and oocyte meiosis. Candidate genes associated with precocious puberty were screened from the SSH libraries, providing valuable insights for further research into goat reproductive biology.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Soraya Mousavi, Roberto Mariotti, Maria Cristina Valeri, Luca Regni, Emanuele Lilli, Emidio Albertini, Primo Proietti, Daniela Businelli, Luciana Baldoni
Summary: This study evaluated the salt tolerance of four olive cultivars and identified key genes involved in salt stress response. The results showed that Koroneiki was the most salt-tolerant cultivar, while Fadak86 and Picual were the most susceptible ones. The expression analysis of candidate genes suggested the important roles of OeNHX7, OeP5CS, OeRD19A, and OePetD in activating a salt tolerance mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Yange Wang, He Shi, Yulu Zhang, Qian Zeng, Tingmei Chen, Chengsen Chai
Summary: This study explored differentially expressed hub genes associated with tumor-infiltrating immune cells in a subtype of breast cancer called claudin-low breast cancer (CL-BCa), using a multi-approach bioinformatics analysis. The results showed an increase in tumor-infiltrating immune cells, especially CD8+ T cells and macrophages, in CL-BCa. Differentially expressed cytokines and claudins were found to be associated with overall survival. The study sheds light on the molecular features of CL-BCa in the immune microenvironment and contributes to the identification of prognosis biomarkers for CL-BCa patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Yan Pan, Marhaba Abdureyim, Qing Yao, Xuejun Li
Summary: The adhesion of tumor cells to endothelial cells leads to changes in gene expression, affecting the metastasis and angiogenesis mechanisms of tumor cells.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Jinyu Li, Gena Huang, Caixia Ren, Ning Wang, Silei Sui, Zuowei Zhao, Man Li
Summary: This study identified the most common differentially expressed genes in various subtypes of BRCA and established a 12-gene prognostic risk model. Evaluation of the risk model using K-M curves, ROC curves, and Cox regression showed good predictive performance and improved accuracy and sensitivity in prognosis. The risk model can assist in individualizing treatment for patients and proposing precise strategies for BRCA therapy.
Article
Environmental Sciences
Stefan Scholz, John W. Nichols, Beate Escher, Gerald T. Ankley, Rolf Altenburger, Brett Blackwell, Werner Brack, Lawrence Burkhard, Timothy W. Collette, Jon A. Doering, Drew Ekman, Kellie Fay, Fabian Fischer, Joerg Hackermueller, Joel C. Hoffman, Chih Lai, David Leuthold, Dalma Martinovic-Weigelt, Thorsten Reemtsma, Nathan Pollesch, Anthony Schroeder, Gerrit Schueuermann, Martin von Bergen
Summary: The concept of the eco-exposome, analogous to the human exposome, aims to describe the totality of internal exposure over the lifetime of ecologically relevant organisms and explore linking exposure to adverse effects. The study discusses methods and technologies using targeted and nontargeted chemical analyses and bioassays to characterize eco-exposome exposure.
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Susann Haehnel, Michael Rade, Nicole Kaiser, Kristin Reiche, Andreas Horn, Dennis Loeffler, Conny Blumert, Felicitas Rapp, Friedemann Horn, Juergen Meixensberger, Christof Renner, Wolf Mueller, Frank Gaunitz, Ingo Bechmann, Karsten Winter
Summary: The study utilized tissue slice cultures to analyze treatment effects at a transcriptional and histological level, finding that slice cultures from long-term survivors showed more apoptosis and slight increase in proliferation. Treatment led to upregulation of DNA damage-related genes and enrichment of genotoxicity pathways. The study also demonstrated the feasibility of transcriptomic analyses and automated histology in tissue slice cultures, with experimental data correlating with clinical outcomes.
Letter
Toxicology
Stefan Scholz, Werner Brack, Beate I. Escher, Joerg Hackermuller, Matthias Liess, Martin von Bergen, Lukas Y. Wick, Ana C. Zenclussen, Rolf Altenburger
ARCHIVES OF TOXICOLOGY
(2022)
Article
Biochemical Research Methods
Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai, Joerg Hackermueller
Summary: Many chemicals in the environment pose risks if not assessed properly; limitations in computational approaches due to lack of labeled training data is a major challenge.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Manuela Voelkner, Felix Wagner, Lisa Maria Steinheuer, Madalena Carido, Thomas Kurth, Ali Yazbeck, Jana Schor, Stephanie Wieneke, Lynn J. A. Ebner, Claudia Del Toro Runzer, David Taborsky, Katja Zoschke, Marlen Vogt, Sebastian Canzler, Andreas Hermann, Shahryar Khattak, Joerg Hackermueller, Mike O. Karl
Summary: Human organoids can provide valuable insights into complex and incurable neuropathologies. In this study, researchers successfully established a human retinal organoid system that replicates various aspects of the human retina, including those within the macula. By combining TNF and HBEGF, the researchers induced the degeneration of photoreceptors, glial pathologies, dyslamination, and scar formation, uncovering a previously unknown pathomechanism. This research could have significant implications for age-related macular degeneration and other related diseases, offering potential therapeutic approaches.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Henry Loeffler-Wirth, Michael Rade, Arsen Arakelyan, Markus Kreuz, Markus Loeffler, Ulrike Koehl, Kristin Reiche, Hans Binder
Summary: Anti-CD19 CAR-T cell immunotherapy is a potential treatment option for B cell lymphomas, but it can lead to severe adverse effects like neurotoxicity. Single-cell RNA sequencing data analysis reveals differences in T cell composition and transcriptional states between patients with different levels of ICANS. The abundance of cycling cells, LAG3-mediated exhaustion, and CAR positive cells varies among patients. These findings provide molecular insights that could help overcome neurotoxicity.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marie Bitenc, Benedicte Grebstad Tune, Maria Melheim, Monica Atneosen-Asegg, Xiaoran Lai, Polona Rajar, Ronnaug Solberg, Lars Oliver Baumbusch
Summary: In this study, the authors tested and validated common techniques for cfDNA extraction and quantification in a piglet model of perinatal asphyxia. They found potential temporal and quantitative changes in the concentrations of cfDNA using qRT-PCR and droplet digital PCR methods. The more sensitive digital PCR methodology might be required to identify minimal responses.
MOLECULAR BIOLOGY REPORTS
(2023)
Review
Chemistry, Multidisciplinary
M. J. B. Amorim, W. Peijnenburg, D. Greco, L. A. Saarimaki, V. Dumit, A. Bahl, A. Haase, L. Tran, J. Hackermuller, S. Canzler, J. J. Scott-Fordsmand
Summary: A Systems Toxicology (ST) approach integrates toxicological concepts with omics technologies and computational data sciences, aiming to integrate New Approach Methodologies (NAMs) into hazard and risk assessment. Adverse Outcome Pathways (AOPs) are important for mechanistic data integration in risk assessment, especially for novel smart and advanced materials. However, there are challenges in the routine usage of NAMs, including omics-based information.
Article
Oncology
Carolin Schimmelpfennig, Michael Rade, Susanne Fuessel, Dennis Loeffler, Conny Blumert, Catharina Bertram, Angelika Borkowetz, Dominik J. Otto, Sven-Holger Puppel, Pia Hoenscheid, Ulrich Sommer, Gustavo B. Baretton, Ulrike Koehl, Manfred Wirth, Christian Thomas, Friedemann Horn, Markus Kreuz, Kristin Reiche
Summary: This study investigated gene fusions in prostate cancer and identified two potential novel fusions, MBTTPS2,L0XNC01::SMS and AMACR::AMACR. The results showed that the number of gene fusions was associated with the prognosis of prostate cancer. However, further validation and assessment of clinical value are needed.
Article
Immunology
Johannes R. Schmidt, Janine Haupt, Sina Riemschneider, Christoph Kaempf, Dennis Loeffler, Conny Blumert, Kristin Reiche, Ulrike Koehl, Stefan Kalkhof, Joerg Lehmann
Summary: In this study, the effects of high-affinity AhR ligand benzo[a]pyrene (BaP) and low-affinity AhR ligand indole-3-carbinol (I3C) on gene expression patterns in murine bone marrow-derived macrophages (BMMs) were compared using mRNA sequencing. The results showed that AhR regulated the expression of over 1,000 genes, involving cellular processes, immune functions, and phenotypic transformation of the cells. Some of the identified genes were previously known to be regulated by AhR, while others were newly discovered to be AhR-regulated.
FRONTIERS IN IMMUNOLOGY
(2023)
Letter
Hematology
Bettina Glatte, Kerstin Wenk, Anja Grahnert, Maik Friedrich, Maximilian Merz, Vladan Vucinic, Luise Fischer, Kristin Reiche, Miriam Alb, Michael Hudecek, Paul Franz, Stephan Fricke, Uwe Platzbecker, Ulrike Koehl, Ulrich Sack, Andreas Boldt, Sunna Hauschildt, Ronald Weiss
Article
Biology
Benedicte Grebstad Tune, Maria Melheim, Monica Asegg-Atneosen, Baukje Dotinga, Ola Didrik Saugstad, Ronnaug Solberg, Lars Oliver Baumbusch
Summary: This study explores selected long non-coding RNAs (lncRNAs) and their protein-coding target genes using a piglet model of perinatal asphyxia. The results show significant changes in lncRNA expression, mainly in the cortex and hippocampus, induced by a brief exposure to 100% oxygen for 3 minutes. The findings suggest that lncRNAs are part of the molecular response to hypoxia-induced damage during perinatal asphyxia, and a better understanding of their regulatory properties may provide novel targets and intervention strategies in the future.
Article
Environmental Sciences
Liza-Marie Beckers, Rolf Altenburger, Werner Brack, Beate I. Escher, Jorg Hackermueller, Enken Hassold, Gianina Illing, Martin Krauss, Janet Krueger, Paul Michaelis, Andreas Schuettler, Sarah Stevens, Wibke Busch
Summary: Aquatic environments are polluted with a wide range of organic micropollutants, posing challenges for risk assessment due to the complexity and diversity of pollutant mixtures. This study suggests that investigating source-specific background pollution in aquatic environments could be a way to approach mixture risk assessment. By preparing a representative mixture of organic micropollutants and comparing it with predicted mixture effects, the study demonstrates that this approach can help identify substances that should be considered in future monitoring efforts and provide measures to estimate wastewater background concentrations and assess mixture risks. The study highlights data gaps that should be addressed for prioritization of effect testing, and offers the approach and mixture for further investigations by authorities and scientists.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Zhipeng Wang, Sven-Bastiaan Haange, Volker Haake, Maike Huisinga, Hennicke Kamp, Roland Buesen, Kristin Schubert, Sebastian Canzler, Joerg Hackermueller, Ulrike Rolle-Kampczyk, Martin von Bergen
Summary: Thyroid hormones play a crucial role in regulating various physiological mechanisms in mammals. The therapeutic drugs PTU and phenytoin have been found to induce hypothyroidism and decrease blood thyroid hormone levels. This study aimed to analyze the impact of these drugs on systemic metabolism by investigating the metabolome of thyroid and liver tissue, as well as blood plasma, in a rat model.
Article
Oncology
Johanne U. Hermansen, Dorota M. Wojcik, Nina Robinson, Jens Pahnke, Hans Kristian Haugland, Ann Helen Jamtoy, Trond Flaegstad, Hanne Halvorsen, Bendik Lund, Lars O. Baumbusch, Monica C. Munthe-Kaas
Summary: This study aimed to establish a prospective and centralized biobank for infants, children, and adolescents diagnosed with cancer in Norway. With judicial and ethical approvals obtained through a consortium, steering committee, and advisory board, pipelines including SOPs for all aspects of the biobank process were developed. By January 1, 2021, approximately 12,000 samples from 510 patients had been included, with a 96% consent and participation rate among newly diagnosed patients.
