Article
Multidisciplinary Sciences
Maryam Momeni, Maryam Rashidifar, Farinaz Hosseini Balam, Amir Roointan, Alieh Gholaminejad
Summary: COVID-19 is a newly recognized respiratory illness. Although candidate gene biomarkers for its diagnosis have been identified, there is still a need for clinically applicable biomarkers. Disease-specific diagnostic biomarkers are important for differential diagnosis and treatment guidance.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Olaia Martinez-Iglesias, Vinogran Naidoo, Juan Carlos Carril, Silvia Seoane, Natalia Cacabelos, Ramon Cacabelos
Summary: There is a lack of effective diagnostic biomarkers for neurodegenerative disorders (NDDs). Gene expression analysis can provide diagnostic value for NDDs and offers an alternative to current diagnostic methods. This study identified specific gene expressions associated with Alzheimer's disease (AD), Parkinson's disease (PD), and vascular/mixed dementia (VaD). APOE, PSEN1, ABCA7, and SNCA mRNA levels showed high diagnostic accuracy for AD and PD, while PICALM had less accuracy as a biomarker for AD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Nuria Sanchez-Baizan, Laia Ribas, Francesc Piferrer
Summary: The study proposes a new method for transcriptomic data analysis, where WGCNA is first applied to utilize the entire dataset followed by filtering with DEGs, which outperformed the traditional method of filtering with DEGs first and then applying WGCNA. The new method showed improved network model fit, node connectivity measures, and provided a more nuanced representation of biological processes through GO terms.
Article
Environmental Sciences
Bongkyun Park, Musun Park, Kyuhyung Jo, Chan-Sik Kim, Su-Jin Baek
Summary: By analyzing the transcriptome of mouse nasal tissues, significant gene expression differences related to nasal inflammation caused by exposure to Korean diesel particulate matter 20 (KDP20) were identified. Potential predictive biomarkers and binding analysis between metal ions and genes were also discovered.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Genetics & Heredity
Farnoosh Abbas-Aghababazadeh, Wei Xu, Benjamin Haibe-Kains
Summary: With advances in high-throughput sequencing technologies, a large amount of -omics data is now available in the biomedical field. However, findings from clinical and biological studies may not be generalizable due to variance in models and analytic methods. Meta-analysis has been proposed as a statistical tool to integrate independent studies and improve the accuracy of biological insights. This study investigates the impact of violating the independence assumption in meta-analyses, specifically focusing on biomarker discoveries using preclinical pharmacogenomics data.
FRONTIERS IN GENETICS
(2023)
Article
Biochemical Research Methods
Ali Al-Fatlawi, Eka Rusadze, Alexander Shmelkin, Negin Malekian, Cigdem Ozen, Christian Pilarsky, Michael Schroeder
Summary: This study introduces a modified version of the NetRank algorithm, which integrates protein associations, co-expressions, and functions with phenotypic association to predict disease progression and treatment outcomes. The evaluation of different cancer type profiles from The Cancer Genome Atlas (TCGA) data demonstrates the strength of NetRank in identifying interpretable biomarker signatures for cancer outcome prediction.
BMC BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Minnie Jacob, Refat M. Nimer, Mohamad S. Alabdaljabar, Essa M. Sabi, Mysoon M. Al-Ansari, Maged Housien, Khalid M. Sumaily, Lina A. Dahabiyeh, Anas M. Abdel Rahman
Summary: This study used liquid chromatography-mass spectrometry (LC-MS) metabolomics to analyze the metabolome of serum from patients with nephrotic syndrome (NS) and found significant changes in 176 metabolites compared to the control group. Dysregulation of arginine, proline, and tryptophan metabolism, as well as arginine, phenylalanine, tyrosine, and tryptophan biosynthesis, were the most common metabolic pathways affected in NS.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Yu Zheng, Yifeng Sun, Yue Kuai, Guoxiang Fu, Huimin An, Jinyun Chen, Jinying Chen, Jiajun Zhu, Yixin Wo, Yiwang Wu, Kaibin Song, Qinghua Xu, Di Wu, Deshuang Huang, Qifeng Wang, Hongming Pan
Summary: The study evaluated a 90-gene expression assay's performance in identifying the tumor origin of multiple primary malignant tumors (MPMTs) and found it to have high accuracy, with important clinical implications for determining the origin of malignant lesions.
CANCER CELL INTERNATIONAL
(2021)
Article
Oncology
A. A. Hamid, H-C Huang, V Wang, Y-H Chen, F. Feng, R. Den, G. Attard, E. M. Van Allen, P. T. Tran, D. E. Spratt, R. Dittamore, E. Davicioni, G. Liu, R. DiPaola, M. A. Carducci, C. J. Sweeney
Summary: The study demonstrates the utility of transcriptomic subtyping for prognostication and potential selection of patients for chemohormonal therapy in mHSPC, and provides proof of concept for biomarker-guided selection of established combination therapies in mHSPC.
ANNALS OF ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lars E. Borm, Alejandro Mossi Albiach, Camiel C. A. Mannens, Jokubas Janusauskas, Ceren Ozgun, David Fernandez-Garcia, Rebecca Hodge, Francisca Castillo, Charlotte R. H. Hedin, Eduardo J. Villablanca, Per Uhlen, Ed S. Lein, Simone Codeluppi, Sten Linnarsson
Summary: EEL FISH is a method that allows for rapid processing of large tissue samples while maintaining high resolution. By electrophoretically transferring RNA, EEL speeds up data acquisition and preserves single-cell resolution, enabling the study of spatial transcriptomes in the mouse brain and the human visual cortex.
NATURE BIOTECHNOLOGY
(2023)
Article
Medicine, Research & Experimental
Stephanie E. Weissinger, N. Zeke Georgantas, Julia C. Thierauf, Rebecca Pellerin, Emma Gardecki, Stephanie Kuehlinger, Lauren L. Ritterhouse, Peter Moeller, Jochen K. Lennerz
Summary: Tissue microarrays (TMA) are essential for high-throughput molecular profiling in translational research. To address the issue of limited tissue in small biopsy specimens or rare tumors, we developed a slide-to-slide (STS) transfer technique that allows the construction of TMAs from individual tissue sections as small as 2 to 5 mm.
LABORATORY INVESTIGATION
(2023)
Article
Biochemical Research Methods
Hukam C. Rawal, Ulavappa Angadi, Tapan Kumar Mondal
Summary: TEnGExA is a tool that allows tissue-enrichment analysis for any number of genes or transcripts, using a read-count or FPKM-value matrix as input. This tool is quick, easy to use, and efficient in providing tissue-enriched gene lists for downstream analysis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Alma Andersson, Joakim Lundeberg
Summary: In this study, a novel method was proposed to analyze spatial transcriptomics data, which simulated the diffusion of individual transcripts to extract genes with spatial patterns, generating satisfactory results on synthetic and real data. Compared to existing methods, this approach seemed to be less influenced by gene expression levels and showed better time performance when run with multiple cores.
Article
Cell Biology
Yi-Ling Wen, Yong Li, Guangcheng Zhu, Zhibing Zheng, Meng Shi, Si Qin
Summary: Crocetin, extracted from Gardenia jasminoides, a traditional Chinese medicine, affects the gene expression profiling of HepG2 cells by upregulating and downregulating specific genes. Bioinformatics analysis shows Crocetin's involvement in cell proliferation, apoptosis, lipid formation, growth factor response, and signal transduction. KEGG pathway analysis indicates regulation of various pathways by Crocetin, with systemic lupus erythematosus being the most significantly affected pathway.
MEDIATORS OF INFLAMMATION
(2021)
Article
Oncology
Amir Shabeer, Sara Mustafa, Rimsha Sadia Bukhari, Mostafa A. Abdel-Maksoud, Saeedah Musaed Almutairi, Wahidah H. Al-Qahtani, Khushboo Chandio, Nazima Yousaf Khan, Jaweria Gul, Mohammed Aufy
Summary: This study identified four hub genes (DNAH1, DNALI1, DNAH9, and CCDC151) and their associated signaling pathways related to the development of head and neck squamous cell carcinoma (HNSC). These hub genes could potentially serve as molecular biomarkers and therapeutic targets in HNSC patients.
AMERICAN JOURNAL OF CANCER RESEARCH
(2023)
Review
Food Science & Technology
Olga Soutourina
Article
Biotechnology & Applied Microbiology
Anna Maikova, Victor Kreis, Anais Boutserin, Konstantin Severinov, Olga Soutourina
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2019)
Review
Genetics & Heredity
Emma Piattelli, Johann Peltier, Olga Soutourina
Article
Biology
Johann Peltier, Audrey Hamiot, Julian R. Garneau, Pierre Boudry, Anna Maikova, Eliane Hajnsdorf, Louis-Charles Fortier, Bruno Dupuy, Olga Soutourina
COMMUNICATIONS BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Pierre Boudry, Emma Piattelli, Emilie Drouineau, Johann Peltier, Anais Boutserin, Maxence Lejars, Eliane Hajnsdorf, Marc Monot, Bruno Dupuy, Isabelle Martin-Verstraete, Daniel Gautheret, Claire Toffano-Nioche, Olga Soutourina
Summary: High-throughput sequencing of RNA immunoprecipitation revealed a diverse set of mRNAs and ncRNAs interacting with the RNA chaperone protein Hfq in C. difficile, shedding light on the post-transcriptional regulatory network of this pathogen.
Article
Physiology
Lydie Cheval, Benoit Viollet, Christophe Klein, Chloe Rafael, Lucile Figueres, Estelle Devevre, Georges Zadigue, Anie Azroyan, Gilles Crambert, Bruno Vogt, Alain Doucet
Summary: The study reveals the mechanism of proliferation of intercalated cells in the renal collecting duct, showing that acid load induces the secretion of Gdf15, which further activates the growth of intercalated cells. This response is mediated through the stimulation of principal cells by vasopressin.
Article
Biochemistry & Molecular Biology
Lilia G. Noriega, Zesergio Melo, Renuga D. Rajaram, Adriana Mercado, Armando R. Tovar, Laura A. Velazquez-Villegas, Maria Castaneda-Bueno, Yazmin Reyes-Lopez, Dongryeol Ryu, Lorena Rojas-Vega, German Magana-Avila, Adriana M. Lopez-Barradas, Mariana Sanchez-Hernandez, Anne Debonneville, Alain Doucet, Lydie Cheval, Nimbe Torres, Johan Auwerx, Olivier Staub, Gerardo Gamba
Summary: SIRT7 interacts with, stabilizes, and modulates the activity of KCC4 through deacetylation, revealing a novel role for SIRT7 in renal physiology.
Article
Microbiology
Anna Maikova, Pierre Boudry, Anna Shiriaeva, Aleksandra Vasileva, Anais Boutserin, Sofia Medvedeva, Ekaterina Semenova, Konstantin Severinov, Olga Soutourina
Summary: CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acid invaders. This study demonstrates the adaptation process of the type I-B CRISPR-Cas system in Clostridioides difficile and its functional link between adaptation and interference machineries. Understanding the functional PAM motifs and activity levels of CRISPR arrays in this pathogen is crucial for future biotechnological and medical applications.
Article
Medicine, Research & Experimental
Marc Fila, Ali Sassi, Gaelle Brideau, Lydie Cheval, Luciana Morla, Pascal Houillier, Christine Walter, Michel Gennaoui, Laure Collignon, Mathilde Keck, Gabrielle Planelles, Naziha Bakouh, Michel Peuchmaur, Georges Deschenes, Ignacio Anegon, Severine Remy, Bruno Vogt, Gilles Crambert, Alain Doucet
Summary: The study identified a variant of ASIC2b responsible for renal sodium retention in the pathological context of idiopathic nephrotic syndrome (INS).
Review
Microbiology
Victor Kreis, Olga Soutourina
Summary: In this review, recent insights into the role of RNAs in modulating interactions between C. difficile and phages are discussed, along with intriguing data from other prokaryotes.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Marine Oberkampf, Audrey Hamiot, Pamela Altamirano-Silva, Paula Belles-Sancho, Yannick D. N. Tremblay, Nicholas DiBenedetto, Roland Seifert, Olga Soutourina, Lynn Bry, Bruno Dupuy, Johann Peltier
Summary: The production and degradation of cyclic diadenosine monophosphate (c-di-AMP) play important roles in the growth, environmental adaptation, and infection of the human enteropathogen Clostridioides difficile. The production of c-di-AMP is essential for growth, potassium uptake, biofilm formation, and cell wall homeostasis, while its degradation is required for osmotolerance and resistance to detergents and bile salts. Additionally, c-di-AMP degradation is important for host colonization.
Article
Multidisciplinary Sciences
Henrik Dimke, Camille Griveau, Wung-Man Evelyne Ling, Gaelle Brideau, Lydie Cheval, Pravina Muthan, Dominik Mueller, Amr Al-Shebel, Pascal Houillier, Caroline Prot-Bertoye
Summary: The kidney plays a critical role in maintaining mineral balance in the body. Dysregulation of calcium and magnesium reabsorption in the renal tubules can lead to familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC), which is characterized by excessive wasting of calcium and magnesium. This study investigated the localization of claudin-19 (CLDN19), a protein involved in mineral reabsorption, in the kidneys and found that it is primarily located in the basolateral membrane of the renal tubules. Additionally, the study showed that CLDN19 interacts with claudin-16 (CLDN16) to regulate permeability in the tubules. These findings provide insights into the pathophysiology of FHHNC and highlight the importance of CLDN19 in maintaining mineral homeostasis in the kidney.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Microbiology
Alexia L. M. Royer, Andrew A. Umansky, Marie-Maude Allen, Julian R. Garneau, Maicol Ospina-Bedoya, Joseph A. Kirk, Gregory Govoni, Robert P. Fagan, Olga Soutourina, Louis-Charles Fortier
Summary: Therapeutic bacteriophages are being considered as alternatives to treat Clostridioides difficile infections. The surface layer protein A (SlpA) is identified as a common receptor used by many phages, which is a significant discovery for the rational design of therapeutic phage cocktails.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Polina Muzyukina, Anton Shkaruta, Noemi M. Guzman, Jessica Andreani, Adair L. Borges, Joseph Bondy-Denomy, Anna Maikova, Ekaterina Semenova, Konstantin Severinov, Olga Soutourina
Summary: CRISPR-Cas systems provide prokaryotic hosts with adaptive immunity against mobile genetic elements. Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit host defense. This study reports the discovery of a novel Acr protein, AcrIB2, which efficiently inhibits interference by the host's CRISPR-Cas system.
Article
Physiology
Lydie Cheval, Naziha Bakouh, Christine Walter, Digne Tembely, Luciana Morla, Genevieve Escher, Bruno Vogt, Gilles Crambert, Gabrielle Planelles, Alain Doucet
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY
(2019)