Article
Biochemistry & Molecular Biology
Fabian Kern, Lena Krammes, Karin Danz, Caroline Diener, Tim Kehl, Oliver Kuechler, Tobias Fehlmann, Mustafa Kahraman, Stefanie Rheinheimer, Ernesto Aparicio-Puerta, Sylvia Wagner, Nicole Ludwig, Christina Backes, Hans-Peter Lenhof, Hagen von Briesen, Martin Hart, Andreas Keller, Eckart Meese
Summary: MiRNAs are regulators of gene expression, and their target genes are not randomly distributed in the transcriptome, but share functional pathways. The HiTmIR strategy efficiently validates target genes and provides a resource for training or benchmarking other target predictors.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Mst Shamima Khatun, Md Ashad Alam, Watshara Shoombuatong, Md Nurul Haque Mollah, Hiroyuki Kurata, Md Mehedi Hasan
Summary: This article reviews the development of bioinformatics tools for miRNA target prediction, discusses the progress and limitations of existing miRNA databases, and explores the challenges and future directions of next-generation algorithms in predicting miRNA targets.
CURRENT MEDICINAL CHEMISTRY
(2022)
Review
Biology
Rayssa M. M. W. Feitosa, Paula Prieto-Oliveira, Helena Brentani, Ariane Machado-Lima
Summary: MicroRNAs (miRNAs) are non-coding RNAs that directly regulate the translation of mRNAs by binding to them. They play important roles in various physiological processes and are associated with disease development. This study presents a systematic review and classification of computational tools for predicting miRNA targets in animals, providing researchers with guidance for tool selection and highlighting the evolution, features, methods, and performance issues of these prediction tools.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Biology
Sedigheh Sadat Mortazavi, Zahra Bahmanpour, Yousef Daneshmandpour, Faranak Roudbari, Roghayeh Sheervalilou, Somayeh Kazeminasab, Babak Emamalizadeh
Summary: MicroRNAs are small endogenous non-coding RNAs that play crucial regulatory roles in biological processes through translational repression or mRNA degradation. The importance of miRNAs has led to the development of multiple databases, each with specific parameters and characteristics for researchers to benefit from. Understanding the classification and information contained in these databases is essential for scientists to quickly find suitable bioinformatics tools and relevant information.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Endocrinology & Metabolism
Dapeng Yin, Zhixin Guo, Xinyu Zhang
Summary: In this study, 130 differentially expressed genes related to diabetic nephropathy (DN) were identified, and 10 hub genes were screened. These hub genes were found to be associated with extracellular matrix, collagen fibrous tissue, transforming growth factor-beta, and advanced glycosylation end products-receptor. Further investigation revealed that matrix metalloproteinase 2 (MMP2) can serve as a biomarker for DN and is involved in the fibrosis process, and miR-106b-5p and miR-93-5p may regulate the expression of MMP2 as upstream signals.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Review
Biochemical Research Methods
Camilo Rebolledo, Juan Pablo Silva, Nicolas Saavedra, Vinicius Maracaja-Coutinho
Summary: Circular RNAs (circRNAs) are non-coding RNA molecules generated from RNA splicing that have regulatory potential over other RNA species. There are various algorithms available for circRNA identification, classified into pseudo-reference-based and split-alignment-based approaches. Data from circRNA transcriptome initiatives are stored in public databases, providing information on different species and functional annotations. This review discusses computational resources for circRNA identification and characterization, including algorithms, predictive tools, and public repositories containing relevant data and information, summarizing their characteristics, reliability, and reported data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biotechnology & Applied Microbiology
Md Mehedi Hasan, Watshara Shoombuatong, Hiroyuki Kurata, Balachandran Manavalan
Summary: DNA N6-methyladenosine (6mA) methylation is an important epigenetic modification that plays key roles in biological processes, and accurate prediction of 6mA sites using bioinformatics tools can vary in performance across different species.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2021)
Article
Genetics & Heredity
Sushil Shakyawar, Siddesh Southekal, Chittibabu Guda
Summary: Identification of miRNA-mRNA interactions is critical and challenging in gene regulation. This study proposed mintRULS, a method that combines miRNA and mRNA features to predict miRNA-target site interactions. The results demonstrated its superior performance compared to existing tools, as well as high accuracy when validated against experimental data.
Article
Genetics & Heredity
Alberto Brusati, Antonia Ratti, Viviana Pensato, Silvia Peverelli, Davide Gentilini, Eleonora Dalla Bella, Marta Nice Sorce, Megi Meneri, Delia Gagliardi, Stefania Corti, Cinzia Gellera, Giuseppe Lauria Pinter, Nicola Ticozzi, Vincenzo Silani
Summary: This study aims to investigate the biological effects of rare variants in miRNA genes on miRNA folding, maturation, and target gene recognition in sporadic ALS patients. The analysis identified several rare variants that altered the secondary structures of miRNA and affected the recognition of target genes. Additionally, some variants were found to be associated with genes related to nervous system development.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Medicinal
Carla Lima, Silas Fernandes Eto, Monica Lopes-Ferreira
Summary: Peptide-protein interactions are crucial for cellular functions and drug design. In silico prediction using bioinformatics and computational tools can help identify drug-target interactions. This study focuses on the TnP family of cyclic peptides and its potential targets, utilizing bioinformatics and computational approaches to predict the structure, binding properties, and interactions of TnP. By identifying integrins as key proteins, the study sheds light on the anti-inflammatory effects of TnP and its possible side effects.
Review
Biochemistry & Molecular Biology
Andres Rincon-Riveros, Duvan Morales, Josefa Antonia Rodriguez, Victoria E. Villegas, Liliana Lopez-Kleine
Summary: Noncoding RNAs play key roles in gene expression regulation by interacting with other biological molecules, and computational biology can enhance our understanding of these interactions. Experimental findings drive advancements in computational methods, which in turn provide new insights for experimental validation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Yang Tai, Chong Zhao, Jinhang Gao, Tian Lan, Huan Tong
Summary: By analyzing miRNA and mRNA expression arrays, we identified 13 differentially expressed miRNAs in cirrhotic samples. These miRNAs were further validated in activated LX2 cells. The miRNA-mRNA interaction networks revealed 361 regulatory pairs and 20 hub genes, primarily involved in collagen and ECM components, immune response, and cell adhesion.
Review
Food Science & Technology
Hena Dhar, Subhash Verma, Sarita Dogra, Shailja Katoch, Rishika Vij, Geetanjali Singh, Mandeep Sharma
Summary: Bovine milk peptides are protein fragments with diverse bioactive properties. They have significant health impact and can be used as natural alternatives for preventing and managing diseases. The article reviews the antimicrobial, immunological, opioid, and anti-hypertensive activities of these peptides and discusses the prediction of new bioactive peptides using computational biology tools.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Genetics & Heredity
Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao
Summary: In this study, we propose a deep learning architecture, DeeReCT-APA, to quantitatively predict the usage of all alternative polyadenylation sites (PASs) of a given gene. Compared to existing methods, DeeReCT-APA outperforms in multiple tasks and can be used to predict the effect of genetic variations on APA patterns.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Immunology
Shi-Ji Li, Zhi-Wen Cai, Hong-Fu Yang, Xu-Dong Tang, Xiao Fang, Le Qiu, Fei Wang, Xu-Lin Chen
Summary: The study identified key miRNA-mRNA axes in potential blood-to-tissue interactions at early burn stage, suggesting plasma exosome-derived miRNAs may impact on the alteration patterns of gene expressions in a burn wound.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Review
Chemistry, Analytical
Ciro Mennella, Susanna Alloisio, Antonio Novellino, Federica Viti
Summary: Technology-aided hand functional assessment is important for clinical decision making, but current applications have limitations and require further research and improvement to enhance their clinical acceptance.
Article
Biotechnology & Applied Microbiology
Stefania Crippa, Anastasia Conti, Valentina Vavassori, Samuele Ferrari, Stefano Beretta, Silvia Rivis, Roberto Bosotti, Serena Scala, Stefania Pirroni, Raisa Jofra-Hernandez, Ludovica Santi, Luca Basso-Ricci, Ivan Merelli, Pietro Genovese, Alessandro Aiuti, Luigi Naldini, Raffaella Di Micco, Maria Ester Bernardo
Summary: Mesenchymal stromal cells (MSCs) have been shown to play a supportive role in the expansion and engraftment of hematopoietic stem and progenitor cells (HSPCs). In this study, we developed a co-culture system using bone marrow (BM)-MSCs to improve the transplantation outcome of CRISPR-Cas9 gene-edited (GE) human HSPCs. We found that BM-MSCs can produce hematopoietic supportive and anti-inflammatory factors that enhance the expansion and clonogenic potential of GE-HSPCs in vitro, leading to improved engraftment and early phase hematological reconstitution in transplanted mice. This study suggests a potential clinical application of BM-MSCs in promoting successful transplantation of GE-HSPCs.
Meeting Abstract
Hematology
Pamela Quaranta, Luca Basso-Ricci, Raisa Jofra Hernandez, Matteo Maria Naldini, Matteo Barcella, Guido Pacini, Carlo Pietrasanta, Lorenza Pugni, Giulia Pais, Fabrizio Benedicenti, Francesca Dionisio, Stefania Giannelli, Ilaria Monti, Silvia Darin, Graziano Barera, Francesca Tucci, Francesca Ferrua, Valeria Calbi, Marco Ometti, Bernhard Gentner, Raffaella Di Micco, Eugenio Montini, Andrea Calabria, Ivan Merelli, Fabio Mosca, Maria Ester Bernardo, Maria Pia Cicalese, Alessandro Aiuti, Serena Scala
Meeting Abstract
Hematology
Annamaria Aprile, Silvia Sighinolfi, Laura Cassina, Mariacarla Panzeri, Mariangela Storto, Stefano Beretta, Ivan Merelli, Alessandra Boletta, Giuliana Ferrari
Article
Biochemistry & Molecular Biology
Giulia Unali, Giovanni Crivicich, Isabel Pagani, Monah Abou-Alezz, Filippo Folchini, Erika Valeri, Vittoria Matafora, Julie A. Reisz, Anna Maria Sole Giordano, Ivan Cuccovillo, Giacomo M. Butta, Lorena Donnici, Angelo D'Alessandro, Raffaele De Francesco, Lara Manganaro, Davide Cittaro, Ivan Merelli, Carolina Petrillo, Angela Bachi, Elisa Vicenzi, Anna Kajaste-Rudnitski
Summary: The interferon-induced transmembrane proteins (IFITM) inhibit endocytic viral entry by binding to phosphatidylinositol 3,4,5-trisphosphate (PIP3), which plays a key role in endosomal antiviral immunity. The level of PIP3 is closely correlated with the potency of endosomal IFITM restriction, and exogenous PIP3 enhances the inhibition of endocytic viruses. These findings elucidate cell-compartment-specific antiviral mechanisms and have potential relevance for the development of broadly acting antiviral strategies.
Article
Biochemistry & Molecular Biology
Paola Bettinaglio, Eleonora Mangano, Viviana Tritto, Roberta Bordoni, Rosina Paterra, Arianna Borghi, Marinella Volonte, Cristina Battaglia, Veronica Saletti, Claudia Cesaretti, Federica Natacci, Mariarosa A. B. Melone, Marica Eoli, Paola Riva
Summary: Spinal neurofibromatosis (SNF) is a form of neurofibromatosis type 1 (NF1) characterized by bilateral neurofibromas involving all spinal roots. The pathogenic mechanisms determining the SNF form are currently unknown. Our study found a higher prevalence of NF1 3' tertile mutations and increased expression of syndecans in SNF, suggesting their potential role in the pathogenesis of SNF.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Materials Science, Biomaterials
Federica Viti, Francesca Micaela Pramotton, Michela Martufi, Raffaella Magrassi, Nicoletta Pedemonte, Mario Nizzari, Francesca Cella Zanacchi, Benedetta De Michele, Manuela Alampi, Martina Zambito, Giuseppe Santamaria, Adriana Bajetto, Sabah Sardar, Valeria Tomati, Paolo Gandullia, Costanza Giampietro, Tullio Florio, Francesco Beltrame, Massimo Vassalli, Isabella Ceccherini
Summary: This study analyzed the morpho-mechanical phenotype of human dermal fibroblasts from patients with VSCM and found that they retained a clear signature of the disease compared to different control groups. The measurement of cellular traction forces was identified as a potential non-specific biomarker of the disease. The authors propose the development of a simple assay based on traction forces to support clinical decision-making or preclinical research.
BIOMATERIALS ADVANCES
(2023)
Article
Multidisciplinary Sciences
Arianna Consiglio, Marco Venturin, Sabrina Briguglio, Clara Rossi, Giorgio Grillo, Stefano Bellosta, Maria Grazia Cattaneo, Flavio Licciulli, Cristina Battaglia
Summary: Long non-coding RNAs (lncRNAs) play a key role in regulating cellular senescence. One particular lncRNA associated with senescence, Senescence Associated Long Non-coding RNA (SALNR), has been found to be down-regulated in various cellular models of senescence. However, our investigation reveals that SALNR may not exist as an independent transcript, but rather as a predicted isoform of the HELLS gene. This finding highlights the importance of HELLS in the senescence and aging process.
Article
Rheumatology
Eleonora Cantoni, Ivan Merelli, Davide Stefanoni, Alessandro Tomelleri, Corrado Campochiaro, Vito Giordano, Maddalena Panigada, Elena M. Baldissera, Laura Merlo Pich, Valentina Natoli, Athanasios Ziogas, Jorge Dominguez-Andres, Giacomo De Luca, Davide Mazza, Samuel Zambrano, Daniela Gnani, Marina Ferrarini, Elisabetta Ferrero, Alessandra Agresti, Barbara Vergani, Biagio Eugenio Leone, Simone Cenci, Angelo Ravelli, Marco Matucci-Cerinic, Angelo D'Alessandro, Leo A. B. Joosten, Lorenzo Dagna, Mihai G. Netea, Raffaella Molteni, Giulio Cavalli
Summary: This study investigated the role of trained immunity (TI) in the pathogenesis of giant cell arteritis (GCA). It was found that monocytes from GCA patients exhibited typical features of TI, including enhanced IL-6 production, immunometabolic changes, and epigenetic changes promoting pro-inflammatory activation. Immunometabolic changes of TI were also observed in myelomonocytic cells in GCA lesions and were required for enhanced cytokine production.
Article
Multidisciplinary Sciences
Matteo Maria Naldini, Gabriele Casirati, Matteo Barcella, Paola Maria Vittoria Rancoita, Andrea Cosentino, Carolina Caserta, Francesca Pavesi, Erika Zonari, Giacomo Desantis, Diego Gilioli, Matteo Giovanni Carrabba, Luca Vago, Massimo Bernardi, Raffaella Di Micco, Clelia Di Serio, Ivan Merelli, Monica Volpin, Eugenio Montini, Fabio Ciceri, Bernhard Gentner
Summary: Relapse in acute myeloid leukemia may be driven by the presence of leukemia stem cells. The authors use single-cell RNA sequencing to identify and characterize leukemia stem cells, and find that miR-126 is a potential marker of resistance. miR-126 high-expressing leukemia stem cells are enriched in chemotherapy-refractory AML and at relapse, and their transcriptional signature can robustly stratify patients for survival.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Martina Zambito, Federica Viti, Alessia G. Bosio, Isabella Ceccherini, Tullio Florio, Massimo Vassalli
Summary: The evaluation of cell elasticity is important due to its impact on physiological and pathological processes. However, single-cell mechanical measurements often vary due to instrumental errors and the nature of the sample. In this study, the authors used a nanoindenter to characterize the experimental procedure and found that technical replicates had minimal influence, but biological conditions significantly affected the results. Experiments should be designed carefully to minimize inhomogeneous scenarios and avoid divergences in measured phenotype.
Review
Gastroenterology & Hepatology
Federica Viti, Roberto De Giorgio, Isabella Ceccherini, Arti Ahluwalia, Maria M. Alves, Chiara Baldo, Giannina Baldussi, Elena Bonora, Osvaldo Borrelli, Luigi Dall'Oglio, Paolo De Coppi, Carlotta De Filippo, Pascal de Santa Barbara, Antonella Diamanti, Carlo Di Lorenzo, Ruggero Di Maulo, Antonio Galeone, Paolo Gandullia, Sohaib K. Hashmi, Florence Lacaille, Laurence Lancon, Salvatore Leone, Maxime M. Mahe, Maria Judit Molnar, Alessandro Palmitelli, Silvia Perin, Alessio Pini Prato, Nikhil Thapar, Massimo Vassalli, Robert O. Heuckeroth
Summary: Visceral myopathy is a rare and life-threatening disease with limited knowledge on its pathogenesis and lack of effective treatments. Current interventions can save lives but severely compromise quality of life. Due to scarce animal models, a collaborative network is needed to advance scientific knowledge and find targeted therapeutic strategies.
DIGESTIVE DISEASES AND SCIENCES
(2023)
Review
Gastroenterology & Hepatology
Federica Viti, Roberto De Giorgio, Isabella Ceccherini, Arti Ahluwalia, Maria M. Alves, Chiara Baldo, Giannina Baldussi, Elena Bonora, Osvaldo Borrelli, Luigi Dall'Oglio, Paolo De Coppi, Carlotta De Filippo, Pascal de Santa Barbara, Antonella Diamanti, Carlo Di Lorenzo, Ruggero Di Maulo, Antonio Galeone, Paolo Gandullia, Sohaib K. Hashmi, Florence Lacaille, Laurence Lancon, Salvatore Leone, Maxime M. Mahe, Maria Judit Molnar, Alessandro Palmitelli, Silvia Perin, Alessio Pini Prato, Nikhil Thapar, Massimo Vassalli, Robert O. Heuckeroth
Summary: Visceral myopathy is a rare and life-threatening disease linked to genetic mutations, with a lack of understanding in its pathogenesis and effective treatments. It is crucial to establish a collaborative network to advance research and provide targeted therapies.
DIGESTIVE DISEASES AND SCIENCES
(2023)
Meeting Abstract
Biotechnology & Applied Microbiology
Michela Milani, Francesco Starinieri, Stefano Beretta, Tiziana Plati, Anna Fabiano, Cesare Canepari, Luigi Aloia, Fabio Russo, Mauro Biffi, Ivan Merelli, Meritxell Huch, Luigi Naldini, Alessio Cantore
Meeting Abstract
Biotechnology & Applied Microbiology
Helena Costa Verdera, Monah Abou Alezz, Eleonora Cavalca, Vasco Meneghini, Elisabeth Mangiameli, Maria Sole Giordano, Inderpal Singh, Klaudia Kuranda, Andrea Ditadi, Ivan Merelli, Angela Gritti, Federico Mingozzi, Anna Kajaste-Rudnitski
