Article
Biochemistry & Molecular Biology
Yohei Miyashita, Osamu Tsukamoto, Ken Matsuoka, Kenta Kamikubo, Yuki Kuramoto, Hai Ying Fu, Tomoya Tsubota, Hirona Hasuike, Toshio Takayama, Hiroaki Ito, Tatsuro Hitsumoto, Chisato Okamoto, Hidetaka Kioka, Ryohei Oya, Haruki Shinomiya, Hideyuki Hakui, Yasunori Shintani, Hisakazu Kato, Masafumi Kitakaze, Yasushi Sakata, Yoshihiro Asano, Seiji Takashima
Summary: Enhancers like CR9 respond to mechanical loads in cardiomyocytes by upregulating natriuretic peptides expressions, and can be affected by drugs inducing cardiac hypertrophy or failure.
Article
Biochemistry & Molecular Biology
Paola Brivio, Giulia Sbrini, Letizia Tarantini, Chiara Parravicini, Piotr Gruca, Magdalena Lason, Ewa Litwa, Chiara Favero, Marco Andrea Riva, Ivano Eberini, Mariusz Papp, Valentina Bollati, Francesca Calabrese
Summary: Epigenetics plays a crucial role in how environmental factors can affect brain function and contribute to central nervous system disorders. Chronic stress was found to mainly impact the expression and methylation of the Gadd45 beta gene, with lurasidone helping to normalize these alterations. MiRNA involvement in gene expression changes was moderate under the experimental conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Ali S. Ropri, Rebecca S. DeVaux, Jonah Eng, Sridar Chittur, Jason Herschkowitz
Summary: Increased breast cancer screening has led to a rise in DCIS diagnosis, emphasizing the need to identify factors influencing DCIS progression to IDC. SE-lncRNAs, which can regulate nearby gene expression, represent novel therapeutic targets. Integrative analysis and cross-referencing with databases revealed differential expression of SE-lncRNAs and alterations in super-enhancers associated with breast cancer progression.
BREAST CANCER RESEARCH
(2021)
Article
Oncology
Yanyao Deng, Liuyang Cheng, Zhicheng Lv, Hongwei Zhu, Xiangrui Meng
Summary: The study found that SNHG7 expression was upregulated in glioma tissues and cell lines, while miR-138-5p expression was downregulated, and the knockdown of SNHG7 expression decreased glioma cell proliferation. Mechanistic studies revealed that SNHG7 downregulated miR-138-5p expression, affecting the expression levels of its target gene EZH2.
Article
Ecology
Y. L. Shen, L. Y. Cheng, T. Zhang, Q. LI, Y. Zhan, N. Yan, E. P. Wang, C. B. Chen
Summary: The problem of continuous cropping obstacle severely hampers the development of the ginseng industry. This study identified miRNAs and target genes related to ginseng crop disorder, providing a theoretical basis for the sustainable development of the ginseng industry.
APPLIED ECOLOGY AND ENVIRONMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jeshima Khan Yasin, Bharat Kumar Mishra, M. Arumugam Pillai, Viswanathan Chinnusamy
Summary: This study identified 63 novel lincRNAs from pigeonpea comprehensive transcriptome assembly, with 43 of them perfectly mapped on the pigeonpea genome. In-depth in-silico analyses were conducted to identify these novel lincRNAs, and the results will facilitate future research on functional characterization of lincRNAs in pigeonpea.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Aalok Shiv, Hari Krishna, Nivedita Sinha, Parichita Priyadarshini, Sarika Sahu, Neelu Jain, Pradeep K. Singh, K. Vinod Prabhu
Summary: MicroRNAs play an important role in modulating pathogen virulence in wheat during leaf rust infection. Different sets of miRNAs are produced in susceptible and resistant genotypes, targeting different genes involved in important biological processes and in virulence.
INDIAN JOURNAL OF GENETICS AND PLANT BREEDING
(2023)
Article
Biochemistry & Molecular Biology
Kimberly N. Griffin, Benjamin William Walters, Haixin Li, Huafeng Wang, Giulia Biancon, Toma Tebaldi, Carolyn B. Kaya, Jean Kanyo, TuKiet T. Lam, Andy L. Cox, Stephanie Halene, Jean-Ju Chung, Bluma J. Lesch
Summary: Argonaute 2 (AGO2) is a protein critical for regulation of mRNA translation and has both cytoplasmic and nuclear functions. Using spermatogenic cells in mice as a model, it was found that AGO2 transiently binds to chromatin and nucleus-specific mRNA transcripts of genes required for sperm production. Knockout of Ago2 resulted in reduced protein levels, abnormal sperm morphology, decreased sperm count, and reduced viability of offspring.
Article
Cell & Tissue Engineering
Alessandro Umbach, Giulia Maule, Eyemen Kheir, Alessandro Cutarelli, Marika Foglia, Luca Guarrera, Luca L. Fava, Luciano Conti, Enrico Garattini, Mineko Terao, Anna Cereseto
Summary: This study presents an efficient method of repairing the NIPBL gene using CRISPR-Cas and HDR induced by inhibiting NHEJ repair. The generated isogenic hiPSCs clones possess regular karyotype and preserved pluripotency.
STEM CELL RESEARCH & THERAPY
(2022)
Article
Biology
Desislava P. Staneva, Stefan Bresson, Tatsiana Auchynnikava, Christos Spanos, Juri Rappsilber, A. Arockia Jeyaprakash, David Tollervey, Keith R. Matthews, Robin C. Allshire
Summary: This study reveals the unique gene expression regulation mechanism in kinetoplastids, a highly divergent lineage of eukaryotes. The researchers identified a complex called SPARC, which consists of SET27 and CRD1, among other components, that is involved in establishing accurate promoter position and directionality.
Article
Health Care Sciences & Services
Matteo Marcatili, Riccardo Borgonovo, Noemi Cimminiello, Ranieri Domenico Cornaggia, Giulia Casati, Cristian Pellicioli, Laura Maggioni, Federico Motta, Chiara Redaelli, Luisa Ledda, Federico Emanuele Pozzi, Michaela Krivosova, Jessica Pagano, Roberto Nava, Fabrizia Colmegna, Antonios Dakanalis, Alice Caldiroli, Enrico Capuzzi, Beatrice Benatti, Bernardo Dell'Osso, Francesca Bertola, Nicoletta Villa, Alberto Piperno, Silvia Ippolito, Ildebrando Appollonio, Carlo Sala, Luciano Conti, Massimo Clerici
Summary: The advent of intra-nasal esketamine (ESK) has the potential to revolutionize the treatment of treatment resistant depression (TRD). However, some patients experience unstable responses and high recurrence rates. These patients require a complex multidisciplinary approach and can benefit from personalized medicine tools.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Meeting Abstract
Hematology
Giulia Biancon, Emma Busarello, Mark D. Lessard, Edward Courvan, Dahyana Arias Escayola, Jennifer VanOudenhove, Veronica Lee, Mathew Krick, Joerg Bewersdorf, Karla M. Neugebauer, Toma Tebaldi, Stephanie Halene
Meeting Abstract
Hematology
Emma Busarello, Zuhairia Ibnat, Giulia Biancon, Jennifer VanOudenhove, Fabio Lauria, Gabriella Viero, Stephanie Halene, Toma Tebaldi
Article
Cell Biology
Hasan H. Oz, Ee-Chun Cheng, Caterina Di Pietro, Toma Tebaldi, Giulia Biancon, Caroline Zeiss, Ping-Xia Zhang, Pamela H. Huang, Sofia S. Esquibies, Clemente J. Britto, Jonas C. Schupp, Thomas S. Murray, Stephanie Halene, Diane S. Krause, Marie E. Egan, Emanuela M. Bruscia
Summary: This study identifies CCR2+ monocytes as a previously neglected contributor to lung damage in CF, driving pathogenic TGF-β signaling and sustaining inflammation by facilitating neutrophil recruitment. Targeting CCR2 to reduce monocyte numbers in CF lungs can ameliorate neutrophil inflammation and prevent tissue damage.
Article
Chemistry, Physical
Kaan oecal, Guido Sanguinetti, Ramon Grima
Summary: Model reduction is a crucial tool for quantitative biologists due to the complexity of mathematical models in biology. In this paper, we demonstrate that common approaches to model reduction for Chemical Master Equation can be viewed as minimizing the Kullback-Leibler divergence between the full model and its reduction. This enables us to transform the task of model reduction into a variational problem that can be solved using numerical optimization methods, and we also derive general expressions for propensities of a reduced system.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Letter
Biotechnology & Applied Microbiology
Sveva Bottini, Claudia Fuoco, Nike Schiavo, Alessandro Bertero, Stefano Biressi, Luciano Conti, Cesare Gargioli
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Maxime Duval, Carlo Yague-Sanz, Tomasz W. Turowski, Elisabeth Petfalski, David Tollervey, Francois Bachand
Summary: Transcription by RNA polymerase I (RNAPI) is essential for producing mature ribosomal RNA (rRNA) in eukaryotic cells. However, the factors and mechanisms that control RNAPI progression and its influence on rRNA processing remain poorly understood. In this study, the authors demonstrate that the RNA-binding protein Seb1 promotes RNAPI pausing along the rDNA, leading to efficient cotranscriptional rRNA processing. This discovery highlights Seb1 as a crucial factor for controlling RNA processing during ribosome biogenesis.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Stefan Bresson, Vadim Shchepachev, David Tollervey
Summary: The fungal cell wall is a crucial target for antifungal compounds, and the cell wall integrity (CWI) pathway regulates transcriptional responses to cell wall damage. In addition, RNA-binding proteins Mrn1 and Nab6 play a complementary role by stabilizing cell wall-related mRNAs. Lack of Nab6 leads to downregulation of these mRNAs, while CWI signaling and Nab6 work together to maintain appropriate cell wall gene expression during stress. Deletion of MRN1 partially alleviates the growth defects associated with Delta nab6, indicating an opposing function in mRNA destabilization. Our findings highlight the importance of a posttranscriptional pathway in cellular resistance to antifungal compounds.
Article
Cell Biology
Valeria Savoca, Julieta Rivosecchi, Alice Gaiatto, Annalisa Rossi, Riccardo Mosca, Irene Gialdini, Lorena Zubovic, Toma Tebaldi, Paolo Macchi, Emilio Cusanelli
Summary: This study reveals that the stability of TERRA transcripts is regulated by the RNA-binding protein associated with lethal yellow mutation (RALY). Depletion of RALY leads to decreased levels of TERRA, impaired localization of TERRA at telomeres, and ultimately telomere damage. Furthermore, TERRA interacts with the poly(A)-binding protein nuclear 1 (PABPN1), suggesting an interplay between RALY and PABPN1 in regulating TERRA stability.
Article
Multidisciplinary Sciences
Martina Paganin, Toma Tebaldi, Fabio Lauria, Gabriella Viero
Summary: expressyouRcell is an easy-to-use R package that visualizes the multi-dimensional variations of transcript and protein levels in dynamic cell pictographs, reducing the complexity of gene expression and protein level changes and improving the quantitative interpretation and communication of results.
Article
Health Care Sciences & Services
Ingrid Battistella, Alessandro Cutarelli, Jacopo Zasso, Massimo Clerici, Carlo Sala, Matteo Marcatili, Luciano Conti
Summary: Astrocytes have important functions in coordinating various homeostatic processes in the central nervous system. A new protocol for generating mature astrocytes from hiPSCs has been developed, allowing for the study of astrocyte functions in human cell contexts and patient-specific settings. The optimized monolayer procedure presented in this study enables the efficient differentiation of hiPSC-derived cortical progenitors into mature astrocytes, providing a valuable tool for investigating the role of these cells in neurodevelopmental and neuropsychiatric diseases and for drug development and biomarker discovery/validation.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Oncology
Daniela Brina, Adele Ponzoni, Martina Troiani, Bianca Cali, Emiliano Pasquini, Giuseppe Attanasio, Simone Mosole, Michela Mirenda, Mariantonietta D'Ambrosio, Manuel Colucci, Ilaria Guccini, Ajinkya Revandkar, Abdullah Alajati, Toma Tebaldi, Deborah Donzel, Fabio Lauria, Nahjme Parhizgari, Aurora Valdata, Martino Maddalena, Arianna Calcinotto, Marco Bolis, Andrea Rinaldi, Simon Barry, Jan Hendrik Rueschoff, Marianna Sabbadin, Semini Sumanasuriya, Mateus Crespo, Adam Sharp, Wei Yuan, Mathew Grinu, Alexandra Boyle, Cynthia Miller, Lloyd Trotman, Nicolas Delaleu, Matteo Fassan, Holger Moch, Gabriella Viero, Johann de Bono, Andrea Alimonti
Summary: In prostate cancer, the secretome is rewired at the translational level to recruit MDSCs, with Hgf, Spp1, and Bgn identified as key regulators. By inhibiting the MNK/eIF4E and AKT pathways, this study provides a therapeutic strategy that combines translation inhibition with immunotherapy to restore immune surveillance in prostate cancer.
