Article
Cell Biology
Julien Paganini, Pierre Faux, Sophie Beley, Christophe Picard, Jacques Chiaroni, Julie Di Cristofaro
Summary: HLA-F has specificities in its structure, expression regulation at the cell membrane, and function. It is detected in various cell types and localizes in the ER and Golgi apparatus. HLA-F binds to activating and inhibitory immune receptors and its expression is associated with specific genotypes and SNPs.
Article
Multidisciplinary Sciences
Mike Thompson, Mary Grace Gordon, Andrew Lu, Anchit Tandon, Eran Halperin, Alexander Gusev, Chun Jimmie Ye, Brunilda Balliu, Noah Zaitlen
Summary: This study presents a method for transcriptome-wide association studies (TWAS) that considers the context-specific and context-shared effects of genetic variants. The authors demonstrate that their method improves the power of TWAS and identifies more genetically predicted genes associated with complex traits. The study highlights the importance of accounting for context-specific effects when analyzing transcriptome data.
NATURE COMMUNICATIONS
(2022)
Article
Pharmacology & Pharmacy
James A. Bjork, Douglas A. Dawson, Jacob O. Krogstad, Kendall B. Wallace
Summary: PFAS, a group of diverse chemicals of public concern, have shown to cause various adverse effects in laboratory animals. Research indicates that the combined exposure to different PFAS generally results in a transcriptional response that is consistently at or below the sum of the individual responses.
Article
Biochemistry & Molecular Biology
Yuan Lou, Sarah A. Woodson
Summary: This study shows that self-cleavage of the glmS ribozyme riboswitch can occur during transcription before the ribozyme is fully synthesized. Co-transcriptional folding of the RNA allows the ribozyme catalytic core to react without the downstream stability domain. Slow sequential folding promotes the formation of the native core structure. Ribozyme self-cleavage at an early stage of transcription is important for the regulation of glmS in B. subtilis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Shao-Pei Chou, Adriana K. Alexander, Edward J. Rice, Lauren A. Choate, Charles G. Danko
Summary: This study investigates how DNA sequence differences affect the dynamics and position of RNA polymerase II (Pol II) during transcription. The researchers found that DNA sequence motifs are key determinants of Pol II initiation and pause positions, and that initiation site selection follows a stochastic process similar to Brownian motion. Additionally, they discovered that differences in transcription termination impact the structure and stability of mature mRNA, and that allelic changes in transcription affect mRNA and ncRNA expression across genomic domains.
Article
Multidisciplinary Sciences
Cedric Debes, Antonios Papadakis, Sebastian Groenke, Oezlem Karalay, Luke S. Tain, Athanasia Mizi, Shuhei Nakamura, Oliver Hahn, Carina Weigelt, Natasa Josipovic, Anne Zirkel, Isabell Brusius, Konstantinos Sofiadis, Mantha Lamprousi, Yu-Xuan Lu, Wenming Huang, Reza Esmaillie, Torsten Kubacki, Martin R. Spaeth, Bernhard Schermer, Thomas Benzing, Roman-Ulrich Mueller, Adam Antebi, Linda Partridge, Argyris Papantonis, Andreas Beyer
Summary: During ageing, impairment of cellular processes such as transcription and RNA splicing compromises physiological homeostasis. This study reveals that transcriptional elongation speed and RNA splicing are correlated with age across different species, and lifespan-extending interventions can reverse these changes. These findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan extension.
Article
Biochemistry & Molecular Biology
Jonathan E. Henninger, Ozgur Oksuz, Krishna Shrinivas, Ido Sagi, Gary LeRoy, Ming M. Zheng, J. Owen Andrews, Alicia Zamudio, Charalampos Lazaris, Nancy M. Hannett, Tong Ihn Lee, Phillip A. Sharp, Ibrahim I. Cisse, Arup K. Chakraborty, Richard A. Young
Summary: This study discusses the mechanisms of feedback control in regulating biological processes, especially in transcription regulation. Research indicates that RNA in transcription initiation promotes condensate formation, while RNA produced during elongation stimulates condensate dissolution. Therefore, transcriptional regulation involves a feedback mechanism where transcribed RNA both stimulates and arrests the process.
Article
Biochemistry & Molecular Biology
Aman Y. Husbands, Antje Feller, Vasudha Aggarwal, Courtney E. Dresden, Ashton S. Holub, Taekjip Ha, Marja C. P. Timmermans
Summary: The START domain enhances the activity of HD-ZIPIII TFs and enables them to bind DNA, providing an answer to a long-standing question in plant development.
Article
Biochemistry & Molecular Biology
Aman Y. Husbands, Antje Feller, Vasudha Aggarwal, Courtney E. Dresden, Ashton S. Holub, Taekjip Ha, Marja C. P. Timmermans
Summary: The START domain of the HD-ZIPIII transcription factors plays a crucial role in promoting homodimerization and increasing transcriptional potency, while also binding to phospholipids. This discovery resolves a long-standing mystery in plant development and highlights the regulatory potential of this evolutionary module.
Article
Biochemistry & Molecular Biology
Yi Zeng, Benjamin J. Fair, Huilin Zeng, Aiswarya Krishnamohan, Yichen Hou, Johnathon M. Hall, Alexander J. Ruthenburg, Yang Li, Jonathan P. Staley
Summary: Previous studies suggested that most vertebrate genes require exon definition for splicing, where spliceosome assembly occurs on exons rather than introns. However, our research found that 90% of introns, including long introns, can splice before the transcription of a downstream exon, indicating that exon definition is not necessary for most human introns. Additionally, splicing timing varies greatly among introns and is influenced by various genetic elements.
Article
Cell Biology
Cecilia Studniarek, Michael Tellier, Pascal G. P. Martin, Shona Murphy, Tamas Kiss, Sylvain Egloff
Summary: The lack of 7SK snRNP has minor impact on global RNAPII transcription under normal conditions, but impairs transcriptional response and reduces viability upon UV-light-induced DNA damage. 7SK is crucial for proper induction of UV-responsive genes and orchestrating the transcriptional response to stress.
Article
Biochemistry & Molecular Biology
Min Liu, Jiafu Zhu, Zhicheng Dong
Summary: Plants have efficient mechanisms for adapting to temperature fluctuations, with primed plants exposed to mild heat stress showing more drastic transcriptional changes compared to naive plants. The study observed accumulation of engaged RNA polymerase II downstream of transcription start sites, with release of 5' pausing being a rate-limiting step for induction of heat shock protein genes.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tatsuya Tsukahara, David H. Brann, Stan L. Pashkovski, Grigori Guitchounts, Thomas Bozza, Sandeep Robert Datta
Summary: The research found that each subtype of olfactory sensory neuron in mice has a unique transcriptome, which is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation and accurately predict responses to odors. The findings suggest a general model where structured transcriptional variation within a cell type reflects individual experience.
Article
Genetics & Heredity
Priscila Saamara Masin, Hugo Alves Visentin, Laise Nayana Sala Elpidio, Ana Maria Sell, Lorena Visentainer, Quirino Alves De Lima Neto, Joana Maira Valentini Zacarias, Patricia Couceiro, Andressa Higa Shinzato, Manuel Santos Rosa, Paulo Rodrigues-Santos, Jeane Eliete Laguila Visentainer
Summary: This study investigated the association between polymorphisms in TLR1 and TLR2 genes and susceptibility/protection against leprosy in southern Brazil. The results showed that certain genotypes in TLR1 and TLR2 were more frequent in the control group, suggesting a potential protective role against leprosy.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Xueyang Dong, Ben G. H. Guthrie, Margaret Alexander, Cecilia Noecker, Lorenzo Ramirez, Nathaniel R. Glasser, Peter J. Turnbaugh, Emily P. Balskus
Summary: This study develops genetic tools for the direct manipulation of Eggerthella lenta and other Coriobacteriia, including shuttle vectors, transformation methods, and genome editing systems. Using these tools, the researchers characterize endogenous promoters and inducible expression systems in Eggerthella lenta, and uncover a novel family of transcriptional regulators in gut Coriobacteriia. Furthermore, they utilize these genetic tools to study the effects of Eggerthella lenta genes on host biology.
NATURE COMMUNICATIONS
(2022)
Review
Endocrinology & Metabolism
Adriana Maggi
Summary: The article explores the sex differences in liver metabolic activities and their evolutionary origins. In mammals, females have adapted their liver functions to support reproductive needs and energy storage. Considering the importance of liver and energy metabolism in diseases, a better understanding of the differences between male and female liver functions could help personalize medicine and pharmacology.
Correction
Pharmacology & Pharmacy
Alessandro Villa, Electra Brunialti, Jessica Dellavedova, Clara Meda, Monica Rebecchi, Matteo Conti, Lorena Donnici, Angelo Reggiani, Vincenzo Lionetti, Paolo Ciana, Raffaele De Francesco
PHARMACOLOGICAL RESEARCH
(2022)
Article
Pharmacology & Pharmacy
Alessandro Villa, Electra Brunialti, Jessica Dellavedova, Clara Meda, Monica Rebecchi, Matteo Conti, Lorena Donnici, Raffaele De Francesco, Angelo Reggiani, Vincenzo Lionetti, Paolo Ciana
Summary: Identifying specific DNA molecules (aptamers) efficiently prevent the interaction and infection of SARS-CoV-2 virus with the human ACE2 receptor, suggesting potential clinical development of these aptamers as inhibitors for SARS-CoV-2 infection.
PHARMACOLOGICAL RESEARCH
(2022)
Article
Oncology
Sara Pizzamiglio, Giulia Cosentino, Chiara M. Ciniselli, Loris De Cecco, Alessandra Cataldo, Ilaria Plantamura, Tiziana Triulzi, Sarra El-abed, Yingbo Wang, Mohammed Bajji, Paolo Nuciforo, Jens Huober, Susan L. Ellard, David L. Rimm, Andrea Gombos, Maria Grazia Daidone, Paolo Verderio, Elda Tagliabue, Serena Di Cosimo, Marilena V. Iorio
Summary: The study evaluated the predictive and prognostic value of basal primary tumor miRNA expression profile in trastuzumab treatment and identified miRNA signatures associated with clinical outcomes. These miRNA markers have the potential to be a useful tool in identifying patients with differential responses to trastuzumab-based neoadjuvant therapy.
Meeting Abstract
Oncology
S. Di Cosimo, C. M. Ciniselli, C. Sotiriou, K. Pogue-Geile, D. Fumagalli, E. de Azambuja, D. Venet, L. De Cecco, N. Pong, V. Cappelletti, E. Tagliabue, Y. Wang, C. Saura Manich, P. G. Nuciforo, S. Kuemmel, L. Pusztai, M. G. Daidone, S. Pizzamiglio, G. Pruneri, P. Verderio
ANNALS OF ONCOLOGY
(2022)
Article
Immunology
Paolo Corradini, Chiara Agrati, Giovanni Apolone, Alberto Mantovani, Diana Giannarelli, Vincenzo Marasco, Veronica Bordoni, Alessandra Sacchi, Giulia Matusali, Carlo Salvarani, Pier Luigi Zinzani, Renato Mantegazza, Fabrizio Tagliavini, Maria Teresa Lupo-Stanghellini, Fabio Ciceri, Silvia Damian, Antonio Uccelli, Daniela Fenoglio, Nicola Silvestris, Fausto Baldanti, Giulia Piaggio, Gennaro Ciliberto, Aldo Morrone, Franco Locatelli, Valentina Sinno, Maria Rescigno, Massimo Costantini
Summary: This study investigated the immune response to the SARS-CoV-2 vaccine in patients with tumors and immune disorders. The results showed that immunosuppressive treatment was a risk factor for a low humoral response, while the booster dose improved both humoral and T-cell responses.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Medical Laboratory Technology
Nouha Setti Boubaker, Aymone Gurtner, Nesrine Trabelsi, Isabella Manni, Ahlem Blel, Ahmed Saadi, Marouene Chakroun, Zeineb Naimi, Selim Zaghbib, Meriam Ksontini, Khedija Meddeb, Soumaya Rammeh, Haroun Ayed, Mohamed Chebil, Giulia Piaggio, Slah Ouerhani
Summary: This study found that HOXA13 plays an important role in the development of bladder cancer but is not associated with prognosis. It may be involved in the early initiation of urothelial tumorigenesis and could serve as a diagnostic marker for patients with NMIBC. Further experimentation on larger validation sets is necessary.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2022)
Article
Cell Biology
Electra Brunialti, Alessandro Villa, Marco Toffoli, Sara Lucas Del Pozo, Nicoletta Rizzi, Clara Meda, Adriana Maggi, Anthony H. V. Schapira, Paolo Ciana
Summary: Microglia are heterogenous cells in the nervous system that have distinct populations contributing to specific processes, including neuroprotection. Our study found that male microglia tend to have a more pro-inflammatory phenotype, while female microglia are more sensitive to glucocerebrosidase inhibition. Furthermore, glucocerebrosidase inhibition impaired the ability of female microglia to enhance the Nrf2-dependent detoxification pathway in neurons.
Article
Multidisciplinary Sciences
Barbara Oliviero, Michele Dei Cas, Aida Zulueta, Roberta Maiello, Alessandro Villa, Carla Martinelli, Elena Del Favero, Monica Falleni, Linda Montavoci, Stefania Varchetta, Dalila Mele, Matteo Donadon, Cristiana Soldani, Barbara Franceschini, Marcello Maestri, Gaetano Piccolo, Matteo Barabino, Paolo Pietro Bianchi, Jesus M. Banales, Stefania Mantovani, Mario U. Mondelli, Anna Caretti
Summary: Cholangiocarcinoma (CCA), a rare cancer with increasing incidence, can be influenced by extracellular vesicles (EV) through cargo molecule transfer. The sphingolipid (SPL) profile of intrahepatic CCA (iCCA)-derived EVs were studied using liquid chromatography-tandem mass spectrometry. iCCA-derived EVs showed downregulation of all SPL species, except poorly-differentiated ones which had higher ceramide and dihydroceramide content. These EVs induced the release of pro-inflammatory cytokines, and inhibiting ceramide synthesis reduced their pro-inflammatory activity. Therefore, iCCA-derived EVs may promote iCCA progression by exporting excessive pro-apoptotic and pro-inflammatory ceramides.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Marco Silvestri, Trung Nghia Vu, Federico Nichetti, Monica Niger, Serena Di Cosimo, Filippo De Braud, Giancarlo Pruneri, Yudi Pawitan, Stefano Calza, Vera Cappelletti
Summary: This study aimed to provide a gene expression-based classification of extrahepatic and intrahepatic cholangiocarcinoma by collecting all available public records. Through unsupervised clustering analysis of gene expression data, four subgroups characterized by different immune infiltrate and signaling pathways were identified in both ICC and ECC. Class predictors were developed using short gene list signatures and subgroups of ICC tumors with different prognosis were identified in an independent dataset.
Letter
Surgery
Armando G. Licata, Chiara M. Ciniselli, Luca Sorrentino, Arianna Micali, Maria Grazia Daidone, Marcello Guaglio, Manuela Gariboldi, Paolo Verderio, Loris De Cecco, Maurizio Cosimelli
BRITISH JOURNAL OF SURGERY
(2023)
Meeting Abstract
Oncology
S. Pizzamiglio, C. M. Ciniselli, E. De Azambuja, D. Agbor-Tarh, A. Moreno-Aspitia, T. Suter, A. Trama, M. G. Daidone, P. Verderio, S. Di Cosimo
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Oncology
Monica Niger, Federico Nichetti, Francesca Dell'Angelo, Vera Cappelletti, Chiara Pircher, Marta Vismara, Christian Cotsoglou, Sherrie Bhoori, Andrea Vingiani, Maria Di Bartolomeo, Filippo Pietrantonio, Filippo de Braud, Giancarlo Pruneri, Maria Grazia Daidone, Vincenzo Mazzaferro
JCO PRECISION ONCOLOGY
(2022)