Article
Agriculture, Dairy & Animal Science
Xiangchun Pan, Jiali Cai, Yifei Wang, Dantong Xu, Yao Jiang, Wentao Gong, Yuhan Tian, Qingpeng Shen, Zhe Zhang, Xiaolong Yuan, Jiaqi Li
Summary: This study provides a comprehensive analysis of gene expression in pigs and reveals the presence of housekeeping genes, tissue-specific genes, and co-expressed genes. The results offer a fresh perspective on the transcriptional regulation of pig tissues.
Article
Multidisciplinary Sciences
Helen C. Schuster, Frank Hirth
Summary: Conserved cis-regulatory elements (CREs) control the expression networks of Engrailed-, Pax2-, and dachshund-related genes, directing the formation and function of midbrain circuits in arthropods and vertebrates. Analysis of 31 sequenced genomes from different animal clades reveals the presence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is found in spiralians, ecdysozoans, and chordates with a brain, indicating a conserved core domain that distinguishes these genes from randomly assembled sequences.
Article
Medicine, Research & Experimental
Chenchen Feng, Chao Song, Yong Jiang, Jun Zhao, Jian Zhang, Yuezhu Wang, Mingxue Yin, Jiang Zhu, Bo Ai, Qiuyu Wang, Fengcui Qian, Yuexin Zhang, Desi Shang, Jiaqi Liu, Chunquan Li
Summary: This study identifies core transcription factors and their regulatory circuits in large cell/tissue samples. The local module analysis highlights the essential functions and prognostic performance of the core circuitry. Tissue-specific core circuits are related to cell identity and exhibit potential for disease markers and cancer immunotherapy.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Multidisciplinary Sciences
Raquel Rouco, Olimpia Bompadre, Antonella Rauseo, Olivier Fazio, Rodrigue Peraldi, Fabrizio Thorel, Guillaume Andrey
Summary: Developmental genes are often controlled by multiple enhancers with similar specificities, making it difficult to fully understand their function when these regulatory elements are deleted. The authors show that deleting one enhancer in the Pitx1 testbed locus leads to regulatory and cellular changes, resulting in altered cell identities and gene expression levels.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Dawei Zhang, Liangcai Shen, Wenjing Wu, Keke Liu, Jin Zhang
Summary: This study identifies the porcine adipose tissue-specific gene LGALS12 and identifies a 4 kb fragment of the LGALS12 promoter that exhibits adipocyte-specific promoter activity. These findings provide new evidence for understanding porcine fat deposition and offer a promoter element for adipose tissue-specific genetic modification in pigs.
Article
Genetics & Heredity
Sofia Battaglia, Kevin Dong, Jingyi Wu, Zeyu Chen, Fadi J. Najm, Yuanyuan Zhang, Molly M. Moore, Vivian Hecht, Noam Shoresh, Bradley E. Bernstein
Summary: The use of targeted nanopore sequencing allowed researchers to analyze chromatin accessibility and DNA methylation on contiguous DNA molecules, leading to the identification of gene regulatory elements such as promoters, enhancers, insulators, and transcription factor binding sites. They also inferred relationships among dynamic elements within immune loci and determined the order of remodeling events during T cell stimulation. Additionally, they phased primary sequences and regulatory elements across the H19/IGF2 locus, revealing primate-specific features and a mechanism that overrides IGF2 imprinting in human cells.
Article
Ecology
Hamsini Suresh, Megan Crow, Nikolas Jorstad, Rebecca Hodge, Ed Lein, Alexander Dobin, Trygve Bakken, Jesse Gillis
Summary: By comparing single-cell expression data from five primate species, researchers discovered extensive gene expression differences between humans and non-human primates, which are associated with various brain disorders. They also found that certain genes have deeply conserved co-expression across non-human animals but divergent co-expression in humans, suggesting their potential role in driving rapid evolutionary changes in brain function.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, John Quackenbush, John Platig
Summary: Understanding how individual genotypes influence gene regulation can improve our understanding of human health and development. EGRET is a method that infers genotype-specific gene regulatory networks to reveal the genetic associations driving complex phenotypes.
Review
Endocrinology & Metabolism
Kimberly A. A. Lewis, Lisa Chang, Julinna Cheung, Bradley E. E. Aouizerat, Laura L. L. Jelliffe-Pawlowski, Monica R. R. McLemore, Brian Piening, Larry Rand, Kelli K. K. Ryckman, Elena Flowers
Summary: Gestational diabetes (GDM) is associated with increased risk for preterm birth and related complications for both the pregnant person and newborn. Changes in gene expression have the potential to characterize complex interactions between genetic and behavioral/environmental risk factors for GDM. Our goal was to summarize the state of the science about changes in gene expression and GDM.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Quantum Science & Technology
Cristhian Roman-Vicharra, James J. Cai
Summary: In this study, a quantum circuit model was proposed to infer gene regulatory networks (GRNs) from single-cell transcriptomic data. The model utilized qubit entanglement to simulate interactions between genes, showing competitive performance and potential for further exploration. The application of the quantum GRN modeling approach to human lymphoblastoid cells successfully predicted regulatory interactions between genes and estimated the strength of these interactions. This work highlights the potential of quantum computing in biology for a better understanding of single-cell GRNs.
NPJ QUANTUM INFORMATION
(2023)
Article
Genetics & Heredity
Hao Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang
Summary: This study introduces a computational framework called RegVar, based on deep neural networks, which accurately predicts the tissue-specific impact of non-coding regulatory variants on target genes. RegVar outperforms current methods in predicting regulatory variants and is capable of assessing the regulatory impact of any variant on its putative target genes in various tissues.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Ryan J. Corbett, Andrea M. Luttman, Juber Herrera-Uribe, Haibo Liu, Nancy E. Raney, Jenna M. Grabowski, Crystal L. Loving, Christopher K. Tuggle, Catherine W. Ernst
Summary: In this study, whole-genome bisulfite sequencing was performed to assess DNA methylation patterns in pig immune cell populations. The study identified differentially methylated regions (DMRs) and observed correlations between differential methylation and gene expression across immune cell populations. Cell-specific low methylation was found to disproportionately impact genes exhibiting enriched expression in the same cell type. The study also revealed cell type-specific enrichment of transcription factor binding motifs in lowly methylated regions. Furthermore, DMRs were enriched for immune capacity GWAS SNPs, suggesting their importance in immune cell development and function. These findings improve the functional annotation of the porcine genome and enhance the understanding of the links between genotype and phenotype.
Article
Biochemistry & Molecular Biology
Peng Xu, Minghui Wang, Neeraj K. Sharma, Mary E. Comeau, Martin Wabitsch, Carl D. Langefeld, Mete Civelek, Bin Zhang, Swapan K. Das
Summary: This study conducted a multiscale gene network analysis of adipose and muscle tissues in African and European populations to reveal the cell-type-specific molecular signatures of insulin resistance. The research identified two adipocyte subtype-enriched modules and modules enriched for stem cells and fibro-adipogenic progenitors that showed opposite insulin sensitivity responses. The study also pinpointed key drivers of insulin resistance through the integration of gene co-expression and causal networks.
Article
Biochemistry & Molecular Biology
Florian Schmidt, Alexander Marx, Nina Baumgarten, Marie Hebel, Martin Wegner, Manuel Kaulich, Matthias S. Leisegang, Ralf P. Brandes, Jonathan Goeke, Jilles Vreeken, Marcel H. Schulz
Summary: STITCHIT is a novel approach to dissect epigenetic variation in a gene-specific manner for the detection of regulatory elements (REMs) without relying on peak calls in individual samples, leading to a more accurate and refined REM detection compared to standard methods across multiple samples. The approach also predicts thousands of putative REMs, suggesting a large portion of the regulome might be uncharted water.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Carly Weiss, Lana Harshman, Fumitaka Inoue, Hunter B. Fraser, Dmitri A. Petrov, Nadav Ahituv, David Gokhman
Summary: The study utilized massively parallel reporter assays to investigate the regulatory effects of modern human-specific variants, revealing that a portion of these variants drove differential gene expression between human populations, particularly in genes related to vocal tract and brain anatomy and function.
Article
Cardiac & Cardiovascular Systems
A. D'Onofrio, F. Mastro, M. Nadali, A. Fiocco, D. Pittarello, P. Aruta, G. Evangelista, G. Lorenzoni, D. Gregori, G. Gerosa
Summary: This single-center retrospective study compared the outcomes of transapical neochordae implantation (NC) versus conventional surgical (CS) mitral valve repair. The results showed that freedom from moderate and severe mitral regurgitation (MR) was worse in patients undergoing NC at 5-year follow-up. However, in patients with isolated P2 prolapse, the freedom from MR was similar between the two groups. Reoperation freedom was lower in the NC group, but similar in patients with isolated P2 prolapse.
INTERACTIVE CARDIOVASCULAR AND THORACIC SURGERY
(2022)
Letter
Cardiac & Cardiovascular Systems
Augusto D'Onofrio, Gino Gerosa
INTERACTIVE CARDIOVASCULAR AND THORACIC SURGERY
(2022)
Review
Cell Biology
Davide Colaianni, Cristiano De Pitta
Summary: MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate protein-coding gene expression post-transcriptionally. They play important roles in the development and function of the fruit fly brain.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lu Chen, Caitlin M. Roake, Paolo Maccallini, Francesca Bavasso, Roozbeh Dehghannasiri, Pamela Santonicola, Natalia Mendoza-Ferreira, Livia Scatolini, Ludovico Rizzuti, Alessandro Esposito, Ivan Gallotta, Sofia Francia, Stefano Cacchione, Alessandra Galati, Valeria Palumbo, Marie A. Kobin, Gian Gaetano Tartaglia, Alessio Colantoni, Gabriele Proietti, Yunming Wu, Matthias Hammerschmidt, Cristiano De Pitta, Gabriele Sales, Julia Salzman, Livio Pellizzoni, Brunhilde Wirth, Elia Di Schiavi, Maurizio Gatti, Steven E. Artandi, Grazia D. Raffa
Summary: This study identifies a neuroprotective role for TGS1 and highlights the impact of defective snRNA maturation on neuronal viability and function.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Angelo Velle, Chiara Pesenti, Tommaso Grassi, Luca Beltrame, Paolo Martini, Marta Jaconi, Federico Agostinis, Enrica Calura, Dionyssios Katsaros, Fulvio Borella, Robert Fruscio, Maurizio D'Incalci, Sergio Marchini, Chiara Romualdi
Summary: In this study, we investigated the expression of isomiRs in different histological subtypes of Stage I epithelial ovarian cancer (EOC) for the first time, aiming to gain new insights into their biological role in tumor growth and progression.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Multidisciplinary Sciences
Simon Lebek, Francesco Chemello, Xurde M. Caravia, Wei Tan, Hui Li, Kenian Chen, Lin Xu, Ning Liu, Rhonda Bassel-Duby, Eric N. Olson
Summary: CRISPR-Cas9 gene editing is a promising therapy for genomic mutations, but current approaches are limited to specific mutations in a small group of patients. This study introduces a cardioprotective strategy that can potentially benefit a broader range of heart disease patients. By using base editing to eliminate oxidation-sensitive methionine residues in the CaMKII6 gene, the researchers demonstrated protection against ischemia/reperfusion injury in human cardiomyocytes and restored heart function in mice.
Article
Multidisciplinary Sciences
Caterina Marchioretti, Giulia Zanetti, Marco Pirazzini, Gaia Gherardi, Leonardo Nogara, Roberta Andreotti, Paolo Martini, Lorenzo Marcucci, Marta Canato, Samir R. Nath, Emanuela Zuccaro, Mathilde Chivet, Cristina Mammucari, Marco Pacifici, Anna Raffaello, Rosario Rizzuto, Andrea Mattarei, Maria A. Desbats, Leonardo Salviati, Aram Megighian, Gianni Soraru, Elena Pegoraro, Elisa Belluzzi, Assunta Pozzuoli, Carlo Biz, Pietro Ruggieri, Chiara Romualdi, Andrew P. Lieberman, Gopal J. Babu, Marco Sandri, Bert Blaauw, Manuela Basso, Maria Pennuto
Summary: Marchioretti and colleagues demonstrate that there are reversible alterations in gene expression related to muscle contraction and mitochondrial respiration in the skeletal muscle of SBMA mice and patients. These alterations are accompanied by calcium accumulation inside the mitochondria, motor dysfunction, and late changes in muscle structure. The deregulation of expression of genes involved in excitation-contraction coupling (ECC) occurs with sexual maturity and androgen increase in the serum. Surgical castration and AR silencing alleviate the early and late pathological processes, indicating an androgen-dependent nature of these alterations.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Elena Groppa, Paolo Martini, Nima Derakhshan, Marine Theret, Morten Ritso, Lin Wei Tung, Yu Xin Wang, Hesham Soliman, Mark Stephen Hamer, Laura Stankiewicz, Christine Eisner, Le Neve Erwan, Chihkai Chang, Lin Yi, Jack H. Yuan, Sunny Kong, Curtis Weng, Josephine Adams, Lucas Chang, Anne Peng, Helen M. Blau, Chiara Romualdi, Fabio M. V. Rossi
Summary: Efficient regeneration requires coordination between multiple cell types. This study analyzes the transcriptome of hematopoietic, stromal, myogenic, and endothelial cells to understand the intercellular networks involved in regeneration. The findings identify VEGFA-driven endothelial engagement as a key differentiating feature in successful and failed regeneration models. Additionally, the study reveals that multiple cell types simultaneously produce most secreted signals, including VEGFA. Deleting VEGFA from stromal and myogenic progenitors shows that spatial compartmentalization of signaling plays a crucial role in intercellular communication networks.
Article
Biochemistry & Molecular Biology
Changwei Shao, Shuai Sun, Kaiqiang Liu, Jiahao Wang, Shuo Li, Qun Liu, Bruce E. Deagle, Inge Seim, Alberto Biscontin, Qian Wang, Xin Liu, So Kawaguchi, Yalin Liu, Simon Jarman, Yue Wang, Hong-Yan Wang, Guodong Huang, Jiang Hu, Bo Feng, Cristiano De Pitta, Shanshan Liu, Rui Wang, Kailong Ma, Yiping Ying, Gabrielle Sales, Tao Sun, Xinliang Wang, Yaolei Zhang, Yunxia Zhao, Shanshan Pan, Xiancai Hao, Yang Wang, Jiakun Xu, Bowen Yue, Yanxu Sun, He Zhang, Mengyang Xu, Yuyan Liu, Xiaodong Jia, Jiancheng Zhu, Shufang Liu, Jue Ruan, Guojie Zhang, Huanming Yang, Xun Xu, Jun Wang, Xianyong Zhao, Bettina Meyer, Guangyi Fan
Summary: This study reveals the molecular architecture and adaptations of the Antarctic krill genome, as well as the population dynamics associated with climate change events. The findings provide valuable insights into the genetic basis of Antarctic krill's ability to survive in the Southern Ocean and offer resources for future Antarctic research.
Article
Biochemistry & Molecular Biology
Irene Zorzan, Riccardo Massimiliano Betto, Giada Rossignoli, Mattia Arboit, Andrea Drusin, Clelia Corridori, Paolo Martini, Graziano Martello
Summary: In human embryos, naive pluripotent cells of the inner cell mass (ICM) generate different cell lineages, including trophoblast cells. In vitro, chemical resetting can convert conventional pluripotent stem cells into naive pluripotent stem cells, which have the potential to efficiently generate trophoblast stem cells. This method can be used to study cell fate transitions and model placental disorders.
Article
Polymer Science
Susanna Tondato, Arianna Moro, Salman Butt, Martina Todesco, Deborah Sandrin, Giulia Borile, Massimo Marchesan, Assunta Fabozzo, Andrea Bagno, Filippo Romanato, Saima Jalil Imran, Gino Gerosa
Summary: Right ventricle outflow tract obstruction (RVOTO), accounting for about 15% of congenital heart diseases, often requires pulmonary valve replacement. This study investigated the use of a new detergent (Tergitol) to decellularize porcine pulmonary valves for scaffold production. The decellularized scaffolds were evaluated for structural integrity, and their compatibility with mesenchymal stem cells was assessed. Tergitol efficiently removed nuclear material while preserving the matrix's structural proteins, making it a potential alternative to Triton X-100.
Article
Genetics & Heredity
Paolo Martini, Jessica Mingardi, Giulia Carini, Stefania Mattevi, Elona Ndoj, Luca La Via, Chiara Magri, Massimo Gennarelli, Isabella Russo, Maurizio Popoli, Laura Musazzi, Alessandro Barbon
Summary: Stress is a major risk factor for psychiatric disorders, and the response to stress involves the regulation of transcriptional programs. In this study, we analyzed the gene expression changes in the prefrontal cortex (PFC) of rats exposed to acute footshock stress. We found alterations in neuronal pathways, glia development, glia-neuron networking, and synaptic function. Furthermore, specific transcription factors were identified as potential master regulators of the acute stress response.
Article
Immunology
Lorenzo Lupi, Anna Bordin, Gabriele Sales, Davide Colaianni, Adriana Vitiello, Alberto Biscontin, Alberto Reale, Alfredo Garzino-Demo, Angelo Antonini, Giancarlo Ottaviano, Carla Mucignat, Cristina Parolin, Arianna Calistri, Cristiano De Pitta
Summary: COVID-19 is a respiratory syndrome that can cause various symptoms, including deficits in smell and taste. Transcriptome analysis of olfactory mucosa revealed altered gene expression levels in patients with persistent olfactory deficits, with associations with inflammatory response and zinc homeostasis.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Medicine, Research & Experimental
Yichi Zhang, Andres Ramirez-Martinez, Kenian Chen, John R. McAnally, Chunyu Cai, Mateusz Z. Durbacz, Francesco Chemello, Zhaoning Wang, Lin Xu, Rhonda Bassel-Duby, Ning Liu, Eric N. Olson
Summary: Mutations in genes encoding nuclear envelope proteins cause nuclear envelopathies, which are characterized by skeletal muscle and heart abnormalities, such as Emery-Dreifuss muscular dystrophy (EDMD). However, the tissue-specific role of the nuclear envelope in these diseases has not been well studied. This study showed that the muscle-specific nuclear envelope protein NET39 is crucial for normal skeletal muscle function and its deficiency leads to key features of EDMD. It was also found that NET39 protects against mechanical stress and DNA damage in muscle cells.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Biochemical Research Methods
Matteo Calgaro, Chiara Romualdi, Davide Risso, Nicola Vitulo
Summary: This article presents benchdamic, a Bioconductor package for benchmarking methods for the identification of differentially abundant taxa.