Article
Neurosciences
Wen Yuan, Sai Ma, Juliana R. Brown, Kwanho Kim, Vanessa Murek, Lucia Trastulla, Alexander Meissner, Simona Lodato, Ashwin S. Shetty, Joshua Z. Levin, Jason D. Buenrostro, Michael J. Ziller, Paola Arlotta
Summary: This study provides an integrated epigenomic and transcriptomic analysis of mouse and marmoset neocortical neuronal classes, revealing differences in regulatory strategies during early and late stages of neuronal development. While early postmitotic neurons utilize more widely shared and evolutionarily conserved molecular regulatory programs, later stages of neuronal maturation are characterized by more brain- and neuron-specific programs with greater evolutionary divergence.
NATURE NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Valentina Botero, Bethany A. Stanhope, Elizabeth B. Brown, Eliza C. Grenci, Tamara Boto, Scarlet J. Park, Lanikea B. King, Keith R. Murphy, Kenneth J. Colodner, James A. Walker, Alex C. Keene, William W. Ja, Seth M. Tomchik
Summary: Neurofibromatosis type 1 is a genetic disorder that affects metabolic homeostasis through a discrete neuronal circuit, leading to increased metabolic rate, feeding, and alterations in lipid stores and turnover kinetics.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ignacio L. Ibarra, Vikram S. Ratnu, Lucia Gordillo, In-Young Hwang, Luca Mariani, Kathryn Weinand, Henrik M. Hammaren, Jennifer Heck, Martha L. Bulyk, Mikhail M. Savitski, Judith B. Zaugg, Kyung-Min Noh
Summary: Neuronal stimulation induced by BDNF involves the activation of enhancers and the cooperation of transcription factors to regulate gene expression and chromatin accessibility. This discovery is important for understanding processes such as neuronal survival, differentiation, synaptic plasticity, and neurodevelopmental disorders.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Plant Sciences
Robert VanBuren, Ching Man Wai, Valentino Giarola, Milan Zupunski, Jeremy Pardo, Michael Kalinowski, Guido Grossmann, Dorothea Bartels
Summary: Resurrection plants have the ability to survive and recover from prolonged periods without water in regions with seasonal drying. This study analyzed the octoploid genome of the model resurrection plant Craterostigma and identified genetic elements associated with desiccation tolerance. The Craterostigma genome contains diverse homeologous genes with different expression profiles, and it also contains a large number of duplicated early light-induced proteins, which are upregulated under water deficit. The study revealed a core network of desiccation-responsive genes across all tissues, with unique expression dynamics in each tissue during recovery.
Article
Biotechnology & Applied Microbiology
Yuqing Hang, Josh Burns, Benjamin T. Shealy, Rini Pauly, Stephen P. Ficklin, Frank A. Feltus
Summary: This study constructed condition-specific gene co-expression networks for normal lung, LUAD, and LUSC, and integrated tissue-specific gene regulatory networks to elucidate biomarker systems for normal and cancerous lung tissue. The findings identified co-expressed genes under common regulatory control that are relevant in lung cancer.
Review
Immunology
Marie-Pierre Piccinni, Raj Raghupathy, Shigeru Saito, Julia Szekeres-Bartho
Summary: During pregnancy, the semi-allogeneic nature of the conceptus makes it vulnerable to attacks from the maternal immune system. Protective mechanisms, such as the effects of progesterone and PIBF on immune functions, work to support a healthy pregnancy outcome. The modulation of cytokine production by progesterone and dydrogesterone, as well as the induction of Treg cells, play crucial roles in maintaining a normal materno-foetal interaction and preventing pregnancy pathologies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Haoyang Li, Juexiao Zhou, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao
Summary: Spatial transcriptomics technologies are utilized to analyze transcriptomes while preserving spatial information, providing high-resolution characterization of transcriptional patterns and tissue architecture reconstruction. Cellular heterogeneity plays a crucial role in deciphering spatial patterns of cell types, and various related methods have been proposed. In this study, we benchmarked 18 existing methods for cellular deconvolution using 50 real-world and simulated datasets, evaluating their accuracy, robustness, and usability. CARD, Cell2location, and Tangram showed the best performance for the cellular deconvolution task. Additionally, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, facilitating users in choosing the optimal method for their specific needs. This comprehensive evaluation of 18 state-of-the-art methods for cellular deconvolution in spatial transcriptomics and the accompanying decision-tree-style guidelines and recommendations are valuable resources for researchers in this field.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Dan Liu, Lulu Yao, Xiaolei Ding, Huan Zhou
Summary: By analyzing large amounts of data, this study identified 22 key genes that play important roles in the immune regulatory mechanism of lung adenocarcinoma (LUAD) and can predict patient survival time and distant metastasis. Additionally, the study identified cell types that are crucial in the immune microenvironment of LUAD. These findings provide potential prognostic markers and therapeutic targets for LUAD.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biotechnology & Applied Microbiology
Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Lijun Wu, Jianwei Zhu, Bin Shao, Pan Deng
Summary: This study introduces a neural network model called CREaTor, which can simulate cis-regulatory patterns up to 2 Mb from target genes and predict specific cis-regulatory patterns in new cell types without prior knowledge of cCRE-gene interactions or additional training, using only RNA-seq and ChIP-seq data.
Article
Multidisciplinary Sciences
Benxia Hu, Hyejung Won, Won Mah, Royce Park, Bibi Kassim, Keeley Spiess, Alexey Kozlenkov, Cheynna A. Crowley, Sirisha Pochareddy, Yun Li, Stella Dracheva, Nenad Sestan, Schahram Akbarian, Daniel H. Geschwind
Summary: This study integrated gene regulatory landscapes of different cell types to explore cell-specific etiologies in brain disorders, revealing involvement of neurons and oligodendrocytes in Alzheimer's disease, and identifying distinct mechanisms for schizophrenia and bipolar disorder.
NATURE COMMUNICATIONS
(2021)
Review
Cell Biology
Y. Grace Chen, Sun Hur
Summary: DSRNA, whether of viral origin or endogenous, can lead to immune disorders or be utilized for immunotherapy. Organisms have mechanisms to recognize and respond to dsRNA to minimize potential infections, with infected and dysregulated cells both triggering immune responses.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Article
Cell Biology
Meena Kusi, Maryam Zand, Li-Ling Lin, Meizhen Chen, Anthony Lopez, Chun-Lin Lin, Chiou-Miin Wang, Nicholas D. Lucio, Nameer B. Kirma, Jianhua Ruan, Tim H. -M. Huang, Kohzoh Mitsuya
Summary: 2-hydroxyglutarate (2HG) suppresses DNA repair, affects chromatin plasticity, and induces cell differentiation and growth in breast cancer cells. Breast tumors with high 2HG exhibit enhanced heterogeneity and adverse prognosis. Ascorbate-2-phosphate can eliminate this heterogeneity and reduce the growth of high 2HG-producing cancer cells.
Review
Pharmacology & Pharmacy
Bin Liu, Feng Pang, Hongsheng Bi, Dadong Guo
Summary: This review provides a comprehensive overview of the involvement of molecular pathways in the therapeutic effects of Gentiopicroside (GPS) on human diseases and the pharmacokinetics of GPS. GPS and its metabolites have been used in traditional Chinese medicine for centuries due to their therapeutic properties and fewer side effects. The pharmacological characteristics and biological functions of GPS include hepatoprotective, anti-inflammatory, antifibrotic, antioxidant, analgesic, antitumor, and immunomodulatory properties. Further research and optimization of the bioavailability and pharmacokinetics of GPS, as well as exploration of additional biomarkers and potential biotransformation pathways, could enhance its clinical applications.
NAUNYN-SCHMIEDEBERGS ARCHIVES OF PHARMACOLOGY
(2023)
Article
Food Science & Technology
Massimo Ferrara, Giancarlo Perrone, Antonia Gallo
Summary: Filamentous fungi produce diverse mycotoxins, which contaminate agricultural commodities and severely impact human and animal health. Understanding the biology, ecology, and genetics of mycotoxin biosynthesis is crucial for preventing its spread in food and feed products and reducing health risks. Recent research has focused on the complex organization of fungal secondary metabolisms and their interaction with environmental factors, providing new insights into the genes, molecular mechanisms, and regulation of mycotoxin biosynthesis.
CURRENT OPINION IN FOOD SCIENCE
(2022)
Review
Cell Biology
Scott Berry, Lucas Pelkmans
Summary: The relationship between mRNA transcript abundance and cell size, as well as the regulation of RNA polymerase II activity and abundance, are discussed in this article. Feedback mechanisms that adjust mRNA synthesis rates, nuclear export, and degradation are also identified, allowing cells to compensate for changes in one aspect by adjusting others. Researchers are integrating findings from different fields to understand the mechanisms underlying transcript homeostasis and its connection to other aspects of the cellular phenotype.
TRENDS IN CELL BIOLOGY
(2022)
