Article
Biochemistry & Molecular Biology
Gyanendra Kumar, Maxime Cuypers, Richard R. Webby, Thomas R. Webb, Stephen W. White
Summary: The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. Baloxavir, an anti-influenza drug, is effective but linked to resistance mutations. By studying complexes of PA(N) with RNA and DNA oligonucleotides, insights are gained on specificity and structural basis of baloxavir resistance mutations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Brendan Todd, Egor P. Tchesnokov, Matthias Gotte
Summary: Baloxavir marboxil is an FDA-approved antiviral prodrug for influenza treatment, with its active form baloxavir acid showing high potency in inhibiting the nuclease activity of the influenza virus. Research reveals that BXA acts as a tight binding inhibitor and the I38T mutation reduces this property.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Min Xu, Judith Risse, Richard Kormelink
Summary: Cap-snatching is a mechanism used by NSVs to initiate genome transcription, with the cap donor source still remaining elusive. Studies suggest that processing bodies may be a potential source for capped RNAs, but conclusive evidence is lacking. Experimental results indicate that downregulation of photosynthesis is partially due to cap-snatching.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Plant Sciences
Wenzhong Lin, Qingchen Zha, Wenwen Zhang, Guanwei Wu, Fei Yan, Zujian Wu, Zhenguo Du
Summary: This study demonstrates the inhibitory effects of antiviral compounds targeting cap-snatching of influenza virus on the transcription of rice stripe virus. The results suggest that these compounds could serve as starting points in developing antivirals against RSV or related plant viruses.
PHYTOPATHOLOGY RESEARCH
(2022)
Article
Virology
Min Xu, Magdalena Mazur, Nigel Gulickx, Hao Hong, Hein Overmars, Xiaorong Tao, Richard Kormelink
Summary: The study found that the nucleocapsid proteins of some plant- and animal-infecting viruses in the order Bunyavirales localize to processing bodies and stress granules in cells, suggesting a more complex mechanism during transcription and cap snatching.
Editorial Material
Oncology
Barbara Pardini, Mihnea P. Dragomir
Summary: The study by Zagorac et al. unveils a novel molecular mechanism in breast cancer involving SOX2, EZH2, and the long noncoding RNA SCIRT. Upregulation of SCIRT may lead to the dedifferentiation of TICs into a less tumorigenic phenotype and offer new therapeutic opportunities.
Article
Virology
Qi Wang, Daining Zhang, Wenjing Feng, Yidi Guo, Xiaoning Sun, Maolin Zhang, Zhenhong Guan, Ming Duan
Summary: This study found that the host lncRNA TSPOAP1-AS1 is significantly induced by influenza A virus (IAV) infection and is involved in viral replication through the regulation of the nuclear factor-kappa B signaling pathway. Overexpression of TSPOAP1-AS1 enhances viral replication, while inhibition of TSPOAP1-AS1 restricts viral replication. TSPOAP1-AS1 also negatively regulates the expression of interferon-stimulated genes.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Lin Deng, Xiaofeng Han, Ziping Wang, Xiaowei Nie, Jinsong Bian
Summary: This review summarizes the research on the classification, biogenesis, biological functions, and molecular mechanisms of noncoding RNA transcripts involved in pulmonary vascular remodeling in pulmonary hypertension (PH). It highlights the utility and challenges of using these noncoding RNAs as biomarkers and therapeutics in PH.
Article
Pharmacology & Pharmacy
Silong Chen, Chengshou Zhang, Lifang Shen, Jianghua Hu, Xiangjun Chen, Yibo Yu
Summary: This review summarizes the research on the role of non-coding RNA (ncRNA) in cataracts. Recent studies have found that ncRNA plays a significant role in cataract formation by regulating cellular activities. Due to its importance in cataracts, further research on novel regulatory mechanisms is urgently needed, and the development of alternative therapies for cataract treatment seems promising.
PHARMACOLOGICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yanwei Zhang, Xiaojuan Chi, Jingyun Hu, Shulin Wang, Senhong Zhao, Yanan Mao, Benqun Peng, Jilong Chen, Song Wang
Summary: Studies have shown that the long noncoding RNA LINC02574 is induced by influenza A virus (IAV) infection and plays a crucial role in inhibiting IAV replication. The expression of LINC02574 is stimulated by viral genomic RNA, poly (I:C), or interferons (IFNs) through the RIG-I-dependent interferon signaling pathway. Knockdown of LINC02574 impairs the expression of type I and type III IFNs, multiple ISGs, and the activation of STAT1 triggered by IAV infection, indicating that LINC02574 positively regulates the innate immune response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Xia-Ming Jiang, Qi-Lin Xin, Kai Liu, Xue-Fang Peng, Shuo Han, Ling-Yu Zhang, Wei Liu, Geng-Fu Xiao, Hao Li, Lei-Ke Zhang
Summary: This study found that severe fever with thrombocytopenia syndrome virus (SFTSV) affects the WNT-CTNNB1 signaling pathway through its cap-snatching activity, and activation of this pathway enhances viral replication while inhibition reduces replication. The downregulation of the WNT-CTNNB1 signaling pathway was also observed for other sNSVs viruses. These findings provide potential therapeutic targets for sNSVs viruses.
Article
Biochemistry & Molecular Biology
Yufan Luo, Liu Liu, Zihao He, Shanshan Zhang, Peipei Huo, Zhihao Wang, Qin Jiaxin, Lianhe Zhao, Yang Wu, Dongdong Zhang, Dechao Bu, Runsheng Chen, Yi Zhao
Summary: Recent advances in RNA engineering have led to the development of RNA-based therapeutics for various applications. However, existing target screening tools often overlook noncoding RNAs and their regulatory relationships relevant to diseases. To address this, researchers have built the TREAT platform, which incorporates a large amount of regulatory relationships between coding and noncoding genes under different physiological conditions. TREAT utilizes graph representation learning with Random Walk Diffusions for disease-relevant target screening and offers design and optimization options for large RNAs or interfering RNAs.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Medicine, Research & Experimental
Xiang He, Xinzhong Li, Yuan Han, Guojun Chen, Tong Xu, Donghua Cai, Yili Sun, Shifei Wang, Yanxian Lai, Zhonghua Teng, Senlin Huang, Wangjun Liao, Yulin Liao, Jianping Bin, Jiancheng Xiu
Summary: This study demonstrates that circChordc1 plays a role in modulating VSMC phenotype and growth, suppressing abdominal aortic aneurysm formation and reducing rupture risk. By inducing vimentin degradation and increasing the activity of the GSK3 beta/beta-catenin pathway, circChordc1 optimizes VSMC phenotype and reverses pathological aneurysm progression.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Review
Virology
Sasidharanpillai Sabeena
Summary: This review discusses the role of noncoding RNAs as diagnostic and prognostic biomarkers in cervical cancer. The existing studies on microRNA signatures in body fluids and cervical cancer tissues lack consistency and lack validated assays. The precise evaluation of immune-associated long noncoding RNA signatures in clinical samples is necessary. Research on the safe delivery methods, toxicities, and side effects of lncRNAs to tumor tissues is needed. Prospective studies on the diagnostic and prognostic roles of circulating lncRNAs and Piwil RNAs in cervical cancer cases are crucial. Comprehensive research is required for the clinical application of lncRNA-based biomarkers, as the impact of noncoding transcripts on molecular pathways is complex. Standardization and validation of deregulated ncRNAs in noninvasive samples of cervical cancer cases are essential.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Virology
Wenhua Kuang, Huanyu Zhang, Yan Cai, Guilin Zhang, Fei Deng, Hailong Li, Zhihong Hu, Yu Guo, Manli Wang, Yiwu Zhou, Peng Gong
Summary: This study reported the crystal structure and catalytic mechanism of the EN enzyme from Ebinur Lake virus (EBIV). Through structural comparison and mutant analysis, the structural characteristics of the active site and the two-metal-ion catalytic mechanism of EBIV EN were revealed.
JOURNAL OF VIROLOGY
(2022)
Review
Biochemical Research Methods
Shibo Wang, Yang Xu, Han Qu, Yanru Cui, Ruidong Li, John M. Chater, Lei Yu, Rui Zhou, Renyuan Ma, Yuhan Huang, Yiru Qiao, Xuehai Hu, Weibo Xie, Zhenyu Jia
Summary: In this study, a highly efficient bivariate genomic selection method was developed and demonstrated significant advantages over univariate methods in predicting traditional traits in rice. The incorporation of the HAT methodology in the 2D BLUP GS model increased computational efficiency by avoiding conventional cross-validation. Selected metabolites can further enhance predictability of traditional traits in the new 2D BLUP-HAT GS method.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Min Jiao, Jingtian Li, Quan Zhang, Xiufeng Xu, Ruidong Li, Peikang Dong, Chun Meng, Yi Li, Lijuan Wang, Wanpeng Qi, Kai Kang, Hongjie Wang, Tao Wang
FRONTIERS IN GENETICS
(2020)
Article
Biochemical Research Methods
Ruidong Li, Shibo Wang, Yanru Cui, Han Qu, John M. Chater, Le Zhang, Julong Wei, Meiyue Wang, Yang Xu, Lei Yu, Jianming Lu, Yuanfa Feng, Rui Zhou, Yuhan Huang, Renyuan Ma, Jianguo Zhu, Weide Zhong, Zhenyu Jia
Summary: This study utilized genomic selection and omics data, particularly the BLUP model and BLUP-HAT method, to predict the prognosis of prostate cancer. The results indicated that these methods performed well in increasing the reliability of outcome prediction.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Xiaoya Gao, Zifeng Huang, Cailing Feng, Chaohao Guan, Ruidong Li, Haiting Xie, Jian Chen, Mingchun Li, Rongfang Que, Bin Deng, Peihua Cao, Mengyan Li, Jianjun Lu, Yihong Huang, Minzi Li, Weihong Yang, Xiaohua Yang, Chunyan Wen, Xiaomei Liang, Qin Yang, Yin-Xia Chao, Ling-Ling Chan, Midori A. Yenari, Kunlin Jin, K. Ray Chaudhuri, Jing Zhang, Eng-King Tan, Qing Wang
Summary: This study aimed to identify key susceptibility gene targets in postmortem brains and blood of Parkinson's disease (PD) patients and healthy controls (HC). Multitiered analysis integrated gene expression data from 244 human postmortem tissues, resulting in the identification of hub node genes related to PD in a consensus module. Validation in 238 subjects revealed promising markers, especially SYNJ1, for discriminating PD from HCs and Parkinson's Plus Syndrome (PPS), highlighting the potential of SYNJ1 in PD diagnosis and treatment.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
A. C. Kalil, T. F. Patterson, A. K. Mehta, K. M. Tomashek, C. R. Wolfe, V. Ghazaryan, V. C. Marconi, G. M. Ruiz-Palacios, L. Hsieh, S. Kline, V. Tapson, N. M. Iovine, M. K. Jain, D. A. Sweeney, H. M. El Sahly, A. R. Branche, J. Regalado Pineda, D. C. Lye, U. Sandkovsky, A. F. Luetkemeyer, S. H. Cohen, R. W. Finberg, P. E. H. Jackson, B. Taiwo, C. I. Paules, H. Arguinchona, N. Erdmann, N. Ahuja, M. Frank, M. Oh, E. -S. Kim, S. Y. Tan, R. A. Mularski, H. Nielsen, P. O. Ponce, B. S. Taylor, L. A. Larson, N. G. Rouphael, Y. Saklawi, V. D. Cantos, E. R. Ko, J. J. Engemann, A. N. Amin, M. Watanabe, J. Billings, M. -C. Elie, R. T. Davey, T. H. Burgess, J. Ferreira, M. Green, M. Makowski, A. Cardoso, S. de Bono, T. Bonnett, M. Proschan, G. A. Deye, W. Dempsey, S. U. Nayak, L. E. Dodd, J. H. Beigel
Summary: Combination treatment with baricitinib plus remdesivir was superior to remdesivir alone in reducing recovery time and accelerating improvement in clinical status among patients with Covid-19, notably among those receiving high-flow oxygen or noninvasive ventilation. The combination was associated with fewer serious adverse events.
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Article
Multidisciplinary Sciences
Jacob E. Lemieux, Katherine J. Siddle, Bennett M. Shaw, Christine Loreth, Stephen F. Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H. Tomkins-Tinch, Lydia A. Krasilnikova, Katherine C. DeRuff, Melissa Rudy, Matthew R. Bauer, Kim A. Lagerborg, Erica Normandin, Sinead B. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber Carter, Cameron Myhrvold, Molly E. Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B. Harris, John A. Branda, David Hooper, Jessie M. Gaeta, Travis P. Baggett, James O'Connell, Andreas Gnirke, Tami D. Lieberman, Anthony Philippakis, Meagan Burns, Catherine M. Brown, Jeremy Luban, Edward T. Ryan, Sarah E. Turbett, Regina C. LaRocque, William P. Hanage, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia M. Pierce, Eric Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn L. MacInnis
Summary: Analysis of 772 complete genomes of SARS-CoV-2 from early in the Boston-area epidemic shows multiple introductions of the virus, with two distinct superspreading events. One at a nursing facility resulted in rapid transmission and significant mortality, while the other at an international business conference led to sustained community transmission and widespread spread. The genetic variation generated by these events differed substantially, indicating varying transmission dynamics in superspreading events.
Article
Multidisciplinary Sciences
Wayne D. Harshbarger, Derrick Deming, Gordon J. Lockbaum, Nattapol Attatippaholkun, Maliwan Kamkaew, Shurong Hou, Mohan Somasundaran, Jennifer P. Wang, Robert W. Finberg, Quan Karen Zhu, Celia A. Schiffer, Wayne A. Marasco
Summary: This study presents structural details of the human antibody 3I14 recognizing HA from various influenza A viruses, highlighting the binding mechanism and potential implications for universal vaccine design.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Chien-Yu Huang, Diana Sanchez Rangel, Xiaobo Qin, Christine Bui, Ruidong Li, Zhenyu Jia, Xinping Cui, Hailing Jin
Summary: Both plant and animal innate immune responses are mediated by membrane-associated receptors and NLRs. The regulation of NLRs is crucial to prevent autoimmune responses, and the chromatin-remodeling protein SWP73A plays a role in suppressing NLR expression and splicing. Bacteria-induced small RNAs can silence SWP73A to activate NLRs during infection.
CELL HOST & MICROBE
(2021)
Article
Cardiac & Cardiovascular Systems
Milka Koupenova, Heather A. Corkrey, Olga Vitseva, Kahraman Tanriverdi, Mohan Somasundaran, Ping Liu, Shaukat Soofi, Rohan Bhandari, Matthew Godwin, Krishna Mohan Parsi, Alyssa Cousineau, Rene Maehr, Jennifer P. Wang, Scott J. Cameron, Jeffrey Rade, Robert W. Finberg, Jane E. Freedman
Summary: The study revealed that platelets in COVID-19 patients contain viral RNA and proteins, and that SARS-CoV-2 can directly influence platelet internalization and cell death, which may contribute to complications like thrombosis.
CIRCULATION RESEARCH
(2021)
Article
Multidisciplinary Sciences
A. L. Gard, R. J. Luu, C. R. Miller, R. Maloney, B. P. Cain, E. E. Marr, D. M. Burns, R. Gaibler, T. J. Mulhern, C. A. Wong, J. Alladina, J. R. Coppeta, P. Liu, J. P. Wang, H. Azizgolshani, R. Fennell Fezzie, J. L. Balestrini, B. C. Isenberg, B. D. Medoff, R. W. Finberg, J. T. Borenstein
Summary: This study integrates human primary airway epithelial cells into a custom-engineered 96-device platform, and applies it to evaluate viral infection kinetics and antiviral agent dosing for influenza A virus and coronavirus infections across various human primary cell populations. This new capability can help address the rapid assessment of therapeutic efficacy against respiratory viruses, including coronaviruses.
SCIENTIFIC REPORTS
(2021)
Article
Virology
Li Jiang, Neha Samant, Ping Liu, Mohan Somasundaran, Jeffrey D. Jensen, Wayne A. Marasco, Timothy F. Kowalik, Celia A. Schiffer, Robert W. Finberg, Jennifer P. Wang, Daniel N. A. Bolon
Summary: Understanding the evolutionary mechanisms that impact drug resistance in influenza A virus (IAV) is crucial for developing surveillance and treatment strategies due to its potential to cause pandemics. A new helper mutation, Y276F, has been identified to rescue the functional defects of the main oseltamivir resistance mutation, H275Y, and contribute to the evolution of drug resistance in IAV.
JOURNAL OF VIROLOGY
(2022)
Article
Medicine, Research & Experimental
Kevin M. Gao, Alan G. Derr, Zhiru Guo, Kerstin Nundel, Ann Marshak-Rothstein, Robert W. Finberg, Jennifer P. Wang
Summary: The study found that macrophages and neutrophils are increased in nasal wash cells of patients infected with COVID-19 and influenza, with an enrichment of specific cell types such as hillock-like epithelial cells, M2-like macrophages, and age-dependent B cells in COVID-19 samples. Compared to influenza, a global decrease in IFN-associated transcripts in neutrophils, macrophages, and epithelial cells was observed in COVID-19 samples.
Article
Critical Care Medicine
Cameron R. Wolfe, Kay M. Tomashek, Thomas F. Patterson, Carlos A. Gomez, Vincent C. Marconi, Mamta K. Jain, Otto O. Yang, Catharine Paules, Guillermo M. Ruiz Palacios, Robert Grossberg, Michelle S. Harkins, Richard A. Mularski, Nathaniel Erdmann, Uriel Sandkovsky, Eyad Almasri, Justino Regalado Pineda, Alexandra W. Dretler, Diego Lopez de Castilla, Angela R. Branche, Pauline K. Park, Aneesh K. Mehta, William R. Short, Susan L. F. McLellan, Susan Kline, Nicole M. Iovine, Hana M. El Sahly, Sarah B. Doernberg, Myoung-don Oh, Nikhil Huprikar, Elizabeth Hohmann, Colleen F. Kelley, Mark Holodniy, Eu Suk Kim, Daniel A. Sweeney, Robert W. Finberg, Kevin A. Grimes, Ryan C. Maves, Emily R. Ko, John J. Engemann, Barbara S. Taylor, Philip O. Ponce, LuAnn Larson, Dante Paolo Melendez, Allan M. Seibert, Nadine G. Rouphael, Joslyn Strebe, Jesse L. Clark, Kathleen G. Julian, Alfredo Ponce de Leon, Anabela Cardoso, Stephanie de Bono, Robert L. Atmar, Anuradha Ganesan, Jennifer L. Ferreira, Michelle Green, Mat Makowski, Tyler Bonnett, Tatiana Beresnev, Varduhi Ghazaryan, Walla Dempsey, Seema U. Nayak, Lori E. Dodd, John H. Beigel, Andre C. Kalil
Summary: In hospitalized patients with COVID-19 requiring supplemental oxygen by low-flow, high-flow, or non-invasive ventilation, baricitinib plus remdesivir and dexamethasone plus remdesivir resulted in similar mechanical ventilation-free survival by day 29, but dexamethasone was associated with significantly more adverse events, treatment-related adverse events, and severe or life-threatening adverse events.
LANCET RESPIRATORY MEDICINE
(2022)
Article
Virology
Ching-Wen Chang, Krishna Mohan Parsi, Mohan Somasundaran, Emma Vanderleeden, Ping Liu, John Cruz, Alyssa Cousineau, Robert W. Finberg, Evelyn A. Kurt-Jones
Summary: Researchers have successfully generated a human cell line for studying SARS-CoV-2 by transducing human ACE2 and TMPRSS2 into A549 cells. These cells are susceptible to infection by SARS-CoV-2, including the delta and omicron variants. Additionally, several antiviral drugs showed strong inhibitory effects against SARS-CoV-2 variants in this cell model.