Review
Cell Biology
Shintaro Komatsu, Hiroki Kitai, Hiroshi I. Suzuki
Summary: MicroRNAs (miRNAs) act as versatile regulators of gene expression at the post-transcriptional level. Recent studies have uncovered the mechanisms involved in miRNA biogenesis, including the processing of both canonical and non-canonical miRNAs. Additionally, the complex interactions between miRNAs and their targets have been explored, revealing target-mediated miRNA degradation and cooperative regulation by multiple miRNAs. These findings highlight the coordinated regulation of miRNA biogenesis and miRNA-target interaction in miRNA biology.
Review
Cell Biology
Charlene Renaud-Pageot, Jean-Pierre Quivy, Marina Lochhead, Genevieve Almouzni
Summary: CENP-A plays a critical role in chromosome segregation and genome integrity maintenance in mammals, but its overexpression is linked to cancer development. Studies have shown that CENP-A overexpression can affect genome integrity, cell fate, and nuclear organization in cancer, highlighting its potential as a target for cancer treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Eduardo Lujan-Soto, Vasti T. Juarez-Gonzalez, Jose L. Reyes, Tzvetanka D. Dinkova
Summary: miRNA zma-miR528 is crucial in maize somatic embryogenesis and plant regeneration, regulating multiple target mRNAs through degradation or translation inhibition mechanisms. It shows differential expression patterns during different stages of the process, suggesting a complex regulatory role in maize development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Ann Dean, Daniel R. Larson, Vittorio Sartorelli
Summary: The virtual meeting sponsored by NCI, NIAMS, and NIDDK at NIH focused on how transcriptional enhancers function within the framework of the folded genome. The discussions emphasized the interaction between levels of organization and their contribution to the spatiotemporal specification of transcription, addressing unresolved questions about enhancer function that are crucial for future research in the field.
GENES & DEVELOPMENT
(2021)
Article
Chemistry, Medicinal
Amu Gubu, Wenbo Su, Xiaoran Zhao, Xueli Zhang, Xinli Fan, Jing Wang, Qian Wang, Xinjing Tang
Summary: Circular AMOs are designed to effectively inhibit microRNA functions with high target specificity and low off-target effects. Compared with linear AMOs, circular AMOs can more effectively reduce the amount of carcinogenic microRNAs and upregulate expression levels of antitumor proteins.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Vincenzo Salemme, Costanza Angelini, Jennifer Chapelle, Giorgia Centonze, Dora Natalini, Alessandro Morellato, Daniela Taverna, Emilia Turco, Ugo Ala, Paola Defilippi
Summary: The scaffold molecule p140Cap, encoded by the SRCIN1 gene, has significant impacts on various cancers, affecting patient survival and disease aggressiveness. Research has shown that p140Cap can influence tumor growth and metastasis by controlling signaling pathways.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Chemistry, Physical
Chuanxian Zhang, Beilei Zhang, Chu Tang, Xiaorui Shi, Bin Guo, Fu Wang
Summary: microRNAs (miRNAs), a class of non-coding small RNAs, play a crucial role in various biological processes and diseases. This study presents a gene-switch system, Gal-miR, which allows visualization and regulation of miRNA activity. By controlling the expression of a downstream luciferase gene using endogenous miRNA machinery, the Gal-miR system converts miRNA-mediated gene silencing into a bioluminescent signal, providing quantitative measurement of miRNA-206 activity during myogenic differentiation. Furthermore, this system effectively inhibits breast cancer cell viability, migration, and invasion by replacing the downstream gene with melittin functional gene, under the control of specific miRNAs. This study offers a powerful genetic design for precise control of transgene expression and visualization of miRNA activity.
Article
Biochemical Research Methods
Ying Li, Qianhuan Guo, Meng Wang, Chengchao Zheng, Kang Yan
Summary: MicroRNAs have been identified as important regulators of post-transcriptional degradation and translational repression in both plants and animals. In this study, the relationship between intronic miRNAs and their host genes in Arabidopsis was investigated using transgenic plants. The results showed that there is an independent relationship between the processing of intronic miRNAs and their host genes in Arabidopsis.
PLANT MOLECULAR BIOLOGY REPORTER
(2022)
Article
Plant Sciences
Chang Liu, Yang Jiang, Ziyi Yun, Kexin Zhang, Mingzhu Zhao, Yi Wang, Meiping Zhang, Zhuo Tian, Kangyu Wang
Summary: Panax ginseng relies on adventitious roots and hairy roots as crucial sources for ginsenoside production. However, miRNA research in ginseng has been limited. In this study, small RNA libraries of ginseng adventitious roots and hairy roots were sequenced, revealing a total of 2432 miRNAs. The miR166 and miR396 families were found to be highly expressed in ginseng. The miRNA expression analysis results were validated using qRT-PCR, and target genes were predicted and analyzed using GO annotation and KEGG pathway analysis. The findings suggest that miRNAs play important roles in metabolic processes in ginseng.
Article
Biochemistry & Molecular Biology
Barbora Hanouskova, Gabriela Vavrova, Martin Ambroz, Iva Bousova, Tommy A. Karlsen, Lenka Skalova, Petra Matouskova
Summary: The study found that miR-137 and miR-29b can inhibit GPx7 expression through certain mechanisms, but no negative correlation between miRNAs and GPx7 was observed during adipogenesis. This suggests that the action of miR-137 and miR-29b in adipogenesis and mature adipocytes must be accompanied by other regulators.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Review
Biochemistry & Molecular Biology
Amrutha Menon, Noraini Abd-Aziz, Kanwal Khalid, Chit Laa Poh, Rakesh Naidu
Summary: This review focuses on the role of miRNA in cancer, therapeutic approaches with miRNAs, and effective delivery into the system. Patents and ongoing clinical trials for miRNA therapy are also summarized.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hongyou Zhao, Bin Yi, Zhipin Liang, Ches'Nique Phillips, Hui-Yi Lin, Adam Riker, Yaguang Xi
Summary: Sulindac inhibits colorectal cancer cell cycle progression through up-regulation of Cyclin G2 and down-regulation of MiR-182, in turn enhancing FOXO3a transcriptional activity. The expression levels of MiR-182/FOXO3a/Cyclin G2 could potentially serve as predictive markers for tumor progression in colorectal cancer.
Review
Cell Biology
Fangfang Yang, Guoyun Xuan, Yixin Chen, Lichao Cao, Min Zhao, Chen Wang, Erfei Chen
Summary: Colorectal cancer is a common type of cancer and a leading cause of mortality worldwide. MicroRNAs play important roles in the development and progression of colorectal cancer, serving as clinical biomarkers and therapeutic targets. However, the complex network of miRNA/target regulation in colorectal cancer remains unclear.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Mengying Zhang, Xiyun Jin, Junyi Li, Yi Tian, Qi Wang, Xinhui Li, Juan Xu, Yongsheng Li, Xia Li
Summary: CeRNASeek is an R package that integrates multiple-omics data to identify and analyze ceRNA-ceRNA interactions. It provides six computational methods and various downstream analyses, suitable for studying the function of ceRNAs in complex diseases.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Anton Tyurin, Daria Shapovalova, Halida Gantseva, Valentin Pavlov, Rita Khusainova
Summary: This study identified miRNA target sites as genetic markers for the development of OA in various ethnic groups, and clarified the association between polymorphic variants in several genes and the incidence of OA.
Article
Biotechnology & Applied Microbiology
Ira W. Deveson, Binsheng Gong, Kevin Lai, Jennifer S. LoCoco, Todd A. Richmond, Jeoffrey Schageman, Zhihong Zhang, Natalia Novoradovskaya, James C. Willey, Wendell Jones, Rebecca Kusko, Guangchun Chen, Bindu Swapna Madala, James Blackburn, Igor Stevanovski, Ambica Bhandari, Devin Close, Jeffrey Conroy, Michael Hubank, Narasimha Marella, Piotr A. Mieczkowski, Fujun Qiu, Robert Sebra, Daniel Stetson, Lihyun Sun, Philippe Szankasi, Haowen Tan, Lin-ya Tang, Hanane Arib, Hunter Best, Blake Burgher, Pierre R. Bushel, Fergal Casey, Simon Cawley, Chia-Jung Chang, Jonathan Choi, Jorge Dinis, Daniel Duncan, Agda Karina Eterovic, Liang Feng, Abhisek Ghosal, Kristina Giorda, Sean Glenn, Scott Happe, Nathan Haseley, Kyle Horvath, Li-Yuan Hung, Mirna Jarosz, Garima Kushwaha, Dan Li, Quan-Zhen Li, Zhiguang Li, Liang-Chun Liu, Zhichao Liu, Charles Ma, Christopher E. Mason, Dalila B. Megherbi, Tom Morrison, Carlos Pabon-Pena, Mehdi Pirooznia, Paula Z. Proszek, Amelia Raymond, Paul Rindler, Rebecca Ringler, Andreas Scherer, Rita Shaknovich, Tieliu Shi, Melissa Smith, Ping Song, Maya Strahl, Venkat J. Thodima, Nikola Tom, Suman Verma, Jiashi Wang, Leihong Wu, Wenzhong Xiao, Chang Xu, Mary Yang, Guangliang Zhang, Sa Zhang, Yilin Zhang, Leming Shi, Weida Tong, Donald J. Johann, Timothy R. Mercer, Joshua Xu
Summary: This study evaluated the performance of five industry-leading ctDNA assays and found that all assays showed high sensitivity, precision, and reproducibility above 0.5% variant allele frequency. However, below this limit, detection became unreliable, especially when input material was limited. The key challenge for ctDNA assays is the reliable sampling of rare ctDNA fragments, with missed mutations being more common than erroneous candidates.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Siqi Bao, Ke Li, Congcong Yan, Zicheng Zhang, Jia Qu, Meng Zhou
Summary: This study summarizes the recent advances and applications of deep learning-based methods in the analysis of scRNA-seq data and specific tools, and investigates the future perspectives and challenges of deep learning techniques in the appropriate analysis and interpretation of scRNA-seq data.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Oncology
Jie Sun, Congcong Yan, Dandan Xu, Zicheng Zhang, Ke Li, Xiaobo Li, Meng Zhou, Dapeng Hao
Summary: This study characterized the immunogenomic landscape of HGSOC and identified prognostic genes associated with favorable outcomes. The results suggest that tumor immunogenicity is the most significant factor related to improved clinical outcomes and response to chemotherapy in HGSOC. Additionally, multiple genomic and transcriptomic determinants of immunogenicity were identified, including copy loss of chromosome 4q and deficiencies in the homologous recombination pathway. Furthermore, an immunological subtype characterized by increased infiltration of activated CD8 T cells and decreased Tregs was associated with favorable prognosis and improved therapeutic efficacy.
BRITISH JOURNAL OF CANCER
(2022)
Article
Biochemistry & Molecular Biology
Weiping Ji, Lu Chen, Wei Yang, Ke Li, Jingting Zhao, Congcong Yan, Cancan You, Minghua Jiang, Meng Zhou, Xian Shen
Summary: This study found that SARS-CoV-2 significantly altered the transcriptional landscape and function of platelets, promoting thrombus formation and affecting energy metabolism. Several key subnetworks and risk genes associated with COVID-19 severity were identified. The study provides insights into the molecular mechanisms of immunothrombosis in COVID-19 and potential therapeutic strategies.
CELL AND BIOSCIENCE
(2022)
Review
Medicine, Research & Experimental
Ke Li, Congcong Yan, Chenghao Li, Lu Chen, Jingting Zhao, Zicheng Zhang, Siqi Bao, Jie Sun, Meng Zhou
Summary: Recent advances in spatially resolved transcriptomics (SRT) have revolutionized biological and medical research, enabling unprecedented insight into tissue and organ functionality and cell communication. This study surveys and summarizes the resources, computational approaches, and tools for analyzing spatial expression variation in SRT studies, highlighting recent advances. It also explores the future prospects and challenges of in silico techniques in SE analysis.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Multidisciplinary Sciences
Binsheng Gong, Ira W. Deveson, Timothy Mercer, Donald J. Johann, Wendell Jones, Weida Tong, Joshua Xu
Summary: This study evaluated the analytical performance of five industry-leading ctDNA assays and demonstrated their high accuracy and reproducibility. By using tailor-made reference samples and assessing multiple key variables, this study provides a valuable dataset for ultra-deep ctDNA sequencing technology.
Article
Multidisciplinary Sciences
Binsheng Gong, Rebecca Kusko, Wendell Jones, Weida Tong, Joshua Xu
Summary: This study developed four reference samples and sequenced them with eight oncopanels at independent test laboratories with ultra-deep sequencing depth. The resulting dataset provided valuable information for assessing the clinical applicability of oncopanels and optimizing bioinformatics pipelines and sequencing parameters.
Article
Medicine, General & Internal
Zicheng Zhang, Lu Chen, Hongyan Chen, Jingting Zhao, Ke Li, Jie Sun, Meng Zhou
Summary: This study conducted a comprehensive analysis of T cell exhaustion (TEX) within the tumor microenvironment (TME). The researchers identified five pan-cancer TEX subsets and revealed tissue-specific patterns and prognostic implications. They also discovered previously unknown TEX-associated cancer genes and developed a machine learning-based gene signature to model the hierarchical stages of TEX.
Article
Biology
Zijian Yang, Yibo Zhang, Ke Xu, Jie Sun, Yue Wu, Meng Zhou
Summary: A deep learning model called DeepDrRVO was developed for early and differential diagnosis of retinal vascular occlusion (RVO). Trained on color fundus photographs, this model achieved high accuracy on different datasets and outperformed conventional classification models. These results highlight the potential benefits of the deep learning model in early RVO detection and differential diagnosis.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Multidisciplinary Sciences
Meng Zhou, Siqi Bao, Tongyang Gong, Qiang Wang, Jie Sun, Jiaqi Li, Minyi Lu, Wanyuan Sun, Jianzhong Su, Hongyan Chen, Zhihua Liu
Summary: This study developed a lncRNA signature predictive of ESCC and validated it across multiple external cohorts. It demonstrated the potential of lncRNAs as non-invasive biomarkers for the early detection of ESCC.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Zicheng Zhang, Hongyan Chen, Dongxue Yan, Lu Chen, Jie Sun, Meng Zhou
Summary: This study investigated the dynamic changes in molecular profiles of T-cell exhaustion (TEX) during immune checkpoint blockade (ICB) treatment, and identified an ICB-associated transcriptional signature consisting of 16 TEX-related genes. A machine-learning model called MLTIP incorporating 16 ITGs achieved reliable predictive power for clinical ICB response. The MLTIP consistently demonstrated superior predictive performance compared to other well-established markers and signatures.
Article
Medicine, General & Internal
Ning Zhao, Zicheng Zhang, Qiang Wang, Lin Li, Zichao Wei, Hongyan Chen, Meng Zhou, Zhihua Liu, Jianzhong Su
Summary: This study characterizes DNA damage repair (DDR) subtypes in esophageal squamous cell carcinoma (ESCC) and investigates their prognostic value. Two distinct DDR subtypes, DDRactive and DDRsilent, are identified, and their independent prognostic values are observed in locoregional ESCC. Additionally, a combination immunotherapy strategy is proposed and validated for high-risk locoregional ESCC tumors.
Article
Biology
Ke Xu, Shenghai Huang, Zijian Yang, Yibo Zhang, Ye Fang, Gongwei Zheng, Bin Lin, Meng Zhou, Jie Sun
Summary: The study presents a deep learning model called DeepDrAMD for the detection and differentiation of AMD subtypes using color fundus photographs (CFPs). The model achieved high performance in AMD detection and classification, surpassing conventional methods and expert-level diagnosis. It offers significant cost savings and efficiency improvements compared to manual reading approaches.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Medical Laboratory Technology
Lu Chen, Rong Ma, Chang Luo, Qin Xie, Xin Ning, Kaidi Sun, Fanling Meng, Meng Zhou, Jie Sun
Summary: This study utilized LC-WGS to analyze genome-wide copy number variations (CNVs) in plasma cfDNA, identifying CNV markers associated with ovarian cancer and developing predictive models for tumor classification. Additionally, certain CNV features associated with survival outcomes and chemotherapy response were discovered.
TRANSLATIONAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ke Li, Lanfang Sun, Yanan Wang, Yixin Cen, Jingting Zhao, Qianling Liao, Wencan Wu, Jie Sun, Meng Zhou
Summary: A recent study utilized single-cell transcriptome data to explore the cellular heterogeneity of macrophages within the uveal melanoma (UM) tumor microenvironment, revealing four distinct macrophage subsets. One subset, M phi-C4, was found to be associated with aggressive tumor behavior and poor survival outcomes. The study also developed a machine-learning-based subtyping system to classify UM subtypes and predict prognosis based on M phi-C4-specific core metagenes. This research deepens our understanding of cellular heterogeneity in UM and highlights the potential therapeutic benefits of targeting macrophages in UM treatment.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2023)
