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Medicine, General & Internal
Kuo-Hao Ho, Tzu-Wen Huang, Chwen-Ming Shih, Yi-Ting Lee, Ann-Jeng Liu, Peng-Hsu Chen, Ku-Chung Chen
Summary: Through the investigation of glycolysis-associated lncRNAs in cancer, we identified a subgroup of patients stratified by different lncRNA profiles, with significant associations to survival rates, gene mutations, molecular subtypes, and immune cell infiltration. This study provides new directions for cancer therapy by revealing the potential roles of glycolysis-associated lncRNAs in cancer progression.
Article
Biochemistry & Molecular Biology
Shital Kumar Mishra, Taole Liu, Han Wang
Summary: The study integrated time-course experimentation and state-of-the-art computational techniques to analyze tens of thousands of zebrafish lncRNAs, revealing rhythmically expressed lncRNAs in the pineal gland and testis. Comparative analyses also identified conserved lncRNA-encoded peptides across different species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Yu-Jian Kang, Jing-Yi Li, Lan Ke, Shuai Jiang, De-Chang Yang, Mei Hou, Ge Gao
Summary: This study introduces the ribosome calculator, which quantitatively models the coding ability of RNAs in the human genome, and successfully predicts transcripts with different coding abilities in various cell types. This suggests that the coding ability of transcripts should be modeled as a continuous spectrum with context-dependent nature.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Nan Wu, Mingzuo Jiang, Haiming Liu, Yi Chu, Dan Wang, Jiayi Cao, Zhiyang Wang, Xin Xie, Yuying Han, Bing Xu
Summary: LINC00941 plays a crucial role in metastatic colorectal cancer by activating the TGF-beta/SMAD2/3 pathway to promote metastasis and invasion.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Multidisciplinary Sciences
Juan Zhang, Ying Ma, Daojun Xie, Yuancheng Bao, Wenming Yang, Han Wang, Huaizhou Jiang, Hui Han, Ting Dong
Summary: This study investigated the lncRNA-mRNA regulation network in a TX WD mouse model, identifying differentially expressed lncRNAs and mRNAs associated with WD liver injury. Functional and pathway analyses revealed enrichment in key processes such as apoptosis and pathways including drug metabolism and signaling pathways. The differential lncRNAs identified may play a role in the pathogenesis and development of WD liver injury.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Wuwen Zhang, Qinshi Wang, Yi Yang, Siyuan Zhou, Ping Zhang, Tongbao Feng
Summary: Exosomes play a crucial role in cell-cell communication within the cancer microenvironment. Exosomal long noncoding RNAs (lncRNAs) are key regulators in cancer development, involved in processes such as cancer cell proliferation, metastasis, drug resistance, and immunomodulation. Changes in exosomal lncRNAs levels often correlate with cancer occurrence and progression, making them valuable biomarkers for cancer diagnosis and prognosis.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Fang Xu, Liya Jiang, Qianwei Zhao, Zhibiao Zhang, Yixian Liu, Shuangshuang Yang, Mengdan Yu, Huiping Chen, Jianying Zhang, Jintao Zhang
Summary: This study analyzed HCC tumor and adjacent normal tissue samples using TMT-labeled tandem mass spectrometry and whole-transcriptome sequencing, identifying 977 differentially expressed proteins and 243 genes, and comprehensively evaluating gene-regulatory circuits in HCC. Bioinformatics analysis revealed involvement of certain miRNAs in regulating hub genes, while crucial coexpression and competing endogenous RNA interaction axes revealed potential functions of lncRNAs and circRNAs in HCC.
Article
Genetics & Heredity
Jingxuan Li, Xueyan Zhao, Yanping Wang, Jiying Wang
Summary: This study sequenced the expression profiles of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) in the longissimus dorsi (LD) muscle of Laiwu pigs to understand their role in the regulation of intramuscular fat (IMF) deposition. The results identified differentially expressed protein-coding genes and noncoding RNAs related to adipogenesis, suggesting their important roles in regulating IMF deposition. A connective network was also constructed, revealing miRNAs that may affect lipid metabolism or adipogenesis. This work provides valuable information for further research on the functions of lncRNAs and circRNAs in IMF deposition.
Article
Biochemistry & Molecular Biology
Dezhong Lv, Zhenghong Chang, Yangyang Cai, Junyi Li, Liping Wang, Qiushuang Jiang, Kang Xu, Na Ding, Xia Li, Juan Xu, Yongsheng Li
Summary: TransLnc is a database that provides experimentally supported and predicted lncRNA peptides in multiple species, with hundreds of thousands of peptides recorded. Various types of evidence supporting the coding potential of lncRNAs are integrated, and users can access lncRNA peptides in 34 tissues and predicted tumor neoantigens.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Min-Qiu Lu, Yu-Qin He, Yin Wu, Hui-Xing Zhou, Yuan Jian, Wen Gao, Li Bao, Wen-Ming Chen
Summary: This study aimed to explore the potential effects of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) patients using two detection methods: high-throughput sequencing and microarray. The study found that certain lncRNAs were aberrantly expressed in MM and identified the top 5 common pathways associated with MM. Furthermore, three microRNAs (miRNAs) were found to constitute competing endogenous RNA (ceRNA) networks in MM. The combination analysis significantly increased our understanding of lncRNAs in MM and identified more overlapping differentially expressed lncRNAs as potential therapeutic targets.
FRONTIERS IN ONCOLOGY
(2023)
Editorial Material
Genetics & Heredity
Claire Wilson, Aditi Kanhere
Summary: This study speculates on the potential role of variants of lncRNAs in cancer development by drawing upon emerging research findings.
TRENDS IN GENETICS
(2021)
Article
Cell Biology
Ye Feng, Ying Xu, Yongjian Gao, Yiying Chen, Xuefeng Wang, Zhi Chen
Summary: SOX2OT is an up-regulated oncogene in CRC, promoting cell proliferation, migration, and invasion. It acts as a competing endogenous RNA to upregulate SOX5 by sponging miR-194-5p, thus affecting tumorgenesis of CRC.
CELL DEATH & DISEASE
(2021)
Article
Multidisciplinary Sciences
Qing Xia, Qibin Yan, Zehua Wang, Qinyuan Huang, Xinying Zheng, Jinze Shen, Lihua Du, Hanbing Li, Shiwei Duan
Summary: This study aimed to construct a prediction model for breast cancer subtypes based on disulfidptosis-related lncRNAs. The random forest algorithm was used to select important lncRNAs, and a prediction model was successfully established. The study also revealed that key lncRNAs were closely related to RNA methylation modification, angiogenesis, and immune infiltrating cells.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Razia Khalid, Hammad Naveed, Zoya Khalid
Summary: Long non-coding RNAs (lncRNAs) have emerged as important players in regulating biological processes and their mutations are associated with complex diseases. In this study, we developed a machine learning model that combines sequence and structure-based features to predict disease-related lncRNAs. Our model outperformed existing methods and achieved the highest F1 score of 76% on the SVM classifier. We also addressed limitations in previous methods by incorporating redundancy checking and oversampling techniques. Combining multiple features, particularly lncRNA sequence mutations, significantly contributed to the prediction of disease-related lncRNAs.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Xiaoying Jiang, Ronghui Lei
Summary: Exosomes are membrane-surrounded extracellular vesicles that mediate intercellular communication by delivering bioactive molecules. Long noncoding RNAs (lncRNAs), a class of non-protein-coding RNAs, play important roles in the development of cardiovascular diseases (CVDs). In this article, we review the current studies on exosomal lncRNAs secreted and absorbed by cardiomyocytes and their functional roles in CVDs, aiming to deepen our understanding of the pathological mechanisms of CVDs and their potential for clinical diagnosis and therapy.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2023)