Review
Biochemistry & Molecular Biology
Cing-Syuan Lei, Hsing-Jien Kung, Jing-Wen Shih
Summary: Oral cancer is a leading malignant tumor worldwide with poor prognosis mainly due to late diagnosis. Valid biomarkers for early detection and effective therapies are urgently needed. lncRNAs play key roles in oral cancer progression and signaling pathways, and their potential as biomarkers or therapeutic targets for oral cancer is being explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Yuqi Wang, Hao Li, Linai Kuang, Yihong Tan, Xueyong Li, Zhen Zhang, Lei Wang
Summary: This article introduces a novel method ICLRBBN for detecting potential lncRNA-disease associations, utilizing internal confidence and radial basis biological network. Research found that ICLRBBN outperformed other methods in terms of AUC values and showed promising potential in practical applications.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Review
Oncology
Aryan Rezaee, Sara Ahmadpour, Ameneh Jafari, Sarehnaz Aghili, Seyed Saeed Tamehri Zadeh, Ali Rajabi, Arash Raisi, Michael R. Hamblin, Maryam Mahjoubin-Tehran, Marzieh Derakhshan
Summary: Gynecologic cancer is a significant cause of death in women worldwide. Recent research has shown that non-coding RNAs play a critical role in the metastasis and invasion of gynecologic cancer.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Seonhyang Jeong, Sunmi Park, Young Suk Jo, Moon Jung Choi, Gibbeum Lee, Seul Gi Lee, Min Chul Choi, Hyun Park, Won Duk Joo, Sang Geun Jung, Jandee Lee
Summary: This study identified and validated Notch-related lncRNAs in ovarian cancer using in silico analyses and experiment, and explored their potential roles in the regulation of Notch signaling and associated genes. The discovery of these lncRNAs significantly contributes to our understanding of the complex interactions between Notch signaling and oncogenic pathways.
Review
Biochemistry & Molecular Biology
Junaid Zafar, Junlin Huang, Xiaoxia Xu, Fengliang Jin
Summary: Over the last decade, there has been a growing interest in long non-coding RNAs (lncRNAs) among scientists. LncRNAs play important roles in various biological processes, and have greatly expanded our understanding of RNA's regulatory potential. However, our knowledge of lncRNAs in insects is limited compared to mammals. This article reviews experimentally validated lncRNAs in insects, as well as lncRNAs identified through bioinformatic tools, and discusses the challenges and future prospects of studying lncRNAs in insects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Yu-Xiao Chen, Jie Ding, Wei-Er Zhou, Xuan Zhang, Xiao-Tong Sun, Xi-Ying Wang, Chi Zhang, Ni Li, Guo-Feng Shao, Shen-Jiang Hu, Jian Yang
Summary: The study identified eight candidate lncRNAs associated with DCM disease and suggested their potential involvement in DCM through ceRNA crosstalk. These findings contribute to the discovery of therapeutic targets and enhance the understanding of DCM pathogenesis.
FRONTIERS IN GENETICS
(2021)
Review
Pharmacology & Pharmacy
Chunmei Zhang, Ning Liu
Summary: Energy metabolism reprogramming is a characteristic feature of tumors, and non-coding RNAs play an important role in regulating glycolysis. This review summarizes the regulatory mechanisms and explores potential therapeutic targets.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Physiology
Shuijin Huang, Dong Jing, Lu Xu, Guanghua Luo, Yanyue Hu, Ting Wu, Yao Hu, Fei Li, Kang He, Wenjing Qin, Yang Sun, Hui Liu
Summary: This study identified chlorantraniliprole-resistance-related lncRNAs in Chilo suppressalis, and found that the upregulated lincRNA MSTRG.7482.1 was involved in chlorantraniliprole resistance.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Reproductive Biology
Jiao Wang, Xiaocui Zhang, Fei Zheng, Qing Yang, Fangfang Bi
Summary: This study utilized The Cancer Genome Atlas and Reactome databases to retrieve ovarian cancer (OC)-related data and identify mitophagy-related long non-coding RNAs (lncRNAs). A prognostic lncRNA signature was constructed to estimate OC prognosis and therapeutic response. The signature showed that patients in the high-risk group had a poorer prognosis, and a ceRNA network was constructed to explore the potential regulatory mechanisms of lncRNAs.
JOURNAL OF OVARIAN RESEARCH
(2023)
Review
Oncology
Wenxiu Chen, Shuna Liu, Fang Wang
Summary: The aberrant expressions of long non-coding RNAs (lncRNAs) in various cancers have been found to affect cancer cells, but their regulatory role in immunity, especially in T cells, also influences cancer development. However, the complex functions and regulatory mechanisms of lncRNAs in T cells need further exploration.
Review
Oncology
Tanchun Cheng, Shouguo Huang
Summary: Metastasis in cervical cancer is not well understood, with non-coding RNAs playing diverse roles in this process. Dysregulation of miRNAs, lncRNAs, and circRNAs is associated with metastasis. They regulate metastasis by influencing metastasis-related genes, epithelial-mesenchymal transition, signaling pathways, and interactions with the tumor microenvironment.
FRONTIERS IN ONCOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Shusuke Toden, Timothy J. Zumwalt, Ajay Goel
Summary: Recent advances have highlighted the importance of non-coding RNAs, particularly microRNAs, in cancer pathogenesis. These ncRNAs have shown potential for therapeutic development in cancer, with early data from pre-clinical studies demonstrating promising results in human trials. While miRNAs have been extensively studied, there is ongoing research to uncover the molecular mechanisms and therapeutic targets of other lesser studied ncRNAs in cancer treatment.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2021)
Review
Plant Sciences
Qingshuai Chen, Kui Liu, Ru Yu, Bailing Zhou, Pingping Huang, Zanxia Cao, Yaoqi Zhou, Jihua Wang
Summary: Long non-coding RNAs (lncRNAs) play vital roles in various biological functions in plant growth and development, interacting with other molecules through roles such as sequestering RNA or DNA, recruiting or hijacking transcription factors, and binding with chromatin modification complexes. So far, 73 lncRNA-molecule interaction pairs have been validated in 16 plant species, indicating the commonality of these regulatory roles in the plant kingdom.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Wenlin Zhang, Yang Yang, Xuedong Zhu, Suyu Yang, Ximei Liao, Honglei Li, Zhexin Li, Qinhong Liao, Jianmin Tang, Guohua Zhao, Lin Wu
Summary: This study identified 744 metabolites and 16,346 lncRNAs in ginger, and revealed the correlations between these lncRNAs and the genes involved in gingerol biosynthesis. A putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling gingerol biosynthesis was proposed for the first time.
Article
Biochemistry & Molecular Biology
Yong Wu, Qinhao Guo, Xingzhu Ju, Zhixiang Hu, Lingfang Xia, Yu Deng, Ping Zhao, Meng Zhang, Yang Shao, Shenglin Huang, Xianghuo He, Hao Wen, Xiaohua Wu
Summary: This study identified an oncogenic lincRNA, LINC00662, in ovarian cancer, which is associated with malignant features and serves as a prognostic indicator. LINC00662 promotes OC cell proliferation and metastasis through interaction with GRP78 and activation of the p38 MAPK signaling pathway.
Review
Oncology
Shadma Fatima, Yafeng Ma, Azadeh Safrachi, Sana Haider, Kevin J. Spring, Fatemeh Vafaee, Kieran F. Scott, Tara L. Roberts, Therese M. Becker, Paul de Souza
Summary: This review emphasizes the importance of immunotherapy in cancer treatment and points out the current issues of high failure rates and serious side effects. Therefore, there is a need for reliable biomarkers to predict patient response to immunotherapy and monitor treatment effects in real-time. It has been found that non-invasive liquid biopsy methods can overcome the limitations of traditional biomarkers and play a significant role in cancer treatment.
Review
Biochemical Research Methods
Abhishek Vijayan, Shadma Fatima, Arcot Sowmya, Fatemeh Vafaee
Summary: Liquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and potential for biomarker discovery. However, the challenges of low concentration of relevant blood-based biosources and sample heterogeneity have hindered biomarker discovery. In this study, 12 feature extraction methods were benchmarked using transcriptomic profiles, and a transformation method called partial least square discriminant analysis showed consistently superior classification performance.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Oncology
Li Zhang, Chi-Lam Au-Yeung, Chunxian Huang, Tsz-Lun Yeung, Sammy Ferri-Borgogno, Barrett C. Lawson, Suet-Ying Kwan, Zheng Yin, Stephen T. Wong, Vienna Thomas, Karen H. Lu, Kay-Pong Yip, James S. K. Sham, Samuel C. Mok
Summary: This study identified the role of ryanodine receptor 1 (RYR1) in uterine serous cancer (USC) progression and demonstrated the efficacy of the repositioned compound dantrolene in treating USC. Inhibition of RYR1 suppressed USC cell proliferation and migration and enhanced apoptosis. The findings provide insight into the mechanism by which RYR1 modulates USC progression and suggest dantrolene as a potential therapeutic agent for improving patient survival.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Seid Miad Zandavi, Forrest C. Koch, Abhishek Vijayan, Fabio Zanini, Fatima Valdes Mora, David Gallego Ortega, Fatemeh Vafaee
Summary: Emerging single-cell technologies provide high-resolution measurements of distinct cellular modalities, but the complexity and inaccuracies in single-cell sequencing measurements can hinder data analysis. This study presents a novel preprocessing method that reduces data complexity, enhances cell-type separation, and enables the identification of rare cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Oncology
Emily K. Colvin, Amanda L. Hudson, Lyndsey L. Anderson, Ramyashree Prasanna Kumar, Iain S. McGregor, Viive M. Howell, Jonathon C. Arnold
Summary: The study shows that phytocannabinoids have anti-cancer effects on mesothelioma cells in vitro and further research is needed to enhance their effects in vivo.
Article
Oncology
Wendy W. Y. Choi, Catherine Sanchez, Jiao Jiao Li, Mojdeh Dinarvand, Hans Adomat, Mazyar Ghaffari, Leila Khoja, Fatemeh Vafaee, Anthony M. Joshua, Kim N. Chi, Emma S. Tomlinson Guns, Elham Hosseini-Beheshti
Summary: EV secreted from cancer cells, which carry distinct cellular components, could be potential markers for disease initiation, progression, and treatment response. The study found significant differences in the composition of EV derived from biological fluids of castration-resistant prostate cancer patients compared to healthy controls. Specific EV proteins common in both serum and urine samples of prostate cancer patients were identified, suggesting their potential as markers for prostate cancer.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Automation & Control Systems
Seid Miad Zandavi, Taha Hossein Rashidi, Fatemeh Vafaee
Summary: The study introduces a hybrid model combining LSTM neural network and dynamic behavioral models to accurately predict the regional spread of COVID-19, outperforming traditional LSTM models. By considering multiple factors, the model enhances prediction accuracy and replicates system behaviors accurately even under uncertainty.
IEEE TRANSACTIONS ON CYBERNETICS
(2022)
Article
Computer Science, Artificial Intelligence
Seid Miad Zandavi, Derong Liu, Vera Chung, Ali Anaissi, Fatemeh Vafaee
Summary: This study proposes a method to transform high-dimensional molecular measurements into two-dimensional images, improving the representation and classification of biological samples using automated image recognition methods.
ARTIFICIAL INTELLIGENCE REVIEW
(2023)
Article
Biochemistry & Molecular Biology
Amani M. Batarseh, Fatemeh Vafaee, Elham Hosseini-Beheshti, Azadeh Safarchi, Alex Chen, Amy Cohen, Annette Juillard, Nicholas Henry Hunt, Michael Mariani, Todd Mitchell, Georges Emile Raymond Grau
Summary: It is found that the pathogenesis of cerebral malaria can be understood by studying the specific lipid composition in the plasma. There are significant changes in lipid components in the plasma of cerebral malaria patients compared to non-cerebral malaria patients. This study provides important evidence for studying the pathophysiology of cerebral malaria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Sammy Ferri-Borgogno, Ying Zhu, Jianting Sheng, Jared K. Burks, Javier A. Gomez, Kwong Kwok Wong, Stephen T. C. Wong, Samuel C. Mok
Summary: A spatial transcriptomics analysis revealed the association between cancer-associated fibroblast (CAF) heterogeneity and long-term survival in patients with advanced high-grade serous ovarian cancer (HGSC). A specific subtype of CAF and its spatial location relative to tumor cells were correlated with long-term survival. Increased APOE-LRP5 cross-talk at the stroma-tumor interface was observed in short-term survivors (STS) compared to long-term survivors (LTS).
Article
Biochemistry & Molecular Biology
Abir Khazaal, Seid Miad Zandavi, Andrei Smolnikov, Shadma Fatima, Fatemeh Vafaee
Summary: Long non-coding RNAs (lncRNAs) have emerged as key regulators in many biological processes, and their dysregulation is associated with numerous diseases, including cancer. Understanding the functional implications of lncRNAs in tumorigenesis can lead to the development of novel biomarkers and therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Hematology
Shruthi Subramanian, Julie A. I. Thoms, Yizhou Huang, Paola Cornejo-Paramo, Forrest C. Koch, Sebastien Jacquelin, Sylvie Shen, Emma Song, Swapna Joshi, Chris Brownlee, Petter S. Woll, Diego Chacon-Fajardo, Dominik Beck, David J. Curtis, Kenneth Yehson, Vicki Antonenas, Tracey O'Brien, Annette Trickett, Jason A. Powell, Ian D. Lewis, Stuart M. Pitson, Maher K. Gandhi, Steven W. Lane, Fatemeh Vafaee, Emily S. Wong, Berthold Goettgens, Hamid Alinejad-Rokny, Jason W. H. Wong, John E. Pimanda
Summary: This study comprehensively characterizes the gene regulatory landscape in rare subpopulations of human hematopoietic stem and progenitor cells (HSPCs), and identifies specific heptad-transcription factor combinations that have distinct roles in regulating hematopoietic differentiation across different cell types. These findings provide valuable insights into adult hematopoiesis and a framework for analyzing aberrant regulatory networks in leukemic cells.
Article
Biochemistry & Molecular Biology
Julie A. Thoms, Forrest C. Koch, Alireza Raei, Shruthi Subramanian, Jason W. H. Wong, Fatemeh Vafaee, John E. Pimanda
Summary: BloodChIP Xtra is a user-friendly database for exploring key transcription factors and chromatin configuration in healthy and leukemia hematopoiesis. It provides rich datasets and an easy-to-use interface for queries and downstream applications.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ihuan Gunawan, Fatemeh Vafaee, Erik Meijering, John George Lock
Summary: Single-cell resolved systems biology methods generate high-dimensional data characterizing cell heterogeneity. Representation learning methods, such as statistical, manifold learning, and neural network approaches, are used to analyze these data by projecting them into lower-dimensional embeddings. This overview compares different representation learning methods and discusses key steps, dependencies, and optimizations in the analysis of single-cell data, providing guidance for researchers in the selection and application of representation learning strategies for current and future single-cell research applications.
CELL REPORTS METHODS
(2023)
Article
Genetics & Heredity
Farhad Alizadeh, Hamid Jazayeriy, Omid Jazayeri, Fatemeh Vafaee
Summary: Ancestry inference of admixed populations is an important issue in anthropology and gene discovery. This study proposes a heuristic function to determine an appropriate window length for local ancestry inference methods, and introduces a method for ancestry inference based on deep conditional random field. Experimental results show that this method is more accurate than existing methods.
JOURNAL OF GENETICS
(2023)