scholarly journals Decoding the Roles of Long Noncoding RNAs in Hepatocellular Carcinoma

2021 ◽  
Vol 22 (6) ◽  
pp. 3137
Author(s):  
Lok-Sze Wong ◽  
Chun-Ming Wong
Keyword(s):  
Hepatocellular Carcinoma ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Future Research ◽  
Research Directions ◽  
Cancer Hallmarks ◽  
Future Research Directions ◽  
Cancer Phenotypes ◽  
Functional Mechanisms

Hepatocellular carcinoma (HCC) is one of the most prevalent malignancies worldwide. HCC is associated with several etiological factors, including HBV/HCV infections, cirrhosis, and fatty liver diseases. However, the molecular mechanism underlying HCC development remains largely elusive. The advent of high-throughput sequencing has unveiled an unprecedented discovery of a plethora of long noncoding RNAs (lncRNAs). Despite the lack of coding capacity, lncRNAs have key roles in gene regulation through interacting with various biomolecules. It is increasingly evident that the dysregulation of lncRNAs is inextricably linked to HCC cancer phenotypes, suggesting that lncRNAs are potential prognostic markers and therapeutic targets. In light of the emerging research in the study of the regulatory roles of lncRNAs in HCC, we discuss the association of lncRNAs with HCC. We link the biological processes influenced by lncRNAs to cancer hallmarks in HCC and describe the associated functional mechanisms. This review sheds light on future research directions, including the potential therapeutic applications of lncRNAs.

RNA Conformation Capture by Proximity Ligation

2020 ◽  
Vol 21 (1) ◽  
pp. 81-100 ◽  
Author(s):  
Grzegorz Kudla ◽  
Yue Wan ◽  
Aleksandra Helwak
Keyword(s):  
High Throughput Sequencing ◽  
Uv Light ◽  
Spatial Proximity ◽  
Future Research ◽  
Research Directions ◽  
Rna Molecules ◽  
Proximity Ligation ◽  
Dna And Rna ◽  
Typical Experiment ◽  
Future Research Directions

RNA proximity ligation is a set of molecular biology techniques used to analyze the conformations and spatial proximity of RNA molecules within cells. A typical experiment starts with cross-linking of a biological sample using UV light or psoralen, followed by partial fragmentation of RNA, RNA–RNA ligation, library preparation, and high-throughput sequencing. In the past decade, proximity ligation has been used to study structures of individual RNAs, networks of interactions between small RNAs and their targets, and whole RNA–RNA interactomes, in models ranging from bacteria to animal tissues and whole animals. Here, we provide an overview of the field, highlight the main findings, review the recent experimental and computational developments, and provide troubleshooting advice for new users. In the final section, we draw parallels between DNA and RNA proximity ligation and speculate on possible future research directions.

scholarly journals The Central Roles of Noncoding RNA in Estrogen-Dependent Female Reproductive System Tumors

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Jiajie Tu ◽  
Huan Yang ◽  
Lei Jiang ◽  
Yu Chen ◽  
Yu Chen ◽  
...  
Keyword(s):  
Reproductive System ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Future Research ◽  
Female Reproductive System ◽  
Research Directions ◽  
New Ideas ◽  
Future Research Directions

The pathogenesis of ovarian and endometrial cancers is closely associated with estrogen-related pathways. These estrogen-dependent tumors seriously threaten the health and quality of life in women. Noncoding RNAs (ncRNAs) are defined as RNAs that do not encode proteins, including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), both of which have been reported in estrogen-dependent female reproductive system tumors. This review systematically summarizes the role of ncRNAs in estrogen-dependent tumors and common patterns of regulatory mechanisms to explore their future research directions in tumor diagnosis, treatment, and prognosis. This may provide new ideas for the potential application of ncRNAs in estrogen-dependent female reproductive system tumors.

Circulating Tumor DNA and Hepatocellular Carcinoma

2019 ◽  
Vol 39 (04) ◽  
pp. 452-462 ◽  
Author(s):  
Ju Dong Yang ◽  
Minetta C. Liu ◽  
John B. Kisiel
Keyword(s):  
Hepatocellular Carcinoma ◽  
Unmet Need ◽  
Circulating Tumor Dna ◽  
Future Research ◽  
Research Directions ◽  
Next Generation Sequencing Technology ◽  
Patients With Cancer ◽  
Future Research Directions ◽  
Tumor Dna ◽  
Detection Technologies

AbstractThere is a clear and unmet need for biomarkers in hepatocellular carcinoma (HCC). Circulating cell free deoxyribonucleic acid (cfDNA) is a fragmented DNA subtype, found in the blood circulation. Circulating tumor DNA (ctDNA) is the fraction of total cfDNA, which originates from the primary tumor or metastases in patients with cancer. Earlier studies reported that quantitative measurement cfDNA has diagnostic and prognostic role for HCC. More recently, improvement in next-generation sequencing technology and better understanding of genetic or epigenetic alteration of HCC have allowed comprehensive analysis of mutational and methylation landscape of ctDNA. Hotspot mutation panels and methylation panels have both shown promising performance. None of these tests have yet been validated in longitudinal cohorts for preclinical detection of HCC. In this article, the authors discuss the currently available ctDNA detection technologies, their diagnostic and prognostic performance in HCC, and future research directions.

scholarly journals Identification and validation of potential key long noncoding RNAs in sorafenib-resistant hepatocellular carcinoma cells

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8624
Author(s):  
Manya Wu ◽  
Xiaoyun Shen ◽  
Yanping Tang ◽  
Caifu Zhou ◽  
Haixia Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Enrichment Analysis ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Advanced Hepatocellular Carcinoma ◽  
Ontology Term ◽  
Huh7 Cells ◽  
Hcc Cells

As the first-line treatment, sorafenib has been used for advanced hepatocellular carcinoma (HCC), but the chemoresistance commonly restricts to the clinical efficiency. In this study, we intend to investigate the genome-wide expression pattern of long noncoding RNAs (lncRNAs) in sorafenib-resistant HCC. Herein, we identified thousands of differentially expressed lncRNAs in sorafenib-resistant HCC cells by high-throughput sequencing compared to the parental. Besides, based on GO (Gene Ontology) term enrichment analysis, these differentially expressed lncRNAs are mainly related to binding and catalytic activity and biological regulation of metabolic processes in both the sorafenib-resistant Huh7 cells (Huh7-S) and sorafenib-resistant HepG2 cells (HepG2-S) compared to the parental cells. Moreover, when analyzed by KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, the differentially expressed genes were significantly related to the tight junction. Among them, the expression of TCONS_00284048 and TCONS_00006019 was consistently up-regulated in sorafenib-resistant HCC cell lines, whereas when either was knocked down, the sensitivity of Huh7-S and HepG2-S cells to sorafenib was increased. Taken together, our data demonstrate that the lncRNA expression profile is significantly altered in sorafenib-resistant HCC cells as well as differentially expressed lncRNAs may play crucial functions on HCC sorafenib resistance and HCC progression.

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