Expanding and Enriching the LncRNA Gene–Disease Landscape Using the GeneCaRNA Database
The GeneCaRNA human gene database is a member of the GeneCards Suite. It presents ~280,000 human non-coding RNA genes, identified algorithmically from ~690,000 RNAcentral transcripts. This expands by ~tenfold the ncRNA gene count relative to other sources. GeneCaRNA thus contains ~120,000 long non-coding RNAs (LncRNAs, >200 bases long), including ~100,000 novel genes. The latter have sparse functional information, a vast terra incognita for future research. LncRNA genes are uniformly represented on all nuclear chromosomes, with 10 genes on mitochondrial DNA. Data obtained from MalaCards, another GeneCards Suite member, finds 1547 genes associated with 1 to 50 diseases. About 15% of the associations portray experimental evidence, with cancers tending to be multigenic. Preliminary text mining within GeneCaRNA discovers interactions of lncRNA transcripts with target gene products, with 25% being ncRNAs and 75% proteins. GeneCaRNA has a biological pathways section, which at present shows 131 pathways for 38 lncRNA genes, a basis for future expansion. Finally, our GeneHancer database provides regulatory elements for ~110,000 lncRNA genes, offering pointers for co-regulated genes and genetic linkages from enhancers to diseases. We anticipate that the broad vista provided by GeneCaRNA will serve as an essential guide for further lncRNA research in disease decipherment.
The Long Non-Coding RNA ENST00000494165 Influence Papillary Thyroid Cancer Cell Proliferation and Invasion - Cytology and Genetics
Long noncoding RNAs (lncRNAs) have recently been identified as crucial biomarkers of papillary thyroid cancer (PTC). In this study, we aimed to investigate the biological function and potential clinical role of lncRNA ENST00000494165 in PTC. From January 2019 to December 2019, 226 PTC patients who underwent preoperative thyroid US-fine needle aspiration biopsy(US-FNAB) and confirmed by postoperative pathology were enrolled at our hospital. Thyroid tissues were collected from FNAB samples and stored in the refrigerator at –80°C. qRT-PCR (quantitative reverse transcriptase-polymerase chain reaction) analysis was performed to detect the relative expression level of ENST00000494165. CCK-8 (Cell Counting Kit-8) and colony formation assay were performed to detect the cell proliferation ability. Cell migration and invasion abilities were evaluated by transwell and scratch assay. We also evaluated the relation between the expression level of ENST00000494165 and the clinicopathological features of PTC. Functional assays demonstrated that the cell proliferation, migration and invasion abilities were all promoted in PTC cell lines when ENST00000494165 expression was overexpressed. The expression of ENST00000494165 in the lymph node metastasis group was significantly higher than that in non-lymph node metastasis group. High level expression of ENST00000494165 was significantly associated with lymph node metastasis of PTC (P < 0.001). The overexpression of ENST00000494165 promoted the progression, migration and invasion abilities of PTC and was significantly correlated with lymph node metastasis in PTC. ENST00000494165 could act as a possible promoter gene and a potential biomarker for PTC.
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Cytology and Genetics