Expression profiling of cancer-related long non-coding RNAs revealed upregulation and biomarker potential of HAR1B and JPX in colorectal cancer

Khajehdehi, Mina; Khalaj‐Kondori, Mohammad; Feizi, Mohammad Ali Hosseinpour

doi:10.1007/s11033-022-07396-z

Cited by 4 publications

(3 citation statements)

References 47 publications

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“…It can serve as a potential biomarker in bone and soft-tissue sarcomas [ 103 ]. Deregulated HAR1B has a greatly higher expression profile in aggressive colorectal cancers [ 104 ]. The association between kidney neoplasms and HAR1B needs further experimental confirmation.…”

Section: Resultsmentioning

confidence: 99%

LDA-VGHB: identifying potential lncRNA–disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine

Peng,

Huang,

et al. 2023

Briefings in Bioinformatics

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Long noncoding RNAs (lncRNAs) participate in various biological processes and have close linkages with diseases. In vivo and in vitro experiments have validated many associations between lncRNAs and diseases. However, biological experiments are time-consuming and expensive. Here, we introduce LDA-VGHB, an lncRNA–disease association (LDA) identification framework, by incorporating feature extraction based on singular value decomposition and variational graph autoencoder and LDA classification based on heterogeneous Newton boosting machine. LDA-VGHB was compared with four classical LDA prediction methods (i.e. SDLDA, LDNFSGB, IPCARF and LDASR) and four popular boosting models (XGBoost, AdaBoost, CatBoost and LightGBM) under 5-fold cross-validations on lncRNAs, diseases, lncRNA–disease pairs and independent lncRNAs and independent diseases, respectively. It greatly outperformed the other methods with its prominent performance under four different cross-validations on the lncRNADisease and MNDR databases. We further investigated potential lncRNAs for lung cancer, breast cancer, colorectal cancer and kidney neoplasms and inferred the top 20 lncRNAs associated with them among all their unobserved lncRNAs. The results showed that most of the predicted top 20 lncRNAs have been verified by biomedical experiments provided by the Lnc2Cancer 3.0, lncRNADisease v2.0 and RNADisease databases as well as publications. We found that HAR1A, KCNQ1DN, ZFAT-AS1 and HAR1B could associate with lung cancer, breast cancer, colorectal cancer and kidney neoplasms, respectively. The results need further biological experimental validation. We foresee that LDA-VGHB was capable of identifying possible lncRNAs for complex diseases. LDA-VGHB is publicly available at https://github.com/plhhnu/LDA-VGHB.

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Section: Resultsmentioning

confidence: 99%

LDA-VGHB: identifying potential lncRNA–disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine

Peng,

Huang,

et al. 2023

Briefings in Bioinformatics

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“…In human chondrocytes, lncRNA urothelial cancer associated 1 increased matrix metallopeptidase 13 expression by suppressing microRNA (miRNA/miR)-204-5p (14). Reports on Just proximal to X-inactive specific transcript (JPX), a lncRNA, have primarily focused on its regulatory effects in various cancers, including hepatocellular carcinoma, colorectal cancer, lung cancer, oral squamous cell carcinoma, and myeloid malignancies (15)(16)(17)(18)(19). Interestingly, Gál et al (20) found that JPX expression was upregulated in adult patients with allergic rhinitis compared with the adult control group.…”

Section: Introductionmentioning

confidence: 99%

Knockdown of lncRNA JPX suppresses IL‑1β‑stimulated injury in chondrocytes through modulating an miR‑25‑3p/PPID axis

et al. 2022

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The aim of this study was to investigate the potential mechanisms of long noncoding (lnc) RNA Just proximal to X-inactive specific transcript (JPX) in interleukin (IL)-1β-stimulated chondrocytes. Human C28/I2 chondrocytes were treated with IL-1β to simulate osteoarthritic (OA) injury. The expression levels of JPX, microRNA (miRNA/miR)-25-3p, and peptidylprolyl isomerase D (PPID) were measured using reverse transcription-quantitative PCR or western blotting. The IL-1β-stimulated injury was assessed using a Cell Counting Kit-8 assay, flow cytometry, and western blot analysis. The targeted relationship between miR-25-3p, JPX, and PPID was verified using a dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. The results showed that JPX expression was upregulated in OA patients and IL-1β-stimulated chondrocytes. JPX knockdown enhanced cell viability and suppressed apoptosis of IL-1β-stimulated chondrocytes. miR-25-3p inhibition rescued the inhibitory effect of JPX knockdown on IL-1β-stimulated injury. PPID overexpression eliminated the effects of JPX knockdown on IL-1β-stimulated chondrocytes. In conclusion, JPX knockdown increased cell viability and reduced apoptosis in IL-1β-stimulated chondrocytes, and this involved modulation of a miR-25-3p/PPID axis.

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“…in the prognostic power (32, 33). As reported, JPX has a pivotal function in the development of several cancers, such as colorectal (34), gastric (35), cervical (36), and lung cancers (37). The function of the other five lncRNAs has not yet been reported, so future research studies will require molecular investigations to explore those functions and mechanisms in HNSCC.…”

mentioning

confidence: 98%

Cuproptosis-related LncRNAs are potential prognostic and immune response markers for patients with HNSCC via the integration of bioinformatics analysis and experimental validation

Zhou

Cheng

et al. 2022

Front. Oncol.

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IntroductionHead and neck squamous cell carcinoma (HNSCC) is a malignant neoplasm typically induced by alcohol and tobacco consumption, ranked the sixth most prevalent cancer globally. This study aimed to establish a cuproptosis-related lncRNA predictive model to assess the clinical significance in HNSCC patients.MethodsThe Cancer Genome Atlas (TCGA) database was utilized to download cuproptosis-related genes, lncRNAs profiles, and selected clinical information of 482 HNSCC samples. Cuproptosis-related lncRNAs were analyzed by Pearson correlation method, with the least absolute shrinkage and selection operator (LASSO) and univariate/multivariate Cox analyses performed to establish the cuproptosis-related lncRNA predictive model. Subsequently, the time-dependent receiver operating characteristics (ROC) and Kaplan-Meier analysis were applied to assess its prediction ability, and the model was verified by a nomogram, univariate/multivariate Cox analysis, and calibration curves. Furthermore, the principal component analysis (PCA), immune analysis, and gene set enrichment analyses (GSEA) were performed, and the 50% inhibitory concentration (IC50) prediction in the risk groups was calculated. Furthermore, the expression of six cuproptosis-related lncRNAs in HNSCC and paracancerous tissues was detected by quantitative real-time PCR (qRT-PCR).ResultsA total of 467 lncRNAs were screened as cuproptosis-associated lncRNAs in HNSCC tissues to establish an eight cuproptosis-related lncRNA prognostic signature consisting of AC024075.3, AC090587.2, AC116914.2, AL450384.2, CDKN2A-DT, FAM27E3, JPX, and LNC01089. For the high-risk group, the results demonstrated a satisfactory predicting performance with considerably worse overall survival (OS). Multivariate Cox regression confirmed that the risk score was a reliable predictive factor (95% CI: 1.089–1.208, hazard ratio =1.147), with the area of 1-, 3-, and 5-year OS under the ROC curve of 0.690, 0.78524, and 0.665, respectively. The differential analysis revealed that JPX was significantly upregulated in HNSCC tissues, while AC024075.3, AC090587.2, AC116914.2, AL450384.2, CDKN2A-DT were downregulated in HNSCC tissues by qRT-PCR assays. In addition, this gene signature was also associated with some immune-related pathways and immune cell infiltration and affected the anti-cancer immune response. Furthermore, Bexarotene, Bleomycin, Gemcitabine, etc., were identified as potential therapeutic compounds for HNSCC.DiscussionsThis novel cuproptosis-related lncRNAs prognostic signature could predict prognosis and help propose novel individual therapeutic targets for HNSCC.

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Expression profiling of cancer-related long non-coding RNAs revealed upregulation and biomarker potential of HAR1B and JPX in colorectal cancer

Cited by 4 publications

References 47 publications

LDA-VGHB: identifying potential lncRNA–disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine

LDA-VGHB: identifying potential lncRNA–disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine

Knockdown of lncRNA JPX suppresses IL‑1β‑stimulated injury in chondrocytes through modulating an miR‑25‑3p/PPID axis

Cuproptosis-related LncRNAs are potential prognostic and immune response markers for patients with HNSCC via the integration of bioinformatics analysis and experimental validation

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