Current insights into the molecular systems pharmacology of lncRNA-miRNA regulatory interactions and implications in cancer translational medicine

Nair, Sujit

doi:10.3934/molsci.2016.2.104

Cited by 12 publications

(10 citation statements)

References 91 publications

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“…For example, AC073335.2, a highly expressed lncRNA in human glioblastoma, is involved in tumorigenesis via acting as a competing endogenous RNA of miR-940 ( Shi et al, 2017 ). MIR100HG was previously reported to act as a regulator of hematopoiesis and oncogenes in many cancers ( Emmrich et al, 2014 ; Nair, 2016 ; Shang et al, 2016 ; Wieczorek and Reszka, 2018 ; Zhang et al, 2018 ). In agreement with our findings, MIR100HG was reported to be down-regulated in MIBC and may serve as a significant biomarker for MIBC ( Wang et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of miR-200c and miR141-Mediated lncRNA-mRNA Crosstalks in Muscle-Invasive Bladder Cancer Subtypes

et al. 2018

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Basal and luminal subtypes of muscle-invasive bladder cancer (MIBC) have distinct molecular profiles and heterogeneous clinical behaviors. The interactions between mRNAs and lncRNAs, which might be regulated by miRNAs, have crucial roles in many cancers. However, the miRNA-dependent crosstalk between lncRNA and mRNA in specific MIBC subtypes still remains unclear. In this study, we first classified MIBC into two conservative subtypes using miRNA, mRNA and lncRNA expression data derived from The Cancer Genome Atlas. Then we investigated subtype-related biological pathways and evaluated the subtype classification performance using Decision Trees, Random Forest and eXtreme Gradient Boosting (XGBoost). At last, we explored potential miRNA-mediated lncRNA-mRNA crosstalks based on co-expression analysis. Our results show that: (1) the luminal subtype is primarily characterized by upregulation of metabolism-related pathways while the basal subtype is predominantly characterized by upregulation of epithelial-mesenchymal transition, metastasis, and immune system process-related pathways; (2) the XGBoost prediction model is consistently robust for classification of the molecular subtypes of MIBC across four datasets (The area under the ROC curve > 0.9); (3) the expression levels of the molecules in the miR-200c and miR141-mediated lncRNA-mRNA crosstalks differ considerably between the two subtypes and have close relationships with the prognosis of MIBC. The miR-200c and miR-141-dependent mRNA-lncRNA crosstalks might be of great significance in tumorigenesis and tumor progression and may serve as the novel prognostic predictors and classification markers of MIBC subtypes.

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Section: Discussionmentioning

confidence: 99%

Identification of miR-200c and miR141-Mediated lncRNA-mRNA Crosstalks in Muscle-Invasive Bladder Cancer Subtypes

et al. 2018

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“…Obviously, miRNAs interact with long noncoding RNAs (lncRNAs) in the pathogenesis of many cancers. For example, UCA1~miR-143, LINC00478~let7c, NR_024015~miR-526b in gastric cancer and so on (Nair, 2016).…”

Section: Mir-326 Role In Cancermentioning

confidence: 99%

Diagnostic biomarker and therapeutic target applications of miR‐326 in cancers: A systematic review

Jadideslam

Ansarin

Sakhinia

et al. 2019

Journal Cellular Physiology

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MicroRNAs (miRNAs) are endogenous mediators of RNA interference and have key roles in the modulation of gene expression under healthy, inflamed, stimulated, carcinogenic, or other cells, and tissues of a pathological state. Many studies have proved the association between miRNAs and cancer. The role of miR-326 as a tumor suppressor miRNA in much human cancer confirmed. We will explain the history and the role of miRNAs changes, especially miR-326 in cancers and other pathological conditions. Attuned with these facts, this review highlights recent preclinical and clinical research performed on miRNAs as novel promising diagnostic biomarkers of patients at early stages, prediction of prognosis, and monitoring of the patients in response to treatment. All related publications retrieved from the PubMed database, with keywords such as epigenetic, miRNA, microRNA, miR-326, cancer, diagnostic biomarker, and therapeutic target similar terms from 1899 to 2018 with limitations in the English language. Recently, researchers have focused on the impacts of miRNAs and their association in inflammatory, autoinflammatory, and cancerous conditions. Recent studies have suggested a major pathogenic role in cancers and autoinflammatory diseases. Investigations have explained the role of miRNAs in cancers, autoimmunity, and autoinflammatory diseases, and so on. The miRNA-326 expression has an important role in cancer conditions and other diseases. K E Y W O R D S cancer, diagnostic biomarker, epigenetic, miR-326, miRNAs, therapeutic target.

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“…This conclusion approves our results:

0.4918. As for CpG site cg24720672, we find some researches about leukemia—a kind of cancer, and we infer it has the similar mechanism in tumor tissue as lung cancer ( Nair, 2016 ; Zhang et al, 2018 ; Jiang et al, 2020 ).…”

Section: Resultsmentioning

confidence: 96%

High-Dimensional Mediation Analysis Based on Additive Hazards Model for Survival Data

Cui

Luo

et al. 2021

Front. Genet.

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Mediation analysis has been extensively used to identify potential pathways between exposure and outcome. However, the analytical methods of high-dimensional mediation analysis for survival data are still yet to be promoted, especially for non-Cox model approaches. We propose a procedure including “two-step” variable selection and indirect effect estimation for the additive hazards model with high-dimensional mediators. We first apply sure independence screening and smoothly clipped absolute deviation regularization to select mediators. Then we use the Sobel test and the BH method for indirect effect hypothesis testing. Simulation results demonstrate its good performance with a higher true-positive rate and accuracy, as well as a lower false-positive rate. We apply the proposed procedure to analyze DNA methylation markers mediating smoking and survival time of lung cancer patients in a TCGA (The Cancer Genome Atlas) cohort study. The real data application identifies four mediate CpGs, three of which are newly found.

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Current insights into the molecular systems pharmacology of lncRNA-miRNA regulatory interactions and implications in cancer translational medicine

Cited by 12 publications

References 91 publications

Identification of miR-200c and miR141-Mediated lncRNA-mRNA Crosstalks in Muscle-Invasive Bladder Cancer Subtypes

Identification of miR-200c and miR141-Mediated lncRNA-mRNA Crosstalks in Muscle-Invasive Bladder Cancer Subtypes

Diagnostic biomarker and therapeutic target applications of miR‐326 in cancers: A systematic review

High-Dimensional Mediation Analysis Based on Additive Hazards Model for Survival Data

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