MicroRNA-3148 acts as molecular switch promoting malignant transformation and adipocytic differentiation of immortalized human bone marrow stromal cells via direct targeting of the SMAD2/TGFβ pathway

Vishnubalaji, Radhakrishnan; Elango, Ramesh; Manikandan, Muthurangan; Siyal, Abdulaziz; Ali, Dalia; Al-Rikabi, Ammar C.; Hamam, Dana; Hamam, Rimi; Benabdelkamel, Hicham; Masood, Afshan; Alanazi, Ibrahim O.; Alfadda, Assim A.; Alfayez, Musaad; Aldahmash, Abdullah; Kassem, Moustapha; Alajez, Nehad M.

doi:10.1038/s41420-020-00312-z

Cited by 3 publications

(2 citation statements)

References 51 publications

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“…The Acridine orange/ethidium bromide (AO/EtBr) fluorescence staining method was used to assess apoptosis/necrosis in TNBC cells, as we described before [ 17 ]. On day 5 post siRNA transfection, TNBC cells were washed twice with PBS and were then stained with dual fluorescent staining solution (100 μg/mL AO and 100 μg/mL EtBr (AO/EtBr, Sigma Aldrich, St. Louis, MO, USA)) for 2 min.…”

Section: Methodsmentioning

confidence: 99%

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes

Vishnubalaji

Alajez

2023

Cells

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Breast cancer (BC) is a heterogeneous disease, which is primarily classified according to hormone receptors and HER2 expression. Despite the many advances in BC diagnosis and management, the identification of novel actionable therapeutic targets expressed by cancerous cells has always been a daunting task due to the large heterogeneity of the disease and the presence of non-cancerous cells (i.e., immune cells and stromal cells) within the tumor microenvironment. In the current study, we employed computational algorithms to decipher the cellular composition of estrogen receptor-positive (ER+), HER2+, ER+HER2+, and triple-negative BC (TNBC) subtypes from a total of 49,899 single cells’ publicly available transcriptomic data derived from 26 BC patients. Restricting the analysis to EPCAM+Lin− tumor epithelial cells, we identified the enriched gene sets in each BC molecular subtype. Integration of single-cell transcriptomic with CRISPR-Cas9 functional screen data identified 13 potential therapeutic targets for ER+, 44 potential therapeutic targets for HER2+, and 29 potential therapeutic targets for TNBC. Interestingly, several of the identified therapeutic targets outperformed the current standard of care for each BC subtype. Given the aggressive nature and lack of targeted therapies for TNBC, elevated expression of ENO1, FDPS, CCT6A, TUBB2A, and PGK1 predicted worse relapse-free survival (RFS) in basal BC (n = 442), while elevated expression of ENO1, FDPS, CCT6A, and PGK1 was observed in the most aggressive BLIS TNBC subtype. Mechanistically, targeted depletion of ENO1 and FDPS halted TNBC cell proliferation, colony formation, and organoid tumor growth under 3-dimensional conditions and increased cell death, suggesting their potential use as novel therapeutic targets for TNBC. Differential expression and gene set enrichment analysis in TNBC revealed enrichment in the cycle and mitosis functional categories in FDPShigh, while ENO1high was associated with numerous functional categories, including cell cycle, glycolysis, and ATP metabolic processes. Taken together, our data are the first to unravel the unique gene signatures and to identify novel dependencies and therapeutic vulnerabilities for each BC molecular subtype, thus setting the foundation for the future development of more effective targeted therapies for BC.

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Section: Methodsmentioning

confidence: 99%

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes

Vishnubalaji

Alajez

2023

Cells

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“… 35 Vishnubalaji et al, demonstrated that miR-3148 acted as molecular switch promoting malignant transformation and adipocytic differentiation of immortalized human bone marrow stromal cells via direct targeting of the SMAD2/TGFβ pathway. 36 Collectively, the above evidence indicated that miR-3148 acted as onco-miRNA in CRC by repressing OTOP2 expression. However, as we have not examined the expression of miR-3148 in the CRC tissues, and whether miR-3148 expression was inversely correlated with OTOP2 expression in CRC tissues remains to be clarified.…”

Section: Discussionmentioning

confidence: 89%

OTOP2, Inversely Modulated by miR-3148, Inhibits CRC Cell Migration, Proliferation and Epithelial–Mesenchymal Transition: Evidence from Bioinformatics Data Mining and Experimental Verification

Guo¹,

Sun²

2022

CMAR

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Introduction Colorectal cancer (CRC) represents one of the most frequent human malignancies with its underlying pathogenesis still unclear. The prevalence of multi-omics in screening biomarkers associated with CRC has largely accelerated our understanding into the pathophysiology of CRC. The present work aimed to mine the Gene Expression Omnibus (GEO) datasets associated with CRC studies and identify potential targets correlated with CRC pathogenesis. Methods We screened the DEGs in GSE50760 and GSE104178 and performed functional Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Furthermore, the overlapped DEGs were subjected to functional GO enrichment and KEGG pathway enrichment analysis. The protein–protein interaction (PPI) network and miRNA-mRNA network were constructed based on the overlapped DEGs. The in vitro functional assays including qRT-PCR, caspase-3 and -9 activity assay, wound healing assay, CCK-8 assay and luciferase reporter assay were performed to determine the role of OTOP2/miR-3148 axis in regulating CRC cell progression. Results Fifty-three overlapped genes were screened over GSE50760 and GSE104178 and ten hub genes were identified by PPI network analysis. Expression levels of GCG, SST, NPY, GUCA2B, PYY, UCN3, GUCA2A, TMEM82 and BEST4 were not correlated with the overall survival of patients with CRC. However, the high expression of otopetrin 2 (OTOP2) in the CRC tissues was significantly correlated with better overall survival of patients with CRC. The expression of OTOP2 in CRC tissues was significantly lowever than that in normal ones. The in vitro functional assays demonstrated that OTOP2 silence reduced caspase-3/-9 activities, promoted cell migration, proliferation and epithelial–mesenchymal transition in HT29 and SW620 cells. Furthermore, miR-3148 could inversely regulate OTOP2 expression in CRC cell lines. Conclusion Collectively, the work suggested the potential role of the OTOP2/miR-3148 axis in the pathophysiology of CRC by mining the GEO database.

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Development of Computational Correlations among Known Drug Scaffolds and their Target-Specific Non-Coding RNA Scaffolds of Alzheimer's Disease

Roy,

Kundu,

Mukherjee

2023

CAR

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Background: Alzheimer's disease is the most common neurodegenerative disorder. Recent development in sciences has also identified the pivotal role of microRNAs (miRNAs) in AD pathogenesis. Objectives: We proposed a novel method to identify AD pathway-specific statistically significant miRNAs from the targets of known AD drugs. Moreover, microRNA scaffolds and corresponding drug scaffolds of different pathways were also discovered. Material and Methods: A Wilcoxon signed-rank test was performed to identify pathway-specific significant miRNAs. We generated feed-forward loop regulations of microRNA-TF-gene-based networks, studied the minimum free energy structures of pre-microRNA sequences, and clustered those microRNAs with their corresponding structural motifs of robust transcription factors. Conservation analyses of significant microRNAs were done, and the phylogenetic trees were constructed. We identified 3’UTR binding sites and chromosome locations of these significant microRNAs. Results: In this study, hsa-miR-4261, hsa-miR-153-5p, hsa-miR-6766, and hsa-miR-4319 were identified as key miRNAs for the ACHE pathway and hsa-miR-326, hsa-miR-6133, hsa-miR-4251, hsa-miR-3148, hsa-miR-10527-5p, hsa-miR-527, and hsa-miR-518a were identified as regulatory miRNAs for the NMDA pathway. These miRNAs were regulated by several AD-specific TFs, namely RAD21, FOXA1, and ESR1. It has been observed that anisole and adamantane are important chemical scaffolds to regulate these significant miRNAs. Conclusion: This is the first study that developed a detailed correlation between known AD drug scaffolds and their AD target-specific miRNA scaffolds. This study identified chromosomal locations of microRNAs and corresponding structural scaffolds of transcription factors that may be responsible for miRNA co-regulation for Alzheimer's disease. Our study provides hope for therapeutic improvements in the existing microRNAs by regulating pathways and targets.

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MicroRNA-3148 acts as molecular switch promoting malignant transformation and adipocytic differentiation of immortalized human bone marrow stromal cells via direct targeting of the SMAD2/TGFβ pathway

Cited by 3 publications

References 51 publications

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes

Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes

OTOP2, Inversely Modulated by miR-3148, Inhibits CRC Cell Migration, Proliferation and Epithelial–Mesenchymal Transition: Evidence from Bioinformatics Data Mining and Experimental Verification

Development of Computational Correlations among Known Drug Scaffolds and their Target-Specific Non-Coding RNA Scaffolds of Alzheimer's Disease

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