Emerging role of non-coding RNAs in the regulation of KRAS

Ghafouri‐Fard, Soudeh; Shirvani-Farsani, Zeinab; Hussen, Bashdar Mahmud; Taheri, Mohammad; Khoshnoud, Reza Jalili

doi:10.1186/s12935-022-02486-1

Cited by 6 publications

(2 citation statements)

References 77 publications

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“…Differential gene expression analysis between R and NR identified 602 DE genes, most of them associated with NR. Many of the top up-regulated genes in R, such as XIST, ENSG00000212939 (LINC01354) and ENSG00000197813 (LINC01420) are long non coding genes (lncRNAs) involved in cell proliferation, increasing the initial sensitivity to cisplatin due to the higher replication rates [37][38][39][40][41] . Additionally, LIPG and RNASE2 genes have also been correlated with proliferation and cancer growth 42,43 and FTCD is a novel candidate to be a tumor suppressor in hepatocellular carcinoma 44 .…”

Section: Discussionmentioning

confidence: 99%

Predicting response to cisplatin-based neoadjuvant chemotherapy for muscle-invasive bladder cancer: transcriptomic features outrank genomic biomarkers

Acedo-Terrades,

Rodriguez-Vida,

Buisan

et al. 2024

Preprint

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Muscle-invasive bladder cancer (MIBC) is associated with poor predictability of response to cisplatin-based neoadjuvant chemotherapy (NAC). Consequently, the benefit of NAC remains unclear for many patients due to the lack of reliable biomarkers predicting treatment response. In order to identify biomarkers and build an integrated and highly accurate model to predict NAC response, we performed a comprehensive transcriptomic and genomic profiling on tumors from 100 MIBC patients. Our results showed that the expression of the top genes associated with response, as well as the expression of growth factor genes and cell cycle regulators are highly correlated with NAC response. Most importantly, we found a novel signature related to the WNT signaling pathway that alone was highly correlated with NAC response and showed high accuracy in predicting NAC response (AUC=0.76). Additionally, mutations in the DNAH family genes (DNAH8, DNAH6 and DNAH10) and deletion in KDM6A were also highly correlated with NAC response. Using our comprehensive molecular analysis as a backbone, we developed two machine learning (ML) models, one incorporating both transcriptomic and genomic features (RF-RW), and the other using only transcriptomic data (RF-R). Both models demonstrated promising performance (AUC=0.82) as predictive models of response to NAC in MIBC. RF-RW and RF-R, after external validation, could potentially change the management of MIBC patients by selecting ideal candidates for NAC.

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Section: Discussionmentioning

confidence: 99%

Predicting response to cisplatin-based neoadjuvant chemotherapy for muscle-invasive bladder cancer: transcriptomic features outrank genomic biomarkers

Acedo-Terrades,

Rodriguez-Vida,

Buisan

et al. 2024

Preprint

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show abstract

“…However, mutations affecting this proto-oncogene are not the only mechanism of its activation. Recently, KRAS has been shown to be regulated by non-coding RNAs (lncRNAs, miRNAs and circRNAs) in the context of cancer development [ 35 ].…”

Section: Discussionmentioning

confidence: 99%

Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia

Dawidowska

Maćkowska-Maślak

Drobna-Śledzińska

et al. 2022

IJMS

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We aimed to identify miRNAs and pathways specifically deregulated in adolescent and young adult (AYA) T-ALL patients. Small RNA-seq showed no major differences between AYA and pediatric T-ALL, but it revealed downregulation of miR-143-3p in T-ALL patients. Prediction algorithms identified several known and putative oncogenes targeted by this miRNA, including KRAS, FGF1, and FGF9. Pathway analysis indicated signaling pathways related to cell growth and proliferation, including FGFR signaling and PI3K-AKT signaling, with the majority of genes overrepresented in these pathways being predicted targets of hsa-miR-143-3p. By luciferase reporter assays, we validated direct interactions of this miRNA with KRAS, FGF1 and FGF9. In cell proliferation assays, we showed reduction of cell growth upon miR-143-3p overexpression in two T-ALL cell lines. Our study is the first description of the miRNA transcriptome in AYA T-ALL patients and the first report on tumor suppressor potential of miR-143-3p in T-ALL. Downregulation of this miRNA in T-ALL patients might contribute to enhanced growth and viability of leukemic cells. We also discuss the potential role of miR-143-3p in FGFR signaling. Although this requires more extensive validation, it might be an interesting direction, since FGFR inhibition proved promising in preclinical studies in various cancers.

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Exploring the Therapeutic Potential of Fe3O4@Glu-Oleuropein Nanoparticles in Targeting KRAS Pathway-Regulating lncRNAs in Colorectal Cancer Cells

Mahdavi Niyaki,

Salehzadeh,

Peymani

et al. 2023

Biol Trace Elem Res

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Emerging role of non-coding RNAs in the regulation of KRAS

Cited by 6 publications

References 77 publications

Predicting response to cisplatin-based neoadjuvant chemotherapy for muscle-invasive bladder cancer: transcriptomic features outrank genomic biomarkers

Predicting response to cisplatin-based neoadjuvant chemotherapy for muscle-invasive bladder cancer: transcriptomic features outrank genomic biomarkers

Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia

Exploring the Therapeutic Potential of Fe3O4@Glu-Oleuropein Nanoparticles in Targeting KRAS Pathway-Regulating lncRNAs in Colorectal Cancer Cells

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