Functional Prediction of Candidate MicroRNAs for CRC Management Using in Silico Approach

Stage-specific treatment of colorectal cancer: A microRNA-nanocomposite approach

Colorectal cancer (CRC) is among the leading causes of cancer mortality. The lifetime risk of developing CRC is about 5% in adult males and females. CRC is usually diagnosed at an advanced stage, and at this point therapy has a limited impact on cure rates and long-term survival. Novel and/or improved CRC therapeutic options are needed. The involvement of microRNAs (miRNAs) in cancer development has been reported, and their regulation in many oncogenic pathways suggests their potent tumor suppressor action. Although miRNAs provide a promising therapeutic approach for cancer, challenges such as biodegradation, specificity, stability and toxicity, impede their progression into clinical trials. Nanotechnology strategies offer diverse advantages for the use of miRNAs for CRC-targeted delivery and therapy. The merits of using nanocarriers for targeted delivery of miRNA-formulations are presented herein to highlight the role they can play in miRNA-based CRC therapy by targeting different stages of the disease.

The chromatin - triple helix connection

Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.

Inhibition of the cell migration, invasion and chemoresistance of colorectal cancer cells through targeting KLF3 by miR-365a-3p

Background: Metastasis and chemoresistance limit treatment efficacy of colorectal cancer (CRC) patients. MicroRNAs (miRNAs) have been believed to be candidate biomarkers for tumor cell proliferation, metastasis and chemoresistance, but the related molecular mechanisms are not clear for prognosis prediction.

Aims: We aimed to investigate the role of miR-365a-3p in metastasis and chemoresistance of CRC.

Methods: The expression levels of miR-365a-3p in clinical CRC tissues were analyzed. The effects of miR-365a-3p expression levels on tumor chemoresistance, invasion and migration were also determined. A dual luciferase reporter gene assay was used to determine the effect of miR-365a-3p on its target gene, Kruppel-like factor 3 (KLF3), and the effect of the miR-365a-3p/KLF3 axis on CRC cell chemoresistance, migration and invasion was further investigated.

Results: In patients with CRC with lymph node or distant organ metastasis or in CRC cell lines, the expression levels of miR-365a-3p were significantly downregulated. In addition, the findings of Transwell assays demonstrated that miR-365a-3p significantly suppressed CRC cell migration and invasion. The dual luciferase reporter gene assay results suggested that miR-365a-3p may play an important role in the regulation of migration, invasion and chemoresistance in CRC cells.

Conclusions: The findings of present study provided evidence to suggest that miR-365a-3p may be a potential tumor suppressor gene in CRC and may inhibit the migration, invasion and chemoresistance of CRC cells. These results suggested that targeting miR-365a-3p/KLF3 axis may represent a potential therapeutic intervention for metastatic disease in patients with CRC.

Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach

The exponential increase in cases and mortality of coronavirus disease (COVID-19) has called for a need to develop drugs to treat this infection. Using in silico and molecular docking approaches, this study investigated the inhibitory effects of Pradimicin A, Lamivudine, Plerixafor and Lopinavir against SARS-CoV-2 M^pro. ADME/Tox of the ligands, pharmacophore hypothesis of the co-crystalized ligand and the receptor, and docking studies were carried out on different modules of Schrodinger (2019-4) Maestro v12.2. Among the ligands subjected to ADME/Tox by QikProp, Lamivudine demonstrated drug-like physico-chemical properties. A total of five pharmacophore binding sites (A3, A4, R9, R10, and R11) were predicted from the co-crystalized ligand and the binding cavity of the SARS-CoV-2 M^pro. The docking result showed that Lopinavir and Lamivudine bind with a higher affinity and lower free energy than the standard ligand having a glide score of -9.2 kcal/mol and -5.3 kcal/mol, respectively. Plerixafor and Pradimicin A have a glide score of -3.7 kcal/mol and -2.4 kcal/mol, respectively, which is lower than the co-crystallized ligand with a glide score of -5.3 kcal/mol. Molecular dynamics confirmed that the ligands maintained their interaction with the protein with lower RMSD fluctuations over the trajectory period of 100 nsecs and that GLU166 residue is pivotal for binding. On the whole, present study specifies the repurposing aptitude of these molecules as inhibitors of SARS-CoV-2 M^pro with higher binding scores and forms energetically stable complexes with M^pro.Communicated by Ramaswamy H. Sarma.

Genomic profiling of microRNA target genes in colorectal cancer

Colorectal cancer is the second and third most common cancer in men and women, respectively, worldwide. Alterations such as genetic and epigenetic are common in colorectal cancer and are the basis of tumor formation. The exploration of the molecular basis of colorectal cancer can drive a better understanding of the disease as well as guide the prognosis, therapeutics, and disease management. This study is aimed at investigating the genetic mutation profile of five candidate microRNAs (hsa-miR-513b-3p, hsa-miR-500b-3p, hsa-miR-500a-3p, hsa-miR-450b-3p, hsa-miR-193a-5p) targeted by seven genes (APC, KRAS, TCF7L2, EGFR, IGF1R, CASP8, and GNAS)) using in silico approaches. Two datasets (dataset 1 from our previous study and dataset two (The Cancer Genome Atlas, Nature 2012) were considered for this study. Protein-protein interaction, expression analysis, and genetic profiling were carried out using STRING, FireBrowse, and cBioPortal, respectively. Protein-protein interaction network showed that epidermal growth factor receptor has the highest connection among the target genes and this can be considered as the hub gene. Relative to other solid tumors, in colorectal cancer, six of the target genes were downregulated and only CASP8 was upregulated. Genes with protein tyrosine kinases domain were frequently altered in colorectal cancer and the most common alteration in these genes/domain are missense mutation. These results could serve as a lead in the identification of driver genes responsible for colorectal cancer initiation and progression. However, the intense mechanism of these results remains unclear and further experimental validation and molecular approaches are the focal points in the nearest future.

Elevated expression of exosomal microRNA-21 as a potential biomarker for the early diagnosis of pancreatic cancer using a tethered cationic lipoplex nanoparticle biochip

Pancreatic cancer (PC) has a poor prognosis due to the lack of effective molecular biomarkers for early diagnosis. Recent studies have investigated the use of exosomal microRNAs (exmiRs) as diagnostic biomarkers in cancer. The present study examined exmiR-21, exmiR-10b and exmiR-212-3p expression in patients with PC and healthy individuals. The expression levels of exmiR-21, exmiR-10b and exmiR-212-3p were examined in the peripheral blood plasma of 36 patients with PC and 65 healthy controls, using tethered cationic lipoplex nanoparticle biochip. The levels of exmiR-21 in the plasma of 34 mice were also evaluated. The expression levels of exmiR-21 and exmiR-10b were significantly greater in patients with PC compared with the control group. The receiver operating characteristic (ROC) analysis indicated that exmiR-21 had better diagnostic performance (P=0.0003; AUC, 0.7171) compared with the other two exmiRs. The diagnostic value of exmiR-21 improved when combined with exmiR-10b (P<0.0001; AUC, 0.791). Furthermore, exmiR-21 was capable of distinguishing patients with early-stage PC from controls and advanced-stage PC (P<0.05, early stage vs. healthy; P<0.001, early stage vs. advanced stage). The results of the present study revealed that the plasma levels of exmiR-21 and exmiR-10b were upregulated in patients with PC. The ROC analyses indicated that exmiR-21 had the best diagnostic performance among the three exmiRs. Furthermore, exmiR-21 was capable of discriminating patients with early-stage PC from healthy controls. These findings indicate the potential of determining the expression of exmiR-21 from serum using a tethered cationic lipoplex nanoparticle biochip as a novel non-invasive strategy for the early diagnosis of PC.