RNA-seq facilitates unbiased genome-wide gene-expression profiling. However, its concordance with the well-established microarray platform must be rigorously assessed for confident uses in clinical and regulatory application. Here we use a comprehensive study design to generate Illumina RNA-seq and Affymetrix microarray data from the same set of liver samples of rats under varying degrees of perturbation by 27 chemicals representing multiple modes of action (MOA). The cross-platform concordance in terms of differentially expressed genes (DEGs) or enriched pathways is highly correlated with treatment effect size, gene-expression abundance and the biological complexity of the MOA. RNA-seq outperforms microarray (90% versus 76%) in DEG verification by quantitative PCR and the main gain is its improved accuracy for low expressed genes. Nonetheless, predictive classifiers derived from both platforms performed similarly. Therefore, the endpoint studied and its biological complexity, transcript abundance, and intended application are important factors in transcriptomic research and for decision-making.

Kinesin family member 4A (KIF4A) was found to be implicated in the regulation of chromosome condensation and segregation during mitotic cell division, which is essential for eukaryotic cell proliferation. However, little is known about the role of KIF4A in colorectal carcinoma (CRC). This study explored the biological function of KIF4A in CRC progression and investigated the potential molecular mechanisms involved. Here, we found that KIF4A was remarkably upregulated in primary CRC tissues and cell lines compared with paired non-cancerous tissues and normal colorectal epithelium. Elevated expression of KIF4A in CRC tissues was significantly correlated with clinicopathological characteristics in patients as well as with shorter overall and disease-free cumulative survival. Multivariate Cox regression analysis revealed that KIF4A was an independent prognostic factor for poor survival in human CRC patients. Functional assays, including a CCK-8 cell proliferation assay, colony formation analysis, cancer xenografts in nude mice, cell cycle and apoptosis analysis, indicated that KIF4A obviously enhanced cell proliferation by promoting cell cycle progression in vitro and in vivo. Furthermore, gene set enrichment analysis, Luciferase reporter assays, and ChIP assays revealed that KIF4A facilitates cell proliferation via regulating the p21 promoter, whereas KIF4A had no effect on cell apoptosis. In addition, Transwell analysis indicated that KIF4A promotes migration and invasion in CRC. Taken together, these findings not only demonstrate that KIF4A contributes to CRC proliferation via modulation of p21-mediated cell cycle progression but also suggest the potential value of KIF4A as a clinical prognostic marker and target for molecular treatments.

Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. In melanoma, tumour cells often experience low glutamine levels, which promote cell dedifferentiation. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in a transgenic melanoma mouse model, and increases sensitivity to a BRAF inhibitor. Metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine in tumours and its downstream metabolite, αKG, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome in tumours. Our data further demonstrate that increase in intra-tumoural αKG concentration drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.

ABSTRACT. To encourage cell adhesion on biomaterial surfaces in a more facile, safe, and lowcost fashion, we have demonstrated a non-covalent approach to spatially conjugate β-cyclodextrin (β-CD) modified peptide sequences onto self-assembled adamantane-terminated polystyrene-b-poly(ethylene oxide) (PS-PEO-Ada) films through inclusion complexing interactions between β-CDs and adamantane. By simply blending various ratios of unmodified PS-PEO with a newly synthesised PS-PEO-Ada, we produced PS polymer films that displayed 2 well-organized adamantine-decorated cylindrical PEO domains with varying average interdomain spacings ranging from 29 to 47 nm. The presence of the adamantane moiety at the terminal end of the PEO chain permitted rapid, and importantly, oriented attachment of β-CD functionalized peptides onto these surfaces. This one-step process not only converted these proven non-adherent PS-PEO surfaces into adherent surfaces, but also permitted precisely controlled presentation and surface distribution of the conjugated peptides. The utility of these surfaces as cell culture substrates was confirmed with human mesenchymal stem cells (hMSCs).We observed that with increasing PS-PEO-Ada content in the PEO cylindrical domains, these novel polymer films displayed improved cell attachment and spreading, with notable differences in hMSC morphology. We further confirmed that this novel PS-PEO-Ada surface provides a flexible platform for facile conjugation of mixtures of β-CDs functionalized with different peptides, specifically RGD and IKVAV peptides. The cell adhesion and spreading assays on these surfaces indicated that the morphologies of hMSCs can be easily manipulated, while no significant changes in cell attachment were observed. The 'lock-and-key' peptide conjugation technique presented in this work is applicable to any substrate that incorporates a moiety capable of forming inclusion complexes with α-, β-and γ-CDs, providing a facile and flexible method by which to construct peptide-conjugated biomaterial substrates for a multitude of applications in fields ranging from cell bioprocessing, regenerative medicine to cell-based assays.

No abstract