Phenotypic, genomic, and transcriptomic heterogeneity in a pancreatic cancer cell line

OBJECTIVES

To evaluate the suitability of the MIA PaCa-2 cell line for studying pancreatic cancer intratumor heterogeneity, we aim to further characterize the nature of MIA PaCa-2 cells' phenotypic, genomic, and transcriptomic heterogeneity.

METHODS

MIA PaCa-2 single-cell clones were established through flow cytometry. For the phenotypic study, we quantified the cellular morphology, proliferation rate, migration potential, and drug sensitivity of the clones. The chromosome copy number and transcriptomic profiles were quantified using SNPa and RNA-seq, respectively.

RESULTS

Four MIA PaCa-2 clones showed distinctive phenotypes, with differences in cellular morphology, proliferation rate, migration potential, and drug sensitivity. We also observed a degree of genomic variations between these clones in form of chromosome copy number alterations and single nucleotide variations, suggesting the genomic heterogeneity of the population, and the intrinsic genomic instability of MIA PaCa-2 cells. Lastly, transcriptomic analysis of the clones also revealed gene expression profile differences between the clones, including the uniquely regulated ITGAV, which dictates the morphology of MIA PaCa-2 clones.

CONCLUSIONS

MIA PaCa-2 is comprised of cells with distinctive phenotypes, heterogeneous genomes, and differential transcriptomic profiles, suggesting its suitability as a model to study the underlying mechanisms behind pancreatic cancer heterogeneity.

Role of MicroRNA Genes miR-1000 and miR-375 in Forming Olfactory Conditional Memory in Drosophila melanogaster

BACKGROUND

Learning and memory are basic aspects of neurogenetics as most of the neurological disorders start with dementia or memory loss. Several genes associated with memory formation have been discovered. MicroRNA genes, miR-1000 and miR-375, were reported to be associated with neural integration and glucose homeostasis in some insects and vertebrates. However, the neuronal function of these genes is yet to be established in D. melanogaster.

OBJECTIVE

The possible role of miR-1000 and miR-375 in learning and memory formation in this fly has been explored in the present study.

METHODS

Both types of appetitive and aversive olfactory conditional learning were tested in the miR- 1000 and miR-375 knockout (KO) strains and compared with the wild one. Five days old third instar larvae were trained by allowing them to be associated with an odor with reward (fructose) or punishment (salt). Then, the larvae were tested to calculate their preferences to the odor they were trained with. Learning Index (LI) values and larval locomotion speed were calculated for all strains.

RESULTS

Knockout strain of miR-1000 showed significant deficiency in both appetitive and aversive memory formation whereas miR-375 KO strain showed a significantly lower response only in appetitive one.

CONCLUSION

The results of the present study indicate an important role of miR-1000 and miR-375 genes in forming short-term memory in D. melanogaster.

DNA-Dependent Protein Kinase Catalytic Subunit: The Sensor for DNA Double-Strand Breaks Structurally and Functionally Related to Ataxia Telangiectasia Mutated

The DNA-dependent protein kinase (DNA-PK) is composed of a DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Ku70/Ku80 heterodimer. DNA-PK is thought to act as the “sensor” for DNA double-stranded breaks (DSB), which are considered the most deleterious type of DNA damage. In particular, DNA-PKcs and Ku are shown to be essential for DSB repair through nonhomologous end joining (NHEJ). The phenotypes of animals and human individuals with defective DNA-PKcs or Ku functions indicate their essential roles in these developments, especially in neuronal and immune systems. DNA-PKcs are structurally related to Ataxia–telangiectasia mutated (ATM), which is also implicated in the cellular responses to DSBs. DNA-PKcs and ATM constitute the phosphatidylinositol 3-kinase-like kinases (PIKKs) family with several other molecules. Here, we review the accumulated knowledge on the functions of DNA-PKcs, mainly based on the phenotypes of DNA-PKcs-deficient cells in animals and human individuals, and also discuss its relationship with ATM in the maintenance of genomic stability.

Epithelial or mesenchymal: Where to draw the line?

Epithelial and mesenchymal cells represent two of the main differentiated cell types in all vertebrates. However, their distinction is not always absolutely clear. Dozens of molecules have been used as markers for each cell type, while emerging evidence questions their validity. The aim of this study was to compare the molecular phenotype of these two cell types. Twenty-two commonly used molecular markers were evaluated by quantitative PCR and immunofluorescence in six lines of human and rat epithelial cells and fibroblasts. The epithelial cells were also examined for their responses to TGFbeta1 stimulation. All of the "markers" tested were found in both epithelial and mesenchymal cells. Some epithelial markers, such as CLDN5, OCLN, DSG1 and TJP1, were expressed even higher in fibroblasts than in epithelial cells. In comparison, mesenchymal markers showed more fidelity, but CDH2 and MMP9 were still significantly higher in epithelial cells than in mesenchymal cells. Furthermore, TGFbeta1 up-regulated epithelial markers CTNNB1 and CTNND1, but suppressed mesenchymal markers, such as S100A4, FGF1 and FGF2. In conclusion, no gene expression is cell-type restricted. Although some of these "markers" are expressed more in one cell type than in the other or differently localized, none of them shows a consistent pattern across species to make them universal markers. Nonetheless, some molecules appear to be better markers than others for a specific cell type. The information provided here is expected to serve as a reference for both basic and clinical researchers in the fields of epithelial-mesenchymal transition, molecular cell typing and cancer diagnosis.