Personalized cancer medicine: next steps in the genomic era

In vitro Cytotoxic Screening of Different Parts from Ornithogalum bungei on Selected Cancer Cells

BACKGROUND

Natural products comprise a large section of pharmaceutical agents in the field of cancer therapy. In the present study, the organic extracts and fractions of various parts of Ornithogalum bungei were investigated for in vitro cytotoxic properties on three human cancer cell lines, hepatocellular carcinoma (HepG2), prostate cancer (PC3), and leukemia (K562) cells.

METHODS

The present experimental study was conducted at Tehran University of Medical Sciences (Tehran, Iran) during 2017-2019. Separately extracted plant materials, including bulbs, stems, and flowers of O. bungei were assessed by the tetrazolium dye-based colorimetric assay (MTT). The selected extracts were submitted to fractionation using vacuum liquid chromatography and after MTT assay, the half maximal inhibitory concentration (IC₅₀ (value for each fraction was determined. The data were analyzed using One-way ANOVA followed by Tukey's post hoc test. P<0.05 was considered statistically significant.

RESULTS

The cytotoxicity of the bulb's methanol extract and the dichloromethane extract of aerial parts increased in a concentration-dependent manner. Additionally, cell viability decreased in a dose-dependent manner. In the HepG2 cell line, the best IC₅₀ values of fractions from DCM extracts of aerial parts were determined to be 19.8±10.2 µg/mL after 24 hours of exposure and 19.39±6.4 µg/mL following 48 hours of exposure. In the PC3 cell line, after 48 hours of exposure, the IC₅₀ values of fractions were unaccountable, while the percentage of inhibition for A6 to A11 in 24 hours of exposure was more than 40 µg/mL.

CONCLUSION

O. bungei growing in Iran showed significant potentials as a cytotoxic agent with selective effects on different cancer cell lines.

Detection and removal of spatial bias in multiwell assays

MOTIVATION

Multiplex readout assays are now increasingly being performed using microfluidic automation in multiwell format. For instance, the Library of Integrated Network-based Cellular Signatures (LINCS) has produced gene expression measurements for tens of thousands of distinct cell perturbations using a 384-well plate format. This dataset is by far the largest 384-well gene expression measurement assay ever performed. We investigated the gene expression profiles of a million samples from the LINCS dataset and found that the vast majority (96%) of the tested plates were affected by a significant 2D spatial bias.

RESULTS

Using a novel algorithm combining spatial autocorrelation detection and principal component analysis, we could remove most of the spatial bias from the LINCS dataset and show in parallel a dramatic improvement of similarity between biological replicates assayed in different plates. The proposed methodology is fully general and can be applied to any highly multiplexed assay performed in multiwell format.

CONTACT

ac2248@columbia.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Molecular Dynamics: New Frontier in Personalized Medicine

The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine.

The bone marrow metastasis niche in retinoblastoma

BACKGROUND

Retinoblastoma (Rb) is a progressive cancer which mainly occurs in children, and which is caused by different genetic or epigenetic alterations that lead to inactivation of both alleles of the RB1 gene. Hereditary and non-hereditary forms of Rb do exist, and the hereditary form is associated with an increased risk of secondary malignancies. Metastasis to distant organs is a critical feature of many tumors, and may be caused by various molecular alterations at different stages. Recognition of these alterations and, thus, insight into the processes underlying the development of metastases may result in novel preventive as well as effective targeted treatment options. Rb is associated with metastases to various organs and tissues, including the bone marrow (BM).

METHODS

Here, we provide an overview of mutations and other molecular changes known to be involved in Rb development and metastasis to the BM. This overview is based on a literature search ranging from 1990 to 2015.

CONCLUSIONS

The various BM metastasis-related molecular changes identified to date may be instrumental for a better diagnosis, prognosis and classification of Rb patients, as well as for the development of novel comprehensive (targeted) therapies.