Identification of candidate genes determining chemosensitivity to anti-cancer drugs of gastric cancer cell lines

Systematic review of comparative transcriptomic studies of cellular resistance to genotoxic stress

The development of resistance by tumor cells to various types of therapy is a significant problem that decreases the effectiveness of oncology treatments. For more than two decades, comparative transcriptomic studies of tumor cells with different sensitivities to ionizing radiation and chemotherapeutic agents have been conducted in order to identify the causes and mechanisms underlying this phenomenon. However, the results of such studies have little in common and often contradict each other. We have assumed that a systematic analysis of a large number of such studies will provide new knowledge about the mechanisms of development of therapeutic resistance in tumor cells. Our comparison of 123 differentially expressed gene (DEG) lists published in 98 papers suggests a very low degree of consistency between the study results. Grouping the data by type of genotoxic agent and tumor type did not increase the similarity. The most frequently overexpressed genes were found to be those encoding the transport protein ABCB1 and the antiviral defense protein IFITM1. We put forward a hypothesis that the role played by the overexpression of the latter in the development of resistance may be associated not only with the stimulation of proliferation, but also with the limitation of exosomal communication and, as a result, with a decrease in the bystander effect. Among down regulated DEGs, BNIP3 was observed most frequently. The expression of BNIP3, together with BNIP3L, is often suppressed in cells resistant to non-platinum genotoxic chemotherapeutic agents, whereas it is increased in cells resistant to ionizing radiation. These observations are likely to be mediated by the binary effects of these gene products on survival, and regulation of apoptosis and autophagy. The combined data also show that even such obvious mechanisms as inhibition of apoptosis and increase of proliferation are not universal but show multidirectional changes.

Dose Issues in Cancer Chemotherapy

In this review, human methotrexate dosing regimens, as well as their relationship to data from in vitro cell culture and in vivo animal and human studies, are discussed. Low-dose, intermediate-dose, and high-dose therapies are covered. Since in vitro and in vivo screenings of potential cancer drugs are commonplace in the development of cancer chemotherapy, comparisons of the three criteria for effectiveness are important.

Genome-Wide DNA Methylation Model for the Diagnosis of Prostate Cancer

Prostate cancer is the most prevalent and the second most lethal malignancy among males in the United States of America. Its diagnosis is almost entirely predicated upon histopathological analysis of the biopsied tissue, and it is associated with a substantial average error. Using genome-wide DNA methylation data derived from 469 prostatic tumor tissue samples and 50 normal prostatic tissue samples and interrogating over 485 000 CpG sites per sample (spanning across gene promoters, CpG islands, shores, shelves, gene bodies, and intergenic and other areas), we were able to develop a mathematical model that classified with a high accuracy (overall sensitivity = 95.31% and overall specificity = 94.00%) tumor tissue versus normal tissue. The methylation β values of five CpG sites, corresponding to the genes LINC01091, RPS15,  SNORA10, and two unknown DNA areas in chromosome 1, provided the input to the model. The model was validated with unknown samples, as well as with a sixfold cross-validation and a leave-one-out cross-validation. This study presents a novel genomic model based on genome-wide DNA methylation analysis of biopsied prostatic tissue that could aid in the diagnosis of prostate cancer and help advance the transition to genomic medicine.

Overexpression of GNAO1 correlates with poor prognosis in patients with gastric cancer and plays a role in gastric cancer cell proliferation and apoptosis

Guanine nucleotide-binding protein (G protein), alpha activating activity polypeptide O (GNAO1) encodes an alpha subunit of the heterotrimeric guanine nucleotide-binding proteins (Gαo), which plays a significant role in the development of various types of cancer, including breast cancer and hepatocellular carcinoma. However, its role in gastric cancer (GC) has not yet been elucidated. In the current study, the expression of Gαo was analyzed by immunohistochemistry in paraffin-embedded tissue sections from 70 patients with GC and its cellular role was examined by small interfering RNA (siRNA)-mediated downregulation. The overexpression of GNAO1 (scores of 2 or 4) was observed in 44 of the 70 patients with GC (62.9%) and the expression of Gαo significantly correlated with the overall survival of the patients with GC after surgery. The median survival rate of patients with a negative or positive expression of Gαo was 61 or 27 months, respectively (P=0.033). The silencing of GNAO1 in GC cells by RNA interference markedly inhibited the proliferation of GC cells and promoted apoptosis by increasing the accumulation of the pro-apoptotic proteins, Puma and Bim, possibly mediated by extracellular signal-regulated kinase 1 and 2 (ERK1/2). This further confirmed the clinical significance of GNAO1, which was overexpressed in GC tissues. To the best of our knowledge, the present study is the first to demonstrate that GNAO1 is overexpressed in GC and that its overexpression correlates with poor prognosis, as it promotes GC cell viability.

Chemical genomics for studying parasite gene function and interaction

With the development of new technologies in genome sequencing, gene expression profiling, genotyping, and high-throughput screening of chemical compound libraries, small molecules are playing increasingly important roles in studying gene expression regulation, gene-gene interaction, and gene function. Here we briefly review and discuss some recent advancements in drug target identification and phenotype characterization using combinations of high-throughput screening of small-molecule libraries and various genome-wide methods such as whole-genome sequencing, genome-wide association studies (GWAS), and genome-wide expression analysis. These approaches can be used to search for new drugs against parasite infections, to identify drug targets or drug resistance genes, and to infer gene function.