Role of rat sarcoma virus mutations in cancer and potential target for cancer therapy

The importance of protein domain mutations in cancer therapy

Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.

Computational design and validation of effective siRNAs to silence oncogenic KRAS

Oncogenic KRAS mutations drive cancer progression in lung, colon, breast, and pancreatic ductal adenocarcinomas. Apart from the current strategies, such as KRAS upstream inhibitors, downstream effector inhibitors, interaction inhibitors, cell cycle inhibitors, and direct KRAS inhibitors, against KRAS-mutated cancers, the therapeutic small interfering RNAs (siRNAs) represent a promising alternative strategy that directly binds with the target mRNA and inhibits protein translation via mRNA degradation. Here, in the present study, we utilized various in silico approaches to design potential siRNA candidates against KRAS mRNA. We have predicted nearly 17 siRNAs against the KRAS mRNA, and further through various criteria, such as U, R, and A rules, GC%, secondary structure formation, mRNA-siRNA duplex stability, Tm (Cp), Tm (Conc), and inhibition efficiency, they have been filtered into 4 potential siRNAs namely siRNA8, siRNA11, siRNA12, and siRNA17. Further, the molecular docking analysis revealed that the siRNA8, siRNA11, siRNA12, and siRNA17 showed higher negative binding energies, such as - 379.13 kcal/mol, - 360.19 kcal/mol, - 288.47 kcal/mol, and - 329.76 kcal/mol, toward the human Argonaute2 protein (hAgo2) respectively. In addition, the normal mode analysis of the hAgo2-siRNAs complexes indicates the structural changes and deformation of the hAgo2 protein upon the binding of siRNA molecules in the dynamic environment which suggests that these siRNAs could be effective. Finally, we conclude that these 4 siRNAs have therapeutic potential against KRAS mRNA and also have to be studied in vitro and in vivo to evaluate their specificity toward mutant KRAS (not degrading wild-type KRAS). Also, the current challenges in the use of siRNA therapeutics could be overcome by the emerging siRNA delivery methods, such as Antibody-siRNA conjugates (ARCs) and Gelatin-Antibody Delivery System (GADS), in the near future and these siRNAs could be employed as potential therapeutic agents against KRAS-mutated cancers.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03767-w.

Oncogenic Ras expression increases cellular formate production

One-carbon units, critical intermediates for cell growth, may be produced by a variety of means, one of which is via the production of formate. Excessive formate accumulation, known as formate overflow and a characteristic of oxidative cancer, has been observed in cancer cells. However, the basis for this high rate of formate production is unknown. We examined the effect of elevated expression of oncogenic Ras (RasV12), on formate production in NIH-3T3 cells (mouse fibroblasts) cultured with either labelled ¹³C-serine or ¹³C-glycine. Formate accumulation by the fibroblasts transformed by RasV12 was increased two-threefold over those by vector control (Babe) cells. The production of formate exceeded the rate of utilization in both cell types. ¹³C-formate was produced almost exclusively from the #3 carbon of ¹³C-serine. Virtually no labelled formate was produced from either the #2 carbon of serine or the #2 carbon of glycine. The increased formate production by RasV12 cells was associated with increased mRNA abundances for enzymes of formate production in both the mitochondria and the cytosol. Thus, we find the oncogenic RasV12 significantly increases formate overflow and may be one way for tumor cells to produce one-carbon units required for enhanced proliferation of these cells and/or for other processes which have not been identified.