Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations in mismatch repair genes in methotrexate-resistant HT-29 cells

Combating Methotrexate Resistance in Cancer Treatment: A Review on Navigating Pathways and Enhancing Its Efficacy With Fat-Soluble Vitamins

Methotrexate (MTX), a potent analogue and antagonist of folic acid, is a first-line treatment for rheumatoid arthritis, IBD and cancer. The development of MTX resistance contributes to the reduced efficacy and development of adverse reactions, forcing clinicians to withdraw treatment early. This drawback requires combinational approaches to combat the resistance and enhance the efficacy and safety of MTX. To provide a brief overview of MTX resistance and strategies to mitigate its aftereffects in cancer therapy, a literature-based search was conducted using keywords such as cancer pathology, MTX mechanism and resistance, S100A4, folate uptake, folate efflux, P-glycoprotein, beta-catenin and anticancer properties of Vitamins A, D, E and K. Investigations encompassing in vitro studies, in vivo studies and clinical trials were reviewed to identify the mechanisms of resistance induced by MTX and the potential benefits of coadministering fat-soluble vitamins with existing anticancer drugs. Derivates of Vitamin A could target cancer stem cells and increase chemotherapy sensitivity in non-small cell lung cancer. Similarly, calcitriol and cytotoxic medications exhibit additive or synergistic effects. Existing research revealed that fat-soluble vitamins can inhibit drug transporters, such as P-glycoprotein, which inhibit drug efflux, improving chemotherapy efficacy in cancer. As personalised medicine continues to evolve, incorporating combination approaches with MTX and fat-soluble vitamins holds promise for enhancing treatment efficacy, which can counteract MTX resistance via multiple pathways and improve the safety profile.

Combating Methotrexate Resistance in Cancer Treatment: A Review on Navigating Pathways and Enhancing Its Efficacy With Fat‐Soluble Vitamins

Methotrexate (MTX), a potent analogue and antagonist of folic acid, is a first‐line treatment for rheumatoid arthritis, IBD and cancer. The development of MTX resistance contributes to the reduced efficacy and development of adverse reactions, forcing clinicians to withdraw treatment early. This drawback requires combinational approaches to combat the resistance and enhance the efficacy and safety of MTX. To provide a brief overview of MTX resistance and strategies to mitigate its aftereffects in cancer therapy, a literature‐based search was conducted using keywords such as cancer pathology, MTX mechanism and resistance, S100A4, folate uptake, folate efflux, P‐glycoprotein, beta‐catenin and anticancer properties of Vitamins A, D, E and K. Investigations encompassing in vitro studies, in vivo studies and clinical trials were reviewed to identify the mechanisms of resistance induced by MTX and the potential benefits of coadministering fat‐soluble vitamins with existing anticancer drugs. Derivates of Vitamin A could target cancer stem cells and increase chemotherapy sensitivity in non–small cell lung cancer. Similarly, calcitriol and cytotoxic medications exhibit additive or synergistic effects. Existing research revealed that fat‐soluble vitamins can inhibit drug transporters, such as P‐glycoprotein, which inhibit drug efflux, improving chemotherapy efficacy in cancer. As personalised medicine continues to evolve, incorporating combination approaches with MTX and fat‐soluble vitamins holds promise for enhancing treatment efficacy, which can counteract MTX resistance via multiple pathways and improve the safety profile.

Targeting the sulfur-containing amino acid pathway in leukemia

sulfur-containing amino acids have been reported to patriciate in gene regulation, DNA methylation, protein synthesis and other physiological or pathological processes. In recent years, metabolism-related molecules of sulfur-containing amino acids affecting the occurrence, development and treatment of tumors have been implicated in various disorders, especially in leukemia. Here, we summarize current knowledge on the sulfur-containing amino acid metabolism pathway in leukemia and examine ongoing efforts to target this pathway, including treatment strategies targeting (a) sulfur-containing amino acids, (b) metabolites of sulfur-containing amino acids, and (c) enzymes and cofactors related to sulfur-containing amino acid metabolism in leukemia. Future leukemia therapy will likely involve innovative strategies targeting the sulfur-containing amino acid metabolism pathway.

Organoids: An Emerging Precision Medicine Model for Prostate Cancer Research

Prostate cancer (PCa) has been known as the most prevalent cancer disease and the second leading cause of cancer mortality in men almost all over the globe. There is an urgent need for establishment of PCa models that can recapitulate the progress of genomic landscapes and molecular alterations during development and progression of this disease. Notably, several organoid models have been developed for assessing the complex interaction between PCa and its surrounding microenvironment. In recent years, PCa organoids have been emerged as powerful in vitro 3D model systems that recapitulate the molecular features (such as genomic/epigenomic changes and tumor microenvironment) of PCa metastatic tumors. In addition, application of organoid technology in mechanistic studies (i.e., for understanding cellular/subcellular and molecular alterations) and translational medicine has been recognized as a promising approach for facilitating the development of potential biomarkers and novel therapeutic strategies. In this review, we summarize the application of PCa organoids in the high-throughput screening and establishment of relevant xenografts for developing novel therapeutics for metastatic, castration resistant, and neuroendocrine PCa. These organoid-based studies are expected to expand our knowledge from basic research to clinical applications for PCa diseases. Furthermore, we also highlight the optimization of PCa cultures and establishment of promising 3D organoid models for in vitro and in vivo investigations, ultimately facilitating mechanistic studies and development of novel clinical diagnosis/prognosis and therapies for PCa.

Promoter from Chinese hamster elongation factor-1a gene and Epstein-Barr virus terminal repeats concatemer fragment maintain stable high-level expression of recombinant proteins

Background

The Chinese hamster ovary (CHO) cell line is the main host for the high-titer production of therapeutic and diagnostic proteins in the biopharmaceutical industry. In most cases, plasmids for efficient protein expression in CHO cells are based on the cytomegalovirus (CMV) promoter. The autologous Chinese hamster eukaryotic translation elongation factor 1α (EEF1A1) promoter is a viable alternative to the CMV promoter in industrial applications. The EEF1A1 promoter and its surrounding DNA regions proved to be effective at maintaining high-level and stable expression of recombinant proteins in CHO cells. EEF1A1-based plasmids' large size can lead to low transfection efficiency and hamper target gene amplification. We hypothesized that an efficient EEF1A1-based expression vector with a long terminal repeat fragment from the Epstein-Barr virus (EBVTR) could be truncated without affecting promoter strength or the long-term stability of target gene expression.

Methods

We made a series of deletions in the downstream flanking region of the EEF1A1 gene, and then in its upstream flanking region. The resulting plasmids, which coded for the enhanced green fluorescent protein (eGFP), were tested for the level of eGFP expression in the populations of stably transfected CHO DG44 cells and the stability of eGFP expression in the long-term culture in the absence of selection agents.

Results

It was shown that in the presence of the EBVTR fragment, the entire downstream flanking region of the EEF1A1 gene could be excluded from the plasmid vector. Shortening of the upstream flanking region of the EEF1A1 gene to a length of 2.5 kbp also had no significant effect on the level of eGFP expression or long-term stability. The EBVTR fragment significantly increased expression stability for both the CMV and EEF1A1 promoter-based plasmids, and the expression level drop during the two-month culture was more significant for both CMV promoter-based plasmids.

Conclusion

Target protein expression stability for the truncated plasmid, based on the EEF1A1 gene and EBVTR fragment, is sufficient for common biopharmaceutical applications, making these plasmid vectors a viable alternative to conventional CMV promoter-based vectors.

Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations in mismatch repair genes in methotrexate-resistant HT-29 cells

DHFR gene amplification is commonly present in methotrexate (MTX)-resistant colon cancer cells and acute lymphoblastic leukemia. In this study, we proposed an integrative framework to characterize the amplified region by using a combination of single-molecule real-time sequencing, next-generation optical mapping, and chromosome conformation capture (Hi-C). We identified an amplification unit spanning 11 genes, from the DHFR gene to the ATP6AP1L gene position, with high adjusted interaction frequencies on chromosome 5 (~2.2 Mbp) and a twenty-fold tandemly amplified region, and novel inversions at the start and end positions of the amplified region as well as frameshift insertions in most of the MSH and MLH genes were detected. These mutations might stimulate chromosomal breakage and cause the dysregulation of mismatch repair. Characterizing the tandem gene-amplified unit may be critical for identifying the mechanisms that trigger genomic rearrangements. These findings may provide new insight into the mechanisms underlying the amplification process and the evolution of drug resistance.

Sequencing a large region of DNA containing many surplus copies of genes linked to drug resistance in colon cancer cells may illuminate how these genomic rearrangements arise. Such regions of gene amplification are highly repetitive, making them impossible to sequence using ordinary methods, and little is known about how they are generated. Using advanced methods, Jeong-Sun Seo at Seoul National University Bundang Hospital in South Korea and co-workers sequenced a region of gene amplification in colon cancer cells. The amplified region was approximately 20 times the length of that in healthy cells and contained many copies of an eleven-gene segment, including a gene implicated in drug resistance. The region also contained mutations in chromosomal repair genes which would disrupt repair pathways. These results illuminate the genetic changes that lead to gene amplification and drug resistance in cancer cells.