Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance

Abstract

Drug resistance continues to impede the success of cancer treatments, creating a need for experimental model systems that are broad, yet simple, to allow the identification of mechanisms and novel countermeasures applicable to many cancer types. To address these needs, we investigated a set of engineered mammalian cell lines with synthetic gene circuits integrated into their genome that evolved resistance to Puromycin. We identified DNA amplification as the mechanism underlying drug resistance in 4 out of 6 replicate populations. Triplex-forming oligonucleotide (TFO) treatment combined with Puromycin could efficiently suppress the growth of cell populations with DNA amplification. Similar observations in human cancer cell lines suggest that TFOs could be broadly applicable to mitigate drug resistance, one of the major difficulties in treating cancer.

Optimizing a CRISPR-Cas13d gene circuit for tunable target RNA downregulation with minimal collateral RNA cutting

“…Over the past two decades, we have developed and refined negative feedback (NF) based synthetic gene circuits for precise gene expression tuning 22–25 . These gene circuits have been applied in yeast 22 , and then developed into mammalian NF (mNF) gene circuits in Chinese hamster 26,27 , and human cells 23,24,28 , revealing surprising phenotypic effects associated with fine-tuned gene expression changes. For instance, using an mNF system to fine-tune metastasis regulator BACH1 expression, we discovered an unexpected non-monotone relationship between its expression and cellular invasion 28 .…”

TTSBBC: triplex target site biomarkers and barcodes in cancer

“…Common uses of TFO technology includes gene modulation by blocking transcription and gene modification through mutagenesis and homologous recombination ( 2 , 10 , 13 ). TFO binding is site-specific ( 14 ), leading to differential responses in cells with varying TTS abundance which can be exploited to target cancer cells with DNA amplification, a related form of genomic instability ( 15 , 16 ). The site-specific nature of TFO binding to TTSs plays an important role in predicting the triplex formations in the genome.…”