December 16, 2019

A new druggable step in the gene expression pathway

Thanks to their expertise in single-molecule imaging of RNAs, researchers from the group of Jeff Chao at the FMI helped to reveal the biological mechanism of a small molecule that restricts Ewing’s sarcoma cell growth. The study - published in Nature Chemical Biology - is further evidence that each step of the gene expression pathway may be druggable, and a great example of a Novartis-FMI collaboration.

Nearly twenty years ago, researchers became interested in a small molecule, called JTE-607, which seemed to play a role in inflammation and have a negative effect on acute myeloid leukemia (AML) cell lines. Despite the compound being tested in various preclinical disease models, its biological target and mode of action remained unknown.

Employing a phenotypic screening approach, a group of researchers at the Novartis Institutes for BioMedical Research (NIBR) led by Nathan Ross, Felix Lohmann, and Rohan Beckwith discovered that in addition to certain forms of AML, Ewing’s sarcoma cell lines were sensitive to JTE-607. This led to a comprehensive target identification effort that identified CPSF3 as the molecular target of JTE-607. CPSF3 is an enzyme that is critical for the processing of pre-mRNAs into mature transcripts.

The beginning of the collaboration with the FMI
To further their understanding of the underlying mode of action, the NIBR team needed a cell-based assay that would allow direct assessment of JTE-607's inhibition of CPSF3. At a NIBR-FMI Epigenetics retreat in Lisbon in 2015, Ross and Lohmann saw the single mRNA imaging tools being pioneered in the lab of Jeff Chao at the FMI and realized that these techniques were ideally suited for characterizing the function of JTE-607 in cells.

"When I started at the FMI, I had no idea of the breadth of research being pursued within NIBR and it was exciting to find out that they had really exciting projects related to RNA biology. I think this study highlights how unbiased phenotypic screens can uncover really exciting and unexpected biology," says Chao.

Using single-molecule fluorescent microscopy, the Chao lab monitored the fate of mRNAs in Ewing’s sarcoma cells where CPSF3 was inhibited by JTE-607. The researchers observed that certain mRNA transcripts accumulated in the nucleus at the site of their transcription. They also revealed that the aberrant RNA processing caused by JTE-607 resulted in the formation of nuclear R-loops (three-stranded DNA-RNA hybrid structures). This negatively affects the expression of key proteins for these cancer cells and ultimately leads to cell death. "We demonstrated that the pharmacological targeting of CPSF3 has an effect on the pre-mRNA processing and in the end the viability of Ewing’s sarcoma cells, thereby offering a potential entry point for therapeutic intervention," says Chao. "Generally, this works illustrates the impact of small molecules on modulating basic RNA processes in disease. It is becoming increasingly clear that all steps of the gene expression pathway, even the ones thought to be lethal for all cells, may be druggable."

NIBR's Felix Lohmann highlights the importance of the collaboration: "The contribution of the Chao group provided key mechanistic insights that were instrumental in bringing the study full circle. In addition to the technology and expertise that enabled characterizing JTE-607's effect in cells, Jeff connected us to Prof. Lori Passmore at the MRC in Cambridge who provided a critical piece of evidence in formally proving that JTE-607 inhibits CPSF3 endonuclease activity. This is a perfect example of a Novartis-FMI collaboration: we each bring our different strengths to the table and combine them to solve an important biological problem."

Original publication:
Ross, N.T., Lohmann, F., Carbonneau, S. et al. CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing’s sarcoma Nat Chem Biol (2019) doi:10.1038/s41589-019-0424-1

FMI A673 cells treated with JTE-607 have increased nucleoplasmic R-loop formation.

"This works illustrates the impact of small molecules on modulating basic RNA processes in disease."
Jeff Chao

"The contribution of the Chao group provided key mechanistic insights that were instrumental in bringing the study full circle."
Felix Lohmann