Targeting MXD1 sensitises pancreatic cancer to trametinib

Abstract

Background The resistance of pancreatic ductal adenocarcinoma (PDAC) to trametinib therapy limits its clinical use. However, the molecular mechanisms underlying trametinib resistance in PDAC remain unclear. Objective We aimed to illustrate the mechanisms of resistance to trametinib in PDAC and identify trametinib resistance-associated druggable targets, thus improving the treatment efficacy of trametinib-resistant PDAC. Design We established patient-derived xenograft (PDX) models and primary cell lines to conduct functional experiments. We also applied single-cell RNA sequencing, Assay for Transposase-accessible Chromatin with sequencing and Cleavage Under Targets and Tagmentation sequencing to explore the relevant molecular mechanism. Results We have identified a cancer cell subpopulation featured by hyperactivated viral mimicry response in trametinib-resistant PDXs. We have demonstrated that trametinib treatment of PDAC PDXs induces expression of transcription factor MAX dimerisation protein 1 (MXD1), which acts as a cofactor of histone methyltransferase mixed lineage leukaemia 1 to increased H3K4 trimethylation in transposable element (TE) loci, enhancing chromatin accessibility and thus the transcription of TEs. Mechanistically, enhanced transcription of TEs produces excessive double-stranded RNAs, leading to the activation of viral mimicry response and downstream oncogenic interferon-stimulated genes. Inhibiting MXD1 expression can recover the drug vulnerability of trametinib-resistant PDAC cells to trametinib. Conclusions Our study has discovered an important mechanism for trametinib resistance and identified MXD1 as a druggable target in treatment of trametinib-resistant PDAC. Data are available on reasonable request. The raw data of the ATAC-seq and CUT & Tag-seq have been deposited in the Gene Expression Omnibus under accession code GSE253341. The raw data of scRNA-seq and RNA-seq have been deposited in the Genome Sequence Archive in BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences under accession number CRA014564 and HRA009296, respectively. The transcriptomic data and clinical information of the TCGA PAAD cohort and GTEx pancreas cohort were downloaded from the UCSC Xena data portal (). The gene boundaries were defined using the GENCODE annotations and the repeat boundaries were defined using the GTF file obtained from the Hammell lab website (downloaded from [https://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE\_GTF/GRCh38\_GENCODE\_rmsk\_TE.gtf.gz][1]). All custom codes used to generate the data in this study are available uponon reasonable request. [1]: https://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/GRCh38_GENCODE_rmsk_TE.gtf.gz