Temporally resolved proteomics identifies nidogen-2 as a co-target in pancreatic cancer that modulates fibrosis and therapeutic efficacy

Pancreatic ductal adenocarcinoma (PDAC) is characterized by increasing fibrosis, which can enhance tumor progression and spread. Here, we undertook an unbiased temporal assessment of the matrisome of the highly-metastatic KPC and poorly-metastatic KPflC genetically engineered mouse models of pancreatic cancer using mass spectrometry proteomics. Our assessment at early-, mid- and late-stage disease reveals an increased abundance of nidogen-2 (NID2) in the KPC model compared to KPflC, with further validation showing that NID2 is primarily expressed by cancer-associated fibroblasts (CAFs). Using biomechanical assessments, second harmonic generation multiphoton imaging and Picrosirius Red staining with birefringence analysis, we show that NID2 reduction by CRISPR interference (CRISPRi) in CAFs reduces stiffness and fibrosis, leading to impaired cancer cell invasion. Intravital imaging with Quantum Dots exhibited improved vascular patency in live NID2-depleted tumors, with enhanced response to gemcitabine/Abraxane (nab-paclitaxel) chemotherapy. In orthotopic models, mice bearing NID2 CRISPRi tumors had significantly reduced liver metastasis and increased survival, highlighting NID2 as a potential new target in PDAC. Overall design: KPC CAF cells (mt-CAF; Vennin et al 2019 Nature Communications DOI: 10.1038/s41467-019-10968-6) were genetically modified via CRISPR inactivation (CRISPRi). There are three cell lines: 1) KPC CAF GFP-1 KRAB, with gRNA targeting GFP-1 as non-targeting control, 2) KPC CAF B500 NID2 KRAB, with gRNA targeting the NID2 gene, 3) KPC CAF C500 NID2 KRAB, w gRNA targeting NID2 gene. RNA sequencing was performed on these 3 different cells in triplicate.