Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models

Abstract

Background The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Here we tested in vivo selection of anti-EGFR SR tumors in CRC patient-derived xenograft (PDX) models as a strategy for a molecular dissection of SR mechanisms. Methods We analyzed 21 KRAS, NRAS, BRAF, and PI3K wildtype CRC patient-derived xenograft (PDX) models for their anti-EGFR sensitivity. Furthermore, 31 anti-EGFR SR tumors were generated via chronic in vivo treatment with cetuximab. A multi-omics approach was employed to address molecular primary and secondary resistance mechanisms. Gene set enrichment analyses were used to uncover SR pathways. Targeted therapy of SR PDX models was applied to validate selected SR pathways. Results In vivo anti-EGFR SR could be established with high efficiency. Chronic anti-EGFR treatment of CRC PDX tumors induced parallel evolution of multiple resistant lesions with independent molecular SR mechanisms. Mutations in driver genes explained SR development in a subgroup of CRC PDX models, only. Transcriptional reprogramming inducing anti-EGFR SR was discovered as a common mechanism in CRC PDX models frequently leading to RAS signaling pathway activation. We identified cAMP and STAT3 signaling activation, as well as paracrine and autocrine signaling via growth factors as novel anti-EGFR secondary resistance mechanisms. Secondary resistant xenograft tumors could successfully be treated by addressing identified transcriptional changes by tailored targeted therapies. Conclusions Our study demonstrates that SR PDX tumors provide a unique platform to study molecular SR mechanisms and allow testing of multiple treatments for efficient targeting of SR mechanisms, not possible in the patient. Importantly, it suggests that the development of anti-EGFR tolerant cells via transcriptional reprogramming as a cause of anti-EGFR SR in CRC is likely more prevalent than previously anticipated. It emphasizes the need for analyses of SR tumor tissues at a multi-omics level for a comprehensive molecular understanding of anti-EGFR SR in CRC.

Lasting response by vertical inhibition with cetuximab and trametinib in KRAS‐mutated colorectal cancer patient‐derived xenografts

“…Gene set enrichment analyses software [25] (V4.3.2) was provided by the Broad Institute of the Massachusetts Institute of Technology and Harvard University (http://www.broad.mit.edu/gsea/). Compared to a previous work [10], this time the hallmark gene sets (V2023.1) were used with default parameters of the GSEA software package; gene set permutation was used. Gene sets with FDR q ‐val ≤ 0.05 were considered appropriate.…”

Pyroptosis-Mediated Molecular Subtypes and Tumor Microenvironment Infiltration Characterization in Colon Cancer

“…RNA-sequencing data and clinical information were obtained from the GEO and TCGA databases. Overall, five eligible CC cohorts (GSE14333, GSE143985, GSE38832, GSE39582, and GSE140973) ( Jorissen et al, 2009 ; Marisa et al, 2013 ; Tripathi et al, 2014 ; Shinto et al, 2020 ; Vangala et al, 2021 ) and The Cancer Genome Atlas—Colon Adenocarcinoma (TCGA-COAD) were included. The primary endpoint was recurrence of the tumor or death, and patients without survival information were removed from further analysis.…”

Liquid biopsy to detect resistance mutations against anti-epidermal growth factor receptor therapy in metastatic colorectal cancer

“…Although resistance mutations in KRAS are most frequent, mutations or amplification of other genes in the EGFR pathway, such as ERBB2 , MEK , BRAF, and MAP2K, could also cause or contribute to anti-EGFR treatment resistance (Figure 1 ). Basic studies using patient-derived xenograft models, where the acquisition of natural resistance by chronic cetuximab exposure is reproduced, have reported the emergence of driver mutations in EGFR , KRAS , MEK1 , and MEK2 [ 56 ]. These results have been documented in real-world clinical settings, where patients were prospectively followed up by liquid biopsy.…”