A RAS-Independent Biomarker Panel to Reliably Predict Response to MEK Inhibition in Colorectal Cancer

Abstract

Background: In colorectal cancer (CRC), mutations of genes associated with the TGF-β/BMP signaling pathway, particularly affecting SMAD4, are known to correlate with decreased overall survival and it is assumed that this signaling axis plays a key role in chemoresistance. Methods: Using CRISPR technology on syngeneic patient-derived organoids (PDOs), we investigated the role of a loss-of-function of SMAD4 in sensitivity to MEK-inhibitors. CRISPR-engineered SMAD4R361H PDOs were subjected to drug screening, RNA-Sequencing, and multiplex protein profiling (DigiWest®). Initial observations were validated on an additional set of 62 PDOs with known mutational status. Results: We show that loss-of-function of SMAD4 renders PDOs sensitive to MEK-inhibitors. Multiomics analyses indicate that disruption of the BMP branch within the TGF-β/BMP pathway is the pivotal mechanism of increased drug sensitivity. Further investigation led to the identification of the SFAB-signature (SMAD4, FBXW7, ARID1A, or BMPR2), coherently predicting sensitivity towards MEK-inhibitors, independent of both RAS and BRAF status. Conclusion: We identified a novel mutational signature that reliably predicts sensitivity towards MEK-inhibitors, regardless of the RAS and BRAF status. This finding poses a significant step towards better-tailored cancer therapies guided by the use of molecular biomarkers.

Human patient derived organoids: an emerging precision medicine model for gastrointestinal cancer research

“…In 2021, Boos SL et al further demonstrated that metastatic CRC PDOs introduced by KRASG12D are an ideal platform to model chemotherapy tolerance ex vivo and AURKA was found to be a therapeutic target in liver metastatic CRC ( Boos et al, 2022 ). Besides, the SMAD4 ( Pfohl et al, 2022 ) mutation and FGFR1 and OXTR ( Tung et al, 2021 ) mutations were knocked out using CRIPSR/CAS9 technology in colon cancer PDOs for reversing drug resistance. Using an organoid platform based on CRISPR/Cas9 knockout technology, Seino T et al found that GATA6 expression regulated Wnt niche independence, which was mainly acquired non-genetically through mutations of driver genes (KRASG12V, CDKN2A, TP53, and SMAD4) during pancreas tumorigenesis ( Seino et al, 2018 ).…”

Multidrug resistance in the standardized treatment of colon cancer harboring a rare fibrosarcoma B-type (BRAF) p.N581I mutation: a case report

“…CRC is the third most diagnosed cancer in the world, and the main cause of death is metastases (1). CRC can be classified into different subtypes, which are characterized by specific molecular and morphological alterations (2).…”