Comparative proteomic analysis of colorectal cancer stem cells reveals potential biomarkers and altered pathways

Colorectal cancer (CRC) initiating/stem cells (CICs/CSCs) represent a rare tumor subpopulation with self-renewal capacity that drives tumor progression, recurrence, therapeutic resistance, and immune evasion. Despite extensive efforts to define CSCs using surface and functional markers, no universally accepted marker exists for CSC isolation and enrichment. Moreover, the molecular mechanisms underlying CSC-associated phenotypes remain incompletely characterized, highlighting the need for unbiased proteome-wide molecular profiling to better define CSC states and identify candidate biomarkers and therapeutic targets.

CSC-enriched spheroids were generated from two colorectal cancer cell lines (SW620 and HCT-116) using three-dimensional, serum-free culture conditions and compared with their corresponding parental adherent cells. Comparative proteomic profiling was performed using mass spectrometry-based label-free shotgun proteomics. Differentially abundant proteins were analyzed using Ingenuity Pathway Analysis (IPA) to identify overrepresented canonical pathways and predict upstream regulators. Selected differentially abundant proteins and predicted upstream regulators were validated by RT-qPCR and/or Western blotting.

Comparative proteomic profiling showed that CSC-enriched spheroids shared convergent pathway-level alterations despite cell line-specific differences in individual protein abundance. IPA pathway and functional analyses predicted activation of metabolic reprogramming, invasion, and hypoxia adaptation, along with predicted suppression of apoptotic pathways. Notably, HMGCS1, a key mevalonate-pathway enzyme, was strongly upregulated at both mRNA and protein levels in CSCs from both cell lines. MYC, MLXIPL, EGF/EGFR, VEGFA, and HIF-related signaling were among the top predicted upstream regulators shaping these alterations. In addition, altered expression of proteins involved in immunosuppressive signaling was observed in CSC-enriched spheroids, with TGF-β signaling emerging as a prominently activated upstream regulator, potentially contributing to CSC-associated epithelial-mesenchymal transition and immunomodulation.

In summary, this study provides a better understanding of key dysregulated pathways and proteins in CRC CSCs, highlighting potential biomarkers and regulatory programs with relevance to stemness, immune modulation, and therapeutic resistance.