Comparing transcriptomic profiles from seven cell lines to elucidate liver metastatic potential

Abstract

Overview: The liver is a vital organ, performing over 500 functions. Metastasis to the liver can disrupt these functions, resulting in poor prognoses. It is not always clear why liver metastasis arises in one case but not another involving the same cancer type. We sought to understand which transcripts and cellular pathways are dysregulated in cell lines shown to metastasize substantially to the liver in a NOD-Scid-Gamma (NSG) mouse-xenograft model. Cancer cell lines of the same type not observed to metastasize to the liver were used for comparison, reducing cell type-specific changes or general pathways associated with cancer not linked to liver metastasis. Three metastatic versus non-metastatic pairs of diverse origin–Merkel cell, colorectal, and pancreatic carcinomas–as well as a normal fibroblast control were used for deep sequencing and transcriptome analysis with subsequent pathway identification. Results: Dysregulated pathways involve cell adhesion, proliferation, and motility (among others), which are consistent with increased malignant potential in the cell lines that support liver metastasis. In addition, dysregulated peroxisome proliferating activated receptor (PPAR) signaling and lipid metabolic / trafficking pathways are candidates for fostering homing to the liver. A surprise was a significant drop in AGR2 expression in cells favoring liver metastasis, while still remaining elevated relative to normal fibroblast controls. Newer clinical data revealed declining levels of AGR2 correlate with higher grade lesions and poorer prognoses in patients with various cancer types. Decreased expression of FOXA2 similarly correlates with clinical data as a prognostic factor. A drop in FOXA2 expression was observed in cell lines favoring liver metastasis, as well as a cell line generated from an NSG-xenograft liver metastasis, which may also explain the liver site preference of select cancer cell lines. Both genes correlate with PPAR signaling dysregulation and either directly or indirectly link to such pathways. Meanwhile, LOXL2 is lower in the cancer cell lines supporting liver metastasis compared to normal fibroblasts, but is substantially elevated relative to paired cancer cell lines which did not metastasize to the liver. LOXL2 is a gene involved in epithelial-mesenchymal transition (EMT), which is expressed at high levels in both normal and cancer-associated fibroblasts. Conclusions: Using only a normal fibroblast control for comparison, or only comparing cancer cells as separate pairs, would have masked several potential candidate genes and pathways linked to liver metastasis. Our findings correlate well with newer clinical data and reinforce biomarkers of disease progression. The dysregulated genes and pathways highlight potential targets to slow disease progression.

Keywords

• Oncology
• Cancer cell lines
• Liver metastases
• Bioinformatics
• Transcriptomic profiles
• Gene ontology