An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer.

Daniela Gerovska,Kai Stühler,Joana Márquez,Gorka Larrinaga,María Armesto,Patricia García Gallastegi,Gereon Poschmann,Charles H Lawrie,Abdel-Majid Khatib,Jon Danel Solano-Iturri,Marcos J Araúzo-Bravo,Iker Badiola

doi:10.3390/cancers12092380

Abstract

(1) Background & Aims: The roles of different cells in the tumor microenvironment (TME) are critical to the metastatic process. The phenotypic transformation of the liver cells is one of the most important stages of the hepatic metastasis progression of colorectal cancer (CRC). Our aim was to identify the major molecules (i.e., genes, miRNAs and proteins) involved in this process. (2) Methods: We isolated and performed whole-genome analysis of gene, miRNA, and protein expression in three types of liver cells (Ito cells, Kupffer cells, and liver sinusoidal endothelial cells) from the TME of a murine model of CRC liver metastasis. We selected the statistically significant differentially expressed molecules using the Student’s t-test with Benjamini-Hochberg correction and performed functional statistically-significant enrichment analysis of differentially expressed molecules with hypergeometric distribution using the curated collection of molecular signatures, MSigDB. To build a gene-miRNA-protein network centered in Brca1, we developed a software package (miRDiana) that collects miRNA targets from the union of the TargetScan, MicroCosm, mirTarBase, and miRWalk databases. This was used to search for miRNAs targeting Brca1. We validated the most relevant miRNAs with real-time quantitative PCR. To investigate BRCA1 protein expression, we built tissue microarrays (TMAs) from hepatic metastases of 34 CRC patients. (3) Results: Using integrated omics analyses, we observed that the Brca1 gene is among the twenty transcripts simultaneously up-regulated in all three types of TME liver cells during metastasis. Further analysis revealed that Brca1 is the last BRCA1-associated genome surveillance complex (BASC) gene activated in the TME. We confirmed this finding in human reanalyzing transcriptomics datasets from 184 patients from non-tumor colorectal tissue, primary colorectal tumor and colorectal liver metastasis of the GEO database. We found that the most probable sequence of cell activation during metastasis is Endothelial→Ito→Kupffer. Immunohistochemical analysis of human liver metastases showed the BRCA1 protein was co-localized in Ito, Kupffer, and endothelial cells in 81.8% of early or synchronous metastases. However, in the greater part of the metachronous liver metastases, this protein was not expressed in any of these TME cells. (4) Conclusions: These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer, and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential TME biomarker.

Highlights

Colorectal cancer (CRC) is the third most common cancer amongst men in developed countries and the second most common amongst women [1]
(4) Conclusions: These results suggest a possible role of the co-expression of BRCA1 in Ito, Kupffer, and sinusoidal endothelial cells in the early occurrence of CRC liver metastases, and point to BRCA1 as a potential tumor microenvironment (TME) biomarker
The treatment of liver metastases focused on fighting the tumor cells that had acquired metastatic capabilities, but this trend has been altered to some extent thanks to the findings related to the tumor microenvironment (TME) rationale [2], based on the “seed and soil” theory [3]

Summary

Introduction

Colorectal cancer (CRC) is the third most common cancer amongst men in developed countries and the second most common amongst women [1]. Most CRCs occur on an existing polyp in the lining of the colon or rectum, which evolves into a malignant tumor. Malignant tumor cells enter the bloodstream and metastasize preferentially in the liver, which accounts for over 70% of metastatic. The treatment of liver metastases focused on fighting the tumor cells that had acquired metastatic capabilities, but this trend has been altered to some extent thanks to the findings related to the tumor microenvironment (TME) rationale [2], based on the “seed and soil” theory [3]. Cancer cells secrete molecular signals to the environment and change the phenotype of the surrounding cells, creating new supporting tumor-survival and growth conditions [4]

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