High-throughput profiling of the tumor-associated macrophages in early phases of synchronous metastatic colorectal cancer

Early synchronous colorectal liver metastasis (CRLM) is a rare clinical condition representing only 20% of CRLM cases that is characterized by the simultaneous presence of primary colorectal cancer (CRC) and metastatic liver lesions. Several studies have highlighted unique immunological tumor microenvironments (TME) in primary tumors and metastatic sites, however, the precise immune mechanisms responsible for the immune evasion specifically in the early phases of this disease remain elusive. This complexity largely arises from the diversity observed in immune cell populations infiltrating and surrounding solid tumors in both the colon and liver, precisely in tumor-associated macrophages (TAMs). Herein, using high-throughput 5’ single-cell RNA sequencing and unsupervised learning algorithms, we investigated the transcriptional changes and phenotypic alterations in matched primary CRC, liver metastases, and peripheral blood samples from three patients who underwent simultaneous colon-liver tumor resection (n samples = 8). To preserve tissue-specific traits and identify inter- and intra-tissue similarities and differences, taking in consideration the whole complexity of this disease, we integrated the three tissues with a deep learning stochastic approach (scVI). Our findings distinct tumor-immune microenvironments between the primary tumor and liver metastasis, with an inverse ratio of inflammatory and immunoregulatory TAMs in the colon and liver, respectively, along with significant functional heterogeneity in both tissues. Pseudotime trajectory analysis (Monocle) revealed a unique monocyte-to-macrophage differentiation pathway in the liver, absent in the colon, along with markedly different transcriptional patterns between the two tissues. Importantly, integrating the liver metastasis data with a public healthy liver scRNA-seq (n samples = 5), our study demonstrated that the metastasis alters the physiological transcriptional characteristics of the liver tissue within the tumor, together with the presence of pathologic liver-specific TAM populations. Additionally, functional enrichment pathway analyses (Reactome) showed a different response between TAMs in the colon and liver, with proliferative pathways specifically in the liver. Overall, our results comprehensively characterize TAMs within primary colon tumor and matched liver metastasis, highlighting their pathophysiological role in the early phases of synchronous CRLM. These insights into TAM involvement could be crucial for developing targeted therapeutic strategies to mitigate the progression of CRLM.