Distinct cell states define the developmental trajectories of mucinous appendiceal neoplasms towards pseudomyxoma metastases

Objective Appendiceal mucinous neoplasms (AMN) start in the appendix. Following appendiceal perforation, these tumor metastasize, leading to pseudomyxoma peritonei (PMP) . We characterized the distinct cell types and states of AMN and PMP. Design Single-cell RNA-seq was conducted on 31 samples including AMNs, PMP metastases and a subset of matched normal appendix or omental tissues. We validated the findings with immunohistochemistry, mass spectrometry on malignant ascites from PMP patients and gene expression data from an independent set of 63 PMPs. Results AMNs and PMPs had epithelial tumor cells with goblet features including the elevated expression of mucin genes. Among these tumors, we identified developmental cell states of the epithelium that ranged from progenitor phase to goblet cell differentiation. Metastatic PMP cells had a distinct cell state with gene expression signatures indicative of mTOR and RAS signaling pathways. A series of cancer genes defined this metastatic cell state. Matched PMP metastases from the same patient differed in their expression signatures. The cell state signatures were validated in external datasets containing 63 PMP patients. AMN and PMP tumor microenvironment (TME) contained CD4 T follicular helper-like cells and cytotoxic CD8 T cells. Conclusion AMN and PMP tumors consisted of progenitor epithelial cells that differentiate into goblet cells. PMP cells had a distinct cell state indicative of metastasis. The TME was infiltrated with T cells, suggesting that immunotherapy is a potential treatment. SUMMARY BOX What is already known about this subject? What are the new findings? How might it impact on clinical practice in the foreseeable future? ### Competing Interest Statement The authors have declared no competing interest.