Distinct gene signatures define the epithelial cell features of mucinous appendiceal neoplasms and pseudomyxoma metastases

Carlos Ayala ¹ Anuja Sathe ² Xiangqi Bai ² Susan Grimes ² Jeanne Shen ³ George Poultsides ¹ Byrne Lee ¹ Hanlee P Ji ^2*

• ¹ Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, United States
• ² Division of Oncology, Department of Medicine, Stanford University, Stanford, United States
• ³ Department of Pathology, School of Medicine, Stanford University, Palo Alto, California, United States

Appendiceal mucinous neoplasms (AMN) are rare tumors of the gastrointestinal tract. They metastasize with widespread abdominal dissemination leading to pseudomyxoma peritonei (PMP), a disease with poor prognosis. There are many questions about the cellular features of origin, differentiation and progression of AMN and PMP. Along these lines, we characterized AMNs, PMPs metastases and matched normal tissues using single-cell RNA-sequencing. We identified previously undescribed cellular features and heterogeneity in AMN and PMP tumors. There were specific gene expression signatures specific to the tumor epithelial cells among the AMN and PMP cells. These signatures included genes indicative of goblet cell differentiation and elevated mucin gene expression. Metastatic PMP cells had a distinct gene expression signature with increased lipid metabolism, inflammatory, JAK-STAT and RAS signaling pathway among others. We observed clonal heterogeneity in a single PMP tumor as well as PMP metastases from the same patient. Our findings were validated with immunohistochemistry, mass spectrometry on malignant ascites from PMP patients and gene expression data from an independent set of PMP tumors.