Single Cell Analysis of Treatment–Resistant Prostate Cancer: Implications of Cell State Changes for Cell Surface Antigen Targeted Therapies
Authors: Zaidi Samir , Park Jooyoung , Chan Joseph M. , Roudier Martine P. , Zhao Jimmy L. , Gopalan Anuradha , Wadosky Kristine M. , Patel Radhika A. , Sayar Erolcan , Karthaus Wouter R. , Kates D. Henry , Chaudhary Ojasvi , Xu Tianhao , Masilionis Ignas , Mazutis Linas , Chaligné Ronan , Obradovic Aleksandar , Linkov Irina , Barlas Afsar , Jungbluth Achim , Rekhtman Natasha , Silber Joachim , Manova–Todorova Katia , Watson Philip A. , True Lawrence D. , Morrissey Colm M. , Scher Howard I. , Rathkopf Dana , Morris Michael J. , Goodrich David W. , Choi Jungmin , Nelson Peter S. , Haffner Michael C. , Sawyers Charles L. 
Published: April 2024

ABSTRACTTargeting cell surface molecules using radioligand and antibody–based therapies has yielded considerable success across cancers. However, it remains unclear how the expression of putative lineage markers, particularly cell surface molecules, varies in the process of lineage plasticity, wherein tumor cells alter their identity and acquire new oncogenic properties. A notable example of lineage plasticity is the transformation of prostate adenocarcinoma (PRAD) to neuroendocrine prostate cancer (NEPC)––a growing resistance mechanism that results in the loss of responsiveness to androgen blockade and portends dismal patient survival. To understand how lineage markers vary across the evolution of lineage plasticity in prostate cancer, we applied single cell analyses to 21 human prostate tumor biopsies and two genetically engineered mouse models, together with tissue microarray analysis (TMA) on 131 tumor samples. Not only did we observe a higher degree of phenotypic heterogeneity in castrate–resistant PRAD and NEPC than previously anticipated, but also found that the expression of molecules targeted therapeutically, namelyPSMA,STEAP1,STEAP2,TROP2, CEACAM5, andDLL3, varied within a subset of gene–regulatory networks (GRNs). We also noted that NEPC and small cell lung cancer (SCLC) subtypes shared a set of GRNs, indicative of conserved biologic pathways that may be exploited therapeutically across tumor types. While this extreme level of transcriptional heterogeneity, particularly in cell surface marker expression, may mitigate the durability of clinical responses to novel antigen–directed therapies, its delineation may yield signatures for patient selection in clinical trials, potentially across distinct cancer types.SIGNIFICANCE STATEMENTTreatment of prostate cancer is rapidly evolving with several promising new drugs targeting different cell surface antigens. Selection of patients most likely to benefit from these therapies requires an understanding of how expression of these cell surface antigens varies across patients and how they change during disease progression, particularly in tumors that undergo lineage plasticity. Using immunohistochemistry and single cell mRNA sequencing, we reveal heterogeneity of cell states across a cohort of advanced disease prostate cancer patients; this heterogeneity is not captured by conventional histology–based designations of adenocarcinoma and neuroendocrine prostate cancer. We show these cell states can be identified by gene regulatory networks that could provide additional diagnostic precision based on their correlation with clinically relevant cell surface antigen expression.