Spatial drivers and pre-cancer populations collaborate with the microenvironment in untreated and chemo-resistant pancreatic cancer
Authors: Zhou Daniel Cui , Jayasinghe Reyka G. , Herndon John M. , Storrs Erik , Mo Chia-Kuei , Wu Yige , Fulton Robert S. , Wyczalkowski Matthew A. , Fronick Catrina C. , Fulton Lucinda A. , Thammavong Lisa , Sato Kazuhito , Zhu Houxiang , Sun Hua , Wang Liang-Bo , Li Yize , Zuo Chong , McMichael Joshua F. , Davies Sherri R. , Appelbaum Elizabeth L. , Robbins Keenan J. , Chasnoff Sara E. , Yang Xiaolu , Liu Ruiyang , Reeb Ashley N. , Wendl Michael C. , Oh Clara , Serasanambati Mamatha , Lal Preet , Varghese Rajees , Mashl R. Jay , Ponce Jennifer , Terekhanova Nadezhda V. , Al Deen Nataly Naser , Yao Lijun , Wang Fang , Chen Lijun , Schnaubelt Michael , Puram Sidharth V. , Kim Albert H. , Song Sheng-Kwei , Shoghi Kooresh I. , Ju Tao , Hawkins William G. , Chen Ken , Chatterjee Deyali , Zhang Hui , Chheda Milan G. , Achilefu Samuel , DeNardo David G. , Oh Stephen T. , Chen Feng , Gillanders William E. , Fields Ryan C. , Ding Li 
Published: January 2021

Pancreatic Ductal Adenocarcinoma (PDAC) is a lethal disease with limited treatment options and poor survival. We studied 73 samples from 21 patients (7 treatment-naïve and 14 treated with neoadjuvant regimens), analyzing distinct spatial units and performing bulk proteogenomics, single cell sequencing, and cellular imaging. Spatial drivers, including mutantKRAS,SMAD4, andGNAQ,were associated with differential phosphosignaling and metabolic responses compared to wild type. Single cell subtyping discovered 12 of 21 tumors with mixed basal and classical features. Trefoil factor family members were upregulated in classical populations, while the basal populations showed enhanced expression of mesenchymal genes, includingVIMandIGTB1. Acinar-ductal metaplasia (ADM) populations, present in 95% of patients, with 46% reduction of driver mutation fractions compared to tumor populations, exhibited suppressive and oncogenic features linked to morphologic states. We identified coordinated expression of TIGIT in exhausted and regulatory T cells and Nectin receptor expression in tumor cells. Higher expression of angiogenic and stress response genes in dendritic cells compared to tumor cells suggests they have a pro-tumorigenic role in remodeling the microenvironment. Treated samples contain a three-fold enrichment of inflammatory CAFs when compared to untreated samples, while other CAF subtypes remain similar. A subset of tumor and/or ADM-specific biomarkers showed differential expression between treatment groups, and several known drug targets displayed potential cross-cell type reactivities. This resolution that spatially defined single cell omics provides reveals the diversity of tumor and microenvironment populations in PDAC. Such understanding may lead to more optimal treatment regimens for patients with this devastating disease.

HIGHLIGHTS

Acinar-ductal metaplasia (ADM) cells represent a genetic and morphologic transition state between acinar and tumor cells.

Inflammatory cancer associated fibroblasts (iCAFs) are a major component of the PDAC TME and are significantly higher in treated samples

Receptor-ligand analysis reveals tumor cell-TME interactions through NECTIN4-TIGIT

Tumor and ADM cell proteogenomics differ between treated and untreated samples, with unique and shared potential drug targets