Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

Abstract

In combination with cell intrinsic properties, interactions in the tumor microenvironment modulate therapeutic response. We leveraged high-plex single-cell spatial transcriptomics to dissect the remodeling of multicellular neighborhoods and cell-cell interactions in human pancreatic cancer associated with specific malignant subtypes and neoadjuvant chemotherapy/radiotherapy. We developed Spatially Constrained Optimal Transport Interaction Analysis (SCOTIA), an optimal transport model with a cost function that includes both spatial distance and ligand-receptor gene expression. Our results uncovered a marked change in ligand-receptor interactions between cancer-associated fibroblasts and malignant cells in response to treatment, which was supported by orthogonal datasets, including an ex vivo tumoroid co-culture system. Overall, this study demonstrates that characterization of the tumor microenvironment using high-plex single-cell spatial transcriptomics allows for identification of molecular interactions that may play a role in the emergence of chemoresistance and establishes a translational spatial biology paradigm that can be broadly applied to other malignancies, diseases, and treatments.

Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response via AP1 dichotomy in pancreatic cancer

“…Altogether, this string of insights provides a potential mechanistic foundation for several recent studies that showed a high degree of heterogeneity in the neoplastic and stromal immune compartments in human PDAC, including hybrid/intermediate/co-expressor CLA/BL subtype states that exist in naive and therapy-treated PDAC tumors 10–16,20,36,37 . We propose that extrinsic regional TNF-α plays an essential role in destabilizing CLA neoplastic cell identity by promoting BL cJUN/AP1-mediated transcriptional programs.…”

“…Complementarily, we here show that JUNB/AP1 acts as a counterpart to promote a favorable CLA phenotypic identity in PDAC. Of note, JUNB/AP1-mediated transcriptional programs can also confer tumor-promoting functions in other cancer types [39][40][41] ; JUN/AP1 TFs are highly context dependent and may co-operate for target gene transcription [41][42][43] or oppose one another 44 Altogether, this string of insights provides a potential mechanistic foundation for several recent studies that showed a high degree of heterogeneity in the neoplastic and stromal immune compartments in human PDAC, including hybrid/intermediate/coexpressor CLA/BL subtype states that exist in naive and therapy-treated PDAC tumors [10][11][12][13][14][15][16]20,36,37 . We propose that extrinsic regional TNF-α plays an essential role in destabilizing CLA neoplastic cell identity by promoting BL cJUN/AP1-mediated transcriptional programs.…”

“…1m ). PDAC has been described to show a remarkable level of plasticity in response to extrinsic signals, via microenvironmental stimuli as well as treatment 16,19,21,36,37 . Hence, we assessed the expression of neoplastic JUNB and GATA6 in a set of treatment-naive, neoadjuvant chemotherapy-treated, and chemo-radiation-treated PDAC specimens ( Fig.…”

“…Here, we investigated the role of neoplastic AP1-mediated epigenetic and transcriptional programs in shaping the local inflammatory TiME, which in turn is critical for intratumoral subtype plasticity and PDAC aggressiveness [10][11][12][13][14][15]20,36,37 . We report that AP1 transcription factors (JUNB/AP1 vs. cJUN/AP1) hold a dichotomous role in maintaining both the plasticity and stability of CLA and BL neoplastic cells via intrinsic epigenetic and transcriptional regulation of lineage gene expression as well as extrinsic inflammatory processes.…”

Enhanced Complement Expression in the Tumor Microenvironment Following Neoadjuvant Therapy: Implications for Immunomodulation and Survival in Pancreatic Ductal Adenocarcinoma

“…Single-cell RNA sequencing (scRNA-seq) is a valuable tool for characterizing TME as it provides insights into cellular heterogeneity and molecular subtypes (17,18). Several scRNA-seq studies have explored the PDAC TME, offering valuable insights into this complex ecosystem (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35). However, scRNA-seq techniques lack spatial context, and are susceptible to cell dissociation-associated artifacts.…”