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Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.

ABSTRACT: Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models against this reference map, we reveal strong culture-specific biases in cancer cell transcriptional state representation driven by altered TME signals. We restore expression state heterogeneity by adding back in vivo-relevant factors and show plasticity in culture models. Further, we prove that non-genetic modulation of cell state can strongly influence drug responses, uncovering state-specific vulnerabilities. This work provides a broadly applicable framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity and manipulating cell state to target associated vulnerabilities.

SUBMITTER: Raghavan S

PROVIDER: S-EPMC8822455 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.

Raghavan Srivatsan S Winter Peter S PS Navia Andrew W AW Williams Hannah L HL DenAdel Alan A Lowder Kristen E KE Galvez-Reyes Jennyfer J Kalekar Radha L RL Mulugeta Nolawit N Kapner Kevin S KS Raghavan Manisha S MS Borah Ashir A AA Liu Nuo N Väyrynen Sara A SA Costa Andressa Dias AD Ng Raymond W S RWS Wang Junning J Hill Emma K EK Ragon Dorisanne Y DY Brais Lauren K LK Jaeger Alex M AM Spurr Liam F LF Li Yvonne Y YY Cherniack Andrew D AD Booker Matthew A MA Cohen Elizabeth F EF Tolstorukov Michael Y MY Wakiro Isaac I Rotem Asaf A Johnson Bruce E BE McFarland James M JM Sicinska Ewa T ET Jacks Tyler E TE Sullivan Ryan J RJ Shapiro Geoffrey I GI Clancy Thomas E TE Perez Kimberly K Rubinson Douglas A DA Ng Kimmie K Cleary James M JM Crawford Lorin L Manalis Scott R SR Nowak Jonathan A JA Wolpin Brian M BM Hahn William C WC Aguirre Andrew J AJ Shalek Alex K AK

Cell 20211201 25

Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), but our understanding of their drivers, stability, and relationship to therapeutic response is limited. To examine these attributes systematically, we profiled metastatic biopsies and matched organoid models at single-cell resolution. In vivo, we identify a new intermediate PDAC transcriptional cell state and uncover distinct site- and state-specific tumor microenvironments (TMEs). Benchmarking models ...[more]

PMID: 34890551

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Project description:BackgroundEarly dissemination to distant organs accounts for the dismal prognosis of patients with pancreatic ductal adenocarcinoma (PDAC). Chronic, dysregulated, persistent and unresolved inflammation provides a preferred tumor microenvironment (TME) for tumorigenesis, development, and metastasis. A better understanding of the key regulators that maintain inflammatory TME and the development of predictive biomarkers to identify patients who are most likely to benefit from specific inflammatory-targeted therapies is crucial for advancing personalized cancer treatment.MethodsThis study identified cell-specific expression of CALB2 in human PDAC through single-cell RNA sequencing analysis and assessed its clinicopathological correlations in tissue microarray using multi-color immunofluorescence. Co-culture systems containing cancer-associated fibroblasts (CAFs) and patient-derived organoids (PDOs) in vitro and in vivo were employed to elucidate the effects of CALB2-activated CAFs on PDAC malignancy. Furthermore, CUT&RUN assays, luciferase reporter assays, RNA sequencing, and gain- or loss-of-function assays were used to unravel the molecular mechanisms of CALB2-mediated inflammatory reprogramming and metastasis. Additionally, immunocompetent KPC organoid allograft models were constructed to evaluate CALB2-induced immunosuppression and PDAC metastasis, as well as the efficacy of inflammation-targeted therapy.ResultsCALB2 was highly expressed both in CAFs and cancer cells and correlated with an unfavorable prognosis and immunosuppressive TME in PDAC patients. CALB2 collaborated with hypoxia to activate an inflammatory fibroblast phenotype, which promoted PDAC cell migration and PDO growth in vitro and in vivo. In turn, CALB2-activated CAFs upregulated CALB2 expression in cancer cells through IL6-STAT3 signaling-mediated direct transcription. In cancer cells, CALB2 further activated Ca2+-CXCL14 inflammatory axis to facilitate PDAC metastatic outgrowth and immunosuppression. Genetic or pharmaceutical inhibition of CXCL14 significantly suppressed CALB2-mediated metastatic colonization of PDAC cells in vivo and extended mouse survival.ConclusionsThese findings identify CALB2 as a key regulator of inflammatory reprogramming to promote PDAC metastatic progression. Combination therapy with αCXCL14 monoclonal antibody and gemcitabine emerges as a promising strategy to suppress distant metastasis and improve survival outcomes in PDAC with CALB2 overexpression.

Project description:BackgroundPancreatic ductal adenocarcinoma (PDAC) is a highly fatal, aggressive cancer due to limited response chemotherapy. The tumor microenvironment (TME) has emerged as a key player in the development of chemoresistance and in malignant progression. In this study, we hypothesized that chemotherapy response is predictable by chemotherapy-related cell types and their differentially expressed genes (DEGs).MethodsDEGs of chemoresistance cell types were identified via single cell analysis and Wilcoxon test. A chemotherapy response signature was established using a random forest model and validated with public datasets. Bulk cell fraction was analyzed using BayesPrism algorithms. Log-rank test was used to analyze survival of PDAC patients.ResultsWe found that natural killer (NK) cells, myeloid cells, and erythroid cells were highly infiltrated in chemo-resistant TME. A total of 36 chemoresistance-related DEGs of chemo-resistant cells were identified in chemo-resistant PDAC. Functional enrichment analysis showed that chemoresistance upregulated various inflammation-related pathways, including TGF-β signaling. Based on these features, we constructed a random forest model to predict the response and survival for PDAC patients, which accurately distinguished high-risk and chemoresistant patients with significantly poorer prognosis in both the training and independent validation datasets. Cox regression analysis indicated that predicted labels were an independent prognostic factor in PDAC. Moreover, deconvolution of TME confirmed higher infiltration levels of M2 macrophage and NK cells in predicted chemoresistance. When combined with chemotherapy response related tumor mutations, the model showed excellent ability in predicting chemotherapy response and survival.ConclusionsThe TME was closely associated with the chemotherapy response and prognosis of PDAC. Our TME-based random forest model predicted chemotherapy response with complementary knowledge to the response-related genetic mutations.

Project description:Rationale: The resistance of pancreatic ductal adenocarcinoma (PDAC) to immunotherapies is caused by the immunosuppressive tumor microenvironment (TME) and dense extracellular matrix. Currently, the efficacy of an isolated strategy targeting stromal desmoplasia or immune cells has been met with limited success in the treatment of pancreatic cancer. Oncolytic virus (OV) therapy can remodel the TME and damage tumor cells either by directly killing them or by enhancing the anti-tumor immune response, which holds promise for the treatment of PDAC. This study aimed to investigate the therapeutic effect of OX40L-armed OV on PDAC and to elucidate the underlying mechanisms. Methods: Murine OX40L was inserted into herpes simplex virus-1 (HSV-1) to construct OV-mOX40L. Its expression and function were assessed using reporter cells, cytopathic effect, and immunogenic cell death assays. The efficacy of OV-mOX40L was then evaluated in a KPC syngeneic mouse model. Tumor-infiltrating immune and stromal cells were analyzed using flow cytometry and single-cell RNA sequencing to gain insight into the mechanisms of oncolytic virotherapy. Results: OV-mOX40L treatment delayed tumor growth in KPC tumor-bearing C57BL/6 mice. It also boosted the tumor-infiltrating CD4+ T cell response, mitigated cytotoxic T lymphocyte (CTL) exhaustion, and reduced the number of regulatory T cells. The treatment of OV-mOX40L reprogrammed macrophages and neutrophils to a more pro-inflammatory anti-tumor state. In addition, the number of myofibroblastic cancer-associated fibroblasts (CAF) was reduced after treatment. Based on single-cell sequencing analysis, OV-mOX40L, in combination with anti-IL6 and anti-PD-1, significantly extended the lifespan of PDAC mice. Conclusion: OV-mOX40L converted the immunosuppressive tumor immune microenvironment to a more activated state, remodeled the stromal matrix, and enhanced T cell response. OV-mOX40L significantly prolonged the survival of PDAC mice, either as a monotherapy or in combination with synergistic antibodies. Thus, this study provides a multimodal therapeutic strategy for pancreatic cancer treatment.

Dataset Information

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.

Publications

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.

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