Molecular profiling and specific targeting of gemcitabine-resistant subclones in heterogeneous pancreatic cancer cell populations

Benedikt Färber; Olga Lapshyna; Axel Künstner; Michael Kohl; Thorben Sauer; Kira Bichmann; Benjamin Heckelmann; Jessica Watzelt; Kim Honselmann; Louisa Bolm; Meike Ten Winkel; Hauke Busch; Hendrik Ungefroren; Tobias Keck; Timo Gemoll; Ulrich F Wellner; Rüdiger Braun

doi:10.3389/fonc.2023.1230382

Molecular profiling and specific targeting of gemcitabine-resistant subclones in heterogeneous pancreatic cancer cell populations

Front Oncol. 2023 Aug 31:13:1230382. doi: 10.3389/fonc.2023.1230382. eCollection 2023.

Authors

Benedikt Färber¹, Olga Lapshyna¹, Axel Künstner^{2

3}, Michael Kohl^{2

4}, Thorben Sauer⁴, Kira Bichmann¹, Benjamin Heckelmann¹, Jessica Watzelt¹, Kim Honselmann¹, Louisa Bolm¹, Meike Ten Winkel¹, Hauke Busch^{2

3}, Hendrik Ungefroren^{5

6}, Tobias Keck¹, Timo Gemoll⁴, Ulrich F Wellner¹, Rüdiger Braun¹

Affiliations

¹ Department of Surgery, University Medical Center Schleswig-Holstein, Lübeck, Germany.
² Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
³ Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany.
⁴ Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, University of Lübeck, Lübeck, Germany.
⁵ First Department of Medicine, University Medical Center Schleswig-Holstein, Lübeck, Germany.
⁶ Institute of Pathology, University Medical Center Schleswig-Holstein, Kiel, Germany.

Abstract

Purpose: Chemotherapy is pivotal in the multimodal treatment of pancreatic ductal adenocarcinoma (PDAC). Technical advances unveiled a high degree of inter- and intratumoral heterogeneity. We hypothesized that intratumoral heterogeneity (ITH) impacts response to gemcitabine treatment and demands specific targeting of resistant subclones.

Methods: Using single cell-derived cell lines (SCDCLs) from the classical cell line BxPC3 and the basal-like cell line Panc-1, we addressed the effect of ITH on response to gemcitabine treatment.

Results: Individual SCDCLs of both parental tumor cell populations showed considerable heterogeneity in response to gemcitabine. Unsupervised PCA including the 1,000 most variably expressed genes showed a clustering of the SCDCLs according to their respective sensitivity to gemcitabine treatment for BxPC3, while this was less clear for Panc-1. In BxPC3 SCDCLs, enriched signaling pathways EMT, TNF signaling via NfKB, and IL2STAT5 signaling correlated with more resistant behavior to gemcitabine. In Panc-1 SCDCLs MYC targets V1 and V2 as well as E2F targets were associated with stronger resistance. We used recursive feature elimination for Feature Selection in order to compute sets of proteins that showed strong association with the response to gemcitabine. The optimal protein set calculated for Panc-1 comprised fewer proteins in comparison to the protein set determined for BxPC3. Based on molecular profiles, we could show that the gemcitabine-resistant SCDCLs of both BxPC3 and Panc-1 are more sensitive to the BET inhibitor JQ1 compared to the respective gemcitabine-sensitive SCDCLs.

Conclusion: Our model system of SCDCLs identified gemcitabine-resistant subclones and provides evidence for the critical role of ITH for treatment response in PDAC. We exploited molecular differences as the basis for differential response and used these for more targeted therapy of resistant subclones.

Keywords: chemotherapy; gemcitabine; intratumor heterogeneity; pancreatic cancer; treatment response.

Grants and funding

This work was supported in part by grants from the German Research Foundation (DFG) through the Clinician Scientist School Lübeck (DFG #413535489), the Junior Funding Program of the University of Lübeck, and the Brigitte and Dr. Konstanze Wegener Foundation (project # 81). AK acknowledges computational support from the OMICS compute cluster at the University of Lübeck. BF is grateful for the support from the doctoral scholarship "Lübeck Medicine of Excellence" and TS for the support from the Ad Infinitum Foundation. We acknowledge financial support by Land Schleswig-Holstein within the funding program Open Access Publikationsfonds.