Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Background Despite major advances in the development of targeted therapies, precision (immuno)oncology approaches for patients with colorectal cancer continue to lag behind other solid cancers. Functional precision oncology – a strategy that is based on perturbing primary tumor cells from cancer patients with drugs – could provide an alternate road forward to personalize treatment. Methods We extend here the functional precision oncology paradigm to measuring phosphoproteome landscapes using patient-derived organoids (PDOs). We first employed steady-state multi-omics (exome sequencing, RNA sequencing, and proteomics) and single-cell characterization of the PDOs. The PDOs were then perturbed with kinase inhibitors (MEKi, PI3Ki, mTORi, TBKi, BRAFi, and TAKi), and large-scale phosphoproteomics profiling using data-independent acquisition was carried out. Further, we used imaging mass-cytometry-based single-cell proteomic profiling of the primary tumors to characterize cellular composition of the tumor-microenvironment (TME) and to quantify heterocellular signaling crosstalk. Results We show that kinase inhibitors induce profound off-target effects resulting in a crosstalk with oncogenic and immune-related pathways. Reconstruction of the topologies of the kinase networks revealed that the patient-specific rewiring of the central EGFR-RAS-MAPK network is unaffected by mutations. Moreover, we show non-genetic heterogeneity of the PDOs and patient- and inhibitor-specific upregulation of stemness and differentiation genes by kinase inhibitors. We complemented our functional profiling by spatial proteomics profiling of the primary tumors using imaging mass cytometry. We quantify spatial heterocellular crosstalk and tumor-immune cell interactions, showing an avoidance of PD1+ immune cells and PD-L1+ tumor cells. Conclusions Collectively, we provide a multi-modal framework for inferring tumor cell intrinsic signaling and external signaling from the TME to inform precision (immuno)-oncology in colorectal cancer.

Authors 29

1. Christina Plattner

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

2. Giorgia Lamberti

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

3. Peter Blattmann

   ETH Zurich · Institute for Molecular Systems Biology

   Affiliation as printed

   Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland

4. Alexander Kirchmair

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

5. Dietmar Rieder

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

6. Zuzana Loncová

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

7. Gregor Sturm

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

8. Stefan J. Scheidl

   Innsbruck Medical University · Universität Innsbruck

   Affiliation as printed

   Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Austria

9. Marieke E. Ijsselsteijn Aachen Department of Pathology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands

10. Georgios Fotakis

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

11. Asma Noureen

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

12. Rebecca Lisandrelli

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

13. Nina Böck

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

14. Niloofar Nemati

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

15. Anne Krogsdam

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

16. Sophia Daum

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

17. Francesca Finotello

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria

18. Antonios Somarakis Aachen Department of Radiology, Leiden University Medical Center

    Leiden University Medical Center

    Affiliation as printed

    Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands

19. Alexander Schäfer

    ETH Zurich · Institute for Molecular Systems Biology

    Affiliation as printed

    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland

20. Doris Wilflingseder

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, Austria

21. Miguel Gonzalez Acera

    Friedrich-Alexander-Universität Erlangen-Nürnberg

    Affiliation as printed

    Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany

22. Dietmar Öfner

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Austria

23. Lukas Alfons Huber

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Cell Biology, Medical University of Innsbruck, Austria

24. Hans C. Clevers

    Hubrecht Institute for Developmental Biology and Stem Cell Research

    Affiliation as printed

    Hubrecht Institute, Utrecht, The Netherlands

25. Henner F. Farin

    Goethe University Frankfurt · Georg Speyer Haus · Frankfurt Cancer Institute · Deutsches Konsortium für Translationale Krebsforschung

    Affiliation as printed

    Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany

    German Cancer Consortium (DKTK), Heidelberg, Germany

    Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus Frankfurt/Main, Germany

26. Florian R. Greten

    Goethe University Frankfurt · Georg Speyer Haus · Frankfurt Cancer Institute · Deutsches Konsortium für Translationale Krebsforschung

    Affiliation as printed

    Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany

    German Cancer Consortium (DKTK), Heidelberg, Germany

    Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus Frankfurt/Main, Germany

27. Ruedi Abersold

    ETH Zurich · Institute for Molecular Systems Biology

    Affiliation as printed

    Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland

28. Noel F.C.C. de Miranda Aachen Department of Pathology, Leiden University Medical Center

    Leiden University Medical Center

    Affiliation as printed

    Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands

29. Zlatko Trajanoski corresponding

    Innsbruck Medical University · Universität Innsbruck

    Affiliation as printed

    Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Austria