Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data

Göran Landberg; Emma Jonasson; Anna Gustafsson; Paul Fitzpatrick; Pauline Isakson; Joakim Karlsson; Erik Larsson; Andreas Svanström; Svanheidur Rafnsdottir; Emma Persson; Daniel Andersson; Jennifer Rosendahl; Sarunas Petronis; Parmida Ranji; Pernilla Gregersson; Ylva Magnusson; Joakim Håkansson; Anders Ståhlberg

doi:10.1016/j.dib.2020.105860

Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data

Data Brief. 2020 Jun 16:31:105860. doi: 10.1016/j.dib.2020.105860. eCollection 2020 Aug.

Authors

Göran Landberg¹, Emma Jonasson¹, Anna Gustafsson¹, Paul Fitzpatrick¹, Pauline Isakson¹, Joakim Karlsson², Erik Larsson², Andreas Svanström¹, Svanheidur Rafnsdottir¹, Emma Persson¹, Daniel Andersson¹, Jennifer Rosendahl³, Sarunas Petronis³, Parmida Ranji¹, Pernilla Gregersson¹, Ylva Magnusson¹, Joakim Håkansson³, Anders Ståhlberg^{1

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Affiliations

¹ Department of Laboratory medicine, Institute of Biomedicine, Sahlgrenska Academy, Sahlgrenska Cancer Center, University of Gothenburg, SE-41390 Gothenburg, Sweden.
² Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-41390 Gothenburg, Sweden.
³ RISE, Research Institutes of Sweden, Bioscience and Materials - Medical Device Technology, SE- 50115 Borås, Sweden.
⁴ Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-41390 Gothenburg, Sweden.
⁵ Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, SE-41390 Gothenburg, Sweden.

Abstract

Patient-derived scaffolds (PDSs) generated from primary breast cancer tumors can be used to model the tumor microenvironment in vitro. Patient-derived scaffolds are generated by repeated detergent washing, removing all cells. Here, we analyzed the protein composition of 15 decellularized PDSs using liquid chromatography-mass spectrometry/mass spectrometry. One hundred forty-three proteins were detected and their relative abundance was calculated using a reference sample generated from all PDSs. We performed heatmap analysis of all the detected proteins to display their expression patterns across different PDSs together with pathway enrichment analysis to reveal which processes that were connected to PDS protein composition. This protein dataset together with clinical information is useful to investigators studying the microenvironment of breast cancers. Further, after repopulating PDSs with either MCF7 or MDA-MB-231 cells, we quantified their gene expression profiles using RNA sequencing. These data were also compared to cells cultured in conventional 2D conditions, as well as to cells cultured as xenografts in immune-deficient mice. We investigated the overlap of genes regulated between these different culture conditions and performed pathway enrichment analysis of genes regulated by both PDS and xenograft cultures compared to 2D in both cell lines to describe common processes associated with both culture conditions. Apart from our described analyses of these systems, these data are useful when comparing different experimental model systems. Downstream data analyses and interpretations can be found in the research article "Patient-derived scaffolds uncover breast cancer promoting properties of the microenvironment" [1].

Keywords: 3d cell culture; Breast cancer; Extracellular matrix; Liquid chromatography-mass spectrometry/mass spectrometry; Patient-derived scaffolds; RNA sequencing.