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Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors

View ORCID ProfileFredrik Salmén, View ORCID ProfileSanja Vickovic, Ludvig Larsson, Linnea Stenbeck, View ORCID ProfileJohan Vallon-Christersson, View ORCID ProfileAnna Ehinger, View ORCID ProfileJari Häkkinen, Åke Borg, View ORCID ProfileJonas Frisén, View ORCID ProfilePatrik L Ståhl, View ORCID ProfileJoakim Lundeberg
doi: https://doi.org/10.1101/358937
Fredrik Salmén
1Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
2Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
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Sanja Vickovic
1Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
6Equal contribution
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Ludvig Larsson
1Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
6Equal contribution
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Linnea Stenbeck
1Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
6Equal contribution
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Johan Vallon-Christersson
3Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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Anna Ehinger
3Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
4Department of Pathology and Cytology, Blekinge County Hospital, Karlskrona, Sweden
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Jari Häkkinen
3Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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Åke Borg
3Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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Jonas Frisén
5Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Patrik L Ståhl
1Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
5Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Joakim Lundeberg
1Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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  • ORCID record for Joakim Lundeberg
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Abstract

The comprehensive analysis of tumor tissue heterogeneity is crucial for determining specific disease states and establishing suitable treatment regimes. Here, we analyze tumor tissue sections from ten patients diagnosed with HER2+ breast cancer. We obtain and analyze multidimensional, genome-wide transcriptomics data to resolve spatial immune cell distribution and identity within the tissue sections. Furthermore, we determine the extent of immune cell infiltration in different regions of the tumor tissue, including invasive cancer regions. We combine cross-sectioning and computational alignment to build three-dimensional images of the transcriptional landscape of the tumor and its microenvironment. The three-dimensional data clearly demonstrates the heterogeneous nature of tumor-immune interactions and reveal interpatient differences in immune cell infiltration patterns. Our study shows the potential for an improved stratification and description of the tumor-immune interplay, which is likely to be essential in treatment decisions.

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Posted June 30, 2018.
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Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Fredrik Salmén, Sanja Vickovic, Ludvig Larsson, Linnea Stenbeck, Johan Vallon-Christersson, Anna Ehinger, Jari Häkkinen, Åke Borg, Jonas Frisén, Patrik L Ståhl, Joakim Lundeberg
bioRxiv 358937; doi: https://doi.org/10.1101/358937
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Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Fredrik Salmén, Sanja Vickovic, Ludvig Larsson, Linnea Stenbeck, Johan Vallon-Christersson, Anna Ehinger, Jari Häkkinen, Åke Borg, Jonas Frisén, Patrik L Ståhl, Joakim Lundeberg
bioRxiv 358937; doi: https://doi.org/10.1101/358937

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