Single-cell heterogeneity of EGFR and CDK4 co-amplification is linked to immune infiltration in glioblastoma
Kacper A. Walentynowicz,
Dalit Engelhardt,
Simona Cristea,
Shreya Yadav,
Ugoma Onubogu,
Roberto Salatino,
Melanie Maerken,
Cristina Vincentelli,
Aashna Jhaveri,
Jacob Geisberg,
Thomas O. McDonald,
Franziska Michor,
Michalina Janiszewska
Affiliations
Kacper A. Walentynowicz
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
Dalit Engelhardt
Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
Simona Cristea
Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Medical Oncology, Harvard Medical School, Boston, MA, USA
Shreya Yadav
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
Ugoma Onubogu
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
Roberto Salatino
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
Melanie Maerken
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
Cristina Vincentelli
Department of Pathology, Mount Sinai Medical Center, Miami Beach, FL, USA
Aashna Jhaveri
Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
Jacob Geisberg
Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
Thomas O. McDonald
Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
Franziska Michor
Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Ludwig Center at Harvard, Boston, MA, USA; Corresponding author
Michalina Janiszewska
Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA; Corresponding author
Summary: Glioblastoma (GBM) is the most aggressive brain tumor, with a median survival of ∼15 months. Targeted approaches have not been successful in this tumor type due to the large extent of intratumor heterogeneity. Mosaic amplification of oncogenes suggests that multiple genetically distinct clones are present in each tumor. To uncover the relationships between genetically diverse subpopulations of GBM cells and their native tumor microenvironment, we employ highly multiplexed spatial protein profiling coupled with single-cell spatial mapping of fluorescence in situ hybridization (FISH) for EGFR, CDK4, and PDGFRA. Single-cell FISH analysis of a total of 35,843 single nuclei reveals that tumors in which amplifications of EGFR and CDK4 more frequently co-occur in the same cell exhibit higher infiltration of CD163+ immunosuppressive macrophages. Our results suggest that high-throughput assessment of genomic alterations at the single-cell level could provide a measure for predicting the immune state of GBM.
