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Caruso FP, Garofano L, D'Angelo F, Yu K, Tang F, Yuan J, Zhang J, Cerulo L, Pagnotta SM, Bedognetti D, Sims PA, Suvà M, Su XD, Lasorella A, Iavarone A, Ceccarelli M. A map of tumor-host interactions in glioma at single-cell resolution. Gigascience 2020; 9:giaa109. [PMID: 33155039 PMCID: PMC7645027 DOI: 10.1093/gigascience/giaa109] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between immune cells and cancer cells is of fundamental importance for the identification of immuno-oncology therapeutic targets. RESULTS We present a novel method, single-cell Tumor-Host Interaction tool (scTHI), to identify significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. We apply our approach to uncover the ligand-receptor interactions in glioma using 6 publicly available human glioma datasets encompassing 57,060 gene expression profiles from 71 patients. By leveraging this large-scale collection we show that unexpected cross-talk partners are highly conserved across different datasets in the majority of the tumor samples. This suggests that shared cross-talk mechanisms exist in glioma. CONCLUSIONS Our results provide a complete map of the active tumor-host interaction pairs in glioma that can be therapeutically exploited to reduce the immunosuppressive action of the microenvironment in brain tumor.
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Affiliation(s)
- Francesca Pia Caruso
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Luciano Garofano
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Fulvio D'Angelo
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Kai Yu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Jinzhou Yuan
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
- Cancer Program, Sidra Medicine, Al Luqta Street, Zone 52, Education City, 26999, Doha Qatar
| | - Jing Zhang
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Luigi Cerulo
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Stefano M Pagnotta
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Davide Bedognetti
- Cancer Program, Sidra Medicine, Al Luqta Street, Zone 52, Education City, 26999, Doha Qatar
- Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, Viale Benedetto XV 10, 16132 Genoa, Italy
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York , NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Mario Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Xiao-Dong Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , NY 10032 USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , NY 10032 USA
- Department of Neurology, Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
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