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Komura D, Isagawa T, Kishi K, Suzuki R, Sato R, Tanaka M, Katoh H, Yamamoto S, Tatsuno K, Fukayama M, Aburatani H, Ishikawa S. CASTIN: a system for comprehensive analysis of cancer-stromal interactome. BMC Genomics 2016; 17:899. [PMID: 27829362 PMCID: PMC5103609 DOI: 10.1186/s12864-016-3207-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/25/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer therapy. However, identifying relevant and druggable cancer-stromal interactions is challenging due to the lack of quantitative methods to analyze whole cancer-stromal interactome. RESULTS We present CASTIN (CAncer-STromal INteractome analysis), a novel framework for the evaluation of cancer-stromal interactome from RNA-Seq data using cancer xenograft models. For each ligand-receptor interaction which is derived from curated protein-protein interaction database, CASTIN summarizes gene expression profiles of cancer and stroma into three evaluation indices. These indices provide quantitative evaluation and comprehensive visualization of interactome, and thus enable to identify critical cancer-microenvironment interactions, which would be potential drug targets. We applied CASTIN to the dataset of pancreas ductal adenocarcinoma, and successfully characterized the individual cancer in terms of cancer-stromal relationships, and identified both well-known and less-characterized druggable interactions. CONCLUSIONS CASTIN provides comprehensive view of cancer-stromal interactome and is useful to identify critical interactions which may serve as potential drug targets in cancer-microenvironment. CASTIN is available at: http://github.com/tmd-gpat/CASTIN .
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Affiliation(s)
- Daisuke Komura
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayuki Isagawa
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuki Kishi
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Graduate School of Interdisciplinary Information Studies, The University of Tokyo, Tokyo, Japan
| | - Ryohei Suzuki
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Graduate School of Information and Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Reiko Sato
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mariko Tanaka
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroto Katoh
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Tatsuno
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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He H, Mack JJ, Güç E, Warren CM, Squadrito ML, Kilarski WW, Baer C, Freshman RD, McDonald AI, Ziyad S, Swartz MA, De Palma M, Iruela-Arispe ML. Perivascular Macrophages Limit Permeability. Arterioscler Thromb Vasc Biol 2016; 36:2203-2212. [PMID: 27634833 DOI: 10.1161/atvbaha.116.307592] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/31/2016] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Perivascular cells, including pericytes, macrophages, smooth muscle cells, and other specialized cell types, like podocytes, participate in various aspects of vascular function. However, aside from the well-established roles of smooth muscle cells and pericytes, the contributions of other vascular-associated cells are poorly understood. Our goal was to ascertain the function of perivascular macrophages in adult tissues under nonpathological conditions. APPROACH AND RESULTS We combined confocal microscopy, in vivo cell depletion, and in vitro assays to investigate the contribution of perivascular macrophages to vascular function. We found that resident perivascular macrophages are associated with capillaries at a frequency similar to that of pericytes. Macrophage depletion using either clodronate liposomes or antibodies unexpectedly resulted in hyperpermeability. This effect could be rescued when M2-like macrophages, but not M1-like macrophages or dendritic cells, were reconstituted in vivo, suggesting subtype-specific roles for macrophages in the regulation of vascular permeability. Furthermore, we found that permeability-promoting agents elicit motility and eventual dissociation of macrophages from the vasculature. Finally, in vitro assays showed that M2-like macrophages attenuate the phosphorylation of VE-cadherin upon exposure to permeability-promoting agents. CONCLUSIONS This study points to a direct contribution of macrophages to vessel barrier integrity and provides evidence that heterotypic cell interactions with the endothelium, in addition to those of pericytes, control vascular permeability.
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Affiliation(s)
- Huanhuan He
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Julia J Mack
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Esra Güç
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Carmen M Warren
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Mario Leonardo Squadrito
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Witold W Kilarski
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Caroline Baer
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Ryan D Freshman
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Austin I McDonald
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Safiyyah Ziyad
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Melody A Swartz
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - Michele De Palma
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.)
| | - M Luisa Iruela-Arispe
- From the Department of Human Genetics (H.H.), Department of Molecular, Cell and Developmental Biology (J.J.M., C.M.W., R.D.F., A.I.M., S.Z., M.L.I.-A.), Molecular Biology Institute (M.L.I.-A.), and Jonsson Comprehensive Cancer Center (M.L.I.-A.), University of California, Los Angeles; Institute for Bioengineering (IBI) (E.G., M.A.S.) and The Swiss Institute for Experimental Cancer Research (ISREC) (M.L.S., C.B., M.A.S., M.D.P., M.L.I.-A.), School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Switzerland; and Institute for Molecular Engineering and Ben May Department of Cancer Research, University of Chicago, IL (W.W.K., M.A.S.).
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