Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models

Kyeongdae Kim; Dahee Shim; Jun Seong Lee; Konstantin Zaitsev; Jesse W. Williams; Ki Wook Kim; Man Young Jang; Hyung Seok Jang; Tae Jin Yun; Seung Hyun Lee; Won Kee Yoon; Annik Prat; Nabil G. Seidah; Jungsoon Choi; Seung Pyo Lee; Sang Ho Yoon; Jin Wu Nam; Je Kyung Seong; Goo Taeg Oh; Gwendalyn J. Randolph; Maxim N. Artyomov; Cheolho Cheong; Jae Hoon Choi

doi:10.1161/CIRCRESAHA.118.312804

Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models

Kyeongdae Kim, Dahee Shim, Jun Seong Lee, Konstantin Zaitsev, Jesse W. Williams, Ki Wook Kim, Man Young Jang, Hyung Seok Jang, Tae Jin Yun, Seung Hyun Lee, Won Kee Yoon, Annik Prat, Nabil G. Seidah, Jungsoon Choi, Seung Pyo Lee, Sang Ho Yoon, Jin Wu Nam, Je Kyung Seong, Goo Taeg Oh, Gwendalyn J. RandolphMaxim N. Artyomov, Cheolho Cheong, Jae Hoon Choi

Research output: Contribution to journal › Article › peer-review

307 Scopus citations

Abstract

Rationale: Monocyte infiltration into the subintimal space and its intracellular lipid accumulation are the most prominent features of atherosclerosis. To understand the pathophysiology of atherosclerotic disease, we need to understand the characteristics of lipid-laden foamy macrophages in the subintimal space during atherosclerosis. Objective: We sought to examine the transcriptomic profiles of foamy and nonfoamy macrophages isolated from atherosclerotic intima. Methods and Results: Single-cell RNA sequencing analysis of CD45 ⁺ leukocytes from murine atherosclerotic aorta revealed that there are macrophage subpopulations with distinct differentially expressed genes involved in various functional pathways. To specifically characterize the intimal foamy macrophages of plaque, we developed a lipid staining-based flow cytometric method for analyzing the lipid-laden foam cells of atherosclerotic aortas. We used the fluorescent lipid probe BODIPY493/503 and assessed side-scattered light as an indication of cellular granularity. BODIPY ^hi SSC ^hi foamy macrophages were found residing in intima and expressing CD11c. Foamy macrophage accumulation determined by flow cytometry was positively correlated with the severity of atherosclerosis. Bulk RNA sequencing analysis showed that compared with nonfoamy macrophages, foamy macrophages expressed few inflammatory genes but many lipid-processing genes. Intimal nonfoamy macrophages formed the major population expressing IL (interleukin)-1β and many other inflammatory transcripts in atherosclerotic aorta. Conclusions: RNA sequencing analysis of intimal macrophages from atherosclerotic aorta revealed that lipid-loaded plaque macrophages are not likely the plaque macrophages that drive lesional inflammation.

Original language	English (US)
Pages (from-to)	1127-1142
Number of pages	16
Journal	Circulation research
Volume	123
Issue number	10
DOIs	https://doi.org/10.1161/CIRCRESAHA.118.312804
State	Published - Jan 1 2018
Externally published	Yes

Bibliographical note

Funding Information:
This work is dedicated to the memory of Cheolho Cheong. We appreciate Erica Lantelme and Dorjan Brinja for fluorescence-activated cell sorting sorting and also thank Inhyuk Jung, Soo Young Cho, and Sung Ho Park for technical assistance and scientific comments, respectively. We thank McDonnell Genome Institute and Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for help with genomic analysis. We thank Dr Eunwoo Nam of Medical statistical office at the Hanyang University College of Medicine for statistical advice.

Funding Information:
This work was supported by grants from the Bio and Medical Technology Development Program of the National Research Foundation and funded by the Korean government (Ministry of Health and Welfare, Ministry of Science and ICT, No. 2016M3A9D5A01952413 and 2018R1A2B6003393 to J.-H. Choi and 2015M3A9B6029138 to G.T. Oh), the Korean Health Technology R&D Project (HI15C0399 to J.-H. Choi), Ministry of Health, Welfare, and Family Affairs, and Canadian Institutes of Health Research (CIHR; FRN 125933 to C. Cheong, CIHR Foundation 148363 and Canada Research Chair 950-231335 to N.G. Seidah), American Heart Association grant 17POST33410473 to J.W. Williams and Government of Russian Federation grant 074-U01 to K. Zaitsev. Genome Technology Access Center at Washington University School of Medicine is partially supported by National Cancer Institute Cancer Center Support grant No. P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA grant No. UL1TR002345 from the National Center for Research Resources (NCRR)—a component of the National Institutes of Health (NIH)—and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official views of NCRR or NIH.

Publisher Copyright:
© 2018 American Heart Association, Inc.

Keywords

Atherosclerosis
Flow cytometry
Foam cells
Macrophages
Mice
RNA-seq

PubMed: MeSH publication types

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1161/CIRCRESAHA.118.312804

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Kim, K., Shim, D., Lee, J. S., Zaitsev, K., Williams, J. W., Kim, K. W., Jang, M. Y., Jang, H. S., Yun, T. J., Lee, S. H., Yoon, W. K., Prat, A., Seidah, N. G., Choi, J., Lee, S. P., Yoon, S. H., Nam, J. W., Seong, J. K., Oh, G. T., ... Choi, J. H. (2018). Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models. Circulation research, 123(10), 1127-1142. https://doi.org/10.1161/CIRCRESAHA.118.312804

Kim, K, Shim, D, Lee, JS, Zaitsev, K, Williams, JW, Kim, KW, Jang, MY, Jang, HS, Yun, TJ, Lee, SH, Yoon, WK, Prat, A, Seidah, NG, Choi, J, Lee, SP, Yoon, SH, Nam, JW, Seong, JK, Oh, GT, Randolph, GJ, Artyomov, MN, Cheong, C & Choi, JH 2018, 'Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models', Circulation research, vol. 123, no. 10, pp. 1127-1142. https://doi.org/10.1161/CIRCRESAHA.118.312804

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title = "Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models",

abstract = " Rationale: Monocyte infiltration into the subintimal space and its intracellular lipid accumulation are the most prominent features of atherosclerosis. To understand the pathophysiology of atherosclerotic disease, we need to understand the characteristics of lipid-laden foamy macrophages in the subintimal space during atherosclerosis. Objective: We sought to examine the transcriptomic profiles of foamy and nonfoamy macrophages isolated from atherosclerotic intima. Methods and Results: Single-cell RNA sequencing analysis of CD45 + leukocytes from murine atherosclerotic aorta revealed that there are macrophage subpopulations with distinct differentially expressed genes involved in various functional pathways. To specifically characterize the intimal foamy macrophages of plaque, we developed a lipid staining-based flow cytometric method for analyzing the lipid-laden foam cells of atherosclerotic aortas. We used the fluorescent lipid probe BODIPY493/503 and assessed side-scattered light as an indication of cellular granularity. BODIPY hi SSC hi foamy macrophages were found residing in intima and expressing CD11c. Foamy macrophage accumulation determined by flow cytometry was positively correlated with the severity of atherosclerosis. Bulk RNA sequencing analysis showed that compared with nonfoamy macrophages, foamy macrophages expressed few inflammatory genes but many lipid-processing genes. Intimal nonfoamy macrophages formed the major population expressing IL (interleukin)-1β and many other inflammatory transcripts in atherosclerotic aorta. Conclusions: RNA sequencing analysis of intimal macrophages from atherosclerotic aorta revealed that lipid-loaded plaque macrophages are not likely the plaque macrophages that drive lesional inflammation. ",

keywords = "Atherosclerosis, Flow cytometry, Foam cells, Macrophages, Mice, RNA-seq",

author = "Kyeongdae Kim and Dahee Shim and Lee, {Jun Seong} and Konstantin Zaitsev and Williams, {Jesse W.} and Kim, {Ki Wook} and Jang, {Man Young} and Jang, {Hyung Seok} and Yun, {Tae Jin} and Lee, {Seung Hyun} and Yoon, {Won Kee} and Annik Prat and Seidah, {Nabil G.} and Jungsoon Choi and Lee, {Seung Pyo} and Yoon, {Sang Ho} and Nam, {Jin Wu} and Seong, {Je Kyung} and Oh, {Goo Taeg} and Randolph, {Gwendalyn J.} and Artyomov, {Maxim N.} and Cheolho Cheong and Choi, {Jae Hoon}",

note = "Funding Information: This work is dedicated to the memory of Cheolho Cheong. We appreciate Erica Lantelme and Dorjan Brinja for fluorescence-activated cell sorting sorting and also thank Inhyuk Jung, Soo Young Cho, and Sung Ho Park for technical assistance and scientific comments, respectively. We thank McDonnell Genome Institute and Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for help with genomic analysis. We thank Dr Eunwoo Nam of Medical statistical office at the Hanyang University College of Medicine for statistical advice. Funding Information: This work was supported by grants from the Bio and Medical Technology Development Program of the National Research Foundation and funded by the Korean government (Ministry of Health and Welfare, Ministry of Science and ICT, No. 2016M3A9D5A01952413 and 2018R1A2B6003393 to J.-H. Choi and 2015M3A9B6029138 to G.T. Oh), the Korean Health Technology R&D Project (HI15C0399 to J.-H. Choi), Ministry of Health, Welfare, and Family Affairs, and Canadian Institutes of Health Research (CIHR; FRN 125933 to C. Cheong, CIHR Foundation 148363 and Canada Research Chair 950-231335 to N.G. Seidah), American Heart Association grant 17POST33410473 to J.W. Williams and Government of Russian Federation grant 074-U01 to K. Zaitsev. Genome Technology Access Center at Washington University School of Medicine is partially supported by National Cancer Institute Cancer Center Support grant No. P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA grant No. UL1TR002345 from the National Center for Research Resources (NCRR)—a component of the National Institutes of Health (NIH)—and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official views of NCRR or NIH. Publisher Copyright: {\textcopyright} 2018 American Heart Association, Inc.",

year = "2018",

month = jan,

day = "1",

doi = "10.1161/CIRCRESAHA.118.312804",

language = "English (US)",

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pages = "1127--1142",

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T1 - Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models

AU - Kim, Kyeongdae

AU - Shim, Dahee

AU - Lee, Jun Seong

AU - Zaitsev, Konstantin

AU - Williams, Jesse W.

AU - Kim, Ki Wook

AU - Jang, Man Young

AU - Jang, Hyung Seok

AU - Yun, Tae Jin

AU - Lee, Seung Hyun

AU - Yoon, Won Kee

AU - Prat, Annik

AU - Seidah, Nabil G.

AU - Choi, Jungsoon

AU - Lee, Seung Pyo

AU - Yoon, Sang Ho

AU - Nam, Jin Wu

AU - Seong, Je Kyung

AU - Oh, Goo Taeg

AU - Randolph, Gwendalyn J.

AU - Artyomov, Maxim N.

AU - Cheong, Cheolho

AU - Choi, Jae Hoon

N1 - Funding Information: This work is dedicated to the memory of Cheolho Cheong. We appreciate Erica Lantelme and Dorjan Brinja for fluorescence-activated cell sorting sorting and also thank Inhyuk Jung, Soo Young Cho, and Sung Ho Park for technical assistance and scientific comments, respectively. We thank McDonnell Genome Institute and Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for help with genomic analysis. We thank Dr Eunwoo Nam of Medical statistical office at the Hanyang University College of Medicine for statistical advice. Funding Information: This work was supported by grants from the Bio and Medical Technology Development Program of the National Research Foundation and funded by the Korean government (Ministry of Health and Welfare, Ministry of Science and ICT, No. 2016M3A9D5A01952413 and 2018R1A2B6003393 to J.-H. Choi and 2015M3A9B6029138 to G.T. Oh), the Korean Health Technology R&D Project (HI15C0399 to J.-H. Choi), Ministry of Health, Welfare, and Family Affairs, and Canadian Institutes of Health Research (CIHR; FRN 125933 to C. Cheong, CIHR Foundation 148363 and Canada Research Chair 950-231335 to N.G. Seidah), American Heart Association grant 17POST33410473 to J.W. Williams and Government of Russian Federation grant 074-U01 to K. Zaitsev. Genome Technology Access Center at Washington University School of Medicine is partially supported by National Cancer Institute Cancer Center Support grant No. P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA grant No. UL1TR002345 from the National Center for Research Resources (NCRR)—a component of the National Institutes of Health (NIH)—and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official views of NCRR or NIH. Publisher Copyright: © 2018 American Heart Association, Inc.

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Rationale: Monocyte infiltration into the subintimal space and its intracellular lipid accumulation are the most prominent features of atherosclerosis. To understand the pathophysiology of atherosclerotic disease, we need to understand the characteristics of lipid-laden foamy macrophages in the subintimal space during atherosclerosis. Objective: We sought to examine the transcriptomic profiles of foamy and nonfoamy macrophages isolated from atherosclerotic intima. Methods and Results: Single-cell RNA sequencing analysis of CD45 + leukocytes from murine atherosclerotic aorta revealed that there are macrophage subpopulations with distinct differentially expressed genes involved in various functional pathways. To specifically characterize the intimal foamy macrophages of plaque, we developed a lipid staining-based flow cytometric method for analyzing the lipid-laden foam cells of atherosclerotic aortas. We used the fluorescent lipid probe BODIPY493/503 and assessed side-scattered light as an indication of cellular granularity. BODIPY hi SSC hi foamy macrophages were found residing in intima and expressing CD11c. Foamy macrophage accumulation determined by flow cytometry was positively correlated with the severity of atherosclerosis. Bulk RNA sequencing analysis showed that compared with nonfoamy macrophages, foamy macrophages expressed few inflammatory genes but many lipid-processing genes. Intimal nonfoamy macrophages formed the major population expressing IL (interleukin)-1β and many other inflammatory transcripts in atherosclerotic aorta. Conclusions: RNA sequencing analysis of intimal macrophages from atherosclerotic aorta revealed that lipid-loaded plaque macrophages are not likely the plaque macrophages that drive lesional inflammation.

AB - Rationale: Monocyte infiltration into the subintimal space and its intracellular lipid accumulation are the most prominent features of atherosclerosis. To understand the pathophysiology of atherosclerotic disease, we need to understand the characteristics of lipid-laden foamy macrophages in the subintimal space during atherosclerosis. Objective: We sought to examine the transcriptomic profiles of foamy and nonfoamy macrophages isolated from atherosclerotic intima. Methods and Results: Single-cell RNA sequencing analysis of CD45 + leukocytes from murine atherosclerotic aorta revealed that there are macrophage subpopulations with distinct differentially expressed genes involved in various functional pathways. To specifically characterize the intimal foamy macrophages of plaque, we developed a lipid staining-based flow cytometric method for analyzing the lipid-laden foam cells of atherosclerotic aortas. We used the fluorescent lipid probe BODIPY493/503 and assessed side-scattered light as an indication of cellular granularity. BODIPY hi SSC hi foamy macrophages were found residing in intima and expressing CD11c. Foamy macrophage accumulation determined by flow cytometry was positively correlated with the severity of atherosclerosis. Bulk RNA sequencing analysis showed that compared with nonfoamy macrophages, foamy macrophages expressed few inflammatory genes but many lipid-processing genes. Intimal nonfoamy macrophages formed the major population expressing IL (interleukin)-1β and many other inflammatory transcripts in atherosclerotic aorta. Conclusions: RNA sequencing analysis of intimal macrophages from atherosclerotic aorta revealed that lipid-loaded plaque macrophages are not likely the plaque macrophages that drive lesional inflammation.

KW - Atherosclerosis

KW - Flow cytometry

KW - Foam cells

KW - Macrophages

KW - Mice

KW - RNA-seq

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Transcriptome analysis reveals nonfoamy rather than foamy plaque macrophages are proinflammatory in atherosclerotic murine models

Abstract

Bibliographical note

Keywords

PubMed: MeSH publication types

UN SDGs

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