An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway

Kevin A. Robertson, Wei Yuan Hsieh, Thorsten Forster, Mathieu Blanc, Hongjin Lu, Peter J. Crick, Eylan Yutuc, Steven Watterson, Kimberly Martin, Samantha J. Griffiths, Anton J. Enright, Mami Yamamoto, Madapura M. Pradeepa, Kimberly A. Lennox, Mark A. Behlke, Simon Talbot, Jürgen Haas, Lars Dölken, William J. Griffiths, Yuqin Wang & 3 others Ana Angulo, Peter Ghazal, Hidde L Ploegh

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway.
LanguageEnglish
Article numbere1002364
Pages1-35
Number of pages35
JournalPLoS Biology
Volume14
Issue number3
DOIs
Publication statusPublished - 3 Mar 2016

Fingerprint

Sterols
MicroRNAs
Interferons
Antiviral Agents
Immunity
Mevalonic Acid
Macrophages
Viruses
Thiouridine
RNA
Enzyme Assays
Invertebrates
Site-Directed Mutagenesis
Cytomegalovirus
Human Influenza
Small Interfering RNA
Mammals
Mass Spectrometry
Transcription Factors
Cholesterol

Keywords

  • sterol
  • cholesterol
  • immune
  • innate
  • microrna

Cite this

Robertson, K. A., Hsieh, W. Y., Forster, T., Blanc, M., Lu, H., Crick, P. J., ... Ploegh, H. L. (Ed.) (2016). An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway. PLoS Biology, 14(3), 1-35. [e1002364]. https://doi.org/10.1371/journal.pbio.1002364
Robertson, Kevin A. ; Hsieh, Wei Yuan ; Forster, Thorsten ; Blanc, Mathieu ; Lu, Hongjin ; Crick, Peter J. ; Yutuc, Eylan ; Watterson, Steven ; Martin, Kimberly ; Griffiths, Samantha J. ; Enright, Anton J. ; Yamamoto, Mami ; Pradeepa, Madapura M. ; Lennox, Kimberly A. ; Behlke, Mark A. ; Talbot, Simon ; Haas, Jürgen ; Dölken, Lars ; Griffiths, William J. ; Wang, Yuqin ; Angulo, Ana ; Ghazal, Peter ; Ploegh, Hidde L (Editor). / An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway. In: PLoS Biology. 2016 ; Vol. 14, No. 3. pp. 1-35.
@article{5362518af9024fa0a4228a7774233214,
title = "An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway",
abstract = "In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway.",
keywords = "sterol, cholesterol, immune, innate, microrna",
author = "Robertson, {Kevin A.} and Hsieh, {Wei Yuan} and Thorsten Forster and Mathieu Blanc and Hongjin Lu and Crick, {Peter J.} and Eylan Yutuc and Steven Watterson and Kimberly Martin and Griffiths, {Samantha J.} and Enright, {Anton J.} and Mami Yamamoto and Pradeepa, {Madapura M.} and Lennox, {Kimberly A.} and Behlke, {Mark A.} and Simon Talbot and J{\"u}rgen Haas and Lars D{\"o}lken and Griffiths, {William J.} and Yuqin Wang and Ana Angulo and Peter Ghazal and Ploegh, {Hidde L}",
year = "2016",
month = "3",
day = "3",
doi = "10.1371/journal.pbio.1002364",
language = "English",
volume = "14",
pages = "1--35",
journal = "PLoS Biology",
issn = "1544-9173",
number = "3",

}

Robertson, KA, Hsieh, WY, Forster, T, Blanc, M, Lu, H, Crick, PJ, Yutuc, E, Watterson, S, Martin, K, Griffiths, SJ, Enright, AJ, Yamamoto, M, Pradeepa, MM, Lennox, KA, Behlke, MA, Talbot, S, Haas, J, Dölken, L, Griffiths, WJ, Wang, Y, Angulo, A, Ghazal, P & Ploegh, HL (ed.) 2016, 'An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway', PLoS Biology, vol. 14, no. 3, e1002364, pp. 1-35. https://doi.org/10.1371/journal.pbio.1002364

An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway. / Robertson, Kevin A.; Hsieh, Wei Yuan; Forster, Thorsten; Blanc, Mathieu; Lu, Hongjin; Crick, Peter J.; Yutuc, Eylan; Watterson, Steven; Martin, Kimberly; Griffiths, Samantha J.; Enright, Anton J.; Yamamoto, Mami; Pradeepa, Madapura M.; Lennox, Kimberly A.; Behlke, Mark A.; Talbot, Simon; Haas, Jürgen; Dölken, Lars; Griffiths, William J.; Wang, Yuqin; Angulo, Ana; Ghazal, Peter; Ploegh, Hidde L (Editor).

In: PLoS Biology, Vol. 14, No. 3, e1002364, 03.03.2016, p. 1-35.

Research output: Contribution to journalArticle

TY - JOUR

T1 - An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway

AU - Robertson, Kevin A.

AU - Hsieh, Wei Yuan

AU - Forster, Thorsten

AU - Blanc, Mathieu

AU - Lu, Hongjin

AU - Crick, Peter J.

AU - Yutuc, Eylan

AU - Watterson, Steven

AU - Martin, Kimberly

AU - Griffiths, Samantha J.

AU - Enright, Anton J.

AU - Yamamoto, Mami

AU - Pradeepa, Madapura M.

AU - Lennox, Kimberly A.

AU - Behlke, Mark A.

AU - Talbot, Simon

AU - Haas, Jürgen

AU - Dölken, Lars

AU - Griffiths, William J.

AU - Wang, Yuqin

AU - Angulo, Ana

AU - Ghazal, Peter

A2 - Ploegh, Hidde L

PY - 2016/3/3

Y1 - 2016/3/3

N2 - In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway.

AB - In invertebrates, small interfering RNAs are at the vanguard of cell-autonomous antiviral immunity. In contrast, antiviral mechanisms initiated by interferon (IFN) signaling predominate in mammals. Whilst mammalian IFN-induced miRNA are known to inhibit specific viruses, it is not known whether host-directed microRNAs, downstream of IFN-signaling, have a role in mediating broad antiviral resistance. By performing an integrative, systematic, global analysis of RNA turnover utilizing 4-thiouridine labeling of newly transcribed RNA and pri/pre-miRNA in IFN-activated macrophages, we identify a new post-transcriptional viral defense mechanism mediated by miR-342-5p. On the basis of ChIP and site-directed promoter mutagenesis experiments, we find the synthesis of miR-342-5p is coupled to the antiviral IFN response via the IFN-induced transcription factor, IRF1. Strikingly, we find miR-342-5p targets mevalonate-sterol biosynthesis using a multihit mechanism suppressing the pathway at different functional levels: transcriptionally via SREBF2, post-transcriptionally via miR-33, and enzymatically via IDI1 and SC4MOL. Mass spectrometry-based lipidomics and enzymatic assays demonstrate the targeting mechanisms reduce intermediate sterol pathway metabolites and total cholesterol in macrophages. These results reveal a previously unrecognized mechanism by which IFN regulates the sterol pathway. The sterol pathway is known to be an integral part of the macrophage IFN antiviral response, and we show that miR-342-5p exerts broad antiviral effects against multiple, unrelated pathogenic viruses such Cytomegalovirus and Influenza A (H1N1). Metabolic rescue experiments confirm the specificity of these effects and demonstrate that unrelated viruses have differential mevalonate and sterol pathway requirements for their replication. This study, therefore, advances the general concept of broad antiviral defense through multihit targeting of a single host pathway.

KW - sterol

KW - cholesterol

KW - immune

KW - innate

KW - microrna

UR - https://pure.ulster.ac.uk/en/publications/an-interferon-regulated-microrna-provides-broad-cell-intrinsic-an-3

U2 - 10.1371/journal.pbio.1002364

DO - 10.1371/journal.pbio.1002364

M3 - Article

VL - 14

SP - 1

EP - 35

JO - PLoS Biology

T2 - PLoS Biology

JF - PLoS Biology

SN - 1544-9173

IS - 3

M1 - e1002364

ER -