UW researchers: Tactics of new Middle East virus suggest treating by altering lung cells? response to infection

[Giuseppe]

[Source: mBio, full text: (LINK). Abstract, edited.]

Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus


Laurence Josset<SUP>a</SUP>, Vineet D. Menachery<SUP>b,c</SUP>, Lisa E. Gralinski<SUP>b,c</SUP>, Sudhakar Agnihothram<SUP>b,c</SUP>, Pavel Sova<SUP>a</SUP>, Victoria S. Carter<SUP>a</SUP>, Boyd L. Yount<SUP>b,c</SUP>, Rachel L. Graham<SUP>b,c</SUP>, Ralph S. Baric<SUP>b,c</SUP>, Michael G. Katze<SUP>a</SUP>
<SUP></SUP>
Author Affiliations: Department of Microbiology, School of Medicine, University of Washington, Seattle, Washington, USA<SUP>a</SUP>; Department of Epidemiology<SUP>b</SUP> and Department of Microbiology and Immunology,<SUP>c</SUP> University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA

Address correspondence to Michael G. Katze, honey@u.washington.edu. L.J. and V.D.M. contributed equally to this work. Invited Editor Michael Buchmeier, University of California, Irvine . Editor Michael Buchmeier, University of California, Irvine


ABSTRACT

A novel human coronavirus (HCoV-EMC) was recently identified in the Middle East as the causative agent of a severe acute respiratory syndrome (SARS) resembling the illness caused by SARS coronavirus (SARS-CoV). Although derived from the CoV family, the two viruses are genetically distinct and do not use the same receptor. Here, we investigated whether HCoV-EMC and SARS-CoV induce similar or distinct host responses after infection of a human lung epithelial cell line. HCoV-EMC was able to replicate as efficiently as SARS-CoV in Calu-3 cells and similarly induced minimal transcriptomic changes before 12 h postinfection. Later in infection, HCoV-EMC induced a massive dysregulation of the host transcriptome, to a much greater extent than SARS-CoV. Both viruses induced a similar activation of pattern recognition receptors and the interleukin 17 (IL-17) pathway, but HCoV-EMC specifically down-regulated the expression of several genes within the antigen presentation pathway, including both type I and II major histocompatibility complex (MHC) genes. This could have an important impact on the ability of the host to mount an adaptive host response. A unique set of 207 genes was dysregulated early and permanently throughout infection with HCoV-EMC, and was used in a computational screen to predict potential antiviral compounds, including kinase inhibitors and glucocorticoids. Overall, HCoV-EMC and SARS-CoV elicit distinct host gene expression responses, which might impact in vivo pathogenesis and could orient therapeutic strategies against that emergent virus.


IMPORTANCE

Identification of a novel coronavirus causing fatal respiratory infection in humans raises concerns about a possible widespread outbreak of severe respiratory infection similar to the one caused by SARS-CoV. Using a human lung epithelial cell line and global transcriptomic profiling, we identified differences in the host response between HCoV-EMC and SARS-CoV. This enables rapid assessment of viral properties and the ability to anticipate possible differences in human clinical responses to HCoV-EMC and SARS-CoV. We used this information to predict potential effective drugs against HCoV-EMC, a method that could be more generally used to identify candidate therapeutics in future disease outbreaks. These data will help to generate hypotheses and make rapid advancements in characterizing this new virus.


Footnotes

Citation Josset L, Menachery VD, Gralinski LE, Agnihothram S, Sova P, Carter VS, Yount BL, Graham RL, Baric RS, Katze MG. 2013. Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus. mBio 4(3):e00165-13. doi:10.1128/mBio.00165-13.

Received 5 March 2013 Accepted 12 April 2013 Published 30 April 2013

Copyright ? 2013 Josset et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.
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[Emily]

UW researchers: Tactics of new Middle East virus suggest treating by altering lung cells? response to infection

http://www.washington.edu/news/2013/04/30/tactics-of-new-middle-east-virus-suggest-treating-by-altering-lung-cells-response-to-infection/

April 30, 2013
Tactics of new Middle East virus suggest treating by altering lung cells? response to infection
By Leila Gray

UW Health Sciences/UW Medicine
A new virus that causes severe breathing distress and kidney failure elicits a distinctive airway cell response to allow it to multiply. Scientists studying the Human Coronavirus-Erasmus Medical Center, which first appeared April 2012 in the Middle East, have discovered helpful details about its stronghold tactics.

Their findings predict that certain currently available compounds might treat the infection. These could act not by killing the virus directly but by keeping lung cells from being forced to create a hospitable environment for the virus to reproduce. The researchers caution that their lab and computer predictions would need to be tested to see if the drugs work clinically.

The results appear in the April 30 issue of mBio, the Journal of the American Society for Microbiology. University of Washington virologist Laurence Josset is lead author of the paper, ?Cell host-response to infection with novel human coronavirus-Erasmus Medical Center predicts potential antivirals and important differences with SARS-coronavirus.? She conducted the research in the laboratory of senior author Michael G. Katze, UW professor of microbiology noted for pioneering systems biology approaches to host and pathogen interactions..

 

[AlaskaDenise]

Re: UW researchers: Tactics of new Middle East virus suggest treating by altering lung cells? response to infection

".....four types of kinase inhibitor and one kind of glucocorticoid....."

Interesting that these drugs are also used to fight cancer - targeting immune system signals or reactivating part of the immune system that the pathogen has silenced - and will hopefully bring better treatments to many diseases.

.

 

[Giuseppe]

Re: UW researchers: Tactics of new Middle East virus suggest treating by altering lung cells? response to infection

Abstract and full PDF: http://www.flutrackers.com/forum/showthread.php?t=204928

(...)


In silico and in vitro evidence for kinase inhibitors as potential
anti-CoV. To test these hypotheses, we first analyzed whether
cells treated with identified kinase inhibitors have gene expression
profiles opposite to the one induced after viral infection. To this
end, we used Connectivity Map (cmap), which is a database of
more than 1,309 drug transcriptional signatures in several cell
lines (22). This data-driven tool allows the identification of molecules
that induce similar or opposite transcriptional changes relative
to the query signature, based on their connectivity scores.

The connectivity score is a value between1 and1, where a high
positive score indicates that the drug induces changes similar to
those induced by viral infection, while a high negative score indicates
that the drug reverses the expression of the HCoV-EMC
signature. Cmap includes transcriptional profiles of several kinase
inhibitors, including two compounds that were predicted to be
potential negative regulators of viral response in IPA upstream
regulator analysis (SB203580 and LY294002). SB203580 had a
connectivity score of 0.733 in MCF7 cells (Data set S1 in the
supplemental material), and LY294002 had negative scores in 4 of
the 5 cell lines tested in cmap (0.281 in HL60,0.146 in MCF7,
0.252 in PC3, and 0.811 in SKMEL5), indicating that these
two drugs reversed the expression profile of HCoV-EMC signature.
Other related kinase inhibitors present in cmap are U0125 (a
derivative of U0126) and SB202190, which both had negative
scores in PC3 cells (0.649 and 0.406, respectively).

To further validate the potential effectiveness of identified kinase
inhibitors, we evaluated the ability of the top predicted negative
upstream regulator, SB203580, to interfere with viral replication
(Fig. 5C). Importantly, this kinase inhibitor was predicted
to regulate genes that wereDEsimilarly by SARS-CoV and HCoVEMC
at late times postinfection (see Table S2 in the supplemental
material) and could therefore inhibit both viruses? replication.

Treating cells with 5
MSB203580 following SARS-CoV infection
resulted in a significant decrease of 20% in the log10 viral titer at
24 hpi (P  0.01); these replication levels are similar to those in
interferon (IFN)-treated cells. SB203580 was less effective against
EMC-CoV, showing no efficacy with posttreatment; however,
pretreatment of infection resulted in significant decreases of 15%
and 7% of the log10 viral titer, at 24 and 48 hpi, respectively (P 
0.01). Efficacy against SARS-CoV can be explained by the fact that
all genes that were DE after SARS-CoV infection were predicted to
be regulated by kinase inhibitors (cluster I and II genes [Fig. 3] and
additional genes specific to SARS-CoV [data not shown]), while
the 8,918 genes specific to HCoV-EMC (clusters III and IV
[Fig. 3]) did not include any kinase inhibitor in their upstream
negative regulators (see Table S2). In addition, host response dynamics
to SARS-CoV and HCoV-EMC were different, with a delayed
and more limited response to SARS-CoV allowing
SB203580 posttreatment to be effective. In contrast, EMC-CoV
rapidly induced host expression changes and thus required
SB203580 pretreatment for measurable effect. As genes specific to
HCoV-EMC were predicted to be negatively regulated by other
classes of molecules (like gemfibrozil, which targets PPAR; z 
2.96), it will be important to determine whether using such molecules
in combination with kinase inhibitors like SB203580 could
provide a better inhibition of viral replication. Together, these
data demonstrate the efficacy of SB203580 against two unique
CoVs and validate in silico approaches to predict effective drug
treatment for emergent viruses.

(...)

While there is no proven effective antiviral therapy against
SARS-CoV (33), several molecules have in vitro antiviral activity,
including ribavirin, lopinavir, and type I IFN, but their benefits for
patients are unclear (33). IFN- pretreatment of cells has been
shown to inhibit HCoV-EMC replication (24), but no direct antiviral
therapies have been reported. Targeting host factors important
for the virus, instead of the virus itself, has been investigated
for HIV (34) and influenza virus (13). For example, inhibiting
upstream regulators (such as NF-B) that control the host response
to influenza virus infection has been shown to reduce virus
replication in vitro and in mice (35). Inhibition of immunophilins
that interact with the viral nonstructural protein 1 (Nsp1) resulted
in potent inhibition of SARS-CoV replication (36, 37). In this
study, we characterized upstream regulators predicted to be activated
(e.g., NF-B and IL-17, which could be targeted with specific
inhibitors) and upstream regulators predicted to be inhibited.

The top five inhibited regulators included one glucocorticoid
and four kinase inhibitors; these drugs may be able to directly
block part of the host response and impact viral replication/pathogenesis.

Among them, LY294002, a potent inhibitor of phosphatidylinositol
3 kinase (PI3K), has known antiviral activity, inhibiting
the replication of influenza virus (38), vaccinia virus (39),
and HCMV (40). SB203580, an inhibitor of p38 MAPK, is also an
effective antiviral against the encephalomyocarditis virus (41),
RSV (42), and HIV (43). LY294002 and SB203580 were also identified
in Connectivity Map, a database of drug-associated gene
expression profiles (22), as molecules reversing components of the
HCoV-EMC gene expression signature. Finally, SB203580
showed promising antiviral results against both HCoV-EMC and
SARS-CoV in our in vitro assay (Fig. 4C). Further extensive studies,
including dose-response tests and tests of other kinases inhibitors,
are ongoing. Nonetheless, these results validate our genomebased
drug prediction, which allows rapid identification of
effective antivirals. Despite central roles of PI3K and MAPK pathways
in regulating multiple cellular processes, many kinase inhibitors
targeting these pathways have been shown to be safe and well
tolerated in vivo (reviewed in references 44 and 45). It has been
hypothesized that mitogenic MAPK and survival PI3K/Akt pathways
may be of major importance only during early development
of an organism and may be dispensable in adult tissues (13). Several
drugs targeting JNK, PI3K, and MEK have shown promising
therapeutic potential in humans against a variety of diseases, including
cancer and inflammatory disorder (44, 45). p38 MAPK
inhibitors have also been evaluated in humans, but the first generation
of molecules, including SB203580, has a high in vivo toxicity
(liver and/or central nervous system). However, development
of novel nontoxic inhibitors (e.g., ML3403) (46), more
selective molecules (e.g., AS1940477) (47), and administration via
inhalation (48) are promising strategies for use of this class of
inhibitor for treatment of pulmonary disease. Overall, these results
indicate that kinase inhibitors could be used as broad anti-
CoV agents which might be combined with other host-targeting
molecules, like peroxisome proliferator-activated receptor 
(PPAR) agonists, to better inhibit HCoV-EMC replication.

In conclusion, using global gene expression profiling, we have
shown that HCoV-EMC induces a dramatic host transcriptional
response, most of which does not overlap the response induced by
SARS-CoV. This study highlights the advantages of highthroughput
?-omics? to globally and efficiently characterize
emerging pathogens. The robust host gene expression analysis of
HCoV-EMC infection provides a plethora of data to mine for
further hypotheses and understanding. Host response profiles can
also be used to quickly identify possible treatment strategies, and
we anticipate that host transcriptional profiling will become a gen-
eral strategy for the rapid characterization of future emerging viruses.

(...)


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