RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation.

Janice Wilson ,Helen E Cumming,Wayne A Schroder,Joy Gardner,Pierre Roques,Phillip I Bird,Linden J Gearing,Roger Le Grand,Bing Tang,Andreas Suhrbier,Yee Suan Poo,Francesca Di Giallonardo,Natalie A Prow,Thuy T Le,Suresh Mahalingam,Linda Hueston,Adam Taylor,Paul J Hertzog,Jonathan Ellis

doi:10.1371/journal.ppat.1006155

Abstract

Chikungunya virus (CHIKV) is an arthritogenic alphavirus causing epidemics of acute and chronic arthritic disease. Herein we describe a comprehensive RNA-Seq analysis of feet and lymph nodes at peak viraemia (day 2 post infection), acute arthritis (day 7) and chronic disease (day 30) in the CHIKV adult wild-type mouse model. Genes previously shown to be up-regulated in CHIKV patients were also up-regulated in the mouse model. CHIKV sequence information was also obtained with up to ≈8% of the reads mapping to the viral genome; however, no adaptive viral genome changes were apparent. Although day 2, 7 and 30 represent distinct stages of infection and disease, there was a pronounced overlap in up-regulated host genes and pathways. Type I interferon response genes (IRGs) represented up to ≈50% of up-regulated genes, even after loss of type I interferon induction on days 7 and 30. Bioinformatic analyses suggested a number of interferon response factors were primarily responsible for maintaining type I IRG induction. A group of genes prominent in the RNA-Seq analysis and hitherto unexplored in viral arthropathies were granzymes A, B and K. Granzyme A-/- and to a lesser extent granzyme K-/-, but not granzyme B-/-, mice showed a pronounced reduction in foot swelling and arthritis, with analysis of granzyme A-/- mice showing no reductions in viral loads but reduced NK and T cell infiltrates post CHIKV infection. Treatment with Serpinb6b, a granzyme A inhibitor, also reduced arthritic inflammation in wild-type mice. In non-human primates circulating granzyme A levels were elevated after CHIKV infection, with the increase correlating with viral load. Elevated granzyme A levels were also seen in a small cohort of human CHIKV patients. Taken together these results suggest granzyme A is an important driver of arthritic inflammation and a potential target for therapy.Trial Registration: ClinicalTrials.gov NCT00281294

Highlights

Chikungunya virus (CHIKV) belongs to a group of mosquito-borne arthritogenic alphaviruses that include the primarily Australian Ross River and Barmah Forest viruses, the African o’nyong-nyong virus, the Sindbis group of viruses and the South American Mayaro virus [1]
We undertook a detailed analysis of the mRNA expression profile during acute and chronic arthritis in an adult wild-type mouse model of CHIKV infection and disease
Granzyme A was prominent in the RNA-Seq data and granzyme A deficient mice showed reduced arthritis, with no effects on viral loads

Summary

Introduction

Chikungunya virus (CHIKV) belongs to a group of mosquito-borne arthritogenic alphaviruses that include the primarily Australian Ross River and Barmah Forest viruses, the African o’nyong-nyong virus, the Sindbis group of viruses and the South American Mayaro virus [1]. The largest documented outbreak of CHIKV disease ever recorded began in 2004 in Africa and spread across the Indian Ocean to Asia, east to Papua New Guinea and several pacific islands, with small outbreaks seen in Europe. In late 2013 the epidemic reached the Americas, spreading through the Caribbean, Central and South America, with autochthonous transmission reported in the USA [2,3]. No effective drug or licensed vaccine is available for human use for any of these alphaviruses; paracetamol/acetaminophen and non-steroidal anti-inflammatory drugs can provide relief from rheumatic symptoms [1,5] and CHIKV vaccines are in development [6,7]

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