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Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys
Steven E. Bosinger, … , Ashley T. Haase, David J. Kelvin
Steven E. Bosinger, … , Ashley T. Haase, David J. Kelvin
Published November 23, 2009
Citation Information: J Clin Invest. 2009;119(12):3556-3572. https://doi.org/10.1172/JCI40115.
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Research Article

Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys

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Abstract

Natural SIV infection of sooty mangabeys (SMs) is nonprogressive despite chronic virus replication. Strikingly, it is characterized by low levels of immune activation, while pathogenic SIV infection of rhesus macaques (RMs) is associated with chronic immune activation. To elucidate the mechanisms underlying this intriguing phenotype, we used high-density oligonucleotide microarrays to longitudinally assess host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs was consistently associated with a robust innate immune response, including widespread upregulation of IFN-stimulated genes (ISGs) in blood and lymph nodes. While SMs exhibited a rapid resolution of ISG expression and immune activation, both responses were observed chronically in RMs. Systems biology analysis indicated that expression of the lymphocyte inhibitory receptor LAG3, a marker of T cell exhaustion, correlated with immune activation in SIV-infected RMs but not SMs. Our findings suggest that active immune regulatory mechanisms, rather than intrinsically attenuated innate immune responses, underlie the low levels of immune activation characteristic of SMs chronically infected with SIV.

Authors

Steven E. Bosinger, Qingsheng Li, Shari N. Gordon, Nichole R. Klatt, Lijie Duan, Luoling Xu, Nicholas Francella, Abubaker Sidahmed, Anthony J. Smith, Elizabeth M. Cramer, Ming Zeng, David Masopust, John V. Carlis, Longsi Ran, Thomas H. Vanderford, Mirko Paiardini, R. Benjamin Isett, Don A. Baldwin, James G. Else, Silvija I. Staprans, Guido Silvestri, Ashley T. Haase, David J. Kelvin

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Figure 2

Divergence in the transcriptome of SMs and RMs.

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Divergence in the transcriptome of SMs and RMs.
(A) PCA of complete gene...
(A) PCA of complete gene-expression profiles measured on each individual array. PCA was performed on the log10-transformed, RMA-normalized intensities on individual arrays (52,024 probe sets per array) using a covariance dispersion matrix and normalized eigenvector scaling. Principal component (PC) no. 1 (37.4%), PC no. 2 (11.7%), and PC no. 3 (7.8%) accounted for 56.9% of the variance in the data. Each colored circle indicates complete expression profiles of individual samples, with similarity between data sets displayed as proximity in 3D space (SIVsmm-infected SMs, blue circles; SIVsmm-infected-RMs, black circles; SIVmac239-infected RMs, red circles). (B) Hierarchical clustering of individual array data sets was performed using a Euclidean metric and average linkage to determine distance between data sets and clusters, respectively. In A and B, data sets from the 3 infection groups are indicated by color: SIVsmm-infected SMs (blue), SIVsmm-infected RMs (black), and SIVmac239-infected RMs (red).

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ISSN: 0021-9738 (print), 1558-8238 (online)

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