Deep Transcriptional Sequencing of Mucosal Challenge Compartment from Rhesus Macaques Acutely Infected with Simian Immunodeficiency Virus Implicates Loss of Cell Adhesion Preceding Immune Activation

Abstract

Pathology resulting from human immunodeficiency virus (HIV) infection is driven by protracted inflammation; the primary loss of CD4؉ T cells is caused by activation-driven apoptosis. Recent studies of nonhuman primates (NHPs) have suggested that during the acute phase of infection, antiviral mucosal immunity restricts viral replication in the primary infection compartment. These studies imply that HIV achieves systemic infection as a consequence of a failure in host antiviral immunity. Here, we used high-dose intrarectal inoculation of rhesus macaques with simian immunodeficiency virus (SIV) SIV mac251 to examine how the mucosal immune system is overcome by SIV during acute infection. The host response in rectal mucosa was characterized by deep mRNA sequencing (mRNA-seq) at 3 and 12 days postinoculation (dpi) in 4 animals for each time point. While we observed a strong host transcriptional response at 3 dpi, functions relating to antiviral immunity were absent. Instead, we observed a significant number of differentially expressed genes relating to cell adhesion and reorganization of the cytoskeleton. We also observed downregulation of genes encoding members of the claudin family of cell adhesion molecules, which are coexpressed with genes associated with pathology in the colorectal mucosa, and a large number of noncoding transcripts. In contrast, at 12 dpi the differentially expressed genes were enriched in those involved with immune system functions, in particular, functions relating to T cells, B cells, and NK cells. Our findings indicate that host responses that negatively affect mucosal integrity occur before inflammation. Consequently, when inflammation is activated at peak viremia, mucosal integrity is already compromised, potentially enabling rapid tissue damage, driving further inflammation. IMPORTANCEThe HIV pandemic is one of the major threats to human health, causing over a million deaths per year. Recent studies have suggested that mucosal antiviral immune responses play an important role in preventing systemic infection after exposure to the virus. Yet, despite their potential role in decreasing transmission rates between individuals, these antiviral mechanisms are poorly understood. Here, we carried out the first deep mRNA sequencing analysis of mucosal host responses in the primary infection compartment during acute SIV infection. We found that during acute infection, a significant host response was mounted in the mucosa before inflammation was triggered. Our analysis indicated that the response has a detrimental effect on tissue integrity, causing increased permeability, tissue damage, and recruitment of SIV target cells. These results emphasize the importance of mucosal host responses preceding immune activation in preventing systemic SIV infection.

African green monkeys avoid SIV disease progression by preventing intestinal dysfunction and maintaining mucosal barrier integrity

“…Any loss of tight junction proteins (i.e., claudin-3), due to cell death or internalization via endocytosis in response to infection would be indicative of a loss of mucosal integrity [60]. In SIV-infected RMs, claudin-3 staining has been used to measure the breakdown in mucosal epithelium continuity, while expression of claudin-encoding genes (i.e., CLDN3) has been shown to be downregulated as early as 3 dpi [132], similar to experimentally-induced IBD [95]. Importantly, at no timepoint post SIVsab infection in AGMs, did we find increases in mucosal apoptosis, proliferation or loss of the mucosal epithelium integrity, in stark contrast with reduced mucosal epithelium integrity in chronically…”

Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)

“…We also identified thousands of transcript sequences that are partially or completely ‘missing’ from current macaque genome assemblies ( 2 ). Many newly identified transcripts were differentially expressed during Ebola virus infection of cynomolgus macaques ( 2 ) or simian immunodeficiency virus infection of rhesus macaques ( 2 , 16 ).…”

“…Also, because the rhesus macaque is a widely used as a model to study HIV/AIDS, we provide a centralized pointer to macaque RNA-seq datasets released by the NHP Functional Genomics Core recently established by NIAID ( http://nhp-fgc.org ). This includes publically released data such as an mRNA-seq dataset of macaque rectal samples from multiple baseline and SIV-infected animals ( 16 ).…”

GASS: genome structural annotation for Eukaryotes based on species similarity

“…The three RNA-Seq and two DNA-Seq datasets to prove the mis-assembly of rheMac3 genome on subsection “Mis-assembly of rheMac3 genome leads to mis-annotations in RefSeq-rheMac3” are from NCBI SRA. The accession numbers for RNA-Seq datasets are SRX424026 [ 31 ], SRX209571 [ 32 ] and SRX518478 [ 33 ]; and the accession number for DNA-Seq datasets are SRX489030 [ 34 ], SRX480828 [ 34 ].…”