GEO DataSets

(Submitter supplied) The mucosa that lines the respiratory and gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Using the simian immunodeficiency virus (SIV) rhesus macaque model, we have performed a comparative analysis of host gene expression in the lung and GI mucosa in response to SIV infection and antiretroviral therapy. Microarrays were used to characterize changes in gene expression in the colonic, jejunal, and pulmonary (lung) mucosa that occur during chronic SIV infection in the presence or absence of antiretroviral therapy.

Organism:

Macaca mulatta

Type:

Expression profiling by array

Dataset:

GDS4993

Platform:

GPL3535

32 Samples

Download data: CEL

Analysis of colon, jejunum and lung from therapy-naïve, SIV-infected males. Gut and lung mucosa are important entry portals for pathogens and provide innate immune defense against infection. Results provide insight into molecular mechanisms underlying mucosal immune response during SIV infection.

Organism:

Macaca mulatta

Type:

Expression profiling by array, count, 2 infection, 3 tissue sets

Platform:

GPL3535

Series:

GSE51615

23 Samples

Download data: CEL

(Submitter supplied) Pathogenic HIV/SIV infection of humans and rhesus macaques (RMs) induces persistently high production of type-I interferon (IFN-I) which is thought to contribute to disease progression. To elucidate the specific role of IFN in SIV pathogenesis, 12 RMs were treated prior to i.v. SIVmac239 infection with a high or a low dose of an antibody (AGS-009) that neutralizes most IFN subtypes, and compared with six mock-infused, SIV-infected controls. more...

Organism:

Macaca mulatta; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

107 Samples

Download data: TXT

(Submitter supplied) We used the ileal loop model to assess the effects of enteric bacteria organisms on host gene expression in intestinal tissue independent of and following early SIV infection. SIV infection in the gut causes rapid and severe immune dysfunction and damage to the intestinal structure, this may alter the intimate interaction with lumenal organisms. This study was performed to determine whether early SIV infection, prior to the depletion of CD4+ T cells, can alter interaction of the host with pathogenic Salmonella serovar Typhimurium (ST) or commensal Lactobacillus plantarum (LP), and to further understand the earliest changes to the intestinal mucosa following SIV infection. more...

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL3535

28 Samples

Download data: CEL

(Submitter supplied) Recent studies of nonhuman primates (NHPs) have suggested that during the acute phase of infection, antiviral mucosal immunity is restricting 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 SIVmac251 to examine how the mucosal immune system is overcome by SIV during acute infection. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13766

23 Samples

Download data: TXT

(Submitter supplied) This study describes differential miRNA expression in small intestinal lamina propria leukocyte samples longitudinally during the course of SIV infection of rhesus macaques. Notably, the T-cell activation associated miR-15b, miR-142-3p, miR-142-5p and miR-150 expression was significantly downregulated at 90 and 180DPI. Further, reporter and overexpression assays validated IRAK1 as a direct miR-150 target. more...

Organism:

Homo sapiens; Macaca mulatta

Type:

Expression profiling by RT-PCR

Platform:

GPL17797

25 Samples

Download data: TXT

(Submitter supplied) We used microarrays to detail the global gene expression changes in the ileum of SIV-infected and uninfected macaques following administration of L. plantarum.

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL3535

12 Samples

Download data: CEL

(Submitter supplied) The mucosa that lines the gastrointestinal (GI) tracts is an important portal of entry for pathogens and provides the frontline of immune defense against HIV infection. Epithelial barrier dysfunction during HIV infection has largely been attributed to the rapid and severe depletion of CD4 T cells in the gastrointestinal (GI) tract. In this study, the poential role of small non-coding microRNA (miRNA) to contribute to epithelial dysfunction was investigated in the non-human primate SIV model and microarrays were utilized to determine changes in mucosal gene expression (non-miRNA) that could be correlated to miRNA modulatiolns. more...

Organism:

Macaca mulatta

Type:

Expression profiling by array

Platform:

GPL3535

6 Samples

Download data: CEL

(Submitter supplied) In acute HIV infection immune activation may provide target cells and drive virus replication, which innate immunity may limit. Thus, the net effects of inflammatory mediators, including type I interferon (IFN-I), are unclear. Here, we block IFN-I signaling during pathogenic acute SIV infection with an IFN-I receptor antagonist. Delayed antiviral gene expression, increased SIV reservoir, increased CD4 T cell depletion and accelerated progression to AIDS and death ensue despite decreased T cell activation. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14954

203 Samples

Download data: TXT

(Submitter supplied) We investigated the effects of rhesus CMV (RhCMV) on composition and function of the immune system in young macaques. Within months of infection, RhCMV was associated with impressive changes in antigen presenting cells, T cells, and NK cells—and marked expansion of innate-memory CD8+ T cells. These cells express high levels of NKG2A/C and the IL-2- and IL-15-receptor beta chain, CD122. IL-15 was sufficient to drive differentiation of the cells in vitro and in vivo. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23949

42 Samples

Download data: CSV

(Submitter supplied) Innate lymphoid cells (ILCs) play critical roles in mucosal barrier defense and tissue homeostasis. While ILCs are depleted in HIV-1 infection, this phenomenon is not a generalized feature of all viral infections. Here we show in untreated SIV-infected rhesus macaques (RMs) that ILC3s are lost rapidly in mesenteric lymph nodes (MLN) yet preserved in SIV+ RMs with pharmacologic or natural control of viremia. more...

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19129

11 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Macaca mulatta; Chlorocebus aethiops

Type:

Expression profiling by high throughput sequencing

4 related Platforms

124 Samples

Download data

(Submitter supplied) We devised a systems biology approach to investigate the early host response to high-dose rectal SIV transmission, by transcriptomic comparative analysis of a natural reservoir host SIV model species, African green monkeys (AGMs – Chlorocebus sabaeus, N=28) and a pathogenic model, rhesus macaques (RMs - Macaca mulatta, N=24).on rectal tissues for both AGMs and RMs.

Organism:

Chlorocebus aethiops; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21120 GPL22096

45 Samples

Download data: TXT

(Submitter supplied) We devised a systems biology approach to investigate the early host response to high-dose rectal SIV transmission, by transcriptomic comparative analysis of a natural reservoir host SIV model species, African green monkeys (AGMs – Chlorocebus sabaeus, N=28) and a pathogenic model, rhesus macaques (RMs - Macaca mulatta, N=24).on rectal tissues for both AGMs and RMs.

Organism:

Chlorocebus aethiops; Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24584 GPL14954

79 Samples

Download data: TXT

(Submitter supplied) We performed RNAseq on whole ileum extracts to investigate the underlying gene expression changes associated with MSC administration during chronic SIV infection.

Organism:

Macaca mulatta

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23949

15 Samples

Download data: TAB

(Submitter supplied) The gastrointestinal tract is a major site of early HIV-1 replication and death of CD4+ T cells. As HIV-1 replicates in the gut, the protective epithelial barrier gets disrupted, leading to the entry of bacteria into the underlying tissue and the bloodstream, leading to inflammation and clinical complications even in HIV-1-infected patients taking antiviral drugs. Counteracting these pathogenic processes may require in-depth understanding of the molecular pathways that HIV-1 and microbes utilize to infect, functionally alter and/or kill CD4+ T cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

24 Samples

Download data: CEL

(Submitter supplied) Mucosal surfaces are continuously exposed to, and challenged by, numerous commensal and pathogenic organisms. To guard against infections, a majority of the thymus-derived T lymphocytes are deployed at the mucosa. Although chemokines are known to be involved in the mucosal lymphocyte deployment, it is not clear whether lymphocytes enter the mucosa through directed migration or enhanced random migration. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

3 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Simultaneous analyses of peripheral and mucosal immune compartments can yield insight into the pathogenesis of mucosal-associated diseases. Although methods to preserve peripheral immune cells are well established, studies involving mucosal immune cells have been hampered by lack of simple storage techniques. We provide a cryopreservation protocol allowing for storage of gastrointestinal (GI) tissue with preservation of viability and functionality of both immune and epithelial cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

72 Samples

Download data: TXT