Dataset: Transcription profiling by array of inguinal lymph nodes of HIV-1-infected individuals

During HIV-1 infection, there is a massive perturbation of host gene expression, but as yet, genome-wide studies have not identified host...

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During HIV-1 infection, there is a massive perturbation of host gene expression, but as yet, genome-wide studies have not identified host genes affecting HIV-1 replication in lymphatic tissue, the primary site of virus-host interactions. In this study, we isolated RNA from the inguinal lymph nodes of 22 HIV-1-infected individuals and utilized a microarray approach to identify host genes critically important for viral replication in lymphatic tissue by examining gene expression associated with viral load. Strikingly, ~95% of the transcripts (558) in this data set (592 transcripts total) were negatively associated with HIV-1 replication. Genes in this subset (1) inhibit cellular activation/proliferation (ex.: TCFL5, SOCS5 and SCOS7, KLF10), (2) promote heterochromatin formation (ex.: HIC2, CREBZF, ZNF148/ZBP-89), (3) increase collagen synthesis (ex.: PLOD2, POSTN, CRTAP), and (4) reduce cellular transcription and translation. Potential anti-HIV-1 restriction factors were also identified (ex.: NR3C1, HNRNPU, PACT). Only ~5% of the transcripts (34) were positively associated with HIV-1 replication. Paradoxically, nearly all these genes function in innate and adaptive immunity, particularly highlighting a heightened interferon system. The predominance of negative correlations as well as the disconnect between host defenses and viral load point to the importance of genes that regulate target cell activation and genes that code for potentially new restriction factors as determinants of viral load rather than conventional host defenses. Total RNA was isolated from the inguinal lymph nodes of 22 HIV-1-infected subjects at different clinical stages (and varying viral loads) and prepared for RNA extraction and hybridization on Affymetrix Human Genome U133 Plus 2.0 microarrays. Replicate arrays were performed for lymph node samples to minimize assay noise and host genes critically important for viral replication in lymphatic tissue were identified by examining gene expression and its association with viral load. Replicates were not performed for samples WB91 and TS35 due to limited amounts of biomaterial.

Species:: human
Samples:: 42
Source:: E-GEOD-21589
PubMed:: 20935203
Updated:: Dec.12, 2014
Registered:: Sep.15, 2014

Factors: (via ArrayExpress)

Sample	PLASMA HIV-1 RNA LEVELS (COPIES/ML)	AGE	PERIPHERAL BLOOD CD4+ T CELLS (CELLS/ML)	ETHNICITY	SEX
GSM538932	14696	41	494	Caucasian	male
GSM538932	14696	41	494	Caucasian	male
GSM538934	3610	26	683	Caucasian	male
GSM538934	3610	26	683	Caucasian	male
GSM538936	439000	51	400	Caucasian	male
GSM538936	439000	51	400	Caucasian	male
GSM538938	32173	32	824	Caucasian	male
GSM538938	32173	32	824	Caucasian	male
GSM538940	19400	23	209	African American	male
GSM538940	19400	23	209	African American	male
GSM538942	24718	37	234	African American	male
GSM538943	484694	59	370	Caucasian	male
GSM538943	484694	59	370	Caucasian	male
GSM538945	100000	30	333	Caucasian	male
GSM538945	100000	30	333	Caucasian	male
GSM538947	100000	42	663	Caucasian	male
GSM538948	71200	34	333	Caucasian	male
GSM538948	71200	34	333	Caucasian	male
GSM538950	27200	23	259	African American	male
GSM538950	27200	23	259	African American	male
GSM538952	15284	32	400	Caucasian	male
GSM538952	15284	32	400	Caucasian	male
GSM538954	122000	34	202	Caucasian	male
GSM538954	122000	34	202	Caucasian	male
GSM538956	174000	49	478	Caucasian	male
GSM538956	174000	49	478	Caucasian	male
GSM538958	46400	63	248	Caucasian	male
GSM538958	46400	63	248	Caucasian	male
GSM538960	100000	36	286	Caucasian	male
GSM538960	100000	36	286	Caucasian	male
GSM538962	20014	39	685	Caucasian	male
GSM538962	20014	39	685	Caucasian	male
GSM538964	31922	35	372	Caucasian	male
GSM538964	31922	35	372	Caucasian	male
GSM538966	4960	49	147	Caucasian	male
GSM538966	4960	49	147	Caucasian	male
GSM538968	35000	43	81	Caucasian	male
GSM538968	35000	43	81	Caucasian	male
GSM538970	12046	40	112	African American	female
GSM538970	12046	40	112	African American	female
GSM538972	10684	45	188	African American	male
GSM538972	10684	45	188	African American	male