Accession	GSE169310
Status	2021/3/23
Title	H3K4me3 histone ChIPseq Analysis Reveals Molecular Mechanisms Responsible for Neutrophil dysfunction in HIV-infected individuals
Organism	Homo sapiens
Experiment type	Genome binding/occupancy profiling by high throughput sequencing
Summary	In this study, we demonstrated dysregulation of DNA transcription in H3K4me3 histone in circulating neutrophils of HIV-infected subjects. Chromatin immunoprecipitation sequencing (ChIPseq) H3K4me3 histone analysis revealed that the most spectacular abnormalities were observed in the exons, introns and promoter-TSS regions. Bioinformatic analysis of Gene Ontology, including biological processes, molecular function and cellular components, demonstrated that the main changes were related to the genes responsible for cell activation, cytokine production, adhesive molecule expression, histone remodeling via upregulation of methyltransferase process and downregulation of NF-kB transcription factor in canonical pathways. Abnormalities within H3K4me3 implicated LPS-mediated NF-kB canonical activation pathway that was a result of low amounts of kB DNA sites within histone H3K4me3, low NF-kB (p65 RelA) and TLR4 mRNA expression as well as reduced free NF-kB (p65 RelA) accumulation in the nucleus. ‘Panoramic view of the landscape gene’ within histone H3K4me3 led us postulate that impairment within the canonical NF-kB cell activation pathway may be the primary phenomenon responsible for neutrophil dysfunction observed in HIV-infected individuals
Samples	GSM ID Sample info Characteristics Description GSM5195429 HIV#11 H3K4me3 cell type:highly purified peripheral blood neutrophils; disease state:HIV infected; chip antibody:anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745; treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt);HOMER results: motif1-45.motif GSM5195430 HC#1 H3K4me3 cell type:highly purified peripheral blood neutrophils; disease state:healthy; chip antibody:anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745; treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt);HOMER results: motif1-45.motif GSM5195431 HC#1 input cell type:highly purified peripheral blood neutrophils; disease state:healthy; chip antibody:none (input); treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) - GSM5195432 HC#2 H3K4me3 cell type:highly purified peripheral blood neutrophils; disease state:healthy; chip antibody:anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745; treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt);HOMER results: motif1-45.motif GSM5195426 HIV#4 H3K4me3 cell type:highly purified peripheral blood neutrophils; disease state:HIV infected; chip antibody:anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745; treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt);HOMER results: motif1-45.motif GSM5195433 HC#17 H3K4me3 cell type:highly purified peripheral blood neutrophils; disease state:healthy; chip antibody:anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745; treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt);HOMER results: motif1-45.motif GSM5195427 HIV#4 input cell type:highly purified peripheral blood neutrophils; disease state:HIV infected; chip antibody:none (input); treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) - GSM5195428 HIV#6 H3K4me3 cell type:highly purified peripheral blood neutrophils; disease state:HIV infected; chip antibody:anti-trimethyl-Histone H3 (Lys4) (MC315, Merck Millipore, cat. 04-745; treatment:2x10^6 neutrophils were incubated without stimulation in RPMI 1640 for 6 h (5%CO2, 20oC, humid atmosphere) MACS2 results: GO (biocyc.txt; bilogical_process.txt; cellular_component.txt; molecular_function.txt; pathwayInteractionDB.txt);HOMER results: motif1-45.motif
Platform	GPL21697  : NextSeq 550 (Homo sapiens)
Literature	34335583