Transcriptome data and gene ontology analysis in human macrophages ingesting modified lipoproteins in the presence or absence of complement protein C1q

We characterized the transcriptional effects of complement opsonization on foam cell formation in human monocyte-derived macrophages (HMDM). RNA-sequencing was used to identify the pathways modulated by complement protein C1q during HMDM ingestion of the atherogenic lipoproteins oxidized low density lipoprotein (oxLDL) and acetylated low density lipoprotein (acLDL). All raw data were submitted to the MIAME-compliant database Gene Expression Omnibus (accession number GEO: GSE80442; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80442). Data presented here include Venn diagram overviews of up- and down-regulated genes for each condition tested, gene ontology analyses of biological processes, molecular functions and cellular components and KEGG pathway analysis. Further investigation of the pathways modulated by C1q in HMDM during ingestion of atherogenic lipoproteins and their functional relevance are described in “Macrophage molecular signaling and inflammatory responses during ingestion of atherogenic lipoproteins are modulated by complement protein C1q” (M.M. Ho, A. Manughian-Peter, W.R. Spivia, A. Taylor, D.A. Fraser, 2016) [1].


Subject area
Biology More specific subject area

Complement and Atherosclerosis
Type of data Tables, Figure  How data was acquired RNA-sequencing was performed using Illumina HiSeq 2500. Gene expression data were input into the DAVID online tool for Gene Ontology and KEGG Pathway analysis.

Data format
Analyzed, raw Experimental factors RNA was isolated from human monocyte-derived macrophages (HMDM) incubated with either oxidized (oxLDL) or acetylated low-density lipoprotein (acLDL) in the presence or absence of C1q.

Experimental features
RNA-seq analysis was performed and data subjected to gene ontology analysis to identify biological processes, molecular functions and cellular components modulated by C1q Data source location

Long Beach, CA
Data accessibility Analyzed data is within this article and raw data is available at the NCBI database at GEO series accession number GEO: GSE80442, http://www.ncbi.nlm.nih.gov/ geo/query/acc.cgi?acc ¼GSE80442

Value of the data
These data provide a list of all genes modulated in human macrophages during foam cell formation.
These data may be used to identify the effect of complement C1q opsonization on macrophage gene expression.
Gene ontology analysis identifies pathways that may provide therapeutic targets for restoring defective foam cell removal in atherosclerosis.

Data
The data shown here include quantification of genes that were up or down-regulated by complement protein C1q in macrophages during ingestion of the atherogenic lipoproteins oxLDL and acLDL and gene ontology analysis. Overlapping upregulated and downregulated genes in the presence of C1q are visualized in Venn diagrams (Fig. 1). Data presented include gene ontology analysis based on biological processes of all significantly modulated genes (Table 1), upregulated genes (Table 2), and downregulated genes (Table 3) due to C1q during ingestion of oxLDL or acLDL and the overlap of the genes in common between lipoprotein treatment. Gene ontology analysis of all modulated genes based on molecular function (Table 4) and cellular component (Table 5) are also provided. Table 6 includes KEGG pathway analysis of all C1q modulated genes based on canonical pathways.

Experimental design
To examine and identify biological processes modulated by C1q during ingestion of modified lipoproteins in an unbiased manner, mRNA was collected from human monocyte-derived macrophages treated with physiologically relevant concentrations of oxidized and acetylated forms of LDL alone, or opsonized with C1q. RNA-seq was performed to identify genes that were up-or downregulated by C1q in macrophages during ingestion of these atherogenic modified lipoproteins.

Cell isolation and lipoprotein treatment
Human monocyte-derived macrophages (HMDM) were prepared from human blood of 10 donors, according to the guidelines and approval of California University Long Beach (CSULB) Institutional Table 1 Gene ontology analysis of all C1q modulated genes based on biological processes.   Review Board and as described [2,3]. RNA was isolated from untreated HMDM or HMDM treated with 10 mg protein/ml oxLDL or acLDL alone, or opsonized with 75 mg/ml C1q. Cells were incubated at 37°C for 3 h in 5% CO 2 as described [1].

RNA isolation and RNA-seq
RNA was isolated and RNA-seq was performed as described [1].

Data analysis
Statistically significant differences in gene expression (p o0.05) were determined using UCI's CyberT in-house software [4]. The overlap of genes determined to be up-or down-regulated by C1q during acLDL or oxLDL treatment was shown with Venn diagrams (Fig. 1). Gene lists of all significantly modulated genes by C1q during ingestion of oxLDL or acLDL (p o0.05) were used as input for gene ontology (GO) analysis (Tables 2,4,5) or KEGG pathway analysis (Table 6) using DAVID (https://david. ncifcrf.gov/) [5]. In addition, resulting upregulated (Table 2) and downregulated (Table 3) gene lists were also used as input separately in DAVID. An adjusted EASE (Expression Analysis Systemic Explore Score) score of 0.05 and a threshold count of 42 genes were used. Benjamini-Hochberg multiple Table 4 Gene ontology analysis of all C1q modulated genes based on molecular function.  testing correction was applied to the p-values. GO terms with FDR q o0.05 were considered significantly enriched within the gene set. The overlap between oxLDL and acLDL gene sets for each GO term was also determined.