Genome-wide expression profiling establishes novel modulatory roles of vitamin C in THP-1 human monocytic cell line
© The Author(s). 2017
Received: 15 September 2016
Accepted: 16 March 2017
Published: 23 March 2017
Vitamin C (vit C) is an essential dietary nutrient, which is a potent antioxidant, a free radical scavenger and functions as a cofactor in many enzymatic reactions. Vit C is also considered to enhance the immune effector function of macrophages, which are regarded to be the first line of defence in response to any pathogen. The THP-1 cell line is widely used for studying macrophage functions and for analyzing host cell-pathogen interactions.
We performed a genome-wide temporal gene expression and functional enrichment analysis of THP-1 cells treated with 100 μM of vit C, a physiologically relevant concentration of the vitamin. Modulatory effects of vitamin C on THP-1 cells were revealed by differential expression of genes starting from 8 h onwards. The number of differentially expressed genes peaked at the earliest time-point i.e. 8 h followed by temporal decline till 96 h. Further, functional enrichment analysis based on statistically stringent criteria revealed a gamut of functional responses, namely, ‘Regulation of gene expression’, ‘Signal transduction’, ‘Cell cycle’, ‘Immune system process’, ‘cAMP metabolic process’, ‘Cholesterol transport’ and ‘Ion homeostasis’. A comparative analysis of vit C-mediated modulation of gene expression data in THP-1cells and human skin fibroblasts disclosed an overlap in certain functional processes such as ‘Regulation of transcription’, ‘Cell cycle’ and ‘Extracellular matrix organization’, and THP-1 specific responses, namely, ‘Regulation of gene expression’ and ‘Ion homeostasis’. It was noteworthy that vit C modulated the ‘Immune system’ process throughout the time-course.
This study reveals the genome-wide effects of physiological levels of vit C on THP-1 gene expression. The multitude of effects impacted by vit C in macrophages highlights its role in maintaining homeostasis of several cellular functions. This study provides a rational basis for the use of the Vitamin C- THP-1 cell model, to study biochemical and cellular responses to stresses, including infection with M. tuberculosis and other intracellular pathogens.
Human leukocytes and cultured cells of leukocyte origin can accumulate vitamin C (vit C) to millimolar concentrations, which is significantly above that in circulating blood where it is estimated to be in the range of about 50-100 μM, and of this at least 95% is in the reduced form [1–4]. Vit C is accumulated in mammalian cells by two types of transporters, namely, sodium-ascorbate co-transporters (SVCTs) for active transport of the reduced form and hexose transporters (GLUTs) for taking up the oxidized form, dehydroascorbate (DHA) . Activated THP-1 cells rapidly accumulate vit C to millimolar concentrations, similar to activated RAW264.7 murine macrophages [6, 7]. Ascorbate is a cytosolic antioxidant and free radical scavenger that operates in concert with lipid-soluble membrane antioxidants, such asα-tocopherol or carotene, and may increase the ability of cells to cope with reactive oxygen metabolites generated by their activated phagocytic apparatus [8, 9]. Vit C also functions as a cofactor for enzymes involved in the biosynthesis of collagen [10, 11] and norepinephrine , and in the amidation of hormones . Several studies have described that adequate circulating levels of vit C are consistent with a decreased risk of varied disease pathologies, such as stroke  or cardiovascular disease . In this context, vit C supplementation has been reported to provide symptomatic relief and to enhance the expression of specific immune response markers . It is noteworthy that most of the studies addressing the effects of vit C at optimum levels (70 μmol/l) on human health considered its supplementation together with other nutrients (usually zinc or within a multivitamin–multimineral formula), whilst a real understanding of its mechanism of action would possibly require its supplementation as a single component .
Mycobacteria-macrophage interactions have been characterized in primary as well as in vitro-differentiated cells to mimic the events that are considered to occur in vivo, namely, the entry and intracellular residence of Mycobacterium tuberculosis (Mtb) within alveolar macrophages [18–20]. Macrophage-like cell lines of human origin are considered as good models for in vitro-differentiated monocyte-derived macrophages ; moreover, they have the advantages of no donor variability of macrophage function, large numbers of cells can be grown reproducibly, cells can be studied at different stages (resting versus activated) and the cells closely model alveolar macrophages for processing of intracellular pathogens, for example Mtb-induced apoptosis . Importantly, the human acute monocytic leukemia cell line, THP-1, develops macrophage functions following the addition of stimulators such as Phorbol myristate acetate (PMA) . These differentiated THP-1 cells showed remarkable phenotypic changes e.g., increased phagocytic activity and HLA-DR expression, increased complement receptor, FcγRI and FcγRII expression , CD11b, and CD14 [24, 25], indicating their similarity but not identity with mature human macrophages. THP-1 cells were found to be a suitable ex vivo infection model for studying Mtb-host interactions and anti-mycobacterials’ action on intracellular bacteria and yielded results comparable to that obtained using monocyte-derived macrophages (MDMs) .
We have reported earlier that tubercle bacilli treated with vit C develop an isoniazid-tolerant phenotype that is considered to be an indicator of bacterial dormancy. The vit C-induced drug tolerant response occurred in vitro as well as in infected THP-1 cells . In view of the ability of vit C to induce a ‘dormant’ phenotype in Mtb, a temporal transcriptome profiling study of baseline gene expression to assess the response of THP-1 cells to vit C was undertaken. It was expected that such an analysis would pave the way for utilizing the vit C-based THP-1 infection model to study interactions of host cells with ‘dormant’ Mtb.
Cell culture conditions
THP-1 cells were grown to confluency in complete RPMI 1640 (Sigma-Aldrich®) medium (c-RPMI) supplemented with 2 mM glutamine, HEPES and sodium bicarbonate with 10% fetal bovine serum (HyClone™) and 1× Penicillin-Streptomycin solution (Sigma-Aldrich®) in 5% CO2, at 37 °C. Cell viability was checked by Trypan Blue exclusion and 99% viable cultures were used for gene expression studies.
Gene expression analysis
Approximately, 8 × 106 THP-1 cells were seeded per T-75 cm2 flask/20 ml c-RPMI in triplicate. Following differentiation with 30 nM phorbol myristate acetate (PMA) for 16–18 h, fresh c-RPMI was added and the cells were rested for 2–3 h. Subsequently, vit C (100 μM, Sigma-Aldrich®) was added to the treated flasks and not in the untreated (UT, control) flasks. At specified time-points (8, 24, 48 and 96 h) cells were harvested (vit C-treated and control flasks), the cell pellet was re-suspended in 1 ml TRI reagent (Molecular Research Center, USA) and stored at -80 °C for the isolation of RNA.
RNA isolation and microarray analysis
Briefly, 1/10th volume of bromochloropropane (Molecular Research Center, USA) was added to thawed THP-1 lysates, vigorously shaken for 10 s and incubated for 10 min at room temperature. The samples were centrifuged at 12,000 rpm for 15 min at 4 °C. Precipitation was carried out in the presence of 1/100th volume of polyacryl carrier and isopropanol (0.6 volumes, for 30 min), centrifuged (12,000 rpm, 4 °C for 15 min), washed with 75% ethanol and then air-dried. Total RNA was dissolved in 100 μl of DEPC-treated water. Ten μg of total RNA was subjected to microarray analysis.
Microarray data processing and analysis
A plan of the microarray analysis is shown in Fig. 1a. Raw signal data from 19 expression arrays were log base 2-transformed and processed by 75th percentile shift normalization using the GeneSpring GX software (Agilent Technologies) as described [27–29]. Further, the robustness of data among the biological replicates for both untreated (UT) and vit C-treated samples was analyzed by hierarchical clustering (Fig. 1b). Next, expression fold change with p-values (student t-test) of all vit C treated conditions was calculated with respect to their time-matched untreated (UT) controls. Genes for analysis were selected by filtration at probe level. If there were multiple probes for the same gene, and they showed similar fold expression values (i.e. either all positives or all negatives), then the gene was selected for analysis, and where different probes for the same gene showed opposite fold expression values (positive and negative), that gene was removed from the analysis. Thus, at every time-point, ~5000 genes were not considered and ~ 25,000 genes were considered for analysis. Significant expression values were determined based on log2 fold change ≥ 1 with Benjamini-Hochberg FDR correction (q ≤0.05). Microarray experiments were performed at Genotypic Technology (Bengaluru, India) and the results are deposited at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73421. The biological significance of the gene expression modulation on vit C-treatment was analyzed using an online enrichment tool GOrilla (Gene Ontology enRIchment anaLysis and visuaLizAtion Tool; http://cbl-gorilla.cs.technion.ac.il, ) using the input option of a single ranked list of genes on the basis of expression value. Gene descriptions explained in the results were obtained from Gene Cards® Human Gene database (http://www.genecards.org/cgi-bin/carddisp.pl?gene).
Intracellular vit C estimation
For vit C estimation, DNPH method was used . The experimental set up was the same as that for gene expression analysis and performed in triplicate. Briefly, at the individual timepoints (8, 24 and 48 h), THP-1 cells (UT and Vit C-treated) were scraped and harvested at 1200 rpm for 10 min. The pellet from two flasks was resuspended in 200 μl water and the suspension was subjected to four consecutive freeze-thaw cycles in chilled ethanol and 37 °C water bath for one minute each. Further, the protocol was same as described .
Viability of vit C-treated THP-1 cells
Briefly, ~5 × 104 THP-1 cells were seeded in a 96-well tissue culture plate in triplicate wells and differentiated with 30 nM PMA for 16-18 h. The cells were washed and allowed to rest for 2-3 h. This was followed by the addition of vit C (100 μM) and the viability of treated and control wells were assessed using MTT at 96 h. Briefly, 20 μL of MTT (Sigma-Aldrich®) (5 mg/mL) was added and incubated for 4–5 h at 37 °C. Following incubation, media was discarded and the formazan crystals were solubilized by adding 200 μL DMSO and the absorbance measured at 590 nm.
Intracellular vit C accumulation
Temporal transcriptome analysis
Whole data enrichment analysis
Next, individual enrichment analysis was performed for the entire temporal data set. GOrilla enrichment tool was used for this analysis, employing the input option of a single ranked list of genes on the basis of expression values. The significantly enriched functional classes (p-value of enrichment ranging from 10-4 to 10-15 with FDR correction, q-value ranging from 10-4 to 10-13) were selected for gaining insights into global responses of THP-1 cells to vit C.
Clustering of predominant functional responses
The functional enrichment is depicted as up- and down-regulated classes (described in sections below) to highlight the diversity in biological processes in response to vit C.
Further, the representation of the data does not exclude the possibility that different genes under a particular GO term respond in different directions. There are functional classes that showed significant enrichment under both up and down-regulated category thereby signifying the differential regulation of genes for the same biological process.
Up-regulated cluster of functional classes
Down-regulated cluster of functional classes
Unique temporal responses
In addition to the common transcriptional response described above, several functional classes showed time-dependent expression following vit C treatment. The classes pertinent to the role of THP-1 cells in macrophage function are discussed in detail.
Early response to vit C (at 8 h)
The enrichment result for the down-regulated classes revealed that the majority of the classes were not obviously linked to the function of macrophages under ex vivo condition. An exceptional class ‘Positive regulation of MAPK cascade’ (Fig 7b) is discussed, as it is under ‘Regulation of signal transduction’ class, which seemed to be a continuous response to vit C (Fig. 4b). The function of these genes (Fig. 7b) covers a wide spectrum of functional processes such as growth and differentiation, cell survival and macrophage function, some genes play an essential role in innate immune response and inflammation and are involved in cytoskeleton reorganization.
Response at 24 h
Predominant enriched GO classes at 24 h in vit C-treated THP-1 cells
Cell cycle checkpoint
Cell cycle phase
Cell cycle phase transition
Cell cycle process
DNA integrity checkpoint
G1/S transition of mitotic cell cycle
M phase of mitotic cell cycle
Mitotic cell cycle
Mitotic cell cycle phase transition
Regulation of transcription involved in G1/S phase of mitotic cell cycle
S phase of mitotic cell cycle
Telomere maintenance via semi-conservative replication
ATP-dependent chromatin remodeling
CENP-A containing nucleosome assembly at centromere
Chromatin assembly or disassembly
Chromatin remodeling at centromere
DNA replication-independent nucleosome assembly
DNA replication-independent nucleosome organization
Telomere maintenance via telomere lengthening
DNA metabolic process
DNA metabolic process
DNA metabolic process
DNA metabolic process
DNA metabolic process
DNA replication initiation
DNA metabolic process
DNA strand elongation
DNA metabolic process
DNA strand elongation involved in DNA replication
DNA metabolic process
DNA unwinding involved in replication
DNA metabolic process
DNA-dependent DNA replication
DNA metabolic process
Double-strand break repair via homologous recombination
DNA metabolic process
Maintenance of fidelity involved in DNA-dependent DNA replication
DNA metabolic process
DNA metabolic process
Nucleotide-excision repair, DNA gap filling
DNA metabolic process
DNA metabolic process
Regulation of DNA metabolic process
DNA metabolic process
Regulation of DNA replication
DNA metabolic process
DNA metabolic process
Telomere maintenance via recombination
DNA metabolic process
Responses at 48 h
Responses at 96 h
Persisting from 48 h onwards were the ‘Immune system process’ and ‘Regulation of cytokine secretion’ classes that reflect vit C to be of paramount importance for immune system function (Fig. 8b). Consistent with this role, the up-regulated classes at 96 h include genes coding for chemokines, coding for molecules involved in antigen presentation (Fig. 8b). Thus, vit C exerts its regulatory role on immune recognition (CD1 and HLA) as well as on levels of cytokines/chemokines, thereby aiding macrophages’ role in innate defence. Importantly, the expression pattern at the later time-point of the study i.e. 96 h, is indicative of a sustained cellular response to vit C.
Among the down-regulated classes, the enrichment of the class ‘Adenylate cyclase modulating GPCR signaling pathway’ indicated a sustained modulatory effect of vit C on cAMP levels and associated signaling (Fig. 8b). A careful examination of the genes involved, revealed the down regulation of genes responsible for the activation of adenylate cyclase (e.g. ADRB2, CALCRL) and also, the inhibition of adenylate cyclase activity (e.g. CHRM2, OPRK1, NPY1R). The plausible underlying explanation could be that it is the balance in the activities of these opposing functions, depending on the stimuli and their duration, which ultimately determines the intracellular levels of cAMP. Linked to the class ‘Chemical ion homeostasis’ described at 48 h, the down regulation of ‘Calcium related signaling using intracellular calcium source’ indicated the modulation of calcium ion-associated signaling pathways on vit C-treatment. The decreased expression of HOMER2 (interacts with Ryanodine receptors (RYR)) and also of the GPCR i.e. GPR143 that stimulates Ca2+ influx into the cytoplasm suggested modulatory effect of vit C on calcium-associated signaling (Fig. 8b).
It is imperative to emphasize that although the temporal response to vit C was analyzed in a step-wise manner, the functional responses clearly reflected an interconnection of the biological pathways, that are integrated in a whole biological system.
The biological role of dietary antioxidant molecules is no longer simply ascribed to their ability to serve as ‘electron donors’; rather, antioxidants such as vit C in the present context, also act by modulating gene expression and signaling. In vivo and in vitro studies have shown that some of the effects of vit C on cells are at the transcriptional level [32–34]. The present study is the first report of the genome-wide effects of vitamin C on gene expression of differentiated THP-1 cells treated with a physiologically relevant concentration of vit C, namely circulating plasma concentration of ~ 100 μM. The intracellular concentration of vit C in THP-1 cells ranged between 20 μM and 80 μM during 8 to 48 h. Macrophages are expected to be constantly exposed to ~ 70 to 100 μM levels of vit C in nutritionally adequate subjects , therefore, the observed modulation of gene expression can be considered as a baseline macrophage-like cell response to physiological concentrations of vit C. It is remarkable that this baseline concentration of vit C mediates widespread changes in gene expression of THP-1 cells as revealed by whole genome enrichment analysis.
Vit C seemed to exert its effect on other notable functional processes in THP-1 cells as well, namely, ‘Cell cycle’, ‘DNA replication’ and ‘Chromosomal organization’ (Table 1) at 24 h and included genes belonging to various GO classes reflecting role of vit C at different steps in the cell cycle such as cell cycle check point, G1 to S transition, genes involved in DNA replication and repair as well as genes involved in chromosomal remodeling. Many reports have explained the effect of vit C on cell cycle processes [45, 46]. Similarly, Belin et al. demonstrated the anti-proliferative role of vit C, potentially due to the inhibition of expression of genes involved in cell division progression . Another noteworthy response to vit C was ‘Extracellular matrix organization’ biological process. ECM organization is a well-known process where vit C plays an essential role. This class was enriched in both up and down regulation (summarized in Fig. 9) and is consistent with the essential cofactor function of vit C in the synthesis of collagen, the main structural component of ECM. Vit C is required for the hydroxylation of proline residues in collagen chains by prolyl hydroxylase , for proper triple helix assembly in the endoplasmic reticulum and for the secretion of procollagen . A study of skin fibroblasts reported the modulatory effects of a stable vit C derivative (AA2P) on ECM remodeling . A comparison of the gene profiles of THP-1 and skin fibroblast cells revealed a similar GO enrichment analysis with a differential selection of genes in these two cell types for the same physiological response. For example, IL-6 is down-regulated in THP-1 cells, whereas this gene is induced in skin fibroblasts .
‘Modulation of Immune response’ is one of the most noteworthy functions of vit C (48 h onwards) [51–55]. Vit C appears to mediate the regulation of various aspects of the immune response, namely, innate receptors, chemokines, antigen presentation, immune signaling and transcriptional regulation. Another interesting class where vit C exerted its effect was ‘Cholesterol transport’. The association between cholesterol metabolism and vit C was observed when chronic latent vitamin C deficiency led to hypercholesterolaemia and cholesterol accumulation in certain tissues , suggesting that deficiency of vitamin C might deregulate cholesterol homeostasis. The THP-1 cell infection model is widely considered as a suitable model for studies of Mtb infection [21, 23]. Interestingly, Mtb infection results in the acquisition of a foam cell phenotype , wherein, Mtb maintains itself within lipid bodies and develops drug tolerance [57, 58]. THP-1 cells have also been established as a model to study atherosclerosis due to its foam cell phenotype . Enrichment analysis in the present study showed down regulation of genes (Fig. 8a) participating in lipase activity (ApoC2, LIPG), uptake (MSR1) and egress (NPC2). Further analysis of ATP-binding cassette transporters, ABCA1 and ABCG1, which play a pivotal role in cholesterol efflux from macrophage foam cells , revealed no significant change in expression. Additionally, nuclear receptors, peroxisome proliferator activated receptors (PPARs) known to exert anti-atherogenic effects by enhancing cholesterol efflux via activation of the liver X receptor (LXR)-ABCA1 pathway [61, 62], showed up regulation by nearly 2-fold at 48 h (PPARα and PPARγ). At physiological levels, the function of vit C in THP-1 cells appears to be more towards balancing the uptake and efflux of cholesterol and thereby preventing the formation of foam cells.
A novel role of vit C was observed to be in ‘Cellular metal ion homeostasis’, particularly in calcium homeostasis as evident by the enrichment of the class ‘Calcium-mediated signaling using intracellular calcium source’ (at 96 h). The decreased expression of genes involved in calcium associated signaling such as GPR143 and HOMER2, indicated the regulation of calcium ion on vit C treatment. There is no report in the literature to the best of our knowledge that has described this regulatory role of vit C. Another ion of interest is iron. Vit C within mammalian systems can regulate cellular iron uptake and metabolism, both at the transcriptional and post-transcriptional levels. The major regulatory factor for the transcriptional control of certain genes involved in iron metabolism is the HIF system that responds to changes in oxygen (O2) tension, intracellular iron and vit C levels. The HIF system includes the O2and iron-regulated proteins, HIF1α and HIF2α [63, 64]. Under conditions of normoxia, high levels of vit C (>100 μM) and iron, prolylhydroxylases are fully active and hydroxylate the 1α subunit at specific proline residues [65, 66], targeting HIF1α for proteasomal degradation [67, 68]. Under the condition of low O2 (3–5% O2, in vivo), low iron, and low vit C, HIF1α /2α proteins are stabilized and activate the transcription of specific genes that contain hypoxia- response elements (HREs), such as genes encoding Tf(TF), TfR1 (TFRC). Interestingly, none of the HIF target genes (described by Lane and Richardson ) showed any change of expression in THP-1 cells on vit C-treatment, possibly owing to the differences in regulatory mechanism under cell culture and in vivo conditions [68, 70, 71].
A comparison with the responses of skin fibroblasts to  suggested that macrophages were far more responsive to treatment with vit C; nearly 294 genes were shown to be differentially regulated in skin fibroblasts at 5 days , in contrast, 874 genes were differentially regulated at the earliest time-point i.e. 8 h in THP-1 cells. The number of DRGs, however, decline from 8 to 96 h.
The absence of cellular response to oxidative stress was a notable finding of this study. It has been reported that pharmacological levels of vit C (0.3 mM to 20 mM) mediate Fenton chemistry that occurs readily in vitro and generates reactive oxygen species . However, due to the non-availability of catalytic metal ions in vivo and in cell culture owing to their sequestration by various metal binding proteins such as ferritin, transferrin, and ceruloplasmin [73, 74], there are minimal chances of the occurrence of Fenton reaction . Thus, the pro-oxidant effect of vit C can be ruled out in the present study as vit C was used at physiological levels and not at pharmacological levels [72, 75].
In conclusion, this genome-wide transcriptome analysis has disclosed that vit C, being an essential dietary component, regulates a wide spectrum of biological processes in THP-1 macrophages. These insights have opened a new dimension to be explored towards understanding the pleiotropic effects of vit C on eukaryotic gene expression and function. The study will also have an impact on curating databases and biological networks. The present findings further point towards the potential utility of the THP-1 cell model for examining the role of vit C in modulating macrophage responses to various stresses, including infection by intracellular pathogens.
We duly acknowledge Dr. Dhiraj Kumar, International Center for Genetic Engineering and Biotechnology, New Delhi and Dr. Sudha Rao and Mohd Aiyaz of Genotypic Pvt. Ltd., Bengaluru, India for valuable discussion during data analysis. The facilities of Biotechnology Information System (BTIS) and Sushma Rani of the Department of Biotechnology, AIIMS are also acknowledged for assistance in microarray data analysis.
JST is thankful to the Department of Biotechnology (DBT) for a Tata Innovation Fellowship and to the Department of Science and Technology, Government of India for the J.C. Bose National fellowship. SDB is thankful to the DBT and the Indian Council of Medical Research (ICMR), Government of India for Junior and Senior Research Fellowships. MN acknowledges the ICMR for a Senior Research Fellowship (SRF) and KS is thankful to the Council of Scientific and Industrial Research, Government of India for a SRF.
Availability of data and materials
The dataset(s) supporting the conclusions of this article are available in the GEO data repository GSE73421 [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73421].
Other supporting information is available as Additional files associated with this manuscript.
SDB performed the THP-1 vit C estimation and setting up of THP-1 vit C – model and RNA extraction for microarray, analysis of data and drafted the manuscript. MN carried out the data analysis. KS performed the THP-1 vit C viability experiment and contributed to discussions regarding the data analysis. JST contributed to the overall study design and writing the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
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