Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip

  • Authors:
    • Weiguo Sui
    • Qiupei Tan
    • Ming Yang
    • Qiang Yan
    • Hua Lin
    • Minglin Ou
    • Wen Xue
    • Jiejing Chen
    • Tongxiang Zou
    • Huanyun Jing
    • Li Guo
    • Cuihui Cao
    • Yufeng Sun
    • Zhenzhen Cui
    • Yong Dai
  • View Affiliations

  • Published online on: March 19, 2015     https://doi.org/10.3892/ijmm.2015.2149
  • Pages: 1467-1479
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Abstract

Systemic lupus erythematosus (SLE) is a chronic, potentially fatal systemic autoimmune disease characterized by the production of autoantibodies against a wide range of self-antigens. To investigate the role of the 5-hmC DNA modification with regard to the onset of SLE, we compared the levels 5-hmC between SLE patients and normal controls. Whole blood was obtained from patients, and genomic DNA was extracted. Using the hMeDIP-chip analysis and validation by quantitative RT-PCR (RT-qPCR), we identified the differentially hydroxymethylated regions that are associated with SLE. There were 1,701 genes with significantly different 5-hmC levels at the promoter region in the SLE patients compared with the normal controls. The CpG islands of 3,826 genes showed significantly different 5-hmC levels in the SLE patients compared with the normal controls. Out of the differentially hydroxymethylated genes, three were selected for validation, including TREX1, CDKN1A and CDKN1B. The hydroxymethylation levels of the three genes were confirmed by RT-qPCR. The results suggested that there were significant alterations of 5-hmC in SLE patients. Thus, these differentially hydroxymethylated genes may contribute to the pathogenesis of SLE. These findings show the significance of 5-hmC as a potential biomarker or promising target for epigenetic-based SLE therapies.

Introduction

Systemic lupus erythematosus (SLE) is a typical systemic autoimmune disease, involving diffuse connective tissues (1) and is characterized by immune inflammation. SLE has a complex pathogenesis (2), involving genetic, immunologic and environmental factors. Thus, it may result in damage to multiple tissues and organs, especially the kidneys (3). SLE arises from a combination of heritable and environmental influences.

Epigenetics, the study of changes in gene expression that occur without changes in the DNA sequence, have been suggested to underlie age-related dysfunction and associated disorders (5). The major epigenetic mechanisms include DNA methylation, histone modifications and microRNAs. Recent findings (4) have shown that epigenetic abnormalities are closely correlated with the pathogenesis of SLE. Epigenetic studies may provide clues to elucidate the pathogenesis of SLE and develop new strategies to treat this disease.

DNA hydroxymethylation (5-hydroxymethylcytosine, 5-hmC) (6,7) is a newly described epigenetic modification. It is an oxidative product of the well-known DNA methylation (5-methylcytosine, 5-mC) and catalyzed by the ten eleven translocation (TET) family of enzymes (8), a family of enzymes dependent on 2-oxoglutarate and Fe(II) in vitro and in vivo.

The methylation of cytosine-guanine dinucleotides (CpG) with C (9) is a common epigenetic modification in mammals and is also widespread in animals and plants. As an important epigenetic modification, 5-mC regulates genomic functions, such as gene transcription, X-chromosome inactivation, imprinting, genetic mutation and chromosome stability (1012). 5-mC is only one component of a dynamic epigenetic regulatory network of DNA modifications that also includes 5-hmC, 5-formylcytosine and 5-carboxylcytosine. The reversible methylation of N6-methyladenosine in RNA has also been demonstrated (13).

5-hmC was first found in bacteriophage DNA in 1952. It was utilized several decades ago, only after its recent identification in DNA from murine brain and stem cells rendered 5-hmC a major focus of epigenomic investigations (14). The lower affinity of methyl-binding proteins to 5-hmC compared with 5-mC suggests that this modification may have a distinct role in gene expression regulation. However, 5-hmC is also involved in the DNA demethylation process (15,16).

To obtain a deeper understanding of the role of 5-hmC with regard to the onset of SLE, we generated genome-wide maps of 5-hmC in patients with SLE and healthy controls by performing hydroxymethyl-DNA immunoprecipitation followed by massively parallel sequencing with an Illumina Genome Analyzer (hMeDIP-chip).

Materials and methods

Patients and controls

Whole blood samples from 15 SLE patients and 15 normal controls were obtained from the 181st Hospital of Guilin (China), between January and September, 2011. The SLE diagnoses were confirmed based on pathology and clinical evidence following the American Rheumatism Association classification criteria (1987).

Written informed consent was obtained from all the subjects or their guardians. The use of biopsy material for studies beyond routine diagnosis was approved by the local ethics committee. This study abides by the Helsinki Declaration on ethical principles for medical research involving human subjects.

Genomic DNA extraction and fragmentation

Blood samples were obtained from SLE patients (n=15, 5 μl per subject pooled into one blood sample) and normal controls (n=15, 5 μl per subject pooled into one blood sample). Genomic DNA (gDNA) was extracted from the SLE patients and normal control blood samples using a DNeasy Blood & Tissue kit (Qiagen, Fremont, CA, USA). The purified gDNA was then quantified and its quality assessed using a Nanodrop ND-1000 (Table I). The genomic DNA from each sample pool was sonicated to ~200–1000 bp using a Bioruptor sonicator (Diagenode, Denville, NJ, USA) on the ‘Low’ setting for 10 cycles of 30 sec ‘ON’ and 30 sec ‘OFF’. The gDNA and each sheared DNA sample were analyzed on an agarose gel.

Table I

DNA quantification and quality assurance by NanoDrop spectrophotometer.

Table I

DNA quantification and quality assurance by NanoDrop spectrophotometer.

Sample IDOD260/2 80 ratioOD260/2 30 ratioConc. (ng/μl)Volume (μl)Total amount (ng)
Control1.812.0541.601004160.00
SLE1.631.8932.381003238.00

[i] For spectrophotometer, the optical density (OD) A260/A280 ratio was required to be close to 1.8 for pure DNA (ratios between 1.7 and 2.0 were acceptable). The OD A260/A230 ratio was required to be >1.8.

GO analysis of differentially expressed 5-hmC

To investigate the specific functions of the differentially expressed 5-hmC in the developmental process of SLE, the 5-hmC targets of each differentially expressed 5-hmC were identified by GO categories. The GO categories are derived from gene ontology, which comprise three structured networks of defined terms that describe gene product attributes.

Pathway analysis of differentially expressed 5-hmC

Pathway analysis is a functional analysis mapping genes to KEGG pathways. To evaluate the effect of SNP-to-gene mapping strategy on pathway analysis, we also mapped SNPs to genes within differentially expressed 5-hmC.

Immunoprecipitation

One microgram of the sonicated genomic DNA was used for immunoprecipitation using a mouse monoclonal anti-5-hydroxymethylcytosine antibody (Diagenode). Prior to immunoprecipitation, the spike-in control sequences were mixed with the genomic DNA fragments. The DNA was then heat-denatured at 94°C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 μl of primary antibody overnight at 4°C with rocking agitation in 400 μl of immunoprecipitation buffer (0.5% BSA in PBS). To recover the immunoprecipitated DNA fragments, 200 μl of anti-mouse IgG magnetic beads were added and incubated for an additional 2 h at 4°C with agitation. After immunoprecipitation, a total of five immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. The washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/ml proteinase K for 2 h at 65°C and then allowed to cool to room temperature. The hMeDIP DNA fragments were purified using Qiagen MinElute columns (Qiagen).

DNA labeling and array hybridization

For DNA labeling, the NimbleGen Dual-Color DNA Labeling kit was used according to the manufacturer’s instructions as detailed in the NimbleGen hMeDIP-chip protocol (NimbleGen Systems, Inc., Madison, WI, USA). DNA (1 μg) from each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample). Then, 100 pmol of deoxynucleoside triphosphates and 100 units of the Klenow fragment (New England Biolabs, Beverly, MA, USA) were added, and the mixture was incubated at 37°C for 2 h. The reaction was stopped by adding 0.1X volume of 0.5 MEDTA, and the labeled DNA was purified by isopropanol/ethanol precipitation. The microarrays were hybridized at 42°C for 16–20 h with Cy3/5-labeled DNA in Nimblegen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc.). Following hybridization, washing was performed using the Nimblegen Wash Buffer kit (Nimblegen Systems, Inc.). For array hybridization, Roche NimbleGen’s Promoter plus CpG Island Array was used, which is a 385K array containing 28,226 CpG islands and well-characterized promoter regions (approximately −800 to +200 bp relative to the TSSs) that were completely covered by ~385,000 probes.

Quantitative RT-PCR verification of 5-hmC

The DNA was reverse transcribed to cDNA using gene-specific primers (Table II). The cycle parameters for the PCR reactions were 95°C for 10 min followed by 40 cycles of a denaturing step at 95°C for 10 sec and an annealing/extension step at 60°C for 60 sec. The relative amount of each gene was described using the equation 2-ΔCt, where ΔCt = (CtmRNA-CtU6). The genes analyzed included TREX1, CDKN1A and CDKN1B.

Table II

Reverse-transcription and RT-qPCR primers.

Table II

Reverse-transcription and RT-qPCR primers.

Gene nameRT-qPCR primersAnnealing temperature (°C)Product length (bp)
TREX1F: 5′-GTGTTCCAAGTGCTGCCAAA-3′
R: 5′-CATAAAGAGCGTGGGCTACATAC-3′60245
CDKN1AF: 5′-AGCCTTCCTCACATCCTCCTT-3′
R: 5′-GACGGCCAGAAAGCCAATC-3′60207
CDKN1BF: 5′-GCCAGCCAGAGCAGGTTT-3′
R: 5′-GATTGACACGGCGAGTCTATTT-3′60224

[i] F, forward; R, reverse.

Results

hMeDIP-chip

Using specific antibodies, we performed hMeDIP-chip (17) on two samples: SLE patients and normal controls. To determine the 5-hmC status of a comprehensive set of human promoters, we enriched the DNA from whole blood samples for hydroxymethylated DNA using hMeDIP-chip methodology combined with microarray detection. The selected platform was a single array design that included 28,226 CpG islands and all the Ref gene promoter regions (approximately −800 to +200 bp relative to the TSSs) that were completely covered by ~385,000 probes. The median probe spacing was 101 bp.

DMR analysis using the MEDME method

To accurately quantify the CpG 5-hmC levels, we used a new analytical methodology, MEDME (modeling experimental data with hMeDIP enrichment), to improve the evaluation and interpretation of the hMeDIP-derived 5-hmC estimates. MEDME utilizes the absolute 5-hmC score (AHS) as the value for DNA hydroxymethylation, which is calculated based on the weighted count of the hydroxymethylated CpG dinucleotides in a 1 kb window centered at each probe. The AHS has been verified to be a more accurate and sensitive measurement of 5-hmC levels than the log-ratio. The MEDME method also provides a relative 5-hmC score (RHS) that normalizes the AHS to the total number of CpGs represented by CpGw. This method allows investigators to obtain a relative measurement of the 5-hmC that is independent of the CpG density of the corresponding region. The RMS is especially useful when comparing regions with different CpG densities.

Promoter classes in relation to CpG frequency

Approximately 70% of human genes are associated with promoter CpG islands, whereas the remaining promoters tend to be depleted in CpGs. The presence of 5-hmC in promoter regions is associated with high levels of transcription, which is consistent with a role for 5-hmC in the maintenance and promotion of gene expression. This effect is also partially dependent on the CpG density of the promoter. Based on the CpG density, the CpG ratio and length of the CpG-rich region, the promoters are subdivided into three classes: high (HCP), low (LCP), and intermediate (ICP) CpG density.

These classes are defined as follows: i) High-CpG-density promoters (HCP) are promoters containing a 500-bp interval within the region from 0.7 kb upstream to 0.2 kb downstream of the TSS with a GC percentage ≥55% and a CpG observed-to-expected ratio (O/E) ≥0.6. ii) Low-CpG-density promoters (LCP) are promoters containing no 500 bp interval with a CpG O/E ≥0.4. iii) Intermediate-CpG-density promoters (ICP) include the remaining promoters that were not classified as HCP or LCP.

CpG island 5-hmC

Mammalian genomes are punctuated by DNA sequences that contain an atypically high frequency of CpG sites termed CpG islands (CGIs). These sequences are characterized as ≥200 bp in length with a GC content of 50% and a CpG O/E of 0.6.

CpG islands can be grouped into three classes based on their distance to RefSeq annotated genes: i) Promoter islands occur from approximately −10 to +0.5 kb around the transcription start site. ii) Intragenic islands occur from 0.5 kb downstream of the transcription start site to the site of transcription termination. iii) Intergenic islands include all other CpG islands that were not classified as being in the promoter or intragenic category (Fig. 1).

Genome-wide profiling of promoter DNA 5-hmC

Based on the data obtained, we examined the CpG content in the pool of hydroxymethylated promoters compared to non-hydroxymethylated promoters that exhibited significant differences in 5-hmC levels between the SLE patients and normal controls. We found that 65.95% of hydroxymethylated genes belonged to the HCP cluster, which is similar to the average occurrence of HCP genes genome-wide (67.82%) (Fig. 2A). Similarly, 69.85% of the non-hydroxymethylated genes were associated with HCPs (Fig. 2A). A detailed analysis of the distribution of the hydroxymethylated probes over these promoters, which contained at least one CpG island by definition, indicated that 75.21% of the HCP genes had a hydroxymethylated probe that overlapped with the CpG island itself (Figs. 1 and 2C). By contrast, ~45% of the ICP and LCP genes were characterized as hydroxymethylated genes (Fig. 2B). We conclude that DNA hydroxymethylation in the blood of SLE patients primarily occurs at HCP promoters or at nonpromoter-CpG islands within HCP genes.

GO analysis of differentially expressed 5-hmC

To investigate the specific functions of the differentially expressed 5-hmC in the developmental process of SLE, the 5-hmC targets of each differentially expressed 5-hmC were identified by GO categories. The GO categories were derived from gene ontology, comprising three structured networks of defined terms that describe gene product attributes. The P-value denotes the significance of GO term enrichment in the differentially expressed 5-hmC list. Thus, the lower the P-value, the more significant the GO term, with P≤0.05 being recommended.

In terms of the GO database, the differentially expressed proteins encoded by these genes were divided into three categories: biological process, cell component and molecular function (Fig. 3). Through GO analysis for differentially expressed 5-hmC genes, we found that 71 differentially expressed 5-hmC genes with annotation terms being linked to the GO biological process categories, 30 being linked to the cell component and 20 being linked to the molecular function, with P<0.01. Details of the cell component categories, molecular function ontology, biological process ontology are presented in Table III.

Table III

Functional analysis of genetic differences of 5-hmC (P<0.01).

Table III

Functional analysis of genetic differences of 5-hmC (P<0.01).

GO IDTermGene (n)P-valueEnrichment score
Molecular function
GO:0005488Binding9758.47676E-065.071770331
GO:0005515Protein binding5740.00069793.156206958
GO:0008601Protein phosphatase type 2A regulator activity60.0023902232.621561587
GO:0005275Amine transmembrane transporter activity140.0027415652.562001469
GO:0046943Carboxylic acid transmembrane transporter activity160.0030325612.518190484
GO:0008198Ferrous iron binding50.0030485522.515906422
GO:0031267Small GTPase binding190.0031121642.506937561
GO:0050662Coenzyme binding260.0031640072.499762629
GO:0005342Organic acid transmembrane transporter activity160.0037386272.427287911
GO:0019903Protein phosphatase binding120.0037954922.420731959
GO:0004683 Calmodulin-dependent protein kinase activity60.0041823282.37858187
GO:0015248Sterol transporter activity50.0042843992.368110104
GO:0015370Solute:sodium symporter activity100.0050964592.292731449
GO:0015293Symporter activity190.0052836762.277063859
GO:0003677DNA binding2100.005453482.263326261
GO:0017016Ras GTPase binding170.0055116192.258720783
GO:0003676Nucleic acid binding2900.0056723652.246235825
GO:0036094Small molecule binding2290.006035272.219303294
GO:0000166Nucleotide binding2150.0062773612.202222878
GO:0019902Phosphatase binding150.0081587072.088378687
Cellular component
GO:0044424Intracellular component9911.25802E-065.900311838
GO:0005622Intracellular10111.96706E-065.706182597
GO:0005737Cytoplasm7511.1809E-054.927788392
GO:0043226Organelle8631.23569E-054.908089407
GO:0043229Intracellular organelle8602.02157E-054.694310928
GO:0044444Cytoplasmic component5560.0001625173.789099975
GO:0043227Membrane-bound organelle7730.0002011613.696456379
GO:0043231Intracellular membrane-bound organelle7710.0002635733.579099179
GO:0005634Nucleus5030.0005115643.291100377
GO:0044422Organelle component5180.0006983633.155918681
GO:0044446Intracellular organelle component5110.0008265813.082714383
GO:0005815Microtubule organizing center540.0015006982.823706722
GO:0044464Cell component11460.0015992782.79607593
GO:0005623Cell11460.001630912.78757007
GO:0015630Microtubule cytoskeleton860.0016725382.776623893
GO:0031988Membrane-bound vesicle850.0021514422.667270359
GO:0000159Protein phosphatase type 2A complex60.0023830192.622872453
GO:0005856Cytoskeleton1630.0026531362.576240518
GO:0030312External encapsulating structure50.0030403182.517080953
GO:0016023Cytoplasmic membrane-bound vesicle820.0035407272.450907507
GO:0031410Cytoplasmic vesicle850.0059383592.226333534
GO:0044428Nuclear component2150.0061102432.213941539
GO:0043228Non-membrane-bound organelle2650.0061882712.208430644
GO:0043232Intracellular non-membrane-bound organelle2650.0061882712.208430644
GO:0031982Vesicle880.0064664932.189331194
GO:0005874Microtubule370.0071220822.147393031
GO:0043240Fanconi anaemia nuclear complex40.0075545272.12179274
GO:0005829Cytosol2010.0075593682.121514538
GO:0008328Ionotropic glutamate receptor complex60.0084723212.071997622
GO:0031974Membrane-enclosed lumen2280.0095287222.020965349
Biological process
GO:0009987Cell process10464.20173E-076.376571542
GO:0006259DNA metabolic process930.0003717823.429711695
GO:0042136Neurotransmitter biosynthetic process60.0004051993.392331799
GO:0051179Localization3740.0005031213.2983276
GO:0033554Cell response to stress1140.0005341863.272307489
GO:0016043Cell component organization3440.0006179723.209030892
GO:0008219Cell death1660.0006361183.19646263
GO:0016265Death1660.0006722123.172493732
GO:0071840Cell component organization or biogenesis3520.0008089433.092082017
GO:0071705Nitrogen compound transport290.0008361393.077721402
GO:0010950Positive regulation of endopeptidase activity180.0009345943.029376965
GO:0012501Programmed cell death1520.0009442283.024923241
GO:0071702Organic substance transport590.0010395572.983151486
GO:0021987Ccerebral cortex development120.0011566392.9368022
GO:0006915Apoptotic process1500.0012753812.894360003
GO:0015697Quaternary ammonium group transport60.0013597212.866550106
GO:0006308DNA catabolic process130.0014399812.841643257
GO:0010952Positive regulation of peptidase activity180.0016483222.782957883
GO:0030301Cholesterol transport120.0018636282.729640865
GO:0015918Sterol transport120.0021660692.664327795
GO:0021543Pallium development150.0024117392.617669728
GO:0042632Cholesterol homeostasis110.002808712.551493105
GO:0055092Sterol homeostasis110.002808712.551493105
GO:0007169Transmembrane receptor protein tyrosine kinase signaling pathway660.0030920992.509746586
GO:0006281DNA repair450.003092752.509655117
GO:0006919Activation of cysteine-type endopeptidase activity involved in apoptotic process140.0031871412.496598699
GO:0097202Activation of cysteine-type endopeptidase activity140.0031871412.496598699
GO:0007049Cell cycle1310.0032468362.488539594
GO:0006950Response to stress2540.0032527882.487744307
GO:0060317Cardiac epithelial to mesenchymal transition50.0032787532.484291311
GO:0015837Amine transport240.0033964312.468977217
GO:0010033Response to organic substance1560.0037034612.431392194
GO:0043280Positive regulation of cysteine-type endopeptidase activity involved in apoptotic process160.0039622.402085511
GO:2001056Positive regulation of cysteine-type endopeptidase activity160.0039622.402085511
GO:0010941Regulation of cell death1190.0044006972.35647858
GO:0034641Cellular nitrogen compound metabolic process4650.0046926552.328581332
GO:0008629Induction of apoptosis by intracellular signals150.0047285012.32527652
GO:0071842Cellular component organization at the cellular level2680.00483972.315181593
GO:0032677Regulation of interleukin-8 production80.0049625692.304293443
GO:0006807Nitrogen compound metabolic process4730.0052089582.283249159
GO:0042981Regulation of apoptotic process1150.0052731372.277930908
GO:0071294Cell response to zinc ion40.0054463252.26389645
GO:0006139 Nucleobase-containing compound metabolic process4310.0056049462.251428588
GO:0006810Transport3020.0059355682.22653772
GO:0071841Cell component organization or biogenesis at the cellular level2750.006113022.213744154
GO:0051716Cell response to stimulus4130.0062392882.204864975
GO:0032365Intracellular lipid transport50.0062668412.20295135
GO:0040007Growth760.0062798452.20205109
GO:0044272Sulfur compound biosynthetic process110.0065282322.185204402
GO:0043067Regulation of programmed cell death1150.0066869962.174768905
GO:0007167Enzyme-linked receptor protein signaling pathway830.0066937132.174332938
GO:0030168Platelet activation280.0073386942.134381237
GO:0015695Organic cation transport70.0074846042.125831149
GO:0014066Regulation of phosphatidylinositol 3-kinase cascade90.0075013082.124863025
GO:0050794Regulation of the cell process6310.0076096032.118638012
GO:0044260Cellular macromolecule metabolic process5300.0077225832.11223743
GO:0042157Lipoprotein metabolic process150.007816962.10696213
GO:0051234Establishment of localization3050.0079998582.096917735
GO:0003203Endocardial cushion morphogenesis40.0080306032.095251834
GO:0042149Cell response to glucose starvation40.0080306032.095251834
GO:0045540Regulation of cholesterol biosynthetic process40.0080306032.095251834
GO:0043065Positive regulation of apoptotic process610.0080932572.091876684
GO:0035556Intracellular signal transduction1730.0081307152.089871248
GO:0032637Interleukin-8 production80.0083619732.077691232
GO:0090304Nucleic acid metabolic process3650.008645382.063215898
GO:0046686Response to cadmium ion70.0090252742.044539606
GO:0006586Indolalkylamine metabolic process60.0091940492.036493163
GO:0009225Nucleotide-sugar metabolic process60.0091940492.036493163
GO:0042430Indole-containing compound metabolic process60.0091940492.036493163
GO:0006974Response to DNA damage stimulus610.0096817092.014047956
GO:0043068Positive regulation of programmed cell death610.0096817092.014047956

[i] GO ID, the ID of gene ontology terms used in the Gene Ontology Project; Term, the name of the gene ontology term; Enrichment score, the enrichment score value of GO ID, which equals [−log10 (P-value)]; P-value, the significance testing value of the GOID, result from the topGO of bioconductor. If the P-value is lower than 1e-299, the P-value will be adjusted as the value of 1e-299.

Pathway analysis of differentially expressed 5-hmC

Pathway analysis is a functional analysis mapping genes to KEGG pathways. The P-value (EASE-score, Fisher P-value or Hypergeometric P-value) denotes the significance of the pathway correlated with the following conditions: the lower the P-value, the more significant the pathway, with P=0.05 as the cut-off value. In order to evaluate the influence of SNP-to-gene mapping strategy on the pathway analysis, we mapped SNPs to genes within differentially expressed 5-hmC.

In terms of the Pathway database, 17 pathways were significant (P<0.05). Differentially expressed 5-hmC is shown in Fig. 4, while details of the pathways are present in Table IV. Furthermore, the CDKN1A and CDKN1B genes contributed to the ErbB (P=0.01073062), P13-Akt (P=0.04341327), and HIF-1 (P=0.04345306) signaling pathways.

Table IV

Transduction pathway analysis in 5-hmC differences genes.

Table IV

Transduction pathway analysis in 5-hmC differences genes.

KEGG
Pathways
Fisher (n)Gene
P-value
Enrichment scoreGenes
Histidine metabolism - Homo sapiens0.00063257683.198888ACY3, ALDH1B1, ALDH3A2, ALDH3B1, HAL, HEMK1, MAOA, WBSCR22
Circadian entrainment - Homo sapiens0.001569437162.804256ADCY4, ADCYAP1R1, CACNA1G, CAMK2D, GNAS, GNG13, GRIA1, GRIN2A, GRIN2C, GRIN2D, KCNJ5, MAPK1, NOS1, PER1, PRKG1, RYR2
Glycerolipid metabolism - Homo sapiens0.005711304102.243265AGPAT3, ALDH1B1, ALDH3A2, CEL, DGKH, DGKQ, DGKZ, GPAM, LIPG, PPAP2A
Calcium signaling pathway - Homo sapiens0.005990646232.222526ADCY4, ADRA1D, ADRB2, ATP2B3, CACNA1G, CAMK2D, CAMK4, CD38, CYSL-TR1, EGFR, GNAS, GRIN2A, GRIN2C, GRIN2D, HTR7, MYLK2, MYLK3, NOS1, P2RX1, PDE1B, PHKG2, PLCD4, RYR2
Amyotrophic lateral sclerosis (ALS) - Homo sapiens0.010419391.982162APAF1, CYCS, DERL1, GRIA1, GRIN2A, GRIN2C, GRIN2D, NEFH, NOS1
ErbB signaling pathway - Homo sapiens0.01073062131.969375CAMK2D, CDKN1A, CDKN1B, CRK, CRKL, EGFR, ELK1, MAPK1, NCK1, NRG2, NRG3, PIK3R3, PTK2
Glycine, serine and threonine metabolism - Homo sapiens0.0182320171.739166BHMT, CTH, DAO, GNMT, MAOA, PSPH, SDSL
Amphetamine addiction - Homo sapiens0.02439724101.612659CAMK2D, CAMK4, CREB3L2, GNAS, GRIA1, GRIN2A, GRIN2C, GRIN2D, MAOA, TH
Cocaine addiction - Homo sapiens0.0266943681.57358BDNF, CREB3L2, GNAS, GRIN2A, GRIN2C, GRIN2D, MAOA, TH
Lysosome - Homo sapiens0.03098124151.508901ABCA2, AP3M1, AP3S2, AP4B1, ARSA, ATP6V0B, ATP6V1H, CLTA, CTNS, CTSL2, HEXB, IGF2R, NPC1, NPC2, SLC17-A5
Glycerophospholipid metabolism - Homo sapiens0.03160531121.50024AGPAT3, CHAT, DGKH, DGKQ, DGKZ, ETNK1, GNPAT, GPAM, LYPLA1, PEMT, PPAP2A, TAZ
Fanconi anemia pathway - Homo sapiens0.0364693881.438072BLM, FANCB, FANCD2, FANCE, FANCF, RPA2, STRA13, WDR48
Alcoholism - Homo sapiens0.03755879201.425288BDNF, CAMK4, CREB3L2, GNAS, GNG13, GRIN2A, GRIN2C, GRIN2D, H2AFV, H2BFM, HIST1H3F, HIST1H4D, HIST2H2AB, HIST2H2BF, HIST2H3D, HIST3H3, MAOA, MAPK1, NTRK2, TH
PI3K-Akt signaling pathway - Homo sapiens0.04341327341.362377BCL2L11, CDKN1A, CDKN1B, CHAD, COL6A1, CREB3L2, EGFR, EPOR, FASLG, FGF1, FLT1, GNG13, HSP90AA1, HSP90B1, INSR, ITGAV, ITGB4, JAK2, KITLG, LAMA5, LAMC3, MAPK1, PIK3R3, PPP2R1A, PPP2R2B, PPP2R3A, PPP2R5E, PRKCZ, PTEN, PTK2, SGK1, THEM4, TLR2, YWHAZ
HIF-1 signaling pathway - Homo sapiens0.04345306131.36198ALDOA, CAMK2D, CDKN1A, CDKN1B, EGFR, FLT1, IFNGR1, INSR, MAPK1, PGK1, PIK3R3, SLC2A1, TF
DNA replication - Homo sapiens0.0435826861.360686MCM2, PCNA, POLA2, RFC2, RNASEH2C, RPA2
Focal adhesion - Homo sapiens0.04412979221.355268BCAR1, CHAD, COL6A1, CRK, CRKL, EGFR, ELK1, FLNC, FLT1, ITGAV, ITGB4, LAMA5, LAMC3, MAPK1, MYL12A, MYLK2, MYLK3, PIK3R3, PPP1R12B, PTEN, PTK2, VCL

[i] Fisher P-value, the enrichment P-value of the Pathway ID using Fisher’s exact test; Enrichment score: the enrichment score value of the pathway ID, which equals [−log10 (P-value)].

Comparison of 5-hmC status between SLE patients and normal controls

By applying the analysis procedure described above to the sequencing results, we found that 1,701 gene promoter regions showed significantly different levels of 5-hmC in the SLE patients compared with the normal controls. Of these genes, 884 exhibited increased 5-hmC and 817 exhibited decreased 5-hmC (Fig. 5A). The CpG islands of 3,826 genes showed significant differences in 5-hmC levels in the SLE patients compared with the normal controls. Of these genes, 2,034 exhibited increased 5-hmC and 1,792 exhibited decreased 5-hmC (Fig. 5B).

Pie chart A shows the chromosomal locations of the 884 genes that were hyper-hydroxymethylated within the promoter region in the SLE patients compared with the normal controls (clockwise from chromosome 1 to the X and Y sex chromosomes). The percentage of genes hyper-hydroxymethylated on chromosome 1 was 10% (Fig. 6A). Pie chart B shows the chromosomal locations of the 2,034 genes that were hyper-hydroxymethylated within the CpG islands in the SLE patients compared with the normal controls (clockwise from chromosome 1 to the X and Y sex chromosomes). The percentage of genes hyper-hydroxymethylated on chromosome 29 was 9% (Fig. 6B).

The 5-hmC modifications of 15 selected genes are shown in Table V. The selected genes showed the greatest differences. Of these genes, we selected three prime repair exonuclease 1 (TREX1), cyclin-dependent kinase inhibitor 1A (p21, Cip1; CDKN1A), and cyclin-dependent kinase inhibitor 1B (p27, Kip1; CDKN1B) for verification. The microarray data were consistent with the RT-qPCR results (Table VI) showing that TREX1, CDKN1A, and CDKN1B exhibited significantly increased levels of 5-hmC. The three genes showed the largest differences in 5-hmC levels and may therefore be associated with SLE.

Table V

The 15 selected genes with hydroxymethylation alterations between SLE and normal controls, identified by hmeDIP-seq.

Table V

The 15 selected genes with hydroxymethylation alterations between SLE and normal controls, identified by hmeDIP-seq.

Peak IDGene namePeak regionPeak scorePeak M-value
4636RTN1Chr14: 59263472-592641214.71 1.26471321387763
3845 S100A7L2Chr1: 151678931-1516798014.55 0.967562504015608
5554ZNRF4Chr19: 5406466-54073104.48 1.10626932760703
5087CPNE7Chr16: 88168557-881692044.37 1.37675784921923
7131FZD3Chr8: 28406910-284077444.35 1.00487584265558
4370LAYNChr11: 110916352-1109174164.32 0.86128687613001
6211LZTR1Chr22: 19665877-196666064.32 1.21336961342519
3824PRMT6Chr1: 107400534-1074010834.23 0.934008953032345
7529VMA21ChrX: 150315981-1503165304.13 1.16048247400229
6560FREM3Chr4: 144840477-1448416314.09 1.18891146363541
3911HIST3H3Chr1: 226679229-2266799634.08 1.33700123117401
6204GNB1LChr22: 18221904-182226334.07 0.77963334561276
6355TREX1Chr3: 48482232-484840482.7 0.450419940777759
6777CDKN1AChr6: 36754464-367630872.66 1.58157470937086
679CDKN1BChr12: 12761568-127665722.03 0.6574848262603

[i] Peak score, the average -log10 (P-value) from probes within the peak. The scores reflect the probability of positive enrichment (cut off = 2). Peak M-value, the median log2-ratio from probes within the peak region. The score reflects the hydroxymethylation level of the region.

Table VI

RT-qPCR verification results.

Table VI

RT-qPCR verification results.

SampleInput-IP
Input-neg
IP/neg
Input (Ct)IP(Ct)%Input (Ct)Neg (Ct)%
TREX1
 SLE26.62829.8272.17826.628NANA
 Normal controls25.64837.8840.00425.648NANA
CDKN1A
 SLE23.37528.6640.51223.375NANA
 Normal controls22.38NANA25.64822.38NA
CDKN1B
 SLE26.47433.430.16126.474NANA
 Normal controls27.28433.5120.26727.284NANA

[i] % Input = 2(CtInput−CtChIP) × Fd × 100%. Fd refers to input dilution factor: For example, when 100 μl sonicated sample was used for hMeDIP and 20 μl sonicated sample was used as Input, Fd =1/5.

Discussion

The 5-hmC modification has been identified in mammalian DNA (6), but its broader role in epigenetics remains to be resolved. Early evidence suggests a few putative mechanisms that have potentially important implications (18): i) Conversion of methylcytosine (5-mC) to 5-hmC may displace methyl-binding proteins (MBPs). MeCP2, for instance, does not bind to 5-hmC. ii) 5-hmC may induce demethylation by interfering with the methylation maintenance function of DNMT1 during cell division. iii) 5-hmC may have its own specific binding proteins that alter the chromatin structure or DNA methylation patterns.

5-hmC was previously observed; however, little is known regarding its subtle interrelationship with other epigenetic modifications and potential functional significance in human disease. In this study, we selected 5-hmC as the target, performed an investigation using hMeDIP-chip, and investigated the hypothesis that 5-hmC is associated with the pathogenesis of SLE. We mainly analyzed the levels of 5-hmC in SLE patients and normal controls. The identified candidate genes with significant differences in 5-hmC levels are shown in Table V. This list includes genes associated with immunity, cell signal transduction, protein transcription and synthesis, ion channels and transporters, and the extracellular matrix.

Of the identified candidate genes, we found that TREX1 was hyper-hydroxymethylated in the SLE patients compared with the normal controls. Three prime repair exonuclease 1 (TREX1) is located on chromosome 3p21.31 and is also known as CRV, AGS1, DRN3 or HERNS. This gene encodes a nuclear protein with 3′ exonuclease activity, which may play a role in DNA repair and serve a proofreading function for DNA polymerase. Mutations in this gene result in Aicardi-Goutieres syndrome, chilblain lupus, Cree encephalitis, and other diseases of the immune system. Alternative splicing of this gene results in multiple transcript variants.

TREX1 plays a key role in the HIV-1 infection process (19). This protein degrades excess HIV-1 DNA, thereby preventing recognition by innate immunity receptors and the type I interferon response. Rare mutations in the TREX1 gene, the major mammalian 3′–5′ exonuclease, have been reported in sporadic SLE cases (20,21). Some of these mutations have also been identified in a rare pediatric neurological condition featuring an inflammatory encephalopathy known as Aicardi-Goutieres syndrome (AGS) (22). The mutations have also been identified in patients with several different human diseases (23), such as Aicardi-Goutieres syndrome 1, and account for all the mutations in retinal vasculopathy with cerebral leukodystrophy. These mutations include null alleles, frameshift mutations and non-synonymous changes in the catalytic domains and the C-terminal region. In AGS, most TREX1 mutations are autosomal recessive and reduce exonuclease activity of the enzyme, in particular a transition of arginine to histidine at position 114 (R114H). Pulliero et al described mutations of the TREX1 gene in Aicardi-Goutières syndrome 1 that increase the ability of T-lymphocytes to inhibit the growth of neoplastic neuronal cells and related angiogenesis (24).

In SLE, most of the mutations reported thus far are heterozygous and are located outside of the catalytic domain in the C-terminal region. The functional significance of these mutations is unknown. To examine the frequency of mutations in the TREX1 gene and their relationship with SLE, Namjou et al (25) genotyped 40 SNPs in the TREX1 genomic region, including previously reported rare SNPs and more common tag SNPs that capture most of the variation in this region. Those authors reported results indicating that TREX1 is involved in the lupus pathogenesis and is most likely essential for the prevention of autoimmunity. Gene Ontology (GO) term analysis shows that TREX1 is mainly associated with the cell process, cellular nitrogen compound metabolic process, cell response to stress, intracellular component, intracellular, binding, and protein binding.

We also observed that CDKN1A was significantly hyper-hydroxymethylated and CDKN1B was significantly hypo-hydroxymethylated in the SLE patients compared with the normal controls. The cyclin-dependent kinase inhibitor 1A (p21, Cip1; CDKN1A) gene is located on chromosome 6p21.2 and is also known as P21, CIP1, SDI1, WAF1, CAP20, CDKN1, MDA-6 or p21CIP1. This gene encodes a potent cyclin-dependent kinase inhibitor. The encoded protein binds to and inhibits the activity of the cyclin-CDK2 or -CDK4 complexes and thus functions as a regulator of G1 cell cycle progression. The expression of this gene is closely regulated by the tumor-suppressor protein p53 and mediates the p53-dependent G1 cell cycle arrest in response to a variety of stress stimuli. This protein can interact with proliferating cell nuclear antigen (PCNA), a DNA polymerase accessory factor, and plays a regulatory role in DNA replication and DNA damage repair. This protein was reported to be specifically cleaved by CASP3-like caspases, which leads to marked activation of CDK2 and may be instrumental in the execution of apoptosis following caspase activation. Multiple alternatively spliced variants have been identified for this gene.

The CDKN1A gene that encodes a cell cycle inhibitor, p21 (WAF1/CIP1), is located in a region associated with SLE susceptibility. Decreased cell levels of p21 are associated with SLE (26,27). Single-nucleotide polymorphisms (SNPs) within the promoter and the first intron of CDKN1A are associated with SLE susceptibility. The minor allele A at nucleotide 899 of CDKN1A is associated with increased susceptibility to SLE and lupus nephritis and decreased cell levels of p21.

The cyclin-dependent kinase inhibitor 1B (p27, Kip1; CDKN1B) encodes a cyclin-dependent kinase inhibitor, which shares a limited similarity with the CDK inhibitor CDKN1A/p21. The encoded protein binds to and prevents the activation of the cyclin E-CDK2 or cyclin D-CDK4 complexes and thus controls G1 cell cycle progression. The degradation of this protein, which is triggered by its CDK-dependent phosphorylation and subsequent ubiquitination by SCF complexes, is required for the cellular transition from quiescence to the proliferative state.

CDKN1B (28) may lead to defects in apoptosis or autophagy and thus increase exposure of nuclear autoantigens to the immune system, and its potential role in autoimmunity is supported by numerous functional studies. CDKN1B encodes p27Kip1, a cyclin-dependent kinase (CDK) inhibitor, which plays a critical role in the inhibition of cell-cycle progression, especially in T lymphocytes. p27Kip1 is essential for the induction of tolerance, a process believed to be at the center of autoimmune diseases such as SLE, and upregulation of p27Kip1 was found to correlate with the induction of anergy in vitro and tolerance in vivo. p27Kip1 is also involved in dendritic cell apoptosis, and the potential roles of the identified susceptibility genes in SLE etiology are noted. GO term analysis indicates that CDKN1A and CDKN1B are strongly associated with the cell process, intracellular component, intracellular, binding, and protein binding.

In this study, we systematically evaluated the genome-wide levels of 5-hmC in the DNA of SLE patients and gained insight into the connections between key genes and 5-hmC in the context of SLE. Our results indicate that 5-hmC is involved in the disease state and these novel candidate genes may become potential biomarkers or future therapeutic targets. Future investigations are needed to clarify the roles of the identified hydroxymethylated candidate genes in the pathogenesis of SLE.

Acknowledgments

The authors are deeply grateful to all the volunteers. This study was supported by the Guangxi Natural Science Foundation (no. 2012GXNSFDA053017) and by the Guangxi Key Laboratory of Metabolic Diseases Research (no. 12-071-32).

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May-2015
Volume 35 Issue 5

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Online ISSN:1791-244X

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Spandidos Publications style
Sui W, Tan Q, Yang M, Yan Q, Lin H, Ou M, Xue W, Chen J, Zou T, Jing H, Jing H, et al: Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip. Int J Mol Med 35: 1467-1479, 2015
APA
Sui, W., Tan, Q., Yang, M., Yan, Q., Lin, H., Ou, M. ... Dai, Y. (2015). Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip. International Journal of Molecular Medicine, 35, 1467-1479. https://doi.org/10.3892/ijmm.2015.2149
MLA
Sui, W., Tan, Q., Yang, M., Yan, Q., Lin, H., Ou, M., Xue, W., Chen, J., Zou, T., Jing, H., Guo, L., Cao, C., Sun, Y., Cui, Z., Dai, Y."Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip". International Journal of Molecular Medicine 35.5 (2015): 1467-1479.
Chicago
Sui, W., Tan, Q., Yang, M., Yan, Q., Lin, H., Ou, M., Xue, W., Chen, J., Zou, T., Jing, H., Guo, L., Cao, C., Sun, Y., Cui, Z., Dai, Y."Genome-wide analysis of 5-hmC in the peripheral blood of systemic lupus erythematosus patients using an hMeDIP-chip". International Journal of Molecular Medicine 35, no. 5 (2015): 1467-1479. https://doi.org/10.3892/ijmm.2015.2149