Biomedical Research

Abstract

In clinical practice, it is difficult to monitor the repeating relapse in patients who have been suffering from systemic lupus erythematosus (SLE). The underlying etiology remains largely unknown. In order to understand the pathogenesis of SLE, the renal tubular cells-derived iPSCs were successfully obtained from urine of SLE patients. Here, with the purpose of identifying differentially expressed genes, highthroughput Illumina sequencing technology were analyzed the mRNA expression in SLE-iPSCs group and control-iPSCs group. Within the 4,254 genes, which were differentiated at least two-fold between the SLE-iPSCs and control-iPSCs, 2,856 genes were up-regulated and 1,398 down-regulated. These differentially expressed genes were involved in 9 cellular components, 9 molecular functions, 8 biological processes and 6 pathways with p-value ≤ 0.05. The clusters of “cellular process”, “intracellular” and “binding” represented the largest group in Process Ontology, Component Ontology, Function Ontology, respectively. Most differentially expressed genes involved in Function of binding, which were reported to be relevant with RNA transcription in SLE. Moreover, alternative splicing events and gene structure refinements of SLE-iPSCs group were greater than those of control-iPSCs group. Occurrence and development of SLE may be related to the excessive alternative spliced genes and events of alternative splicing. Using large cohorts of patient samples with long-term clinical follow-up data deserves for further investigation and research. Thus, it could assess the usefulness of the pathogenesis of SLE.

Keywords

Systemic lupus erythematosus-induced pluripotent stem cells (SLE- iPSCs), RNA sequence, Differentially expressed genes.

Introduction

Systemic lupus erythematosus (SLE) is the prototype of complex autoimmune disease characterized by the production of autoantibodies which results in widespread immunologic abnormalities and immune complex formation [1]. The patients can present variable manifestations and the nature courses are alternately remissions and relapses. Till now, although a lot of related researches have been undertaken [2], SLE patients still have no effective cures, whose treatments are often based upon long-term broad-spectrum immune suppressive regimes in the current therapeutic management. It has also become a major public health problem. Therefore, a rational approach for therapeutic design requires a detailed understanding of disease pathogenesis, and systematic characterization of the molecular and cellular basis of signaling abnormalities within the immune system and their relationship to regulation of gene expression remain critical for understanding [3].

The possibility of reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers an opportunity to generate pluripotent patient-specific cell lines, which can be conductive to studying pathogenesis of model human diseases [4]. Also, these iPSCs lines are powerful tools for drug discovery and the development of cellular transplantation therapies [4]. Generation of iPSCs from urine, fibroblasts and keratinocytes of disease patients has been reported [5-8]. To study SLE pathogenesis, renal tubular cells derived iPSCs were successfully established from urine of SLE patients [9]. In this study, high-throughput Illumina sequencing technology was utilized to further study the model cells of SLE-iPSCs.

Recently, the high-throughput Illumina Genome Analyzer provides a powerful approach to identify differentially expressed genes for the given cell, tissue and organism [10-12]. It can increase transcript sensitivity and identify novel transcripts, single nucleotide polymorphisms as well as splicing events [13]. Sequencing technology is developing rapidly, which results in the discovery of new disease genes. Actually, numerous chromosomal loci may harbor susceptibility genes [14,15]. By using the high-throughput Illumina sequencing platform, this study detects the mRNA expression in SLE-iPSCs group and control-iPSCs group, analyzes the two groups of differentially expressed genes and then identifies novel transcripts and splicing events. Further studies of gene regulation at transcriptional levels could help us to determine the pathogenesis of SLE comprehensively and accurately.

Materials and Methods

Materials

All the studies and other procedures were approved by the ethics committee of the Shenzhen People’s Hospital (Shenzhen, China) or the Guangzhou Institutes of Biomedicine and Health (Guangzhou, China). One patient, at the age of 39, was diagnosed as active SLE with SLEDAI>8. Moreover, one subject, age and sex matched, was recruited as healthy controls. To generate human iPSCs clone, renal tubular cells from urine of SLE patients were reprogrammed. Furthermore, SLE-iPSCs clone and control-iPSCs clone were identified [9]. Morphology was identified as well [9] (Figure 1). All of the samples were collected and immediately frozen in liquid nitrogen and stored at - 80°C.

Figure 1: Morphological characteristics appeared at days 6-7 posttransduction. a The SLE-iPSCs were picked at day 19, Matrigel 10×; b Alkaline phosphatase (AP)-positive SLE-iPSCs were imaged using light microscope, feeder 10X.

RNA extraction, cDNA library construction and sequencing

The SLE-iPSCs and Control-iPSCs were utilized for RNA extraction, and total RNA of iPSCs was extracted as described previously [16]. The individual RNA samples were quantified and examined spectrophotometrically for protein contamination (A260/A280 ratio) and reagent contamination (A260/A230 ratio), which were prior to library construction.

The cDNA library was carried out at the Beijing Genomics Institute (BGI, Shenzhen, Guangdong, China) by using the Illumina manufacturer’s instructions. The main reagents and supplies were the Illumina Gene Expression Sample Prep Kit and the Solexa Sequencing Chip (flowcell), and the main instruments were the Illumina Cluster Station and the Illumina HiSeq^TM 2000 System. In a nutshell, it is to extract the total RNA from samples. mRNA is enriched by utilizing the oligo (dT) magnetic beads and removing rRNA from the total RNA with kit. Through the fragmentation buffer, the mRNA is fragmented into short fragments (about 200~700 bp), Then, the first-strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand cDNA. The double strand cDNA is purified with QiaQuick PCR extraction kit. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by agarose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeqTM 2000.

Bioinformatics analysis of sequencing data

Primary sequencing data produced by Illumina HiSeq^TM 2000, called raw reads, is subjected to quality control (QC). To determine whether a resequencing step is necessary, the QC of alignment will be performed. Raw reads were filtered to remove reads with adapters, unknown bases of more than 10% and low quality reads (which are defined as reads having more than 50% bases with quality value ≤ 10). After filtering, the remaining reads, which are called “clean reads”, will be aligned to the reference sequences with SOAP2 [17]. Then, QC of alignment is performed again. The alignment data is utilized to calculate the distribution of reads on reference genes and perform coverage analysis. If alignment results pass QC, we will proceed with downstream analysis including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and SNP detection.

Gene expression analysis

Results of gene expression contain gene expression levels and differential expression analysis. The levels of gene expression were measured as numbers of reads per kilobase of exon model in a gene per million mapped reads (RPKM), which can be directly utilized to compare the differences of gene expression among the samples.

According to Differentially Expressed Genes (DEGs), we utilize ‘FDR(false discovery rate) ≤ 0.001 [18] and the absolute value of log2-Ratio ≥ 1 ’as the thresholds to judge the significance of DEGs. Then, more stringent criteria with smaller FDR and bigger fold change value can be applied to identify DEGs. These Differentially Expressed Genes were annotated in Gene Ontology (GO) and KEGG pathway analysis.

GO enrichment analysis maps all DEGs to GO terms in the database (http://www.geneontology.org/), calculating gene numbers for each term. Beyond that, the calculated p-value goes through Bonferroni Correction [19], taking corrected pvalue ≤ 0.05 as a threshold. GO terms fulfilling this condition are defined as significantly enriched GO terms in DEGs. This analysis can recognize the main biological functions exercised by DEGs.

Result

High-throughput sequencing and reads mapping

In order to identify SLE-related genes, transcript profiling of iPSCs was performed using RNA-Seq. Clean reads are mapped to genome sequence by using SOAP2 aligner.

Through mapping of reads to entire genome sequence, a total of 26,749,056 and 26,855,414 high-quality reads were obtained for the SLE-iPSCs and the control-iPSCs, respectively (Table 1). After discarding the low quality tags, 2,407,415,040 and 2,416,987,260 tags remained in the SLE-iPSCs and controliPSCs, respectively. 23,488,075 (87.81%) and 23,928,072 (89.10%) reads were mapped to the whole genome, 16,513,998 (61.74%) and 15,718,886 (58.53%) reads were perfect match in the SLE-iPSCs and control-iPSCs, respectively. 795,112 reads were expressed exclusively in the SLE-iPSCs, which were possibly related to the SLE development. Further analysis revealed that 21,382,507 unique tags (79.94%) and 21,937,249 (81.69%) were exclusively matched in the SLE-iPSCs and control-iPSCs, respectively. These data indicate that approximately 80% of the transcripts are expressed in the SLEiPSCs and control-iPSCs (Table 1).

Table 1: The SLE-iPSC and control-iPSC reads were mapped to the human Genome.

Gene structure refinement

Mapping to genome allows for potential discovery of novel exons and novel 5’ and 3’ ends. This can increase sensitivity and specificity due to recognition of potential reads through transcripts from neighboring genes. Transcripts were assembled with reads by Cufflinkss [20]. Through comparing assembled transcripts and gene annotation from reference sequences, it’s possible to find assembled transcripts that can extend 5’ or 3’ end of gene annotation, and therefore refine gene structure. 6,985 and 2,935 gene structures were refined in the SLE-iPSCs and control-iPSCs, respectively. Gene structure refinements in the SLE-iPSCs were apparently higher than those in the control-iPSCs (Figure 2).

Figure 2: Number extend 5’ or 3’ end of Gene structure refinement between SLE- iPSC and control-iPSC.

Novel transcript regions were also detected using Cufflinkss. As a novel transcript, an assembled transcript must meet three requirements. This means that the transcript must be at least 200 bp away from annotated gene, the transcript is of length over 180 bp and the sequencing depth is no less than 2. In our experiment, 792 and 973 novel transcribed regions were found in the SLE-iPSCs and control-iPSCs, respectively.

Alternative splicing analysis

To generate a mature mRNA, the introns must be removed and exons joined together in the process of pre-mRNA splicing [21]. Many pre-mRNAs in humans and other metazoans undergo the process of alternative splicing (AS) where multiple mRNA isoforms are produced from a single gene locus. In order to detect gene junctions, we perform an “intact” alignment using SOAPsplice to map complete reads to the reference genome. The remaining reads, initially unmapped reads (IUM reads), are mapped with the spliced alignment algorithm. We mainly detect four kinds of alternative spliced events, exon skipping, intron retention, alternative 5’ splice site and alternative 3’ splice site (Figures 3 and 4). Our results indicate that SLE-iPSCs have a higher rate of alternative splicing, compared with the control-iPSCs (Figure 4). And alternatively spliced genes of SLE-iPSCs are significantly higher than those of control-iPSCs (Figure 3). Disruption of normal splicing or splicing misregulation has been observed in a large number of diseases, which has been reviewed extensively [22-24]. The results clearly show that different organisms have different levels of alternative splicing, as well as alternatively spliced genes. Occurrence and development of SLE may be related to the excessive alternatively spliced genes and events of alternative splicing.

Figure 3: Genes of Alternative Splicing in SLE-iPSC and controliPSC.

Figure 4: Events of Alternative Splicing in SLE-iPSC and controliPSC.

Global analysis of gene expression

One of the primary goals of transcriptome sequencing is to compare gene expression levels in different genotypes. We estimated the expression levels of genes between the SLEiPSCs and the control-iPSCs. The expressed levels are measured in “reads per kilobase of exon model per million mapped reads” (RPKM), and the expression level of one gene is the sum of the RPKM values of its isoforms [25]. A total of 18,142 annotated genes were detected with RPKM>0. Using the P-value ≤ 0.05 and FDR ≤ 0.001 as threshold value, 4,254 genes were detected at least two-fold difference between the SLE-iPSCs and control-iPSCs (Figure 5). 2,856 genes and 1,398 genes represent a higher and lower abundance of more than two fold than those of control-iPSCs, respectively. The blue dots representing differentially expressed genes are less than two-fold between the two libraries, which are arbitrarily designated as ‘‘no difference in expression’’. We observe that parts of the dots are on the axis. Red dots of Y-axis indicate that genes only express in SLE-iPSCs, and green dots of Xaxis only express in control-iPSCs. The differentially expressed genes with ten-fold or greater are shown in Tables 2 and 3. We find that most differential expressed genes are involved in binding, ion binding, GTPase regulator activity, nucleoside- triphosphatase regulator activity of Function Ontology (Table 3) and so on.

Table 2: Up-regulated of the differential expressed genes with ten-fold or greater.

Table 3: Down-regulated of the differential expressed genes with tenfold or greater.

Figure 5: Comparison of gene expression levels between the SLEiPSC and control-iPSC.

Gene ontology functional enrichment analysis of differentially expressed genes (DEGs)

Gene Ontology (GO) is an international standardized gene functional classification system, which offers a dynamic update and a strictly defined concept to comprehensively describe the properties of genes and their products in any organism.

Using the P-value ≤ 0.05 as the threshold value, 4,254 differentially expressed genes were categorized into 30 functional groups (Tables 4-6), which included 9 molecular functions (Table 4), 9 cellular components (Table 5) and 8 biological processes (Table 6).

Table 4: The classification of differentially expressed genes in different category based on function ontology.

Table 5: The classification of differential expressed genes in different category based on component ontology.

Table 6: The classification of differential expressed genes in different category based on process ontology.

According to biological process, 3,067 differentially expressed genes were involved in biological process. The genes involved in cellular process (2264) [GO: 0009987] were enriched more significantly than other seven biological processes. The next representative terms were metabolic process (macromolecule metabolic process, cellular macromolecule metabolic process, cellular protein metabolic process) (Table 6). According to cellular component, 3,350 differentially expressed genes were involved in cellular component. The most representative GO term was intracellular (GO: 0005622), the next representative GO term was organelle (GO: 0043226), which was carried out at the intracellular level and results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of an intracellular component (Table 5). The significantly enriched transcripts on the Function Ontology were 2,825 DEGs, which associated with the GO term of binding [GO: 0005488], the differentially expressed genes were also involved in ion binding, cation binding, metal ion binding, transition metal ion binding. The remaining of differentially expressed genes was categorized into regulator activity (GTPase regulator activity, nucleosidetriphosphatase regulator activity) and exchange factor activity (guanyl-nucleotide exchange factor activity, Ras guanylnucleotide exchange factor activity). Alessandra B and Pernis reported that deregulation of Rho GTPase-mediated pathways might play a role in the pathogenesis of SLE [26].

Pathway enrichment analysis for DEGs

Genes usually interact with each other in certain biological functions. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database contains a record of all known networks of molecular interactions in cells and the variants of these pathways that are specific to particular organisms [27]. Pathway enrichment analysis helps us to understand what biological functions the genes have and how these genes interact with each other. In this study, the KEGG database can be used to analyze the potential involvement of differentially expressed genes.

Pathways with Q-value ≤ 0.05 were significantly enriched in differentially expressed genes. The differentially expressed genes were categorized into six pathways. The most representative pathway is purine metabolism, and then 4.42% of differentially expressed genes were involved in pathways in cancer (Table 7). Purinergic signaling not only regulated numerous organ systems, but also involved in embryonic development, injury and pain [28]. Moreover, there is evidence that purinergic receptors play a role in the regulation of behaviours and immunity [29]. Our result shows most significant difference of expressed genes in SLE-iPSCs involve in purine metabolism.

Table 7: Pathway enrichment analysis for DEGs.

Discussion

During the past few years, new NGS technologies have been developed with applications in complete genome sequencing, metagenomic sequencing, Chip-Seq, small RNA sequencing, transcriptome profiling, and others. Yukinori Okada et al [30] uses genome-wide association studies (GWAS) to discovery of susceptibility genes of SLE. And Graham, Deborah S Cunninghame [31] indicates that GWAS has been shown to be a powerful way of identifying novel susceptibility genes in SLE.

Our study provides the first comprehensive insight into the transcriptome of SLE- iPSCs using Illumina HiSeqTM 2000, as a powerful next generation RNA sequencing platform. We calculated the number of differentially expressed genes between SLE- iPSCs and control-iPSCs based on RPKM. 4,254 genes were considered to be significant difference, classified using Gene Ontology (GO) and KEGG Pathway. The clusters of “cellular process”, “intracellular” and “binding” represented the largest group in Process Ontology, Component Ontology and Function Ontology, respectively. Most differentially expressed genes involved in Function of binding (Tables 2 and 3), such as up-regulated hemoglobin, forkhead box B1, basic helix-loop-helix family and down- regulated eukaryotic translation initiation factor 1A, transcription elongation regulator 1-like and so on. Most of them were reported to be relevant with RNA transcription in SLE [32]. Bhatnagar et al. [33] showed that human Hemoglobin (Hb) was demonstrated in the sera of systemic lupus erythematosus (SLE). In addition, heterogeneous nuclear ribonucleoprotein H2 was significant difference in the study, which was consistent with our previous results [34]. Siapka et al. also demonstrated that hnRNP had a predominant nuclear localization and exerted multiple functions, including regulation of alternative splicing, transport of mRNA and regulation of translation [35].

Alternative splicing has recently emerged as a major mechanism for expanding and regulating the repertoire of gene functions [36]. Alternatively spliced proteins are involved in many biological processes like apoptosis [37]. The effects of these polymorphisms on splicing efficiency are believed to contribute significantly to disease severity and susceptibility [38]. Most alternative splicing events affect the coding sequence, subsequently amino acid sequence. Recently, a number of observations indicate physiological or pathological significance of alternative splicing and its role in the genetic background of diseases [39], such as immune diseases [40]. About one third of AS events result in splice variants containing premature termination codon, or leading to nonsense-mediated decay of the RNA product [41]. Many disease- associated mutations also affect pre-mRNA alternative splicing, usually causing inappropriate exon skipping [42]. Our result indicates that four types of exon skipping, intron retention, alternative 5’ splice site and alternative 3’ splice site in SLE-iPSCs are higher than those in control-iPSCs. Exon skipping in SLE-iPSCs is the biggest difference among the four types of alternatives. Studies have shown that up to 50% of point mutations responsible for genetic diseases in humans cause aberrant splicing [43,44]. The most common phenotype of point mutations that affect splicing, however, is exon skipping [43,45]. A family-based analysis of Caucasian and Chinese populations shows a significant association between the major alleles of a three alternative splicing CR2 and lupus susceptibility [46]. KB Douglas et al. also confirm the association of these three CR2 variants, and identify two additional CR2 variants significantly associated with SLE susceptibility. Therefore, aberrant exon skipping is closely related to the pathogenesis of SLE, and as the most common phenotype of alternatives because it is not usually amenable to correction.

Conclusion

The high-throughput Illumina sequencing technology is a powerful approach to identification of differentially expressed genes. We used the Illumina sequencing technology to detect the mRNAs expression in SLE-iPSCs group and control-iPSCs group; 4,254 genes were detected at least two-fold difference between the SLE-iPSCs and control-iPSCs, 2,856 genes were up-regulated and 1,398 down-regulated. Some differentially expressed genes only express in SLE-iPSCs or control-iPSCs. The 4,254 differentially expressed genes were annotated in Gene Ontology (GO) and KEGG pathway analysis. We found that the DEGs involved in 9 cellular components, 9 molecular functions, 8 biological processes and 6 pathways with p-value ≤ 0.05. The clusters of “cellular process”, “intracellular” and “binding” represented the largest group in Process Ontology, Component Ontology, Function Ontology, respectively. Most differentially expressed genes involved in Function of binding, which were reported to be relevant with RNA transcription in SLE. Moreover, we also proceeded with other downstream analysis including gene structure refinement, alternative splicing and novel transcript prediction. Alternative splicing events and gene structure refinement of SLE-iPSCs group were greater than those of control-iPSCs group. The results clearly showed that different organisms had different levels of alternative splicing, as well as alternatively spliced genes. Occurrence and development of SLE may be related to the excessive alternatively spliced genes and events of alternative splicing. In the future, further investigation is necessary for using large cohorts of patient samples with long-term clinical follow-up data, to assess the usefulness of the pathogenesis of SLE.

Acknowledgements

We thank the patients and healthy volunteers who participated in this study.

Conflict of Interest

No financial relationship exists between any of the authors and any commercial interest with a vested interest in the outcome of the study.

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