Accounting for cellular heterogeneity is critical in epigenome-wide association studies
© Jaffe and Irizarry; licensee BioMed Central Ltd. 2014
Received: 16 October 2013
Accepted: 4 February 2014
Published: 4 February 2014
Epigenome-wide association studies of human disease and other quantitative traits are becoming increasingly common. A series of papers reporting age-related changes in DNA methylation profiles in peripheral blood have already been published. However, blood is a heterogeneous collection of different cell types, each with a very different DNA methylation profile.
Using a statistical method that permits estimating the relative proportion of cell types from DNA methylation profiles, we examine data from five previously published studies, and find strong evidence of cell composition change across age in blood. We also demonstrate that, in these studies, cellular composition explains much of the observed variability in DNA methylation. Furthermore, we find high levels of confounding between age-related variability and cellular composition at the CpG level.
Our findings underscore the importance of considering cell composition variability in epigenetic studies based on whole blood and other heterogeneous tissue sources. We also provide software for estimating and exploring this composition confounding for the Illumina 450k microarray.
Epigenome-wide association studies (EWAS) of human disease are becoming increasingly common. DNA methylation (DNAm) is of particular interest because it is dynamic across the lifetime, affected by environmental insults, and previously implicated in developmental disorders and cancer . In these studies, DNAm levels are measured genome-wide at thousands to millions of sites in hundreds of individuals to identify loci where these levels are associated with quantitative traits or disease [1, 2]. Because existing cohort studies that extensively characterize participants often store blood samples, the most widely available tissue for subsequent/retrospective EWAS is whole blood. Furthermore, many studies measure genome-wide DNAm in blood as obtaining disease-relevant tissues is often invasive and/or impossible. With many of these studies completed, few disease-associated loci have been reported outside of cancer , type 1 diabetes , and rheumatoid arthritis . Instead a series of papers reporting age-related changes of DNAm profiles have been published [6–14].
Age-related changes in DNAm have been previously reported and functionally described by Chu et al. . In this carefully designed study, fluorescence-activated cell sorting (FACS) was used to separate peripheral blood into pure cellular populations. DNAm was measured in four genomic regions, selected using biological insight, and modest age-related changes were found in CD4+ and CD8+ T cells. In contrast, the above-mentioned EWAS measured DNAm for all CpGs selected by the array manufacturers and used whole blood as a source tissue. Whole blood is a heterogeneous collection of different cell types, each with a very different DNA methylation profile [16, 17]. Observed whole blood DNAm profiles are therefore mixtures of the cell type profiles. In a seminal paper, Houseman et al.  describe a statistical method that can accurately estimate relative proportions of cell type components in whole blood. Using practically the same statistical approach, Guintivano et al.  describe a method for estimating neuron and non-neuron components in brain samples. However, currently there are no published statistical solutions to parsing age effects by cell type from observed whole blood DNAm measurements.
We examined data from five publicly available studies (Additional file 1) and found strong evidence of cell composition changes across age. Furthermore, we find high levels of confounding between age-related variability and cell composition. We report findings that underscore the importance of accounting for cell composition variability in epigenetic studies based on whole blood and other heterogeneous tissue sources.
Results and discussion
DNAm profiles show large between cell type differences
We downloaded Illumina HumanMethylation450 BeadChip (Illumina 450k) data from flow-sorted neutrophils (granulocytes), lymphocytes (CD8+ and CD4+ T cells, CD56+ natural killer cells and CD19+ B cells) and CD14+ monocytes from six adult male samples (mean age 38 ± 13.6 years) as previously described  and confirmed that sorted blood cell types have unique DNAm profiles (Figure S1 in Additional file 2). In fact 63.5% of the CpGs on the Illumina 450k array showed differences with P < 0.05 across these cell types (Figure S1C in Additional file 2).
In sorted samples, cell type explains a larger percentage of variability than age
Given these results, for the purposes of our analysis, we assumed that, for the selected 600 CpGs, the cell type-specific DNAm profiles are the same for all ages. Although we know this assumption does not hold true for all CpGs , the results of this section suggest that it is reasonable for most CpGs, and our 600 CpG profile in particular. To demonstrate this, we interrogated two publicly available datasets - the Reinius et al.  Illumina 450k data on 6 men (sample ages were obtained from the authors) and Illumina 27k data from sorted CD4+ T cells and monocytes  on 24 and 26 subjects, respectively (see Materials and methods). First, we removed CpG probes that showed age associations (at P < 0.05) in the Reinius et al.  dataset when picking cell-type-discriminating probes for the cell composition estimation. Additionally, in Rakyan et al.  (which was a larger sample) we found that the percentage of variance explained by cell type was much greater than that explained by age within each cell type with most CpGs showing no significant association with age (Figure S2 in Additional file 2). Furthermore, among the 23 CpGs appearing on the Illumina 27k array that were among the 600 cell-type discriminating CpGs (from the Illumina 450k), only one probe (cg03439703) had a p-value < 0.05 when testing for association with age in both CD4+ T cells (P = 0.003) and monocytes (P = 0.047).
Varying cell composition may explain apparent age-associated differences
We downloaded all publicly available DNAm studies in peripheral blood measured with the Illumina 450k array (Additional file 1), re-normalized the data, and applied our method to obtain cell composition estimates for each sample. Note that only three of the studies were focused on finding age-related changes in DNAm [8, 10, 11], but all studies recorded age information. Figure 1 demonstrates that peripheral blood samples indeed appear to be a mixture of pure cellular components, and differences in DNAm may potentially arise merely from differences in the relative proportions of these components rather than site-specific changes in specific cellular populations (Figure 1C).
Cell type proportions change with age following monotonic patterns
Cellular composition correlates strongly with global DNAm profiles
Confounding between cell composition and age leads to false positives
To determine the adverse effects at the single locus level of the observed confounding between age, cell composition, and DNAm, we reexamined the CpGs reported in the literature to be associated with age [6–13] across several different measurement platforms (Additional file 4). For each of the CpGs reported to associate with age on the Illumina 450k array (n = 134,489), we tested between-to-within cell type variability on the sorted DNAm data and found that 86.7% of these had P < 0.05 across cell type (Figure S5 in Additional file 2).
Improved biological interpretation after composition filtering
We removed results from Johansson et al.  (which reporting one-third of the array was differentially methylated) then mapped the remaining 5,237 age-associated CpGs (Additional file 4) to human genes using the database provided by Triche . For each Gene Ontology category  with more than 25 annotated gene IDs we counted the number of CpGs associated with a gene in that category and formed an observed count to expected count ratio (see Materials and methods). We then filtered this list by removing CpGs associated with cell composition and recomputed the observed to expected ratios. With the unfiltered list, 10 of the top 20 enriched categories were clearly related to the immune system while only three were related to development, whereas in the filtered list 9 of the top 20 were associated with developmental processes and only 4 to immune response (Additional file 5).
Whole blood has been one of the most widely used source tissues in EWAS. Here we demonstrate that, in these studies, cellular composition explains much of the observed variability in DNAm. Therefore, when the outcome of interest correlates with cell composition, as age does, failure to account for cellular heterogeneity may result in many false positives. For binary outcomes, for example, we may observe differences between cases and controls, not due to the real differences in DNAm, but rather due to cases and controls having different blood cell counts (Figure 1).
While our re-analysis of publicly available data does not necessarily suggest that all reported age-related DNAm changes in blood are false positives, it certainly suggests that one should account for cellular composition. We therefore recommend that users of the Illumina 450k array studying whole blood perform the cell composition estimation (using, for example, the estimateCellCounts function we have added to the minfi Bioconductor package) and check for possible confounding. If confounding is present, we recommend the use of our table (Additional file 3; also available in the FlowSorted.Blood.450k Bioconductor package) that summarizes cell-type variability for each CpG. Those CpGs with methylation values highly associated with cell-type variability should be treated with skepticism, and we strongly recommend that CpGs associated with both composition and the covariate of interest be validated using FACS-derived cellular populations.
Note that due to the high levels of confounding we currently do not recommend regression approaches for adjustment purposes, but we note that RUV performed best for reducing the composition-based confounding. However, when there is no or minimal confounding, the added unaccounted variability may result in false negatives. In such cases popular factor-based 'batch' correction methodology, like surrogate variable analysis , and RUV  can empirically estimate and control for cell-type composition.
Note that these confounding problems are not confined to blood, but rather any tissue source that contains a mixture of cell types. Here, careful study design, via targeted validation employing cell sorting within the tissue of interest, can help isolate cell type-specific changes, such as age-related DNAm changes in the pure cellular populations of blood beyond the preliminary negative findings in CD4+ T cells and monocytes from Rakyan et al. . These may better explain observed biological effects, specifically, which epigenetic marks mediate risk for disease or associate with a trait. Characterizing and exploring the effects of cellular heterogeneity is therefore a necessary step in the analysis of genome-wide DNAm data in any heterogeneous tissue source, especially peripheral blood.
Materials and methods
Sample and study selection
There were five publicly available datasets on the Illumina 450k platform [5, 8, 10, 11, 26] performed on blood samples in the Gene Expression Omnibus (GEO) available through the National Center for Biotechnology Information (NCBI) as of February 2013 . We also downloaded cell sorted data described in the Results section from Reinius et al.  (GSE35069). Because study and age were almost perfectly confounded, and because there were very strong effects of study in the processed GEO data, we required 'raw' methylated (M) and unmethylated (U) channels from the Illumina 450k to preprocess and normalize all of the samples together, including the cell-sorted dataset. One study, Horvath et al., was not included in the manuscript because the GEO entry lacked raw data. Samples were dropped according to three criteria: 1) missing an age in the database (N = 11); 2) known to be cell-sorted, according to published manuscripts (N = 2, from Heyn et al.); and 3) hypothesized to be cell-sorted, based on granulocyte count values (Figure S7 in Additional file 2), including all centenarian samples from Heyn et al (N = 19), as all appeared to be only granulocytes, and 21 samples from Harris et al., which appeared to be granulocyte-depleted (the manuscript refers to a subset of samples being sorted, but it was not available information in the GEO entry). This left 1,098 samples across 5 studies.
We performed across-array quantile normalization within the M and U channels separately to normalize intensities across samples. Before normalization, we dropped probes on the sex chromosomes (chromosome X = 11,232 and chromosome Y = 416) and also probes that contained an annotated SNP (via dbSNP 137 Common database) in the CpG site (N = 16,756) and at the single base extension site (N = 7,880). This left 456,655 autosomal probes across the epigenome. After normalization, DNAm measurements on the logit scale were calculated as log2(M/U), and then transformed to Illumina’s 'beta' scale (proportion methylation, between 0 and 1). This approach is similar to the 'ABNorm' approach described by Sun et al. , but we use the logit transform described above rather than the Illumina approach [M/(M + U + 100)] for calculating the beta values.
Empirically estimating cellular composition using the Illumina 450k microarray
We tailored the algorithm designed by Houseman et al.  for the Illumina 27k array to the Illumina 450k array. Briefly, the Houseman algorithm identified 500 CpGs that discriminated cellular composition in flow-sorted cell populations (consisting of CD4+ and CD8+ T cells, B cells, monocytes, natural killer cells, and granulocytes). The algorithm then fits a nonlinear random effects model at each of these CpGs, estimating the coefficient for each cellular component, and then uses these coefficients to predict the relative proportion of each cellular component in peripheral blood samples.
However, there were several reasons that prevented the direct use of Houseman et al.’s algorithm on the 1,098 blood samples obtained on the Illumina 450k. First, while 473 of the 500 composition-discriminating CpGs were present on the Illumina 450k, these probes exhibited slightly different behavior in the two arrays (Figure S8 in Additional file 2). Second, 291 CpGs used by Houseman et al.’s algorithm contained an annotated SNPs (by rs number in the dbSNP137 database) at the CpG site of interest (N = 57), at the single base extension site following the CpG (N = 34) or in the probe sequence itself (N = 200). Problems detailing the inclusion of SNPs in the design of the Illumina 450k have been discussed previously [29, 30], and given our data are from a genetically heterogeneous population, we elected to exclude some of these probes.
We therefore obtained flow-sorted data, including the same six cellular components on six adult male subjects on the Illumina 450k platform , and derived our own similar blood composition algorithm using linear modeling across 600 composition-discriminating probes. We computed t-statistics for each cell type after removing probes that associated with age (at P ≤ 0.05), comparing that particular cell type with all others, and selected among the CpGs showing differences at P < 10-8 the 100 most differentially methylated probes by effect size, 50 hypermethylated and 50 hypomethylated. One outlying CD8+ T cell was excluded for the sake of composition estimation. The choices of 50 and 10-8 were somewhat arbitrary, but in-sample cross-validation (via leaving out one sample per cell type, training the model on the remaining 30 samples, and then predicting the 6 left out samples) demonstrated nearly perfect concordance between our estimates of cellular composition and the true values (Figure S9 in Additional file 2).
We also validated the overall algorithm using publicly available brain data from Guintivano et al. , which consisted of flow-sorted NeuN + and NeuN- cellular populations from the dorsolateral prefrontal cortex as training data, and then mixture data containing 10% NeuN+/90% NeuN-, 20% NeuN+/80% NeuN-, …, 90% NeuN+/10% NeuN- and bulk tissue data with FACS-derived counts of NeuN + cells as testing data. We processed the data (quantile normalization, dropping probes with SNPs and on sex chromosomes), picked 50 hypo- and hyper-methylated probes, and implemented the algorithm. The algorithm successfully recovered the mixture experiment (correlation = 0.9995; Figure S10A in Additional file 2) and predicted the FACS-derived counts from bulk tissue with moderate accuracy (correlation = 0.786). Lastly, we expect similar accuracy in blood (<10% on the Illumina 27k) as Houseman et al. , as we have adapted the algorithm to the Illumina 450k without changing the regression calibration approach.
Software to implement the estimation of cellular compositions from cell-sorted DNAm data is available in the minfi Bioconductor package . Publicly available cell-sorted data, to be used in conjunction with the minfi package, are available in the FlowSorted.Blood.450k Bioconductor package.
Previously published solution does not generally adjust for confounding
Guintivano et al.  also provide software that implements a method that they claim can transform data to eliminate (or at least reduce) the confounding effect of cell type heterogeneity on methylation profiles. Although the software is developed for brain, and only for two cell types, one could envision extensions applicable to cases with more cell types such as blood.
However, we offer a mathematical proof demonstrating that the solution offered in the paper only adjusts for confounding in a very special case. To understand the transformation we downloaded the accompanying software package CETS (version 0.99.2) and deciphered it from the R code. Here is a mathematical description of what the transformation does.
Thus, the signal is recovered only when the difference between the individual profiles and the average profiles are the same across cell type, which is not a reasonable, nor useful, assumption.
Variability in sorted cell populations
We downloaded publicly available data from Rakyan et al.  at GEO accession GSE20242, which consisted of sorted adult blood samples for monocyte and CD4+ T-cell populations. Linear regression models including i) age, ii) cell type, iii) both age, cell type, and their interaction term were fit at every probe. We summarized each fit with the adjusted R2 (coefficient of determination) . We then examined the P-values for the age terms within each cellular population at our 600 probes from the Illumina 450k used to estimate cellular composition that were also present on the Illumina 27k (n = 23).
Analysis of reported age-associated differentially methylated regions
We downloaded tables for statistically significant age-associated differentially methylated probes or regions (DMRs) from the supplementary material of published manuscripts listed in Additional file 4. For each reported age-associated DMR, we identified the F-statistic (and resulting marginal P-value) for that probe for the effect of composition in the publicly available sorted Illumina 450k data .
We applied naïve regression adjustment (for example, adjusting for cell type estimates) and two-step RUV using k = 10 (principal components) in Alisch et al.  and k = 30 in Hannum et al. , which were determined using diagnostic plots across a range of k values. Univariate regression modeling for Hannum et al.  included a categorical 'plate' adjustment variable, as plate and age were strongly associated, and plate and DNAm estimates were also associated. The RUV method requires control probes that are affected by the confounder (cell composition) but not the outcome of interest. We therefore used our 600 probes used to estimate cell type proportion since we showed these had no relation to age in at least two cell types. While it is possible that they are age associated in other cell types the results summarized in Figure S2 in Additional file 2 suggest that this is a useful approximation. With these control probes in place we then let the algorithm estimate the surrogate variables.
We assessed functional significance through enrichment using pre-defined gene sets with the Gene Ontology database. First we mapped each CpG to its Entrez Gene ID  for background enrichment (311,817/456,655 probes had an annotated Entrez Gene ID). For each gene set with 25 or more genes, we assessed the number of CpGs that mapped to each gene set. Then we assessed the number of reported age DMR CpGs in the existing gene sets, before (n = 4,691/5,237 mapped to an Entrez ID) and after (n = 1,090/1,209 mapped to an Entrez ID) removing probes that correlated with composition (f-statistic P-value <1 × 10-4 and DNAm range >10%). The observed verses expected ratios were computed for every gene set before and after this composition filtering, and are presented in Additional file 5.
epigenome-wide association study
fluorescence-activated cell sorting
Gene Expression Omnibus
Remove Unwanted Variation
We thank Tomas Ekström and Lars Klareskog for providing age information from the EIRA study, associated with the Liu et al. dataset . We also thank E Andrés Houseman for providing the code used in his manuscript .
Lieber Institute for Brain Development Intramural Research Fund, National Institute of Health (NIH): National Institute of General Medical Sciences (2R01GM083084) and National Human Genome Research Institute/Center for Inherited Disease Research (1X01HG006605-01).
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