Introduction
Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome are caused by pathogenic variants in
FOXP3, a transcription factor critical for the development of functional regulatory T-cells (T
regs) [
1]. IPEX patients usually present with rapidly progressing multiple autoimmunity, including autoimmune diabetes (typically neonatal diabetes; NDM; onset < 6 months), life-threatening enteropathy, and atopic dermatitis. It is this classic triad of symptoms that is often the catalyst for genetic testing. However, the clinical, immunological, and molecular phenotype is heterogeneous, and increasingly, patients are reported with atypical features or a milder clinical course [
2‐
4]. For progressive or syndromic genetic disorders such as IPEX syndrome, an early and accurate genetic diagnosis can provide insight into prognosis and direct monitoring and treatment plans, often improving outcomes [
5].
Gene panel testing has revolutionized genetic testing and highlighted the phenotypic variability associated with monogenic diseases such as IPEX syndrome, with pathogenic variants being reported in individuals without all the classic features of the genetic disorder [
6‐
8]. In such cases, assigning pathogenicity to novel variants can be difficult and may rely on waiting for additional features to develop. Isolated NDM may be the first and only feature at testing for IPEX, which overlaps with > 30 other monogenic disorders including other “Tregopathies” (sometimes termed IPEX-like disorders) [
3,
9,
10]. Variant interpretation is further complicated by a high proportion of maternally inherited variants making co-segregation analysis difficult and an alternatively spliced isoform of
FOXP3 which makes variants in exon 2 challenging to interpret.
Functional immune analyses can assist with understanding the impact of a
FOXP3 variant. However, these techniques require fresh blood samples to be rapidly processed by specialist laboratories, which can be prohibitive due to cost, expertise needed, and remoteness of patients to the laboratory [
10,
11]. Quantitative assessment of immune cells by methylation-specific qPCR is an alternative option for the analysis of human leukocyte populations and can be used to quantify different cell types in whole-blood derived DNA [
12]. This cost-effective method does not rely on fresh samples and can be easily performed in a genomics laboratory using existing samples taken for genetic testing. The T
reg cell-specific demethylated region (Foxp3 TSDR) is an imprinted region within the
FOXP3 locus that controls and stabilizes expression of
FOXP3. De-methylation of the TSDR allows for stable
FOXP3 expression and subsequent maintenance of T
reg identity [
13]. T
reg count by flow cytometry is very tightly correlated with the number of cells with demethylation of the TSDR in healthy individuals but appears to be unphysiologically high in individuals with IPEX [
14].
We report a large cohort of patients with IPEX syndrome (n = 65) resulting from a hemizygous FOXP3 pathogenic variant identified by custom gene panel testing for monogenic NDM. We assessed whether genetically diagnosing IPEX at presentation with isolated NDM could offer a window in which to monitor and intervene before patients become critically ill. We then sought to assess if the number of cells characterized by a demethylated FOXP3 TSDR could have diagnostic and prognostic value in atypical IPEX.
As described in the method section, we determined the number of blood cells with demethylated FOXP3 TSDR or a region in the CD4 locus specifically demethylated in T helper cells (demethylated CD4). These counts were initially analyzed relative to the number of all nucleated blood cells determined by the number of demethylated copies of a region of the GAPDH gene previously been shown to be demethylated in all cells (demethylated GAPDH). Based on these counts, we quantified the percentage of Tregs (% demethylated FOXP3 TSDR) and CD4 + T helper cells (% demethylated CD4) in leukocytes as well as the percentage of Tregs within the T helper cells (% demethylated FOXP3 TSDR/demethylated CD4 + , henceforth referred to as %TSDR/CD4).
Discussion
We have shown, in the largest single-center series of IPEX patients, that identifying and accurately diagnosing IPEX early at initial presentation with infancy-onset diabetes could offer an opportunity to monitor patients before the onset of life-threatening features. Measurement of demethylation at the T-reg specific demethylated region (TSDR), a specific marker of thymic derived regulatory T cells [
17], represented as a proportion of all T helper cells (as measured by demethylation at a CD4 T helper cell specific demethylated region) could be useful for interpreting novel variants of uncertain significance in
FOXP3, facilitating early diagnosis where clinical features are not sufficiently informative (i.e., patients have isolated diabetes). The %TSDR/CD4 was raised in individuals with IPEX compared to healthy controls, individuals with non-autoimmune monogenic neonatal diabetes, and non-IPEX monogenic autoimmunity with overlapping phenotype. In addition, we found evidence that a higher %TSDR/CD4 value correlates with the severity of phenotype in our cohort, suggesting this may be a marker of disease severity.
We found the presenting feature was diabetes in 77%. This is higher than previous reports and likely reflects referral bias as we offer research-funded genetic testing to any individual diagnosed with diabetes before 6 months (
www.diabetesgenes.org). Diagnosing IPEX rapidly after presentation with isolated NDM allows time for additional monitoring, for example, by testing for diagnostic autoantibodies (e.g., antienterocyte autoantibodies for enteropathy), which can appear before overt clinical disease [
1]. It may therefore allow patients immunosuppressive treatment options (e.g., Sirolimus) that delay or reduce the development of additional, life-threatening symptoms. Currently, hematopoietic stem cell transplantation (HSCT) is the only curative therapy for IPEX, and survival after HSCT is significantly impacted by disease severity [
18]. Amelioration of insulin dependency has been reported in an adolescent treated with HSCT 1 month after diabetes onset [
19], suggesting the period from onset may also impact efficacy. This further underlines the importance of rapid genetic testing and variant classification. We found that individuals with a higher %TSDR/CD4 had more systems affected.
In healthy subjects, the number of DNA copies demethylated at the TSDR faithfully reflects the number of functional (i.e., suppressive) Tregs and measurement correlates closely with quantification of Tregs from flow cytometry data [
14,
20]. A similar association was also found between demethylation of the CD4 locus and the number of CD4 + T helper cells, among others [
14,
16]. However, upon mutation of the Treg-defining FOXP3 gene and protein, the association is disrupted. In individuals with IPEX syndrome, functional Tregs are largely absent, and one of the most typical Treg markers, intracellular antibody staining of FOXP3, may no longer work [
21]. At the same time, the number of cells counted by other Treg surface markers (e.g., CD4( +), CD25( +), and CD127(low)) may no longer reflect fully functional Tregs [
1,
10,
21,
22] which are highly variable in individuals with IPEX syndrome [
23]. Indeed, a breakdown of correlation between surface Treg markers and
FOXP3 TSDR demethylation was recently shown in 15 IPEX patients whose FOXP3 expression was independent of TSDR demethylation [
23]. We were not able to measure regulatory T cell number or function in our cohort to assess whether TSDR quantification is related to Treg function in our cohort, as we were not able to obtain fresh samples for analysis.
We have demonstrated the utility of an established and relatively inexpensive test (methylation specific qPCR) which can aid
FOXP3 variant classification and offer some insight into severity of IPEX symptoms. The utility of this measurement is demonstrated by our patient with a novel missense variant in the alternatively spliced exon two who had isolated diabetes at age 5 years but in whom the TSDR/CD4 value was raised leading to reclassification of the variant as likely pathogenic. Critically, measuring TSDR/CD4 does not require additional samples from patients and can even be run on dried blood spots [
14]. It is important to note, however, that our data are cross sectional with variable follow-up periods and rely on comprehensive reporting of symptoms by referring clinicians. A recent study on 15 individuals with IPEX syndrome showed that demethylation at the TSDR increased gradually with disease progression, having normal values in new-born blood spot samples from individuals with pathogenic
FOXP3 variants that increased as IPEX syndrome developed in early life [
23].
Previous studies have shown that the epigenetic measurement of lineage-specific differentially methylated loci may be useful for quantifying the immune system in individuals with primary immune disorders. This contrasts to individuals with IPEX where demethylation of the TSDR is unphysiologically high. In a recent pre-printed study currently under review, a population of cells from 4 IPEX patients were shown to have demethylated FOXP3 TSDR but not markers of Treg phenotype (CD25 and FOXP3). These cells originated both from the effector T cell compartment and from “regulatory T cells” that, due to the
FOXP3 mutation, gained effector functions such as the secretion of Th17 and Th2 cytokines [
24]. This provides tantalizing evidence for the underlying mechanism for the increased %TSDR/CD4 in IPEX syndrome we have shown. A previous study showed reduced cells with TSDR demethylation (i.e., lower “Treg” as measured by methylation analysis) in individuals with non-IPEX Tregopathies that did not correlate with flow cytometric analysis of FOXP3 positive cells [
25]. This is in contrast to our data where individuals with other Tregopathies had similar TSDR/CD4 ratios to healthy controls.
Identifying IPEX at initial presentation with diabetes offers a critical window of time to begin monitoring patients and intervening if necessary. All males with NDM should have rapid comprehensive genetic testing that includes FOXP3. Measurement of %TSDR/CD4 could be an important additional tool to aid classification of variants in IPEX syndrome facilitating early diagnosis and improved outcomes, particularly in cases with atypical clinical features. Importantly, this biomarker seems to be specific to IPEX syndrome rather than a general marker of Treg insufficiency, which is common in other monogenic autoimmune conditions. Finally, we found that %TSDR/CD4 may be linked to severity; therefore, further longitudinal studies are warranted.
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