Abstract
BackgroundNephrotic syndrome (NS) is a heterogenous kidney disease, with subgroups of patients exhibiting distinct patterns of treatment response, disease progression and recurrence after kidney transplant. Epigenetic mechanisms, such as DNA methylation (DNAm), can induce stable but reversible changes in
gene expression without any change in the underlying DNA sequence; these mechanisms can also be altered by environmental influences. DNAm has shown potential as a patient stratification tool in other diseases but has not been comprehensively explored in NS. Therefore, the hypothesis underpinning this
thesis is that peripheral blood cell DNAm profiles from people with NS can be used for subgroup segregation, as well as providing mechanistic insights into disease pathogenesis.
Methods
A systematic review of NS epigenetic studies was performed and informed the decision to investigate DNAm rather than another epigenetic mechanism. A range of bioinformatic analyses were used to identify differences in peripheral blood cell DNAm patterns between NS subgroups and to derive DNAmbased subgroup classification models. Podocyte cell line experiments, alongside patient DNAm data, were used to investigate the effect of steroid treatment on DNAm and candidate genes. The biological relevance of the observed DNAm-NS relationships was untangled by using whole blood gene expression data from NS patients, and by evaluating potential causal relationships using Mendelian Randomization.
Results
Multi-site DNAm-based NS subgroup classification models performed well, demonstrating better accuracy than a published NS polygenic risk score. DNAm site cg25345365 in ZBTB16 was identified as a potential NS subgroup biomarker; this finding appeared to be biologically significant as DNAm levels at this site were associated with whole blood ZBTB16 gene expression levels across the NS subgroups. Furthermore, it was discovered that steroid treatment reduced DNAm at cg25345365 in NS patients, with suggestive evidence that this response may be blunted for a subgroup of patients who are resistant to this treatment. In a podocyte cell line, steroid therapy dramatically increased ZBTB16 transcript
levels, suggesting a functional protective role for ZBTB16 within the podocyte.
Conclusions
DNAm in peripheral blood is useful for NS subgroup segregation and offers unique insights into NS. External validation of the DNAm-based NS subgroup classification models is now a priority. Further laboratory work is also required to unpick the specific biological mechanism behind the observed relationship between cg25345365 DNAm, ZBTB16 expression and NS, both in peripheral blood cells and the podocyte.
| Date of Award | 13 May 2025 |
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| Original language | English |
| Awarding Institution |
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| Supervisor | Moin Saleem (Supervisor), Matthew J Suderman (Supervisor) & Gavin I Welsh (Supervisor) |