Pharmacoepigenomics: a key determinant in resolving epigenomic parameters in pathogenesis, and treatment response in complex diseases

Glucocorticoid-mediated acetylated regulation of glucocorticoid receptor and Histone3/Histone4 influence glucocorticoid heterogeneity in children patients with primary nephrotic syndrome

BACKGROUND

Glucocorticoid (GC) response heterogeneity has been recognized as an unfavorable prognostic factor, yet the underlying mechanism remains elusive. In this study, we endeavored to investigate the potential causes from an epigenetic perspective.

METHODS

The protein expression levels of the glucocorticoid receptor (GR), acetylated GC receptor (Ac-GR), acetylated histone3 (Ac-H3), histone4 (Ac-H4), and the activity of nuclear factor-κB (NF-κB) were quantified in the peripheral blood lymphocytes of patients exhibiting diverse GC responses.

RESULTS

Before GC treatment, the study included 32 children with steroid-sensitive nephrotic syndrome (SSNS) and 15 children with steroid-resistant nephrotic syndrome (SRNS). The expression levels of Ac-GR, Ac-H3, Ac-H4, and NF-κB activity were significantly different among the control, SSNS, and SRNS groups (p-values < 0.05). Specifically, the expressions were relatively low in the control group, moderately high in the SSNS group, and significantly elevated in the SRNS group. After GC treatment, the expressions of Ac-GR, Ac-H3, Ac-H4, and NF-κB activity decreased in the SSNS children (mean = 0.397, SD = 0.049, p = 4.42E-11 for NF-κB; mean = 0.429, SD = 0.107, p = 8.41E-6 for Ac-GR, mean = 0.652, SD = 0.126, p = 5.38E-8 for Ac-H3, and mean = 0.599, SD = 0.098, p = 1.24E-7 for Ac-H4), while they increased in the SRNS patients (mean = 0.576, SD = 0.064, p = 4.53E-5 for NF-κB, mean = 0.498, SD = 0.113, p = 8.81E-3 for Ac-GR). The correlations among these expressions differed between the SSNS and SRNS groups. In the SSNS group, a positive correlation was identified between NF-κB (mean = -0.156, SD = 0.090) activity and Ac-GR (mean = -0.148, SD = 0.157) protein expression after GC treatment (r = 0.392, p = 0.026), whereas a negative correlation was observed in the SRNS group (mean = 0.195, SD = 0.130 for NF-κB, mean = 0.173, SD = 0.221 for Ac-GR, r = -0.367, p = 0.178). Additionally, a positive correlation for the difference between Ac-H3 and Ac-H4 expressions was observed in the SSNS group (mean = -0.239, SD = 0.190 for Ac-H3, mean = -0.203, SD = 0.168 for Ac-H4, r = 0.394, p = 0.026), which was absent in the SRNS group.

CONCLUSION

The expression levels of Ac-GR, Ac-H3, and Ac-H4 differed significantly among children's patients with primary nephrotic syndrome (PNS) who manifested distinct GC responses. It is suggested that GC therapy may has a direct impact on the acetylation of GR, H3, and H4.

Pharmacogenetics in IBS: update and impact of GWAS studies in drug targets and metabolism

INTRODUCTION

Medications are frequently prescribed for patients with irritable bowel syndrome (IBS) or disorders of gut brain interaction. The level of drug metabolism and modifications in drug targets determine medication efficacy to modify motor or sensory function as well as patient response outcomes.

AREAS COVERED

The literature search included PubMed searches with the terms: pharmacokinetics, pharmacogenomics, epigenetics, clinical trials, irritable bowel syndrome, disorders of gut brain interaction, and genome-wide association studies. The main topics covered in relation to irritable bowel syndrome were precision medicine, pharmacogenomics related to drug metabolism, pharmacogenomics related to mechanistic targets, and epigenetics.

EXPERT OPINION

Pharmacogenomics impacting drug metabolism [CYP 2D6 (cytochrome P450 2D6) or 2C19 (cytochrome P450 2C19)] is the most practical approach to precision medicine in the treatment of IBS. Although there are proof of concept studies that have documented the importance of genetic modification of transmitters or receptors in altering responses to medications in IBS, these principles have rarely been applied in patient response outcomes. Genome-wide association (GWAS) studies have now documented the association of symptoms with genetic variation but not the evaluation of treatment responses. Considerably more research, particularly focused on patient response outcomes and epigenetics, is essential to impact this field in clinical medicine.

Longitudinal early epigenomic signatures inform molecular paths of therapy response and remission in depressed patients

Introduction

The etiology of major depressive disorder (MDD) involves the interaction between genes and environment, including treatment. Early molecular signatures for treatment response and remission are relevant in a context of personalized medicine and stratification and reduce the time-to-decision. Therefore, we focused the analyses on patients that responded or remitted following a cognitive intervention of 8 weeks.

Methods

We used data from a randomized controlled trial (RCT) with MDD patients (N = 112) receiving a cognitive intervention. At baseline and 8 weeks, blood for DNA methylation (Illumina Infinium MethylationEPIC 850k BeadChip) was collected, as well as MADRS. First, responders (N = 24; MADRS-reduction of at least 50%) were compared with non-responders (N = 60). Then, we performed longitudinal within-individual analyses, for response (N = 21) and for remission (N = 18; MADRS smaller or equal to 9 and higher than 9 at baseline), respectively, as well as patients with no change in MADRS over time. At 8 weeks the sample comprised 84 individuals; 73 patients had DNA methylation for both time-points. The RnBeads package (R) was used for data cleaning, quality control, and differential DNA-methylation (limma). The within-individual paired longitudinal analysis was performed using Welch's t-test. Subsequently gene-ontology (GO) pathway analyses were performed.

Results

No CpG was genome-wide significant CpG (p < 5 × 10-8). The most significant CpG in the differential methylation analysis comparing response versus non-response was in the IQSEC1 gene (cg01601845; p = 1.53 × 10-6), linked to neurotransmission. The most significant GO-terms were linked to telomeres. The longitudinal response analysis returned 67 GO pathways with a p < 0.05. Two of the three most significant pathways were linked to sodium transport. The analysis for remission returned 46 GO terms with a p-value smaller than 0.05 with pathways linked to phosphatase regulation and synaptic functioning. The analysis with stable patients returned mainly GO-terms linked to basic cellular processes.

Discussion

Our result suggest that DNA methylation can be suitable to capture early signs of treatment response and remission following a cognitive intervention in depression. Despite not being genome-wide significant, the CpG locations and GO-terms returned by our analysis comparing patients with and without cognitive impairment, are in line with prior knowledge on pathways and genes relevant for depression treatment and cognition. Our analysis provides new hypotheses for the understanding of how treatment for depression can act through DNA methylation and induce response and remission.

The Role of Histone Post-Translational Modifications in Merkel Cell Carcinoma

Merkel Cell Carcinoma (MCC) is a rare but highly aggressive form of non-melanoma skin cancer whose 5-year survival rate is 63%. Merkel cell polyomavirus (MCPyV), a small DNA tumor virus, is the etiological agent of MCC. Although representing a small proportion of MCC cases, MCPyV-negative MCCs have also been identified. The role of epigenetic mechanisms, including histone post-translational modifications (PTMs) in MCC, have been only partially determined. This review aims to describe the most recent progress on PTMs and their regulative factors in the context of MCC onset/development, providing an overview of current findings on both MCC subtypes. An outline of current knowledge on the potential employment of PTMs and related factors as diagnostic and prognostic markers, as well as novel treatment strategies targeting the reversibility of PTMs for MCC therapy is provided. Recent research shows that PTMs are emerging as important epigenetic players involved in MCC onset/development, and therefore may show a potential clinical significance. Deeper and integrated knowledge of currently known PTM dysregulations is of paramount importance in order to understand the molecular basis of MCC and improve the diagnosis, prognosis, and therapeutic options for this deadly tumor.