Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs.

Profiling of circulating cell-free DNA (cfDNA) by tissue-specific base modifications, such as 5-methylcytosines (5mC), may enable the monitoring of ongoing pathophysiological processes. Nanopore sequencing allows genome-wide 5mC detection in cfDNA without bisulphite conversion. The aims of this study were: i) to find differentially methylated regions (DMRs) of cfDNA associated with obesity in Göttingen minipigs using Nanopore sequencing, ii) to validate a subset of the DMRs using methylation-specific PCR (MSP-PCR), and iii) to compare the cfDNA DMRs with those from whole blood genomic DNA (gDNA). Serum cfDNA and gDNA were obtained from 10 lean and 7 obese Göttingen Minipigs both with experimentally induced myocardial infarction and sequenced using Oxford Nanopore MinION. A total of 1,236 cfDNA DMRs (FDR<0.01) were associated with obesity. In silico analysis showed enrichment of the adipocytokine signalling, glucagon signalling, and cellular glucose homoeostasis pathways. A strong cfDNA DMR was discovered in PPARGC1B, a gene linked to obesity and type 2 diabetes. The DMR was validated using MSP-PCR and correlated significantly with body weight (P < 0.05). No DMRs intersected between cfDNA and gDNA, suggesting that cfDNA originates from body-wide shedding of DNA. In conclusion, nanopore sequencing detected differential methylation in minute quantities (0.1-1 ng/µl) of cfDNA. Future work should focus on translation into human and comparing 5mC from somatic tissues to pinpoint the exact location of pathology.

Oxford nanopore sequencing can reveal changes in methylation patterns associated with obesity in minute quantities of cell-free DNA from serum.Bisulphite conversion and methylation-specific PCR can be used to validate differentially methylated regions in cell-free DNA.A differentially methylated region in an intronic region of the PPARGC1B gene was found associated with obesity.Differentially methylated regions in cell-free DNA could be useful as early risk markers of certain diseases and pathologies.

Electrocardiography and heart rate variability in Göttingen Minipigs: Impact of diurnal variation, lead placement, repeatability and streptozotocin-induced diabetes.

BACKGROUND: The Göttingen Minipig is widely used in preclinical research and safety pharmacology, but standardisation of porcine electrocardiography (ECG) is lacking. The aim of this study was to investigate diurnal effects, change over time and choice of lead on ECG morphology and heart rate variability (HRV) in healthy and streptozotocin (STZ) induced diabetic Göttingen Minipigs. METHODS: Diabetes was experimentally induced using STZ in 11 Göttingen Minipigs (DIA). Seven controls (CON) were included. 24-h ECG was recorded at baseline and four months. Morphological parameters (QRS and T wave duration, P- and T-wave amplitude, PR and QT (Bazett's (QTcb) or Fridericia (QTcf) correction) intervals and ST segment), presence of cardiac arrhythmias, heart rate (HR) and HRV (time and frequency domain) were analysed. RESULTS: Four months after induction, DIA had decreased P-wave amplitude (P < 0.0001) and T-wave duration (P = 0.017), compared to CON. QTcb was lower in DIA, but not in CON. Both groups had decreased HR (P < 0.0001) and QRS duration (lead II, P = 0.04) and length of PR-segment increased (lead I and II, P < 0.01) while selected HRV parameters also increased (all P < 0.01). Time of day influenced HR, QRS duration, PR segment, ST segment, T- and P-wave amplitude and some parameters of HRV. Inter- and intra-observer variability of morphological measurements was low (<6%). CONCLUSION: ECG parameters were influenced by time setting, diurnal variation and lead. Some ECG and HRV changes were found in diabetic minipigs four months after STZ induction. The findings underline the need for standardisation of ECG and HRV in Göttingen Minipigs.