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Series GSE125929 Query DataSets for GSE125929
Status Public on Jan 31, 2020
Title 5-Hydroxymethylcytosines in Circulating Cell-free DNA Reveal Vascular Complications of Type 2 Diabetes
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary BACKGROUND: Long-term complications of type 2 diabetes (T2D), such as macrovascular and microvascular events, are the major causes for T2D-related disability and mortality. A clinically convenient, non-invasive approach for monitoring the development of these complications would improve the overall life quality of patients with T2D and help reduce healthcare burden through preventive interventions.
METHODS: A selective chemical labeling strategy for 5-hydroxymethylcytosines (5hmC-Seal) was used to profile genome-wide 5hmCs, an emerging class of epigenetic markers implicated in complex diseases including diabetes, in circulating cell-free DNA (cfDNA) from a collection of Chinese patients (n = 62). Differentially modified 5hmC markers between patients with T2D with and without macrovascular/microvascular complications were analyzed under a case-control design.
RESULTS: Statistically significant changes in 5hmC markers were associated with T2D-related macrovascular/microvascular complications, involving genes and pathways relevant to vascular biology and diabetes, including insulin resistance and inflammation. A 16-gene 5hmC marker panel accurately distinguished patients with vascular complications from those without (testing set: AUC = 0.85, 95%CI, 0.73-0.96), outperforming conventional clinical variables such as urinary albumin. In addition, a separate 13-gene 5hmC marker panel could distinguish patients with single complications from those with multiple complications (testing set: AUC = 0.84, 95%CI, 0.68-0.99), showing superiority over conventional clinical variables.
CONCLUSIONS: The 5hmC markers in cfDNA reflected the epigenetic changes in patients with T2D who developed macrovascular/microvascular complications. The 5hmC-Seal assay has the potential to be a clinically convenient, non-invasive approach that can be applied in the clinic to monitor the presence and severity of diabetic vascular complications.
Overall design Differential 5hmC markers between T2D patients with and without macrovascular/microvascular complications were analyzed in a Chinese patient cohort (n = 62).
Contributor(s) Zhang W, Liu S, He C, Yang Y, Zeng C
Citation(s) 31575611
Submission date Jan 30, 2019
Last update date May 01, 2020
Contact name Wei Zhang
Organization name Northwestern University
Department Preventive Medicine
Street address 680 N Lake Shore Drive, Suite 1400
City Chicago
State/province IL
ZIP/Postal code 60611
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (62)
GSM3585157 SEQ772
GSM3585158 SEQ552
GSM3585159 SEQ773
BioProject PRJNA517967
SRA SRP182983

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125929_5hmC_Count_Matrix.csv.gz 1.6 Mb (ftp)(http) CSV
GSE125929_Clinical.SampleInfo_V1.csv.gz 695 b (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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