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Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer

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Abstract

Background

5-Hydroxymethylcytosine-enriched gene profiles and regions show tissue-specific and tumor specific. There is a potential value to explore cell-free DNA 5-hydroxymethylcytosine feature biomarkers for early gastric cancer detection.

Methods

A matched case‒control study design with 50 gastric cancer patients and 50 controls was performed to sequence the different 5-hydroxymethylcytosine modification features of cell free DNA. Significantly differential 5-hydroxymethylcytosine modification genes were identified to construct a gastric cancer diagnostic model. Data set from GEO was used as an external testing set to test the robustness of the diagnostic model.

Results

Accounting for more than 90% of 5-hydroxymethylcytosine peaks were distributed in the gene body in both the gastric cancer and control groups. The diagnostic model was developed based on five different 5-hydroxymethylcytosine modification genes, FBXL7, PDE3A, TPO, SNTG2 and STXBP5. The model could effectively distinguish gastric cancer patients from controls in the training (AUC = 0.95, sensitivity = 88.6%, specificity = 94.3%), validation (AUC = 0.87, sensitivity = 73.3%, specificity = 93.3%) and testing (AUC = 0.90, sensitivity = 81.9%, specificity = 90.2%) sets. The risk scores of the controls from the model were significantly lower than those of gastric cancer patients in both our own data (P < 0.001) and GEO external testing data (P < 0.001), and no significant difference between different TNM stage patients (P = 0.09 and 0.66). Furthermore, there was no significant difference between the healthy control and benign gastric disease patients in the testing set from GEO (P = 0.10).

Conclusions

The characteristics of 5-hydroxymethylcytosine in cell free DNA are specific to gastric cancer patients, and the diagnostic model constructed by five genes’ 5-hydroxymethylcytosine features could effectively identify gastric cancer patients.

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Data availability

The raw and processed 5hmc-Seal data of the model development in the current study are available in GEO database as GSE246110.

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Acknowledgements

We thank the supporting from the National Natural Science Foundation of China (81874279 and 82373664), Natural Science Foundation of Jilin Province (YDZJ202201ZYTS064), and the Department of Finance Jilin Province (JLSWSRCZX2021-073).

Funding

Naural Science Foundation of Jilin Province, YDZJ202201ZYTS064, Yingli Fu, National Natural Science Foundation of China, 81874279, Jing Jiang, 82373664, Jing Jiang, Department of Finance of Jilin Province, JLSWSRCZX2021-073, Xueyuan Cao.

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Author notes

  1. Yingli Fu and Jing Jiang have contributed equally.

Authors and Affiliations

  1. Division of Clinical Epidemiology, The First Hospital of Jilin University, Changchun, China

    Yingli Fu, Jing Jiang, Yanhua Wu, Donghui Cao & Zhifang Jia

  2. Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China

    Yangyu Zhang & Yuzheng Zhang

  3. Department of Hospital Infection Management, China-Japan Union Hospital of Jilin University, Changchun, China

    Dongming Li, Yingnan Cui & Yuzheng Zhang

  4. Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China

    Xueyuan Cao

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  1. Yingli Fu
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Contributions

Yingli Fu and Jing Jiang conceptualized and wrote the main text and figures, Yingli Fu and Jing Jiang contributed equally. Xueyuan Cao, Yanhua Wu and Zhifang Jia analyzed information and made suggestions for improvement. Donghui Cao, Yangyu Zhang, Dongming Li, Yingnan Cui, and Yuzheng Zhang revised the overall text to provide accuracy. All authors read and approved the final manuscript.

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Correspondence to Xueyuan Cao.

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This study was reviewed and approved by the Ethics Committee at The First Hospital of Jilin University (NO. 19K118-001). Written informed consent was obtained from each participant, and biospecimens were collected as approved by the Institutional Review Boards (IRBs) responsible at the First Hospital of Jilin University.

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10120_2024_1493_MOESM8_ESM.eps

Supplementary file8 Fig. 1.Classification value of model involved each individual gene and the model distinguish probability for other type of cancer.( a.ROC curves for each individual gene 5hmC level and the complex predicted score with combined data of our own data and GEO validation data. b.ROC curves for the colon, liver, pancreas and thyroid cancer separately with data from the GEO data (GSE98570).) (EPS 2127 KB)

10120_2024_1493_MOESM9_ESM.eps

Supplementary file9 Fig. 2. Correlation between 5hmC change and gene expression.(a.The log2 fold change of 5hmC in GC patients’ cfDNA vs. controls’ cfDNA were compared to the log2 fold change of 5hmC in tumor vs. adjacent tissues. 5hmC changes in the tumor is positively associated with 5hmC changes in the cfDNA for 350 genes with different 5hmC. b.The log2 fold changes of gene expression in tumor vs. adjacent tissues were compared to the log2 fold change of 5hmC in tumor vs. adjacent tissues. Gene expression changes in the tumor is positively associated with 5hmC changes in the tumor for 350 5hmC differential genes.) (EPS 2994 KB)

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Fu, Y., Jiang, J., Wu, Y. et al. Genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA as noninvasive diagnostic markers for gastric cancer. Gastric Cancer (2024). https://doi.org/10.1007/s10120-024-01493-7

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