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DNA methylation marker in DNA of host T cells and peripheral blood mononuclear cells (PBMCs) of cancer patients

A methylation marker and methylation technology, applied in the determination/testing of microorganisms, biochemical equipment and methods, etc., can solve unexplained problems

Active Publication Date: 2018-01-05
BEIJING YOUAN HOSPITAL CAPITAL MEDICAL UNIV +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, whether the peripheral host immune system exhibits unique DNA methylation in response to cancer states associated with cancer progression has not been elucidated

Method used

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  • DNA methylation marker in DNA of host T cells and peripheral blood mononuclear cells (PBMCs) of cancer patients
  • DNA methylation marker in DNA of host T cells and peripheral blood mononuclear cells (PBMCs) of cancer patients
  • DNA methylation marker in DNA of host T cells and peripheral blood mononuclear cells (PBMCs) of cancer patients

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0083] Example 1. DNA Methylation Markers in Peripheral Blood Mononuclear Cells (PBMCs) Associated with HCC Cancer Clinical Progression Stage

[0084] patient sample

[0085] HCC clinical progression stage was diagnosed according to the European Association for the Study of the Liver and European Organization for Cancer Therapy and Research EASL-EORTC clinical practice guidelines: management of hepatocellular carcinoma. Patients were divided into four groups, including BLC-0 (Stage 1), BLC-A (Stage 2), BLC-3 (Stage 3), and BLC-C / D (Stage 4). For the sake of simplicity, the above-mentioned phases refer to phases 1 to 4 in the drawings and embodiments of the present invention. Confirm the diagnosis of chronic hepatitis B according to the American Association for the Study of Liver Diseases AASLD practice guidelines for hepatitis B, and the AASLD recommendations for the diagnosis of chronic hepatitis C, and testing, management, and treatment of hepatitis C. Strict exclusion cri...

Embodiment 2

[0100] Example 2. Unique and overlapping differential methylation sites are associated with different HCC clinical progression stages, and can distinguish HCC from hepatitis B and hepatitis C

[0101] The inventors described differentially methylated CGs between healthy controls and each HCC clinical progression stage by using the implementation of the Bioconductor package Limma (50) in ChAMP. The number of differentially methylated CG sites between each HCC clinical progression stage and healthy controls (p-7 ) increased with the progress of clinical stage; stage 1 (BLC-0) was 14,375; stage 2 (BLC-A) was 22,018; stage 3 (BLC-B) was 30,709; stage 4 (BLC -Phase C / D) is 54580. The significance of the overlap between two groups was determined using R-based hypergeometric Fisher's exact test. Significant overlap exists between cancer stages ( Figure 3A ), which implies that there are affected common markers in all stages of clinical progression of HCC (p-297 ).

[0102] The ra...

Embodiment 3

[0108] Example 3: Cancer clinical progression stage-specific DNA methylation markers are used to predict unknown samples from patients by minus-one Pearson cluster analysis, thereby detecting HCC cancers in early clinical progression stages and distinguishing early clinical progression stages of HCC cancer and chronic hepatitis

[0109] Differential methylation sites for each HCC clinical progression stage were obtained by comparing 10 healthy controls and 10 clinical progression stage-specific HCC patients. Other clinical progression stages and hepatitis B and C samples were not "trained" by these differentially methylated CGs ("training" was applied to the model to obtain differentially methylated sites), they served as "cross-validation" for unknown samples " set to address the following questions: First, can markers derived from a stage of clinical progression of the cancer correctly classify HCC samples that were not "trained" by these markers? Second, could the DNA meth...

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Abstract

According to the present invention, it is found that a DNA methylation marker exists in the DNA of host T cells and peripheral blood mononuclear cells (PBMCs) of cancer patients. The invention discloses CG IDs derived from PBMCs DNA, wherein the clinical progression staging of hepatocellular carcinoma (HCC) and chronic hepatitis can be predicted through the methylation level of the CG IDs in the DNA of PBMCs or T cells. The present invention further discloses a kit for predicting HCC by using the identified CG IDs, and applications of a pyrosequencing DNA methylation experiment, a receiver operating characteristic (ROC) experiment, a penalized regression experiment and hierarchical clustering analysis in prediction of HCC. According to the present invention, any one of technicists in the field can obtain the DNA methylation marker for any cancers and the clinical progression staging of any cancers; and the DNA methylation marker (CG IDs) is used for diagnosing cancers, different clinical progression staging of cancers, the response of patients undergoing treatment to treatment, and chronic hepatitis B or chronic hepatitis C.

Description

technical field [0001] The present invention relates to DNA methylation markers in human DNA, especially in the field of molecular diagnosis. Background technique [0002] Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world (1), and it is particularly prevalent in Asia. And the incidence of HCC is highest in areas where hepatitis B is prevalent, suggesting a possible causal relationship (2). Follow-up of high-risk patients such as those with chronic hepatitis and early diagnosis of transition from chronic hepatitis to HCC can improve the cure rate. At present, the long-term survival rate of patients with HCC is extremely low, because HCC is almost always diagnosed in the middle and late stages. If diagnosed early, liver cancer can be effectively treated with >80% cure rate. Advances in diagnostic imaging have improved the non-invasive detection of HCC (3, 4). However, current diagnostic methods, which include imaging and immunoassays using sing...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886C12Q1/6883
Inventor 李宁摩西·斯义夫苏菲·彼得罗普洛斯张永宏
Owner BEIJING YOUAN HOSPITAL CAPITAL MEDICAL UNIV
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