Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data

Zheng, Xubin; Wu, Qiong; Wu, Haonan; Leung, Kwong‐Sak; Wong, Man‐Hon; Liu, Xueyan; Cheng, Lixin

doi:10.3389/fcell.2021.671302

Cited by 15 publications

(9 citation statements)

References 52 publications

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“…Technically, data integration is necessary for a large-scale study to obtain accurate biomarkers [55]. The primary challenge lies on integrating various cohorts, due to the technical variation between platforms and the batch effect from different experiments [56]. To address this issue, the relative expression of gene pairs in each sample rather than the absolute expression value of a single gene was taken into account.…”

Section: Discussionmentioning

confidence: 99%

Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer

Cheng

Zheng

Leung

et al. 2022

Preprint

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Understanding the regulatory mechanisms in serous ovarian carcinoma (SOC) is critical for its diagnosis and targeted therapy. However, some critical motifs in the competing endogenous RNA (ceRNA) network in SOC were still undiscovered. We profiled a whole transcriptome of eight human SOCs and eight controls and constructed a ceRNA network including mRNAs, lncRNAs, and circRNAs. We hypothesized the noncoding RNA's competing endogenous gene pairs (ceGPs) relationship for the mRNA-ncRNA-mRNA motifs in the ceRNA network. Then, we proposed the denoised individualized pair analysis of gene expression (deiPAGE) to identify mRNA-ncRNA-mRNA motifs from integrated multi-cohorts. 18 cricRNA's ceGPs (cceGPs) were identified and fused as an indicator (SOC index) for SOC discrimination, which carried a high predictive capacity in independent cohorts. The index was negatively correlated with the CD8+/CD4+ ratio in tumour-infiltration, reflecting the migration and growth of tumour cells in ovarian cancer progression.

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Section: Discussionmentioning

confidence: 99%

Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer

Cheng

Zheng

Leung

et al. 2022

Preprint

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“…Previously, we observed that using the expression value of lncRNAs or coding genes directly may lead to deviation, because high-throughput platforms are sensitive to various forms of technical variations (22,34). Moreover, the generated continuous measurements were not measurable and comparable between different states due to the global biological alteration, even though they were preprocessed by plausible normalization methods (20,21).…”

Section: Discussionmentioning

confidence: 99%

Blood Circulating miRNA Pairs as a Robust Signature for Early Detection of Esophageal Cancer

et al. 2021

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Esophageal cancer (EC) is a common malignant tumor in the digestive system which is often diagnosed at the middle and late stages. Noninvasive diagnosis using circulating miRNA as biomarkers enables accurate detection of early-stage EC to reduce mortality. We built a diagnostic signature consisting of four miRNA pairs for the early detection of EC using individualized Pairwise Analysis of Gene Expression (iPAGE). Profiling of miRNA expression identified 496 miRNA pairs with significant relative expression change. Four miRNA pairs consistently selected from LASSO were used to construct the final diagnostic model. The performance of the signature was validated using two independent datasets, yielding both AUCs and PRCs over 0.99. Furthermore, precision, recall, and F-score were also evaluated for clinical application, when a fixed threshold is given, resulting in all the scores are larger than 0.92 in the training set, test set, and two validation sets. Our results suggested that the 4-miRNA signature is a new biomarker for the early diagnosis of patients with EC. The clinical use of this signature would have improved the detection of EC for earlier therapy and more favorite prognosis.

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“…These methods are mainly based on the principle of bisulfite conversion or MSRE digestion. , The bisulfite-based conversion reaction is considered as a gold-standard method for determining DNA methylation, which is primarily to convert unmethylated cytosine (C) to uracil (U) by bisulfite. However, the process needs to be carried out under acidic and high-temperature conditions, which will cause DNA degradation and detection failure. , The MSRE-based method provides a bisulfite-independent way for determination of DNA methylation. The MSRE is a class of restriction endonucleases that are sensitive to methylated bases at their recognition sites, thereby distinguishing methylated from unmethylated sequences. , These endonucleases perform under mild conditions, which avoid DNA degradation .…”

Section: Introductionmentioning

confidence: 99%

“…However, the process needs to be carried out under acidic and high-temperature conditions, which will cause DNA degradation and detection failure. 11,12 The MSRE-based method provides a bisulfite-independent way for determination of DNA methylation. The MSRE is a class of restriction endonucleases that are sensitive to methylated bases at their recognition sites, thereby distinguishing methylated from unmethylated sequences.…”

Section: ■ Introductionmentioning

confidence: 99%

Endonuclease-Assisted PAM-free Recombinase Polymerase Amplification Coupling with CRISPR/Cas12a (E-PfRPA/Cas) for Sensitive Detection of DNA Methylation

et al. 2022

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DNA methylation is considered as a potential cancer biomarker. The evaluation of DNA methylation level will contribute to the prognosis and diagnosis of cancer. Herein, we propose a novel assay based on endonuclease-assisted protospacer adjacent motif (PAM)-free recombinase polymerase amplification coupling with CRISPR/Cas12a (E-PfRPA/Cas) for sensitive detection of DNA methylation. The methylation-sensitive restriction enzyme (MSRE) is first used to selectively digest unmethylated DNA, while the methylated target remains structurally intact. Therefore, the methylated target can initiate the RPA reaction to generate a large amount of double-stranded DNA (dsDNA). To avoid the dependence of PAM site of CRISPR/Cas12a, one of the RPA primers is designed with 5′phosphate terminuses. After treating with Lambda, the sequence with 5′-phosphate modification will be degraded, leaving the singlestranded DNA (ssDNA). The CRISPR/Cas12a can accurately locate ssDNA without PAM, then initiating its trans-cleavage activity for further signal amplification. Meanwhile, non-specific amplification can be also avoided under Lambda, effectively filtering the detection background. Benefiting from the specificity of MSRE, the high amplification efficiency of Lambda-assisted RPA, and the self-amplification effect of CRISPR/Cas, the E-PfRPA/Cas assay shows outstanding sensitivity and selectivity, and as low as 0.05% of methylated DNA can be distinguished. Moreover, the lateral flow assay is also introduced to exploit the point-of-care diagnostic platform. Most importantly, the proposed method shows high sensitivity for determination of genomic DNA methylation from cancer cells, indicating its great potential for tumor-specific gene analysis.

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Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data

Cited by 15 publications

References 52 publications

Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer

Circular RNA’s competing endogenous gene pair as motif in serous ovarian cancer

Blood Circulating miRNA Pairs as a Robust Signature for Early Detection of Esophageal Cancer

Endonuclease-Assisted PAM-free Recombinase Polymerase Amplification Coupling with CRISPR/Cas12a (E-PfRPA/Cas) for Sensitive Detection of DNA Methylation

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