Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites

Liu, Hui; Chen, Jianming; Chen, Haifeng; Xia, Jie; Wang, Ouxi; Xie, Jiajing; Li, Meifeng; Guo, Zheng; Chen, Guoping; Yan, Haidan

doi:10.1080/15592294.2020.1827720

Cited by 8 publications

(8 citation statements)

References 35 publications

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“…A method based on DNA methylation profiles has recently been used to distinguish gliomas from BM, and has been tested in the identification of the origin of BM with known primary, correctly classifying 95% of the samples. Data on BM-CUP are not available [63]. Liquid biopsies collect and analyse circulating tumour cells (CTCs) and cell-free tumour (ctDNA) in body fluids (such as cerebrospinal fluid (CSF) and plasma); these can be a surrogate of tumour tissue in the management of both primary and secondary brain tumours [64].…”

Section: Gene Expression Profiling: a New Frontiermentioning

confidence: 99%

Brain Metastasis from Unknown Primary Tumour: Moving from Old Retrospective Studies to Clinical Trials on Targeted Agents

Balestrino

Rudà

Soffietti

2020

Cancers

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Brain metastases (BMs) are the most common intracranial tumours in adults and occur up to 3–10 times more frequently than primary brain tumours. BMs may be the cause of the neurological presenting symptoms in patients with otherwise previously undiagnosed cancer. In up to 15% of patients with BMs, the primary tumour cannot be identified. These cases are known as BM of cancer of unknown primary (CUP) (BM-CUP). CUP has an early and aggressive metastatic spread, poor response to chemotherapy, and poor prognosis. The pathogenesis of CUP seems to be characterized by a specific underlying pro-metastatic signature. The understanding of BM-CUP, despite its relative frequency and unfavourable outcome, is still incomplete and clear indications on management are missing. Advances in diagnostic tools, molecular characterization, and target therapy have shifted the paradigm in the approach to metastasis from CUP: while earlier studies stressed the importance of finding the primary tumour and deciding on treatment based on the primary diagnosis, most recent studies focus on the importance of identifying targetable molecular markers in the metastasis itself. The aim of this review is to summarize current evidence on BM-CUP, from the diagnosis and pathogenesis to the treatment, with a focus on available studies and ongoing clinical trials.

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Section: Gene Expression Profiling: a New Frontiermentioning

confidence: 99%

Brain Metastasis from Unknown Primary Tumour: Moving from Old Retrospective Studies to Clinical Trials on Targeted Agents

Balestrino

Rudà

Soffietti

2020

Cancers

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“…The relative methylation levels (RMLs) of gene pairs have been reported to be robust to batch effects [7,15], which allowed us to integrate normal controls from different sources for a disease. Thus, we developed a RML-based method, termed RankDMG, to analyze methylation data in the three special scenarios.…”

Section: Discussionmentioning

confidence: 99%

RankDMG: a differentially methylated gene analysis method for three special scenarios

Fan

Zheng

Chen

et al. 2023

Preprint

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Background Common methods of identification of differentially methylated genes (DMGs) mainly detect differences between case and control groups, which cannot tell whether a gene is differentially methylated in a specific disease sample (first scenario), and are not applicable for the study with no normal control (one-phenotype, second scenario). Also, these methods have low detection capacity at the control-limited (third) scenario. Results we developed a method, termed RankDMG, to analyze DNA methylation data in the three special scenarios. For the individualized DMG analysis, RankDMG showed remarkable performances in simulated and real data, independent of measured platforms. Using DMGs detected by common methods as ‘gold standard’, the DMGs identified by RankDMG using only one-phenotype data were comparable to those detected by common methods using case-control samples. Moreover, even when the number of disease samples reduced to five, RankDMG could also identify disease-related DMGs for control-limited data. Conclusion RankDMG provides a novel tool to dissect the inter-individual heterogeneity of tumor at epigenetic level, and it could analyze the one-phenotype and control-limited methylation data. RankDMG is provided as an open source tool via https://github.com/FunMoy/RankDMG.

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“…DNA methylation, a ubiquitous epigenetic silencing mechanism, exhibits a greater level of universality than somatic mutations, 82 tissue-specificity, and relative stability, 83 rendering it an attractive avenue to discriminate MLCs. Despite a lack of comprehensive research on MLCs, DNA methylation profiles have been leveraged to identify the tissue origin of unknown primary malignancies based on mapping to a comprehensive atlas, 77 intra-sample methylation orderings of the CpG sites, 84 similarity of regional patterns to a specific cancer type, 82 tightly coupled CpG sites termed methylation haplotypes 85 and so on. These mechanisms have demonstrated promise for molecular analysis of clonal relatedness.…”

Section: Potential Molecule-based Methods For Discriminating Mlcsmentioning

confidence: 99%

Towards the molecular era of discriminating multiple lung cancers

Wang¹,

Yuan²,

Jiang³

et al. 2023

eBioMedicine

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Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites

Cited by 8 publications

References 35 publications

Brain Metastasis from Unknown Primary Tumour: Moving from Old Retrospective Studies to Clinical Trials on Targeted Agents

Brain Metastasis from Unknown Primary Tumour: Moving from Old Retrospective Studies to Clinical Trials on Targeted Agents

RankDMG: a differentially methylated gene analysis method for three special scenarios

Towards the molecular era of discriminating multiple lung cancers

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