Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma

Burgener, Justin M.; Zou, Jinfeng; Zhao, Zhen; Zheng, Yangqiao; Shen, Shu Yi; Huang, Shao Hui; Keshavarzi, Sareh; Xu, Wei; Liu, Feifei; Liu, Geoffrey; Waldron, John; Weinreb, Ilan; Spreafico, Anna; Siu, Lillian L.; Almeida, John R. de; Goldstein, David P.; Hoffman, Michael M.; Carvalho, Daniel D. De; Bratman, Scott V.

doi:10.1158/1078-0432.ccr-21-0110

Cited by 67 publications

(79 citation statements)

References 45 publications

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“…Inference of copy number profiles and sequencing multiple genes using NGS to identify “trunk” mutations can help mitigate these sources of variability. Another emerging method is the detection of methylated ctDNA, which has characteristic patterns in distinct tumor types; notably, there are numerous recurrent cancer-specific DNA methylation aberrations, and these can be measured using PCR- and NGS-based assays ( 47 – 51 ). The strength of methylated DNA as a biomarker is that it does not rely on the presence of specific mutations.…”

Section: Introductionmentioning

confidence: 99%

Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges

et al. 2022

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Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.

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Section: Introductionmentioning

confidence: 99%

Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges

et al. 2022

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“…25–31 Recently, a study by Burgener et al did demonstrate tumor-naïve detection of ctDNA by simultaneously profiling mutations and methylation. 32…”

Section: Discussionmentioning

confidence: 99%

Plasma cell-free DNA methylome profiling in pre- and post-surgery oral cavity squamous cell carcinoma

Patel

Padhya

Huang

et al. 2022

Preprint

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Purpose: Head and neck squamous cell carcinoma cancer (HNSCC), a highly heterogeneous disease that involves multiple anatomic sites, is a leading cause of cancer-related mortality worldwide. Although the utility of noninvasive biomarkers based on circulating cell-free DNA (cfDNA) methylation profiling has been widely recognized, limited studies have been reported so far regarding the dynamics of cfDNA methylome in oral cavity squamous cell carcinoma (OCSCC). It is hypothesized in this study that comparison of methylation profiles in pre- and post-surgery plasma samples will reveal OCSCC-specific prognostic and diagnostic biomarkers. Materials and methods: Matched plasma samples from eight patients with OCSCC were collected at Moffitt Cancer Center before and after surgical resection. Plasma-derived cfDNA was analyzed by cfMBD-seq, which is a high-sensitive methylation profiling assay. Differential methylation analysis was then performed based on the matched samples profiled. As a strategy to further prioritize tumor-specific targets, top differential methylated regions (DMRs) were called by reanalyzing methylation data from paired tumor and normal tissue collected in the TCGA head and neck cancer cohort. Results: In the top 200 HNSCC-specific DMRs detected based on the TCGA dataset, a total of 23 regions reached significance in the plasma-based DMR test. The top five validated DMR regions (ranked by the significance in the plasma study) are located in the promoter regions of genes PENK, NXPH1, ZIK1, TBXT and CDO1, respectively. The genome-wide cfDNA DMR analysis further highlighted candidate biomarkers located in genes SFRP4, SOX1, IRF4 and PCDH17. The prognostic relevance of candidate genes was confirmed by survival analysis using the TCGA data. Conclusion: This study supports the utility of cfDNA-based methylome profiling as a promising noninvasive biomarker source for OCSCC and HNSCC.

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“…Because these non-genetic signatures are unique to their cells of origin, they could provide a novel marker of tissue-specific pathologies. There is growing interest in using these new approaches as cancer biomarkers that may be complementary to tracking tumor mutations [ 82 , 106 , 150 , 151 , 152 , 153 , 154 , 155 ]. Furthermore, cell-free DNA epigenetic markers have been shown to be associated with normal tissue injury [ 92 , 156 , 157 , 158 ], raising the possibility that cell-free DNA methylation, fragmentomics, and/or cell-free RNA could identify radiation-induced normal tissue toxicity.…”

Section: Liquid Biopsies To Monitor Cancer Treatment Responsementioning

confidence: 99%

Liquid Biopsies for Molecular Biology-Based Radiotherapy

Blomain

Moding

2021

IJMS

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Molecular alterations drive cancer initiation and evolution during development and in response to therapy. Radiotherapy is one of the most commonly employed cancer treatment modalities, but radiobiologic approaches for personalizing therapy based on tumor biology and individual risks remain to be defined. In recent years, analysis of circulating nucleic acids has emerged as a non-invasive approach to leverage tumor molecular abnormalities as biomarkers of prognosis and treatment response. Here, we evaluate the roles of circulating tumor DNA and related analyses as powerful tools for precision radiotherapy. We highlight emerging work advancing liquid biopsies beyond biomarker studies into translational research investigating tumor clonal evolution and acquired resistance.

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Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma

Cited by 67 publications

References 45 publications

Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges

Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges

Plasma cell-free DNA methylome profiling in pre- and post-surgery oral cavity squamous cell carcinoma

Liquid Biopsies for Molecular Biology-Based Radiotherapy

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