Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics

Song, Ping; Wu, Lucia R.; Yan, Yan Helen; Zhang, Jinny X; Chu, Tianqing; Kwong, Lawrence N.; Patel, Abhijit A.; Zhang, David Y.

doi:10.1038/s41551-021-00837-3

Cited by 118 publications

(92 citation statements)

References 150 publications

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“…As biomarkers, there are several differences between eccDNA and linear circulating cfDNA, and eccDNA is more advantageous in some respects (Table 5 ). 289 , 290 First, eccDNAs are resistant to exonuclease digestion due to their closed circular structure. Therefore, they are more stable than their linear counterparts.…”

Section: Potential Applications Of Eccdnamentioning

confidence: 99%

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Yang

Jia

et al. 2022

Sig Transduct Target Ther

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Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.

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Section: Potential Applications Of Eccdnamentioning

confidence: 99%

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Yang

Jia

et al. 2022

Sig Transduct Target Ther

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“…To date, molecular hallmarks, assessed directly in primary tumor tissue, drive therapy and predict prognosis in several types of solid malignancies [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]; however, often, their evaluation is not reliable and presents some limitations [ 18 , 19 , 20 , 21 ]. Circulating tumor DNA (ctDNA), DNA released from cancer cells into the bloodstream or other body fluids, has been increasingly investigated as a “liquid biopsy” and proved to enable comprehensive genomic profiling of several tumors at various time points [ 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ]. Further, the analysis of cfDNA was shown to be a viable, inexpensive, and less-invasive method to diagnose and monitor cancer hence circumventing the well-known shortcomings of invasive tissue biopsies [ 26 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Circulating Cell-Free DNA in Renal Cell Carcinoma: The New Era of Precision Medicine

Francini

Fanelli

Pederzoli

et al. 2022

Cancers

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Tumor biopsy is still the gold standard for diagnosing and prognosis renal cell carcinoma (RCC). However, its invasiveness, costs, and inability to accurately picture tumor heterogeneity represent major limitations to this procedure. Analysis of circulating cell-free DNA (cfDNA) is a non-invasive cost-effective technique that has the potential to ease cancer detection and prognosis. In particular, a growing body of evidence suggests that cfDNA could be a complementary tool to identify and prognosticate RCC while providing contemporary mutational profiling of the tumor. Further, recent research highlighted the role of cfDNA methylation profiling as a novel method for cancer detection and tissue-origin identification. This review synthesizes current knowledge on the diagnostic, prognostic, and predictive applications of cfDNA in RCC, with a specific focus on the potential role of cell-free methylated DNA (cfMeDNA).

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“…For instance, exosomes present a lipid bilayer, which gives them stability in the bloodstream or during bulk storage, preserving their content against degradation. In addition, their presence in biological fluids is greater compared to CTCs and their genetic material provides more information than cfDNA fragments alone [37,38].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Exosomal Cargo Provides Accurate Clinical, Histologic and Mutational Information in Non-Small Cell Lung Cancer

Durendez-Saez

Calabuig

Torres‐Martínez

et al. 2022

Cancers

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Lung cancer is a malignant disease with high mortality and poor prognosis, frequently diagnosed at advanced stages. Nowadays, immense progress in treatment has been achieved. However, the present scenario continues to be critical, and a full comprehension of tumor progression mechanisms is required, with exosomes being potentially relevant players. Exosomes are membranous vesicles that contain biological information, which can be transported cell-to-cell and modulate relevant processes in the hallmarks of cancer. The present research aims to characterize the exosomes’ cargo and study their role in NSCLC to identify biomarkers. We analyzed exosomes secreted by primary cultures and cell lines, grown in monolayer and tumorsphere formations. Exosomal DNA content showed molecular alterations, whereas RNA high-throughput analysis resulted in a pattern of differentially expressed genes depending on histology. The most significant differences were found in XAGE1B, CABYR, NKX2-1, SEPP1, CAPRIN1, and RIOK3 genes when samples from two independent cohorts of resected NSCLC patients were analyzed. We identified and validated biomarkers for adenocarcinoma and squamous cell carcinoma. Our results could represent a relevant contribution concerning exosomes in clinical practice, allowing for the identification of biomarkers that provide information regarding tumor features, prognosis and clinical behavior of the disease.

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Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics

Cited by 118 publications

References 150 publications

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Extrachromosomal circular DNA: biogenesis, structure, functions and diseases

Circulating Cell-Free DNA in Renal Cell Carcinoma: The New Era of Precision Medicine

Analysis of Exosomal Cargo Provides Accurate Clinical, Histologic and Mutational Information in Non-Small Cell Lung Cancer

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