Cell-Free Nucleic Acids: New Insights into Physico-Chemical Properties, Analytical Considerations, and Clinical Applications—2nd Edition

Dear Colleagues,

Through programmed or accidental cell degradation, as well as through purported extrusion from live cells, genetic material is continuously dispelled from different tissues and cells into body fluids. The capture and analysis of these cell-free DNA (cfDNA) molecules open up an unprecedented window of access for the minimally invasive characterization of inherited genetic codes, as well as of static and temporal genomic changes that result from disease, environmental insults, and other means.

Until recently, the profiling of classical cfDNA mutations for the characterization of solid tumors and fetal genetic abnormalities has attracted the most attention. However, from the rapidly growing body of evidence, the picture emerges that not only is the scope of potential clinical applications of cfDNA analysis much wider than initially thought, but there is still much to be learned about the characteristics of cfDNA both as a molecular entity and as a biological phenomenon in general. Unsurprisingly, studies of the complete physico-chemical features of cfDNA molecules (e.g., DNA methylation, sequence motifs, histone modifications, nucleosome density and spacing, and fragment end-point patterns) as they relate to a variety of contexts has moved rapidly to the front and will, in the next couple of years, likely become the principle center of interest in the research field.

Within this context, the goal of this Special Issue is to advance the emerging perspective on the importance of a holistic knowledge on cfDNA. This is crucial for accelerating our understanding of this intriguing biological phenomenon, and to fully harness its potential in both basic research and clinical settings. Therefore, authors are invited to submit original research and review papers that are focused on, but not limited to, the following topics:

• Nomenclature.
• The current status of cfDNA research:
• The many different domains of research;
• Important and emerging concepts in the cfDNA research field;
• New technologies and opportunities;
• Defining the edges of knowledge in the research field;
• Highlighting neglected topics and areas of cfDNA research.
• The clinical scope of cfDNA as a biomarker:
• Assessments of different diseases and conditions (e.g., exercise, cancer, fetal genetic abnormalities, sepsis, clonal hematopoiesis, and cardiovascular metabolic, inflammatory, autoimmune, hypoxic, and ischemic diseases);
• Assessment of different diseases in animals.
• Preanalytical optimization, standardization, and quality control:
• Comparative analysis of methods and technologies;
• Development and testing of tailored methods and bioinformatics approaches;
• Enrichment strategies for circulating tumor DNA.
• New insights into the biology and structure of cfDNA:
• Biological and physico-chemical properties of cfDNA;
• cfDNA size analysis (fragmentomics);
• Possible origins of cfDNA (consideration of apoptosis, necrosis, and active release);
• Possible biological functions of cfDNA;
• Possible detrimental effects of cfDNA.
• Analysis and management of high-throughput datasets.
• Exciting applications of cfDNA analysis in oncology:
• Epigenetic characterization of cfDNA and tissue-specific signatures;
• Gauging the use of cfDNA as a tool for early cancer detection;
• Stratification and monitoring targeted therapies in early and advanced cancers;
• Clonal evolution of cancer in response to the microenvironment and immune response;
• Plasma TMB and beyond for stratification and monitoring in immune therapies;
• Liquid biopsy approaches for cell-based immune therapies;
• Monitoring minimal residual disease in cancer;
• Combinatorial diagnostic power of multimarker or multi-parameter assessments (inclusion of proteins, extracellular vesicles, and other nucleic acid species);
• Longitudinal assessments of cfDNA.

Dr. Abel Bronkhorst
Prof. Dr. Stefan Holdenrieder
Guest Editors

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• cell-free DNA
• circulating tumor DNA
• liquid biopsy
• cancer management
• clinical oncology

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