Circulating cell-free nucleic acids of plasma in human aging, healthy aging and longevity: current state of knowledge

Circulating cell-free nucleic acids (ccfNAs) of plasma are a remarkable source of genetic, epigenetic and transcriptomic materials originating from different cells, tissues and organs of an individual. They have been increasingly studied over the past decade as they can carry several important pieces of information about the health status of an individual, which makes them biomarkers of choice for non-invasive diagnosis of numerous diseases and health conditions. However, few studies have investigated variations of plasma ccfNAs in healthy subjects, particularly in relation to aging, healthy aging and longevity, despite the great variability of these biological processes among individuals. Here, we reviewed several studies that focused on the analysis of circulating cell-free DNA (ccfDNA) and microRNAs (ccfmiRNAs) during aging and in the elderly, including some on exceptionally long-lived individuals, i.e., centenarians. After a brief overview of the types, origins and functions of plasma ccfNAs, we described the variations of both ccfDNA and ccfmiRNAs during aging as well as the identification of several potential ccfDNA-based and ccfmiRNA-based biomarkers of aging, healthy aging and/or longevity. We finally highlighted some prospects offered by ccfNAs for the understanding and improvement of healthy aging and longevity.

An Overview of Circulating Cell-Free Nucleic Acids in Diagnosis and Prognosis of Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer due to its molecular heterogeneity and poor clinical outcomes. Analysis of circulating cell-free tumor nucleic acids (ctNAs) can improve our understanding of TNBC and provide efficient and non-invasive clinical biomarkers that may be representative of tumor heterogeneity. In this review, we summarize the potential of ctNAs to aid TNBC diagnosis and prognosis. For example, tumor fraction of circulating cell-free DNA (TFx) may be useful for molecular prognosis of TNBC: high TFx levels after neoadjuvant chemotherapy have been associated with shorter progression-free survival and relapse-free survival. Mutations and copy number variations of TP53 and PIK3CA/AKT genes in plasma may be important markers of TNBC onset, progression, metastasis, and for clinical follow-up. In contrast, the expression profile of circulating cell-free tumor non-coding RNAs (ctncRNAs) can be predictive of molecular subtypes of breast cancer and thus aid in the identification of TBNC. Finally, dysregulation of some circulating cell-free tumor miRNAs (miR17, miR19a, miR19b, miR25, miR93, miR105, miR199a) may have a predictive value for chemotherapy resistance. In conclusion, a growing number of efforts are highlighting the potential of ctNAs for future clinical applications in the diagnosis, prognosis, and follow-up of TNBC.

Liquid biopsy as a tool for predicts of severe COVID-19 and hospitalised community-acquired pneumonia

Cell-free DNA (cfDNA) is released into the circulation after apoptosis, necrosis, and active secretion from cells. In a healthy individual, cfDNA is present in small amounts, has a short half-life, and is predominantly derived from circulating hematopoietic cells. The composition and quantity of cfDNA dramatically changes during pathological conditions. Indeed, several studies reported elevated cfDNA concentration as a potential noninvasive biomarker in many diseases.

AIM

The aim of the study was evaluation of the circulating cell-free DNA in patients with severe Covid-19 in comparison with patients with hospitalised community-acquired pneumonia (with and without hyperglycemia and type 2 diabetes mellitus) to determine the specificity, sensitivity and cutoff value of cfDNA for each nosology.

MATERIALS AND METHODS

The studies were carried out on the basis of city and regional hospitals in the Luhansk region between 2015 to 2021. Were examined in the study 28 patients with a positive diagnosis of COVID-19 according to PCR analysis (14 women and 14 men), 60 patients with community- acquired pneumonia (CAP) (30 women and 30 men), 101 patients with community-acquired pneumonia and hyperglicemia (CAP+HH) (44 women and 57 men), 70 patients with type 2 diabetes mellitus (T2DM) (37 women and 33 men), 42 patients with community-acquired pneumonia in combination with type 2 diabetes mellitus (CAP+T2DM) (27 women and 15 men). The control group consisted of 81 healthy volunteer donor (46 women and 35 men). DNA fragmentation was measured with the diphenylamine assay. Statistical and graphical analyses were done using Statistica 7.0 StatSoft software and using GraphPad Prism version 9.0 (GraphPad Software, La Jolla, CA, USA) software.

RESULTS

We found 3-4-fold higher concentration of serum cfDNA levels in COVID-19 patients (womens and mens) compared with healthy controls. Similarly, the levels of cfDNA were 1,5- to 2-fold higher in pneumoniawomens and pneumonia-mens, pneumonia+hyperglycemia-womens and pneumonia+hyperglycemia-mens pneumonia+Type2 Diabetes-womens and pneumonia+Type2 Diabetes-mens, compared with healthy controls. Our results indicate cfDNA profiles on admission can discriminate between patients with COVID-19 and community-acquired pneumonia at risk of severe disease and death with better performance than previously reported inflammatory markers.

CONCLUSIONS

Circulating cell-free nucleic acids (cfDNA) are novel potential biomarkers of COVID-19 and community-acquired pneumonia identified. Our study is one of the first to analyze cfDNA level (the cutoff value of cfDNA concentration) for prediction of COVID-19 and community-acquired pneumonia (with and without complications and comorbidity diseases).

Novel Molecular Markers in Glioblastoma-Benefits of Liquid Biopsy

Glioblastoma is a primary Central Nervous System (CNS) malignancy with poor survival. Treatment options are scarce and despite the extremely heterogeneous nature of the disease, clinicians lack prognostic and predictive markers to characterize patients with different outcomes. Certain immunohistochemistry, FISH, or PCR-based molecular markers, including isocitrate dehydrogenase1/2 (IDH1/2) mutations, epidermal growth factor receptor variant III (EGFRvIII) mutation, vascular endothelial growth factor overexpression (VEGF) overexpression, or (O6-Methylguanine-DNA methyltransferase promoter) MGMT promoter methylation status, are well-described; however, their clinical usefulness and accuracy is limited, and tumor tissue samples are always necessary. Liquid biopsy is a developing field of diagnostics and patient follow up in multiple types of cancer. Fragments of circulating nucleic acids are collected in various forms from different bodily fluids, including serum, urine, or cerebrospinal fluid in order to measure the quality and quantity of these markers. Multiple types of nucleic acids can be analyzed using liquid biopsy. Circulating cell-free DNA, mitochondrial DNA, or the more stable long and small non-coding RNAs, circular RNAs, or microRNAs can be identified and measured by novel PCR and next-generation sequencing-based methods. These markers can be used to detect the previously described alterations in a minimally invasive method. These markers can be used to differentiate patients with poor or better prognosis, or to identify patients who do not respond to therapy. Liquid biopsy can be used to detect recurrent disease, often earlier than using imaging modalities. Liquid biopsy is a rapidly developing field, and similarly to other types of cancer, measuring circulating tumor-derived nucleic acids from biological fluid samples could be the future of differential diagnostics, patient stratification, and follow up in the future in glioblastoma as well.

Circulating cell-free nucleic acids as biomarkers in colorectal cancer screening and diagnosis - an update

Introduction: Screening methods for one of the most frequently diagnosed malignancy, colorectal cancer (CRC), have limitations. Circulating cell-free nucleic acids (cfNA) hold clinical relevance as screening, prognostic and therapy monitoring markers. Area covered: In this review, we summarize potential CRC-specific cfNA biomarkers, the recently developed sample preparation techniques, their applications, and pitfalls. Expert opinion: Automated extraction of cfDNA is highly reproducible, however, cfDNA yield is less compared to manual isolation. Quantitative and highly sensitive detection techniques (e.g. digital PCR, NGS) can be applied to analyze genetic and epigenetic changes. Detection of DNA mutations or methylation in cfDNA and related altered levels of mRNA, miRNA, and lncRNA may improve early cancer recognition, based on specific, CRC-related patterns. Detection of cfDNA mutations (e.g. TP53, KRAS, APC) has limited diagnostic sensitivity (40-60%), however, methylated DNA including SEPT9, SFRP1, SDC2 can be applied with higher sensitivity (up to 90%) for CRC. Circulating miRNAs (e.g. miR-21, miR-92, miR-141) provide comparably high sensitivity for CRC as the circulating tumor cell mRNA markers (e.g. EGFR, CK19, CK20, CEA). Automation of cfNA isolation coupled with quantitative analysis of CRC-related, highly sensitive biomarkers may enhance CRC screening and early detection in the future.