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Circulating Cell-Free Nucleic Acids and Cancers
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Circulating Cell-Free Nucleic Acids and Cancers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 24051

Special Issue Editor

Dr. Bruna Scaggiante

E-Mail Website
Guest Editor
Department of Life Sciences, University of Trieste, Valerio 28, 34127 Trieste, Italy
Interests: biological fluids; cancer; cancer biomarkers; cfDI; cfDNA; cfNA; copy number variation; ctDNA; ddPCR; disease-free survival; epigenetic; epigenetic sequencing; exosome; extracellular vesicle; genotyping; liquid biopsy; miRNA; mRNA; mutation; ncRNA; next- generation sequencing; overall survival; progression-free survival; recurrence-free survival; whole-exome sequencing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Improvements in the molecular diagnosis and prognosis of cancer and better evaluation of the therapeutic intervention are urgently needed to offer more personalized treatment to patients.

In this respect, the liquid biopsy has great potential for precision medicine, especially for solid tumors: It is applicable for screening, diagnosis, prognosis, and for the predictive value and monitoring of the disease. Liquid biopsy is a versatile and minimally invasive procedure and the availability of high-throughput technologies allows the analysis of very small quantities of targets.

In a liquid biopsy, the targeting of circulating cell-free nucleic acids (cfNA), is one of the most interesting aspects because many cancer biomarkers, already identified in the tissue, can be found in circulating cell-free DNA (cfDNA). In cfDNA, a fraction of tumor DNA (ctDNA) can be searched by identifying both the cancer-related mutations and the copy number variation of specific genes. The cancer-related methylation status of selected genes in cfDNA can also be measured. Moreover, it has been demonstrated that ctDNA quantity can be related to the integrity index of the cfDNA, (cfDI), i.e., the fraction of long over short-nested fragments of the same DNA target. Many studies indicate that ctDNA analysis can depict tumor heterogeneity. Recently, the role of circulating-free RNA molecules (cfRNA) in diagnosis, prognosis, and therapy responsiveness is emerging. In general, studies on cfNA have a high translational potential for clinical practice, as in EGFR mutations validated by FDA in 2016 for NSCLC. Finally, the analysis of cfNA has the advantage of being highly specific but simpler and lower costing than analyses using circulating tumor cells. Thus, they can be useful to facilitate therapeutic decision-making and to predict tumor burden after therapies or the acquired treatment resistance.

Topics of interest for this Special Issue include but are not limited to the following:

  • Liquid biopsy targeting cfNA for cancer molecular diagnostic
  • Clinical validity and utility of cfNA analysis for tumors
  • Epigenetic markers for cancer by liquid biopsy
  • Extracellular Vesicle biomarkers in liquid biopsy
  • New insights in cfNA biomarkers (cfDNA, ctDNA, cfDI and cfRNA) for screening, diagnosis, prognosis, follow-up and therapeutic management of tumors
  • New techniques to evaluate cfNA
  • Liquid biopsy on Exosome for cancer diagnostic

Dr. Bruna Scaggiante
Guest Editor

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Keywords

  • Biological fluids
  • Cancer
  • Cancer biomarkers
  • cfDI
  • cfDNA
  • cfNA
  • Copy number variation
  • ctDNA
  • ddPCR
  • Disease-free survival
  • Epigenetic
  • Epigenetic sequencing
  • Exosome
  • Extracellular vesicle
  • Genotyping
  • Liquid biopsy
  • miRNA
  • mRNA
  • mutation
  • ncRNA
  • Next-generation sequencing
  • Overall survival
  • Progression-free survival
  • Recurrence-free survival
  • Whole-exome sequencing

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Published Papers (7 papers)

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Research

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14 pages, 1932 KiB  
Article
Molecular Beacon for Detection miRNA-21 as a Biomarker of Lung Cancer
by Daniela Alexandre, Bernardo Teixeira, André Rico, Salete Valente, Ana Craveiro, Pedro V. Baptista and Carla Cruz
Int. J. Mol. Sci. 2022, 23(6), 3330; https://doi.org/10.3390/ijms23063330 - 19 Mar 2022
Cited by 12 | Viewed by 3707
Abstract
Lung cancer (LC) is the leading cause of cancer-related death worldwide. Although the diagnosis and treatment of non-small cell lung cancer (NSCLC), which accounts for approximately 80% of LC cases, have greatly improved in the past decade, there is still an urgent need [...] Read more.
Lung cancer (LC) is the leading cause of cancer-related death worldwide. Although the diagnosis and treatment of non-small cell lung cancer (NSCLC), which accounts for approximately 80% of LC cases, have greatly improved in the past decade, there is still an urgent need to find more sensitive and specific screening methods. Recently, new molecular biomarkers are emerging as potential non-invasive diagnostic agents to screen NSCLC, including multiple microRNAs (miRNAs) that show an unusual expression profile. Moreover, peripheral blood mononuclear cells’ (PBMCs) miRNA profile could be linked with NSCLC and used for diagnosis. We developed a molecular beacon (MB)-based miRNA detection strategy for NSCLC. Following PBMCs isolation and screening of the expression profile of a panel of miRNA by RT-qPCR, we designed a MB targeting of up-regulated miR-21-5p. This MB 21-5p was characterized by FRET-melting, CD, NMR and native PAGE, allowing the optimization of an in-situ approach involving miR-21-5p detection in PBMCs via MB. Data show the developed MB approach potential for miR-21-5p detection in PBMCs from clinical samples towards NSCLC. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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18 pages, 5121 KiB  
Article
Circular RNA hsa_circ_0000190 Facilitates the Tumorigenesis and Immune Evasion by Upregulating the Expression of Soluble PD-L1 in Non-Small-Cell Lung Cancer
by Yung-Hung Luo, Yi-Ping Yang, Chian-Shiu Chien, Aliaksandr A. Yarmishyn, Afeez Adekunle Ishola, Yueh Chien, Yuh-Min Chen, Ping-Hsing Tsai, Tzu-Wei Lin, Mong-Lien Wang and Shih-Hwa Chiou
Int. J. Mol. Sci. 2022, 23(1), 64; https://doi.org/10.3390/ijms23010064 - 22 Dec 2021
Cited by 24 | Viewed by 4146
Abstract
Lung cancer is the leading cause of death from cancer in Taiwan and throughout the world. Immunotherapy has revealed promising and significant efficacy in NSCLC, through immune checkpoint inhibition by blocking programmed cell death protein (PD)-1/PD-1 ligand (PD-L1) signaling pathway to restore patients’ [...] Read more.
Lung cancer is the leading cause of death from cancer in Taiwan and throughout the world. Immunotherapy has revealed promising and significant efficacy in NSCLC, through immune checkpoint inhibition by blocking programmed cell death protein (PD)-1/PD-1 ligand (PD-L1) signaling pathway to restore patients’ T-cell immunity. One novel type of long, non-coding RNAs, circular RNAs (circRNAs), are endogenous, stable, and widely expressed in tissues, saliva, blood, urine, and exosomes. Our previous results revealed that the plasma level of hsa_circ_0000190 can be monitored by liquid-biopsy-based droplet digital PCR and may serve as a valuable blood-based biomarker to monitor the disease progression and the efficacy of immunotherapy. In this study, hsa_circ_0000190 was shown to increase the PD-L1 mRNA-mediated soluble PD-L1 (sPD-L1) expression, consequently interfering with the efficacy of anti-PD-L1 antibody and T-cell activation, which may result in immunotherapy resistance and poor outcome. Our results unraveled that hsa_circ_0000190 facilitated the tumorigenesis and immune evasion of NSCLC by upregulating sPD-L1 expression, potentially developing a different aspect in elucidating the molecular immunopathogenesis of NSCLC. Hsa_circ_0000190 upregulation can be an effective indicator for the progression of NSCLC, and hsa_circ_0000190 downregulation may possess a potential therapeutic value for the treatment of NSCLC in combination with immunotherapy. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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14 pages, 2769 KiB  
Article
ANK2 Hypermethylation in Canine Mammary Tumors and Human Breast Cancer
by Johannes J. Schabort, A-Reum Nam, Kang-Hoon Lee, Seok Won Kim, Jeong Eon Lee and Je-Yoel Cho
Int. J. Mol. Sci. 2020, 21(22), 8697; https://doi.org/10.3390/ijms21228697 - 18 Nov 2020
Cited by 13 | Viewed by 3021
Abstract
Canine mammary tumors (CMT) constitute the most common tumor types found in female dogs. Understanding this cancer through extensive research is important not only for clinical veterinary applications, but also in the scope of comparative oncology. The use of DNA methylation as a [...] Read more.
Canine mammary tumors (CMT) constitute the most common tumor types found in female dogs. Understanding this cancer through extensive research is important not only for clinical veterinary applications, but also in the scope of comparative oncology. The use of DNA methylation as a biomarker has been noted for numerous cancers in the form of both tissue and liquid biopsies, yet the study of methylation in CMT has been limited. By analyzing our canine methyl-binding domain sequencing (MBD-seq) data, we identified intron regions of canine ANK2 and EPAS1 as differentially methylated regions (DMGs) in CMT. Subsequently, we established quantitative methylation specific PCR (qMSP) of ANK2 and EPAS1 to validate the target hypermethylation in CMT tissue, as well as cell free DNA (cfDNA) from CMT plasma. Both ANK2 and EPAS1 were hypermethylated in CMT and highlighted as potential tissue biomarkers in CMT. ANK2 additionally showed significant hypermethylation in the plasma cfDNA of CMT, indicating that it could be a potential liquid biopsy biomarker as well. A similar trend towards hypermethylation was indicated in HBC at a specific CpG of the ANK2 target on the orthologous human region, which validates the comparative approach using aberrant methylation in CMT. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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15 pages, 1737 KiB  
Article
Unique Interplay between Molecular miR-181b/d Biomarkers and Health Related Quality of Life Score in the Predictive Glioma Models
by Rytis Stakaitis, Aiste Pranckeviciene, Giedrius Steponaitis, Arimantas Tamasauskas, Adomas Bunevicius and Paulina Vaitkiene
Int. J. Mol. Sci. 2020, 21(20), 7450; https://doi.org/10.3390/ijms21207450 - 9 Oct 2020
Cited by 9 | Viewed by 2252
Abstract
In the last decade, an increasing amount of research has been conducted analyzing microRNA expression changes in glioma tissue and its expressed exosomes, but there is still sparse information on microRNAs or other biomarkers and their association with patients’ functional/psychological outcomes. In this [...] Read more.
In the last decade, an increasing amount of research has been conducted analyzing microRNA expression changes in glioma tissue and its expressed exosomes, but there is still sparse information on microRNAs or other biomarkers and their association with patients’ functional/psychological outcomes. In this study, we performed a combinational analysis measuring miR-181b and miR-181d expression levels by quantitative polymerase chain reaction (qPCR), evaluating isocitrate dehydrogenase 1 (IDH1) single nucleotide polymorphism (SNP), and O-6-methylguanine methyltransferase (MGMT) promoter methylation status in 92 post-surgical glioma samples and 64 serum exosomes, including patients’ quality of life evaluation applying European Organization for Research and Treatment of Cancer (EORTC) questionnaire for cancer patients (QLQ-30), EORTC the Brain Cancer-Specific Quality of Life Questionnaire (QLQ-BN20), and the Karnofsky performance status (KPS). The tumoral expression of miR-181b was lower in grade III and glioblastoma, compared to grade II glioma patients (p < 0.05). Additionally, for the first time, we demonstrated the association between miR-181 expression levels and patients’ quality of life. A positive correlation was observed between tumoral miR-181d levels and glioma patients’ functional parameters (p < 0.05), whereas increased exosomal miR-181b levels indicated a worse functional outcome (p < 0.05). Moreover, elevated miR-181b exosomal expression can indicate a significantly shorter post-surgical survival time for glioblastoma multiforme (GBM) patients. In addition, both tumoral and exosomal miR-181 expression levels were related to patients’ functioning and tumor-related symptoms. Our study adds to previous findings by demonstrating the unique interplay between molecular miR-181b/d biomarkers and health related quality of life (HRQOL) score as both variables remained significant in the predictive glioma models. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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14 pages, 1353 KiB  
Article
The Circulating Nucleic Acid Characteristics of Non-Metastatic Soft Tissue Sarcoma Patients
by Nicholas Eastley, Aurore Sommer, Barbara Ottolini, Rita Neumann, Jin-Li Luo, Robert K. Hastings, Thomas McCulloch, Claire P. Esler, Jacqueline A. Shaw, Robert U. Ashford and Nicola J. Royle
Int. J. Mol. Sci. 2020, 21(12), 4483; https://doi.org/10.3390/ijms21124483 - 24 Jun 2020
Cited by 9 | Viewed by 2430
Abstract
Soft tissue sarcomas (STS) are rare, malignant tumours with a generally poor prognosis. Our aim was to explore the potential of cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) analysis to track non-metastatic STS patients undergoing attempted curative treatment. The analysed cohort [...] Read more.
Soft tissue sarcomas (STS) are rare, malignant tumours with a generally poor prognosis. Our aim was to explore the potential of cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) analysis to track non-metastatic STS patients undergoing attempted curative treatment. The analysed cohort (n = 29) contained multiple STS subtypes including myxofibrosarcomas, undifferentiated pleomorphic sarcomas, leiomyosarcomas, and dedifferentiated liposarcomas amongst others. Perioperative cfDNA levels trended towards being elevated in patients (p = 0.07), although did not correlate with tumour size, grade, recurrence or subtype, suggesting a limited diagnostic or prognostic role. To characterise ctDNA, an amplicon panel covering three genes commonly mutated in STSs was first trialled on serial plasma collected from nine patients throughout follow-up. This approach only identified ctDNA in 2.5% (one in 40) of the analysed samples. Next custom-designed droplet digital PCR assays and Ion AmpliSeq™ panels were developed to track single nucleotide variants identified in patients’ STSs by whole exome sequencing (1–6 per patient). These approaches identified ctDNA in 17% of patients. Although ctDNA was identified before radiologically detectable recurrence in two cases, the absence of demonstrable ctDNA in 83% of cases highlights the need for much work before circulating nucleic acids can become a useful means to track STS patients. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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Review

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16 pages, 994 KiB  
Review
Liquid Biopsy as a Source of Nucleic Acid Biomarkers in the Diagnosis and Management of Lynch Syndrome
by Gergely Buglyó, Jakub Styk, Ondrej Pös, Ádám Csók, Vanda Repiska, Beáta Soltész, Tomas Szemes and Bálint Nagy
Int. J. Mol. Sci. 2022, 23(8), 4284; https://doi.org/10.3390/ijms23084284 - 13 Apr 2022
Cited by 11 | Viewed by 3043
Abstract
Lynch syndrome (LS) is an autosomal dominant inherited cancer predisposition disorder, which may manifest as colorectal cancer (CRC), endometrial cancer (EC) or other malignancies of the gastrointestinal and genitourinary tract as well as the skin and brain. Its genetic cause is a defect [...] Read more.
Lynch syndrome (LS) is an autosomal dominant inherited cancer predisposition disorder, which may manifest as colorectal cancer (CRC), endometrial cancer (EC) or other malignancies of the gastrointestinal and genitourinary tract as well as the skin and brain. Its genetic cause is a defect in one of the four key DNA mismatch repair (MMR) loci. Testing of patients at risk is currently based on the absence of MMR protein staining and detection of mutations in cancer tissue and the germline, microsatellite instability (MSI) and the hypermethylated state of the MLH1 promoter. If LS is shown to have caused CRC, lifetime follow-up with regular screening (most importantly, colonoscopy) is required. In recent years, DNA and RNA markers extracted from liquid biopsies have found some use in the clinical diagnosis of LS. They have the potential to greatly enhance the efficiency of the follow-up process by making it minimally invasive, reproducible, and time effective. Here, we review markers reported in the literature and their current clinical applications, and we comment on possible future directions. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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15 pages, 1062 KiB  
Review
Current Status of Circulating Tumor DNA Liquid Biopsy in Pancreatic Cancer
by Miles W. Grunvald, Richard A. Jacobson, Timothy M. Kuzel, Sam G. Pappas and Ashiq Masood
Int. J. Mol. Sci. 2020, 21(20), 7651; https://doi.org/10.3390/ijms21207651 - 16 Oct 2020
Cited by 39 | Viewed by 4268
Abstract
Pancreatic cancer is a challenging disease with a low 5-year survival rate. There are areas for improvement in the tools used for screening, diagnosis, prognosis, treatment selection, and assessing treatment response. Liquid biopsy, particularly cell free DNA liquid biopsy, has shown promise as [...] Read more.
Pancreatic cancer is a challenging disease with a low 5-year survival rate. There are areas for improvement in the tools used for screening, diagnosis, prognosis, treatment selection, and assessing treatment response. Liquid biopsy, particularly cell free DNA liquid biopsy, has shown promise as an adjunct to our standard care for pancreatic cancer patients, but has not yet been universally adopted into regular use by clinicians. In this publication, we aim to review cfDNA liquid biopsy in pancreatic cancer with an emphasis on current techniques, clinical utility, and areas of active investigation. We feel that researchers and clinicians alike should be familiar with this exciting modality as it gains increasing importance in the care of cancer patients. Full article
(This article belongs to the Special Issue Circulating Cell-Free Nucleic Acids and Cancers)
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