Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology

Current Pharmaceutical Biotechnology ◽

10.2174/1389201021666201211102710 ◽

2020 ◽

Vol 21 ◽

Author(s):

Suman Kumar Ray ◽

Sukhes Mukherjee

Keyword(s):

Tumor Cells ◽

Liquid Biopsy ◽

Cancer Metastasis ◽

Nuclear Dna ◽

Fragment Size ◽

Body Fluids ◽

Response To Therapy ◽

Significant Information ◽

Cell Free Dna ◽

Free Dna

: Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.

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Molecular characterisation of longitudinally collected circulating cell-free DNA in HPV+ve and HPV-ve oropharyngeal cancer

10.1101/2020.09.07.20189704 ◽

2020 ◽

Author(s):

John P Thomson ◽

Sophie J Warlow ◽

Martyna Adamowicz ◽

Helen Thain ◽

Kate Cuschieri ◽

...

Keyword(s):

Deep Sequencing ◽

Clinical Decision Making ◽

Fragment Size ◽

Clinical Care ◽

Significant Risk ◽

Post Treatment ◽

Response To Therapy ◽

Cell Free Dna ◽

Tissue Biopsy ◽

Free Dna

Oropharyngeal squamous cell carcinoma (OPSCC) is an increasing global health problem and is divided into two types dependent on association with human papillomavirus (HPV), with a more favourable prognosis in virus-associated tumours. Current methods of establishing viral aetiology, assessing response to therapy and clinical monitoring rest on tissue biopsy, clinical examination and post-treatment imaging. However, tissue biopsy is invasive and carries significant risk of morbidity, and post-treatment scans are frequently indeterminate. Analysis of cell-free DNA (cfDNA) from the circulation provides a minimally invasive method for detecting and monitoring cancer-derived DNA fragments, with the potential for enhancing clinical care. Through the longitudinal collection of 166 blood samples in 67 OPSCC patients we evaluate the utility of three cfDNA analysis methods: droplet digital PCR (ddPCR) and fragment size analysis in both HPV+ve and HPV-ve disease, and ultra-deep sequencing in patients with HPV-ve disease. We show that ddPCR analysis of cfDNA for five HPV types (16, 18, 31, 33 & 35) is strongly concordant with existing clinical assays (p16 immunohistochemistry (IHC) and quantitative PCR analysis of solid tumour tissue) and that cfDNA fragment size was reduced in OPSCC patients compared to healthy controls. Sequential ddPCR measurements of cfDNA HPV copy number showed a decrease to undetectable levels in all 30 HPV+ve patients in at least one of their post-treatment samples and a corresponding increase in cfDNA fragment size in patients who had a complete response to chemoradiotherapy. In two HPV+ve patients, clinical decision-making based on HPV ddPCR of cfDNA may have led to earlier detection of relapse in one patient or avoided surgical exploration in a second patient, which led to resection of tissue that did not harbour malignancy. In HPV-ve disease, ultra-deep sequencing identified tumour-derived somatic mutations of circulating cfDNA in genes such as TP53 and members of the ERBB family that are potential markers of therapeutic responsiveness and patient prognosis. Together our data suggest that analysis of circulating cfDNA can enhance current clinical strategies for assessing therapeutic response and disease monitoring in both HPV+ve and HPV-ve OPSCC.

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Cell-Free DNA and Circulating Tumor Cells: Comprehensive Liquid Biopsy Analysis in Advanced Breast Cancer

Clinical Cancer Research ◽

10.1158/1078-0432.ccr-17-2092 ◽

2017 ◽

Vol 24 (3) ◽

pp. 560-568 ◽

Cited By ~ 58

Author(s):

Giovanna Rossi ◽

Zhaomei Mu ◽

Alfred W. Rademaker ◽

Laura K. Austin ◽

Kimberly S. Strickland ◽

...

Keyword(s):

Breast Cancer ◽

Advanced Breast Cancer ◽

Tumor Cells ◽

Circulating Tumor Cells ◽

Liquid Biopsy ◽

Advanced Breast ◽

Cell Free Dna ◽

Free Dna

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Purification and quantification of circulating cell-free DNA from body fluids with DANAGENE Circulating System applied to Liquid Biopsy

BioTechniques ◽

10.2144/000114410 ◽

2016 ◽

Vol 60 (4) ◽

Author(s):

David Navarro ◽

A. Navarro ◽

A. Martinez-Murcia ◽

Adriana Lasa

Keyword(s):

Liquid Biopsy ◽

Body Fluids ◽

Cell Free Dna ◽

Free Dna ◽

Circulating Cell Free Dna

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The role of mucin cell-free DNA detection as a new marker for the study of acellular pseudomyxoma peritonei of appendicular origin by liquid biopsy

Therapeutic Advances in Medical Oncology ◽

10.1177/1758835920928233 ◽

2020 ◽

Vol 12 ◽

pp. 175883592092823 ◽

Cited By ~ 1

Author(s):

Damián García-Olmo ◽

Susana Olmedillas-López ◽

Delia Cortés-Guiral ◽

Pedro Villarejo ◽

Irene López Rojo ◽

...

Keyword(s):

Tumor Cells ◽

Pseudomyxoma Peritonei ◽

Liquid Biopsy ◽

Magnetic Bead ◽

Plasma Electron ◽

Kras Mutations ◽

Cell Free Dna ◽

Post Surgery ◽

Free Dna ◽

Cytokine Levels

Background: Acellular pseudomyxoma peritonei ( aPMP) is a rare peritoneal malignancy characterized by the accumulation of large amounts of mucin (lacking tumor cells) in the peritoneum. Many cases account for several kilograms of mucin to be screened by the pathologist. This is a comprehensive study of three patients with aPMP, whose tumors showed KRAS mutation, allowing for the tracking of this marker by liquid biopsy. Methods: Pre and post-surgery plasma, and mucin removed during cytoreductive surgery were collected from the patients. KRAS mutations were analyzed using droplet digital polymerase chain reaction (ddPCR). Mucin was injected in mice. KRAS and cytokine levels were measured in plasma of the mice using ddPCR and a magnetic bead-based assay. Mucin microbiome was analyzed by 16S rRNA sequencing. Results: KRAS mutations were detected in mucin cell-free DNA (cfDNA) from the three patients but not in the pre or post-surgery plasma. Electron microscopy detected microparticles (diameter <0.4 µm) in mucin. Mucin from one patient grew up inside the peritoneal cavity of mice and human KRAS was identified in mucin cfDNA, but not in plasma. All mucins showed the same bacterial profile. Cytokine levels were slightly altered in mice. Conclusions: The three aPMP patients included in this study shared some common aspects: the absence of tumor cells in mucin, the presence of KRAS mutated cfDNA in mucin, and the absence of this tumor-derived mutation in the bloodstream, providing additional information to the routine pathological examinations and suggesting that mucin cfDNA could potentially play a role in aPMP recurrence and prognosis.

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BIOM-56. THE INTEGRATION OF A LIQUID BIOPSY PROGRAM INTO THE CARE OF PEDIATRIC BRAIN TUMOR PATIENTS

Neuro-Oncology ◽

10.1093/neuonc/noaa215.053 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii13-ii14

Author(s):

Alexandra Miller ◽

Luca Szalontay ◽

Hamza Ahmad ◽

Nancy Bouvier ◽

Irene Rodriguez-Sanchez ◽

...

Keyword(s):

Liquid Biopsy ◽

Tumor Tissue ◽

Clinical Care ◽

High Grade Glioma ◽

Response To Therapy ◽

Low Grade ◽

High Grade ◽

Cell Free Dna ◽

Free Dna ◽

Minimal Residual

Abstract Pediatric CNS tumors remain the leading cause of cancer-related death in children and adolescents. Safe sampling of tumor tissue for diagnostic purposes may be difficult if not impossible. Detection of minimal residual or recurrent disease prior to definitive clinical or radiographic progression may allow earlier initiation of novel therapies and ultimately improve overall survival. Given the rarity of serial sampling of tumor tissue, our understanding of molecular evolution in response to therapy remains limited. Recent technological advances have led to the development of “liquid biopsy” assays, which detect cell-free DNA (cfDNA) in blood, cerebrospinal fluid (CSF) or other bodily fluids. Here, we report our initial clinical experience with the recently established MSK Kids pediatric neuro-oncology liquid-biopsy program at Memorial Sloan Kettering Cancer Center (MSKCC) using MSK-IMPACT, which is clinically validated by the New York State Department of Health for CSF cell-free DNA (cfDNA)vprofiling. All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. Samples from 29 unique patients were sequenced. Histopathology included high-grade glioma (5); low-grade glioma (2); medulloblastoma (8); pineoblastoma (3); retinoblastoma (4); other (7). CSF cfDNA could be detected in 18/42 samples (43%) and 12/29 patients (34%). CSF cfDNA was more commonly detected in higher-grade, disseminated tumors such as high-grade glioma (60%), medulloblastoma (38%), and pineoblastoma (100%). Low-grade lesions without leptomeningeal involvement did not result in detectable CSF cfDNA shedding (86% were negative). In a subset of patients, MSK-IMPACT identified previously unrecognized molecular actionable targets (e.g. BRAF-KIAA1549 fusion); or the detection of “minimal residual disease” prior to the detection of tumor recurrence by conventional diagnostics, impacting clinical care decisions. Future directions include integration of CSF cfDNA into prospective clinical trials as a correlative biomarker.

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