scholarly journals Quantification of plasma cell-free DNA levels in dogs with various tumors

2019 ◽  
Vol 31 (6) ◽  
pp. 836-843 ◽  
Author(s):  
Michihito Tagawa ◽  
Genya Shimbo ◽  
Hisashi Inokuma ◽  
Kazuro Miyahara
Keyword(s):  
Disease Progression ◽  
Distant Metastasis ◽  
Malignant Tumors ◽  
Clinical Stage ◽  
Extracellular Dna ◽  
Dna Integrity ◽  
Healthy Controls ◽  
Cell Free Dna ◽  
Free Dna ◽  
Integrity Index

Circulating cell-free DNA (cfDNA) is extracellular DNA released into the bloodstream by apoptotic or necrotic tumor cells, with cfDNA determination proposed as a noninvasive, sensitive marker for the diagnosis of human cancer. We evaluated cfDNA quantification as a diagnostic and prognostic tool in dogs with various tumors. We quantified plasma cfDNA concentration by absolute real-time PCR of long interspersed nuclear elements in 50 dogs with malignant tumors, 13 dogs with benign tumors or nodules, and 11 healthy controls. Six patients with malignant tumors were followed-up, and plasma cfDNA was quantified throughout disease progression. We found that plasma cfDNA concentrations were significantly elevated in dogs with malignant tumors compared with dogs with benign nodules or healthy controls. The DNA integrity index (the ratio between long and short cfDNA fragments) was significantly lower in dogs with malignant tumors compared to healthy controls. Significantly higher cfDNA levels and a lower DNA integrity index were observed in dogs with lymphoma or leukemia, hemangiosarcoma, and distant metastasis; cfDNA levels correlated well with clinical stage and tended to increase during or before periods of disease progression, suggesting potential efficacy of cfDNA for the detection of distant metastasis and to monitor the clinical stage of neoplasia.

scholarly journals Pleural fluid cell-free DNA integrity index to identify cytologically negative malignant pleural effusions including mesotheliomas

BMC Cancer ◽  
2012 ◽  
Vol 12 (1) ◽  
Author(s):  
Krishna B Sriram ◽  
Vandana Relan ◽  
Belinda E Clarke ◽  
Edwina E Duhig ◽  
Morgan N Windsor ◽  
...  
Keyword(s):  
Pleural Fluid ◽  
Dna Integrity ◽  
Pleural Effusions ◽  
Cell Free Dna ◽  
Malignant Pleural Effusions ◽  
Free Dna ◽  
Integrity Index ◽  
Fluid Cell

scholarly journals AB0061 INVOLVEMENT OF CELL-FREE DNA IN THE DIFFERENTIATION OF OSTEOCLASTS – IMPLICATIONS FOR CLINICAL RESEARCH

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1332.1-1332
Author(s):  
P. Škubica ◽  
J. Horinkova ◽  
M. Gregová ◽  
K. Pavelka ◽  
M. Husakova ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Rheumatic Diseases ◽  
Extracellular Dna ◽  
Future Research ◽  
Tartrate Resistant Acid Phosphatase ◽  
Healthy Controls ◽  
Cytokine Network ◽  
Cell Free Dna ◽  
Total N ◽  
Free Dna

Background:Cell-free DNA (cfDNA) is a molecule with undisputable immunogenic potential[1]. Its role is well established in etiopathogenesis of systemic lupus erythematosus and many reports suggest it may play an important role in other rheumatic diseases[2]. Patients suffering from rheumatic diseases are at higher risk of osteoporosis[3], which may be a consequence of increased generation of osteoclasts (OC). Traditionally, increased formation of OC is attributed to changes in cytokine network[4]. It is not yet known whether cfDNA can also act on mononuclear precursors and influence their differentiation into OC.Objectives:The aim of this study was to assess role of cfDNA in differentiation of bone resorbing cells in rheumatic diseases. For this purpose, deoxyribonuclease I (DNAse) was employed to eliminate cfDNA from sera of patients and healthy controls (HC) used for cell culture.Methods:In order to evaluate effects of cfDNA on osteoclastogenesis, anin vitroexperiment of peripheral blood monocytes (PBM) cultures was designed. Axial spondyloarthritis (AxSpA) was chosen as a model of rheumatic disease. Sera of AxSpA patients (total n=13) and healthy controls (total n=13) were collected and subsequently used in cell cultures. PBM of 13 healthy donors were cultured in presence of 25 ng/ml macrophage colony-stimulating factor (M-CSF), 0,5 ng/ml receptor-activator of nuclear factor kappa B ligand (RANKL) and 10 % of pooled AxSpA or HC sera, respectively. Serum counterpart treated with DNAse was used in parallel. After 14 days, cells were stained for tartrate-resistant acid phosphatase (TRAP) and counted. TRAP positive cells with 3 or more nuclei were recognized as OC.Results:On average, differentiation of OC in presence of AxSpA sera led to higher osteoclastogenesis compared to DNAse-treated counterpart (137 vs. 61; p < 0.01). In a similar way, treatment of HC sera with DNAse greatly diminished osteoclastogenesis compared to untreated sera (17 vs. 111; p < 0.05). Overall, the effect of cfDNA depletion in HC sera regarding OC differentiation was more than 2,5× higher than the effect of cfDNA depletion in AxSpA sera (p < 0.001).Conclusion:Results of our pilot study indicate possible involvement of cfDNA in osteoclastogenesis. Decrease in number of OC after cfDNA depletion in both AxSpA sera and HC sera suggests that cfDNA effect in osteoclastogenesis is non-specific with respect to healthy condition and may represent universal link between innate immunity and bone metabolism. Lower effect of cfDNA depletion in AxSpA sera on osteoclastogenesis is very possibly owing to presence of other inflammatory molecules, which influence osteoclastogenesis. Future research might identify cfDNA as useful therapeutic target to decrease osteoporosis risk not only in patients with rheumatic and autoimmune diseases, where pathological bone resorption is imminent, but also in general aging population.References:[1]Pisetsky, D. S. (2012). The origin and properties of extracellular DNA: from PAMP to DAMP. Clinical Immunology, 144(1), 32-40.[2]Lood, C. J., & Duvvuri, B. (2019). Cell-free DNA as a biomarker in autoimmune rheumatic diseases. Frontiers in immunology, 10, 502.[3]Maruotti, N., Corrado, A., & Cantatore, F. P. (2014). Osteoporosis and rheumatic diseases. Reumatismo, 125-135.[4]Amarasekara, D. S., Yu, J., & Rho, J. (2015). Bone loss triggered by the cytokine network in inflammatory autoimmune diseases. Journal of immunology research, 2015.Acknowledgments:Project MH CR 00023728 & MEYS CR Progres Q43Disclosure of Interests:Patrik Škubica: None declared, Jana Horinkova: None declared, Monika Gregová Consultant of: Novartis, Abbvie, Paid instructor for: Novartis, Speakers bureau: Novartis, Abbvie, MSD, Karel Pavelka Consultant of: Abbvie, MSD, BMS, Egis, Roche, UCB, Medac, Pfizer, Biogen, Speakers bureau: Abbvie, MSD, BMS, Egis, Roche, UCB, Medac, Pfizer, Biogen, Marketa Husakova Speakers bureau: Novartis, Pavlina Dankova: None declared

scholarly journals A novel decision tree model based on chromosome imbalances in cell-free DNA and CA-125 in the differential diagnosis of ovarian cancer

2021 ◽  
pp. 172460082199235
Author(s):  
Weina Zhang ◽  
Yu-min Zhang ◽  
Yuan Gao ◽  
Shengmiao Zhang ◽  
Weixin Chu ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Differential Diagnosis ◽  
Decision Tree ◽  
Copy Number ◽  
Malignant Tumors ◽  
Copy Number Variations ◽  
Ca 125 ◽  
Benign Tumors ◽  
Cell Free Dna ◽  
Free Dna

Objective: CA-125 is widely used as biomarker of ovarian cancer. However, CA-125 suffers low accuracy. We developed a hybrid analytical model, the Ovarian Cancer Decision Tree (OCDT), employing a two-layer decision tree, which considers genetic alteration information from cell-free DNA along with CA-125 value to distinguish malignant tumors from benign tumors. Methods: We consider major copy number alterations at whole chromosome and chromosome-arm level as the main feature of our detection model. Fifty-eight patients diagnosed with malignant tumors, 66 with borderline tumors, and 10 with benign tumors were enrolled. Results: Genetic analysis revealed significant arm-level imbalances in most malignant tumors, especially in high-grade serous cancers in which 12 chromosome arms with significant aneuploidy ( P<0.01) were identified, including 7 arms with significant gains and 5 with significant losses. The area under receiver operating characteristic curve (AUC) was 0.8985 for copy number variations analysis, compared to 0.8751 of CA125. The OCDT was generated with a cancerous score (CScore) threshold of 5.18 for the first level, and a CA-125 value of 103.1 for the second level. Our most optimized OCDT model achieved an AUC of 0.975. Conclusions: The results suggested that genetic variations extracted from cfDNA can be combined with CA-125, and together improved the differential diagnosis of malignant from benign ovarian tumors. The model would aid in the pre-operative assessment of women with adnexal masses. Future clinical trials need to be conducted to further evaluate the value of CScore in clinical settings and search for the optimal threshold for malignancy detection.

scholarly journals Probing of breast cancer using a combination of plasma and urinary circulating cell-free DNA

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Zhigang Zuo ◽  
Jiying Tang ◽  
Xiaojun Cai ◽  
Feng Ke ◽  
Zhenzong Shi
Keyword(s):  
Breast Cancer ◽  
Early Stage ◽  
Pik3ca Mutation ◽  
Early Stage Breast Cancer ◽  
Healthy Controls ◽  
Cell Free Dna ◽  
Clinical Sensitivity ◽  
Free Dna ◽  
Urine Specimens ◽  
Circulating Cell Free Dna

Abstract Monitoring of early-stage breast cancer is critical in promptly addressing disease relapse. Circulating cell-free DNA provides a minimally invasive and sensitive means to probing the disease. In a longitudinal analysis of 250 patients with early breast cancer, we compared the circulating cell-free DNA recovered from both plasma and urine specimens. For comparison, 50 healthy controls were also recruited. Specific mutations associated with the disease were profiled to determine the clinical sensitivity and specificity. Correlations of recovered concentrations of cell-free DNA with outcomes were examined to address early prognostication. PIK3CA mutation profiling in both plasma and urinary cell-free DNA showed an agreement of 97.2% compared with the results obtained for tumor tissues. The analysis of healthy controls revealed that cell-free DNA measurements were stable and consistent over time. Over the short 6-month period of monitoring, our analyses showed declines in recovered cell-free DNA; these findings may aid physicians in stratifying patients at higher risk for relapse. Similar results were observed in both plasma and urine specimens (hazard ratios: 2.16 and 2.48, respectively). Cell-free DNA presents a novel and sensitive method for the monitoring of early-stage breast cancer. In the present study, serial measurements of both plasma and urine specimens were useful in probing the disease.

scholarly journals Cell-free DNA integrity for the monitoring of breast cancer: Future perspectives?

2018 ◽  
Vol 9 (2) ◽  
pp. 26-32 ◽  
Author(s):  
Navid Sobhani ◽  
Daniele Generali ◽  
Fabrizio Zanconati ◽  
Marina Bortul ◽  
Bruna Scaggiante
Keyword(s):  
Breast Cancer ◽  
Dna Integrity ◽  
Future Perspectives ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Detection of Circulating Tumor DNA in Patients With Leiomyosarcoma With Progressive Disease

2019 ◽  
pp. 1-11 ◽  
Author(s):  
Matthew L. Hemming ◽  
Kelly Klega ◽  
Justin Rhoades ◽  
Gavin Ha ◽  
Kate E. Acker ◽  
...  
Keyword(s):  
Disease Progression ◽  
Tumor Size ◽  
Disease Burden ◽  
Progressive Disease ◽  
Circulating Tumor Dna ◽  
Tumor Burden ◽  
Blood Draw ◽  
Cell Free Dna ◽  
Free Dna ◽  
Tumor Dna

Purpose Leiomyosarcoma (LMS) is a soft-tissue sarcoma characterized by multiple copy number alterations (CNAs) and without common recurrent single-nucleotide variants. We evaluated the feasibility of detecting circulating tumor DNA (ctDNA) with next-generation sequencing in a cohort of patients with LMS whose tumor burden ranged from no evidence of disease to metastatic progressive disease. Patients and Methods We evaluated cell-free DNA in plasma samples and paired genomic DNA from resected tumors from patients with LMS by ultra-low passage whole-genome sequencing. Sequencing reads were aligned to the human genome and CNAs that were identified in cell-free DNA and tumor DNA by ichorCNA software to determine the presence of ctDNA. Clinical data were reviewed to assess disease burden and clinicopathologic features. Results We identified LMS ctDNA in 11 (69%) of 16 patients with disease progression and total tumor burden greater than 5 cm. Sixteen patients with stable disease or low disease burden at the time of blood draw were found to have no detectable ctDNA. Higher ctDNA fraction of total cell-free DNA was associated with increasing tumor size and disease progression. Conserved CNAs were found between primary tumors and ctDNA in each case, and recurrent CNAs were found across LMS samples. ctDNA levels declined after resection of progressive disease in one case and became detectable upon disease relapse in another individual patient. Conclusion These results suggest that ctDNA, assayed by a widely available sequencing approach, may be useful as a biomarker for a subset of patients with uterine and extrauterine LMS. Higher levels of ctDNA correlate with tumor size and disease progression. Liquid biopsies may assist in guiding treatment decisions, monitoring response to systemic therapy, surveying for disease recurrence, and differentiating benign and malignant smooth muscle tumors.

scholarly journals Tissue and Cell-Free DNA-Based Epigenomic Approaches for Cancer Detection

2019 ◽  
Vol 66 (1) ◽  
pp. 105-116 ◽  
Author(s):  
Alessandro Leal ◽  
David Sidransky ◽  
Mariana Brait
Keyword(s):  
Cancer Detection ◽  
Cancer Diagnosis ◽  
Malignant Tumors ◽  
Unmet Need ◽  
Clinical Routine ◽  
Commercial Development ◽  
Cell Free Dna ◽  
Cancer Management ◽  
Diagnosis And Prognosis ◽  
Free Dna

Abstract BACKGROUND Over 9 million people die of cancer each year worldwide, reflecting the unmet need for effective biomarkers for both cancer diagnosis and prognosis. Cancer diagnosis is complex because the majority of malignant tumors present with long periods of latency and lack of clinical presentation at early stages. During carcinogenesis, premalignant cells experience changes in their epigenetic landscapes, such as differential DNA methylation, histone modifications, nucleosome positioning, and higher orders of chromatin changes that confer growth advantage and contribute to determining the biologic phenotype of human cancers. CONTENT Recent progress in microarray platforms and next-generation sequencing approaches has allowed the characterization of abnormal epigenetic patterns genome wide in a large number of cancer cases. The sizable amount of processed data also comes with challenges regarding data management and assessment for effective biomarker exploration to be further applied in prospective clinical trials. Epigenetics-based single or panel tests of genes are being explored for clinical management to fulfill unmet needs in oncology. The advance of these tests to the clinical routine will depend on rigorous, extensive, and independent validation in well-annotated cohort of patients and commercial development of clinical routine–friendly and adequate procedures. SUMMARY In this review we discuss the analytic validation of tissue and cell-free DNA-based epigenomic approaches for early cancer detection, diagnosis, and treatment monitoring and the clinical utility of candidate epigenetic alterations applied to colorectal, glioblastoma, breast, prostate, bladder, and lung cancer management.

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