scholarly journals The Specific Gravity-Free Method for the Isolation of Circulating Tumor KRAS Mutant DNA and Exosome in Colorectal Cancer

Micromachines ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 987
Author(s):  
Tae Hee Lee ◽  
Eunsook Park ◽  
Young-gon Goh ◽  
Han Byul Lee ◽  
Woo Sun Rou ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Specific Gravity ◽  
Medical Technology ◽  
Alginate Bead ◽  
Area Under The Curve ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Buffy Coat ◽  
Isolation System ◽  
Tumor Dna

Background: Circulating tumor DNA (ctDNA) and exosome have been widely researched in the field of medical technology and diagnosis platforms. The purpose of our study was to improve the capturing properties of ctDNA and exosome, which involved combining two beads using approaches that may provide a new method for cancer diagnoses. Methods: We present a dual isolation system including a polydopamine (PDA)–silica-coated alginate bead for circulating tumor DNA (ctDNA) capture and an anti-CD63 immobilized bead for exosome capture. We examined the ctDNA mutation in pre-operative plasma samples obtained from 91 colorectal cancer (CRC) patients using a droplet digital PCR (ddPCR). Results: The area under the curve (AUROC) of ctKRAS G12D mutation in the buffy coat was 0.718 (95% CI: 0.598−0.838; p = 0.001). Patients with CRC that had unmethylation of MLH1 and MSH2 showed significantly higher buffy coat ctKRAS G12D mutations, ascites ctKRAS G12D mutations, miR-31-5, and mixed scores than the patients with a methylation of MLH1 and MSH2. Conclusion: Our proposed alginate bead using the specific gravity-free method suggests that the screening of mutated ctKRAS DNA and miR-31-5 by liquid biopsy aids in identifying the patients, predicting a primary tumor, and monitoring in the early detection of a tumor.

scholarly journals Small EVs-Associated DNA as Complementary Biomarker to Circulating Tumor DNA in Plasma of Metastatic Colorectal Cancer Patients

2021 ◽  
Vol 14 (2) ◽  
pp. 128
Author(s):  
Silvia Galbiati ◽  
Francesco Damin ◽  
Dario Brambilla ◽  
Lucia Ferraro ◽  
Nadia Soriani ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Metastatic Colorectal Cancer ◽  
Cancer Patients ◽  
Digital Pcr ◽  
Extracellular Vesicle ◽  
Circulating Tumor Dna ◽  
Mutation Status ◽  
Promising Practice ◽  
Colorectal Cancer Patients ◽  
Tumor Dna

It is widely accepted that assessing circular tumor DNA (ctDNA) in the plasma of cancer patients is a promising practice to evaluate somatic mutations from solid tumors noninvasively. Recently, it was reported that isolation of extracellular vesicles improves the detection of mutant DNA from plasma in metastatic patients; however, no consensus on the presence of dsDNA in exosomes has been reached yet. We analyzed small extracellular vesicle (sEV)-associated DNA of eleven metastatic colorectal cancer (mCRC) patients and compared the results obtained by microarray and droplet digital PCR (ddPCR) to those reported on the ctDNA fraction. We detected the same mutations found in tissue biopsies and ctDNA in all samples but, unexpectedly, in one sample, we found a KRAS mutation that was not identified either in ctDNA or tissue biopsy. Furthermore, to assess the exact location of sEV-associated DNA (outside or inside the vesicle), we treated with DNase I sEVs isolated with three different methodologies. We found that the DNA inside the vesicles is only a small fraction of that surrounding the vesicles. Its amount seems to correlate with the total amount of circulating tumor DNA. The results obtained in our experimental setting suggest that integrating ctDNA and sEV-associated DNA in mCRC patient management could provide a complete real-time assessment of the cancer mutation status.

Difference in appearance of KRAS mutated circulating tumor DNA in patients with metastatic colorectal cancer during treatments.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23025-e23025
Author(s):  
Yuji Takayama ◽  
Koichi Suzuki ◽  
Kosuke Ichida ◽  
Taro Fukui ◽  
Fumiaki Watanabe ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Metastatic Colorectal Cancer ◽  
Kras Mutation ◽  
Treatment Resistance ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Oil Droplets ◽  
Tumor Tissues ◽  
The Difference ◽  
Tumor Dna

e23025 Background: Emergence of KRAS mutation in blood is observed in colorectal cancer patients who undergo chemotherapy, but its clinical significance is not well known. In this study, we focused on the difference in appearance of KRAS mutated circulating tumor DNA (MctDNA) and elucidated its association with treatments. Methods: Four hundred and fifty-one plasma samples were collected prospectively from 85 patients (pts) who underwent chemotherapy due to metastatic colorectal cancer in 2014 - 2016. Seven types of KRAS mutation in MctDNA were detected by droplet digital PCR creating oil droplets. To exclude false positive detection, mutation was validated. MctDNA amplified in oil droplets was selectively sorted by On-chip sorting system and mutation was determined by Sanger sequencing. Results: KRAS assessment in tumor tissues showed 29 pts with KRAS mutation (MT), 56 pts without KRAS mutation (WT). Among 29 pts with MT, KRAS assessment in plasma displayed 23 pts with MctDNA and 6 pts without MctDNA. The type of mutation in MctDNA was consistent with that detected in tumor tissues, indicating mutual exclusivity in KRAS mutation was confirmed. In 56 pts with WT, 28 pts showed MctDNA during treatments. Difference in appearance of MctDNA was recognized in several treatments. Gradual increase in detection of MctDNA was observed with anti-EGFR antibody, resulted in treatment resistance. Transient spike elevation was frequently seen in TAS-102, which associated with drug response. No specific appearance was recognized during treatments with other drugs including anti-VEGF antibody. MctDNA in oil droplets were successfully sorted even if a few droplets were targeted, and mutation was confirmed. Conclusions: Difference in appearance of MctDNA may associate with treatment response in patients with metastatic colorectal cancer during treatments. [Table: see text]

scholarly journals A Study of Hypermethylated Circulating Tumor DNA as a Universal Colorectal Cancer Biomarker

2016 ◽  
Vol 62 (8) ◽  
pp. 1129-1139 ◽  
Author(s):  
Sonia Garrigou ◽  
Geraldine Perkins ◽  
Fanny Garlan ◽  
Corinne Normand ◽  
Audrey Didelot ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Genetic Material ◽  
Surrogate Marker ◽  
Digital Pcr ◽  
Tumor Stage ◽  
Circulating Tumor Dna ◽  
Tumor Evolution ◽  
Highly Sensitive ◽  
Tumor Dna

Abstract BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a good candidate for tracking tumor dynamics in different cancer types, potentially avoiding repeated tumor biopsies. Many different genes can be mutated within a tumor, complicating procedures for tumor monitoring, even with highly sensitive next-generation sequencing (NGS) strategies. Droplet-based digital PCR (dPCR) is a highly sensitive and quantitative procedure, allowing detection of very low amounts of circulating tumor genetic material, but can be limited in the total number of target loci monitored. METHODS We analyzed hypermethylation of 3 genes, by use of droplet-based dPCR in different stages of colorectal cancer (CRC), to identify universal markers for tumor follow-up. RESULTS Hypermethylation of WIF1 (WNT inhibitory factor 1) and NPY (neuropeptide Y) genes was significantly higher in tumor tissue compared to normal tissue, independently of tumor stage. All tumor tissues appeared positive for one of the 2 markers. Methylated ctDNA (MetctDNA) was detected in 80% of metastatic CRC and 45% of localized CRC. For samples with detectable mutations in ctDNA, MetctDNA and mutant ctDNA (MutctDNA) fractions were correlated. During follow-up of different stage CRC patients, MetctDNA changes allowed monitoring of tumor evolution. CONCLUSIONS These results indicate that MetctDNA could be used as a universal surrogate marker for tumor follow-up in CRC patients, and monitoring MetctDNA by droplet-based dPCR could avoid the need for monitoring mutations.

scholarly journals Monitoring the effect of first-line treatment in RAS/RAF mutated metastatic colorectal cancer by serial analysis of tumor specific DNA in plasma.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 3593-3593
Author(s):  
Caroline Brenner Thomsen ◽  
Torben Hansen ◽  
Rikke Fredslund Andersen ◽  
Jan Lindebjerg ◽  
Lars Henrik Jensen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Metastatic Colorectal Cancer ◽  
Lead Time ◽  
Progressive Disease ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
First Line ◽  
Fractional Abundance ◽  
Risk Of Progression ◽  
Tumor Dna

3593 Background: Personalized medicine calls for an early indicator of treatment failure. Circulating tumor DNA (ctDNA) is a promising marker in this setting and our prospective study explored the association between disease control and change of ctDNA during first line chemotherapy in patients with RAS/RAF mutated metastatic colorectal cancer (mCRC). Methods: The present study included 138 mCRC patients receiving standard first line combination chemotherapy. In patients with a RAS/RAF mutated tumor the same mutation was quantified in the plasma using droplet digital PCR (ddPCR). The fractional abundance of ctDNA (ctDNA level) was assessed in plasma before treatment start and at every treatment cycle until radiologically defined progressive disease (PD). Results: RAS/RAF mutations were detected in the plasma from 77 patients (94% of patients with a tumor mutation). Twenty patients progressed on treatment and 57 stopped treatment without progression. The presence of a RAS/RAF mutation in plasma correlated to overall survival (OS) with a median of 24.2 months for patients with a wild-type tumor compared to 12.7 months for patients with a mution in plasma. A substantial increase in ctDNA level was highly associated with progression on treatment (risk ratio = 4.58, 95%CI = 1.99-10.51, p < 0.0001). Furthermore, with a stable ctDNA level the chance of non-progression was 88.2% (range 76.1-95.6%). The first substantial increase in ctDNA level occurred at a median of 51 days (range 14-133 days) before radiologically confirmed PD. Conclusions: The results indicate that ctDNA level may be predictive of treatment effect in patients with mCRC. An increase was observed to correlate with high risk of progression with a relevant lead time, whereas an unchanging ctDNA level related to stable disease.

INVESTIGATION KRAS MUTATION IN CIRCULATION TUMOR DNA IN DIFFERENT STAGES OF COLORECTAL CANCER

2019 ◽  
Vol 65 (5) ◽  
pp. 701-707
Author(s):  
Vitaliy Shubin ◽  
Yuriy Shelygin ◽  
Sergey Achkasov ◽  
Yevgeniy Rybakov ◽  
Aleksey Ponomarenko ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Plasma Volume ◽  
Kras Mutation ◽  
Stage Iv ◽  
Circulating Tumor Dna ◽  
Stage Ii ◽  
Kras Gene ◽  
Kras Mutations ◽  
Droplet Pcr ◽  
Tumor Dna

To determine mutations in the plasma KRAS gene in patients with colorectal cancer was the aim of this study. The material was obtained from 44 patients with colorectal cancer of different stages (T1-4N0-2bM0-1c). Plasma for the presence of KRAS gene mutation in circulating tumor DNA was investigated using digital droplet polymerase chain reaction (PCR). KRAS mutations in circulating tumor DNA isolated from 1 ml of plasma were detected in 13 (30%) patients with cancer of different stages. Of these, with stage II, there were 3 patients, with III - 5 and with IV - 5. Patients who did not have mutations in 1 ml of plasma were analyzed for mutations of KRAS in circulating tumor DNA isolated from 3 ml of plasma. Five more patients with KRAS mutations were found with II and III stages. The highest concentrations of circulating tumor DNA with KRAS mutation were found in patients with stage IV. The increase in plasma volume to 3 ml did not lead to the identification of mutations in I stage. This study showed that digital droplet PCR allows identification of circulating tumor DNA with the KRAS mutations in patients with stage II-IV of colon cancer. The results can be used to determine the degree of aggressiveness of the tumor at different stages of the disease, but not the 1st, and it is recommended to use a plasma volume of at least 3 ml.

Clinical applications of circulating tumor DNA in monitoring breast cancer drug resistance

2020 ◽  
Vol 16 (34) ◽  
pp. 2863-2878
Author(s):  
Yang Liu ◽  
Qian Du ◽  
Dan Sun ◽  
Ruiying Han ◽  
Mengmeng Teng ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Drug Resistance ◽  
Digital Pcr ◽  
Circulating Tumor Dna ◽  
Resistance Mechanisms ◽  
Clinical Applications ◽  
Current Status ◽  
Cancer Drug ◽  
Genomic Alteration ◽  
Tumor Dna

Breast cancer is one of the leading causes of cancer-related deaths in women worldwide. Unfortunately, treatments often fail because of the development of drug resistance, the underlying mechanisms of which remain unclear. Circulating tumor DNA (ctDNA) is free DNA released into the blood by necrosis, apoptosis or direct secretion by tumor cells. In contrast to repeated, highly invasive tumor biopsies, ctDNA reflects all molecular alterations of tumors dynamically and captures both spatial and temporal tumor heterogeneity. Highly sensitive technologies, including personalized digital PCR and deep sequencing, make it possible to monitor response to therapies, predict drug resistance and tailor treatment regimens by identifying the genomic alteration profile of ctDNA, thereby achieving precision medicine. This review focuses on the current status of ctDNA biology, the technologies used to detect ctDNA and the potential clinical applications of identifying drug resistance mechanisms by detecting tumor-specific genomic alterations in breast cancer.

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