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For patients with T1a muscularis mucosae (MM) esophageal squamous cell carcinoma (ESCC) with lymphovascular invasion (LVI) or T1b submucosal (SM) ESCC, endoscopic resection is non-curative, and adjuvant treatment entailing esophagectomy or definitive chemoradiotherapy is necessary. This is because about 30% of these cases have lymph node (LN) metastasis. The purpose of this study was to test the utility of a CRP genetic polymorphism test kit for determining the risk of LN metastasis with the aim of eliminating additional invasive adjuvant therapy.This is a retrospective, multi-institutional, observational study. The CRP 1846CT genetic polymorphisms were identified using a fully automated genotyping system. The primary end points were an 85% negative predictive value (NPV) for diagnosis of LN metastasis in pT1a (MM) and 80% NPV in pT1b (SM1) patients.A total of 742 ESCC (105 pMM, 166 pSM1 and 471 pSM2-3) patients who had received esophagectomy with 2- or 3-field LN dissection at 65 institutions were enrolled. According to this test, patients with the C/C and C/T genotypes were considered to be low risk. The NPVs using this test were 82.8% in pMM and 71.7% in pSM1 patients.CRP 1846CT genetic polymorphism is not a useful diagnostic indicator for determining the risk of LN metastasis; however, the possibility that CRP gene polymorphisms are involved in the mechanism of lymph node metastasis in solid tumors still remains.

Purpose Less-invasive early diagnosis of lung cancer is essential for improving patient survival rates. The purpose of this study is to demonstrate that serum comprehensive miRNA profile is high sensitive biomarker to early-stage lung cancer in direct comparison to the conventional blood biomarker using next-generation sequencing (NGS) technology combined with automated machine learning (AutoML). Methods We first evaluated the reproducibility of our measurement system using Pearson’s correlation coefficients between samples derived from a single pooled RNA sample. To generate comprehensive miRNA profile, we performed NGS analysis of miRNAs in 262 serum samples. Among the discovery set (57 patients with lung cancer and 57 healthy controls), 1123 miRNA-based diagnostic models for lung cancer detection were constructed and screened using AutoML technology. The diagnostic faculty of the best performance model was evaluated by inspecting the validation samples (74 patients with lung cancer and 74 healthy controls). Results The Pearson’s correlation coefficients between samples derived from the pooled RNA sample ≥ 0.98. In the validation analysis, the best model showed a high AUC score (0.98) and a high sensitivity for early stage lung cancer (85.7%, n = 28). Furthermore, in comparison to carcinoembryonic antigen (CEA), a conventional blood biomarker for adenocarcinoma, the miRNA-based model showed higher sensitivity for early-stage lung adenocarcinoma (CEA, 27.8%, n = 18; miRNA-based model, 77.8%, n = 18). Conclusion The miRNA-based diagnostic model showed a high sensitivity for lung cancer, including early-stage disease. Our study provides the experimental evidence that serum comprehensive miRNA profile can be a highly sensitive blood biomarker for early-stage lung cancer.

Accurate detection of myeloproliferative neoplasms (MPN)-associated gene mutations is necessary to correctly diagnose MPN. However, conventional gene testing has various limitations, including the requirement of skilled technicians, cumbersome experimental procedures, and turnaround time of several days. The gene analyzer i-densy IS-5320 allows gene testing using the quenching probe-Tm method. Specifically, pretreatment of samples including DNA extraction, amplification and detection of genes, and analysis of results are performed in a fully automatic manner after samples and test reagents are added into this system, which is compact and can be easily installed in a laboratory. The aim of this study is to investigate the sensitivity and specificity associated with the simultaneous detection of MPN-associated gene mutations.We conducted an analysis of MPN-associated genes using i-densy IS-5320. We analyzed 384 samples (171 JAK2 V617F mutations, 10 JAK2 exon12 mutations, 104 CALR mutations, and 26 MPL mutations) that had been examined using conventional approaches such as allele-specific polymerase chain reaction (PCR), droplet digital PCR, and the direct sequencing method.The detection accuracy of JAK2 V617F, JAK2 exon 12, CALR, and MPL was 100.0% (383/383), 99.7% (383/384), 100.0% (370/370), and 99.7% (377/378), respectively. There was a strong positive correlation between the JAK2 V617F allele burden measured using conventional methods and i-densy IS-5320 (r = .989).Overall, i-densy IS-5320 exhibited good accuracy in terms of analyzing MPN-associated genes; thus, it can serve as a replacement for conventional methods of MPN-associated gene testing.

Simple Summary Circulating tumor cell (CTC) detection is a non-invasive and easy way to collect and separate single cells to use as tumor biomarkers. In this article, we show the feasibility and clinical value of RNA sequencing of CTCs at the single-cell level by exploiting CTC-FIND with SMART-Seq v4 technologies in patients with metastatic colorectal cancer (mCRC). CTCs were classified by epithelial, epithelial-mesenchymal transition (EMT), and stem cell-related gene expression. A patient who had EMT gene expressing CTCs showed significantly shorter PFS and OS regardless of epithelial CTCs presence. Therefore, the presence of CTCs expressing EMT-related genes at the single-cell level may be ofprognostic value and a potential biomarker for risk stratification in patients with refractory mCRC who are considered to have highly heterogeneous features. Abstract Background: Circulating tumor cells (CTCs) are a prognostic marker in patients with metastatic colorectal cancer (mCRC). However, little is known about the characterization of CTCs in mCRC at the single-cell level using RNA sequencing. The purpose of this study was to validate the capability to detect and isolate single CTCs for single-cell RNA sequencing (scRNA-seq) and to identify clinical significance at a single CTC level. Methods: Single CTCs from 27 mCRC patients were collected by CTC-FIND, which is comprised of filter separation and immunomagnetic depletion to collect ultra-pure CTC samples. To address tumor heterogeneity, CTCs were collected without relying on any traditional CTC markers, such as epithelial and mesenchymal cell antigens, and were undertaken by scRNA-seq using SMART-Seq v4. Results: We identified 59 single CTCs which were classified into four groups by epithelial, epithelial-mesenchymal transition (EMT) and stem cell-related gene expression. Patients receiving second or later-line treatment who had EMT gene expressing CTCs had a significantly shorter PFS and OS. Conclusions: Exploiting CTC-FIND with SMART-Seq v4 showed that scRNA-seq of CTCs may shed new insight into tumor heterogeneity of mCRC and that the presence of CTCs expressing EMT-related genes at the single-cell level could have prognostic value in mCRC patients.

Pancreatic β-cell mass (BCM) has a central importance in the pathophysiology of diabetes mellitus. Recently, pancreatic β-cell-specific imaging, especially positron emission tomography (PET) with exendin-based probes, has emerged for non-invasive evaluation of BCM. We developed a novel exendin-based probe labeled with fluorine-18, [18F]FB(ePEG12)12-exendin-4 (18F-Ex4) for PET imaging. We subsequently conducted a first-in-human phase 1 study of 18F-Ex4 PET/computed tomography (CT) and investigated the safety and utility for visualizing the pancreas. Six healthy male subjects were enrolled in this study. A low dose (37.0 MBq) of 18F-Ex4 PET/CT was administered (first cohort: n = 2), and subsequently a higher dose (74.0 MBq) was administered (second cohort: n = 4). In the first and second cohorts, 38.6 ± 4.8 and 71.1 ± 4.8 MBq of 18F-Ex4 were administered, respectively. No serious adverse events were observed in both groups. Only one participant in the first cohort showed transient hypoglycemia during the PET scans. 18F-Ex4 PET/CT successfully visualized the pancreas in all participants. The mean standardized uptake value of the pancreas was found to be higher than that in the surrounding organs, except for the bladder and kidney, during the observation. Dosimetry analyses revealed the effective systemic doses of 18F-Ex4 as 0.0164 ± 0.0019 mSv/MBq (first cohort) and 0.0173 ± 0.0020 mSv/MBq (second cohort). 18F-Ex4 PET/CT demonstrated the safety and utility for non-invasive visualization of the pancreas in healthy male subjects. 18F-Ex4 is promising for clinical PET imaging targeting pancreatic β cells.

Liquid biopsy with circulating free DNA (cfDNA) is a recommended alternative method of re-biopsy. Quality control with cfDNA is indispensable for precise examinations, and it is desirable to achieve high-quality cfDNA separation. We investigated two issues: the influence of pre-analytical procedures on cfDNA analysis performed as a routine procedure in a standard clinical laboratory, and the extent of deterioration of cfDNA quality due to long-term storage. Comparisons among blood collection tube types, storage temperatures, and periods of blood separation were performed in terms of cfDNA quantification, cfDNA size distribution, and detection of EGFR mutations. Quality of cfDNA was better with collection tubes containing 3.2% sodium citrate than with those containing EDTA 2K, and was maintained with storage at 4° C for up to 72 h after blood collection, equivalent to results with cell-stabilizing blood collection tubes. Analysis of cfDNA stored for 7 years showed that samples with low allele frequency (AF) deteriorated more readily than samples with high AF. Despite the same storage period and extraction method, AF of plasma stored for 7 years was remarkably lower than that of cfDNA. However, deterioration due to long-term plasma storage was overcome by changing the DNA extraction method from a silica membrane spin column to a cellulose magnetic beads system. These results can guide the establishment of standardized pre-analytical procedures for liquid biopsy with cfDNA.

PIK3CA mutations are common activating mutations associated with breast cancer (occurring in 20-30% of all cases) and are potent predictive markers for responses to PI3K inhibitors. Thus, it is important to develop sensitive methods to detect these mutations. We established a novel detection method using a quenching probe (QP) system to identify PIK3CA mutations, using DNA from 309 breast cancer tissues. In a developmental cohort, we determined the optimal detection threshold of the QP system with human tumor DNA from 119 freshly frozen tumor samples. We found a 96% concordance rate with the QP system between DNA from 26 matching fresh-frozen specimens and formalin-fixed paraffin-embedded (FFPE) specimens from the same patients, and known PIK3CA mutation status in the developmental cohort. In a validation cohort, we evaluated whether the threshold for judging mutations using the QP system with frozen specimen-derived DNA was applicable with FFPE-derived DNA. In the validation cohort, 30 DNA samples from 190 FFPE-derived DNA samples with known PIK3CA mutation status were analyzed by direct sequencing (DS) and droplet digital PCR, in a blinded manner. The sensitivity and specificity of the droplet digital PCR results were 100% and 100% (QP system), and 60% and 100% (DS), respectively. We also analyzed the relationship between clinical outcomes and the PIK3CA mutational status of 309 breast cancer samples, including the developmental cohort and validation cohort samples. Multivariate analysis suggested that PIK3CA mutations, especially H1047R, were prognostic factors of relapse-free survival. Our novel detection system could be more useful than DS for detecting clinical PIK3CA mutations.

The clinical utility of plasma DNA for detecting cancer-specific mutations has rapidly achieved recognition, but reliability has not been established because of relatively low mutation-detection rates compared with those from tissue re-biopsy. To address this shortcoming we examined efficiency, in terms of mutation detection, of an automated DNA extraction system that uses cellulose magnetic beads. A fully automated, highly sensitive point-mutation-detection method, mutation-biased PCR and quenching probe (MBP-QP) system, was used for this study. Plasma DNA was extracted from 61 plasma samples collected from patients with advanced non-small cell lung cancer. Extraction was performed manually with 200 μl plasma (200-M) by using a silica membrane spin column system or an automated system using 200 μl (200-A) or 1000 μl (1000-A) plasma. Median DNA yield quantified by real-time PCR was 4.4, 4.5, and 17.3 ng with the three methods, respectively. Sensitivity for detecting epidermal growth factor receptor (EGFR) L858R point mutation was 36.6%, 58.5%, and 77.5%, and specificity was 93.3%, 100%, and 96.7%, respectively. Concordance rates were 60.6%, 76.1%, and 85.7%. The size distribution of plasma DNA with automated extraction was bimodal with modes at about 170 bp and 5 Kb, and plasma DNA of both sizes included tumor-derived DNA. In this report, we demonstrate that automated DNA extraction using cellulose magnetic beads can improve mutation-detection rates with plasma DNA in association with two overall sizes of DNA fragments recovered by this DNA isolation system. Examining the biological characteristics of these fragments will be the subject of further investigation.

Genetic analysis, rather than simply counting the number of circulating tumor cells (CTCs), which are rare cancer cells in peripheral blood, has great potential for non-invasive biopsy or "liquid biopsy." However, a practical problem in conventional enrichment of CTCs is that the isolated target cells are mixed with numerous residual leukocytes, and are suspended in a large volume. Hence, further isolation (i.e., cytokeratin (CK)-positive cell picking) or DNA purification is required for downstream genetic analysis after isolation. Here, we propose a novel cancer marker-free method of CTC enrichment by size-based Filtration and Immunomagnetic Negative selection followed by Dielectrophoretic concentration (CTC-FIND) for direct detection of genetic mutations in rare cancer cells suspended in whole blood. A combination of two independent isolation methods based on physical (filtration) and biochemical properties (immunomagnetic negative selection) in CTC-FIND allowed highly efficient cancer marker-free purification (5.1-log depletion of leukocytes). The isolated cells were trapped and concentrated using a microfluidic step-channel device using dielectrophoresis for discrimination and downstream genetic analysis. The feasibility of cancer marker-free enrichment by CTC-FIND was successfully demonstrated by directly detecting mutations in various cancer cells with a very high sensitivity of 1 cell per mL, including EpCAM and CK-negative cells, which were used to spike 8 mL of whole blood. Thus, CTC-FIND can be used with liquid biopsy to detect genetic mutations in wide-ranging CTC subsets, independent of cancer cell-specific marker expression.

Although mechanisms of acquired resistance to 1st and 3rd generation EGFR-TKI continue to be elucidated, there have been few clinical investigations into the mechanisms of acquired resistance to the 2nd generation EGFR-TKI afatinib. We analyzed data from 20 patients with advanced lung adenocarcinoma who acquired resistance to afatinib, including resistance during EGFR-TKI re-challenge. We examined EGFR T790M and C797S mutations, BRAF V600E mutation, and MET amplification with the MBP-QP method and with droplet digital PCR using ctDNA and re-biopsy samples obtained before and after afatinib treatment. Just before afatinib treatment, 15 of the 20 patients were T790M negative and five were positive. Among the T790M negative patients, 40.0% (6/15) became positive at the time of PD under afatinib. In patients positive for T790M, changes in T790M allele frequency were correlated with afatinib treatment efficacy. C797S was not detected in any patients just before afatinib treatment, but it appeared after treatment in three patients, although with very low allele frequency. Two of these three patients, although positive for both C797S and T790M, achieved PR to osimertinib. However, PFS of these patients was somewhat shorter than that of patients positive for T790M only. BRAF V600E was detected in one patient at PD under afatinib. MET amplification was not detected in this study. T790M is associated with acquired resistance to afatinib, as with 1st generation EGFR-TKI, but with somewhat lower frequency. The influence of C797S on resistance to afatinib is less than that of T790M, but C797S might cause shorter PFS under osimertinib.

3041 Background: CTCs are a promising diagnostic and prognostic biomarker in colorectal cancer. The analysis of CTCs at the single-cell level may allow to capture tumor heterogeneity and identify novel prognostic and predictive markers in mCRC. Our aim was to evaluate whether the transcriptome profile of CTCs was associated with progression-free survival (PFS) in pts receiving treatment for mCRC and whether we could identify significant differences based on pts’ ethnicity. Methods: Single CTCs were prospectively collected from 25 pts undergoing treatment for mCRC at the USC/Norris Comprehensive Cancer Center between April and October 2019. Pre-treatment peripheral blood was processed using CTC-FIND comprised filter separation and immunomagnetic depletion of CD45/50-expressing cells to collect ultra-pure CTCs samples. After isolation to single cell, CTCs were processed by single cell RNA-sequence (scRNAseq). Principal component analysis was used for clustering expression data. DESeq2 was used to identify differentially expressed genes between pts with short ( < 150 days) and long term ( > 150 days) PFS, as well as between Hispanic and non-Hispanic ethnicity with control for FDR ( Q < 0.1). Ingenuity pathway analyses (IPA) of enriched pathway networks were performed. Results: Main pts characteristics were as follow: median age = 52 years; M/F = 18/7; Hispanics/non-Hispanics = 7/18; treatment line (n pts) = 1st (5), 2nd (11), ≥ 3rd (9). We identified 59 single CTC and CTC cluster from 22/25 pts (range 1-9, median = 2/pt). scRNAseq analysis identified two separate clusters of pts based on PFS (short term vs long term). Hispanic pts were mainly distributed within the short term PFS cluster. The IPA of the network of top 40 enriched pathways showed several pathways related with metabolism, such as Sirtuin signaling, mitochondrial dysfunction and oxidative phosphorylation, and IL6/JAK/STAT signaling pathways in pts with short term PFS ( Q < 0.05). When comparing Hispanic vs non-Hispanic pts, we detected enrichment of neuroinflammation signaling pathway in Hispanics, including CXCL8 (fold change, FC: 11.04), GAD2 (FC: 4.77), IRAK3 (FC: 17.06), PLCG2 (FC: 4.65) and TYROBP (FC: 8.43) (all Q < 0.05). Conclusions: In our study CTCs transcriptome profiles showed an association with PFS in pts receiving treatment for mCRC, with an enrichment in mitochondria-related pathways and IL6/JAK/STAT signaling in the CTCs of pts with shorter PFS. Additionally, CTCs scRNAseq identified differentially expressed genes in Hispanic pts, displaying enrichment in neuroinflammation signaling. These results highlight the potential of CTCs molecular profiling as a tool to identify novel prognostic and predictive biomarkers in mCRC and actionable molecular pathways which may impact tumor spread and treatment response

Circulating tumor cells (CTCs) are a promising biomarker for cancer liquid biopsy. To evaluate the CTC capture bias and detection capability of the slit filter-based CTC isolation platform (CTC-FIND), we prospectively compared it head to head to a selection-free platform (AccuCyte&reg, CyteFinder&reg, system). We used the two methods to determine the CTC counts, CTC positive rates, CTC size distributions, and CTC phenotypes in 36 patients with metastatic cancer. Between the two methods, the median CTC counts were not significantly different and the total counts were correlated (r = 0.63, p &lt, 0.0001). The CTC positive rate by CTC-FIND was significantly higher than that by AccuCyte&reg, system (91.7% vs. 66.7%, p &lt, 0.05). The median diameter of CTCs collected by CTC-FIND was significantly larger (13.0 &mu, m, range 5.2&ndash, 52.0 vs. 10.4 &mu, 44.2, p &lt, 0.0001). The distributions of CTC phenotypes (CK+EpCAM+, CK+EpCAM&minus, or CK&minus, EpCAM+) detected by both methods were similar. These results suggested that CTC-FIND can detect more CTC-positive cases but with a bias toward large size of CTCs.

It has been reported that colon cancer patients with KRAS and BRAF mutations that lie downstream of epidermal growth factor receptor (EGFR) acquire resistance against therapy with anti‑EGFR antibodies, cetuximab and panitumumab. On the other hand, some reports say KRAS codon 13 mutation (p.G13D) has lower resistance against anti-EGFR antibodies, thus there is a substantial need for detection of specific KRAS mutations. We have established a state-of-the-art measurement system using QProbe (QP) method that allows simultaneous measurement of KRAS codon 12/13, p.G13D and BRAF mutation, and compared this method against Direct Sequencing (DS) using 182 specimens from colon cancer patients. In addition, 32 biopsy specimens were processed with a novel pre-treatment method without DNA purification in order to detect KRAS/BRAF. As a result of KRAS mutation measurement, concordance rate between the QP method and DS method was 81.4% (144/177) except for the 5 specimens that were undeterminable. Among them, 29 specimens became positive with QP method and negative with DS method. BRAF was measured with QP method only, and the mutation detection rate was 3.9% (6/153). KRAS measurement using a simple new pre-treatment method without DNA extraction resulted in 31 good results out of 32, all of them matching with the DS method. We have established a simple but highly sensitive simultaneous detection system for KRAS/BRAF. Moreover, introduction of the novel pre-treatment technology eliminated the inconvenient DNA extraction process. From this research achievement, we not only anticipate quick and accurate results returned in the clinical field but also contribution in improving the test quality and work efficiency.

Most circulating tumor cell (CTC) detection methods have technical limitations, allowing the detection of only cells expressing epithelial antigens, and they cannot identify if the CTCs are alive or dead. Herein, we constructed a novel CTC detection system comprised of filter separation and 5-aminolevulinic acid (5-ALA)-based labeling, termed “Fs-ALA”. Blood specimens (7.5 mL) were subjected to this method. Cells enriched on the filter were incubated with 5-ALA and Hoechst 33342 as positive markers for CTCs. Images of the whole filter surface were obtained using a fluorescence microscope. No 5-ALA positive cells were detected in healthy blood specimens. The Fs-ALA method was capable of detecting not only EpCAM-positive, but also EpCAM-negative tumor cells. In the Fs-ALA method, one or more CTCs were detected in samples from 13 of 18 (72.2%) colorectal cancer patients. The Fs-ALA method had a significantly higher CTC detection rate than CellSearch™ in colorectal cancer patients ( P 0.05), and only the former was capable of identifying live cells. This method is highly efficient for detecting CTC populations having undergone phenotypic changes, such as epithelial–mesenchymal transition.

Re-challenge with epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKI) has been suggested to potentially improve survival in certain populations of patients with advanced lung cancer, but predictive markers for the success of EGFR-TKI re-challenge have not been identified. The present study analyzed 16 re-challenges with EGFR-TKI undertaken in 12 patients with lung adenocarcinoma by investigating T790M and hepatocyte growth factor (HGF) in plasma coupled with clinical characteristics. EGFR mutations in plasma DNA were detected using the wild inhibiting PCR and quenched probe system for exon 19 deletions, and T790M and L858R were detected using the mutation-biased PCR and quenched probe system. HGF levels in the plasma were measured by enzyme-linked immunosorbent assay, and the ratio of HGF levels prior to re-challenge to those prior to the previous EGFR-TKI treatment was calculated. Two re-challenges demonstrated partial response, six remained as stable disease and eight had progressive disease (PD). A total of 4 of the 5 patients with a history of T790M positivity based on plasma DNA levels had PD. A total of 7 of the 8 patients who had ≥1.5-fold elevation of HGF prior to re-challenge with EGFR-TKI suffered PD. Elevation of the HGF ratio to ≥1.5 was significantly associated with poor response to EGFR-TKI re-challenge. Having no history of T790M and an HGF ratio

KRAS mutations have been recognized as predictive markers of primary resistance to anti-EGFR-antibodies in colorectal cancer patients. In addition, newly detected KRAS mutations have been reported to be related with acquired resistance to chemotherapy containing anti-EGFR antibody. Considering this evidence, monitoring of KRAS mutations is indispensable for making treatment decisions, and the method should be non-invasive allowing repeated examinations. Recently, we established a novel automated sensitive detection system for KRAS mutations, named mutation-biased PCR quenching probe system (MBP-QP). The goal of our study was to investigate the potential for monitoring KRAS mutations during treatment with anti-EGFR antibodies. The detection limit of MBP-QP using a control plasmid containing KRAS mutations was 1-9 copies, and 0.05-0.3% mutant plasmid was detectable in a mixture of wild type and mutants. One-hundred twenty colorectal cancer patients were genotyped for KRAS mutations with MBP-QP as well as polymerase chain reaction reverse sequence-specific oligonucleotide (PCR-rSSO), which has already been applied to cancer tissue samples in the clinical setting. Concordance rates between plasma DNA and cancer tissues were 68% with MBP-QP and 66% with PCR-rSSO, indicating that these systems are equivalent in terms of detecting KRAS mutations with plasma DNA. KRAS mutations in plasma DNA were frequently observed in systemic metastatic cancer patients, and in three patients KRAS mutations appeared after chemotherapy containing anti-EGFR antibody. A prospective study is needed for clarifying whether KRAS mutations detected in plasma DNA are predictive markers of treatment efficacy with anti-EGFR antibody.

Introduction: Detection of epidermal growth factor receptor ( EGFR) mutations is indispensable to determine an appropriate lung cancer treatment. Although retreatment often prolongs survival, how to select the appropriate population for retreatment has not been clarified. Methods: We used novel methods to identify EGFR mutations: wild inhibiting polymerase chain reaction (PCR) and quenched probe system (WIP-QP) for exon 19 deletions and mutation-biased PCR and quenched probe system for L858R. After the detection limits were determined, we examined DNA isolated from lung cancer specimens and circulating plasma DNA samples of 39 adenocarcinoma patients whose primary tumors harbored EGFR exon 19 deletions or L858R. Results: Detection limit was 0.005 to 0.04 ng in genomic DNA and 0.1% to 0.3% in mutant plasmids. The results of cancer tissue specimens were identical to those with existing systems (nucleic acid-locked nucleic acid PCR clamp or cycleave PCR), except for two samples that showed both exon 19 deletions and L858R. One of the two samples was confirmed to harbor L858R mutation by allele-specific oligonucleotide PCR; the other one did not. Exon 19 deletions and L858R were detected in 44.7% and 8.7% of patients, using plasma DNA, among those who carried the identical abnormalities in primary tumors all of cases that evidenced pathological stage IV except for one patient, suggesting that EGFR mutations might be preferentially detected in plasma DNA obtained from patients in advanced stages. Serial monitoring of these mutations with T790M, a gate keeper mutation, demonstrated correlation with disease state. Conclusions: Our novel detection systems for EGFR mutations could be useful not only at the beginning of treatment but also for monitoring using plasma DNA for deciding appropriate treatment, including rechallenge with EGFR-tyrosine kinase inhibitors.

An efficient method for cell trapping onto a designated location and reduction of the sample volume is required to reduce the risk of sample losses during the discrimination and molecular characterization of low-abundant cells suspended in a large volume of the sample. In this study, we propose a novel microfluidic device that allows for highly efficient trapping of the cancer cells onto a designated location and correction of the trapped cells with a significantly reduced sample volume. The microfluidic device, which utilizes dielectrophoresis cell trapping, consists of an attraction-zone to control the vertical position of the cells and a trap-zone to capture the target cells by drastically decreasing the flow velocity around the cells with a sharply increased channel height. The device showed that 92 ± 9% of the introduced cancer cells were trapped on a designated location (500-μm behind the step) with a high inlet flow rate of 100 μl min−1. The trapped cells were corrected with a one-hundredth volume ...

Background Genetic analysis of circulating tumor cells (CTCs) is useful as a liquid biopsy. However, there are 3 challenging issues in processing of CTC samples for clinical use of the analysis: [1] numerous residual blood cells in processed samples, [2] loss of CTCs that do not express epithelial markers, and [3] very laborious process. Here, we developed a novel system capable of overcoming all of these problems. Methods Our CTC analysis system is composed of 3 steps: [1] filtering of whole blood followed by immunostaining and magnetic labeling of cells trapped on the filter, [2] depletion of white blood cells (WBCs) in the cells recovered from the filter by magnetic separation, and [3] trapping the resultant cells at an observation chamber in a microfluidic enrichment device using dielectrophoresis, followed by recovering them as a concentrated sample after fluorescence microscope observation. SNV and CNV analysis was conducted using the collected concentrated sample, and the system performance was substantiated. Genetic mutations of the cells in the collected sample were detected by the Quenching Probe method. On the other hand for CNV analysis, cells in the collected concentrated sample were immobilized on slide glass and analysis of gene amplification conducted by FISH. Results With SNV analysis, our system successfully detected EGFR, KRAS or PIK3CA mutations of cancer cell lines spiked in 8 mL of whole blood (Table). The detection sensitivity of our method was 1 cell/mL, and both the cancer cells and their genetic mutations were detected within 9 hours of starting the processing of whole blood. Additionally, with CNV analysis, HER2 gene amplification was confirmed with cell lines spiked in 8 mL of blood. This detection result was obtained within 48 hours. Conclusion Our system would be useful for the analysis of gene mutations in a wide range of CTC types independent of certain epithelial antigens, such as CK and EpCAM, and can be used for various genetic analyses. Table Results of spiking test for SNV analysisSpiked cell linesExpected count[cells/8ml]No. of detected spiked cells [cells]No. of detected remained WBCs [cells]Detected genotypesNCI-H197512979EGFR L858RNCI-H16508225EGFR exon19 deletionSW6208648KRAS codon12, 13SNU-1124154KRAS codon12, 13MCF-777341PIK3CA G1633A Citation Format: Hidenori Takagi, Masahiro Kozuka, Hiroshi Ito, Soo Hyeon Kim, Mitsuharu Hirai, Teruo Fujii. Genetic analysis using a novel high-purity enrichment system for circulating tumor cells independent of epithelial cell antigen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3782. doi:10.1158/1538-7445.AM2017-3782

The usefulness of liquid biopsy to detect mutations from cancer patients has been well recognized today. However, because the mutation detection rates from plasma DNA were relatively lower than those of tissue re-biopsy, its clinical utility has not been confirmed yet. As previously we reported, we have developed fully automatic high-sensitive point mutation detecting system named mutation-biased PCR and quenched probe (MBP-QP) system for liquid biopsy. Recently, the importance of pre-analytical procedures for plasma DNA anazysis has been highlighted. In this study, we examined whether the automatic DNA extraction system can improve the mutation detection rate in our MBP-QP system. Sixty-one plasma samples were obtained from advanced non-small cell lung cancer patients, and plasma DNA extraction was performed from 200μl plasma by manually (200-M), and 200μl (200-A), 1000μl (1000-A) plasma by automatically. We used silica membrane spin column system for manual DNA extraction, and magnet beads system for automatic DNA extraction procedure. The median DNA concentrations quantified by quantitative real-time PCR of 200-M, 200-A, 1000-A were 4.92, 6.00, 20.1 ng/mL plasma, respectively. In terms of the epidermal growth factor receptor (EGFR) L858R point mutation detection, the sensitivity of 200-M, 200-A, 1000-A were 36.6%, 58.5%, 77.5%, that of the specificity were 93.3%, 100%, 96.7%, and the concordance rates were 60.6%, 76.1%, 85.7%, respectively. The size distribution of automatically extracted plasma DNA represented two peaks characteristics at 170 bp and 5 kb. In this study, we indicate the automatic DNA extraction can improve mutation detection rates in plasma DNA. Citation Format: Chiho Nakashima, Akemi Sato, Tomonori Abe, Tomomi Nakamura, Kazutoshi Komiya, Eisaburo Sueoka, Shinya Kimura, Naoko Sueoka-Aragane, Junichi Kato, Mitsuharu Hirai. Automatic DNA extraction system can improve the EGFR point mutation detection rate of liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2751. doi:10.1158/1538-7445.AM2017-2751

JAK2V617F is a common mutation in chronic myeloproliferative diseases (CMPDs). We have developed a system utilizing JAK2V617F-specific guanine quenching probe (QP-system) to detect JAK2V617F. With QP-system, results can be obtained from 100 microl of blood within 90 min. We compared QP-system with direct sequencing using 42 CMPD patients' specimens. JAK2V617F was detected in 25 specimens by QP-system, while direct sequencing failed to detect JAK2V617F in 7 of those 25. The presence of JAK2V617F mutation in these 7 specimens was confirmed by allele-specific PCR. These findings indicate that QP-system is more sensitive and useful than direct sequencing for diagnoses of CMPDs.

Purpose Gene polymorphism and genetic mutation are related to the therapeutic effect of many drugs, and a simple genetic test method is preferred. To meet this demand, we have developed a platform for genetic testing called i-densy, which can complete fully automated gene polymorphism analysis from whole blood in approximately 90 minutes, and compared it with the existing test method. Also, recent reports indicate that DNA derived from cancer cells are liberated in blood (it is called “circulating cell-free DNA”). Using the i-densy, we here tested EGFR gene T790M mutation in circulating cell-free DNA from a sample derived from advanced lung cancer patient with EGFR-TKI aquired resistance, and then compared with the existing test method. Methods The i-densy newly developed can perform fully automated gene polymorphism testing from 70μL of whole blood and allows typing of 3 polymorphisms or mutations in a single reaction. Four samples can be tested at once with this instrument, and testing is also possible using oral mucosa or purified nucleic acid instead of whole blood. In addition to the i-densy, circulating cell-free DNA was also tested using Mutation Biased PCR (MBP) method that can preferentially amplify mutation sequence. Results As a result of using the i-densy with whole blood for gene testing on 1236C>T, 3435C>T and 2677 G>(T/A) polymorphism of ABCB1 gene related to toxicity and pharmacokinetics of EGFR-TKI erlotinib, results of 1236C>T and 3435C>T matched with that of Taqman assay method and 2677 G>(T/A) matched with Direct sequencing method for all 20 samples. We also extracted free DNA from peripheral blood plasma of a patient, and tested EGFR T790M mutation using Mutation Biased PCR (MBP) method, PNA-LNA PCR clamp method and Cycleave method. Among 19 patients with acquired resistance to EGFR-TKI, number of patients tested positive for T790M were 10 (53%) using MBP method, 3 (16%) using PNA-LNA PCR method and 5 (26%) using Cycleave method. Also, when using MBP method, there was not a single case with T790M mutation detected among cases with continued therapeutic effect or which EGFR-TKI is not used. Conclusion The i-densy newly developed has been identified to be simple and fast that allows accurate gene polymorphism from whole blood, and also confirmed to be useful in clinical practice. As a result of EGFR gene T790M mutation testing from circulating cell-free DNA using the i-densy and MBP method, appearance ratios of acquired resistance mutation were very close to each other (approximately 50%), indicating the high detection performance compared to other methods. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2089. doi:1538-7445.AM2012-2089

Although EGFR tyrosine kinase inhibitors (EGFR-TKIs) have great response to lung adenocarinoma with EGFR activating mutations, acquired resistance eventually developed. The half of these patients has the gatekeeper T790M mutation of EGFR in lung cancer tissue. A non-invasive mutation detection system is desired considering the difficulty in obtaining tissue specimens during disease progression_the majority of lung cancer recurrences occur in distant sites. We report a novel non-invasive monitoring system, MBP-QP (mutation-biased PCR and quenching probe) method, to detect the mutation using plasma DNA. The MBP-QP method is combined with mutated biased PCR and genotyping based on the analysis of a melting curve of probe DNA which is bound to the target mutated site using a fluorescence quenching probe. The detection limit was 2 copies of control plasmid, and 0.2 ng of genomic DNA isolated from a lung caner cell line harboring T790M. 0.3 % mutant plasmid could be detected in the mixture of plasmids inserted with EGFR exon 20 with or without T790M. With this method, T790M mutations were detected in plasma DNA of 50% of patients who acquired resistance, but not in primary EGFR-TKI non-responders, patients responding to treatment, or patients not treated with EGFR-TKI, which is consistent with the clinical course. The non-invasive MBP-QP method enabled us to monitor T790M repeatedly and will be useful for determining appropriate lung cancer treatment strategies in practice. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4117. doi:10.1158/1538-7445.AM2011-4117

Abstract 2590 Poster Board II-566 Chronic myelogenous leukemia (CML) is caused by a consistent genetic abnormality, termed the Philadelphia chromosome (Ph). It results in the production of BCR-ABL fusion protein, a constitutively active tyrosine kinase. Imatinib mesylate (IM, Gleevec®), the first generation tyrosine kinase inhibitor (TKI), has revolutionized therapy for CML patients. However, resistance for IM develops in a significant proportion of cases, and is predominantly mediated by single point mutations within the BCR-ABL kinase domain. Second generation TKIs such as dasatinib (Sprycel®) and nilotinib (Tasigna®) represent viable alternatives for IM-resistant or intolerant CML patients. Each mutated BCR-ABL has different sensitivity to those TKIs. Thus, it is significantly important to detect early the existence of BCR-ABL mutations and their specificities in treating Ph+ leukemias. We have developed a novel automated method that has high sensitivity to detect a few copies of mutation sequences that are mixed in many copies of normal sequences. This method consists of PCR amplification step and Tm (melting temperature) analysis step that uses a quenching probe. And we have already shown that this system has clinical efficacy in JAK2V617F mutation that is one of the genetic hallmarks of chronic myeloproliferative diseases. (Tanaka R, et al. Leuk Res, 2008). When a whole blood sample or a purified DNA sample reacts with reagents, PCR and Tm analysis automatically processed in the same tube, and whole procedure finishes in approximately 1 hour. The detection of mutation is extremely accurate because the quenching probe is designed perfectly matched for mutated sequence. As Tm value of mutation sequence is higher than that of normal one, it is easy to detect the existence of mutation from the Tm analysis data. We have constructed the probes for 14 mutations concerned for IM-resistance (M244V, G250E, Q252H, Y253F, Y253H, E255V, E255K, T315I, T315A, F317L, M351T, E355G, F359V, and H396R). Considering the clinical significance of T315I mutation, which renders resistance to all currently available TKIs, we refined this method to higher sensitivity for detecting T315I mutation. First, we analyzed the sensitivity of this system on BCR-ABL. In dilution assays using wt and mutated plasmid, the system reliably quantified the mutation in a population containing as few as 3.0% mutant. Moreover, for T315I setting, we successfully detected as few as 0.3% (30 copies from 10,000 copies) mutations by a higher-sensitive assay. Next, we examined the clinical samples. Each sample was also examined by direct sequencing in comparison to our method. Kinase domain mutations were identified in 24 of the 50 (48%) patients. Our automated analysis was enabled to detect mutations in 19 patients, including p-loop mutations (G250E: n=3; E255K: n= 5), IM-binding domain mutations (T315I: n=10), and an activation-loop mutation (H396R: n=1). And all the positive cases (19 of 19) showed a concordance with the result of direct sequencing. On the other hand, 5 cases were detected just by direct sequencing, but all that cases were out of our setting mutations (Q252E, V379I, S417F, E459K). Impressively, in one case, only higher-sensitivity assay could reveal T315I mutation, although it was detected as a wild type both by direct sequence and our usual method. It suggests that the higher-sensitive system could detect low amount of T315I mutation in the earlier stage of disease. In conclusion, sensitivity of our system (3%) is significantly greater than that of direct sequencing (15 – 25%), and results can be obtained within one hour. By the serial monitoring, it is demonstrated the availability of the higher-sensitive analysis (0.3%) to detect T315I mutation. This rapid and accurate detection of clinically significant mutations enables us to contribute to better clinical practice in treating Ph+ leukemia patients, such as in selecting alternative strategies of IM dose escalation, second generation TKIs, or allogeneic stem cell transplantation. Disclosures: No relevant conflicts of interest to declare.

The JAK2 V617F substitution mutation (JAK2V617F) is one of the genetic hallmarks of chronic myeloproliferative diseases (CMPDs), such as polycythemia vera (PV), essential thrombocythemia (ET), or chronic idiopathic myelofibrosis (CIMF). Accurate and rapid detection of this mutation is essential for diagnosing and treating CMPDs today. We have developed a novel, rapid, sensitive and fully-automated single nucleotide polymorphism (SNP) detection system, termed ARKRAY SNP Detection System (ASDS), and used it to detect JAK2V617F in patients with CMPDs. With ASDS, diagnosis requires only 100ml of whole blood (or DNA), and the system automatically performs DNA extraction and PCR. The detection of both wild type and mutant jak2 alleles from PCR amplicons was measured by the increase in fluorescence produced by the dissociation of a JAK2V617F-specific guanine-quenching probe, and was completed within 75 minutes. In dilution assays of HEL cells (a JAK2V617F-positive leukemia cell line) using MYL cells (a chronic myelogenous leukemia (CML)-derived cell line with wild type JAK2), the system reliably quantified the mutation in a cell population containing as few as 1.0% mutant cells (Figure). We tested 44 samples from CMPDs patients using ASDS and direct sequencing (DS) (13 PV, 23 ET, 3 CIMF, 1 chronic myelomonocytic leukemia (CMMoL), 1 chronic neutrophilic leukemia (CNL), 3 unclassifiable CMPD (uCMPD)), which included samples from 3 post-allogenic bone marrow transplantation (BMT) patients with CIMF or uCMPD. Using ASDS, we detected JAK2V617F in 12/13 PV, 13/23 ET, 0/1 CIMF without BMT, 1/1 CMMoL, 0/1 CNL and 1/3 uCMPD. Overall, these results were comparable to previous results using relatively sensitive detection strategies, such as allele-specific PCR (AS-PCR). One of the 3 post-BMT CIMF samples was positive for JAK2V617F, which indicated that there were residual disease clones after BMT. ASDS detected JAK2V617F in one PV and eight ET patients, while DS failed to detect the mutation in these same samples, which clearly indicated that ASDS has a higher sensitivity than DS. JAK2V617F was absent in all samples from secondary erythrocytemia and healthy volunteers. Collectively, these results demonstrate that ASDS is a powerful and convenient tool for detecting JAK2V617F. With its associated high sensitivity, convenience and rapidity, this system will enable “Point-of-care” testing in clinical laboratories and “Patient-oriented” therapy for CMPDs. ASDS could also be applied to the detection of other point mutations relevant to cancer treatment, such as mutations in the BCR-ABL kinase domain that are associated with CML. Download : Download high-res image (133KB) Download : Download full-size image Figure