Molecular Analysis Of Circulating Tumor Cells Research Articles

Molecular profiling using next generation sequencing with high-purity enrichment of circulating tumor cells.

e15054 Background: In the field of liquid biopsy, coupled with next generation sequencing (NGS), circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) can serve as an alternative substrate to tumor tissue for mutation detection and companion diagnostic purpose. Emerging evidence suggests that complementary sequential CTCs and ctDNA profiling offers promising benefits for prognosis and treatment. In contrast to well-established ctDNA extraction methods, the process of isolation of intact CTCs for NGS analysis has not yet been fully elucidated. Here we show that isolation and harvesting of viable CTCs using CytoGen's Smart Biopsy™ System achieves high CTC purity for NGS analysis in breast cancer and non-small cell lung cancer (NSCLC). Methods: Targeted panel sequencing for CTC was developed to detect representative mutated genes using the Oncomine™ Comprehensive Assay Plus (501 genes) and the Oncomine™ Pan-Cancer Cell-Free Assay (52 genes). Analytical validation was performed with breast cancer cells MDA-MB-231 (50 to 5 cells) and NSCLC cells H358 (10 and 5 cells) which were spiked into 5 mL of healthy blood to mimic CTCs. CytoGen's Smart Biopsy™ System was applied to isolate the CTCs. Subsequently, CD45 depletion and whole genome amplification were performed. Sequencing was performed on Ion S5™ XL Systems using an Ion 550™ chip kit. The sequencing data were then analyzed using the Ion Torrent software with the default configurations. Results: As a result of targeted panel sequencing with Oncomine™ Comprehensive Assay Plus, representative breast cancer mutation genes (BRAF, KRAS, TP53, NF2 and NOTCH3) were detected in at least 20 MDA-MB-231 cells. In the results using Oncomine™ Pan-Cancer Cell-Free Assay, mutated genes (BRAF, KRAS and TP53) were successfully detected in as few as 5 MDA-MB-231 cells and, in addition, KRAS mutation was detected even with only 5 H358 cells. These results suggest that CytoGen's Smart Biopsy™ System could be applied to detect representative mutated genes in clinical breast cancer and NSCLC patient samples with detection technology that require high sensitivity and specificity. Conclusions: Molecular analysis of CTCs is a challenge since CTCs are very rare in the blood and there are technical limitations in isolating CTCs with sufficient purity for NGS analysis. In this study, we developed the process for NGS analysis on very small number of high-purity CTCs using CytoGen's Smart Biopsy™ System. Taken together with the results from our ongoing clinical trials, this process could provide information for the diagnosis and appropriate treatment of breast cancer and NSCLC patients.

Abstract 3691: Molecular profiling using next generation sequencing with high purity enrichment of circulating tumor cells

Abstract Purpose: In the area of liquid biopsy, coupled with next generation sequencing (NGS), circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) can serve as an alternative substrate to tumor tissue for mutation detection and companion diagnostic purpose. Emerging evidence shows that complementary sequential CTCs and ctDNA profiling provide promising benefit for prognosis and treatment. In contrast to well-established ctDNA extraction methods, the process of isolating intact CTCs for NGS analysis is yet to be fully elucidated. Here, we show that the isolation and harvest of viable CTCs by CytoGen’s Smart Biopsy™ System enable the attainment of sufficiently high purity for NGS analysis in metastatic breast cancer. Methods: Targeted panel sequencing for CTC was developed to detect representative mutated genes, using the Oncomine™ Comprehensive Assay Plus (501 genes) and the Oncomine™ Pan-Cancer Cell-Free Assay (52 genes). Analytical validation was performed with breast cancer cells MDA-MB-231 (50 to 5 cells) which were spiked into 5 mL healthy blood, to mimic CTC. The CytoGen’s Smart Biopsy™ system was applied to isolate the CTC. Then, CD45 depletion and whole genome amplification were performed. Sequencing was carried out on Ion S5™ XL systems using an Ion 550™ Chip Kit. Subsequently, sequencing data was analyzed using Ion Torrent software with default configurations. Results: As a result of targeted panel sequencing using Oncomine™ Comprehensive Assay Plus, representative mutated genes (BRAF, KRAS, TP53, NF2 and NOTCH3) in breast cancer were detected in at least 20 MDA-MB-231 cells. In the results using Oncomine™ Pan-Cancer Cell-Free Assay, mutated genes (BRAF, KRAS and TP53) were successfully detected even with only 5 MDA-MB-231 cells. These results suggest that clinical sample of breast cancer could be applied with promising sensitivity and specificity for detection of representative mutated genes. Conclusion: Molecular analysis of CTCs is a challenge since CTCs are very rare in the blood and there are technical limitations in isolating CTCs with sufficient purity. In this study, we developed the process for NGS analysis on very low number of CTCs with high purity, isolated using CytoGen's Smart Biopsy™ system. Overall, these process could provide information for diagnosis and appropriate treatment of metastatic breast cancer along with the results of our ongoing clinical trials. Citation Format: Sehwan Park, Jaesung Choi, Aejin Jeong, Hanbyeol Kim, Jiyoun Oh, Ingeon Jang, Hoin Kang, Jihyun Lee, Sehyung Pak, Min-Ji Song, Jung Won Kim, Hai-Chon Lee. Molecular profiling using next generation sequencing with high purity enrichment of circulating tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3691.

Beyond Circulating Tumor Cell Enumeration: Cell-Based Liquid Biopsy to Assess Protein Biomarkers and Cancer Genomics Using the RareCyte® Platform.

The practice of medicine has steadily employed less invasive methods to obtain information derived from the tumor to guide clinical management of patients. Liquid biopsy—the sampling of blood—is a non-invasive method for generating information previously only available from tissue biopsies of the tumor mass. Analysis of fragmented circulating tumor DNA in the plasma is clinically used to identify actionable mutations and detect residual or recurrent disease. Plasma analysis cannot, however, assess cancer phenotypes, including the expression of drug targets and protein biomarkers. Circulating tumor cells (CTCs) are intact cancer cells that have entered the blood that have the potential for distant metastasis. While enumeration of CTCs is prognostic of outcome, recently developed technology allows for the interrogation of protein biomarkers on CTCs that could be predictive of response. Furthermore, since CTCs contain intact whole cancer genomes, isolating viable CTCs detected during therapy could provide a rational approach to assessing mutational profiles of resistance. Identification, characterization and molecular analysis of CTCs together will advance the capacity of liquid biopsy to meet the requirements of twenty-first century medicine.

Non-Invasive Profiling of Advanced Prostate Cancer via Multi-Parametric Liquid Biopsy and Radiomic Analysis.

Integrating liquid biopsies of circulating tumor cells (CTCs) and cell-free DNA (cfDNA) with other minimally invasive measures may yield more comprehensive disease profiles. We evaluated the feasibility of concurrent cellular and molecular analysis of CTCs and cfDNA combined with radiomic analysis of CT scans from patients with metastatic castration-resistant PC (mCRPC). CTCs from 22 patients were enumerated, stained for PC-relevant markers, and clustered based on morphometric and immunofluorescent features using machine learning. DNA from single CTCs, matched cfDNA, and buffy coats was sequenced using a targeted amplicon cancer hotspot panel. Radiomic analysis was performed on bone metastases identified on CT scans from the same patients. CTCs were detected in 77% of patients and clustered reproducibly. cfDNA sequencing had high sensitivity (98.8%) for germline variants compared to WBC. Shared and unique somatic variants in PC-related genes were detected in cfDNA in 45% of patients (MAF > 0.1%) and in CTCs in 92% of patients (MAF > 10%). Radiomic analysis identified a signature that strongly correlated with CTC count and plasma cfDNA level. Integration of cellular, molecular, and radiomic data in a multi-parametric approach is feasible, yielding complementary profiles that may enable more comprehensive non-invasive disease modeling and prediction.

Abstract PS2-11: Ctc-her2+ a novel subset in stage IVaggressive: Molecular correlations, outcome and clinical characteristics in metastatic breast cancer

Abstract Background The enumeration of Circulating Tumor Cells (CTCs) in the peripheral blood of patients (pts) with metastatic breast cancer (MBC) showed prognostic value independent of clinic-pathological characteristics and proposed as a new tool for Stage IV stratification. Molecular characterization of CTCs with analysis of standard HER2 and estrogen-receptor (ER) status provides additional predictive value. The presence of HER2 positive CTCs (CTCs-HER2+) has been documented in pts with HER2 negative MBC and suggestive of tumor heterogeneity. The molecular features associated with the detection of these cells and the clinical significance of CTCs-HER2+ remains of unclear clinical significance. The lack of validated prospective trials limits the use of this immunophenotypic characterization as a prognostic and predictive factor. We conducted an analysis of a large cohort of patients with MBC evaluated for CTCs enumeration (CTCs+), molecular analysis of CTCs (CTCs-HER2+) and ctDNA. Methods The IRB-approved study prospectively analyzed blood samples of pts with MBC enrolled before starting a new line of therapy. Samples were collected from pts treated at Northwestern University (Chicago, IL) between 2016 and 2020. ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health) with a specific focus on the detection of ERBB2 mutations. CTCs were enumerated through CellSearch™ (Menarini Silicon Biosystems, Bologna, Italy), and characterized for HER2 expression using the CellSearch CXC Kit. HER2+ CTCs were divided in 4 different categories (0,1+,2+,3+), leaning on fluorescence intensity, as previously reported by Riethdorf et al. Pts with <5 CTCs (stage IV indolent ) were excluded from the analysis. The cHER2 ratio, defined as the sum of 2+ CTCs and 3+ CTCs divided by the total number of HER2+ CTCs was used to split the remaining pts in 2 different subgroups: cHER2 ratio> 0.75 (cHER2high), cHER2 ratio<0.75 (cHER2low). Pts' characteristics and genomic alterations were compared between these two subgroups and a long-rank test was performed to analyze the outcome (progression-free survival, PFS). Results A total of 247 pts with MBC about to start new therapy were enrolled. 136 patients (55%) demonstrated CTCs count ≥ 5 (stage IV aggressive). Of these, 111 pts had a blood sample bearing HER2+ CTCs. 88 pts were classified as cHER2low, while 32 were allocated in the second subgroup (cHER2high). The clinic subtype distribution of the two groups was as follows: 65% ER+, 19% HER2+ and 16% TNBC among cHER2low, compared to 55% ER+, 38% HER2+ and 7% TNBC among cHER2high pts. The HER2+ subtype was significantly more represented in the cHER2high group (p<0.05), along with ERBB2 mutations (p<0.05). We observed a total of 89 events (progression to treatment), 67 and 22 respectively. The median PFS was 87 days in the cHER2low and 209 days among cHER2high pts (log Rank test, p<0.001). Conclusion This study shows a significant association between the cHER2 ratio and outcome in pts with Stage IV aggressive disease, suggesting a potential predictive/prognostic role of this biomarker among MBC pts bearing CTC-HER2+. cHER2high pts, in which blood was collected a prevalent number of CTC-HER2+ 2+ and 3+, were more likely to have a HER2 FISH amplification by tissue biopsy and ERBB2 gene alteration by ctDNA. These findings, taken together, suggest a potential role of these subsets of CTC-HER2+ in the characterization of the HER2+ metastatic disease. The cHER2low is intrinsically characterized by a higher percentage of CTC-HER2+ 1+. This CTC-HER2+ subset of cells is commonly detected among all subtypes but, more frequently in ER+ disease and their significance remains unclear. Exploring the underlying biological nature of the CTC-HER2+ 1+ could allow to better understand the role these cells in the natural evolution of the MBC. Citation Format: Paolo D'Amico, Qiang Zhang, Lorenzo Gerratana, Youbin Zhang, Ami Shah, Carolina Reduzzi, Andrew Davis, Saya Jacob, Firas Wehbe, Amir Behdad, Giuseppe Curigliano, Massimo Cristofanilli. Ctc-her2+ a novel subset in stage IVaggressive: Molecular correlations, outcome and clinical characteristics in metastatic breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS2-11.

Emerging Microfluidic Technologies for the Detection of Circulating Tumor Cells and Fetal Nucleated Red Blood Cells

Blood tests have been a powerful tool for the clinical analysis of many diseases. With the advances in microfluidic technology, two more specific indicators from the circulation system, namely, emerging "liquid biopsy" of circulating tumor cells (CTCs) and fetal nucleated red blood cells (fNRBCs), can be screened and analyzed as a simple blood test for the noninvasive diagnosis of cancers as well as fetal disorders. The unique feature of precisely manipulating a trace of fluid endows microfluidic devices with the ability to isolate CTCs or fNRBCs from numerous blood cells with high performance, which undoubtedly facilitates biomedical applications of these two kinds of rare cells. In this review, advanced developments in microfluidic technologies focusing on the detection and sorting of rare CTCs and fNRBCs from peripheral blood are summarized. The development of microfluidic devices incorporated with various multifunctional microstructures and nanomaterials for enhancing the sensitivity, purity, and viability of CTC or fNRBC detection enables CTC molecular analysis and fNRBC-based noninvasive prenatal diagnosis (NIPD). These microfluidics-based approaches provide great potential opportunities in noninvasive cancer diagnosis or NIPD applications.

Circulating Tumor Cells in Early and Advanced Breast Cancer; Biology and Prognostic Value.

Breast cancer metastasis is the leading cause of cancer deaths in women and is difficult to combat due to the long periods in which disseminated cells retain a potential to be re-activated and start the relapse. Assessing the number and molecular profile of circulating tumor cells (CTCs) in breast cancer patients, especially in early breast cancer, should help in identifying the possibility of relapse in time for therapeutic intervention to prevent or delay recurrence. While metastatic breast cancer is considered incurable, molecular analysis of CTCs still have a potential to define particular susceptibilities of the cells representing the current tumor burden, which may differ considerably from the cells of the primary tumor, and offer more tailored therapy to the patients. In this review we inspect the routes to metastasis and how they can be linked to specific features of CTCs, how CTC analysis may be used in therapy, and what is the current status of the research and efforts to include CTC analysis in clinical practice.

Capture and selective release of multiple types of circulating tumor cells using smart DNAzyme probes.

The effective capture, release and reanalysis of circulating tumor cells (CTCs) are of great significance to acquire tumor information and promote the progress of tumor therapy. Particularly, the selective release of multiple types of CTCs is critical to further study; however, it is still a great challenge. To meet this challenge, we designed a smart DNAzyme probe-based platform. By combining multiple targeting aptamers and multiple metal ion responsive DNAzymes, efficient capture and selective release of multiple types CTCs were realized. Sgc8c aptamer integrated Cu2+-dependent DNAzyme and TD05 aptamer integrated Mg2+-dependent DNAzyme can capture CCRF-CEM cells and Ramos cells respectively on the substrate. With the addition of Cu2+ or Mg2+, CCRF-CEM cells or Ramos cells will be released from the substrate with specific selectivity. Furthermore, our platform has been successfully demonstrated in the whole blood sample. Therefore, our capture/release platform will benefit research on the molecular analysis of CTCs after release and has great potential for cancer diagnosis and individualized treatment.

Clonality of circulating tumor cells in breast cancer brain metastasis patients

BackgroundThe incidence of brain metastases in breast cancer (BCBM) patients is increasing. These patients have a very poor prognosis, and therefore, identification of blood-based biomarkers, such as circulating tumor cells (CTCs), and understanding the genomic heterogeneity could help to personalize treatment options.MethodsBoth EpCAM-dependent (CellSearch® System) and EpCAM-independent Ficoll-based density centrifugation methods were used to detect CTCs from 57 BCBM patients. DNA from individual CTCs and corresponding primary tumors and brain metastases were analyzed by next-generation sequencing (NGS) in order to evaluate copy number aberrations and single nucleotide variations (SNVs).ResultsCTCs were detected after EpCAM-dependent enrichment in 47.7% of the patients (≥ 5 CTCs/7.5 ml blood in 20.5%). The CTC count was associated with ERBB2 status (p = 0.029) of the primary tumor as well as with the prevalence of bone metastases (p = 0.021). EpCAM-independent enrichment revealed CTCs in 32.6% of the patients, especially among triple-negative breast cancer (TNBC) patients (70.0%). A positive CTC status after enrichment of either method was significantly associated with decreased overall survival time (p < 0.05). Combining the results of both enrichment methods, 63.6% of the patients were classified as CTC positive. In three patients, the matched tumor tissue and single CTCs were analyzed by NGS showing chromosomal aberrations with a high genomic clonality and mutations in pathways potentially important in brain metastasis formation.ConclusionThe detection of CTCs, regardless of the enrichment method, is of prognostic relevance in BCBM patients and in combination with molecular analysis of CTCs can help defining patients with higher risk of early relapse and suitability for targeted treatment.

Quantification of activated and exhausted immune cell populations and simultaneous characterization of circulating tumor cells (CTCs) in peripheral blood of cancer patients receiving checkpoint inhibitor therapy.

e14033 Background: Immune checkpoint inhibitors (ICIs) are becoming standard treatment options in many indications. However, a substantial portion of patients will not respond. Single biomarkers such as PD-L1 are insufficiently accurate to predict patient benefit. We sought to expand the Epic Sciences non-invasive liquid biopsy platform to identify predictive, peripheral blood biomarkers for ICIs using both molecular analyses of CTCs and immune cell changes. Methods: Blood samples from prostate, kidney, and bladder cancer patients treated with ICIs were collected at baseline and on-therapy and sent to Epic Sciences. Nucleated cells were plated on glass slides and stained with CTC (pan-CK, CD45, PD-L1 and DAPI) and immune panels for activation (CD4, CD8, Ki-67, and DAPI) and exhaustion (CD8, Ki-67, PD-1, Lag-3, Tim-3, and DAPI). Changes in populations of immune cells and circulating tumor cells were assessed using high throughput digital pathology. Results: CTCs were detected in 73% (24/33) patients, of which 12% (4/33) had PD-L1+ CTCs detected. No PD-L1+ CTCs were detected in the nine on-therapy samples tested. Of 14 patients with matched samples, 57% (8/14) patients had an increase in activated CD4+ leukocytes and 36% (5/14) patients had an increase in activated CD8+ leukocytes in on-therapy samples compared to baseline. The exhaustion assay was performed on a subset (6 of 14) of matched samples. In baseline and on-therapy samples, one patient had higher levels of exhausted CD8+ leukocytes compared to healthy donor controls, and two patients had lower levels versus controls. No change in exhausted CD8+ leukocytes was observed from baseline to on-therapy. Conclusions: We developed a liquid biopsy-based platform that can simultaneously measure biomarkers in CTCs and leukocytes from a single peripheral blood sample. Changes in activated and exhausted immune cell populations with ICI treatment were detected and PD-L1 expression on CTCs was evaluated. Efforts to further stratify immune and rare cell populations are ongoing.

Enrichment and mutation detection of circulating tumor cells from blood samples.

The potential of circulating tumor cells (CTCs) in the diagnosis and prognosis of cancer patients has become increasingly attractive. However, molecular analysis of CTCs is hindered by low sensitivity and a high level of background leukocytes in CTC enrichment technologies. We have developed a novel protocol using a microfluidic device, which enriches and retrieves CTCs from blood samples. The principle of CTC capturing is that tumor cells are larger and less deformable than normal blood cells. To evaluate the potential of utilizing Celsee PREP100 in CTC molecular analysis, we prepared prostate cancer cell lines PC3 and LNCaP, retrieved the captured cells and analyzed them using PCR amplicon sequencing. We were able to recover an average of 79% of 110-1,100 PC3 and 60–1,500 LNCaP cells, and detect the p.K139fs*3 deletion of the p53 gene in PC3 cells and p.T877A mutation of the androgen receptor gene in LNCaP cells. Next, we spiked these two types of cells into normal donor blood samples, captured the cells and analyzed them using PCR amplicon sequencing. The PC3 and LNCaP cells were captured and retrieved with the ratio of captured CTCs to the background leukocytes reaching 1:1.5 for PC3 and 1:2.9 for LNCaP cells. We further revealed that the p.K139fs*3 deletion and p.T877A mutation can be detected in the captured PC3 and LNCaP cells, respectively. We successfully validated this approach using clinical blood samples from patients with metastatic prostate cancer. Our results demonstrated a novel approach for CTC enrichment and illustrated the potential of CTC molecular characterization for diagnosis, prognosis and treatment selection of patients with metastatic malignancy.

Circulating tumor cells in patients with head and neck squamous cell carcinoma: Feasibility of detection and quantitation.

The purpose of this study was to present our findings that because circulating tumor cells (CTCs) exist in extremely low numbers, their detection and quantification are challenging. Peripheral blood samples were collected from 32 patients with head and neck squamous cell carcinoma (HNSCC), and were subjected to the CellSieve Microfiltration Assay using a low-pressure filtration system. The CTCs captured by the filter were stained with an antibody cocktail (anti-cytokeratin (CK) 8, 18, and 19, anti-epithelial cell adhesion molecule (EpCAM), and anti-CD45 antibodies). The CTCs were detected in 29 of 32 patients (90.6%). Although patients with advanced disease had a significantly higher number of CTCs, the clinical N classification was not associated with the CTC count. After treatment, the CTC count showed a significant decrease. The CTCs were successfully detected and quantified in patients with HNSCC by using a low-pressure filtration system equipped with precision microfilters. Further studies using a larger number of patient samples and/or molecular analysis of CTCs are warranted.

Abstract 1717: Orthogonal identification of circulating tumor cells (CTCs) using single cell low pass whole-genome sequencing (WGS) and copy-number alteration (CNA) analysis

Abstract Introduction: Presence of circulating tumor cells has prognostic value in multiple malignancies, and molecular analysis of CTCs is currently ongoing in numerous clinical trials. Most CTC enrichment methods rely on standard epithelial and leukocyte markers (CK+CD45-), so recovered cells are assumed to be of epithelial origin but never shown to be bona fide tumor cells. Conversely, atypical cells lacking the characteristic marker profile may not be analyzed, even though they may represent important tumor subpopulations. Here we evaluate a rapid, non-exhaustive, and cost-effective first-pass genomic analysis of individual candidate CTCs. This approach allows efficient upfront CNA-based confirmation that a given cell is of tumor origin, while leaving abundant DNA for deeper subsequent analysis in cells of interest. Methods: Whole peripheral blood of metastatic prostate cancer patients was enriched for CTCs using the CellSearch® system (Janssen Diagnostics) under an IRB-approved protocol, and 5 samples with &amp;gt;5 CTCs were selected for further study. Next, the DEPArray™ v2 system (Menarini Silicon Biosystems) was used to identify and isolate single CTCs (CK+CD45-DAPI+) and paired white blood cells (WBCs; CK-CD45+DAPI+) from the enriched samples. In addition, cells negative for both cytokeratin and CD45 but with characteristic malignant morphology (large with high nuclear-cytoplasmic ratio) were isolated. Recovered single cells were whole-genome amplified with Ampli1™ WGA and quality controlled by Ampli1 QC. Ampli1 LowPass kit was then used to prepare NGS libraries for absolute CNA profiling by low-pass WGS. Results: Thirty-three single CTCs (CK+CD45-DAPI+) and 30 WBCs (CK-CD45+DAPI+), as well as 47 putative CTCs with non-conventional phenotype (CK-CD45-DAPI+) were isolated. Single-cell WGA products with high Genome-Integrity Index (QC score ≥3) were prioritized for CNA analysis. Ampli1 LowPass data demonstrated copy number gains/losses confirming tumor origin of the CK+ cells, while WBCs showed a normal profile. In addition, a portion of the cells having non-conventional phenotype also demonstrated copy number alterations consistent with tumor origin. Discussion: We demonstrate a WGA and low-pass WGS approach on single CTCs sorted from enriched peripheral blood, which offers a dual benefit: i) it allows rapid, non-exhaustive upfront identification of bona fide tumor cells for further study, and ii) it reveals genetic similarities and diversities (vis a vis copy number alteration) across CTCs of classical as well as non-conventional phenotypes, which may better represent clonal diversity. In a clinical setting, this molecular approach may be more effective for reliably identifying and characterizing heterogeneous CTCs, yielding profiles that more accurately reflect disease evolution and inform treatment strategies. Citation Format: Gareth Morrison, Valeria Sero, Yucheng Xu, Jacek Pinski, Sue Ingles, David Quinn, Claudio Forcato, Genny Buson, Chiu-Ho Webb, Kyle Horvath, Aditi Khurana, Gianni Medoro, Suman Verma, Matthew Moore, Philip Cotter, Nicolò Manaresi, Farideh Bischoff, Amir Goldkorn. Orthogonal identification of circulating tumor cells (CTCs) using single cell low pass whole-genome sequencing (WGS) and copy-number alteration (CNA) analysis [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 1717. doi:10.1158/1538-7445.AM2017-1717

Enumeration, Dielectrophoretic Capture, and Molecular Analysis of Circulating Tumor Cells.

The identification of therapeutically targetable mutations in circulating tumor cells (CTCs) from cancer patient blood is increasingly used to personalize patient care. Here, we describe a novel approach for the enumeration, capture, and molecular analysis of CTCs from blood using an FDA-approved CTC enrichment and enumeration platform followed by dielectrophoretic capture and next-generation sequencing.

Personalized Treatment Through Detection and Monitoring of Genetic Aberrations in Single Circulating Tumor Cells.

Circulating tumor cells (CTCs) present a viable alternative to access tumor materials other than primary biopsies in cancer. This disease is among the most widespread in the world and is difficult to target because of its complex nature, challenges in getting quality samples and dynamic temporal changes in response to treatment. Conventional methods of detection and monitoring the disease profile do not suffice to be able to target the heterogeneity that exists at the cellular level. CTCs have been identified as a possible substitute for tumor tissue samples, and can be used to complement current disease management. Challenges in CTCs molecular analysis lie in the purity of the sample, which is masked by the presence of large quantities of white blood cells (WBCs) . In this chapter, we present a microfluidic biochip platform that performs secondary purification to isolate single CTCs efficiently. Studying single CTCs will allow for sensitive detection of critical mutations and addressing intercellular variances that will be otherwise missed easily due to low mutation frequencies when evaluating bulk cell retrieval. Using the biochip, we isolated single CTCs, and conducted personalized integrated EGFR mutational analysis using conventional polymerase chain reaction (PCR) and Sanger sequencing. We also demonstrated that high quality next generation sequencing (NGS) libraries can be readily generated from these samples. In our initial study, we revealed that the dominant EGFR mutations such as L858R and T790M could be detected in Non Small Cell Lung Cancer (NSCLC) patients with low CTC counts. We envision the biochip will enable efficient isolation of rare single cells from samples. This technology coupled with downstream molecular characterization of CTCs will aid in realizing the personalized medicine for cancer patients.

Abstract 4967: Label-free collection of prostate circulating tumor cells using microfluidic Vortex technology

Abstract BACKGROUND Prostate cancer is among the most common cancers in men worldwide. Better markers than Prostate Specific Antigen (PSA) are still needed for the detection and monitoring of disease progression. Circulating Tumor Cells (CTCs) are shed into the blood stream from primary tumor(s) and may play key roles in the metastatic process. Liquid biopsies have emerged as a promising approach, with a correlation between the CTC numbers and patient prognosis for prostate cancer. CTCs have also been shown to enable early detection of recurrence, and could be potential candidates for guiding cancer therapy in real-time [1]. Current CTC enrichment technologies, including immuno-affinity and size-based filtration methods, have focused on high capture efficiency with sometimes tedious sample preparation and overall low purity. METHOD Here, we describe the use of the microfluidic Vortex Chip [2] for rapid and size-based isolation of CTCs from the blood of 23 patients with advanced prostate cancer, and 10 healthy donors; 5 being &amp;lt;30 years old, 5 age-matched with the patient cohort. Requiring no upstream sample preparation, blood was diluted 10-fold and processed through the highly parallelized Vortex Chip at 8 mL/min (800 μL/min whole blood). Larger cells (predominantly CTCs) were captured in microscale vortices produced on the Chip, released into a small volume and collected off-chip for CK, PSA, CD45 and DAPI immunostaining and enumeration. RESULTS Preliminary work with LNCaP prostate cancer cells spiked in blood showed a 29% capture efficiency and 50% purity. In vitro cell assays confirmed that cells enriched with Vortex chip were alive and proliferating for up to 7 days. For 23 patient samples, CTCs were captured (0.5 - 20 CTCs/mL) with high purity (3.6 - 72.3%), in less than 1H, without prior sample preparation. 11.5% of the cells collected were CK and PSA-negative, but some were identified as undergoing epithelial-mesenchymal transition (EMT) following staining for vimentin and N-cadherin. Few atypical cells were also isolated from age-matched healthy donors (0.7 - 2.8 CTCs/mL), while none was detected in younger healthy donors. Using a threshold calculated from the age-matched healthy donors (3.31 CTCs/mL = mean + 2CV), 70% of the patients were characterized as “positive for CTCs”. No correlation was found between CTC counts and elevated PSA level. CONCLUSION These results demonstrate the ability to rapidly collect pure populations of CTCs in metastatic prostate cancer, independent of surface marker expression, without prior sample preparation. Future studies will use chips with optimized capture performance, sample recycling, and will include CTC molecular analysis by targeted panel sequencing. A larger cohort of healthy donors is also being examined to determine a statistically-robust CTC baseline for this size-based capture approach. [1] Scher Hi, et al., J. Clin. Oncol. 2015 [2] Sollier E, et al., Lab Chip 2014 Citation Format: Edward Pao, Corinne Renier, Clementine Lemaire, James Che, Melissa Matsumoto Di Carlo, Melanie Triboulet, Sandy Srivinas, Stefanie S. Jeffrey, Rajan P. Kulkarni, Matthew Rettig, Elodie Sollier, Dino Di Carlo. Label-free collection of prostate circulating tumor cells using microfluidic Vortex technology. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4967.

PD32-11 GENE EXPRESSION ANALYSIS OF BONE METASTASIS AND CIRCULATING TUMOR CELLS FROM METASTATIC CASTRATE-RESISTANT PROSTATE CANCER PATIENTS

You have accessJournal of UrologyProstate Cancer: Advanced (including Drug Therapy) III1 Apr 2016PD32-11 GENE EXPRESSION ANALYSIS OF BONE METASTASIS AND CIRCULATING TUMOR CELLS FROM METASTATIC CASTRATE-RESISTANT PROSTATE CANCER PATIENTS Won-Jin Cho, Michael Cher, Daniel Oliveira, Abdo Najy, Leandro Mainetti, Elisabeth Heath, Kim Hyeong-Reh, and R. Daniel Bonfil Won-Jin ChoWon-Jin Cho More articles by this author , Michael CherMichael Cher More articles by this author , Daniel OliveiraDaniel Oliveira More articles by this author , Abdo NajyAbdo Najy More articles by this author , Leandro MainettiLeandro Mainetti More articles by this author , Elisabeth HeathElisabeth Heath More articles by this author , Kim Hyeong-RehKim Hyeong-Reh More articles by this author , and R. Daniel BonfilR. Daniel Bonfil More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.02.687AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Characterization of gene expression in bone metastasis is critical to the identification of therapeutic targets and prognostic/predictive biomarkers in metastatic castrate-resistant prostate cancer (mCRPC). Although bone marrow tissue can be obtained for molecular analysis, bone marrow biopsy (BMBx) is relatively invasive. In contrast, circulating tumor cells (CTCs) can be obtained by simple blood draw, and in mCRPC, CTCs likely emanate from bone metastases. Herein, we wished to establish a sensitive method to analyze gene expression in BMBxs and CTCs and to determine whether potential biomarkers present in bone lesions are mirrored in CTCs. METHODS Areas of relatively pure prostate cancer tissue were collected from BMBxs using laser capture microdissection. CTCs were enriched from blood using the CellSearch® platform. RNA from these two sources was amplified linearly using an Eberwine-based procedure to obtain antisense mRNA (aRNA). In this pilot study, the expression of 8 genes was assessed using RT-PCR. In control experiments, the efficiency of CTC isolation and linearity of RNA amplification were determined by comparing relative gene expression levels in non-amplified RNAs from large numbers of cultured PC3 cells and amplified aRNAs from small numbers of PC3 cells spiked in normal blood and recovered using the CellSearch® system. RESULTS RNAs were successfully extracted from as few as 1-5 CTCs in blood samples. The relative expression levels of reference genes were maintained after RNA amplification. The integrity of the amplified RNA was demonstrated by RT-PCR analysis using primer sets that target the 5′-end, middle, and 3′-end of reference mRNAs. Besides epithelial- and prostate-specific genes, Interleukin-6 was the only gene expressed in all CTCs analyzed. In this pilot study, we found partial concordance between gene expression patterns in CTCs and microdissected prostate cancer tissue from bone metastases of the same patients. CONCLUSIONS aRNA amplification through in vitro transcription may serve as a useful method for gene analysis in small numbers of CTCs and tumor cells microdissected from BMBxs. To our knowledge, this is the first comparative study of gene expression in CTCs and BMBxs from individual mCRPC patients. Our exploratory study in this small cohort of patients suggests that molecular analysis of CTCs might reveal gene expression patterns that might be missed by analysis of single BMBx sites. © 2016FiguresReferencesRelatedDetails Volume 195Issue 4SApril 2016Page: e764-e765 Advertisement Copyright & Permissions© 2016MetricsAuthor Information Won-Jin Cho More articles by this author Michael Cher More articles by this author Daniel Oliveira More articles by this author Abdo Najy More articles by this author Leandro Mainetti More articles by this author Elisabeth Heath More articles by this author Kim Hyeong-Reh More articles by this author R. Daniel Bonfil More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Circulating tumor cells in breast cancer beyond the genotype of primary tumor for tailored therapy.

Although TNM staging based on tumor, node lymph status and metastasis status-is the most widely used method in the clinic to classify breast cancer (BC) and assess prognosis, it offers limited information for different BC subgroups. Circulating tumor cells (CTCs) are regarded as minimal residual disease and are proven to have a strong relationship with BC. Detection of ≥5 CTCs per 7.5 mL in peripheral blood predicts poor prognosis in metastatic BC irrespective of other clinical parameters, whereas, in early-stage BC, detection of CK19(+) CTCs are also associated with poor prognosis. Increasing data and clinical trials show that CTCs can improve prognostic accuracy and help tailor treatment for patients with BC. However, heterogeneous CTCs in the process of an epithelial-mesenchymal transition (EMT) in BC makes it a challenge to detect these rare cells. Moreover, the genotypic and phenotypic features of CTCs are different from primary BC tumors. Molecular analysis of CTCs in BC may benefit patients by identifying those amenable to tailored therapy. We propose that CTCs should be used alongside the TNM staging system and the genotype of primary tumor to guide tailored BC diagnosis and treatment.

Whole Genome Amplification in Genomic Analysis of Single Circulating Tumor Cells.

Investigation of the genome of organisms is one of the major basics in molecular biology to understand the complex organization of cells. While genomic DNA can easily be isolated from tissues or cell cultures of plant, animal or human origin, DNA extraction from single cells is still challenging. Here, we describe three techniques for the amplification of genomic DNA of fixed single circulating tumor cells (CTC) isolated from blood of cancer patients. This amplification is aimed to increase DNA amounts from those of one cell to yields sufficient for different DNA analyses such as mutational analysis including next-generation sequencing, array-comparative genome hybridization (CGH), and quantitative measurement of gene amplifications. Molecular analysis of CTC as liquid biopsy can be used to identify therapeutic targets in personalized medicine directed, e.g. against human epidermal growth factor receptor 2 (HER2) or epidermal growth factor receptor (EGFR) and to stratify the patients to those therapies.

Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer.

Small-cell lung cancer (SCLC), an aggressive neuroendocrine tumor with early dissemination and dismal prognosis, accounts for 15-20% of lung cancer cases and ∼200,000 deaths each year. Most cases are inoperable, and biopsies to investigate SCLC biology are rarely obtainable. Circulating tumor cells (CTCs), which are prevalent in SCLC, present a readily accessible 'liquid biopsy'. Here we show that CTCs from patients with either chemosensitive or chemorefractory SCLC are tumorigenic in immune-compromised mice, and the resultant CTC-derived explants (CDXs) mirror the donor patient's response to platinum and etoposide chemotherapy. Genomic analysis of isolated CTCs revealed considerable similarity to the corresponding CDX. Most marked differences were observed between CDXs from patients with different clinical outcomes. These data demonstrate that CTC molecular analysis via serial blood sampling could facilitate delivery of personalized medicine for SCLC. CDXs are readily passaged, and these unique mouse models provide tractable systems for therapy testing and understanding drug resistance mechanisms.