Isolation Of Circulating Tumor Cells Research Articles

Abstract PO4-13-08: Mechanical conditioning (MeCo) score is higher in circulating tumor cells (CTCs) compared to primary tumors in early-stage breast cancer and even higher in metastases compared to CTCs in metastatic breast cancer

Abstract Background: The mechanical conditioning (MeCo) score is a gene expression signature that is acquired early by cancer cells in the primary breast tumor and is reflective of their responsiveness to matrix stiffness (fibrotic-like matrix rigidity). Further, chromatin remodeling in response to stiffness allows cancer cells to retain their aggressive features even in the absence of mechanical stimulation by the primary tumor microenvironment, for instance, during their dissemination through the circulation in metastasis. Importantly, patients who have high MeCo score tumors are at higher risk of developing metastatic breast cancer, compared to low MeCo scores (p< 0.0001; HR=2.2, 95%CI 1.7-2.7; Watson et al 2021, PMID: 34192535). Moreover, circulating tumor cells (CTCs) are associated with higher rate of metastatic dissemination, making CTC detection in the circulation of breast cancer patients a significant prognostic biomarker for breast cancer metastasis. Beyond their enumeration per blood volume units, specific prognostic features of CTCs are not fully explored. We sought to determine whether, compared to primary tumors, CTCs retain high MeCo scores and whether these scores are maintained during late-stage breast cancer in the metastatic sites. Methods: CTCs were isolated from peripheral blood of two patient cohorts: stage II-III breast cancer patients using immunomagnetic enrichment/FACS methodology (Lang et al 2018, PMID: 29868978) and of metastatic breast cancer patients using ANGLE Parsortix microfluidics system (Ring et al 2022, PMID: 35000083). Gene expression profiling using RNA-seq was performed in CTCs and in matching primary tumors (PT) and metastases (MET) for the early-stage and late-stage cohorts, respectively. A quantile normalization approach was used to allow comparison across cohorts. MeCo scores were computed for all samples as per Watson et al 2021. Wilcoxon matched-pairs signed rank test was performed for comparison of MeCo scores from matching samples within each cohort; Mann-Whitney unpaired test was used to compared MeCo scores of CTCs across cohorts. Results: In 12 pairs of early-stage breast cancer patient CTCs and PT, MeCo scores of CTCs were significantly higher than their matched PTs (p=0.026). Furthermore, in 26 pairs of metastatic patient’s CTCs and MET, MeCo scores of METs were significantly higher than matching CTCs (p=0.0004). MeCo scores of CTCs were similar between early- and late-stage breast cancer despite differing CTC isolation strategies (epitope-dependent and microfluidics size gradient). 98% of genes in the MeCo score were present in the evaluable CTC, MET and PT samples. Conclusions: Our results show that the MeCo score is higher in CTCs compared to PTs and in METs compared to CTCs in early- and late-stage breast cancer, respectively. Therefore, the MeCo score is progressively higher throughout the metastatic cascade in breast cancer. These findings demonstrate that mechanical conditioning is retained during metastatic progression, even as cancer cells transition through the circulation where the initial induction by matrix stiffness is lost. Further, these findings support that cancer cells with higher MeCo scores are more competent with–and potentially selected for by–metastatic progression. Importantly, these findings provide a novel feature of CTCs, mechanical conditioning (MeCo), which is associated with higher capacity for metastasis. Further, since the CTC MeCo score is elevated even in early-stage breast cancer, it could provide, in addition to CTC enumeration, a potential prognostic tool to predict metastatic risk in breast cancer patients. Citation Format: Gus Mouneimne, Adam Watson, Adam Grant, Daniel Campo, Alexander Ring, Pushpinder Bains, Julie Lang. Mechanical conditioning (MeCo) score is higher in circulating tumor cells (CTCs) compared to primary tumors in early-stage breast cancer and even higher in metastases compared to CTCs in metastatic breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-13-08.

Research progress of cell membrane biomimetic nanoparticles for circulating tumor cells

Early detection of cancer is crucial to reducing fatalities and improving patient outcomes. Metastasis is the first stage of aggressive cancers, often occurring before primary lesions can be seen. It occurs when cancerous cells disseminate to distant, non-malignant organs through the bloodstream, known as circulating tumor cells (CTCs). CTCs, or cancer tumor cells, are valuable indicators for predicting treatment response, metastasis progression, and disease progression. However, they are primarily used for research due to challenges like heterogeneity, separation from blood, and lack of clinical validation. Only a few methods have been approved for clinical use. One area of research is the isolation and identification of CTCs, which could significantly impact early cancer detection and prognosis. Current technologies using whole-blood samples use size, immunoaffinity, and density approaches, along with positive and negative enrichment techniques. Surface modification of nanomaterials is important for effective cancer therapies because it improves their ability to target and reduces interactions with healthy tissues. Consequently, researchers have created biomimetic nanoparticles covered with cell membranes using functional, targeted, and biocompatible coating technology. Nanoparticles with membranes can target specific cells, stay in circulation for longer, and avoid immune responses, which makes them much better at capturing CTCs. This study examines the current opportunities and difficulties associated with using cell membrane–coated nanoparticles as a capture technique for CTCs. In addition, we examine potential future developments in light of the current obstacles and investigate areas that require further research to fully understand its growing clinical possibilities.

Microfluidic-SERS Technologies for CTC: A Perspective on Clinical Translation.

Enumeration and phenotypic profiling of circulating tumor cells (CTCs) provide critical information for clinical diagnosis and treatment monitoring in cancer. To achieve this goal, an integrated system is needed to efficiently isolate CTCs from patient samples and sensitively evaluate their phenotypes. Such integration would comprise a high-throughput single-cell processing unit for the isolation and manipulation of CTCs and a sensitive and multiplexed quantitation unit to detect clinically relevant signals from these cells. Surface-enhanced Raman scattering (SERS) has been used as an analytical method for molecular profiling and in vitro cancer diagnosis. More recently, its multiplexing capability and power to create distinct molecular signatures against their targets have garnered attention. Here, we share our insights into the combined power of microfluidics and SERS in realizing CTC isolation, enumeration, and detection from a clinical translation perspective. We highlight the key operational factors in CTC microfluidic processing and SERS detection from patient samples. We further discuss microfluidic-SERS integration and its clinical utility as a paradigm shift in clinical CTC-based cancer diagnosis and prognostication. Finally, we summarize the challenges and attempt to look forward to what lies ahead of us in potentially translating the technique into real clinical applications.

Detecting androgen receptor (AR), AR variant 7 (AR-V7), prostate-specific membrane antigen (PSMA), and prostate-specific antigen (PSA) gene expression in CTCs and plasma exosome-derived cfRNA in patients with metastatic castration-resistant prostate cancer (mCRPC) by integrating the VTX-1 CTC isolation system with the QIAGEN AdnaTest

BackgroundTherapies for metastatic castration-resistant prostate cancer (mCRPC) include targeting the androgen receptor (AR) with androgen receptor inhibitors (ARIs) and prostate-specific membrane antigen (PSMA). Having the ability to detect AR, AR splice variant 7 (AR-V7), or PSMA in circulating tumor cells (CTCs) or circulating exosomal cell-free RNA (cfRNA) could be helpful to guide selection of the appropriate therapy for each individual patient. The Vortex Biosciences VTX-1 system is a label-free CTC isolation system that enables the detection of the expression of multiple genes in both CTCs and exosomal cfRNA from the same blood sample in patients with mCRPC. Detection of both AR-V7 and PSMA gene expression in both CTCs and cfRNA simultaneously has not yet been reported.MethodsTo characterize the combined VTX-1-AdnaDetect workflow, 22Rv1 cancer cells were spiked into blood from healthy donors and processed with the VTX-1 to mimic patient samples and assess performances (capture efficiency, purity, AR and AR-V7 expression). Then, we collected 19 blood samples from 16 patients with mCRPC and therapeutic resistance to androgen receptor inhibitors (ARIs). Plasma was separated and the plasma-depleted blood was processed further with the VTX-1 to collect CTCs. Both plasma exosomal cfRNA and CTCs were subsequently analyzed for AR, AR-V7, PSMA, and prostate-specific antigen (PSA) mRNA expression using the AdnaTest ProstateCancerPanel AR-V7 assay.ResultsAR-V7 expression could be detected in 22Rv1 cells spiked into blood from healthy volunteers as well as in CTCs and plasma-derived exosomal cfRNA from patients with mCRPC by processing blood with the VTX-1 CTC isolation system followed by the AdnaTest ProstateCancerPanel AR-V7 assay. 94.7% of patient blood samples (18/19) had detectable AR expression in either CTCs or exosomal cfRNA (16 in CTCs, 12 in cfRNA). 15.8% of the 19 patient blood samples (3/19) were found to have AR-V7-positive (AR-V7+) CTCs, one of which was also AR-V7+ in the exosomal cfRNA analysis. 42.1% of patient blood samples (8/19) were found to be PSMA positive (PSMA+): 26.3% (5/19) were PSMA+ in the CTC analysis and 31.6% (6/19) were PSMA+ in the exosomal cfRNA analysis. Of those 8 PSMA+ samples, 2 had detectable PSMA only in CTCs, and 3 had detectable PSMA only in exosomal cfRNA.ConclusionVTX-1 enables isolation of CTCs and plasma exosomes from a single blood draw and can be used for detecting AR-V7 and PSMA mRNA in both CTCs and cfRNA in patients with mCRPC and resistance to ARIs. This technology facilitates combining RNA measurements in CTCs and exosomal cfRNA for future studies to develop potentially clinically relevant cancer biomarker detection in blood.

Trajectory analysis of circulating tumor cells through contorted deterministic lateral displacement array for unruptured trapping: a simulation study

During the multistage process of cancer spread, fragments of cells branch out from the primitive tumor tissue and scatter throughout the body by blood flow stream or lymph, which are termed as circulating tumor cells (CTCs), regarded as an important biomarker for early cancer diagnosis. Deterministic lateral displacement (DLD) is one of the most efficient passive type particle isolation techniques which functions on asymmetrical laminar flow diversion around the placed microposts forming an array, based on the critical dimeter of the device. In this simulation study, complete trajectory analysis of CTCs and WBCs has been performed using COMSOL Multiphysics software with respect to the angular orientation of sample inlet channel. A simulated model of an asymmetric DLD array-based microfluidic device with latest empirical expression for critical diameter has been presented with optimized sample inlet orientation so as to maintain perfect separation efficiency of CTCs along with arrangement for unruptured trapping of CTCs and WBCs. The approximate CTC isolation efficiency was obtained above 95% for sample inlet inclinations up to 0.5°, and further tilt showed reduction in efficiency. Migration angle of CTC trajectory for the modeled device was obtained around 15° for both the sample inlet orientations leading to least intermingling of CTCs and WBCs. A smaller number of CTC–WBC interaction points was observed for clockwise sample inlet tilt compared to the anticlockwise displacement reducing possibilities of cell rupture. The shear rate around central microposts was found to be higher as well in clockwise sample inlet orientation. This simulation study establishes that sample inlet clockwise tilting of maximum around 0.5°–0.7° leads to better CTC isolation and provides better chances of unruptured trapping of cells at the designated outlets. The results of this study provide an approach toward further optimization of DLD devices' functioning and, thus, could help fabricate better DLD-based microfluidic devices for efficient trapping of CTCs.

Orthotopic model for the analysis of melanoma circulating tumor cells

Metastatic melanoma, a highly lethal form of skin cancer, presents significant clinical challenges due to limited therapeutic options and high metastatic capacity. Recent studies have demonstrated that cancer dissemination can occur earlier, before the diagnosis of the primary tumor. The progress in understanding the kinetics of cancer dissemination is limited by the lack of animal models that accurately mimic disease progression. We have established a xenograft model of human melanoma that spontaneously metastasizes to lymph nodes and lungs. This model allows precise monitoring of melanoma progression and is suitable for the quantitative and qualitative analysis of circulating tumor cells (CTCs). We have validated a flow cytometry-based protocol for CTCs enumeration and isolation. We could demonstrate that (i) CTCs were detectable in the bloodstream from the fourth week after tumor initiation, coinciding with the lymph node metastases appearance, (ii) excision of the primary tumor accelerated the formation of metastases in lymph nodes and lungs as early as one-week post-surgery, accompanied by the increased numbers of CTCs, and (iii) CTCs change their surface protein signature. In summary, we present a model of human melanoma that can be effectively utilized for future drug efficacy studies.

The Role of Circulating Tumor Cells as a Liquid Biopsy for Cancer: Advances, Biology, Technical Challenges, and Clinical Relevance.

Cancer remains a leading cause of mortality worldwide, with metastasis significantly contributing to its lethality. The metastatic spread of tumor cells, primarily through the bloodstream, underscores the importance of circulating tumor cells (CTCs) in oncological research. As a critical component of liquid biopsies, CTCs offer a non-invasive and dynamic window into tumor biology, providing invaluable insights into cancer dissemination, disease progression, and response to treatment. This review article delves into the recent advancements in CTC research, highlighting their emerging role as a biomarker in various cancer types. We explore the latest technologies and methods for CTC isolation and detection, alongside novel approaches to characterizing their biology through genomics, transcriptomics, proteomics, and epigenetic profiling. Additionally, we examine the clinical implementation of these findings, assessing how CTCs are transforming the landscape of cancer diagnosis, prognosis, and management. By offering a comprehensive overview of current developments and potential future directions, this review underscores the significance of CTCs in enhancing our understanding of cancer and in shaping personalized therapeutic strategies, particularly for patients with metastatic disease.

Abstract 3711: Procedure establishment of EGFR mutation test with circulating tumor cells of lung cancer by in vitro assay

Abstract Introduction: Non-small cell lung cancer (NSCLC) is the most common subtype, accounting for approximately 80% of lung cancer. The treatment for NSCLC has significantly improved since the introduction of targeted therapies. Epidermal growth factor receptor (EGFR) mutations are the most frequently found genetic alterations in NSCLC, and deletion of exon 19 is a representative example. Searching for this mutation may provide important clues to the use of EGFR tyrosine kinase inhibitors in NSCLC. So, the detection of EGFR mutation is important step in cancer diagnosis and determining the drug treatment strategy, but the detection of mutation with tissues has limitations such as clinical challenge to poorly accessible tumor tissues before and after treatment. The aim of this study was to explore the feasibility and utility of implementation of EGFR molecular testing from circulating tumor cells (CTC) in NSCLC. Here, we developed and optimized the procedure of mutated EGFR detection in CTC after isolation with CytoGen’s Smart BiopsyTM CTC isolator by cobas® EGFR Mutation Test. This EGFR mutation test in CTC showed the potential to overcome the limitations of tissue biopsy with high sensitivity and specificity in an in vitro assay. Method: PC-9 cells were used the positive control of EGFR mutation (EGFR exon 19 deletion). Limit of detection (LOD) was performed with PC-9 cells (200 cells to 5 cells, 6 points) spiked into blood sample (5mL, healthy donor) to mimic CTC in the blood of lung cancer patient. CTC were isolated from spiked samples using CytoGen’s Smart BiopsyTM CTC isolator, subsequently cobas® EGFR Mutation Test was carried out to detect of EGFR mutation. Results: In in vitro experiments of recovery test using cell lines spiked into blood from healthy donor, the recovery rate of CytoGen’s Smart Biopsy TM CTC isolator showed over 80%. As a result of LOD test, EGFR exon19 deletion mutation of PC-9 cells was clearly detected even in the smallest number of cells were spiked into blood (5 cells in 5mL blood) and was not detected at all in the negative controls. The result suggested that CytoGen’s Smart Biopsy TM CTC isolator can isolate CTC with high recovery rate and apply the test of oncogenic mutations including EGFR mutation in CTC. Conclusions: Confirmation of EGFR mutation is important step in the diagnosis and selection of optimal drug for cancer patients. However, tissue biopsy has several limitations such as difficulties to get tissue samples and inaccurate information due to invasive method and tumor heterogeneity. Detection of EGFR mutation in CTC might overcome and make up for limitations of tissue biopsy. In this study, we optimized the EGFR mutation detection procedure of intact live CTC isolated by CytoGen’s Smart BiopsyTM CTC isolator. Citation Format: Jihyun Lee, Hoin Kang, Min Hyung Kim, Jubi Lee, Hyoyong Kim, Soee Kim, Hae Ung Lee, Hai-Chon Lee, Jung Won Kim. Procedure establishment of EGFR mutation test with circulating tumor cells of lung cancer by in vitro assay [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 3711.

Abstract 3689: Optimizing CTC isolation techniques for molecular characterization of circulating tumor cells in clear cell renal cell carcinoma: A comparative study of EpCAM-based and density-based methods

Abstract Introduction: Renal cell carcinoma (RCC) belongs to the most invasive cancers with the high molecular intrapatient heterogeneity. Circulating tumor cells (CTCs) are cells that detach from the tumor, reflecting the activity of the metastatic procedure. The most popular CTCs isolation methods are based on EpCAM signal detection on epithelial tumor cells. The clear cell RCC (ccRCC) originate from epithelial entity, since that is the EpCAM-based method suitable to isolate CTCs in this cancer. However, the prone of CTCs to EMT is known, which may in consequence downregulate the EpCAM expression and change the cell profile (hybrid phenotype). This is one of the points challenging the CTCs isolation by RCC disease. In our study, we compare the effectivity of antibody-based and density-based isolations technics in ccRCC patients to detect potential markers in CTCs. Purpose: Our aim was to find a precise and costs effective method to isolate and characterize CTCs from ccRCC patients. Materials and Methods: Prospective blood samples (3mL) from pulmonary and/or osseous metastatic ccRCC patients were collected during the immunotherapy and from the healthy donors. CTCs were isolated using EpCAM beads (RCC n=13; healthy n=15) or density-based (RCC n=13; healthy n=15) method. Expression of potential RCC biomarkers (mucin-1 (Muc1), androgen receptor (AR)) was identified using qPCR (Real-Time PCR) followed by dPCR (digital PCR), the results status received from both methods was evaluated. Summary: Based on our prior results, we first isolated CTCs based on EpCAM beads. Using qPCR we analyzed expression of genes, which we previously associated to the RCC (Muc1, PD-L1, AR). The results revealed differences in Muc1 (40% of tested patients positive but none of the healthy donors), when PD-L1 did not differed and AR was not detected. Applying more precise dPCR did neither show any expression. We continued our investigations with isolation of CTCs using density-based method. We confirmed more frequent expression of Muc1 by RCC Patients than by donors, as in our EpCAM cohort. PD-L1 was similar in both groups. Results of AR obtained using qPCR were confusing, showing deviations within same patients. The use of dPCR displayed significant differences in expression between RCC patients (77%; median [range] 0.28 [0.00 - 0.62] and donors (60%; 0.04 [0.00 - 0.51] confirming dPCR as optimal tool for molecular CTC characterization. Conclusions: Based on our results we demonstrate higher expression of Muc1 and AR in CTCs of metastatic ccRCC patients. The isolation technic should be adapted to the disease status and treatment choice. Further investigations confirming Muc1 and AR as ccRCC biomarkers are required. Citation Format: Joanna Bialek, Anne Muthe, Stefan Yankulov, Felix Kawan, Georgios Gakis, Gerit Theil. Optimizing CTC isolation techniques for molecular characterization of circulating tumor cells in clear cell renal cell carcinoma: A comparative study of EpCAM-based and density-based methods [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 3689.

Abstract 7505: Detection validation of androgen-receptor splice variant 7 in circulating tumor cells of prostate cancer by double-check assays

Abstract Introduction: Androgen-receptor splice variant 7 (AR-V7) is constitutively activated isoform of AR and has been associated with resistance towards AR targeting therapies and development into mCRPC. Confirmation of AR-V7 expression is important step in prostate cancer diagnosis and determining the drug, but the detection of AR-V7 with tissues has limitations such as clinical challenge to poorly accessible tumor tissues before and after treatment. Here, we developed the method of AR-V7 detection in circulating tumor cells (CTC) after isolation with CytoGen’s Smart BiopsyTM CTC isolator by in vitro assays of qPCR and immunofluorescence (IF) with high sensitivity and specificity, overcoming the limitations of tissue biopsy. Method: qPCR and IF methods were developed for high sensitivity and specificity of AR-V7 detection. Sensitivity and specificity were tested using AR-V7 positive cells (VCaP and 22Rv1) and negative cells (PC-3 and Raji). Limit of detection (LOD) test of AR-V7 expression was performed with AR-V7 positive cells (200 cells to 50 cells, 3 points) mixed with Raji cells (1 × 10^5cells). Then, AR-V7 positive cells (200 cells to 50 cells, 3 points) were spiked into peripheral blood mononuclear cells (PBMC) of blood sample (5mL, healthy donor) to mimic CTC after isolation by CytoGen’s Smart BiopsyTM CTC isolator, subsequently AR-V7 expression was tested with qPCR and IF assay. Results: AR-V7 expression was clearly detected by qPCR and IF in the LOD test of AR-V7 positive cells mixed with Raji cells and was not detected at all in the negative controls. The similar clear results were also observed in the spiking test of AR-V7 positive cells into PBMC isolated by CytoGen’s Smart BiopsyTM CTC isolator, suggesting that clinical samples of prostate cancer could be applied with excellent sensitivity and specificity for AR-V7. Conclusions: AR-V7 expresses only a part of cancer tissue, so it is difficult to accurately diagnose with traditional histological assays. Detection of AR-V7 in intact live CTC isolated by CytoGen’s Smart BiopsyTM CTC isolator might overcome limitations of tissue biopsy. In this study, we developed the method to detect AR-V7 in CTC with high sensitivity and specificity with qPCR and IF assay, and presented the results of verifying AR-V7 expression by double check using two kinds of assays. We plan to conduct clinical validation of the developed method through additional study using patient samples. Citation Format: Hoin Kang, Jihyun Lee, Min Hyung Kim, Soee Kim, Hyoyong Kim, Jubi Lee, Hae Ung Lee, Hai-Chon Lee, Jung Won Kim. Detection validation of androgen-receptor splice variant 7 in circulating tumor cells of prostate cancer by double-check assays [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 7505.

Abstract 3750: Dual isolation and profiling of circulating tumor cells and circulating tumor DNA from a single liquid sample using the Genesis Cell Isolation System and Droplet Digital PCR

Abstract Introduction: Recent advances in technology support the use of liquid biopsy as a noninvasive method for cancer monitoring and diagnosis. Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) are both regarded as key liquid biopsy biomarkers, offering significant disease-related molecular insights. Despite their potential, dual isolation and profiling have been challenged in a clinical setting by the lack of established platforms and optimized protocols that support this approach. The Genesis System with Celselect SlidesTM captures CTCs based on size and deformability, then the enriched cells can be recovered for subsequent downstream analysis. Concurrently, Droplet Digital PCR (ddPCRTM) can be utilized to interrogate cell-free DNA (cfDNA) to determine the presence of a range of DNA aberrations present in ctDNA. This study, using a model lung CTC-ctDNA sample, illustrates the feasibility of this dual-biomarker approach to detect cancer-associated nucleic acid mutations simultaneously with CTC enumeration, using commercially available kits and instruments. Methods: To model lung cancer samples, blood samples were prepared by spiking in two model circulating markers, cultured cancer cells (model CTCs, human ㅣlung cancer cell line A549) and fragmented genomic DNA containing EGFR mutations (model ctDNA, multiplexed 23 ctDNA [~145 bp band > 95%]), into whole blood from a healthy donor prior to enrichment/extraction. Plasma isolation from the whole blood model samples was performed using either two-step centrifugation or Ficoll-Paque PLUS solution for plasma/buffy coat separation. The extracted plasma layer was used for ctDNA separation, while the remaining cell layer was used for CTC isolation on the Genesis System with a modified protocol. Results: The Genesis System isolated 78-79% of spiked cancer cells in whole blood at a concentration of 40 cells/ml. Despite additional plasma separation steps and liquid handling, the system isolated CTCs spiked in with minimal cell loss (<6%). With an optimized ctDNA extraction, more than 70% of spiked ctDNA in blood samples in the size range of 120-220 bp was extracted. Using the Bio-Rad QX200 ddPCR System and ddPCR EGFR T790M Mutation Detection Assay, blood samples with the model ctDNA spiked in showed positive droplets (17 copies) for EGFR T790M while control blood samples without model ctDNA spiked in showed no positive droplets. Discussion and Conclusions: This work illustrates an optimized protocol for the dual isolation and profiling of CTCs and ctDNA from a single blood sample by using an automated CTC isolation platform and high-sensitivity ddPCR based ctDNA mutation detection. This protocol enables comprehensive liquid biopsy studies using a single blood sample from cancer patients with readily available instruments and kits, which can be applied to many other cancers. Citation Format: Yoon-Tae Kang, Abiodun Bodunrin, Errile Pusod, Kris Simonyi, Adam Corner, David Coe, Michelle Racey, Elizabeth J. Dreskin. Dual isolation and profiling of circulating tumor cells and circulating tumor DNA from a single liquid sample using the Genesis Cell Isolation System and Droplet Digital PCR [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 3750.

Abstract 7495: Validation of microfluidic isolation of circulating pancreatic tumor cells from blood

Abstract Background. Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis and is the fourth leading cause of cancer-related deaths in the US. PDAC is diagnosed in the late stages, which limits treatment options and yields poor clinical outcomes. Recurrence is a significant issue for patients undergoing surgery for PDAC. Circulating tumor cells (CTCs) are thought to be a potential mediator of recurrence, facilitating the formation of secondary tumor sites after surgery. Thus, there is a need to isolate CTCs to improve understanding of disease recurrence, to ultimately improve outcomes. Herein, we aim to validate our inertial microfluidic (iMF) system for isolating pancreatic CTCs from blood. We also benchmark our iMF system to a commercially available immunomagnetic negative selection system, EasySep™, and quantify target cell recovery and cell enrichment. Methods. Our iMF system employs the differential cell sizes of CTCs from blood cells and inertial migration of such cells in a straight microchannel (150 µm × 50 µm × 24 mm) to enrich CTCs from blood. The iMF system sample flow rate used is 100 µL/min, with a 200 µL/min PBS buffer flow rate. The EasySep™ Direct Human CTC Enrichment kit targets CD2, CD14, CD16, CD19, CD45, CD61, CD66b, and Glycophorin to remove blood cells from the sample using magnetic particles, thereby separating them from CTCs. We spiked low cell concentrations of 50, 100, and 500 Hoechst-stained pancreatic carcinoma cells, PANC1, in 1 mL of healthy blood then captured using either EasySep™ or iMF. Cell enumeration was performed after centrifugation or Cytospin. Results. PANC1 cells and WBCs have average sizes of 18 µm and 8.4 µm, respectively. We characterized our iMF device to capture cells ≥ 12 µm, which yields capture of most PANC1 cells. Indeed, our iMF system achieved 82.8±19.2%, 72.5±16.3%, and 59.3±3.8% recovery for 50, 100, and 500 cell-spikes in lysed blood, respectively. For the same 50, 100, and 500 cell-spikes, the total iMF CTC yields after Cytospin were 46.3±11.8, 44.3±9.1, and 32.7±2.1%, while the total CTC yields from EasySep™ were 4.6±3, 5.3±2.1, 8.3±1%, respectively. When we processed whole blood directly, EasySep™ had lower cell recovery, 3.8±0.2, 4.6±1, and 3.3±0.4%, respectively. Our system also demonstrated 8 × higher target cell enrichment compared to EasySep™. Blood lysis before iMF separation did not drastically affect the recovery of target cells. Conclusions. We determined that our system has improved performance over the commercial isolation system, EasySep™, thereby validating the effectiveness of microfluidic isolation for PDAC. In future studies, we can then use our iMF system in CTC isolation from routine blood draws from PDAC patients undergoing surgical resection. We may then isolate real patient samples and study relevant phenotypes of PDAC CTCs which may therefore be used for identifying certain mechanisms of PDAC progression. Citation Format: Celine Macaraniag, Ifra Khan, Jian Zhou, Pier Cristoforo Giulianotti, Alain Borgeat, Gina Votta-Velis, Ian Papautsky. Validation of microfluidic isolation of circulating pancreatic tumor cells from blood [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 7495.

Abstract 5166: A multiplexed immunofluorescence assay to assess Rb and phospho-Rb as predictive biomarkers for CDK4/6 inhibitors in HR+/HER2- breast cancer

Abstract Introduction: Cyclin-dependent kinases 4/6 inhibitors (CDK4/6i) are used as the first-line treatment of advanced/metastatic or high-risk HR+/HER2- breast cancer (BC) that make up about 60-70% of all cases. However, nearly 50% of patients exhibit drug resistance. Therefore, biomarkers that predict CDK4/6i response are needed to spare patients from toxicities and high costs. Resistance to CDK4/6i [palbociclib, ribociclib, and abemaciclib] is associated with the aberrant or loss of Retinoblastoma (Rb). A decline in phospho-Rb (pRb) levels on therapy is also associated with CDK4/6i response. We aimed to develop a multiplex immunofluorescence (IF) assay to assess Rb and pRb levels that can be used on circulating tumor cells (CTCs) to predict tumor response to CDK4/6i. Here, we report the selection of internal controls for Rb and pRb, assay repeatability and reproducibility, as well as compatibility of the CTC isolation protocol with the assay. Methods: Rb and pRb expression was evaluated by western blotting (WB) and IF in parental (P), estrogen deprivation-resistant (EDR), palbociclib-resistant (PalboR), and EDR/PalboR derivatives of two HR+/HER2- cell lines (MCF7 and T47D), Rb1 KO cells of MCF7 and T47D, as well as triple-negative cell lines, BT549 and MDA-MB-468. IF-stained cells were imaged using Leica STED SP8 confocal microscope and Zeiss Axioscan 7. The concordance between IF and WB results was assessed using a Bland-Altman plot. Selectivity and specificity of the assay as well as repeatability and reproducibility between investigators were also assessed. Blood from healthy subjects was used to test the compatibility of the ScreenCell® filtration system to isolate CTC with the IF assay. Results: Our initial approach utilized indirect IF staining for Rb and pRb using the same primary antibodies as WB. On the Bland-Altman plot, most data points were relatively close to the bias line, suggesting that the difference between the two methods was acceptable. The analytical range for mean Rb and pRb staining intensity was 0.744 - 46.779 and 1.001 - 52.919, respectively. Based on WB and IF data, we nominated T47D PalboR and MDA-MB-468 cells as negative controls for Rb and pRb expression. The selectivity and specificity were 100% and 70%, respectively, for the Rb expression and 99% and 61% for pRb, respectively. The IF assay was repeatable and reproducible between two investigators. The ScreenCell® CTC isolation method was not compatible with the assay, as Rb and pRb expression was either not detected or limited when processed using FC2 or PBTFC buffer, irrespective of the antigen retrieval. Conclusion: We have selected internal cell line controls for Rb and pRb and are in the process of optimizing signal-to-noise ratio and specificity using conjugated antibodies. We are also testing the compatibility of other CTC isolation methods with the IF assay. Citation Format: Mantasha Tabassum, Shivaani Suresh Kanna, Wangjia Cao, Mothaffar Rimawi, George E Miles, Meghana V Trivedi. A multiplexed immunofluorescence assay to assess Rb and phospho-Rb as predictive biomarkers for CDK4/6 inhibitors in HR+/HER2- breast cancer [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 5166.

A Detachable Magnetic Nanodevice for the Efficient Capture and Subtype Identification of Circulating Tumor Cells

AbstractThe effective capture and accurate identification of heterogeneous circulating tumor cells (CTCs) aid in guiding clinical diagnosis and personalized treatment of tumors. Herein, a core‐satellite‐sized magnetic separable nanodevice (denoted as MS‐RI) is developed for the capture and subtype identification of heterogeneous CTCs by identifying the protein targets of CTCs in vitro and imaging intracellular nucleic acid targets of CTCs in situ. Upon the separation of CTCs by MS‐RI using aptamers as capture elements, the programmatically dissociated satellite particles aim to internalize into the cells for simultaneous profiling of microRNA‐21 and microRNA‐141. By virtue of the validated magnetic separation of the core structure, the high affinity of the aptamer, and the high sensitivity of the recognition imaging (RI) module, MS‐RI allows the isolation and subtyping of CTCs in clinical samples from breast cancer patients. This strategy of combining extracellular recognition and intracellular imaging pioneers a new paradigm for the capture and precision subtyping of heterogeneous CTCs.

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.

Abstract 3692: Genomic profiling with the novel single-cell IMPACT assay reveals evidence of genetic heterogeneity among CTCs in late-stage breast cancer patients

Abstract Introduction: Liquid biopsy enables minimally invasive molecular profiling of systemic cancer for diagnosis, therapy selection and longitudinal monitoring of minimal residual disease. Cell-based liquid biopsy methods are particularly well suited to examine the extent of genetic heterogeneity and clonal diversity among metastatic cancer cells, which are believed to be the major determinants of therapeutic failure. However, isolation and molecular profiling of circulating tumor cells (CTCs) from body fluids is challenging due to methodological constrains. Methods: To overcome these challenges, we have developed a workflow for detection, isolation, and mutational profiling of CTCs. The workflow utilizes the FDA-approved CellSearch System® and a novel method for single-cell Integrated Mutation Profiling of Actionable Cancer Targets (scIMPACT). Our workflow was optimized for reliable detection of copy number variations (CNVs) and single nucleotide variations (SNVs) in single CTCs. The method was then applied to 31 CTCs alongside with 15 matched germline samples. Results: After implementation of a customized Bayesian neural network based algorithm, accounting for biases introduced during amplification of single-cell DNA and prioritizing the detected mutations, we achieved a sensitivity of 91% and a specificity of 96%, AUC = 0.98. The CTC analysis revealed presence of CNVs affecting known oncogenes and tumor suppressor genes (including MYC, CCND1, FGF4, TP53 and RB1) as well as SNVs classified as pathogenic (e.g., ARID1A Q775*). Notably, in the examined specimens most of the chromosomal aberrations (51-82%) were clonal across all cells of a given patient. In contrast, most of the detected somatic SNVs (67-96%) were sub-clonal and thus present only in a subset of CTCs. Conclusion: In summary, the novel scIMPACT workflow enabled reliable and accurate genomic profiling of patient-derived CTCs in late-stage breast cancer patients. Our proof-of-concept study revealed evidence of genetic diversity of SNVs among the examined CTCs, which might have been acquired late in progression but relevant for therapy escape in the studied cases. Further analyses are still needed for assessing the generalizability of our finding as well as for deeper understanding of the molecular basis orchestrating the establishment and maintenance of heterogeneous genotypes of CTCs in breast cancer. Citation Format: Zbigniew T. Czyż, Clara Chaiban, Adithi Ravikumar Varadarajan, Cäcilia Köstler, Vadim Dechand, Jonas Grote, Thomas Ragg, Bernhard Polzer, Jens Warfsmann, Christoph A. Klein. Genomic profiling with the novel single-cell IMPACT assay reveals evidence of genetic heterogeneity among CTCs in late-stage breast cancer patients [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 3692.

Abstract 7497: Advancing multi-biomarker CTC assay and CDx development through the automated GenoCTC system

Abstract Introduction: The successful outcomes observed in clinical trials emphasize the effectiveness of therapeutic approaches relying on biomarker tests, particularly in the development of cancer drugs. The parallel development of a drug and its associated predictive biomarker is considered an ideal strategy for achieving rapid and successful drug development in precision medicine. In this context, we employ an automated circulating tumor cell (CTC) isolation platform, known as GenoCTC, to facilitate the development of biomarker-driven CTC assays, with the ultimate goal of developing companion diagnostic (CDx) tests. Method: This study employed the 5th generation GenoCTC device, a fully automated system designed for marker-based CTC enrichment using immune magnetophoresis. We confirmed the isolation of CTCs through spiking tests, utilizing cancer biomarkers such as cMET, Mesothelin (MSLN), and Claudin 3 (CLDN3). cMET is a biomarker extensively studied in various cancers, particularly non-small cell lung cancer. We previously showed the prognostic significance of cMET expressing CTCs in HR+ and HER2- metastatic breast cancer patients. MSLN and CLDN3 are tumor-associated proteins showing overexpression across diverse cancer types, with a potential for the development of antibody-based cytotoxic drugs. The GenoCTC device allows efficient separation of CTCs expressing these biomarkers, ensuring high accuracy, precision, specificity, and sensitivity. Simultaneously, therapeutic drugs directed at these markers are progressing through phase trials or preclinical studies. Conclusion: Our results show that cMET, MSLN, and CLDN3 are potential markers for the development of biomarker tests, that can improve the patient selection process for personalized therapy targeting these biomarkers. Citation Format: Chaithanya Chelakkot, Jieun Park, Chae Rin Kim, Yeonu Lee, Yu Rim Lee, Saehyung Lee, Jun Young Choi, Young Ho Moon, Yoon-La Choi, Young Kee Shin, Hun Seok Lee. Advancing multi-biomarker CTC assay and CDx development through the automated GenoCTC system [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 7497.

Size effect of dynamic bioactive magnetic particles on regulated isolation of tumor cells

Circulating tumor cells (CTCs) are critical biomarkers in cancer metastasis, yet their isolation from the bloodstream remains a challenging task due to their low abundance. This study introduces a method for the efficient isolation of CTCs, utilizing dynamic biointerface-based magnetic particles (DBMPs), with a particular emphasis on the role of particle size. We have developed three distinct sizes DBMPs specifically tailored for effective CTCs interaction, leveraging the unique properties of polydopamine (PDA) coatings and phenylboronic acid (PBA)-modified capture peptides through reversible catechol-boronate interactions. Comparative analysis of DBMPs of varying sizes was assessed under uniform experimental conditions for their capture and release efficiencies. The findings reveal a clear distinction: smaller particles (DBMP1 and DBMP2) achieved greater efficiency in capturing CTCs, whereas the larger particles (DBMP3) were more effective in releasing them. This difference is ascribed to the varied interaction dynamics between the particles and CTCs. Furthermore, we have fine-tuned DBMP3 to optimize CTC capture while still maintaining a high efficiency in cell release. The integration of these DBMPs into a magnetic isolation framework is poised to significantly enhance CTCs isolation methods, marking a pivotal advancement in cancer diagnostics and management.

Abstract 7498: Acoustophoresis enriches tumor cell clusters from patients with metastatic prostate cancer

Abstract Purpose: A subset of aggressive prostate cancers (PCa) progress to invade surrounding tissue to form distant metastases by shed of circulating tumor cells (CTCs). However, due to the scarcity of CTCs among the millions of nucleated blood cells, there is an unmet need to improve CTC isolation assays. Our technique Acoustophoresis uses standing ultrasound waves in a flow-through microfluidic chamber to discriminate cells based on their size, density, and compressibility. Method: We analyzed the effectiveness of acoustophoretic circulating tumor cell (CTC) isolation from 6 mL PFA fixed red blood cell lysed blood from 12 metastatic prostate cancer patients and 20 healthy control subjects and compared it to the golden standard CellSearch. For acoustic cell separation, cells were diluted in 12 mL PBS based buffer and separated by acoustophoresis and analyzed by imaging flow cytometry using a standardized antibody panel (EpCAM, cytokeratin, CD45, CD66b, DAPI). Generally, CTCs, and clusters migrate faster than white blood cells (WBCs) when exposed to ultrasound in the microchannel during acoustophoresis and can therefore be separated from nucleated blood cells. Major findings: Our pilot study shows that acoustophoresis finds both singlets and clusters of CTCs in patients as well as aggregates of CTCs and WBCs. In total, 67 cancer cell containing cell clusters were identified. Most identified cell clusters were small, containing less than 4 cells. In addition, acoustophoresis is a label-free separation technique, and could therefore identify additional subclasses of CTCs among the detected CTCs with e.g., EpCAM low/- expression. Further, we provide extensive data for the effect of storage time on acoustophoretic separation performance for fixed prostate cancer cell line cells and WBCs. Demonstrating that sample processing can be done up to 72 hours after blood sampling. We believe this is to date the most comprehensive study of acoustic separation of CTCs in patients and control subjects. Conclusion: Label-free acoustophoresis is a potential method for future non-invasive molecular interrogation of metastatic cancers. We believe Acoustophoresis is a promising technology for CTC enrichment with the possibility to detect new subclasses of CTCs as well as cell clusters not detectable with CellSearch. CTC-clusters has previously been proposed as a promising and potent predictor to monitor progressive disease and is associated with earlier onset of metastatic disease and poor prognosis, which makes acoustophoresis ability to identify clusters of high interest. Citation Format: Cecilia Magnusson, Per Augustsson, Andreas Lenshof, Andreas Josefsson, Anders Bjartell, Yvonne Ceder, Hans Lilja, Thomas Laurell. Acoustophoresis enriches tumor cell clusters from patients with metastatic prostate cancer [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 7498.

Abstract 2771: Increased mtDNA copy number via EPOR signaling: A potential mechanism for metastatic dissemination in head and neck squamous cell carcinoma

Abstract Introduction: Head and Neck Squamous cell carcinoma (HNSCC) is characterized by high degree of invasion, locoregional metastasis, relapse which leads to overall poor prognosis. The molecular mechanism responsible for aggressiveness is poorly understood. A better understanding of molecular pathways involved shall precede the identification of newer diagnostic tools and therapeutic targets. We explored EPOR signaling pathway in Circulating tumor cells (CTCs) and HNSCC cell lines. Methods and Results: By using a validated in-house CTC isolation protocol, which addresses various drawbacks of currently available techniques and isolates CTCs suitable for various downstream molecular analysis, we isolated CTCs from HNSCC patients. The whole transcriptome analysis was performed from CTCs using ultra-low cell number RNA sequencing and corresponding primary tumors in 24 paired samples. We found a significant transcriptomic heterogeneity in CTCs, which are associated with overall disease outcome in HNSCC patients. To explore the plausible molecular pathways, we also identified 521 differentially expressed genes in CTCs with respect to primary tumors and various canonical pathways including oxidative phosphorylation, TCA cycle, cytokine-cytokine receptor interaction signaling, and ECM receptor interaction were enriched in CTC samples. Overexpression of erythropoietin receptor (EPOR) along with various genes encoded by mitochondrial genome and genes involved in maintenance of mtDNA in CTCs as compared to primary tumors was an important finding from our data. When analyzed in depth, there was a significant positive correlation between various genes involved in mtDNA maintenance (ABAT, NT5M) and encoded by mitochondrial genome (MT-ND1, MT-ND2, MT-ND4, MT-ND5, MT-ND6, MT-CO1, MT-CO2, MT-ATP6, MT-CYTB) with EPOR expression in our RNA seq data which is also substantiated by analyzing TCGA data. We confirmed these findings experimentally in HNSCC cell lines Cal 27 and FaDu. It was also observed that metastatic cell line FaDu has significantly higher mtDNA content as compared to non-metastatic cell line Cal 27, which was correlated with EPOR expression. Treatment with low dose Erythropoietin (0.1IU/mL) which a natural ligand for EPOR, enhanced mtDNA content in both the cell lines at low doses and boosted the metastatic capability while minimal effect on cell proliferation was observed. Conclusion: EPOR signaling might promote the metastatic ability of cancer cells and may act as a potential target for cancer dissemination and metastasis. Citation Format: Anshika Chauhan, Geeta S. Boora, Sahana Ghosh, Subrata K. Patra, Roshan K. Verma, Jaimanti Bakshi, Debajyoti Chatterjee, Radhika Srinivasan, Sushmita Ghoshal, Arindam Maitra, Arnab Pal. Increased mtDNA copy number via EPOR signaling: A potential mechanism for metastatic dissemination in head and neck squamous cell carcinoma [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 2771.