Characterization Of Circulating Tumor Cells Research Articles

Abstract PO1-16-02: Correlation of Circulating Tumor Cells (CTC) with Clinical Characteristics, Pathological Factors, and Treatment Response in Patients with Metastatic Breast Cancer (MBC)

Abstract Background: Circulating Tumor Cells (CTC) can be isolated in 40-80% of patients with metastatic breast cancer (MBC). High levels of CTC, defined as ≥5/7.5 ml of blood are associated with shorter progression-free survival and overall survival. CTC can be tested for clinically relevant biomarkers, such as ER, and HER2 status, and have the potential to guide therapy as well as help with disease monitoring. We investigated CTC detection rate, its correlation with clinical characteristics, pathological characteristics, and response to treatment in patients with any type of metastatic breast cancer who progressed on at least one line of therapy. Methods: Eligible patients with MBC were enrolled in the IMAGE-II study (Individualized Molecular Analyses Guide Efforts in Breast Cancer) NCT02965755, in which we obtained archival tissue as part of the standard of care, and prospectively collected serial blood samples for CTC analysis. We compared CTC levels and biomarker status with clinical factors, tissue-based pathology, and molecular biomarkers. We assessed whether changes in CTC count correlated with treatment response. Blood samples were collected at baseline (Day 1), after 1-2 weeks of therapy, after 8-12 weeks, and at subsequent restaging (every 8-12 weeks). Medical records were reviewed every 3 months for ongoing treatment response, and death. Samples were processed at the Biocept CLIA-certified Laboratory. CTC were enumerated by the presence of CD45- and DAPI+ cells. Further CTC characterization was performed by antibody staining of specific protein biomarkers (ER, HER2). Fisher’s exact test was used to evaluate the association between baseline CTC < 5 and ≥5/7.5ml with patient characteristics. McNemar’s test was used to assess discordance between tissue-based and CTC-defined markers. Results: Between 1/26/2018 and 12/31/22 baseline samples were collected from 70 women with a median age of 56 (36-82) who were enrolled at four study sites. CTC was detected in 59 (84%) of participants. Baseline CTC counts were < 5/7.5 ml in 37/59 (63%) and ≥5/7.5 ml in 22/59 (37%) of participants. Differences between breast cancer subtype and CTC-receptor status were observed (Table 1). Among the 41 patients who were ER-positive, 31 (76%) were CTC ER-negative(p< 0.001). Among 29 patients who were ER-negative, 4 (14%) were CTC ER-Positive (P< 0.001). Among the 7 patients who were HER2 positive, 2(29%) were HER2 positive on CTC. Among 63 patients who were HER2 negative, 7(11%) had HER2 expression on their CTC. The discordance in the classification of HER2 wasn't statistically significant (p=0.77). Elevated CTC at baseline was more frequently detected in younger participants (< 50 years old) (55% vs 27%; P=0.22), in Black women compared to White (60 % vs 29 %, P=0.27), and in participants with visceral vs non-visceral metastasis (52% vs 28 %, P=0.40). Patients with CTC ≥5 vs < 5/7.5mL at baseline had a shorter duration of anti-HER2-based therapy (61.5 vs 836 days, p=0.04). There were no statistically significant differences among participants who received chemotherapy agents (316.5 vs 365.5 days, P=0.88), endocrine therapy (376 vs 490 days, P=0.89), or overall therapy (272 vs 390 days, P=0.21). Conclusions: We observed significant differences in the expression of ER between tumor tissue and CTC, which can be partly due to tumor evolution over time. Additionally, participants who are young, Black, and those who have visceral metastasis may have higher CTC counts. Higher CTC counts were associated with a shorter duration of anti-HER2 therapy. Although it didn’t meet statistical significance, a similar trend was observed in patients who received chemotherapy and endocrine therapy. Table 1: MBC Tissue-Based Subtype and CTC-receptor status at baseline Citation Format: Asnakech Bayable, Tingchang Wang, Amanda Blackford, Jessica Tao, Jenna Canzoniero, Seoho Lee, Faith Too, Barbara Blouw, Mary Wilkinson, Rima Couzi, Antonio Wolff, Christie Hiton, Ben Park, Vered Stearns, Cesar Santa-Maria. Correlation of Circulating Tumor Cells (CTC) with Clinical Characteristics, Pathological Factors, and Treatment Response in Patients with Metastatic Breast Cancer (MBC) [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 PO1-16-02.

Acoustic Enrichment of Heterogeneous Circulating Tumor Cells and Clusters from Metastatic Prostate Cancer Patients.

There are important unmet clinical needs to develop cell enrichment technologies to enable unbiased label-free isolation of both single cell and clusters of circulating tumor cells (CTCs) manifesting heterogeneous lineage specificity. Here, we report a pilot study based on the microfluidic acoustophoresis enrichment of CTCs using the CellSearch CTC assay as a reference modality. Acoustophoresis uses an ultrasonic standing wave field to separate cells based on biomechanical properties (size, density, and compressibility), resulting in inherently label-free and epitope-independent cell enrichment. Following red blood cell lysis and paraformaldehyde fixation, 6 mL of whole blood from 12 patients with metastatic prostate cancer and 20 healthy controls were processed with acoustophoresis and subsequent image cytometry. Acoustophoresis enabled enrichment and characterization of phenotypic CTCs (EpCAM+, Cytokeratin+, DAPI+, CD45-/CD66b-) in all patients with metastatic prostate cancer and detected CTC-clusters composed of only CTCs or heterogeneous aggregates of CTCs clustered with various types of white blood cells in 9 out of 12 patients. By contrast, CellSearch did not detect any CTC clusters, but detected comparable numbers of phenotypic CTCs as acoustophoresis, with trends of finding a higher number of CTCs using acoustophoresis. Our preliminary data indicate that acoustophoresis provides excellent possibilities to detect and characterize CTC clusters as a putative marker of metastatic disease and outcomes. Moreover, acoustophoresis enables the sensitive label-free enrichment of cells with epithelial phenotypes in blood and offers opportunities to detect and characterize CTCs undergoing epithelial-to-mesenchymal transitioning and lineage plasticity.

Abstract 3702: Dissecting circulating tumor cells phenotype in a cohort of locally advanced non-small cell lung cancer patients undergoing neoadjuvant chemotherapy

Abstract Background: Platinum-based neoadjuvant chemotherapy (pb-NACT) is the primary treatment approach for locally advanced non-small cell lung cancer (LA-NSCLC), despite offering only a limited overall survival (OS) gain. Cisplatin-induced cell damage has been shown to activate the SDF-1/CXCR4 axis in preclinical models of NSCLC, resulting in the recruitment of a cell subset co-expressing the stemness marker CD133 and CXCR4 (SDF-1 receptor) at distant sites. These cells, known as metastasis-initiating cells (MIC), exhibit prometastatic activity. By longitudinally monitoring circulating tumor cells (CTC) in the blood of LA-NSCLC patients (pts) undergoing pb-NACT, our objective is to assess the potential prognostic significance of CTC number and phenotype. Methods: Between February 2019 and August 2023, a total of 61 pts with LA-NSCLC undergoing pb-NACT, were included in the study. Blood samples were obtained at baseline (T1), post-pb-NACT (T2), and post-surgery (T3) for the characterization of CTC, including total CTC, CXCR4+CTCs, and CXCR4+CD133+ MIC. This characterization utilized a validated marker-independent strategy combining Parsortix and DEPArrayTM technologies. Logistic regression models were employed to examine the association between CTC subsets and the response to pb-NACT (Disease Control Rate [DCR], Overall Response Rate [ORR]), while Cox-regression models were used to assess their association with survival endpoints (event-free survival [EFS], OS, disease-free survival [DFS]). Results: Out of the 61 enrolled patients, 34 had available CTC data for analysis. In this population, DCR was 64.7%, and the ORR 29.4%. Surgery was performed in 14 pts (41.2%). At baseline (T1), elevated levels of CXCR4+CTCs were linked to a lower DCR (10 vs 3/mL, odds ratio [OR]=0.02, 95% confidence interval [CI]: 0-0.40, p=0.008), as well as shorter EFS (10 vs 3/mL, HR=4.20, 95% CI: 1.84-9.58, p=0.002) and OS (10 vs 3/mL, HR=3.14, 95% CI: 1.25-7.88, p=0.004). At the post- CT time point (T2), higher levels of MIC were associated with shorter EFS (3 vs 0/mL, HR=1.41, 95% CI: 1.00-1.99, p=0.047) and OS (3 vs 0/mL, HR=1.55, 95% CI: 1.03-2.34, p=0.035). Although the sample size was limited, a higher number of MIC at the post-surgery time point (T3) showed a trend toward reduced DFS. Discussion: CTC could serve as a novel biomarker for assessing the effectiveness of pb-NACT in LA-NSCLC. Elevated levels of CXCR4+CTC both at baseline and after pb-NACT, along with increased MIC post-pb-NACT and post-surgery, indicate unfavorable prognostic factors for survival. Specifically, a higher baseline of CXCR4+CTCs may be linked to a suboptimal response to treatment, suggesting the potential need for treatment intensification in patients exhibiting elevated CXCR4+CTC baseline levels. Citation Format: Rita Leporati, Teresa Beninato, Sara Iadecola, Chiara Andreon, Fabio Murianni, Melissa Balsamo, Antonia Martinetti, Benedetta Lombardi Stocchetti, Laura Mazzeo, Sara Manglaviti, Mario Occhipinti, Marta Brambilla, Arsela Prelaj, Claudia Proto, Rosalba Miceli, Luca Roz, Gabriella Sozzi, Filippo De Braud, Giuseppe Lo Russo, Giulia Bertolini. Dissecting circulating tumor cells phenotype in a cohort of locally advanced non-small cell lung cancer patients undergoing neoadjuvant chemotherapy [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 3702.

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.

Advancements in Circulating Tumor Cell Research: Bridging Biology and Clinical Applications.

Circulating tumor cells (CTCs) are cells released from the primary and metastatic tumor and intravasate into the blood or lymphatic vessels, where they are transported to distant sites and act as seeds that initiate cancer metastases or the development of further lesions. Recent advances in CTC research have shown their relevance as prognostic markers for early and metastatic disease detection, predictive biomarkers for relapse, and response to medical intervention or therapy. The rapidly evolving landscape of CTC biology has opened new avenues for understanding cancer progression, metastasis, and treatment response. Additionally, translating these findings into clinical applications holds promise for improving cancer diagnostics, prognosis, and personalized therapeutic strategies. This review discusses the significance of CTCs in cancer research and their associated challenges. We explore recent developments in the detection and characterization of CTCs and their implications in cancer research and clinical practice.

Research progress of CTC, ctDNA, and EVs in cancer liquid biopsy

Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and extracellular vehicles (EVs) have received significant attention in recent times as emerging biomarkers and subjects of transformational studies. The three main branches of liquid biopsy have evolved from the three primary tumor liquid biopsy detection targets—CTC, ctDNA, and EVs—each with distinct benefits. CTCs are derived from circulating cancer cells from the original tumor or metastases and may display global features of the tumor. ctDNA has been extensively analyzed and has been used to aid in the diagnosis, treatment, and prognosis of neoplastic diseases. EVs contain tumor-derived material such as DNA, RNA, proteins, lipids, sugar structures, and metabolites. The three provide different detection contents but have strong complementarity to a certain extent. Even though they have already been employed in several clinical trials, the clinical utility of three biomarkers is still being studied, with promising initial findings. This review thoroughly overviews established and emerging technologies for the isolation, characterization, and content detection of CTC, ctDNA, and EVs. Also discussed were the most recent developments in the study of potential liquid biopsy biomarkers for cancer diagnosis, therapeutic monitoring, and prognosis prediction. These included CTC, ctDNA, and EVs. Finally, the potential and challenges of employing liquid biopsy based on CTC, ctDNA, and EVs for precision medicine were evaluated.

Isolation of Viable Epithelial and Mesenchymal Circulating Tumor Cells from Breast Cancer Patients.

Circulating tumor cells (CTCs) undergoing epithelial-mesenchymal transition (EMT) may exhibit more aggressive features than epithelial CTCs and are more frequently observed during disease progression. Therefore, detection and characterization of both epithelial and mesenchymal CTCs in cancer patients are urgently needed to allow for a better understanding of the metastatic process and more effective treatment. Here we describe a method for detection and isolation of viable epithelial and mesenchymal CTCs from peripheral blood of breast cancer patients. The method is based on density gradient centrifugation, multiplex immunofluorescent staining, and negative anti-CD45 selection. Cells obtained after the procedure are suitable for genomic or transcriptomic profiling, and they can also be isolated by micromanipulation for single-cell analysis.

Circulating Tumour Cells: Detection and Application in Advanced Non-Small Cell Lung Cancer.

Non-small cell lung cancer (NSCLC) is one of the deadliest diseases worldwide. Tissue biopsy is the current gold standard for the diagnosis and molecular profiling of NSCLC. However, this approach presents some limitations due to inadequate tissue sampling, and intra- and intertumour heterogenicity. Liquid biopsy is a noninvasive method to determine cancer-related biomarkers in peripheral blood, and can be repeated at multiple timepoints. One of the most studied approaches to liquid biopsies is represented by circulating tumour cells (CTCs). Several studies have evaluated the prognostic and predictive role of CTCs in advanced NSCLC. Despite the limitations of these studies, the results of the majority of studies seem to be concordant regarding the correlation between high CTC count and poor prognosis in patients with NSCLC. Similarly, the decrease of CTC count during treatment may represent an important predictive marker of sensitivity to therapy in advanced NSCLC. Furthermore, molecular characterization of CTCs can be used to provide information on tumour biology, and on the mechanisms involved in resistance to targeted treatment. This review will discuss the current status of the clinical utility of CTCs in patients with advanced NSCLC, highlighting their potential application to prognosis and to treatment decision making.

A microfluidic device for enhanced capture and high activity release of heterogeneous CTCs from whole blood

Circulating tumor cells (CTCs) are tumor cells that spontaneously detach from the primary focus, and early detection and characterization of CTCs is vital for cancer diagnosis and appropriate treatment. Current methods commonly use EpCAM to capture CTCs, but this results in a loss of information on other CTC subsets (EpCAM-negative cells) due to the heterogeneity of CTCs. Here, we report a novel microfluidic device that integrates the capture and release of heterogeneous CTCs directly from whole blood. A spiral chip was designed for the separation of differently sized cells, and larger CTCs were effectively separated from smaller blood cells with a 98% recovery rate. CD146-containing magnetic beads were used to complement the EpCAM-based CTC capture methods, and the capture efficiency of Fe3O4@Gelatin@CD146/EpCAM increased by 20% over Fe3O4@Gelatin@EpCAM. Finally, MMP-9 was employed to release CTCs with high efficiency and less damage by degrading gelatins on the surface of Fe3O4. The established method was successfully applied to CTC capture and release in a simulated patient's whole blood. The developed method achieved enhanced capture and high activity release of heterogeneous CTCs with less interference by blood cells, which contributes to the early detection and clinical downstream analysis of CTCs.

Automated Image Analysis for Characterization of Circulating Tumor Cells and Clusters Sorted by Magnetic Levitation.

Magnetic levitation-based sorting technologies have revolutionized the detection and isolation of rare cells, including circulating tumor cells (CTCs) and circulating tumor cell clusters (CTCCs). Manual counting and quantification of these cells are prone to time-consuming processes, human error, and inter-observer variability, particularly challenging when heterogeneous cell types in 3D clusters are present. To overcome these challenges, we developed "Fastcount," an in-house MATLAB-based algorithm for precise, automated quantification and phenotypic characterization of CTCs and CTCCs, in both 2D and 3D. Fastcount is 120 times faster than manual counting and produces reliable results with a ±7.3% deviation compared to a trained laboratory technician. By analyzing 400 GB of fluorescence imaging data, we showed that Fastcount outperforms manual counting and commercial software when cells are aggregated in 3D or staining artifacts are present, delivering more accurate results. We further employed Fastcount for automated analysis of 3D image stacks obtained from CTCCs isolated from colorectal adenocarcinoma and renal cell carcinoma blood samples. Interestingly, we observed a highly heterogeneous spatial cellular composition within CTCCs, even among clusters from the same patient. Overall, Fastcount can be employed for various applications with lab-chip devices, such as CTC detection, CTCC analysis in 3D and cell detection in biosensors.

Monitoring epithelial, epithelial-mesenchymal, and mesenchymal circulating tumor cells on papillary thyroid cancer following thyroidectomy: A prospective cohort study.

6097 Background: Monitoring the effectiveness of cancer-removal surgery is challenging in most cases. Therefore, robust and non-invasive techniques have been developed, and liquid biopsy is an apparent method for that purpose. In this prospective cohort study, we examined whether one type of liquid biopsy, an enumeration of circulating tumor cells (CTCs), can monitor the effectiveness of thyroidectomy in patients with papillary thyroid cancer (PTC). Methods: From January 2021 to January 2022, we recruited 62 PTC patients who had operated on isthmectomy, lobectomy, and total thyroidectomy for this study at Seoul National University Bundang Hospital. The blood samples from the recruited patients were collected before surgery and two weeks and three months after the surgery for CTC detection. We collected peripheral blood samples by venipuncture from each patient in EDTA tubes and stored them at 4°C until isolation and characterization of CTCs (within 6 hours). Results: We found the CTCs in 87% (54/62) of PTC patients, with an average number of 8.0. This number significantly decreased after thyroidectomy, with an average of 5.3 and 4.3 post-operation of two weeks and three months, respectively. In the peripheral blood of PTC patients, the CTCs with epithelial-mesenchymal and mesenchymal phenotypes were significantly more frequent than the epithelial phenotype of CTCs. Furthermore, PTC patients with lymphatic invasion, lymph node metastasis, or BRAF V600E mutation showed significantly decreased CTC count after surgery. Conclusions: PTC patients had a significantly higher number of CTCs undergoing epithelial-mesenchymal transition and showed a significant decrease in CTC count after surgery. This indicates that liquid biopsy using CTC enumeration can satisfy the purpose of monitoring the effectiveness of cancer-removal surgery. Clinical trial information: KCT0008179.

Concordance between liquid and tissue biopsy in participants with newly diagnosed recurrent breast cancer.

1028 Background: Tissue biopsy is recommended to confirm breast cancer (BC) recurrence. Liquid biopsy [including circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA)] is a non-invasive approach for detecting cancer that may provide information to identify treatment choices and replace invasive biopsies. This ongoing study aims to assess the concordance between tissue and liquid biopsy testing in subjects presenting with suspicion of distant recurrence from BC. Methods: Patients with suspected metastatic BC were enrolled; tumour characteristics and treatment were recorded. Blood samples were collected within 30 days before tissue biopsy, or within 7-28 days after tissue biopsy and before any systemic or radiation treatment. Samples were shipped to EPIC Sciences and processed within 96 hours; after plasma isolation, nucleated cells were plated; slides and plasma were banked. CTCs were identified using Epic Sciences digital imaging and machine learning algorithms. Single-cell isolation for genomic ctDNA analysis was performed. Cell free DNA was analyzed using a validated NGS panel to detect ctDNA alterations. The presence of metastases was classified as suspicious, highly suspicious, definitely metastatic BC or other by the treating oncologist based on the patient's clinical presentation and biopsy pathology results. Epic Sciences classified samples into similar categories based on CTC and ctDNA assay results. These classifications were performed independently. Sensitivity of the Epic Sciences methodology to detect metastatic BC (as determined by the treating oncologist), and its false positive rate were calculated. Results: 100 patients were enrolled from June 2020 to October 2022; shipping delays precluded EPIC assays in six patients; 94 patients were analyzed. Of 83 cases deemed suspicious, highly suspicious, or definitely metastatic BC by the treating oncologist, 61 were also deemed so by Epic Sciences (sensitivity of 73.5%, 95% confidence interval, CI 63.1% - 81.9%). Of 66 cases assigned as suspicious, highly suspicious, or definitely metastatic BC by the Epic Sciences, 4 had new primary cancers (3 lung cancer, 1 hepatocarcinoma), for a false positive rate of 6.1% (95% CI 1.9% - 15.0%). One additional case was classified as un-specified adenocarcinoma (possibly breast) by the treating oncologist; resolution awaits further follow-up. Conclusions: Preliminary results show that 73.5% of distant BC recurrences were correctly identified by liquid biopsy. A small number of false positive results occurred in patients with other new primary cancers. Additional analyses with CTC characterization are ongoing. [Table: see text]

Circulating tumor cells (CTCs) dynamics after CDK4/6i for hormone-receptor positive (HR+) metastatic breast cancer (MBC): A biomarker analysis of the PACE randomized phase II study.

1059 Background: PACE is a multicenter randomized phase II trial investigating palbociclib (P) in combination with fulvestrant (F) after progression on any CDK4/6 inhibitor (CDK4/6i), with or without the PD-L1 inhibitor avelumab (A), in HR+/HER2- MBC. CTCs are rare cells in the blood stream whose detection is associated with worse outcome and treatment resistance. Methods: Eligible patients (pts) had HR+/HER2- MBC with prior progression after ≥ 6 months (mo) of AI and CDK4/6i for MBC, or during/within 12 mo in the adjuvant setting, with ≤ 1 prior chemotherapy for MBC. Pts were randomized 1:2:1 to F, F+P, or F+P+A. CTC detection and enumeration were performed utilizing CellSearch (Menarini Silicon Biosystems) at baseline (BL), at time of first tumor assessment (TTA1), and at progression. Results were dichotomized using the standard CTC threshold (≥ 5 CTCs/7.5 ml) into a novel prognostic classification: StageIVindolent and StageIVaggressive (Cristofanilli et al 2019). Concurrent ctDNA Sequencing was performed using Guardant360 (Guardant Health). Results: Of the 220 randomized pts, 203 (92%) had sample available for BL CTC enumeration, 155 had detectable CTCs (70.5%), and 99 (48.8%) were StageIVaggressive. De novo disease at initial diagnosis was associated with StageIVaggressive (47.5% vs 30.8% StageIVindolent), and distribution of visceral versus non-visceral disease was similar across the two CTCs groups. StageIVaggressive represented 38.3%, 54.8%, and 46.2% of the F, F+P and F+P+A treatment groups, respectively. BL CTCs were prognostic in the overall cohort; median PFS was 5.7mo vs 3.5mo for StageIVindolent vs StageIVaggressive (HR: 1.69, 90%CI 1.27,2.24, P<0.001). Median PFS for the F, F+P and F+P+A arms was 1.9mo, 4.6mo and 5.4mo in StageIVaggressive compared to 8.2mo, 5.3mo and 8.3mo in StageIVindolent. Among patients in the StageIVaggressive subgroup, the F+P and F+P+A arms demonstrated improved outcomes compared to F alone. (F+P vs F HR 0.43, 90% CI 0.25-0.71, and F+P+A vs F HR 0.26, 90% CI 0.14-0.49). No benefit of F+P or F+P+A over F was observed in the StageIVindolent subgroup (F+P vs F HR 1.45, 90% CI 0.87 - 2.40 and F+P+A vs F HR 1.06, 90% CI 0.61 - 1.84, each p(interaction)<0.01). Changes in StageIV CTC characterization (indolent vs aggressive) between BL and TTA1 among the subset of 175/203 pts with both timepoints available are reported. Conclusions: Baseline CTC enumeration is prognostic in patients receiving F with or without CDK4/6i. The StageIVaggressive subgroup may derive preferential benefit with combinations of F+P or F+P+A over F alone. Findings should be confirmed in other studies. ctDNA analyses are ongoing. Clinical trial information: NCT03147287 . [Table: see text]

Transcriptome Profiling of Circulating Tumor Cells to Predict Clinical Outcomes in Metastatic Castration-Resistant Prostate Cancer.

The clinical utility of circulating tumor cells (CTC) as a non-invasive multipurpose biomarker is broadly recognized. The earliest methods for enriching CTCs from whole blood rely on antibody-based positive selection. The prognostic utility of CTC enumeration using positive selection with the FDA-approved CellSearchTM system has been demonstrated in numerous studies. The capture of cells with specific protein phenotypes does not fully represent cancer heterogeneity and therefore does not realize the prognostic potential of CTC liquid biopsies. To avoid this selection bias, CTC enrichment based on size and deformability may provide better fidelity, i.e., facilitate the characterization of CTCs with any phenotype. In this study, the recently FDA-approved Parsortix® technology was used to enrich CTCs from prostate cancer (PCa) patients for transcriptome analysis using HyCEADTM technology. A tailored PCa gene panel allowed us to stratify metastatic castration-resistant prostate cancer (mCRPC) patients with clinical outcomes. In addition, our findings suggest that targeted CTC transcriptome profiling may be predictive of therapy response.

Abstract 3370: Liquid biopsy approaches to determine tumor cell heterogeneity in advanced prostate cancer

Abstract Aggressive variants of prostate cancer (AVPC) emerge from prostate adenocarcinoma following enduring therapeutic pressure. They grow independent of the androgen receptor, progress rapidly and can show traits of neuroendocrine (NE) differentiation. As progression to AVPC is not well detected by prostate specific antigen monitoring, new biomarkers are urgently needed. The aim of this study is to evaluate the detection of circulating tumor cells (CTCs) in combination with gene expression analysis of NE genes to identify AVPC patients with neuroendocrine traits. Blood samples were collected from patients suffering from AVPC (n=78, including 25 patients with histological evidence of NEPC) as well as from patients with hormone-sensitive prostate cancer (HSPC) as controls (n=12) at the University Medical Center Hamburg-Eppendorf. CTC counts were determined by CellSearch analysis. In parallel, CTCs were immuno-magnetically enriched using the AdnaTest and bulk gene expression of prostate-specific and NE genes was analyzed by semi-quantitative PCR. From a subset of patients, CTCs were additionally enriched by Parsortix to compare gene expression of CTCs with EpCAM-based or size-based CTC enrichment. Using CellSearch analysis, CTCs were found in 88.9 % of AVPC patients. CTC counts ranged between 0 – 20,000 CTCs/7.5 ml of blood with a median of 32 CTCs/7.5 ml. Similarly, 81.8 % of NEPC patients were positive for CTCs with a median count of 35 CTCs/7.5 ml (range 0-13,000). In contrast, CTCs were found in only 50 % of HSPC patients at lower concentrations (median count of 0.5 CTCs/7.5 ml, range 0-34). CTC counts were significantly elevated in AVPC and NEPC patients compared to HSPC (p = 0.002, p = 0.012), but no significant differences were found between AVPC and NEPC samples.In 93.8 % of AVPC samples, CTCs expressed prostate-specific genes such as KLK3 or PSMA. At least one of the NE transcripts was detected in 37.5 % of AVPC patients. In CTCs from NEPC patients, the positivity for prostate markers was significantly reduced to 66.6 % (p = 0.01) and the positivity for NE markers was increased to 61.1 %. A random Forrest model trained on all analyzed transcripts allowed for a distinction of HSPC and NEPC with an AUC of 79.5 %. Comparison of CTC enrichment strategies in a subset of 13 patients showed similar NE marker detection by size-based enrichment (53.8 % NE-positive) compared to the AdnaTest (61.5 % NE-positive). AVPC and NEPC patients show a high CTC burden that will allow subsequent molecular analyses, and CTC counts allowed a distinction between blood samples from HSPC and NEPC patients. Gene expression analysis revealed a high degree of inter-patient heterogeneity for neuroendocrine-specific transcripts with a reduction of prostate markers in NEPC patients. Future molecular characterization and longitudinal monitoring of CTCs will shed more light on the evolution of AVPC and NEPC. Citation Format: Lina Merkens, Sarah Greimeier, Sabine Riethdorf, Klaus Pantel, Gunhild von Amsberg, Stefan Werner. Liquid biopsy approaches to determine tumor cell heterogeneity in advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3370.

Abstract 1031: Specific gene alterations of HER2 positive single circulating tumor cell (CTC) compared to autologous leukocytes in metastatic breast cancer (MBC)

Abstract Introduction: Monitoring of CTC in MBC showed ability to predict treatment resistance and outcome. HER2 is one of the most important tumor markers which is associated with rapid cell division and the metastasis and prognosis of MBC in the clinic. More recently, we reported single CTC gene mutation is a key point to distinguish metastasis capability in MBC (2022 AACR and 2022 ASCO). Herein, we report specific gene alterations in HER2+ single CTC compared to autologous leukocytes in MBC. Methods: Whole blood sample (7.5ml/each) was collected from MBC patient before therapy. CTC enumeration was performed in FDA approved CellSearch™ System and then the single HER2+ CTC and leukocytes were isolated by using DEPArrayTM System (Menarini). The single cell DNA was isolated and then the initial library was prepared by using Ampli1™ Whole Genome Amplification, Ampli1™ QC Kit (Menarini) and AMPure XP kit (Beckman Coulter). The exome capture was performed by TruSeq DNA Exome kit (illumine). The sequencing was prepared by NextSeq 500 mid output V2.5 kit and was performed on the NextSeq 500 (Illumina). Results: We identified 107 CTCs including 55 HER2+ CTCs and 14 CTC-clusters. Autologous single HER2+ CTC (HER2+CK+CD45−, Group 1), HER2+CK−CD45+ leukocyte (Group 2) and HER2−CK−CD45+ leukocyte (Group 3) were isolated and sequenced respectively. The sequencing data was processed following the GATK pipeline and annotated using SnpEff. There were 486,119 counts (56.69%) for intron variants, 175,819 counts (20.51%) for intergenic variants, 70,334 counts (8.20%) for exon variants, 50,370 counts (5.87%) for downstream genes, 45,915 counts (5.36%) for upstream genes and others (3.37%) in HER2+ CTC. Meanwhile, there were 71,848 (8.76%) and 0 counts for exon variants found in Group 2 and Group 3 respectively. There were 79 gene variants ((SNP and Ins-Del) identified to have the highest impact effect (≥20) on HER2+ CTC chromosome, when there were 85 and 0 highest impact gene variants were identified in Group 2 and Group 3 respectively. The specific gene alterations in Group 1 compared to Group 2 includes CCNA2, FOLH1, BRD4, SAMHD1, CYP17A1, IDE, HPGDS and CTNNB1 Among the top 50 high impact gene variants, there were 26 genes alteration sites are same in both Group 1 and Group 2, including FECH, HDAC8, CYP11B2, TTN(6 sites), RAN, CD207, HK1, CASP1(2 sites), BRCA1, PIK3CG (3 sites), APEX1(4 sites), KIF11, SIRT5 (2 sites), XYLB and CHKA. Conclusion: Genomic characterization of HER2 positive single CTCs elucidated specific gene alterations associated with disease metastasis compared to autologous leukocytes in MBC. The newfound HER2+CK−CD45+ cells with gene alterations maybe a new kind of cancer transformed leukocytes which need further validation. Specific gene alterations will help to develop novel drugs aimed at the eradication of CTCs using molecularly driven therapies for disease metastasis. Citation Format: Qiang Zhang, Lorenzo Gerratana, Zhe Ji, Xinkun Wang, Paolo D’Amico, Seema Singhal, Youbin Zhang, Andrew A. Davis, Ami N. Shah, William Gradishar. Specific gene alterations of HER2 positive single circulating tumor cell (CTC) compared to autologous leukocytes in metastatic breast cancer (MBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1031.

Abstract 3385: A pipeline for mRNA analysis on circulating tumor cells (CTCs) collected and stored in preservative tubes

Abstract Introduction: Circulating tumor cells (CTCs) are associated with prognosis in breast cancer. In addition to enumeration, there is great interest in the molecular characterization of CTCs. Nonetheless, this is technically challenging, especially with regards to RNA analysis, which requires immediate CTC processing to avoid RNA degradation. The purpose of this study was to evaluate the performance of the CellRescueTM preservative tubes in preserving RNA, and to optimize a method for mRNA expression analysis on CTCs up to 4 days after blood collection. Methods: Ten blood sample from one healthy donor (10 mL each) were collected into CellRescueTM tubes and spiked-in with 5 (n=4) or 500 (n=4) MCF7; two tubes were used for white blood cell (WBC) collection on day (d) 1, 2, 4, and 8 (4 mL used for each timepoint). The spiked-in samples were processed for CTC enrichment on d2 and d4 using CellSearch® (cs5d2, cs500d2, cs5d4, cs500d4) or Parsortix® (p5d2, p500d2, p5d4, p500d4). RNA was extracted, quantified, and subjected to reverse transcription to cDNA. Half cDNA from each sample was analyzed through TaqMan real-time PCR (in technical duplicates) for the detection of 3 transcripts of interest: ACTB (housekeeping), CD45 (WBC marker), and EPCAM (tumor cell marker). Considering the low amount of RNA, the second half of cDNA for each sample underwent preamplification of the 3 target transcripts, followed by real-time PCR (with technical triplicates) to evaluate whether this could increase sensitivity. Results: RNA quantification by Qubit was 11.6, 23, 9.9 and 4.8 ng/uL in WBC samples collected on d1, d2, d4 and d8, respectively. Thus, using CellRescueTM tubes, RNA was preserved up to 8 days, with a slight reduction in RNA quantity on d8. For spiked-in samples, RNA was below detection at any timepoint. Real-time PCR analysis of CD45 and ACTB in WBC samples confirmed a similar quantity of transcripts across all timepoints. For spiked-in samples processed with CellSearch®, CTCs were detected only after preamplification and when 500 MCF7 were present. For spiked-in samples processed with Parsortix®, 500 CTCs were detected both at d2 and d4, regardless of preamplification. Preamplification allowed for the detection of 5 CTCs as well, but only at d2. The spiked-in samples confirmed that by using CellRescueTM tubes, RNA is preserved up to 4 days, with slight transcript signal decrease between D2 and D4. Conclusions: With the developed pipeline, it is possible to detect 500 CTCs after blood storage for up to 4 days, and as low as 5 CTCs after 2-days storage. The enrichment methods can however affect the detection. More tests need to be performed to define the pipeline’s sensitivity using different enrichment methods and with different numbers of cells. Using this pipeline, up to a total of 100 gene expression assays of interest can be evaluated in a single sample. Citation Format: Eleonora Nicolo, Marwa Manai, Youbin Zhang, Laura Munoz Arcos, Strickland Kaylan, Paolo D'Amico, Huiping Liu, Giuseppe Curigliano, Carolina Reduzzi, Massimo Cristofanilli. A pipeline for mRNA analysis on circulating tumor cells (CTCs) collected and stored in preservative tubes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3385.

Abstract P5-06-01: A Multi-center Clinical Study to Harvest and Characterize Circulating Tumor Cells from Patients with Metastatic Breast Cancer Using the Parsortix® PC1 System in support of FDA clearance

Abstract Background: Circulating tumor cells (CTCs) captured from the blood of cancer patients may serve as a non-invasive surrogate source of tumor material to investigate tumor characteristics in real-time. However, the only FDA-cleared CTC assay is limited to the enumeration of surface marker-defined epithelial cells and not designed for further characterization of the CTCs identified. The Parsortix® PC1 system is a semi-automated microfluidic device capable of capturing and harvesting CTCs from peripheral blood based on cell size and deformability, making it cell-surface marker agnostic. Here, we demonstrate that the Parsortix® PC1 system enables the enrichment and capture of CTCs from the blood of patients with metastatic breast cancer (MBC) and their interrogation using evaluation techniques commonly available in clinical laboratories. Methods: As part of a multicenter clinical trial (NCT03427450), peripheral blood samples from 216 patients with MBC and 205 healthy volunteers (HVs) were prospectively collected at four different clinical sites located throughout the United States. Each subject provided two separate blood samples collected into K2EDTA Vacutainer® tubes to be processed using the Parsortix® PC1 system on the same day. The cells harvested from one of the blood samples collected from each subject by the Parsortix® PC1 system were deposited onto cytology slides using a cytocentrifugation method and stained with Wright-Giemsa reagents using an automated stainer. The stained slides were subjected to cytopathological evaluation by a board-certified pathologist to enumerate CTCs. As proof of principle, cells harvested from the second blood sample were evaluated using one of three additional techniques: molecular profiling by qRT-PCR, RNA sequencing, or cytogenetic analysis of HER2 amplification by FISH. Results: Cytologic examination identified one or more cells as a CTC in 48.5% (95% CI of 41.5 – 55.4%) of the 194 patients with MBC and 9.9% (95% CI of 6.4 – 14.9%) of the 192 HVs. The results from the qRT-PCR evaluation (102 HVs and 74 MBC patients) showed differential expression of cancer-related genes (KRT19, EPCAM, and TWIST1) in the patients with MBC compared to the HVs. Results from the RNA sequencing (53 HVs and 16 MBC patients) showed differential expression of several genes involved in the Kegg Cancer Pathway in the patients with MBC compared to the HVs. The results from the HER2 FISH evaluation (38 HVs and 101 MBC patients) showed that while the majority of the CTC identified had normal HER2/CEP17 ratios, detection of HER2 amplification was possible. Conclusions: The Parsortix PC1 system is capable of capturing and harvesting CTCs from the peripheral blood of patients with MBC. Harvested cells can be evaluated using standard orthogonal methodologies such as gene expression and FISH to identify and characterize CTCs. Based in part on the above results, the FDA granted a De Novo classification request (DEN200062) for the Parsortix PC1 device in May of 2022. Citation Format: Evan Cohen, Gitanjali Jayachandran, Richard Moore, Massimo Cristofanilli, Julie E. Lang, Joseph Khoury, Michael F. Press, Heather McBride, Kyu Kwang Kim, Negar Khazan, Qiang Zhang, Youbin Zhang, Roberta Guzman, Michael C. Miller, James Reuben, Naoto T. Ueno. A Multi-center Clinical Study to Harvest and Characterize Circulating Tumor Cells from Patients with Metastatic Breast Cancer Using the Parsortix® PC1 System in support of FDA clearance [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-06-01.

Quantification and Characterization of CTCs and Clusters in Pancreatic Cancer by Means of the Hough Transform Algorithm

Circulating Tumor Cells (CTCs) are considered a prognostic marker in pancreatic cancer. In this study we present a new approach for counting CTCs and CTC clusters in patients with pancreatic cancer using the IsofluxTM System with the Hough transform algorithm (Hough-IsofluxTM). The Hough-IsofluxTM approach is based on the counting of an array of pixels with a nucleus and cytokeratin expression excluding the CD45 signal. Total CTCs including free and CTC clusters were evaluated in healthy donor samples mixed with pancreatic cancer cells (PCCs) and in samples from patients with pancreatic ductal adenocarcinoma (PDAC). The IsofluxTM System with manual counting was used in a blinded manner by three technicians who used Manual-IsofluxTM as a reference. The accuracy of the Hough-IsofluxTM approach for detecting PCC based on counted events was 91.00% [84.50, 93.50] with a PCC recovery rate of 80.75 ± 16.41%. A high correlation between the Hough-IsofluxTM and Manual-IsofluxTM was observed for both free CTCs and for clusters in experimental PCC (R2 = 0.993 and R2 = 0.902 respectively). However, the correlation rate was better for free CTCs than for clusters in PDAC patient samples (R2 = 0.974 and R2 = 0.790 respectively). In conclusion, the Hough-IsofluxTM approach showed high accuracy for the detection of circulating pancreatic cancer cells. A better correlation rate was observed between Hough-IsofluxTM approach and with the Manual-IsofluxTM for isolated CTCs than for clusters in PDAC patient samples.

Prognostic value of integrated liquid biopsies in patients (pts) with metastatic urothelial cancer (mUC).

547 Background: Despite recent therapeutic advancements for patients with mUC, including checkpoint inhibitors (CPIs), anti-FGFR and antibody-drug conjugates (ADCs), biomarker data to predict therapeutic response and identify mechanisms of resistance remain limited. Ongoing randomized clinical trials evaluating the combination of CPIs and ADCs in these pts underscore the need to develop biomarkers to better understand who might best respond to these therapies. Here, we employ a liquid biopsy approach to molecularly characterize circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), including those isolated with Trop-2, the target of the novel drug Sacituzumab Govitecan and Datopotamab Deruxtecan. Methods: 104 blood samples serially collected from pts being treated for mUC were used for CTC collection using anti-EpCAM and Trop-2 antibodies in parallel. CTCs were isolated and stained for immune markers PD-L1 and HLA I using the VERSA (Versatile Exclusion-based Rare Sample Analysis) platform. Plasma was isolated for paired analysis of CTC and ctDNA content. CTCs were analyzed for enumeration and single-cell protein analysis. Overall survival (OS) was defined from time of sample collection, and survival analyses were performed using the Kaplan-Meier method. Results: We observed significantly shorter OS in pts with higher CTC burden (≥ 20 CTCs/7.5 mL blood) in samples captured with either EpCAM (median 34.1 vs 3.1 mo, P < 0.01) or Trop-2 (median 34.1 vs 6.2 months, P < 0.01). Furthermore, EpCAM and Trop-2 CTC burdens were higher at progression timepoints relative to responding or stable timepoints, when stratified according to treatment modality (table). Inter and intra-patient heterogeneous PD-L1 and HLA I expression and co-expression was observed on CTCs although no significant differences were seen globally between EpCAM and Trop-2 CTCs. In a cohort of pts treated with CPIs, we observed dynamic phenotypic changes in the ratio of HLA:PD-L1 that differed between EpCAM and Trop-2 CTCs. ctDNA analysis identified concordant increases in tumor fraction and acquired genomic mutations. When examined longitudinally across individual pts, these findings in tandem with changes in enumeration, suggest the emergence of different CTC subpopulations that may serve as biomarkers of resistance. Conclusions: We identify the prognostic significance of CTC enumeration with parallel EpCAM and Trop-2 CTC isolation and demonstrate the utility of a liquid biopsy assay that can detect pharmacodynamic changes in CTC burden and immune marker expression throughout the course of treatment. [Table: see text]