Profiling Of Circulating Tumor Cells Research Articles

Abstract PO1-16-05: Matched multi-analyte and multi-omic liquid biopsy of cell-free DNA, circulating tumor cells and extracellular vesicles in HER2-positive metastatic breast cancer patients

Abstract Background: Liquid biopsy, specifically cell-free DNA (cfDNA) mutation analysis, has recently entered clinical practice for treatment decision-making in hormone receptor (HR)-positive (+)/HER2-negative (-) metastatic breast cancer (mBC) patients. However, we showed that the analysis of multiple liquid biopsy analytes in the course of treatment in this BC subgroup has additive value. Since no multi-analyte studies are currently available for the subgroup of HER2+ mBC patients, we here studied multiple analytes [cfDNA, circulating tumor cells (CTCs) and extracellular vesicles (EVs)] and utilized our multi-omics perspective (CpG island methylation, mutations and mRNA expression) to get insight into their utility in therapy management of HER2+ mBC. Methods: 2x 9 ml blood was drawn from 21 HER2+ (HR+ n=16 and HR- n=5) mBC patients at the time of disease progression and at two consecutive staging time points. CTCs and their mRNA were isolated from 2x5 ml blood by positive immunomagnetic selection targeting EpCAM, EGFR and HER2 (AdnaTest EMT2/StemCell Select/Detect). Plasma of CTC-depleted blood was used for cfDNA isolation, while mRNA from EVs was isolated from 4 ml pre-filtered plasma by affinity-based binding to a spin column (exoRNeasy) using the remaining blood. The mRNA purified from CTCs and EVs by Oligo-dT beads was reverse transcribed, pre-amplified and analyzed by a multi-marker (18 genes) qPCR panel. qPCR data was normalized to CD45 (for CTC analysis) and data of 20 healthy female donor controls to identify BC specific overexpression signals with a specificity of >90% for all targets. Variants in the cfDNA were analyzed with a customized QIAseq Targeted DNA Panel with unique molecular indices (UMIs) and high coverage (mean 22.000x), while CpG island methylation in the cfDNA was analyzed with a customized QIAseq Targeted Methyl Panel with UMIs covering 9786 CpG sites (mean 900x). Consumables: QIAGEN, Germany. Results: In general, substantial differences occurred between the CTC and EV mRNA profiles. Transcripts involved in the PI3K pathway (mTOR, AKT2, PIK3CA) as well as ERBB2 signals were significantly more prevalent in CTCs compared to EVs and mTOR, ERCC1, SRC, AKT2 und PIK3CA CTC overexpression signals were found in >50% of these patients. In contrast, PARP1, AURKA, SRC und ERCC1 signals were significantly more prominent in the EVs and detected in >50% of the patients. ERCC1 signals were present in EVs with highest prevalence whereas ERBB2 signals were only present in CTCs. ERBB3+ CTCs were only detected in patients showing disease progression. Currently, cfDNA mutations as well as cfDNA CpG island methylation are under evaluation and the complete multi-analyte and multi-omic data set as well as their relation to clinical outcome will have been finalized to be presented at the meeting. Conclusion: We successfully established a workflow for parallel isolation of multiple liquid biopsy analytes from a minimized blood volume in HER2+ mBC. Preliminary mRNA profile results for CTCs and EVs show the complementary nature of these two liquid biopsy analytes. Besides the multi-analyte nature of this workflow, the pending results for genomic and epigenomic information will show which one of the analytes, alone or in combination, will help to optimize therapy management in HER2+ mBC patients. Citation Format: Sabine Kasimir-Bauer, Markus Storbeck, Ioanna Andreou, Siegfried hauch, Oliver Hoffmann, Rainer Kimmig, Corinna Keup. Matched multi-analyte and multi-omic liquid biopsy of cell-free DNA, circulating tumor cells and extracellular vesicles in HER2-positive metastatic breast cancer patients [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 PO1-16-05.

Abstract LB094: Assessment of minimal residual disease in lung cancer patients treated with osimertinib using liquid biopsy

Abstract Purpose: Drug tolerance has emerged as one of the major mechanisms driving resistance to targeted therapies (TT), but a comprehensive understanding of the dynamics and molecular heterogeneity underlying the adaptive drug response in patients is still lacking. Here, we used iterative liquid biopsies from osimertinib-treated lung cancer patients to monitor and characterize minimal residual disease (MRD) using both circulating tumor DNA (ctDNA) and circulating tumor cells (CTC). Experimental design: LUNG-RESIST (NCT04222335) is a prospective research study enrolling EGFR-mutant adenocarcinoma patients treated by osimertinib frontline. We collected blood samples at baseline, 1 month and every 3 months until progression. CtDNA was used to monitor the initial EGFR mutation (EGFRm) by digital PCR, and to identify new potential biomarkers of resistance by next-generation sequencing (NGS). CTC were enriched and isolated based on their size, absence of leucocyte staining and viability, to perform single-cell transcriptomic and genomic analyses. Results: 40 patients have been enrolled with a median progression-free survival (mPFS) of 14.5 months (95%CI, 8.5-24.5 months). 28/40 (70%) patients had detectable EGFRm in ctDNA at baseline, and decreased ctDNA level could be measured in 25/26 (96%) patients after 1 month of treatment, with a complete clearance in 15/26 (58%) patients. 7/11 (64%) patients without clearance at 1 month relapsed within 9 months. Clinical relapse could be anticipated 3 months ahead based on ctDNA increase for 9/20 (45%) patients. CTC-like cells have been collected at baseline and MRD (between 1 and 3 months) from respectively 31/40 (78%) and 29/40 (73%) patients, and at clinical progression for 12/22 (54%) patients who relapsed, for a total number of 1,510 cells. The number of CTC-like cells decreased after 1 month of treatment in 18/29 (62%) patients, and increased again in 7/12 (58%) patients at the time of clinical relapse. The results of NGS analyses on ctDNA and single-cell transcriptomic and genomic analyses on CTC will be presented at the congress, and should provide a better insight into the dynamics of molecular events occurring throughout the adaptive response in patients. Conclusion: We report the first molecular profiling of both ctDNA and CTC during the adaptive response to osimertinib in lung cancer patients. Monitoring the response and predicting the clinical outcome for EGFR-mutant lung cancer patients undergoing TT treatment can be done using ctDNA level as a biomarker. The isolation of CTC-like cells represents a non-invasive approach to study drug tolerance and ultimately develop new combinatory treatments to prevent relapse. Citation Format: Celia Delahaye, Anne Casanova, Estelle Clermont-Tarenchon, Aurelia Doussine, Juan-Pablo Cerapio, Anaïs Anton, Emma Devienne, Vincent Dongay, Julie Milia, Gilles Favre, Olivier Calvayrac, Anne Pradines, Julien Mazieres. Assessment of minimal residual disease in lung cancer patients treated with osimertinib using liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB094.

Abstract 7043: Genomic profiling of DLL3-positive and negative CTCs in small cell lung cancer

Abstract BACKGROUND: Delta-like ligand 3 (DLL3), an atypical Notch family protein implicated in neuroendocrine tumorigenesis, has emerged as a promising therapeutic target in small cell lung cancer (SCLC), prompting numerous clinical trials investigating DLL3-targeted treatments. Exploring DLL3 in circulating tumor cells (CTCs) through liquid biopsy, coupled with comprehensive genomic analysis, presents an invaluable and minimally-invasive avenue for monitoring disease progression. This approach holds the potential to tailor personalized treatment strategies, emphasizing the critical need for in-depth investigations into both DLL3-positive and negative cell genomic compositions. METHODS: This study examined blood collected in CellSave preservative tubes from stage I (n=17) and stage IV (n=12) SCLC patients, as well as healthy donors (n=10). The CELLSEARCH® platform was employed to count EpCAM-enriched CTCs and evaluate DLL3 protein expression. Subsequently, individual CTCs were isolated based on the presence and absence of DLL3 expression using the DEPArray™ PLUS. The isolated DLL3-negative and positive CTCs were subjected to low-pass sequencing using the Ampli1™ LowPass Kit to uncover genomic aberrations. RESULTS: CTCs were absent in the healthy control group. In stage I patients, CTCs were identified in 5.8% of blood samples, while in stage IV patients, they were present in 50% of samples, with an average CTC count of 148 in stage IV. Among a total of 2074 detected CTCs, 460 were DLL3-positive, accounting for 6-28% of EpCAM-enriched CTCs in individual patients. Analysis of >300 copy number alteration (CNA) profiles of sorted single cells revealed considerable inter-patient and intra-patient heterogeneity, delineating recurrent clonality and specific genomic alterations in DLL3-negative CTCs. In contrast, DLL3-positive cells showed more stochastic CNA profiles, suggestive of apoptosis-related DNA fragmentation. CONCLUSIONS: Integrating CellSearch, DEPArray, and low-pass sequencing provides a minimally-invasive approach to compare genomic characteristics in DLL3-positive and negative CTCs from SCLC patients. Extension of this approach to a larger patient cohort and employing machine learning algorithms will facilitate identification of patterns within diverse CNA profiles, improving patient stratification and predicting treatment responses for personalized therapeutic strategies in SCLC. Citation Format: Zoltan Simandi, Thai Bui, Alberto Ferrarini, Steven Hepburn, Richard G. Del Mastro. Genomic profiling of DLL3-positive and negative CTCs in small cell lung 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 7043.

Abstract 2757: Investigating regulatory drivers of prostate cancer metastasis in circulating tumor cells

Abstract Prostate cancer is the most common cancer in men and the second-leading cause of death. Most prostate cancer deaths are due to metastasis, particularly to the bone. Metastasis occurs when cells from the primary tumor travel through the blood as circulating tumor cells (CTCs) and settle in metastatic sites. CTCs are difficult to collect from patients, and understanding the relationships between CTCs and the tumor phenotypes of origin could reveal mechanisms of cancer metastasis. Hence, we utilized several genetically engineered mouse models (GEMMs) of metastatic prostate cancer to evaluate tumor phenotypes and CTCs. We compared the tumor phenotypes of several GEMMs of metastatic prostate cancer and identified a level of heterogeneity among tumors, particularly focusing on a GEMM that demonstrated severe metastasis, especially to the bone. Next, we analyzed CTCs from this GEMM and focused our analysis on transcriptional states that are regulated by proteins called master regulators (MRs). MRs control the expression of groups of genes called regulons, and pharmacologically inhibiting these MRs may lead to reversal of cancer phenotypes. We hypothesized that these MRs may be mechanistic drivers of CTC cell state in prostate cancer metastasis. We investigated MRs enriched in CTCs from mice and screened and validated Lap2, the lamina-associated polypeptide 2 protein, as a regulatory driver in mice with metastatic prostate cancer. Analysis of bulk RNA-seq profiles from primary and metastatic prostate samples in The Cancer Genome Atlas and Stand Up to Cancer cohorts, respectively, revealed that the regulon-based activity of Lap2 was significantly higher in the latter group. Moreover, analysis of single-cell RNA-seq profiles of CTCs isolated from prostate cancer patients confirmed aberrant Lap2 activity. Finally, the role of Lap2 was assessed in human tissue from an engineered multi-organ-on-a-chip model of metastasis. Silencing of Lap2 production in cells dissociated from mouse CTC-derived organoids inhibited extravasation to the bone in the model, suggesting a critical role for Lap2 in metastasis. Our findings illustrate the unique transcriptional profile of prostate cancer CTCs associated with their metastatic potential. We identified Lap2 as a novel driver of CTC dissemination and metastasis in mice and validated its activity in human prostate cancer, which can aid future therapies to prevent metastatic progression in patients. Citation Format: Aunika Zheng, Aleksandar Obradovic, Kacey Ronaldson-Bouchard, Gordana Vunjak-Novakovic, Andrea Califano, Peter A. Sims, Cory Abate-Shen, Arianna Giacobbe. Investigating regulatory drivers of prostate cancer metastasis in 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 2757.

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 3694: Genomic profiling of single cancer cells using the novel single-cell integrated mutational profiling of actionable cancer targets (scIMPACT) assay

Abstract Liquid biopsy provides opportunities to guide therapy decisions using biomarkers such as circulating tumor cells (CTCs) even years after the primary tumor resection. For this, novel methods permitting the genomic profiling of CTCs are needed to characterize systemic cancer spread and identify clinically targetable genomic alterations. Hence, we developed an assay based on the FDA-approved MSK-IMPACT® assay to analyze the genomes of single-cells. We present a series of benchmarking experiments using well-characterized cell lines to demonstrate the performance of our new Single-Cell Integrated Mutation Profiling of Actionable Cancer Targets (scIMPACT) assay.The scIMPACT assay was developed using Ampli1® WGA products of single-cell and pool samples. The workflow consists of an optimized library preparation protocol followed by targeted sequencing with the scIMPACT panel. A bioinformatics mutation calling workflow facilitates the detection of single nucleotide variations (SNVs), indels, and copy number variations (CNVs). To account for WGA associated bias, we developed an in-house proprietary machine learning based classifier algorithm. Two sample collectives were prepared and used for training and validating the workflow. The first collective, including genomic libraries of MDA-MB-453, BT474, BT549 and ZR-75.1 samples, was used for training of the mutation detection workflow. The second collective, consisting of HCC1395/HCC1395BL cell lines representing matched tumor and normal cells, was used to validate the performance of the assay. The scIMPACT assay identified somatic mutations in all WGA products as predicted from bulk gDNA samples and published literature. Notably, evidence of genetic heterogeneity was reported at the single cell level. Pertaining to the SNV detection, the training collective displayed 91% sensitivity and 96% specificity (AUC=0.98) while the validation collective demonstrated similar performance with 84% sensitivity and 96% specificity (AUC=0.90) proving the applicability of our workflow across different datasets. Furthermore, CNV analysis showed high concordance between matching gDNA and WGA samples. Our workflow enables mutational profiling with high specificity and sensitivity and accurate CNV detection in single cells. The scIMPACT assay has been successfully adapted to analyze samples at the single-cell level. Therefore, our method can be applied for the genomic profiling of patient-derived CTCs. Citation Format: Clara Chaiban, Adithi Ravikumar Varadarajan, Jonas Grote, Thomas Ragg, Isabell Blochberger, Vadim Dechand, Jens Warfsmann, Christoph A. Klein, Zbigniew T. Czyż. Genomic profiling of single cancer cells using the novel single-cell integrated mutational profiling of actionable cancer targets (scIMPACT) 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 3694.

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.

Integrin-associated transcriptional characteristics of circulating tumor cells in breast cancer patients.

Integrins enable cell communication with the basal membrane and extracellular matrix, activating signaling pathways and facilitating intracellular changes. Integrins in circulating tumor cells (CTCs) play a significant role in apoptosis evasion and anchor-independent survival. However, the link between CTCs expressing different integrin subunits, their transcriptional profile and, therefore, their functional activity with respect to metastatic potential remains unclear. Single-cell RNA sequencing of CD45-negative cell fraction of breast cancer patients was performed. All CTCs were divided into nine groups according to their integrin profile. СTCs without the gene expression of integrins or with the expression of non-complementary α and β subunits that cannot form heterodimers prevailed. Only about 15% of CTCs expressed integrin subunits which can form heterodimers. The transcriptional profile of CTCs appeared to be associated with the spectrum of expressed integrins. The lowest potential activity was observed in CTCs without integrin expression, while the highest frequency of expression of tumor progression-related genes, namely genes of stemness, epithelial-mesenchymal transition (EMT), invasion, proinflammatory chemokines and cytokines as well as laminin subunits, were observed in CTCs co-expressing ITGA6 and ITGB4. Validation on the protein level revealed that the median of integrin β4+ CTCs was higher in patients with more aggressive molecular subtypes as well as in metastatic breast cancer patients. One can expect that CTCs with ITGA6 and ITGB4 expression will have pronounced metastatic potencies manifesting in expression of EMT and stemness-related genes, as well as potential ability to produce chemokine/proinflammatory cytokines and laminins.

Kinetics and Biology of Circulating Tumor Cells (CTCs) and Measurable Residual Disease (MRD): Two Dynamic High-Risk Clones in Multiple Myeloma (MM)

BACKGROUND CTCs and MRD are two small clones associated with a high risk of progression in smoldering MM (SMM) and post treatment relapse in active MM. Despite growing knowledge about their clinical significance and biological features, these questions remain unanswered: 1) What is the prognostic value of CTC and MRD kinetics? 2) Is MM dissemination and on-treatment resistance driven by specific genomic alterations? 3) Are CTCs and MRD genetically related? AIM Analyze the kinetics and molecular features of CTCs and MRD in SMM and MM patients. METHODS CTC kinetics were investigated using NGF in 164 SMM patients with ≥3 assessments collected every 6 months in the iMMunocell study. MRD kinetics were investigated using NGF in 277 MM patients with ≥4 assessments in BM aspirates after induction, transplant, consolidation, and yearly during maintenance (GEM2012MENOS65-GEM2014MAIN trials). Unsupervised clustering based on CTC and MRD kinetics was performed using CONNECTOR. Molecular features of BM tumor cells at diagnosis were compared to paired CTCs in 94 SMM and MM patients and to paired MRD in 96 MM patients. In 10 cases, genomic data from tripartite BM tumor cells, CTCs, and MRD was available. Tumor samples were isolated based on patient-specific aberrant phenotypes using FACS. Whole exome and RNA-seq were performed in 343 and 217 samples, respectively. RESULTS Based on the assessment of CTCs in 754 PB samples, SMM patients clustered into 3 groups: sustained undetectable (n = 20), stable (n = 71) and evolving (n = 73) CTC levels. With a median follow-up of 2 years, the respective 2y progression-free rates were 100%, 94% and 81% ( P =.003). Risk stratification based on CTC kinetics (C-index 0.68) outperformed a single baseline assessment (C-index 0.61) and, along with the IMWG 20/2/20 model, had independent prognostic value (HR 3.4; P = .01). Patients with high risk cytogenetics showed more frequently evolving CTC levels. Studying genetic drivers of tumor egress, we found CTCs to closely resemble BM tumor cells (88% concordance at copy number [CNA] and somatic mutational [SNV] level). No recurrent cell-specific SNV or CNA was identified. CTC's transcriptional profile revealed 268 DEGs enriched in interferon alpha, gamma response and cell-adhesion pathways. Next, the prognostic value of MRD dynamics was analyzed according to 1,759 assessments, identifying 3 patient clusters: sustained undetectable (n = 100), stable (n = 104), and evolving (n = 73) MRD levels. Respective 6-year rates of PFS after consolidation were 90%, 75% and 5% ( P <.001), and of OS were 94%, 95% and 66% ( P<.001). Risk stratification based on MRD kinetics (C-index 0.82) outperformed a single MRD assessment before maintenance (C-index 0.62), the R-ISS (C-index 0.57) and R2-ISS (C-index 0.61) at diagnosis. MRD cells showed heterogeneous genomic evolution (60% median concordance) diverging from BM tumor cells at diagnosis due to de novo CNA and SNV that emerged at a subclonal level, particularly after transplant. After induction, MM driver mutations were detected or remained clonal in 13/19 (68%) MRD, whereas after transplant, this was true for only 5/13 (38%) MRD. No recurrent cell-specific SNV or CNA was identified. The transcriptional signature of MRD was treatment dependent, with common molecular features of on-treatment resistance found in all 96 patient-paired samples analyzed after various treatment stages. The 334 DEGs were commonly enriched in KRAS signaling hallmarks. Genomic profiles of tripartite BM tumor cells, CTCs and MRD from 10 MM patients confirmed a patient-specific mutational landscape with genomic heterogeneity in MRD. For instance, one patient exhibited BRAF & DIS3 mutations and del(13q) detected at baseline in BM tumor cells and CTCs, which persisted in MRD. After induction, de novo clonal SNVs, including a NEK11 mutation, emerged, followed by the appearance of 3 subclonal CNA after transplant, possibly contributing to resistance. CONCLUSIONS This is the largest dataset analyzing the kinetics and molecular features of CTCs and MRD in SMM and active MM. We showed superior prognostic value of CTC and MRD kinetics over single assessments. Tumor dissemination seems to be driven by transcriptional priming rather than acquired secondary genetic events, while on-treatment resistance is linked to genomic and transcriptional evolution, without recurrent genetic alterations and with common molecular signatures of resistance.

Advances in the role of circulating tumor cell heterogeneity in metastatic small cell lung cancer

AbstractSmall cell lung cancer (SCLC), a highly aggressive malignancy, is rapidly at an extensive stage once diagnosed and is one of the leading causes of death from malignancy. In the past decade, the treatment of SCLC has largely remained unchanged, and chemotherapy remains the cornerstone of SCLC treatment. The therapeutic value of adding immune checkpoint inhibitors to chemotherapy for SCLC is low, and only a few SCLC patients have shown a response to immune checkpoint inhibitors. Circulating tumor cells (CTCs) are tumor cells shed from solid tumor masses into the peripheral circulation and are key to tumor metastasis. Single‐cell sequencing has revealed that the genetic profiles of individual CTCs are highly heterogeneous and contribute to the poor outcome and prognosis of SCLC patients. Theoretically, phenotypic analysis of CTCs may be able to predict the diagnostic significance of new potential targets for metastatic tumors. In this paper, we will discuss in depth the heterogeneity of CTCs in SCLC and the value of CTCs for the diagnosis and prognosis of SCLC and as relevant tumor markers in metastatic SCLC.

Application of multicolor flow cytometry in liquid biopsy of breast cancer

As a result of the clinical study NCT04817501 “Phenotypic characterization of circulating tumor cells (CTCs) in tumors of the female reproductive system”, we developed a method for preoperative prediction of a recurrence risk in patients with stage T1 endometrial cancer (Patent No. 2762493 of 21.12.2021).The article presents a clinical case of the use of multicolor flow cytometry in liquid biopsy of breast cancer (BC). CTCs were detected in the blood of a patient with T2N0M0 BC, stage IIA before the initiation of treatment. Using multicolor flow cytometry, various CTC phenotypes were studied and the Her2/neu and ki-67 markers were determined. These markers were also studied in the biopsy and surgical material of the BC tissue using immunohistochemistry. As a result of the study, it was shown that the molecular profile of CTCs in the blood taken before fine needle aspiration biopsy coincided with that of cancer cells in the BC tissue. In addition, the calculated risk of tumor progression before biopsy predicted recurrence of cancer in this patient 20 months before its occurrence. The obtained results show the practical utility of multicolor flow cytometry in liquid biopsy of cancers. The ability to evaluate CTCs by various molecular parameters can be useful for diagnosing, predicting, monitoring, and determining treatment strategies for cancer patients.

Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer

Circulating tumor cells (CTCs) and epigenetic alterations are involved in the development of metastasis from solid tumors, such as colorectal cancer (CRC). The aim of this study was to characterize the DNA methylation profile of metastasis-competent CTCs in CRC. The DNA methylome of the human CRC-derived cell line CTC-MCC-41 was analyzed and compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells. The association between methylation and the transcriptional profile of CTC-MCC-41 was also evaluated. Differentially methylated CpGs were validated with pyrosequencing and qMSP. Compared to primary and metastatic CRC cells, the methylation profile of CTC-MCC-41 was globally different and characterized by a slight predominance of hypomethylated CpGs mainly distributed in CpG-poor regions. Promoter CpG islands and shore regions of CTC-MCC-41 displayed a unique methylation profile that was associated with the transcriptional program and relevant cancer pathways, mainly Wnt signaling. The epigenetic regulation of relevant genes in CTC-MCC-41 was validated. This study provides new insights into the epigenomic landscape of metastasis-competent CTCs, revealing biological information for metastasis development, as well as new potential biomarkers and therapeutic targets for CRC patients.

Deciphering the Biology of Circulating Tumor Cells through Single-Cell RNA Sequencing: Implications for Precision Medicine in Cancer.

Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment, single cell isolation, and bioinformatic tools applied for this purpose. Furthermore, we elucidated the translational knowledge from the transcriptomic profile of individual CTCs and the biology of cancer metastasis for developing effective therapeutics through targeting key pathways in CTCs.

Novel method for highly multiplexed gene expression profiling of circulating tumor cells (CTCs) captured from the blood of women with metastatic breast cancer

BackgroundEnumeration of circulating tumor cells (CTCs) has proven clinical significance for monitoring patients with metastatic cancers. Multiplexed gene expression profiling of CTCs is a potential tool for assessing disease status and monitoring treatment response. The Parsortix® technology enables the capture and harvest of CTCs from blood based on cell size and deformability. The HyCEAD™ (Hybrid Capture Enrichment Amplification and Detection) assay enables simultaneous amplification of short amplicons for up to 100 mRNA targets, and the Ziplex™ instrument quantifies the amplicons for highly sensitive gene expression profiling down to single cell levels. The aim of the study was to functionally assess this system.MethodsThe HyCEAD/Ziplex platform was used to quantify the expression levels for 72 genes using as little as 20 pg of total RNA or a single cultured tumor cell. Assay performance was evaluated using cells or total RNA spiked into Parsortix harvests of healthy donor blood. The assay was also evaluated using total RNA obtained from Parsortix harvests of blood from metastatic breast cancer (MBC) patients or healthy volunteers (HVs).ResultsUsing genes with low expression in WBC RNA and/or in unspiked Parsortix harvests from HVs, the assay distinguished between the different breast cancer and ovarian cancer cell lines with as little as 20 pg of total RNA (equivalent to a single cell) in the presence of 1 ng of WBC RNA. Single cultured cells spiked into Parsortix harvests from 10 mL of HV blood were also detected and distinguished from each other. CVs from repeatability experiments were less than 20%. Hierarchical clustering of clinical samples differentiated most MBC patients from HVs.ConclusionHyCEAD/Ziplex provided sensitive quantification of expression of 72 genes from 20 pg of total RNA from cultured tumor cell lines or from single cultured tumor cells spiked into lysates from Parsortix harvests of HV blood. The HyCEAD/Ziplex platform enables the quantification of selected genes in the presence of residual nucleated blood cells in Parsortix harvests. The HyCEAD/Ziplex platform is an effective tool for multiplexed molecular characterization of mRNA in small numbers of tumor cells harvested from blood.

Luminal and basal subtyping of circulating tumor cells and influence on outcomes in patients with metastatic castration-resistant prostate cancer.

e17034 Background: Luminal and basal subtyping using PAM50 classifier and the prostate cancer classification system (PCS) have been shown to predict outcomes and treatment response in prostate cancer (PCa). However, these genomic classifiers rely on the acquisition of tumor samples, which are usually not available in patients with metastatic castration resistant PCa (mCRPC). Circulating tumor cells (CTC) are tumors cells shed into bloodstream and can serve as surrogates of tumor. In this study, we aimed to subtype circulating tumor cells with PAM50 and PCS classifiers and evaluate their prognostic performance in mCRPC patients. Methods: A CTC RNA assay was developed by combining NanoVelcro microfluidic system for enriching CTCs and Nanostring nCounter system for PAM50 and PCS profiling of CTCs. The PAM50 and PCS genes were refined through a bioinformatic pipeline to ensure the specific profiling of CTCs. The classification and prognostic performance of the refined CTC-PAM50 and CTC-PCS gene panels were validated in GenomeDx GRID database. For the clinical study, 50 blood samples from mCRPC patients before the initiation of androgen receptor signaling inhibitors (ARSI) (n = 34) or taxanes (n = 16) were analyzed with the CTC RNA assay. Kaplan-Meier analysis and log-rank test were used to evaluate the association between CTC-PAM50/PCS subtypes and survival. Results: The refined CTC-PAM50 (36 genes) and CTC-PCS (40 genes) classifiers retained their original classification and prognostic performance in the GenomeDx GRID cohort. In the clinical study, the CTC RNA assay classified the 50 mCRPC patients into luminal A (n = 14), luminal B (n = 22), and basal (n = 14) by CTC-PAM50 classifier; and PCS1 (n = 5), PCS2 (n = 24), and PCS3 (n = 21) by CTC-PCS classifier. Overall, patients assigned as PCS1 subtype had shorter overall survival than other subtypes (hazard ratio [HR] = 4.8). In addition, basal or PCS1 subtype showed worse biochemical progression free survival than other subtypes (ARSI group: Basal: HR = 2.5; PCS1: HR = 6.9. Taxanes group: Basal: HR = 5.0; PCS1: HR = 7.2). Conclusions: Luminal and basal subtyping of CTCs is prognostic and provides a noninvasive method for molecular profiling mCRPC patients.

HERCULES: A prostate cancer (PC) sequencing panel for parallel analysis of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs).

5036 Background: In metastatic PC, tracking genomic alterations over time and with treatment can predict disease outcomes, guide treatment, and identify novel therapeutic targets. Analysis of peripheral blood ctDNA offers a non-invasive liquid biopsy for genomic profiling, but ctDNA often comprises a small portion of total cell-free DNA (cfDNA) in the blood, requiring high depth of sequencing which may still miss PC-relevant variants. We and others have shown that single CTCs captured from the same blood sample yield additional PC-relevant genomic data when combined with ctDNA profiling, but currently there is no assay that can be applied uniformly to both analytes. Here, we present a new amplicon-based sequencing panel capable of detecting PC-relevant variants in both cfDNA and single CTCs. Methods: PC-relevant genes were curated by overlapping reviews of cBioPortal for cancer genomics, the catalogue of somatic mutations in cancer (COSMIC), and PC-relevant genomic literature. HERCULES targets 36 genes with 258 amplicons covering PC-associated mutations and copy number variations. AmpliSeq HD targeted sequencing technology was applied for analysis of both cfDNA and CTCs. Analytical validation was performed sequentially, first using AcroMetrix and Seracare DNA control samples, then single and pooled LNCap and PC3 PC cells and cfDNA, then 8 patient peripheral blood samples of matched plasma cfDNA and single CTCs captured using the RareCyte platform from participants in SWOG S1802, an ongoing CTEP/CIRB-approved phase 3 trial for men with metastatic PC. Results: In DNA control samples with allele frequencies of 1%, 0.25%, and 0.1%, HERCULES displayed sensitivity of 100%, 75%, and 50%, respectively. In matched single cells and cfDNA from cell lines, HERCULES detected 100% of database-annotated somatic variants in cfDNA and in pools of 2 or more cells, and it identified >90% of variants in single cells. In 16 matched patient samples of cfDNA and single CTCs, with read coverage depths of >50,000x for 20ng cfDNA and >1,500x for single CTCs, HERCULES detected shared variants (mean N per sample = 6.1) as well as unique somatic variants (mean of 1.1 CTC variants not called in the cfDNA, and 4.1 cfDNA variants not called in the CTCs). Conclusions: HERCULES is, to our knowledge, the first PC-specific targeted sequencing panel capable of parallel genomic profiling of both ctDNA and CTCs. In our preliminary analytical validation, it detected somatic variants with high sensitivity in matched cfDNA and CTC samples. With additional validation, HERCULES has the potential to augment conventional ctDNA profiling by illuminating both cell-free and cellular genomic evolution during PC treatment and progression.

Abstract 2140: DNA damage response in circulating tumor cells shows predictive value for metastatic breast cancer patients receiving CDK4/6 inhibitors

Abstract Background: Resistance to CDK4/6 inhibitors (CDK4/6i), like Palbociclib and Ribociclib, plus endocrine therapy (TX) is an omnipresent topic for metastatic (M), hormone receptor-positive/HER2-negative (HR+/HER2-) breast cancer (BC) patients (pts). Circulating tumor cells (CTCs) represent the oncogenic heterogeneity in real time. Here, we aim to identify markers of resistance to CDK4/6i by mRNA profiling of CTCs. Methods: Blood of 90 HR+/HER2-MBC pts drawn before CDK4/6i plus endocrine TX (baseline: n=57 pts first line; n=33 second or more line pts), 19 HR+/HER2-MBC pts receiving endocrine monoTX (control group) and matched samples of 78/62 of these 109 pts after six months of TX/at progression (PD) were analyzed. Isolation of CTCs was conducted using the AdnaTest EMT2/StemCell Select. Expression profiling was conducted with preamplified cDNA utilizing QuantiNova LNA Probe assays targeting 25 genes. qPCR data were normalized to CD45 and data of 20 healthy female donors. Consumables: QIAGEN, Germany. Only results with Benjamini Hochberg corrected p<0.05 in univariate Cox regression and multivariate Cox regression with non-adjusted p<0.05 are demonstrated. Results: At baseline, in pts treated with CDK4/6i in the first line, CETN2 (HR 3.6)/MLH3 (HR 4)/E2F1 (HR 5.3) overexpression signals in CTCs correlated significantly with shorter progression-free survival (PFS) and shorter overall survival [(baseline to death, OS) (HR 8.3/HR 4.9/HR 3.8)], whereas ESR1 signals correlated with a shorter OS (HR 4.4). After six months of TX, in CDK4/6i treated pts, CXCR4 and CETN2 signals correlated with a shorter PFS and the signal dynamics from baseline to six months of CXCR4, CETN2 and PCNA also correlated with a shorter PFS. At PD, STAT1 signals were identified as potential Ribociclib specific resistance markers and Hippo pathway inhibition as a potential new approach for postCDK4/6i TX, because TEAD2 and WWTR1 correlated with shorter remaining time to death. Conclusion: We identified overexpression of transcripts involved in DNA damage response mechanisms (CETN2, MLH3 and/or PCNA) at baseline to have predictive and/or prognostic value in first line CDK4/6i treated pts while signal dynamics of CETN2 and PCNA to six months of TX could serve as monitoring marker in these pts. Currently, further longitudinal blood sampling over the course of treatment is underway to give a deeper insight in resistance development under CDK4/6i treatment. Citation Format: Corinna Keup, Charlotte Gruber, Stefanos Ioannis Moukas, Mitra Tewes, Hans-Christian Kolberg, Rainer Kimmig, Sabine Kasimir-Bauer. DNA damage response in circulating tumor cells shows predictive value for metastatic breast cancer patients receiving CDK4/6 inhibitors [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 2140.

Abstract P5-02-25: Transcriptional profiling of CTCs in metastatic breast cancer patients in the course of CDK4/6 inhibition

Abstract Background: De novo resistance defined as progression within six months and acquired resistance are one of the major problems in the subset of metastatic (M), hormone receptor-positive/HER2-negative (HR+/HER2-) breast cancer (BC) patients without visceral crisis receiving CDK4/6 inhibitors (CDK4/6i) plus endocrine therapy (TX). Here, we aim to identify predictive and monitoring markers of CDK4/6i resistance by conducting transcriptional profiling of circulating tumor cells (CTCs) that represent a real-time snapshot of the heterogeneity. Methods: Blood of (A) 60 HR+/HER2- MBC patients drawn at baseline of Palbociclib plus endocrine TX (TX as first line n=31, second or more lines n=29), (B) 19 HR+/HER2- MBC patients drawn before the initiation of endocrine monoTX (control) and matched blood samples of these patients after six months under TX (n=72) and at the time of progression (n=42) were analyzed. To enlarge the global CDK4/6i cohort at baseline, blood of (C) 32 patients before the initiation of Ribociclib plus endocrine TX was also drawn. Patients with progression within six months were defined as non-responders. Isolation of CTCs was conducted using positive immunomagnetic selection (AdnaTest EMT2/StemCell Select) and preamplified cDNA was analyzed by a multimarker qPCR panel utilizing QuantiNova LNA Probe assays targeting 25 genes involved in the DNA damage -, MAPK -, STAT -, Hippo – pathway or cell cycle, chemokine sensing, multidrug resistance and cell adhesion. qPCR data was normalized to CD45 and data of 20 healthy female donor controls to identify BC CTC specific overexpression signals with a specificity of >90% for all targets. Consumables: QIAGEN, Germany. Statistical analysis included log-rank testing and univariate Cox regression. Results: For first line CDK4/6i treated patients at baseline, CETN2 and E2F1 signals correlated significantly with worse progression-free survival (PFS) while CETN2 signals also related significantly to non-response. Furthermore, CETN2 and PCNA signals were significantly associated with worse overall survival (OS). Analyzing the Palbociclib cohort after six months of TX, PCNA signals correlated significantly with a decreased PFS while EpCAM signals showed a significant association with OS. In addition, CETN2, CXCR4, EpCAM, MLH3, WWTR1 signals after six months were shown to correlate significantly with a decreased OS and PFS and MAPK1 signals were only found in the non-responders. While non-response was related to appearing (from baseline to six months under TX) ABCC2, JUN and MAPK1 signals, disappearing ABCC2 signals were only found in the responders. Dynamics of ABCC2, CXCR4, EpCAM, JUN, MAPK1, MLH3, STAT1 and WWTR1 signals from baseline to six months under TX correlated significantly with OS and CXCR4 signal dynamics significantly with a worse PFS. At the time of progression, the presence of E2F1, JUN, MAPK1 and STAT1 signals correlated significantly with a decreased OS and in comparison to baseline analysis, the prevalence of ABCC2, EpCAM, E2F1, CETN2 and CXCR4 signals increased. Conclusion: CTC overexpression signals at baseline of targets involved in the cell cycle (CETN2 and E2F1) might be predictive markers for de novo resistance to CDK4/6i as first line TX, while ABCC2 (multidrug resistance), EpCAM (cell adhesion), E2F1, CETN2 and CXCR4 (chemokine sensing) signals could indicate acquired resistance to Palbociclib. In case of disease progression, E2F1, JUN (cell cycle) and targets of the MAPK- and STAT- pathway could be relevant targets for therapeutic strategies beyond Palbociclib TX. Monitoring and prognostic value was shown for single and repeated measurement of signals under TX in genes involved in resistance, cell cycle progression, DNA damage response (MLH3, PCNA), chemokine sensing, cell adhesion and the MAPK-, STAT- and Hippo (WWTR1) pathway. Citation Format: Sabine Kasimir-Bauer, Charlotte Gruber, Stefanos Moukas, Mitra Tewes, Hans-Christian Kolberg, Rainer Kimmig, Corinna Keup. Transcriptional profiling of CTCs in metastatic breast cancer patients in the course of CDK4/6 inhibition [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 P5-02-25.

Abstract P6-01-29: Serial genomic analysis of circulating free DNA and change of immune-related gene signature in triple negative and HER2 positive advanced, metastatic breast cancer

Abstract Background: Circulating tumor cells (CTCs) and circulating free DNA (cfDNA) have a promising role for detecting early response and progression in breast cancer. Furthermore, change of immune-related gene signature during systemic treatment influence the treatment response of breast cancer. Herein we report the outcome of serial genomic analysis of CTC, cfDNA and change of immune-related gene signature in advanced, metastatic triple negative breast cancer (TNBC) and HER2 positive breast cancer (BC). Methods: Serial whole blood were prospectively collected in 18 early or advanced, and 10 metastatic BC patients periodically during systemic chemotherapy. CTC was isolated from whole blood through EpCAM positive bead selection, and ctDNA was isolated from plasma. For genomic profiling of CTC and ctDNA, Oncomine™ Comprehensive Assay Plus and Oncomine™ Pan-Cancer cfDNA assay (included BRCA1, BRCA2 and MYCN customized panel) was performed and analyzed, respectively. Total RNA was extracted using whole blood and analyzed using Nanostring Pancancer Immunology Panel. Results: Total 61 serial samples were obtained from 28 patients during the study. At baseline, FGFR4 mutation was the most commonly detected (10 patients, 76.9%) with median variant of allele frequency (VAF) of 54.5% (range 20.87~99.8%) in advanced and metastatic TNBC based on CTC analysis. In case of cfDNA, 11 patients (84.6%) showed TP53 mutation with low VAF (median 1.8%, range 0.1~12.3%). In HER2 positive BC, FGFR4 was also the most common mutation (5 patients [62.5%]; median VAF 57.9%) in CTC analysis and TP53 was most frequently detected (5 patients, [62.5%]; median VAF 3.0%) in cfDNA analysis. In three pathogenic gBRCA1 mutated patients, BRCA1 was identically detected in 2 patients based on CTC analysis and in 3 patients based on cfDNA analysis with VAF of approximately 50%. There were no significant changes of VAF in target mutations of CTC and cfDNA during systemic treatment, irrespective of tumor response and subtype. However, in one patients who harbored 13 mutations detected based on baseline CTC analysis, showed disappearance of 12 mutations in final CTC analysis with partial response based on radiologic findings. In contrary, there was another patient who gained multiple mutations during CTC analysis during neoadjuvant chemotherapy (NAC) with gain of tumor mutational burden (TMB). She did not achieve pathologic complete response and RCB score was 3 after completion of NAC. Most TNBC patients who received NAC and showed partial response, TMB showed gradual decrease during treatment. Baseline immune-related gene signatures were compared between HER2(+) BC and TNBC, and type 1 interferon signaling pathway was upregulated in HER2 (+) BC compared to TNBC. Conclusions: Our study suggest that serial follow up CTC and ctDNA, immune-related gene signature is feasible and reflect the general characteristics of baseline characteristics and dynamic molecular alteration of breast cancer. Further analysis with larger patient sample and correlation with tumor tissue is warranted in the future. Citation Format: Jieun Lee, Kabsoo Shin, Seung Yeon Joe, Hayoon Lee, Byung Hee Jeon, Ahwon Lee. Serial genomic analysis of circulating free DNA and change of immune-related gene signature in triple negative and HER2 positive advanced, metastatic breast cancer [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 P6-01-29.

Metabolomic analysis of circulating tumor cells derived liver metastasis of colorectal cancer

Metabolic reprogramming is one of the essential features of tumor that may dramatically contribute to metastasis and collapse. The metabolic profiling is investigated on the patient derived tissue and cancer cell line derived mouse metastasis xenograft. As well-recognized “seeds” for remote metastasis of tumor, role of circulating tumor cells (CTCs) in the study of metabolic reprogramming feature of tumor is yet to be elucidated. More specifically, whether there is difference of metabolic features of liver metastasis in colorectal cancer (CRC) derived from either CTCs or cancer cell line is still unknown. In this study, comprehensive untargeted metabolomics was performed using high performance liquid chromatography-mass spectrometry (HPLC-MS) in liver metastasis tissues from CT26 cells and CTCs derived mouse models. We identified 288 differential metabolites associated with the pathways such as one carbon pool by folate, folate biosynthesis and histidine metabolism through bioinformation analysis. Multiple gene expression was upregulated in the CTCs derived liver metastasis, specifically some specific enzymes. These results indicated that the metabolite phenotype and corresponding gene expression in the CTCs derived liver metastasis tissues was different from the parental CT26 cells, displaying a specific up-regulation of mRNAs involved in the above metabolism-related pathways. The metabolic profile of CTCs was characterized on the liver metastatic process in colorectal cancer. The invasion ability and chemo drug tolerance of the CTCs derived tumor and metastasis was found to be overwhelming higher than cell line derived counterpart. Identification of the differential metabolites will lead to a better understanding of the hallmarks of the cancer progression and metastasis, which may suggest potential attractive target for treating metastatic CRC.