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1.
PLoS Biol ; 20(1): e3001527, 2022 01.
Article in English | MEDLINE | ID: mdl-35089911

ABSTRACT

CRISPR-associated nucleases are powerful tools for precise genome editing of model systems, including human organoids. Current methods describing fluorescent gene tagging in organoids rely on the generation of DNA double-strand breaks (DSBs) to stimulate homology-directed repair (HDR) or non-homologous end joining (NHEJ)-mediated integration of the desired knock-in. A major downside associated with DSB-mediated genome editing is the required clonal selection and expansion of candidate organoids to verify the genomic integrity of the targeted locus and to confirm the absence of off-target indels. By contrast, concurrent nicking of the genomic locus and targeting vector, known as in-trans paired nicking (ITPN), stimulates efficient HDR-mediated genome editing to generate large knock-ins without introducing DSBs. Here, we show that ITPN allows for fast, highly efficient, and indel-free fluorescent gene tagging in human normal and cancer organoids. Highlighting the ease and efficiency of ITPN, we generate triple fluorescent knock-in organoids where 3 genomic loci were simultaneously modified in a single round of targeting. In addition, we generated model systems with allele-specific readouts by differentially modifying maternal and paternal alleles in one step. ITPN using our palette of targeting vectors, publicly available from Addgene, is ideally suited for generating error-free heterozygous knock-ins in human organoids.


Subject(s)
DNA/genetics , Deoxyribonuclease I/metabolism , Genetic Loci , Organoids/metabolism , Recombinational DNA Repair , Staining and Labeling/methods , Alleles , Base Sequence , CRISPR-Associated Protein 9/genetics , CRISPR-Associated Protein 9/metabolism , Colon/cytology , Colon/metabolism , DNA/metabolism , DNA End-Joining Repair , Deoxyribonuclease I/genetics , Electroporation/methods , Epithelial Cells/cytology , Epithelial Cells/metabolism , Fluorescent Dyes/chemistry , Fluorescent Dyes/metabolism , Gene Knock-In Techniques , Genetic Vectors , Genome, Human , Heterozygote , Humans , Organoids/cytology
2.
Cytometry A ; 103(11): 881-888, 2023 11.
Article in English | MEDLINE | ID: mdl-37461156

ABSTRACT

The median number of circulating tumor cells (CTCs) detected in 7.5 mL of peripheral blood by CellSearch (PB-CS) in patients with metastatic prostate cancer is in the order of 1-10, which means many samples have insufficient tumor cells for comprehensive characterization. A significant increase is obtained through diagnostic leukapheresis (DLA), however, only 2%-3% of the DLA product can be processed per CellSearch test, limiting the gain. We processed aliquots from 30 DLA products of metastatic prostate cancer patients consisting of 0.2 × 109 leukocytes using CellSearch (DLA-CS) as well as the newly introduced reduced enrichment reagent protocol (RER), which uses 10-fold less enrichment reagents than DLA-CS. The number of tumor cells and the total number of captured cells were determined using the CellTracks Analyzer. Additionally, for six DLA samples, a 1.0 × 109 leukocyte aliquot was processed (RER+), using twofold less enrichment reagents than DLA-CS. A median 2.7-fold reduction in leukocyte co-enrichment was found between DLA-CS and RER methods without any loss in tumor cell recovery (Wilcoxon Signed Ranks Test, p = 0.953). Using 1.0 × 109 leukocyte aliquots a fourfold increase in tumor cells was found compared to DLA-CS and a 19-fold increase compared to PB-CS was obtained. The here-introduced RER protocol results in a higher final sample purity without any loss in tumor cell recovery while using 10-fold less CellSearch capture reagent. With this improved method, 26% of the leukapheresis sample can now be processed using reagents from a single CellSearch test, enabling the obtainment of a sufficient number of CTCs for comprehensive characterization in most metastatic prostate cancer patients.


Subject(s)
Neoplastic Cells, Circulating , Prostatic Neoplasms , Male , Humans , Neoplastic Cells, Circulating/pathology , Leukapheresis/methods , Prostatic Neoplasms/diagnosis , Biomarkers, Tumor
3.
Br J Cancer ; 126(3): 409-418, 2022 02.
Article in English | MEDLINE | ID: mdl-34848855

ABSTRACT

BACKGROUND: Circulating tumour cells (CTCs) can be used to monitor cancer longitudinally, but their use in non-small cell lung cancer (NSCLC) is limited due to low numbers in the peripheral blood. Through diagnostic leukapheresis (DLA) CTCs can be obtained from larger blood volumes. METHODS: Patients with all stages of NSCLC were selected. One total body blood volume was screened by DLA before and after treatment. Peripheral blood was drawn pre- and post DLA for CTC enumeration by CellSearch. CTCs were detected in the DLA product (volume equalling 2 × 108 leucocytes) and after leucocyte depletion (RosetteSep, 9 mL DLA product). Single-cell, whole-genome sequencing was performed on isolated CTCs. RESULTS: Fifty-six patients were included. Before treatment, CTCs were more often detected in DLA (32/55, 58%) than in the peripheral blood (pre-DLA: 18/55, 33%; post DLA: 13/55, 23%, both at p < 0.01). CTCs per 7.5 mL DLA product were median 9.2 times (interquartile range = 5.6-24.0) higher than CTCs in 7.5 mL blood. RosetteSEP did not significantly improve CTC detection (pretreatment: 34/55, 62%, post treatment: 16/34, 47%) and CTCs per mL even decreased compared to DLA (p = 0.04).. Patients with advanced-stage disease with DLA-CTC after treatment showed fewer tumour responses and shorter progression-free survival (PFS) than those without DLA-CTC (median PFS, 2.0 vs 12.0 months, p < 0.01). DLA-CTC persistence after treatment was independent of clinical factors associated with shorter PFS (hazard ratio (HR) = 5.8, 95% confidence interval (CI), 1.4-35.5, p = 0.02). All evaluable CTCs showed aneuploidy. CONCLUSIONS: DLA detected nine times more CTCs than in the peripheral blood. The sustained presence of CTCs in DLA after treatment was associated with therapy failure and shortened PFS. TRIAL REGISTRATION: The study was approved by the Medical Ethical Committee (NL55754.042.15) and was registered in the Dutch trial register (NL5423).


Subject(s)
Biomarkers, Tumor/blood , Carcinoma, Non-Small-Cell Lung/mortality , Leukapheresis/methods , Lung Neoplasms/mortality , Neoplastic Cells, Circulating/pathology , Single-Cell Analysis/methods , Aged , Carcinoma, Non-Small-Cell Lung/blood , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/pathology , Cell Count , Female , Humans , Lung Neoplasms/blood , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , Male , Middle Aged , Progression-Free Survival , Survival Rate , Treatment Outcome , Whole Genome Sequencing/methods
4.
Pharmacogenomics J ; 21(2): 152-164, 2021 04.
Article in English | MEDLINE | ID: mdl-33011741

ABSTRACT

Genetic variation may mediate the increased risk of cardiovascular disease (CVD) in chemotherapy-treated testicular cancer (TC) patients compared to the general population. Involved single nucleotide polymorphisms (SNPs) might differ from known CVD-associated SNPs in the general population. We performed an explorative genome-wide association study (GWAS) in TC patients. TC patients treated with platinum-based chemotherapy between 1977 and 2011, age ≤55 years at diagnosis, and ≥3 years relapse-free follow-up were genotyped. Association between SNPs and CVD occurrence during treatment or follow-up was analyzed. Data-driven Expression Prioritized Integration for Complex Trait (DEPICT) provided insight into enriched gene sets, i.e., biological themes. During a median follow-up of 11 years (range 3-37), CVD occurred in 53 (14%) of 375 genotyped patients. Based on 179 SNPs associated at p ≤ 0.001, 141 independent genomic loci associated with CVD occurrence. Subsequent, DEPICT found ten biological themes, with the RAC2/RAC3 network (linked to endothelial activation) as the most prominent theme. Biology of this network was illustrated in a TC cohort (n = 60) by increased circulating endothelial cells during chemotherapy. In conclusion, the ten observed biological themes highlight possible pathways involved in CVD in chemotherapy-treated TC patients. Insight in the genetic susceptibility to CVD in TC patients can aid future intervention strategies.


Subject(s)
Antineoplastic Agents/therapeutic use , Cardiovascular Diseases/genetics , Neoplasms, Germ Cell and Embryonal/drug therapy , Neoplasms, Germ Cell and Embryonal/genetics , Organoplatinum Compounds/therapeutic use , Testicular Neoplasms/drug therapy , Testicular Neoplasms/genetics , Adolescent , Adult , Cohort Studies , Endothelial Cells/drug effects , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study/methods , Genomics/methods , Genotype , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide/genetics , Young Adult
5.
Clin Chem ; 67(4): 631-641, 2021 03 31.
Article in English | MEDLINE | ID: mdl-33491069

ABSTRACT

BACKGROUND: Multiple technologies are available for detection of circulating tumor cells (CTCs), but standards to evaluate their technical performance are still lacking. This limits the applicability of CTC analysis in clinic routine. Therefore, in the context of the CANCER-ID consortium, we established a platform to assess technical validity of CTC detection methods in a European multi-center setting using non-small cell lung cancer (NSCLC) as a model. METHODS: We characterized multiple NSCLC cell lines to define cellular models distinct in their phenotype and molecular characteristics. Standardized tumor-cell-bearing blood samples were prepared at a central laboratory and sent to multiple European laboratories for processing according to standard operating procedures. The data were submitted via an online tool and centrally evaluated. Five CTC-enrichment technologies were tested. RESULTS: We could identify 2 cytokeratin expressing cell lines with distinct levels of EpCAM expression: NCI-H441 (EpCAMhigh, CKpos) and NCI-H1563 (EpCAMlow, CKpos). Both spiked tumor cell lines were detected by all technologies except for the CellSearch system that failed to enrich EpCAMlow NCI-H1563 cells. Mean recovery rates ranged between 49% and 75% for NCI-H411 and 32% and 76% for NCI-H1563 and significant differences were observed between the tested methods. CONCLUSIONS: This multi-national proficiency testing of CTC-enrichment technologies has importance in the establishment of guidelines for clinically applicable (pre)analytical workflows and the definition of minimal performance qualification requirements prior to clinical validation of technologies. It will remain in operation beyond the funding period of CANCER-ID in the context of the European Liquid Biopsy Society (ELBS).


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Neoplastic Cells, Circulating , Biomarkers, Tumor , Carcinoma, Non-Small-Cell Lung/diagnosis , Cell Line, Tumor , Humans , Lung Neoplasms/diagnosis
6.
Platelets ; 32(4): 440-443, 2021 May 19.
Article in English | MEDLINE | ID: mdl-32552252

ABSTRACT

The study of extracellular vesicles (EVs) in plasma requires removal of cells including platelets. At present, a two-step centrifugation protocol is recommended and commonly used. A simpler protocol that is less operator dependent is likely to improve the quality of plasma samples collected for EV research. The objective of this study is to develop an easy, fast and clinically applicable centrifugation protocol to produce essentially platelet-free plasma with a high yield for EV research. We compared the two-step centrifugation protocol to a single-step protocol at 5,000 g for 20 minutes. The removal of platelets was computationally predicted and experimentally validated. Flow cytometry was used to detect residual platelets and platelet-derived (CD61+) EVs. The single-step protocol at 5,000 g (i) is less laborious and approximately ten minutes faster, (ii) removes platelets as effective as the two-step centrifugation protocol, and (iii) has a ~ 10% higher plasma yield, whereas (iv) the recovery of platelet-derived EVs is comparable. For future research on plasma EVs we recommend the newly developed, easy and fast single-step protocol for preparation of platelet-free plasma for research on plasma biomarkers including EVs.


Subject(s)
Blood Platelets/metabolism , Centrifugation/methods , Extracellular Vesicles/metabolism , Humans
7.
Br J Cancer ; 122(6): 801-811, 2020 03.
Article in English | MEDLINE | ID: mdl-31937922

ABSTRACT

BACKGROUND: Circulating tumour cells (CTCs) in blood associate with overall survival (OS) of cancer patients, but they are detected in extremely low numbers. Large tumour-derived extracellular vesicles (tdEVs) in castration-resistant prostate cancer (CRPC) patients are present at around 20 times higher frequencies than CTCs and have equivalent prognostic power. In this study, we explored the presence of tdEVs in other cancers and their association with OS. METHODS: The open-source ACCEPT software was used to automatically enumerate tdEVs in digitally stored CellSearch® images obtained from previously reported CTC studies evaluating OS in 190 CRPC, 450 metastatic colorectal cancer (mCRC), 179 metastatic breast cancer (MBC) and 137 non-small cell lung cancer (NSCLC) patients before the initiation of a new treatment. RESULTS: Presence of unfavourable CTCs and tdEVs is predictive of OS, with respective hazard ratios (HRs) of 2.4 and 2.2 in CRPC, 2.7 and 2.2 in MBC, 2.3 and 1.9 in mCRC and 2.0 and 2.4 in NSCLC, respectively. CONCLUSIONS: tdEVs have equivalent prognostic value as CTCs in the investigated metastatic cancers. CRPC, mCRC, and MBC (but not NSCLC) patients with favourable CTC counts can be further prognostically stratified using tdEVs. Our data suggest that tdEVs could be used in clinical decision-making.


Subject(s)
Extracellular Vesicles/metabolism , Neoplasm Metastasis/physiopathology , Neoplasms/complications , Neoplastic Cells, Circulating/metabolism , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Neoplasms/blood , Neoplasms/mortality , Survival Analysis
8.
Nanomedicine ; 24: 102109, 2020 02.
Article in English | MEDLINE | ID: mdl-31669420

ABSTRACT

Extracellular Vesicles (EVs) can be used as biomarkers in diseases like cancer, as their lineage of origin and molecular composition depend on the presence of cancer cells. Recognition of tumor-derived EVs (tdEVs) from other particles and EVs in body fluids requires characterization of single EVs to exploit their biomarker potential. We present here a new method based on synchronized Rayleigh and Raman light scattering from a single laser beam, which optically traps single EVs. Rapidly measured sequences of the Rayleigh scattering amplitude show precisely when an individual EV is trapped and the synchronously acquired Raman spectrum labels every time interval with chemical information. Raman spectra of many single EVs can thus be acquired with great fidelity in an automated manner by blocking the laser beam at regular time intervals. This new method enables single EV characterization from fluids at the single particle level.


Subject(s)
Extracellular Vesicles/chemistry , Spectrum Analysis, Raman , Extracellular Vesicles/metabolism , Humans , PC-3 Cells , Particle Size
9.
Int J Cancer ; 144(12): 3127-3137, 2019 06 15.
Article in English | MEDLINE | ID: mdl-30536653

ABSTRACT

The need for a liquid biopsy in non-small cell lung cancer (NSCLC) patients is rapidly increasing. We studied the relation between overall survival (OS) and the presence of four cancer biomarkers from a single blood draw in advanced NSCLC patients: EpCAMhigh circulating tumor cells (CTC), EpCAMlow CTC, tumor-derived extracellular vesicles (tdEV) and cell-free circulating tumor DNA (ctDNA). EpCAMhigh CTC were detected with CellSearch, tdEV in the CellSearch images and EpCAMlow CTC with filtration after CellSearch. ctDNA was isolated from plasma and mutations present in the primary tumor were tracked with deep sequencing methods. In 97 patients, 21% had ≥2 EpCAMhigh CTC, 15% had ≥2 EpCAMlow CTC, 27% had ≥18 tdEV and 19% had ctDNA with ≥10% mutant allele frequency. Either one of these four biomarkers could be detected in 45% of the patients and all biomarkers were present in 2%. In 11 out of 16 patients (69%) mutations were detected in the ctDNA. Two or more unfavorable biomarkers were associated with poor OS. The presence of EpCAMhigh CTC and elevated levels of tdEV and ctDNA was associated with a poor OS; however, the presence of EpCAMlow CTC was not. This single tube approach enables simultaneous analysis of multiple biomarkers to explore their potential as a liquid biopsy.


Subject(s)
Carcinoma, Non-Small-Cell Lung/diagnosis , Liquid Biopsy/methods , Lung Neoplasms/diagnosis , Adult , Aged , Aged, 80 and over , Biomarkers, Tumor/blood , Biomarkers, Tumor/genetics , Carcinoma, Non-Small-Cell Lung/blood , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Case-Control Studies , Circulating Tumor DNA/blood , Circulating Tumor DNA/genetics , Epithelial Cell Adhesion Molecule/blood , Female , Humans , Lung Neoplasms/blood , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Male , Middle Aged , Mutation , Neoplasm Staging , Neoplastic Cells, Circulating/pathology , Survival Rate
10.
Breast Cancer Res Treat ; 175(2): 451-458, 2019 Jun.
Article in English | MEDLINE | ID: mdl-30756285

ABSTRACT

PURPOSE: The estrogen (ER), progesterone (PR), and HER2 status are essential in guiding treatment decisions in breast cancer patients. In daily life, the ER/PR/HER2 status is expected to be commonly tested twice, i.e., at diagnosis using material from tumor needle biopsies, and after tumor resection using full tumor tissue material. This study explored the discordance of ER/PR/HER2 between tumor needle biopsies and full tumor resection material using real-world patient-level data from Dutch breast cancer patients. METHODS: Pathology reports of 11,054 breast cancer patients were derived from PALGA (Dutch Pathology Registry). Discordance was calculated for multiple combinations of the ER/PR/HER2 receptor status. The influence of patient and tumor characteristics on the probability of having discordant test results was analyzed using multiple logistic regression models (separately for ER, PR and HER2). RESULTS: For 1279 patients (14.4%), at least one of the receptors (ER/PR/HER2) was determined on both biopsy and tumor tissue material. The majority had concordant test results for ER (n = 916; 94.8%), PR (n = 1170; 86.7%), and HER2 (n = 881; 98.1%). Patients having an ER- and HER2-positive but PR-negative biopsy classification, BR grade III, and < 10% tumor tissue remaining after neoadjuvant therapy (NAT) have the highest probability of ER discordant test results (OR 4.991; p = 83.31%). The probability of discordance in PR is based on different sets of patient and tumor characteristics. Potential cost savings from omitting multiple tests if concordance can be perfectly predicted can be up to €205,000 yearly. CONCLUSIONS: Double testing of ER/PR/HER2 is less common than expected. Discordance in ER/PR/HER2 test results between tumor needle biopsy taken at the time of diagnosis and tumor resection material is very low, especially in patients not receiving any form of neoadjuvant therapy. These results imply that a substantial number of tests can potentially be omitted in specific subgroups of breast cancer patients.


Subject(s)
Biomarkers, Tumor/genetics , Biopsy , Breast Neoplasms/diagnosis , Adult , Aged , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Breast Neoplasms/surgery , Estrogen Receptor alpha/genetics , Estrogens/genetics , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Middle Aged , Neoadjuvant Therapy , Netherlands/epidemiology , Progesterone/genetics , Receptor, ErbB-2/genetics , Receptors, Progesterone/genetics
11.
Int J Mol Sci ; 20(3)2019 Jan 23.
Article in English | MEDLINE | ID: mdl-30678037

ABSTRACT

The availability of viable tumor cells could significantly improve the disease management of cancer patients. Here we developed and evaluated a method using self-seeding microwells to obtain single circulating tumor cells (CTC) and assess their potential to expand. Conditions were optimized using cells from the breast cancer cell line MCF-7 and blood from healthy volunteers collected in EDTA blood collection tubes. 43% of the MCF-7 cells (nucleus+, Ethidium homodimer-1-, Calcein AM+, α-EpCAM+, α-CD45-) spiked into 7.5 mL of blood could be recovered with 67% viability and these could be further expanded. The same procedure tested in metastatic breast and prostate cancer patients resulted in a CTC recovery of only 0⁻5% as compared with CTC counts obtained with the CellSearch® system. Viability of the detected CTC ranged from 0⁻36%. Cell losses could be mainly contributed to the smaller size and greater flexibility of CTC as compared to cultured cells from cell lines and loss during leukocyte depletion prior to cell seeding. Although CTC losses can be reduced by fixation, to obtain viable CTC no fixatives can be used and pore size in the bottom of microwells will need to be reduced, filtration conditions adapted and pre-enrichment improved to reduce CTC losses.


Subject(s)
Cell Separation , Immunophenotyping , Neoplastic Cells, Circulating/metabolism , Biomarkers , Breast Neoplasms , Cell Culture Techniques , Cell Line, Tumor , Cell Separation/methods , Cell Survival , Female , Humans , Immunophenotyping/methods , Male , Neoplastic Cells, Circulating/pathology , Prostatic Neoplasms
12.
Int J Cancer ; 143(10): 2584-2591, 2018 11 15.
Article in English | MEDLINE | ID: mdl-30006930

ABSTRACT

Frequently, the number of circulating tumor cells (CTC) isolated in 7.5 mL of blood is too small to reliably determine tumor heterogeneity and to be representative as a "liquid biopsy". In the EU FP7 program CTCTrap, we aimed to validate and optimize the recently introduced Diagnostic LeukApheresis (DLA) to screen liters of blood. Here we present the results obtained from 34 metastatic cancer patients subjected to DLA in the participating institutions. About 7.5 mL blood processed with CellSearch® was used as "gold standard" reference. DLAs were obtained from 22 metastatic prostate and 12 metastatic breast cancer patients at four different institutions without any noticeable side effects. DLA samples were prepared and processed with different analysis techniques. Processing DLA using CellSearch resulted in a 0-32 fold increase in CTC yield compared to processing 7.5 mL blood. Filtration of DLA through 5 µm pores microsieves was accompanied by large CTC losses. Leukocyte depletion of 18 mL followed by CellSearch yielded an increase of the number of CTC but a relative decrease in yield (37%) versus CellSearch DLA. In four out of seven patients with 0 CTC detected in 7.5 mL of blood, CTC were detected in DLA (range 1-4 CTC). The CTC obtained through DLA enables molecular characterization of the tumor. CTC enrichment technologies however still need to be improved to isolate all the CTC present in the DLA.


Subject(s)
Breast Neoplasms/blood , Breast Neoplasms/pathology , Neoplastic Cells, Circulating/pathology , Prostatic Neoplasms, Castration-Resistant/blood , Prostatic Neoplasms, Castration-Resistant/pathology , Female , Humans , Leukapheresis/methods , Liquid Biopsy/methods , Male
13.
Anal Chem ; 90(19): 11290-11296, 2018 10 02.
Article in English | MEDLINE | ID: mdl-30157378

ABSTRACT

Mammalian cells release extracellular vesicles (EVs) into their microenvironment that travel the entire body along the stream of bodily fluids. EVs contain a wide range of biomolecules. The transported cargo varies depending on the EV origin. Knowledge of the origin and chemical composition of EVs can potentially be used as a biomarker to detect, stage, and monitor diseases. In this paper, we demonstrate the potential of EVs as a prostate cancer biomarker. A Raman optical tweezer was employed to obtain Raman signatures from four types of EV samples, which were red blood cell- and platelet-derived EVs of healthy donors and the prostate cancer cell lines- (PC3 and LNCaP) derived EVs. EVs' Raman spectra could be clearly separated/classified into distinct groups using principal component analysis (PCA) which permits the discrimination of the investigated EV subtypes. These findings may provide new methodology to detect and monitor early stage cancer.


Subject(s)
Extracellular Vesicles/metabolism , Prostatic Neoplasms/diagnosis , Prostatic Neoplasms/pathology , Spectrum Analysis, Raman/methods , Blood Platelets/pathology , Erythrocytes/pathology , Humans , Male
14.
Cytometry A ; 93(12): 1202-1206, 2018 12.
Article in English | MEDLINE | ID: mdl-30246927

ABSTRACT

For using counts of circulating tumor cells (CTCs) in the clinic to aid a physician's decision, its reported values will need to be accurate and comparable between institutions. Many technologies have become available to enumerate and characterize CTCs, thereby showing a large range of reported values. Here we introduce an Open Source CTC scoring tool to enable comparison of different reviewers and facilitate the reach of a consensus on assigning objects as CTCs. One hundred images generated from two different platforms were used to assess concordance between 15 reviewers and an expert panel. Large differences were observed between reviewers in assigning objects as CTCs urging the need for computer recognition of CTCs. A demonstration of a deep learning approach on the 100 images showed the promise of this technique for future CTC enumeration. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.


Subject(s)
Cell Count/methods , Flow Cytometry/methods , Neoplastic Cells, Circulating/pathology , Carcinoma, Non-Small-Cell Lung/pathology , Consensus , Humans , Lung Neoplasms/pathology
15.
Clin Chem ; 63(10): 1633-1641, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28784692

ABSTRACT

BACKGROUND: Identification, enumeration, and characterization of extracellular vesicles (EVs) are hampered by the small size of EVs, a low refractive index, and low numbers of antigens on their surface. METHODS: We investigated the potential of a 48-multiplex surface plasmon resonance imaging (SPRi) system to perform EV phenotyping. Antigen surface density of 11 antigens was measured on the human breast cancer cell lines HS578T, MCF7, and SKBR3 and their EVs by use of both SPRi and the widely used flow cytometry (FCM). RESULTS: For cells, the SPRi and FCM signals for antigen exposure correlated (RHS578T cells2 = 0.66, RMCF7 cells2 = 0.78, RSKBR3 cells2 = 0.60). With regard to EVs, SPRi detected 31 out of 33 tested antibody-EV pairs, whereas our flow cytometer detected 5 antibody-EV pairs because of high blank and isotype control signals. For HS578T-derived EVs, the SPRi and FCM signals correlated (R2HS578T EVs = 0.98). However, on MCF7- and SKBR3-derived EVs, insufficient antigens were detected by our flow cytometer. To confirm that the SPRi responses correlated with mean antigen density on EVs, the SPRi responses of EVs were correlated with antigen density on parental cells as measured by FCM (RHS578T2 = 0.77, RMCF72 = 0.49, RSKBR32 = 0.52). CONCLUSIONS: SPRi responses correlate with mean antigen density. Moreover, SPRi detects lower antigen-exposure levels than FCM because SPRi measures an ensemble of EVs binding to the sensor surface, whereas FCM detects antigens of single EV.


Subject(s)
Antigens/analysis , Breast Neoplasms/pathology , Breast/pathology , Extracellular Vesicles/pathology , Surface Plasmon Resonance/methods , Antibodies/chemistry , Antigens, Neoplasm/analysis , Cell Line, Tumor , Female , Flow Cytometry , Humans , Immunoassay/methods
16.
Chemistry ; 23(17): 4180-4186, 2017 Mar 23.
Article in English | MEDLINE | ID: mdl-28139850

ABSTRACT

A DNA-sensing platform is developed by exploiting the easy surface functionalization of metal-organic framework (MOF) particles and their highly parallelized fluorescence detection by flow cytometry. Two strategies were employed to functionalize the surface of MIL-88A, using either covalent or non-covalent interactions, resulting in alkyne-modified and biotin-modified MIL-88A, respectively. Covalent surface coupling of an azide-dye and the alkyne-MIL-88A was achieved by means of a click reaction. Non-covalent streptavidin-biotin interactions were employed to link biotin-PNA to biotin-MIL-88A particles mediated by streptavidin. Characterization by confocal imaging and flow cytometry demonstrated that DNA can be bound selectively to the MOF surface. Flow cytometry provided quantitative data of the interaction with DNA. Making use of the large numbers of particles that can be simultaneously processed by flow cytometry, this MOF platform was able to discriminate between fully complementary, single-base mismatched, and randomized DNA targets.


Subject(s)
DNA/analysis , Ferric Compounds/chemistry , Metal-Organic Frameworks/chemistry , Peptide Nucleic Acids/chemistry , Alkynes/chemistry , Azides/chemistry , Biotin/chemistry , Click Chemistry , Cycloaddition Reaction , Fluorescence , Fluorescent Dyes/chemistry , Particle Size , Polyethylene Glycols/chemistry , Streptavidin/chemistry , Surface Properties
17.
Int J Mol Sci ; 18(2)2017 02 09.
Article in English | MEDLINE | ID: mdl-28208771

ABSTRACT

Reviews on circulating biomarkers in breast cancer usually focus on one single biomarker or a selective group of biomarkers. An overview summarizing the discovery and evaluation of all blood-based biomarkers in metastatic breast cancer is lacking. This systematic review aims to identify the available evidence of known blood-based biomarkers in metastatic breast cancer, regarding their clinical utility and state-of-the-art position in the validation process. The initial search yielded 1078 original studies, of which 420 were assessed for eligibility. A total of 320 studies were included in the final synthesis. A Development, Evaluation and Application Chart (DEAC) of all biomarkers was developed. Most studies focus on identifying new biomarkers and search for relations between these biomarkers and traditional molecular characteristics. Biomarkers are usually investigated in only one study (68.8%). Only 9.8% of all biomarkers was investigated in more than five studies. Circulating tumor cells, gene expression within tumor cells and the concentration of secreted proteins are the most frequently investigated biomarkers in liquid biopsies. However, there is a lack of studies focusing on identifying the clinical utility of these biomarkers, by which the additional value still seems to be limited according to the investigated evidence.


Subject(s)
Biomarkers, Tumor/blood , Breast Neoplasms/blood , Breast Neoplasms/diagnosis , Breast Neoplasms/mortality , Female , Humans , Neoplasm Metastasis , Neoplasm Staging , Prognosis
18.
Anal Biochem ; 504: 1-3, 2016 07 01.
Article in English | MEDLINE | ID: mdl-27040182

ABSTRACT

We simulated, using Comsol Multiphysics, the excretion of antibodies by single hybridoma cells and their subsequent binding on a surface plasmon resonance imaging (SPRi) sensor. The purpose was to confirm that SPRi is suitable to accurately quantify antibody (anti-EpCAM) excretion. The model showed that antibody loss by diffusion away from the sensor was less than 1%. Unexpectedly, more than 99% of the excreted antibodies were captured on the sensor. These data prove the remarkable phenomenon that the SPRi output of cellular antibody excretion and its subsequent binding, performed under the conditions described here, is directly usable for quantification of single cell antibody production rates.


Subject(s)
Antibodies/metabolism , Antibody Formation , Hybridomas/immunology , Hybridomas/metabolism , Surface Plasmon Resonance , Antibodies/immunology , Diffusion , Epithelial Cell Adhesion Molecule/immunology , Humans , Hybridomas/pathology
19.
Anal Biochem ; 500: 21-3, 2016 May 01.
Article in English | MEDLINE | ID: mdl-26878776

ABSTRACT

The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)).


Subject(s)
Biosensing Techniques , Kinetics , Ligands , Surface Plasmon Resonance/methods
20.
Analyst ; 141(10): 3068-76, 2016 05 10.
Article in English | MEDLINE | ID: mdl-27077142

ABSTRACT

A practical way to realize on-chip sample preparation for point-of-care diagnostics is to store the required reagents on a microfluidic device and release them in a controlled manner upon contact with the sample. For the development of such diagnostic devices, a fundamental understanding of the release kinetics of reagents from suitable materials in microfluidic chips is therefore essential. Here, we study the release kinetics of fluorophore-conjugated antibodies from (sub-) µm thick gelatin layers and several ways to control the release time. The observed antibody release is well-described by a diffusion model. Release times ranging from ∼20 s to ∼650 s were determined for layers with thicknesses (in the dry state) between 0.25 µm and 1.5 µm, corresponding to a diffusivity of 0.65 µm(2) s(-1) (in the swollen state) for our standard layer preparation conditions. By modifying the preparation conditions, we can influence the properties of gelatin to realize faster or slower release. Faster drying at increased temperatures leads to shorter release times, whereas slower drying at increased humidity yields slower release. As expected in a diffusive process, the release time increases with the size of the antibody. Moreover, the ionic strength of the release medium has a significant impact on the release kinetics. Applying these findings to cell counting chambers with on-chip sample preparation, we can tune the release to control the antibody distribution after inflow of blood in order to achieve homogeneous cell staining.


Subject(s)
Antibodies/chemistry , Gelatin , Microfluidic Analytical Techniques , Blood Cells , Cell Separation , Fluorescent Dyes , Humans , Kinetics , Staining and Labeling
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