Small extracellular vesicles detection using dielectrophoresis-based microfluidic chip for diagnosis of breast cancer.

Small extracellular vesicles (sEVs) reflect the genotype and phenotype of original cells and are biomarkers for early diagnosis and treatment monitoring of tumors. Yet, their small size and low density make them difficult to isolate and detect in body fluid samples. This study proposes a novel acDEP-Exo chip filled with transparent micro-beads, which formed a non-uniform electrical field, and finally achieved rapid, sensitive, and tunable sEVs capture and detection. The method requires only 20-50 µL of sample, achieved a limit of detection (LOD) of 161 particles/µL, and can detect biomarkers within 13 min. We applied the chip to analyze the two markers of sEV's EpCAM and MUC1 in clinical plasma samples from breast cancer (BC) patients and healthy volunteers and found that the combined evaluation of sEV's biomarkers has extremely high sensitivity, specificity and accuracy. The present study introduces an alternative approach to sEVs isolation and detection, has a great potential in real-time sEVs-based liquid biopsy.

Molecular Genomic Assessment Using a Blood-based mRNA Signature (NETest) is Cost-effective and Predicts Neuroendocrine Tumor Recurrence With 94% Accuracy.

INTRODUCTION: Identification of residual disease after neuroendocrine tumor (NET) resection is critical for management. Post-surgery imaging is insensitive, expensive, and current biomarkers ineffective. We evaluated whether the NETest, a multigene liquid biopsy blood biomarker, correlated with surgical resection and could predict recurrence. METHODS: Multicenter evaluation of NET resections over 24 months (n = 103): 47 pancreas, 26 small bowel, 26 lung, 2 appendix, 1 duodenum, 1 stomach. Surgery: R0 (83), R1/R2 (20). One millilitre of blood was collected at D0 and posroperative day (POD) 30. Transcript quantification by polymerase chain reaction (normal: ≤20), CgA by NEOLISA (normal ≤108 ng/mL). Standard-of-care (SoC) follow-up costs were calculated and compared to POD30 NETest-stratification approach. Analyses: Wilcoxon-paired test, Chi-square test. D BIOMARKERS: NETest: 103 of 103 (100%)-positive, whereas 23 of 103 (22%) were CgA-positive (Chi-square = 78, P < 0.0001).In the R0 group, the NETest decreased 59 ± 28 to 26 ± 23 (P < 0.0001); 36% (30/83) remained elevated. No significant decrease was evident for CgA. In the R1/R2 group the NETest decreased but 100% remained elevated. CgA levels did not decrease.An elevated POD30 NETest was present in R0 and 25 (83%) developed radiological recurrences. Normal score R0 s (n = 53) did not develop recurrence (Chi-square = 56, P < 0.0001). Recurrence prediction was 94% accurate with the NETest. COST EVALUATION: Using the NETest to stratify postoperative imaging resulted in a cost-savings of 42%. CONCLUSION: NETest diagnosis is more accurate than CgA (100% vs 22%). Surgery significantly decreased NETest. An elevated POD30 NETest predicted recurrence with 94% accuracy and post-surgical POD30 NETest follow-up stratification decreased costs by 42%. CgA had no surgical utility. Further studies would define the accuracy and cost-effectiveness of the NETest in the detection of postoperative recurrent disease.

Technical validation of a new microfluidic device for enrichment of CTCs from large volumes of blood by using buffy coats to mimic diagnostic leukapheresis products.

Diagnostic leukapheresis (DLA) enables to sample larger blood volumes and increases the detection of circulating tumor cells (CTC) significantly. Nevertheless, the high excess of white blood cells (WBC) of DLA products remains a major challenge for further downstream CTC enrichment and detection. To address this problem, we tested the performance of two label-free CTC technologies for processing DLA products. For the testing purposes, we established ficollized buffy coats (BC) with a WBC composition similar to patient-derived DLA products. The mimicking-DLA samples (with up to 400 × 106 WBCs) were spiked with three different tumor cell lines and processed with two versions of a spiral microfluidic chip for label-free CTC enrichment: the commercially available ClearCell FR1 biochip and a customized DLA biochip based on a similar enrichment principle, but designed for higher throughput of cells. While the samples processed with FR1 chip displayed with increasing cell load significantly higher WBC backgrounds and decreasing cell recovery, the recovery rates of the customized DLA chip were stable, even if challenged with up to 400 × 106 WBCs (corresponding to around 120 mL peripheral blood or 10% of a DLA product). These results indicate that the further up-scalable DLA biochip has potential to process complete DLA products from 2.5 L of peripheral blood in an affordable way to enable high-volume CTC-based liquid biopsies.

Purification of HCC-specific extracellular vesicles on nanosubstrates for early HCC detection by digital scoring.

We report a covalent chemistry-based hepatocellular carcinoma (HCC)-specific extracellular vesicle (EV) purification system for early detection of HCC by performing digital scoring on the purified EVs. Earlier detection of HCC creates more opportunities for curative therapeutic interventions. EVs are present in circulation at relatively early stages of disease, providing potential opportunities for HCC early detection. We develop an HCC EV purification system (i.e., EV Click Chips) by synergistically integrating covalent chemistry-mediated EV capture/release, multimarker antibody cocktails, nanostructured substrates, and microfluidic chaotic mixers. We then explore the translational potential of EV Click Chips using 158 plasma samples of HCC patients and control cohorts. The purified HCC EVs are subjected to reverse-transcription droplet digital PCR for quantification of 10 HCC-specific mRNA markers and computation of digital scoring. The HCC EV-derived molecular signatures exhibit great potential for noninvasive early detection of HCC from at-risk cirrhotic patients with an area under receiver operator characteristic curve of 0.93 (95% CI, 0.86 to 1.00; sensitivity = 94.4%, specificity = 88.5%).

Pre-analytical factors affecting the establishment of a single tube assay for multiparameter liquid biopsy detection in melanoma patients.

The combination of liquid biomarkers from a single blood tube can provide more comprehensive information on tumor development and progression in cancer patients compared to single analysis. Here, we evaluated whether a combined analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and circulating cell-free microRNA (miRNA) in total plasma and extracellular vesicles (EV) from the same blood sample is feasible and how the results are influenced by the choice of different blood tubes. Peripheral blood from 20 stage IV melanoma patients and five healthy donors (HD) was collected in EDTA, Streck, and Transfix tubes. Peripheral blood mononuclear cell fraction was used for CTC analysis, whereas plasma and EV fractions were used for ctDNA mutation and miRNA analysis. Mutations in cell-free circulating DNA were detected in 67% of patients, with no significant difference between the tubes. CTC was detected in only EDTA blood and only in 15% of patients. miRNA NGS (next-generation sequencing) results were highly influenced by the collection tubes and could only be performed from EDTA and Streck tubes due to hemolysis in Transfix tubes. No overlap of significantly differentially expressed miRNA (patients versus HD) could be found between the tubes in total plasma, whereas eight miRNA were commonly differentially regulated in the EV fraction. In summary, high-quality CTCs, ctDNA, and miRNA data from a single blood tube can be obtained. However, the choice of blood collection tubes is a critical pre-analytical variable.

Two-site evaluation of a new workflow for the detection of malignant cells on the Sysmex XN-1000 body fluid analyzer.

INTRODUCTION: The presence of high fluorescent cells (HF-BF) on the Sysmex XN-1000 hematology analyzers has gained interest regarding the prediction of malignant cells in body fluids, but lacks sensitivity. We aimed to increase this sensitivity by combining HF-BF value, automated results, and clinical information. METHODS: We evaluated a new workflow for the management of body fluids in the hematology laboratory, including the HF-BF criterion and clinical information. In two laboratories, 1623 serous fluids were retrospectively analyzed on the XN-1000 BF mode. All samples were morphologically screened for malignant cells. Optimal HF-BF cutoffs were determined to predict their presence. Thereafter, the added value of clinical information was evaluated. Other reflex testing rules (eosinophilic count >5% and presence of the WBC Abnormal Scattergram flag) were also used to refine our workflow. RESULTS: Optimal HF-BF cutoffs in the two hematology centers were 108 and 45 cells/µL, yielding a sensitivity/specificity of 66.7/93.6% and 86.8/66.6% for malignant cell detection. When adding clinical information, sensitivity/specificity evolved to 100.0/68.9% and 100.0%/not determined. Of 104 samples containing malignant cells, 97 had positive clinical information; the remainder had a HF-BF > cutoff. CONCLUSION: Combining clinical information and HF-BF reached 100% sensitivity for malignant cell detection in body fluid analysis. Lack of robustness of the optimal HF-BF cutoff deserves the use of local cutoffs. Rapid automated results reporting from the XN-1000 BF mode are also feasible in clinical practice. Prospective evaluation of the workflow is needed before its implementation in clinical practice.

Dynamically Monitoring the Clonal Evolution of Lung Cancer Based on the Molecular Characterization of Circulating Tumor Cells Using Aptamer Cocktail-Modified Nanosubstrates.

Dynamically monitoring the clonal evolution of lung cancer and performing molecular analyses on tumor cells are challenging but necessary tasks to adjust therapeutic interventions and evaluate treatment efficacy. Circulating tumor cells (CTCs), as a "liquid biopsy", may offer an auxiliary tool to identify phenotypic transformation of solid tumors at primary or metastatic sites and uncover their corresponding molecular variation. Herein, we developed an aptamer-modified PEG-PLGA-nanofiber (PPN) microfluidic system optimized for recognizing rare CTC subtypes in lung cancer patients. This unique purification system can be adopted to monitor the clonal evolution of solid tumors by following the intrinsic immunophenotypes of CTCs, while significantly enhancing capture efficiency for polyclonal-derived tumor cells, further facilitating therapeutic evaluation via dynamic CTC enumeration. Combining with downstream single-cell sequencing, the aptamer-modified-PPN microfluidic system was able to provide early insight into tumor heterogeneity and predict histologic transformation in advance, broadening its clinical applications in lung cancer patients.

Unbiased enrichment of urine exfoliated cells on nanostructured substrates for sensitive detection of urothelial tumor cells.

BACKGROUND: Early detection of urothelial carcinoma (UC) by noninvasive diagnostic methods with high accuracy is still underscored. This study aimed to develop a noninvasive assay incorporating both enrichment of urine exfoliated cells and immunoassays for UC detection. METHODS: Polystyrene dishes were exposed to oxygen plasma and modified with 3-aminopropyltriethoxysilane to prepare amine-functionalized nanostructured substrates (NS). Performance characterization of NS was evaluated by atomic force microscope and X-ray photoelectron spectroscopy. Urine exfoliated cells were captured by NS and then immunostained to detect urinary tumor cells (UTCs), which was called UTC assay. The receiver operating characteristic (ROC) curve, area under ROC curve (AUC), and Youden index were used to find the cutoff value of UTC assay. ROC analysis and McNemar test were used to compare the diagnostic accuracy of UTC assay with cytology. Kappa test was used to analyze the agreement of UTC assay and cytology with pathological diagnosis. RESULTS: Nanostructured substrates had good cell binding yields of nucleated cells and tumor cells. CK20+ CD45- CD11b- cells were considered as UTCs. UTC number ≥ 1 per sample could be considered as a positive result. By AUC and Kappa analysis, UTC assay showed good performance in UC detection. McNemar test demonstrated that UTC assay had a superior sensitivity even in low-grade subgroup and a similar specificity compared to cytology in UC diagnosis. CONCLUSIONS: Nanostructured substrates could be used to enrich the exfoliated cells from urine samples. UTC assay with NS has the potential to play a role in UC detection. The value of this assay still needs additional validation by large, multi-center studies.

Detection of circulating tumor DNA (ctDNA) by digital droplet polymerase chain reaction (dd-PCR) in liquid biopsies.

Circulating tumor DNA (ctDNA) analyses are minimally invasive and accessible for risk stratification or treatment response monitoring of cancer patients. Compared to tumor biopsy analysis, they are not only less invasive, but also provide a more representative picture, allowing capturing both tumor heterogeneity and multiple tumor sites. Development of new technologies such as droplet-based digital PCR (ddPCR) has greatly improved the sensitivity, specificity and precision of the detection of rare ctDNA sequences in the pool of total circulating free DNA. In this chapter, we discuss the application of ddPCR in the analysis of ctDNA, and present the protocols for obtaining variant allele frequency or copy number variation analysis.

Spatially Engineered Janus Hybrid Nanozyme toward SERS Liquid Biopsy at Nano/Microscales.

Nanomaterials with intrinsic enzyme-mimicking properties (nanozymes) have been widely considered as artificial enzymes in biomedicine. However, manipulating inorganic nanozymes for multivariant targeted bioanalysis is still challenging because of the insufficient catalytic efficiency and biological blocking effect. Here, we rationally designed a spatially engineered hollow Janus hybrid nanozyme vector (h-JHNzyme) based on the bifacial modulation of Ag-Au nanocages. The silver face inside the h-JHNzyme served as an interior gate to promote the enzymatic activity of the Ag-Au nanozyme, whereas two-dimensional DNAzyme-motif nanobrushes deposited on the exterior surface of the h-JHNzyme endowed it with the targeting function and tremendously enhanced the peroxidase-mimicking activity. We demonstrated that the spatially separated modulation of the h-JHNzyme propelled it as a powerful "all-in-one" enzymatic vector with excellent biocompatibility, specific vectorization, remarkable enzymatic performance, and clinical practicability. Further, we programmed it into a stringent catalytic surface-enhanced Raman scattering (SERS) liquid biopsy platform to trace multidimensional tumor-related biomarkers, such as microRNAs and circulating tumor cells, with a limit of detection of fM and single cell level, respectively. The developed enzymatic platform showed great potential in facilitating reliable quantitative SERS liquid biopsy for on-demand clinical diagnosis.

Origami-paper-based device for microvesicle/exosome preconcentration and isolation.

Microvesicles and exosomes are promising liquid biopsy biomarkers. However, conventional isolation techniques damage and contaminate the biomarkers. We developed an origami-paper-based device for effective isolation of biomarkers with less damage and in fewer steps. The multi-folded device enables the preconcentration of the microvesicles/exosomes on specific layers (∼5-fold) by the ion concentration polarization technique and they were simply isolated from the rest of the sample by unfolding the device.

A novel microneedle device for controlled and reliable liquid biopsy of the human inner ear.

Sensorineural hearing loss is the most common sensory deficit worldwide, yet our understanding of the underlying pathophysiology is limited by the challenges of access to the inner ear in a safe and reliable manner. We present a novel microneedle device for trans-round window membrane liquid biopsy, which utilizes controlled depth of perforation and microliter aspiration control to safely biopsy fluids of the inner ear. Of eleven devices tested in fresh frozen human temporal bones, seven demonstrated alignment between electrical, visual and tactile detection of round window membrane perforation, and nine were successful in aspiration of meaningful diagnostic samples from the perilymphatic space. Purity of the average perilymph sample was 69% for a 5 µL sample volume, equivalent to 3.5 µL attributable to perilymph. Diagnostic success was shown both by transmastoid facial recess and transcanal tympanotomy approach. This device can enable new advances in the understanding of inner ear pathology, and brings us one step closer to liquid biopsy of the inner ear becoming a routine part of clinical care.

Integrated Microfluidic Device for Enrichment and Identification of Circulating Tumor Cells from the Blood of Patients with Colorectal Cancer.

Integrated device with high purity for circulating tumor cell (CTC) identification has been regarded as a key goal to make CTC analysis a "bench-to-bedside" technology. Here, we have developed a novel integrated microfluidic device that can enrich and identify the CTCs from the blood of patients with colorectal cancer. To enrich CTCs from whole blood, microfabricated trapping chambers were included in the miniaturized device, allowing for the isolation of tumor cells based on differences in size and deformability between tumor and normal blood cells. Microvalves were also introduced sequentially in the device, enabling automatic CTC enrichment as well as immunostaining reagent delivery. Under optimized conditions, the whole blood spiked with caco-2 cells passing through the microfluidic device after leukocyte depletion and approximately 73% of caco-2 cells were identified by epithelial cell adhesion molecule (EpCAM) staining. In clinical samples, CTCs were detectable from all patients with advanced colorectal cancer within 3 h. In contrast, the number of CTCs captured on the device from the blood of healthy donors was significantly lower than that from the patients, suggesting the utilization of the integrated device for further molecular analyses of CTCs.

Comparison of cytological adequacy and pain scale score in ultrasound-guided fine-needle aspiration of solid thyroid nodules for liquid-based cytology with with 23- and 25-gauge needles: a single-center prospective study.

In ultrasound (US)-guided fine-needle aspiration (FNA) of solid thyroid nodules (STN) using liquid-based cytology (LBC), the most appropriate needle size for LBC remains unclear. This study compared the cytological adequacy and complications associated with using 23- and 25-gauge needles in US-guided FNA of STNs using LBC. US-guided FNA was performed in consecutive patients by one radiologist to diagnose STNs ≥ 5 mm in the largest diameter. The one-sampling technique through a single needle puncture and multiple to-and-fro needle motions was used in each patient. The 23- and 25-guage needles were used consecutively each day. After FNA, the pain and complications experienced by each patient were investigated by a nurse, who was blinded to the information of needle gauge used. A cytopathologist retrospectively analyzed the cytological adequacy and cellularity of the cases. Of the 99 STNs, eight (8.1%) exhibited inadequate cytology (4 each with 23- and 25-gauge needles). The rate of cytological adequacy was not statistically different between the groups (p = 0.631). The mean pain scale values with 23- and 25-gauge needles were 2.1 ± 1.3 and 1.6 ± 1.3, respectively (p = 0.135). There were no significant complications in either group. In conclusion, both 23- and 25-gauge needles are useful in LBC because cytological adequacy and complications were not statistically different with both sizes of the needles.

Liquid biopsy using the nanotube-CTC-chip: capture of invasive CTCs with high purity using preferential adherence in breast cancer patients.

In this paper, we report the development of the nanotube-CTC-chip for isolation of tumor-derived epithelial cells (circulating tumor cells, CTCs) from peripheral blood, with high purity, by exploiting the physical mechanisms of preferential adherence of CTCs on a nanotube surface. The nanotube-CTC-chip is a new 76-element microarray technology that combines carbon nanotube surfaces with microarray batch manufacturing techniques for the capture and isolation of tumor-derived epithelial cells. Using a combination of red blood cell (RBC) lysis and preferential adherence, we demonstrate the capture and enrichment of CTCs with a 5-log reduction of contaminating WBCs. EpCAM negative MDA-MB-231/luciferase-2A-green fluorescent protein (GFP) cells were spiked in the blood of wild mice and enriched using an RBC lysis protocol. The enriched samples were then processed using the nanotube-CTC-chip for preferential CTC adherence on the nanosurface and counting the GFP cells yielded anywhere from 89% to 100% capture from the droplets. Electron microscopy (EM) studies showed focal adhesion with filaments from the cell body to the nanotube surface. We compared the nanotube preferential adherence to collagen adhesion matrix (CAM) scaffolding, reported as a viable strategy for CTC capture in patients. The CAM scaffolding on the device surface yielded 50% adherence with 100% tracking of cancer cells (adhered vs. non-adhered) versus carbon nanotubes with >90% adherence and 100% tracking for the same protocol. The nanotube-CTC-chip successfully captured CTCs in the peripheral blood of breast cancer patients (stage 1-4) with a range of 4-238 CTCs per 8.5 ml blood or 0.5-28 CTCs per ml. CTCs (based on CK8/18, Her2, EGFR) were successfully identified in 7/7 breast cancer patients, and no CTCs were captured in healthy controls (n = 2). CTC enumeration based on multiple markers using the nanotube-CTC-chip enables dynamic views of metastatic progression and could potentially have predictive capabilities for diagnosis and treatment response.

[Clinical study of brush liquid-based cytology combined with automatic immunohistochemistry in the classification and diagnosis of lung cancer].

Objective: To explore the feasibility of bronchoscopic brushing liquid-based slide cytology combined with automatic immunocytochemistry (ICC) for pathological typing of lung cancer. Methods: A liquid-based thin-prep was prepared from 171 bronchoscopic brushing specimens of patients with pulmonary lesions. ICC was detected by automatic immunohistochemistry instrument while cytomorphological diagnosis was made. The results were compared with those of histopathological diagnosis. Results: Among 171 patients, 130 (76.0%) could be classified by cell morphology alone, including 31 squamous cell carcinomas, 44 adenocarcinomas and 55 small cell carcinomas; 162 (94.7%) could be classified by cell morphology combined with ICC, including 38 squamous cell carcinomas, 61 adenocarcinomas and 63 small cell carcinomas (P<0.001). According to the gold standard of histopathological diagnosis, the coincidence rate of cytomorphology combined with ICC was higher than that of cell morphology alone. The coincidence rate of squamous cell carcinoma was increased from 85.2% to 97.1% (P=0.093), adenocarcinoma from 92.5% to 98.0% (P<0.001), and small cell carcinoma from 96.1% to 98.3% (P=0.465). Conclusion: The combination of liquid-based thin-prep cytology and automatic immunohistochemistry can effectively improve the accuracy of pathological typing of brushing specimens under fiberoptic bronchoscopy, and provide more objective diagnostic results for clinical treatment.

Fast and efficient microfluidic cell filter for isolation of circulating tumor cells from unprocessed whole blood of colorectal cancer patients.

Liquid biopsy offers unique opportunities for low invasive diagnosis, real-time patient monitoring and treatment selection. The phenotypic and molecular profile of circulating tumor cells (CTCs) can provide key information about the biology of tumor cells, contributing to personalized therapy. CTC isolation is still challenging, mainly due to their heterogeneity and rarity. To overcome this limitation, a microfluidic chip for label-free isolation of CTCs from peripheral blood was developed. This device, the CROSS chip, captures CTCs based on their size and deformability with an efficiency of 70%. Using 2 chips, 7.5 ml of whole blood are processed in 47 minutes with high purity, as compared to similar technologies and assessed by in situ immunofluorescence. The CROSS chip performance was compared to the CellSearch system in a set of metastatic colorectal cancer patients, resulting in higher capture of DAPI+/CK+/CD45- CTCs in all individuals tested. Importantly, CTC enumeration by CROSS chip enabled stratification of patients with different prognosis. Lastly, cells isolated in the CROSS chip were lysed and further subjected to molecular characterization by droplet digital PCR, which revealed a mutation in the APC gene for most patient samples analyzed, confirming their colorectal origin and the versatility of the technology for downstream applications.

Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells.

Molecular analysis of circulating tumor cells (CTCs) at single-cell resolution offers great promise for cancer diagnostics and therapeutics from simple liquid biopsy. Recent development of massively parallel single-cell RNA-sequencing (scRNA-seq) provides a powerful method to resolve the cellular heterogeneity from gene expression and pathway regulation analysis. However, the scarcity of CTCs and the massive contamination of blood cells limit the utility of currently available technologies. Here, we present Hydro-Seq, a scalable hydrodynamic scRNA-seq barcoding technique, for high-throughput CTC analysis. High cell-capture efficiency and contamination removal capability of Hydro-Seq enables successful scRNA-seq of 666 CTCs from 21 breast cancer patient samples at high throughput. We identify breast cancer drug targets for hormone and targeted therapies and tracked individual cells that express markers of cancer stem cells (CSCs) as well as of epithelial/mesenchymal cell state transitions. Transcriptome analysis of these cells provides insights into monitoring target therapeutics and processes underlying tumor metastasis.