Negative enrichment strategy combined with site-specific derivatization for the C-terminomics.

Protein C-termini containing valuable biological information plays a vital role in various physiological processes, such as protein localization, protein recognition, and signal transduction in organisms. However, C-terminal peptide identification is still challenging due to their low abundance and similar physicochemical properties to other digested peptides. Herein, we developed a simple and mild strategy for the enrichment of C-terminal peptides that incorporates selectively 2-pyridinecarbaldehyde (2-PCA) derivatization of α-amine with negative enrichment by NHS resin. Two synthesized peptides were utilized to evaluate the efficiency of 2-PCA derivatization and optimize the coupling conditions of NHS resin. The feasibility of the method was further validated by enriching the C-terminus of the bovine serum albumin (BSA). Finally, this method was successfully applied to the C-terminus analysis of mouse brain tissue, identifying 404 protein C-termini with physicochemical properties unbiasedly. Additionally, the GO and KEGG analyses revealed that these identified proteins are crucial for proper brain function. In summary, our proposed method is effective and has the potential to facilitate comprehensive C-terminal analysis of proteins. SIGNIFICANCE: Effective enrichment methods are essential for the identification of the proteins C-terminus. In this study, a mild and simple method for negative C-terminal enrichment combined with site-specific derivatization was developed. The enrichment process was simplified and minimized sample loss simultaneously, using 2-PCA derivatization which has high α-amino specificity. Up to 346C-terminal proteins were identified in mouse brain tissue unbiasedly and reliably. This approach has the potential to facilitate comprehensive analysis of protein C-termini in a variety of biological contexts.

The Protocol of Circulating Tumor Cell Detection.

The detection of CTCs is related to the development of tumors and can be used in medical fields such as early diagnosis, postoperative evaluation, monitoring treatment, and predicting disease prognosis. This article focuses on the entire process of CTC detection, including negative enrichment isolation and immunofluorescence in situ hybridization detection.

Single-Cell Identification of Melanoma Biomarkers in Circulating Tumor Cells.

The current standard for investigating tumors is surgical biopsy, which is costly, invasive, and difficult to perform serially. As an adjunct, circulating tumor cells (CTCs)-cells that have broken away from the primary tumor or metastatic sites-can be obtained from a blood draw and offer the potential for obtaining serial genetic information and serving as biomarkers. Here, we detail the potential for melanoma CTCs to serve as biomarkers and discuss a clinically viable methodology for single-cell CTC isolation and analysis that overcomes previous limitations. We explore the use of melanoma CTC biomarkers by isolating and performing single-cell RNA sequencing on CTCs from melanoma patients. We then compared transcriptional profiles of single melanoma CTCs against A375 cells and peripheral blood mononuclear cells to identify unique genes differentially regulated in circulating melanoma tumor cells. The information that can be obtained via analysis of these CTCs has significant potential in disease tracking.

[Optimization and evaluation of protein C-terminal peptide enrichment strategy based on arginine cleavage].

As unique biomarkers, protein C-termini are involved in various biological processes such as protein trafficking, subcellular relocation, and signal transduction. Dysregulation of protein C-terminal status is critical during the development of various diseases, including cardiovascular, neurodegenerative, and metabolic diseases and cancer. Thus, global profiling of protein C-termini is of great value in providing mechanistic insight into biological or pathological processes, as well as for identifying potential new targets for therapeutic treatment. Polymer-based negative enrichment is a prominent C-terminomics strategy with advantages of universal applicability and parallel sample preparation. Compared with other methods of such a strategy, the profiling depth of the approaches based on enzymatic cleavage of Arg residues still needs to be improved. This greatly limits our understanding of the physiological functions and molecular mechanisms of C-termini. To add a more powerful tool for C-terminomics, Arg cleavage-based negative enrichment C-terminomics was optimized and evaluated. First, the sample preparation process was optimized. A one-pot enrichment platform based on a V-shaped filter was established, which reduced sample loss, avoided cross-contamination between reactions, and shortened sample preparation time. In addition, the protein-level acetylation conditions were investigated with the optimal labeling conditions as follows: triple coupling using 5 mmol/L Ac-NHS at pH 7.0 and 500 mmol/L ammonium for 15 min provided minimized acetylation rates (acetylation labeling efficiencies of Ser, Thr, and Tyr were lower than 4%, 2%, and 1%, respectively), along with the highest peptide-spectrum match number and satisfactory Lys labeling efficiency (up to 98%). These optimized conditions would not only minimize acetylation, but also facilitate the identification of C-terminal peptides. Second, it was speculated that the unexpected low identification rate was primarily caused by the interference of the large number of organic compounds accumulated during the peptide-level reactions, including reagents, organic buffering agents, and their complex side-reaction products. Therefore, the conditions for StageTip-based fractionation, including pH, the amount of Empore C18 beads, and the number of fractions, were optimized. As a result, by separating the sample enriched from 300 µg proteome into seven fractions, sample complexity was largely decreased and a total of 696 C-termini were identified in duplicates from strict data filtration, that is, percolator false discovery rate (FDR)<0.01, ion score≥20, and C-terminal amidation by ethanolamine. If only peptide FDR<0.01 was considered, the identified C-termini further increased to 933, which was among the largest C-terminome datasets obtained from the polymer-based strategy. Furthermore, compared with the results of a previous study, the optimized method would be a practical strategy for broader C-terminome coverage. Finally, to further broaden the coverage of the sub-C-terminome generated by Arg-specific cleavage, this study explored a new method in which ArgN-specific cleavage (cleavage at the N-terminal of Arg by LysargiNase) was combined with different N-terminal protections (dimethylation and acetylation). Among all the combinations, the additional use of the "LysargiNase+N-terminal acetylation" method increased 47% more identifications of unique C-termini on the basis of "trypsin+N-terminal demethylation" and the two covered 87% of the total C-termini. Therefore, the parallel use of the two methods would further expand the coverage of Arg-cleaved C-terminal peptides. With the analysis of the physicochemical properties of the peptides identified by the two methods, the reason why the C-terminal peptides identified by different strategies are complementary was explained. In conclusion, in this study, the optimized C-terminomics platform can deeply profile Arg cleavage-generated C-terminal peptides using a polymer-based approach. This method provides a powerful tool for the global characterization of protein C-termini.

Circulating Tumor Cells Correlate With Prognosis in Head and Neck Squamous Cell Carcinoma.

BACKGROUND: To investigate the relationship of circulating tumor cells (CTCs) and the clinical characteristic parameters and prognosis in patients with head and neck squamous cell carcinoma (HNSCC). METHODS: The retrospective clinical study included 95 patients with HNSCC who after surgery in Shanghai Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine between December 2015 and December 2016. All patients were followed up for survival until the end of June 2019. The CTCs detection was performed by negative enrichment (NE) immunofluorescence-in situ hybridization (im-FISH) of chromosome 8. RESULTS: Patients with higher CTCs counts are associated with a worse prognosis with an area under the receiver operator characteristic (ROC) curve of 0.756 [95% confidence interval (CI) 0.640-0.872, p = 0.001]. The CTCs-positive rate of HNSCC patients was 58.9% (56/95) by using the cut-point of 3. Both the chi-square test and binary logistic regression analysis showed that the N stage and clinical stage were significantly associated with CTCs-positive in patients with HNSCC (p < 0.05). Further Non-parametric test analysis indicated that more CTCs counts were detected in late N and clinical stages patients (p < 0.001). The Kaplan-Meier survival analysis indicated that CTCs-positive were correlated with shorter progression-free survival (PFS) (p < 0.001) and overall survival (OS) (p = 0.001). Further, the CTCs-positive was an independent prognostic factor for PFS and OS according to the Cox multivariate regression analysis (p < 0.05). CONCLUSION: More CTCs were associated with N stage, clinical stage, poor prognosis in patients with HNSCC, which might be used as a prognostic biomarker.

Directed evolution approach to enhance efficiency and speed of outgrowth during single cell subcloning of Chinese Hamster Ovary cells.

Chinese Hamster Ovary (CHO) cells are the working horse of the pharmaceutical industry. To obtain high producing cell clones and to satisfy regulatory requirements single cell cloning is a necessary step in cell line development. However, it is also a tedious, labor intensive and expensive process. Here we show an easy way to enhance subclonability using subcloning by single cell sorting itself as the selection pressure, resulting in improved subcloning performance of three different host cell lines. These improvements in subclonability also lead to an enhanced cellular growth behavior during standard batch culture. RNA-seq was performed to shed light on the underlying mechanisms, showing that there is little overlap in differentially expressed genes or associated pathways between the cell lines, each finding their individual strategy for optimization. However, in all three cell lines pathways associated with the extracellular matrix were found to be enriched, indicating that cells struggle predominantly with their microenvironment and possibly lack of cell-to-cell contact. The observed small overlap may hint that there are multiple ways for a cell line to achieve a certain phenotype due to numerous genetic and subsequently metabolic redundancies.

Clinical significance of circulating tumor cells and metabolic signatures in lung cancer after surgical removal.

BACKGROUND: Lung cancer (LC) remains the deadliest form of cancer globally. While surgery remains the optimal treatment strategy for individuals with early-stage LC, what the metabolic consequences are of such surgical intervention remains uncertain. METHODS: Negative enrichment-fluorescence in situ hybridization (NE-FISH) was used in an effort to detect circulating tumor cells (CTCs) in pre- and post-surgery peripheral blood samples from 51 LC patients. In addition, targeted metabolomics analyses, multivariate statistical analyses, and pathway analyses were used to explore surgery-associated metabolic changes. RESULTS: LC patients had significantly higher CTC counts relative to healthy controls with 66.67% of LC patients having at least 1 detected CTC before surgery. CTC counts were associated with clinical outcomes following surgery. In a targeted metabolomics analysis, we detected 34 amino acids, 147 lipids, and 24 fatty acids. When comparing LC patients before and after surgery to control patients, metabolic shifts were detected via PLS-DA and pathway analysis. Further surgery-associated metabolic changes were identified when comparing LA (LC patients after surgery) and LB (LC patients before surgery) groups. We identified SM 42:4, Ser, Sar, Gln, and LPC 18:0 for inclusion in a biomarker panel for early-stage LC detection based upon an AUC of 0.965 (95% CI 0.900-1.000). This analysis revealed that SM 42:2, SM 35:1, PC (16:0/14:0), PC (14:0/16:1), Cer (d18:1/24:1), and SM 38:3 may offer diagnostic and prognostic benefits in LC. CONCLUSIONS: These findings suggest that CTC detection and plasma metabolite profiling may be an effective means of diagnosing early-stage LC and identifying patients at risk for disease recurrence.

Circulating tumour cells as prognosis predictive markers of neoadjuvant chemotherapy-treated breast cancer patients.

In this study, we detected and measured the count of circulating tumour cells (CTCs) in breast cancer (BC) patients who were treated by neoadjuvant chemotherapy (NAC) in order to assess the clinical validity of CTCs. A total of 96 patients with locally advanced BC and who were treated by NAC were enrolled in this study. The CTC count in the peripheral blood was estimated by negative enrichment-fluorescence in situ hybridization before and after NAC. The clinicopathological data of the patients were recorded. CTCs were detected in 59 of the 96 patients with BC before NAC. Particularly, the detection rate of CTCs was significantly lower in human epidermal growth factor receptor-2 (HER-2)-negative patients than in HER-2-positive patients. CTCs were significantly fewer after NAC than before NAC. The CTC-detection sensitivity in the NAC efficacy evaluation was 75.5% (40/53), while the specificity was 72.1% (31/43). The CTC consistency analysis with clinical effects (Response Evaluation Criteria in Solid Tumors Version 1.1 Standard) was described as moderate (kappa = 0.476, P < 0.001). Thus, our findings suggest that CTC detection is a potential new approach to assess the efficacy of NAC.

Improvement of sensitive and specific detection of circulating tumor cells using negative enrichment and immunostaining-FISH.

BACKGROUND: Circulating tumor cells (CTCs) provide an opportunity to obtain pivotal biological information required for the development of personalized medicine. However, the current assays of CTCs' detection face serious challenges regarding specificity and sensitivity. METHODS: In this study, we developed a novel strategy that combined negative enrichment (NE), immunocytochemistry CD45 staining and fluorescence in situ hybridization (FISH) to identify, enumerate and characterize CTCs. CTCs were identified as DAPI+/CD45-/Chromosome multiploid. The assay was evaluated with different cancer cell lines including lung, breast, esophageal and gastric cancer. And then, the developed assay was applied in cancer patients to explore the possibility of clinical application and whether CTC number was related to clinicopathological factors. RESULTS: The average recover rate of esophageal cancer cell line Eca-109 using negative enrichment was higher than 80% and the multiploid cells rate of four cancer cell lines were >96%, which demonstrate the NE-FISH platform is favorable for CTCs detection. CTCs count was significantly higher in lung cancer patients than healthy controls and benign lung disease with an area under ROC curve of 0.905 (95% confidence interval 0.866-0.944, P < .001). Using a cutoff value of 2 CTCs, the positive rate of detecting lung, gastric, breast and esophageal cancer patients were 71.33%, 86.21%, 76.77% and 78.35%, respectively. Besides, CTCs could be detected in stage I with the positive rate of 64.15% for lung cancer, 83.33% for gastric cancer, 78.95% for breast cancer and 68.18% for esophageal cancer, which may promote the early diagnose and influence the treatment decision for better management of those cancer in clinic. CONCLUSIONS: Our study showed that CTCs could be detected in diverse cancers using the novel NE-FISH platform with high sensitivity and specificity. Therefore, analysis of CTCs with NE-FISH has a clear potential to improve the management of cancer patients in clinical use.

Improved detection of EGFR mutations in the tumor cells enriched from the malignant pleural effusion of non-small cell lung cancer patient.

Previous studies focus on developing high sensitive PCR-related technologies to detect EGFR gene mutation in malignant pleural effusion (MPE) of non-small cell lung cancer patient (NSCLC) instead of improving the quality of clinical samples themselves. We therefore hypothesized that the enrichment of tumor cells in MPE could improve the quality of MPE for the more accurate detection of EGFR gene mutation in the patients with NSCLC. MPE were collected from 28 patients with NSCLC. The tumor cells in MPE were firstly enriched by the depletion of leukocytes with bi-antibodies and identified by multiple flow cytometry. CastPCR was performed to detect the deletions in exon 19 (DelEGFR19) and point mutations in 20 (T790M, c.2369C>T) and 21 (L858R, c.2573T>G) of EGFR. All the detected mutations were confirmed their presence by Sanger sequencing. Before enrichment, the tumor cells in MPE were detected in 46.4% (13/28) of samples and the median value of the percentage of the tumor cells was only 0.64% including 3 (10.7%, 3/28) of samples more than 10% on it. After enrichment, the tumor cells were detected in all samples (100%) and the median value of the percentage of tumor cells was increased to 40.8% including only one (3.6%, 1/28) less than 10% on it. EGFR gene mutations were detected in 28.6% (8/28) and 42.9% (12/28) of the samples before and after enrichment, respectively. The sensitivity on the detection rate was relatively increased by 44.4%. Moreover, the mutations can be confirmed their presence by Sanger sequencing in 6 samples before enrichment (75%, 6/8) and 11 samples (91.7%, 11/12) after enrichment. It is valuable to improve the quality of the sample by the enrichment of the tumor cells from MPE for the following genetic analysis.

Circulating tumor cell detection: A direct comparison between negative and unbiased enrichment in lung cancer.

Circulating tumor cells (CTCs), isolated as a 'liquid biopsy', may provide important diagnostic and prognostic information. Therefore, rapid, reliable and unbiased detection of CTCs are required for routine clinical analyses. It was demonstrated that negative enrichment, an epithelial marker-independent technique for isolating CTCs, exhibits a better efficiency in the detection of CTCs compared with positive enrichment techniques that only use specific anti-epithelial cell adhesion molecules. However, negative enrichment techniques incur significant cell loss during the isolation procedure, and as it is a method that uses only one type of antibody, it is inherently biased. The detection procedure and identification of cell types also relies on skilled and experienced technicians. In the present study, the detection sensitivity of using negative enrichment and a previously described unbiased detection method was compared. The results revealed that unbiased detection methods may efficiently detect >90% of cancer cells in blood samples containing CTCs. By contrast, only 40-60% of CTCs were detected by negative enrichment. Additionally, CTCs were identified in >65% of patients with stage I/II lung cancer. This simple yet efficient approach may achieve a high level of sensitivity. It demonstrates a potential for the large-scale clinical implementation of CTC-based diagnostic and prognostic strategies.

Negative Enrichment of Circulating Tumor Cells in Blood Using a Microfluidic Chip.

The enumeration and analysis of circulating tumor cells (CTCs) is an increasing interest for monitoring disease progression or response to treatment, specifically as a companion diagnostic for new anticancer drugs, and for research into the mechanisms of disease progression and metastases. Ideally, CTCs would be enriched from very small samples, with minimal handling, high recovery, and no requirement for the expression of specific surface markers. Here, we describe negative enrichment as the preferred approach for cancer cell isolation using a microfluidic platform.

An integrated on-chip platform for negative enrichment of tumour cells.

The study of cancer cells in blood, popularly called circulating tumour cells (CTCs), has exceptional prospects for cancer risk assessment and analysis. Separation and enrichment of CTCs by size-based methods suffer from a well-known recovery/purity trade-off while methods targeting certain specific surface proteins can lead to risk of losing CTCs due to Epithelial to Mesenchymal Transition (EMT) and thus adversely affect the separation efficiency. A negative selection approach is thus preferred for tumour cell isolation as it does not depend on biomarker expression or defines their physical property as the separation criteria. In this work, we developed a microfluidic chip to isolate CTCs from whole blood samples without targeting any tumour specific antigen. This chip employs a two-stage cell separation: firstly, magnetophoresis depletes the white blood cells (WBCs) from a whole blood sample and is then followed by a micro-slit membrane that enables depleting the red blood cells (RBCs) and retaining only the tumour cells. By creating strong magnetic field gradients along with customized antibody complexes to target WBCs, we are able to remove >99.9% of WBCs from 1:1 diluted blood at a sample processing rate of 500µL/min. This approach achieves an average of >80% recovery of spiked tumour cells from 2mL of whole blood in a total assay processing time of 50min without multiple processing steps.

Microfluidic immunomagnetic cell separation from whole blood.

Immunomagnetic-based separation has become a viable technique for the separation of cells and biomolecules. Here we report on the design and analysis of a simple and efficient microfluidic device for high throughput and high efficiency capture of cells tagged with magnetic particles. This is made possible by using a microfluidic chip integrated with customized arrays of permanent magnets capable of creating large magnetic field gradients, which determine the effective capturing of the tagged cells. This method is based on manipulating the cells which are under the influence of a combination of magnetic and fluid dynamic forces in a fluid under laminar flow through a microfluidic chip. A finite element analysis (FEA) model is developed to analyze the cell separation process and predict its behavior, which is validated subsequently by the experimental results. The magnetic field gradients created by various arrangements of magnetic arrays have been simulated using FEA and the influence of these field gradients on cell separation has been studied with the design of our microfluidic chip. The proof-of-concept for the proposed technique is demonstrated by capturing white blood cells (WBCs) from whole human blood. CD45-conjugated magnetic particles were added into whole blood samples to label WBCs and the mixture was flown through our microfluidic device to separate the labeled cells. After the separation process, the remaining WBCs in the elute were counted to determine the capture efficiency, and it was found that more than 99.9% WBCs have been successfully separated from whole blood. The proposed design can be used for positive selection as well as for negative enrichment of rare cells.

Isolation and characterization of living circulating tumor cells in patients by immunomagnetic negative enrichment coupled with flow cytometry.

BACKGROUND: This study was aimed at establishing a sensitive and specific isolation, characterization, and enumeration method for living circulating tumor cells (CTCs) in patients with colorectal carcinoma. METHODS: Quantitative isolation and characterization of CTCs were performed through a combination of immunomagnetic negative enrichment and fluorescence-activated cell sorting. Isolated CTCs were identified by immunofluorescence staining. The viability and purity of the sorted cells were determined by flow cytometry. Blood samples spiked with HCT116 cells (range, 3-250 cells) were used to determine specificity, recovery, and sensitivity. The method was used to enumerate, characterize, and isolate living CTCs in 10 mL of blood from patients with colorectal carcinoma. RESULTS: The average recovery of HCT116 cells was 61% or more at each spiking level, and the correlation coefficient was 0.992. An analysis of samples from all 18 patients with colorectal carcinoma revealed that 94.4% were positive for CTCs with an average of 33 ± 24 CTCs per 10 mL of blood and with a diameter of 14 to 20 µm (vs 8-12 µm for lymphoma). All patients were CD47(+) , with only 4.3% to 61.2% being CD44(+) . The number of CTCs was well correlated with the patient TNM stage and could be detected in patients at an early cancer stage. The sorted cells could be recultured, and their viability was preserved. CONCLUSIONS: This method provides a novel technique for highly sensitive and specific detection and isolation of CTCs in patients with colorectal carcinoma. This method complements the existing approaches for the de novo functional identification of a wide variety of CTC types. It is likely to help in predicting a patient's disease progression and potentially in selecting the appropriate treatment.