Highly multiplexed simultaneous detection of RNAs and proteins in single cells

Precise gene expression measurement has been fundamental to developing an advanced understanding of the roles of biological networks in health and disease. To enable detection of expression signatures specific to individual cells we developed PLAYR (Proximity Ligation Assay for RNA). PLAYR enables highly multiplexed quantification of transcripts in single cells by flow- and mass-cytometry and is compatible with standard antibody staining of proteins. With mass cytometry, this currently enables simultaneous quantification of more than 40 different mRNAs and proteins. The technology was demonstrated in primary cells to be capable of quantifying multiple gene expression transcripts while the identity and the functional state of each analyzed cell was defined based on the expression of other transcripts or proteins. PLAYR now enables high throughput deep phenotyping of cells to readily expand beyond protein epitopes to include RNA expression, thereby opening a new venue on the characterization of cellular metabolism.

Biomarker detection for disease diagnosis using cost-effective microfluidic platforms

Early and timely detection of disease biomarkers can prevent the spread of infectious diseases, and drastically decrease the death rate of people suffering from different diseases such as cancer and infectious diseases. Because conventional diagnostic methods have limited application in low-resource settings due to the use of bulky and expensive instrumentation, simple and low-cost point-of-care diagnostic devices for timely and early biomarker diagnosis is the need of the hour, especially in rural areas and developing nations. The microfluidics technology possesses remarkable features for simple, low-cost, and rapid disease diagnosis. There have been significant advances in the development of microfluidic platforms for biomarker detection of diseases. This article reviews recent advances in biomarker detection using cost-effective microfluidic devices for disease diagnosis, with the emphasis on infectious disease and cancer diagnosis in low-resource settings. This review first introduces different microfluidic platforms (e.g. polymer and paper-based microfluidics) used for disease diagnosis, with a brief description of their common fabrication techniques. Then, it highlights various detection strategies for disease biomarker detection using microfluidic platforms, including colorimetric, fluorescence, chemiluminescence, electrochemiluminescence (ECL), and electrochemical detection. Finally, it discusses the current limitations of microfluidic devices for disease biomarker detection and future prospects.

Regulation of the Contribution of Integrin to Cell Attachment on Poly(2-Methoxyethyl Acrylate) (PMEA) Analogous Polymers for Attachment-Based Cell Enrichment

Cell enrichment is currently in high demand in medical engineering. We have reported that non-blood cells can attach to a blood-compatible poly(2-methoxyethyl acrylate) (PMEA) substrate through integrin-dependent and integrin-independent mechanisms because the PMEA substrate suppresses protein adsorption. Therefore, we assumed that PMEA analogous polymers can change the contribution of integrin to cell attachment through the regulation of protein adsorption. In the present study, we investigated protein adsorption, cell attachment profiles, and attachment mechanisms on PMEA analogous polymer substrates. Additionally, we demonstrated the possibility of attachment-based cell enrichment on PMEA analogous polymer substrates. HT-1080 and MDA-MB-231 cells started to attach to poly(butyl acrylate) (PBA) and poly(tetrahydrofurfuryl acrylate) (PTHFA), on which proteins could adsorb well, within 1 h. HepG2 cells started to attach after 1 h. HT-1080, MDA-MB-231, and HepG2 cells started to attach within 30 min to PMEA, poly(2-(2-methoxyethoxy) ethyl acrylate-co-butyl acrylate) (30:70 mol%, PMe2A) and poly(2-(2-methoxyethoxy) ethoxy ethyl acrylate-co-butyl acrylate) (30:70 mol%, PMe3A), which suppress protein adsorption. Moreover, the ratio of attached cells from a cell mixture can be changed on PMEA analogous polymers. These findings suggested that PMEA analogous polymers can be used for attachment-based cell enrichment.

Improvement of the fluorescence intensity during a flow cytometric analysis for rice protoplasts by localization of a green fluorescent protein into chloroplasts

Protoplasts have been a useful unicellular system for various molecular biological analyses based on transient expression and single cell analysis using fluorescence-activated cell sorting (FACS), widely used as a powerful method in functional genomics. Despite the versatility of these methods, some limits based on low fluorescence intensity of a flow cytometric analysis (FCA) using protoplasts have been reported. In this study, the chloroplast targeting of fluorescent proteins (FPs) led to an eight-fold increase in fluorescence intensity and a 4.5-fold increase of transfection ratio from 14.7% to 65.7% as compared with their targeting into the cytoplasm. Moreover, the plot data of FCA shows that 83.3% of the K-sGFP population is under the threshold level, regarded as a non-transgenic population with background signals, while 65.7% of the K-sGFP population is spread on overall intervals. To investigate the reason underlying this finding, mRNA/protein levels and transfection efficiency were analyzed, and results suggest that mRNA/protein levels and transfection ratio are not much different between K-sGFP and KR-sGFP. From those results, we hypothesized that the difference of fluorescence intensity is not only derived from cellular events such as molecular level or transfection efficiency. Taken together, we suggest that the translocation of FPs into chloroplasts contributes to the improvement of fluorescence intensity in FCA and, apparently, plays an important role in minimizing the loss of the transfected population. Our study could be usefully applicable for highly sensitive FACS and FCA-investigations of green tissue.

Circulating endothelial cells and their subpopulations: role as predictive biomarkers in antiangiogenic therapy for colorectal cancer

Several anticancer therapies have been developed to block angiogenesis, a key mechanism in tumor growth and metastasis. The predominantly cytostatic action of these compounds makes an assessment of their clinical activities inadequate if based only on the reduction of the tumor dimensions, as this may not reflect their true biologic efficacy. Thus, it is crucial to identify biomarkers that permit the recognition of potentially responsive subjects and to spare toxicity in those who are unlikely to benefit from treatment. Circulating endothelial cells (CECs) have been recently indicated as potential surrogate biomarkers of angiogenesis in several types of cancer. The possibility of rapidly quantifying these cells represents a promising tool for monitoring the clinical outcome of tumors with the potential to assess response to various treatments. However, the identification and quantification of CECs is technically difficult and not well standardized. A variety of methods to detect CECs in patients with solid tumors have been used; these are based on different technical approaches, combinations of surface markers, sample handling, and staining protocols. With an expanding interest in the field of potential clinical applications for CECs in oncology, the development of standardized protocols for analysis is mandatory. The aim of this review was to critically summarize the available data concerning the clinical value of CECs and their subpopulations as biomarkers of antiangiogenic therapy in patients with metastatic colorectal cancer.

Flow cytometry protocols for surface and intracellular antigen analyses of neural cell types

Flow cytometry has been extensively used to define cell populations in immunology, hematology and oncology. Here, we provide a detailed description of protocols for flow cytometric analysis of the cluster of differentiation (CD) surface antigens and intracellular antigens in neural cell types. Our step-by-step description of the methodological procedures include: the harvesting of neural in vitro cultures, an optional carboxyfluorescein succinimidyl ester (CFSE)-labeling step, followed by surface antigen staining with conjugated CD antibodies (e.g., CD24, CD54), and subsequent intracellar antigen detection via primary/secondary antibodies or fluorescently labeled Fab fragments (Zenon labeling). The video demonstrates the most critical steps. Moreover, principles of experimental planning, the inclusion of critical controls, and fundamentals of flow cytometric analysis (identification of target population and exclusion of debris; gating strategy; compensation for spectral overlap) are briefly explained in order to enable neurobiologists with limited prior knowledge or specific training in flow cytometry to assess its utility and to better exploit this powerful methodology.

Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo

In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, whole-transcriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.

A non-parametric Bayesian model for joint cell clustering and cluster matching: identification of anomalous sample phenotypes with random effects

Background

Flow cytometry (FC)-based computer-aided diagnostics is an emerging technique utilizing modern multiparametric cytometry systems.

The major difficulty in using machine-learning approaches for classification of FC data arises from limited access to a wide variety of anomalous samples for training. In consequence, any learning with an abundance of normal cases and a limited set of specific anomalous cases is biased towards the types of anomalies represented in the training set. Such models do not accurately identify anomalies, whether previously known or unknown, that may exist in future samples tested. Although one-class classifiers trained using only normal cases would avoid such a bias, robust sample characterization is critical for a generalizable model. Owing to sample heterogeneity and instrumental variability, arbitrary characterization of samples usually introduces feature noise that may lead to poor predictive performance. Herein, we present a non-parametric Bayesian algorithm called ASPIRE (anomalous sample phenotype identification with random effects) that identifies phenotypic differences across a batch of samples in the presence of random effects. Our approach involves simultaneous clustering of cellular measurements in individual samples and matching of discovered clusters across all samples in order to recover global clusters using probabilistic sampling techniques in a systematic way.

Results

We demonstrate the performance of the proposed method in identifying anomalous samples in two different FC data sets, one of which represents a set of samples including acute myeloid leukemia (AML) cases, and the other a generic 5-parameter peripheral-blood immunophenotyping. Results are evaluated in terms of the area under the receiver operating characteristics curve (AUC). ASPIRE achieved AUCs of 0.99 and 1.0 on the AML and generic blood immunophenotyping data sets, respectively.

Conclusions

These results demonstrate that anomalous samples can be identified by ASPIRE with almost perfect accuracy without a priori access to samples of anomalous subtypes in the training set. The ASPIRE approach is unique in its ability to form generalizations regarding normal and anomalous states given only very weak assumptions regarding sample characteristics and origin. Thus, ASPIRE could become highly instrumental in providing unique insights about observed biological phenomena in the absence of full information about the investigated samples.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-314) contains supplementary material, which is available to authorized users.

Deconvolution of the gene expression profiles of valuable banked blood specimens for studying the prognostic values of altered peripheral immune cell proportions in cancer patients

Background

The altered composition of immune cells in peripheral blood has been reported to be associated with cancer patient survival. However, analysis of the composition of peripheral immune cells are often limited in retrospective survival studies employing banked blood specimens with long-term follow-up because the application of flow cytometry to such specimens is problematic. The aim of this study was to demonstrate the feasibility of deconvolving blood-based gene expression profiles (GEPs) to estimate the proportions of immune cells and determine their prognostic values for cancer patients.

Methods and Results

Here, using GEPs from peripheral blood mononuclear cells (PBMC) of 108 non-small cell lung cancer (NSCLC) patients, we deconvolved the immune cell proportions and analyzed their association with patient survival. Univariate Kaplan-Meier analysis showed that a low proportion of T cells was significantly associated with poor patient survival, as was the proportion of T helper cells; however, only the proportion of T cells was independently prognostic for patients by a multivariate Cox regression analysis (hazard ratio = 2.23; 95% CI, 1.01–4.92; p = .048). Considering that altered peripheral blood compositions can reflect altered immune responses within the tumor microenvironment, based on a tissue-based GEPs of NSCLC patients, we demonstrated a significant association between poor patient survival and the low level of antigen presentation, which play a critical role in T cell proliferation.

Conclusions

These results demonstrate that it is feasible to deconvolve GEPs from banked blood specimens for retrospective survival analysis of alterations of immune cell composition, and suggest the proportion of T cells in PBMC which might reflect the antigen presentation level within the tumor microenvironment can be a prognostic marker for NSCLC patients.

Recent advances in the molecular characterization of circulating tumor cells

Although circulating tumor cells (CTCs) were first observed over a century ago, lack of sensitive methodology precluded detailed study of these cells until recently. However, technological advances have now facilitated the identification, enumeration, and characterization of CTCs using a variety of methods. The majority of evidence supporting the use of CTCs in clinical decision-making has been related to enumeration using the CellSearch® system and correlation with prognosis. Growing evidence also suggests that CTC monitoring can provide an early indication of patient treatment response based on comparison of CTC levels before and after therapy. However, perhaps the greatest potential that CTCs hold for oncology lies at the level of molecular characterization. Clinical treatment decisions may be more effective if they are based on molecular characteristics of metastatic cells rather than on those of the primary tumor alone. Molecular characterization of CTCs (which can be repeatedly isolated in a minimally invasive fashion) provides the opportunity for a "real-time liquid biopsy" that allows assessment of genetic drift, investigation of molecular disease evolution, and identification of actionable genomic characteristics. This review focuses on recent advances in this area, including approaches involving immunophenotyping, fluorescence in situ hybridization (FISH), multiplex RT-PCR, microarray, and genomic sequencing.

DNA-directed assembly of antibody-fluorophore conjugates for quantitative multiparametric flow cytometry

Multiparametric flow cytometry offers a powerful approach to single-cell analysis with broad applications in research and diagnostics. Despite advances in instrumentation, progress in methodology has lagged. Currently there is no simple and efficient method for antibody labeling or quantifying the number of antibodies bound per cell. Herein, we describe a DNA-directed assembly approach to fluorescent labeling that overcomes these barriers. Oligonucleotide-tagged antibodies and microparticles can be annealed to complementary oligonucleotides bearing fluorophores to create assay-specific labeling probes and controls, respectively. The ratio of the fluorescence intensity of labeled cells to the control particles allows direct conversion of qualitative data to quantitative units of antibody binding per cell. Importantly, a single antibody can be labeled with any fluorophore by using a simple mix-and-match labeling strategy. Thus, any antibody can provide a quantitative probe in any fluorescent channel, thus overcoming major barriers to the use of flow cytometry as a technique for systems biology and clinical diagnostics.

Tumor-reactive CD8+ T cells in metastatic gastrointestinal cancer refractory to chemotherapy

PURPOSE

To evaluate whether patients with metastatic gastrointestinal adenocarcinomas refractory to chemotherapy harbor tumor-reactive cytotoxic T cells.

EXPERIMENTAL DESIGN

Expansion of CD8(+) tumor-infiltrating lymphocytes (TIL) and cancer cell lines was attempted from gastrointestinal cancer metastases in 16 consecutive patients for the study of antitumor immune recognition. Retroviral transduction of genes encoding T-cell receptors (TCR) was used to define HLA-restriction elements and specific reactivity.

RESULTS

TIL were expanded from metastases in all patients, and new tumor cell lines were generated in 5 patients. Autologous tumor recognition without cross-reactivity against allogeneic HLA-matched gastrointestinal tumors was found in CD8(+) TIL from 3 of these 5 patients. In a patient with gastric cancer liver metastases, the repertoire of CD8(+) TIL was dominated by cytolytic sister clones reactive to 2 out of 4 autologous cancer cell lines restricted by HLA-C*0701. From the same patient, a rare CD8(+) TIL clone with a distinct TCR recognized all four cancer cell lines restricted by HLA-B*4901. In a patient with bile duct cancer, two distinct antitumor cytolytic clones were isolated from a highly polyclonal CD8(+) TIL repertoire. TCRs isolated from these clones recognized epitopes restricted by HLA-A*0201. In a third patient, CD8(+) TIL reactivity was progressively lost against an autologous colon cancer cell line that displayed loss of HLA haplotype.

CONCLUSIONS

This study provides a basis for the development of immunotherapy for patients with advanced gastrointestinal malignancies by first establishing the presence of naturally occurring tumor-reactive CD8(+) TIL at the molecular level.

Phenotype and function of T cells infiltrating visceral metastases from gastrointestinal cancers and melanoma: implications for adoptive cell transfer therapy

Adoptive cell transfer of tumor-infiltrating lymphocytes (TILs) can mediate cancer regression in patients with metastatic melanoma, but whether this approach can be applied to common epithelial malignancies remains unclear. In this study, we compared the phenotype and function of TILs derived from liver and lung metastases from patients with gastrointestinal (GI) cancers (n = 14) or melanoma (n = 42). Fewer CD3(+) T cells were found to infiltrate GI compared with melanoma metastases, but the proportions of CD8(+) cells, T cell differentiation stage, and expression of costimulatory molecules were similar for both tumor types. Clinical-scale expansion up to ~50 × 10(9) T cells on average was obtained for all patients with GI cancer and melanoma. From GI tumors, however, TIL outgrowth in high-dose IL-2 yielded 22 ± 1.4% CD3(+)CD8(+) cells compared with 63 ± 2.4% from melanoma (p < 0.001). IFN-γ ELISA demonstrated MHC class I-mediated reactivity of TIL against autologous tumor in 5 of 7 GI cancer patients tested (9% of 188 distinct TIL cultures) and in 9 of 10 melanoma patients (43% of 246 distinct TIL cultures). In these assays, MHC class I-mediated up-regulation of CD137 (4-1BB) expression on CD8(+) cells suggested that 0-3% of TILs expanded from GI cancer metastases were tumor-reactive. This study implies that the main challenge to the development of TIL adoptive cell transfer for metastatic GI cancers may not be the in vitro expansion of bulk TILs, but the ability to select and enrich for tumor-reactive T cells.

Technical advance: autofluorescence-based sorting: rapid and nonperturbing isolation of ultrapure neutrophils to determine cytokine production

The technical limitations of isolating neutrophils without contaminating leukocytes, while concurrently minimizing neutrophil activation, is a barrier to determining specific neutrophil functions. We aimed to assess the use of FACS for generating highly pure quiescent neutrophil populations in an antibody-free environment. Peripheral blood human granulocytes and murine bone marrow-derived neutrophils were isolated by discontinuous Percoll gradient and flow-sorted using FSC/SSC profiles and differences in autofluorescence. Postsort purity was assessed by morphological analysis and flow cytometry. Neutrophil activation was measured in unstimulated-unsorted and sorted cells and in response to fMLF, LTB4, and PAF by measuring shape change, CD62L, and CD11b expression; intracellular calcium flux; and chemotaxis. Cytokine production by human neutrophils was also determined. Postsort human neutrophil purity was 99.95% (sem=0.03; n=11; morphological analysis), and 99.68% were CD16(+ve) (sem=0.06; n=11), with similar results achieved for murine neutrophils. Flow sorting did not alter neutrophil activation or chemotaxis, relative to presorted cells, and no differences in response to agonists were observed. Stimulated neutrophils produced IL-1β, although to a lesser degree than CXCL8/IL-8. The exploitation of the difference in autofluorescence between neutrophils and eosinophils by FACS is a quick and effective method for generating highly purified populations for subsequent in vitro study.

Combined flow cytometric analysis of surface and intracellular antigens reveals surface molecule markers of human neuropoiesis

Surface molecule profiles undergo dynamic changes in physiology and pathology, serve as markers of cellular state and phenotype and can be exploited for cell selection strategies and diagnostics. The isolation of well-defined cell subsets is needed for in vivo and in vitro applications in stem cell biology. In this technical report, we present an approach for defining a subset of interest in a mixed cell population by flow cytometric detection of intracellular antigens. We have developed a fully validated protocol that enables the co-detection of cluster of differentiation (CD) surface antigens on fixed, permeabilized neural cell populations defined by intracellular staining. Determining the degree of co-expression of surface marker candidates with intracellular target population markers (nestin, MAP2, doublecortin, TUJ1) on neuroblastoma cell lines (SH-SY5Y, BE(2)-M17) yielded a combinatorial CD49f^-/CD200^high surface marker panel. Its application in fluorescence-activated cell sorting (FACS) generated enriched neuronal cultures from differentiated cell suspensions derived from human induced pluripotent stem cells. Our data underlines the feasibility of using the described co-labeling protocol and co-expression analysis for quantitative assays in mammalian neurobiology and for screening approaches to identify much needed surface markers in stem cell biology.

Flow cytometry: a flexible tool for biomarker research

Flow cytometry is increasingly recognized as an invaluable technology in biomarker research. Owing to its multiparametric nature it can provide highly detailed information on any single cell in a heterogeneous population. Its versatility means it can be conducted in both the preclinical and clinical setting, generating biomarker data that can drive decisions pertaining to dose selection in clinical trials, treatment options for cancer sufferers and even suitability of patients to receive transplants. Most tissue types can be utilized by the flow cytometrist, allowing the technology to be applied to many fields of research, yet consensus still needs to be reached on standardization, regulation and validation of multiparametric flow cytometry assays. In parallel, continual innovation in analysis software to manage the huge datasets that can be generated is also needed. Nevertheless, the flexibility of flow cytometry means that it remains at the forefront of both routine and exploratory biomarker studies.

Inter-laboratory assessment of flow cytometric monocyte HLA-DR expression in clinical samples

BACKGROUND

Diminished expression of human leukocyte antigen DR on circulating monocytes (mHLA-DR) is a reliable indicator of immunosuppression in critically ill patients, predictive of both adverse outcome and septic complications. The objective of the present work was to test, in an inter-laboratory clinical study, a standardized protocol for mHLA-DR measurement by flow cytometry.

METHODS

mHLA-DR was assessed in fresh whole blood according to a standardized staining protocol. Cells were analyzed on different flow cytometers (FC500, Navios, FACS Canto II) in different laboratories (Lyon and Grenoble). Results were expressed as numbers of antibodies bound per cell (AB/C).

RESULTS

Correlations between results were excellent (Pearson and interclass correlation coefficients > 0.98). Coefficients of variations for intra-assay precision ranged from 1.9 to 3.2%.

CONCLUSION

The present report highlights the robustness of this standardized flow cytometric protocol for mHLA-DR measurement in multicentric clinical studies.