Profiling CD antigens on leukaemias with an antibody microarray

New insight on the role of Helicobacter pylori cagA in the expression of cell surface antigens with important biological functions in gastric carcinogenesis

BACKGROUND

Expression of cluster of differentiation (CD) antigens changes according to disease status and inflammation. Profiles of CD antigens expression in gastric cancer patients are different based on the status of H. pylori infection.

AIMS

We conducted this study to profile CD antigen markers in gastric adenocarcinoma cells (AGS cell line) infected with distinct cytotoxin-associated gene A (cagA) genotypes of H. pylori clinical isolates.

METHODS

The AGS cells were infected with H. pylori isolates with different cagA genotypes, and CD antigens expression was determined using DotScan™ antibody microarray. Formation of "hummingbird" phenotype was determined, and the percentage was calculated.

RESULTS

H. pylori strains harboring cagA upregulated the expression of CD antigen involved in cancer stem cell formation (CD55), but downregulated CD antigens involved in immune regulation (CD40 and CD186) and cell adhesion (CD44). CD54 (neutrophil adhesion) and CD71 (iron transfer) were highly downregulated in the gastric cells infected with Western cagA isolates compared with East Asian isolates. CD antigen expression was different in the cells infected with H. pylori harboring different CagA EPIYA (Glu-Pro-Ile-Tyr-Ala) numbers, in which higher repression of CD54 and CD15 (Lewis x antigen) were observed in the isolate with the highest number of EPIYA motif. Furthermore, higher downregulation of CD15 was observed in the infected gastric cells with high percentage of "hummingbird" phenotype than that of low percentage of "hummingbird" phenotype.

CONCLUSION

Our study demonstrated the critical roles of CD antigens in the CagA pathogenesis and should be investigated further.

Maternal exposure to di-2-ethylhexyl phthalate (DEHP) depresses lactation capacity in mice

Increasing evidence shows that di-2-ethylhexyl phthalate (DEHP), mostly commonly used phthalate for the production of flexible polyvinyl chloride (PVC), has the potential to induce serious health risks in humans. However, the understanding of DEHP-induced lactation performance remains largely unknown. We sought to investigate the adverse effects of DEHP on lactation and examine the underlying mechanism linking DEHP exposure with the lactation alterations. We successfully adapted a maternal DEHP exposure model in female pregnant/lactating mice. Then we determined effects of DEHP exposure on food intake, body weight and milk production as well as the alterations in endocrine factors in lactating mice. The integrated metabonomic and transcriptomic analyses of the mammary gland were performed to measure the changed metabolites and genes related to DEHP exposure-induced lactation alterations. We observed the reduced food intake with elevated blood leptin and the decreased milk yield as well as the reduced levels of serum prolactin, growth hormone, insulin-like growth factor 1 and insulin after exposed to DEHP. Furthermore, 208 metabolites and 3452 genes were separately identified as differentially expressed features associated with DEHP exposure. Integrated metabonomic and transcriptomic analyses demonstrated that DEHP caused lactation depression mainly through impairing energy generation, inducing stress responses along with the hypoactivation of inflammation, reducing the production of antioxidants, disrupting hormone homeostasis and repressing the synthesis of milk constituents (the lower glucose availability for lactose synthesis; the disruption of milk fat globule membrane for lipid droplet formation; the ribosomal dysfunction and disruption of post-modifications for milk protein synthesis). We demonstrated that DEHP disrupted several lactation-related hormone homeostasis and multiple processes like energy insufficiency, inflammation activation, oxidative stress aggravation and disturbance of milk production in the mammary gland of female lactating mice. Our results provide valuable information for the health risk of plastic additive (DEHP) on female lactation dysfunction.

A Proposal for Nomenclature in Myeloid C-Type Lectin Receptors

Myeloid C-type lectin receptors (CLRs) comprise a family of receptors expressed by immune myeloid cells that share homologous C-type lectin domains. The implication of these CLRs in the regulation of homeostasis and activation of myeloid cells has generated a buoyant growth in the number of studies involving these receptors. Since their first description, diverse nomenclature has been used to refer to each of them, ranging from systematic classifications, such as gene name or cluster of differentiation, to non-systematic ones that include terminology based on gene expression patterns or function. In this review, we aim to summarize the different names used for the main myeloid CLRs and analyze which of them have been more frequently used in the literature. In addition, we have examined the evolution of the terminology applied to these myeloid CLRs over time. Based on this analysis, we propose a consensus alias for each of those myeloid CLRs. However, we acknowledge that systematicity is required beyond this terminology based on use frequency. Therefore, we have included gene names as the standardization tool to gather the maximum agreement. We suggest that a standard nomenclature consisting of both gene names and consensus alias should be included at least in scientific abstracts, which would help to identify relevant literature, saving time and effort and fostering the research in this field in a more systematic manner.

Capturing B type acute lymphoblastic leukemia cells using two types of antibodies

One way to monitor minimal residual disease (MRD) is to screen cells for multiple surface markers using flow cytometry. In order to develop an alternative microfluidic based method, isolation of B type acute lymphoblastic cells using two types of antibodies should be investigated. The immunomagnetic beads coated with various antibodies are used to capture the B type acute lymphoblastic cells. Single beads, two types of beads and surface immobilized antibody were used to measure the capture efficiency. Both micro and nanosize immunomagnetic beads can be used to capture B type acute lymphoblastic cells with a minimum efficiency of 94% and maximum efficiency of 98%. Development of a microfluidic based biochip incorporating immunomagnetic beads and surface immobilized antibodies for monitoring MRD can be an alternative to current cost and time inefficient laboratory methods. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2737, 2019.

Interfacing antibody-based microarrays and digital holography enables label-free detection for loss of cell volume

Background:

We introduce the combination of digital holographic microscopy (DHM) and antibody microarrays as a powerful tool to measure morphological changes in specifically antibody-captured cells. The aim of the study was to develop DHM for analysis of cell death of etoposide-treated suspension cells.

Results/methodology:

We demonstrate that the cell number, mean area, thickness and volume were noninvasively measured by using DHM. The cell number was stable over time, but the two cell lines showed changes of cell area and cell irregularity after treatment. The cell volume in etoposide-treated cells was decreased, whereas untreated cells showed stable volume.

Conclusion:

Our results provide proof of concept for using DHM combined with antibody-based microarray technology for detecting morphological changes in captured cells.

We use an innovative technique that combines digital holographic microscopy and the capture of cells with antibody microarrays as a powerful tool to measure cellular morphological changes. With this technique, the cells can be noninvasively viewed in 3D over time. We obtain results showing changes in cellular parameters including cell area, thickness and volume of the captured cells after treatment with the cell death-inducing drug etoposide. The cell volume in etoposide-treated cells showed a decrease, while untreated cells remained stable. Digital holographic microscopy combined with antibody microarray technology can be a future method for detecting morphological changes in treated cancer cells.

Exosome enrichment of human serum using multiple cycles of centrifugation

In this work, we compared the use of repeated cycles of centrifugation at conventional speeds for enrichment of exosomes from human serum compared to the use of ultracentrifugation (UC). After removal of cells and cell debris, a speed of 110 000 × g or 40 000 × g was used for the UC or centrifugation enrichment process, respectively. The enriched exosomes were analyzed using the bicinchoninic acid assay, 1D gel separation, transmission electron microscopy, Western blotting, and high-resolution LC-MS/MS analysis. It was found that a five-cycle repetition of UC or centrifugation is necessary for successful removal of nonexosomal proteins in the enrichment of exosomes from human serum. More significantly, 5× centrifugation enrichment was found to provide similar or better performance than 5× UC enrichment in terms of enriched exosome protein amount, Western blot band intensity for detection of CD-63, and numbers of identified exosome-related proteins and cluster of differentiation (CD) proteins. A total of 478 proteins were identified in the LC-MS/MS analyses of exosome proteins obtained from 5× UCs and 5× centrifugations including many important CD membrane proteins. The presence of previously reported exosome-related proteins including key exosome protein markers demonstrates the utility of this method for analysis of proteins in human serum.

Fundamentals and application of magnetic particles in cell isolation and enrichment: a review

Magnetic sorting using magnetic beads has become a routine methodology for the separation of key cell populations from biological suspensions. Due to the inherent ability of magnets to provide forces at a distance, magnetic cell manipulation is now a standardized process step in numerous processes in tissue engineering, medicine, and in fundamental biological research. Herein we review the current status of magnetic particles to enable isolation and separation of cells, with a strong focus on the fundamental governing physical phenomena, properties and syntheses of magnetic particles and on current applications of magnet-based cell separation in laboratory and clinical settings. We highlight the contribution of cell separation to biomedical research and medicine and detail modern cell-separation methods (both magnetic and non-magnetic). In addition to a review of the current state-of-the-art in magnet-based cell sorting, we discuss current challenges and available opportunities for further research, development and commercialization of magnetic particle-based cell-separation systems.

Surface antigen profiles of leukocytes and melanoma cells in lymph node metastases are associated with survival in AJCC stage III melanoma patients

There is an urgent need to identify more accurate prognostic biomarkers in melanoma patients, particularly in those with metastatic disease. This study aimed to identify melanoma and leukocyte surface antigens predictive of survival in a prospective series of AJCC stage IIIb/c melanoma patients (n = 29). Live cell suspensions were prepared from melanoma metastases within lymph nodes (LN). The suspensions were immuno-magnetically separated into CD45⁺ (leukocyte) and CD45⁻ (non-hematopoietic, enriched melanoma cell) fractions. Surface antigens on CD45⁻ and CD45⁺ cell populations were profiled using DotScan™ microarrays (Medsaic Pty. Ltd.) and showed differential abundance levels for 52 and 78 antigens respectively. Associations of the surface profiles with clinicopathologic and outcome data (median follow-up 35.4 months post LN resection) were sought using univariate (log-rank test) and multivariate (Wald’s test; modelled with patient’s age, gender and AJCC staging at LN recurrence) survival models. CD9 (p = 0.036), CD39 (p = 0.004) and CD55 (p = 0.005) on CD45⁺ leukocytes were independently associated with distant metastasis-free survival using multivariate analysis. Leukocytes with high CD39 levels were also significantly associated with increased overall survival (OS) in multivariate analysis (p = 0.016). LNs containing leukocytes expressing CD11b (p = 0.025), CD49d (p = 0.043) and CD79b (p = 0.044) were associated with reduced OS on univariate analysis. For enriched melanoma cells (CD45⁻ cell populations), 11 surface antigens were significantly correlated with the disease-free interval (DFI) between diagnosis of culprit primary melanoma and LN metastasis resection. Nine antigens on CD45⁺ leukocytes also correlated with DFI. Following validation in independent datasets, surface markers identified here should enable more accurate determination of prognosis in stage III melanoma patients and provide better risk stratification of patients entering clinical trials.

Current status of biomarkers for prostate cancer

Prostate cancer (PCa) is a leading cause of cancer-related death of men globally. Since its introduction, there has been intense debate as to the effectiveness of the prostate specific antigen (PSA) test as a screening tool for PCa. It is now evident that the PSA test produces unacceptably high rates of false positive results and is not prognostic. Here we review the current status of molecular biomarkers that promise to be prognostic and that might inform individual patient management. It highlights current efforts to identify biomarkers obtained by minimally invasive methods and discusses current knowledge with regard to gene fusions, mRNA and microRNAs, immunology, and cancer-associated microparticles.

High-throughput on-chip leukemia diagnosis

Advances in lab-on-a-chip technologies enabled programmable, reconfigurable, and scalable manipulation of a variety of laboratory procedures. Samples, reagents, and fluids can be precisely controlled; buffer temperature, pH, and concentration control systems as well as a variety of detection systems can be integrated on a small chip. These advantages have attracted attention in various fields of clinical application including leukemia diagnosis and research. A lot of research on lab-on-a-chip based diagnosis has been reported and the field is rapidly expanding. This review describes recent developments of lab-on-a-chip technologies as solutions to challenges for high-throughput leukemia diagnosis.

Using digital RNA counting and flow cytometry to compare mRNA with protein expression in acute leukemias

BACKGROUND

The diagnosis of malignant hematologic diseases has become increasingly complex during the last decade. It is based on the interpretation of results from different laboratory analyses, which range from microscopy to gene expression profiling. Recently, a method for the analysis of RNA phenotypes has been developed, the nCounter technology (Nanostring® Technologies), which allows for simultaneous quantification of hundreds of RNA molecules in biological samples. We evaluated this technique in a Swiss multi-center study on eighty-six samples from acute leukemia patients.

METHODS

mRNA and protein profiles were established for normal peripheral blood and bone marrow samples. Signal intensities of the various tested antigens with surface expression were similar to those found in previously performed Affymetrix microarray analyses. Acute leukemia samples were analyzed for a set of twenty-two validated antigens and the Pearson Correlation Coefficient for nCounter and flow cytometry results was calculated.

RESULTS

Highly significant values between 0.40 and 0.97 were found for the twenty-two antigens tested. A second correlation analysis performed on a per sample basis resulted in concordant results between flow cytometry and nCounter in 44-100% of the antigens tested (mean = 76%), depending on the number of blasts present in a sample, the homogeneity of the blast population, and the type of leukemia (AML or ALL).

CONCLUSIONS

The nCounter technology allows for fast and easy depiction of a mRNA profile from hematologic samples. This technology has the potential to become a valuable tool for the diagnosis of acute leukemias, in addition to multi-color flow cytometry.

Life on a microarray: assessing live cell functions in a microarray format

Microarray technology outgrew the detection of simple intermolecular interactions, as incubation of slides with living cells opened new vistas. Cell-based array technology permits simultaneous detection of several different cell surface molecules, allowing the complex characterization of cells with an amount of information that is hardly assessed by any other technique. Furthermore, binding of cells to printed antibodies or ligands may induce their activation, and consequently the outcome of these interactions, such as phosphorylation, gene expression, secretion of various products; differentiation, proliferation and apoptosis of the cells are also measurable on arrays. Moreover, since cells can be transfected with printed vectors, over- or under-expression of selected genes is also achievable simultaneously, creating a nice tool for assessing the function of a given gene. The enormously high-throughput cell-based microarray technology enables testing the effect of external stimuli on a scale that was earlier unthinkable. This review summarizes the possible applications of cell-based arrays.

Protein microarrays for systems biology

Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer, diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics, proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as high-throughput, miniaturized, and capable of parallel analysis, protein microarrays have already become an important technology platform for systems biology. In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays, and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.