Proximity ligation measurement of the complex between prostate specific antigen and alpha1-protease inhibitor

A facile and label-free electrochemical aptasensor for tumour-derived extracellular vesicle detection based on the target-induced proximity hybridization of split aptamers

Facile detection of tumour-derived extracellular vesicles (EVs) is crucial to cancer diagnosis. Herein, a facile and label-free electrochemical aptasensor was fabricated to detect tumour-derived EVs based on the target-induced proximity hybridization of split aptamers. In this assay, two designed oligonucleotide probes containing fragments of a protein tyrosine kinase-7 (PTK7) aptamer were used to recognize and capture EVs containing PTK7. In the presence of target EVs, the aptamer-target ternary complex could induce proximity hybridization and form a DNA duplex on the electrode. The DNA duplex could bind more electroactive Ru(NH3)63+ through electrostatic attraction, resulting in an increased cathodic current signal. By virtue of the excellent electrochemical signal reporter RuHex, the specificity of the aptamer and proximity ligation, a facile EV electrochemical aptasensor with a detection limit of 6.607 × 105 particles per mL was realized. Furthermore, this aptasensor showed good selectivity to distinguish different tumour-derived EVs and was applied to detect EVs in complex biological samples. The proposed electrochemical aptasensor can be further extended to the detection of other EVs, thus showing great potential in clinical diagnosis.

Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues

Immunohistochemistry (IHC) is the accepted standard for spatial analysis of protein expression in tissues. IHC is widely used for cancer diagnostics and in basic research. The development of new antibodies to proteins with unknown expression patterns has created a demand for thorough validation. We have applied resources from the Human Protein Atlas project and the Antibody Portal at National Cancer Institute to generate protein expression data for 12 proteins across 39 cancer cell lines and 37 normal human tissue types. The outcome of IHC on consecutive sections from both cell and tissue microarrays using two independent antibodies for each protein was compared with in situ proximity ligation (isPLA), where binding by both antibodies is required to generate detection signals. Semi-quantitative scores from IHC and isPLA were compared with expression of the corresponding 12 transcripts across all cell lines and tissue types. Our results show a more consistent correlation between mRNA levels and isPLA as compared to IHC. The main benefits of isPLA include increased detection specificity and decreased unspecific staining compared to IHC. We conclude that implementing isPLA as a complement to IHC for analysis of protein expression and in antibody validation pipelines can lead to more accurate localization of proteins in tissue.

Proximity Ligation Real-Time PCR: A protein-based confirmatory method for the identification of semen and sperm cells from sexual assault evidence

The positive identification of seminal fluids in sexual assault crimes is considered crucial evidence to determine whether a sexual act occurred or not. However, current presumptive methods lack specificity and sensitivity. Confirmation of semen by microscopic examination of spermatozoa is laborious, time consuming, and can sometimes lead to negative or inconclusive results. Here we report the use of the Proximity Ligation Real-Time PCR (PLiRT-PCR) assay as an attractive and promising confirmatory method for the identification of semen and sperm proteins using two polyclonal antibodies, Prostate Specific Antigen (PSA) and Sperm-Specific Protein (SP10), respectively. PLiRT-PCR, relies on protein recognition by pairs of proximity probes (antibody-DNA conjugates) that give rise to a ligated DNA strand. The ligated DNA strand is then amplified and detected by qPCR.

Biomarker development, from bench to bedside

This review describes studies performed by our group and other laboratories in the field aimed at development of biomarkers not only for cancer but also for other diseases. The markers covered include tumor-associated trypsin inhibitor (TATI), tumor-associated trypsin (TAT), human chorionic gonadotropin (hCG), prostate-specific antigen (PSA) and their various molecular forms, their biology and diagnostic use. The discovery of TATI was the result of a hypothesis-driven project aimed at finding new biomarkers for ovarian cancer among urinary peptides. TATI has since proved to be a useful prognostic marker for several cancers. Recently, it has been named Serine Peptidase Inhibitor Kazal Type 1 (SPINK1) after being rediscovered by several groups as a tumor-associated peptide by gene expression profiling and proteomic techniques and shown to promote tumor development by stimulating the EGF receptor. To explain why a trypsin inhibitor is strongly expressed in some cancers, research focused on the protease that it inhibited led to the finding of tumor-associated trypsin (TAT). Elevated serum concentrations of TAT-2 were found in some cancer types, but fairly high background levels of pancreatic trypsinogen-2 limited the use of TAT-2 for cancer diagnostics. However, trypsinogen-2 and its complex with α1-protease inhibitor proved to be very sensitive and specific markers for pancreatitis. Studies on hCG were initiated by the need to develop more rapid and sensitive pregnancy tests. These studies showed that serum from men and non-pregnant women contains measurable concentrations of hCG derived from the pituitary. Subsequent development of assays for the subunits of hCG showed that the β subunit of hCG (hCGβ) is expressed at low concentrations by most cancers and that it is a strong prognostic marker. These studies led to the formation of a working group for standardization of hCG determinations and the development of new reference reagents for several molecular forms of hCG. The preparation of intact hCG has been adopted as the fifth international standard by WHO. Availability of several well-defined forms of hCG made it possible to characterize the epitopes of nearly 100 monoclonal antibodies. This will facilitate design of immunoassays with pre-defined specificity. Finally, the discovery of different forms of immunoreactive PSA in serum from a prostate cancer patient led to identification of the complex between PSA and α1-antichymotrypsin, and the use of assays for free and total PSA in serum for improved diagnosis of prostate cancer. Epitope mapping of PSA antibodies and establishment of PSA standards has facilitated establishment well-standardized assays for the various forms of PSA.

Elevated Serum GAD65 and GAD65-GADA Immune Complexes in Stiff Person Syndrome

Glutamic acid decarboxylase 65 (GAD65) and autoantibodies specific for GAD65 (GADA) are associated with autoimmune diseases including Stiff Person Syndrome (SPS) and Type 1 diabetes (T1D). GADA is recognized as a biomarker of value for clinical diagnosis and prognostication in these diseases. Nonetheless, it remains medically interesting to develop sensitive and specific assays to detect GAD65 preceding GADA emergence, and to monitor GADA-GAD65 immune complexes in blood samples. In the present study, we developed a highly sensitive proximity ligation assay to measure serum GAD65. This novel assay allowed detection of as little as 0.65 pg/ml GAD65. We were also able to detect immune complexes involving GAD65 and GADA. Both free GAD65 and GAD65-GADA levels were significantly higher in serum samples from SPS patients compared to healthy controls. The proximity ligation assays applied for detection of GAD65 and its immune complexes may thus enable improved diagnosis and better understanding of SPS.

Recent progress in prostate-specific antigen and HIV proteases detection

Proteases mediate a wide variety of biological events and have a critical role in the development of many diseases. Protease detection methods can be hindered by the limitation of assay safety, sensitivity, specificity, time constraints and ease of on-site analysis. Notably, the implementation of various detection methods on biosensing platforms translates them into practical biosensing applications. Currently, the detection of prostate cancer and AIDS at the earliest occasion is one of the major research obstacles. Therefore, recent advances focus on the development of portable detection systems toward point-of-care testing. These detection systems should be highly sensitive and specific for the detection of their prognostic biomarkers, such as the prostate-specific antigen and HIV load assay for prostate cancer and AIDS, respectively. These methods will also facilitate decision-making on a treatment regimen.

Assembling DNA through affinity binding to achieve ultrasensitive protein detection

Recent advances in DNA assembly and affinity binding have enabled exciting developments of nanosensors and ultrasensitive assays for specific proteins. These sensors and assays share three main attractive features: 1) the detection of proteins can be accomplished by the detection of amplifiable DNA, thereby dramatically enhancing the sensitivity; 2) assembly of DNA is triggered by affinity binding of two or more probes to a single target molecule, thereby resulting in increased specificity; and 3) the assay is conducted in solution with no need for separation, thus making the assay attractive for potential point-of-care applications. We illustrate here the principle of assembling DNA through affinity binding, and we highlight novel applications to the detection of proteins.

PSA forms complexes with α1-antichymotrypsin in prostate

BACKGROUND

PSA is the most useful prostate cancer marker. However, its levels are increased also in some non-malignant conditions. In circulation, the majority of PSA is complexed with protease inhibitors, including α(1) -antichymotrypsin (ACT). The proportion of the PSA-ACT complex is higher in patients with prostate cancer than in controls without cancer. The expression of ACT has been shown to be higher in prostate cancer than in benign prostatic hyperplasia. However, results regarding the extent which PSA forms complexes within the prostate and whether there are differences in complex formation between normal and malignant prostatic tissue are inconsistent and limited.

METHODS

We studied complex formation of PSA secreted by cultured human prostate tissues and in the tissue by in situ proximity ligation assay (PLA). Free, total and active PSA, and the PSA-ACT complex were determined in tissue culture media by immunoassays, immunoblotting, and chromatographic methods.

RESULTS

The majority of PSA in tissue culture medium was free and enzymatically active. However, a significant proportion (1.6 ± 0.5%) of immunoreactive PSA was found to be complexed with ACT. Complex formation was confirmed by in situ PLA, which showed more intense staining of PSA-ACT in cancers with Gleason grade 3 than in adjacent benign tissues from the same patients.

CONCLUSIONS

These results show that PSA forms complexes already within the prostate and that PSA-ACT levels are increased in moderately differentiated prostate cancer tissue. This may explain, at least partially, why the ratio of serum PSA-ACT to total PSA is increased in prostate cancer.

In situ quantification of HER2-protein tyrosine kinase 6 (PTK6) protein-protein complexes in paraffin sections from breast cancer tissues

Background:

Protein tyrosine kinase 6 (PTK6; breast tumour kinase) is overexpressed in up to 86% of the invasive breast cancers, and its association with the oncoprotein human epidermal growth factor receptor 2 (HER2) was shown in vitro by co-precipitation. Furthermore, expression of PTK6 in tumours is linked with the expression of HER2.

Method and results:

In this study, we used the proximity ligation assay (PLA) technique on formalin-fixed paraffin sections from eighty invasive breast carcinoma tissue specimens to locate PTK6–HER2 protein–protein complexes. Proximity ligation assay signals from protein complexes were assessed quantitatively, and expression levels showed a statistically significant association with tumour size (P=0.015) and course of the cancer disease (P=0.012).

Conclusion:

Protein tyrosine kinase 6 forms protein complexes with HER2 in primary breast cancer tissues, which can be visualised by use of the PLA technique. Human epidermal growth factor receptor 2–PTK6 complexes are of prognostic relevance.

Semisynthetic DNA-protein conjugates for biosensing and nanofabrication

Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.

Sensitive plasma protein analysis by microparticle-based proximity ligation assays

Detection of proteins released in the bloodstream from tissues damaged by disease can promote early detection of pathological conditions, differential diagnostics, and follow-up of therapy. Despite these prospects and a plethora of candidate biomarkers, efforts in recent years to establish new protein diagnostic assays have met with limited success. One important limiting factor has been the challenge of detecting proteins present at trace levels in complex bodily fluids. To achieve robust, sensitive, and specific detection, we have developed a microparticle-based solid-phase proximity ligation assay, dependent on simultaneous recognition of target proteins by three antibody molecules for added specificity. After capture on a microparticle, solid-phase pairs of proximity probes are added followed by washes, enabling detection and identification of rare protein molecules in blood while consuming small amounts of sample. We demonstrate that single polyclonal antibody preparations raised against target proteins of interest can be readily used to establish assays where detection depends on target recognition by three individual antibody molecules, recognizing separate epitopes. The assay was compared with state-of-the-art sandwich ELISAs for detection of vascular endothelial growth factor, interleukin-8 and interleukin-6, and it was found to be superior both with regard to dynamic range and minimal numbers of molecules detected. Furthermore, the assays exhibited excellent performance in undiluted plasma and serum as well as in whole blood, producing comparable results for nine different antigens. We thus show that solid-phase proximity ligation assay is suitable for validation of a variety of protein biomarkers over broad dynamic ranges in clinical samples.