Assay For Detection Of Protein Research Articles

DNA-Assisted CRISPR-Cas12a Enhanced Fluorescent Assay for Protein Detection in Complicated Matrices.

Proteins are important biological macromolecules that perform a wide variety of functions in the cell and human body, and can serve as important biomarkers for early diagnosis and prognosis of human diseases as well as monitoring the effectiveness of disease treatment. Hence, sensitive and accurate detection of proteins in human biospecimens is imperative. However, at present, there is no ideal method available for the detection of proteins in clinical samples, many of which are present at ultralow (less than 1 pM) concentrations and in complicated matrices. Herein, we report an ultrasensitive and selective DNA-assisted CRISPR-Cas12a enhanced fluorescent assay (DACEA) for protein detection with detection limits reaching as low as attomolar concentrations. The high assay sensitivity was accomplished through the combined DNA barcode amplification (by using dual-functionalized AuNPs) and CRISPR analysis, while the high selectivity and high resistance to the matrix effects of our method were accomplished via the formation of protein-antibody sandwich structure and the specific recognition of Cas12a (under the guidance of crRNA) toward the designed target ssDNA. Given its ability to accurately and sensitively detect trace amounts of proteins in complicated matrices, the DACEA protein assay platform pioneered in this work has a potential application in routine protein biomarker testing.

Simultaneous detection of membrane protein and mRNA at single extracellular vesicle level by droplet microfluidics for cancer diagnosis

IntroductionSimultaneous detection of proteins and mRNA within a single extracellular vesicle (EV) enables comprehensive analysis of specific EVs subpopulations, significantly advancing cancer diagnostics. However, developing a sensitive and user-friendly approach for simultaneously detecting multidimensional biomarkers in single EV is still challenging. ObjectivesTo facilitate the analysis of multidimensional biomarkers in EVs and boost its clinical application, we present a versatile droplet digital system facilitating the concurrent detection of membrane proteins and mRNA at the single EV level with high sensitivity and specificity. MethodsThe antibody-DNA conjugates were firstly prepared for EVs protein biomarkers recognition and signal transformation. Coupling with the assembled triplex droplet digital PCR system, a versatile droplet digital analysis assay for simultaneous detection of membrane protein and mRNA at a single EV level was developed. ResultsOur new droplet digital system displayed high sensitivity and specificity. Additionally, its clinical application was validated in a breast cancer cohort. As expected, this assay has demonstrated superior performance in distinguishing breast cancer from healthy individuals and benign controls through combined detection of EVs protein and mRNA markers compared to any single kind marker detections, especially for patients with breast cancer at early stage (AUC=0.9229). ConclusionConsequently, this study proposes a promising strategy for accurately identifying and analyzing specific EV subgroups through the co-detection of proteins and mRNA at the single EV level, holding significant potential for future clinical applications.

Levels of the HtrA1 Protein in Serum and Vitreous Humor Are Independent of Genetic Risk for Age-Related Macular Degeneration at the 10q26 Locus.

The purpose of this study was to determine if levels of the HtrA1 protein in serum or vitreous humor are influenced by genetic risk for age-related macular degeneration (AMD) at the 10q26 locus, age, sex, AMD status, and/or AMD disease severity, and, therefore, to determine the contribution of systemic and ocular HtrA1 to the AMD disease process. A custom-made sandwich ELISA assay (SCTM ELISA) for detection of the HtrA1 protein was designed and compared with three commercial assays (R&D Systems, MyBiosource 1 and MyBiosource 2) using 65 serum samples. Concentrations of HtrA1 were thereafter determined in serum and vitreous samples collected from 248 individuals and 145 human donor eyes, respectively. The SCTM ELISA demonstrated high specificity, good recovery, and parallelism within its linear detection range and performed comparably to the R&D Systems assay. In contrast, we were unable to demonstrate the specificity of the two assays from MyBioSource using either recombinant or native HtrA1. Analyses of concentrations obtained using the validated SCTM assay revealed that genetic risk at the 10q26 locus, age, sex, or AMD status are not significantly associated with altered levels of the HtrA1 protein in serum or in vitreous humor (P > 0.05). HtrA1 levels in serum and vitreous do not reflect the risk for AMD associated with the 10q26 locus or disease status. Localized alteration in HTRA1 expression in the retinal pigment epithelium, rather than systemic changes in HtrA1, is the most likely driver of elevated risk for developing AMD among individuals with risk variants at the 10q26 locus.

Characterization of humoral immune responses against SARS-CoV-2 accessory proteins in infected patients and mouse model

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, encodes several accessory proteins that have been shown to play crucial roles in regulating the innate immune response. However, their expressions in infected cells and immunogenicity in infected humans and mice are still not fully understood. This study utilized various techniques such as luciferase immunoprecipitation system (LIPS), immunofluorescence ​assay (IFA), and western ​blot (WB) to detect accessory protein-specific antibodies in sera of COVID-19 patients. Specific antibodies to proteins 3a, 3b, 7b, 8 and 9c can be detected by LIPS, but only protein 3a antibody was detected by IFA or WB. Antibodies against proteins 3a and 7b were only detected in ICU patients, which may serve as a marker for predicting disease progression. Further, we investigated the expression of accessory proteins in SARS-CoV-2-infected cells and identified the expressions of proteins 3a, 6, 7a, 8, and 9b. We also analyzed their ability to induce antibodies in immunized mice and found that only proteins 3a, 6, 7a, 8, 9b and 9c were able to induce measurable antibody productions, but these antibodies lacked neutralizing activities and did not protect mice from SARS-CoV-2 infection. Our findings validate the expression of SARS-CoV-2 accessory proteins and elucidate their humoral immune response, providing a basis for protein detection assays and their role in pathogenesis.

Abstract 5566: Streamlining tissue sample preparation: A comparative study on the efficiency and reproducibility of the Omni-Stainer™ dewaxing and HIER protocol

Abstract The evolution of life sciences research has entailed a shift toward understanding cellular functions within tissue microenvironments, with an emphasis on cell- and tissue-specific relationships. A key challenge in these endeavors is the need for accurate data acquisition, which can be impeded by variability in the multistep manual assay preparations. In the quest for developing reliable and efficient tissue sample preparation workflows, two protocols using multiple dewaxing agents have been compared: the Omni-Stainer™ Dewaxing and HIER antigen retrieval protocol from Parhelia Biosciences, Inc. and the analogous one on Leica BOND Rx. The objective of this research was to assess the efficiency and reproducibility of these methods in the context of a four-color morphology immunostaining used for GeoMx DSP RNA and protein detection assays (Nanostring). We examined the efficiency of automated dewaxing using various non-toxic xylene alternatives, including C12-15 alkyl Benzoate, diethylene glycol, methyl octanoate or methyl decanoate, and compared them to the proprietary Leica Bond Dewaxing solution. Then, we compared the quality of post-HIER immunostaining using two different four-antibody panels on human jejunum samples. After several rounds of optimization, we found that the V4 of the open-source Omni-Stainer™ dewax-HIER protocol resulted in identical quality of morphology immunostaining compared to proprietary Leica Bond protocol. This study validates the Omni-Stainer™ Dewaxing and HIER protocol as a viable and efficient approach for automation of sample prep for GeoMx DSP studies. Citation Format: Nikolay Samusik, Yury Goltsev, Noemi Kedei. Streamlining tissue sample preparation: A comparative study on the efficiency and reproducibility of the Omni-Stainer™ dewaxing and HIER protocol [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5566.

Directed differentiation of human embryonic stem cells into parathyroid cells and establishment of parathyroid organoids.

Differentiation of human embryonic stem cells (hESCs) into human embryonic stem cells-derived parathyroid-like cells (hESC-PT) has clinical significance in providing new therapies for congenital and acquired parathyroid insufficiency conditions. However, a highly reproducible, well-documented method for parathyroid differentiation remains unavailable. By imitating the natural process of parathyroid embryonic development, we proposed a new hypothesis about the in vitro differentiation of parathyroid-like cells. Transcriptome, differentiation marker protein detection and parathyroid hormone (PTH) secretion assays were performed after the completion of differentiation. To optimize the differentiation protocol and further improve the differentiation rate, we designed glial cells missing transcription factor 2 (GCM2) overexpression lentivirus transfection assays and constructed hESCs-derived parathyroid organoids. The new protocol enabled hESCs to differentiate into hESC-PT. HESC-PT cells expressed PTH, GCM2 and CaSR proteins, low extracellular calcium culture could stimulate hESC-PT cells to secrete PTH. hESC-PT cells overexpressing GCM2 protein secreted PTH earlier than their counterpart hESC-PT cells. Compared with the two-dimensional cell culture environment, hESCs-derived parathyroid organoids secreted more PTH. Both GCM2 lentiviral transfection and three-dimensional cultures could make hESC-PT cells functionally close to human parathyroid cells. Our study demonstrated that hESCs could differentiate into hESC-PT in vitro, which paves the road for applying the technology to treat hypoparathyroidism and introduces new approaches in the field of regenerative medicine.

Establishment and methodological evaluation of a chemiluminescence assay for detection of anti-envelope protein (E1, E2) antibodies in the serum of hepatitis C virus-infected patients.

To establish a chemiluminescence method for detecting anti-E1 and anti-E2 antibodies in the serum of patients with hepatitis C virus (HCV) infection. The microplate was coated with recombinant envelope proteins E1 and E2 by indirect method, respectively, and the kits for detecting anti-E1 and anti-E2 antibodies were prepared. The methodological indexes were evaluated. The methodological indexes of the kits were as follows: precision test (the variation coefficient of anti-E1 antibody 6.71%-8.95% for within run and 9.91%-12.16% for between run, the variation coefficient of anti-E2 antibody 6.06%-8.44% for within run and 10.77%-13.98% for between run, respectively). The blank limit and detection limit were 1.18 RLIR and 3.16 RLIR for the anti-E1 antibody, and 1.26 RLIR and 3.32 RLIR for the anti-E2 antibody, respectively. The correlation coefficients (r) of anti-E1 and anti-E2 were 0.9963 and 0.9828, the analysis and measurement ranges (AMR) were 1.66-41.28 RLIR and 1.55-19.46 RLIR, and the average recovery was 96.4% and 93.7%, respectively. The rheumatoid factor and other positive serum samples had no interference or cross-reaction to the test, and the kits were stable within 15 months. The positive rates of anti-E1 and anti-E2 antibodies in 45 patients with HCV infection were 35.6% (16/45) and 44.4% (20/45), respectively. The kits for detecting anti-E1 and anti-E2 meet the requirements of methodology, and can be used in screening diagnosis, disease monitoring, prognosis evaluation, disease mechanism, and epidemiological studies of HCV infection. The HCV envelope proteins E1 and E2 have an immune response in HCV-infected patients.

Evaluation of ELISA Test Kits for Detection of Milk Protein in Frying Oil Treated at Different Temperatures

Milk is a common ingredient in fried foods. Allergen cross-contact can occur through the reuse of frying oil. To enable assessment of the allergy risk of reused oil, methods for quantification of milk protein in oil are needed. This study evaluated four commercial ELISA test kits in comparison with the 660 nm total protein assay for the detection of milk protein in oil after frying. Corn oil spiked with nonfat or whole milk powder were fried at 150 °C or 180 °C for 3 min and were analyzed by ELISA kits either directly or after preextraction with phosphate-buffered saline containing 0.05% Tween (PBST). All four ELISA kits performed well in quantifying milk protein in unheated oil, achieving normalized recoveries of 72.1–115.9% compared with that determined in reference solutions (PBST spiked with nonfat or whole milk powder, 100%). Frying lowered the amount of protein detected, but the extent of reduction differed between test kits. In nonfat milk powder-spiked oil fried at 150 °C, normalized recoveries determined by Veratox Total Milk and BioKits BLG Assay (49.9% and 43.6%, respectively) were higher than that determined by the 660 nm assay (25.4%). Normalized recoveries determined by ELISA Systems Casein and Beta-Lactoglobulin (BLG) kits were substantially lower (9.7% and 2.4%, respectively). In samples fried under typical frying temperature (180 °C), very little protein (0.1–7.4%) was detected. Inclusion of PBST preextraction improved the detection of the two test kits targeting BLG but lowered the level of protein detected by Veratox and ELISA Systems Casein in fried samples. Overall, the ELISA kits evaluated could effectively quantify milk protein in unheated oil without the need to remove the oil phase prior to analysis. Heat treatment was the key factor negatively affecting protein quantitation. Such impact needs to be considered when ELISA test results are used for assessing the allergy risk of reused frying oil.

A Multiplex GPCR‐Mediated Peptide Tagging System for a Growing Yeast Synthetic Biology Toolbox

AbstractStraightforward methods for specifically detecting and quantifying proteins are essential for both basic and applied research and notably in synthetic biology. Previously we demonstrated that the yeast mating pathway could be hijacked to detect species‐specific fungal peptide pheromones using their corresponding mating GPCRs. Here we asked if our yeast biosensor could detect proteins in addition to peptides – a question not previously resolved in the literature. As such, we repurposed the Saccharomyces cerevisiae fungal mating pheromone α‐factor as a peptide tag and fused it terminally and internally to the protein Smt3. Our biosensor was able to detect the tagged protein in the nanomolar range using fluorescence as a read‐out. We extended the assay to four additional orthogonal peptide pheromone tags, demonstrating a cheap, non‐labor‐intensive, and high‐throughput assay compatible with multiplexing for protein detection. With its ability to detect proteins our living yeast biosensor could be useful for the optimization of protein producing cell‐factories, for building logic gates and myriad other applications in synthetic biology.

Aptamer-enhanced particle aggregation inhibition assay for simple homogeneous protein detection using DNA aptamer and thermo-responsive magnetic nanoparticles

A simple and sensitive homogeneous protein detection system is required for the early detection of biomarkers. Thermo-responsive magnetic particles (TM) have already been developed to achieve easy bound/free separation at the homogeneous protein detection system, but they are still limited owing to the requirement of secondary antibodies and negatively charged polymers, and it is challenging to control the TM aggregation behavior because of the size of the TM. Therefore, at new method to control TM aggregation behavior that is simple, easy, and highly sensitive is required. In this study, we developed a DNA aptamer-based TM assay as a simple protein detection system without additional secondary molecular recognition elements or negatively charged polymer. In the first attempt, a DNA aptamer was modified on the TM surface, and its aggregation behavior was monitored depending on the target molecule concentration. The TM aggregation rate during the heating process decreased depending on the amount of the DNA aptamer and increased depending on the target protein level. This suggests that the DNA aptamer prevented TM aggregation owing to its negative charge and achieved target protein detection owing to the cancellation of repulsion. Capturable aptamers were used in the TM assay to improve the sensitivity and limit of detection. The designed Capture DNA was modified on the TM surface, and the aptamer was captured in the presence of the target protein through a conformational change. Eventually, Capturable aptamer-based TM assay achieved a sub-nanomolar limit of detection and higher sensitivity than that of our initial investigation. Through this study and the ease of the DNA aptamer design, it was shown that the DNA aptamer-modified TM assay enabled the development of a simple and sensitive homogeneous protein detection system.

An aptamer-based sandwich assay for detection of alpha-defensin human neutrophil protein 1 on a microfluidic platform.

The diagnosis of periprosthetic joint infection (PJI) remains a labor-intensive and challenging issue, with life-threatening complications associated with misdiagnoses. Superior diagnostic approaches are therefore urgently needed, and synovial biomarkers are gaining substantial attention in this capacity. A new aptamer-based sandwich assay was developed where the aptamer probes specific to one such biomarker, alpha-defensin human neutrophil protein 1 (HNP 1), was integrated herein into a new microfluidic platform. The magnetic beads coated with the primary aptamer probe were able to bind the target protein with high affinity and high specificity in synovial fluid and a fluorescent-labelled secondary aptamer were further used to quantify HNP 1 in a sandwich approach. Up to four clinical samples with low volume (∼50μL each) in a much faster assay including detection within <60min with 100% accuracy (with totally 13 clinical samples without the need of sample pretreatment) through the use of the aptamer-based sandwich assay were automatically detected on a single chip. The wide dynamic range of this compact device, 0.5-100mg/L, highlights its utility for future PJI diagnostics in the clinic.

Pharmacokinetics of Monoclonal Antibody and Antibody Fragments in The Mouse Eye Following Intravitreal Administration

Mice are rarely used in pharmacokinetic (PK) studies of ocular therapeutics due to the small size of their eyes and challenges in drug administration, tissue collection, and analysis of drug concentrations. Therefore, ocular PK of protein therapeutics in mouse eye following intravitreal (IVT) administration is not known. Here, we have presented the first of its kind investigation, to study the PK of 4 different size non-binding protein therapeutics in mouse plasma, cornea/ICB, vitreous humor, retina, and posterior cup (including choroid) following IVT administration. Administered proteins include trastuzumab (150 kDa) and F(ab)2 (100 kDa), Fab, and scFv (27 kDa) fragments of trastuzumab. An imaging and injection apparatus suitable for performing small (50 nL) IVT injections in mice was developed, and techniques for enucleation of the eye and dissection of ocular tissues were developed. Furthermore, a sensitive enzyme-linked immunosorbent assay (ELISA) for detection of proteins in very small amounts of ocular tissues were developed. It was observed that elimination from the vitreous chamber was the primary driver of PK in the cornea/ICB, retina, posterior cup, and plasma. Trastuzumab displays first-order kinetics in the vitreous humor with a half-life of 18.8 h. F(ab)2, Fab, and ScFv show biphasic PK profiles with distribution phases becoming more rapid as molecular weight decreases, and terminal elimination becoming longer as molecular weight decreases, with terminal half-lives of 16.3, 20.6, and 48.9 h, respectively. The mean residence times of trastuzumab, F(ab)2, Fab, and scFv in the vitreous humor were 26.0, 12.2, 10.7, and 8.16 h, respectively. It was found that the mean residence time in vitreous humor doubles with an increase in molecular weight of ∼69 kDa. Interestingly, the PK of proteins measured in the un-injected eye suggest the presence of a pathway for drug transfer between the eyes, which needs to be further validated. Overall, the findings presented here pave the way for drug discovery and development studies of protein therapeutics for ophthalmic indications in mice.

Abstract 1033: Evaluation of HER2 status in circulating tumor cells isolated using the Parsortix® system

Abstract Background: Evaluation of HER2 status in tissue from breast cancer patients is a standard test for clinical diagnosis and treatment. However, tissue biopsy is invasive and repeated testing is generally not possible. Liquid biopsy allows minimally invasive, repeat sample collection for regular monitoring. This study combined ANGLE’s Parsortix® PR1 Research System*, an epitope-independent microfluidic device that isolates and harvests rare cells from blood based on size and deformability, with two downstream assays: an Immunofluorescence (IF) assay for HER2 protein detection and an IF assay combined with FISH targeting HER2 gene amplification, to determine HER2 status on circulating tumor cells (CTCs). Methods: Blood was collected from healthy volunteers into Streck Cell-Free DNA tubes. Two aliquots of blood from each donor were spiked with cultured SKBR3 (HER2+) and Hs 578T (HER2-) breast cancer cells and then processed using Parsortix® PR1 instruments. Captured cells were harvested and spun onto positively charged slides. One slide per donor was stained using ANGLE’s IF panel for CTC detection, consisting of a nuclear dye, antibodies targeting epithelial and mesenchymal markers, and antibodies targeting blood cell markers. After imaging, slides were de-stained and processed using a commercially available HER2 FISH kit. Cancer cells identified by the IF panel were re-imaged to examine FISH signal. Cells were considered HER2+ if the ratio of HER2 foci to CEP17 foci was ≥2. The second slide was stained using the same IF CTC panel in combination with an antibody targeting HER2 protein. HER2 expression was analyzed based on intensity of fluorescence signal. Same workflow was implemented in a small cohort of breast cancer patients with blood processed 72-144 hours post-draw using Parsortix® PC1 Clinical System. Results: The numbers of epithelial and mesenchymal CTCs detected on each slide were comparable in both assays. In HER2 FISH-stained samples, 97.3% of the SKBR3 cells and 13.3% of the Hs 578T cells harvested showed HER2 amplification. This data was consistent with the literature (~20% of Hs 578T cells tend to form isochromosomes, altering the HER2/CEP17 ratio). In IF-only stained samples, 96.8% of the SKBR3 cells and 0% of the Hs578T cells harvested overexpressed HER2 protein. In patient samples, CTCs were identified in 80% of the donors (mean: 21; median: 6; range: 0-200), with 17% of the CTC-positive donors having ≥1 CTC overexpressing HER2 protein. Conclusions: This study demonstrates the feasibility of HER2 evaluation using IF for protein expression and HER2 FISH for gene amplification on CTCs enriched from blood using the Parsortix® systems. It also demonstrates that blood collection in Streck tubes is suitable for both assays, with the advantage of allowing longer blood sample storage and facilitating batch shipping and processing of clinical samples. *Research Use Only. Not for use in diagnostic procedures. Citation Format: Nerea Borreguero-Munoz, Alex Young, Jessica Kimber, Mariacristina Ciccioli, Anne-Sophie Pailhes-Jimenez. Evaluation of HER2 status in circulating tumor cells isolated using the Parsortix® system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1033.

Fabrication of CuInZnS/ZnS Quantum Dot Microbeads by a Two-Step Approach of Emulsification-Solvent Evaporation and Surfactant Substitution and Its Application for Quantitative Detection.

CuInS2 quantum dots (CIS QDs) are considered to be promising alternatives for Cd-based QDs in the fields of biology and medicine. However, high-quality hydrophobic CIS QDs are difficult to be transferred to water due to their 1-dodecylmercaptan (DDT) ligands. Therefore, the fluorescence and stability of the prepared aqueous CIS QDs is not enough to meet the requirement for sensitive detection. Here, as large as 13 nm CuInZnS/ZnS QDs with DDT ligands were first synthesized, and then, CuInZnS/ZnS microbeads (QBs) containing thousands of QDs were successfully fabricated by a two-step approach of emulsion-solvent evaporation and surfactant substitution. Through emulsion-solvent evaporation, the CuInZnS/ZnS QDs formed microbeads in the microemulsion with dodecyl trimethylammonium bromide (DTAB), and the Förster resonance energy transfer (FRET) has been effectively overcome. Then, CO-520 was introduced to substitute DTAB to improve the stability and water solubility. Lastly, the microbeads were coated with a SiO2 shell and carboxylated. Subsequently, the constructed QBs (∼210 nm) were used as labels in a fluorescence immunosorbent assay (FLISA) for quantitative detection of heart type fatty acid binding protein (H-FABP), and the limit of detection was 0.48 ng mL-1, which indicated a greatly improved detection sensitivity compared to that of the Cd-free QDs. The highly fluorescent and stable CuInZnS/ZnS QBs will have great application prospects in many biological fields.

Optimization of Biotinylated RNA or DNA Pull-Down Assays for Detection of Binding Proteins: Examples of IRP1, IRP2, HuR, AUF1, and Nrf2.

Investigation of RNA- and DNA-binding proteins to a defined regulatory sequence, such as an AU-rich RNA and a DNA enhancer element, is important for understanding gene regulation through their interactions. For in vitro binding studies, an electrophoretic mobility shift assay (EMSA) was widely used in the past. In line with the trend toward using non-radioactive materials in various bioassays, end-labeled biotinylated RNA and DNA oligonucleotides can be more practical probes to study protein-RNA and protein-DNA interactions; thereby, the binding complexes can be pulled down with streptavidin-conjugated resins and identified by Western blotting. However, setting up RNA and DNA pull-down assays with biotinylated probes in optimum protein binding conditions remains challenging. Here, we demonstrate the step-by step optimization of pull-down for IRP (iron-responsive-element-binding protein) with a 5'-biotinylated stem-loop IRE (iron-responsive element) RNA, HuR, and AUF1 with an AU-rich RNA element and Nrf2 binding to an antioxidant-responsive element (ARE) enhancer in the human ferritin H gene. This study was designed to address key technical questions in RNA and DNA pull-down assays: (1) how much RNA and DNA probes we should use; (2) what binding buffer and cell lysis buffer we can use; (3) how to verify the specific interaction; (4) what streptavidin resin (agarose or magnetic beads) works; and (5) what Western blotting results we can expect from varying to optimum conditions. We anticipate that our optimized pull-down conditions can be applicable to other RNA- and DNA-binding proteins along with emerging non-coding small RNA-binding proteins for their in vitro characterization.

A microfluidic dual-aptamer sandwich assay for rapid and cost-effective detection of recombinant proteins

While monitoring expression of recombinant proteins is essential for obtaining high-quality biopharmaceutical and biotechnological products, existing assays for recombinant protein detection are laborious, time-consuming and expensive. This paper presents a microfluidic approach to rapid and cost-effective detection of tag-fused recombinant proteins via a dual-aptamer sandwich assay. Our approach addresses limitations in current methods for both dual-aptamer assays and generation of aptamers for such assays by first using microfluidic technology to isolate the aptamers rapidly and then employing these aptamers to implement a microfluidic dual-aptamer assay for tag-fused recombinant protein detection. The use of microfluidic technology enables the fast generation of aptamers and rapid detection of recombinant proteins with minimized consumption of reagents. In addition, compared with antibodies, aptamers as low-cost affinity reagents with an ability of reversible denaturation further decreases the cost of recombinant protein detection. For demonstration, an aptamer pair is isolated rapidly toward His-tagged IgE within two days, and then used in the microfluidic dual-aptamer assay for detecting His-tagged IgE in cell culture media within 10 min and with a limit of detection of 7.1 nM.

Development of alkaline phosphatase-scFv and its use for one-step enzyme-linked immunosorbent assay for His-tagged protein detection.

A histidine (His)-tag is composed of six His residues and typically exerts little influence on the structure and solubility of expressed recombinant fusion proteins. Purification methods for recombinant proteins containing His-tags are relatively well-established, thus His-tags are widely used in protein recombination technology. We established a one-step enzyme-linked immunosorbent assay (ELISA) for His-tagged recombinant proteins. We analyzed variable heavy and light chains of the anti-His-tag monoclonal antibody 4C9 and used BLAST analyses to determine variable zones in light (VL) and heavy chains (VH). VH, VL, and alkaline phosphatase (ALP) regions were connected via a linker sequence and ligated into the pGEX-4T-1 expression vector. Different recombinant proteins with His tags were used to evaluate and detect ALP-scFv activity. Antigen and anti-His-scFv-ALP concentrations for direct ELISA were optimized using the checkerboard method. ZIKV-NS1, CHIKV-E2, SCRV-N, and other His-tag fusion proteins demonstrated specific reactions with anti-His-scFv-ALP, which were accurate and reproducible when the antigen concentration was 50 µg mL-1 and the antibody concentration was 6.25 µg mL-1. For competitive ELISA, we observed a good linear relationship when coating concentrations of recombinant human anti-Müllerian hormone (hAMH) were between 0.78 and 12.5 µg mL-1. Our direct ELISA method is simple, rapid, and accurate. The scFv antibody can be purified using a prokaryotic expression system, which provides uniform product quality and reduces variations between batches.

Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST.

Advanced gastrointestinal stromal tumour (GIST) is characterised by genomic perturbations of key cellcycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximising response to therapeutic CDK4/6 inhibition. Targeted next-generation sequencing and multiplexed protein imaging were used to detect cellcycle regulator aberrations in GIST clinical samples. The impact of inhibitors of CDK2, CDK4 and CDK2/4/6 was determined through cellproliferation and proteindetection assays. CDK-inhibitor resistance mechanisms were characterised in GIST cell lines after long-term exposure. We identify recurrent genomic aberrations in cellcycle regulators causing co-activation of the CDK2 and CDK4/6 pathways in clinical GIST samples. Therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation. Moreover, RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) are mechanisms of acquired CDK-inhibitor resistance in GIST. These studies establish the biological rationale for CDK2 and CDK4/6 co-inhibition as a therapeutic strategy in patients with advanced GIST, including metastatic GIST progressing on tyrosine kinase inhibitors.

Abstract A013: CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance

Abstract Advanced GIST is characterized by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor (CDK4/6i) therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximizing response to therapeutic CDK4/6 inhibition. Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples (N=18), including 8 metastatic TKI-resistant GISTs. Multiple metastases were analyzed in 3 patients. The impact of CDK2i (CDK2 inhibitor-II), CDK4/6i (palbociclib or abemaciclib), and CDK2/4/6i (PF-06873600) was determined through cell proliferation and protein detection assays in vitro and in vivo. Mechanisms of acquired CDK2i and CDK4/6i resistance were characterized in GIST cell lines after long-term exposure. The results demonstrate recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways. Identical aberrations of p16, RB1, and TP53 were present in all metastases from 3 patients. We show that therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation (P&amp;lt;0.01). Intact RB1 predicted response to treatment, whereas RB1-deficient models were resistant. Moreover, we identify RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) as mechanisms of acquired CDK inhibitor resistance in GIST. The CCND1 rearrangement deleted the cyclin D1 C-terminal Thr286 and Thr288 residues which mediate cyclin D1 proteasomal degradation, resulting in overexpression of an abnormal cyclin D1. CDK inhibitor resistance properties were corroborated by lentiviral transduction of the CCND1 fusion gene into fusion-negative GIST, leiomyosarcoma, and breast cancer cells. These studies establish the biologic rationale for CDK2 and CDK4/6 co-inhibition as therapeutic strategy in patients with advanced GIST, including patients with metastatic GIST progressing on TKIs. In addition, these findings expand the spectrum of potential CDK inhibitor resistance mechanisms with translational potential for improving cell cycle targeted therapies in other cancer types. Citation Format: Inga-Marie Schaefer, Matthew L. Hemming, Meijun Z. Lundberg, Matthew P. Serrata, Isabel Goldaracena, Ninning Liu, Peng Yin, Joao A. Paulo, Steven P. Gygi, Suzanne George, Jeffrey A. Morgan, Monica M. Bertagnolli, Ewa T. Sicinska, Adrian Mariño-Enríquez, Jason L. Hornick, Chandrajit P. Raut, George D. Demetri, Wen-Bin Ou, Sinem K. Saka, Jonathan A. Fletcher. CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A013.

Rapid magneto-enzyme-linked immunosorbent assay for ultrasensitive protein detection

Protein-based diagnostics are the standard of care for screening and diagnosing a broad range of diseases and medical conditions. The current gold standard method for quantifying proteins in clinical specimens is the enzyme-linked immunosorbent assay (ELISA), which offers high analytical sensitivity, can process many samples at once, and is widely available in many diagnostic laboratories worldwide. However, running an ELISA is cumbersome, requiring multiple liquid handling and washing steps, and time-intensive (∼2 − 4 h per test). Here, we demonstrate a unique magneto-ELISA that utilizes dually labeled magnetic nanoparticles (DMPs) coated with horseradish peroxidase (HRP) and an HRP-conjugated detection antibody, enabling rapid immunomagnetic enrichment and signal amplification. For proof of concept, this assay was used to detect Plasmodium falciparum histidine-rich protein 2 (PfHRP2), a malaria parasite biomarker, which exhibited a lower limit of detection of 2 pg mL−1 (33 fM) in human serum. Measurements of PfHRP2 in clinical blood samples from individuals with and without P. falciparum infection revealed that this magneto-ELISA offers a superior diagnostic accuracy compared to a commercial PfHRP2 ELISA kit. We also demonstrate the versatility of this platform by adapting it for the detection of SARS-CoV-2 nucleocapsid protein, which could be detected at concentrations as low as 8 pg mL−1 (174 fM) in human serum. In addition to its high analytical performance, this assay can be completed in 30 min, requires no specialized equipment, and is compatible with standard microplate readers and ELISA protocols, allowing it to integrate readily into current clinical practice.