Multiplexed real-time PCR using universal reporters

COVID-19 susceptibility, severity, clinical outcome and Toll-like receptor (7) mRNA expression driven by TLR7 gene polymorphism (rs3853839) in middle-aged individuals without previous comorbidities

Background

Toll-like receptors are implicated in the pathophysiology of the severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory disease (MERS), according to several studies. The whole-genome sequencing of SARS-CoV-2 revealed that the TLR7 gene could be implicated in the virus's pathogenesis since the virus includes ssRNA patterns that could bind to TLR7.

Aim

The purpose of this study was to look into the function of the TLR7 (rs3853839) C/G polymorphism and the expression of TLR7 mRNA transcript in the development, severity and progression of COVID-19.

Subjects and methods

A case-control study included 285 participants who were divided into two groups: 150 middle-aged people with COVID 19 who had no previous co-morbidities and 135 healthy volunteers who served as controls. TaqMan test was used to genotype the TLR7 (rs3853839) C/G polymorphism, and real-time PCR was used to determine the relative expression of its mRNA transcript. The level of IL-6 in serum was determined using the ELISA method as an indicator of cytokine storm and COVID-19 severity.

Results

The GG genotype was shown to be much more common in COVID-19 patients (38.7%) than controls (4.4%), with an OR of 19.86 (95% CI: 7.85; 50.22) and was linked to disease severity and poor clinical outcomes (hospitalization, respiratory failure, cardiac complications, ICU admission and mechanical ventilation).As a result, the G allele was considerably higher in cases (57.0%), while the C allele was significantly higher in controls (p = 0.001). The GG genotype was found to be substantially more common in patients who were severely/critically unwell. TLR7 mRNA expression levels were significantly higher in COVID-19 patients (2.44 ± 0.89) than in controls (1.06 ± 0.46) (p = 0.001). TLR7 mRNA levels were highest in COVID 19 patients with the GG genotype (rs3853839). Patients with the GG genotype had considerably lower WBC counts, but significantly higher serum ferritin, CRP, IL-6 and D dimer levels (P = 0.045, 0.001, 0.023, 0.033, 0.001, respectively).

Conclusion

The GG form of the TLR7 SNP (rs3853839) could be a genetic risk factor for COVID-19 infection, severe illness and poor clinical outcome. TLR7 mRNA expression was also elevated in COVID-19 patients who were severely/critically unwell and had a bad outcome, suggesting that they could be used as COVID-19 prognostic biomarkers.

A pilot study on gene expression of endoplasmic reticulum unfolded protein response in chronic kidney disease

BACKGROUND

Chronic kidney disease (CKD) is a worldwide public health problem due to its increasing prevalence worldwide. Endoplasmic reticulum (ER) stress has been shown to play a role in the pathogenesis of various renal diseases in humans. It leads to the activation of the unfolded protein response (UPR) which triggers three known trans membrane sensors in the ER: activating transcription factor 6 (ATF6), inositol-requiring enzyme I (IRE1), and PKR (double-stranded RNA-dependent protein kinase)-like ER protein kinase (PERK). The activation of these signal transduction pathways can result in cell death, inflammation, and fibrosis in the context of CKD.

OBJECTIVES

The aim of this study was to detect the level of gene expression of activating transcription factor 6 (ATF6), inositol-requiring enzyme I (IRE1), and PKR (double-stranded RNA-dependent protein kinase)-like ER protein kinase (PERK) in chronic kidney disease patients.

SUBJECTS AND METHODS

This study was carried out on eighty subjects, 50 patients with CKD (25 with hypertension and 25 without hypertension) and 30 healthy subjects served as controls. All studied subjects underwent laboratory investigations, including CBC, Serum Lipid profile: Total cholesterol, Triglycerides, HDL-cholesterol and LDL-cholesterol, liver and kidney functions, fasting and 2 h postprandial blood glucose and HbA1C, serum level of IL6 and gene expression of ATF6, IRE1 and PERK using real time PCR technique.

RESULTS

There was a significant increase in relative quantitation (RQ) of gene expression of IRE1, ATF6 and PERK in chronic kidney patient groups with hypertension and without hypertension compared to control group. Also, there was a significant positive correlation of PERK and ATF6 gene expressions and a significant negative correlation of PERK gene expressions and GFR in groups I&II.

CONCLUSION

Endoplasmic reticulum (ER) stress occurs in CKD with activation of gene expression of three trans-membrane sensors in the ER: activating transcription factor 6 (ATF6), inositol-requiring enzyme I (IRE1), and PKR (double-stranded RNA-dependent protein kinase)-like ER protein kinase (PERK).

Role of oxidative stress and vascular endothelial growth factor expression in pterygium pathogenesis and prevention of pterygium recurrence after surgical excision

PURPOSE

To assess the roles of oxidative stress and vascular endothelial growth factor (VEGF) in pterygium pathogenesis and prevention of pterygium recurrence after surgical excision.

METHODS

Surgically removed pterygium tissue from 35 pterygium patients and normal conjunctival samples from 15 patients matched for age and sex (used as controls) constituted the study samples. The conjunctival samples were preserved at - 80 °C until analysis. Catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH) and total antioxidant (TAO) enzymatic activity and the levels of nitric oxide (NO), malondialdehyde (MDA) and VEGF were studied in both groups. To evaluate the recurrence rate after surgical excision, the pterygium patients were further subdivided into three groups according to the adjuvant therapy used to prevent recurrence. Group 1 consisted of 10 patients who were treated with 0.2 mg mitomycin-c (MMC) for 2 min. Group 2 consisted of 12 patients treated with subconjunctival bevacizumab injection after surgical removal of the pterygium. Group 3 consisted of 13 patients who underwent combined treatment with 0.2 mg of MMC for 2 min and subconjunctival bevacizumab injection. The follow-up of patients in the three groups ranged from 7 to 15 months.

RESULTS

The activities of CAT, SOD, GSH and TAO were significantly lower in pterygium samples than in normal conjunctival samples (p < 0.0001 each). The levels of MDA (p = 0.046), NO (p < 0.0001) and VEGF (p < 0.0001) were significantly higher in pterygium patients than in controls. The lowest recurrence rate after surgical excision was that of the third group.

CONCLUSIONS

Oxidative stress and VEGF could play a role in the pathogenesis of pterygium as indicated by decreased antioxidant enzymatic activity and increased levels of VEGF in the pterygium tissue and the role of MMC and anti-VEGF therapy in decreasing the recurrence rate after surgical excision.

Cell-free long non-coding RNAs (LY86-AS1 & HCG27_201and GAS5) as biomarkers for pre-diabetes and type 2 DM in Egypt

Background

Increasing interest has been focused on lncRNAs as potential markers in the pathogenesis and progression of numerous diseases.

Aim

We aimed to investigate the expression pattern and role of cell-free lncRNAs (GAS5, HCG27_201 and LY86-AS1) in pre-diabetic, diabetic and T2DM groups.

Subjects & methods

Quantification of the expression level of cell-free lncRNAs (GAS5, HCG27_201 and LY86-AS1) was performed by real-time PCR in 210 individuals classified in diabetic (T2DM), pre-diabetic and control groups.

Results

Significant differences were observed in the relative expression level of lncRNAs (GAS5, LY86-AS1 and HCG27_201) among the three studied groups. The LncRNA expression levels decreased gradually from the control to the pre-diabetic group and reached the lowest values in the T2DM group. The A receiver operating characteristic curve (ROC) was applied to identify a cut-off value for each of the three genes among our groups. The three lncRNAs showed promising results in discriminating between the diabetic patients and controls, with HCG27_201 gene expression having the best performance. Furthermore, lncRNA expression was able to predict the future development of DM in the pre-diabetics because ROC analysis among diabetics and pre-diabetics revealed considerable results. GAS5 gene expression showed the best performance. Additionally, HCG27_201 expression was the most valuable biomarker for differentiating between pre-diabetics and controls and presented a sensitivity of 91% and specificity of 64%.

Conclusions

We concluded that cell free lncRNAs (GAS5, LY86-AS1 and HCG27_201) could be considered promising diagnostic and predictive biomarkers for DM and that HCG27_201 could act as a potential diagnostic biomarker for pre-diabetes.

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lncRNAs are involved in T2DM pathological process.

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lncRNA showed ability to predict development of DM.

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GAS5, LY86-AS1 and HCG27_201 could be considered as diagnostic biomarkers for DM.

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The three studied lncRNA could also be considered as predictive biomarkers for DM.

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HCG27_201 could act as a potential diagnostic biomarker for pre-diabetes.

Human Epidermal Growth Factor Receptor-3 mRNA Expression as a Prognostic Marker for Invasive Duct Carcinoma not Otherwise Specified

INTRODUCTION

Breast cancer is the most common cancer in women and the Erythroblastosis Oncogene B(ErbB) receptor family holds crucial role in its pathogenesis. Human Epidermal Growth Factor Receptor 3 (HER-3) gene over expression in breast tissue has been associated with aggressive clinical behaviour and bad prognosis.

AIM

To evaluate HER-3 mRNA expression level as a prognostic marker for breast cancer and to correlate its level with other established prognostic parameters.

MATERIALS AND METHODS

This study was carried out on specimens of 100 cases that were divided into 40 patients presented with fibroadenoma and 60 patients presented with Invasive Ductal Carcinoma (IDC) not otherwise specified and underwent modified radical mastectomy. All specimens were investigated for HER-2/neu, ER and PR expression by Immunohistochemistry (IHC) and quantitative assay of HER-3 mRNA expression using real time PCR technique.

RESULTS

There was a significant high HER3 mRNA level in carcinoma cases compared to fibroadenoma. In malignant cases, HER3 mRNA level was significantly associated with advanced T stage, advanced N stage, number of positive lymph nodes, large tumour size and cases associated with an adjacent in situ component. Moreover, HER-3 mRNA level was of highest values in Her-2/neu positive group followed by triple negative cases with the lowest level in luminal group (p<0.05).

CONCLUSION

HER-3 gene is upregulated in IDC especially those carrying poor prognostic features. HER-3 mRNA level may identify a subset of patients with a poor prognosis, and who could undergo further evaluation for the efficacy of HER3 targeted anticancer therapy.

BCL6 mRNA Expression Level in Invasive Duct Carcinoma not otherwise Specified

INTRODUCTION

B-Cell Lymphoma 6 (BCL6) has an oncogenic role in tumourigenesis of various malignancies. It represses genes involved in terminal differentiation and plays complementary role with Signal Transducer and Activator of Transcription 3 (STAT3) in triple-negative breast cancer cellular function.

AIM

To evaluate the expression of BCL6 in cancer breast and determine its correlation with the clinico-pathological features including the molecular subtype of breast carcinoma.

MATERIALS AND METHODS

This prospective case control study was carried out on 150 patients, divided into 100 cases of invasive duct carcinoma not otherwise specified and 50 benign breast lesions including fibroadenoma and fibrocystic disease. Fresh tissues were excised, which were then subjected to RNA extraction. The BCL6 mRNA level was assessed using real-time reverse transcription Polymerase Chain Reaction (PCR).

RESULTS

There was a significant higher levels of BCL6 mRNA in malignant cases compared to benign ones (p<0.001). The level of BCL6 mRNA was higher in cases showing advanced tumor stage (p<0.04), triple negative subtype and associated in situ component (p<0.001) compared to cases with an early stage, luminal or Her 2-neu positive subtypes and those lacking in situ component.

CONCLUSION

BCL6 is up-regulated in breast cancer and is associated with poor prognostic features such as advanced stage and triple negative molecular subtype. BCL6 inhibitors might be considered as targeted therapy for breast cancer.

Sequence-Specific Biosensing of DNA Target through Relay PCR with Small-Molecule Fluorophore

Polymerase chain reaction coupled with signal generation offers sensitive recognition of target DNA sequence; however, these procedures require fluorophore-labeled oligonucleotide probes and high-tech equipment to achieve high specificity. Therefore, intensive research has been conducted to develop reliable, convenient, and economical DNA detection methods. The relay PCR described here is the first sequence-specific detection method using a small-molecule fluorophore as a sensor and combines the classic 5'-3' exonuclease activity of Taq polymerase with an RNA mimic of GFP to build a label-free DNA detection platform. Primarily, Taq polymerase cleaves the 5' noncomplementary overhang of the target specific probe during extension of the leading primer to release a relay oligo to initiate tandem PCR of the reporting template, which encodes the sequence of RNA aptamer. Afterward, the PCR product is transcribed to mRNA, which could generate a fluorescent signal in the presence of corresponding fluorophore. In addition to high sensitivity and specificity, the flexibility of choosing different fluorescent reporting signals makes this method versatile in either single or multiple target detection.

A new, multiplex, quantitative real-time polymerase chain reaction system for nucleic acid detection and quantification

Quantitative real-time polymerase chain reaction (qPCR) has emerged as a powerful investigative and diagnostic tool with potential to generate accurate and reproducible results. qPCR can be designed to fulfil the four key aspects required for the detection of nucleic acids: simplicity, speed, sensitivity, and specificity. This chapter reports the development of a novel real-time multiplex quantitative PCR technology, dubbed PrimRglo™, with a potential for high-degree multiplexing. It combines the capacity to simultaneously detect many viruses, bacteria, or nucleic acids, in a single reaction tube, with the ability to quantitate viral or bacterial load. The system utilizes oligonucleotide-tagged PCR primers, along with complementary fluorophore-labelled and quencher-labelled oligonucleotides. The analytic sensitivity of PrimRglo technology was compared with the widely used Taqman(®) and SYBR green detection systems.

Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications

BACKGROUND

Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents.

CONTENT

We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications.

SUMMARY

The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.

Mediator probe PCR: a novel approach for detection of real-time PCR based on label-free primary probes and standardized secondary universal fluorogenic reporters

BACKGROUND

The majority of established techniques for monitoring real-time PCR amplification involve individual target-specific fluorogenic probes. For analysis of numerous different targets the synthesis of these probes contributes to the overall cost during assay development. Sequence-dependent universal detection techniques overcome this drawback but are prone to detection of unspecific amplification products. We developed the mediator probe PCR as a solution to these problems.

METHODS

A set of label-free sequence-specific primary probes (mediator probes), each comprising a target-specific region and a standardized mediator tag, is cleaved upon annealing to its target sequence by the polymerases' 5' nuclease activity. Release of a mediator triggers signal generation by cleavage of a complementary fluorogenic reporter probe.

RESULTS

Real-time PCR amplification of human papillomavirus 18 (HPV18), Staphylococcus aureus, Escherichia coli, and Homo sapiens DNA dilution series showed exceptional linearity when detected either by novel mediator probes (r(2) = 0.991-0.999) or state-of-the-art hydrolysis probes (TaqMan probes) (r(2) = 0.975-0.993). For amplification of HPV18 DNA the limits of detection were 78.3 and 85.1 copies per 10-μL reaction when analyzed with the mediator probe and hydrolysis probe, respectively. Duplex amplification of HPV18 target DNA and internal standard had no effects on back calculation of target copy numbers when quantified with either the mediator probe PCR (r(2) = 0.998) or the hydrolysis probe PCR (r(2) = 0.988).

CONCLUSIONS

The mediator probe PCR has equal performance to hydrolysis probe PCR and has reduced costs because of the use of universal fluorogenic reporters.

High-throughput Universal Probe Salmonella Serotyping (UPSS) by nanoPCR

Salmonella enterica subsp. enterica serovar identification is of great importance with respect to outbreak monitoring and case verification. Therefore rapid, sensitive and cost efficient detection of Salmonella spp. is indispensable within microbiology labs. To amalgamate single tube isolate identification with Salmonella typing, we developed the high-throughput Universal Probe Salmonella Serotyping (UPSS) technique based on nano liter PCR. In comparison to the classical approach, where O- and H-antisera are applied, the UPSS relies on specific gene content amplification of Salmonella spp. by a universal TaqMan assay for all markers and identification of the specific amplicon pattern. To enable high-throughput technology we employed a chip format containing 1024 wells loaded by an automated liquid-handling system which allowed us to perform TaqMan PCR reactions in volumes of 100nL per well. Herein we present proof of principle of the UPSS method by the use of a test panel of 100 previously serotyped Salmonella isolates to successfully verify the usability, accuracy and feasibility of the newly developed UPSS approach. We found that the methodology of the UPSS technology is capable of unequivocally identifying 30 Salmonella serotypes on a single chip within 3 hours but can be highly parallelized by the use of multiple PCR machines. Therefore the UPSS method offers a robust and straightforward molecular alternative for Salmonella detection and typing that saves expensive chemistry and can be easily automated.

Evaluation of the LightCycler 1536 Instrument for high-throughput quantitative real-time PCR

Quantitative real-time PCR (qPCR) is a frequently used, sensitive and accurate method to study gene expression profiles. However, its throughput was so far limited for routine laboratories to 384 reactions per run based on the limitations of the available instruments. Recently, the LightCycler 1536 Instrument was launched providing a high-throughput solution for qPCR with the analysis of 1536 reactions in approximately 45 min. We assessed the accuracy and sensitivity of this novel technology for the analysis of gene expression profiles in combination with the Innovadyne Nanodrop Express pipetting robot. We compared expression profiles obtained for 42 genes in 71 samples between the Universal ProbeLibrary and the LightCycler 1536 Instrument and SYBR Green I and the ABI PRISM 7900HT system. We found that the results were highly reproducible between both systems. Beside the higher throughput, the advantage of the LightCycler 1536 Instrument was the reduced consumption of reagents and sample material.