TaqMan PCR Research Articles

CRISPR-Cas12a based HSV DNA detection method using quantum dot-labeled immunochromatographic strips

Herpes simplex virus (HSV) infection poses a significant public health challenge, particularly affecting vulnerable populations such as pregnant women, newborns, and immunocompromised individuals. Traditional diagnostic methods for HSV are often time-consuming, requiring specialized expertise and infrastructure, resulting in delays and limitations in resource-limited regions. In this research, we established a novel detection method that integrates CRISPR-Cas12a with Recombinase Assisted Amplification (RAA), enabling the sensitive and specific detection of HSV DNA. Compared to TaqMan PCR, our CRISPR-Cas12a-based lateral flow assay (CRI-LFA) using universal primers demonstrated a sensitivity of 90.38 %, specificity of 98.08 %, positive predictive value (PPV) of 100 %, negative predictive value (NPV) of 91.22 %, kappa value of 0.904, and an area under the receiver operating characteristic curve (AUC) of 0.973. The subsequent typing tests on our platform for HSV-1 and HSV-2 showed a sensitivity of 100 % (95 % CI: 74.12 %–100 %) and 95.83 % (95 % CI: 86.02 %–99.26 %), respectively. Specificity was 97.85 % (95 % CI: 92.49 %–99.62 %) for HSV-1 and 96.64 % (95 % CI: 85.39 %–98.54 %) for HSV-2. The kappa values were 0.906 for HSV-1 and 0.883 for HSV-2, with PPV of 84.6 % and 97.7 %, and NPV of 100 % and 91.7 %, respectively. Our portable paper strip assay provides a convenient and user-friendly testing option suitable for decentralized settings. This approach has the potential to facilitate early detection and enhance public health efforts in controlling HSV transmission.

Does the LPA genotype have a role in coronary artery disease risk beyond Lp(a) values?

Abstract Introduction High lipoprotein(a) [Lp(a)] concentrations are one of the most important genetically determined risk factors for coronary artery disease (CAD). Many functional single nucleotide polymorphisms (SNPs) of the LPA gene have pronounced effects on Lp(a) concentrations. Studies show that rs3798220 polymorphism is strongly associated with Lp(a) concentration and also with risk of CAD. Goal: To evaluate if LPA rs3798220 T>C is associated with CAD beyond its effect on Lp(a) levels. Methods We performed a case-control study with 3,157 individuals (1,721 CAD patents and 1,436 controls). The LPA rs3798220 T>C was genotyped with the TaqMan PCR assay (Applied Biosystems 7300 Real-Time). This variant has a minor allele frequency (MAF) <2%; hence, the risk homozygous CC is a rare genotype, and we used the heterozygous CT in our analysis. Laboratory analysis was performed, and Lp(a) biochemical levels were measured in the cases and controls. Chi-squared tests were used to determine differences by genotype in CAD association (in cases and controls). We also reported a multivariate logistic regression to test if this LPA variant is still independently associated with CAD after adjustment to Lp(a) levels and traditional risk factors for CAD. Results Wild-type genotype TT was increased in the group without CAD, whereas the genotype TC was higher in patients with CAD (p<0.0001). After multivariate logistic regression, adjusted for traditional risk factors, the TC genotype remained in the equation as an independent risk factor for CAD (OR=2.36; 95%CI: 1.54–3.61; p<0.0001). When the multivariate regression analysis is adjusted for traditional risk factors plus Lp(a) levels, the TC genotype remains in the equation as independently associated with CAD despite being substantially attenuated (OR=1.67; 95%CI: 1.07–2.60; p=0.025). Conclusion LPA rs3798220 T>C may be an independent risk factor for CAD beyond the effect of rising Lp(a) levels. Perhaps testing for the genetic determinants of Lp(a) relative to direct measurement of Lp(a) level could provide additional prognostic utility.

Diabetes Mellitus influence in Lipoprotein(a) gene expression and association to coronary artery disease

Abstract Introduction Lp(a) and type 2 diabetes mellitus are both known and established risk factors for the development of coronary artery disease (CAD). Lp(a) levels are 75% to 95% heritable and predominately determined by single-nucleotide variants at the LPA gene; rs3798220 is one of the most studied variants and accounts for a significant portion of Lp(a) levels. Whether diabetes could influence the LPA rs3798220 account for Lp(a) levels is unknown. Aim Evaluate whether there is a different association between polymorphism LPA rs3798220 T>C and Lp(a) levels and their association with CAD in diabetic and non-diabetic populations. Methods 3,209 subjects (mean age 59.3±8.9 years, 76.3% male were selected from the data set of the Research Center. The LPA rs3798220 T>C was genotyped with the TaqMan PCR assay (Applied Biosystems 7300 Real-Time). This genetic variant has a minor allele frequency (MAF) <2%; hence, the risk homozygous CC is a rare genotype, and we used the heterozygous CT in our analysis. Lp(a) biochemical levels were measured in all participants. From the 3,209 participants, 810 had diabetes, and 2399 were no diabetics. For each group, chi-squared tests were used to determine the association of CAD prevalence by genotype, and t-tests were used to evaluate differences in CAD prevalence by Lp(a) levels. Results In non-diabetic subjects, LPA TC was significantly associated with CAD in non-diabetic subjects compared with TT (p<0.0001). Similarly, Lp(a) was higher in the CAD population (37.2±39.7) compared to the healthy population (25.6±30.0) (p<0.0001). In diabetic group, Lp(a) was higher in the CAD population (38.5±41.4) compared to the population without CAD (23.9±29.2) (p<0.0001). Nevertheless, there was no difference in genotype between CAD and non-CAD patients (p=0.710). Conclusion The LPA rs3798220 T>C variant in non-diabetic group can explain high Lp(a) levels and their association with CAD. However, in patients with diabetes, Lp(a) is elevated in CAD patients besides the fact that no significant genotype differences were displayed. Non-genetic influences like behavioural factors or even epigenetic changes may probably explain high Lp(a) levels in this population.

Droplet Digital PCR for Acinetobacter baumannii Diagnosis in Bronchoalveolar Lavage Samples from Patients with Ventilator-Associated Pneumonia.

Advanced diagnostic technologies have made accurate and precise diagnosis of pathogens easy. Herein, we present a new diagnostic method, droplet digital PCR (ddPCR), to detect and quantify Acinetobacter baumannii in mini bronchoalveolar lavage (mini-BAL) samples. A. baumannii causes ventilator-associated pneumonia (VAP), a severe healthcare infection affecting patients' lungs. VAP carries a high risk of morbidity and mortality, making its timely diagnosis crucial for prompt and effective management. Methodology. The assay performance was evaluated by comparing colonization data, quantitative culture results, and different generations of PCR (traditional PCR and Real-Time PCR-qPCR Taqman® and SYBR® Green). The ddPCR and qPCR Taqman® prove to be more sensitive than other molecular techniques. Reasonable analytical specificity was obtained with ddPCR, qPCR TaqMan®, and conventional PCR. However, qPCR SYBR® Green technology presented a low specificity, making the results questionable in clinical samples. DdPCR detected/quantified A. baumanni in more clinical samples than other methods (38.64% of the total samples). This emerging ddPCR technology offers promising advantages such as detection by more patients and direct quantification of pathogens without calibration curves.

Development of a qPCR Assay for the Detection and Quantification of the Fungal Pathogen Calonectria canadiana on Conifers

ABSTRACTA real‐time PCR TaqMan assay was developed for the detection of Calonectria canadiana, a fungal pathogen responsible for damping off, root rot and seedling blight in conifer forest nurseries in central and eastern North America. While highly significant in Quebec Forest nurseries, coniferous seedling mortality decreased significantly when nurseries transitioned from bare root to container seedling production. However, over the past few years, this pathogen has re‐emerged as a threat and millions of container white spruce seedlings were culled in two nurseries in eastern Quebec. A sensitive detection and quantification assay for C. canadiana was essential to investigate the biological and environmental factors driving this new epidemic. We designed primers and a TaqMan probe targeting the internal transcribed spacer (ITS) of C. canadiana. The resulting Ccan TaqMan assay successfully differentiated C. canadiana from other soil‐borne pathogens of the Nectriaceae encountered in Quebec Forest nurseries. The limit of detection of the assay was established at eight copies of C. canadiana ITS. The Ccan TaqMan assay quickly identified the presence of the pathogen in both symptomatic and asymptomatic white spruce (Picea glauca) seedlings. Furthermore, we demonstrated that the pathogen was more easily detected when DNA was extracted from necrotic needles at the base of the stem rather than from necrotic roots. This molecular tool will greatly aid in understanding the biology and epidemiology of C. canadiana.

The Relationship between HERV, Interleukin, and Transcription Factor Expression in ZIKV Infected versus Uninfected Trophoblastic Cells.

Zika virus (ZIKV) is an arbovirus with maternal, sexual, and TORCH-related transmission capabilities. After 2015, Brazil had the highest number of ZIVK-infected pregnant women who lost their babies or delivered them with Congenital ZIKV Syndrome (CZS). ZIKV triggers an immune defense in the placenta. This immune response counts with the participation of interleukins and transcription factors. Additionally, it has the potential involvement of human endogenous retroviruses (HERVS). Interleukins are immune response regulators that aid immune tolerance and support syncytial structure development in the placenta, where syncytin receptors facilitate vital cell-to-cell fusion events. HERVs are remnants of ancient viral infections that integrate into the genome and produce syncytin proteins crucial for placental development. Since ZIKV can infect trophoblast cells, we analyzed the relationship between ZIKV infection, HERV, interleukin, and transcription factor modulations in the placenta. To investigate the impact of ZIKV on trophoblast cells, we examined two cell types (BeWo and HTR8) infected with ZIKV-MR766 (African) and ZIKV-IEC-Paraíba (Asian-Brazilian) using Taqman and RT2 Profiler PCR Array assays. Our results indicate that early ZIKV infection (24-72 h) does not induce differential interleukins, transcription factors, and HERV expression. However, we show that the expression of a few of these host defense genes appears to be linked independently of ZIKV infection. Future studies involving additional trophoblastic cell lineages and extended infection timelines will illuminate the dynamic interplay between ZIKV, HERVs, interleukins, and transcription factors in the placenta.

Development of the novel gene chip and restriction fragment length polymorphism (RFLP) methods for rapid detection of Mycobacterium tuberculosis complex in broth culture

BackgroundTuberculosis (TB) is a major global public health issue. Prompt and accurate TB diagnosis is crucial for starting appropriate treatments and preventing the disease's spread. Current diagnostic techniques are either slow or expensive. This study aimed to create and evaluate a new, fast, highly reliable, and cost-effective TB detection method using a gene chip and Restriction Fragment Length Polymorphism (RFLP) analysis on Mycobacteria Growth Indicator Tubes (MGIT) specimens. MethodsWe assessed the effectiveness of a novel gene chip and RFLP methods targeting the 16S rRNA gene of Mycobacterium tuberculosis in 2000 MGIT culture-positive specimens. RFLP analysis identified the AfeI restriction site within the M. tuberculosis complex (MTBC) genome. Discrepancies were investigated through extensive sequencing and Cobas TaqMan PCR analysis, along with reviewing patient profiles. ResultsBoth methods showed high efficacy in detecting MTBC in broth cultures, with the gene chip method achieving a sensitivity of 99.27 %, specificity of 98.35 %, and the RFLP method showing a sensitivity of 98.18 %, specificity of 99.31 %. False negatives in two isolates were due to a mutation in the AfeI site. Additionally, five cases showed MTBC presence when nontuberculous Mycobacterium species grew in cultures. ConclusionOur novel gene chip and RFLP methods are effective for rapid highly-reliable and cost-effective M. tuberculosis detection in MGIT specimens. Both gene chip and RFLP methods are suitable for resource-limited settings, offering an economical advantage. These methods have significant potential to improve clinical TB diagnosis.

O07 RENAL DENERVATION IMPROVES RIGHT VENTRICULAR FUNCTION, RESTORES MYOCARDIAL NOREPINEPHRINE LEVELS AND REVERSES VENTRICULAR SPECIFICITY OF SELECTED MARKERS IN HYPERTENSIVE RATS WITH HEART FAILURE INDUCED BY VOLUME OVERLOAD

Background and objective: Despite the known anti-hypertensive effect of renal denervation (RDN), its influence on the cardiac function, particularly of the right ventricle (RV) and the cardiac sympathetic nervous system in heart failure (HF) is poorly understood. This study aimed to investigate the effect of RDN on RV function, myocardial norepinephrine (NE), and left versus right ventricular (LV/RV) dominance of HF markers in HF induced by aorto-caval fistula (ACF). Methods: ACF was created in hypertensive Ren-2 transgenic rats. RDN was performed by phenol application. Cardiac function was measured by echocardiography and pressure-volume analysis. NE levels were measured using an ELISA kit, protein expression was assessed by western blotting, gene expression by TaqMan PCR assay, and ROS by Amplex Red assay. Results: RDN in ACF rats decreased RV hypertrophy and dilatation, decreased RV end-systolic pressure and end-diastolic pressure, improved RV function (Ees +45%, FAC +20%), decreased HF gene markers Nppa, Tgm2, Myh7/6 ratio, and increased SOD2 protein expression. RDN decreased plasmatic NE levels, increased NE in RV, and decreased monoamine oxidase (MAO-A) in RV. NE levels and SOD2 were more dominant in RV than LV in control (sham/intact) rats and ACF changed their specificity towards RV dominance, while RDN had no effect in these parameters in ACF on ventricular specificity. In sham/intact rats dominant for LV were hemodynamic parameters Ees, EDPVR, and molecular markers Mao-a, ROS production by MAO-A, Nppa, Myh7, Myh7/6 ratio, Tgm2, Uchl1, and Beta1/Chrm2 ratio. ACF changed the dominance of these selected markers from LV to RV. Interestingly, RDN reversed dominance back towards LV in gene markers Mao-a, Nppa, Myh7, Tgm2, Uchl1, and Beta1/Chrm2 ratio. Conclusions: RDN decreased RV ESP and EDP, improved RV systolic function, restored NE levels, decreased RV gene expression of selected HF markers, and reversed their RV/LV dominance, probably by reduction of central sympathetic nerve drive and alternations of the cardiac sympathetic nervous system.

Pitfalls When Determining HNA-1 Genotypes and Finding Novel Alleles.

Genetic variation in the FCGR3B gene is responsible for different variants of human neutrophil antigen 1 (HNA-1). Laboratory techniques currently utilized for routine HNA-1 genotyping, predominantly PCR-sequence-specific primer (PCR-SSP) and PCR-sequence-based typing (PCR-SBT), lack specificity for FCGR3B. This study compares the capabilities and limitations of existing technologies including an in-house TaqMan PCR, a commercial PCR-SSP test, PCR-SBT and multiplex ligation-dependent probe amplification (MLPA) with those of a long-read nanopore sequencing assay. Testing was performed with both related and unrelated Danish samples with different copy numbers and/or rare alleles. Long-read nanopore sequencing was validated by blind testing of ten English samples. The results showed that FCGR3B copy numbers correlate with a dose-dependent distribution of alleles that complicates genotyping by TaqMan PCR, PCR-SSP and PCR-SBT, due to co-amplification of the homologous FCGR3A gene. MLPA can correctly quantify the dose-dependent distribution but not detect novel variants. Long-read nanopore sequencing showed high specificity for FCGR3B and was able to detect dosage-dependent distribution, and rare and novel variants that were previously not described. Current HNA-1 genotyping methods cannot produce unambiguous allele-level results, whereas long-read nanopore sequencing has shown the potential to resolve observed ambiguities, identify new HNA-1 variants and allow definitive allele assignment.

Association of glutamine synthetase polymorphisms rs2296521, rs10911021 and rs12136955 with plasma ammonia concentration in valproic acid-treated Egyptian epilepsy patients.

The use of valproic acid (VPA) in the treatment of some psychiatric and neurological disorders such as bipolar disorder, migraines, and epilepsy is associated with hyperammonemia. However, the mechanism of this negative effect of VPA is unclear. In this study, we investigate gene glutamate-ammonia ligase (GLUL) polymorphisms for the glutamine synthetase (GS) enzyme, a key enzyme that catalyzes the removal of ammonia by incorporating it with glutamate to form glutamine, and we investigate whether it has a relationship with the emergence of hyperammonemia during VPA-based therapy. We enrolled 180 Egyptian epilepsy patients in this study. Patient history, general and neurological examination and blood samples from arm veins were taken. Real time TaqMan PCR polymorphism for three polymorphism SNPs (rs2296521, rs10911021 and rs12136955) of GLUL was done. We assessed the relationship between the patient features, including three GLUL polymorphisms, and the development of hyperammonemia during VPA-based therapy. We found that the ammonia levels showed a positive correlation with VPA treatment duration (p = 0.015) and a negative correlation with carbamazepine total dose per day (p = 0.027) and with WBCs count (p = 0.026). Also, female patients having rs2296521 SNPs with the A allele and patients having rs10911021 SNPs with the C allele were at high risk for elevated plasma ammonia levels. Moreover, patients having rs12136955 SNPs with the A allele or associated hypertension as a co-morbidity were at high risk for elevated plasma ammonia levels. Female patients who have rs2296521 with the A allele, rs10911021 with the C allele, or rs12136955 with the A allele, are independent risk factors for elevated plasma ammonia levels during VPA-based therapy. Moreover, carbamazepine combined therapy may protect against the development of hyperammonemia in VPA-treated patients.

Abstract Tu057: Renal denervation enhances right ventricular function, reduces myocardial damage, and restores myocardial sympathetic signaling in rats with heart failure induced by volume overload

Introduction: Heart failure (HF) is associated with chronically increased sympathetic nervous activity with depleted norepinephrine (NE) in the myocardium. Despite the known anti-hypertensive effect of renal denervation (RDN), its influence on the function of the right ventricle (RV) and the cardiac sympathetic nervous system in HF is not well comprehended. Hypothesis: RDN improves RV function by reducing central sympathetic drive and changes of a sympathetic nervous branch in the heart. Aims: To investigate the effect of RDN on RV function, HF markers, myocardial NE, and its metabolism in RV in HF induced by aorto-caval fistula (ACF). Methods: HF was induced by ACF in Ren-2 transgenic rats (TGR). One week later, the RDN was performed by phenol application. Two weeks after RDN, RV function was measured by pressure-volume analysis and RV tissue was collected. Echocardiography was done once a week, during the entire experiment. NE levels were measured using an ELISA kit, protein expression was assessed by western blotting, gene expression by TaqMan PCR gene expression assay, and ROS by oxidation of Amplex Red assay. Results: The ACF increased RV weight, RV dimensions (RVD1, RVD2, RVD3), end-systolic (ESP) and end-diastolic pressure (EDP), reduced RV systolic function (end-systolic elastance - Ees, fractional area change - FAC) and ventricular-arterial coupling (Ees/Ea ratio), increased gene expression of HF markers collagen I/III ratio, natriuretic peptide A (Nppa), myosine heavy chain 7/6 (Myh7/6) ratio, transglutaminase 2 (Tgm2), and decreased superoxide dismutase 2 (SOD2) protein expression. ACF increased plasmatic NE levels, depleted NE in RV, decreased tyrosine hydroxylase protein expression in RV, and increased gene, protein expression, and activity of monoamine oxidase A (MAO-A). RDN decreased RV hypertrophy and dilatation (RVD1, RVD2, RVD3), decreased RV ESP (-7 mmHg, p=0.004) and EDP (-2.2 mmHg, p=0.003), improved RV function (Ees +45%, p=0.03, FAC +20%, p=0.005, Ees/Ea ratio +46%, p=0.02), decreased HF markers collagen I/III ratio, Nppa, Tgm2, Myh7/6 ratio, and increased SOD2 protein expression. RDN decreased plasmatic NE levels, increased NE in RV (+32%, p=0.03), and decreased MAO-A in RV. Conclusions: RDN decreased RV ESP and EDP, improved RV systolic function, restored NE levels, and decreased RV gene expression of selected HF markers, probably by reduction of central sympathetic nerve drive and alterations of the cardiac sympathetic nervous system.

The Prevalence of Rickettsial and Rickettsial-Like Diseases in Patients with Undifferentiated Febrile Illness - Hainan Province, China, 2018-2021.

Rickettsial and Rickettsial-like diseases, resulting from obligate intracellular Gram-negative bacteria, pose a growing public health threat in China. To assess the current prevalence of these diseases on Hainan Island, a study was conducted on 9 bacterial pathogens found in patients with undifferentiated febrile illness (UFI) treated in Haikou between 2018 and 2021 using a TaqMan Polymerase Chain Reaction (TaqMan PCR) array. Blood samples (n=503) were collected from patients with UFI between 2018 and 2021. The samples were screened for Rickettsia spp., Orientia tsutsugamushi (O. tsutsugamushi), Anaplasma. phagocytophilum (A. phagocytophilum), Ehrlichia chaffeensis, Coxiella burnetii, Chlamydia psittaci, Brucella spp., Burkholderia pseudomallei, and Borrelia burgdorferi using a TaqMan PCR array. Positive samples (Ct<35) underwent confirmation through nested PCR, sequencing, and phylogenetic analysis. O. tsutsugamushi and A. phagocytophilum were detected in the patients at positive rates of 14.51% (73/503) and 5.57% (28/503), respectively. Co-infection of O. tsutsugamushi and A. phagocytophilum was identified in scrub typhus (ST) positive populations from Hainan (10.96%, 8/73), Guangxi (61.54%, 8/13), and Yunnan (5.36%, 3/56) provincial-level administrative divisions (PLADs) of China. An increased prevalence rate of ST and a decreased prevalence of rickettsioses were observed in patients with UFI in Hainan compared to a decade ago. The co-infection of O. tsutsugamushi and A. phagocytophilum poses a current public health threat in China.

P-266 Profiling redox effects induced by micro-nanoplastics in the female reproductive system: insights from human granulosa cells

Abstract Study question Are nano-microplastics (NMPs) taken up into human granulosa cells causing redox alterations? Summary answer NMPs enter into human granulosa cells and influence viability, energy production and antioxidant response. What is known already In recent decades, anthropogenic activities have increased the production of global plastic with millions of tons produced every year. Under the action of different physical, chemical or biological agents, plastic waste breaks down into (NMP) particles that propagate in the environment posing threats for human health. NMPs translocate from digestive tract to circulatory systems reaching organs and cells, including female gonads. Nevertheless, there is insufficient knowledge of their effects on reproductive functions in mammals to allow for an accurate risk assessment to be conducted and any risks managed in animal and human being contexts. Study design, size, duration Human ovarian granulosa cells (KGN cell line) were exposed to NMPs of different sizes (40 nm, 70 nm, 100 nm, and 200 nm) at concentrations ranging from 5 to 1000 μg/ml for 24 h and then processed for cellular and biochemical analyses Participants/materials, setting, methods NMPs uptake by granulosa cells was tested by the employment of fluorescent NMPs and observation under confocal laser scanning microscopy. Cell viability was assed by Cell Counting Kit8. The effects of NMPs on mitochondrial bioenergetics was evaluated by MitoStress kit (Seahorse Xfe96, Agilent). ATP production was evaluated by Cell Titer-Glo ATP assay kit (Promega). Key enzymes of antioxidant response were analysed at transcript and protein level by using real-time Taqman PCR and Western blotting, respectively. Main results and the role of chance We demonstrated that NMPs are taken up by granulosa cells at all tested concentrions along with significant decrease of cell vitality with all sizes and concentrations. Seahorse analysis revealed an altered bioenergetic profiles. ATP levels increase at 70, 100 and 200 nm (one way ANOVA p = 0.001) at all tested concentrations (one way ANOVA p &amp;lt; 0.001). The gene and protein expression of catalase (CAT) superoxide dismutase 1 (SOD1) and superoxide dismutase 2 (SOD2) increased at 5 and 100 µg/ml with all sizes except 100 nm, whereas the level of sirtuins (SIRT1 and SIRT3) transcripts and protein decreased. Reduced levels of phosphorylated NRF2, the transcription factor that activates antioxidant responsive elements (ARE)-mediated gene expression were observed. Limitations, reasons for caution The use of human cell lines requires careful consideration when transferring to human testing. Wider implications of the findings Our results contribute to understanding the effects of NMPs on mammalian fertility in order to find possible protective approaches. Considering that the level of susceptibility of mammalian female germ cells to NMPs is still unknown, present results contribute to evidence-based strategies allowing living and working in a health promoting environment. Trial registration number Effects of combined exposure to nano/microplastics and plastic additives on mammalian female fertility (CUP E53D2301100006)

Study of gene polymorphisms in Toll-like receptor 2 in patients with acute lymphoblastic leukemia

ObjectivesAcute Lymphoblastic Leukemia (ALL) is a multifactorial disease that results from the interaction between multiple genetic factors. ALL is characterized by uncontrolled production of hematopoietic precursor cells of the lymphoid progenitors within the bone marrow. The development of hematological malignancies has been associated with malignant-like cells that express low levels of immunogenic surface molecules, thus, facilitating their escape from cellular antineoplastic immune responses. This risk may be partly influenced by variations in polymorphic genes that control immune function and regulation. Toll-like receptors (TLRs) are well known pattern recognition receptors playing key role in innate immune response. Abnormal expression and dysregulation of TLRs will provide an opportunity for cancer cells to escape from the immune system and enhance their proliferation and angiogenesis. Toll-like receptor 2 (TLR2) play an essential role in innate immunity. Single nucleotide polymorphisms (SNPs) are present in a number of TLR genes and have been associated with various disorders. MethodsIn this study, 265 subjects have been divided into two groups included 150 patients with ALL and115 healthy volunteers. All subjects were genotyped using TaqMan PCR techniques. In total, Five SNPs were statistically evaluated in the TLR2 (rs1898830 A/G, rs3804099 T/C, rs3804100 T/C, rs1339 T/C, and rs1337 C/G), which may influence the susceptibility of ALL. Minor allele frequency and genotype distribution were compared across the study groups, and the relative risk and differences between patients and controls were estimated. Moreover, the mRNA expression level was evaluated in patients with ALL and the matched healthy individuals by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). ResultsTLR2 rs1898830 A/G; rs3804099 T/C; rs3804100 T/C; rs1339 T/C, were significantly decrease the risk in our population, overall and for certain subtypes and ALL samples exhibited significant increase in the mRNA levels of TLR2. ConclusionsThis study shows that TLR2 could be an independent prognostic factor of ALL risks in the Saudi population. Suggesting that genetic variation in genes associated with an immune response may be important in the etiology of ALL. In addition, the results herein revealed that TLR2 overexpression is associated with ALL and has diverse biological significance in the context of the complex relationship between inflammation and cancer development. Therefore, these data could open further studies to explore the possible clinical relevance of TLRs as pathological markers for Leukemia and enhance the strategies regarding hematological malignancies prevention based on their gene expression.

EPEN-06. IDENTIFICATION OF CSF MIRNA BIOMARKERS FOR THE EARLY DETECTION OF MEASURABLE RESIDUAL DISEASE IN PAEDIATRIC EPENDYMOMA: A BIOMECA STUDY

Abstract BACKGROUND Ependymoma (EPN) is the second most common malignant paediatric brain tumour. 50% of children relapse. Detection of Measurable Residual Disease (MRD) via MRI is difficult and lacks sensitivity for very early recurrence, necessitating an urgent need for identifying new, robust biomarkers for the early diagnosis, prognosis, and clinical management of disease progression in EPN. We hypothesise that microRNA (miRNA) quantification in the cerebrospinal fluid (CSF) will have clinical utility in the early detection of MRD in these patients. PATIENTS/METHODS A discovery cohort of EPN CSF samples (n=12) from patients enrolled on the SIOP Ependymoma II clinical trial (trials.gov identifier: NCT02265770) and control leukaemia CSF samples (n=8) underwent RNA-sequencing (QIAGEN) after total RNA extraction using QIAGEN miRNeasy Serum/Plasma kit. The EPN cohort consisted of infratentorial (IT; n=9), supratentorial (ST; n=1) and spinal (SP; n=2) cases taken prior to, or at, resection (primary/relapse). RESULTS Raw sequencing data entered a quality-control pipeline (Tally/Cutadapt), followed by alignment to miRBase-v22 (https://mirbase.org/) using Chimira (PMID:26093149). Two outlying (infratentorial) EPN samples were removed, leaving a 10 (IT+ST+SP) versus 8 comparison. Extracted raw counts were normalised across samples using DESeq2 (PMID:25516281) and 87 differentially-expressed miRNAs identified (adj-p&amp;lt;0.05). EPN samples completely segregated from controls on clustering/heatmap analysis. From these 87 miRNAs, a core set of 53 were overlapping in comparisons removing spinal (IT+ST remaining) and supratentorial (IT alone) samples. These miRNAs underwent combined ranking by adjusted-p and abundance (normalised count) values, and top-ranking candidates taken forward for confirmation using highly-sensitive Taqman PCR, prior to validation in additional samples. CONCLUSION Circulating miRNA quantification offers promise for EPN diagnosis and MRD detection. Further CSF study in larger patient cohorts, and serum/plasma analysis, are now warranted.

USE OF TAQMAN ARRAY TO INVESTIGATE INFECTION IN DIABETIC FOOT WOUNDS

IntroductionDiabetic foot disease is a major public health problem with an annual NHS expenditure in excess of £1 billion. Infection increases risk of major amputation fivefold. Due to the polymicrobial nature of diabetic foot infections, it is often difficult to isolate the correct organism with conventional culture techniques, to deliver appropriate narrow spectrum antibiotics. Rapid DNA-based technology using multi-channel arrays presents a quicker alternative and has previously been used effectively in intensive care and respiratory medicine.MethodsWe gained institutional and Local Ethics Committee approval for a prospective cohort study of patients with clinically infected diabetic foot wounds. They all had deep tissue samples taken in clinic processed with conventional culture and real-time PCR TaqMan array.Results50 samples were taken from 39 patients between October 2020 and March 2022. 84% of patient were male, 88% had type 2 diabetes. The ulcers were of variable chronicity prior to sampling (range 1–113 weeks) and mean HbA1c was 67.2mmol/mol. Ulcers were on the heel (3), midfoot (6) and forefoot (41). Minimum follow up was 3 months. 6 ulcers healed, 24 patients were admitted due to foot disease, there were 2 major amputations and 4 deaths. TaqMan array results were available a mean of 4.3 days earlier than culture results. 9 patients had negative conventional cultures and 8 were negative onarray testing. 17 patients had the same organisms detected on culture and array. 16 of these 17 had additional organisms detected by array. The most frequent organisms detected on array that were not detected by culture were Staphylococcus spp., Enterobacter, Pseudomonas and fungi.ConclusionTaqMan array shows promise in detecting infecting organisms from diabetic foot wounds and providing earlier results than standard culture, which may enable appropriate and timely antibiotic therapy.

#228 APOL1 variants and chronic kidney disease in Morocco: case control study

Abstract Background and Aims APOL1 genetic variants account for much of the excess risk of chronic and end stage kidney disease, which results in a significant global health disparity for persons of African ancestry. We estimate the lifetime risk of kidney disease in APOL1 dual-risk allele individuals to be at least 15%. These genetic variants were never tested in north African patients and this is the first study aimed to search the existence of this variants in general Moroccan people and patients with chronic kidney disease. Method This is a case control multi center study including Moroccan adult with GFR less than 60 ml per min secondary to unknown etiology or nephroangiosclerosis. Patients with known nephropathy or diabetes were excluded. Between July 2014 and June 2017, patients and 100 controls were enrolled for testing APOL1 variants. ADN extraction was done by isolate II Blood DNA kit and nucleic acid concentration by spectrophotometry. The allele frequency was calculated by PCR TaqMan. Results During the inclusion period 117 patients with chronic kidney disease from unknown etiology and 8 patients with nephroangiosclerosis were included from all the twelve Moroccan regions. There mean age was 49 years and more than 60% were males. The age of end stage renal disease was 42 years. Testing APOL1 variants did not find G1 or G2 classic mutations but we find a G2 deletion and a new mutation GAT to AAT in two patients. We find also a silent mutation AGA to AGG that we are exploring in a family investigation. Conclusion APOL1 genetic variants as described in the literature are not significantly present in Moroccan patient with chronic kidney disease and cannot be yet used as a risk factor in our context. However we find a new mutation needing a wide exploration in a bigger cohort

#1358 The association between TNFRSF1B rs1061624 polymorphism and hypertension in end-stage kidney disease patients on dialysis

Abstract Background and Aims In chronic kidney disease (CKD), hypertension (HT) is commonly found during its development and is a leading cause for its progression. HT, dyslipidemia and visceral obesity are among the components of metabolic syndrome (MetS) and seem to associate with progression of CKD to end-stage kidney disease (ESKD). Enhanced levels of soluble tumor necrosis factor receptor 2 (sTNFR2) are known to associate with progressive CKD; and this biomarker was reported as an independent predictor of all-cause mortality in ESKD patients under dialysis. Concerning the TNFRSF1B gene, the polymorphism rs1061624 (A &amp;gt; G), located in the 3′-untranslated region (3′-UTR), was associated with the development of HT in men and with increased risk of MetS. The aim of this study was to determine the genotype frequencies of TNFRSF1B rs1061624 in ESKD patients with and without HT, and to evaluate its relationship with the circulating levels of some MetS biomarkers. Method We studied 277 ESKD patients on dialysis (recruited between 2016-2019), 170 diagnosed with HT and 107 without HT (no-HT group); age, sex, body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP) and statin therapy were recorded. Real time PCR TaqMan SNP genotyping assay was used to assess genotype frequencies of TNFRSF1B rs1061624. We also evaluated the conventional lipid profile and the levels of oxidized low-density lipoprotein, adiponectin and leptin. Results The genotype frequencies in patients with and without HT were different (P = 0.002); the AA genotype was less frequent in HT than in no-HT group, while GG and AG genotypes were more frequent. Considering the AA genotype carriers, HT ESKD patients (n = 23), compared to the no-HT group (n = 33), presented lower adiponectin levels (P = 0.025); for the AG genotype carriers, HT group (n = 89) presented a trend towards lower adiponectin concentrations (P = 0.055), and were younger than no-HT patients (n = 48; P&amp;lt;0.001); in both comparisons, groups were matched for sex, BMI and number of patients under statins treatment, and in the first case also for age. Considering GG genotype, HT patients (n = 58) only differed from no-HT subjects (n = 26) in SBP, that was higher (P&amp;lt;0.001). Among HT patients, AG genotype carriers presented higher DBP (P = 0.004), lower values of leptin (P = 0.012) and leptin/adiponectin ratio (P = 0.022) and were younger (P&amp;lt;0.001) than GG genotype patients; compared to AA carriers, cholesterol levels were lower (P = 0.012). For the no-HT group, AG genotype patients presented lower DBP (P = 0.008) than AA genotype carriers. Conclusion The genotype frequencies were different in ESKD patients with and without HT, being G allele more frequent in HT. The HT ESKD patients with the AA or the AG genotypes seem to present lower adiponectin levels than the ESKD no-HT patients with the same genotypes. Acknowledgements This work was financed by CESPU, through the project SNPsCKD-GI2-CESPU-2022; FCT, in the scope of the project UIDP/04378/2020 and UIDB/04378/2020 of the Research Unit on Applied Molecular Biosciences—UCIBIO and the project LA/P/0140/2020 of the Associate Laboratory Institute for Health and Bioeconomy—i4HB.

Sex- Specific Effects of Chronic Unpredictable Stress on Renal Mitochondrial Function in C57BL/6 Mice

Background: The kidneys play a central role in long term control of blood pressure. Chronic psychological stress has been linked to hypertension, inflammation, and is associated with both an increased prevalence and progression of renal disease. However, the molecular and cellular mechanisms by which chronic stress alters renal function are not fully understood, and data on sex specific differences in renal and blood pressure responses to stress are limited. The impact of stress to cause local inflammation and mitochondrial dysfunction in the kidneys is not clear and represents a potential mechanism leading to renal dysfunction and hypertension. The chronic unpredictable stress (CUS) model induces psychological stress in rodents thus allowing the study of integrated physiological changes to the kidney in response to stress. Hypothesis: Exposing mice to CUS will lead to increased blood pressure that is associated with decreased renal mitochondrial function and renal inflammation. Methods: To investigate the link between stress, renal mitochondrial function, inflammation, and blood pressure, we exposed adult male and female C57BL/6 mice to CUS for 28 consecutive days. Blood pressure was measured via tail cuff on the 28th day of stress. 24 hours later, mice were euthanized and estrous cycle phase in females was determined by vaginal cytology. Kidney mitochondrial oxygen consumption was assessed using the Oroboros respirometer on the pole ends of the left kidneys. NLR family pyrin domain containing 3 (NLRP3) expression was measured in the right kidney using Real-Time TaqMan PCR. Results: Mean arterial pressure was elevated in both stressed males (in mmHg, 106±4 vs 87±4, n&lt;11, p&lt;0.01) and females (131± 6 vs 94±11 n&lt;4, p&lt;0.01) compared to non-stressed mice. While maximal electron transport capacity (ETS), a measure of mitochondrial function, was unchanged in CUS male kidneys, stressed females in the receptive (estrus and proestrus) phase of the estrous cycle exhibited a significant decrease in renal ETS compared to non-stressed females (in pmol O2/mg protein, 14.4±0.9 vs 11.4±0.7, n=11, p&lt;0.05). Renal mRNA expression of NLRP3 was increased in CUS males (35%± 7.7, n=8, p&lt;0.01) but unchanged in CUS females. Conclusion: These data suggest potential mechanistic differences in stress-induced hypertension in renal mitochondria (decreased ETS in stressed females) and inflammasome level (increased NLRP3 in stressed males) between male and female mice. This work was supported by P20GM109091 (F.H.), R01HL130972-01A1, R01HL5949, BX000168-10A1, BX005320 (F.G.S.), R01DK132948 (C.W. &amp; F.P.) R01 MH129798 (SKW); VA VISN7 RDA (F.H.),, 1U54HL169191-01 &amp; BX002604 (M.J.R.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the abstract. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Validation of a simplified small-scale DNA extraction protocol from wine by quantitative real-time PCR

In the present study, we compared a simplified small-scale purification protocol to obtain DNA admixtures out of wine, with our large-scale published method. The extraction methods must provide DNA free of PCR inhibitors, that can interfere with DNA amplification. To evaluate the efficiency of grapevine’s nuclear DNA extraction from wine, the new protocol was also compared in terms of purity and yield to the DNA obtained out of grapevine’s (Vitis vinifera) leaf tissue, using a commercial kit. Two single-copy nuclear genes, nine-cis-epoxy carotenoid dioxygenase 2 (NCED2), and prefoldin subunit 5-like (PS5) were amplified in DNA extracted from wine and grapevine by real-time TaqMan PCR to determine the presence of inhibitors in relation to the diversity of starting biological matrix. This study showed that the small-scale, simpler method for extracting DNA from wine produced effective results in terms of inhibitor presence and purity. Furthermore, even though the initial biological matrix was more complicated, the grapevine nuclear DNA that was removed from wine was qualitatively equivalent to the DNA that was isolated from the leaves.