Sensitive Method Research Articles

Improving onchocerciasis elimination surveillance: trials of odour baited Esperanza Window Traps to collect black fly vectors and real-time qPCR detection of Onchocerca volvulus in black fly pools

Abstract Background Entomological data for onchocerciasis surveillance relies on sampling black flies through human landing collectors in the field and laboratory testing of the flies for infection using pooled screening O-150 PCR-ELISA assay. Both techniques require improvements. This study aimed to optimize the Esperanza Window Trap (EWT) for black fly collection. We tested alternative carbon dioxide (CO2) mimics to attract black flies to the traps. Additionally, we evaluated new quantitative PCR (qPCR) methods that target mitochondrial DNA markers and have been proposed to enhance the sensitivity and specificity for detecting Onchocerca volvulus infections in blackflies. Methods Traps baited with low, medium and high release rates of either 2-butanone or cyclopentanone as CO2 mimics were field tested against traps baited with organically generated CO2 in four ecological zones in Nigeria: Guinea savannah, derived savannah, rainforest and montane forest. The performance of EWTs baited with CO2 or in combination with 2-butanone (low release) were subsequently evaluated against the human landing collection (HLC). Trap scaling was also pilot tested by comparing two EWTs to a single HLC team. Collected black flies were used to test detection of O. volvulus in black flies using Ov ND5 real-time PCR (qPCR) compared to the conventional pool screening O-150 PCR. Results EWTs baited with 2-butanone caught similar numbers of black flies (Simulium damnosum s.l.) to those baited with CO2, while cyclopentanone collected significantly fewer flies in all locations. The low release of 2-butanone was the most effective overall, although HLCs collected higher numbers of black flies than EWT baited with CO2 either singly or in combination with low-release 2-butanone. The combination of two EWTs baited with CO2 and deployed 100 m apart from each other collected similar numbers of flies as one HLC. More black fly pools were positive for O. volvulus by Ov ND5 qPCR compared with O-150 PCR in derived savannah (31.15 vs. 15.57%), montane forest (11.54 vs. 0%) and rainforest (23.08 vs. 2.56%), with only one positive pool in Guinea savannah detected by both methods. Conclusions The 2-butanone has potential to be used in xenomonitoring as a standardized replacement for organically generated CO2. Ov ND5 qPCR detected more positive pools than O-150 PCR. The positive pools found in foci hitherto considered to have interrupted/eliminated onchocerciasis highlight the need for more sensitive and specific methods that support programmatic assessments to identify and combat recrudescence. Graphical Abstract

A sustainable HPTLC approach for green assessment of Tyrosine to phenylalanine ratio in chronic kidney disease

AbstractThe kidney is considered the main site for the net release of Tyrosine (Tyr) to the circulation through hydroxylation of Phenylalanine (Phe) using phenylalanine hydroxylase enzyme. In chronic kidney disease (CKD) patients the enzyme activity is impaired, therefore the serum concentration ratio of Tyr/Phe is reduced compared to healthy individuals. This motivates us to develop a cost effective, green, simple, sensitive, and selective HPTLC method to measure the levels of Tyr and Phe in serum samples. The analysis was carried out using acetonitrile: ethanol: 25% ammonia solution: ethyl acetate (6.5: 1.5: 1: 0.5) as a mobile phase. Rf values were 0.55 ± 0.05 for Phe and 0.39 ± 0.05 for Tyr. Densitometry scanning was performed using UV detector and dual wavelengths of 210 and 225 nm were obtained. A linear correlation was observed between the levels of Phe and Tyr, ranging from 50 to 700 ng band− 1 and 50 to 600 ng band− 1, respectively, under the optimum conditions. The method selectivity, linearity, precision, accuracy, and robustness were all confirmed in accordance with ICH recommendations. Calculations of the separation and resolution factors, number of theoretical plates, and height equivalent to theoretical plates prove to the chromatographic system accuracy and high separation efficiency. The developed method exhibits an acceptable eco-scale when measuring the method greenness using AGREE and GAPI softwares. It was applied for the determination of Phe and Tyr concentrations in human serum samples.

Ammonia and temperature sensing applications using fluorometric and colorimetric microparticles and polymeric films doped with BODIPY-emitters.

Fourfunctionalized BODIPY derivatives(BDP1 to BDP4) were synthesizedand their optical properties investigatedboth in solution and when incorporated into a solid matrix. Recognizing the versatility of BODIPY derivatives and the increasing interest in developing new luminescent organic dyes embedded in polymers, the BODIPY derivatives were dispersed into two types of polymeric matrices: Poly(methyl methacrylate) (PMMA) and Thermoplastic Polyurethane (TPU), both as films and microparticles. This resulted in eight new BODIPY-doped polymer films and eight types of BODIPY-doped polymeric microparticles for use in aqueous solutions. The integration of the BODIPY dyes into the polymeric matrices combines the unique properties of the polymer films, such as porosity, flexibility, and elasticity, with the excellent photophysical characteristics of the BODIPYs. Importantly, the dispersion minimized issues such as aggregation-caused quenching commonly observed in solid-state luminescent materials. The thermometric responses of all polymer films were evaluated by studying their solid-state emission spectra in the 25-200°C temperature range. The reversibility of these temperature-induced changes was also assessed, revealing excellent recovery of luminescence. These promising results suggest these materials could have applications as fluorescent thermometric sensors. Furthermore, we explored the potential of the brominated (BDP3) and chalcogenated (BDP4) BODIPY derivatives as ammonia sensors. The two derivatives produced yellow fluorescent products upon interaction with the analyte. Kinetic studies using solid-state emission spectra of BDP4@TPU and BDP4@PMMA showed significant differences in reaction rates (minutes for BDP4@TPU and hours in the case of BDP4@PMMA) attributable to the higher permeability of TPU when compared with PMMA. Detection and quantification of ammonia concentration were conducted by means of simple photographic analysis, measuring the "R" (red) and "G" (green) components of RGB color parameters. Theresults from the photographic method correlated well with the results from fluorimetric spectroscopy studies. The photographic analysis is straightforward, portable, and does not require expensive equipment. Finally, we successfully applied polymeric microparticles doped with BODIPYs to detect ammonia in water, demonstrating their effectiveness without the need for organic solvents. This highlights their potential for environmental monitoring and other applications requiring sensitive and selective detection methods.

Split Probe-Induced Protein Translational Amplification for Nucleic Acid Detection.

Nucleic acid detection is important in a wide range of applications, including disease diagnosis, genetic testing, biotechnological research, environmental monitoring, and forensic science. However, the application of nucleic acid detection in various fields is hindered by the lack of sensitive, accurate, and inexpensive methods. This study introduces a simple approach to enhance the sensitivity for the accurate detection of nucleic acids. Our approach combined a split-probe strategy with in vitro translational amplification of reporter protein for signal generation to detect nucleic acids with high sensitivity and selectivity. This approach enables target-mediated translational amplification of reporter proteins by linking split probes in the presence of a target microRNA (miRNA). In particular, the fluorescence split-probe sensor adopts a reporter protein with various fluorescence wavelength regions, enabling the simultaneous detection of multiple target miRNAs. Moreover, luminescence detection by merely altering the reporter protein sequence can substantially enhance the sensitivity of detection of target miRNAs. Using this system, we analyzed and quantified target miRNAs in the total RNA extracted from cell lines and cell-derived extracellular vesicles with high specificity and accuracy. This split-probe sensor has potential as a powerful tool for the simple, sensitive, and specific detection of various target nucleic acids.

Development and Validation of Rapid and Cost-Effective RP-HPLC/UV Method for Determination of Cetirizine/Levocetirizine in Blood Plasma of Smokers and Non Smokers: a Two Cohort Comparative Study.

In this research study, a simple, rapid, sensitive, and cost-effective Reverse Phase High Performance Liquid Chromatography method was developed and validated for determination of Cetirizine and Levocetirizine in human plasma. The drugs were separated on an ACE Generix100-5 C18 RP (250 × 4.6mm, 5μm) column, using Acetonitrile and Distilled water pH7 (59:41v/v) as mobile phase with a flow rate of 1.5mL/min, retention time of 3.39 ± 0.02min, detection wavelength of 230nm, and column oven temperature at 26°C. The drug was extracted from human plasma using Methanol, the percent recovery was 97%. The LOD and LOQ for Cetirizine and Levocetirizine were 0.5ng and 1ng. The method was linear over the concentration range of 0.5-1000ng /mL for Cetirizine and Levocetirizine. The method was applied for analysis of drugs in plasma following oral administration of Cetirizine (10mg) and Levocetirizine (5mg) in smokers and nonsmokers of Pashtun ethnicity belonging from different districts of Khyber Pakhtunkhwa, Pakistan. The difference between Cetirizine plasma levels in smokers and non-smokers was significant with p -value 0.0279.

Highly Sensitive and Robust LC-MS/MS Method for Determination up to 15 Small Molecule Nitrosamine Impurities in Pharmaceutical Drug Substances.

Nitrosamine impurities have been classified as probable human carcinogens for decades. These impurities were reported in water, food, tobacco, pesticides, and plastics but received attention in mid-2018 when N-nitrosodimethylamine (NDMA) was reported in valsartan drug products. Subsequently, it was revealed that several small molecule and complex nitrosamine impurities can form in any active pharmaceutical ingredient (API) or drug product in which secondary or tertiary amines are present (as API or as impurities) along with a nitrosating agent. Consequently, regulators have provided several guidelines for the risk assessment of nitrosamine formation during manufacturing, storage, or from contaminated supply chains. This has led to a demand for validated analytical methods that quantify N-nitrosamine impurities in pharmaceutical products. In this study, a highly sensitive and robust analytical method was developed and validated for quantitatively determining up to 15 small nitrosamines at low levels (0.01 ppm) in sartan drug substances. The study also suggests that this method can be extended not only to corresponding sartan drug products but could also be used as a generic screening method to test a variety of drug substances, and drug products with the minimum required optimization of method conditions.

Electrochemical biosensors for dopamine.

Dopamine (DA), a key catecholamine, plays a pivotal role in the regulation of human cognition and emotions. It has profound effects on the hormonal, memory, and cardiovascular systems. Anomalies like Alzheimer's, Parkinson's, schizophrenia, and senile dementia are linked to abnormal DA levels. Consequently, the precise determination of DA levels in biological systems is critical for the accurate diagnosis and treatment of these disorders. Among all analytical techniques, electrochemical studies provide the most selective and highly sensitive methods for detecting DA in biological samples. Ascorbic acid and uric acid are two examples of small biomolecules that can obstruct the detection of DA in biological fluids. To address this issue, numerous attempts have been made to modify bare electrodes to separate the signals of these substances and enhance the electrocatalytic activity towards DA. Various surface modifiers, including coatings, conducting polymers, ionic liquids, nanomaterials, and inorganic complexes, have been employed in the modification process. Despite the reported success in DA detection using electrochemical sensors, many of these approaches are deemed too complex and costly for real-world applications. Therefore, this review aims to provide an overview of DA electrochemical biosensors that are practical for real-world applications.

Sensitive and reliable detection of KIT p.D816V mutation in decalcified archival bone marrow trephines.

The majority of mastocytosis cases are characterized by an activating mutation in the KIT gene in codon 816. The detection of this alteration is of importance for proper diagnostic workup. Therefore, reliable and sensitive methods for the detection of KIT Codon 816 hotspot mutations in various types of patient samples are required. Since mutated cancer genes are often overexpressed, we evaluated the feasibility and sensitivity of KIT p.D816V detection by analysing mRNA/cDNA instead of genomic DNA. From 80 bone marrow trephines harboring a KIT p.D816 mutation, seven were only mutated by mRNA/cDNA pyrosequencing and 11 only by digital PCR analysis of genomic DNA. These results clearly demonstrate that detection of clinically relevant mutations in mRNA extracted from routinely processed decalcified archival bone marrow trephines is not only possible in a reliable fashion but under many circumstances advantageous. This enables the direct correlation of genomic data with high-quality morphological evaluation.

Abstract B018: Plasma-based circulating tumor tissue modified viral (TTMV)-HPV DNA for detection of recurrent HPV-driven anal cancer

Abstract Purpose: Squamous cell carcinoma of the anus (SCCA) is primarily driven by human papillomavirus (HPV) infection. Up to 30% of patients experience recurrence, necessitating improved surveillance strategies. Liquid biopsies have shown promise as a tool in oncology. This study investigates the clinical performance of circulating tumor tissue modified viral (TTMV)- HPV DNA in the post-treatment surveillance of SCCA. Patients and methods: This central IRB-approved retrospective cohort study included 117 patients diagnosed with HPV-driven SCCA from seven U.S. centers who had ≥1 TTMV-HPV DNA tests (NavDx®, Naveris, Inc., Waltham, MA) performed between March 2020 and June 2024. TTMV-HPV DNA for HPV subtypes 16, 18, 31, 33, and 35 were analyzed using droplet digital PCR. The diagnostic accuracy of TTMV-HPV DNA was evaluated by comparing test results with clinical evidence of SCCA recurrence determined through anoscopy, radiology, and/or tissue biopsy. Recurrence is defined as either a positive biopsy or subsequent salvage therapy. Results: Patients were primarily female (73%) with a median age 63 years. Median follow-up after initial treatment was 19 months. Forty-seven patients (40%) had pretreatment TTMV-HPV DNA testing, with a baseline detectability of 85.1% (40/47, 95% CI: 74.9–95.3). Of these, 24 were re-tested within 3 months post-treatment and 18 had undetectable TTMV-HPV DNA (75%). Those patients whose scores became undetectable had significantly longer recurrence-free survival than those whose scores remained detectable (log-rank test, p=0.01). One hundred and four patients (89%) underwent post-treatment testing, of which 91 provided relevant data for the analysis. Of these 91 patients, 27 (29.7%) experienced recurrence. Post-treatment testing demonstrated a per- patient sensitivity of 85.7% (24/28, 95% CI: 72.8-98.7). Of four patients with a false negative test, only one had biopsy-confirmed recurrence, whereas the remaining recurrences were not biopsied prior to starting salvage treatment. The positive predictive value of a single positive test was 97.6% (40/41; 95% CI: 92.8–100.0). One patient remains in active follow-up. Of the true positive post-treatment tests, 58% (14/24) predicted recurrence before clinical detection, with a median lead time of 59 days (range: 10–536). There were 141 negative post-treatment tests across 66 patients. This yielded a per-test specificity and negative predictive value of 99.3% (136/137, 95% CI: 97.8-100.0) and 97.2% (136/140, 95% CI: 94.9-99.9), respectively. Indeterminate TTMV-HPV DNA tests were rare (5/268,1.9%). However, clinically indeterminate findings (CIFs) were common, with 141 post-treatment CIFs identified across 52/117 patients (44.4%). TTMV-HPV DNA testing was able to correctly predict recurrence status in 94.3% of CIF cases. Conclusion: TTMV-HPV DNA testing is a sensitive and specific surveillance method for detecting early recurrence of HPV-driven SCCA. Citation Format: Shane Lloyd, Rafi Kabarriti, James Jabalee, Tyler Slater, Corbin Jacobs, Sean Inocencio, Michael Rutenberg, Chance Matthiesen, Kasha Neff, Gene-Fu F Liu, Tiffany M Juarez, Catherine DV Fitz, Stanley Liauw. Plasma-based circulating tumor tissue modified viral (TTMV)-HPV DNA for detection of recurrent HPV-driven anal cancer [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B018.

Abstract B057: Base-error model (BEM) for improved detection of ctDNA in lymph samples of HPV-negative head and neck cancer patients

Abstract Introduction: Previously we demonstrated that ctDNA present in lymphatic exudate collected via surgical drains (“lymph”) outperformed plasma for detecting minimal residual disease (MRD) in head and neck squamous cell carcinoma (HNSCC) patients through a targeted sequencing (TS) approach. However, artifacts introduced during library preparation and sequencing remain challenges to sensitive low allelic fraction mutation detection. To enhance the performance of the TS approach, we characterized the background noise in lymph samples and developed a base-error model (BEM) that reduces sequencing artifacts and maximizes ctDNA signal. Methods: Lymph and blood were collected from 44 HPV-negative HNSCC patients postoperatively at 24 hours along with resected tumor. Cell-free DNA was extracted from lymph and sequenced using a custom TS panel with unique molecular identifiers (UMI). Somatic mutations were identified by tumor and blood exome sequencing (200x). Five patients had <2 mutations in tumor and were excluded. Two patients were censored due to lack of clinical data, yielding 17 patients with disease recurrence (REC) and 20 with no evidence of disease (NED) with >1 year of follow-up. Tumor-specific variants were force-called in lymph using a custom pipeline. A BEM of each tumor variant was built using a series of high-quality lymph reference samples to quantify the background noise. BEM was fit by Weibull distribution if more than 5 non-zero non-reference alleles were observed at a tumor variant position across the reference samples. Otherwise, Gaussian distribution was used to fit BEM. Force-called variants were considered artifacts if the variant allele fraction (VAF) was not greater than BEM cutoff controlled by false discovery rate. Patients were considered MRD positive if the mean VAF was greater than the estimated limit of detection. The Kaplan-Meier (KM) estimator with log-rank test and Cox proportional-hazards model were used for survival analyses. Results: Background noise was observed in reference lymph samples across all 12 nucleotide substitution classes. Out of 299 single nucleotide variants (SNVs), 94 were determined as artifacts by BEM. Among the artifacts, 77 were C/G to A/T mutations, indicating that the majority of recurrent background artifact in TS is likely the result of oxidative damage. The artifacts had VAFs ranging from 0.004% to 0.12% with median of 0.02%. Incorporation of BEM in lymph TS showed significantly improved specificity (sensitivity (SN) = 71%, specificity (SP) = 65%; p = 0.027, Hazard ratio (HR) = 3.07) compared to the same cohort without BEM (SN = 76%, SP = 30%, p = 0.60, HR = 1.34). Conclusions: BEM is a sensitive and robust method to improve ctDNA detection accuracy in TS. We demonstrated its utility in improving recurrence prediction in a HNSCC cohort. Given its advantages, we envision that BEM will prove useful as a general strategy for deep sequencing applications requiring precise digital quantification of low frequency alleles in TS. Citation Format: Zhuosheng Gu, Maciej Pacula, Seka Lazare, Noah Earland, Marra S. Francis, Adam Harmon, Megan Long, Aadel A. Chaudhuri, Jose P. Zevallos, Wendy Winckler. Base-error model (BEM) for improved detection of ctDNA in lymph samples of HPV-negative head and neck cancer patients [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B057.

CRISPR-Cas13a-Based Lateral Flow Assay for Detection of Bovine Leukemia Virus

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (EBL), which presents worldwide prevalence. BLV caused substantial economic loss in China around the 1980s; then, it could not be detected for some time, until recently. Due to its latent and chronic characteristics, the efficient and accurate detection of BLV is of utmost significance to the timely implementation of control measures. Therefore, this study harnessed the recombinase-aided amplification (RAA), clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 13a (Cas13a) technology, and lateral flow (LF) strips to develop an efficient method for detection of BLV. In this method, isothermal amplification of the targeted pol gene is performed at 37 °C with a detection threshold of 1 copy/µL, and the procedure is completed in 100 min. This assay demonstrated high selectivity for BLV, as indicated by the absence of a cross-reaction with six common bovine pathogens. Remarkably, 100 blood samples from dairy cows were tested in parallel with a conventional quantitative polymerase chain reaction (qPCR) and this method and the results showed 100% agreement. Furthermore, this method exhibited good repeatability. In conclusion, in this study, we established a sensitive and specific method for BLV detection, which shows promise for application in BLV surveillance.

Abstract B006: Qualitative research study on the use of minimal residual disease as an intermediate endpoint in multiple myeloma clinical trials in Saudi Arabia

Abstract Introduction: The U.S. Food and Drug Administration has recently considered minimal residual disease (MRD) as an acceptable accelerated approval endpoint in multiple myeloma (MM). Meta-analysis studies have shown the clinical benefit of MRD negativity in certain hematological cancers such as MM. Objectives: This qualitative research study, with a unique focus on the Saudi context, aims to assess the opinions and experiences of hematology and oncology specialists and consultants in Saudi Arabia. The study is particularly interested in their views on the use of MRD as an intermediate endpoint in early-phase clinical trials for fast-track drug approval by the Saudi Food and Drug Authority in the context of multiple myeloma. This includes assessing the use of MRD in both newly diagnosed and relapsed/refractory MM. The secondary objective is to gather information about the feasibility and availability of sensitive MRD detection methods in real-world medical practice and clinical trials in Saudi Arabia. Study Design: The study will involve interviewing 30 registered male or female physicians specialized in hematology and oncology in Saudi Arabia. The physicians will be included in the study using purposive sampling methods. The study will collect the physicians’ opinions and experiences about MRD. The interviews will be conducted through a single focus group and several face-to- face interviews or performed online, using ZOOM. Participants should have more than one year of experience post-residency or post-fellowship training. The predetermined set of semi- structured questions will cover topics such as the definition of MRD, its clinical and research significance, MRD detection thresholds, duration of MRD negativity, and its correlation with other clinical endpoints, such as progression-free survival and overall survival. The interviews will be conducted by scientific oncology and hematology evaluation experts at the Saudi Food and Drug Authority, who play a crucial role in this study. The study will consist of 5–10 semi- structured one-to-one interviews and focused group discussions of as few as four participants. Before starting any interview, participants will complete consent forms, including the study’s goals and who will conduct the study. Qualitative data will be prepared and analyzed by an expert in data analysis, ensuring the highest research standards. The results will be presented using descriptive and interpretive methods. Citation Format: Albandari A Alnasser, Tariq H Alqurayshah. Qualitative research study on the use of minimal residual disease as an intermediate endpoint in multiple myeloma clinical trials in Saudi Arabia [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B006.

Enhancing detection of various pancreatic lesions on endoscopic ultrasound through artificial intelligence: a basis for computer-aided detection systems.

Endoscopic ultrasound (EUS) is the most sensitive method for evaluation of pancreatic lesions but is limited by significant operator dependency. Artificial intelligence (AI), in the form of computer-aided detection (CADe) systems, has shown potential in increasing accuracy and bridging operator dependency in several endoscopic domains. However, the complexity of integrating AI into EUS is far more challenging. This aims to develop and test the basis for a CADe system for real-time detection and segmentation of all pancreatic lesions. In this single-center study EUS studies of pancreatic findings were included. Lesions were outlined by two expert (>5years performing EUS) endoscopists, and the two leading types of models were benchmarked. The models' performance was evaluated through per-pixel intersection over union (IoU). A total of 1497 EUS images from 165 patients were evaluated. The dataset included malignancies, neuroendocrine tumors, benign cysts, chronic and acute pancreatitis, normal fatty pancreas, and benign lesions. The best model demonstrated detection and segmentation on the test set with a mean IoU of 0.73, achieving a PPV, NPV, total accuracy, and ROC of 0.82, 0.96, 0.95, and 0.95, respectively. The algorithm is adaptable for real-time processing. We developed and tested deep learning models for real-time detection and segmentation of pancreatic lesions during EUS with promising results. This constitutes the basis for a CADe system for EUS, which could be valuable in future detection and evaluation of pancreatic lesions. Further studies for validation and generalization are underway.

Characterization of variably protease-sensitive prionopathy by capillary electrophoresis.

Variably Protease Sensitive Prionopathy (VPSPr) is a rare human prion disease that, like Creutzfeldt-Jakob disease (CJD), results in the deposition of abnormally folded prion protein aggregates in the brain and is ultimately fatal. Neuropathology and clinical features of VPSPr are heterogeneous. However, the key discriminating feature is the relative sensitivity of the pathological prion protein to proteinase digestion compared to that typically seen in other human prion cases. Three major fragments of 23, 17 and 7kDa are characteristic of the disease following digestion with proteinase K. We recently reported the utility of the highly adaptive and reproducible ProteinSimple™ capillary electrophoresis (CE) system to perform protein separation of PK digested prion protein in CJD. Consequently, we explored capillary-based electrophoresis (CE) technology as a sensitive method to detect and characterize VPSPr in a cohort of 29 cases. The unique 7kDa fragment has high intensity, particularly in cases with the codon 129 VV genotype, but can be missed by regular Western blotting due to the small size. However, this fragment is readily detected by CE in all cases. In addition, the flexibility of CE produced highly reproducible, semi-quantitative data for determining relative proteinase K sensitivity and epitope mapping of representative cases from each codon 129 genotype (VV, MV and MM).

Abstract A053: Liquid biopsy-based detection of triple negative breast cancer using DNA methylation biomarkers

Abstract Triple-negative breast cancer (TNBC) presents significant clinical challenges due to its aggressive phenotype, rapid progression, and limited targeted treatment options. TNBC often mimics benign lesions on ultrasound and metastatic features can be missed in routine mammography screening leading to misdiagnosis and delayed treatment. These limitations led us to investigate whether a blood-based liquid biopsy could provide a non-invasive, sensitive method for early TNBC detection, potentially overcoming the constraints of conventional imaging techniques. To discover biomarkers for TNBC, we performed targeted bisulfite sequencing on a cohort of 46 breast cancer solid tissue biopsy samples, comprising 19 TNBC and 27 non-TNBC cases. We identified 150 differentially methylated regions (mean length 703bp) separating TNBC and non-TNBC samples. Upon linking each region to its nearest gene, we observed several genes previously associated with prognosis and survival (HOXB3, PAX9, SOX9) substantiating the clinical relevance of these biomarkers. Using public TCGA data (369 breast cancer samples), we integrated expression and methylation data and observed directionally consistent changes. For example, HOXB3 showed increased methylation at its associated differential regions and decreased expression in TNBC cases. To ascertain whether these biomarkers could be useful in a liquid biopsy approach, we performed targeted bisulfite- sequencing on cell-free DNA samples derived from prospectively collected patients with breast cancer. All samples had independent tissue-based assessment of ER, PR and HER2 using immunohistochemistry or in situ hybridization. We then built a feed-forward neural network classifier with classes TNBC and non-TNBC that used transfer-learning and the identified biomarkers to learn methylation signatures in the biopsy samples and map them to cell-free DNA. To emulate clinical workflow, where subtyping follows cancer diagnosis and tissue of origin identification, we evaluated cfDNA samples correctly identified as breast cancer using two independent machine learning models trained using 2,393 prospectively collected multi- indication cancer and non-cancer samples (NCT05435066). Subsequent TNBC subtyping of breast cancer-positive cases (N=56) accurately identified 77% (10/13) of TNBC samples and 91% (39/43) of non-TNBC cases, with overall accuracy of 84%. The estimated tumor content range for correctly predicted TNBC samples was 0.5-33% with the three mis-classified samples all showing very low tumor content (0.22%, 0.28%, 0.59%). Non-TNBC cases showed a tumor content range of 0.07-36% for correct and 2.3-14% for misclassified samples. In conclusion, we identified novel methylation biomarkers that distinguish TNBC in the cell-free DNA of patients without needing invasive tissue biopsies. The high sensitivity of our assay at low tumor fractions has the potential to improve outcomes through earlier intervention and may enable earlier screening in high-risk groups, monitoring of minimal residual disease and longitudinal monitoring during treatment. Citation Format: Jocelyn Charlton, Shiva Farashahi, Kade Pettie, Elie Massaad, Josh Hubbell, Feras Hantash, Kieran I Chacko. Liquid biopsy-based detection of triple negative breast cancer using DNA methylation biomarkers [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A053.

Abstract B007: A qualitative research study on hematology and oncology consultants’ experiences and opinions on using minimal residual disease (MRD) as a fast-track approval endpoint in early-phase clinical trials in multiple myeloma in Saudi Arabia

Abstract Introduction: The U.S. Food and Drug Administration recently considered the minimal residual disease (MRD) as an acceptable accelerated approval endpoint in multiple myeloma (MM). The data from the meta-analysis studies established the clinical benefit of MRD negativity in certain hematological cancers such as MM. Objectives: The primary objective of this qualitative research study is to assess hematology and oncology consultants’ opinions and experiences on the adequacy of using minimal residual disease (MRD) as an intermediate endpoint in early- phase clinical trials in multiple myeloma (MM) for fast-track approval of drugs and biological products in the Saudi Food and Drug Authority. That may include using MRD in MM in both settings: newly diagnosed and relapsed/refractory MM. The secondary objective is to gather information about the feasibility and availability of sensitive methods for detecting MRD in the context of real-world medical practice and clinical trials in Saudi Arabia. Study Design: The study design is a qualitative approach to interviewing 30 registered male, or female physicians specialized in hematology and oncology in Saudi Arabia. The interviews will be conducted in two ways: a single focus group and several face-to-face interviews. The participants should have more than 1 year of experience post-fellowship training. The participants will be invited for an interview via email or phone. A predetermined set of semi-structured questions is to be asked in the same order to each participant. The topic of questions will include the definition of MRD, clinical and research significance of MRD, MRD detection thresholds (e.g., 10^-5 vs. 10^-6), duration of MRD negativity at the complete response, correlation with other clinical endpoints such as progression-free survival (PFS) and overall survival (OS). The interviews will be conducted by scientific oncology and hematology evaluation experts at the Saudi Food and Drug Authority who have considerable experience in engaging in personal discussion. This qualitative study has about 5–10 semi-structured one-to-one interviews of hematology and oncology consultants performed at a convenient time for each doctor. Moreover, the discussions in focus groups can be as small as four participants. Qualitative data will be prepared and analyzed by an expert in data analysis. Citation Format: Tariq Hassan Alqurayshah, Albandari Alnasser, Tariq Alqurayshah. A qualitative research study on hematology and oncology consultants’ experiences and opinions on using minimal residual disease (MRD) as a fast-track approval endpoint in early-phase clinical trials in multiple myeloma in Saudi Arabia [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B007.

Detection of Ochratoxin A in Maize and Its Potential Impact on Avian Pathology in Romanian Farms

Ochratoxin A (OTA) is a nephrotoxic mycotoxin that commonly contaminates maize, posing significant health risks to both poultry and humans. In this study, a rapid and sensitive method utilizing ultra-performance liquid chromatography coupled with fluorescence detection (UPLC-FLD) was developed for the quantification of OTA levels in maize. The method utilizes immunoaffinity column purification for improved specificity. Accuracy and precision were validated in line with European Union Reference Laboratory (EURL-MP) guidelines, meeting regulatory standards for linearity, trueness, detection and quantification limits, precision, and uncertainty, as per European Commission Regulation (EC) No. 401/2006 and its amendments. The method demonstrated an average recovery rate of 116.78% for maize, with RSDwR values (within-laboratory reproducibility) of 12.72%. Furthermore, OTA occurrence and its possible effects were investigated in several farms in South Romania, where necropsy and histopathological analyses of poultry revealed severe kidney damage, including renal tubular degeneration.

Bright middle cerebellar peduncle sign in multiple system atrophy with predominant cerebellar ataxia is more apparent in double-inversion recovery imaging than in conventional imaging.

Multiple system atrophy (MSA) is a neurodegenerative disorder that presents as parkinsonism, cerebellar ataxia, and autonomic dysfunction. Magnetic resonance imaging (MRI) findings of MSA are reported to be the atrophy of the putamen/pons/cerebellum, hot cross bun sign, and bright middle cerebellar peduncle (MCP) sign. Here, we assessed the sensitivity of detecting the bright MCP sign in patients with MSA cerebellar variant (MSA-C) using a double inversion recovery (DIR) procedure, comparing it to the sensitivity of detection by T2-weighted image (T2WI) and fluid-attenuated inversion recovery (FLAIR) sequences on conventional MRI. We evaluated 6 MSA-C patients and 6 control patients (multiple sclerosis, neuromyelitis optica, and spinocerebellar atrophy). Characteristics of all the patients were collected, and MRI was analyzed. Two neurologists independently evaluated the visualization of the bright MCP sign using a 4-point visual grade from Grade 0 to Grade 3. Differences in grade between DIR and T2WI or FLAIR were statistically analyzed. Also, as a quantitative analysis, the signal intensity of the MCP lesion was compared with that of the ipsilateral thalamus, and the MCP/thalamus ratio was evaluated. As a result, DIR more sensitively showed the bright MCP signs of MSA-C patients than T2WI or FLAIR. Also, the bright MCP sign deteriorated and expanded over time in the cases we followed with MRI. We also evaluated hot cross bun sign in the pons, but the hot cross bun sign in MSA-C patients was not significantly different between the DIR and conventional MRI sequences. The DIR procedure can be a more sensitive method for detecting the involvement of MCP lesions in MSA-C.

Causal associations of ischemic stroke, metabolic factors, and related medications with epilepsy: a Mendelian randomization study

BackgroundEarlier researches have demonstrated that ischemic stroke, metabolic factors, and associated medications may influence the risk of epilepsy. Nevertheless, the causality between these elements and epilepsy remains inconclusive. This study aims to examine whether ischemic stroke, metabolic factors, and related medications affect the overall risk of epilepsy.MethodsWe used single nucleotide polymorphisms associated with ischemic stroke, hypothyroidism, hypertension, blood glucose levels, high cholesterol, serum 25-Hydroxyvitamin D levels, testosterone, HMG CoA reductase inhibitors, and beta-blocking agents as instrumental variables in a Mendelian randomization technique to investigate causality with epilepsy. Multiple sensitivity methods were performed to evaluate pleiotropy and heterogeneity.ResultsThe IVW analysis revealed positive associations between ischemic stroke (OR = 1.29; p = 0.020), hypothyroidism (OR = 1.05; p = 0.048), high blood pressure (OR = 1.10; p = 0.028), high cholesterol (OR = 1.10; p = 0.024), HMG CoA reductase inhibitors (OR = 1.19; p = 0.003), beta-blocking agents (OR = 1.20; p = 0.006), and the risk of epilepsy. Conversely, blood glucose levels (OR = 0.79; p = 0.009), serum 25-Hydroxyvitamin D levels (OR = 0.75; p = 0.020), and testosterone (OR = 0.62; p = 0.019) exhibited negative associations with the risk of epilepsy. Sensitivity analyses confirmed the robustness of these findings (p > 0.05).ConclusionOur research suggests that ischemic stroke, hypothyroidism, high blood pressure, high cholesterol, HMG CoA reductase inhibitors, and beta-blockers may increase the risk of epilepsy, whereas serum 25-Hydroxyvitamin D levels and blood glucose levels may reduce the risk.

The efficacy of high pressure liquid chromatography (HPLC) in detecting congenital glycosylation disorders (CDG)

Abstract Objectives Congenital disorders of glycosylation (CDG) are a family of rare inherited metabolic disorders. This study aimed to examine the carbohydrate-deficient transferrin (CDT) screening results of 1,328 patients with suspected CDG by using transferrin- high pressure liquid chromatography (Tf- HPLC) method and to evaluate the performance of the method as a reference diagnostic tool. Methods Relative CDT levels (CDT concentrations expressed as percent of total transferrin) were determined in serum samples by HPLC. The method sensitivity, specificity and positive predictive value (PPV) were further calculated. Results Abnormal transferrin isoform profile consistent with CDG Type-I and CDG Type-II were determined in 50 cases; in 44 cases asiolo-Tf (7.63 ± 5.44 %) and disialo-Tf (36.29 ± 9.04 %), in six cases monosialo-Tf (3.95 ± 0.95 %) and trisialo-Tf (25.05 ± 4.46 %) were determined and decreased tetrasialo-Tf (49.75 ± 11.59 %) was identified in all cases. Two cases having abnormal CDT pattern were molecularly diagnosed with hereditary fructose intolerance and galactosemia and 11 cases diagnosed with CDG based on clinical and molecular analysis showed a normal pattern. The sensitivity, specificity and positive predictive values of Tf-HPLC method were 81.96 %, 99% and 96 %, respectively. Conclusions Tf-HPLC is a useful, highly sensitive, cost-advantageous and reliable method for the detection and preliminary diagnosis of CDG for laboratories working with large sample series.