Clinical Molecular Diagnostics Research Articles

Advancements in mass spectrometry-based proteomics: anew era in pathology research and diagnostics.

Mass spectrometry (MS)-based proteomics is rapidly transforming pathology research and diagnostics by enabling comprehensive studies of protein expression and post-translational modifications (PTMs). This article discusses recent advancements in MS-based proteomics, focusing on emerging technologies in sample preparation, MS instrumentation, and data analysis. These developments are scrutinized for their applications in clinical cohort studies and molecular pathology diagnostics. The article reviews innovations in automated sample preparation, chromatography systems, advanced MS technologies, and proteomic data analysis in the context of pathology. Specific applications such as liquid biopsy, spike-in heavy peptide panels, immunopeptidomics, and PTM screening are highlighted alongside opportunities for data integration. Recent technological improvements have significantly increased the throughput, precision, and scope of proteomic studies, enabling the analysis of large clinical cohorts and small specimens with unprecedented sensitivity. Advanced MS techniques have broadened applications, opening new avenues for discovery and diagnosis of marker proteins and therapeutic targets. Advancements in MS-based proteomics have created new opportunities in clinical research and diagnostics. By facilitating more comprehensive and integrated analyses of proteomes, these technologies are set to play apivotal role in the future of personalized medicine and pathology research.

Evaluating Use of Generative Artificial Intelligence in Clinical Pathology Practice: Opportunities and the Way Forward.

Generative artificial intelligence (GAI) technologies are likely to dramatically impact health care workflows in clinical pathology (CP). Applications in CP include education, data mining, decision support, result summaries, and patient trend assessments. To review use cases of GAI in CP, with a particular focus on large language models. Specific examples are provided for the applications of GAI in the subspecialties of clinical chemistry, microbiology, hematopathology, and molecular diagnostics. Additionally, the review addresses potential pitfalls of GAI paradigms. Current literature on GAI in health care was reviewed broadly. The use case scenarios for each CP subspecialty review common data sources generated in each subspecialty. The potential for utilization of CP data in the GAI context was subsequently assessed, focusing on issues such as future reporting paradigms, impact on quality metrics, and potential for translational research activities. GAI is a powerful tool with the potential to revolutionize health care for patients and practitioners alike. However, GAI must be implemented with much caution considering various shortcomings of the technology such as biases, hallucinations, practical challenges of implementing GAI in existing CP workflows, and end-user acceptance. Human-in-the-loop models of GAI implementation have the potential to revolutionize CP by delivering deeper, meaningful insights into patient outcomes both at an individual and population level.

B-225 Bridging the Gap Between Clinical Microbiology and Molecular Diagnostics: Correlation of PCR Cycle Threshold Values for Establishing Semi-Quantitative CFU/mL Ranges of Bacterial Targets

Abstract Background Molecular diagnostics (MolDx) has surpassed culture in the clinical microbiology laboratory. Wong (2023) states PCR is more sensitive than urine culture in detecting polymicrobial infections (para. 8), marking an advantage in MolDX for urinary tract infections. This advancement poses a challenge for clinicians in treatment decision-making. To address requests for numerical MolDx result ranges, a validation accessed semi-quantitative Colony Forming Units per milliliter (CFU/mL) through the assessment of PCR cycle threshold (CT) values. Methods Bacterial targets of UTI and STI PCR panels were inoculated in nutrient broth (Hardy diagnostics cat#K43) and incubated overnight in a shaking incubator at 35±2°C. The density of the cultures was measured using the OD600 function of a NanoDrop One/One after 18-24 hour incubation. The density of stock cultures was adjusted to 106 CFU/mL. Serial dilutions of stock were made in 1:10 steps covering the range of 106 to 100 CFU/mL. The stock and dilutions were extracted, and PCR was performed in a minimum of 2 replicates of each sample for the UTI and STI PCR panels. Mean CT values, standard deviations and coefficients of variation were calculated for each sample. The linearity of CT values within each organism’s stock and dilution samples were assessed by evaluating the CT differences between each dilution step. Corresponding CFU/mL concentrations were tabulated against each mean CT value. Results The average CT values for reportable CFU/mL ranges were established for each stock and dilution. Mean CT values for each CFU/mL breakdown across all organisms were also calculated, along with standard deviations, to investigate universal CT-CFU/mL correlations. A final interpretation table (Table 1) was constructed according to the universal range calculations. Conclusions The study confirmed correlation between CT values and CFU/mL ranges. Further data analysis and comparison with other laboratories’ results will enhance accuracy and precision of reportable CFU/mL ranges.

Decoding pediatric spinal tumors: a single-center retrospective case series on etiology, presentation, therapeutic strategies, and outcomes

IntroductionSpinal tumors (ST) often result in dire prognosis, carrying risks such as permanent paralysis, sensory loss, and sphincter dysfunction. Data on their incidence and etiology in pediatric populations are markedly scant. Our study investigates the etiology, clinical manifestation, treatment, and outcomes of pediatric ST.MethodsWe conducted a retrospective review of our institutional pediatric oncology and neurosurgery database, examining 14 patients under 18 years admitted with ST due to oncological diseases since 2005. We analyzed the clinical presentations, evaluations, molecular diagnostics and treatments for these patients.ResultsThe study spanned 15 years and included 14 pediatric patients, each diagnosed with distinct spinal tumor entity. The mean patient age was approximately 19.6 ± 10.1 months. Severe axial pain along the vertebral column was observed in 13 patients, while acute neurological deterioration manifested in 7 patients. As a first-line intervention, 13 patients underwent decompressive surgery through laminectomy and tumor resection, and only one patient received chemotherapy solely. Before surgery, seven patients were unable to walk; post-surgery, six of them regained their ability to ambulate. The diagnosis encompassed a range of neoplasms: two instances of Ewing sarcoma, 3 instances of teratoma, one case presenting an atypical teratoid Rhabdoid tumor, two instances each of low-grade astrocytoma and neuroblastoma, and single instances of ependymoma, meningioma, rhabdomyosarcoma, and embryonal tumors with multilayered rosettes (ETMRs). Three patients succumbed two years after initiating therapy.ConclusionDespite their rarity, intraspinal tumors in pediatric patients pose substantial therapeutic challenges. The intertwined complexities of the disease entity and the patient’s neurological status demand swift initiation of an individualized therapeutic strategy. This crucial step helps optimize outcomes for this patient cohort, who frequently grapple with debilitating health conditions. Inclusion of these patients within a registry is mandatory to optimize treatment outcomes due to their rarity in pediatric population.

Basics in diagnostics and therapy of allergic diseases for ENT consultations

Allergies play a pivotal role in the daily practice of ENT specialists. Allergic symptoms induced by inhalant allergens are widespread in the population and can manifest through a wide range of symptoms, including rhinorrhea, sneezing, conjunctival redness, cough and dyspnea. Inconsistent diagnosis and treatment of allergic conditions can lead to reduced quality of life, decreased work performance, and socioeconomically significant secondary diseases. In addition to the medical history, the skin prick test and serological IgE diagnostics are the most important diagnostic procedure for detecting type-I allergies. To clarify clinical relevance, molecular diagnostics and nasal provocation testing may be employed. The key to effective treatment lies in a comprehensive allergological diagnosis coupled with a detailed patient history. General treatment recommendations such as allergen avoidance and nasal irrigation should complement pharmacological therapy. In the treatment of allergic rhinitis topical steroids are first line treatment options. The primary goal of treatment is symptom control, and if control is insufficient, causal therapy through specific allergen immunotherapy is recommended. Challenges in the ENT clinic involve selecting the necessary diagnostics and appropriate, effective treatments. Hence, using diagnostic and treatment algorithms, as well as standardized patient history questionnaires, can serve as invaluable tools in daily patient interactions, especially considering limited time availability.

Target recycle initiated entropy driven assembly strategy for sensitive, enzyme-free, and portable miRNA detection

MicroRNA (miRNA) is a pivotal biomarker in the diagnosis of various cancers, including bladder cancer (BCa). Despite their significance, the low abundance of miRNA presents a substantial challenge for sensitive and reliable detection. We introduce an innovative, highly sensitive assay for miRNA expression quantification that is both enzyme-free and portable. This method leverages the synergy of target recycling and entropy-driven assembly (EDA) for enhanced sensitivity and specificity. The proposed method possesses several advantages, including i) dual signal amplification through target recycling and EDA, which significantly boosts sensitivity with a lower limit of detection of 2.54 fM; ii) elimination of enzyme requirements, resulting in a cost-effective and stable signal amplification process; and iii) utilization of a personal glucose meter (PGM) for signal recording, rendering the method portable and adaptable to diverse settings. In summary, this PGM-based approach holds promising potential for clinical molecular diagnostics, offering a practical and efficient solution for miRNA analysis in cancer detection.

Abstract 1771: NYU Langone Genome PACT - Genome Profiling of Actionable Cancer Targets (LG-PACT) for clinical patient molecular diagnostics and treatment

Abstract Next-generation sequencing (NGS) for the detection of somatic variants has become the tool of choice in a variety of molecular oncology fields and in the clinic. Its use ranges from sequencing entire tumor genomes and transcriptomes to targeted clinical diagnostic gene panels. The NYU Langone Genome PACT assay is a qualitative in vitro diagnostic test that uses targeted next generation sequencing of formalin-fixed paraffin-embedded (FFPE) tumor tissue matched with normal specimens from patients to detect gene alterations in a 607-gene panel. Indications for testing are cancer (solid tumors or hematological malignancies) where a mutational profile from multiple genes would be informative for disease stratification, prognosis, or treatment options including targeted therapies and eligibility for clinical trials. The test is intended to provide information on somatic mutations including point mutations, copy number aberrations, and small insertions/deletions (indels) for diagnostic and treatment decisions. LG-PACT is a United States Food and Drug Administration (FDA) approved diagnostic test. The clinical interpretation of sequencing data of molecular tumor markers from NGS encompasses automated variant calling tools with human interpretation. The final mostly manual review of data is intensive, involving highly trained scientists, encompassing literature review, interpretation and tier classification by pathologists, who then provide a complete molecular diagnostic report to the treating oncologists. Since January 2022 to present (October 2023) we have provided clinical genomic reports for 1029 oncological cases from 124 different cancers and their subtypes, including Brain (489 cases incl. meningioma, glioma and glioblastoma), Gastrointestinal (123), Lung (114), among others. We first present the technical challenges of validating an NGS oncological diagnostic targeted assay for appropriate clinical grade accuracy and sensitivity acceptable for patient care. We show how copy number alterations provide a more comprehensive description of the tumors genomic profile. We then outline the actionability of targeted panel sequencing for our current patient cohort. Where analysis of variant detection has led to 47% (490) of our clinical tumor samples containing known tier 1 therapeutic variants. We conclude with presenting case studies that identify both the clinical utility and informatic challenges of variant calling specific to gene panel sequencing e.g., i) the capture of potential targetable rare and novel indels and multivariant mutations in exons 19 and 20 of EGFR, and ii) a unique KIT tandem duplication event in a gastrointestinal stromal tumor (GIST). We demonstrate the value in precision oncology for multiple cancer types and how the capture of unique variants can provide better targeted treatment options to cancer patients. Citation Format: Varshini Vasudevaraja, Yiying Yang, Jonathan Serrano, Kazimierz Wrzeszczynski, Matija Snuderl. NYU Langone Genome PACT - Genome Profiling of Actionable Cancer Targets (LG-PACT) for clinical patient molecular diagnostics and treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1771.

Diagnostic challenges in cutaneous leishmaniasis due to atypical Leishmania infantum: pathologists' insights from re-emergence zones.

Leishmaniasis, a parasitic infection affecting both humans and animals, is increasingly spreading across Mediterranean and European regions, largely driven by human migration and environmental changes. In countries like Türkiye and across Europe, which have seen large influxes of migrants, the incidence of cutaneous leishmaniasis (CL) is rising, with cases now appearing in cities where the disease was previously undocumented. In these previously non-endemic areas, physicians unfamiliar with the characteristic lesions may misdiagnose CL, particularly in cases with only cutaneous manifestations. This study aims to evaluate the impact of re-emerging CL on the routine diagnostic practices of pathologists in Türkiye, by retrospectively reviewing cases. We conducted a retrospective analysis of CL cases diagnosed between 2013 and 2022 at a single pathology center in Türkiye, covering multiple provinces. Twelve cases of CL were identified and analyzed based on clinical presentation, pre-diagnosis, histopathological findings, and molecular diagnostics. DNA extraction and PCR were performed on paraffin-embedded tissue samples to identify the Leishmania species involved. Out of the twelve CL cases reviewed, seven exhibited morphological findings strongly suggestive of CL (MFSS of CL), warranting further microbiological evaluation. All patients presented with non-healing skin lesions characterized by central ulceration, crater-like formations, or papulonodular lesions. Notably, CL was included in the clinical pre-diagnosis in only 58.3% of cases, while it was not considered in the remaining 41.7% of cases. Clinicians initially pre-diagnosed skin tumors in six cases (50%), four of which led to wide surgical excision. Histopathological examination in all cases revealed chronic or mixed (acute/chronic) inflammation, predominantly rich in histiocytes. To further investigate the role of Leishmania species in the pre-diagnosis, DNA extraction and PCR were performed on paraffin-embedded tissue samples, identifying L. infantum as the causative agent in 10 cases and L. major in two cases. Notably, L. infantum was the causative agent in all five cases initially misdiagnosed as skin tumors, which were also associated with a granulomatous type of chronic inflammation.

CRISPR/Cas13a catalyzed self-assembly of quantum dot-DNA hydrogel for microRNA assay

Taking the advantages of outstanding precision in target recognition and trans-cleavage ability, the RNA-guided CRISPR-Cas systems have shown great promise in cancer diagnostics. Here, we developed a novel detection system based on CRISPR-Cas-catalyzed formation of quantum dot-DNA (QD-DNA) hydrogel for sensitive miRNA assay. After target miRNA recognition and Cas-mediated cleavage of the uracil ribonucleotide-embedded hairpin DNA (rU-HD), the cleaved rU-HD released primer DNA, which triggered toehold-mediated strand displacement (TMSD) amplification to form trefoil DNA quenchers. The trefoil DNA quenchers hybridized with DNA functionalized quantum dots (DNA-QDs) to construct self-assembled QD-DNA hydrogel and the fluorescence of the QDs could be efficiently quenched by the modified black hole quencher at the 3′ terminal of the trefoil DNA quenchers. This assay, termed CRISPR-Cas-catalyzed TMSD based QD-DNA hydrogel (Cas-TMSD-QDH), was applied for the sensitively detection of miR-17 and the limit of detection was as low as 182aM. The Cas-TMSD-QDH assay showed an accurate detection of miR-17 levels in different cell lines and the detection accuracy is confirmed by qRT-PCR. Besides, the assay was able to assess miR-17 levels in serum sample, revealing great potential for miRNAs assay in clinical molecular diagnostics.

Target Recognition Initiated Self-Assembly-Based Signal Amplification Strategy for Sensitive and Colorimetric Staphylococcus aureus Detection and Diagnosis of Skin Infection.

Staphylococcus aureus (S. aureus), as a Gram-positive bacterium, is commonly encountered in various infectious diseases, such as acute skin and soft tissue infections. Despite that many efforts have been made, sensitive and reliable quantitative determination of S. aureus remains a huge challenge. Here, we depict a novel colorimetric approach for sensitive and accurate detection by combining allosteric probe-based target recognition and chain extension-based dual signal recycling. The single-strand DNA (ssDNA) products generated by the chain extension process lead to the liberation of G-quadruplex sequences, which can fold into active DNAzyme under the assistance of hemin. The active DNAzyme can work as peroxidase mimics to catalyze the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS2-)-H2O2 system, causing the color change of the system. Eventually, the method exhibits a wide detection range from 103cfu/mL to 106cfu/mL. The limit of detection of the approach was determined 232cfu/mL. Considering the robust capability of the approach in S. aureus detection, we believe that it will be a potential alternative tool for biomedical research and clinical molecular diagnostics.

DNA tetrahedron-based CRISPR bioassay for treble-self-amplified and multiplex HPV-DNA detection with elemental tagging.

Sensitive quantification of multiple analytes of interest is of great significance for clinical diagnosis. CRISPR Cas platforms offer a strategy for improving the specificity, sensitivity, and speed of nucleic acid-based diagnostics, while their multiplex analysis capability is still limited and challenging. Herein, we develop a novel DNA Tetrahedron (DTN)-supported biosensor based on the spatially separated CRISPR Cas self-amplification strategy and multiple-metal-nanoparticle tagging coupled with inductively coupled plasma mass spectrometry (ICP-MS) detection to improve the sensitivity and feasibility of the platform for multiplex detection of HPV-DNA (HPV-16, HPV-18 and HPV-52). Given target DNA induces robust trans-cleavage activity of the Cas12a/crRNA duplex, and the surrounding corresponding single-stranded DNA (ssDNA) linker are cleaved into short fragments that are unable to bond metal-nanoparticle probes (197Au, 107Ag, 195Pt) onto DTN modified magnetic beads probe (MBs-DTN), resulting in obvious ICP-MS signal change. Of note, compared with ssDNA functionalized MBs, a higher Signal-to-Noise Ratio was obtained by using MBs-DTN in our system, further amplifying the signal by regulating probes on the surface of MBs. As expected, the HPV-DNA could be detected with detection limits as low as 218fM and be multiplexed assayed at one test with high accuracy and specificity by this proposed strategy. Furthermore, we demonstrated that the HPV-DNA in cervical swab samples could be detected, showing high consistency with DNA sequencing results. We believe that this work provides a promising option in designing CRISPR based multiplex detection system for high sensitivity, good specificity, and clinical molecular diagnostics.

Copy number variation (CNV) calling of MET, MYC, and ERBB2 using PiVAT bioinformatic platform.

e15145 Background: CNV in tumor-associated genes such as MET, MYC and ERBB2 amplification can lead to cancer progression and poor survival in multiple cancers, and is associated with treatment regimen decision. Whole genome sequencing (WGS) and comprehensive genomic profiling (CGP) panels covering hundreds of genes are currently used to detect CNV in hospitals and CLIA-accredited laboratories. However, cost and complex workflow of WGS/CGP restrict their application in clinical molecular diagnostics. CGP panel covering dozens of genes based on targeted amplicon sequencing (TAS) method is preferred, but it is not ideal to detect CNV accurately due to unique methodology. Here we established a CNV calling toolkit in PiVAT bioinformatic platform to solve CNV calling problems in small-size TAS panel. Methods: 46 CNV positive (CNV+) and 14 CNV negative (CNV-) samples were sequenced using MGISEQ-2000 with a paired end, 2x100 read length protocol and adapter sequences were trimmed from 3’ ends of each read. PiVAT’s CNV calling method is based on double coverage normalization, including one per-sample normalization and one per-amplicon normalization. CNV- samples were used as normalization references. MET, MYC and ERBB2 copy number was investigated to determine sensitivity, specificity, precision, and accuracy of the overall test. Copy number deletion is defined as ratio < 0.8 and amplification is defined as ratio > 1.2. PiVAT CNV output calls were compared against excepted copy number to calculate and plot the concordance. CNVkit and Control-FREEC, 2 other CNV calling tools, were chosen as comparators to compare ERBB2, MET and MYC copy number levels with PiVAT’s CNV caller. Results: Sequencing results from all 46 CNV+ samples showed high coverage uniformity, with > 90% of sites having base coverage depth > 20% of mean coverage for all samples. Average mapping rate and on-target rate of sequencing run, analyzed by PiVAT, were 98.98±0.41% and 98.39±0.45%. Results from PiVAT showed a sensitivity of 97.83% and a specificity of 100% for MET, MYC, ERBB2 amplifications. PiVAT estimated copy number more accurately compared with CNVkit and Control-FREEC. PiVAT’s R2, measuring degree of difference from expected copy number, was greater than CNVkit and Control-FREEC for MET, MYC and ERBB2, with values at 0.78, 0.69 and 0.96, respectively. In contrast, CNVkit and Control-FREEC were on average 77.38% and 164.04% worse. For CNVkit and Control-FREEC, many of MET, MYC and ERBB2 CNV calls were seen at a much lower magnitude than expected. Conclusions: Our studies have shown that PiVAT is a reliable tool for calling CNVs. PiVAT’s sensitivity and accuracy were calculated to be > 97%. And PiVAT outperformed other CNV calling tools, CNVkit and Control-FREEC. This demonstrates that PiVAT’s CNV caller can be used to provide CNV results from TAS panel, and guide relevant cancer diagnosis and clinical decision more accurately.

Overview of Molecular Detection Technologies for MET in Lung Cancer.

MET tyrosine kinase receptor pathway activation has become an important actionable target in solid tumors. Aberrations in the MET proto-oncogene, including MET overexpression, the activation of MET mutations, MET mutations that lead to MET exon 14 skipping, MET gene amplifications, and MET fusions, are known to be primary and secondary oncogenic drivers in cancer; these aberrations have evolved as predictive biomarkers in clinical diagnostics. Thus, the detection of all known MET aberrations in daily clinical care is essential. In this review, current molecular technologies for the detection of the different MET aberrations are highlighted, including the benefits and drawbacks. In the future, another focus will be on the standardization of detection technologies for the delivery of reliable, quick, and affordable tests in clinical molecular diagnostics.

Abstract 2115: Zero-waste molecular diagnostics from biopsy needle wash water

Abstract Background: Over the past decade, the WHO classification of brain tumors has increasingly integrated molecular diagnostics into official classification criteria. However, biopsy tissue is precious due to high morbidity associated with repeat biopsies, and usually earmarked for histology, leaving little or no tissue for clinical molecular diagnostics. We have identified that the fluid used to wash biopsy needles after cores contains excess tumor DNA and cells that can be diagnostically useful. Additional research of tumor DNA and tumor tissue recovered from biopsy needle washes provides an opportunity for improvement in the diagnosis and treatment for brain tumor patients, while utilizing material that is otherwise thrown away. Methods: In two cases, surgeons were instructed to save 5-15ml of fluid used to wash biopsy needles. Isothermal targeted amplification of H3.3 and H3.1 histone genes was performed on raw wash fluid. Resulting amplicons were sequenced using an Oxford Nanopore MinION. DNA extracted from wash fluid was subjected to NGS sequencing via the Illumina TruSight Oncology 500 panel and compared to a CLIA certified NGS sequencing results from clinically indicated biopsy tissue. Results: For case 1, 5ul of raw wash fluid was subjected to rapid Loop-mediated Isothermal Amplification (LAMP) targeting the H3.1 and H3.3 K27M histone mutations and immediately sequenced using a MinION sequencer via rapid library preparation. Sequencing revealed a H3.3 K27M histone mutation present in wash fluid at 12% variant allele fraction (VAF). The variant call (99.99% CI) was available 1hr5mins after acquisition of material. For case 2, 5ml of wash fluid was processed using a cell-free DNA extraction kit resulting in ~250ng of recovered DNA. A LAMP assay targeting the H3.3 K27M mutation was performed on extracted DNA from wash fluid. Sequencing revealed an H3.3 K27M histone mutation present at 55% VAF, which was later corroborated using digital droplet PCR. Clinically indicated tissue from both biopsies was submitted for cancer panel sequencing in a CLIA certified setting. DNA extracted from wash fluid from both cases was subjected to Illumina TruSight Oncology 500 panel sequencing. In both cases, the panel was able to corroborate all SNV mutations reported by clinical sequencing that were also covered by the panel. Accrual of needle wash specimens is ongoing, with multiple monthly procedures. Conclusions: Large amounts of diagnostically useful material is present in biopsy needle wash fluid, which is usually discarded. Isothermal assays coupled with MinION sequencing can rapidly identify clinically relevant point mutations directly from wash fluid (e.g. IDH1), and enough DNA was recovered from wash fluid from both case-studies to submit for targeted cancer panel sequencing. These results suggest biopsy needle wash fluid should be considered a first-class diagnostic resource in any cancer. Citation Format: Jack Wadden, Vishal John, Seongbae Kong, Kait Verbal, Amy K. Bruzek, Wajd Al-Holou, Jason A. Heth, Hugh Garton, Carl Koschmann. Zero-waste molecular diagnostics from biopsy needle wash water [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2115.

Engineering m6A demethylation-activated DNAzyme for visually and sensitively sensing fat mass and obesity-associated protein

Fat mass and obesity-associated protein (FTO) regulating the N6-methyladenine (m6A, the most pervasive epigenetic modification) levels within the nucleus has been identified as a potential biomarker for cancer diagnosis and prognosis. However, current methods for FTO detection are complicated or/and not sensitive enough for practical application. Herein, we propose a colorimetric biosensor for detecting FTO based on a delicate design of m6A demethylation-activated DNAzyme. Specifically, an m6A-blocked DNAzyme is constructed as a switch of the biosensor that can be turned on by target FTO. The decreased thermal stability resulting from substrate cleavage leads to a DNAzyme recycling to produce multiple primers. Then the rolling circle amplification (RCA) reactions can be initiated to generate G-quadruplex-DNAzymes catalyzing 2,2-azino-bis-(3-ethylben-zthiazoline-6-sulfonic acid (ABTS) oxidation which can be readily observed by the naked eye. Quantitative detection can also be achieved with a limit of detection (LOD) down to 69.9 fM, exhibiting higher sensitivity than previous reports. Therefore, this biosensor opens a simple and sensitive way to achieve visual assay of FTO via triple signal amplification. In addition, our biosensor has been successfully applied to FTO detection in clinical samples, which shows great potential in clinical molecular diagnostics.

A color-based FHGC approach facilities DNA-based clinical molecular diagnostics

A color-based FHGC approach facilities DNA-based clinical molecular diagnostics

Development of a Biosensor for fast point-of-care Blood Analysis of Troponin.

We present the development of novel tetrapolar EIS biosensor for the detect of troponin. Troponin has considerable diagnostic power and provide invaluable prognostic information for risk stratification. of acute coronary syndromes. Clinical Relevance- A feasibility study was undertaken to assess the diagnostic performance of serial cardiac troponin measurements which is excellent as these structural proteins are unique to the heart and thus sensitive and specific of damage to the myocardium. clinical molecular diagnostics and home healthcare. Troponin's biosensors would provide point-of-care and rapid decision making for the early detection of CS. Clinically relevant window of cTnI testing, concentrations from 10pM to 0.1μM were achieved.

Combining CRISPR/Cas12a with isothermal exponential amplification as an ultrasensitive sensing platform for microRNA detection

MicroRNA (miRNA) is considered as a potential biomarker in the diagnosis of cancer. Thus, a new diagnostic technique with high sensitivity and selectivity is crucial for miRNA detection in clinical testing. Herein, we presented a sensing platform based on CRISPR/Cas12a and isothermal exponential amplification reaction (EXPAR) to realize ultrasensitive analysis of miRNA. MiRNA-27a (miR-27a) was chosen as a model target. In this sensing platform, a miR-27a-triggered cascade EXPAR process was introduced to achieve a mass of activators. The resultant activators could hybrid specifically with crRNA of CRISPR/Cas12a system, triggering the multiple-turnover trans-cleavage activity of Cas12a for achieving signal amplification. The sensing platform rendered a wide detection (ranging from 100 aM to 10 nM) and a low limit of detection (90 aM). In particular, this strategy achieved ultrasensitive detection of the other microRNA biomarkers such as let-7a and miR-141 by the flexible design of the region of template, which demonstrated the universal detection ability. Furthermore, an excellent selectivity feature was obtained by the discrimination of microRNA family members and base mismatch analysis. The proposed sensing platform also was able to assess miR-27a levels in breast cancer cell and serum sample, revealing a promising application in clinical molecular diagnostics.

Tissue-specific genotype-phenotype correlations among USH2A-related disorders in the RUSH2A study.

We assessed genotype-phenotype correlations among the visual, auditory, and olfactory phenotypes of 127 participants with Usher syndrome (USH2) (n =80) or nonsyndromic autosomal recessive retinitis pigmentosa (ARRP) (n = 47) due to USH2A variants, using clinical data and molecular diagnostics from the Rate of Progression in USH2A Related Retinal Degeneration (RUSH2A) study. USH2A truncating alleles were associated with USH2 and had a dose-dependent effect on hearing loss severity with no effect on visual loss severity within the USH2 subgroup. A group of missense alleles in an interfibronectin domain appeared to be hypomorphic in ARRP. These alleles were associated with later age of onset, larger visual field area, better sensitivity thresholds, and better electroretinographic responses. No effect of genotype on the severity of olfactory deficits was observed. This study unveils a unique, tissue-specific USH2A allelic hierarchy with important prognostic implications for patient counseling and treatment trial endpoints. These findings may inform clinical care or research approaches in others with allelic disorders or pleiotropic phenotypes.

Next-generation sequencing of cerebrospinal fluid for clinical molecular diagnostics in pediatric, adolescent and young adult brain tumor patients.

Safe sampling of central nervous system tumor tissue for diagnostic purposes may be difficult if not impossible, especially in pediatric patients, and an unmet need exists to develop less invasive diagnostic tests. We report our clinical experience with minimally invasive molecular diagnostics using a clinically validated assay for sequencing of cerebrospinal fluid (CSF) cell-free DNA (cfDNA). All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. We analyzed 64 CSF samples from 45 pediatric, adolescent and young adult (AYA) patients (pediatric = 25; AYA = 20) with primary and recurrent brain tumors across 12 histopathological subtypes including high-grade glioma (n = 10), medulloblastoma (n = 10), pineoblastoma (n = 5), low-grade glioma (n = 4), diffuse leptomeningeal glioneuronal tumor (DLGNT) (n = 4), retinoblastoma (n = 4), ependymoma (n = 3), and other (n = 5). Somatic alterations were detected in 30/64 samples (46.9%) and in at least one sample per unique patient in 21/45 patients (46.6%). CSF cfDNA positivity was strongly associated with the presence of disseminated disease at the time of collection (81.5% of samples from patients with disseminated disease were positive). No association was seen between CSF cfDNA positivity and the timing of CSF collection during the patient's disease course. We identified three general categories where CSF cfDNA testing provided additional relevant diagnostic, prognostic, and/or therapeutic information, impacting clinical assessment and decision making: (1) diagnosis and/or identification of actionable alterations; (2) monitor response to therapy; and (3) tracking tumor evolution. Our findings support broader implementation of clinical CSF cfDNA testing in this population to improve care.