Molecular Diagnosis & Therapy最新文献

Leishmaniasis remains a significant public health challenge, particularly in endemic regions with limited resources. Traditional diagnostic methods, including microscopy, culture, and serology, though widely utilized, often suffer from limitations such as variable  sensitivity, time delays, and the need for specialized infrastructure. Some of these limitations have been addressed with the emergence of molecular diagnostic techniques. Quantitative PCR (q-PCR), loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA) assays have improved  the diagnostic sensitivity and specificity, enabling species identification and detection of asymptomatic infections. Further, nanodiagnostics and portable sequencing technologies such as the MinION™, along with lab-on-chip platforms, are revolutionizing the diagnostic landscape of leishmaniasis by offering point-of-care (POC) options for remote settings and field-based diagnosis. This review provides an in-depth analysis of these cutting-edge advances, discusses their application in resource-constrained settings, and evaluates their potential to reshape the future of leishmaniasis diagnosis and management.

Introduction: Anorectal melanoma is a rare neoplasm with an aggressive behavior and poor prognosis. Recently, recurrent gene mutations related to anorectal melanoma have been identified in a small series of cases, and this holds promise for targeted therapies, analogous to cutaneous melanoma. The purpose of this study was to analyze testing rates and prevalence of mutations in anorectal melanoma in the Dutch population.

Methods: The Netherlands Cancer Registry and the Dutch Nationwide Pathology Databank were queried for all patients with a diagnosis of anorectal melanoma (2009-2019) and for whom a molecular analysis was performed. The genes that were tested and mutations that were reported were recorded. Mutation status was correlated with clinical characteristics.

Results: In the period 2009-2019, 121 patients were diagnosed with anorectal melanoma. A molecular analysis was performed for 81 (67%) using single gene testing and various next-generation sequencing panels. Testing rates increased from 53% in 2009-2012 to 73% in 2016-2019. In 29/81 (36%) analyzed tumors, one or more mutations were reported: mutations in KIT (16/70, 23%), CTNNB1 (3/20, 15%), NRAS (6/60, 10%), BRAF non-V600E (4/74, 5%), GNAS (1/19, 5%), KRAS (1/28, 4%), BRAF V600E (1/74, 1%), and SF3B1 (1/1). In this cohort, a positive correlation was found between BRAF mutation status and age. Mutation status did not correlate with sex, date of diagnosis, tumor stage or surgical treatment. Survival was not influenced by any mutation status.

Conclusion: KIT was the most frequently mutated gene in the 81 analyzed anorectal melanomas in the period 2009-2019. With the increasing testing rates and use of next generation sequencing, the molecular landscape of anorectal melanomas is gradually being revealed. Adoption of broad mutation analysis will reveal potentially actionable targets for treatment of patients with anorectal melanoma.

Rabies, a neglected zoonosis, claims approximately 60,000 lives globally each year. One of the significant challenges in rabies control efforts is the lack of surveillance data and underreporting, stemming from inadequate diagnostic facilities, particularly in low- and middle-income countries. At present, the World Health Organization recognizes the fluorescent antibody test (FAT) on postmortem brain specimens as the "gold standard" for confirming rabies in humans and animals. In this opinion article, we highlight several limitations of FAT and advocate for superior alternatives to replace it as the reference diagnostic technique for rabies. We argue that molecular techniques, specifically PCR-based methods, offer rapid, accurate, and convenient means of laboratory confirmation for rabies. Their implementation is now feasible due to the expanded technical and logistical capabilities achieved during the COVID-19 pandemic.

Objectives: To investigate whether 18F-fluorodeoxyglucose positron emission tomography-computed tomography ([¹⁸F]F-FDG PET/CT) metabolic parameters were associated with histology and to assess their prognostic role in patients with thymic lesions.

Patients and methods: In total, 116 patients (49/67 M/F; mean age 59.5 years) who underwent preoperative [¹⁸F]F-FDG PET/CT and thymectomy from 2012 to 2022 were retrospectively analyzed. Associations between histology and metabolic parameters (maximum standardized uptake value (SUVmax), mean standardized uptake value (SUVmean), peak standardized uptake value (SUVpeak), total lesion glycolysis (TLG), metabolic tumor volume (MTV), ratio between target lesion and liver SUVmax (rPET), quotient of SUVpeak in the tumor residual and SUVmean in a 20-cm³ volume of interest (qPET), and tumor-to-mediastinum (T/M) were analyzed. Freedom from recurrence (FFR) was determined and compared using the Kaplan-Meier and the log-rank test. The median follow-up was 38 months (range 14-72 months).

Results: In total, 27 thymic hyperplasia, 41 low-risk thymomas (LRT) (types A, AB, and B1), and 48 high-risk thymomas (HRT) (B2, B3 thymoma, and carcinoma) were included. SUVmax, SUVmean, SUVpeak, rPET, qPET, and T/M were significantly higher in HRT than LRT and hyperplasia (p < 0.001). TLG and MTV were significantly higher in patients with LRT (p < 0.001). Only rPET, qPET, and T/M remained significantly higher in HRT than in LRT subgroups (p = 0.042, p = 0.049, and p = 0.028, respectively). SUVmax, SUVmean, and SUVpeak cutoffs of < 4.3, < 2.87, and 4.03, respectively, significantly distinguished patients with longer FFR (p = 0.009, p = 0.05, and p = 0.05).

Conclusions: Positron emission tomography (PET) metabolic parameters could help to differentiate thymic histotypes. Standardized uptake value (SUV)-based parameters appear promising to predict recurrent disease.

Hearing loss represents a highly prevalent and debilitating sensory disorder affecting roughly one in five people worldwide. In a majority of patients with congenital hearing loss, genetic mutations cause the disease. Up until recently, therapeutic options for individuals with hearing loss were limited to hearing aids and different types of auditory implants. However, after numerous years of intensive basic and translational research, gene therapy strategies are now being investigated in clinical trials. First results show significant hearing improvement in treated patients, highlighting gene therapy's role as a promising treatment for certain forms of genetic hearing loss. In this article, we provide an overview of genetic hearing loss and inner ear gene therapy research including relevant strategies that have been established in animal models and will likely be investigated in human patients soon. Furthermore, we summarize and contextualize the novel findings of recently completed and ongoing clinical trials, and discuss future hurdles needed to be overcome to allow for a broad and safe clinical application of inner ear gene therapy.

To better understand ovarian cancer lethality and treatment resistance, sophisticated computational approaches are required that address the complexity of the tumor microenvironment, genomic heterogeneity, and tumor evolution. The ovarian cancer tumor ecosystem consists of multiple tumors and cell types that support disease growth and progression. Over the last two decades, there has been a revolution in -omic methodologies to broadly define components and essential processes within the tumor microenvironment, including transcriptomics, metabolomics, proteomics, genome sequencing, and single-cell analyses. While most of these technologies comprehensively characterize a single biological process, there is a need to understand the biological and clinical impact of integrating multiple -omics platforms. Overall, multi-omics is an intriguing analytic framework that can better approximate biological complexity; however, data aggregation and integration pipelines are not yet sufficient to reliably glean insights that affect clinical outcomes.

Introduction: Testing for homologous recombination deficiency (HRD) as a biomarker in relation to poly (ADP-ribose) polymerase inhibitor (PARPi) treatment in ovarian cancer is done by sequencing of the BRCA1/2 genes and/or by assessing a genomic instability signature. Here we present data obtained with two different methods for genomic instability testing: the Oncomine™ Comprehensive Assay Plus (OCA Plus) NGS panel and the OncoScan CNV assay.

Methods: The retrospective analytical study included 80 ovarian cancer samples of patients previously referred to clinical Myriad testing (reference cohort), and 50 ovarian cancer samples from patients collected as part of the Pelvic Mass study. OCA Plus NGS libraries were sequenced with the Ion S5™XL Sequencer and analyzed with the Ion Reporter™ Software v5.20 for calculation of the genomic instability metric (GIM). In addition, all samples were tested with the OncoScan CNV FFPE Assay and analyzed with a previously published R-algorithm for generation of an in-house genomic instability score (in-house GIS).

Results: The OCA Plus assay had a concordance to the reference of 89% on samples with a tumor fraction ≥ 30% (auto-calculated or via molecular estimation). A total of 15 samples in the reference cohort had a calculated tumor fraction < 30% in the OCA Plus assay. In these, the concordance to reference was only 60%. For the OncoScan CNV in-house GIS a local cutoff point of ≥ 50 was calculated. This gave a concordance to the reference of 85%, with 91% of the samples in the reference cohort passing quality control (QC) on tumor fraction. Both assays had a high sensitivity for the detection of genomic instability in samples with pathogenic or likely pathogenic BRCA1/2 mutations, with 12/13 being GIM positive (OCA Plus assay) and 13/13 being in-house GIS positive (OncoScan CNV assay).

Conclusions: The OCA Plus assay and the OncoScan CNV assay show a high but not complete concordance to reference standard homologous recombination deficiency (HRD) detection. The main reason for QC failure or non-concordance in our study was a low tumor fraction estimated in the assay, despite the selection of material by a pathologist with an inclusion criterion of > 30% tumor. QC steps should include careful tumor content evaluation, and results on samples with < 30% tumor should not be reported.

Digital PCR (dPCR) has been used in the field of virology since its inception. Technological innovations in microfluidics more than a decade ago caused a sharp increase in its use. There is an emerging consensus that dPCR now outperforms quantitative PCR (qPCR) in the basic parameters such as precision, sensitivity, accuracy, repeatability and resistance to inhibitors. These strengths have led to several current applications in quantification, mutation detection and environmental DNA and RNA samples. In high throughput scenarios, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the cost and throughput still significantly hampered the adaption of dPCR. There is much unexplored potential within the multiplexing capabilities of dPCR. This will allow simultaneous multi-target quantification and can also partially alleviate the throughput and cost drawback. In this review, we discuss the strengths and weaknesses of dPCR with a focus on virology applications and we discuss future applications. Finally, we discuss recent evolutions of the technology in the form of real-time dPCR and digital high-resolution melting.

Compromising between accuracy and rapidity is an important issue in analytics and diagnostics, often preventing timely and appropriate reactions to disease. This issue is particularly critical for infectious diseases, where reliable and rapid diagnosis is crucial for effective treatment and easier containment, thereby reducing economic and societal impacts. Diagnostic technologies are vital in disease modeling, tracking, treatment decision making, and epidemic containment. At the point-of-care level in modern healthcare, accurate diagnostics, especially those involving genetic-level analysis and nucleic acid amplification techniques, are still needed. However, implementing these techniques in remote or non-laboratory settings poses challenges because of the need for trained personnel and specialized equipment, as all nucleic acid-based diagnostic techniques, such as polymerase chain reaction and isothermal nucleic acid amplification, require temperature cycling or elevated and stabilized temperatures. However, in smart food packaging, there are approved and commercially available methods that use temperature regulation to enable autonomous heat generation without external sources, such as chemical heaters with phase change materials. These approaches could be applied in diagnostics, facilitating point-of-care, electricity-free molecular diagnostics, especially with nucleic acid-based detection methods such as isothermal nucleic acid amplification. In this review, we explore the potential interplay between self-heating elements, isothermal nucleic acid amplification techniques, and phase change materials. This paves the way for the development of truly portable, electricity-free, point-of-care diagnostic tools, particularly advantageous for on-site detection in resource-limited remote settings and for home use.