Molecular Diagnosis & Therapy最新文献

{"title":"Optimization of Metagenomic Next-Generation Sequencing Workflow with a Novel Host Depletion Method for Enhanced Pathogen Detection.","authors":"Yen-Chia Chen, Po-Hsiang Liao, Yen-Wen Chen, David Hung-Tsang Yen, Chorng-Kuang How, Chia-Ming Chang","doi":"10.1007/s40291-025-00797-3","DOIUrl":"https://doi.org/10.1007/s40291-025-00797-3","url":null,"abstract":"<p><strong>Introduction: </strong>Sepsis is a critical condition requiring timely and accurate pathogen identification. Traditional blood cultures are slow and often yield low sensitivity. Metagenomic next-generation sequencing (mNGS) offers broad and rapid pathogen detection but is hindered by excessive human DNA background in blood samples. This study evaluated a novel Zwitterionic Interface Ultra-Self-assemble Coating (ZISC)-based filtration device designed to deplete host cells and enhance microbial DNA recovery for improved mNGS diagnostics.</p><p><strong>Methods: </strong>We assessed the novel filter's performance in depleting white blood cells (WBCs) while preserving microbial integrity using spiked blood samples. Comparisons were made with other host depletion techniques, including differential lysis and CpG-methylated DNA removal. Analytical sensitivity was tested using spiked microbial communities at varying genome equivalents (GEs). Clinical validation involved eight blood culture-positive sepsis patient samples, processed with and without filtration, for both genomic DNA (gDNA) and cell-free DNA (cfDNA)-based mNGS. All libraries were sequenced on a NovaSeq600 with at least 10 million reads per sample.</p><p><strong>Results: </strong>The novel filter achieved > 99% WBC removal across various blood volumes and allowed unimpeded passage of bacteria and viruses. Compared to other depletion methods, the novel filtration was more efficient, less labor-intensive, and preserved microbial reads. mNGS with filtered gDNA detected all expected pathogens in 100% (8/8) of clinical samples, with an average microbial read count of 9351 reads per million (RPM), over tenfold higher than unfiltered samples (925 RPM). In contrast, cfDNA-based mNGS showed inconsistent sensitivity and was not significantly enhanced by filtration (1251-1488 RPM). Finally, the novel filtration did not alter the microbial composition, making it suitable for accurate pathogen profiling.</p><p><strong>Conclusion: </strong>The workflow with the novel host depletion method significantly enhanced the analytical sensitivity of gDNA-based mNGS by reducing the host DNA background and enriching microbial content. This approach improved diagnostic yield in sepsis and may be a valuable tool for further clinical infectious disease diagnostics.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":""},"PeriodicalIF":4.1,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recurrent and Novel Pathogenic Variants in Genes Involved with Hearing Loss in the Pakistani Population.","authors":"Madiha Shadab, Afif Ben-Mahmoud, Luis Nicolás Martínez Völter, Ansar Ahmed Abbasi, Bonsu Ku, Ahsan Ejaz, Zahid Latif, Vijay Gupta, Daniel Owrang, Mi-Hyeon Jang, Zijin Zhang, Rahema Mohammad, Henry Houlden, Hyung-Goo Kim, Barbara Vona","doi":"10.1007/s40291-025-00782-w","DOIUrl":"10.1007/s40291-025-00782-w","url":null,"abstract":"<p><strong>Background: </strong>Molecular diagnostic rates for hereditary hearing loss vary by genetic ancestry, highlighting the importance of population-specific studies. In Pakistan, where consanguineous marriages are prevalent, genetic research has identified many autosomal recessive genes, advancing understanding of rare and novel hearing loss mechanisms. This study aimed to identify pathogenic genetic variants in 31 families from Azad Kashmir, Pakistan, presenting non-syndromic hearing loss.</p><p><strong>Methods: </strong>We conducted exome sequencing and bioinformatics analysis, and targeted gene sequencing on 31 Pakistani families with hearing loss.</p><p><strong>Results: </strong>We identified ten pathogenic, three likely pathogenic variants, and one variant of uncertain significance, comprising six nonsense, four missense, three frameshift, and one deep intronic variant, across ten hearing loss-associated genes (MYO15A, GJB2, SLC26A4, TMC1, HGF, TMIE, SLC19A2, KCNE1, ILDR, PCDH15 and MYO6) in 25 families. The overall diagnostic rate, including families with pathogenic and likely pathogenic variants, was 77.4%. GJB2 was the most frequently affected gene, identified in seven families. Thirteen out of 14 identified variants were homozygous. Notably, we identified two novel variants: MYO15A (NM_016239.4, DFNB3) c.870C>G, p.(Tyr290*) and MYO6 (NM_016239.4, DFNB37) c.3465del, p.(Pro1156Leufs*9). Additionally, we identified c.10475dupA, p.(Leu3493Alafs*25) in MYO15A (NM_016239.4, DFNB3) and c.617T>A, p.(Leu206*) in SLC26A4 (NM_000441.2, DFNB4), previously documented in ClinVar but unpublished. We also propose SLC19A2 as a candidate gene presenting as non-syndromic hearing loss, despite its association with thiamine-responsive megaloblastic anemia syndrome.</p><p><strong>Conclusion: </strong>Our work expands the genotypic and phenotypic spectrum of hearing loss by emphasizing the importance of investigating under-represented groups to identify unique genetic variants and clinical characteristics. Such efforts deepen understanding of genetic diversity in under-represented populations to improve diagnosis and treatment strategies.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"519-537"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144081635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell-Free HPV-DNA in Screening, Diagnosis, Prognosis, and Treatment Response Monitoring of Cervical Cancer.","authors":"Nayara Nascimento Toledo Silva, Ana Carolina Silva Santos, Isadora Oliveira Ansaloni Pereira, Glenda Nicioli da Silva, Angélica Alves Lima","doi":"10.1007/s40291-025-00790-w","DOIUrl":"10.1007/s40291-025-00790-w","url":null,"abstract":"<p><p>Persistent infection with high-risk human papillomavirus (HPV) is a significant factor in cervical cancer (CC) development. Although CC screening programs have reduced the incidence of this neoplasm, the number of deaths remains high, especially in developing countries: CC remains the fourth most common neoplasm in the female population globally. Currently, an HPV test has been replacing cytological analysis because it is a more sensitive screening method. However, the collection of gynecological material is still necessary, which can be a barrier to adherence to testing in the target population. Host cells presenting with a viral infection release fragments of their DNA into circulation, known as cell-free DNA (cfDNA); this allows detection through venous puncture, a routine procedure in clinical laboratories. Thus, the objective of this review was to evaluate the role of cfDNA of HPV (cfHPV-DNA) as an alternative tool for CC screening, diagnosis, prognosis, and treatment response monitoring. Furthermore, the development of sensitive methods, such as droplet digital PCR (ddPCR) and next-generation sequencing (NGS), have proven useful in identifying tumor markers for CC. The specificity of the primers, the size of the target DNA fragments, and variables such as sample type and volume, in addition to the cfDNA extraction kit used, can influence the results of cfHPV-DNA detection. Although the detection of cfHPV-DNA in plasma and serum of patients with CC is feasible, there were conflicting results regarding cfHPV-DNA detection in the blood circulation of patients with premalignant lesions. On the other hand, when CC is already established, the detection and quantification of cfHPV-DNA have shown potential as a biomarker for tumor staging, prognosis definition, and treatment response monitoring.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"483-497"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Dynamics as a Precision Therapy: A Perspective on Epileptic Encephalopathies.","authors":"Raffaele Falsaperla, Vincenzo Sortino, Federica Maria Sipala, Simone Ronsisvalle, Piero Pavone","doi":"10.1007/s40291-025-00780-y","DOIUrl":"10.1007/s40291-025-00780-y","url":null,"abstract":"","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"425-429"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Research Progress on Signal Conversion Based on Aptamer Combined CRISPR/Cas System in Biosensors.","authors":"Yihua Wang, Hui Li, Sijian Luo, Min Zhong, Jinbo Liu, Baolin Li","doi":"10.1007/s40291-025-00785-7","DOIUrl":"10.1007/s40291-025-00785-7","url":null,"abstract":"<p><p>The CRISPR/Cas system has been extensively used in the fields of biology, food safety, and environmental monitoring. This is in part because its can to be used in combination with isothermal amplification-mediated signal amplification technology along with its extraordinary trans-cleavage ability, which has initiated a new era of biosensing applications. The popularity of functional nucleic acids has enabled aptamers to convert non-nucleic acid substances into programmable nucleic acid sequences through methods such as direct detection, lock activation, sandwich design, induction of conformations, and split aptamers. Additionally, CRISPR/Cas systems have been extended beyond nucleic acid detection to include ions, small molecules, proteins, cells, bacteria, viruses, and other non-nucleic acid-based target substances. This article provides a brief overview of the mechanisms of action of four Cas proteins, the generation of aptamers, and their combined applications. Moreover, we focus on the research progress of biosensors based on aptamer-based signal conversion combined with the CRISPR/Cas system.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"499-518"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327538","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FAPI-Targeted Molecular Imaging: Transforming Insights into Post-Ischemic Myocardial Remodeling?","authors":"Luca Filippi, Marco Alfonso Perrone, Orazio Schillaci","doi":"10.1007/s40291-025-00778-6","DOIUrl":"10.1007/s40291-025-00778-6","url":null,"abstract":"<p><p>Post-ischemic myocardial remodeling significantly impacts clinical outcomes after acute myocardial infarction (MI), involving structural and functional changes such as ventricular dilation, infarct wall thinning, and fibrosis development. These processes, driven by inflammatory cascades, neurohormonal activation, and extracellular matrix remodeling, result in impaired cardiac output and an increased risk of heart failure. Imaging with fibroblast activation protein inhibitors (FAPI) has emerged as a promising non-invasive tool for assessing myocardial fibrosis via positron emission tomography (PET) or single-photon emission computed tomography (SPECT), targeting activated fibroblasts; the mediators of reparative and fibrotic processes. This innovative approach enables precise visualization and quantification of fibrosis dynamics, surpassing traditional imaging modalities. Preclinical studies using [⁶⁸Ga]Ga-FAPI PET/computed tomography (CT) demonstrated the tracer's specificity for fibroblast activation and its peak uptake in the infarct border zone at day 6 post-MI. These findings, corroborated by histology and autoradiography, highlight its potential for tracking reparative fibrosis. Clinical translation of FAPI imaging was recently achieved with [⁶⁸Ga]Ga-FAPI-46 PET/magnetic resonance imaging (MRI), showing persistent fibroblast activity beyond infarct zones and strong correlations with myocardial injury markers. Complementary research on [^99mTc]Tc-HFAPi SPECT imaging in patients post-MI established its predictive value for left ventricular remodeling, emphasizing its cost-effectiveness and accessibility compared with PET. These advancements underscore FAPI-based imaging's potential to transform risk stratification and therapeutic guidance in post-MI care.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"435-442"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227512/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nectin-4-Targeting Radiotracers: Novel Theranostic Agents for Precision Oncology in Cancer.","authors":"Giorgia Speltri, Ilham Badrane, Rebecca Napolitano, Alessandra Boschi, Licia Uccelli, Luca Filippi, Massimo Guidoboni, Matteo Brunelli, Federica Lancia, Petra Martini, Antonella Iudicello, Corrado Cittanti, Mirco Bartolomei, Luca Urso","doi":"10.1007/s40291-025-00786-6","DOIUrl":"10.1007/s40291-025-00786-6","url":null,"abstract":"<p><p>Nectin cell adhesion molecule 4 (Nectin-4) is specifically overexpressed in most cancers of epithelial origin but downregulated in normal tissue, representing an ideal target for positron emission tomography imaging. The development of positron emission tomography imaging probes targeting Nectin-4 has gained significant attention in recent years, especially after the approval in December 2019 by the US Food and Drug Administration of enfortumab vedotin-an antibody drug conjugate targeting Nectin-4-in patients with locally advanced or metastatic bladder cancer. This article aims to comprehensively review original research articles discussing preclinical development or early translational clinical applications of radiolabeled probes targeting Nectin-4. The main radioactive compounds investigated belong to two classes, antibody-based radiopharmaceuticals and peptide-drug conjugates, in particular novel bicyclic peptides. While monoclonal antibody-based probes have demonstrated theranostic potential in preclinical studies, their clinical application has been hindered by their slow pharmacokinetic properties. However, peptide-based positron emission tomography/computed tomography tracers offer several advantages, such as ease of handling in synthesis, a more favorable biodistribution, and lower immunogenicity and have been tested in preliminary clinical experiences.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"453-463"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making Sense of Missense: Benchmarking MutScore for Variant Interpretation in Inherited Cardiac Diseases.","authors":"Alessandra Pia Porretta, Véronique Fressart, Elodie Surget, Charles Morgat, Adrien Bloch, Anne Messali, Vincent Algalarrondo, Géraldine Vedrenne, Etienne Pruvot, Antoine Leenhardt, Isabelle Denjoy, Fabrice Extramiana","doi":"10.1007/s40291-025-00784-8","DOIUrl":"10.1007/s40291-025-00784-8","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Accurate interpretation of genetic variants still represents a major challenge. According to current recommendations from the American College of Medical Genetics and Genomics (ACMG), variant interpretation relies on a comprehensive analysis including, among others, computational data for prediction of variant pathogenicity. However, the predictive accuracy of in silico tools is often limited, and results are frequently inconsistent. In the current study, we evaluated the predictive performance of a previously described innovative classifier (MutScore) for missense variants in our cohort of probands with inherited cardiac diseases (InCDs).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;We retrospectively reviewed missense variants detected in our cohort of probands with InCDs. Variants were analyzed with four in silico tools commonly used in our diagnostic pipelines (CADD, Polyphen-2, Alpha-missense and Revel) and with MutScore, a new meta-predictor combining data on variant location with the output of 16 existing predictors. For each variant, we recorded the original classification (established according to scientific evidence available at the time of molecular diagnosis) and the updated classification performed at the present time, according to ACMG standards.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We detected 252 missense variants in our cohort of 517 patients affected by InCDs. MutScore was the most proficient tool in classifying variants (0.89 maximum area under the curve [95% confidence interval (CI) 0.85-0.94]). Compared to Revel, the second-best predictor, MutScore showed superior sensitivity (73% vs 57%) at the maximum tolerated false-positive rate of 10%, higher specificity (0.83 vs 0.36) and a markedly lower false-positive rate (0.17 vs 0.64), supporting a more nuanced and accurate assessment, especially for benign or likely benign variants. MutScore also appeared to perform better for variants located in genes associated with channelopathies than for variants in cardiomyopathy-related genes. Notably, when comparing the original and updated classification, 27% (69/252) of missense variants underwent a change in classification over the 9-year follow-up period. Among these, reclassification had a significant impact on clinical management in one third of cases (i.e., variants of uncertain significance upgraded to pathogenic or likely pathogenic variants or vice versa), with a 4.8% increase in molecular diagnosis of InCDs over the 9-year period.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;Our study supports the excellent performance of MutScore in a real-life dataset of missense variants associated with the rare subset of InCDs. MutScore represents a promising application of artificial intelligence with major potential in cardiogenetics to improve diagnostic precision in clinical practice. In addition, our results highlight the importance of periodic reanalysis of variants, incorporating newly available scientific evidence, as attested by","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"539-552"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12227508/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Potential of a Cell-Free DNA Methylation-Based Blood Test in Colorectal Cancer Screening.","authors":"Angeliki Margoni, Athanasios G Papavassiliou","doi":"10.1007/s40291-025-00783-9","DOIUrl":"10.1007/s40291-025-00783-9","url":null,"abstract":"","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"431-434"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056776","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revakinagene Taroretcel: First Approval.","authors":"Sheridan M Hoy","doi":"10.1007/s40291-025-00787-5","DOIUrl":"10.1007/s40291-025-00787-5","url":null,"abstract":"<p><p>Revakinagene taroretcel (revakinagene taroretcel-lwey; ENCELTO™) is an encapsulated cell-based gene therapy containing 200,000-440,000 allogeneic retinal pigment epithelial (RPE) cells expressing recombinant human ciliary neurotrophic factor (rhCNTF). Available as a single-dose intravitreal implant, it has been developed by Neurotech Pharmaceuticals, Inc. for the treatment of chronic retinal diseases. In March 2025, revakinagene taroretcel received its first approval for the treatment of adults with idiopathic macular telangiectasia (MacTel) type 2 in the USA. It is the first US FDA-approved treatment for this disease. Revakinagene taroretcel has been granted Orphan Drug Designation for retinitis pigmentosa and Fast Track Designation for retinitis pigmentosa and dry age-related macular degeneration in the USA. This article summarises the milestones in the development of revakinagene taroretcel leading to this first approval for the treatment of adults with idiopathic MacTel type 2 in the USA.</p>","PeriodicalId":49797,"journal":{"name":"Molecular Diagnosis & Therapy","volume":" ","pages":"553-561"},"PeriodicalIF":4.1,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144334321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}