BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060890
Govardhan Rathnaiah, Joann B Sweasy
{"title":"Protein-Protein Interactions in Base Excision Repair.","authors":"Govardhan Rathnaiah, Joann B Sweasy","doi":"10.3390/biom15060890","DOIUrl":"10.3390/biom15060890","url":null,"abstract":"<p><p>The Base Excision Repair (BER) pathway involves a highly coordinated series of protein-protein interactions that facilitate the recognition, excision, and repair of damaged bases. Key enzymes such as DNA glycosylases, apurinic/apyrimidinic endonuclease 1 (APE1), polynucleotide kinase-phosphatase (PNKP), DNA polymerase b (Pol β), ligase IIIα (LigIIIα), poly (ADP-ribose) polymerases PARP1 and PARP2, and X-ray repair cross-complementing protein 1 (XRCC1) catalyze BER in a tightly regulated molecular network. These interactions ensure the seamless handoff of DNA intermediates between the core enzymes of the BER pathway. Understanding the details of protein-protein interactions in BER provides valuable insights into the molecular underpinnings of DNA repair processes. In this review, we focus on protein-protein interactions between the components of the single-nucleotide BER (SN-BER) pathway and other proteins that interact with BER components and regulate the coordination of the pathway. We also briefly discuss the interactions of other proteins that interact with the components of SN-BER based on functional evidence.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060889
Dominyka Švedaitė, Anastasija Kriučkova, Augustas Morkvėnas, Vitalijus Karabanovas, Gintautas Stankūnavičius, Vigilija Klima, Jaunius Urbonavičius, Rūta Ivanec-Goranina
{"title":"Application of Free and Encapsulated DNA Tracers in Surface Water Studies in Lithuanian Climatic Conditions.","authors":"Dominyka Švedaitė, Anastasija Kriučkova, Augustas Morkvėnas, Vitalijus Karabanovas, Gintautas Stankūnavičius, Vigilija Klima, Jaunius Urbonavičius, Rūta Ivanec-Goranina","doi":"10.3390/biom15060889","DOIUrl":"10.3390/biom15060889","url":null,"abstract":"<p><p>The applicability of free and encapsulated DNA as tracers in surface water studies in Lithuanian climatic conditions was evaluated. Tracer DNA synthesis and analysis were performed using real-time polymerase chain reaction (RT-PCR). Alginate and chitosan were used to obtain the microcapsules with DNA, and their sizes were determined using an atomic force microscopy. The Murlė stream in the city of Vilnius was chosen for field experiments using the prepared tracers. It was found that both types of tracers may be applied to surface water studies, but the relative concentration recovery of encapsulated DNA tracers is 3-6 times higher than that of free DNA tracers. It was concluded that the alginate/chitosan capsules protect DNA from the sandy layer in Murlė stream, direct UV exposure and other environmental factors that could degrade DNA. To our knowledge, this is the first report about free and encapsulated DNA tracer application in surface water studies in Lithuania.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190598/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060887
Emily Barr, Maude Comtois-Cabana, Andressa Coope, Sylvana M Coté, Michael S Kobor, Chaini Konwar, Sonia Lupien, Marie-Claude Geoffroy, Michel Boivin, Nadine Provençal, Nicole L A Catherine, Jessica K Dennis, Isabelle Ouellet-Morin
{"title":"Early-Life Adversity and Epigenetic Aging: Findings from a 17-Year Longitudinal Study.","authors":"Emily Barr, Maude Comtois-Cabana, Andressa Coope, Sylvana M Coté, Michael S Kobor, Chaini Konwar, Sonia Lupien, Marie-Claude Geoffroy, Michel Boivin, Nadine Provençal, Nicole L A Catherine, Jessica K Dennis, Isabelle Ouellet-Morin","doi":"10.3390/biom15060887","DOIUrl":"10.3390/biom15060887","url":null,"abstract":"<p><p>Youth exposed to early-life adversity (ELA) are at greater risk for poorer physical and mental health outcomes in adolescence and adulthood. Although the biological mechanisms underlying these associations remain elusive, DNA methylation (DNAm) has emerged as a potential pathway. DNAm-based measures of epigenetic age have been associated with ELA, indicating accelerated aging. According to the stress sensitization hypothesis, prenatal adversity may further heighten sensitivity to subsequent stressors in childhood and adolescence. This study examined the associations between ELA and six epigenetic aging measures, considering both the timing of adversity and the participant's sex. Data were drawn from the Quebec Longitudinal Study of Child Development, with two cumulative indices of ELA derived from prospectively collected data: the Perinatal Adversity and the Child and Adolescent Adversity indices. Higher Perinatal Adversity scores were associated with accelerated DunedinPACE scores. No significant associations were found between ELA and the other epigenetic clocks, nor did we find support for the stress sensitization hypothesis-though a sex-specific trend emerged among girls. The findings suggest that DunedinPACE may be more sensitive to variations in ELA than other clocks. Future research should systematically investigate sex-dimorphic associations between ELA and epigenetic aging, with particular attention to the impact of perinatal adversity.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060896
Sixin Guo, Binwei Duan, Jianchao Chen, Mingyang Cui, Canbei You, Hanyin Wei, Xiazi Huang, Li Deng, Kai Zhang
{"title":"Genome-Wide Identification of DNA Methyltransferases (Dnmts) in Fish and Its Potential Roles During Sex Change in Blackhead Seabream.","authors":"Sixin Guo, Binwei Duan, Jianchao Chen, Mingyang Cui, Canbei You, Hanyin Wei, Xiazi Huang, Li Deng, Kai Zhang","doi":"10.3390/biom15060896","DOIUrl":"10.3390/biom15060896","url":null,"abstract":"<p><p>DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in multiple important biological processes in fish, such as gonadal development. The cellular DNA methylation level is tightly regulated by DNA methyltransferases (Dnmt). However, detailed investigations of this family in fish are very scarce. In this study, our results confirmed that teleost genomes contain 4 to 16 <i>Dnmt</i> genes, with diversity likely resulting from a combination of whole-genome duplication (WGD), tandem duplication, and gene loss. Differences were observed in tissue distribution, transcription abundance, and protein structure of <i>Dnmt</i> duplicates, supporting their subfunctionalization or neofunctionalization after duplication. Interestingly, we found that fish <i>Dnmt3b</i> duplicates likely have acquired the functions of mammalian <i>Dnmt3l</i>, which may compensate for the absence of fish <i>Dnmt3l</i>. Furthermore, transcriptome analysis and qPCR results indicated that DNA methyltransferase genes (<i>Dnmt1</i>, <i>Dnmt3aa</i>, <i>Dnmt3ab</i>, <i>Dnmt3ba</i>, and <i>Dnmt3bb.1</i>) possibly play important roles in the natural sex change of protandrous hermaphrodite blackhead seabream (<i>Acanthopagrus schlegelii</i>) and inferred that global remodeling of gonadal DNA methylation, regulated by DNA methyltransferase genes, was closely associated with sex change in sequentially hermaphroditic fishes. Overall, our results may help provide a better understanding of the evolution and function of DNA methyltransferases in fish.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060891
Hui Xiang, Runtian Wu, Man Xiao, Jianhui An, Longchen Shang, Yexing Tao, Lingli Deng
{"title":"Influence of the Maillard Reaction on the Properties of Gelatin/Zein Nanofibers Loaded with Dihydromyricetin Prepared by Electro-Blowing Spinning.","authors":"Hui Xiang, Runtian Wu, Man Xiao, Jianhui An, Longchen Shang, Yexing Tao, Lingli Deng","doi":"10.3390/biom15060891","DOIUrl":"10.3390/biom15060891","url":null,"abstract":"<p><p>This study investigated gelatin/zein nanofibers loaded with dihydromyricetin (0-20%, relative to protein weight), before and after the Maillard reaction (60 °C with 50% relative humidity for 6 h). Scanning electron microscopy and diameter distribution analysis indicated that dihydromyricetin incorporation increased the fiber diameter from 692 ± 133 to 922 ± 121 nm, while the nanofibers maintained a uniform morphology following the Maillard reaction. Fourier transform infrared spectroscopy revealed that dihydromyricetin formed hydrogen bonds with protein molecules. X-ray diffraction results indicate that dihydromyricetin was uniformly dispersed within the gelatin/zein nanofibers. The addition of dihydromyricetin improved the thermal stability of the nanofibers. Furthermore, after the Maillard reaction, the nanofibers with dihydromyricetin demonstrated enhanced water resistance. Mechanical testing revealed that nanofibers containing 20% dihydromyricetin after the Maillard reaction exhibited a considerably higher elastic modulus of approximately 90 MPa. In addition, nanofibers containing dihydromyricetin exhibited notable antioxidant activity and antibacterial properties against <i>Escherichia coli</i> and <i>Staphylococcus aureus</i>. In summary, gelatin/zein nanofibers containing high concentrations of dihydromyricetin exhibited favorable physical and functional properties, supporting their suitability as effective delivery systems for dihydromyricetin in active packaging applications.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dynamic 3D-Network Coating Composite Enables Global Isolation of Phosphopeptides, Stepwise Separation of Mono- and Multi-Phosphopeptides, and Phosphoproteomics of Human Lung Cells.","authors":"Linlin Liu, Zhenhua Chen, Danni Wang, Weida Liang, Binbin Wang, Chenglong Xia, Yinghua Yan, Chuanfan Ding, Xiaodan Meng, Hongze Liang","doi":"10.3390/biom15060894","DOIUrl":"10.3390/biom15060894","url":null,"abstract":"<p><p>Protein phosphorylation is one of the most common and important post-translational modifications (PTMs) and is highly involved in various biological processes. Ideal adsorbents with high sensitivity and specificity toward phosphopeptides with large coverage are therefore essential for enrichment and mass spectroscopy-based phosphoproteomics analysis. In this study, a newly designed IMAC adsorbent composite was constructed on the graphene matrix coated with mesoporous silica. The outer functional 3D-network layer was prepared by free radical polymerization of the phosphonate-functionalized vinyl imidazolium salt monomer and subsequent metal immobilization. Due to its unique structural feature and high content of Ti<sup>4+</sup> ions, the resulting phosphonate-immobilized adsorbent composite G@mSiO<sub>2</sub>@PPFIL-Ti<sup>4+</sup> exhibits excellent performance in phosphopeptide enrichment with a low detection limit (0.1 fmol, tryptic β-casein digest) and superior selectivity (molar ratio of 1:15,000, digest mixture of β-casein and bovine serum albumin). G@mSiO<sub>2</sub>@PPFIL-Ti<sup>4+</sup> displays high tolerance to loading and elution conditions and thus can be reused without a marked decrease in enrichment efficacy. The captured phosphopeptides can be released globally, and mono-/multi-phosphopeptides can be isolated stepwise by gradient elution. When applying this material to enrich phosphopeptides from human lung cell lysates, a total of 3268 unique phosphopeptides were identified, corresponding to 1293 phosphoproteins. Furthermore, 2698 phosphorylated peptides were found to be differentially expressed (<i>p</i> < 0.05) between human lung adenocarcinoma cells (SPC-A1) and human normal epithelial cells (Beas-2B), of which 1592 were upregulated and 1106 were downregulated in the cancer group. These results demonstrate the material's superior enrichment efficiency in complex biological samples.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060892
Chang Dai, Raouf A Khalil
{"title":"Calcium Signaling Dynamics in Vascular Cells and Their Dysregulation in Vascular Disease.","authors":"Chang Dai, Raouf A Khalil","doi":"10.3390/biom15060892","DOIUrl":"10.3390/biom15060892","url":null,"abstract":"<p><p>Calcium (Ca<sup>2+</sup>) signaling is a fundamental regulatory mechanism controlling essential processes in the endothelium, vascular smooth muscle cells (VSMCs), and the extracellular matrix (ECM), including maintaining the endothelial barrier, modulation of vascular tone, and vascular remodeling. Cytosolic free Ca<sup>2+</sup> concentration is tightly regulated by a balance between Ca<sup>2+</sup> mobilization mechanisms, including Ca<sup>2+</sup> release from the intracellular stores in the sarcoplasmic/endoplasmic reticulum and Ca<sup>2+</sup> entry via voltage-dependent, transient-receptor potential, and store-operated Ca<sup>2+</sup> channels, and Ca<sup>2+</sup> elimination pathways including Ca<sup>2+</sup> extrusion by the plasma membrane Ca<sup>2+</sup>-ATPase and Na<sup>+</sup>/Ca<sup>2+</sup> exchanger and Ca<sup>2+</sup> re-uptake by the sarco(endo)plasmic reticulum Ca<sup>2+</sup>-ATPase and the mitochondria. Some cell membranes/organelles are multifunctional and have both Ca<sup>2+</sup> mobilization and Ca<sup>2+</sup> removal pathways. Also, the individual Ca<sup>2+</sup> handling pathways could be integrated to function in a regenerative, capacitative, cooperative, bidirectional, or reciprocal feed-forward or feed-back manner. Disruption of these pathways causes dysregulation of the Ca<sup>2+</sup> signaling dynamics and leads to pathological cardiovascular conditions such as hypertension, coronary artery disease, atherosclerosis, and vascular calcification. In the endothelium, dysregulated Ca<sup>2+</sup> signaling impairs nitric oxide production, reduces vasodilatory capacity, and increases vascular permeability. In VSMCs, Ca<sup>2+</sup>-dependent phosphorylation of the myosin light chain and Ca<sup>2+</sup> sensitization by protein kinase-C (PKC) and Rho-kinase (ROCK) increase vascular tone and could lead to increased blood pressure and hypertension. Ca<sup>2+</sup> activation of matrix metalloproteinases causes collagen/elastin imbalance and promotes vascular remodeling. Ca<sup>2+</sup>-dependent immune cell activation, leukocyte infiltration, and cholesterol accumulation by macrophages promote foam cell formation and atherosclerotic plaque progression. Chronic increases in VSMCs Ca<sup>2+</sup> promote phenotypic switching to mesenchymal cells and osteogenic transformation and thereby accelerate vascular calcification and plaque instability. Emerging therapeutic strategies targeting these Ca<sup>2+</sup>-dependent mechanisms, including Ca<sup>2+</sup> channel blockers and PKC and ROCK inhibitors, hold promise for restoring Ca<sup>2+</sup> homeostasis and mitigating vascular disease progression.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060888
Jun Yang, Binyang Deng, Pingan Liao, Siyu Lin, Liqi Zheng, Xing Yang, Fei Wang, Chao Zhai, Lixin Ma
{"title":"Improving the Catalytic Activity and Thermostability of FAST-PETase with a Multifunctional Short Peptide.","authors":"Jun Yang, Binyang Deng, Pingan Liao, Siyu Lin, Liqi Zheng, Xing Yang, Fei Wang, Chao Zhai, Lixin Ma","doi":"10.3390/biom15060888","DOIUrl":"10.3390/biom15060888","url":null,"abstract":"<p><p>Previous reports indicated that self-assembling amphipathic peptide S1v1 (AEAEAHAH)<sub>2</sub> significantly enhances the soluble expression, thermostability, and activity of the target proteins when fused to them. In order to obtain high-efficiency enzymes for the large-scale degradation of polyethylene terephthalate (PET), this multifunctional peptide was fused to the N- and C-terminus of FAST-PETase, a variant of <i>Ideonella sakaiensis</i> PETase (<i>Is</i>PETase), with a PT-linker (TTVTTPQTS) harbored between the target protein and the multifunctional peptide. Consistent with previous reports, S1v1 increased the solubility of FAST-PETase slightly. Moreover, it increased the activity of FAST-PETase dramatically. The amount of terephthalic acid (TPA) and mono(2-hydroxyethyl) terephthalic acid (MHET) released from PET substrate after 24 h of digestion at 50°C by fusion enzymes bearing N- and C-terminal S1v1 tag was approximately 2.9- and 4.6-fold that of FAST-PETase, respectively. Furthermore, the optimal temperature and thermostability of the fusion proteins increased in comparison with FAST-PETase. The present study provides a novel strategy to improve the depolymerization efficiency of FAST-PETase.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-18DOI: 10.3390/biom15060898
Lowell Welburn, Amir Milad Moshref Javadi, Luong Nguyen, Salil Desai
{"title":"Prospects and Trends in Biomedical Microelectromechanical Systems (MEMS) Devices: A Review.","authors":"Lowell Welburn, Amir Milad Moshref Javadi, Luong Nguyen, Salil Desai","doi":"10.3390/biom15060898","DOIUrl":"10.3390/biom15060898","url":null,"abstract":"<p><p>Designing and manufacturing devices at the micro- and nanoscales offers significant advantages, including high precision, quick response times, high energy density ratios, and low production costs. These benefits have driven extensive research in micro-electromechanical systems (MEMS) and nano-electromechanical systems (NEMS), resulting in various classifications of materials and manufacturing techniques, which are ultimately used to produce different classifications of MEMS devices. The current work aims to systematically organize the literature on MEMS in biomedical devices, encompassing past achievements, present developments, and future prospects. This paper reviews the current research trends, highlighting significant material advancements and emerging technologies in biomedical MEMS in order to meet the current challenges facing the field, such as ensuring biocompatibility, achieving miniaturization, and maintaining precise control in biological environments. It also explores projected applications, including use in advanced diagnostic tools, targeted drug delivery systems, and innovative therapeutic devices. By mapping out these trends and prospects, this review will help identify current research gaps in the biomedical MEMS field. By pinpointing these gaps, researchers can focus on addressing unmet needs and advancing state-of-the-art biomedical MEMS technology. Ultimately, this can lead to the development of more effective and innovative biomedical devices, improving patient care and outcomes.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
BiomoleculesPub Date : 2025-06-17DOI: 10.3390/biom15060883
Wei Yen Chan, Ashleigh Stewart, Russell J Diefenbach, Elin S Gray, Jenny H Lee, Richard A Scolyer, Georgina V Long, Helen Rizos
{"title":"Pre-Amplification of Cell-Free DNA: Balancing Amplification Errors with Enhanced Sensitivity.","authors":"Wei Yen Chan, Ashleigh Stewart, Russell J Diefenbach, Elin S Gray, Jenny H Lee, Richard A Scolyer, Georgina V Long, Helen Rizos","doi":"10.3390/biom15060883","DOIUrl":"10.3390/biom15060883","url":null,"abstract":"<p><p>Circulating tumour DNA (ctDNA) is a promising biomarker for personalised oncology. However, its clinical utility is limited by detection sensitivity, particularly in early-stage disease. T-Oligo Primed Polymerase Chain Reaction (TOP-PCR) is a commercial amplification approach utilising an efficient \"half-adapter\" ligation design and a single-primer-based PCR strategy. This study evaluated the clinical value and application of cell-free DNA (cfDNA) pre-amplification. cfDNA amplification with TOP-PCR preserved DNA size profiles and resulted in a 22 bp size increase due to the half-adaptor ligation. Gene target amplification rates varied, showing lower efficiency for the GC-rich TERT promoter amplicon and higher efficiency for the <i>BRAF</i> and <i>TP53</i> amplicons. Optimised pre-amplification (20 ng cfDNA input and 5-7 cycles of PCR) enhanced ctDNA detection sensitivity and expanded sample availability for the detection of multiple tumour-informed mutations. Importantly, PCR errors emerged in pre-amplified cfDNA samples, underscoring the necessity for negative controls and the establishment of stringent mutation positivity thresholds.</p>","PeriodicalId":8943,"journal":{"name":"Biomolecules","volume":"15 6","pages":""},"PeriodicalIF":4.8,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12191314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144494456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}