Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models

Sauer, Carolin M; Heider, Katrin; Belic, Jelena; Boyle, Samantha E; Hall, James A.; Couturier, Dominique-Laurent; An, Angela; Reinius, Marika; Hosking, Karen; Vias, Maria; Rosenfeld, Nitzan; Brenton, James D.

doi:10.15252/emmm.202215729

Cited by 9 publications

(2 citation statements)

References 47 publications

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“…The quandary at hand revolves around the dexterous identification and capture of scant ctDNA fractions amid the backdrop of copious cell-free DNA (cfDNA), while preempting the distorting influence of clonal hematopoiesis on detection fidelity. [138] Prevailing modalities of imaging and the conventional repository of blood biomarkers, though valuable, bespeak limitations in their sensitivity, primarily when tasked with delineating postoperative MRD status. Their pragmatic utility in the clinical domain is concomitantly curtailed.…”

Section: Detection Of Nucleic Acidsmentioning

confidence: 99%

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Nanozyme‐Enhanced Electrochemical Biosensors: Mechanisms and Applications

Yang,

Guo,

Wang

et al. 2023

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Nanozymes, as innovative materials, have demonstrated remarkable potential in the field of electrochemical biosensors. This article provides an overview of the mechanisms and extensive practical applications of nanozymes in electrochemical biosensors. First, the definition and characteristics of nanozymes are introduced, emphasizing their significant role in constructing efficient sensors. Subsequently, several common categories of nanozyme materials are delved into, including metal‐based, carbon‐based, metal‐organic framework, and layered double hydroxide nanostructures, discussing their applications in electrochemical biosensors. Regarding their mechanisms, two key roles of nanozymes are particularly focused in electrochemical biosensors: selective enhancement and signal amplification, which crucially support the enhancement of sensor performance. In terms of practical applications, the widespread use of nanozyme‐based electrochemical biosensors are showcased in various domains. From detecting biomolecules, pollutants, nucleic acids, proteins, to cells, providing robust means for high‐sensitivity detection. Furthermore, insights into the future development of nanozyme‐based electrochemical biosensors is provided, encompassing improvements and optimizations of nanozyme materials, innovative sensor design and integration, and the expansion of application fields through interdisciplinary collaboration. In conclusion, this article systematically presents the mechanisms and applications of nanozymes in electrochemical biosensors, offering valuable references and prospects for research and development in this field.

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Section: Detection Of Nucleic Acidsmentioning

confidence: 99%

“…The quandary at hand revolves around the dexterous identification and capture of scant ctDNA fractions amid the backdrop of copious cell‐free DNA (cfDNA), while preempting the distorting influence of clonal hematopoiesis on detection fidelity. [ 138 ]…”

Section: Practical Applications Of Nanozymes Electrochemical Sensorsmentioning

confidence: 99%

Nanozyme‐Enhanced Electrochemical Biosensors: Mechanisms and Applications

Yang,

Guo,

Wang

et al. 2023

Small

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Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA

Hua,

Zhou,

et al. 2024

Nat Commun

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Aberrant DNA methylation patterns have been used for cancer detection. However, DNA hemi-methylation, present at about 10% CpG dinucleotides, has been less well studied. Here we show that a majority of differentially hemi-methylated regions (DHMRs) in liver tumor DNA or plasma cells free (cf) DNA do not overlap with differentially methylated regions (DMRs) of the same samples, indicating that DHMRs could serve as independent biomarkers. Furthermore, we analyzed the cfDNA methylomes of 215 samples from individuals with liver or brain cancer and individuals without cancer (controls), and trained machine learning models using DMRs, DHMRs or both. The models incorporated with both DMRs and DHMRs show a superior performance compared to models trained with DMRs or DHMRs, with AUROC being 0.978, 0.990, and 0.983 in distinguishing control, liver and brain cancer, respectively, in a validation cohort. This study supports the potential of utilizing both DMRs and DHMRs for multi-cancer detection.

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Preparation and processing of dried blood spots for microRNA sequencing

Morgunova,

Ibrahim,

Chen

et al. 2023

Biology Methods and Protocols

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Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs – small non-coding RNAs that regulate gene activity at the post-transcriptional level – are emerging as critical markers and mediators of disease, including cancer, infectious diseases and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral microRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of microRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of microRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based microRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.

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Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models

Cited by 9 publications

References 47 publications

Nanozyme‐Enhanced Electrochemical Biosensors: Mechanisms and Applications

Nanozyme‐Enhanced Electrochemical Biosensors: Mechanisms and Applications

Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA

Preparation and processing of dried blood spots for microRNA sequencing

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