Biology subjects

Korbie, D.

Publications and source records attributed to Korbie, D..

6 recordsLinked to original sources

bioRxiv2025

Tracking breast cancer progression using Methylscape

Cancer progression is intricately driven by epigenetic reprogramming, where aberrant DNA methylation patterns reshape gene regulation and cellular phenotypes. These alterations include promoter hypermethylation of tumour suppressor genes and global hypomethylation, collectively fuelling oncogenesis and disease advancement. We previously introduced the Methylscape--a distinct cancer-specific DNA methylation landscape characterized by clustered promoter hypermethylation and gene body hypomethylation--that enhances DNAs physical affinity for gold surfaces. In this study, we demonstrate that Methylscape can be leveraged to monitor cancer progression. Using a breast cancer epithelial-mesenchymal transition (EMT) model, we observe an increase in Methylscape enrichment of mesenchymal-state DNA during EMT, suggesting that this method can sensitively detect subtle epigenetic remodelling linked to tumour progression. Using a gold-based DNA desorption enrichment strategy coupled with methylation sequencing and qPCR, we show that hypermethylated regions are preferentially enriched. Finally, we developed a low-cost, disposable screen-printed electrode platform for stage-specific breast cancer monitoring. Together, these findings establish Methylscape as a promising biophysical biomarker for non-invasive and real-time monitoring of cancer progression, advancing its potential for clinical translation.

bioengineering↗

bioRxiv2024

DIYNAFLUOR: An Affordable DIY Plug-and-Play Nucleic Acid Fluorometer for eDNA Quantification in Resource Limited Settings

Nucleic Acid (NA) fluorometry is widely employed for quantifying environmental DNA (eDNA) samples and their downstream DNA sequencing libraries, owing to its sensitivity, accuracy, and speed. However, the high cost of NA fluorometers presents a barrier to eDNA sequencing in resource limited settings (RLSs). For instance, at [~]$1.5-3.3k USD, current NA fluorometers present a greater capital cost than ONTs $1k USD portable MinION third-generation Nanopore sequencing platform. The collapse of international scientific device and consumable supply chains during the COVID-19 pandemic also highlighted the need for distributed manufacturing of molecular research tools to mitigate the impact of increased pricing to RLSs. To address these challenges, we have developed the "DIYNAFLUOR" (DIY Nucleic Acid FLUORometer), a portable, open-source, <$40 USD NA fluorometer, designed using readily available off-the-shelf components, simple 3D-printed parts, and plug-and-play, solder-free assembly. The DIYNAFLUOR was primarily designed to be compatible with the popular DNA-centric Qubit High Sensitivity (HS) and Broad Range (BR) assay kits. Notably, the DIYNAFLUOR demonstrated an in-assay Limit of Detection with the Qubit HS kit of 0.0028 ng/L, and an average absolute bias of 0.018 ng/L across a 0-10 ng/L working range using a 2-point linear calibration methodology. Device verification was performed by comparative measurements with a Qubit 4 fluorometer in a busy biotechnology laboratory, and build instructions were validated through assembly and qualification of three DIYNAFLUOR devices by researchers outside the primary design team. We also describe a custom "extreme"low-cost assay, <13{cents} USD per-measurement, that uses SYBR Safe dye to quantify DNA across a working range of 0-0.5 ng/L. This assay reports a lower sensitivity and accuracy than commercial kits but may be of use to RLSs in times of extreme resource constraints or as a teaching tool for STEM educators. To demonstrate its practical application for field-based eDNA analysis in RLSs, the DIYNAFLUOR was used to perform all quality control measurements throughout the preparation of a 16S and 18S metabarcoding library generated from eDNA extracted from Australian lake water, leading to the successful identification of Australian fauna via Nanopore sequencing. Finally, configurations of the DIYNAFLUOR for RNA and Protein quantification are briefly described. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/626200v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@28244dorg.highwire.dtl.DTLVardef@16749acorg.highwire.dtl.DTLVardef@15c31aorg.highwire.dtl.DTLVardef@bc03e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Unraveling cfDNA Fragmentation Patterns: Linking Chromatin Architecture to Cancer Diagnostic Sensitivity

Circulating cell-free DNA (cfDNA) liquid biopsies offer a powerful, non-invasive approach for cancer diagnostics, leveraging DNA fragments primarily released during apoptosis. Using droplet digital PCR on cfDNA samples from 88 breast and colorectal cancer patients, we uncovered highly consistent nucleosome breakpoints across individuals. Proximity to these cfDNA breakpoints diminishes the sensitivity of somatic mutation assays, including those targeting IDH1 and NRAS hotspot mutations, underscoring the importance of precise nucleosome positioning data. We introduce a probabilistic nucleosome protection scoring method that enables high-resolution mapping of nucleosome positions and cfDNA breakpoints. These maps reveal distinct nucleosome spacing patterns between heterochromatin and euchromatin, corresponding to different chromatin fiber topologies. Analysis of X-chromosome inactivation further supports the topoisomer model: heterochromatins 187 bp nucleosome repeat length differs from euchromatins 182 bp, generating wave interference patterns in nucleosome signals. Our findings suggest that loop-mediated transitions from T2 to T1 topoisomers shape chromatin accessibility and cfDNA fragmentation, advancing the diagnostic potential of liquid biopsy assays. HighlightsO_LINucleosome breakpoint conservation impacts somatic mutation assay sensitivity C_LIO_LIProbabilistic protection scoring enhances cfDNA nucleosome peak resolution C_LIO_LIChromatin states exhibit unique nucleosome spacing linked to distinct topologies, influencing cfDNA fragmentation C_LIO_LIChromosome X-inactivation phasing analyses reveal waveform interference in nucleosome positioning signals C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/623159v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@65893corg.highwire.dtl.DTLVardef@14c986org.highwire.dtl.DTLVardef@ba9306org.highwire.dtl.DTLVardef@10a7364_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2021

An analytical pipeline for DNA Methylation Array Biomarker Studies

DNA methylation is one of the most commonly studied epigenetic biomarkers, due to its role in disease and development. The Illumina Infinium methylation arrays still remains the most common method to interrogate methylation across the human genome, due to its capabilities of screening over 480, 000 loci simultaneously. As such, initiatives such as The Cancer Genome Atlas (TCGA) have utilized this technology to examine the methylation profile of over 20,000 cancer samples. There is a growing body of methods for pre-processing, normalisation and analysis of array-based DNA methylation data. However, the shape and sampling distribution of probe-wise methylation that could influence the way data should be examined was rarely discussed. Therefore, this article introduces a pipeline that predicts the shape and distribution of normalised methylation patterns prior to selection of the most optimal inferential statistics screen for differential methylation. Additionally, we put forward an alternative pipeline, which employed feature selection, and demonstrate its ability to select for biomarkers with outstanding differences in methylation, which does not require the predetermination of the shape or distribution of the data of interest. AvailabilityThe Distribution test and the feature selection pipelines are available for download at: https://github.com/uqjlu8/DistributionTest

bioinformatics↗

bioRxiv2020

Transcriptional comparison of Testicular Adrenal Rest Tumors with fetal and adult tissues

Testicular Adrenal Rest Tumors (TART) are a common complication of unknown origin in patients with Congenital Adrenal Hyperplasia. These benign tumors may derive from cells of adrenal origin or from pluripotent progenitor cells from the fetal adrenogonadal primordium. By comparing the transcriptome of TART with fetal- and adult-testis and adrenal tissues, this study aims to unravel the origin of TART. Targeted transcriptome sequencing was followed by unsupervised clustering-, differential expression-, functional enrichment- and pathway analyses. Immunohistochemistry demonstrated co-expression of adrenal-specific CYP11B1 and testis-specific HSD17B3 in TART, indicating the existence of a distinct TART cell exhibiting both adrenal- and testicular characteristics. Principal component analysis indicated that the TART transcriptome was distinct from either adrenal or testis fetal tissue, making a progenitor-like phenotype of TART unlikely. Rather, TART appears to originate from -or differentiate into-a mature cell type, with both adrenal- and testicular characteristics. The present study, the first to describe the TART transcriptome, expands knowledge about the identity and functional characteristics of TART and identifies clinically targetable pathways associated with fibrosis.

molecular biology↗

bioRxiv2018

MiR-29b-1-5p is altered in BRCA1 mutant tumours and is a biomarker in basal- like breast cancer

Depletion of BRCA1 protein in mouse mammary glands results in defects in lactational development and increased susceptibility to mammary cancer. Extensive work has focussed on the role of BRCA1 in the normal breast and in the development of breast cancer, the cell of origin for BRCA1 tumours and the protein-coding genes altered in BRCA1 deficient cells. However, the role of non-coding RNAs in BRCA1-deficient cells is poorly understood. To evaluate miRNA expression in BRCA1 deficient mammary cells, RNA sequencing was performed on the mammary glands of Brca1 knockout mice. We identified 140 differentially expressed miRNAs, 9 of which were also differentially expressed in human BRCA1 breast tumours or familial non-BRCA1 patients and during normal gland development. We show that BRCA1 binds to putative cis-elements in promoter regions of the miRNAs and regulates their expression, and that four miRNAs (miR-29b-1-5p, miR-664, miR-16-2 and miR-744) significantly stratified the overall survival of basal-like tumours. Importantly the prognostic value of miR-29b-1-5p was higher in significance than several commonly used clinical biomarkers. These results emphasize the role of Brca1 in modulating expression of miRNAs and highlights the potential for BRCA1 regulated miRNAs to be informative biomarkers associated with BRCA1 loss and survival in breast cancer.

cancer biology↗