Publications by authors named "Buys de Barbanson"
Article Synopsis
- - The study focuses on glioblastoma (GBM), a dangerous brain cancer, and how patient-derived cancer organoids (PGOs) can help understand how tumors respond to treatments and why they sometimes don't work.
- - Researchers created PGOs from GBM samples and tested how they respond to a cancer drug called temozolomide (TMZ), finding that different organoids had different reactions based on their unique genetic traits.
- - The results show that PGOs can keep the important genetic differences of the tumors and could be used in the future to tailor treatments to individual patients and discover new drug targets.
Organoid evolution models complemented with integrated single-cell sequencing technology provide a powerful platform to characterize intra-tumor heterogeneity (ITH) and tumor evolution. Here, we conduct a parallel evolution experiment to mimic the tumor evolution process by evolving a colon cancer organoid model over 100 generations, spanning 6 months in time. We use single-cell whole-genome sequencing (WGS) in combination with viral lineage tracing at 12 time points to simultaneously monitor clone size, CNV states, SNV states, and viral lineage barcodes for 1,641 single cells.
View Article and Find Full Text PDFRegulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells.
View Article and Find Full Text PDFPost-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow.
View Article and Find Full Text PDFMolecular characterization of Barrett's esophagus at single-cell resolution.
Proc Natl Acad Sci U S A
November 2021
Barrett's esophagus (BE) is categorized, based on morphological appearance, into different stages, which correlate with the risk of developing esophageal adenocarcinoma. More advanced stages are more likely to acquire chromosomal instabilities, but stage-specific markers remain elusive. Here, we performed single-cell DNA-sequencing experiments (scDNAseq) with fresh BE biopsies.
View Article and Find Full Text PDFArticle Synopsis
- The regulation of messenger RNA (mRNA) levels in mammalian cells can be affected by how quickly mRNA is made and broken down.
- Traditional methods measured these rates in bulk populations, but understanding them in dynamic situations like cell differentiation requires analyzing individual cells.
- A new method was developed to track both new and existing mRNA in thousands of single cells, uncovering important strategies that influence gene expression during the cell cycle and differentiation processes.
Article Synopsis
- Advances in microfluidics and low sequencing costs have revolutionized single-cell sequencing technology, allowing for the analysis of thousands to millions of cells in one experiment.
- This rapid data generation presents unique challenges in data science, which the text identifies as central to the future of single-cell biology.
- The article provides an overview of eleven key challenges, including motivating research questions and open problems, making it relevant for both experienced researchers and newcomers to the field.
Wnt dependency and Lgr5 expression define multiple mammalian epithelial stem cell types. Under defined growth factor conditions, such adult stem cells (ASCs) grow as 3D organoids that recapitulate essential features of the pertinent epithelium. Here, we establish long-term expanding venom gland organoids from several snake species.
View Article and Find Full Text PDFThe culturing of mini-organs (organoids) in three-dimensions (3D) presents a simple and powerful tool to investigate the principles underlying human organ development and tissue self-organization in both healthy and diseased states. Applications of single molecule analysis are highly informative for a comprehensive understanding of the complexity underlying tissue and organ physiology. To fully exploit the potential of single molecule technologies, the adjustment of protocols and tools to 3D tissue culture is required.
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