Biology subjects

Madsen, J. G. S.

Publications and source records attributed to Madsen, J. G. S..

5 recordsLinked to original sources

bioRxiv2025

Single Nucleus Multiome Analysis Reveals Early Inflammatory Response to High-Fat Diet in Mouse Pancreatic Islets

In periods of sustained hyper-nutrition, pancreatic {beta}-cells undergo functional compensation through transcriptional upregulation of gene programs driving insulin secretion. This adaptation is essential for maintaining systemic glucose homeostasis and metabolic health. Using single nuclei multiomics, we have mapped the early transcriptional compensation mechanisms in murine islets of Langerhans exposed to high-fat diet (HFD) for one and three weeks. We show that {beta}-cells exhibit the largest transcriptional response to HFD, characterized by early activation of proinflammatory eRegulons and downregulation of {beta}-cell identity genes, particularly in a distinct subset of {beta}-cells. Our observations translate to humans, as we observe an increase in the inflammatory gene signatures in human {beta}-cells in pre-diabetes and diabetes. Collectively, these observations point to cellular cross-talk through proinflammatory signaling as a central and early driver of {beta}-cell dysfunction that limits the compensatory capacity of {beta}-cells, which is closely linked to the development of diabetes.

cell biology↗

bioRxiv2025

PAF15-PCNA assembly exhaustion governs lagging strand replication and replisome integrity

Genome replication in eukaryotic cells is surveyed by the S-phase checkpoint, which orchestrates sequential replication origin activation to avoid exhaustion of hitherto poorly defined rate-limiting replisome components. Here, we find that excessive activation of replication origins depletes chromatin-bound PCNA and lagging strand components, thereby limiting additional PCNA loading at new origins when checkpoint control is disrupted. PAF15 (PCNA-associated factor 15) emerges as a dosage-sensitive regulator of PCNA, delineating the dynamic range of global genome duplication and defining distinct roles for PCNA on the leading and lagging strands. Through its high-affinity PIP motif and interaction within the DNA encircling channel of PCNA, PAF15 stabilizes PCNA exclusively on the lagging strand, optimizing and rate-limiting lagging strand processing. On the other hand, misregulation of PAF15--whether by overexpression or mislocalization to the leading strand--impairs replication fork progression and leads to cell death. These defects are mitigated by TIMELESS and CLASPIN, which restrain PAF15-PCNA interactions beyond the lagging strand. E2F4-mediated repression orchestrates PAF15 expression in normal and cancer cells, maintaining its optimal dosage for lagging strand-specific interactions with PCNA. Thus, the S-phase checkpoint functions in concert to restrict origin activation when lagging strand PAF15-PCNA assembly is exhausted, linking a previously concealed strand-specific rate limitation to overall replication dynamics.

biochemistry↗

bioRxiv2025

Single cell-resolved transcriptional dynamics of human subcutaneous adipose tissue during lifestyle- and bariatric surgery-induced weight loss

During sustained weight gain, human white adipose tissue undergoes dramatic remodeling that may compromise adipose tissue function and lead to obesity comorbidities such as cardiometabolic disease. These comorbidities can be at least partially reversed by weight loss; however, the degree to which human adipose tissue is remodeled during weight loss is currently unclear. Here, we have used snRNA-seq combined with bulk RNA-seq and 3D light microscopy to investigate the cellular and transcriptional alterations in abdominal subcutaneous adipose tissue (ASAT) from a unique cohort of obese individuals undergoing initially modest (8-10%) lifestyle-induced weight loss followed by a more dramatic (20-45%) bariatric surgery-induced weight loss. We show that in response to this weight loss, ASAT in both males and females underwent dramatic compositional and transcriptional remodeling. Most notably, surgery-indued weight loss led to an increase in the adipose vascular compartment, a dramatic reduction in proinflammatory immune cells, and a tissue-wide reduction in inflammatory gene signatures. In response to modest weight loss, we observed an increase in specific progenitor populations and an induction of proadipogenic genes, indicating that this process is important for the early adaptation of AT to weight loss that might contribute to the early overall beneficial effects on insulin sensitivity and systemic inflammation.

cell biology↗

bioRxiv2024

Limitations in mitochondrial programming restrain the differentiation and maturation of human stem cell-derived β cells

Pluripotent stem cell (SC)-derived islets offer hope as a renewable source for {beta} cell replacement for type 1 diabetes (T1D), yet functional and metabolic immaturity may limit their long-term therapeutic potential. Here, we show that limitations in mitochondrial transcriptional programming impede the formation of SC-derived {beta} (SC-{beta}) cells. Utilizing transcriptomic profiling, assessments of chromatin accessibility, mitochondrial phenotyping, and lipidomics analyses, we observed that SC-{beta} cells exhibit reduced oxidative and mitochondrial fatty acid metabolism compared to primary human islets that are related to limitations in key mitochondrial transcriptional networks. Surprisingly, we found that reductions in glucose-stimulated mitochondrial respiration in SC-islets were not associated with alterations in mitochondrial mass, structure, or genome integrity. In contrast, SC-islets show limited expression of targets of PPAR, which regulate mitochondrial programming, yet whose functions in {beta} cell differentiation are unknown. Importantly, treatment with WY14643, a potent PPAR agonist, induced expression of mitochondrial targets, improved insulin secretion, and increased the formation of SC-{beta} cells both in vitro and following transplantation. Thus, PPAR-dependent mitochondrial programming promotes the differentiation of SC-{beta} cells and may be a promising target to improve {beta} cell replacement efforts for T1D.

developmental biology↗

bioRxiv2023

Automatic quality control of single-cell and single-nucleus RNA-seq using valiDrops

Single-cell and single-nucleus RNA-sequencing (sxRNA-seq) measures gene expression in individual cells or nuclei, which enables unbiased characterization of cell types and states in tissues. However, the isolation of cells or nuclei for sxRNA-seq can introduce artifacts, such as cell damage and transcript leakage. This can distort biological signals and introduce contamination from debris. Thus, the identification of barcodes con-taining high-quality cells or nuclei is a critical analytical step in the processing of sxRNA-seq data. Here, we present valiDrops, which is a novel data-adaptive method to identify high-quality barcodes and flag dead cells. In valiDrops, barcodes are initially filtered using data-adaptive thresholding on community-standard quality metrics and subsequently, valiDrops uses a novel clustering-based approach to identify barcodes with biological distinct signals. We benchmark valiDrops and existing methods and find that the biological signals from cell types and states are more distinct, easier to separate and more consistent after filtering by valiDrops. Finally, we show that valiDrops can be used to predict and flag dead cells with high accuracy. This novel classifier can further improve data quality or be used to identify dead cells to interrogate the biology of cell death. Thus, valiDrops is an effective and easy-to-use method to remove barcodes associated with low quality cells or nuclei from sxRNA-seq datasets, thereby improving data quality and biological interpretation. Our method is openly available as an R package at www.github.com/madsen-lab/valiDrops.

bioinformatics↗