Biology subjects

Hansen, M. S.

Publications and source records attributed to Hansen, M. S..

4 recordsLinked to original sources

bioRxiv2025

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets

Alternative splicing is an essential mechanism for generating protein diversity by producing distinct isoforms from a single gene. Dysregulation of splicing that affects pancreatic function and immune tolerance has been linked to both type 1 and type 2 diabetes. Next-generation sequencing technologies, with their short read lengths, are limited in their ability to accurately detect splice variants. Long-read sequencing technologies offer the potential to overcome these limitations by providing full-length transcript information; however, their application in single-cell RNA sequencing has been hindered by technical challenges, including insufficient read lengths and higher error rates. Furthermore, cell types that produce high levels of a single transcript, such as islet endocrine cells, can obscure identification of lower abundance transcripts. In this study, we optimized a protocol for single-cell long-read sequencing in pancreatic islets to improve read length and transcript detection. Our findings demonstrate that 5 library preparation protocols outperform 3 protocols, resulting in better transcript identification. Furthermore, we show that targeted depletion of insulin transcripts enhances the detection of informative reads, highlighting the utility of transcript depletion strategies. This optimized protocol enables isoform-specific gene expression analysis and reveals differential transcript usage across the various cell types in pancreatic islets. By leveraging this approach, we gain deeper insights into the transcriptomic complexity and cellular heterogeneity within pancreatic islets. Article HighlightsO_LIThis study addresses the limitations of current single-cell long-read RNA-sequencing (sclrRNA-seq) technologies in detecting full-length transcripts and isoform diversity, particularly in pancreatic islets. C_LIO_LIWe demonstrate that optimizing single-cell library preparation protocols reproducibly enhances read length and transcript identification in pancreatic islets. C_LIO_LI5 capture methods, combined with targeted insulin depletion and extended reverse transcription, significantly improved read length and isoform detection compared to standard protocols, while maximizing the number of informative reads. C_LIO_LIThese improvements yield longer reads in single-cell experiments, substantially enhancing transcript identification and enabling more accurate analysis of isoform diversity. C_LI

genomics↗

bioRxiv2024

Diminished gap junction coupling under diabetogenic conditions does not drive loss of functional β-cell sub-populations

Within the islets of Langerhans, gap junction coupling is important for synchronizing oscillatory free-calcium activity ([Ca2+]) and regulating pulsatile insulin release. In islets from multiple models of diabetes, gap junction coupling is disrupted, and [Ca2+] synchronization and pulsatile insulin is lost. Functional sub-populations have been identified within the islet that are linked to driving synchronized [Ca2+] and insulin release. These sub-populations can be disrupted under conditions associated with diabetes such as glucolipotoxicity and inflammatory environments, and their loss may drive islet dysfunction. Here we investigated how loss of gap junction coupling influences functional subpopulations under diabetogenic environments. We treated islets with a cocktail of pro-inflammatory cytokines, and protected gap junction coupling via co-treatment with a Cx36 peptide S293 that was previously shown to specifically prevent a decline in gap junction permeability and synchronized [Ca2+] dynamics. We performed calcium imaging and ChR2 stimulation, analyzed islet [Ca2+] dynamics and the presence of functional sub-populations including hubs and first-responders. 1h or 24h cytokine-treatment disrupted gap junction coupling, which was fully prevented by S293 peptide co-treatment. Treatment with pro-inflammatory cytokines decreased the recruitment of [Ca2+] upon ChR2 stimulation, increased the time between first and last responding cells upon glucose stimulation, and reduced the number and consistency of hub cells. When preserving gap junction coupling by S293 during cytokine treatment, the presence and consistency of these sub-populations was only marginally improved. We therefore concluded that while gap junction coupling is important for functional sub-populations to exert their influence on islet function, restoration of gap junctions alone is not sufficient to recover functional sub-populations upon diabetogenic conditions. Thus, preventing a disruption to intrinsic {beta}-cell properties that define functional subpopulations is likely important for preserving these sub-populations during diabetes.

biophysics↗

bioRxiv2022

GIP receptor reduces osteoclast activity and improves osteoblast survival by activating multiple signaling pathways

Bone is a dynamic tissue that is remodeled throughout life by bone resorbing osteoclasts and bone forming osteoblasts, to adapt to physiological or mechanical demands. These processes are impaired in osteoporosis, and understanding how bone remodeling is regulated could improve anti-osteoporotic treatments. Clinical investigations show that short-term treatment with glucose-dependent insulinotropic polypeptide (GIP) acutely decreases serum markers of bone resorption and may increase bone formation. However, evidence for direct effects of GIP intracellular signaling and functions in mature human osteoclasts and osteoblasts have not been investigated. We report that the GIP receptor (GIPR) is robustly expressed in mature human osteoclasts. Exposure of osteoclasts to GIP inhibits osteoclastogenesis, delays bone resorption, and increases osteoclast apoptosis by acting upon multiple signaling pathways (cAMP, Src, Akt, calcium, p38) to impair nuclear translocation of nuclear factor of activated T cells 1 (NFATc1) and nuclear factor-{kappa}B (NF{kappa}B). Human osteoblasts also express GIPR, and GIP improves osteoblast survival via cAMP and Akt-mediated pathways. GIP treatment of co-cultures of osteoclasts and osteoblasts also decreased bone resorption. Antagonizing GIPR with GIP(3-30)NH2 abolished the effects of GIP on osteoclasts and osteoblasts. This study demonstrates that GIP inhibits bone resorption and improves survival of human osteoblasts, which could increase bone mass and strength, supporting clinical investigations of the effect of GIP on bone. Moreover, this study demonstrates that GIPR agonism could be beneficial in the treatment of disorders of bone remodeling, such as osteoporosis. One-sentence SummaryGIP acts directly on bone cells to regulate bone remodeling

cell biology↗

bioRxiv2021

TGF-β modulates cell fate in human ES cell-derived foregut endoderm by inhibiting multiple endogenous signaling pathways

Genetic differences between pluripotent stem cell lines causes variable activity of extra-cellular signaling pathways, which limits the reproducibility of directed differentiation protocols. Here we used human embryonic stem cells (hESCs) to interrogate how exogenously provided factors modulate endogenous signaling events during specification of foregut endoderm lineages. We find that TGF-{beta}1 activates an OTX2/LHX1 gene regulatory network that promotes anterior fate by antagonizing endogenous Wnt signaling. In contrast to Porcupine inhibition, the effects of TGF-{beta}1 cannot be reversed by exogenous Wnt ligands, suggesting that induction of SHISA proteins and intracellular accumulation of Fzd receptors make TGF-{beta}1 treated cells refractory to Wnt signaling. Subsequently, TGF-{beta}1-mediated inhibition of Bmp- and Wnt-signaling suppresses liver- and promotes pancreas fate. However, pancreas differentiation is delayed by TGF-{beta}1-induced CYP26A1 expression and inhibition of RA signaling. Our study thus identifies multiple mechanisms of crosstalk between major developmental signaling pathways during foregut patterning.

developmental biology↗