Biology subjects

Blum, B.

Publications and source records attributed to Blum, B..

11 recordsLinked to original sources

bioRxiv2026

Capture-(Hi)C analysis with PostChicago: Integrative metaprofiling and quantitative comparison of chromatin interactions

Functionally linking enhancers to gene promoters at high resolution often entails analysis of 3C datasets, including viewpoint-based methods such as Capture-(Hi)C. Quantitative comparison across samples and experiments, together with visualization and integration of promoter interactions with other datasets are of critical importance. While existing statistical tools identify significant interactions and quantify underlying signal, systematically comparing the shape and extent of this signal across large sets of intervals remains challenging. Moreover, experimental artefacts, such as inefficient crosslinking, can affect downstream interpretation, but are difficult to detect systematically. Here we introduce PostChicago, an R/Bioconductor package that fills this gap. Building upon the widely used interaction-calling package Chicago, PostChicago provides a complete workflow for quality control, visualization, integration and quantitative analysis of promoter interactions between multiple samples, including annotation and quantification of genomic regions based on external datasets. PostChicago extends visual quantitative comparisons beyond individual viewpoints by computing normalized metaprofiles around large sets of intervals that visualize the distribution of interaction signal, enabling comparison between narrow and broad interaction patterns. We further demonstrate how PostChicago can identify experimental crosslinking artefacts. Together, PostChicago enables integrative, shape-sensitive analysis and quality control of promoter Capture-(Hi)C datasets at a scale that would otherwise require extensive custom scripting.

bioinformatics↗

bioRxiv2026

Stromal and Neuronal Sources of Slit2/3 Ligands in the Adult Pancreas Exhibit Distinct Expression Patterns Independent of Robo2 Receptor Expression in the Islet

Pancreatic islets regulate blood glucose homeostasis. Although islet architecture is stable under homeostatic conditions, increased metabolic demand drives compensatory islet expansion. In mice, islets are organized as a {beta} cell core surrounded by a mantle of and {delta} cells. The formation of islet architecture during development requires expression of Roundabout receptors 1 and 2 (Robo1/2) in endocrine cells and of Slits 2 and 3 (Slit2/3) from islet-extrinsic sources. Furthermore, expression of Robo2 in endocrine cells is required to maintain islet architecture in the adult mouse. However, the cellular sources of Slit2/3 in the adult pancreas and their expression dynamics during islet expansion remain unknown. Here, we identify distinct stromal populations, including fibroblasts and pericytes, as well as neurons within intrapancreatic ganglia, as the sources of Slit2/3. We further show that Slit3 expression is increased in Ob/Ob mice, and that SLIT2 expression is elevated in stromal cell populations of humans with type 2 diabetes. The expression of neither Slit2 nor Slit3 was affected by deletion of Robo2 in {beta} cells. Together, these findings define the cellular origins of Slit2/3 and their expression dynamics in the adult pancreas, supporting a potential role for Slit signaling in the diabetic islet microenvironment.

developmental biology↗

bioRxiv2026

Genome-wide cell type-specific and sex-specific transcriptional dysregulation in the islet of Langerhans underlies islet dysfunction in Down syndrome-related diabetes

Individuals with Down syndrome (trisomy of human chromosome 21) are at a significantly higher risk of developing type 2 diabetes (T2D) than the general population. Systemic metabolic defects in Down syndrome have been linked to gene expression dysregulation in peripheral tissues like the liver, muscle, brain, and adipose. However, the contribution of gene expression dysregulation in the islets of Langerhans to the increased risk of T2D in Down syndrome has not been explored. Here we show that trisomic Ts65Dn mice, a common Down syndrome mouse model, are glucose intolerant and display reduced {beta}-to- cell ratio compared to disomic controls. Using single cell RNA sequencing on islets from Ts65Dn mice we found genome-wide, cell type-specific, and sex-specific transcriptional dysregulation in trisomic islets compared to controls. The Down syndrome-associated transcriptional signature revealed important islet defects, both at the cell autonomous level and at the whole-islet level, increasing T2D susceptibility. Our results put forth innate islet defects as a central underlying cause of Down syndrome-related T2D, warranting additional studies.

developmental biology↗

bioRxiv2026

Chemo-omic pipeline enables discovery of prion synaptotoxic pathways and inhibitory drugs

Prion propagation, in which the cellular prion protein (PrPC) is conformationally converted into an infectious structure (PrPSc), is now well understood. However, the molecular mechanism responsible for the neurotoxicity of prions remains unclear. Synaptic loss is one of the earliest events in both in vivo and in vitro models of prion disease. We previously developed a neuronal cell culture model to analyze the mechanisms of prion-induced synaptic degeneration in a physiologically relevant setting. Using this system, we showed that exposure of hippocampal neurons to PrPSc engages a NMDAR/p38 mitogen-activated protein kinase (MAPK) signaling pathway that results in rapid, PrPC-dependent loss of synaptic transmission and retraction of dendritic spines. To comprehensively identify the components of this synaptotoxic signaling pathway, we measured changes in the phosphoproteome and transcriptome of hippocampal neurons exposed to PrPSc while they were undergoing the process of dendritic spine retraction. We then used these data as input into the L1000 and P100 databases of transcriptomic and proteomic drug signatures, leading to the discovery of 17 compounds that were able to prevent PrPSc-induced spine retraction. These compounds converged on three protein kinase targets: Ca2+/calmodulin-dependent protein kinase II (CaMKII), protein kinase C (PKC), and glycogen synthase kinase 3{beta} (GSK3{beta}). Using immunocytochemical staining, we confirmed that PrPSc treatment of hippocampal neurons induced phosphorylation of the three kinases and caused their rapid translocation to dendritic spines. Along with N-methyl-D-aspartate receptors (NMDARs) on the neuronal surface, which trigger an initial influx of Ca2+ in response to PrPSc, these kinases constitute key nodes in a signaling network that mediates prion synaptotoxicity. Taken together, our results provide new insights into the mechanisms of prion neurotoxicity, and they identify novel molecular targets and inhibitory compounds that can be utilized for therapy of prion diseases. AUTHOR SUMMARYThe mechanism by which prions propagate is now well established, but how they cause neurodegenerative changes is still uncertain. The earliest effects of prion infection occur at the level of the synapse, and we previously established an experimental system using cultured hippocampal neurons to assay prion synaptotoxicity. To search comprehensively for components of the synaptotoxic signaling pathway, we employed a novel, small-molecule discovery pipeline based on the transcriptomic and phosphoproteomic profiles of prion-treated neurons. This approach converged on inhibitors of three different protein kinases (Ca2+/calmodulin-dependent protein kinase II, protein kinase C, and glycogen synthase kinase 3{beta}), which, along with N-methyl-D-aspartate receptors, constitute key nodes in a prion synaptotoxic signaling network that can be targeted for therapeutic benefit.

neuroscience↗

bioRxiv2022

Islet architecture in adult mice is actively maintained by Robo2 expression in beta cells

Pancreatic islets of Langerhans have a non-random spatial architecture, which is important to proper glucose homeostasis. Islet architecture forms during embryonic development, in a morphogenesis process partially involving expression of Roundabout (Robo) receptors in {beta} cells, and their ligand, Slit, in the surrounding mesenchyme. Whether islet architecture is set during development and remains passive in adulthood, or whether it requires active maintenance throughout life, has not been determined. To distinguish between these two models, we conditionally deleted Robo2 in {beta} cells of adult mice and observed their islet architecture following a two-month chase. Here, we show that deleting Robo2 in adult {beta} cells causes significant loss of islet architecture without affecting {beta} cell identity, maturation, or stress, indicating that Robo2 plays a role in actively maintaining adult islet architecture. Understanding the factors required to maintain islet architecture, and thus optimize islet function, is important for developing future diabetes therapies.

developmental biology↗

bioRxiv2021

Platelet proteome analysis reveals an early hyperactive phenotype in SARS-CoV-2-infected humanized ACE2 mice

Coronavirus disease-2019 (COVID-19) provokes a hypercoagulable state with increased incidence of thromboembolism and mortality. Platelets are major effectors of thrombosis and hemostasis. Suitable animal models are needed to better understand COVID-19-associated coagulopathy (CAC) and underlying platelet phenotypes. Here, we assessed K18-hACE2 mice undergoing a standardized SARS-CoV-2 infection protocol to study dynamic platelet responses via mass spectrometry-based proteomics. In total, we found significant changes in >1,200 proteins. Strikingly, protein alterations occurred rapidly by 2 days post-infection (dpi) and preceded outward clinical signs of severe disease. Pathway enrichment analysis of 2dpi platelet proteomes revealed that SARS-CoV-2 infection upregulated complement-coagulation networks (F2, F12, CFH, CD55/CD59), platelet activation-adhesion-degranulation proteins (PF4, SELP, PECAM1, HRG, PLG, vWF), and chemokines (CCL8, CXCL5, CXCL12). When mice started to lose weight at 4dpi, pattern recognition receptor signaling (RIG-I/MDA5, CASP8, MAPK3), and interferon pathways (IFIT1/IFIT3, STAT1) were predominant. Interestingly, SARS-CoV-2 spike protein in the lungs was observed by immunohistochemistry, but in platelets was undetected by proteomics. Similar to patients, K18-hACE2 mice during SARS-CoV-2 infection developed progressive lymphohistiocytic interstitial pneumonia with platelet aggregates in the lungs and kidneys. In conclusion, this model recapitulates activation of coagulation, complement, and interferon responses in circulating platelets, providing valuable insight into platelet pathology during COVID-19. Key PointsO_LISARS-CoV-2-infected humanized ACE2 mice recapitulate platelet reprogramming towards activation-degranulation-aggregation. C_LIO_LIComplement/coagulation pathways are dominant in platelets at 2 days post-infection (dpi), while interferon signaling is dominant at 4dpi. C_LI

immunology↗

bioRxiv2021

Macrophages govern antiviral responses in human lung tissues protected from SARS-CoV-2 infection

The majority of SARS-CoV-2 infections among healthy individuals result in asymptomatic to mild disease. However, the immunological mechanisms defining effective lung tissue protection from SARS-CoV-2 infection remain elusive. Unlike mice solely engrafted with human fetal lung xenograft (fLX), mice co-engrafted with fLX and a myeloid-enhanced human immune system (HNFL mice) are protected against SARS-CoV-2 infection, severe inflammation, and histopathology. Effective control of viral infection in HNFL mice associated with significant macrophage infiltration, and the induction of a potent macrophage-mediated interferon response. The pronounced upregulation of the USP18-ISG15 axis (a negative regulator of IFN responses), by macrophages was unique to HNFL mice and represented a prominent correlate of reduced inflammation and histopathology. Altogether, our work shed light on unique cellular and molecular correlates of lung tissue protection during SARS-CoV-2 infection, and underscores macrophage IFN responses as prime targets for developing immunotherapies against coronavirus respiratory diseases. HIGHLIGHTSO_LIMice engrafted with human fetal lung xenografts (fLX-mice) are highly susceptible to SARS-CoV-2. C_LIO_LICo-engraftment with a human myeloid-enriched immune system protected fLX-mice against infection. C_LIO_LITissue protection was defined by a potent and well-balanced antiviral response mediated by infiltrating macrophages. C_LIO_LIProtective IFN response was dominated by the upregulation of the USP18-ISG15 axis. C_LI

microbiology↗

bioRxiv2021

The Anna Karenina model of beta cell maturation in development and their dedifferentiation in type 1 and type 2 diabetes

Loss of mature {beta} cell function and identity, or {beta} cell dedifferentiation, is seen in all types of diabetes mellitus. Two competing models explain {beta} cell dedifferentiation in diabetes. In the first model, {beta} cells dedifferentiate in the reverse order of their developmental ontogeny. This model predicts that dedifferentiated {beta} cells resemble {beta} cell progenitors. In the second model, {beta} cell dedifferentiation depends on the type of diabetogenic stress. This model, which we call the "Anna Karenina" model, predicts that in each type of diabetes, {beta} cells dedifferentiate in their own way, depending on how their mature identity is disrupted by any particular diabetogenic stress. We directly tested the two models using a {beta} cell-specific lineage-tracing system coupled with RNA-sequencing in mice. We constructed a multidimensional map of {beta} cell transcriptional trajectories during the normal course of {beta} cell postnatal development and during their dedifferentiation in models of both type 1 diabetes (NOD) and type 2 diabetes (BTBR-Lepob/ob). Using this unbiased approach, we show here that despite some similarities between immature and dedifferentiated {beta} cells, {beta} cells dedifferentiation in the two mouse models is not a reversal of developmental ontogeny and is different between different types of diabetes.

developmental biology↗

bioRxiv2020

SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway

SARS-CoV-2 can infect multiple organs, including lung, intestine, kidney, heart, liver, and brain. The molecular details of how the virus navigates through diverse cellular environments and establishes replication are poorly defined. Here, we performed global proteomic analysis of the virus-host interface in a newly established panel of phenotypically diverse, SARS-CoV-2-infectable human cell lines representing different body organs. This revealed universal inhibition of interferon signaling across cell types following SARS-CoV-2 infection. We performed systematic analyses of the JAK-STAT pathway in a broad range of cellular systems, including immortalized cell lines and primary-like cardiomyocytes, and found that several pathway components were targeted by SARS-CoV-2 leading to cellular desensitization to interferon. These findings indicate that the suppression of interferon signaling is a mechanism widely used by SARS-CoV-2 in diverse tissues to evade antiviral innate immunity, and that targeting the viral mediators of immune evasion may help block virus replication in patients with COVID-19.

microbiology↗

bioRxiv2020

Morphogenesis of the islets of Langerhans is guided by extra-endocrine Slit2/3 signals

The spatial architecture of the islets of Langerhans is vitally important for their correct function, and alterations in islet morphogenesis often result in diabetes mellitus. We have previously reported that Roundabout (Robo) receptors are required for proper islet morphogenesis. As part of the Slit-Robo signaling pathway, Robo receptors work in conjunction with Slit ligands to mediate axon guidance, cell migration, and cell positioning in development. However, the role of Slit ligands in islet morphogenesis has not yet been determined. Here we report that Slit ligands are expressed in overlapping and distinct patterns in both endocrine and non-endocrine tissues in late pancreas development. We show that function of either Slit2 or Slit3, which are predominantly expressed in the pancreatic mesenchyme, is required and sufficient for islet morphogenesis, while Slit1, which is predominantly expressed in the {beta} cells, is dispensable for islet morphogenesis. We further show that Slit functions as a repellent signal to {beta} cells. These data suggest that clustering of endocrine cells during islet morphogenesis is guided, at least in part, by repelling Slit2/3 signals from the pancreatic mesenchyme.

developmental biology↗

bioRxiv2019

Islet architecture controls synchronous β cell response to glucose in the intact mouse pancreas in vivo

The spatial architecture of the islets of Langerhans is hypothesized to facilitate synchronized insulin secretion between {beta} cells, yet testing this in vivo in the intact pancreas is challenging. Robo {beta}KO mice, in which the genes Robo1 and Robo2 are deleted selectively in {beta} cells, provide a unique model of altered islet spatial architecture without loss of {beta} cell differentiation or islet damage from diabetes. Combining Robo {beta}KO mice with intravital microscopy, we show here that Robo {beta}KO islets lose synchronized intra-islet Ca2+ oscillations between {beta} cells in vivo. We provide evidence that this loss is not due to a {beta} cell-intrinsic function of Robo, loss of Connexin36 gap junctions, or changes in islet vascularization, suggesting that the islet architecture itself is required for synchronized Ca2+ oscillations. These results have implications for understanding structure-function relationships in the islets during progression to diabetes as well as engineering islets from stem cells.

developmental biology↗