Biology subjects

Sterr, M.

Publications and source records attributed to Sterr, M..

17 recordsLinked to original sources

bioRxiv2026

MAFA drives pancreatic islet maturation through coordination of cell growth, metabolic maturation, and resilience to stress.

Stem cell-derived islets (SC-islets) are a promising source for replacing the loss of insulin-secreting {beta} cells in insulin-dependent diabetes patients, but compared to their primary human counter parts, SC-islets are considered functionally immature and do not immediately regulate blood glucose after transplantation. To better understand the molecular underpinnings of {beta} cell maturation, we genetically engineered human pluripotent stem cells (hPSCs) to control the induction of the {beta} cell-maturing transcription factor MAFA or a MAFA S64F mutant variant associated with premature {beta} cell aging and senescence in SC-islets. We employ a combination of in vitro assays, multi-omics analyses, and murine in vivo transplantation studies to demonstrate that MAFA remodeling of the SC-islet transcriptional landscape promotes SC-islet biogenesis and metabolic maturation giving rise to greater SC-islet resilience and insulin secretory capacity. Parallel MAFA S64F studies highlight the importance for compensatory mechanisms for sustaining accelerated oxidative metabolism and enhanced insulin secretion without inducing intracellular stress responses and islet dysfunction. Overall, these results reveal MAFA-governed transcriptional changes that drive SC-islet functional maturation, which provides the foundation for maturing SC-islets in vitro, preserving {beta} cell integrity, and improving SC-islet cell replacement therapies.

cell biology↗

bioRxiv2026

The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking

A central challenge in single-cell biology is distinguishing disease-associated remodeling from normal cellular heterogeneity. Addressing this challenge requires healthy reference frameworks that capture cellular diversity across individuals, technologies, and biological contexts. Here we present the Human Pancreas Cell Atlas (HPCA), a reference atlas of the healthy human pancreas integrating 815,126 single-cell and single-nucleus transcriptomes from 109 donors across 12 studies, diverse technologies, and demographics. Using benchmarked integration and community-driven annotations, HPCA defines 94 cell types and transcriptional states spanning endocrine, exocrine, immune, and stromal compartments. The atlas identifies rare endocrine populations, including a putative, spatially supported polyhormonal alpha-beta-delta state, and provides a unified framework for interpreting pancreatic cellular variation across diverse biological and demographic covariates. Projection of disease and model-system datasets onto HPCA contextualized endocrine and epithelial remodeling relative to healthy pancreatic states. Diabetes-associated endocrine cells remained embedded within the healthy endocrine state space while exhibiting disease-specific changes, as supported by spatial and eQTL concordance analyses. Integration with a pancreatic ductal adenocarcinoma atlas resolved injury-associated and malignant epithelial ecosystem regions across donors. Finally, the HPCA enables quantitative benchmarking of murine diabetes models and stem-cell-derived islets against human pancreatic reference states. Together, the HPCA establishes a healthy transcriptional coordinate system for interpreting disease-associated pathophysiology, experimental perturbation, and regenerative fidelity, illustrating how reference atlases can function as analytical frameworks rather than static cell catalogs.

bioinformatics↗

bioRxiv2025

Endocrine-enriched stem cell-derived islets improve long-term safety in vivo

Fully differentiated stem cell-derived islets (SC-islets) are proven to normalise blood glucose in type 1 diabetic patients. However, the presence of off-target cell types and the immature SC-islet function upon transplantation remain unresolved problems. Here, we established sorting strategies to generate SC-islets with defined glucagon-producing SC-- and insulin-producing {beta}-cell ratios and assessed their safety and efficacy in vitro and in vivo. Engineering SC-islets is beneficial to the insulin response in vitro, which does not translate to improved glycaemic regulation in vivo. Importantly, hormone-producing endocrine cell enrichment and thus off-target cell type depletion eliminated the risk for unwanted outgrowth in vivo. Single cell analysis defined off-target cells in vitro and in vivo and identified marker genes to assess SC-islet quality and define safety release criteria before graft transplantation. This study highlights the importance of determining the SC-islet composition and establishing rigorous quality controls to ensure long-term safety for {beta}-cell replacement therapy.

bioengineering↗

bioRxiv2025

Benchmarking porcine pancreatic ductal organoids for drug screening applications

Primary human pancreatic ductal organoids (HPDO) have emerged as a model to study pancreas biology and disease. Yet, donor material availability, and a lack of extensive benchmarking limits the range of applications. To address this gap, we established porcine pancreatic ductal organoids (PPDO) as a system from an easily obtainable source to model pancreatic ductal/progenitor biology. We benchmarked PPDO to HPDO and primary porcine pancreas using single-cell RNA sequencing (scRNA-Seq). We observed no overt phenotypic differences in PPDO derived from distinct developmental stages, with a WNT signaling enriched population characterizing PPDO. PPDO exhibited differentiation potential towards mature ductal cells and limited potential towards endocrine lineages. We used PPDO as a platform to assess the safety of FDA-approved drugs and showed conserved toxicity of statins and -adrenergic receptor inhibitors between PPDO and HPDO cultures. Overall, our results highlight the PPDO as a model for mammalian duct/progenitor applications.

developmental biology↗

bioRxiv2024

Single-cell multiome uncovers differences in glycogen metabolism underlying species-specific speed of development

Embryos from different mammalian species develop at characteristic timescales. These timescales are recapitulated during the differentiation of pluripotent stem cells in vitro. Specific genes and molecular pathways that modulate cell differentiation speed between mammalian species remain to be determined. Here we use single-cell multi-omic analysis of neural differentiation of mouse, cynomolgus and human pluripotent cells to identify regulators for differentiation speed. We demonstrate that species-specific transcriptome dynamics are mirrored at the chromatin level, but that the speed of neural differentiation is insensitive to manipulations of cell growth and cycling. Exploiting the single-cell resolution of our data, we identify glycogen storage levels regulated by UDP-glucose pyrophosphorylase 2 (UGP2) as a species-dependent trait of pluripotent cells, and show that lowered glycogen storage in UGP2 mutant cells is associated with accelerated neural differentiation. The control of energy storage could be a general strategy for the regulation of cell differentiation speed.

developmental biology↗

bioRxiv2024

Resolving human α versus β cell fate allocation for the generation of stem cell-derived islets

Generating stem cell-derived glucagon-producing (SC- cells) and insulin-producing {beta} cells (SC-{beta} cells) allows to engineer an in vitro biomimetic of the islet of Langerhans, the micro-organ controlling blood glucose, however, there is still a major knowledge gap in the mode and mechanism by which human SC- and {beta} cells are specified. Mouse studies postulated that Aristaless Related homeobox (Arx) and Paired box 4 (Pax4) transcription factors cross-inhibit each other in endocrine progenitors to promote or {beta} cell fate allocation, respectively. To test this model in human, we generated an ARXCFP/CFP; PAX4mCherry/mCherry double knock-in reporter induced pluripotent stem cell (iPSC) line to combine time-resolved cell lineage labeling with high-resolution single cell multiomic analysis. Strikingly, lineage labelling and tracing, proteomic and gene regulatory network (GRN) analysis and potency assays revealed a human specific mode and regulatory logic of versus {beta} cell fate allocation. Importantly, pharmacological perturbation using drugs previously proposed to trigger -to-{beta} cell transdifferentiation or identified via our GRN analysis led to enhanced endocrine induction and directed vs {beta} cell fate commitment. Thus, shedding light on basic mechanisms of endocrine induction and fate segregation not only paves the way to engineer islets from pluripotent stem cells, but also has broader implications for cell-replacement therapy, disease modelling and drug screening.

cell biology↗

bioRxiv2024

Chronic intermittent fasting impairs β-cell maturation and function in adolescent mice

Intermittent fasting (IF) is a nutritional lifestyle intervention with broad metabolic benefits, but whether the impact of IF depends on the individuals age is unclear. Here, we investigated the effects of IF on systemic metabolism and pancreatic islet function in old, middle-aged, and young mice. Short-term IF improved glucose homeostasis across all age groups, without altering islet function and morphology. In contrast, while chronic IF was beneficial for adult mice, it resulted in impaired {beta}-cell function in the young. Using scRNAseq, we delineated that the {beta}-cell maturation and function score were reduced in young mice. In human islets, a similar pattern was observed in Type 1 (T1D), but not in Type 2 diabetes (T2D), suggesting that the impact of chronic IF in adolescence is linked to the development of {beta}-cell dysfunction. Our study suggests considering the duration of IF in younger people, as it may enhance rather than reduce diabetes outcomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/590140v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1676dd1org.highwire.dtl.DTLVardef@15ac993org.highwire.dtl.DTLVardef@167f577org.highwire.dtl.DTLVardef@247e4e_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LILong-term IF impairs {beta}-cell function in adolescent mice. C_LIO_LIIF-induced impaired {beta}-cell function is associated with impaired proliferative capacity and lower levels of mature cells. C_LIO_LIIF-induced impaired {beta}-cell function is associated with a transcriptional change highly conserved in type 1-, but not type 2 diabetes. C_LI

physiology↗

bioRxiv2024

Capture of Human Neuromesodermal and Posterior Neural Tube Axial Stem Cells

The spinal cord, nerves, and skeletal muscles arise from neuromesodermal progenitors (NMPs). We have developed a growth-factor screening strategy, utilizing ES and iPS cells, facilitating the indefinite self-renewal of two types of human axial stem cells (AxSCs), closely resembling mouse NMPs (NM-AxSCs) and posterior neural tube progenitors (N-AxSCs). Under specific regimens-- Wnt/CHIR99021, FGF2, and TGF-{beta} inhibitor SB431542 (CFS) and excluding FGF2 (CS), respectively--these AxSCs self-renew and sustain telomeres. Single cell transcriptomics and proteomics have revealed expression of posterior growth-zone and dorsoventral neural tube markers in NM-AxSCs, and correspondingly, differentiation to a wide spectrum of neural tube neurons and myocytes. N-AxSCs rapidly matured into dorsal sensory subsets and neural crest. Crucially, neither AxSC type produces teratomas, and analogous mouse NM-AxSCs integrated successfully into the neural tube and somites. Capturing of AxSCs from patient and GMP ES / iPS cells without transgenesis unveils ontogeny and promises modeling and therapy in neuropathies.

developmental biology↗

bioRxiv2024

Space-time dynamics of genome replication studied with super-resolved microscopy

Genome replication requires duplication of the complete set of DNA sequences together with nucleosomes and epigenetic signatures. Notwithstanding profound knowledge on mechanistic details of DNA replication, major problems of genome replication have remained unresolved. In this perspective article, we consider the accessibility of replication machines to all DNA sequences in due course, the maintenance of functionally important positional and structural features of chromatid domains during replication, and the rapid transition of CTs into prophase chromosomes with two chromatids. We illustrate this problem with EdU pulse-labeling (10 min) and chase experiments (80 min) performed with mouse myeloblast cells. Following light optical serial sectioning of nuclei with 3D structured illumination microscopy (SIM), seven DNA intensity classes were distinguished as proxies for increasing DNA compaction. In nuclei of cells fixed immediately after the pulse-label, we observed a relative under-representation of EdU-labeled DNA in low DNA density classes, representing the active nuclear compartment (ANC), and an over-representation in high density classes representing the inactive nuclear compartment (INC). Cells fixed after the chase revealed an even more pronounced shift to high DNA intensity classes. This finding contrasts with previous studies of the transcriptional topography demonstrating an under-representation of epigenetic signatures for active chromatin and RNAPII in high DNA intensity classes and their over-representation in low density classes. We discuss these findings in the light of current models viewing CDs either as structural chromatin frameworks or as phase-separated droplets, as well as methodological limitations that currently prevent an integration of this contrasting evidence for the spatial nuclear topography of replication and transcription into a common framework of the dynamic nuclear architecture.

cell biology↗

bioRxiv2023

Mapping cells through time and space with moscot

Single-cell genomics technologies enable multimodal profiling of millions of cells across temporal and spatial dimensions. Experimental limitations prevent the measurement of all-encompassing cellular states in their native temporal dynamics or spatial tissue niche. Optimal transport theory has emerged as a powerful tool to overcome such constraints, enabling the recovery of the original cellular context. However, most algorithmic implementations currently available have not kept up the pace with increasing dataset complexity, so that current methods are unable to incorporate multimodal information or scale to single-cell atlases. Here, we introduce multi-omics single-cell optimal transport (moscot), a general and scalable framework for optimal transport applications in single-cell genomics, supporting multimodality across all applications. We demonstrate moscots ability to efficiently reconstruct developmental trajectories of 1.7 million cells of mouse embryos across 20 time points and identify driver genes for first heart field formation. The moscot formulation can be used to transport cells across spatial dimensions as well: To demonstrate this, we enrich spatial transcriptomics datasets by mapping multimodal information from single-cell profiles in a mouse liver sample, and align multiple coronal sections of the mouse brain. We then present moscot.spatiotemporal, a new approach that leverages gene expression across spatial and temporal dimensions to uncover the spatiotemporal dynamics of mouse embryogenesis. Finally, we disentangle lineage relationships in a novel murine, time-resolved pancreas development dataset using paired measurements of gene expression and chromatin accessibility, finding evidence for a shared ancestry between delta and epsilon cells. Moscot is available as an easy-to-use, open-source python package with extensive documentation at https://moscot-tools.org.

bioinformatics↗

bioRxiv2022

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

Multiple pancreatic islet single-cell RNA sequencing (scRNA-seq) datasets have been generated to study development, homeostasis, and diabetes. However, there is no consensus on cell states and pathways across conditions as well as the value of preclinical mouse models. Since these challenges can only be resolved by jointly analyzing multiple datasets, we present a scRNA-seq cross-condition mouse islet atlas (MIA). We integrated over 300,000 cells from nine datasets with 56 samples, varying in age, sex, and diabetes models, including an autoimmune type 1 diabetes (T1D) model (NOD), a gluco-/lipotoxicity T2D model (db/db), and a chemical streptozotocin (STZ) {beta}-cell ablation model. MIA is a curated resource for interactive exploration and computational querying, providing new insights inaccessible from individual datasets. The {beta}-cell landscape of MIA revealed new disease progression cell states and cross-publication differences between previously suggested marker genes. We show that in the STZ model {beta}-cells transcriptionally correlate to human T2D and mouse db/db, but are less similar to human T1D and mouse NOD. We observe different pathways shared between immature, aged, and diabetes model {beta}-cells. In conclusion, our work presents the first comprehensive analysis of {beta}-cell responses to different stressors, providing a roadmap for the understanding of {beta}-cell plasticity, compensation, and demise.

bioinformatics↗

bioRxiv2022

Hypercaloric diet triggers transient molecular rearrangements of astrocytes selectively in the arcuate nucleus

Hypothalamic astrocytes are particularly affected by energy-dense food consumption. How the anatomical location of these glial cells and their spatial molecular distribution in the arcuate nucleus of the hypothalamus (ARC) determine the cellular response to a high caloric diet remains unclear. In this study, we investigated their distinctive molecular responses following the exposure to a high-fat high-sugar (HFHS) diet, specifically in the ARC. Using RNA sequencing and proteomics, we showed that astrocytes have a distinct transcriptomic and proteomic profile dependent on their anatomical location, with a major proteomic reprogramming in hypothalamic astrocytes. By ARC single-cell sequencing, we observed that a HFHS diet dictates time- and cell-specific transcriptomic responses, revealing that astrocytes have the most distinct regulatory pattern compared to other cell types. Lastly, we topographically and molecularly characterized astrocytes expressing glial fibrillary acidic protein and/or aldehyde dehydrogenase 1 family member L1 in the ARC, of which the abundance was significantly increased, as well as the alteration in their spatial and molecular profiles, with a HFHS diet. Together, our results provide a detailed multi-omics view on the spatial and temporal changes of astrocytes particularly in the ARC during different time points of adaptation to a high caloric diet.

neuroscience↗

bioRxiv2022

True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin

Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggested only modest compaction differences ([~]2-10x) between active and inactive nuclear compartments (ANC and INC). Here, we present maps of nuclear landscapes with true-to-scale DNA-densities, ranging from <5 Mbp/{micro}m3 to >300 Mbp/{micro}m3. Maps were generated from individual human and mouse cell nuclei with single-molecule localization microscopy at [~]20 nm lateral and [~]100 nm axial resolution and supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription and replication into nuclei of living cells, demonstrated their localization and movements within the ANC and exclusion from the INC.

cell biology↗

bioRxiv2021

Multi-omics and 3D-imaging reveal bone heterogeneity and unique calvaria cells in neuroinflammation

The meninges of the brain are an important component of neuroinflammatory response. Diverse immune cells move from the calvaria marrow into the dura mater via recently discovered skull-meninges connections (SMCs). However, how the calvaria bone marrow is different from the other bones and whether and how it contributes to human diseases remain unknown. Using multi-omics approaches and whole mouse transparency we reveal that bone marrow cells are highly heterogeneous across the mouse body. The calvaria harbors the most distinct molecular signature with hundreds of differentially expressed genes and proteins. Acute brain injury induces skull-specific alterations including increased calvaria cell numbers. Moreover, TSPO-positron-emission-tomography imaging of stroke, multiple sclerosis and neurodegenerative disease patients demonstrate disease-associated uptake patterns in the human skull, mirroring the underlying brain inflammation. Our study indicates that the calvaria is more than a physical barrier, and its immune cells may present new ways to control brain pathologies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/473988v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@978194org.highwire.dtl.DTLVardef@bc45e8org.highwire.dtl.DTLVardef@91afdborg.highwire.dtl.DTLVardef@b06bc6_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBone marrow across the mouse body display heterogeneity in their molecular profile C_LIO_LICalvaria cells have a distinct profile that is relevant to brain pathologies C_LIO_LIBrain native proteins are identified in calvaria in pathological states C_LIO_LITSPO-PET imaging of the human skull can be a proxy of neuroinflammation in the brain C_LI Supplementary Videos can be seen at: http://discotechnologies.org/Calvaria/

cell biology↗

bioRxiv2021

A strategy to address dissociation-induced compositional and transcriptional bias for single-cell analysis of the human mammary gland

Single-cell transcriptomics provide insights into cellular heterogeneity and lineage dynamics that are key to better understanding normal mammary gland function as well as breast cancer initiation and progression. In contrast to murine tissue, human mammary glands require laborious dissociation protocols to isolate single cells. This leads to unavoidable procedure-induced compositional and transcriptional bias. Here, we present a new strategy on how to identify and minimize systematic error by combining different tissue dissociation strategies and then directly comparing composition and transcriptome of isolated cells using single-cell RNA sequencing and flow cytometry. Depending on the tissue isolation strategy, we found dramatic differences in abundance and heterogeneity of certain stromal cells types. Moreover, we identified lineage-specific dissociation-induced gene expression changes that, if left unchecked, could lead to misinterpretation of cellular heterogeneity and, since the basal epithelial population is particularly affected by this, wrongful assignment of putative stem cell populations.

cell biology↗

bioRxiv2020

Wnt/PCP-primed intestinal stem cells directly differentiate into enteroendocrine or Paneth cells

A detailed understanding of intestinal stem cell (ISC) self-renewal and differentiation is required to better treat chronic intestinal diseases. However, different models of ISC lineage hierarchy1-6 and segregation7-12 are debated. Here we report the identification of Lgr5+ ISCs that express Flattop (Fltp), a Wnt/planar cell polarity (PCP) reporter and effector gene. Lineage labelling revealed that Wnt/PCP-activated Fltp+ ISCs are primed either towards the enteroendocrine or the Paneth cell lineage in vivo. Integration of time-resolved lineage labelling with genome-wide and targeted single-cell gene expression analysis allowed us to delineate the ISC differentiation path into enteroendocrine and Paneth cells at the molecular level. Strikingly, we found that both lineages are directly recruited from ISCs via unipotent transition states, challenging the existence of formerly predicted bi- or multipotent secretory progenitors7-12. Transitory cells that mature into Paneth cells are quiescent and express both stem cell and secretory lineage genes, indicating that these cells are the previously described Lgr5+ labelretaining cells7. Wnt/PCP-activated Lgr5+ ISCs are indistinguishable from Wnt/{beta}-catenin-activated Lgr5+ ISCs based on the expression of stem-cell signature or secretory lineagespecifying genes but possess less self-renewal activity. This suggests that lineage priming and cell-cycle exit is triggered at the post-transcriptional level by polarity cues and a switch from canonical to non-canonical Wnt/PCP signalling. Taken together, we identified the Wnt/PCP pathway as a new niche signal and polarity cue regulating stem cell fate. Active Wnt/PCP signalling represents one of the earliest events in ISC lineage priming towards the Paneth and enteroendocrine cell fate, preceding lateral inhibition and expression of secretory lineagespecifying genes. Thus, our findings provide a better understanding of the niche signals and redefine the mechanisms underlying ISC lineage hierarchy and segregation.

developmental biology↗

bioRxiv2019

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2.

Pioneer transcription factors (PTF) can recognize their binding sites on nucleosomal DNA and trigger chromatin opening for recruitment of other non-pioneer transcription factors. However, critical properties of PTFs are still poorly understood, such as how these transcription factors selectively recognize cell type-specific binding sites and under which conditions can they can initiate chromatin remodelling. Here we show that early endoderm binding sites of the paradigm PTF Foxa2 are epigenetically primed by low levels of active chromatin modifications in embryonic stem cells (ESC). Priming of these binding sites is supported by preferential recruitment of Foxa2 to endoderm binding sites compared to lineage-inappropriate binding sites, when ectopically expressed in ESCs. We further show that binding of Foxa2 is required for chromatin opening during endoderm differentiation. However, increased chromatin accessibility was only detected on binding sites which are synergistically bound with other endoderm transcription factors. Thus, our data suggest that binding site selection of PTFs is directed by the chromatin environment and that chromatin opening requires collaboration of PTFs with additional transcription factors.

genomics↗