Biology subjects

Reinhardt, S.

Publications and source records attributed to Reinhardt, S..

16 recordsLinked to original sources

bioRxiv2026

Baseline regulatory programs in larval and adult neural progenitors converge towards an injury-induced state after spinal cord injury

Regeneration after spinal cord injury requires progenitor cells to convert injury-associated signals into coordinated remodeling of gene regulatory programs. Mammalian spinal progenitors show limited neurogenic output after injury, whereas zebrafish regenerate spinal neurons and recover motor function. To investigate the regulatory changes that allow ependymo-radial glia (ERG) cells, the progenitor cells of the zebrafish spinal cord, to generate new neurons, we combined single-nucleus gene expression and chromatin accessibility profiling across embryonic, larval, and adult stages with topic-based gene regulatory network (GRN) inference. We found that larval and adult ERGs enter the injury response from distinct regulatory baselines: larval progenitors are characterized by a gliogenic program, whereas adult progenitors maintain a comparatively quiescent state. Following injury, both populations gradually change their baseline programs and shift towards a lesion-associated module marked by stress-responsive and chromatin-associated regulators, including jun, hmga1a, hmga2, ybx1, and foxj1a. The shift away from homeostatic states is supported by decreased expression of the Notch-associated regulators nuclear factor I A (nfia) and hey1 in larvae, while in adults, downregulation of the same nuclear factor and other TFs such as bhlhe41 is associated with quiescence exit. Pathway analysis showed stage-specific alterations after injury, characterized predominantly by extracellular signaling and cytoskeletal reorganization in larvae and by metabolic and translational remodeling in adults. Despite divergence from the homeostatic states, injury-induced larval and adult GRNs remain distinct from embryonic hERG regulatory programs. Thus, larval and adult progenitors follow different trajectories from their baselines towards a related lesion-reactive state, in which shared regeneration-associated features are acquired within respective contexts.

bioinformatics↗

bioRxiv2026

ILK binding to β1 Integrin is indirectly mediated by Kindlin-2

Integrin-linked kinase (ILK) and kindlin-2 (K2) are key components of focal adhesions (FAs) that regulate cell-matrix adhesion and integrin signaling. Both proteins directly bind each other, but how they influence each others localization to FAs and binding to integrins remains a subject of ongoing debate. Here, we establish a sensitive workflow to study protein-protein interactions in cells by combining methods from biochemistry, cell biology and super-resolution microscopy. Together with an analytical framework this approach allowed us to distinguish direct from indirect molecular interactions and construct detailed interaction networks. Disrupting the ILK-K2 interaction reduced ILK localization to FAs and compromised integrin function, whereas K2 recruitment was unaffected. Our interdisciplinary approach also revealed that ILK does not directly bind {beta}1-integrin cytosolic domains in vitro and in cells. Instead, ILK was recruited to integrins exclusively through a K2-dependent mechanism, primarily via K2 bridging ILK and {beta}1 integrins. These findings define the hierarchical relationship between ILK and K2 in FAs and highlight the essential role of K2-mediated ILK recruitment for integrin adhesion and signaling. Significance StatementHow cells anchor to their environment is a fundamental question in biology. Integrins provide such a connection by bridging the extracellular matrix and the cytoskeleton. A central regulator of the integrin machine is Integrin-linked kinase (ILK). How ILK is recruited to {beta}1 integrins is hotly debated since its discovery more than 30 years ago. By integrating cell biology and biochemistry with super-resolution DNA-PAINT microscopy and a novel spatial analysis framework, we demonstrate that ILK does not bind directly to integrin cytoplasmic tails. Instead, we found that ILK is recruited by kindlin-2 (K2) to active, adhesion plaque-resident integrins. This work resolves a long-standing controversy in cell biology and establishes a versatile workflow for distinguishing direct from indirect protein-protein interactions in situ.

cell biology↗

bioRxiv2026

Mesenchymal stroma cell-derived stem cell factor mediates cross-species compatibility of the hematopoietic stem cell niche.

The regulation of human hematopoietic stem cell (HSC) function within its native bone marrow microenvironment remains poorly understood due to the limitations of existing humanized models. Here, we present a non-conditioned human HSC xenotransplantation platform that serves as a physiologically relevant in vivo surrogate to study these complex cellular interactions. Using this system, we uncover a dynamic, cross-species communication between human HSCs and the murine niche, revealing a profound cellular and molecular plasticity of the bone marrow microenvironment in response to humanization. Upon engraftment, platelet-derived growth factor receptor alpha positive (Pdgfra+) mesenchymal stromal cells (MSCs) undergo significant numerical expansion and a major transcriptional shift, transitioning from a mixed adipo- and osteo-primed state toward a leptin receptor positive (Lepr+) predominantly adipo-primed, hematopoiesis-supporting signature. Functional validation demonstrates that this niche plasticity is a critical determinant of stem cell engraftment: the targeted depletion of Lepr+ MSCs or the genetic deletion of stem cell factor results in the rapid mobilization and lack of engraftment of human HSCs, respectively. Our findings establish niche plasticity as a primary regulator of human HSC function and demonstrate the utility of this cross-species platform as a modular genetic toolbox for precise in vivo engineering of the bone marrow microenvironment. Ultimately, this adaptable system provides a powerful framework for elucidating human stem cell biology and advancing bone marrow transplantation therapies.

cell biology↗

bioRxiv2026

Dynamic myosin 10 coupling to DCC and β1 integrin is mediated by intrinsically disordered regions during filopodial transport and patterning

Intrinsically disordered regions (IDRs) are key mediators of protein-protein interactions. IDRs are important components of Myosin 10 (Myo10) and cargo complexes that influence neuronal development and cell growth, yet how IDRs dictate Myo10s cargo affinity and selectivity is not fully understood. Here, we investigate how the actin motor protein Myo10 engages two distinct cargo receptors, DCC and {beta}1 integrin, in cellular protrusions known as filopodia. Using hydrogen-deuterium exchange mass spectrometry (HDX-MS), cross-linking mass spectrometry (XL-MS), live-cell imaging, and super-resolution microscopy, we show that Myo10 decodes IDR elements through two complementary mechanisms: disorder-to-order transitions and "fuzzy" binding. The cytoplasmic portion of DCC binds Myo10 via a weakly helical P3 motif that acts as a preformed recognition element, while additional disordered motifs contribute to affinity through dynamic, weak interactions. In contrast, the {beta}1 integrin tail interacts with Myo10 through short NPxY motifs that remain disordered. Both cargos engage a common Myo10 surface but also contact distinct sites. Super-resolution DNA-PAINT imaging reveals distinct patterning of cargo with Myo10 along and around filopodia. Concentration measurements show that DCC is primarily bound while {beta}1 integrin exhibits a broader range of occupancy along the filopodial shaft. Multiple additive weak contacts and a shared binding site implies that DCC can out-compete integrin for Myo10 binding, which causes redistribution of active {beta}1 integrin from the filopodial tip to the shaft. Our findings illustrate a tunable, multivalent binding strategy that allows Myo10 to selectively coordinate diverse signaling cargos, demonstrating how regulated disorder within IDRs is one mechanism underlying cargo binding and cellular signaling.

biophysics↗

bioRxiv2024

Canonical and non-canonical PRC1 differentially contribute to the regulation of neural stem cell fate

Neocortex development is characterized by sequential phases of neural progenitor cell (NPC) expansion, neurogenesis and gliogenesis. Polycomb-mediated epigenetic mechanisms are known to play important roles in regulating the lineage potential of NPCs during development. The composition of Polycomb Repressive Complex 1 (PRC1) is highly diverse in mammals and was hypothesized to contribute to context-specific regulation of cell fate. Here, we have performed side-by-side comparison of the role of canonical PRC1.2/1.4 and non-canonical PRC1.3/1.5, all of which are expressed in the developing neocortex, in NSC proliferation and differentiation. We found that the deletion of Pcgf2/4 in NSCs led to a strong reduction in proliferation and to altered lineage fate, both during the neurogenic and gliogenic phase, whereas Pcgf3/5 played a minor role. Mechanistically, genes encoding stem cell and neurogenic factors were bound by PRC1 and differentially expressed upon Pcgf2/4 deletion. Thus, rather than different PRC1 sub-complexes contributing to different phases of neural development, we found that canonical PRC1 played a more significant role in NSC regulation during proliferative, neurogenic and gliogenic phases compared to non-canonical PRC1.

developmental biology↗

bioRxiv2023

Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin

Zebrafish faithfully regenerate their fins after amputation which includes restoration of bone tissue and a component of cell plasticity. It is currently unclear how different cell populations of the regenerate divide labor to allow for efficient regenerate growth and proper patterning. Here, we studied lineage relationships of FACS-enriched epidermal, blastemal and bone forming fin regenerate cells by single cell (sc) RNA sequencing, lineage tracing, targeted osteoblast ablation and electron microscopy to show that the majority of osteoblasts in the outgrowing regenerate derive from osterix+ osteoblasts, while mmp9+ cells give rise to a limited cell number at the fin segment joints. A third population of distal blastema cells contributes to distal osteoblast progenitors, suggesting compartmentalization during appendage regeneration. Fin elongation and bone formation are carried out by distinct regenerate cell populations, and these variably depend on Fgf signaling. Ablation of osterix+ osteoblasts irreversibly impairs patterning of segment joints, and prevents bone matrix formation in the proximal regenerate. The resulting reduced regenerate length is partially compensated for by the distal regenerate which shows increased Wnt signaling activity. Surprisingly, ablation of joint cells does not abolish the formation of segment joints. Our study characterizes rare fin regenerate cell populations, indicates intricate osteoblast-blastema lineage relationships, inherent detection and compensation of impaired regeneration, and demonstrates zonation of the elongating regenerate. Furthermore, it sheds light on the variable dependence of bone formation on growth factor signaling.

developmental biology↗

bioRxiv2023

CD38 promotes hematopoietic stem cell dormancy via c-Fos

A subpopulation of deeply quiescent, so-called dormant hematopoietic stem cells (dHSCs) resides at the top of the hematopoietic hierarchy and serves as a reserve pool for HSCs possessing the greatest long-term blood repopulation capacity. The state of dormancy protects the HSC pool from exhaustion throughout life, however excessive dormancy may block an efficient response to hematological stresses. The mechanisms of HSC dormancy remain elusive, mainly due to the absence of surface markers that allow dHSC prompt isolation. Here, we identify CD38 as a novel surface marker for murine dHSCs that is broadly applicable. Moreover, we demonstrate that cyclic adenosine diphosphate ribose (cADPR), the product of CD38 cyclase activity, regulates the expression of the transcription factor c-Fos by increasing cytoplasmic Ca2+ concentration. Strikingly, we uncover that c-Fos drives HSCs dormancy through the induction of the cell cycle inhibitor p57Kip2. Moreover, we found that CD38 ecto-enzymatic activity at the neighboring CD38-positive cells can promote human HSC quiescence. Together, CD38/cADPR/Ca2+/cFos/p57Kip2 axis maintains HSC dormancy. Pharmacological manipulations of this pathway can provide new strategies to expand dHSCs for transplantation or to activate them during hematological stresses.

cell biology↗

bioRxiv2021

Predictive framework of macrophage activation

Macrophages populate every organ during homeostasis and disease, displaying features of tissue imprinting and heterogeneous activation. The disjointed picture of macrophage biology that emerged from these observations are a barrier for integration across models or with in vitro macrophage activation paradigms. We set out to contextualize macrophage heterogeneity across mouse tissues and inflammatory conditions, specifically aiming to define a common framework of macrophage activation. We built a predictive model with which we mapped the activation of macrophages across 12 tissues and 25 biological conditions, finding a striking commonality and finite number of transcriptional profiles, which we modelled as defined stages along four conserved activation paths. We verified this model with adoptive cell transfer experiments and identified transient RELM[a] expression as a feature of macrophage tissue engraftment. We propose that this integrative approach of macrophage classification allows the establishment of a common predictive framework of macrophage activation in inflammation and homeostasis. One Sentence SummaryWe propose an integrative approach of macrophage classification that allows the establishment of a common framework of macrophage activation in inflammation and homeostasis.

immunology↗

bioRxiv2021

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ cells to diabetes recovery in zebrafish

Regeneration-competent species possess the ability to reverse the progression of severe diseases by restoring the function of the damaged tissue. However, the cellular dynamics underlying this capability remain unexplored. Here, we use single-cell transcriptomics to map de novo {beta}-cell regeneration during induction and recovery from diabetes in zebrafish. We show that the zebrafish has evolved two distinct types of somatostatin-producing {delta}-cells, which we term {delta}1- and {delta}2-cells. Moreover, we characterize a small population of glucose-responsive islet cells, which share the hormones and fate-determinants of both {beta}- and {delta}1-cells. The transcriptomic analysis of {beta}-cell regeneration reveals that {beta}/{delta} hybrid cells constitute a prominent source of insulin-expression during diabetes recovery. Using in vivo calcium imaging and cell tracking, we further show that the hybrid cells form de novo and acquire glucose-responsiveness in the course of regeneration. The overexpression of dkk3, a gene enriched in hybrid cells, increases their formation in the absence of {beta}-cell injury. Finally, interspecies comparison shows that plastic {delta}1-cells are partially related to PP-cells in the human pancreas. Our work provides an atlas of {beta}-cell regeneration and indicates that the rapid formation of glucose-responsive hybrid cells contributes to the resolution of diabetes in zebrafish

developmental biology↗

bioRxiv2021

Loss of SETD1B results in the redistribution of genomic H3K4me3 in the oocyte

Histone 3 lysine 4 trimethylation (H3K4me3) is an epigenetic mark found at gene promoters and CpG islands. H3K4me3 is essential for mammalian development, yet mechanisms underlying its genomic targeting are poorly understood. H3K4me3 methyltransferases SETD1B and MLL2 are essential for oogenesis. We investigated changes in H3K4me3 in Setd1b conditional knockout (cKO) oocytes using ultra-low input ChIP-seq, with comparisons to DNA methylation and gene expression analyses. H3K4me3 was redistributed in Setd1b cKO oocytes showing losses at active gene promoters associated with downregulated gene expression. Remarkably, many regions also gained H3K4me3, in particular those that were DNA hypomethylated, transcriptionally inactive and CpG-rich, which are hallmarks of MLL2 targets. Consequently, loss of SETD1B disrupts the balance between MLL2 and de novo DNA methyltransferases in determining the epigenetic landscape during oogenesis. Our work reveals two distinct, complementary mechanisms of genomic targeting of H3K4me3 in oogenesis, with SETD1B linked to gene expression and MLL2 to CpG content. Graphical AbstractIn oogenesis, SETD1B and CXXC1 target H3K4me3 to actively transcribed gene promoters, while MLL2 targets transcriptionally inactive regions based on underlying CpG composition (upper panel). When SETD1B is ablated, H3K4me3 is lost at a subset of active promoters, resulting in downregulation of transcription (lower panel). Loss of SETD1B alters the activity of MLL2, permitting MLL2 to deposit H3K4me3 at CpG-rich regions, many of which should otherwise be DNA methylated. Thus, it is evident that MLL2 and de novo DNMTs compete for genomic occupancy late in oogenesis, and loss of SETD1B disrupts the balance of these mechanisms. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

developmental biology↗

bioRxiv2020

Hematopoietic lineages diverge within the stem cell compartment

Hematopoietic stem cells (HSCs) produce a highly diverse array of cell lineages. To assay hematopoietic differentiation with minimal experimental perturbation, non-invasive methods for heritable labeling1-3 or barcoding4-7 of HSCs in vivo have recently been developed and used to study lineage fate of HSCs in physiological conditions. However, the differentiation pathways leading from HSCs to mature cells remain controversial8, with suggested models ranging from gradual lineage restriction in a branching cascade of progenitors to HSCs already making ultimate lineage decisions. Here we show, by iterating HSC fate-mapping, mitotic history tracking, single-cell RNA-sequencing and computational inference, that the major differentiation routes to megakaryocytes, erythro-myeloid cells and lymphocytes split within HSCs. We identify the hitherto elusive self-renewing source of physiological hematopoiesis as an HSC subpopulation co-expressing high levels of Sca-1 and CD201. Downstream, HSCs reduce Sca-1 expression and enter into either thrombopoiesis or erythro-myelopoiesis, or retain high Sca-1 levels and the ability to generate lymphocytes. Moreover, we show that a distinct population of CD48-/lo megakaryocyte progenitors links HSCs to megakaryocytes. This direct thrombopoiesis pathway is independent of the classical pathway of megakaryocyte differentiation via multipotent progenitors and becomes the dominant platelet production line upon enhanced thrombopoietin signaling. Our results define a hierarchy of self-renewal and lineage decisions within HSCs in native hematopoiesis. Methodologically, we provide a blueprint for mapping physiological differentiation pathways of stem cells and probing their regulation.

systems biology↗

bioRxiv2020

Single-cell transcriptome analysis reveals cell-cell communication and thyrocyte diversity in the zebrafish thyroid gland

The thyroid gland regulates growth and metabolism via production of thyroid hormone in follicles composed of thyrocytes. So far, thyrocytes have been assumed to be a homogenous population. To uncover genetic heterogeneity in the thyrocyte population, and molecularly characterize the non-thyrocyte cells surrounding the follicle, we developed a single-cell transcriptome atlas of the zebrafish thyroid gland. The 6249-cell atlas includes profiles of thyrocytes, blood vessels, lymphatic vessels, immune cells and fibroblasts. Further, the thyrocytes could be split into two sub-populations with unique transcriptional signature, including differential expression of the transcription factor pax2a. To validate thyrocyte heterogeneity, we generated a CRISPR/Cas9-based pax2a knock-in line, which demonstrated specific pax2a expression in the thyrocytes. However, a population of pax2a-low mature thyrocytes interspersed within individual follicles could be distinguished, corroborating heterogeneity within the thyrocyte population. Our results identify and validate transcriptional differences within the nominally homogenous thyrocyte population. One-line summarySingle-cell analysis uncovers latent heterogeneity in thyroid follicular cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/891630v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@f6df3org.highwire.dtl.DTLVardef@fb8c59org.highwire.dtl.DTLVardef@bb5be1org.highwire.dtl.DTLVardef@8d174e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Proliferative behavior of hematopoietic stem cells revisited: No evidence for mitotic memory

The proliferative activity of adult hematopoietic stem cells (HSCs) is controversially discussed. Inducible fluorescent histone 2B fusion protein (H2B-FP) transgenic mice are important tools for tracking the mitotic history of murine HSCs in label dilution experiments. A recent study proposed that the most primitive HSCs divide only four times, to then enter permanent quiescence. We observed that background fluorescence due to leaky H2B-FP expression, occurring in all H2B-FP transgenes independent of label induction, accumulated with age in primitive HSCs with high repopulation potential. We argue that this background had been misinterpreted as retention of induced label and permanent quiescence. We found cell division-independent half-lives of H2B-FPs to be short, which had led to overestimation of HSC divisional activity. Our data do not support HSC mitotic memory and entry into permanent quiescence after few divisions, but show that primitive HSCs of adult mice continue to cycle rarely.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/745729v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@1b97626org.highwire.dtl.DTLVardef@fbc702org.highwire.dtl.DTLVardef@1c66b60org.highwire.dtl.DTLVardef@1b38f69_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Gene expression-based identification of antigen-responsive CD8+ T cells on a single-cell level

CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors and self antigens. Here, we asked how human cognate antigen-responsive CD8+ T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labelled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8+ T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8+ T cells from unselected populations. Gene response profiles of CD8+ T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors.\n\nOne-sentence summaryIdentification of genes, gene sets, and development of a machine learning-based classifier that distinguishes antigen-responsive CD8+ T cells on a single-cell level.

immunology↗

bioRxiv2019

Redox potential defines functional states of adult hippocampal stem cells

Intracellular redox states regulate the balance between stem cell maintenance and activation. Increased levels of reactive oxygen species (ROS) are linked to proliferation and lineage specification. In contrast to this general principle, we show that in the hippocampus of adult mice it is the quiescent neural stem cells (NSCs) that maintain the highest ROS levels (hiROS). Classifying NSCs based on intracellular ROS content identified subpopulations with distinct molecular profiles, corresponding to functional states. Shifts in ROS content primed cells for a subsequent transition of cellular state, with lower cellular ROS content marking activity and differentiation. Physical activity, a known physiological activator of adult hippocampal neurogenesis, recruited the quiescent hiROS NSCs into proliferation via a transient Nox2-dependent ROS surge. In the absence of Nox2, baseline neurogenesis was unaffected, but the activity-induced increase in proliferation disappeared. These results describe a novel mechanism linking the modulation of cellular ROS by behavioral cues to the maintenance and activation of adult NSCs.\n\nHighlightsO_LIQuiescent adult hippocampal stem cells are characterized by high intracellular ROS\nC_LIO_LIChanges in intracellular ROS content precede changes in cellular state\nC_LIO_LIAcute physical activity recruits quiescent cells into active proliferation\nC_LIO_LIThis recruitment is marked by a Nox2-dependent ROS spike in hiROS stem cells and represents an independent mode of cell cycle entry\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/606186_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (65K):\norg.highwire.dtl.DTLVardef@1bbb7ddorg.highwire.dtl.DTLVardef@1241536org.highwire.dtl.DTLVardef@1ec9c32org.highwire.dtl.DTLVardef@102d527_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2018

Machine learning based classification of cells into chronological stages using single-cell transcriptomics.

Age-associated deterioration of cellular physiology leads to pathological conditions. The ability to detect premature aging could provide a window for preventive therapies against age-related diseases. However, the techniques for determining cellular age are limited, as they rely on a limited set of histological markers and lack predictive power. Here, we implement GERAS (GEnetic Reference for Age of Single-cell), a machine learning based framework capable of assigning individual cells to chronological stages based on their trans criptomes. GERAS displays greater than 90% accuracy in classifying the chronological stage of zebrafish and human pancreatic cells. The framework demonstrates robustness against biological and technical noise, as evaluated by its performance on independent samplings of single-cells. Additionally, GERAS determines the impact of differences in calorie intake and BMI on the aging of zebrafish and human pancreatic cells, respectively. We further harness the predictive power of GERAS to identify genome-wide molecular factors that correlate with aging. We show that one of these factors, junb, is necessary to maintain the proliferative state of juvenile beta-cells. Our results showcase the applicability of a machine learning framework to classify the chronological stage of heterogeneous cell populations, while enabling to detect pro-aging factors and candidate genes associated with aging.

bioinformatics↗