Biology subjects

Zhang, S. Y.

Publications and source records attributed to Zhang, S. Y..

9 recordsLinked to original sources

bioRxiv2025

3' Nucleotide Asymmetry Directs miRNA Strand Selection

Accurate microRNA (miRNA) strand selection is essential for defining the regulatory landscape of the miRNA-induced silencing complex (miRISC). While 5' nucleotide identity and duplex thermodynamics have been proposed to bias strand choice, these features cannot fully explain in vivo strand preferences. Here, we uncover a conserved and previously unrecognized role for 3' nucleotide asymmetry in directing miRNA strand selection in Caenorhabditis elegans and human cells. A favorable 3' terminal nucleotide on the passenger strand promotes selective loading of the opposing guide strand into miRISC, revealing a cooperative interplay between 5' and 3' terminal asymmetries that ensures precise strand discrimination. These findings establish a unified, evolutionarily conserved mechanism for miRNA duplex sorting and expand the fundamental rules governing small RNA biogenesis.

molecular biology↗

bioRxiv2024

Modeling Hereditary Diffuse Leukoencephalopathy with Axonal Spheroids using microglia-sufficient brain organoids

Hereditary diffuse leukoencephalopathy with axonal spheroids (HDLS) is a rare, fatal, adult-onset neurodegenerative disease that is most often caused by mutations affecting the Colony Stimulating factor-1 Receptor (CSF-1R). To understand how CSF-1R-mutation affects human microglia - the specialized brain-resident macrophages of the central nervous system - and the downstream consequences for neuronal cells, we used a macrophage and forebrain organoid co-culture system based on induced pluripotent stem cells generated from two patients with HDLS, with CSF-1R gene-corrected isogenic organoids as controls. Macrophages derived from iPSC (iMacs) of patients exhibited a metabolic shift towards the glycolytic pathway and reduced CSF-1 sensitivity, which was associated with higher levels of IL-1{beta} production and an activated inflammatory phenotype. Single-cell RNA sequencing revealed that iMacs adopt a reactive state that leads to impaired regulation of neuronal cell populations in organoid cultures, thereby identifying microglial dysregulation and specifically IL-1{beta} production as key contributors to the degenerative neuro-environment in HDLS.

neuroscience↗

bioRxiv2023

The Topological Properties of the Protein Universe

Deep learning methods have revolutionized our ability to predict protein structures, allowing us a glimpse into the entire protein universe. As a result, our understanding of how protein structure drives function is now lagging behind our ability to determine and predict protein structure. Here, we describe how topology, the branch of mathematics concerned with qualitative properties of spatial structures, provides a lens through which we can identify fundamental organizing features across the known protein universe. We identify topological determinants that capture global features of the protein universe, such as domain architecture and binding sites. Additionally, our analysis also identified highly specific properties, so-called topological generators, that can be used to provide deeper insights into protein structure-function and evolutionary relationships. We used our approach to determine structural, functional and disease consequences of mutations, explain differences in properties of proteins in mesophiles and thermophiles, and the likely structural and functional consequences of polymorphisms in a protein. Overall, we present a practical methodology for mapping the topology of the known protein universe at scale.

bioinformatics↗

bioRxiv2023

Approximate Bayesian Computation for Inferring Waddington Landscapes from Single Cell Data

Single cell technologies allow us to gain insights into cellular processes at unprecedented resolution. In stem cell and developmental biology snapshot data allows us to characterise how the transcriptional state of cells changes between successive cell types. Here we show how approximate Bayesian computation (ABC) can be employed to calibrate mathematical models against single cell data. In our simulation study we demonstrate the pivotal role of the adequate choice of distance measures appropriate for single cell data. We show that for good distance measures, notably optimal transport distances, we can infer parameters for mathematical models from simulated single cell data. We show that the ABC posteriors can be used to characterise parameter sensitivity and identify dependencies between different parameters, and to infer representations of the Waddington or epigenetic landscape, which forms a popular and interpretable representation of the developmental dynamics. In summary, these results pave the way for fitting mechanistic models of stem cell differentiation to single cell data.

systems biology↗

bioRxiv2023

Dynamical information enables inference of gene regulation at single-cell scale

Cell dynamics and biological function are governed by intricate networks of molecular interactions. Inferring these interactions from data is a notoriously difficult inverse problem. The majority of existing network inference methods work at the population level to construct population-averaged representations of gene interaction networks, and thus do not naturally allow us to infer differences in gene regulation activity across heterogeneous cell populations. We introduce locaTE, an information theoretic approach that leverages single cell dynamical information together with geometry of the cell state manifold to infer cell-specific, causal gene interaction networks in a manner that is agnostic to the topology of the underlying biological trajectory. We find that factor analysis can give detailed insights into the inferred cell-specific GRNs. Through extensive simulation studies and applications to three experimental datasets spanning mouse primitive endoderm formation, pancreatic development, and haematopoiesis, we demonstrate superior performance and the generation of additional insights compared to standard static GRN inference methods. We find that locaTE provides a powerful, efficient and scalable network inference method that allows us to distill cell-specific networks from single cell data. Graphical abstractCell-specific network inference from estimated dynamics and geometry LocaTE takes as input a transition matrix P that encodes inferred cellular dynamics as a Markov chain on the cell state manifold. By considering the coupling (X{tau}, X-{tau}), locaTE produces an estimate of transfer entropy for each cell i and each pair of genes (j, k). Downstream factor analyses can extract coherent patterns of interactions in an unsupervised fashion. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/523176v4_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@12dc737org.highwire.dtl.DTLVardef@722a08org.highwire.dtl.DTLVardef@1258a03org.highwire.dtl.DTLVardef@1880a1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2021

Secretory MPP3 reinforce myeloid differentiation trajectory and amplify myeloid cell production

Recent lineage tracing analyses revealed multipotent progenitors (MPP) to be major functional contributors to steady-state hematopoiesis (1-6). However, we are still lacking a precise resolution of myeloid differentiation trajectories and cellular heterogeneity in MPPs. Here, we found that myeloid-biased MPP3 (2, 3) are functionally and molecularly heterogeneous, with a distinct subset of myeloid-primed secretory cells with high endoplasmic reticulum (ER) volume and Fc{gamma}R expression. We show that Fc{gamma}R+/ERhigh MPP3 are a transitional population for rapid production of granulocyte/macrophage progenitors (GMP), which directly amplify myelopoiesis through inflammation-triggered secretion of cytokines in the local bone marrow (BM) microenvironment. Our results identify a novel regulatory function for a subset of secretory MPP3 that controls myeloid differentiation through lineage-priming and cytokine production, and act as a self-reinforcing amplification compartment in stress and disease conditions. One-Sentence SummaryA secretory subset of multipotent hematopoietic progenitors augment myelopoiesis in stress and diseases conditions.

immunology↗

bioRxiv2021

Hematopoiesis at single cell resolution spanning human development and maturation

Hematopoiesis is a process of constitutive regeneration whereby hematopoietic stem and progenitor cells (HSPCs) replenish mature blood cells. During maturation and aging, HSPCs shift their output to support the demands of prenatal development and postnatal maturation both at homeostasis and in response to stress. How HSPC ontogeny changes throughout life is unknown; studies to date have largely focused on specific individual ages, particularly at single cell resolution. Here, we performed single cell RNA-seq of human HSPCs from early prenatal development into mature adulthood. We observed shifts in HSPC transcriptional states and differentiation trajectories over time. We identified age-specific gene expression patterns throughout human maturation and developed methods for identifying, prospectively purifying, and functionally validating age-specific HSC states. Together, our findings define the temporal maturation of human HSPCs and uncover principles applicable to age-biased blood diseases. SummarySingle cell RNA sequencing reveals that the mechanisms of human hematopoietic stem and progenitor cell (HSPC) fate commitment change over a lifetime from gestation to mature adulthood.

developmental biology↗

bioRxiv2021

Stromal inflammation is a targetable driver of hematopoietic aging

Hematopoietic aging is marked by a loss of regenerative capacity and skewed differentiation from hematopoietic stem cells (HSC) leading to dysfunctional blood production. Signals from the bone marrow (BM) niche dynamically tailor hematopoiesis, but the effect of aging on the niche microenvironment and the contribution of the aging niche to blood aging still remains unclear. Here, we characterize the inflammatory milieu in the aged marrow cavity that drives both stromal and hematopoietic remodeling. We find decreased numbers and functionality of osteogenic mesenchymal stromal cells (MSC) at the endosteum and expansion of pro-inflammatory perisinusoidal MSCs with deterioration of sinusoidal endothelium in the central marrow, which together create a degraded and inflamed old niche. Molecular mapping at single cell resolution confirms disruption of cell identities and enrichment of inflammatory response genes in niche populations. Niche inflammation, in turn, drives chronic activation of emergency myelopoiesis pathways in old HSCs and multipotent progenitors (MPP), which promotes myeloid differentiation at the expense of lymphoid and erythroid commitment and hinders hematopoietic regeneration. Remarkably, niche deterioration, HSC dysfunction and defective hematopoietic regeneration, can be improved by blocking inflammatory IL-1 signaling. Our results demonstrate that targeting niche inflammation is a tractable strategy to restore blood production during aging.

cell biology↗

bioRxiv2018

Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid

BackgroundTransposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species.\n\nResultsWe have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~108, which is ~2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported.\n\nConclusionWe have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research.

microbiology↗