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Biology subjects

Klein, A. M.

Publications and source records attributed to Klein, A. M..

At least 19 recordsLinked to original sources

Tree diversity intensifies soil microorganism-tree interactions

O_LIA productivity-driven higher nutrient demand of trees in diverse mixtures is frequently reported. Yet, it remains unclear how tree diversity influences microorganisms-plants interactions, in which microbes facilitate tree nutrient acquisition in exchange for carbon (C) to meet the resource demand of both. C_LIO_LIUsing a long-term tree diversity experiment in the subtropics, we assessed microbial investment in C-, nitrogen (N)-, and phosphorus (P)-acquiring enzymes in litter and mineral soil, testing the effects of tree species richness and mycorrhizal type (arbuscular (AM)- vs. ectomycorrhizal (EcM)-associated tree species). C_LIO_LIWith increasing tree species richness, microbial investment in C acquisition decreased, while investment in N and/or P acquisition increased in litter and in mineral soil. In mineral soil of AM-associated tree mixtures, ecoenzymatic stoichiometry revealed a shift from microbial investment in C toward P acquisition as tree species richness increased. C_LIO_LIOur findings suggest that tree diversity strengthens microbe-tree interactions in terms of C-for-nutrient exchange. This highlights the key role of soil microorganisms, particularly in AM symbiosis, shaping tree diversity-biogeochemical feedbacks. C_LI

ecology↗

A single-cell transcriptomic atlas of inner ear morphogenesis in zebrafish

The inner ear constitutes different cell types next to one another: the sensory patches whose hair cells synapse with neurons, the thin channels of three semicircular canals whose perpendicular organization enables detection of directional head rotation, and the endolymphatic duct and sac whose conditional epithelial barrier relieves excess pressure and promotes fluid pressure homeostasis. How the ears component cell states are established during development has remained unknown. We use single-cell RNA sequencing to distinguish cell states within the developing ear with wild-type zebrafish embryos and lmx1bb mutants that exhibit defects in canal and sac morphogenesis. We identify the earliest marker for the semicircular canal-genesis zone (ccn1l1), unexpected genes in the endolymphatic sac that suggest a role for tissue contraction in its function (smtnb), parallel gene sets for sensory patches in the neuromast and ear, and a conserved role for cell-cycle pausing (cdkn1bb expression in the canals and sac as previously observed in the developing mouse ear). This atlas provides the most comprehensive transcriptional profiling of the developing inner ear, identifying new molecular leads to understand ear morphogenesis. Summary statementSingle-cell transcriptomic analysis of developing wild-type and lmx1bb mutant zebrafish reveals cell-states and effectors that distinguish the inner ears sensory patches, semicircular canals, endolymphatic duct and sac, and periotic mesenchyme.

developmental biology↗

Multi-stage single-cell atlas of Botryllus schlosseri asexual development unveils dedifferentiating bud founder cells

Colonial tunicates are the only chordates capable of forming fully functional bodies from somatic tissues through non-embryonic development, known as budding. In Botryllus schlosseri, this agametic process, termed peribranchial budding, generates new zooids in a stereotyped, cyclical manner from a cluster of cells within the peribranchial epithelium. Despite detailed morphological characterization, the molecular and cellular underpinnings of budding initiation remain poorly understood. Here, we present the first single-cell transcriptomic atlas of B. schlosseri peribranchial budding, encompassing multiple stages from pre-budding to near-mature zooid. This high-resolution atlas captures the diversity of cell types involved in budding and their dynamics enabling precise cluster annotation and lineage trajectory inference. While circulating mesenchymal cells exhibit transcriptional hallmarks of stem-like states, we found no definitive evidence of broad contribution to bud onset and early morphogenesis beyond hematopoietic and gonadal lineages. Instead, we identified a distinct founder cell population arising from peribranchial epithelium, marked by a unique transcriptional profile and progressive acquisition of developmental potency. This supports a model in which budding is initiated by dedifferentiation of committed epithelial cells rather than activation of multi- or pluripotent stem cells. Furthermore, we highlight signaling pathways, including GNRHR-like receptors, that may couple metabolic state with developmental progression. Altogether, our data suggest that peribranchial budding in B. schlosseri is driven by potential reprogramming within epithelial tissues. This work provides a foundational resource for studying non-embryonic development and the evolution of regenerative strategies in chordates.

developmental biology↗

Immune cell type divergence in a basal chordate

Evolutionary adaptations often occur at the level of cell types and cellular function. Innate immune cells are a promising system for studying cell type evolution, as they are widespread across metazoans, have several conserved functions, and are under selective pressure from pathogens. However, molecular characterizations of invertebrate immune cells are limited, and it remains unclear whether invertebrate immune cell types are homologous to those in vertebrates. Here we use single-cell RNA sequencing, in situ hybridization, and live reporters to define the identity of blood cell states from a basal chordate, Ciona robusta. We find evidence that C. robusta circulating blood contains a differentiation hierarchy that gives rise to at least eight major morphotypes, constituting approximately half of mature blood cell states. The mature cell states include phagocytes, as well as cells variously expressing vanadium-binding proteins, carbonic anhydrases, pattern recognition receptors, cytokines, and complement factors. Despite the expression of homologs to vertebrate immune components, extensive divergence between tunicate and vertebrate immune cells obscures cell state homology. Altogether, this work modernizes blood cell classifications in C. robusta and extends the known repertoire of immune cells within chordates.

evolutionary biology↗

Multi-step genomics on single cells and live cultures in sub-nanoliter capsules

Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multi-step assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extension to live-cell assays.

genomics↗

Tissue Fluidity: A Double-Edged Sword for Multicellular Patterning

The organization of cells into spatial patterns is a fundamental aspect of multicellularity. One major mechanism underlying tissue patterning is adhesion-based cell sorting, in which a heterogeneous mixture of cell types spontaneously separates into distinct domains based on differences in adhesion protein expression. Here, we identify tissue fluidity--the extent to which cells can move freely within a tissue--as a critical regulator of adhesion-based sorting. First, we describe a physically well-understood minimal tissue model that can integrate both tissue fluidity and adhesion-based sorting, and demonstrate that this model can quantitatively reproduce experimentally measured sorting dynamics in a fibroblast cell culture assay. We go on to show that altering tissue fluidity by any mechanism in the model leads to substantial changes in the rate or accuracy of sorting (or both). We further demonstrate that the balance between cell motility, which acts to fluidize the tissue, and homotypic cell-cell adhesion, which acts to solidify the tissue, sensitively tunes a fundamental trade-off between the rate and accuracy of sorting--such that sorting can only occur when motility and adhesion are tightly coupled. Intriguingly, best fits of the simulations to the experiments across a range of adhesion protein expression conditions suggest that cells may naturally scale their motility strength with their adhesion strength - thereby maintaining a permissive fluidity for sorting. Overall, our results indicate that tissue fluidity must be tightly regulated for sorting to occur, and that cells may have evolved a mechanism to naturally co-regulate their mechanical properties in order to sustain a patterning-competent fluidity. Statement of SignificanceTissue fluidity, or the ability of cells to freely rearrange within a tissue, is a universal property of multicellular organisms that plays central roles in development, cancer, and wound healing. Here, we identify tissue fluidity as a critical regulator of a major mechanism of multicellular patterning - adhesion-based cell sorting. The results of our combined experimental-computational investigation suggest that tissues can readily tune their fluidity in order to freeze, catalyze, or erase multicellular patterns - carrying significant implications for our understanding of how patterns are formed in development, lost in diseases affecting tissue organization (e.g., cancer), regained through the processes of wound healing and regeneration, and can be engineered in the creation of synthetic organoid and embryoid systems. One sentence summaryBiophysical modeling demonstrates how tissue fluidity is a key regulator of the rate and accuracy of adhesion-based sorting.

cell biology↗

IL-17A primes an early progenitor compartment to tune the erythropoietic feedback circuit

Feedback control of erythropoiesis exemplifies conflicting goals in tissue homeostasis: maintaining fast reactivity to stress while minimizing proliferative burden on progenitors in the steady state. Here we show that these conflicting goals are tuned through the combinatorial action of cytokines. We find that IL-17A, a pro-inflammatory cytokine, mediates striking synergism with the negative feedback signal erythropoietin (Epo) in vivo, accelerating the erythropoietic response to hypoxia. A model of erythropoietic control shows increased reactivity may occur through two cell circuit designs, with one having far lower constitutive progenitor burden in normoxia. IL-17A acts through this optimal design by sensitizing progenitors to Epo, a model supported by multiple experimental observations. We suggest that IL-17A signals impending hypoxia during infections, tuning erythropoiesis in favor of a faster stress response. Our study highlights IL-17A as a potential erythropoietic therapeutic agent and serves as a model of homeostatic tuning in stem and progenitor cell circuits.

systems biology↗

Global decoupling of cell differentiation from cell division in early embryo development

As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. In the absence of cell division, differentiation slows down in some cell types, and cells exhibit global stress responses. While differentiation is robust to blocking cell division, the proportions of cells across cell states are not. This work simplifies our understanding of the role of cell division in development and showcases the utility of combining embryo-wide perturbations with single-cell RNA sequencing to uncover the role of common biological processes across multiple tissues.

developmental biology↗

A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells

Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.

genomics↗

A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells

Cellular lineage histories along with their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have limited barcode diversity and poor single-cell lineage coverage, thus precluding their use in tissues composed of millions of cells. Here, we developed DARLIN, an improved Cas9 barcoding mouse line that utilizes terminal deoxynucleotidyl transferase (TdT) to enhance insertion events over 30 CRISPR target sites, stably integrated into 3 distinct genomic loci. DARLIN is inducible, has an estimated ~1018 lineage barcodes across tissues, and enables detection of usable barcodes in ~60% of profiled single cells. Using DARLIN, we examined fate priming within developing hematopoietic stem cells (HSCs) and revealed unique features of HSC migration. Additionally, we adapted a method to jointly profile DNA methylation, chromatin accessibility, gene expression, and lineage information in single cells. DARLIN will enable widespread high-resolution study of lineage relationships and their molecular signatures in diverse tissues and physiological contexts.

developmental biology↗

A map of signaling responses in the human airway epithelium

Receptor-mediated signaling plays a central role in tissue regeneration, and it is dysregulated in disease. Here, we build a signaling-response map for a model regenerative human tissue: the airway epithelium. We analyzed the effect of 17 receptor-mediated signaling pathways on organotypic cultures to determine changes in abundance and phenotype of all epithelial cell types. This map recapitulates the gamut of known airway epithelial signaling responses to these pathways. It defines convergent states induced by multiple ligands and diverse, ligand-specific responses in basal-cell and secretory-cell metaplasia. We show that loss of canonical differentiation induced by multiple pathways is associated with cell cycle arrest, but that arrest is not sufficient to block differentiation. Using the signaling-response map, we show that a TGFB1-mediated response underlies specific aberrant cells found in multiple lung diseases and identify interferon responses in COVID-19 patient samples. Thus, we offer a framework enabling systematic evaluation of tissue signaling responses.

systems biology↗

The secreted neuronal signal Spock1 regulates the blood-brain barrier

The blood-brain barrier (BBB) is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick-quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally-expressed Spock1 is cell non-autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix (ECM), increased endothelial transcytosis, and altered pericyte-endothelial interactions. Furthermore, a single dose of recombinant SPOCK1 partially restores BBB function in spock1 mutants by quenching gelatinase activity and restoring vascular expression of BBB genes including mcamb. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM, thereby regulating pericyte-endothelial interactions and downstream vascular gene expression. One-Sentence SummarySpock1 is a signal secreted by neurons that induces barrier properties in the brain vasculature

neuroscience↗

Learning dynamics by computational integration of single cell genomic and lineage information

A goal of single cell genome-wide profiling is to reconstruct dynamic transitions during cell differentiation, disease onset, and drug response. Single cell assays have recently been integrated with lineage tracing, a set of methods that identify cells of common ancestry to establish bona fide dynamic relationships between cell states. These integrated methods have revealed unappreciated cell dynamics, but their analysis faces recurrent challenges arising from noisy, dispersed lineage data. Here, we develop coherent, sparse optimization (CoSpar) as a robust computational approach to infer cell dynamics from single-cell genomics integrated with lineage tracing. CoSpar is robust to severe down-sampling and dispersion of lineage data, which enables simpler, lower-cost experimental designs and requires less calibration. In datasets representing hematopoiesis, reprogramming, and directed differentiation, CoSpar identifies fate biases not previously detected, predicting transcription factors and receptors implicated in fate choice. Documentation and detailed examples for common experimental designs are available at https://cospar.readthedocs.io/.

developmental biology↗

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change

Despite the global importance in ecological processes, the Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. In this study, we used a combination of deep shotgun metagenomics and a machine learning approach to compare physiological strategies of microbial communities between contrasting forest and pasture soils. We showed that microbial communities (bacteria, archaea and viruses), and the composition of protein-coding genes are distinct in each ecosystem. The diversities of these metagenomic datasets are strongly correlated, indicating that the protein-coding genes found in any given sample of these soil types are predictable from their taxonomic lineages. Shifts in metagenome profiles reflected potential physiological differences caused by forest-to-pasture conversion with alterations in gene abundances related to carbohydrate and energy metabolisms. These variations in these gene contents are associated with several soil factors including C/N, temperature and H++Al3+ (exchangeable acidity). These data underscore that microbial community taxa and protein-coding genes co-vary. Differences in gene abundances for carbohydrate utilization, energy, amino acid, and xenobiotic metabolisms indicate alterations of physiological strategy with forest-to-pasture conversion, with potential consequences to C and N cycles. Our analysis also indicated that soil virome was altered and shifts in the viral community provide insights into increased health risks to human and animal populations.

microbiology↗

Belowground changes to community structure alter methane-cycling dynamics in Amazonia

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with changes to ecosystem processes, including substantial increases in soil methane (CH4) emission. The drivers of this change in CH4 flux are not well understood. To address this knowledge gap, we measured soil CH4 flux, environmental conditions, and belowground microbial community attributes across a land use change gradient (old growth primary forest, cattle pasture, and secondary forest regrowth) in two Amazon Basin regions. Primary forest soils exhibited CH4 uptake at modest rates, while pasture soils exhibited CH4 emission at high but variable rates. Secondary forest soils exhibited low rates of CH4 uptake, suggesting that forest regrowth following pasture abandonment could reverse the CH4 sink-to-source trend. While few environmental variables were significantly associated with CH4 flux, we identified numerous microbial community attributes in the surface soil that explained substantial variation in CH4 flux with land use change. Among the strongest predictors were the relative abundance and diversity of methanogens, which both increased in pasture relative to forests. We further identified individual taxa that were associated with CH4 fluxes and which collectively explained ~50% of flux variance. These taxa included methanogens and methanotrophs, as well as taxa that may indirectly influence CH4 flux through acetate production, iron reduction, and nitrogen transformations. Each land type had a unique subset of taxa associated with CH4 fluxes, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, our results suggest that changes in CH4 flux from agricultural conversion could be driven by microbial responses to land use change in the surface soil, with both direct and indirect effects on CH4 cycling. This demonstrates the central role of microorganisms in mediating ecosystem responses to land use change in the Amazon Basin.

ecology↗

Community structure ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here we argue that this stems from at least three issues: 1) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge, 2) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge and 3) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4)-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and include environmental covariates in statistical analyses to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4 oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.

ecology↗

ERK2 phosphorylates the epigenetic regulator CXXC-finger protein 1 (Cfp1)

BackgroundThe Ras-Raf-MEK-ERK signaling pathway is essential for proper development and homeostatic regulation in eukaryotic cells and underlies progression of several types of cancer. Many pathway functions are performed by extracellular signal-regulated kinase (ERK)1 and 2 (ERK1/2), serine/threonine protein kinases of the mitogen-activated protein kinase (MAPK) family that interact with a large number of substrates and are highly active in the nucleus.\n\nResultsWe identified the epigenetic regulator CXXC-finger protein 1 (CFP1) as a protein that interacts with ERK2 on chromatin. CFP1 is involved in multiple aspects of chromatin regulation, including histone methylation and DNA methylation. Here, we demonstrate the overlapping roles for ERK1/2 and CFP1 in regulation of immediate early gene (IEG) induction. Our work suggests multiple modes of co-regulation and demonstrates that CFP1 is required for an optimal signal-dependent response. We also show that CFP1 is an ERK2 substrate in vitro and identify several phosphorylation sites. Furthermore, we provide evidence that Su(var)3-9, Enhancer-of-zeste and Trithorax (Set)1b, a CFP1-interacting histone methylase, is phosphorylated by ERK2 and is regulated by CFP1.\n\nConclusionOur work highlights ERK1/2 interactions with chromatin regulators that contribute to MAPK signaling diversity in the nucleus.

cell biology↗

Lineage tracing on transcriptional landscapes links state to fate during differentiation

A challenge in stem cell biology is to associate molecular differences among progenitor cells with their capacity to generate mature cell types. Though the development of single cell assays allows for the capture of progenitor cell states in great detail, these assays cannot definitively link cell states to their long-term fate. Here, we use expressed DNA barcodes to clonally trace single cell transcriptomes dynamically during differentiation and apply this approach to the study of hematopoiesis. Our analysis identifies functional boundaries of cell potential early in the hematopoietic hierarchy and locates them on a continuous transcriptional landscape. We reconstruct a developmental hierarchy showing separate ontogenies for granulocytic subtypes and two routes to monocyte differentiation that leave a persistent imprint on mature cells. Finally, we use our approach to benchmark methods of dynamic inference from single-cell snapshots, and provide evidence of strong early fate biases dependent on cellular properties hidden from single-cell RNA sequencing.

systems biology↗