Biology subjects

Lin, Z.

Publications and source records attributed to Lin, Z..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Nephrectomy and high-salt diet inducing pulmonary hypertension and kidney damage by increasing Ang II concentration in rats

BackgroundPulmonary hypertension (PH) is a common complication in patients with chronic kidney disease (CKD), affecting prognosis. However, the pathogenesis is not clear, and the lack of a stable animal model is a significant factor. MethodsIn this study, a rat model of chronic kidney disease with pulmonary hypertension (CKD-PH) was developed through 5/6 nephrectomy combined with a high-salt diet. The models hemodynamics and pathological changes in multiple organs were dynamically assessed. Lung tissues and serum were collected from the model rats to measure the expression of ACE2, the expression levels of vascular active components related to the renin-angiotensin-aldosterone system (RAAS), and changes in the serum metabolic profile of the model. ResultsAfter 14 weeks post-surgery, the CKD-PH rat model exhibited significant changes in hemodynamic parameters indicative of pulmonary arterial hypertension, along with alterations such as right ventricular hypertrophy. However, no evidence of pulmonary vascular remodeling was observed. An imbalance in the renin-angiotensin-aldosterone system was identified in the CKD-PH rat models. Downregulation of ACE2 expression was observed in pulmonary tissues. The serum metabolic profile of the CKD-PH rat models showed distinct differences compared to the sham surgery group. ConclusionsThe development of pulmonary arterial hypertension in CKD-PH rats may be primarily attributed to the disruption of the renin-angiotensin-aldosterone system (RAAS), coupled with a decrease in ACE2 expression in pulmonary vascular endothelial tissues and metabolic disturbances.

pathology↗

bioRxiv2024

PP2B-dependent cerebellar plasticity sets the amplitude of an innate reflex during juvenile development

Throughout life, the cerebellum plays a central role in the coordination and optimization of movements, using cellular plasticity to adapt a range of behaviors. If these plasticity processes establish a fixed setpoint during development, or continuously adjust behaviors throughout life, is currently unclear. Here, by spatiotemporally manipulating the activity of protein phosphatase 2B (PP2B), an enzyme critical for cerebellar plasticity, we examined the consequences of disrupted plasticity on the performance and adaptation of the vestibulo-ocular reflex (VOR). We find that, in contrast to Purkinje cell specific deletion starting early postnatally, acute pharmacological as well as adult-onset genetic deletion of PP2B affects all forms of VOR adaptation, but not the level of VOR itself. Next, we show that Purkinje cell-specific genetic deletion of PP2B in juvenile mice leads to a progressive loss of the protein PP2B and a concurrent change in the VOR, in addition to the loss of adaptive abilities. Finally, re-expressing PP2B in adult mice that lack PP2B expression from early in development, rescues VOR adaptation, but does not affect the performance of the reflex. Together, our results indicate that chronic or acute, genetic or pharmacological block of PP2B disrupts the adaptation of the VOR. In contrast, only the absence of plasticity during cerebellar development affects the setpoint of VOR, an effect that cannot be corrected after maturation of the cerebellum. These findings suggest that cerebellar plasticity influences behavior in two ways, through direct control of behavioral adaptation and via long-term effects initiated in the juvenile period. Significance StatementEarly damage to motor adaptation structures, such as the cerebellum, has been linked to neurodevelopmental disorders persisting into adulthood. Understanding these long-term effects requires disentangling the persistent, long-term effects of disrupted development from the acute, ongoing effects directly caused by the continuous presence of the disruption. Here, we demonstrate that disruptions during early development affect both basal level and adaptation, whereas late, adult-onset disruption of cerebellar plasticity only affects the ability to adapt, not the setpoint of an innate reflex. Our findings that specifically the absence of plasticity during cerebellar development affects the setpoint of VOR, which cannot be corrected by re-instating plasticity after maturation of the cerebellum, supports the concept of a sensitive developmental period for setting innate reflexes.

neuroscience↗

bioRxiv2024

Binding profiles for 954 Drosophila and C. elegans transcription factors revealtissue specific regulatory relationships

A catalog of transcription factor (TF) binding sites in the genome is critical for deciphering regulatory relationships. Here we present the culmination of the modERN (model organism Encyclopedia of Regulatory Networks) consortium that systematically assayed TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). We describe key features of these datasets, comprising 604 TFs identifying 3.6M sites in the fly and 350 TFs identifying 0.9 M sites in the worm. Applying a machine learning model to these data identifies sets of TFs with a prominent role in promoting target gene expression in specific cell types. TF binding data are available through the ENCODE Data Coordinating Center and at https://epic.gs.washington.edu/modERNresource, which provides access to processed and summary data, as well as widgets to probe cell type-specific TF-target relationships. These data are a rich resource that should fuel investigations into TF function during development.

genomics↗

bioRxiv2023

Viruses that 'infect' viruses: Cas12f1 and Cas9 gene drive in HSV1

Synthetic CRISPR-Cas9 gene drive has been developed as a potential tool to control harmful species. However, Cas9 gene drive faces high resistance rate and mitigation strategies developed so far are difficult to implement. Furthermore, studying the resistance to gene drive is time consuming and challenging in higher organisms. We here tackled these two challenges simultaneously by generating Cas9 and Un1Cas12f1 gene drive in a fast-replicating DNA virus, HSV1. We assessed the transmission dynamics and resistance formation through phenotypical staining and next-generation sequencing, and demonstrated that HSV1 supported fast and effective transmission of gene drives, and the Un1Cas12f1 gene drives yielded greater conversion and lower resistance than did the Cas9 gene drives. This positions the Un1Cas12f1 gene drive as a promising alternative, and HSV1 emerges as a dependable and swift platform for gene drive assessment. The gene drive viruses function like pathogens that specifically infect viruses, offering potential applications in attenuating viral infections.

microbiology↗

bioRxiv2023

Liquid-liquid phase separation within dense-core vesicles in sympathetic adrenal chromaffin cells

The neural communication process heavily relies on vesicular release of neurotransmitters and/or neuromodulators primarily from synaptic vesicles (SVs) or dense-core vesicles (DCVs), within neurons and neuroendocrine cells. SVs ([~]40 nm) are responsible for releasing classical neurotransmitters, while DCVs (100-500 nm in diameter) release both classic neurotransmitters and neuropeptides. DCVs contain a variety of neuropeptides, hormones, and neurotransmitters, playing crucial roles in diverse physiological processes, such as brain development, neurogenesis, and synaptic plasticity. However, the biogenesis of DCVs and the sorting mechanism of different neuropeptides into DCVs remained largely unknown. Recent studies have revealed that liquid-liquid phase separation (LLPS) of matrix protein-chromogranins plays pivotal roles in the formation of DCVs and the sorting process of neurotransmitters/neuromodulators in endocrine cells. Here we highlight recent advancements in mechanisms of LLPSs regulation of DCVs [1, 2], which selectively affect release of some co-transmitters (catecholamines) but not others (i.e. ATP) [3]. We term this phenomenon "1-2-2": 1 vesicle, 2 transmitters (catecholamine and ATP), 2 release modes (quanta and sub-quanta).

neuroscience↗

bioRxiv2023

Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells

The cell membrane proteome is the primary biohub for cell communication, yet we are only beginning to understand the dynamic protein neighborhoods that form on the cell surface and between cells. Proximity labeling proteomics (PLP) strategies using chemically reactive probes are powerful approaches to yield snapshots of protein neighborhoods but are currently limited to one single resolution based on the probe labeling radius. Here, we describe a multi-scale PLP method with tunable resolution using a commercially available histological dye, Eosin Y, which upon visible light illumination, activates three different photo-probes with labeling radii ranging from [~]100 to 3000 [A]. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor (EGFR) and orthogonally validated >20 neighbors using immuno-assays and AlphaFold-Multimer prediction that generated plausible binary interaction models. We further profiled the protein neighborhoods of cell-cell synapses induced by bi-specific T-cell engagers (BiTEs) and chimeric antigen receptor (CAR)T cells at longer length scales. This integrated multi-scale PLP platform maps local and distal protein networks on cell surfaces and between cells. We believe this information will aid in the systematic construction of the cell surface interactome and reveal new opportunities for immunotherapeutics.

biochemistry↗

bioRxiv2023

A large-scale volumetric correlated light and electron microscopy study localizes Alzheimer's disease-related molecules in the hippocampus

Connectomics using volume-electron-microscopy enables mapping and analysis of neuronal networks, revealing insights into neural circuit function and dysfunction. In Alzheimers disease (AD), where amyloid-{beta} (A{beta}) and hyperphosphorylated-Tau (pTau) are implicated, connectomics offers an approach to unravel how these molecules contribute to circuit alterations by enabling the study of these molecules within the context of the complete local neuronal and glial milieu. We present a volumetric-correlated-light-and-electron microscopy (vCLEM) protocol using fluorescent nanobodies to localize A{beta} and pTau within a large-scale connectomics dataset from the hippocampus of the 3xTg AD mouse model. A key outcome of this work is a publicly accessible vCLEM dataset, featuring fluorescent labeling of A{beta} and pTau in the ultrastructural context with segmented neurons, glia, and synapses. This dataset provides a unique resource for exploring AD pathology in the context of connectomics and fosters collaborative opportunities in neurodegenerative disease research. As a proof-of-principle, we uncovered new localizations of A{beta} and pTau, including pTau-positive spine-like protrusions at the axon initial segment and changes in the number and size of synapses near A{beta} plaques. Our vCLEM approach facilitates the discovery of both molecular and structural alterations within large-scale EM data, advancing connectomics research in Alzheimers and other neurodegenerative diseases.

neuroscience↗

bioRxiv2023

RhoGDI phosphorylation by PKC regulates its interaction with death receptor p75NTR to gate axon growth and neuron survival pathways

Although transmembrane receptors engage multiple signaling pathways simultaneously, each pathway is typically investigated individually. How receptors juggle their interactions with different downstream effectors and the conditions under which distinct pathways are prioritized remains poorly understood. Here we show that the outcome of death receptor p75NTR signaling is determined through competition of effectors for interaction with its intracellular domain, in turn dictated by the nature of the incoming ligand. While NGF induces release of RhoGDI through recruitment of RIP2, thus decreasing RhoA activity in favor of NFkB signaling, MAG induces PKC-mediated phosphorylation of the RhoGDI N-terminus, thus promoting its interaction with the juxtamembrane domain of p75NTR, disengaging RIP2, and enhancing RhoA activity in detriment of NF-kB. This results in growth cone collapse, stunted neurite outgrowth and apoptosis in cerebellar granule neurons. If presented simultaneously, MAG prevails over NGF. The NMR solution structure of the complex between the RhoGDI N-terminus and p75NTR juxtamembrane domain reveals previously unknown structures of these proteins and clarifies the mechanism of p75NTR activation. These results show how ligand-directed competition between RIP2 and RhoGDI for p75NTR engagement determine axon growth and neuron survival. Similar principles are likely at work in other receptors engaging multiple effectors and signaling pathways.

neuroscience↗

bioRxiv2023

Transcriptional coupling of telomeric retrotransposons with the cell cycle

Instead of employing telomerases to safeguard chromosome ends, dipteran species maintain their telomeres by transposition of telomeric-specific retrotransposons (TRs): in Drosophila, these are HeT-A, TART, and TAHRE. Previous studies have shown how these TRs create tandem repeats at chromosome ends, but the exact mechanism controlling TR transcription has remained unclear. Here we report the identification of multiple subunits of the transcription cofactor Mediator complex and transcriptional factors Scalloped (Sd, the TEAD homolog in flies) and E2F1-Dp as novel regulators of TR transcription and telomere length in Drosophila. Depletion of multiple Mediator subunits, Dp, or Sd increased TR expression and telomere length, while over-expressing E2F1-Dp or knocking down the E2F1 regulator Rbf1 (Retinoblastoma-family protein 1) stimulated TR transcription, with Mediator and Sd affecting TR expression through E2F1-Dp. The CUT&RUN analysis revealed direct binding of CDK8, Dp, and Sd to telomeric repeats. These findings highlight the essential role of the Mediator complex in maintaining telomere homeostasis by regulating TR transcription through E2F1-Dp and Sd, revealing the intricate coupling of TR transcription with the host cell-cycle machinery, thereby ensuring chromosome end protection and genomic stability during cell division.

cell biology↗

bioRxiv2023

Phase-Precession-Like Effects in the Anterior Insula Cortex during Reward Expectancy

Reward expectancy shapes behavioral performance by coordinating the allocation of cognitive resources, which incorporates the involvement of the anterior insular cortex (AIC). To investigate the electrophysiological mechanisms of the AIC during reward expectancy, we collected intracranial electroencephalographic data from epilepsy patients undergoing clinical monitoring. Subjects navigated a virtual T-maze containing rewards at three predetermined locations. We focused on the period immediately before entering the reward zone, termed the reward expectancy stage. During this stage, we identified the reward-specific brain patterns (RBPs) that were preactivated in the AIC. This pre-activation preceded the emergence of robust phase-amplitude coupling (PAC), where theta oscillations (5-7 Hz) modulated gamma activities (75-110 Hz). The PAC strength correlated positively with the pre-activation level of RBPs, implying the potential role of oscillatory coordination in amplifying preactivated reward representations. Strikingly, this PAC effect exhibited a specific temporal structure that peak gamma activity became progressively coupled to earlier theta phases as reward approached, mirroring the theta phase precession phenomenon previously observed in frontal and temporal lobes. We refer to this dynamic as phase-precession-like effect (PPLE). Moreover, subjects exhibiting PPLE in the AIC presented greater trial-by-trial improvements in response latency. Taken together, these findings shed light on the electrophysiological mechanisms of the AIC underlying reward expectancy.

neuroscience↗

bioRxiv2023

A muscle hypertrophy-derived myokine reprograms the stromal vascular fractions differentiation towards thermogenic adipocytes in subcutaneous adipose tissue

Skeletal muscle plays a significant role in both local and systemic energy metabolism; however, the cross-talk between skeletal muscle and adipose tissue remains largely unexplored. In this study, we identify the HIF2-Bambi-Thbs4 axis as a critical driver of muscle hypertrophy and metabolic improvement. Deletion of Bambi induces muscle hypertrophy and oxidative switching, thereby enhancing local and systemic metabolism under conditions of rodent chow and high-fat diets (HFD). Other than the metabolic regulation of skeletal muscle hypertrophy, we hypothesize that a portion of this improvement may be attributed to the metabolic reprogramming of the stromal vascular fraction (SVFs) of iWAT, promoting the development of beige adipocytes. Leveraging multi-omics approaches, we establish Thbs4 as a newly identified, muscle hypertrophy-derived myokine that serves as an essential regulator of this metabolic reprogramming. Thbs4 is upregulated in skeletal muscle during hypertrophy and aerobic exercise, localizes to the iWAT membrane, and facilitates the transformation of white adipocytes into beige adipocytes under conditions such as cold exposure, muscle hypertrophy, or aerobic exercise. Moreover, overexpression of Thbs4 elevates its plasma levels and leads to the transformation of white to beige adipocytes, therefore offering long-term protection against HFD-induced metabolic disorders. Conversely, Thbs4 knockout (Thbs4-KO) disrupts the metabolic reprogramming of SVFs and exacerbates metabolic syndromes induced by an HFD, mirroring the observed decline in Thbs4 levels in aged mice. Therefore, our findings underscore Thbs4s potential as both a long-term metabolic protective factor and a therapeutic target for the treatment of metabolic disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/558627v1_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1178e6org.highwire.dtl.DTLVardef@1184d4eorg.highwire.dtl.DTLVardef@7b592aorg.highwire.dtl.DTLVardef@1b0b03_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBambi, a direct target gene of HIF2 in skeletal muscle, when deleted, triggers muscle hypertrophy and the transformation of white into beige adipocytes, improving systemic energy metabolism. C_LIO_LIThe metabolic reprogramming of stromal vascular fractions (SVFs) contributes to the observed improvements in energy metabolism and adipocyte hyperplasia. C_LIO_LIThbs4, a novel myokine produced in skeletal muscle during hypertrophy and aerobic exercise, plays a key role in the transformation of white into beige adipocytes. C_LIO_LIOverexpression of Thbs4 provides enduring protection against high-fat diet (HFD)-induced metabolic disorders, demonstrating its potential as a therapeutic target. C_LIO_LIThbs4 deletion abrogates the beneficial metabolic reprogramming of SVFs and exacerbates HFD-induced metabolic syndromes, further underlining its crucial role in metabolic regulation. C_LI

physiology↗

bioRxiv2023

SMB controls decompartmentalization in Arabidopsis root cap cells to execute programmed cell death

Programmed cell death (PCD) is a fundamental cellular process crucial to development, homeostasis, and immunity in multicellular eukaryotes. In contrast to our knowledge on the regulation of diverse animal cell death subroutines, information on execution of PCD in plants remains fragmentary. Here we make use of the accessibility of the Arabidopsis thaliana root cap to visualize the execution process of developmentally controlled PCD. We identify a succession of selective decompartmentalization events and ion fluxes that are controlled by a gene regulatory network downstream of the NAC transcription factor SOMBRERO (SMB). Surprisingly, breakdown of the large central vacuole is a relatively late and variable event, preceded by an increase of intracellular calcium levels and acidification, release of mitochondrial matrix proteins, leakage of nuclear and endoplasmic reticulum lumina, and release of fluorescent membrane reporters into the cytosol. Elevated intracellular calcium levels and acidification are sufficient to trigger cell death execution specifically in cells that are rendered competent to undergo PCD by SMB activity, suggesting that these ion fluxes act as PCD-triggering signals.

plant biology↗

bioRxiv2023

Correlative single-cell X-ray tomography and X-ray fluorescence imaging

X-ray tomography (XRT) and X-ray fluorescence (XRF) imaging are two non-invasive imaging techniques to study cellular structures and chemical element distributions, respectively. However, correlative X-ray tomography and fluorescence imaging for the same cell have yet to be routinely realized due to challenges in sample preparation and X-ray radiation damage. Here we report an integrated experimental and computational workflow for achieving correlative multi-modality X-ray imaging of a single cell. The method consists of the preparation of radiation-resistant single-cell samples using live-cell imaging-assisted chemical fixation and freeze-drying procedures, targeting and labeling cells for correlative XRT and XRF measurement, and computational reconstruction of the correlative and multi-modality images. With XRT, cellular structures including the overall structure and intracellular organelles are visualized, while XRF imaging reveals the distribution of multiple chemical elements within the same cell. Our correlative method demonstrates the feasibility and broad applicability of using X-rays to understand cellular structures and the roles of chemical elements and related proteins in signaling and other biological processes.

cell biology↗

bioRxiv2023

SR2: Sparse Representation Learning for Scalable Single-cell RNA Sequencing Data Analysis

Single-cell RNA-sequencing (scRNA-seq) technology has been widely used to measure the transcriptome of cells in complex and heterogeneous systems. Integrative analysis of multiple scRNA-seq data can transform our understanding of various aspects of biology at the single-cell level. Many computational methods are proposed for data integration. However, few methods for scRNA-seq data integration explicitly model variation from heterogeneous biological conditions for interpretation. Modeling the variation helps understand the effect of biological conditions on complex biological systems. Our study proposes SR2 to capture gene expression patterns from heterogeneous biological conditions and discover cell identity simultaneously. Therefore, it can uncover the effect of biological conditions on the gene expression of cells and simultaneously achieve state-of-the-performance in cell identity discovery in our comprehensive comparison. Notably, SR2 is extended to model the effects of biological conditions on gene expression for cell populations, thus uncovering the effect of biological conditions on gene expression for cell populations and identifying putative condition-associated cell populations. To improve its scalability, we incorporate a batch-fitting strategy to ensure it is scalable to scRNA-seq data with arbitrary sample sizes. Moreover, the broad applicability of SR2 in biomedical studies has been demonstrated via applications. The complete package of SR2 is available at https://github.com/kai0511/SR2.

bioinformatics↗

bioRxiv2023

Synthetic Frizzled agonist and LRP antagonist for high-efficiency Wnt/β-catenin signaling manipulation in organoid cultures and in vivo

Wnt/{beta}-catenin signaling and its dysregulation play critical roles in the fate determination of stem cells and the pathology of various diseases. However, the application of translated Wnt ligand in regenerative medicine is hampered by its hydrophobicity and cross-reactivity with Frizzled (FZD) receptors. Here, we generate an engineered water-soluble, FZD subtype-specific agonist, RRP-pbFn, for high-efficiency Wnt/{beta}-catenin signaling activation. In the absence of direct binding to LRP5/6, RRP-pbFn stimulates Wnt/{beta}-catenin signaling more potently than surrogate Wnt. RRP-pbFn supports the growth of a variety of mouse and human organoids, and induces the expansion of liver and intestine progenitors in vivo. Meanwhile, we develop a synthetic LRP antagonist, RRP-Dkk1c, which exhibits heightened effectiveness in attenuating Wnt/{beta}-catenin signaling activity compared to Dkk1, thereby abolishing the formation of CT26-derived colon cancer xenograft in vivo. Together, these two paired Wnt/{beta}-catenin signaling manipulators hold great promise for biomedical research and potential therapeutics.

synthetic biology↗

bioRxiv2023

A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

Teleost fish form the largest group of vertebrates, making them critically important for the study on the mechanisms of brain evolution. In fact, teleosts show a tremendous variety of adaptive behaviors similar to birds and mammals, however, the neural basis mediating these behaviors remains elusive. We performed a systematic comparative survey of the goldfish telencephalon; the seat of plastic behavior, learning and memory in vertebrates. We delineated and mapped goldfish telencephalon cell types using single-cell RNA-seq and spatial transcriptomics, resulting in de novo molecular neuroanatomy parcellation. Glial cells were highly conserved across 450 million years of evolution separating mouse and goldfish, while neurons showed diversity and modularity in gene expression. Specifically, somatostatin (SST) interneurons, famously interspersed in the mammalian isocortex for local inhibitory input, were curiously aggregated in a single goldfish telencephalon nucleus, but molecularly conserved. Cerebral nuclei including the striatum, a hub for motivated behavior in amniotes, had molecularly and spatially conserved goldfish homologues. We further suggest different elements of a hippocampal formation across the goldfish pallium. Together, our atlas provides new insights to organization and evolution of vertebrate forebrains and may serve as a resource for the functional study underlying cognition in teleost fish. TeaserDetailed mapping of goldfish forebrain cells unwraps how 450 million years of evolution may have impacted brain function

neuroscience↗

bioRxiv2023

Immuno-Engineered Mitochondria for Efficient Therapy of Acute Organ Injuries via Modulation of Inflammation and Cell Repair

Acute organ injuries represent a major public health concern, and despite recent advances in organ support therapy, managing patients with organ failure stemming from such injuries remains a formidable challenge. The pathogenesis of acute organ injuries is driven by a cascade of inflammatory reactions and mitochondrial dysfunction-mediated cell damage, two interrelated events that fuel a vicious cycle of disease progression. In this study, we engineered neutrophil membrane-fused mitochondria (nMITO) that inherit the injury-targeting and broad-spectrum anti-inflammatory activities from neutrophil membrane proteins while retaining the cell-repairing activity of mitochondria. We demonstrated that nMITO can effectively block the inflammatory cascade and replenish mitochondrial function to simultaneously modulate these two key mechanisms in diverse acute organ injuries. Furthermore, by virtue of the {beta}-integrin inherited from neutrophils, nMITO exhibit selective homing to injured endothelial cells and can be efficiently delivered to damaged tissue cells via tunneling nanotubes, amplifying their regulatory effects on local inflammation and cell injury. In mouse models of acute myocardial injury, acute liver injury, and acute pancreatitis, nMITO effectively ameliorated immune dysfunction and repaired damaged tissues. Our findings suggest that nMITO represents a promising therapeutic strategy for managing acute organ injuries.

bioengineering↗

bioRxiv2023

In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development

Protein translational control is highly regulated step in the gene expression program during mammalian development that is critical for ensuring that the fetus develops correctly and that all of the necessary organs and tissues are formed and functional. Defects in protein expression during fetal development can lead to severe developmental abnormalities or premature death. Currently, quantitative techniques to monitor protein synthesis rates in a developing fetus (in utero) are limited. Here, we developed a novel in utero stable isotope labeling approach to quantify tissue-specific protein dynamics of the nascent proteome during mouse fetal development. Fetuses of pregnant C57BL/6J mice were injected with isotopically labeled lysine (Lys8) and arginine (Arg10) via the vitelline vein at various gestational days. After treatment, fetal organs/tissues including brain, liver, lung, and heart were harvested for sample preparation and proteomic analysis. We show that the mean incorporation rate for injected amino acids into all organs was 17.50 {+/-} 0.6%. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates (kobs) were calculated between 3.81E-5 and 0.424 hour-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver versus brain), however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates which correlated with known physiological changes during mouse development.

systems biology↗