Biology subjects

Peng, G.

Publications and source records attributed to Peng, G..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Learning phenotype associated signature in spatial transcriptomics with PASSAGE

Spatially resolved transcriptomics (SRT) is poised to advance our understanding of cellular organization within complex tissues under various physiological and pathological conditions at unprecedented resolution. Despite the development of numerous computational tools that facilitate the automatic identification of statistically significant intra-/inter-slice patterns (like spatial domains), these methods typically operate in an unsupervised manner, without leveraging sample characteristics like physiological/pathological states. Here we present PASSAGE (Phenotype Associated Spatial Signature Analysis with Graph-based Embedding), a rationally-designed deep learning framework for characterizing phenotype-associated signatures across multiple heterogeneous spatial slices effectively. In addition to its outstanding performance in systematic benchmarks, we have demonstrated PASSAGEs unique capability in identifying sophisticated signatures in multiple real-world datasets. The full package of PASSAGE is available at https://github.com/gao-lab/PASSAGE.

bioinformatics↗

bioRxiv2024

Dual nuclease single-cell lineage tracing by Cas9 and Cas12a

Single-cell lineage tracing based on CRISPR/Cas9 gene editing enables the simultaneous linkage of cell states and lineage history at a high resolution. Despite its immense potential in resolving the cell fate determination and genealogy within an organism, existing implementations of this technology suffer from limitations in recording capabilities and considerable barcode dropout. Here, we introduce DuTracer, a versatile tool, which utilizes two orthogonal gene editing systems to record deep cell lineage history at single-cell resolution in an inducible manner. DuTracer shows the ability of enhanced lineage recording with minimized target dropouts and deepened tree depth. Application of DuTracer in mouse embryoid bodies and neuromesodermal organoids illustrates the lineage relationship of different cell types and proposes potential lineage-biased molecular drivers. Moreover, we have developed an entropy-based approach to quantify the lineage recording ability of DuTracer in cell differentiation models. Together, DuTracer facilitates the precise and regulatory interrogation of cellular lineages of complex biological processes.

developmental biology↗

bioRxiv2023

Systematic comparison of sequencing-based spatial transcriptomic methods

Recent advancements of sequencing-based spatial transcriptomics (sST) have catalyzed significant advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare six sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, significantly impacting the effective resolutions. Furthermore, we observed that spatial transcriptomic data demonstrate unique attributes beyond merely adding a spatial axis to single-cell data, including an enhanced ability to capture patterned rare cell states along with specific markers, albeit being influenced by multiple factors including sequencing depth and resolution. Our study assists biologists in sST platform selection, and helps foster a consensus on evaluation standards and establish a framework for future benchmarking efforts that can be used as a gold standard for the development and benchmarking of computational tools for spatial transcriptomic analysis.

genomics↗

bioRxiv2023

Deletion of FNDC5/Irisin modifies murine osteocyte function in a sex-specific manner

Irisin, released from exercised muscle, has been shown to have beneficial effects on numerous tissues but its effects on bone are unclear. We found significant sex and genotype differences in bone from wildtype (WT) mice compared to mice lacking Fndc5 (KO), with and without calcium deficiency. Despite their bone being indistinguishable from WT females, KO female mice were partially protected from osteocytic osteolysis and osteoclastic bone resorption when allowed to lactate or when placed on a low-calcium diet. Male KO mice have more but weaker bone compared to WT males, and when challenged with a low-calcium diet lost more bone than WT males. To begin to understand responsible molecular mechanisms, osteocyte transcriptomics was performed. Osteocytes from WT females had greater expression of genes associated with osteocytic osteolysis and osteoclastic bone resorption compared to WT males which had greater expression of genes associated with steroid and fatty acid metabolism. Few differences were observed between female KO and WT osteocytes, but with a low calcium diet, the KO females had lower expression of genes responsible for osteocytic osteolysis and osteoclastic resorption than the WT females. Male KO osteocytes had lower expression of genes associated with steroid and fatty acid metabolism, but higher expression of genes associated with bone resorption compared to male WT. In conclusion, irisin plays a critical role in the development of the male but not the female skeleton and protects male but not female bone from calcium deficiency. We propose irisin ensures the survival of offspring by targeting the osteocyte to provide calcium in lactating females, a novel function for this myokine.

physiology↗

bioRxiv2023

Cell context-specific Synthetic lethality Prediction and Mechanism Analysis

Synthetic lethality (SL) holds significant promise as a targeted cancer therapy by selectively eliminating tumor cells while sparing normal cells. However, the discovery of SL gene pairs has encountered tremendous challenges, including high costs and low efficiency of experimental methods. Current computational approaches only provide limited insights because of overlooking the crucial aspects of cellular context dependency and mechanistic understanding of SL pairs. To overcome these challenges, we have developed SLWise, a deep-learning model capable of predicting SL interactions in diverse cellular backgrounds. We evaluated SLWise using a real world ground truth standard. The evaluation demonstrated that SLWise outperformed benchmark models in SL prediction. Additionally, we proposed a novel analysis scheme called SLAD-CE (Synthetic Lethal Associated Gene Detection and Cell Damage Evaluation) for the identification of abnormal essential genes induced by SL gene pairs and tracking the extent of cell damage. Leveraging the cell-line-specific input feature L1000 and employing Gene Set Enrichment Analysis (GSEA), SLAD-CE provides valuable insights into the underlying mechanisms of SLWise-predicted gene pairs. The combined utilization of SLWise and SLAD-CE offers an approach for predicting and analyzing SL interactions in specific cellular contexts. Our findings highlight the potential of SLWise and SLAD-CE in advancing SL-based therapies by improving prediction accuracy and enhancing mechanistic understanding, ultimately contributing to the development of effective precision treatments for cancer.

cancer biology↗

bioRxiv2023

Using graph-based model to identify cell specific synthetic lethal effects

Synthetic lethal (SL) pairs are pairs of genes whose simultaneous loss-of-function results in cell death, while a damaging mutation of either gene alone does not affect the cells survival. This makes SL pairs attractive targets for precision cancer therapies, as targeting the unimpaired gene of the SL pair can selectively kill cancer cells that already harbor the impaired gene. Limited by the difficulty of finding true SL pairs, especially on specific cell types, the identification of SL targets still relies on expensive, time-consuming experimental approaches. In this work, we utilized various cell-line specific omics data to design a deep learning model for predicting SL pairs on particular cell-lines. By incorporating multiple types of cell-specific omics data with a self-attention module, we represent gene relationships as graphs. Our approach demonstrates the potential to facilitate the discovery of cell-specific SL targets for cancer therapeutics, providing a tool to unearth mechanisms underlying the origin of SL in cancer biology. Our approach allows for prediction of SL pairs in a cell-specific manner and enhances cancer precision medicine. The code and data of our approach can be found at https://github.com/promethiume/SLwise HighlightsO_LIFew computational methods can systematically predict SL pairs at a cell-specific level, and their performance may not generalize well to clinical scenarios due to the heterogeneity of cancer types. C_LIO_LIThe SLWise utilizes various cell-line specific omics data to design a deep learning model with a graph-based representation and self-attention mechanism. C_LIO_LIThis approach allows for the prediction of SL pairs in a cell-specific manner, providing valuable insights on effectively identifying the cell-type specific SL targets for personalized treatment strategies. C_LI

bioinformatics↗

bioRxiv2023

The leptin receptor has no role in delta-cell control of beta-cell function in the mouse

Leptin inhibits insulin secretion from isolated islets from multiple species, but the cell type that mediates this process remains elusive. Mouse models have been used to explore this question. Ablation of the leptin receptor (Lepr) throughout the pancreatic epithelium results in altered glucose homeostasis, ex vivo insulin secretion, and calcium dynamics. However, the removal of Lepr from neither alpha nor beta cells mimics these results. Because Lepr is enriched in the delta cells of human islets, we used a mouse model to test whether delta cells mediate the diminished glucose-stimulated insulin secretion in response to leptin. However, ablation of Lepr within mouse delta cells had no impact on glucose homeostasis or insulin secretion. We further demonstrate that Lepr is not appreciably expressed within mouse delta cells.

molecular biology↗

bioRxiv2023

Time, Space and Single-Cell Resolved Molecular Trajectory of Cell Populations and the Laterality of the Body Plan at Gastrulation

Understanding of the molecular drivers of lineage diversification and tissue patterning during primary germ layer development requires in-depth knowledge of the dynamic molecular trajectories of cell lineages across a series of developmental stages of gastrulation1-7. Through computational modeling, we constructed at single-cell resolution a spatio-temporal compendium of the molecular trajectories of germ-layer derivatives in gastrula-stage mouse embryos. This molecular atlas infers the developmental trajectories of single-cell populations and the molecular network activity underpinning the specification and differentiation of the germ-layer lineages. Analysis of the heterogeneity of cellular composition of cell populations at defined positions in the epiblast revealed progressive diversification of cell types, mirroring the process of lineage allocation during gastrulation. A novel observation is the difference in the contribution of cells on contralateral sides of the epiblast to mesoderm derivatives of the early organogenesis embryo, and the enhanced BMP signaling activity in right-side mesoderm of E7.5 embryo. Perturbation of BMP signaling activity at late gastrulation led to randomization of left-right (L-R) molecular asymmetry in the lateral mesoderm of early-somite-stage embryo. Our findings indicate the asymmetric BMP activity during gastrulation may be critical for the symmetry breaking process associated with specification of L-R body asymmetry ahead of the acquisition of functionality of the L-R organizer.

developmental biology↗

bioRxiv2023

FOXM1 acts sexually dimorphically to regulate functional β-cell mass

The transcription factor FOXM1 regulates {beta}-cell proliferation and insulin secretion. Our previous work demonstrates that expressing an activated form of FOXM1 (FOXM1*) in {beta} cells increases {beta}-cell proliferation and mass in aged male mice. Additionally, FOXM1* enhances {beta}-cell function even in young mice, in which no {beta}-cell mass elevation occurs. Here, we demonstrate that FOXM1 acts in a sexually dimorphic manner in the {beta} cell. Expression of FOXM1* in female mouse {beta} cells does not affect {beta}-cell proliferation or glucose tolerance. Transduction of male but not female human islets with FOXM1* enhances insulin secretion in response to elevated glucose. Estrogen contributes to diabetes susceptibility differences between males and females, and the estrogen receptor (ER) is the primary mediator of {beta}-cell estrogen signaling. We show that FOXM1* can rescue impaired glucose tolerance in female mice with a pancreas-wide ER deletion. Further, FOXM1 and ER binding sites overlap with each other and with other {beta}-cell-enriched transcription factors, including ISL1, PAX6, MAF, and GATA. These data indicate that FOMX1 and ER cooperate to regulate {beta}-cell function and suggest a general mechanism contributing to the lower incidence of diabetes observed in women.

molecular biology↗

bioRxiv2022

Three-dimensional molecular architecture of mouse organogenesis

Mammalian embryos have sophisticated cell organizations that are orchestrated by molecular regulation at cellular and tissue level. It has recently been appreciated that the cells that make up the animal body themselves harbor significant heterogeneity in the context of both cellular and particularly spatial dimension. However, current spatial transcriptomics profiling of embryonic tissues either lack three-dimensional representation or are restricted to limited depth and organs. Here, we reported a holistic spatial transcriptome atlas of all major organs at embryonic day 13.5 of mouse embryo and delineated a 3D rendering of the molecular regulation of embryonic patterning. By integrating with corresponding single-cell transcriptome data, the spatial organogenesis atlas provides rich molecular annotation of the dynamic organ nature, spatial cellular interaction, embryonic axes and divergence of cell fates underlying mammalian development, which would pave the way for precise organ-engineering and stem-cell based regenerative medicine.

developmental biology↗

bioRxiv2022

Spatiotemporal orchestration of multicellular transcriptional programs and communications in spinal cord injury

While spinal cord injury (SCI) involves a complex cascade of cellular and pathological changes that last for months to years, the most dramatic and comprehensive molecular rewiring and multicellular re-organization occur in the first few days, which determine the overall progression and prognosis of SCI, yet remain poorly understood. Here, we resolved the spatiotemporal architecture of multicellular gene expression in a mouse model of acute SCI, and revealed the coordinated gene co-expression networks, the upstream regulatory programs, and in situ cell-cell interactions that underlay the anatomic disorganization as well as the immune and inflammatory responses conferring the secondary injury. The spatial transcriptomic analysis highlights that the genes and cell types in the white matter (WM) play a more active and predominant role in the early stage of SCI. In particular, we identified a distinct population of WM-originated, Igfbp2-expressing reactive astrocytes, which migrated to the grey matter and expressed multiple axon/synapse-supporting molecules that may foster neuron survival and spinal cord recovery in the acute phase. Together, our dataset and analyses not only showcase the spatially-defined molecular features endowing the cell (sub)types with new biological significance but also provide a molecular atlas for disentangling the spatiotemporal organization of the mammalian SCI and advancing the injury management.

neuroscience↗

bioRxiv2022

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Spinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs.

cell biology↗

bioRxiv2022

Kiaa1024L/Minar2 is essential for hearing by regulating cholesterol distribution in hair bundles

Unbiased genetic screens implicated a number of uncharacterized genes in hearing loss, suggesting some biological processes required for auditory function remain unexplored. Loss of Kiaa1024L/Minar2, a previously understudied gene, caused deafness in mice, but how it functioned in hearing was unclear. Here we show that disruption of kiaa1024L/minar2 causes hearing loss in the zebrafish. Defects in mechanotransduction, longer and thinner hair bundles, and enlarged apical lysosomes in hair cells are observed in kiaa1024L/minar2 mutant. In cultured cells, Kiaa1024L/Minar2 is mainly localized to lysosomes and its overexpression recruits cholesterol and increases cholesterol labeling. Strikingly, an accessible pool of cholesterol is highly enriched in the hair bundle membrane, and loss of kiaa1024L/minar2 reduces cholesterol localization to the hair bundles. Decreasing cholesterol levels aggravates, while increasing cholesterol levels rescues hair cell defects in kiaa1024L/minar2 mutant. Therefore cholesterol plays an essential role in the hair bundles, and Kiaa1024L/Minar2 regulates cholesterol distribution and homeostasis to ensure normal hearing.

neuroscience↗

bioRxiv2022

Simultaneously spatiotemporal gene expression and chromatin accessibility for mouse brain development

Brain are complex biological tissues which function relies on coordinated anatomical and molecular structure comprised by a large number of specialized cells. The spatial architecture of brain which is key to the understanding of its physiological and pathological significance is formed during embryo development. However, the molecular basis for discrete neuroanatomical domains particularly in the context of spatial organization of the brain is inadequate. Here, we introduced microfluidic indexing based spatial ATAC and RNA sequencing (MISAR-seq), a method for joint profiling of chromatin accessibility and gene expression with spatial information retained in the developing mouse brain. Our study has established a direct means to spatially determine the coordination between chromatin accessibility and transcriptome, identified the chromatin potential to define cell fate determination of brain organization, and uncovered spatiotemporal regulatory principles during mammalian brain development.

developmental biology↗

bioRxiv2022

Spatial and molecular anatomy of germ layers in the gastrulating primate embryo

During mammalian embryogenesis, spatial regulation of gene expression and cell signaling are functionally coupled with lineage specification, patterning of tissue progenitors and germ layer morphogenesis. While the mouse model has been instrumental for our understanding of mammalian development, comparatively little is known about human and non-human primate gastrulation due to the restriction of both technical and ethical issues. Here, we present a morphological and molecular survey of spatiotemporal dynamics of cell types populating the non-human primate embryos during gastrulation. We performed serial sections of Cynomolgus monkeys (Macaca fascicularis) gastrulating embryos at 1-day temporal resolution from E17 to E21, and reconstructed three-dimensional digital models based on high-resolution anatomical atlas that revealed the dynamic changes in the geography of the mesoderm and primitive streaks. Spatial transcriptomics identified unique gene profiles that correspond to distinct germ layers and cross-species spatiotemporal transcriptome analysis revealed a developmental coordinate of germ layer segregation between mouse and primate. Furthermore, we identified species-specific transcription programs during gastrulation. These results offer important insights into evolutionarily conserved and divergent processes during mammalian gastrulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/474719v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1058f45org.highwire.dtl.DTLVardef@105cborg.highwire.dtl.DTLVardef@12362d7org.highwire.dtl.DTLVardef@2e2346_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightO_LIA high-resolution anatomical atlas of Cynomolgus gastrulation embryos C_LIO_LICreated a three-dimensional digital template from serial sections of five developmental stages C_LIO_LIA two-dimensional spatiotemporal transcriptome of the germ layers of gastrulating embryos C_LIO_LICross-species comparison infers conservation of functional attributes of regulome and signaling activity in germ layer formation C_LI

developmental biology↗

bioRxiv2022

Stem embolism vulnerability curve depends on methods used: is there a fifth mechanism of cavitation?

A long-established ecological paradigm predicts a functional relationship determining vulnerability to cavitation: vulnerability increases with vessel hydraulic efficiency and vessel diameter. Even within a species, big vessels cavitate before small ones. Some centrifuge methods for measuring vulnerability are prone to artifacts due to nano-particles seeding early embolism, as the particles are drawn into vessels during measurements. Both the Sperry and Cochard rotors are prone to early cavitation due to nano-particles drawn into long and wide vessels in Robinia pseudoacacia and Quercus acutissima, whereas extraction centrifuge methods produce vulnerability curves more resistant to cavitation. Sufficient nano-particles pass through the stems to seed early embolism in all rotor designs. For several years, people have thought that early embolism is induced by nano-particles present in laboratory water. One new hypothesis is that the origin of nano-particles is from cut-open living cells but a much bigger study including many species is required to confirm this idea. This paper confirms the hypothesis in comparisons between short-vesselled Acer, and long-vesselled Robinia, and Quercus. Our new results and a review of old results justifies bigger study. Hypothetical nano-particles might explain why different methods for measuring vulnerability curves cause different T50 = tensions causing 50% loss of hydraulic conductivity. Hence the hypothesis for future research should be that the open-vessel artifact is consistent with long vessels surrounded by cut open living cells. One sentence SummaryNano-particles induced early cavitation in species with vessel lengths about [1/4] the stem length used in all centrifuge rotors, and the origin of nano-particles might be from living cells nearby vessels

physiology↗

bioRxiv2021

A quadratic analytical solution of root pressure generation provides insights about bamboo and other species

We derived a steady-state model of whole root pressure generation through the combined action of all parallel segments of fine roots. This may be the first complete analytical solution for root pressure, which can be applied to complex roots/shoots. The osmotic volume of a single root is equal to that of the vessel lumen in fine roots and adjacent apoplastic spaces. Water uptake occurs via passive osmosis and active solute uptake ([Formula], osmol s-1), resulting in the osmolal concentration Cr (mol{middle dot}kg-1 of water) at a fixed osmotic volume. Solute loss occurs via two passive processes: radial diffusion of solute Km (Cr-Csoil), where Km is the diffusional constant and Csoil is the soil-solute concentration) from fine roots to soil and mass flow of solute and water into the whole plant from the end of the fine roots. The proposed model predicts the quadratic function of root pressure [Formula], where b and c are the functions of plant hydraulic resistance, soil water potential, solute flux, and gravitational potential. The present study investigates the theoretical dependencies of Pr on the factors detailed above and demonstrates the root pressure-mediated distribution of water through the hydraulic architecture of a 6.8-m-tall bamboo shoot. One sentence SummaryAn analytical solution for root pressure is derived and illustrated by applying it to the measured hydraulic architecture of a 7-meter bamboo shoot.

physiology↗

bioRxiv2021

A Unit Pipe Pneumatic model to simulate gas kinetics during measurements of embolism in excised angiosperm xylem

O_LIThe Pneumatic method has been introduced to quantify embolism resistance in plant xylem of various organs. Despite striking similarity in vulnerability curves between the Pneumatic and hydraulic methods, a modeling approach is highly needed to demonstrate that xylem embolism resistance can be accurately quantified based on gas diffusion kinetics. C_LIO_LIA Unit Pipe Pneumatic (UPPn) model was developed to estimate gas diffusion from intact conduits, which were axially interconnected by interconduit pit membranes. The physical laws used included Ficks law for diffusion, Henrys law for gas concentration partitioning between liquid and gas phases at equilibrium, and the ideal gas law. C_LIO_LIThe UPPn model showed that 91% of the extracted gas came from the first two series of embolized, intact conduits, and only 9% from the aqueous phase after 15 s of simulation. Embolism resistance measured with a Pneumatic apparatus was systematically overestimated by 2 to 17%, corresponding to a typical measuring error of 0.11 MPa for P50 (the water potential equivalent to 50% of the maximum amount of gas extracted). C_LIO_LIBecause results from the UPPn model are supported by experimental evidence, there is a good theoretical and experimental basis for applying the pneumatic method to research on embolism resistance of angiosperms. C_LI

plant biology↗