Project description:Understanding complex biological processes requires precise spatiotemporal mapping of proliferative and transcriptional dynamics. Current spatial transcriptomics methods are tailored to capture protein-coding transcripts and static snapshots, obscuring non-coding RNAs and dynamic cellular events. We developed SPTEdU-seq, integrating spatial full-length total transcriptomics with optics-free 5-ethynyl-2’-deoxyuridine (EdU) tracking to concurrently profile global gene expression and proliferation dynamics at cellular resolution. SPTEdU-seq demonstrates ultrahigh sensitivity in detecting coding/non-coding transcripts and splicing isoforms, and bypasses imaging through its single-molecule probe design. Applied to the developing and adult mouse brains, it revealed spatial lncRNA patterns, reconstructed cortical trajectories through enhanced RNA velocity and enabled spatiotemporal lineage tracing of embryonic neurodevelopment. To demonstrate its applicability across pathological contexts, SPTEdU-seq was applied to murine ischemic stroke as well as mouse and human renal tumors. It mapped regeneration dynamics, reconstructed astrocyte-to-neuron reprogramming trajectories through transient intermediates, and identified a pro‑repair niche in which newborn cells enhance neighboring developmental potency after stroke. Crucially, SPTEdU-seq simultaneously profiles newborn and resident cells within intact microenvironments, uncovering previously inaccessible interaction networks during tissue remodeling and tumor invasion. SPTEdU-seq also identified tumor‑associated splicing in mouse renal tumors and showed potential for molecular diagnosis by detecting 3p loss via CNV in human renal cell carcinoma. SPTEdU-seq establishes a powerful framework for investigating cell fate dynamics across regenerative medicine, development, and tumor biology.
Project description:Dynamic remodeling in architecture and function of mammalian brain, especially in primate, rely on a precisely orchestrated molecular and cellular regulation at distinct levels. Here, we applied comprehensive RNA-seq and CAGE-Seq analysis to characterize dynamics of lncRNA expression in Rhesus macaque brain across postnatal development and aging. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities respectively. Highly spatiotemporal- and sex-specific dynamic changes in lncRNA but mRNA expression and the negative correlation between lncRNAs and mRNAs, functionally associate with brain development and aging, especially in the neocortex. Together with in situ hybridization (ISH) and quantitative real time-PCR (qRT-PCR) data, our findings provide an initial insight into spatial-, age- and sex-related dynamics of lncRNA expression during postnatal brain development and aging in macaque, implying that high dynamics of lncRNA expression might represent a previously unappreciated regulatory system in shaping brain architecture and function.
Project description:Dynamic remodeling in architecture and function of mammalian brain, especially in primate, rely on a precisely orchestrated molecular and cellular regulation at distinct levels. Here, we applied comprehensive RNA-seq and CAGE-Seq analysis to characterize dynamics of lncRNA expression in Rhesus macaque brain across postnatal development and aging. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities respectively. Highly spatiotemporal- and sex-specific dynamic changes in lncRNA but mRNA expression and the negative correlation between lncRNAs and mRNAs, functionally associate with brain development and aging, especially in the neocortex. Together with in situ hybridization (ISH) and quantitative real time-PCR (qRT-PCR) data, our findings provide an initial insight into spatial-, age- and sex-related dynamics of lncRNA expression during postnatal brain development and aging in macaque, implying that high dynamics of lncRNA expression might represent a previously unappreciated regulatory system in shaping brain architecture and function.
Project description:Genetic studies have revealed an essential role for cytosine DNA methylation in gene regulation. However, its spatiotemporal distribution in the developing embryo remains obscure. Here, we profiled the DNA methylation landscape of 12 mouse tissues/organs at 8 developmental stages spanning from early embryo to birth. In-depth analysis of such spatiotemporal epigenome maps uncovered widespread regulatory DNA element dynamics during embryogenesis. We systematically delineated methylation variants that likely drive gene transcription, whose human counterparts are enriched for genetic risk factors of human diseases. Strikingly, these predicted regulatory elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. Key transcription factors, essential for early tissue/organ development, accumulate non-CG methylation within their gene bodies, coinciding with transcriptional repression during late stage fetal development. These spatiotemporal epigenomic datasets provide a valuable resource for studies of gene regulation during mammalian tissue/organ progression and the possible origins of human developmental diseases.
Project description:Differences between species promote stable coexistence in a resource-limited environment. These differences can result from interspecies competition leading to character shifts, a process referred to as character displacement. While character displacement is often interpreted as a consequence of genetically fixed trait differences between species, it can also be mediated by phenotypic plasticity in response to the presence of another species. Here, we test whether phenotypic plasticity leads to a shift in proteome allocation during co-occurrence of two bacterial species from the abundant, leaf-colonizing families Sphingomonadaceae and Rhizobiaceae in their natural habitat. Upon mono-colonizing of the phyllosphere, both species exhibit specific and shared protein functions indicating a niche overlap. During co-colonization, quantitative differences in the protein repertoire of both bacterial populations occur as a result of bacterial coexistence in planta. Specifically, the Sphingomonas strain produces enzymes for the metabolization of xylan, while the Rhizobium strain reprograms its metabolism to beta-oxidation of fatty acids fueled via the glyoxylate cycle and adapts its biotin acquisition. We demonstrate the conditional relevance of cross-species facilitation by mutagenesis leading to loss of fitness in competition in planta. Our results show that dynamic character displacement and niche facilitation mediated by phenotypic plasticity can contribute to species coexistence.
Project description:Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse in different organs. In bone, niche macrophages express estrogen receptor (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of ER in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in metastatic niche and functionally tie ER signaling in macrophages to T cell exclusion during metastatic colonization.
Project description:Microenvironment niches determine cellular fates of metastatic cancer cells. However, robust and unbiased approaches to identify niche components and their molecular profiles are lacking. We established Sortase A-Based Microenvironment Niche Tagging (SAMENT), which selectively labels cells encountered by cancer cells during metastatic colonization. SAMENT was applied to multiple cancer models colonizing the same organ and the same cancer to different organs. Common niche features include macrophage enrichment and T cell depletion. Macrophage niches are phenotypically diverse in different organs. In bone, niche macrophages express estrogen receptor (ER) and exhibit active ER signaling in male and female hosts. Conditional knockout of ER in macrophages significantly retarded bone colonization by allowing T cell infiltration. ER expression was also discovered in human bone metastases of both genders. Collectively, we identified a unique population of ER+ macrophages in metastatic niche and functionally tie ER signaling in macrophages to T cell exclusion during metastatic colonization.