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Single-cyst transcriptome analysis of Drosophila male germline stem cell lineage.
The Drosophila male germline stem cell (GSC) lineage provides a great model to understand stem cell maintenance, proliferation, differentiation and dedifferentiation. Here, we use the Drosophila GSC lineage to systematically analyze the transcriptome of discrete but continuously differentiating germline cysts. We first isolated single cysts at each recognizable stage from wild-type testes, which were subsequently applied for RNA-seq analyses. Our data delineate a high-resolution transcriptome atlas in the entire male GSC lineage: the most dramatic switch occurs from early to late spermatocyte, followed by the change from the mitotic spermatogonia to early meiotic spermatocyte. By contrast, the transit-amplifying spermatogonia cysts display similar transcriptomes, suggesting common molecular features among these stages, which may underlie their similar behavior during both differentiation and dedifferentiation processes. Finally, distinct differentiating germ cell cyst samples do not exhibit obvious dosage compensation of X-chromosomal genes, even considering the paucity of X-chromosomal gene expression during meiosis, which is different from somatic cells. Together, our single cyst-resolution, genome-wide transcriptional profile analyses provide an unprecedented resource to understand many questions in both germ cell biology and stem cell biology fields.
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A single-cell atlas of the peripheral immune response to severe COVID-19.
There is an urgent need to better understand the pathophysiology of Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2. Here, we apply single-cell RNA sequencing (scRNA-seq) to peripheral blood mononuclear cells (PBMCs) of 7 patients hospitalized with confirmed COVID-19 and 6 healthy controls. We identify substantial reconfiguration of peripheral immune cell phenotype in COVID-19, including a heterogeneous interferon-stimulated gene (ISG) signature, HLA class II downregulation, and a novel B cell-derived granulocyte population appearing in patients with acute respiratory failure requiring mechanical ventilation. Importantly, peripheral monocytes and lymphocytes do not express substantial amounts of pro-inflammatory cytokines, suggesting that circulating leukocytes do not significantly contribute to the potential COVID-19 cytokine storm. Collectively, we provide the most thorough cell atlas to date of the peripheral immune response to severe COVID-19.
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Single-cell profiling reveals IFI44L as a central regulator of immune dysregulation in high HIV viral load.
Human Immunodeficiency Virus (HIV) infection impairs the immune system, diminishing its ability to defend against pathogens and increasing susceptibility to infections and diseases. To gain a comprehensive understanding of the heterogeneity, functions, and regulatory mechanisms of immune cells affected by different HIV viral loads, we investigated the biological impacts of HIV infection on the human body. We reanalyzed a publicly available peripheral blood mononuclear cell (PBMC) single-cell RNA sequencing dataset (GSE157829) comprising three people living with HIV with high viral load (HL-HIV), three people living with HIV with low viral load (LL-HIV), and one healthy control donor. We constructed single-cell immune atlases that represent different viral load profiles. We also analyzed the dynamic changes in specific immune cell subpopulations to gain insights into their signaling pathways, developmental trajectories, and key transcriptional regulators. At the single-cell level, non-classical monocyte subpopulations, specifically ncMono_LYN_TCF7L2 and ncMono_IL32, functioned as immunosurveillance elements but also activated pro-inflammatory pathways, leading to immune activation. B_CD83 subpopulation was critical in B cell development, facilitating B cell differentiation and tolerance. Naive.T_TNFAIP3 subpopulation exhibited anti-inflammatory effects and protected against aberrant apoptosis. Central memory T (TCM)_TCF7_CCR7 subpopulation played a crucial role in regulating the expansion of HIV-specific CD8+ T cells and maintaining the immune response. Additionally, we observed a significant enrichment of IFI44L-positive subpopulations across different cell types, particularly in HL-HIV samples. Our findings demonstrate that HIV infection increases the complexity of immune cell subpopulations. Notably, IFI44L has emerged as a potential disease hub gene in HL-HIV samples, highlighting its potential as a novel biomarker for HIV.
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One section, two worlds: single-cell integration of MALDI-MSI and spatial transcriptomics on the same single tissue section.
Understanding tissue complexity requires spatially resolved multi-omics data at single-cell resolution. Here, we present a workflow integrating high-resolution matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with Xenium spatial transcriptomics (SPT) on a single tissue section. This strategy ensures pixel-scale spatial correspondence between metabolic and transcriptomic features, avoiding misalignment issues of serial sections, where even minor offsets result in sampling different cells. We investigated MALDI-MSI compatibility with downstream SPT revealing that the number of transcripts per cell decreased by ~ 30% after MSI, whilst cell recovery and cell-type assignments are preserved. Validated using mouse brain and demonstrated using human glioblastoma tissues, we achieved pixel-scale modality co-registration, enabling per-cell MALDI spectra extraction aligned with gene expression. Integrated clustering revealed enhanced cell-type resolution and identified metabolic heterogeneity within transcriptionally defined populations. This facilitates precise correlations of a cell's function and its biochemical state, providing a holistic view of cellular function, heterogeneity, and interaction in health and disease. Our workflow provides a scalable path to multi-omic atlases, advancing both data integration and translational research.
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Unveiling novel double-negative prostate cancer subtypes through single-cell RNA sequencing analysis.
Recent advancements in single-cell RNA sequencing (scRNAseq) have facilitated the discovery of previously unrecognized subtypes within prostate cancer (PCa), offering new insights into cancer heterogeneity and progression. In this study, we integrated scRNAseq data from multiple studies, comprising publicly available cohorts and data generated by our research team, and established the Human Prostate Single cell Atlas (HuPSA) and Mouse Prostate Single cell Atlas (MoPSA) datasets. Through comprehensive analysis, we identified two novel double-negative PCa populations: KRT7 cells characterized by elevated KRT7 expression and progenitor-like cells marked by SOX2 and FOXA2 expression, distinct from NEPCa, and displaying stem/progenitor features. Furthermore, HuPSA-based deconvolution re-classified human PCa specimens, validating the presence of these novel subtypes. We then developed a user-friendly web application, "HuPSA-MoPSA" ( https://pcatools.shinyapps.io/HuPSA-MoPSA/ ), for visualizing gene expression across all newly established datasets. Our study provides comprehensive tools for PCa research and uncovers novel cancer subtypes that can inform clinical diagnosis and treatment strategies.
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A single-cell atlas of the peripheral immune response in patients with influenza A virus infection.
Influenza A virus (IAV) remains a pressing global health concern, yet our understanding of the specific nature and functional roles of certain circulating cell subsets in relation to this viral infection remains unclear. We performed single-cell RNA sequencing (scRNA-seq) on single-cell whole-blood (scWB) isolated from various populations using the Singleron Matrix platform. Our investigation showed a significant upregulation of the IFN-stimulated gene, IFN-α-inducible protein 27 (IFI27), in patients affected by IAV infection and further found that the heightened expression of IFI27 was primarily concentrated in specific immune cell populations, including monocytes and conventional dendritic cells (cDCs). Notably, we identified a specific subset of neutrophils, neutrophil_ISG15, which implicates interferon (IFN) signaling in IAV infection. Our findings provide a comprehensive understanding of the cellular subtypes and molecular characteristics of scWB across different populations with IAV infection.
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Comprehensive ceRNA Profiling Uncovers Clinically Relevant Hub lncRNAs in Glioblastoma.
Long non-coding RNAs (lncRNAs) can function as competing endogenous RNAs (ceRNAs) that rewire post-transcriptional regulation in glioblastoma (GBM). Previous GBM studies have focused on either single lncRNA ceRNA axis in isolation or used in silico predictions with small patient cohorts (< 200). In this study, we integrated RNA-seq data from 372 TCGA-GBM tumors, 5 matched adjacent TCGA-normal brain and 2 931 GTEx-normal brain (n = 3 308) samples to build an experimentally informed ceRNA atlas. Limma-voom differential analysis, intersection with 2 experimentally supported interaction databases (ENCORI and miRTarBase) distilled 517 high-confidence lncRNA-miRNA-mRNA triplets. Twelve hub lncRNAs coordinated 3 downregulated miRNAs and 262 target mRNAs enriched for cell-cycle, p53 signaling and homologous recombination pathways. Two co-expressed hubs, CYTOR and MIR4435-2HG, were significantly over-expressed in GBM tumors in comparison with normal brain tissue and independently predicted poor overall survival (log-rank P < .01). Their shared 25 targets include oncogenic YBX1, MDM4 and TGFBR1 mRNAs, underscoring the redundant regulation of oncogenic pathways, suggesting the need to explore combination lncRNA inhibition strategies. This population-scale analysis prioritizes CYTOR and MIR4435-2HG for functional interrogation and offers a framework for exploring biomarkers and RNA-targeted strategies in GBM.
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Single-cell transcriptomics reveals conserved cell identities and fibrogenic phenotypes in zebrafish and human liver.
The mechanisms underlying liver fibrosis are multifaceted and remain elusive with no approved antifibrotic treatments available. The adult zebrafish has been an underutilized tool to study liver fibrosis. We aimed to characterize the single-cell transcriptome of the adult zebrafish liver to determine its utility as a model for studying liver fibrosis. We used single-cell RNA sequencing (scRNA-seq) of adult zebrafish liver to study the molecular and cellular dynamics at a single-cell level. We performed a comparative analysis to scRNA-seq of human liver with a focus on hepatic stellate cells (HSCs), the driver cells in liver fibrosis. scRNA-seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA-seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish. Human and zebrafish HSCs show conservation of transcriptional profiles, and we uncover collectin subfamily member 11 (colec11) as a novel, conserved marker for zebrafish HSCs. To demonstrate the power of scRNA-seq to study liver fibrosis using zebrafish, we performed scRNA-seq on our zebrafish model of a pediatric liver disease with mutation in mannose phosphate isomerase (MPI) and characteristic early liver fibrosis. We found fibrosis signaling pathways and upstream regulators conserved across MPI-depleted zebrafish and human HSCs. CellPhoneDB analysis of zebrafish transcriptome identified neuropilin 1 as a potential driver of liver fibrosis. Conclusion: This study establishes the first scRNA-seq atlas of the adult zebrafish liver, highlights the high degree of similarity to human liver, and strengthens its value as a model to study liver fibrosis.
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Alterations in Astrocyte Subpopulations in Glioma and Identification of Cuproptosis-Related Genes Using Single-Cell RNA Sequencing.
PURPOSE: Mitochondrial metabolism is essential for energy production and the survival of brain cells, particularly in astrocytes. Cuproptosis is a newly identified form of programmed cell death that occurs due to the disruption of mitochondrial metabolism caused by excessive copper toxicity. However, the relationship between cuproptosis-related genes (CRGs) in the tumor microenvironment (TME) and the prognosis of gliomas remains unclear. PATIENTS AND METHODS: In this study, we utilized 32,293 cells obtained from three in-house single-cell RNA sequencing (scRNA-seq) datasets, along with 6,148 cells acquired from the Chinese Glioma Genome Atlas (CGGA) involving 14 glioma patients, to identify and validate the TME of gliomas. RESULTS: Based on an analysis of 32,293 single cells, we investigated intra-tumor heterogeneity, intercellular communication, and astrocyte differentiation trajectories in gliomas. Our findings revealed that the TGFβ signaling pathway exhibited a higher relative strength in astrocyte subpopulations. Additionally, we identified a novel three-gene signature (CDKN2A, SOX2, and MPC1) was identified for prognostic prediction. Furthermore, glioma patients with a high-risk score demonstrated poorer overall survival (OS) compared to those with a low-risk score in both training and testing datasets (P training set < 0.001; P test set = 0.037). CONCLUSION: Our study revealed the prognostic value of the CRGs in astrocytes exhibiting tumor immunosuppressive characteristics in glioma. We established a novel three-gene prognostic model that offers new insights into the prognosis and treatment strategies for gliomas.
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Single-nucleus transcriptomic atlas reveals autophagy and hormone signaling in early grapevine (Vitis vinifera L.) tendril versus inflorescence determination.
Understanding the early specification of tendrils versus inflorescences in grapevine is key for developmental biology and agricultural applications. Here, we performed a comparative anatomical and cyto-histological analysis of lateral buds from the tendril-prone cultivar "Pinot Noir" ("PN") and the inflorescence-prone cultivar "Einset Seedless" ("EinS"). Our results show that cytological differences between tendril and inflorescence primordia emerge early during floral initiation, prior to any visible structural divergence. In particular, rib zone (RZ) cells in the uncommitted lateral meristem (UM) of "PN" differentiated into vacuolated pith cells more rapidly than those in "EinS." We subsequently applied single-nucleus RNA sequencing (snRNA-seq) to 50 052 nuclei from lateral buds of both cultivars, generating a cell type-resolved transcriptional atlas. Reconstruction of shoot apical meristem (SAM) and UM developmental trajectories revealed accelerated SAM differentiation in "PN." Together with cyto-histological observations of a less abundant UM mantle zone and lower cell cycle gene activity in UM cells, these findings indicate that both accelerated SAM differentiation and reduced UM proliferative activity restrict complete inflorescence formation in "PN," which is consistent with the anatomical differences observed. Analyzing UM and inflorescence meristem differentiation trajectories distinguished inflorescences- and tendril-specific differentiation trajectories, and revealed the involvement of the autophagy and hormone signal transduction pathway in early tendril versus inflorescence determination. Furthermore, transcription factors from the GRF, B3, S1Fa-like, WRKY, GATA, and C2H2 families showed expression patterns correlated with tendril specification. These results provide key insights into the differentiation of homologous reproductive structures in grapevine, thereby advancing the theoretical framework for early tendril versus inflorescence specification and supporting future applied research.