Integrative single-nucleus transcriptomic analysis identifies UBE2C+ proliferative tumor cells and immune-stromal regulatory crosstalk in small cell lung cancer
Aug 2026· Frontiers in Immunology· Vol 17· 0 citations· 69 references
Medicine
TL;DR
This study identified UBE2C+ proliferative tumor cells as a functionally relevant malignant subpopulation in SCLC and links this state to immune-stromal communication networks within the tumor microenvironment and provides a systems-level framework for investigating the cancer-immunity regulome in SCLC.
Abstract
Background Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy characterized by rapid proliferation, early dissemination, and limited durable benefit from current chemoimmunotherapy. Although immune checkpoint blockade has modestly improved clinical outcomes, the regulatory logic linking malignant cell states to the tumor immune microenvironment remains incompletely understood. Here, we applied an integrative single-nucleus transcriptomic framework to dissect tumor cell heterogeneity, regulatory programs, and immune-stromal communication networks in SCLC. Methods Publicly available Single-nucleus RNA sequencing data from primary and metastatic SCLC samples were analyzed using Seurat-based clustering, inferCNV-based malignant cell identification, differential expression analysis, pathway enrichment, metabolic and stemness scoring, pseudotime trajectory reconstruction, CellChat-mediated cell-cell communication inference, and transcription factor regulatory module analysis. A UBE2C-enriched proliferative tumor cell subpopulation was prioritized for functional validation. siRNA-mediated UBE2C knockdown was performed in DMS114 and NCI-H446 SCLC cell lines, followed by qRT-PCR, CCK-8, colony formation, transwell migration, and Annexin V/PI apoptosis assays. Results Using snRNA-seq, we identified multiple cell types and resolved a UBE2C+ subpopulation with marked proliferative features. UBE2C+ subpopulation displayed strong G2/M-phase enrichment, elevated mitotic and cell cycle programs. And pseudotime analysis positioned C3 UBE2C+ tumor cells at a proliferative state during tumor cell state evolution. Cell-cell communication analysis suggested that this subpopulation might interact with macrophages and fibroblasts through GRN-SORT1 and THBS1-CD47/CD36 signaling axes, indicating a potential link between proliferative tumor states and candidate communication axes. Transcription factor module analysis further revealed enrichment of cell cycle-associated regulators, including MYBL2, NFYB, E2F2, TGIF1, and RXRG, in the C3 subpopulation. Functionally, UBE2C knockdown significantly suppressed proliferation, clonogenic growth, and migration while increasing apoptosis in SCLC cells. Conclusions This study identified UBE2C+ proliferative tumor cells as a functionally relevant malignant subpopulation in SCLC and links this state to immune-stromal communication networks within the tumor microenvironment. By integrating single-nucleus transcriptomics, regulatory network inference, intercellular communication analysis, and in vitro validation, our findings nominate UBE2C as a potential candidate functional regulator and provide a systems-level framework for investigating the cancer-immunity regulome in SCLC.
Integrative single-cell RNA sequencing analysis of publicly available datasets from non-small cell lung cancer and breast cancer is performed to systematically map transcriptional heterogeneity and regulatory networks within the TME, providing a systems-level framework of TME organization.
M. O. Odubote, Chiemeka Elochi Emeribe· bioRxiv· 0 citations
Single-cell transcriptomics of publicly available BLCA data identifies two transcriptionally distinct fibroblast states in adjacent tissue and supports an exploratory ligand–receptor interaction framework, warranting prospective validation with primary CAF populations and adequately powered multi-specimen cohorts.
Yan-Dong He, Wen-Long Lu, Guan-Qun Ju et al.· Frontiers in Cell and Develo...· 0 citations
These findings define the cellular organization and molecular programs that shape the cSCC microenvironment and provide insights into the coordinated immune, stromal, and epithelial interactions involved in cSCC progression.
Yong He, Ting Tian, Liming Li et al.· Frontiers in Immunology· 0 citations
Colorectal cancer liver metastasis (CRLM) develops within a liver-specific immune and stromal microenvironment, yet the natural killer (NK)-cell adaptations associated with this metastatic niche remain incompletely defined.
We integrated human single-cell RNA sequencing, an exploratory murine cross-species comparison, spatial transcriptomics, bulk transcriptomic cohorts, donor-level pseudobulk analyses, cell-cell communication, pseudotime and in silico perturbation analyses, together with multiplex immunofluorescence, conditioned-medium assays, ELISA and immunoblotting.
Across 73,486 cells from six anatomical sites, NK cells showed lower relative representation within the recovered T/NK compartment in primary tumors and liver metastases, while the residual compartment showed inflammatory remodeling. NK-cell reclustering identified CD56-associated and CD16-associated CCL4 source clusters that were analyzed jointly as a CCL4-enriched NK-cell transcriptional state characterized by NF-κB, TNF, MAPK and JAK-STAT programs. In paired GSE164522 samples from 10 patients, this state was independently recovered, with nominally higher CCL4-associated signal in liver metastases than in primary tumors that did not remain significant after Benjamini-Hochberg correction. Spatial and communication analyses associated the state with SPP1-positive macrophage and stromal programs without establishing causality. Tissue imaging, conditioned-medium assays, ELISA and immunoblotting provided complementary marker-level and model-system support for CCL4-associated inflammatory activity and NF-κB pathway responsiveness.
CRLM is associated with altered NK-cell representation among recovered cells and a reproducible CCL4-enriched inflammatory NK-cell transcriptional state. Its association with inflammatory and myeloid-stromal programs across independent, spatial and model-system analyses provides a focused framework for future lineage-restricted and
in vivo
studies.
Li-Hong Lin, Michael Xu, Xiao-Chun Gu et al.· Frontiers in Immunology· 0 citations
Intratumoral heterogeneity of malignant epithelial cells limits prognostic stratification and therapeutic development in NPC, yet transcriptionally distinct malignant epithelial states and their associated molecular programs remain poorly characterized. We aimed to identify clinically relevant malignant epithelial states and define their associated molecular programs in NPC. Fresh normal nasopharyngeal tissue, primary NPC, and nodal metastases were profiled by scRNA-seq, yielding 27,330 cells. Malignant epithelial states were characterized by transcriptomic reclustering, cell-cycle analysis, CNV inference, pseudotime trajectory analysis, and pathway enrichment analyses. An independent public scRNA-seq cohort (GSE150825) was reanalyzed to validate the identified malignant epithelial state and its associated molecular programs. TUBB4B function was examined using knockdown and overexpression assays, cell-cycle analysis, clonogenic assays, and xenograft experiments. Clinical relevance was evaluated by immunohistochemistry and immunofluorescence in NPC tissue sections and by survival analysis in an independent NPC tissue microarray cohort with long-term follow-up. We identified a malignant epithelial state occupying an early branch of the inferred pseudotime trajectory, characterized by increased inferred CNV burden and increased cell-cycle engagement, and further distinguished by coordinated microtubule- and cilium-associated transcriptional programs and selective enrichment of TUBB4B expression. Reanalysis of GSE150825 identified a phenotypically similar malignant epithelial state subpopulation with concordant microtubule- and cilium-associated pathway enrichment. TUBB4B localized to mitotic structures; its knockdown reduced the proportion of cells in G2/M phase, whereas overexpression increased PCNA expression, clonogenic growth, and xenograft tumor growth. In clinical tissue sections, TUBB4B expression was higher in NPC than in normal nasopharyngeal epithelium and was accompanied by an increased Ki-67-positive area. In the tissue microarray cohort, high cytoplasmic TUBB4B expression was associated with significantly worse overall survival and progression-free survival using a data-derived cut-off, and remained associated with overall survival after adjustment for staging in multivariable Firth penalized Cox models, although this association was attenuated using an alternative cut-off. We identify a TUBB4B-linked malignant epithelial transcriptional program in NPC associated with proliferation, inferred CNV burden, and adverse clinical outcome in this cohort. These findings provide a transcriptionally resolved framework for understanding malignant epithelial heterogeneity in NPC progression and nominate TUBB4B as a candidate prognostic biomarker and potential therapeutic vulnerability warranting further validation.
Xiasang Chen, W. Liao, Meiqian Xu et al.· Journal of Translational Med...· 0 citations
A comprehensive single-cell multiomic analysis of primary human T cells exposed to exosomes derived from 17 genomically diverse TNBC cell lines and 35 patient samples uncovered conserved and subtype-specific immunomodulatory programs induced by TNBC exosomes.
Sanam Rezaei Benam, S. Maleknia, Kent Williams et al.· Signal Transduction and Targ...· 0 citations
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