Dec 2024· bioRxiv· Vol 17· 0 citations· 135 references
MedicineBiology
TL;DR
INvestigating SIGnaling network of specific cell subpopulation in Heterogeneous Tissue, a new platform technology combining fluorescence-activated cell sorting with ultra-sensitive mass spectrometry to enable phosphoproteomic characterization of rare and discrete cell subpopulations from fixed tissues, uncovered a global rewiring of signaling networks with tumor cell dissemination.
Abstract
Dysregulation of intracellular signaling networks underpins cancer. However, a systems-level elucidation of how signaling networks within distinct cell subpopulations drive cancer progression in vivo has been unattainable due to technical limitations. We developed INSIGHT (INvestigating SIGnaling network of specific cell subpopulation in Heterogeneous Tissue), a new platform technology combining fluorescence-activated cell sorting with ultra-sensitive mass spectrometry to enable phosphoproteomic characterization of rare and discrete cell subpopulations from fixed tissues. We demonstrated the broad utility of INSIGHT by analyzing the oligodendroglial cell-specific signaling network in the mouse brain. We then applied INSIGHT to investigate the rare, disseminated tumor cell subpopulation in glioblastoma patient-derived xenograft models. INSIGHT uncovered a global rewiring of signaling networks with tumor cell dissemination, marked by a transition from proliferation-associated signaling in the primary tumor cells to signaling associated with postsynapse, neuronal migration, and ion homeostasis in disseminated tumor cells. We reveal interconnections between signaling circuitries within the networks, with numerous proteins, including GluA2, exhibiting altered phosphorylation without protein expression changes, emphasizing the role of post-translational modifications in glioblastoma dissemination. We validated key phosphorylation changes and inferred differentially active kinases with tumor spread to offer new systems-level insights into glioblastoma dissemination mechanisms in vivo. INSIGHT is generally applicable to a wide range of biological systems without genetic engineering and provides quantitative phosphorylation and protein expression data for selected cell subpopulations from heterogeneous tissues.
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
Background Glioblastoma (GBM) is a highly heterogeneous and vascularized malignancy in which the mesenchymal (MES) subtype is associated with poor prognosis, extensive macrophage infiltration and resistance to therapy. However, the signaling mechanisms integrating vascular remodeling with inflammatory tumor-macrophage crosstalk remain incompletely understood. Methods We integrated magnetic resonance imaging-derived vascular phenotyping with transcriptomic analyses of human glioblastoma cohorts to identify molecular pathways associated with highly vascular tumors. Functional studies using glioblastoma cell lines, THP-1-derived macrophages and co-culture systems were performed to investigate the role of PI3K signaling in tumor-macrophage communication. Finally, an independent single-cell transcriptomic cohort of primary human glioblastoma was interrogated to determine whether the identified inflammatory programs were conserved in malignant cells from patient tumors. Results Integrated imaging-transcriptomic analyses identified highly vascular glioblastomas as tumors enriched for the MES subtype, increased macrophage infiltration and activation of PI3K-associated signaling. Pharmacological inhibition of PI3K reduced the expression of macrophage-recruiting cytokines and impaired the ability of glioblastoma cells to educate macrophages toward an immunosuppressive phenotype. Reciprocally, tumor-educated macrophages enhanced inflammatory signaling, immune checkpoint expression and migratory capacity in glioblastoma cells, whereas IL-6 blockade attenuated these effects, identifying IL-6 as a key mediator of this bidirectional communication. To determine whether these inflammatory programs were conserved in human disease, we analyzed an independent single-cell transcriptomic dataset of primary glioblastomas. MES-like malignant cells exhibited the strongest inflammatory transcriptional programs among the four malignant transcriptional states, including higher NF-κB activation program scores and tumor-macrophage communication signature scores. At the tumor level, MES-like enrichment was positively associated with higher inflammatory program activity, supporting the clinical relevance of the proposed signaling axis. Conclusions Together, our findings identify PI3K signaling as a central regulator integrating vascular remodeling with inflammatory tumor-macrophage communication in mesenchymal glioblastoma. These results provide a mechanistic framework linking PI3K signaling, macrophage education and the MES phenotype, and provide a rationale for therapeutic strategies aimed at disrupting inflammatory signaling within the glioblastoma microenvironment.
Rebeca Burgos-Panadero, María Rosado-Sanz, V. Montosa-i-Micó et al.· bioRxiv· 0 citations
Single-cell breast cancer atlases reveal malignant, immune, and stromal diversity; however, how the recurrent signaling pathways drive untreated malignant-cell states and could inform combination therapy remains unclear. Here, we analyzed 15,753 malignant cells from untreated primary breast tumors using a cell-resolved network framework. Individual transcriptomes were projected onto a protein–protein interaction network, partitioned into Leiden communities, and annotated by pathway enrichment. Pathway recurrence was evaluated against matched null models preserving community size, protein-network degree, and gene detection rate. Before null correction, recurrent pathways included PI3K/AKT, MAPK, JAK/STAT, and HIF-1 (hypoxia-inducible factor 1) signaling. After correction, HIF-1 emerged as the dominant recurrent signal across patients, indicating convergence of diverse upstream pathways on a shared hypoxia- and stress-adaptive malignant-cell program. The recurrent JAK/STAT, cAMP, glucagon, oxytocin, and thyroid hormone signaling suggest inflammatory, metabolic, and endocrine crosstalk. These findings support rational drug combinations targeting HIF-1 together with upstream PI3K/AKT/mTOR, MAPK, or JAK/STAT signaling.
B. R. Yavuz, Hyunbum Jang, Ruth Nussinov· bioRxiv· 0 citations
Integrated analyses show that MBM exhibits dynamic bidirectional signaling across tumor cells, endothelium, and microglia, collectively driving invasion and proliferation.
Kevin Zhang, Mao Yang, Ming Yuang et al.· Neuro-Oncology Advances· 0 citations
Multiple myeloma (MM) persists within a specialized bone marrow niche in which malignant plasma cells, immune dysfunction, inflammatory signaling, and metabolic stress reinforce one another. To resolve this ecosystem at compartment-level resolution, we integrated public single-cell RNA sequencing data with pathway scoring, cell-cell communication inference, independent clinical validation, multiplex immunofluorescence, and metabolic perturbation experiments. Analysis of 95,940 bone marrow cells identified 32 annotated populations and revealed broad microenvironmental remodeling in MM, including plasma-cell expansion, altered cytotoxic and dendritic-cell compartments, TAM-associated inflammatory programs, and lineage-specific hematopoietic perturbations. Hallmark pathway analysis identified recurrent immunometabolic programs, including IL6-JAK-STAT3, TNFα-NFκB, mTORC1 signaling, oxidative phosphorylation, unfolded protein response, hypoxia, and checkpoint/exhaustion-associated pathways. CellChat analysis showed disease-associated rewiring of ligand-receptor networks involving malignant plasma cells, TAMs, dendritic cells, and T/NK subsets, with checkpoint-enriched communication and clinically relevant plasma-cell and CD274 survival associations. Serum IL-6 was elevated in an independent clinical validation cohort. Multiplex immunofluorescence confirmed PD-L1-positive plasma cells, C1QA/C1QB/C1QC-positive TAMs expressing LAG3, and CD8-positive/LAG3-positive cytotoxic T cells. Mechanistically, malignant plasma cells showed transcriptional activation of LDH-associated glycolytic/lactate programs and ASCT2/SLC1A5-GLS-linked glutamine-metabolic programs, nominating these pathways as functional vulnerabilities. Accordingly, the LDH inhibitor galloflavin and the ASCT2/SLC1A5 glutamine-transport inhibitor V-9302 suppressed RPMI-8226 viability in dose- and time-dependent manners; their combination produced synergistic anti-myeloma activity supported by Bliss synergy, combination-index analysis, observed-versus-expected inhibition, and apoptosis-related validation. Together, these findings support an IL6-centered immunometabolic communication circuit linking malignant plasma cells, TAMs, and dysfunctional T cells, and identify cooperative glycolytic/lactate and glutamine-dependent metabolic vulnerabilities with therapeutic relevance in MM.
De-Long Lang, Jing Wu, Jiayou Zhang et al.· Frontiers in Immunology· 0 citations
This human iPSC-derived tumor–brain organoid platform provides a reliable and scalable system for studying complex tumor-neural interactions and exploring therapeutic approaches that aim to eliminate the tumor while preserving neural function.
Ewa Grassin, H. Chintalapudi, Xianjun Dong et al.· bioRxiv· 0 citations
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