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Mechanism- and Immune Landscape-Based Ranking of Therapeutic Responsiveness of 22 Major Human Cancers to Next Generation Anti-CTLA-4 Antibodies.
BACKGROUND: CTLA-4 was the first immune checkpoint targeted for cancer therapy and the first target validated by the FDA (Food and Drug Administration) after approval of the anti-CTLA-4 antibody, Ipilimumab. However, clinical response rates to anti-CTLA-4 antibodies are lower while the rates of immunotherapy-related adverse events (irAE) are higher than with anti-PD-1 antibodies. As a result, the effort to target CTLA-4 for cancer immunotherapy has stagnated. To reinvigorate CTLA-4-targeted immunotherapy, we and others have reported that rather than blocking CTLA-4 interaction with its cognate targets, CD80 and CD86, anti-CTLA-4 antibodies achieve their therapeutic responses through selective depletion of regulatory T cells in the tumor microenvironment. Accordingly, we have developed a new generation of anti-CTLA-4 antibodies with reduced irAE and enhanced antibody-dependent cell-mediated cytotoxicity/phagocytosis (ADCC/ADCP). A major unresolved issue is how to select appropriate cancer types for future clinical development. METHODS: We generated a landscape of the immune tumor microenvironment from RNAseq and genomic data of 7279 independent cancer samples belonging to 22 cancer types from The Cancer Genomics Atlas (TCGA) database. Based primarily on genomic and RNAseq data from pre-treatment clinical samples of melanoma patients who were later identified as responders and nonresponders to the anti-CTLA-4 antibody Ipilimumab, we identified 5 ranking components of responsiveness to anti-CTLA-4, including CTLA-4 gene expression, ADCC potential, mutation burden, as well as gene enrichment and cellular composition that favor CTLA-4 responsiveness. The total ranking number was calculated by the sum of 5 independent partitioning values, each comprised of 1-3 components. RESULTS: Our analyses predict metastatic melanoma as the most responsive cancer, as expected. Surprisingly, non-small cell lung carcinoma (NSCLC) is predicted to be highly responsive to anti-CTLA-4 antibodies. Single-cell RNAseq analysis and flow cytometry of human NSCLC-infiltrating T cells supports the potential of anti-CTLA-4 antibodies to selectively deplete intratumoral Treg. CONCLUSIONS: Our in silico and experimental analyses suggest that non-small cell lung carcinoma will likely respond to a new generation of anti-CTLA-4 monoclonal antibodies. Our approach provides an objective ranking of the sensitivity of human cancers to anti-CTLA-4 antibodies. The comprehensive ranking of major cancer types provides a roadmap for clinical development of the next generation of anti-CTLA-4 antibodies.
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Multiphase enhanced computed tomography features captured by delta radiomics reveal prognosis and tumor heterogeneity in patients with hepatocellular carcinoma treated with transarterial chemoembolization.
BACKGROUND: Although transarterial chemoembolization (TACE) is a widely used locoregional therapy for intermediate-stage hepatocellular carcinoma (HCC), there is substantial inter-patient heterogeneity in treatment response. This study aimed to develop a delta radiomic model based on pre-treatment enhanced computed tomography (CT) to predict the prognosis of HCC patients undergoing TACE and to reveal tumor heterogeneity. METHODS: A total of 269 patients treated with TACE between January 2016 and June 2020 were enrolled from two medical centers and divided into three cohorts: a training cohort (n = 126), an internal validation cohort (n = 84), an external test cohort (n = 59). Radiological features of the tumor area were extracted on multiple phases of CT before treatment, and progression-free survival (PFS) was predicted through the least absolute shrinkage and selection operator Cox (LASSO-Cox) regression algorithm. Overall survival (OS) was evaluated using the Kaplan-Meier curve. Genetic and tumor microenvironment differences related to the prognosis of TACE were analyzed in 23 patients with CT from The Cancer Genome Atlas (TCGA). Single-cell data from the comprehensive Gene Expression Omnibus (GEO) public database were used to explore the expression of different genes in cells. RESULTS: The area under the receiver operating characteristic curves of the delta radiomic model for predicting 2-year PFS in TACE-treated patients were 0.812, 0.720, and 0.807 in the training, internal validation, and external test cohorts, respectively. The Rad-score was calculated based on radiomic features selected through LASSO. The Rad-score stratified patients into high- and low-risk groups, with significant differences in OS across all cohorts. The high-risk group had a higher immune score. It is worth noting that in the immune infiltration analysis, there were significant differences in B cells, resting CD4 memory T cells, active natural killer cells, and mast cells among different risk groups. CONCLUSIONS: The delta radiomics model based on multiphase enhanced CT accurately predicts prognosis and reflects tumor heterogeneity in HCC patients treated with TACE, and contributes to treatment planning.
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Focal Adhesion Kinase-Dependent Reprogramming of IFN-γ Signaling through PYK2 Coinhibition Sensitizes Melanoma to Immune Checkpoint Blockade.
Immune checkpoint blockade has transformed melanoma therapy but is frequently limited by acquired resistance. Focal adhesion kinase (FAK) and its homolog PYK2 are nonreceptor tyrosine kinases that coordinate cell-matrix adhesion and cytoskeletal signaling. In this study, we define the distinct roles of FAK (as the principal scaffold) and PYK2 (in a supportive capacity) in IFN-γ-mediated immune checkpoint blockade resistance. Label-free phosphoproteomic profiling revealed that IFN-γ stimulation drives extensive phosphorylation across pathways governing cytoskeletal remodeling, transcriptional regulation, mRNA splicing, and ribosomal RNA biogenesis. Selective FAK inhibition markedly suppressed IFN-γ-induced signal transducer and activator of transcription 1 and PD-L1 upregulation, and the addition of PYK2 blockade achieved maximal suppression, culminating in enhanced CD8+ T-cell-mediated tumor cytotoxicity. In an anti-PD-1-resistant murine melanoma model, high tumoral FAK expression correlated with treatment failure. Analysis of The Cancer Genome Atlas-Skin Cutaneous Melanoma cohort showed that FAK levels associate with immunosuppressive gene signatures, whereas in an independent clinical dataset (GSE91061), patients exhibiting post-treatment downregulation of FAK experienced improved outcomes. Single-cell RNA sequencing distinguished tumor cell-intrinsic FAK expression from PYK2 enrichment in immune subsets. Together, these data position FAK as the dominant driver of IFN-γ-dependent resistance, with PYK2 playing a subsidiary role, and suggest that selective FAK targeting-potentially combined with limited PYK2 inhibition-may overcome immune checkpoint blockade resistance in melanoma.
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Spatial characterization of skin lesions in discoid and systemic lupus erythematosus.
Lupus erythematosus (LE) skin lesions are associated with significant dysregulation of the local immune microenvironment. However, the spatial distribution and interactions between stromal and immune cells within affected tissues remain poorly characterized. In this study, we employed Stereo-seq to construct a single-cell resolution spatial transcriptomic atlas of lesional skin from patients with discoid lupus erythematosus (DLE) and systemic lupus erythematosus (SLE). Our analysis revealed that keratinocyte subpopulations in distinct differentiation states presented cell type-specific profiles of inflammatory mediator expression. Notably, a subset of stress keratinocytes located predominantly at the epidermis-dermis interface mediated the recruitment of T cells and plasma cells, potentially through an IFN-γ-JAK-STAT axis driving CXCL9/10/11-CXCR3 signaling, and these effects were more pronounced in active SLE lesions compared to chronic DLE lesions. Spatial profiling revealed immune cell niches resembling tertiary lymphoid structures (TLS), which were particularly prominent in chronic DLE and SLE lesions. These lupus-associated TLS structures were characterized by the coordinated infiltration of multiple cell subsets, including age-associated B cells, precursors of germinal center B cells, naïve B cells, regulatory T cells, T peripheral helper and/or T follicular helper cells, memory T cells, and CCL14+ vascular endothelial cells, which presented the spatial characteristics of the lymphoid follicle-like structures in chronic LE skin lesions. Collectively, our findings provide a comprehensive spatial characterization of the cellular components and molecular features within LE skin lesions.
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A hypoxia-responsive migrasome-related lncRNA signature predicts prognosis and suggests the MSC-AS1/ITGA5 axis as a potential therapeutic target in head and neck squamous cell carcinoma.
Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy associated with dismal prognosis. Migrasomes, a unique class of migration-dependent extracellular vesicles, have emerged as pivotal mediators of intercellular crosstalk within the tumor microenvironment. However, the clinical implications and regulatory mechanisms of migrasome-related long non-coding RNAs (MRLs) in HNSCC remain largely unexplored. Herein, we retrieved transcriptomic and clinical data of HNSCC from The Cancer Genome Atlas (TCGA) and established a prognostic signature using LASSO-Cox regression analysis, which was further internally validated in a randomly split subset of the TCGA cohort as internal validation. We systematically characterized the immune microenvironment and drug sensitivity profiles stratified by this signature, and identified the cellular distribution of core MRLs via single-cell RNA sequencing. Functional experiments were performed in clinical specimens and HNSCC cell lines using RT-qPCR, Western blot, CCK-8, and wound-healing assays. Consequently, a 10-MRL prognostic model was constructed to effectively stratify patients into high- and low-risk groups with significantly divergent overall survival, representing an independent prognostic factor in the context of the available clinical covariates from TCGA. High-risk patients exhibited an immunosuppressive tumor microenvironment and activation of oncogenic pathways (NF-κB, JAK-STAT). Mechanistically, MSC-AS1 was upregulated in HNSCC and facilitated cell proliferation and migration. Hypoxia upregulated the MSC-AS1/ITGA5 axis and increased VEGFA/PD-L1 expression, along with changes in the migrasome-related protein TSPAN4, suggesting a potential association with migrasome-related molecular features, which requires direct experimental validation. Collectively, our findings establish a novel MRL-based signature for prognostic prediction in HNSCC and highlight the hypoxia-responsive MSC-AS1/ITGA5 axis as a promising target for combinatorial therapeutic strategies.
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Serum response factor is essential for endometrial function and prevention of inflammatory fibrosis.
Pregnancy requires a supportive uterine environment facilitated by steroid hormone-regulated differentiation of endometrial stromal fibroblasts into decidual cells and tight control of inflammation. Serum response factor (SRF) is a widely expressed transcription factor essential for mesenchymal cell growth and differentiation with noted roles in hormonal regulation of muscle tissues but little characterization in reproductive organs. Here, we reveal that endometrial SRF is dysregulated in human endometriosis and is critical for female reproductive success in mice through regulation of endometrial stromal and epithelial cells. Immunohistochemical analysis identified decreased endometrial SRF expression in infertile endometriosis patient tissues. RNAi-based SRF knockdown in human endometrial stromal cells resulted in disrupted cytoskeletal structure, viability, and decidual response. Conditional Srf knockout mice (Srfd/d) generated using the PgrCre were infertile with implantation failure, lack of decidual response, and development of severe endometrial fibrosis. Single-cell RNA sequencing identified dramatic changes in Srfd/d endometrial cell populations including large-scale myeloid immune cell infiltration. Srfd/d stromal fibroblasts displayed aberrant cytoskeletal and extracellular matrix gene expression and downregulation of genes important for decidual growth response. Srf-deficient epithelial cells displayed the most prominent dysregulation, strongly overexpressing estrogenic innate inflammatory genes including C3 and Lcn2 and fibrogenic genes Mmp7 and Fbln1, all of which paralleled patterns in human endometriosis patient data that we identified through comparative analysis using a published single-cell atlas. These results demonstrate the profound impact of SRF on endometrial homeostasis with relevance to human endometriosis-related infertility.
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Identification of novel cuproptosis-related lncRNA signatures to predict the prognosis and immune microenvironment of breast cancer patients.
BACKGROUND: Cuproptosis is a new modality of cell death regulation that is currently considered as a new cancer treatment strategy. Nevertheless, the prognostic predictive value of cuproptosis-related lncRNAs in breast cancer (BC) remains unknown. Using cuproptosis-related lncRNAs, this study aims to predict the immune microenvironment and prognosis of BC patients. and develop new therapeutic strategies that target the disease. METHODS: The Cancer Genome Atlas (TCGA) database provided the RNA-seq data along with the corresponding clinical and prognostic information. Univariate and multivariate Cox regression analyses were performed to acquire lncRNAs associated with cuproptosis to establish predictive features. The Kaplan-Meier method was used to calculate the overall survival rate (OS) in the high-risk and low-risk groups. High risk and low risk gene sets were enriched to explore functional discrepancies among risk teams. The mutation data were analyzed using the "MAFTools" r-package. The ties of predictive characteristics and immune status had been explored by single sample gene set enrichment analysis (ssGSEA). Last, the correlation between predictive features and treatment condition in patients with BC was analyzed. Based on prognostic risk models, we assessed associations between risk subgroups and immune scores and immune checkpoints. In addition, drug responses in at-risk populations were predicted. RESULTS: We identified a set of 11 Cuproptosis-Related lncRNAs (GORAB-AS1, AC 079922.2, AL 589765.4, AC 005696.4, Cytor, ZNF 197-AS1, AC 002398.1, AL 451085.3, YTH DF 3-AS1, AC 008771.1, LINC 02446), based on which to construct the risk model. In comparison to the high-risk group, the low-risk patients lived longer (p < 0.001). Moreover, cuproptosis-related lncRNA profiles can independently predict prognosis in BC patients. The AUC values for receiver operating characteristics (ROC) of 1-, 3-, and 5-year risk were 0.849, 0.779, and 0.794, respectively. Patients in the high-risk group had lower OS than those in the low-risk group when they were divided into groups based on various clinicopathological variables. The tumor burden mutations (TMB) correlation analysis showed that high TMB had a worse prognosis than low-TMB, and gene mutations were found to be different in high and low TMB groups, such as PIK3CA (36% versus 32%), SYNE1 (4% versus 6%). Gene enrichment analysis indicated that the differential genes were significantly concentrated in immune-related pathways. The predictive traits were significantly correlated with the immune status of BC patients, according to ssGSEA results. Finally, high-risk patients showed high sensitivity in anti-CD276 immunotherapy and conventional chemotherapeutic drugs such as imatinib, lapatinib, and pazopanib. CONCLUSION: We successfully constructed of a cuproptosis-related lncRNA signature, which can independently predict the prognosis of BC patients and can be used to estimate OS and clinical treatment outcomes in BRCA patients. It will serve as a foundation for further research into the mechanism of cuproptosis-related lncRNAs in breast cancer, as well as for the development of new markers and therapeutic targets for the disease.
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EPAS1 prevents telomeric damage-induced senescence by enhancing transcription of TRF1, TRF2, and RAD50.
Telomeres are nucleoprotein structures located at the end of each chromosome, which function in terminal protection and genomic stability. Telomeric damage is closely related to replicative senescence in vitro and physical aging in vivo. As relatively long-lived mammals based on body size, bats display unique telomeric patterns, including the up-regulation of genes involved in alternative lengthening of telomeres (ALT), DNA repair, and DNA replication. At present, however, the relevant molecular mechanisms remain unclear. In this study, we performed cross-species comparison and identified EPAS1, a well-defined oxygen response gene, as a key telomeric protector in bat fibroblasts. Bat fibroblasts showed high expression of EPAS1, which enhanced the transcription of shelterin components TRF1 and TRF2, as well as DNA repair factor RAD50, conferring bat fibroblasts with resistance to senescence during long-term consecutive expansion. Based on a human single-cell transcriptome atlas, we found that EPAS1 was predominantly expressed in the human pulmonary endothelial cell subpopulation. Using in vitro-cultured human pulmonary endothelial cells, we confirmed the functional and mechanistic conservation of EPAS1 in telomeric protection between bats and humans. In addition, the EPAS1 agonist M1001 was shown to be a protective compound against bleomycin-induced pulmonary telomeric damage and senescence. In conclusion, we identified a potential mechanism for regulating telomere stability in human pulmonary diseases associated with aging, drawing insights from the longevity of bats.
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M2 macrophage-based classification identifies DOK3 as a driver of pro-tumoral polarization and migration in glioblastoma.
BACKGROUND: Glioblastoma (GBM) is the most aggressive primary brain tumor, characterized by limited therapeutic options and dismal prognosis. Among the components of the immunosuppressive tumor microenvironment (TME), M2-polarized macrophages are pivotal mediators of tumor progression, yet the molecular mechanisms underlying their polarization and pro-tumoral functions remain inadequately understood. METHODS: We integrated bulk and single-cell RNA sequencing datasets from CGGA, TCGA, and GSE131928. M2 macrophage infiltration was quantified using the xCell algorithm, and unsupervised clustering of M2-associated genes was first performed to define macrophage-centered immune subtypes, further refined by XGBoost and LASSO modeling. Based on the molecular features of the most immunosuppressive subtype, a macrophage-associated risk score based on CTSB, LITAF, and DOK3 was constructed and validated across independent cohorts for prognostic and immune relevance. Functional validation was performed by silencing DOK3 in THP-1-derived macrophages, followed by co-culture with glioma cells to assess macrophage polarization and tumor cell behavior. RESULTS: Elevated M2 macrophage infiltration correlated with reduced tumor purity, spatial heterogeneity, and worse survival. Three immune subtypes (C1-C3) were identified; notably, the C1 subtype exhibited the highest M2 infiltration, strongest immunosuppressive features, and poorest prognosis. The derived macrophage-based risk score robustly stratified patient survival and correlated with CD163 expression and immune checkpoint activation. Single-cell analysis revealed predominant DOK3 expression in macrophages and microglia. Functional assays demonstrated that DOK3 knockdown reduced CD163 expression and attenuated glioma cell invasiveness, supporting its role in promoting M2 polarization and tumor aggressiveness. CONCLUSION: This integrative analysis identifies DOK3 as a pivotal regulator of M2 macrophage polarization and a driver of glioblastoma progression. Together, immune subtyping and the simplified macrophage-based risk model represent complementary strategies, with the latter providing a practical tool for prognostic stratification. Targeting DOK3 offers a promising therapeutic strategy to reprogram the TME and improve clinical outcomes in patients with GBM.
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The transcriptomic and spatial organization of telencephalic GABAergic neuronal types.
The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.