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C1ORF112 drives lung adenocarcinoma progression through e2f8-mediated transcriptional activation.
BACKGROUND: Lung adenocarcinoma (LUAD) remains a leading cause of cancer mortality, with poor prognosis driven by metastasis and therapeutic resistance. Chromosome 1 open reading frame 112 (C1ORF112) encodes a nuclear protein involved in DNA replication and repair, but its role in LUAD is unclear. To systematically investigate the clinical relevance, functional impact, and transcriptional regulation of C1ORF112 in LUAD through integrative bioinformatic and experimental approaches. METHODS: C1ORF112 expression and prognostic significance were analyzed using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Single-cell RNA sequencing defined cellular localization and communication patterns. Functional enrichment, protein-protein interaction (PPI), and transcription factor prediction analyses were performed. In vitro assays and xenograft models assessed biological functions and transcriptional regulation by E2F8. RESULTS: C1ORF112 was significantly upregulated in LUAD and correlated with poor overall survival (OS). Single-cell analysis showed elevated expression in malignant cells, fibroblasts, endothelial cells, and mast cells, accompanied by increased communication with M2 macrophages and exhausted CD8+ T cells. Overexpression of C1ORF112 inhibited apoptosis and promoted proliferation in LUAD cells, while xenografts exhibited accelerated tumor growth and increased Ki67 expression. Mechanistically, E2F8 directly bound the C1ORF112 promoter, enhancing its transcription and inhibiting downstream p53 signaling. CONCLUSIONS: Our integrative analysis suggests that C1ORF112 exhibits oncogenic properties in LUAD by promoting tumor survival, proliferation, and potentially remodeling the tumor microenvironment. The transcriptional activation by E2F8 highlights the E2F8-C1ORF112 axis as a candidate prognostic biomarker and therapeutic vulnerability, though prospective clinical validation and drug sensitivity studies are warranted.
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Comprehensive pan-cancer investigation: unraveling the oncogenic, prognostic, and immunological significance of Abelson interactor family member 3 gene in human malignancies.
Background: Abelson interactor Family Member 3 (ABI3) encodes protein that not only suppresses the ectopic metastasis of tumor cells but also hinders their migration. Although ABI3 had been found to modulate the advancement of diverse neoplasms, there is no comprehensive pan-cancer analysis of its effects. Methods: The transcriptomics data of neoplasm and normal tissues were retrieved from the Genomic Data Commons (GDC) data portal, and UCSC XENA database. To gather protein information for ABI3, Human Protein Atlas (HPA) and GeneMANIA websites were utilized. Additionally, Tumor Immune Single-cell Hub (TISCH) database was consulted to determine the primary cell types expressing ABI3 in cancer microenvironments. Univariate Cox regression approach was leveraged to evaluate ABI3's prognostic role across cancers. The Cbioportal and Gene Set Cancer Analysis (GSCA) website were leveraged to scrutinize the genomic landscape information across cancers. TIMER2.0 was leveraged to probe the immune cell infiltrations associated with ABI3 across cancers. The associations of ABI3 with immune-related genes were analyzed through Spearman correlation method. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were utilized to search associated biological pathways. The CellMiner database and molecular docking were implemented to identify potential interactions between the ABI3 protein and specific anticarcinogen. Findings: ABI3 expression and its ability to predict prognosis varied distinct tumor, with particularly high expression observed in Tprolif cells and monocytes/macrophages. Copy number variation (CNV) and methylation negatively correlated with ABI3 expression in the majority of malignancies. Corresponding mutation survival analysis indicated that the mutation status of ABI3 was strongly connected to the prognosis of LGG patients. ABI3 expression was linked to immunotherapeutic biomarkers and response in cancers. ESTIMATE and immune infiltrations analyses presented ABI3 association with immunosuppression. ABI3 was significantly correlated with immunoregulators and immune-related pathways. Lastly, prospective ABI3-targeted drugs were filtered and docked to ABI3 protein. Interpretation: Our study reveals that ABI3 acts as a robust tumor biomarker. Its functions are vital that could inhibit ectopic metastasis of tumor cells and modulate cellular adhesion and migration. The discoveries presented here may have noteworthy consequences for the creation of fresh anticancer suppressors, especially those targeting BRCA.
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Upregulation of HCFC1 expression promoted hepatocellular carcinoma progression through inhibiting cell cycle arrest and correlated with immune infiltration.
Background: Host cell factor 1 (HCFC1) was reported associated with the progression of a variety of cancers. However, its role in the prognosis and immunological characteristics of hepatocellular carcinoma (HCC) patients has not been revealed. Methods: The expression and prognostic value of HCFC1 in HCC were investigated from the Cancer Genome Atlas (TCGA) dataset and a cohort of 150 HCC patients. The associations between HCFC1 expression with somatic mutational signature, tumor mutational burden (TMB), and microsatellite instability (MSI) were investigated. Next, the correlation of HCFC1 expression with immune cell infiltration was investigated. In vitro, cytological experiments were conducted to verify the role of HCFC1 in HCC. Results: HCFC1 mRNA and protein upregulated in HCC tissues and correlated to poor prognosis. Multivariate regression analysis based on a cohort of 150 HCC patients revealed that high HCFC1 protein expression was an independent risk factor for prognosis. Upregulation of HCFC1 expression was associated with TMB, MSI, and tumor purity. HCFC1 expression showed a significant positive association with B cell memory, T cell CD4 memory, macrophage M0, and a significant positive association with immune checkpoint-related gene expression in the tumor microenvironment. HCFC1 expression negatively correlated to ImmuneScore, EstimateScore, and StromalScore. The single-cell RNA sequencing analysis demonstrated that the malignant cells and immune cells (B cells, T cells, and macrophages) represented high HCFC1 expression in HCC tissues. Functional analysis revealed that HCFC1 was remarkably correlated with cell cycle signaling. HCFC1 knockdown inhibited the proliferation, migration, and invasion capacity while promoting the apoptosis of HCC cells. At the same time, the cell-cycle-related proteins such as Cyclin D1 (CCND1), Cyclin A2 (CCNA2), cyclin-dependent kinase 4 (CDK4), and cyclin-dependent kinase 6 (CDK6) were downregulated. Conclusion: Upregulation of HCFC1 predicted undesirable prognosis of HCC patients and promoted tumor progression through inhibiting cell cycle arrest.
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Deciphering the transcriptional regulatory network driving lung adenocarcinoma progression.
Normal type II alveolar epithelial cells transform into lung adenocarcinoma through intermediate stages of adenocarcinoma in situ and minimally invasive adenocarcinoma, eventually becoming invasive adenocarcinoma. Transcription factors (TFs) are pivotal in tumorigenesis and development, etc. In this study, we modeled the malignant transformation of AT2 cells into lung adenocarcinoma using single-cell profiling, focusing on TF-mediated transcriptional repression or activation as a key mechanism. We analyzed data from 29 motifs database, including Jaspar, Bergman, Transfac and cisBP, compiling a collection of 18,422 motifs. By integrating Motif analysis to deduce the target genes regulated by transcription factors exhibiting activity alterations across various progression stages of lung adenocarcinoma, and subsequently determining the intersection between these target genes and the differentially expressed genes at each stage, we can pinpoint the target genes that are both differentially expressed and under the regulation of key transcription factors at each stage. Consequently, the regulatory mechanism of TFs on target genes in lung adenocarcinoma was speculated. Furthermore, the transcriptional regulatory network reveals that TFs modulate signaling pathways, cellular metabolism, and biological processes during the transformation process. In addition, leveraging six transcription factors (REBF2, CEBPB, TFCP2, IRF6, ETV4, and BHLHE40) that exhibit progressively increasing activity during the progression of lung adenocarcinoma, we developed a pivotal progression model score, termed the "Lung Adenocarcinoma Transformation TFs Upregulation" (LUAD-TTFs-UP) score, to predict both the progression and prognosis of this disease.
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A spatial and temporal transcriptomic atlas of mouse intestinal regeneration in the jejunum.
The intestinal epithelium exhibits a remarkable capacity for regeneration following injury, yet the spatial and temporal dynamics of the damage-repair cycle remain incompletely understood. We present a spatial transcriptomics atlas of ionizing radiation-induced injury and repair in the mouse jejunum, capturing mRNA from 16,921 genes across approximately 26 million bins at 2-µm resolution in 23 biological samples spanning six days post-irradiation. Analysis reveals transcriptional patterns and niche signals undetectable by bulk or single-cell approaches, including spatially restricted interferon-target gene activation, an altered differentiation trajectory in the lower villus during early repair, two transcriptionally distinct crypt regenerative cell populations, and global transcriptional upregulation consistent with hypertranscription as a hallmark of intestinal regeneration, with evidence for hypertranscription extending to human Crohn's disease. In this work, we provide a spatiotemporal atlas of mouse intestinal regeneration at subcellular 2-µm resolution that will inform future therapeutic strategies for inflammatory bowel diseases and gastrointestinal pathologies arising from injury or cancer therapy.
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High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration.
PURPOSE: To elucidate the clinical and prognostic role of PDZ and LIM domain protein (PDLIM) genes and the association to epithelial-mesenchymal transition (EMT) and immune cell infiltration in patients with prostate cancer (PRAD). METHODS: The data of RNA-seq, DNA methylation, and clinical features of PRAD patients were collected from The Cancer Genome Atlas (TCGA) database to define the prognostic value of PDLIM gene expression and the association with EMT and immune cell infiltration. A tissue microarray including 134 radical prostatectomy specimens was served as validation by immunohistochemistry (IHC) staining analysis. RESULTS: The mRNA levels of PDLIM1/2/3/4/6/7 were significantly downregulated, while PDLIM5 was upregulated in PRAD (P < 0.05). High expression of PDLIM2 mRNA suggests poor progression free interval in PRAD patients. DNA methylation of PDLIM2 was correlated with its mRNA expression level, and that the cg22973076 methylation site in PDLIM2 was associated with shorter PFI (P < 0.05) in PRAD. Single-sample gene-set enrichment and gene functional enrichment results showed that PDLIM2 was correlated with EMT and immune processes. Spearman's test showed a significant correlation with six reported EMT signatures and several EMT signature-related genes. Tumor microenvironment analysis revealed that the PDLIM2 mRNA expression was positively correlated with the immune score, stromal score, and various tumor infiltrating immune cells. Additionally, the results showed that patients in the high-PDLIM2 mRNA expression group may be more sensitive to immune checkpoint blockade therapy. Finally, IHC analysis further implicated the protein level of PDLIM2 was upregulated in PRAD and acts as a novel potential biomarker in predicting tumor progression. CONCLUSION: Our study suggests that PDLIM family genes might be significantly correlated with oncogenesis and the progression of PRAD. PDLIM2 correlated with EMT and immune cell infiltration by acting as an oncogene in PRAD, which may serve as a potential prognostic biomarker for PRAD patients.
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A palmitoylation-associated three-gene signature predicts prognosis, immune features, and drug sensitivity in gastric cancer: functional validation of CTHRC1.
BACKGROUND: Gastric cancer (GC) is a heterogeneous malignancy that requires improved molecular tools for prognostic stratification. Protein palmitoylation regulates membrane localization and signaling, but the clinical relevance of palmitoylation-related genes (PRGs) in GC remains unclear. METHODS: Gene Expression Omnibus, The Cancer Genome Atlas, and GeneCards data were integrated to identify PRGs. Differential expression analysis, weighted gene co-expression network analysis, and three machine-learning algorithms were used to select key genes. Diagnostic and prognostic performance was evaluated in TCGA-STAD, platform-specific GEO cohorts, and an institutional cohort of 80 paired tissues. Immune infiltration, single-cell RNA sequencing, immunotherapy-related indices, and GDSC-based drug sensitivity were analyzed. CTHRC1 was further examined using clinical specimens, cell assays, and xenografts. RESULTS: Thirteen differentially expressed PRGs were identified, and SERPINE1, CTHRC1, and EGR1 were selected. The integrated diagnostic model achieved AUCs of 0.935 in TCGA-STAD, 1.000 in GSE54129, and 0.916 in GSE118916, respectively. The three-gene score stratified overall survival in the total, training, and testing TCGA-STAD cohorts and in GSE84437, GSE236522, and the institutional cohort. It remained independently associated with survival in multivariable analysis. High-risk tumors showed increased stromal and immune scores, altered immune-cell composition, higher checkpoint expression, and higher TIDE scores. Single-cell analysis localized SERPINE1 and CTHRC1 mainly to fibroblast-related compartments. CTHRC1 knockdown reduced GC-cell proliferation, clonogenicity, migration, invasion, and xenograft growth while increasing apoptosis. CONCLUSION: The SERPINE1/CTHRC1/EGR1 signature provides prognostic and immune-stromal information in GC, and the experiments support a tumor-promoting role for CTHRC1. The findings define a palmitoylation-associated transcriptional framework but do not establish a palmitoylation-dependent mechanism.
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Integrating bulk and single-cell RNA sequencing analysis to reveal characterization of mechanical stimulus-related genes and prognostic signatures in breast cancer.
OBJECTIVES: To identify molecular clusters and establish a scoring model based on mechanical stimulus-related genes (MSRGs) for predicting the prognosis of breast cancer patients and understanding the role of mechanical stimuli in the breast tumor microenvironment (TME). METHODS: We utilized bulk and single-cell RNA sequencing analysis to characterize MSRGs associated with breast cancer prognosis. Unsupervised consensus molecular clustering was applied to identify distinct clusters based on overall survival-associated MSRGs from The Cancer Genome Atlas (TCGA) database. The scoring model was constructed by LASSO-Cox method and validated. Additionally, single-cell RNA sequencing analysis, along with in vitro and in vivo experiments, were conducted to further investigate the role of the model in breast cancer. RESULTS: We identified 23 overall survival-associated MSRGs and established two molecular subgroups with distinct survival outcomes. A prognostic signature incorporating 15 MSRGs was developed and validated, demonstrating its predictive capability for overall survival of breast cancer patients. The nomogram integrating clinical characteristics and the mechanical stimulus-related risk score exhibited promising predictive accuracy. The low-risk group displayed an immune "hot" phenotype with increased immune cell infiltration, while the high-risk group exhibited resistance to conventional chemotherapy but potential sensitivity to Sepantronium bromide. By using the SCISSOR algorithm, we provide evidence at single-cell resolution for the impact of mechanical stimulation on tumor immune microenvironment. The in vivo and in vitro assays demonstrated that knockdown of TEX19 significantly suppressed breast tumor proliferation. CONCLUSION: We developed a pioneering prognostic signature incorporating MSRGs in breast cancer, with a particular focus on mechanical stimuli may influence breast cancer prognosis by remodeling the immune microenvironment. The findings highlighted the importance of personalized treatment strategies and provide new insights into the role of mechanical forces in breast tumor biology.
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An Activated Dendritic-Cell-Related Gene Signature Indicative of Disease Prognosis and Chemotherapy and Immunotherapy Response in Colon Cancer Patients.
Accumulating evidence has underscored the prognostic value of tumor-infiltrating immune cells in the tumor microenvironment of colon cancer (CC). In this retrospective study, based on publicly available transcriptome profiles and clinical data from the Gene Expression Omnibus and The Cancer Genome Atlas databases, we derived and verified an activated dendritic cell (aDC)-related gene signature (aDCRS) for predicting the survival outcomes and chemotherapy and immunotherapy response of CC patients. We quantified the infiltration abundance of 22 immune cell subtypes via the "CIBERSORT" R script. Univariate Cox proportional hazards (PHs) regression was used to identify aDC as the most robust protective cell type for CC prognosis. After selecting differentially expressed genes (DEGs) significantly correlated with aDC infiltration, we performed univariate Cox-PH regression, LASSO regression, and stepwise multivariate Cox-PH regression successively to screen out prognosis-related genes from selected DEGs for constructing the aDCRS. Receiver operating characteristic (ROC) curves and Kaplan-Meier (KM) analysis were employed to assess the discriminatory ability and risk-stratification capacity. The "oncoPredict" package, Cancer Treatment Response gene signature DataBase, and Tumor Immune Dysfunction and Exclusion algorithm were utilized to estimate the practicability of the aDCRS in predicting response to chemotherapy and immune checkpoint blockade. Gene set enrichment analysis and single-cell RNA sequencing analysis were also implemented. Furthermore, an aDCRS-based nomogram was constructed and validated via ROC curves, calibration plots and decision curve analysis. In conclusion, aDCRS and an aDCRS-based nomogram will facilitate precise prognosis prediction and individualized therapeutic interventions, thus improving the survival outcomes of CC patients in the future.
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Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH.
The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the human cortex and how cellular organization varies across species remain unclear. In this study, we performed spatially resolved single-cell profiling of 4000 genes using multiplexed error-robust fluorescence in situ hybridization (MERFISH), identified more than 100 transcriptionally distinct cell populations, and generated a molecularly defined and spatially resolved cell atlas of the human middle and superior temporal gyrus. We further explored cell-cell interactions arising from soma contact or proximity in a cell type-specific manner. Comparison of the human and mouse cortices showed conservation in the laminar organization of cells and differences in somatic interactions across species. Our data revealed human-specific cell-cell proximity patterns and a markedly increased enrichment for interactions between neurons and non-neuronal cells in the human cortex.