Deregulated transcription factors in the emerging cancer hallmarks

Tumors and their microenvironments: Learning from pediatric brain pathologies

Early clues to tumors and their microenvironments come from embryonic development. Here we review the literature and consider whether the embryonic brain and its pathologies can serve as a better model. Among embryonic organs, the brain is the most heterogenous and complex, with multiple lineages leading to wide spectrum of cell states and types. Its dysregulation promotes neurodevelopmental brain pathologies and pediatric tumors. Embryonic brain pathologies point to the crucial importance of spatial heterogeneity over time, akin to the tumor microenvironment. Tumors dedifferentiate through genetic mutations and epigenetic modulations; embryonic brains differentiate through epigenetic modulations. Our innovative review proposes learning developmental brain pathologies to target tumor evolution-and vice versa. We describe ways through which tumor pharmacology can learn from embryonic brains and their pathologies, and how learning tumor, and its microenvironment, can benefit targeting neurodevelopmental pathologies. Examples include pediatric low-grade versus high-grade brain tumors as in rhabdomyosarcomas and gliomas.

Nuclear-localized metabolic enzymes: emerging key players in tumor epigenetic regulation

Advancements in tumor research have highlighted the potential of epigenetic therapies as a targeted approach to cancer treatment. However, the application of these therapies has faced challenges due to the issue of substrate availability since the discovery of epigenetic modifications. Interestingly, metabolic changes are closely associated with epigenetic changes, and notably, certain metabolic enzymes exhibit nuclear localization within epigenetically active cellular contexts. This suggests that nuclear localization of metabolic enzymes may provide a mechanistic foundation for addressing substrate availability issues in epigenetic regulation. To date, there has been limited progress in synthesizing this information systematically. In this study, we provide an overview of the interplay between metabolic enzymes and epigenetic mechanisms, highlighting their critical roles. Subsequently, we summarize recent advances regarding the nuclear localization of metabolic enzymes, shedding light on their emerging roles in epigenetic regulation and oncogenesis.

Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs

Understanding the role of transcription and transcription factors (TFs) in cellular identity and disease, such as cancer, is essential. However, comprehensive data resources for cell line-specific TF-to-target gene annotations are currently limited. To address this, we employed a straightforward method to define regulons that capture the cell-specific aspects of TF binding and transcript expression levels. By integrating cellular transcriptome and TF binding data, we generated regulons for 40 common cell lines comprising both proximal and distal cell line-specific regulatory events. Through systematic benchmarking involving TF knockout experiments, we demonstrated performance on par with state-of-the-art methods, with our method being easily applicable to other cell types of interest. We present case studies using three cancer single-cell datasets to showcase the utility of these cell-type-specific regulons in exploring transcriptional dysregulation. In summary, this study provides a valuable pipeline and a resource for systematically exploring cell line-specific transcriptional regulations, emphasizing the utility of network analysis in deciphering disease mechanisms.

Identification of ETV4 as a prognostic biomarker and correlates with immune cell infiltration in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSC) is a common malignant tumor with high incidence and mortality rates. ETS variant transcription factor 4 (ETV4), an important transcription factor, plays a key role in various cancers. However, the role of ETV4 in HNSC remains unclear. This study aimed to explore the potential prognostic value and oncogenic effects of ETV4 in HNSC. We analyzed ETV4 expression in HNSC patients' data from the TCGA database, alongside clinical pathological characteristics. The STRING and GEPIA databases were utilized to explore ETV4's interaction proteins and expression related genes. Gene Set Enrichment Analysis (GSEA) was performed on the stratified TCGA-HNSC cohort based on ETV4 expression levels. The correlation between ETV4 expression and immune cells, immune checkpoints, immune regulatory genes was further analyzed using R packages and TISIDB database. Finally, knockdown ETV4 in nasopharyngeal carcinoma cells (NPCs) using siRNA and evaluate cell proliferation, migration, and invasion using CCK-8, wound healing, clone formation, and Transwell assays. ETV4 was significantly overexpressed in HNSC and closely related with clinical pathological characteristics and prognosis. GSEA enrichment analysis showed significant enrichment of ETV4 in multiple immune suppression pathways. Further immune-related analysis indicated that ETV4 negatively correlated with most immune cells, immune checkpoints, tumor-infiltrating lymphocyte type characteristic molecules, immunoinhibitors, immune activators and MHC molecules. Knocking down ETV4 significantly inhibited the proliferation, migration and invasion of NPCs. ETV4 may serve as a prognostic biomarker and immunotherapy target in HNSC. High expression of ETV4 may have a negative regulatory effect on the immune level, matrix components and immune regulatory molecules.

Participation of lipids in the tumor response to photodynamic therapy and its exploitation for therapeutic gain

Hydroperoxides of unsaturated membrane lipids (LOOHs) are the most abundant non-radical intermediates generated by photodynamic therapy (PDT) of soft tissues such as tumors and have far longer average lifetimes than singlet oxygen or oxygen radicals formed during initial photodynamic action. LOOH-initiated post-irradiation damage to remaining membrane lipids (chain peroxidation) or to membrane-associated proteins remains largely unrecognized. Such after-light processes could occur during clinical oncological PDT, but this is not well-perceived by practitioners of this therapy. In general, the pivotal influence of lipids in tumor responses to PDT needs to be better appreciated. Of related importance is the fact that most malignant tumors have dramatically different lipid metabolism compared with healthy tissues, and this too is often ignored. The response of tumors to PDT appears especially vulnerable to manipulations within the tumor lipid microenvironment. This can be exploited for therapeutic gain with PDT, as exemplified here by the combined treatment with the antitumor lipid edelfosine.

Identification and Validation of Epithelial Cell Centre Regulatory Transcription Factors in the Gastric Cancer Microenvironment

Purpose

To identify the epithelial cell centre regulatory transcription factors in the gastric cancer (GC) microenvironment and provide a new strategy for the diagnosis and treatment of GC.

Methods

The GC single-cell dataset was downloaded from the Gene Expression Omnibus (GEO) database. The regulatory mechanisms of transcription factors in both pan-cancer and GC microenvironments were analysed using the Cancer Genome Atlas (TGCA) database. Real-time quantitative PCR (RT-qPCR) was used to determine the mRNA expression levels of Prospero homeobox gene 1 (PROX1) and Endothelial PAS domain-containing protein 1 (EPAS1) in the human gastric mucosal normal epithelial cell line (GES-1) and the GC cell line (AGS). Immunohistochemistry (IHC) was used to determine the amounts of PROX1 and EPAS1 protein expression in GC and adjacent tissues. GC patients' overall survival (OS) was tracked through outpatient, Inpatient case inquiry, or phone follow-up.

Results

The single-cell data from GSE184198 was re-annotated, resulting in nine cell subsets: T cells (13364), NK cells (606), B cells (2525), Epithelial cells (2497), DC cells (1167), Fibroblast cells (372), Endothelial cells (271), Neutrophils cells (246) and Macrophage cells (420). Analysis of cell subgroup signalling pathways revealed that communication intensity between epithelial cells and smooth muscle cells was highest. Transcription factors PROX1 and EPAS1 were notably active in epithelial cells. Cell communication analysis indicated that IFNG may interact with IFNGR1/2 and LIF with IL6ST and LIFR to regulate the downstream PROX1 and EPAS1. PROX1 and EPAS1 were upregulated and negatively correlated with tumour mutation burden (TMB). They also exhibited high positive correlations with immune checkpoints CTLA4 and PDCD1LG2, as well as with chemokines CCL24 and CXCL12 and their receptors CCR3 and CCR4. Additionally, PROX1 and EPAS1 were positively correlated with immunosuppressive factors ADORA2A, CD160, IL10, TGFBR1, KDR and CSF1R, as well as with immunostimulators CD276, PVR, TNFRSF25, ULBP1, CXCL12 and ENTPD1. In GC tissues and AGS, PROX1 and EPAS1 were both substantially expressed. In the meantime, they showed a positive correlation with clinicopathological features such TNM stage and degree of differentiation. In GC patients, the up-regulated group's PROX1 and EPAS1 prognosis was noticeably poorer than the down-regulated group's.

Conclusion

PROX1 and EPAS1 are likely central regulatory transcription factors in the epithelial cells of the GC environment, regulated by IFNG and LIF. They may contribute to GC progression by modulating the tumour's immune microenvironment.

CPNE7 promotes colorectal tumorigenesis by interacting with NONO to initiate ZFP42 transcription

Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related death globally. Also, there is still a lack of effective therapeutic strategies for CRC patients owing to a poor understanding of its pathogenesis. Here, we analysed differentially expressed genes in CRC and identified CPNE7 as a novel driver of colorectal tumorigenesis. CPNE7 is highly expressed in CRC and negatively correlated with patients' prognosis. Upregulation of CPNE7 promotes proliferation and metastasis of cancer cells in vitro and in vivo, and vice versa. Mechanistically, CPNE7 interacts with NONO to initiate ZFP42 transcription, thus promoting CRC progression. Moreover, ZFP42 knockdown inhibits tumor cell proliferation and migration while promoting apoptosis. Notably, delivery of CPNE7 shRNA or the small molecule gramicidin, which blocks the interaction between CPNE7 and NONO, hinders tumor growth in vivo. In conclusion, our findings demonstrate that the CPNE7-NONO-ZFP42 axis promotes colorectal tumorigenesis and may be a new potential therapeutic target.

Emerging roles of long non-coding RNA FOXP4-AS1 in human cancers: From molecular biology to clinical application

Forkhead box P4 antisense RNA 1 (FOXP4-AS1) is a long non-coding RNA (lncRNA) situated on the human chromosome 6p21.1 locus. Previous research has demonstrated that FOXP4-AS1 is dysregulated in various cancers and exhibits a dual purpose as a tumor suppressor or oncogene in specific types of cancer. The levels of FOXP4-AS1 are significantly correlated with clinical features of cancer as well as prognosis. Additionally, FOXP4-AS1 is stimulated by transcription factors ATF3, YY1, PAX5, and SP4. The molecular mechanisms of FOXP4-AS1 in cancer are quite complex. It competitively sponges multiple miRNAs, bidirectionally regulates the levels of host gene FOXP4, activates the PI3K/AKT, Wnt/β-catenin, and ERK/MAPK signaling pathways, and recruits chromatin-modifying enzymes or interacts with other proteins to regulate malignant phenotypes of tumors, including proliferation, invasion, epithelial-mesenchymal transition (EMT), and angiogenesis. In this review, we provide an overview of the latest developments in FOXP4-AS1 oncology research, outlines its molecular regulatory networks in cancer, and discusses its prospective relevance as a cancer therapeutic target as well as a biomarker for prognosis and diagnosis.

MiR-137 mediated high expression of TIGD1 promotes migration, invasion, and suppresses apoptosis of lung adenocarcinoma

OBJECTIVES

Tigger transposable element-derived 1 (TIGD1) expression and its underlying functions and regulatory mechanisms in lung adenocarcinoma (LUAD) remain unknown. Therefore, we intended to explore the expression, potential functions, and regulatory mechanisms of TIGD1 in LUAD.

MATERIALS AND METHODS

TIGD1 expression in LUAD tissues was determined by immunohistochemistry analysis of a tissue microarray. Functional experiments were conducted to determine how TIGD1 affects LUAD tumorigenesis and metastasis. The molecular mechanisms by which TIGD1 induces LUAD progression were determined.

RESULTS

TIGD1 was upregulated in LUAD tissues and was related to lymph node metastases. TIGD1 knockdown suppressed LUAD cell proliferation, migration, and invasion, while promoted cell apoptosis. Furthermore, decreased metastatic nodules were observed in the TIGD1 knockdown mouse metastasis model. Moreover, microarray analysis was performed to determine the potential downstream genes of TIGD1 in LUAD. Hallmark pathway analysis revealed that the downstream genes of TIGD1 were involved in epithelial-mesenchymal transition (EMT). Western blotting confirmed that vimentin and TWIST was downregulated in TIGD1 knockdown cells, while E-cadherin was upregulated. Ingenuity pathway and hallmark pathway analyses revealed that TIGD1 regulated the interleukin-6 signaling pathway and related gene members. Western blotting, quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay indicated that downregulation of TIGD1 decreased interleukin-6 and CXCL1 expression. TIGD1 expression was negatively correlated with immune infiltration in LUAD. The upstream microRNA of TIGD1 was predicted, and subsequent luciferase reporter gene experiments confirmed the interactions between miR-137 and TIGD1. The expression of miR-137 was significantly downregulated in LUAD tissues and miR-137 suppressed the proliferation, migration, and invasion of LUAD cells, partially through negatively regulating the expression of TIGD1.

CONCLUSION

Our findings suggest that TIGD1, which was regulated by miR-137, contributed to LUAD progression by promoting cell proliferation, migration, invasion, and EMT and suppressing cell apoptosis.

Role of Specificity Protein 1 (SP1) in Cardiovascular Diseases: Pathological Mechanisms and Therapeutic Potentials

In mammals, specificity protein 1 (SP1) was the first Cys2-His2 zinc finger transcription factor to be isolated within the specificity protein and Krüppel-like factor (Sp/KLF) gene family. SP1 regulates gene expression by binding to Guanine-Cytosine (GC)-rich sequences on promoter regions of target genes, affecting various cellular processes. Additionally, the activity of SP1 is markedly influenced by posttranslational modifications, such as phosphorylation, acetylation, glycosylation, and proteolysis. SP1 is implicated in the regulation of apoptosis, cell hypertrophy, inflammation, oxidative stress, lipid metabolism, plaque stabilization, endothelial dysfunction, fibrosis, calcification, and other pathological processes. These processes impact the onset and progression of numerous cardiovascular disorders, including coronary heart disease, ischemia-reperfusion injury, cardiomyopathy, arrhythmia, and vascular disease. SP1 emerges as a potential target for the prevention and therapeutic intervention of cardiac ailments. In this review, we delve into the biological functions, pathophysiological mechanisms, and potential clinical implications of SP1 in cardiac pathology to offer valuable insights into the regulatory functions of SP1 in heart diseases and unveil novel avenues for the prevention and treatment of cardiovascular conditions.