PurposeThe heterogeneous nuclear ribonucleoprotein (HNRNP) family plays pivotal roles in multiple aspects of RNA metabolism. Recent studies suggest that HNRNP dysregulation can promote tumor development. Therefore, this study aims to systematically characterize the expression profiles, immunological associations, and prognostic significance of HNRNP family members in LUAD.MethodsComprehensive transcriptomic and proteomic analyses were conducted using TCGA, GTEx, GEO, and CPTAC LUAD cohorts. Differential expression, immune infiltration, and survival analyses were performed using bioinformatics approaches including ssGSEA, TIDE, and Cox regression modeling. Functional enrichment and alternative splicing profiling were further applied to explore potential mechanisms, with a focus on HNRNPC.ResultsMultiple HNRNP genes were significantly overexpressed in LUAD tissues across datasets. Their expression levels positively correlated with tumor stage, metastasis, recurrence, and TP53 mutation status. High expression of several HNRNPs was associated with poor overall survival, with HNRNPC identified as an independent prognostic indicator in both TCGA and GEO cohorts. Elevated HNRNP expression was linked to reduced immune cell infiltration and lower stromal, immune, and ESTIMATE scores, alongside increased TIDE and Exclusion scores, suggesting immunosuppressive roles in the tumor microenvironment. Functionally, HNRNPC was associated with the activation of cell cycle progression and DNA damage repair. Alternative splicing analysis revealed that HNRNPC predominantly regulates exon skipping events, with enriched downstream pathways involved in chromatin remodeling and transcriptional regulation.ConclusionThis study highlights the critical roles of HNRNP family members in LUAD, identifying HNRNPC as a key prognostic biomarker and potential intervention candidate to improve patient outcomes.

Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide. MicroRNAs (miRNAs) are key regulators of tumorigenesis. This study investigated the role of the miR-192/215-early growth response protein 1 (EGR1) axis in GC and explored its therapeutic implications. Combinatorial molecular approaches including dual-luciferase reporter assays and western blot analyses were employed to authenticate EGR1 as a direct target of miR-192/215. Multi-modal data analysis incorporating The Cancer Genome Atlas datasets and our institutional cohort (n=56) was conducted to delineate EGR1 expression profiles across clinicopathological GC stages. Pharmacological modulation studies were implemented to characterize the dose- and time-dependent effects of epigallocatechin-3-gallate (EGCG) on the miR-192/215-EGR1 axis. EGR1 is a direct target of miR-192/215, with its expression negatively regulated by these miRNAs. Clinical analysis revealed significantly reduced EGR1 expression in tumors of early-stage GC (stage I) and cases with superficial invasion depth (T1) (p<0.05), suggesting a tumor-promoting role in the early stages of the disease. Higher EGR1 levels were associated with poorer overall survival, highlighting its potential as a prognostic biomarker (p<0.05). Furthermore, treatment of cells with EGCG transiently up-regulated miR-192/215 and down-regulated EGR1, highlighting its therapeutic potential. This study highlights the miR-192/215-EGR1 axis as a critical regulator of GC progression and a promising therapeutic target. EGCG may serve as an adjunct therapy for GC. Future studies should focus on the regulatory mechanisms of EGR1, its interaction with the tumor microenvironment, and clinical validation of EGCG and other agents targeting this axis.

Circular RNAs play significant roles in the development and progression of various cancers through diverse mechanisms, including the translation of novel proteins. Ferroptosis, a recently identified form of cell death, is associated with tumorigenesis in several cancers; however, its pathological mechanisms in gastric cancer (GC) remain unclear. Here, we found that circTUBGCP3 expression was elevated in GC tissues compared with normal gastric tissues. Moreover, circTUBGCP3 can be translated into a previously undescribed protein, TUBGCP3-230aa. In vitro and in vivo functional analyses demonstrated that both circTUBGCP3 and TUBGCP3-230aa promote rapid GC cell proliferation, with TUBGCP3-230aa exerting independent biological effects. Enolase 1 (ENO1), a glycolytic enzyme, was identified as an interacting partner of TUBGCP3-230aa, leading to activation of the glycolytic pathway and inhibition of ferroptosis in GC cells in vitro and in vivo. Mechanistically, TUBGCP3-230aa stabilizes ENO1 through posttranslational regulation, thereby repressing ferroptosis. Together, our results identify circTUBGCP3 and TUBGCP3-230aa as potential biomarkers for GC and uncover a novel mechanism of ferroptosis regulation, which may represent a promising therapeutic target. Furthermore, our findings highlight a critical moonlighting function of ENO1 in GC and underscore its potential as a novel target for cancer therapy.

Gastric cancer (GC) is one of the most common and lethal malignancies in developing countries, with particularly high prevalence in China. Circular RNAs (circRNAs) have garnered increasing attention for their roles in disease pathogenesis. While circRNAs can be translated, there have been few investigations into the biological functions of “translatable circRNAs” in the initiation and progression of gastric adenocarcinoma. In this study, we identified a circRNA, circMAP3K13, which inhibits the proliferation and migration of GC cells. CircMAP3K13 was found to encode a previously unreported 26 kDa protein, designated MAP3K13-232aa. Mechanistically, MAP3K13-232aa binds directly to the kinase domain of IKKα and enhances its activity, thereby promoting NF-κB signaling. This activation leads to upregulation of NLRP3 and increased cisplatin-induced pyroptosis in GC cells. Moreover, MAP3K13-232aa enhances pyroptosis and reduces tumorigenicity and metastasis in vivo. Taken together, both circMAP3K13 and its encoded protein MAP3K13-232aa represent potential therapeutic targets in GC.

Background/Aim: Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide. MicroRNAs (miRNAs) are key regulators of tumorigenesis. This study investigated the role of the miR-192/215-early growth response protein 1 (EGR1) axis in GC and explored its therapeutic implications. Materials and Methods: Combinatorial molecular approaches including dual-luciferase reporter assays and western blot analyses were employed to authenticate EGR1 as a direct target of miR-192/215. Multi-modal data analysis incorporating The Cancer Genome Atlas datasets and our institutional cohort (n=56) was conducted to delineate EGR1 expression profiles across clinicopathological GC stages. Pharmacological modulation studies were implemented to characterize the dose- and time-dependent effects of epigallocatechin-3-gallate (EGCG) on the miR-192/215-EGR1 axis. Results: EGR1 is a direct target of miR-192/215, with its expression negatively regulated by these miRNAs. Clinical analysis revealed significantly reduced EGR1 expression in tumors of early-stage GC (stage I) and cases with superficial invasion depth (T1) (p<0.05), suggesting a tumor-promoting role in the early stages of the disease. Higher EGR1 levels were associated with poorer overall survival, highlighting its potential as a prognostic biomarker (p<0.05). Furthermore, treatment of cells with EGCG transiently up-regulated miR-192/215 and down-regulated EGR1, highlighting its therapeutic potential. Conclusion: This study highlights the miR-192/215-EGR1 axis as a critical regulator of GC progression and a promising therapeutic target. EGCG may serve as an adjunct therapy for GC. Future studies should focus on the regulatory mechanisms of EGR1, its interaction with the tumor microenvironment, and clinical validation of EGCG and other agents targeting this axis.

The lack of effective, targeted therapies for gastric cancer (GC) continues to limit patient survival. Circular RNAs (circRNAs), known to act as epigenetic regulators, may also encode functional proteins. In this study, RNA-seq combined with ribosome profiling (Ribo-seq) of human GC cells identified a non-canonically translated circRNA, circSEMA3C, which encodes a novel 319-amino-acid (aa) protein, SEMA3C-319aa. Functionally, both circSEMA3C and SEMA3C-319aa suppressed GC cell viability and tumor growth in vitro and in vivo. Using proteomics and metabolomics, we found that SEMA3C-319aa targets ferroptosis-associated metabolites and metabolic pathways in GC. Notably, SEMA3C-319aa upregulated the production of polyunsaturated fatty acid chains and inhibited glutathione metabolism-particularly the GSH cycle-thereby suppressing GPX4 activity. Mechanistically, SEMA3C-319aa binds to LDHA and, via its non-canonical nuclear localization signal (NLS), sequence shuttles LDHA into the nucleus, where it enhances transcription of the E3 ligase PARK2, promoting GPX4 degradation. Furthermore, combination treatment with SEMA3C-319aa and the GPX4 inhibitor RSL3 was more effective than monotherapy in vivo. Taken together, our findings reveal a novel NLS-dependent nuclear translocation mechanism mediated by SEMA3C-319aa and identify a new ferroptosis pathway in GC. SEMA3C-319aa may offer a promising adjuvant therapeutic strategy for GC.

INTRODUCTION:Gastric cancer (GC) is a common malignancy, which is associated with high rates of morbidity and mortality. Despite therapeutic advancements, there is an overall lack of effective treatment options for patients with GC, particularly those with advanced and metastatic disease. The roles of circular (circ)RNAs in tumorigenesis are being increasingly recognized, among which circRNAs are defined as miRNA/protein sponges, scaffolds, or protein coding templates. OBJECTIVES:The aim of the present study is to investigate the functions of circATM in GC and elucidate the underlying molecular mechanism. METHODS:By circRNA sequencing in GC tissues, we identified a novel 526 nt circRNA, circATM, generating from exons 3-6 of the ATM gene. Through circRNA pull-down and RNA immunoprecipitation assays, we identified PARP1 as one of circATM binding proteins. The EdU, colony formation, wound healing, dual-luciferase reporter, cell cycle assays were employed to evaluated circATM functions in vitro. The GC xenograft model was used to determine the role of circATM in vivo. RESULTS:Knocking down circATM promoted GC cells growth in vivo and in vitro. Meanwhile, the overexpression of circATM increased the levels of p16, p21, and p27, and decreased those of β-catenin and c-Myc. Furthermore, we identified PARP1 as a circATM-interacting partner. Mechanistically, circATM bound to the zinc finger motif of Ⅱ-Ⅲ domains of PARP1 to block its recruitment to sites of DNA damage, triggering cell cycle arrest and sequestering β-catenin from the PARP1/β-catenin/TCF4 complex, leading to the suppression of Wnt/β-catenin signaling. Additionally, circATM facilitated the ubiquitin-proteasome degradation of PARP1, further jeopardizing its ability to mediate DNA damage repair. CONCLUSION:Taken together, we defined circATM as a novel gastric tumor suppressor via interacting with PARP1, which indicate that circATM may be a promising biomarker for the diagnosis and therapy of GC.

Supplementary Tables S1 & S2 from Reprimo Methylation Is a Potential Biomarker of Barrett's-Associated Esophageal Neoplastic Progression

Supplementary Figure S1 from Reprimo Methylation Is a Potential Biomarker of Barrett's-Associated Esophageal Neoplastic Progression

The majority of glucose in tumor cells is converted to lactate despite the presence of sufficient oxygen and functional mitochondria, a phenomenon known as the "Warburg effect" or "aerobic glycolysis". Aerobic glycolysis supplies large amounts of ATP, raw material for macromolecule synthesis, and also lactate, thereby contributing to cancer progression and immunosuppression. Increased aerobic glycolysis has been identified as a key hallmark of cancer. Circular RNAs (circRNAs) are a type of endogenous single-stranded RNAs characterized by covalently circular structures. Accumulating evidence suggests that circRNAs influence the glycolytic phenotype of various cancers. In gastrointestinal (GI) cancers, circRNAs are related to glucose metabolism by regulating specific glycolysis-associated enzymes and transporters as well as some pivotal signaling pathways. Here, we provide a comprehensive review of glucose-metabolism-associated circRNAs in GI cancers. Furthermore, we also discuss the potential clinical prospects of glycolysis-associated circRNAs as diagnostic and prognostic biomarkers and therapeutic targets in GI cancers.

Circular RNAs (circRNAs) form a class of endogenous single-stranded RNA transcripts that are widely expressed in eukaryotic cells. These RNAs mediate post-transcriptional control of gene expression and have multiple functions in biological processes, such as transcriptional regulation and splicing. They serve predominantly as microRNA sponges, RNA-binding proteins, and templates for translation. More importantly, circRNAs are involved in cancer progression, and may serve as promising biomarkers for tumor diagnosis and therapy. Although traditional experimental methods are usually time-consuming and laborious, substantial progress has been made in exploring potential circRNA-disease associations by using computational models, summarized signaling pathway data, and other databases. Here, we review the biological characteristics and functions of circRNAs, including their roles in cancer. Specifically, we focus on the signaling pathways associated with carcinogenesis, and the status of circRNA-associated bioinformatics databases. Finally, we explore the potential roles of circRNAs as prognostic biomarkers in cancer.

Supplementary Table S1 from Hypermethylation of Tachykinin-1 Is a Potential Biomarker in Human Esophageal Cancer

Supplementary Table 1 from Pituitary Tumor-Transforming 1 Increases Cell Motility and Promotes Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma

Supplementary Figure Legends 1-2 from A Multicenter, Double-Blinded Validation Study of Methylation Biomarkers for Progression Prediction in Barrett's Esophagus

Peptidylarginine deiminase 4 (PAD4), a Ca2+-dependent enzyme, catalyzes the conversion of arginine to citrulline and has been strongly associated with many malignant tumors. However, the molecular mechanisms of PAD4 in the development and progression of colorectal cancer (CRC) remain unclearly defined. In our study, PAD4 expression was increased in CRC tissues and cells, and was closely related to tumor size, lymph node metastasis. Moreover, the transcription factor KLF9 directly bound to PADI4 gene promoter, leading to overexpression of PAD4 in CRC cells, which augmented cell growth and migration. We revealed that PAD4 interacted with and citrullinated glycogen synthase kinase-3β (GSK3β) in CRC cells, and GSK3β Arg-344 was the dominating PAD4-citrullination site. Furthermore, IgL2 and catalytic domains of PAD4 directly bound to the kinase domain of GSK3β in CRC cells. Mechanistically, PAD4 promoted the transport of GSK3β from the cytoplasm to the nucleus, thereby increasing the ubiquitin-dependent proteasome degradation of nuclear cyclin-dependent kinase inhibitor 1 (CDKN1A). Our study is the first to reveal the details of a critical PAD4/GSK3β/CDKN1A signaling axis for CRC progression, and provides evidence that PAD4 is a potential diagnosis biomarker and therapeutic target in CRC.

Circular RNA (circRNA) is characterized by a specific covalently closed ring structure. The back-splicing of precursor mRNA is the main way of circRNA generation, and various cis/trans-acting elements are involved in regulating the process. circRNAs exhibit multiple biological functions, including serving as sponges of microRNAs, interacting with proteins to regulate their stabilities and abilities, and acting as templates for protein translation. Autophagy participates in many physiological and pathological processes, especially it plays a vital role in tumorigenesis and carcinoma progression. Increasing numbers of evidences have revealed that circRNAs are implicated in regulating autophagy during tumor development. Until now, the roles of autophagy-associated circRNAs in carcinoma progression and their molecular mechanisms remain unclear. Here, the emerging regulatory roles and mechanisms of circRNAs in autophagy were summarized. Furtherly, the effects of autophagy-associated circRNAs on cancer development were described. We also prospected the potential of autophagy-associated circRNAs as novel therapeutic targets of tumors and as biomarkers for cancer diagnosis and prognosis.

Abstract Background Transcatheter arterial chemoembolization (TACE) is the mainstay of therapy for intermediate-stage hepatocellular carcinoma (HCC); yet its efficacy varies between patients with the same tumor stage. Accurate prediction of TACE response remains a major concern to avoid overtreatment. Thus, we aimed to develop and validate an artificial intelligence system for real-time automatic prediction of TACE response in HCC patients based on digital subtraction angiography (DSA) videos via a deep learning approach. Methods This retrospective cohort study included a total of 605 patients with intermediate-stage HCC who received TACE as their initial therapy. A fully automated framework (i.e., DSA-Net) contained a U-net model for automatic tumor segmentation (Model 1) and a ResNet model for the prediction of treatment response to the first TACE (Model 2). The two models were trained in 360 patients, internally validated in 124 patients, and externally validated in 121 patients. Dice coefficient and receiver operating characteristic curves were used to evaluate the performance of Models 1 and 2, respectively. Results Model 1 yielded a Dice coefficient of 0.75 (95% confidence interval [CI]: 0.73–0.78) and 0.73 (95% CI: 0.71–0.75) for the internal validation and external validation cohorts, respectively. Integrating the DSA videos, segmentation results, and clinical variables (mainly demographics and liver function parameters), Model 2 predicted treatment response to first TACE with an accuracy of 78.2% (95%CI: 74.2–82.3), sensitivity of 77.6% (95%CI: 70.7–84.0), and specificity of 78.7% (95%CI: 72.9–84.1) for the internal validation cohort, and accuracy of 75.1% (95% CI: 73.1–81.7), sensitivity of 50.5% (95%CI: 40.0–61.5), and specificity of 83.5% (95%CI: 79.2–87.7) for the external validation cohort. Kaplan-Meier curves showed a significant difference in progression-free survival between the responders and non-responders divided by Model 2 (p = 0.002). Conclusions Our multi-task deep learning framework provided a real-time effective approach for decoding DSA videos and can offer clinical-decision support for TACE treatment in intermediate-stage HCC patients in real-world settings.

Circular RNAs (circRNAs) are covalently closed, endogenous molecules that are widespread in eukaryotes. Recent evidence indicates that circRNAs play important roles in carcinogenesis. Several circRNAs have been reported to comprise translatable RNA; however, whether circRNAs encode functional proteins remains unknown. In our study, circRNA sequencing was carried out using five pathologically diagnosed gastric carcinoma (GC) samples and their paired adjacent normal tissues, we characterized the circRNA GSPT1 (circGSPT1), which is expressed at low levels in GC. Antibody detections, and mass spectrometry were used to validate active circRNA translation. The spanning junction open reading frame in circGSPT1, driven by an internal ribosome entry site (IRES), encodes a functional peptide, termed GSPT1-238aa. Interestingly, GSPT1-238aa tends to select the start codon used to initiate translation. This is the first finding of selective translation driven by IRES. CircGSPT1 and GSPT1-238aa halted the proliferation, migration, and invasion in GC cells in vitro. We also confirmed that the vimentin/Beclin1/14-3-3 complex interacts with GSPT1-238aa and modulates autophagy via the PI3K/AKT/mTOR signaling pathway in GC cells. Our study reveals that GSPT1-238aa, a novel protein encoded by circGSPT1, halts GC tumorigenesis. We also provide insights into the function and underlying molecular mechanisms of GSPT1-238aa in GC and suggest that this protein represents a novel target for GC treatment.

Gastric cancer (GC) is one of the most common malignant tumors and ranks third in cancer mortality globally. Although, a lot of advancements have been made in diagnosis and treatment of gastric cancer, there is still lack of ideal biomarker for the diagnosis and treatment of gastric cancer. Due to the poor prognosis, the survival rate is not improved much. Circular RNAs (circRNAs) are single-stranded RNAs with a covalently closed loop structure that don’t have the 5′-3′ polarity and a 3′ polyA tail. Because of their circular structure, circRNAs are more stable than linear RNAs. Previous studies have found that circRNAs are involved in several biological processes like cell cycle, proliferation, apoptosis, autophagy, migration and invasion in different cancers, and participate in some molecular mechanisms including sponging microRNAs (miRNAs), protein translation and binding to RNA-binding proteins. Several studies have reported that circRNAs play crucial role in the occurrence and development of different types of cancers. Although, some studies have reported several circRNAs in gastric cancer, more studies are needed in searching new biomarkers for gastric cancer diagnosis and treatment. Here, we investigated potential circRNA biomarkers for GC using next-generation sequencing (NGS) data collected from 5 paired GC samples. A total of 45,783 circRNAs were identified in all samples and among them 478 were differentially expressed (DE). The gene ontology (GO) analysis of the host genes of the DE circRNAs showed that some genes were enriched in several important biological processes, molecular functions and cellular components. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that some host genes were enriched in several GC related pathways. The circRNA-miRNA-gene interaction network analysis showed that two circRNAs circCEACAM5 and circCOL1A1 were interacted with gastric cancer related miRNAs, and their host genes were also the important therapeutic and prognostic biomarkers for GC. The experimental results also validated that these two circRNAs were DE in GC compared to adjacent normal tissues. Overall, our findings suggest that these two circRNAs circCEACAM5 and circCOL1A1 might be the potential biomarkers for the diagnosis and treatment of GC.