GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

Mitochondrial ribosomal protein L3 (MRPL3): An early diagnostic biomarker and potential molecular target in pancreatic cancer

Pancreatic cancer (PanCa) is projected to become the second major cause of cancer-related mortality by 2030. The current diagnostic and treatment strategies offer only marginal benefits in overall survival. This highlights the need to discover new biomarkers and targets for the treatment of PanCa. Dysregulated mitochondrial ribosome biogenesis occurs in PanCa and can be utilized as a potential biomarker and molecular target for its management. In this study, we established MRPL3 (Mitochondrial Ribosomal Protein L3) as a potential biomarker and its role in expression of ETC (Electron Transport Chain) components. We employed an integrated approach combining the in silico and experimental validation. Our findings demonstrate that the expression of MRPL3 is upregulated during PanCa in ductal adenocarcinoma and other single cell populations of pancreas. Amongst various grades, the highest expression of MRPL3 was observed in grade 1 human PanCa tumors. MRPL3 is involved in the growth of PanCa cells and the targeted knock-down of MRPL3 leads to decrease in the expression of ETC components. Moreover, in silico analysis identified that MRPL3 undergoes alternative splicing that gives rise to six coding and four non-coding variants. The MRPL3-001 isoform arising from ENSG00000114686.8 variant was found to be the most abundant in PanCa. Pathway enrichment analysis showed that MRPL3 is positively associated with cell growth and proliferation while negatively associated with cell lineage commitment and differentiation. These results represent MRPL3 as a promising early biomarker and molecular target for PanCa which warrant further investigation for its clinical applications.

HELQ upregulates PARP1 to drive platinum resistance and predict therapeutic response in ovarian cancer

POLQ-like helicase (HELQ), an evolutionarily conserved 3'-5' DNA helicase, is markedly overexpressed in platinum-resistant ovarian cancer (OC), which is correlated with a poor prognosis. However, the mechanisms linking HELQ with resistance to platinum-based chemotherapy remain unkonwn. Our study presents both in vitro and in vivo evidence that elevated HELQ expression is linked to increased chemoresistance in OC models, with reduced HELQ levels enhancing their sensitivity to platinum agents. The expression of γH2AX, RPA1 and 53BP1 determined by immunofluorescence and western blot indicated that HELQ could promote platinum-induced DNA damage repair. HELQ was found to promote OC platinum resistance by regulating the expression of poly (ADP-ribose) polymerase 1(PARP1), which could be reversed by PARP1 downregulation. Furthermore, in vitro experiments showed that HELQ overexpression sensitizes OC cells to PARP inhibitors (PARPi). Immunohistochemical analysis indicates that diminished HELQ expression in tumor tissues correlates with disease progression in patients with first-line maintenance therapy with PARPi, whereby higher expression levels predict improved progression-free survival. Notably, we found a positive correlation between PARP1 and HELQ expression. In conclusion, HELQupregulats PARP1 to promote platinum resistance in OC and warrants consideration as an emerging biomarker for monitoring therapeutic responses to chemotherapy and PARPi treatment in ovarian cancer.

In Silico Drug Repurposing Against PSMB8 as a Potential Target for Acute Myeloid Leukemia Treatment

PSMB8 emerges as a prominent gene associated with cancer survival, yet its potential therapeutic role in acute myeloid leukemia (AML) remains unexplored within the existing literature. The principal aim of this study is to systematically screen an expansive library of molecular entities, curated from various databases to identify the prospective inhibitory agents with an affinity for PSMB8. A comprehensive assortment of molecular compounds obtained from the ZINC15 database was subjected to molecular docking simulations with PSMB8 by using the AutoDock tool in PyRx (version 0.9.9) to elucidate binding affinities. Following the docking simulations, a select subset of molecules underwent further investigation through comprehensive ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis employing AdmetSar and SwissADME tools. Finally, RMSD, RMSF, Rg, and H bond analyses were conducted via GROMACS to determine the best conformationally dynamic molecule that represents the candidate agent for the study. Following rigorous evaluation, Adozelesin, Fiduxosin, and Rimegepant have been singled out based on considerations encompassing bioavailability scores, compliance with filter criteria, and acute oral toxicity levels. Additionally, ligand interaction analysis indicates that Adozelesin and Fiduxosin exhibit an augmented propensity for hydrogen bond formation, a factor recognized for its facilitative role in protein-ligand interactions. After final analyses, we report that Fiduxosin may offer a treatment possibility by reversing the low survival rates caused by PSMB8 high activation in AML. This study represents a strategic attempt to repurpose readily available pharmaceutical agents, potentially obviating the need for de novo drug development, and thereby offering promising avenues for therapeutic intervention in specific diseases.

Apigenin inhibits recurrent bladder cancer progression by targeting VEGF-β

Bladder cancer is a major global health concern with high incidence and mortality rates. Both muscle-invasive bladder cancer (MIBC) and recurrent non-muscle-invasive bladder cancer (NMIBC) present significant challenges in treatment. Apigenin, a naturally occurring flavonoid, has shown promise in inhibiting the growth of bladder cancer cells, however, its therapeutic mechanism remains unclear. Single-cell RNA sequencing (scRNA-seq) data analysis and drug target screening were performed. Differentially expressed genes (DEGs) and potential therapeutic targets of apigenin were identified. Molecular docking was utilized to evaluate the binding affinity between apigenin and VEGF-β. In vitro assays were conducted to evaluate the association of VEGF-β and apigenin. Drug target screening identified 51 common targets between apigenin and bladder cancer, with VEGF-β emerging as a dominant gene. Molecular docking confirmed a high binding affinity between apigenin and VEGF-β. VEGF-β was significantly upregulated in fibroblasts from recurrent bladder cancer, correlating with increased tumor malignancy. Enhanced cell communication in VEGF-β-positive fibroblasts contributed to tumor progression. In vitro experiments demonstrated that VEGF-β promotes tumor cell proliferation, migration, and invasion. Apigenin significantly inhibits bladder cancer progression by targeting VEGF-β. The upregulation of VEGF-β in fibroblasts from recurrent bladder cancer highlights its potential as a diagnostic marker and therapeutic target. This study underscores the promise of apigenin as a chemopreventive and therapeutic agent for recurrent bladder cancer.

Identification of TMEM100's role in immune infiltration regulation and construction of an endogenous RNA network in prostate cancer through pan-cancer analysis

BACKGROUND

Prostate adenocarcinoma (PRAD) is a prevalent urinary tumor with an elusive etiology. While transmembrane protein 100 (TMEM100) plays diverse roles in various cancers, its involvement in prostate cancer remains unexplored. Herein, we aim to elucidate the impact of TMEM100 on prostate cancer diagnosis and progression.

METHODS

Utilizing data from the TCGA database, we analyzed mRNA sequences, clinical information, and methylation data. Prognostic analysis was conducted using the GEPIA database, and a nomogram was developed using the "rms" package in R software. Drug sensitivity was assessed using the "pRRophetic" package. The correlation between TMEM100 and immune infiltration was investigated using the TIMER and TISDIB databases. Methylation levels were evaluated using Perl and R software. The competitive endogenous RNA (ceRNA) network was constructed using the starBase database. Functional assays including qRT-PCR, CCK8, EdU, and IHC assays were employed to evaluate TMEM100's role in PRAD.

RESULTS

TMEM100 expression was significantly reduced in prostate cancer tissues compared to normal tissues, correlating with poor prognosis in PRAD. The multivariable model nomogram demonstrated enhanced prediction of PFI. Additionally, the low-expression TMEM100 group exhibited lower IC50 values for several chemotherapy drugs. TMEM100 was closely associated with various immune cell types, immunomodulators, and chemokines, exerting anti-tumor effects. Higher methylation levels of TMEM100 were observed in PRAD, with specific CpG sites showing significant correlation. TMEM100 hypermethylation correlated with immune infiltration in PCa. Furthermore, a TMEM100-related ceRNA network was constructed in PRAD, corroborating TMEM100's role in PCa through functional experiments.

CONCLUSION

TMEM100 downregulation, through modulation of immune infiltration and epigenetic mechanisms, correlates with poor prognosis and tumor cell proliferation in PRAD.

SIRPα blockade therapy potentiates immunotherapy by inhibiting PD-L1+ myeloid cells in hepatocellular carcinoma

Tumor-infiltrating myeloid cells (TIMs) are pivotal cell populations involved in the immunosuppressive tumor immune microenvironment (TIME). However, there has been little success in large-scale clinical trials of myeloid cell modulators. We aim to investigate potential molecular targets for TIMs and disclose the underlying mechanism. Using mass cytometry by time of flight (CyTOF), we analyzed 24 spontaneous HCC tissues from mouse. Orthotopic and subcutaneous tumor models were established with or without anti-SIRPα antibody treatment. Patient-derived tumor xenografts model (PDX) was used to identify the CD47-SIRPα axis blocked therapy. In 24 murine spontaneous HCC tissues, we observed that the proportion of myeloid-derived suppressor cells (MDSCs) plus macrophages accounts for 40-90% of TIMs and SIRPα was highly expressed in TIMs, especially in macrophages and MDSCs. Through in vivo experiments, we showed that anti-SIRPα therapy inhibited tumor growth, accompanied by increased CD8+ T cells infiltration and decreased TIMs including MDSCs and macrophages. We found that anti-SIRPα inhibited immunosuppressive function, migration and PD-L1 expression of myeloid cells. In a series of in vivo experiments, we demonstrated the anti-tumor and immune-active effect of SIRPα-blocked therapy. Mechanistically, anti-SIRPα inhibited the immunosuppressive function and PD-L1 expression of TIMs through downregulating PI3K/AKT signaling in myeloid cells. At last, anti-SIRPα enhanced the antitumor effect of anti-PD-L1 therapy in orthotopic and spontaneous murine models. Together, SIRPα blocked therapy reversed the immunosuppressive TIME, which provides a promising therapeutic rationale for increasing the efficacy of anti-PD-L1 therapy in treating HCC.

Potential mechanism of Camellia luteoflora against colon adenocarcinoma: An integration of network pharmacology and molecular docking

BACKGROUND

Camellia luteoflora is a unique variety of Camellia in China which is only distributes in Chishui City, Guizhou Province and Luzhou City, Sichuan Province. Its dried leaves are used by local residents as tea to drink with light yellow and special aroma for health care. It has high potential economic medicinal value. Colon adenocarcinoma (COAD) is the third most frequent malignancy and its incidence and mortality is increasing. However, the current common treatments for COAD bring great side effects. In recent years, natural products and their various derivatives have shown significant potential to supplement conventional therapies and to reduce associated toxicity while improving efficacy. In order to overcome the limitations of traditional treatment methods, the global demand and development of natural anti-COAD drugs were increasingly hindered.

AIM

To investigate the potential targets and mechanisms of Camellia luteoflora anti-COAD.

METHODS

Nuclear magnetic resonance and mass spectrometry was used to identified the compounds of Camellia luteoflora. Network pharmacology analysis and survival analysis was used in this study to investigate the anti-COAD effect and mechanism of Camellia luteoflora.

RESULTS

Firstly, a total of 13 compounds were identified. Secondly, 10 active ingredients for 204 potential targets were screened and protein-protein interaction analysis showed that TP53, STAT3, ESR1, MAPK8, AKR1C3, RELA, CYP19A1, CYP1A1, JUN and CYP17A1 were hub targets. GO and KEGG enrichment analyses revealed that Camellia luteoflora exerted anti-COAD effect through multiple functions and pathways. Then, the analysis of survival and stage indicated that TP53 was highly expressed in COAD and the overall survival of high-TP53 and high-CYP19A1 COAD patients was significantly shorter than the low group and there was significant difference in MAPK and RELA expression between different stages. Finally, the molecular docking results demonstrated the binding affinities and sites between active ingredients and TP53, STAT3, ESR1.

CONCLUSION

Our study systematically demonstrated the potential anti-COAD mechanism of Camellia luteoflora and provided a theoretical basis for its further application in the COAD treatment.

Identification of CWH43 as a novel prognostic biomarker and therapeutic target in clear cell renal cell carcinoma by a multi-omics approach and correlation with autophagy progression

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) poses significant challenges due to its asymptomatic nature and poor prognosis at advanced stages. Identifying novel biomarkers is essential for enhancing prognostic accuracy and therapeutic strategies. This study explores the CWH43 gene, utilizing multi-omics data to determine its role in ccRCC.

METHODS

Genomic, transcriptomic, and methylation data from TCGA-KIRC and GEO databases were analyzed to evaluate CWH43 expression and clinical impact. Bioinformatics tools assessed correlations with patient outcomes and pathway involvement.

RESULTS

CWH43 expression was significantly reduced in ccRCC tissues and correlated with advanced disease stages and poor patient survival. Enrichment analyses revealed CWH43's involvement in critical cancer pathways, such as autophagy and immune response modulation, suggesting its significant role in ccRCC pathophysiology. Lower CWH43 levels were associated with increased tumor progression and immune evasion, impacting the tumor microenvironment.

CONCLUSION

This study highlights the utility of multi-omics data in identifying CWH43 as a novel prognostic biomarker for ccRCC. Integrating CWH43 into clinical practice could refine prognostic assessments and guide personalized therapy strategies, aligning with advancements in modern oncology. Further research is warranted to explore CWH43's mechanisms and therapeutic potential.

Identification of metabolism-associated molecular classification for effect and prognosis in lung adenocarcinoma based on multidatabases including the cancer genome atlas and gene expression omnibus

Background

Lung adenocarcinoma is a highly heterogeneous group of diseases with distinct molecular genetic features, pathological characteristics, metabolic profiles, and clinical behaviors. However, the clinical relevance of metabolic characteristics of lung adenocarcinoma remains unclear. This study aimed to describe the molecular characteristics of lung adenocarcinoma.

Methods

The gene expression profiles of 1037 lung adenocarcinoma samples were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. This study is based on sample data from 2006 to 2020. The long-time span and sufficient sample size ensure the robustness of the research findings. Using unsupervised transcriptome analysis, we identified three distinct subtypes (C1, C2, and C3). We then compared the prognostic traits, transcriptome characteristics, metabolic signatures, immune infiltration, clinical features, and drug sensitivity of the lung adenocarcinoma subclasses. A classifier was generated to determine lung adenocarcinoma classification, and we verified the clinical value of this classifier in other tumors.

Results

Our results indicated that C1 possessed the most abundant metabolic pathways. Compared with C2 and C3, C1 possessed 35 metabolic pathways that exhibited significant differences. The immune score, matrix score, and immune infiltration for subtype C1 were significantly lower than those for subtypes C2 and C3, suggesting that C1 is a metabolically active subtype. Five metabolic pathways were observed in C2. Subtype C2 was associated with the best prognosis and exhibited the lowest tumor mutation burden and copy number variation. Subtype C3 comprised five metabolic pathways. Immune checkpoint analysis revealed that C3 cells may potentially benefit from immunotherapy.

Conclusions

Our study deepens the understanding of the metabolic characteristics of lung adenocarcinoma and may provide valuable information for immunotherapy.

P65-Driven MIR4435-2HG Enhances Prognostic Value and Mediates Oxaliplatin Resistance via the miR-378G/ABCB9 Axis in Colorectal Cancer

Long non-coding RNA MIR4435-2HG has emerged as a pivotal oncogenic factor across various cancers. However, its role in chemoresistance, particularly in colorectal cancer (CRC), remains unclear. This work demonstrates that MIR4435-2HG is significantly overexpressed in CRC tissues, correlating with poor prognosis and resistance to oxaliplatin (L-OHP) based chemotherapy. Mechanistically, MIR4435-2HG binds to miR-378g, leading to elevated ABCB9 levels, a crucial factor in drug resistance. Both in vitro and in vivo experiments indicate that the MIR4435-2HG/miR-378g/ABCB9 axis confers L-OHP resistance in CRC cells by reducing DNA damage and enhancing cell survival. Additionally, P65, a component of the NF-κB pathway, directly promotes MIR4435-2HG transcription, triggering subsequent chemoresistance. Based on these results, MIR4435-2HG is recognized as a reliable prognostic marker and serves as a target for therapeutic strategies, presenting new approaches to counteract L-OHP resistance and enhance CRC patient outcomes.

Deciphering ETS2: An indispensable conduit to cancer

E26 Transformation-Specific homolog 2 (ETS2) is a founding member of the ETS family of transcription factors and has been implicated in several developmental and survival functions. The predominant route of its action is by directly binding and regulating the promoters of its target genes, although it can function through other regulatory mechanisms as well. In this review, a comprehensive understanding of the contribution of ETS2 in health and disease is described with specific focus on cancer. ETS2 demonstrates extreme complexity as it can act as a double-edged sword in cancer with tumour suppressive or oncogenic functions in a context specific manner. Here, we delineate the different signalling pathways, post-translational modifications, miRNA regulations and protein-protein interactions that illustrate the role of ETS2 as an emerging biomarker with special emphasis on its contribution to 'hallmarks of cancer'. Given the evidently opposing effects of ETS2 in different cancers, elucidating the critical mechanisms in its development and progression can validate ETS2's potential as a novel therapeutic target. Finally, we provide insights into frontier areas of research focus that implicate ETS2 and can translate into clinical outcomes.

PSAT1 regulated by STAT4 enhances the proliferation, invasion and migration of ovarian cancer cells via the PI3K/AKT pathway

Epithelial ovarian cancer, the most prevalent form of ovarian cancer, is a health concern worldwide. Phosphoserine aminotransferase 1 (PSAT1), as the rate‑limiting enzyme in serine synthesis, is key in the conversion of 3‑phosphoglycerate to serine. The present study explored the role of PSAT1 expression in epithelial ovarian tumors. Gene Expression Profiling Interactive Analysis was used for gene expression and survival analyses. The effects of PSAT1 overexpression and knockdown on invasion, migration, proliferation and cell cycle progression of ovarian cancer cell lines were investigated both in vitro and in vivo. Western blotting was conducted to assess alterations in PI3K/AKT signalling pathway proteins. Database and tissue sample data confirmed that PSAT1 was significantly upregulated in ovarian cancer. Preliminary functional investigations indicated that PSAT1 was involved in modulation of invasion and migration, demonstrating the capacity of PSAT1 to enhance expression of the PI3K/AKT signalling pathway. These findings suggested that PSAT1 served a critical role in the onset and progression of ovarian cancer, thereby offering a theoretical basis for early detection and therapeutic strategies.

Pan-Cancer Analysis and Experimental Validation of CEND1 as a Prognostic and Immune Infiltration-Associated Biomarker for Gliomas

Cell cycle exit and neuronal differentiation 1 (CEND1), highly expressed in the brain, is a specific transmembrane protein which plays a tumor suppressor role. This study is performed to investigate the role of CEND1 in various cancers through pan-cancer analysis, and further investigate its functions in gliomas by cell experiments. The expression and subcellular localization of CEND1 in different cancer types were analyzed utilizing the data from the GEPIA, UCSC, UALCAN and HPA databases. Relationships of CEND1 expression with prognosis, immunomodulation-related genes, immune checkpoint genes, microsatellite instability (MSI), tumor mutation burden (TMB) and RNA modifications were analyzed based on the TCGA database. The ESTIMATE algorithm was utilized to evaluate tumors' StromalScore, Immune Score, and ESTIMATES Score. The cBioPortal database was employed to analyze the categories and frequencies of CEND1 gene alterations. Biological functions and co-expression patterns of CEND1 in gliomas were explored using the LinkedOmics database, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. The interactions between CEND1 and drugs were explored employing the Comparative Toxicogenomics Database and molecular docking technology. Cell experiments were conducted to analyze triptonide's effects on glioma cells through CCK-8, flow cytometry and qRT-PCR. CEND1 was lowly expressed in gliomas, and high CEND1 expression was correlated to better overall survival of glioma patients (HR = 0.65, P = 0.02). Deep deletion was the main type of hereditary change of CEND1 mutation. CEND1 expression was markedly associated with immune infiltration, TMB, MSI, and RNA modification in various tumors (r > 0.3, P < 0.05). CEND1 co-expressed genes in gliomas were markedly correlated with immune responses and cell cycle (FDR < 0.05). Triptonide could bind well to CEND1 (-5.0 kcal/mol), and triptonide could facilitate CEND1 expression in glioma cells and cell apoptosis, and block the cell cycle progression (P < 0.05). CEND1 serves as a potential biomarker for pan-cancer. Particularly in gliomas, CEND1 is a key regulator of cell apoptosis and cell cycle, and a potential target for glioma treatment.

COPS5 Triggers Ferroptosis Defense by Stabilizing MK2 in Hepatocellular Carcinoma

Sorafenib, which is proven to serve as a potent ferroptosis inducer, is used as a first-line treatment for patients with advanced hepatocellular carcinoma (HCC), but it has limited clinical benefits, mainly due to drug resistance. Herein, using genome-wide CRISPR/Cas9 knockout screening and multiple functional studies, this work identifies COP9 signalosome subunit 5 (COPS5) as a driver of sorafenib resistance and a suppressor of ferroptosis in HCC. Consistently, the amplification and overexpression of COPS5 are frequently observed in clinical HCC samples, which are associated with poor patient prognosis and might predict patient response to sorafenib therapy. Mechanistically, COPS5 stabilized mitogen-activated protein kinase 2 (MK2) through deubiquitination and, in turn, induced the activation of heat shock protein beta-1 (HSPB1), a ferroptosis repressor, thereby protecting HCC cells from ferroptosis and consequently leading to sorafenib resistance and tumor progression, while its own expression could be induced by sorafenib treatment via activating transcription factor 4 (ATF4)-activated transcription. Furthermore, pharmacological inhibition of COPS5/MK2 synergize with sorafenib to induce ferroptosis and suppress HCC progression. This data reveals the crucial role of COPS5 in triggering ferroptosis defense and sorafenib resistance through the activation of the MK2-HSPB1 axis in HCC and highlights the potential of targeting COPS5/MK2 combined with sorafenib as a promising strategy for treating HCC.

Characterizing the immune landscape of tumor-infiltrating lymphocytes in non-small cell lung cancer

Tumor-Infiltrating Lymphocytes (TILs) immunotherapy is a highly promising treatment for Non-small Cell Lung Cancer (NSCLC), which is responsible for 18% of all cancer-related deaths. The heterogeneity of TILs remains poorly understood. Here, we utilized combined single-cell RNA (scRNA)/T cell receptor sequencing (scTCR-seq) data from lung adenocarcinoma (LUAD) patients. Naïve CD4+ and effector memory CD8+ T cells were increased in tumor tissue compared with circulating blood samples. Activated signaling pathways were detected, and GZMA was identified as a potential novel diagnostic biomarker. During the transitional phase, macrophages (FTL) and dendritic (AIF1) cells transported the most CD3 TCR clones to T cells, while cytotoxicity CD8+ T (NKG7) cells transported to terminal exhausted CD8+ T cells. In both transition and expansion phases, T helper cells (CXCL13) are transported to regulatory T cells (Tregs). Additionally, we investigated the expression profiles of key cytokines, checkpoint receptors, and their ligands. Cytotoxicity CD8+ T cells (CCL5 and IFNG), T helper cells (FTL, TNFRSF4, and TIGIT), and regulatory T cells (CTLA4, TIGIT and FTL) exhibited functional roles in both primary and metastatic tumor stages. Taken together, our study provides a single-cell resolution of the TIL immune landscape and suggests potential treatment strategies to overcome drug resistance.

Targeting ETHE1 inhibits tumorigenesis in vitro and in vivo by preventing aerobic glycolysis in gastric adenocarcinoma cells

Gastric adenocarcinoma (GAC) is a prevalent form of cancer that frequently displays abnormal metabolism characterized by increased aerobic glycolysis. Therefore, inhibition of glycolysis may exhibit therapeutic potential for the management of advanced or recurrent gastric cancer. Analysis of ethylmalonic encephalopathy protein 1 (ETHE1) expression levels in 30 pairs of cancerous and paracancerous tissues, and 50 tumor tissue sections collected from patients with GAC revealed that ETHE1 expression was upregulated in cancerous tissues compared with in paracancerous tissues. Advanced tumor stage, lymph node metastasis and Tumor-Node-Metastasis stage were associated with high ETHE1 expression. Knockdown of ETHE1 expression in GAC cells resulted in a significant inhibition of cell proliferation and in cell cycle arrest, accompanied by downregulated levels of cyclin D1 and cyclin-dependent kinase 4. ETHE1 knockdown also resulted in increased apoptosis of GAC cells, and increased caspase-3 and caspase-9 activity. Additionally, the expression levels of proteins associated with aerobic glycolysis were downregulated following ETHE1 knockdown, which may reduce glucose consumption, lactic acid production and ATP levels. In the in vivo experiments, suppressed tumor growth and increased tumor cell apoptosis were observed in the xenograft tumor model in animals injected with ETHE1-knockdown GAC cells. In summary, knockdown of ETHE1 inhibited aerobic glycolysis, promoted apoptosis and inhibited tumor cell proliferation in GAC cells. These results highlight ETHE1 as a promising molecular target for the treatment of GAC potentially using an adjuvant to target it, offering a novel approach in the exploration of targeted therapeutic drugs for GAC.

MICAL1 Mediates TGF-β1-Induced Epithelial-to-Mesenchymal Transition and Metastasis of Hepatocellular Carcinoma by Activating Smad2/3

Epithelial-mesenchymal transition (EMT) induced by transforming growth factor-β (TGF-β) is involved in hepatocellular carcinoma (HCC) growth and metastasis. Our study aimed to investigate the role of molecules interacting with CasL 1 (MICAL1) in regulating TGF-β-triggered EMT in HCC and the related mechanisms. After detecting MICAL1 expression and prognostic value in HCC, in vitro assays including CCK-8 assay, EdU staining, flow cytometry assay, Transwell assay, western blotting, and RT-qPCR and in vivo metastasis assay was conducted to evaluate the influence of MICAL1 knockdown on the proliferation and apoptosis as well as TGF-β-induced EMT and metastasis of Huh7 and MHCC97H cells. MICAL1 was highly expressed in HCC, and its high expression was related to histological grade, TNM stage, and shorter overall survival of HCC patients. MICAL1 silencing suppressed proliferation, promoted apoptosis, and curbed TGF-β1-triggered cytoskeletal remodeling, EMT, and metastasis of HCC cells. MICAL1 knockdown impeded TGF-β1-induced upregulation in phosphorylated-Smad2/3 protein levels and reduced Smad2/3 mRNA levels in HCC cells. MICAL1 downregulation enhanced the polyubiquitination and proteasomal degradation of TβRI. Additionally, MICAL1 silencing suppressed tumor growth and lung metastasis in Huh7-derived xenograft mouse models. Collectively, MICAL1 knockdown impairs TGF-β1-stimulated EMT and metastasis of HCC cells by restraining Smad2/3 phosphorylation and activation.

TGFβ2 Promotes the Construction of Fibrotic and Immunosuppressive Tumor Microenvironment in Pancreatic Adenocarcinoma: A Comprehensive Analysis

Pancreatic adenocarcinoma (PAAD) was characterized by dense fibrotic stroma and immunosuppressive tumor microenvironment (TME). TGFβ signaling pathways are highly activated in human cancers. However, the role of TGFβ2 in TME of PAAD remains to be elucidated. In this study, we showed that TGFβ2 was expressed at a relatively high level in PAAD tissues or cancer cells. Moreover, its high expression predicted unfavorable prognosis. In PAAD, gene set enrichment analysis showed that TGFβ2 correlated positively with leukocyte transendothelial migration, but negatively with aerobic metabolism, including oxidative phosphorylation. Results in Tumor and Immune System Interaction Database showed that TGFβ2 correlated with the infiltration of tumor-associated macrophages (TAMs), which could be attributed to that TGFβ2 promote CCL2 expression in PAAD. Moreover, correlation analysis showed that TGFβ2 could trigger cancer-associated fibroblasts (CAFs) activation in PAAD. The drug sensitivity analysis may indicate that patients with TGFβ2 high expression have higher sensitivity to chemotherapeutics, but the sensitivity to targeted drugs is still controversial. TGFβ2 could promote expansion of CAFs and infiltration of TAMs, thus participating in the construction of a fibrotic and immunosuppressive TME in PAAD. Targeting TGFβ2 could be a promising therapeutic approach, which needs to be elucidated by clinical and experimental evidences.

A comprehensive review and in silico analysis of the role of survivin (BIRC5) in hepatocellular carcinoma hallmarks: A step toward precision

Hepatocellular carcinoma (HCC) is a complex malignancy driven by the dysregulation of multiple cellular pathways. Survivin, a key member of the inhibitor of apoptosis (IAP) family, plays a central role in HCC tumorigenesis and progression. Despite significant research, a comprehensive understanding of the contributions of survivin to the hallmarks of cancer, its molecular network, and its potential as a therapeutic target remains incomplete. In this review, we integrated bioinformatics analysis with an extensive literature review to provide deeper insights into the role of survivin in HCC. Using bioinformatics tools such as the Human Protein Atlas, GEPIA, STRING, TIMER, and Metascape, we analyzed survivin expression and its functional associations and identified the top 20 coexpressed genes in HCC. These include TK1, SPC25, SGO2, PTTG1, PRR11, PLK1, NCAPH, KPNA2, KIF2C, KIF11, HJURP, GTSE1, FOXM1, CEP55, CENPA, CDCA3, CDC45, CCNB2, CCNB1 and CTD-2510F5.4. Our findings also revealed significant protein-protein interactions among these genes, which were enriched in pathways associated with the FOXM1 oncogenic signaling cascade, and biological processes such as cell cycle regulation, mitotic checkpoints, and diseases such as liver neoplasms. We also discussed the involvement of survivin in key oncogenic pathways, including the PI3K/AKT, WNT/β-catenin, Hippo, and JAK/STAT3 pathways, and its role in modulating cell cycle checkpoints, apoptosis, and autophagy. Furthermore, we explored its interactions with the tumor microenvironment, particularly its impact on immune modulation through myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages, and natural killer cell function in HCC. Additionally, we highlighted its involvement in alkylglycerone phosphate synthase (AGPS)-mediated lipid reprogramming and identified important gaps in the survivin network that warrant further investigation. This review also examined the role of survivin in cancer stemness, inflammation, and virally mediated hepatocarcinogenesis. We evaluated its potential as a diagnostic, prognostic, predictive, and pharmacodynamic biomarker in HCC, emphasizing its relevance in precision medicine. Finally, we summarized emerging survivin-targeted therapeutics and ongoing clinical trials, underscoring the need for novel strategies to effectively target survivin in HCC.

Metformin regulates ferroptosis in Skin cutaneous melanoma via ATF3/NRF2 axis

BACKGROUND

To explore the effects of metformin on the proliferation and ferroptosis of skin cutaneous melanoma (SKCM) and its potential molecular mechanisms, providing a new theoretical basis and strategy for the treatment of cutaneous melanoma.

METHODS

The CCK-8 experiment was used to detect the effect of metformin on the proliferation of skin cutaneous melanoma cells. Kits were used to detect glutathione (GSH) content, reactive oxygen species (ROS), lipid peroxide (LPO), and malondialdehyde (MDA) levels to evaluate ferroptosis-related indicators. RNA-seq sequencing and related analyses were used to screen differentially expressed genes and explore their involved biological functions and signaling pathways. Western blot was used to detect the expression levels of ATF3 and NRF2 proteins and analyze the regulatory effect of metformin on the ATF3/NRF2 axis.

RESULTS

Metformin significantly reduced the proliferation ability of skin cutaneous melanoma cells. The treated cells showed a decrease in GSH content and an accumulation of ROS, LPO, and MDA, suggesting that ferroptosis was regulated. RNA-seq analysis found 2068 differentially expressed genes, of which 897 were up-regulated and 1171 were down-regulated. The related pathways such as iron metabolism disorders and ferroptosis were activated. After metformin treatment, the expression of ATF3 mRNA in cells increased and was positively correlated with the concentration, while the expression in SKCM tissues decreased. At the same time, the expression of ATF3 protein increased and the expression of NRF2 protein decreased, suggesting that metformin may induce ferroptosis through the ATF3/NRF2 axis.

CONCLUSION

Metformin can induce ferroptosis by regulating ATF3/NRF2 axis, which may be a novel strategy for improving the treatment of skin cutaneous melanoma.

MiR-125b suppresses bladder Cancer cell growth and triggers apoptosis by regulating IL-6/IL-6R/STAT3 axis in vitro and in vivo

Bladder cancer (BLCA) is an aggressive malignancy characterized by limited therapeutic options and a poor prognosis. Research has indicated that abnormally expressed miRNAs play a significant role in the pathogenesis of BLCA, although the specific mechanisms remain unclear. MiR-125b plays a tumor suppressor role in a variety of cancers and affects the biological processes of cancer cells such as proliferation, invasion, migration and apoptosis by regulating different signaling pathways. Elucidation of the molecular mechanisms underlying miR-125b may provide clinical therapeutic strategies for bladder cancer. Here, miR-125b was downregulated whereas its targets IL-6R and STAT3 were upregulated in BLCA, as evidenced by bioinformatics analysis. Kaplan-Meier analysis confirmed that miR-125b serves as an independent prognostic factor linked to overall survival (OS) in patients with bladder cancer. Furthermore, overexpression of miR-125b significantly inhibited BLCA cell proliferation, migration, and invasion, while promoting apoptosis, as evidenced by an increased Bax/Bcl-2 ratio and activated cleaved caspase-3. Further investigations demonstrated that miR-125b directly targets and downregulates both IL-6R and STAT3. In a xenograft model, miR-125b overexpression effectively inhibited tumor growth in bladder cancer by blocking IL-6/IL-6R and STAT3 signaling pathways. Collectively, these findings broaden our understanding of the mechanism by which miR-125b acting as a BLCA suppressor in apoptotic regulation by targeting the IL-6/IL-6R/STAT3 signaling pathway, providing novel insights regarding the design of novel miRNA based therapeutic strategies against BLCA.

Comprehensive assessment of cleavage and polyadenylation specificity factors in hepatocellular carcinoma: Expression, prognostic significance and immune infiltration analysis

Hepatocellular carcinoma (HCC), a prevalent and highly malignant form of liver cancer, poses significant global health challenges. Previous studies have suggested that alterations in cleavage and polyadenylation specificity factors (CPSFs) play a role in the development and prognosis of HCC. Despite these insights, a thorough evaluation of CPSFs' expression levels, prognostic value and association with immune infiltration in HCC is lacking. To address this gap, the present study conducted a systematic analysis leveraging multiple bioinformatics databases to elucidate the functions of CPSFs in HCC. To comprehensively investigate the role of CPSFs in HCC, a diverse array of bioinformatics tools and publicly accessible datasets were utilized. The present study investigated the gene expression patterns, clinicopathological correlations, and diagnostic and prognostic capabilities of CPSFs. Furthermore, genetic variations, co-expression networks and the role of CPSFs in immune cell infiltration and tumor-related pathways were examined. To elucidate the biological functions of CPSF-associated genes, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were integrated. For experimental validation, reverse transcription-quantitative polymerase chain reaction was used to assess gene expression and the Cell Counting Kit-8 assay was utilized to evaluate the effects of CPSFs on HCC cell proliferation. Our analysis offers valuable insights into the molecular mechanisms through which CPSFs contribute to HCC progression. The current findings suggest that CPSFs, particularly CPSF1, CPSF3, CPSF4 and CPSF6, exhibit significant transcriptional upregulation in HCC, with their overexpression closely tied to advanced tumor progression. These CPSFs showed diagnostic and prognostic significance in HCC. Additionally, CPSF expression was associated with immune cell infiltration and activation status. Functional enrichment analysis indicated that CPSF1, CPSF3, CPSF4, CPSF6 and CPSF7 are involved in cancer-related signaling pathways, highlighting their role in tumor immune modulation. Experimental validation demonstrated that the expression of CPSF3 and CPSF7 was notably greater in the HCC cell lines than in the normal liver cells. Knockdown of CPSF3 and CPSF7 inhibited HCC cell proliferation, suggesting their potential oncogenic roles. This research offers an in-depth evaluation of the expression patterns, prognostic relevance and immune modulation-related functions of CPSFs in HCC. The observed upregulation of CPSFs in HCC, coupled with their association with poor clinical outcomes and immune system activation, highlights their potential as prognostic indicators. Nonetheless, additional experimental studies are needed to fully elucidate the molecular mechanisms and clinical significance of CPSFs in HCC.

Suppression of NRF2 by photodynamic action to enhance bortezomib-triggered DNA damage for synergistic colorectal cancer therapy

Anti-tumor agent bortezomib (BTZ) showed poor efficacy in colorectal cancer (CRC), which is attributed to the high expression of KEAP1-NRF2, an essential anti-oxidative system. Oxidative DNA damage is one of the critical mechanisms by which photodynamic therapy (PDT) induces apoptosis in tumor cells, which can be considered an important tool for early non-invasive treatment of CRC. The present work aims to explore the role and mechanism of PDT synergizing with BTZ in the treatment of CRC. The findings showed slight decrease in cell viability in BTZ-treated CRC cells of SW480 and SW620. KEAP1-NRF2 was highly expressed in CRC as revealed by GEPIA, TIMER databases, and in vitro experiments, conferring antioxidant activity. Further investigation revealed BTZ bound KEAP1, resulting in KEAP1-NRF2 decoupling, which was manifested as downregulation of KEAP1 and upregulation of NRF2. CO-IP test provides in-depth confirmation that BTZ impaired NRF2 ubiquitination. When SW480 and SW620 cells were co-treated with the chlorin e6 (Ce6)-PDT and BTZ, the expression of NRF2 was reduced with increased ROS generation and enhanced DNA damage. The combination of PDT and BTZ exhibited robust anti-CRC efficacy, characterized by increased apoptosis in SW480 and SW620 cells and dramatic inhibition of tumor growth in SW480 cell-bearing mice. To summarize, Ce6-mediated PDT combined with BTZ suppresses NRF2 and thus enhances DNA damage against CRC. The present study uncovered the molecular mechanism of redox in CRC and recommends an effective intervention strategy with PDT.

Non-canonical Wnt co-receptors ROR1/ROR2 are differentially regulated by hypoxia in colon cancer cells

ROR1 and ROR2 co-receptors are transducers of non-canonical Wnt responses that promote an aggressive phenotype in several cancer types, including colon cancer. It has been demonstrated that hypoxia promotes tumor progression through the action of Hypoxia Inducible Factors (HIFs). An in silico analysis revealed that ROR2 is overexpressed in the advanced clinical stages of colon cancer. In line with this, ROR1 and ROR2 were found to be only expressed in malignant colon cells compared to non-malignant ones. The blockade of either ROR1 or ROR2 impaired colon cancer cells' colony formation abilities and the migration capacity of them. Additionally, the silencing of the ROR2 co-receptor blocked the metastatic ability of colon cancer cells in a xenografted mice model. We found that while silencing HIF-1α did not significantly reduce ROR1 or ROR2 expression, inhibiting HIF-2α and HIF-3α expression greatly decreased the protein levels of both co-receptors in colon cancer cells. The HIF-1α subunit expression is induced in acute hypoxia, whereas HIF-2α and HIF-3α show higher activity in chronic hypoxia, which may be functionally relevant since hypoxia induced a decrease in the constitutive active β-catenin transcriptional activity in SW480 cells. While both ROR1 and ROR2 stimulate proliferation and migration under normoxic conditions, the exposure of cells to hypoxia increased the expression of ROR1 or ROR2, depending on the Wnt cellular context, Thus, our results indicate that hypoxia partially represses β-catenin transcriptional activity and activates non-canonical Wnt signaling by regulating ROR1/ROR2 expression to induce an aggressive migrating and metastatic phenotype in colon cancer cells.

TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets

Publicly accessible expression data produced by large consortium projects like TCGA and GTEx are increasing in number and size at an unprecedented rate. Their utility cannot be underestimated given the diversity of valuable tools widely used to interrogate these data and the many discoveries of biological and clinical significance already garnered from these datasets. However, there remain undiscovered ways to mine these rich resources and a continuing need to provide researchers with easily accessible and user-friendly applications for complex or bespoke analyses. We introduce TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT), a bioinformatics application automating the stratification and subsequent differential expression analysis of cohort data to provide further insights into gene regulation. TRANSECT works by defining two groups within a cohort based on disparate expression of a gene or a gene set and subsequently compares the groups for differences in global expression. Akin to reverse genetics minus the inherent requirement of in vitro or in vivo perturbations, cell lines or model organisms and all the while working within natural physiological limits of expression, TRANSECT compiles information about global transcriptomic change and functional outcomes. TRANSECT is freely available as a command line application or online at https://transect.au.

Identification of ZNF384 as a regulator of epigenome in leukemia

Leukemia is a complex hematologic cancer driven by genetic and epigenetic changes that impact gene expression. Understanding these molecular mechanisms is essential for improving leukemia diagnosis and prognosis. This study examines the role of the zinc finger protein ZNF384 in the epigenome and its influence on gene regulation in leukemia. We analyzed next-generation sequencing data from The Encyclopedia of DNA Elements (ENCODE), integrating datasets such as chromatin immunoprecipitation sequencing (ChIP-seq) of ZNF384 and regulatory histone marks, RNA sequencing (RNA-seq), and Hi-C data from K562 and GM12878 cells. Additionally, we used RNA-seq from K562 ZNF384 knock-down (KD) cells generated via CRISPR interference (CRISPRi) to validate our findings. This enabled us to explore the chromatin interaction patterns of ZNF384 and its regulatory impact. Our results demonstrate that ZNF384 associates with promoters and enhancers in K562 and GM12878 cells, facilitating increased transcription levels. We also found ZNF384 enriched at topologically associating domain (TAD) boundaries and chromatin loops, suggesting a role in three-dimensional (3D) chromatin organization. Furthermore, we identified a significant binding of ZNF384 at SINE-Alu elements in both K562 and GM12878 cells. In summary, this study highlights the regulatory role of ZNF384 in the leukemia epigenome and its impact on gene expression. Understanding the oncogenic implications of ZNF384 may improve leukemia diagnosis and prognosis.

KLF13 promotes esophageal cancer progression and regulates triacylglyceride and free fatty acid metabolism through GPIHBP1

Kruppel-Like Factor 13 (KLF13) has strong effects on cancer occurrence and progression. Nevertheless, the role of KLF13 in oesophagal cancer (EC) remain elusive. In this study, we detected the expression of KLF13 in EC tissues and cells using immunohistochemistry, western blot, and real-time PCR, and found that KLF13 was upregulated in EC tissues and cells compared to normal controls. High expression of KLF13 indicated a poor prognosis for EC patients. Further, function studies in vitro and in vivo were performed to explore the role of KLF13 in EC cell progression. The results revealed that KLF13 knockdown suppressed EC cell proliferation, migration, epithelial-mesenchymal transition, increased cell apoptosis and cell cycle arrest in vivo and inhibited tumour growth in vitro. Conversely, KLF13 overexpression in EC cells had the opposite consequences. Mechanically, differentially expressed genes downstream of KLF13 were identified by RNA-seq and ChIP-seq. We found that there is a positive correlation between triacylglyceride and free fatty acid levels and KLF13 expression levels. A lipid-related gene, Glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 (GPIHBP1), was identified as a downstream gene of KLF13 using luciferase and chromatin immunoprecipitation assays, whose expression was positively regulated by KLF13. Finally, in vitro and in vivo recovery assays using shRNAs and overexpression plasmids confirmed that KLF13 has an oncogenic role in EC progression through GPIHBP1. Collectively, KLF13 can promote EC progression, triacylglyceride and free fatty acid metabolism through GPIHBP1. Therefore, molecular therapies targeting KLF13 and GPIHBP1 may be effective treatments against EC.

RUNX1/SLAMF3 Axis Drives Immunosuppression to Contribute to Colorectal Cancer Liver Metastasis by Blocking Phagocytosis and Depleting C1QC+ Tumor-Associated Macrophages

Colorectal cancer liver metastasis (CRLM) is a leading cause of death in colorectal cancer (CRC) patients and is characterized by an immunosuppressive tumor microenvironment (TME). This study employs mouse in vivo selection to isolate highly metastatic CRLM derivatives for profiling their transcriptomic, proteomic, and metabolomic alterations associated with CRLM. Notably, the expression of SLAMF3 is significantly upregulated in CRLM derivatives and its knockdown effectively suppresses CRLM in mice. RUNX1 transcriptionally upregulates SLAMF3 expression and combined targeting of the RUNX1/SLAMF3 axis synergistically suppresses liver metastasis in mice. In parallel, SLAMF3 suppresses macrophage-mediated phagocytosis of CRC cells through the SHP-1/2/mTORC1 pathway. Conversely, SLAMF3 knockdown promotes M1 polarization in liver metastases and activates the CCL signaling pathway between macrophages and CD8+ T cells. It also reduces the exhausted CD8+ T cells in liver metastases and the expression of inhibitory receptors PD-1 and TIM-3, thus alleviating the immunosuppressive TME. Clinically, activation of the RUNX1/SLAMF3 axis is closely associated with CRLM progression and correlates with a reduced proportion of clinically beneficial C1QC⁺ tumor-associated macrophages (TAMs). Collectively, these findings identify the RUNX1/SLAMF3 axis as a key driver of immunosuppressive TME remodeling and CRLM progression, highlighting its potential as a promising therapeutic target for CRLM.

Integrated pan-cancer analysis revealed therapeutic targets in the ABC transporter protein family

Next-generation sequencing technology enables uniform and impartial assessment of cancer diagnoses and prognosis. However, such studies are mostly type-specific, and capturing shared genomic abnormalities responsible for neoplastic transformation and progression is a challenging task. Pan-cancer analysis offers insights into the shared and unique molecular mechanisms driving cancer. We conducted an integrated gene-expression analysis using 10,629 samples from 30 distinct cancer types characterized by The Cancer Genome Atlas (TCGA). A gene co-expression network was constructed and genes overlapping between the selected modules and Differentially Expressed Genes (DEGs) were designated as genes of interest. Following a comprehensive literature review, ATP binding cassette subfamily A member 10 (ABCA10) and ATP binding cassette subfamily B member 5 (ABCB5) were selected as key candidates for downstream analysis due to the absence of systematic pan-cancer analysis of these genes. This study presents a unique contribution as the first comprehensive pan-cancer analysis of ABCA10 and ABCB5, highlighting their roles in tumor biology and clinical outcomes. We employed a variety of bioinformatics tools to explore the role of these genes across different tumors. Our research demonstrated that ABCA10 shows reduced expression, while ABCB5 displays variable expression patterns across tumors, indicating their opposing roles and flexible functions in pan-cancer. In many cancer patients, these expression patterns are correlated with worse survival outcomes. Furthermore, immunotherapy responses and immune infiltration across a variety of tumor types are associated with the expression levels of both ABCA10 and ABCB5. These results imply that ABCA10 and ABCB5 could serve as valuable predictive markers and potential therapeutic targets across various cancers.

Systematic Exploration of Potential Toxicity Targets and Molecular Mechanisms of Emerging Short-Chain PFAS Substitutes: PFBA- and PFBS-Induced Hepatocellular Carcinoma Based on Toxicity Network Analysis, Machine Learning, and Biomimetic Calculations

Perfluorobutanoic acid (PFBA) and perfluorobutanesulfonic acid (PFBS) are short-chain alternatives to traditional perfluoroalkyl and polyfluoroalkyl substances (PFASs). Long-term exposure to these pollutants is closely associated with hepatocellular carcinoma (HCC). However, the toxic targets and mechanisms underlying PFBA- and PFBS-induced HCC remain unclear. To address this knowledge gap, this study employed a multifaceted approach encompassing network toxicology, molecular docking, and molecular dynamic simulation. Thirty-six core targets associated with PFBA- and PFBS-induced HCC were identified, and 12 key genes were initially screened through network toxicity analysis. Subsequently, based on the TCGA and ICGC datasets, three classical algorithms were applied to screen key genes: PPARG, ESR1, and ALB. Further exploration of the HCC-related dataset from the GEO database identified six critical genes: PPARG, ESR1, CD36, ABCA1, ACACA, and ALB. Survival analysis and ROC analysis based on the TCGA dataset revealed and validated the strong association between the expression levels of key genes (PPARG, ESR1, and ACACA). Single-gene GSEA showed that these three key genes may induce HCC through multiple biological pathways via interfering with the normal growth and development of hepatocytes and promoting inflammation and cell proliferation. Ultimately, molecular dynamics demonstrated the strong binding affinities between PFBA, PFBS, and the three protein receptors, with the best stability and flexibility of the interaction between PFBS and PPARG. These findings provide insights into the theoretical foundation for applying network toxicology, molecular docking, and molecular dynamic simulations in environmental pollutant research.

Unraveling the Oncogenic Characteristics of the Cytolinker, Plectin, in Esophageal Squamous Cell Carcinoma

BACKGROUND & AIMS

Tissue mechanics involved in carcinogenesis by regulating cell morphology and structure, cell-cell, and cell-extracellular matrix (ECM) interactions are not fully understood. Plectin, a cytolinker and a critical component of the cell-ECM adhesion complex hemidesmosome (HD), plays an important role in the regulation of epithelial tissue mechanics, but its functions in carcinogenesis remain elusive.

METHODS

We used cellular and molecular methods and multiple systems, including a 2-dimensional (2-D) esophageal keratinocyte Ca2+-dependent differentiation system, a 3-dimensional (3-D) esophageal keratinocyte organoid system, and tissue samples of normal rat and human esophageal stratified squamous epithelium (SSE), N-nitroso-N-methylbenzylamine (NMBzA)-induced rat esophageal squamous cell carcinoma (ESCC), and human ESCC, to determine the role(s) of plectin in regulating SSE homeostasis and ESCC carcinogenesis.

RESULTS

We show that plectin is ubiquitously expressed in all proliferative and differentiative cell types in esophageal SSE. However, the localization of plectin in different cell types is controlled by plectin crosslinking to different macromolecular structures, such as HD, desmosome (DSM), and cytoskeletal filaments, and its expression is regulated by the ESCC oncogenic drivers and transcription factors, p63 and/or Notch1. Plectin functions by coupling plectin-associated HD, DSM, and cytoskeletal components together with plectin regulators p63 and Notch1, to maintain cell anchorage, proliferation/differentiation, and stratification of esophageal SSE tissue homeostasis. Perturbation of plectin expression and localization leads to the disruption of SSE homeostasis and the involvement in ESCC carcinogenesis.

CONCLUSIONS

Plectin is involved in maintaining SSE homeostasis, and misexpression of plectin through its genetic alterations or transcriptional dysregulations perturbs the compositions, stoichiometries, and localizations of plectin, HD, DSM, and the cytoskeleton underlying the oncogenic characteristics of plectin.

Potassium Iodide Induces Apoptosis in Salivary Gland Cancer Cells

Salivary gland cancers (SGCs) pose a therapeutic challenge due to their aggressive nature and limited treatment options. Ion transporters, particularly the sodium/iodide symporter (SLC5A5), which transport iodine in the form of iodide anion (I-) into cells, have emerged as potential therapeutic targets in tumors of glandular origin. Our research indicates that SLC5A5 is expressed predominantly in ductal cells of human and murine SGC cells. We assessed the effects of potassium iodide (KI), a source of iodide ions. KI treatment reduced SGC cell proliferation and viability without impacting migration. KI increased ROS levels and triggered caspase-dependent apoptosis, as indicated by the upregulation of the pro-apoptotic protein BAX, downregulation of the anti-apoptotic protein Bcl-2, and induction of SGC cell shrinkage. KI did not affect NF-κB or TNF-α and SLC5A5 expression. Adding the antioxidant N-acetylcysteine reversed KI-induced growth inhibition, underscoring ROS-induced oxidative stress's crucial role in growth inhibition. While KI administered in drinking water to mice increased epidermal growth factor (EGF) expression in non-malignant salivary gland tissues, KI decreased EGF receptor (EGFR) expression in malignant SGC cell cultures, where EGFR signaling is frequently dysregulated in SGCs but promoted AKT phosphorylation. Combining KI and anti-EGFR treatment did not yield synergistic anti-SGC cell effects. The study underscores the therapeutic potential of KI as a standalone treatment in vitro for SGC cells. However, the upregulation of EGF in non-malignant tissues and, therefore, the possibility to enhance EGFR-driven signals and AKT phosphorylation after KI treatment in cancer patients could indicate a risk of rendering SGC cells more drug resistant, warranting further investigation to optimize its clinical application.

Elucidating the Anti-Diabetic Mechanisms of Mushroom Chaga (Inonotus obliquus) by Integrating LC-MS, Network Pharmacology, Molecular Docking, and Bioinformatics

Diabetes mellitus is characterized by insulin resistance, impaired glucose homeostasis, and dysregulated glucose metabolism, leading to complications. Inonotus obliquus (Chaga) has shown potential anti-diabetic effects, but the bioactive compounds and molecular targets remain unclear. This study aimed to identify the bioactive components of Chaga and elucidate their anti-diabetic mechanisms using LC-MS compound screening, network pharmacology, molecular docking, and bioinformatics analyses. Chaga extract was prepared using 95% ethanol, and bioactive compounds were identified through UHPLC-QE-MS analysis. Target prediction was conducted using Swiss Target Prediction and SEA databases, while diabetes-related targets were retrieved from GeneCards. A PPI network was constructed using STRING and analyzed for GO and KEGG enrichment. Molecular docking was performed using AutoDock Vina, and gene expression was validated using the GSE7014 dataset and GEPIA database, with immune cell infiltration analyzed through CIBERSORT. UHPLC-QE-MS identified 30 bioactive compounds from Chaga, including 21 triterpenoids, four flavonoids, and two diterpenoids. Network pharmacology predicted 432 anti-diabetic targets, with 167 core targets enriched in key pathways, primarily the PI3K/Akt signaling pathway. Molecular docking revealed strong binding affinities of five key compounds with seven core targets. Bioinformatics analysis validated significant expression changes in ESR1, IL6, and SRC, while immune cell infiltration analysis showed correlations between core targets and immune cell subtypes. This study highlights the anti-diabetic potential of Chaga by identifying key bioactive compounds and their interactions with central diabetic targets. Further in vitro and in vivo studies are needed to validate these findings.

Molecular Targets and Mechanisms of Piperine Against Breast Cancer: A Network Pharmacology, Molecular Docking Analysis, and Toxicity Prediction

Breast cancer is still one of the major causes of cancer-related death worldwide, which highlights the need for cutting-edge therapeutic strategies. An alkaloid called piperine, which comes from Piper longum, has demonstrated encouraging anticancer effects. Piperine modulates different cancer signaling pathways and enzymes such as P53, apoptosis, and cell cycle regulation. Protein function and signaling pathway enrichment studies were made easier using the DAVID Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, while the SwissTarget Prediction database was used to identify the target genes for piperine. Using STRING, Cytoscape, and the CytoHubba degree approach, protein-protein interaction networks were investigated. Ninety-three possible piperine target sites in breast cancer were found, most of which were connected to important cancer pathways. The therapeutic effect of piperine was demonstrated by analysis of KEGG pathways, molecular functions, cellular components, and biological processes. Following the identification of the top ten hub gene targets, further molecular docking and dynamic simulations (iMODS server) were performed on SRC, HSP90AA1, MTOR, and MDM2 to evaluate binding affinity, flexibility, and stability. These results were confirmed by survival, correlation, and Humane FP analyses, highlighting the function of piperine in focusing on the genes responsible with pathogenic breast cancer. This thorough investigation opens the door for more research and clinical uses by demonstrating piperine's potential as a new therapeutic agent for the treatment of breast cancer.

Glucosylceramide Synthase, a Key Enzyme in Sphingolipid Metabolism, Regulates Expression of Genes Accounting for Cancer Drug Resistance

Emergent cancer drug resistance and further metastasis can mainly be attributed to altered expression levels and functional activities of multiple genes of cancer cells under chemotherapy. In response to challenge with anticancer drugs, enhanced ceramide glycosylation catalyzed by glucosylceramide synthase (GCS) confers drug resistance and enrichment with cancer stem cells. p53 mutations, which gain function in tumor progression, are prevalently extant in ovarian cancers. Via integrated gene expression assessments, we characterized GCS-responsive genes in ovarian cancer cells treated with dactinomycin. NCI/ADR-RES cells dominantly expressed a p53 mutant (7 aa deleted in exon-5) and displayed anti-apoptosis; however, silencing GCS expression rendered these cells sensitive to dactinomycin-induced apoptosis. Microarray analyses of NCI/ADR-RES and its GCS transfected sublines found that elevated GCS expression or ceramide glycosylation was associated with altered expression of 41 genes, notably coding for ABCB1, FGF2, ALDH1A3, apolipoprotein E, laminin 2, chemokine ligands, and IL6, with cellular resistance to induced apoptosis and enrichment with cancer stem cells, promoting cancer progression. These findings were further corroborated through integrated genomic analyses of ovarian cancer from The Cancer Genome Atlas (TCGA) and cancer resistance to platinum-based chemotherapy. Altogether, our present study indicates that altered ceramide glycosylation can modulate expression of these GCS-responsive genes and alter cancer cell attributes under chemotherapy.

A panel of three serum microRNAs as a potential diagnostic biomarker for renal cell carcinoma

Hitherto there is no praiseworthy noninvasive methods in the early diagnosis of renal cell carcinoma (RCC). MicroRNAs (miRNAs) could be utilized as molecular markers for diverse malignancies. In this study, we aim to discern potential miRNAs as markers for screening RCC. We employed quantitative reverse transcription-polymerase chain reaction (RT-qPCR) to detect expression levels of candidate miRNAs in serum specimens of 108 RCC patients and 112 health volunteers. Diagnostic values of miRNAs were appraised, and panel was constructed by dint of receiver operating characteristic curves, the area under the ROC curve and backward stepwise logistic regression analysis. Moreover, we capitalized on bioinformatics analysis for exploration of miRNAs biological functions. The expression of five miRNAs (miR-30c-5p, miR-142-3p, miR-206, miR-223-3p, miR-200c-5p) were markedly alteration in serum specimens of RCC patients and health subjects. A three-miRNA panel combining miR-30c-5p, miR-142-3p and miR-206 was constructed and could discriminate RCC patients and healthy subjects satisfactorily with 0.872 (0.811-0.919, P < 0.001) AUC, 81.25% sensitivity and 86.90% specificity. ATF3 and MYC seem to be potential targets of the three-miRNA panel. The novel miRNA-based panel may perform as potential noninvasive markers to discriminate RCC patients and healthy subjects in advance.

Dissecting PTPN7-driven aggressiveness in IDH-wildtype astrocytomas: multi-omics, clinical validation, and spatial transcriptomics for prognostic insights

BACKGROUND

Gliomas, particularly IDH-wildtype astrocytomas, remain highly aggressive and resistant to current therapies. Despite advances in molecular classification, effective therapeutic targets are still limited. Consequently, identifying new targets is essential to improve patient survival. PTPN7, a tyrosine phosphatase implicated in MAPK signaling, is known to play roles in various malignancies but remains underexplored in gliomas. This study examines the prognostic significance, spatial distribution, and immune-related functions of PTPN7, aiming to elucidate its potential as a prognostic role and therapeutic target in glioma treatment.

MATERIALS AND METHODS

We analyzed PTPN7 mRNA expression in gliomas via TCGA, CGGA, and single-cell RNA sequencing (GSE131928 and GSE89567). Kaplan determined prognostic significance-Meier and uni-/multi-variate Cox survival analyses. Gene set enrichment analysis (GSEA) was used to identify dysregulated pathways, immune signatures, and cell-type enrichments. We also applied CIBERSORT to evaluate the relationships between PTPN7 expression and 12-principal cell states and 22 immune populations. Spatial transcriptomics (Ivy Glioblastoma Atlas, 10 × Genomics Visium) mapped PTPN7 distribution; these findings were corroborated by immunohistochemistry-validated protein expression in 70 cases.

RESULTS

Pan-cancer analysis revealed PTPN7 overexpression in multiple malignancies, including glioma. Notably, PTPN7 was significantly elevated in IDH-wildtype astrocytomas, correlating with higher tumor grades and poorer overall survival. GSEA indicated that high PTPN7 is linked to T-cell differentiation, macrophage/monocyte activation, and dendritic cell-associated pathways. Both immune deconvolution and single-cell analyses showed that PTPN7 positively correlates with myeloid series and T-cell populations, supported by additional GSEA findings. In the Ivy dataset and spatial transcriptomics, PTPN7 was concentrated in peri-necrotic, cellular tumor, and slightly lower in the infiltrating border regions, consistent with immune interaction sites. Immunohistochemical data further demonstrated high PTPN7 expression tracks with increased tumor grade, reaching statistical significance in IDH-wildtype astrocytomas and confirming its clinical relevance.

CONCLUSION

This study positions PTPN7 as a prognostic biomarker and immune modulator in gliomas, particularly IDH-wildtype astrocytomas. Its expression correlates with tumor aggressiveness and immune infiltration, potentially driving glioma progression. Targeting PTPN7 may disrupt immune evasion and support tumor eradication, indicating a promising therapeutic avenue in immunotherapy-based strategies.

Homeobox C6 plays an oncogenic role in bladder cancer

BACKGROUND

Bladder cancer (BLCA) is a common urological tumor. Homeobox C6 (HOXC6) is an HOX family gene that has an oncogenic effect in various malignancies.

AIM

To investigate the expression and function of HOXC6 in BLCA.

METHODS

This study employed immunohistochemistry, along with global chip and sequencing data for BLCA, to comprehensively evaluate the protein and mRNA expression of HOXC6 in BLCA. RNA interference technology was employed to knock down the mRNA expression of HOXC6 in BLCA cells, and the impact of reduced HOXC6 expression on cellular function was assessed. Additionally, we explored the potential mechanisms of HOXC6 in BLCA by aggregating HOXC6 chromatin immunoprecipitation sequencing data.

RESULTS

The immunohistochemistry results, sequencing data, and microarray data revealed that both the mRNA and protein expressions of HOXC6 in BLCA were notably greater than the expressions in non-cancerous tissues. Knocking down the expression of HOXC6 considerably limited the function of cell proliferation, migration, and invasion abilities of BLCA cells, elevated cell apoptosis, and triggered the G0/G1 phase blockade. The potential target genes of HOXC6 were enriched in pathways such as chemical carcinogenesis and reactive oxygen species. A notable positive correlation between HOXC6 mRNA expression and its target gene timeless circadian regulator (TIMELESS) was revealed. Notable binding peak signals for HOXC6 were identified in the promoter region of TIMELESS.

CONCLUSION

HOXC6 is upregulated in BLCA and may influence the cellular functions of BLCA by regulating the expression of the target gene TIMELESS.

piR-RCC Suppresses Renal Cell Carcinoma Progression by Facilitating YBX-1 Cytoplasm Localization

PIWI-interacting RNAs (piRNAs), a novel category of small non-coding RNAs, are widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Little is known about their function and mechanism in renal cell carcinoma (RCC) progression. Herein, a down-regulated piRNA in RCC, termed piR-hsa-28489 (designated as piR-RCC), is identified to impede RCC progression both in vivo and in vitro. Mechanistically, piR-RCC directly interacts with Y-box binding protein 1 (YBX-1), thus impeding p-AKT-mediated YBX-1 phosphorylation and its subsequent nuclear translocation. Moreover, YBX-1 coordinates the transcription of ETS homologous factor (EHF) as a repressor factor. Consequently, piR-RCC enhances EHF expression, leading to the inhibition of RCC proliferation and metastasis. Based on these, a biomimetic nanoparticle platform is constructed to achieve RCC-specific targeted delivery of piR-RCC. The nanoparticles are fabricated using a cell membrane coating derived from cancer cells and used to encapsulate and deliver piR-RCC plasmids to renal orthotopic implantation in mice, hindering RCC progression. This study illustrates piR-RCC/YBX-1/EHF signaling axis in RCC, offering a promising therapeutic avenue for RCC.

Ero1a, the most strongly hypoxia-induced protein in PASMCs, promotes the development of hypoxia- and monocrotaline-induced pulmonary hypertension in rats

AIMS

Pulmonary hypertension (PH) is a progressive and life-threatening condition characterized by elevated pressure in the pulmonary circulation, leading to right heart dysfunction and ultimately heart failure. Pulmonary artery smooth muscle cells (PASMCs) are key players in group 3 PH (due to lung diseases and/or hypoxia) progression, where their aberrant proliferation and migration drive vascular remodeling. Dysregulated proteins in PASMCs are critical in PH development. Our research was designed to investigate the most promising potential therapeutic targets for PH.

MATERIALS AND METHODS

Proteomics was used to identify the most significantly upregulated protein in PASMCs under hypoxia. siRNA or plasmid transfection was used to silence or overexpress Ero1a. The proliferation, migration, and apoptosis of PASMCs were assessed respectively. Both hypoxia and monocrotaline-induced pulmonary hypertension model were established in animals. The expression of Ero1a was reduced to explore its role in PH. Bioinformatic analysis were conducted to investigate the signaling pathways involved in the disease progression.

KEY FINDINGS

Ero1a was confirmed as the most significantly upregulated protein in PASMCs under hypoxia. Silencing Ero1a reduced PASMC proliferation, migration, and apoptosis resistance under both normoxic and hypoxic conditions, while overexpression of Ero1a had the opposite effect. Exposure of rats to hypoxia, along with intraperitoneal injection of MCT solution, induced PH. However, knockdown of Ero1a alleviated all these pathological features. The HIF1-Ero1a-Apelin/APJ signaling axis was speculated to mediate the functional role of Ero1a in PH.

SIGNIFICANCE

Our study identifies that targeting Ero1a may represent a promising therapeutic strategy for pulmonary hypertension.

Induction of cell death by the CXCR2 antagonist SB225002 in colorectal cancer and stromal cells

Molecular targeted therapies have had great success in cancer treatment due to their high efficacy and selectivity. Identifying specific prognostic/predictive biomarkers helps clinicians stratify patients according to individual characteristics and improves patient quality of life in terms of disease control and survival. In our previous work, we identified Interleukin-8 as an important prognostic biomarker according to specific genomic alterations of colorectal cancers, leading us to investigate the effects of its axis inhibition, by targeting the Interleukin-8 receptors CXCR1 and CXCR2. Here, we show that dual CXCR1/2 inhibition does not affect colorectal cancer cell viability, whereas CXCR2-selective inhibition by SB225002 reduces cell viability in responder colorectal cancer cell lines. More specifically, these responder cells undergo programmed cell death upon SB225002 treatment, while non responder cell lines incur in a reversible G2/M arrest. Interestingly, the same response in terms of inhibition of cell viability also occurs in the stromal compartment (normal fibroblasts): however, in this compartment, the G2/M block is non reversible, hence leading to non-apoptotic cell death. These findings suggest that SB225002 could be a potential therapeutic agent in colorectal cancer, by affecting not only cell viability, but also tumor-stroma interactions.

LZTS2 methylation as a potential diagnostic and prognostic marker in LIHC and STAD: Evidence from bioinformatics and in vitro analyses

The rising mortality rate from cancer, driven by the absence of reliable biomarkers, highlights the pressing need for advanced diagnostic and prognostic strategies. This study investigates LZTS2's role as a pan-cancer biomarker, emphasizing its predictive value for immunotherapy and therapeutic targeting. Unlike existing biomarkers such as AFP in hepatocellular carcinoma or HER2 in gastric cancer, which exhibit tissue-specific utility, LZTS2 demonstrates unique cross-cancer applicability, as evidenced by its consistent dysregulation in both liver hepatocellular carcinoma (LIHC) and stomach adenocarcinoma (STAD) alongside emerging associations with other malignancies. Leveraging advanced bioinformatics tools and databases including UALCAN, KM-plotter, and The Cancer Genome Atlas (TCGA), alongside experimental validation in LIHC and STAD cell lines, we analyze LZTS2 expression patterns and their clinical relevance. Notably, LZTS2's dual role-acting as a tumor suppressor in some cancers while promoting oncogenesis in others-distinguishes it from conventional single-function markers, offering novel insights into its regulatory versatility. Our findings reveal that LZTS2 mutations and expression levels are closely associated with cancer progression and patient survival, solidifying its potential as a prognostic biomarker. Notably, LZTS2 expression correlates with various clinicopathological parameters, underscoring its significance in cancer biology. Pathway analysis highlights LZTS2's involvement in critical biological processes, providing actionable insights for therapeutic interventions. Quantitative real-time polymerase chain reaction (qRT-PCR) and quantitative methylation-specific PCR (qMSP) experimental validations confirm these results, further establishing LZTS2's utility as a multi-dimensional biomarker that integrates genetic, epigenetic, and immunological features-a capability rarely observed in existing markers. This comprehensive analysis positions LZTS2 as a pivotal player in cancer progression, opening promising avenues for enhanced clinical management.

GEPIA3: Enhanced drug sensitivity and interaction network analysis for cancer research

The GEPIA series has provided robust and widely used tools for pan-cancer analysis of gene expression data. In the post-genomic era, a major challenge lies in deconvoluting complex regulatory relationship influenced by multiple factors and discovering gene-based precision therapeutics. Here we present GEPIA3, an advanced version of GEPIA that provides a comprehensive analysis of gene/protein interactions across various cancer types. This version facilitates the investigation of treatment sensitivity utilizing both real-world patient data and cell line screens for over 1000 therapeutic agents, as well as the integration of RNA alterations derived from the pan-cancer analysis of whole genomes project. GEPIA3 represents a significant enhancement of the original platform, enabling in-depth exploration of gene regulation and cancer phenotypes, thereby supporting the identification of novel biomarkers and therapeutic targets. GEPIA3 is publicly accessible at https://gepia3.bioinfoliu.com.

USP41 plays carcinogenic roles in human cutaneous melanoma through PI3K/Akt signaling pathway

Cutaneous melanoma is a malignant tumor with a high mortality rate. Ubiquitin-specific protease 41 (USP41) has recently been reported to be overexpressed in various malignancies. However, its role in melanoma remains unclear. Gene Expression Profiling Interactive Analysis (GEPIA) was used to perform pan-cancer analysis using data from the the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Melanoma tissue microarray (TMA), clinical patient tissues, and cells were used to explore USP41 expression profiles by immunohistochemistry (IHC), RT-qPCR or Western blotting. Small interfering RNAs (siRNAs) were used to knock down USP41 in melanoma cells. Cell proliferation, migration, and invasion were assessed using CCK-8, EdU staining, wound healing, and transwell assays, respectively. Cell apoptosis was detected by flow cytometry and TUNEL staining. GEPIA revealed that USP41 is highly expressed in most human cancers, including melanoma. USP41 is overexpressed in melanoma tumor tissues and cells. IHC showed that USP41 was positively stained in melanoma tissues and was significantly correlated with the TNM stage of melanoma. USP41 knockdown inhibited cell proliferation, migration, and invasion while promoting cell apoptosis and inhibiting phosphorylated PI3K, AKT, and mTOR in the PI3K/AKT signaling pathway. The results indicate that USP41 may play a carcinogenic role in melanoma partly via the PI3K/AKT signaling pathway, suggesting that USP41 may be an effective therapeutic target for the treatments of cutaneous melanoma.

Multi-Omics Pan-Cancer Profiling of HSD17B10 Unveils Its Prognostic Potential, Metabolic Regulation, and Immune Microenvironment Interactions

This study systematically analyzed the expression and clinical significance of Hydroxysteroid 17-beta dehydrogenase type 10 (HSD17B10) in 33 cancers by integrating TCGA, GTEx, and other multi-omics databases. HSD17B10 was highly expressed in 14 cancers, like GBM and LGG, but low in 5, such as KIRC. Its expression correlated closely with overall survival (OS) and disease-free survival (DFS). In GBM-LGG, LGG, and other cancers, high HSD17B10 expression was linked to lower survival rates, indicating that it could be an independent prognostic marker. HSD17B10 also had a two-way relationship with the tumor's immune microenvironment. In cancers such as GBM-LGG, high expression correlated positively with immune/stromal scores. However, in most cancers like LUAD, it was negatively associated with B- and T-cell infiltration. Epigenetic analysis showed that low methylation in the HSD17B10 promoter region might drive its high expression in tumors such as SARC, and specific methylation sites (e.g., CG26323797) were significantly related to patient survival. Functional enrichment analysis revealed that HSD17B10 participated in tumor progression by regulating oxidative phosphorylation, mitochondrial metabolism, and RNA methylation. Single-cell and spatial transcriptome data further demonstrated that HSD17B10 had a cell-type-specific expression pattern in colorectal cancer. This study provides a theoretical basis for HSD17B10 as a pan-cancer prognostic marker and therapeutic target.

Gemcitabine resistance by CITED4 upregulation via the regulation of BIRC2 expression in pancreatic cancer

BACKGROUND

Gemcitabine (GEM) is used as a first-line therapy for patients diagnosed with any stage of pancreatic cancer (PC); however, patient survival is poor because of GEM resistance. Thus, new approaches to overcome GEM resistance in PC are urgently needed. Here, we aimed to establish an in vivo drug-resistant PC model and identify genes involved in GEM resistance. We focused on one of these factors, CITED4, and elucidated its mechanisms of action in GEM resistance in PC.

METHODS

L3.6pl, a GEM-sensitive PC cell line, was orthotopically injected into the pancreas of BALB/c nude mice to establish a GEM-resistant PC animal model. Transcriptomic data from control or GEM-resistant tumor-derived cells were analyzed. GEM resistance was evaluated using cell viability, clonogenicity, and apoptosis assays. An apoptosis array was used to identify genes downstream of CITED4. A CITED4 knockout-mediated GEM sensitivity assay was performed in an orthotopic xenograft mouse model using PANC-1 cells, which are GEM-resistant cells.

RESULTS

From the RNA sequencing data of isolated GEM-resistant PC cells and The Cancer Genome Atlas dataset, 15 GEM resistance-related genes were found to be upregulated, including CITED4, the gene encoding a type of CBP/p300-interacting transactivator implicated in several cancers. CITED4 knockdown in drug-resistant cells reduced cell proliferation and migration but increased apoptosis. To identify the molecular mechanism underlying CITED4-mediated induction of GEM resistance, alterations in Baculoviral IAP Repeat Containing 2 (BIRC2) levels were observed using an apoptosis array. BIRC2 expression was downregulated following CITED4 knockdown in GEM-resistant PC cell lines. Furthermore, chromatin immunoprecipitation and promoter assays showed that BIRC2 was directly regulated by CITED4. Consistent with the CITED-knockdown experiments, silencing of BIRC2 increased the sensitivity of L3.6pl-GEM-resistant and PANC-1 cell lines to GEM. Furthermore, CITED4 knockout using the CRISPR-Cas9 system in PANC-1 cells increased the sensitivity to GEM in orthotopic mice. Moreover, elevated CITED4 and BIRC2 expression levels were associated with poorer outcomes in human PC clinical samples.

CONCLUSIONS

Collectively, these results indicate that CITED4 regulates GEM resistance via inhibition of apoptosis by upregulating BIRC2 expression in PC cells. Therefore, CITED4 may serve as a valuable diagnostic marker and therapeutic target for GEM-resistant PC.

Alcohol consumption and esophageal cancer risk: unveiling DLEU2 as a key immune modulator through Mendelian randomization and transcriptomic analysis

Esophageal cancer (EC) is a leading cause of cancer-related mortality globally, with alcohol consumption being a significant risk factor. However, the genetic and molecular mechanisms linking alcohol intake to EC remain unclear. This study utilized Mendelian randomization analysis to establish a causal relationship between alcohol consumption and EC (OR: 4.11 [95% CI 1.83-9.23]). Transcriptomic analysis identified 83 differentially expressed genes (log₂ fold change > 1, false discovery rate [FDR] < 0.05), among which DLEU2 was uniquely transcribed into a long non-coding RNA (lncRNA). Pan-cancer analysis revealed its association with the tumor immune microenvironment and cancer progression. Single-cell RNA sequencing localized DLEU2 expression predominantly to T cells, particularly exhausted subpopulations, and pseudo-temporal analysis demonstrated increased DLEU2 expression during late T cell differentiation stages, co-expressing immune suppression markers, with consistent expression patterns observed across multiple patient-derived samples. Additionally, cell communication analysis suggested that DLEU2 modulates TNF signaling through TNFRSF1A/B pathways, contributing to immune evasion and poor prognosis. These findings position DLEU2 as a pivotal regulator of the immune landscape in EC and a potential prognostic biomarker and therapeutic target.

ZC3H12D gene expression exhibits dual effects on the development and progression of lung adenocarcinoma

While precision oncology requires robust biomarkers, current predictors for lung adenocarcinoma (LUAD) often show limited clinical utility. This study investigates the multifaceted roles of ZC3H12D, a novel immunomodulatory molecule, in LUAD progression and tumor microenvironment regulation. Multi-omics analyses integrated ZC3H12D transcriptomic (511 tumors vs 59 normals), proteomic (74 tumors vs 69 normals), and single-cell RNA-seq data (15 tumors vs 11 normals). Immunohistochemistry validated ZC3H12D expression in 51 matched pairs. Computational biology approaches assessed immune infiltration, genomic instability (TMB/MSI/HRD), and pathway enrichment. Functional validation employed ZC3H12D knockdown in PC9 cells with colony formation and transwell assays. Multi-omics verification confirmed ZC3H12D upregulation in LUAD at both mRNA and protein levels (p < 0.001), with single-cell resolution revealing predominant localization in tumor-infiltrating immune cells. Moreover, ZC3H12D expression positively correlated with immune regulatory genes while inversely associating with genes involved in cellular respiration. Its expression was also linked to clinical markers such as TMB, MSI, HRD, tumor purity, and ploidy. Notably, high ZC3H12D expression revealed Immune-infiltrated microenvironment and favorable prognosis, despite silencing ZC3H12D resulted in significant inhibition of tumor cell proliferation and invasion in vitro (p < 0.001). Our findings demonstrate that high ZC3H12D expression in immune cells appears to enhance antitumor immune activity, whereas lower expression in malignant cells contributes to reduced cellular proliferation and migration. This spatial duality challenges conventional biomarker paradigms and provides mechanistic insights for developing cell type-targeted therapies.

Upregulated Expression of SHMT2 Predicts Poor Survival of Lung Adenocarcinoma

Backgrounds: Serine hydroxy methyltransferase 2 (SHMT2) exerts an essential function in the cellular serine/glycine biosynthesis and one-carbon metabolism. Accumulative evidence revealed that SHMT2 was involved in cancer initiation and development in several types of carcinomas such as glioma, intrahepatic cholangiocarcinoma and colorectal cancer. However, expression and role of SHMT2 in lung adenocarcinoma (LUAD) had not been fully investigated. Methods: Transcriptional information of SHMT2 was retrieved from TCGA database. mRNA and protein expression of SHMT2 were analyzed in LUAD tissues alongside adjacent normal lung tissues using quantitative RT-PCR and immunohistochemical staining. The prognostic significance of SHMT2 in LUAD was assessed through both univariate and multivariate statistical analyses. Results: SHMT2 was higher in LUAD tissues than that in adjacent lung tissues on transcriptional level, mRNA level, and protein level. Elevated SHMT2 protein levels were associated with increased tumor size, positive lymph node metastasis, and more advanced TNM stages. LUAD patients with high SHMT2 level had worse prognosis. Conclusions: Our research indicated that elevated SHMT2 expression is strongly linked to adverse clinical characteristics and poor prognosis in LUAD patients. Consequently, SHMT2 may represent a novel prognosis marker and a promising therapeutic target regarding the treatment of LUAD.

Nebulized inhalation of extracellular vesicles containing SPOCK2 suppresses lung adenocarcinoma progression via MAPK inhibition

Aberrant expression of SPARC/osteonectin, cwcv and kazal-like domains proteoglycan 2 (SPOCK2) plays a role in the development and progression of several human cancers. However, the importance of its expression and function in lung adenocarcinoma (LUAD) remains unclear. The present study aimed to elucidate the role of SPOCK2 in the growth of LUAD and propose a novel therapeutic insight for LUAD through SPOCK2. SPOCK2 protein expression was significantly reduced in LUAD tissues and cells by Immunohistochemical assay and Western blot. CCK-8, colony formation, and Transwell assays were used to demonstrate that SPOCK2 overexpression inhibited both proliferation and migration of LUAD cells in vitro. This inhibition of tumor growth was further confirmed by a LUAD xenograft mouse model in vivo. To explore downstream target signal of SPOCK2 in LUAD, RNA transcriptome sequencing was performed and enrichment analysis showed an association between SPOCK2 expression and the MAPK pathway. Furthermore, HEK293T cells were modified with SPOCK2, and extracellular vesicles (EVs) containing SPOCK2 (SPOCK2-EVs) were collected through ultra-high-speed centrifugation. Interestingly, co-culture with SPOCK2-EVs significantly increased SPOCK2 levels within LUAD cells. Furthermore, SPOCK2-EVs effectively inhibited LUAD growth in vitro and in vivo studies. Because directly injecting SPOCK2-EVs into tumors presents challenges for internal organs, we investigated the efficacy of nebulized SPOCK2-EVs for LUAD treatment. Consistent with our findings from intratumoral injection, nebulized inhalation of SPOCK2-EVs resulted in significant inhibition of LUAD growth. These results strongly suggest that SPOCK2 released by HEK293T-EVs can effectively inhibit LUAD tumor growth and hold promise for future clinical translation in cancer therapy.