An EGFR/HER2-targeted conjugate sensitizes gemcitabine-sensitive and resistant pancreatic cancer through different SMAD4-mediated mechanisms

A heterogeneous graph transformer framework for accurate cancer driver gene prediction and downstream analysis

Accurately predicting cancer driver genes remains a formidable challenge amidst the burgeoning volume and intricacy of cancer genomic data. In this investigation, we propose HGTDG, an innovative heterogeneous graph transformer framework tailored for precisely predicting cancer driver genes and exploring downstream tasks. A heterogeneous graph construction module is central to the framework, which assembles a gene-protein heterogeneous network leveraging the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and protein-protein interactions sourced from the STRING (search tool for recurring instances of neighboring genes) database. Moreover, our framework introduces a pioneering heterogeneous graph transformer module, harnessing multi-head attention mechanisms for nuanced node embedding. This transformative module proficiently captures distinct representations for both nodes and edges, thereby enriching the model's predictive capacity. Subsequently, the generated node embeddings are seamlessly integrated into a classification module, facilitating the discrimination between driver and non-driver genes. Our experimental findings evince the superiority of HGTDG over existing methodologies, as evidenced by the enhanced performance metrics, including the area under the receiver operating characteristic curves (AUROC) and the area under the precision-recall curves (AUPRC). Furthermore, the downstream analysis utilizing the newly identified cancer driver genes underscores the efficacy and versatility of our proposed framework.

Identification of toll-like receptor 2 as a key regulator of neuronal apoptosis in vascular dementia by bioinformatics analysis and experimental validation

BACKGROUND

Vascular dementia (VaD), the second most prevalent type of dementia, lacks a well-defined cause and effective treatment. Our objective was to utilize bioinformatics analysis to discover the fundamental disease-causing genes and pathological mechanisms in individuals diagnosed with VaD.

METHODS

To identify potential pathogenic genes associated with VaD, we conducted weighted gene co-expression network analysis (WGCNA), differential expression analysis, and protein-protein interaction (PPI) analysis. The exploration of potential biological mechanisms involved the utilization of Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis. Moreover, a bilateral common carotid artery stenosis (BCAS) mouse model of VaD was established, and the expression of the hub gene, its relationship with cognitive function and its potential pathogenic mechanism were verified by cognitive behavior tests, cerebral blood flow measurement, Western blotting, and immunofluorescence experiments.

RESULTS

This study identified 293 DEGs from the brain cortex of VaD patients and healthy controls, among these genes, the Toll-like receptor 2 (TLR2) gene was identified as hub gene, and it was associated with the apoptosis-related pathway PI3K/AKT.The BCAS model demonstrated that the use of TLR2 inhibitors greatly enhanced the cognitive function of the mice (p < 0.05). Additionally, there was a notable decrease in the number of apoptotic cells in the brain cortex of the mice (p < 0.01). Moreover, significant alterations in the levels of proteins related to the PI3K/AKT pathway and cleaved-caspase3 proteins were detected (p < 0.05).

CONCLUSIONS

TLR2 plays a role in the pathophysiology of VaD by enhancing the neuronal apoptotic pathway, suggesting it could be a promising therapeutic target.

PHF12 regulates HDAC1 to promote tumorigenesis via EGFR/AKT signaling pathway in non-small cell lung cancer

BACKGROUND

Lung cancer stands as the second most prevalent malignant neoplasm worldwide. Addressing the underlying mechanisms propelling the progression of non-small cell lung cancer is of paramount importance. In this study, we have elucidated the pivotal role of PHF12 in this context.

MATERIALS AND METHODS

We harnessed clinical lung cancer tissue samples and non-small cell lung cancer cell lines to discern the expression pattern of PHF12. In vitro assays probing cell proliferation were conducted to substantiate the functional impact of PHF12. Furthermore, an in vivo Xenograft model was employed to dissect the role of PHF12. Employing ChIP assays and qRT-PCR, we delved into the intricate binding dynamics between PHF12 and HDAC1. Mechanistic insights into the PHF12-HDAC1 axis in lung cancer progression were pursued via RNA-seq and GSEA analyses.

RESULTS

Notably, PHF12 exhibited a substantial upregulation within tumor tissue, concomitant with its correlation to HDAC1. The trilogy of cell proliferation assays, transwell assays, and the Xenograft model collectively underscored the promoting influence of PHF12 on lung cancer proliferation, both in vitro and in vivo. The ChIP assay unveiled the transcriptional regulatory role of PHF12 in governing HDAC1 expression. This correlation extended to both mRNA and protein levels. PHF12 promotes NSCLC progression through regulating HDCA1 expression. Intriguingly, the rescue of function within NSCLC cell lines post PHF12 knockdown was achievable through HDAC1 overexpression. Additionally, our findings unveiled the capacity of the PHF12-HDAC1 axis to activate the EGFR/AKT signaling pathway, thereby further corroborating its significance in lung cancer progression.

CONCLUSION

Our study identified PHF12 as an oncogenic role in lung cancer proliferation and migration for the first time. PHF12 transcriptionally regulate HDAC1 and activate EGFR/AKT signaling pathway in NSCLC progression. PHF12 may serve as an important target in lung cancer therapy.

Induced dual-target rebalance simultaneously enhances efficient therapeutical efficacy in tumors

Multiple gene abnormalities are major drivers of tumorigenesis. NF-κB p65 overactivation and cGAS silencing are important triggers and genetic defects that accelerate tumorigenesis. However, the simultaneous correction of NF-κB p65 and cGAS abnormalities remains to be further explored. Here, we propose a novel Induced Dual-Target Rebalance (IDTR) strategy for simultaneously correcting defects in cGAS and NF-κB p65. By using our IDTR approach, we showed for the first time that oncolytic adenovirus H101 could reactivate silenced cGAS, while silencing GAU1 long noncoding RNA (lncRNA) inhibited NF-κB p65 overactivation, resulting in efficient in vitro and in vivo antitumor efficacy in colorectal tumors. Intriguingly, we further demonstrated that oncolytic adenoviruses reactivated cGAS by promoting H3K4 trimethylation of the cGAS promoter. In addition, silencing GAU1 using antisense oligonucleotides significantly reduced H3K27 acetylation at the NF-κB p65 promoter and inhibited NF-κB p65 transcription. Our study revealed an aberrant therapeutic mechanism underlying two tumor defects, cGAS and NF-κB p65, and provided an alternative IDTR approach based on oncolytic adenovirus and antisense oligonucleotides for efficient therapeutic efficacy in tumors.

Driver Mutations in Pancreatic Cancer and Opportunities for Targeted Therapy

Pancreatic cancer is the sixth leading cause of cancer-related mortality globally. As the most common form of pancreatic cancer, pancreatic ductal adenocarcinoma (PDAC) represents up to 95% of all pancreatic cancer cases, accounting for more than 300,000 deaths annually. Due to the lack of early diagnoses and the high refractory response to the currently available treatments, PDAC has a very poor prognosis, with a 5-year overall survival rate of less than 10%. Targeted therapy and immunotherapy are highly effective and have been used for the treatment of many types of cancer; however, they offer limited benefits in pancreatic cancer patients due to tumor-intrinsic and extrinsic factors that culminate in drug resistance. The identification of key factors responsible for PDAC growth and resistance to different treatments is highly valuable in developing new effective therapeutic strategies. In this review, we discuss some molecules which promote PDAC initiation and progression, and their potential as targets for PDAC treatment. We also evaluate the challenges associated with patient outcomes in clinical trials and implications for future research.

SMAD4 endows TGF-β1-induced highly invasive tumor cells with ferroptosis vulnerability in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is an extremely aggressive malignancy prone to recurrence and metastasis. Studies show that tumor cells with increased invasive and metastatic potential are more likely to undergo ferroptosis. SMAD4 is a critical molecule in the transforming growth factor β (TGF-β) pathway, which affects the TGF-β-induced epithelial-mesenchymal transition (EMT) status. SMAD4 loss is observed in more than half of patients with PDAC. In this study, we investigated whether SMAD4-positive PDAC cells were prone to ferroptosis because of their high invasiveness. We showed that SMAD4 status almost determined the orientation of transforming growth factor β1 (TGF-β1)-induced EMT via the SMAD4-dependent canonical pathway in PDAC, which altered ferroptosis vulnerability. We identified glutathione peroxidase 4 (GPX4), which inhibited ferroptosis, as a SMAD4 down-regulated gene by RNA sequencing. We found that SMAD4 bound to the promoter of GPX4 and decreased GPX4 transcription in PDAC. Furthermore, TGF-β1-induced high invasiveness enhanced sensitivity of SMAD4-positive organoids and pancreas xenograft models to the ferroptosis inducer RAS-selective lethal 3 (RSL3). Moreover, SMAD4 enhanced the cytotoxic effect of gemcitabine combined with RSL3 in highly invasive PDAC cells. This study provides new ideas for the treatment of PDAC, especially SMAD4-positive PDAC.

Advanced renal pelvis carcinoma patient with an ERBB2 insertion mutation: a case report

The prognosis of renal pelvis cancer is poor and therapeutic options are limited, especially for patients with advanced disease. In this report, we present a case of advanced renal pelvis carcinoma in a male patient in his 60s, characterized by an activating mutation in ERBB2. Clinical evaluation resulted in a pathological diagnosis of renal pelvis carcinoma with liver metastasis. Immunohistochemistry staining results suggested that CK, P63, and PAX8 were positively expressed, while Sy, CK7, CK20, S100, PAX8, and HEP1 were negatively expressed. Furthermore, next-generation sequencing results showed an activating mutation in the ERBB2 gene. The patient initially received a trastuzumab-based combination therapy, which led to a significant reduction in ERBB2 mutation frequency and a stable condition after three treatment cycles. However, following continuous treatment for 4 months, the patient developed drug resistance that resulted in disease relapse. Subsequently, the patient received apatinib treatment, but the therapeutic response was not satisfactory. The patient's condition underwent rapid deterioration and he ultimately succumbed to the disease. This case underscores the potential benefit of trastuzumab for treating ERBB2-mutated advanced renal pelvis cancer, but further highlights that overcoming drug resistance remains a crucial challenge for long-term efficacy.

CircLDLRAD3 inhibits Oral squamous cell carcinoma progression by regulating miR-558/Smad4/TGF-β

Oral squamous cell carcinoma (OSCC) is a malignant neoplasm with high mortality and morbidity. The role of circRNA and its molecular mechanism in OSCC remains largely unknown. The study aims to explore the role of a novel circular RNA (circLDLRAD3) in OSCC and its underlying mechanism. PCR and fluorescence in situ hybridization were used to explore the expression features of circLDLRAD3 in OSCC. The effects of circLDLRAD3 on the behaviour of OSCC were investigated using CCK-8, colony formation assay, transwell and animal experiments. Bioinformatics analysis along with dual luciferase reporter assay and RIP assay were used to reveal the interaction between circLDLRAD3, miR-558 and Smad4. It was revealed that circLDLRAD3 exhibited low expression status in OSCC. CircLDLRAD3 inhibits proliferation, migration, and invasion of OSCC cells both in vitro and in vivo. Mechanistically, circLDLRAD3 could bind with miR-558 to positively regulate its target gene Smad4 expression. Rescue experiments further confirmed both miR-558 overexpression and Smad4 knockdown could reverse the influence of circLDLRAD3 on OSCC phenotypes. Moreover, circLDLRAD3 regulate the TGF-β signalling pathways to influence EMT through miR-558/Smad4 axis. Our study found that circLDLRAD3 is downregulated in OSCC and verified its tumour suppressor function and mechanism in OSCC through sponging miR-558 to regulate miR-558/Smad4/TGF-β axis. The characterization of such regulating network uncovers an important mechanism underlying OSCC progression, which could provide promising targets targeted therapy strategies for OSCC in the future.

SMAD Proteins in TGF-β Signalling Pathway in Cancer: Regulatory Mechanisms and Clinical Applications

Suppressor of mother against decapentaplegic (SMAD) family proteins are central to one of the most versatile cytokine signalling pathways in metazoan biology, the transforming growth factor-β (TGF-β) pathway. The TGF-β pathway is widely known for its dual role in cancer progression as both an inhibitor of tumour cell growth and an inducer of tumour metastasis. This is mainly mediated through SMAD proteins and their cofactors or regulators. SMAD proteins act as transcription factors, regulating the transcription of a wide range of genes, and their rich post-translational modifications are influenced by a variety of regulators and cofactors. The complex role, mechanisms, and important functions of SMAD proteins in tumours are the hot topics in current oncology research. In this paper, we summarize the recent progress on the effects and mechanisms of SMAD proteins on tumour development, diagnosis, treatment and prognosis, and provide clues for subsequent research on SMAD proteins in tumours.

Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer

Background

Chemoresistance is a major hurdle to improving the prognosis of pancreatic cancer (PC). This study aimed to identify key genes regulating chemoresistance and develop a chemoresistance-related gene signature for prognosis prediction.

Methods

A total of 30 PC cell lines were subtyped according to gemcitabine sensitivity data from the Cancer Therapeutics Response Portal (CTRP v2). Differentially expressed genes (DEGs) between gemcitabine-resistant and gemcitabine-sensitive cells were subsequently identified. These upregulated DEGs associated with prognostic values were incorporated to build a LASSO Cox risk model for The Cancer Genome Atlas (TCGA) cohort. Four datasets (GSE28735, GSE62452, GSE85916, and GSE102238) from the Gene Expression Omnibus (GEO) were used as an external validation cohort. Then, a nomogram was developed based on independent prognostic factors. The responses to multiple anti-PC chemotherapeutics were estimated by the "oncoPredict" method. Tumor mutation burden (TMB) was calculated using the "TCGAbiolinks" package. Analysis of the tumor microenvironment (TME) was performed using the "IOBR" package, while the TIDE and "easier" algorithms were employed to estimate immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducted to validate the expression and functions of ALDH3B1 and NCEH1.

Results

A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1. Bulk and single-cell RNA sequencing analyses indicated that all five genes were highly expressed in tumor samples. This gene signature was not only an independent prognostic factor but also a biomarker forecasting chemoresistance, TMB, and immune cells. In vitro experiments suggested that ALDH3B1 and NCEH1 were involved in PC progression and gemcitabine chemoresistance.

Conclusion

This chemoresistance-related gene signature links prognosis with chemoresistance, TMB, and immune features. ALDH3B1 and NCEH1 are two promising targets for treating PC.

Exploring the therapeutic mechanisms of Gleditsiae Spina acting on pancreatic cancer via network pharmacology, molecular docking and molecular dynamics simulation

Pancreatic cancer is one of the most aggressive tumors and also has a low survival rate. The dried spines of Gleditsia sinensis Lam are known as "Gleditsiae Spina" and they mostly contain flavonoids, phenolic acids, terpenoids, steroids, and other chemical components. In this study, the potential active components and molecular mechanisms of Gleditsiae Spina for treating pancreatic cancer were systematically revealed by network pharmacology, molecular docking and molecular dynamics simulations (MDs). RAC-alpha serine/threonine-protein kinase (AKT1), cellular tumor antigen p53 (TP53), tumor necrosis factor α (TNFα), interleukin-6 (IL6) and vascular endothelial growth factor A (VEGFA) were common targets of Gleditsiae Spina, human cytomegalovirus infection signaling pathway, AGE-RAGE signaling pathway in diabetic complications, and MAPK signaling pathway were critical pathways of fisetin, eriodyctiol, kaempferol and quercetin in the treatment of pancreatic cancer. Molecular dynamics simulations (MDs) results showed that eriodyctiol and kaempferol have long-term stable hydrogen bonds and high binding free energy for TP53 (-23.64 ± 0.03 kcal mol-1 and -30.54 ± 0.02 kcal mol-1, respectively). Collectively, our findings identify active components and potential targets in Gleditsiae Spina for the treatment of pancreatic cancer, which may help to explore leading compounds and potential drugs for pancreatic cancer.