Prognostic prediction and immune infiltration analysis based on ferroptosis and EMT state in hepatocellular carcinoma

The Role of Chemokine (C-C Motif) Ligand 7 (CCL7) in Hepatocellular Carcinoma: Expression, Function, and Mechanisms

AIM

AHepatocellular carcinoma (HCC) is a malignant neoplasm characterized by a poor prognosis, with its incidence rising globally. Chemokine (C-C motif) ligand 7 (CCL7), a chemokine protein, has been implicated in the progression of various cancers. Nonetheless, the specific role of CCL7 in HCC has yet to be elucidated. This study seeks to examine the expression and functional role of CCL7 in the context of HCC.

MATERIALS & METHODS

Western blot and immunohistochemistry were used to detect the expression of CCL7 in HCC tissues and cell lines. Cell Counting Kit 8 (CCK8) assay, clonogenic assay, and transwell assay were performed to examine the effects of CCL7 on SNU-878 cells. Immunofluorescence was used to analyze the expression of proteins associated with epithelial interstitial transformation (EMT). Western blot was used to detect the activation of the PI3K/AKT pathway. In vivo tumorigenesis experiments were performed to assess the role of CCL7 in HCC tumorigenesis.

RESULTS

The results showed that the expression of CCL7 was up-regulated in HCC tissues, and exogenous CCL7 promoted the proliferation, migration, invasion, and EMT of SNU-878 cells and VEGF secretion by SNU-878 cells. Furthermore, CCL7 stimulated the activation of the PI3K/AKT pathway. Further analysis revealed that CCL7 targeted CCR1 and CCR2 to enhance the growth, and metastasis of SNU-878 cells and VEGF secretion by SNU-878 cells. CCR1/CCR2 silencing prevented CCL7 from activating the PI3K/AKT signaling pathway in SNU-878 cells. Moreover, CCL7 facilitated HCC tumorigenesis and VEGF expression in vivo.

CONCLUSION

Our findings indicate that CCL7 plays a promoting role in HCC growth and tumorigenesis, potentially via targeting CCR1 and CCR2 and activating the PI3K/AKT pathway.

Cellular Membrane Protein GRINA is Highly Expressed and Associated with Survival Outcomes in Liver Cancer Patients

OBJECTIVE

Hepatocellular carcinoma (HCC), a lethal cancer with high global mortality, may be targeted through ferroptosis, an iron-dependent form of cell death. Despite its potential, the prognostic value of ferroptosis in HCC is underexplored.

METHODS

Our study leveraged single-cell and bulk sequencing datasets to identify ferroptosis-related genes and developed a prognostic model via Cox and LASSO regression analyses. Survival and mutation analyses led to the creation of a nomogram for predicting patient prognosis. Furthermore, we investigated the role of GRINA, a ferroptosis-related gene, through functional assays, including cell proliferation, colony formation, and metastatic potential analyses. We also assessed mitochondrial abnormalities, intracellular iron, and ROS levels in GRINA-knockdown cells.

RESULTS

The developed ferroptosis-related model classified HCC patients into risk groups, revealing notable survival disparities. High-risk patients presented increased immune checkpoint gene expression. The nomogram revealed robust prognostic accuracy. Additionally, we found that GRINA suppression reduced HCC cell proliferation, colony formation, and metastatic potential. Cells with GRINA knockdown presented mitochondrial abnormalities and increased intracellular iron and ROS levels.

CONCLUSIONS

By analysing multiomics sequencing data, we established a connection between ferroptosis-related risk groups and the tumor immune microenvironment. These findings provide novel insights into the role of ferroptosis in HCC and suggest that GRINA inhibition is a potential therapeutic strategy, leading to mitochondrial damage and the induction of ferroptosis in HCC cell lines.

Targeting ferroptosis: the role of non-coding RNAs in hepatocellular carcinoma progression and therapy

One of the most common tumors is hepatocellular carcinoma (HCC), and the prognosis for late-stage HCC is still not good. It is anticipated that improved outcomes would result from a deeper comprehension of the pathophysiology of HCC. Ferroptosis as a new discovered cell death type is linked to the progression of HCC and may be crucial for its detection, prevention, therapy, and prognosis. Numerous studies suggest that epigenetic alterations mediated by non-coding RNAs (ncRNA) might influence cancer cell susceptibility to ferroptosis. This study elucidates the processes of ferroptosis and delineates the paths by which ncRNAs influence HCC by modulating ferroptosis. Furthermore, it offers significant insights into ferroptosis-associated ncRNAs, intending to discover novel therapeutic approaches for HCC. It also explores innovative concepts for the future use of ncRNA-based ferroptosis-targeted therapeutics.

The heterogeneity of neutrophils in cancer and its implication for therapeutic targeting

Neutrophils have a pivotal role in safeguarding the host against pathogens and facilitating tissue remodeling. They possess a large array of tools essential for executing these functions. Neutrophils have a critical role in cancer, where they are largely associated with negative clinical outcome and resistance to therapy. However, the specific role of neutrophils in cancer is complex and controversial, owing to their high functional diversity and acute sensitivity to the microenvironment. In this Perspective, we discuss the accumulated evidence that suggests that the functional diversity of neutrophils can be ascribed to two principal functional states, each with distinct characteristics: classically activated neutrophils and pathologically activated immunosuppressive myeloid-derived suppressor cells. We discuss how the antimicrobial factors in neutrophils can contribute to tumor progression and the fundamental mechanisms that govern the pathologically activated myeloid-derived suppressor cells. These functional states play divergent roles in cancer and thus require separate consideration in therapeutic targeting.

Bidirectional crosstalk between the epithelial-mesenchymal transition and immunotherapy: A bibliometric study

Immunotherapy has recently attracted considerable attention. However, currently, a thorough analysis of the trends associated with the epithelial-mesenchymal transition (EMT) and immunotherapy is lacking. In this study, we used bibliometric tools to provide a comprehensive overview of the progress in EMT-immunotherapy research. A total of 1,302 articles related to EMT and immunotherapy were retrieved from the Web of Science Core Collection (WOSCC). The analysis indicated that in terms of the volume of research, China was the most productive country (49.07%, 639), followed by the United States (16.89%, 220) and Italy (3.6%, 47). The United States was the most influential country according to the frequency of citations and citation burstiness. The results also suggested that Frontiers in Immunotherapy can be considered as the most influential journal with respect to the number of articles and impact factors. "Immune infiltration," "bioinformatics analysis," "traditional Chinese medicine," "gene signature," and "ferroptosis" were found to be emerging keywords in EMT-immunotherapy research. These findings point to potential new directions that can deepen our understanding of the mechanisms underlying the combined effects of immunotherapy and EMT and help develop strategies for improving immunotherapy.

Progress in research of ferroptosis in gastrointestinal tumors

Ferroptosis is a non-apoptotic and oxidation-damaged regulated cell death caused by iron accumulation, lipid peroxidation, and subsequent plasma membrane rupture. Ferroptosis is the main cause of tissue damage caused by iron overload and lipid peroxidation. With the deepening of the research in recent years, the understanding of the occurrence and treatment of tumors has made a major breakthrough, which brings new strategies for anti-cancer treatment. This paper reviews the relationship between ferroptosis and gastrointestinal tumors, the research of ferroptosis in cancer prevention and treatment, and the role of ferroptosis in the prevention and treatment of gastrointestinal tumors.

Research progress of ferroptosis regulating lipid peroxidation and metabolism in occurrence and development of primary liver cancer

As a highly aggressive tumor, the pathophysiological mechanism of primary liver cancer has attracted much attention. In recent years, factors such as ferroptosis regulation, lipid peroxidation and metabolic abnormalities have emerged in the study of liver cancer, providing a new perspective for understanding the development of liver cancer. Ferroptosis regulation, lipid peroxidation and metabolic abnormalities play important roles in the occurrence and development of liver cancer. The regulation of ferroptosis is involved in apoptosis and necrosis, affecting cell survival and death. Lipid peroxidation promotes oxidative damage and promotes the invasion of liver cancer cells. Metabolic abnormalities, especially the disorders of glucose and lipid metabolism, directly affect the proliferation and growth of liver cancer cells. Studies of ferroptosis regulation and lipid peroxidation may help to discover new therapeutic targets and improve therapeutic outcomes. The understanding of metabolic abnormalities can provide new ideas for the prevention of liver cancer, and reduce the risk of disease by adjusting the metabolic process. This review focuses on the key roles of ferroptosis regulation, lipid peroxidation and metabolic abnormalities in this process.

Amentoflavone reverses epithelial-mesenchymal transition in hepatocellular carcinoma cells by targeting p53 signalling pathway axis

Epithelial-mesenchymal transition (EMT) and its reversal process are important potential mechanisms in the development of HCC. Selaginella doederleinii Hieron is widely used in Traditional Chinese Medicine for the treatment of various tumours and Amentoflavone is its main active ingredient. This study investigates the mechanism of action of Amentoflavone on EMT in hepatocellular carcinoma from the perspective of bioinformatics and network pharmacology. Bioinformatics was used to screen Amentoflavone-regulated EMT genes that are closely related to the prognosis of HCC, and a molecular prediction model was established to assess the prognosis of HCC. The network pharmacology was used to predict the pathway axis regulated by Amentoflavone. Molecular docking of Amentoflavone with corresponding targets was performed. Detection and evaluation of the effects of Amentoflavone on cell proliferation, migration, invasion and apoptosis by CCK-8 kit, wound healing assay, Transwell assay and annexin V-FITC/propidium iodide staining. Eventually three core genes were screened, inculding NR1I2, CDK1 and CHEK1. A total of 590 GO enrichment entries were obtained, and five enrichment results were obtained by KEGG pathway analysis. Genes were mainly enriched in the p53 signalling pathway. The outcomes derived from both the wound healing assay and Transwell assay demonstrated significant inhibition of migration and invasion in HCC cells upon exposure to different concentrations of Amentoflavone. The results of Annexin V-FITC/PI staining assay showed that different concentrations of Amentoflavone induces apoptosis in HCC cells. This study revealed that the mechanism of Amentoflavone reverses EMT in hepatocellular carcinoma, possibly by inhibiting the expression of core genes and blocking the p53 signalling pathway axis to inhibit the migration and invasion of HCC cells.

Ferroptosis and hepatocellular carcinoma: the emerging role of lncRNAs

Hepatocellular carcinoma is the most common form of primary liver cancer and poses a significant challenge to the medical community because of its high mortality rate. In recent years, ferroptosis, a unique form of cell death, has garnered widespread attention. Ferroptosis, which is characterized by iron-dependent lipid peroxidation and mitochondrial alterations, is closely associated with the pathological processes of various diseases, including hepatocellular carcinoma. Long non-coding RNAs (lncRNAs), are a type of functional RNA, and play crucial regulatory roles in a variety of biological processes. In this manuscript, we review the regulatory roles of lncRNAs in the key aspects of ferroptosis, and summarize the research progress on ferroptosis-related lncRNAs in hepatocellular carcinoma.

BCLAF1-induced HIF-1α accumulation under normoxia enhances PD-L1 treatment resistances via BCLAF1-CUL3 complex

Bcl-2-associated transcription factor-1 (BCLAF1), an apoptosis-regulating protein of paramount significance, orchestrates the progression of various malignancies. This study reveals increased BCLAF1 expression in hepatocellular carcinoma (HCC) patients, in whom elevated BCLAF1 levels are linked to escalated tumor grades and diminished survival rates. Moreover, novel BCLAF1 expression is particularly increased in HCC patients who were not sensitive to the combined treatment of atezolizumab and bevacizumab, but not in patients who had tumors that responded to the combined regimen. Notably, overexpression of BCLAF1 increases HCC cell proliferation in vitro and in vivo, while the conditioned medium derived from cells overexpressing BCLAF1 strikingly enhances the tube-formation capacity of human umbilical vein endothelial cells. Furthermore, compelling evidence demonstrates that BCLAF1 attenuates the expression of prolyl hydroxylase domain protein 2 (PHD2) and governs the stability of hypoxia-inducible factor-1α (HIF-1α) under normoxic conditions without exerting any influence on transcription, as determined by Western blot and RT‒qPCR analyses. Subsequently, employing coimmunoprecipitation and immunofluorescence, we validated the reciprocal interaction between BCLAF1 and Cullin 3 (CUL3), through which BCLAF1 actively upregulates the ubiquitination and degradation of PHD2. The Western blot and RT‒qPCR results suggests that programmed death ligand-1 (PD-L1) is one of the downstream responders to HIF-1α in HCC. Thus, we reveal the pivotal role of BCLAF1 in promoting PD-L1 transcription and, through binding to CUL3, in promoting the accumulation of HIF-1α under normoxic conditions, thereby facilitating the ubiquitination and degradation of PHD2.

Ferroptosis of immune cells in the tumor microenvironment

Ferroptosis is a distinct form of cell death driven by the accumulation of peroxidized lipids. Characterized by alterations in redox lipid metabolism, ferroptosis has been implicated in a variety of cellular processes, including cancer. Induction of ferroptosis is considered a novel way to kill tumor cells, especially cells resistant to radiation and chemotherapy. However, in recent years, a new paradigm has emerged. In addition to promoting tumor cell death, ferroptosis causes potent immune suppression in the tumor microenvironment (TME) by affecting both innate and adaptive immune responses. In this review, we discuss the dual role of ferroptosis in the antitumor and protumorigenic functions of immune cells in cancer. We suggest strategies for targeting ferroptosis, taking into account its ambiguous role in cancer.

Sensitivity Analysis for Survival Prognostic Prediction with Gene Selection: A Copula Method for Dependent Censoring

Prognostic analysis for patient survival often employs gene expressions obtained from high-throughput screening for tumor tissues from patients. When dealing with survival data, a dependent censoring phenomenon arises, and thus the traditional Cox model may not correctly identify the effect of each gene. A copula-based gene selection model can effectively adjust for dependent censoring, yielding a multi-gene predictor for survival prognosis. However, methods to assess the impact of various types of dependent censoring on the multi-gene predictor have not been developed. In this article, we propose a sensitivity analysis method using the copula-graphic estimator under dependent censoring, and implement relevant methods in the R package "compound.Cox". The purpose of the proposed method is to investigate the sensitivity of the multi-gene predictor to a variety of dependent censoring mechanisms. In order to make the proposed sensitivity analysis practical, we develop a web application. We apply the proposed method and the web application to a lung cancer dataset. We provide a template file so that developers can modify the template to establish their own web applications.

Identification of biomarkers co-associated with M1 macrophages, ferroptosis and cuproptosis in alcoholic hepatitis by bioinformatics and experimental verification

Backgrounds

Alcoholic hepatitis (AH) is a major health problem worldwide. There is increasing evidence that immune cells, iron metabolism and copper metabolism play important roles in the development of AH. We aimed to explore biomarkers that are co-associated with M1 macrophages, ferroptosis and cuproptosis in AH patients.

Methods

GSE28619 and GSE103580 datasets were integrated, CIBERSORT algorithm was used to analyze the infiltration of 22 types of immune cells and GSVA algorithm was used to calculate ferroptosis and cuproptosis scores. Using the "WGCNA" R package, we established a gene co-expression network and analyzed the correlation between M1 macrophages, ferroptosis and cuproptosis scores and module characteristic genes. Subsequently, candidate genes were screened by WGCNA and differential expression gene analysis. The LASSO-SVM analysis was used to identify biomarkers co-associated with M1 macrophages, ferroptosis and cuproptosis. Finally, we validated these potential biomarkers using GEO datasets (GSE155907, GSE142530 and GSE97234) and a mouse model of AH.

Results

The infiltration level of M1 macrophages was significantly increased in AH patients. Ferroptosis and cuproptosis scores were also increased in AH patients. In addition, M1 macrophages, ferroptosis and cuproptosis were positively correlated with each other. Combining bioinformatics analysis with a mouse model of AH, we found that ALDOA, COL3A1, LUM, THBS2 and TIMP1 may be potential biomarkers co-associated with M1 macrophages, ferroptosis and cuproptosis in AH patients.

Conclusion

We identified 5 potential biomarkers that are promising new targets for the treatment and diagnosis of AH patients.