Development of machine learning models for patients in the high intrahepatic cholangiocarcinoma incidence age group.

BACKGROUND: Intrahepatic cholangiocarcinoma (ICC) has a poor prognosis and is understudied. Based on the clinical features of patients with ICC, we constructed machine learning models to understand their importance on survival and to accurately determine patient prognosis, aiming to develop reference values to guide physicians in developing more effective treatment plans. METHODS: This study used machine learning (ML) algorithms to build prediction models using ICC data on 1,751 patients from the SEER (Surveillance, Epidemiology, and End Results) database and 58 hospital cases. The models' performances were compared using receiver operating characteristic curve analysis, C-index, and Brier scores. RESULTS: A total of eight variables were used to construct the ML models. Our analysis identified the random survival forest model as the best for prognostic prediction. In the training cohort, its C-index, Brier score, and Area Under the Curve values were 0.76, 0.124, and 0.882, respectively, and it also performed well in the test cohort. Kaplan-Meier survival analysis revealed that the model could effectively determine patient prognosis. CONCLUSIONS: To our knowledge, this is the first study to develop ML prognostic models for ICC in the high-incidence age group. Of the ML models, the random survival forest model was best at prognosis prediction.

Comprehensive analysis of scRNA-Seq and bulk RNA-Seq data reveals dynamic changes in tumor-associated neutrophils in the tumor microenvironment of hepatocellular carcinoma and leads to the establishment of a neutrophil-related prognostic model.

BACKGROUND: Analysis of hepatocellular carcinoma (HCC) single-cell sequencing data was conducted to explore the role of tumor-associated neutrophils in the tumor microenvironment. METHODS: Analysis of single-cell sequencing data from 12 HCC tumor cores and five HCC paracancerous tissues identified cellular subpopulations and cellular marker genes. The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were used to establish and validate prognostic models. xCELL, TIMER, QUANTISEQ, CIBERSORT, and CIBERSORT-abs analyses were performed to explore immune cell infiltration. Finally, the pattern of tumor-associated neutrophil roles in tumor microenvironmental components was explored. RESULTS: A total of 271 marker genes for tumor-associated neutrophils were identified based on single-cell sequencing data. Prognostic models incorporating eight genes were established based on TCGA data. Immune cell infiltration differed between the high- and low-risk groups. The low-risk group benefited more from immunotherapy. Single-cell analysis indicated that tumor-associated neutrophils were able to influence macrophage, NK cell, and T-cell functions through the IL16, IFN-II, and SPP1 signaling pathways. CONCLUSION: Tumor-associated neutrophils regulate immune functions by influencing macrophages and NK cells. Models incorporating tumor-associated neutrophil-related genes can be used to predict patient prognosis and immunotherapy responses.

Involvement of adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1 in diallyl trisulfide-induced cytotoxicity in hepatocellular carcinoma cells.

It has been demonstrated that APPL1 (adaptor protein, phosphotyrosine interacting with PH domain and leucine zipper 1) is involved in the regulation of several growth-related signaling pathways and thus closely associated with the development and progression of some cancers. Diallyl trisulfide (DAT), a garlic-derived bioactive compound, exerts selective cytotoxicity to various human cancer cells through interfering with pro-survival signaling pathways. However, whether and how DAT affects survival of human hepatocellular carcinoma (HCC) cells remain unclear. Herein, we tested the hypothesis of the involvement of APPL1 in DAT-induced cytotoxicity in HCC HepG2 cells. We found that Lys 63 (K63)-linked polyubiquitination of APPL1 was significantly decreased whereas phosphorylation of APPL1 at serine residues remained unchanged in DAT-treated HepG2 cells. Compared with wild-type APPL1, overexpression of APPL1 K63R mutant dramatically increased cell apoptosis and mitigated cell survival, along with a reduction of phosphorylation of STAT3, Akt, and Erk1/2. In addition, DAT administration markedly reduced protein levels of intracellular TNF receptor-associated factor 6 (TRAF6). Genetic inhibition of TRAF6 decreased K63-linked polyubiquitination of APPL1. Moreover, the cytotoxicity impacts of DAT on HepG2 cells were greatly attenuated by overexpression of wild-type APPL1. Taken together, these results suggest that APPL1 polyubiquitination probably mediates the inhibitory effects of DAT on survival of HepG2 cells by modulating STAT3, Akt, and Erk1/2 pathways.

Protective Mechanism of MIF Inhibitor ISO-1 on Intrahepatic Bile Duct Cells in Rats with Severe Acute Pancreatitis.

AIMS: This study aimed to explore the protection mechanism of ISO-1 on severe acute pancreatitis-associated intrahepatic bile duct (IBD) injury in rats. METHODS: Forty-eight specific-pathogen-free male Wistar rats were randomly divided into four groups (N = 12): a sham operation group (SO group), a severe acute pancreatitis model group (SAP group), a ISO-1 treatment group (ISO-1 + SAP group), and a ISO-1 control group (ISO-1 + SO group). All rats were killed after 12 h of being made models. Immunohistochemistry was used to detect the expression of MIF and P38 in IBD cells. MIF mRNA expression in IBD cells was observed using real-time fluorescent quantitative polymerase chain reaction (real-time PCR). In addition, Western blotting was performed to detect the protein expression of P38, phosphorylated P38 (P-P38), nuclear factor-κB (NF-κB p65), and tumor necrosis factor alpha (TNF-α). Enzyme-linked immunosorbent assays were used to analyze the levels of TNF-α, IL-1ß, and IL-6 in the IBD of rats. RESULTS: Compared with SAP, after treatment with ISO-1, the pathological injuries of pancreas, liver, and IBD cells in ISO-1 treatment group remarkably relieved. The expression of MIF in the IBD cells was significantly downregulated both at mRNA and at protein levels in ISO-1 treatment group. Besides, the protein expression levels of P38, P-P38, NF-κBp65, TNF-α, IL-1ß, and IL-6 in the IBD in rats were also significantly decreased in ISO-1 treatment group (all P < 0.05). CONCLUSION: ISO-1 may protect the IBD cells, reduce pathological injuries, and reduce the inflammatory response in SAP rats. Its mechanisms may be via inhibiting the expression of MIF and then blocking the activation of p38-MAPK and NF-κB signaling pathway.

Upregulation of ubiquitin-conjugating enzyme E2Z is associated with human hepatocellular carcinoma.

UBE2Z, a member of ubiquitin-conjugating enzymes, has been reported to participate in multiple biological processes. However, its roles in hepatocellular carcinoma (HCC) remain undiscovered. This study aimed at investigating the functions of UBE2Z in HCC. Firstly, we evaluated UBE2Z expression in HCC and identified associations among UBE2Z expression, clinicopathological features, copy number alterations, DNA methylation, and survival of patients using data from the Cancer Genome Atlas (TCGA). As a result, UBE2Z was remarkably overexpressed in HCC tissues relative to normal liver tissues (P < 0.05). High UBE2Z expression was significantly correlated with age, advanced TNM stage, histological grade, vascular invasion, elevated serum alpha-fetoprotein expression (AFP), worse overall survival (OS) and disease-free survival (DFS) of HCC patients (all P < 0.05). Besides, data mining in UCSC Xena Browser showed that UBE2Z DNA amplification which was significantly associated with its expression was common (108 out of 364) in HCC, and that the level of UBE2Z DNA methylation was negatively associated with its expression (Pearson's correlation = -0.4, P < 0.0001). After analyzing the datasets from TCGA, we further confirmed the up-regulation of UBE2Z in 60 HCC tissues and several HCC cell lines. Finally, functional assays were performed and showed that knockdown UBE2Z using small interfering RNA (siRNA) could significantly restrain tumor cell proliferation and suppress cell migration and cell invasion through repressing the expression of MMP2 and MMP9. Meanwhile, UBE2Z knockdown could effectively reduce the expression of p-ERK, p-p38, p-JNK, p-Stat3 and p-JAK2, suggesting that UBE2Z might promote HCC progression by targeting ERK and stat3 signaling pathway. These findings implied that UBE2Z might be considered as a prognostic biomarker in HCC and provided a potential therapeutic tumor-associated antigen for HCC.

Overexpression of PARPBP Correlates with Tumor Progression and Poor Prognosis in Hepatocellular Carcinoma.

BACKGROUND: PARP1-binding protein (PARPBP/PARI/C12orf48), a negative regulator of homologous recombination (HR), has been suggested to function as an oncogene in cervical, lung, and pancreatic cancer. OBJECTIVE: To investigate the expression profile of PARPBP and its role in hepatocellular carcinoma (HCC). METHODS: Using data from the Cancer Genome Atlas and Human Protein Atlas databases, PARPBP expression level and its clinical implication in HCC were identified by t test and Chi-square test. The prognostic value of PARPBP in HCC was evaluated by Kaplan-Meier method, Cox regression analysis, and nomogram. Gene set enrichment analysis (GSEA) was used to screen biological pathways correlated with PARPBP expression in HCC. RESULTS: PARPBP was significantly upregulated in HCC tissues compared with normal liver tissues (P < 0.05). High PARPBP expression was significantly associated with elevated serum AFP level, vascular invasion, poor tumor differentiation, and advanced TNM stage (all P < 0.05). Kaplan-Meier analyses suggested that upregulation of PARPBP was correlated with worse overall survival (OS) and recurrence-free survival (RFS) in HCC. Multivariate analyses further confirmed that PARPBP upregulation was an independent indicator of poor OS and RFS (all P < 0.05). The prognostic nomograms based on PARPBP mRNA expression and TNM stage were superior to those based on the TNM staging system alone (all P < 0.05). Besides, PARPBP DNA copy gain and miR-139-5p downregulation were associated with PARPBP upregulation in HCC. GSEA revealed that "cell cycle," "HR," "DNA replication," and "p53 signaling" pathways were enriched in high PARPBP expression group. CONCLUSION: PARPBP may be a promising prognostic biomarker and candidate therapeutic target in HCC.

Macrophage Migration Inhibitor Promoted the Intrahepatic Bile Duct Injury in Rats with Severe Acute Pancreatitis.

BACKGROUND: Macrophage migration inhibitory factor (MIF) is involved in many acute and chronic inflammatory diseases. However, its role in intrahepatic bile duct (IBD) cell damage associated with severe acute pancreatitis (SAP) remains unclear. AIMS: This study was aimed to identify the role of MIF and its underlying mechanisms in SAP complicated by IBD cell damage. METHODS: Forty-eight specific-pathogen-free male Wistar rats were randomly divided into four groups (N = 12): a sham operation group (SO group) and three SAP model groups (SAP-3h, SAP-6h, and SAP-12h). Immunohistochemistry was used to detect the expression of MIF and P38 in IBD cells. MIF mRNA expression in IBD cells was observed using real-time fluorescent quantitative polymerase chain reaction (real-time PCR). In addition, Western blotting was performed to detect the protein expression of P38, phosphorylated P38 (P-P38), nuclear factor-κB (NF-κB p65), and tumor necrosis factor alpha (TNF-α). Enzyme-linked immunosorbent assays were used to analyze the levels of TNF-α, IL-1ß, and IL-6 in the IBD of rats. RESULTS: Compared with the SO group, the expression of MIF in the IBD was significantly upregulated both at mRNA and at protein levels in the SAP group. Besides, the protein expression levels of P38, P-P38, NF-κB, p65, TNF-α, IL-1ß, and IL-6 in the IBD in rats were also significantly increased in the SAP group and the levels increased gradually as acute pancreatitis progressed (all P < 0.05). CONCLUSIONS: MIF may promote the IBD injury and inflammatory reaction in SAP via activating the P38-MAPK and NF-κB signaling pathways.

Microwave-assisted liver resection vs. clamp crushing liver resection in cirrhosis patients with hepatocellular carcinoma.

PURPOSE: This study aimed to evaluate the safety and effectiveness of microwave-ablation-assisted liver resection (MW-LR) and clamp crushing liver resection (CC-LR) in cirrhotic patients with hepatocellular carcinoma (HCC). MATERIALS AND METHODS: From July 2005 to January 2015, cirrhotic HCC patients who underwent CC-LR (n = 191) or MW-LR (n = 112) were retrospectively analysed. We compared morbidity, mortality, disease-free survival (DFS) time and overall survival time between the CC-LR and MW-LR groups. RESULTS: The blood loss volume was significantly higher in the CC-LR group (mean of 752 ml) than that in the MW-LR group (mean of 253 ml, p < 0.001). The abdominal abscess rate was higher in the MW-LR group (8.9%) than that in the CC-LR group (3.1%, p = 0.029). The 30-day mortality rate (1.5% vs. 0.8%) and postoperative complication rate (32.9% vs. 25.0%) were both similar between the CC-LR and MW-LR groups. MW-LR provided a survival benefit over CC-LR at 1, 3 and 5 years in the entire population (93.5% vs. 87.0%, 77.0% vs. 62.5% and 50.0% vs. 36.5%, respectively; p = 0.003). In a subgroup analysis, MW-LR provided a survival benefit over CC-LR for Barcelona Clinic Liver Cancer stage A (BCLC-A) HCC (p = 0.026) and stage B (BCLC-B) HCC (p = 0.035) patients and provided DFS benefits for BCLC-A HCC patients (p = 0.036). CONCLUSIONS: MW-LR is a safe and feasible procedure for HCC patients with a cirrhotic liver history.

Quercetin suppresses the chymotrypsin-like activity of proteasome via inhibition of MEK1/ERK1/2 signaling pathway in hepatocellular carcinoma HepG2 cells.

The proteasomal system is a promising target for cancer treatment. Quercetin (Que), a flavonoid compound with antitumor ability, displays the inhibitory effect on proteasome activity. However, the underlying molecular mechanisms are ill defined. The present study found that Que treatment significantly reduced the chymotrypsin-like protease activity of proteasome whereas the trypsin- and caspase-like protease activities remained unchanged in HepG2 cancer cells, along with activation of p38 MAPK and JNK and reduction of ERK1/2 phosphorylation. Que-reduced proteasome activity could not be reverted by inhibition of p38 MAPK and JNK signaling pathway. In addition, MEK1 overexpression or knockdown upregulated or downregulated the chymotrypsin-like protease activity of proteasome, respectively. Both Que and MEK1/ERK1/2 inhibitor attenuated the expression levels of proteasome ß subunits. These results indicate that Que-induced suppression of MEK1/ERK1/2 signaling and subsequent reduction of proteasome ß subunits is responsible for its inhibitory impacts on proteasome activity.

Staurosporine suppresses survival of HepG2 cancer cells through Omi/HtrA2-mediated inhibition of PI3K/Akt signaling pathway.

Staurosporine, which is an inhibitor of a broad spectrum of protein kinases, has shown cytotoxicity on several human cancer cells. However, the underlying mechanism is not well understood. In this study, we examined whether and how this compound has an inhibitory action on phosphatidylinositol 3-kinase (PI3K)/Akt pathway in vitro using HepG2 human hepatocellular carcinoma cell line. Cell viability and apoptosis were determined using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and terminal deoxyribonucleotidyl transferase-mediated dUTP-digoxigenin nick end labeling (TUNEL) assay, respectively. Glutathione S-transferase (GST) pull-down assay and co-immunoprecipitation were performed to detect protein-protein interactions. Small interfering RNA (siRNA) was used to silence the expression of targeted protein. We found that staurosporine significantly decreased cell viability and increased cell apoptosis in a concentration- and time-dependent manner in HepG2 cancer cells, along with the decreased expressions of PDK1 protein and Akt phosphorylation. Staurosporine was also found to enhance Omi/HtrA2 release from mitochondria. Furthermore, Omi/HtrA2 directly bound to PDK1. Pharmacological and genetic inhibition of Omi/HtrA2 restored protein levels of PDK1 and protected HepG2 cancer cells from staurosporine-induced cell death. In addition, staurosporine was found to activate autophagy. However, inhibition of autophagy exacerbated cell death under concomitant treatment with staurosporine. Taken together, our results indicate that staurosporine induced cytotoxicity response by inhibiting PI3K/Akt signaling pathway through Omi/HtrA2-mediated PDK1 degradation, and the process provides a novel mechanism by which staurosporine produces its therapeutic effects.

Caffeine inhibits migration in glioma cells through the ROCK-FAK pathway.

AIMS: Glioma is the most malignant brain tumor that has the ability to migrate and invade the CNS. In this study, we investigated the signaling mechanism of caffeine on the migration of glioma cells. METHODS: The effect of caffeine on cell migration was evaluated using Transwell and wound healing assays. The expression of the focal adhesion complex as it related to cell migration was assayed using Western blotting and immunostaining. RESULTS: Caffeine decreased the migration of rat C6 and human U87MG glioma cells and down-regulated the expression of phosphorylated focal adhesion kinase (p-FAK) and p-paxillin. Caffeine also decreased p-FAK staining at the edge of glioma cells and disassembled actin stress fibers. Additionally, caffeine elevated expression of phosphorylated myosin light chain (p-MLC), an effect that could be blocked by Y27632, a rho-associated protein kinase (ROCK) inhibitor, but not myosin light chain kinase inhibitor, ML-7. Y27632 also inhibited the caffeine-reduced expression of p-FAK and p-paxillin as well as cell migration. CONCLUSION: Caffeine decreased the migration of glioma cell through the ROCK-focal adhesion complex pathway; this mechanism may be useful as part of clinical therapy in the future.

The Clinical Evaluation of Laparoscopic Transcystic Duct Common Bile Duct Exploration in Elderly Choledocholithiasis.

UNLABELLED: Aims: To evaluate the feasibility and safety of Laparoscopic transcystic duct common bile duct exploration(LTCBDE) in elderly patients. METHODOLOGY: Between Jan 2010 and Dec 2011, 308 elderly patients (age 65 years) with CBD stones underwent surgery. 165 were initially treated with LTCBDE, 143 patients underwent open choledocholithotomy surgery. Two groups were compared with operative duration, incidence of postoperative complication, and the average days of in hospital. RESULTS: The LTCBDE was performed successfully in 157 of 165 patients 95.15%. 3 cases were converted to laparotomy and the other 5 were changed to laparoscopic choledocholithotomy and T-tube drainage. All he elderly patients receiving LTCBDE were dealt with primary closure of cystic duct. There were no severe complications such as bleeding and residual stones.The average duration of surgery was 102 ± 35 min and the mean blood loss 43 ± 20 ml. The postoperative hospital day was 3 ± 0.5 days. 143 patients underwent open choledocholithotomy surgery. There were 2 (1.4%) cases abdominal wall incision infection, 5 (3.5%) cases pulmonary infection, 2 (1.4%) bile leakage, and 1 (0.7%) local bile leakage for part T-tube pulled out postoperation. The operation duration was about 120 ± 30 minutes, and postoperative hospital day 7 ± 1.5 days CONCLUSIONS: Elective LTCBDE to treat CBD stones in elderly patients is safe and effective.

S100A16 is a potential target for reshaping the tumor microenvironment in the hypoxic context of liver cancer.

BACKGROUND: The research on the S100 family has garnered significant attention; however, there remains a dearth of understanding regarding the precise role of S100A16 in the tumor microenvironment of liver cancer. METHOD: Comprehensive analysis was conducted on the expression of S100A16 in tumor tissues and its correlation with hypoxia genes. Furthermore, an investigation was carried out to examine the association between S100A16 and infiltration of immune cells in tumors as well as immunotherapy. Relevant findings were derived from the analysis of single cell sequencing data, focusing on the involvement of S100A16 in both cellular differentiation and intercellular communication. Finally, we validated the expression of S100A16 in liver cancer by Wuhan cohort and multiplexed immunofluorescence to investigate the correlation between S100A16 and hypoxia. RESULT: Tumor tissues displayed a notable increase in the expression of S100A16. A significant correlation was observed between S100A16 and genes associated with hypoxic genes. Examination of immune cell infiltration revealed an inverse association between T cell infiltration and the level of S100A16 expression. The high expression group of S100A16 exhibited a decrease in the expression of genes related to immune cell function. Single-cell sequencing data analysis revealed that non-immune cells predominantly expressed S100A16, and its expression levels increased along with the trajectory of cell differentiation. Additionally, there were significant variations observed in hypoxia genes as cells underwent differentiation. Cellular communication identified non-immune cells interacting with immune cells through multiple signaling pathways. The Wuhan cohort verified that S100A16 expression was increased in liver cancer. The expression of S100A16 and HIF was simultaneously elevated in endothelial cells. CONCLUSION: The strong association between S100A16 and immune cell infiltration is observed in the context of hypoxia, indicating its regulatory role in shaping the hypoxic tumor microenvironment in liver cancer.

Clinical Features and Prognostic Models in Patients with Intrahepatic Cholangiocarcinoma: a Population-Based Analysis.

BACKGROUND: This study aims to construct a risk classification system and a nomogram in intrahepatic cholangiocarcinomafor patients (ICC). METHODS: Three thousand seven hundred thirty-seven patients diagnosed with ICC between 2010 and 2015 were selected from the Surveillance, Epidemiology and End Results. The consistency index, time-dependent receiver operating characteristic curve, and the calibration plots were adopted to evaluate the effective performance of nomogram. Decision curve analysis (DCA), net reclassification index (NRI), and comprehensive discrimination improvement (IDI) were used to compare the advantages and disadvantages of two models. Kaplan-Meier curve showed the difference in prognosis among different groups. RESULTS: Ten variables were selected to establish the nomogram for ICCA. The C-index (training cohort: 0.765, P < 0.05; validation cohort: 0.776, P < 0.05) and the time-dependent AUCs (the training cohort: the values of 1, 3, 5 years were 0.836, 0.873, and 0.888; the validation cohort: the values of 1, 3, 5 years were 0.833, 0.838, and 0.881) showed satisfactory discrimination. The calibration curves also revealed that the nomogram was consistent with the actual observations. The NRI (training cohort: 1-, 3-, 5-year CSS: 0.879, 0.94, 0.771; validation cohort: 1-, 3-, 5-year CSS: 0.905, 0.945, 0.717) and IDI (training cohort: 1-, 3-, 5-year CSS: 0.24, 0.23, 0.22; validation cohort: 1-, 3-, 5-year CSS: 0.24, 0.46, 0.27) (P < 0.05) (compared with AJCC staging). DCA showed that the new model was more practical and had better recognition than AJCC staging. CONCLUSIONS: A new risk stratification system for ICC patients has been developed, which can be a practical tool for patient management.

Construction and validation of a nomogram for patients with multiple hepatocellular carcinoma: A SEER-based study.

BACKGROUND: American Joint Committee on Cancer (AJCC)-TNM system doesn't accurately predict prognosis. Our study was designed to identify prognostic factors in patients with multiple hepatocellular carcinoma (MHCC), establish and validate a nomogram model to predict the risk and overall survival (OS) of MHCC patients. METHODS: We selected eligible HCC patients from the Surveillance, Epidemiology, and End Results (SEER) database, used univariate and multivariate COX regression to determine prognostic factors in MHCC patients, and used these factors to build a nomogram. The accuracy of the prediction was evaluated using the C-index, receiver operating characteristic (ROC) and calibration curve. Decision curve analysis (DCA), net reclassification index (NRI) and integrated discrimination improvement (IDI) were used to compare the nomogram with AJCC-TNM staging system. Finally, the prognosis of different risks was analyzed using Kaplan-Meier (K-M) method. RESULTS: 4950 eligible patients with MHCC were enrolled in our study and randomly assigned to the training cohort and test cohort in a 7:3 ratio. After COX regression analysis, age, sex, histological grade, AJCC-TNM stage, tumor size, alpha-fetoprotein (AFP), surgery, radiotherapy and chemotherapy in total 9 factors could be used to independently determine OS of patients. the above factors were used to construct a nomogram, and the consistency C-index was 0.775. C-index, DCA, NRI and IDI showed that our nomogram was superior to the AJCC-TNM staging system. K-M plots for OS were performed using the log-rank test, the P-value of which was <0.001. CONCLUSIONS: The practical nomogram can provide more accurate prognostic prediction for multiple hepatocellular carcinoma patients.

Analysis of M2 macrophage-associated risk score signature in pancreatic cancer TME landscape and immunotherapy.

Background: M2 macrophages perform an influential role in the progression of pancreatic cancer. This study is dedicated to explore the value of M2 macrophage-related genes in the treatment and prognosis of pancreatic cancer. Methods: RNA-Seq and clinical information were downloaded from TCGA, GEO and ICGC databases. The pancreatic cancer tumour microenvironment was revealed using the CIBERSORT algorithm. Weighted gene co-expression network analysis (WGCNA) was used to detect M2 macrophage-associated gene modules. Univariate Cox regression, Least absolute shrinkage and selection operator (LASSO) regression analysis and multivariate Cox regression were applied to develop the prognostic model. The modelling and validation cohorts were divided into high-risk and low-risk groups according to the median risk score. The nomogram predicting survival was constructed based on risk scores. Correlations between risk scores and tumour mutational load, clinical variables, immune checkpoint blockade, and immune cells were further explored. Finally, potential associations between different risk models and chemotherapeutic agent efficacy were predicted. Results: The intersection of the WGCNA results from the TCGA and GEO data screened for 317 M2 macrophage-associated genes. Nine genes were identified by multivariate COX regression analysis and applied to the construction of risk models. The results of GSEA analysis revealed that most of these genes were related to signaling, cytokine receptor interaction and immunodeficiency pathways. The high and low risk groups were closely associated with tumour mutational burden, immune checkpoint blockade related genes, and immune cells. The maximum inhibitory concentrations of metformin, paclitaxel, and rufatinib lapatinib were significantly differences on the two risk groups. Conclusion: WGCNA-based analysis of M2 macrophage-associated genes can help predict the prognosis of pancreatic cancer patients and may provide new options for immunotherapy of pancreatic cancer.

Tumor-associated endothelial cell prognostic risk model and tumor immune environment modulation in liver cancer based on single-cell and bulk RNA sequencing: Experimental verification.

BACKGROUND: To build a prognostic and immunotherapeutic response prediction model for liver cancer based on marker genes of tumor-associated endothelial cell (TEC). METHOD: Single cell sequencing data from Gene Expression Omnibus (GEO) liver cancer patients were utilized to identify TEC subpopulations. Models were built from transcriptomic and clinical data of TCGA liver cancer patients. The GSE76427 and ICGC databases were used as independent validation sets. Time-dependent receiver operating characteristic (ROC) curves and Kaplan-Meier curves were used to verify the ability of the model to predict survival. XCELL, TIMER, QUANTISEQ, CIBERSORT, CIBERSORT-ABS, and ssGSEA were applied to evaluate tumor immune cell infiltration. The TIDE score was used to predict the effect of immunotherapy. Immune blockade checkpoint gene, tumor mutational load and GSVA enrichment analyses were further explored. The expression levels of candidate genes were measured and validated by real-time PCR between liver cancer tissues and adjacent nontumor liver tissues. RESULTS: Eighty-seven genes were identified as marker genes for TECs. IGFBP3, RHOC, S100A16, FSCN1, and CLEC3B were included in the constructed prognostic model. Time-dependent ROC curve values were higher than 0.700 in both the model and validation groups. The low risk group exhibited high immune cell infiltration and function than the higher risk group. The TIDE score indicated that the low-risk group benefited more from immunotherapy than the high-risk group. The risk score and multiple immune blockade checkpoint genes and immune-related pathways were strongly correlated. CONCLUSION: Novel signatures of TEC marker genes showed a powerful ability to predict prognosis and immunotherapy response in patients with liver cancer.

Integrated analysis of single-cell and bulk RNA-sequencing identifies a signature based on NK cell marker genes to predict prognosis and immunotherapy response in hepatocellular carcinoma.

BACKGROUND: Prognostic modeling of NK cell marker genes in patients with hepatocellular carcinoma based on single cell sequencing and transcriptome data analysis. METHODS: Marker genes of NK cells were analyzed according to single cell sequencing data of hepatocellular carcinoma. Univariate Cox regression, lasso regression analysis, and multivariate Cox regression were performed to estimate the prognostic value of NK cell marker genes. TCGA, GEO and ICGC transcriptomic data were applied to build and validate the model. Patients were divided into high and low risk groups based on the median risk score. XCELL, timer, quantitative sequences, MCP counter, EPIC, CIBERSORT and CIBERSORT-abs were performed to explore the relationship between risk score and tumor microenvironment in hepatocellular carcinoma. Finally the sensitivity of the model to chemotherapeutic agents was predicted. RESULTS: Single-cell sequencing identified 207 marker genes for NK cells in hepatocellular carcinoma. Enrichment analysis suggested that NK cell marker genes were mainly involved in cellular immune function. Eight genes were selected for prognostic modeling after multifactorial COX regression analysis. The model was validated in GEO and ICGC data. Immune cell infiltration and function were higher in the low-risk group than in the high-risk group. The low-risk group was more suitable for ICI and PD-1 therapy. Half-maximal inhibitory concentrations of Sorafenib, Lapatinib, Dabrafenib, and Axitinib were significantly different on the two risk groups. CONCLUSION: A new signature of hepatocyte NK cell marker genes possesses a powerful ability to predict prognosis and immunotherapeutic response in patients with hepatocellular carcinoma.

Advances in Promoting the Efficacy of Chimeric Antigen Receptor T Cells in the Treatment of Hepatocellular Carcinoma.

HCC, one of the most common and deadly cancers worldwide, develops from hepatocytes and accounts for more than 90% of primary liver cancers. The current widely used treatment modalities are far from meeting the needs of liver cancer patients. CAR-T cell therapy, which has recently emerged, has shown promising efficacy in lymphoma and hematologic cancers, but there are still many challenges to overcome in its application to the clinical treatment of HCC, including osmotic barriers, the inhibition of hepatocellular carcinoma microenvironment activity, the limited survival and killing ability of CAR-T cells, and inevitable side effects, among others. As a result, a number of studies have begun to address the suboptimal efficacy of CAR-T cells in HCC, and many of these schemes hold good promise. This review focuses on advances in the past five years aimed at promoting the efficacy of CAR-T cell therapy for treatment of HCC.

A Practical Nomogram and Risk Stratification System Predicting Cancer-Specific Survival for Hepatocellular Carcinoma Patients With Severe Liver Fibrosis.

Objective: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths worldwide. This study aims to construct a novel practical nomogram and risk stratification system to predict cancer-specific survival (CSS) in HCC patients with severe liver fibrosis. Methods: Data on 1,878 HCC patients with severe liver fibrosis in the period 1975 to 2017 were extracted from the Surveillance, Epidemiology, and End Results database (SEER). Patients were block-randomized (1,316 training cohort, 562 validation cohort) by setting random seed. Univariate and multivariate COX regression analyses were employed to select variables for the nomogram. The consistency index (C-index), the area under time-dependent receiver operating characteristic curve (time-dependent AUC), and calibration curves were used to evaluate the performance of the nomogram. Decision curve analysis (DCA), the C-index, the net reclassification index (NRI), and integrated discrimination improvement (IDI) were used to compare the nomogram with the AJCC tumor staging system. We also compared the risk stratification of the nomogram with the American Joint Committee on Cancer (AJCC) staging system. Results: Seven variables were selected to establish the nomogram. The C-index (training cohort: 0.781, 95%CI: 0.767-0.793; validation cohort: 0.793, 95%CI = 95%CI: 0.779-0.798) and the time-dependent AUCs (the training cohort: the values of 1-, 3-, and 5 years were 0.845, 0.835, and 0.842, respectively; the validation cohort: the values of 1-, 3-, and 5 years were 0.861, 0.870, and 0.876, respectively) showed satisfactory discrimination. The calibration plots also revealed that the nomogram was consistent with the actual observations. NRI (training cohort: 1-, 2-, and 3-year CSS: 0.42, 0.61, and 0.67; validation cohort: 1-, 2-, and 3-year CSS: 0.26, 0.52, and 0.72) and IDI (training cohort: 1-, 3-, and 5-year CSS:0.16, 0.20, and 0.22; validation cohort: 1-, 3-, and 5-year CSS: 0.17, 0.26, and 0.30) indicated that the established nomogram significantly outperformed the AJCC staging system (P < 0.001). Moreover, DCA also showed that the nomogram was more practical and had better recognition. Conclusion: A nomogram for predicting CSS for HCC patients with severe liver fibrosis was established and validated, which provided a new system of risk stratification as a practical tool for individualized treatment and management.