Background and Aims:Dysregulated lipid metabolism contributes to hepatocellular carcinoma (HCC) progression, but the prognostic value and mechanistic roles of lipid metabolism-related long noncoding RNAs (LRLs) remain insufficiently characterized. This study aimed to construct and validate an LRL-based prognostic model and to investigate the biological function and metabolic mechanism of AC026412.3 in HCC. Methods:Transcriptomic and clinical data from the The Cancer Genome Atlas Liver Hepatocellular Carcinoma cohort were analyzed to identify LRLs based on their correlation with curated lipid metabolism genes. Differential expression, univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox analyses were performed to construct a prognostic signature, which was evaluated using Kaplan-Meier survival and time-dependent receiver operating characteristic (ROC) analyses. Functional enrichment analyses Gene Ontology [GO], Kyoto Encyclopedia of Genes and Genomes [KEGG] and gene set enrichment analysis [GSEA], mutation profiling, tumor mutational burden, immune infiltration estimation, and consensus clustering were applied to characterize associated features. A key LRL was identified through integrated bioinformatic screening and prioritization. Its biological role was assessed by quantitative reverse transcription polymerase chain reactionq (RT-PCR), western blotting, BODIPY staining, colony formation, Transwell assays, and xenograft models. RNA sequencing followed by pathway enrichment analysis was conducted to explore underlying mechanisms. Results:A three-LRL signature (AL031985.3, NRAV, and AC026412.3) stratified HCC patients into distinct risk groups with significantly different survival outcomes and demonstrated independent prognostic value. AC026412.3 was markedly upregulated in HCC and associated with poor prognosis. Functional assays demonstrated that AC026412.3 promoted proliferation, invasion, and tumor growth while reducing lipid accumulation. Mechanistically, AC026412.3 upregulated solute carrier family 22 member 5 (SLC22A5), enhanced fatty acid β-oxidation, and increased adenosine triphosphate (ATP) production, thereby driving metabolic reprogramming. Conclusions:This study establishes a robust LRL-based prognostic model and identifies AC026412.3 as a key regulator of lipid metabolic reprogramming via the SLC22A5-fatty acid β-oxidation axis, highlighting its potential as a biomarker and therapeutic target in HCC.

Gallbladder cholesterol polyp (GCP) and gallbladder adenoma (GA) are easily confused in clinical diagnosis. This study aims to establish a nomogram prediction model for preoperative prediction of the risk of GA patients. We retrospectively collected clinical data of GCP or GA patients who underwent laparoscopic cholecystectomy (LC) between January 2020 and April 2023. We compared and analyzed the differences between the GCP group and the GA group. The data were divided into a training set and a validation set in a 7:3 ratio. Independent risk factors were determined using LASSO and Logistic regression analysis, and a nomogram model was established. The model was comprehensively validated and evaluated using the area under the ROC curve (AUC), Hosmer–Lemeshow test and clinical decision curve analysis (DCA). This study ultimately included 497 patients. The independent predictors of the nomogram model include blood type (O-type blood, OR 2.00, 95

Cholangiocarcinoma is a common malignant tumor that seriously endangers physical and mental health. Elevated serum ferritin levels are correlated with reduced survival and increased recurrence rates in various cancers. The present study aimed to evaluate the potential of serum ferritin as a prognostic biomarker in cholangiocarcinoma. Immunoassay was used to detect ferritin protein in the serum of 120 cholangiocarcinoma patients and to compare the diagnostic utility of the conventional tumour markers CEA, CA19-9 and CA125. The median DFS for all patients was 420 days (range, 1.0-51.8 months). Median survival was 991 days (range, 2.1–51.8 months) and 361 days (range, 1.0-51.8 months) in the low- and high-ferritin level groups, respectively (P < 0.001). Patients with cholangiocarcinoma with low ferritin expression (≤ 196.5 ng/ml) had significantly higher disease-free survival than those with high ferritin expression (> 196.5 ng/ml). The findings of multivariate analyses showed serum ferritin (P = 0.001), CA19-9 (P = 0.037), Tbil (P = 0.017), and Ki67 (P = 0.008), lymph node metastasis (P = 0.040) and no lymph node dissection (P<0.001) were considered as independent factors affecting the prognosis. Ferritin levels had statistically significant relationship between patient’s CA19-9 level, Vascular invasion, CD34/31 expression and Postoperative adjuvant therapy (P < 0.05). These results indicate that serum ferritin is prognostically associated with patients with cholangiocarcinoma and may serve as a valuable prognostic biomarker for patients with cholangiocarcinoma.

Background: Immune escape is a critical barrier to effective cancer immunotherapy for cancers such as hepatocellular carcinoma (HCC). The aim of this study was to identify prognostic genes associated with immune escape and to analyse immune infiltration in HCC. Methods: The TCGA-LIHC cohort gene expression matrix and TCGA cohort were downloaded from the UCSC Xena and TCGA databases, respectively, for differential expression analysis, as well as for clinical data and survival information. Additionally, gene expression matrices from HCC tumor tissue samples were downloaded from the ICGC database to validate prognostic models. Subsequently, enrichment analysis utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were conducted. Risk modeling was subsequently performed, followed by univariate and multivariate Cox regression analyses, as well as LASSO regression analysis. Overall survival (OS) curves, receiver operating characteristic (ROC) curves, and nomograms were also generated. Finally, immune infiltration analysis was performed by single-sample genomic enrichment analysis (ssGSEA) and GeneMANIA to predict the functions and pathways of associated with prognostic genes. Results: A total of 4489 differential expression genes were obtained, including 3259 up-regulated, and 1230 down-regulated. Among them, 2123 GO biological functions and 334 KEGG results were enriched. Subsequently, eight differential genes related to immune escape became candidate genes. Finally, we constructed a risk model using three genes, CEP55, GPAA1 and PIGU, and demonstrated better results. The results of immune infiltration showed that the prognostic genes affected the patient's condition through these immune cells. Subsequently, we performed drug sensitivity analysis and finally discovered that CEP55 and PIGU were positively associated with five drugs in the high-risk group. And these three key prognostic genes have high expression levels in HCC tumor tissues. Conclusion: Our study found that three prognostic genes: CEP55, GPAA1 and PIGU have good prognostic value for HCC patients, and are the pivotal prognostic biomarkers.

Intrahepatic cholangiocarcinoma (ICCA), the second most prevalent primary liver cancer, is linked to a poor prognosis. However, the role of histone lactylation-related epigenetic modifications in ICCA remains poorly understood. This study aimed to identify reliable prognostic biomarkers and establish a foundation for targeted therapies. Specifically, this study integrated single-cell RNA sequencing (scRNA-seq), bulk transcriptomic data from TCGA-ICCA and GSE107943, and a curated list of histone lactylation-related genes. Cell–cell communication analysis revealed a significant CXCL12–CXCR4 interaction between apCAFs and vCAFs (p < 0.01). Prognostic markers were identified through regression models, and a risk signature was developed and validated using ROC curves. Five genes—STMN1, UBE2T, CENPF, C5orf34, and FAM72C—were established as prognostic indicators. FAM72C exhibited a negative correlation with plasmacytoid dendritic cells (cor = − 0.355), while CENPF correlated negatively with mast cells (cor = − 0.386) (p < 0.05). Drug sensitivity analysis revealed that the IC50 values of 10 candidate compounds, including AZD6482, BX.798, and Bicalutamide, exhibited significant differences between the two groups (p < 0.05). RT-qPCR confirmed the overexpression of STMN1, UBE2T, CENPF, and FAM72C in ICCA tissues. Overall, this study highlights the significance of histone lactylation-associated prognostic genes and potential therapeutic targets in ICCA, providing insights into tumor microenvironment modulation and precision treatment approaches.

BACKGROUND: Cancer-associated fibroblasts (CAFs), integral components of the tumor microenvironment, substantially influence cholangiocarcinoma (CCA) progression and clinical outcomes. This study aimed to identify CAF-related genes implicated in CCA pathogenesis. METHODS: Differentially expressed genes (DEGs) between CCA and non-tumorous samples were extracted from the Gene Expression Omnibus GSE107943 dataset, then intersected with cancer-associated fibroblast signature genes (CAFSGs) to derive DE-CAFSGs. Mendelian randomization (MR) analysis was subsequently conducted to determine causally linked biomarkers. The diagnostic efficacy of these biomarkers was evaluated via receiver operating characteristic (ROC) curve analysis using data from GSE107943 and the TCGA-CHOL cohort. Functional annotation of representative DE-CAFSGs was performed through single-gene gene set enrichment analysis. The expression trends of these biomarkers were preliminarily explored using RT-PCR, Western blotting, and immunohistochemistry. RESULTS: A total of 135 DE-CAFSGs were identified, among which GRN, PLXNC1, and ORMDL3 emerged as CCA-associated biomarkers. GRN and PLXNC1 were identified as risk-associated, while ORMDL3 exhibited a protective association. Each demonstrated robust discriminatory capacity, with area under the ROC curve values exceeding 0.8 in both datasets. Enrichment analysis revealed significant associations with pathways including retinol metabolism, cytochrome P450-mediated drug metabolism, and the complement and coagulation cascades. CONCLUSION: GRN, PLXNC1, and ORMDL3 represent key CAF-associated genes in CCA, shedding light on potential molecular mechanisms of disease development.

BACKGROUND:Gallstones are common lesions that often require surgical intervention. Laparoscopic cholecystectomy is the treatment of choice for symptomatic gallstones. Preoperatively, the anatomical morphology of the cystic duct (CD), needs to be accurately recognized, especially when anatomical variations occur in the CD, which is otherwise prone to bile duct injury. However, at present, there is no optimal classification system for CD morphology applicable in clinical practice, and the relationship between anatomical variations in CDs and gallstones remains to be explored.AIM:To create a more comprehensive clinically applicable classification of the morphology of CD and to explore the correlations between anatomic variants of CD and gallstones.METHODS:A total of 300 patients were retrospectively enrolled from October 2021 to January 2022. The patients were divided into two groups: The gallstone group and the nongallstone group. Relevant clinical data and anatomical data of the CD based on magnetic resonance cholangiopancreatography (MRCP) were collected and analyzed to propose a morphological classification system of the CD and to explore its relationship with gallstones. Multivariate analysis was performed using logistic regression analyses to identify the independent risk factors using variables that were significant in the univariate analysis.RESULTS:Of the 300 patients enrolled in this study, 200 (66.7%) had gallstones. The mean age was 48.10 ± 13.30 years, 142 (47.3%) were male, and 158 (52.7%) were female. A total of 55.7% of the patients had a body mass index (BMI) ≥ 24 kg/m2. Based on the MRCP, the CD anatomical typology is divided into four types: Type I: Linear, type II: n-shaped, type III: S-shaped, and type IV: W-shaped. Univariate analysis revealed differences between the gallstone and nongallstone groups in relation to sex, BMI, cholesterol, triglycerides, morphology of CD, site of CD insertion into the extrahepatic bile duct, length of CD, and angle between the common hepatic duct and CD. According to the multivariate analysis, female, BMI (≥ 24 kg/m2), and CD morphology [n-shaped: Odds ratio (OR) = 10.97, 95% confidence interval (95%CI): 5.22-23.07, P < 0.001; S-shaped: OR = 4.43, 95%CI: 1.64-11.95, P = 0.003; W-shaped: OR = 7.74, 95%CI: 1.88-31.78, P = 0.005] were significantly associated with gallstones.CONCLUSION:The present study details the morphological variation in the CD and confirms that CD tortuosity is an independent risk factor for gallstones.

BACKGROUD:Fibroblasts turn into cancer associated fibroblasts (CAFs) in the tumor microenvironment, which play an important role in tumor progression. However, the mechanism is unclear.AIMS:To investigate the role of CAFs with HS6ST1-overexpression in cell migration and invasion effects.METHODS:Human primary CAFs were isolated and identified from intrahepatic cholangiocarcinoma. mRNA profiles differences between CAFs and NFs were examined by using transcriptome sequencing. Using Transwell® migration assays, ICCA cells (RBE and HUCCT1) with NF-CM, CAF-CM, CAFsNC-CM, and CAFsHS6ST1-CM were analyzed. Immunohistochemical staining were used to analyze the expression of HS6ST1 in CAF in 152 patients with ICCA. Overall survival (OS) was compared based on CAF HS6ST1 expression were analysed. The relationship between clinicopathological parameters and survival was also examined.RESULTS:Successfully isolated CAFs is positive staining with αSMA, FSP-1, FAP, and PDGFR-β. Transcriptome sequencing showed that differently expressed genes were enriched in the function of the extracellular matrix and chemokine signaling pathway. HS6ST1 is differentially expressed between CAFs and NFs, and associated with the migration and invasion of ICCA cells. Moreover, HS6ST1 positive expression of CAFs predicted unfavorable prognosis in patients with intrahepatic cholangiocarcinoma and showed correlation with the presence of lymph node metastasis.CONCLUSION:HS6ST1 is new possibilities for targeting the CAFs to reduce cholangiocarcinoma growth and metastasis.

The FGF/FGFR signaling axis deregulation of the fibroblast growth factor receptor (FGFR) family is closely related to tumorigenesis, tumor progression and drug resistance to anticancer therapy. And fibroblast growth factor receptor 3 (FGFR3) is one member of this family. In this study, we aimed to investigate the effect of siRNA-induced knockdown of FGFR3 on the biological behaviors of intrahepatic cholangiocarcinoma (ICC). The expression levels of FGFR3 were determined in three intrahepatic cholangiocarcinoma cell lines RBE, HUCCT1 and HCCC9810 cell lines by Western blot. FGFR3 expression in RBE cell line was knocked down by siRNA. Our study found that knockdown of FGFR3 inhibited the migration, invasion and proliferation of ICC cells using Wound healing assay, Transwell migration and invasion assays and Cell proliferation assay. And significantly down-regulated the protein expression levels of MMP2, cyclinD1, and NCadherin, but had no significant effect on MMP9, cyclinD3, vimentin, E-cadherin protein. In addition, we found that ERK/c-Myc presumably is its signaling pathway by bioinformatics analysis and Western blot verification. To sum up, knockdown of FGFR3 inhibited the migration, invasion and proliferation of ICC cells. It demonstrated that FGFR3 probably becomes a therapeutic target for ICC and increases the proportion of potentially curable intrahepatic cholangiocarcinoma patients treated with FGFR inhibitors.

Additional file 4: Table S3.The miRNA enrichment analysis results of dysregulated miRNAs.

BACKGROUND:Gallbladder carcinoma (GBC) is a highly malignant tumor with a poor overall prognosis. This study aimed to identify the characteristic microRNAs (miRNAs) of GBC and the competing endogenous RNA (ceRNA) regulatory mechanisms.METHODS:The microarray data of GBC tissue samples and normal gallbladder (NGB) tissue samples from the Gene Expression Omnibus (GEO) database was downloaded. GBC-related differentially expressed miRNAs (DE-miRNAs) were identified by inter-group differential expression analysis and weighted gene co-expression network analysis (WGCNA). Machine learning algorithms were used to screen the characteristic miRNA based on the intersect between least absolute shrinkage and selection operator (LASSO) and Support vector machine-recursive feature elimination (SVM-RFE). Based on the differential expression analysis of GEO database, the ceRNA network of characteristic miRNA was predicted and constructed. The biological functions of the ceRNA network were revealed by carrying out the gene enrichment analysis was implemented. We further screened the key genes of ceRNA network and constructed a protein-protein interaction (PPI) network, and predicted and generated the transcription factors (TFs) network of signature miRNAs. The expression of characteristic miRNA in clinical samples was verified by quantitative real-time polymerase chain reaction (qRT-PCR).RESULTS:A total of 131 GBC-related DE-miRNAs were obtained. The hsa-miR-4770 was defined as characteristic miRNA for GBC. The ceRNA network containing 211 mRNAs, one miRNA, two lncRNAs, and 48 circRNAs was created. Gene enrichment analysis suggested that the downstream genes were mainly involved in actin filament organization, cell-substrate adhesion, cell-matrix adhesion, reactive oxygen species metabolic process, glutamine metabolic process and extracellular matrix (ECM)-receptor interaction pathway. 10 key genes in the network were found to be most correlated with disease, and involved in cell cycle-related processes, p53, and extrinsic apoptotic signaling pathways. The qRT-PCR result demonstrated that hsa-miR-4770 is down-regulated in GBC, and the expression trend is consistent with the public database.CONCLUSIONS:We identified hsa-miR-4770 as the characteristic miRNA for GBC. The ceRNA network of hsa-miR-4770 may play key roles in GBC. This study provided some basis for potential pathogenesis of GBC.

Abstract Background and Aims: Gallbladder carcinoma (GBC) is a highly malignant tumor with a poor overall prognosis. This study aimed to identify the characteristic microRNAs (miRNAs) of GBC and the competing endogenous RNA (ceRNA) regulatory mechanisms. Methods GBC-related differentially expressed miRNAs (DE-miRNAs) were authenticated by differential expression analysis and weighted gene co-expression network analysis (WGCNA). The characteristic miRNA was extracted by least absolute shrinkage and selection operator (LASSO) and Support vector machine-recursive feature elimination (SVM-RFE). Targeting genes (mRNAs), upstream circularRNAs (circRNAs), and long noncoding RNAs (lncRNAs) prediction for the characteristic miRNAs was conducted by using the Starbase database. The lncRNA(circRNA)-miRNA-mRNA network was created by Cytoscape software. Gene Ontology (GO) and KEGG enrichment analysis was implemented by clusterProfiler R package. The varElect was applied to analyse the target genes, and search for functions and interactions by GeneMANIA. The expression of characteristic miRNA in clinical samples was verified by quantitative real-time polymerase chain reaction (RT-qPCR). Results A total of 131 GBC-related DE-miRNAs were obtained. The hsa-miR-4770 was defined as characteristic miRNA for GBC. The ceRNA network containing 211 mRNAs, 1 miRNA, 2 lncRNAs, and 48 circRNAs was created. The downstream genes were mainly involved in actin filament organization, cell-substrate adhesion, cell-matrix adhesion, reactive oxygen species metabolic process, glutamine metabolic process and extracellular matrix (ECM)-receptor interaction pathway. 10 key genes in the network, namely BRCA1, CHEK2, RB1, CASP8, PTGS2, CD44, KRT19, CDK1, PVT1, and MXRA5 were found to be most correlated with disease. Multiple genes involved in cell cycle-related processes, p53 related pathway, and extrinsic apoptotic signaling pathway. RT-qPCR result demonstrated that the expression trends of hsa-miR-4770 was consistent with the public database. Conclusion We identified hsa-miR-4770 as the characteristic miRNA for GBC. The ceRNA network of hsa-miR-4770 may play key roles in GBC. This study provided a little basis for potential pathogenesis of GBC.

Purpose: Intrahepatic cholangiocarcinoma (ICC) can invade and metastasize. EIF5A2 is involved in the invasive metastatic process of several digestive malignancies. However, its role in ICC is yet to be elucidated. Methods: Immunohistochemistry (IHC) and Western blot (WB) were used to detect the level of EIF5A2 in the tumor specimens of ICC patients and evaluate the correlation between its expression and clinicopathological characteristics. The significance of EIF5A2 in the prognosis of ICC patients was further evaluated by Kaplan-Meier and Cox regression analysis. In addition, CCK-8, EdU, Transwell invasion, and scratch assays were utilized to detect tumor cell proliferation, invasion, and metastasis. Furthermore, the role of EIF5A2 in ICC cells was evaluated after modification of EIF5A2 expression. Results: The level of EIF5A2 protein was significantly higher in ICC than in adjacent tissues. This high expression in the tumor samples was significantly associated with malignant phenotypes, such as lymph node metastasis (LNM), microvascular or bile duct invasion, and poor differentiation. ICC patients with high expression of EIF5A2 had short overall survival and a high cumulative recurrence rate. The multifactorial analysis showed that EIF5A2 is an independent prognostic marker. Furthermore, high levels of EIF5A2 may activate the PI3K/AKT/mTOR signaling pathway and upregulate Cyclin D1, Cyclin D3, MMP2, and MMP9 to promote ICC cell proliferation, migration, and invasion. Conclusion: The current study found that EIF5A2 promotes ICC progression and is a prognostic biomarker and candidate therapeutic target for ICC patients. (c) 2022 The Authors. Published by Elsevier Masson SAS.

Background The need for intraoperative endoscopic nasobiliary drainage during laparoscopic cholecystectomy and laparoscopic common bile duct exploration with primary closure is controversial in the treatment of cholecystolithiasis combined with choledocholithiasis. The aim of this study was to evaluate the safety and efficacy of laparoscopic cholecystectomy + laparoscopic common bile duct exploration + intraoperative endoscopic nasobiliary drainage + primary closure (LC + LCBDE + IO-ENBD + PC). The safety of different intubation methods in IO-ENBD was also evaluated. Method From January 2018 to January 2022, 168 consecutive patients with cholecystolithiasis combined with choledocholithiasis underwent surgical treatment in our institution. Patients were divided into two groups: group A ( n = 96) underwent LC + LCBDE + IO-ENBD + PC and group B ( n = 72) underwent LC + LCBDE + PC. Patient characteristics, perioperative indicators, complications, stone residual, and recurrence rates were analyzed. Group A was divided into two subgroups. In group A 1 , the nasobiliary drainage tube was placed in an anterograde way, and in group A 2 , nasobiliary drainage tube was placed in an anterograde–retrograde way. Perioperative indicators and complications were analyzed between subgroups. Results No mortality in the two groups. The operation success rates in groups A and B were 97.9% (94/96) and 100% (72/72), respectively. In group A, two patients were converted to T-tube drainage. The stone clearance rates of group A and group B were 100% (96/96) and 98.6% (71/72), respectively. Common bile duct diameter was smaller in group A [10 vs. 12 mm, P < 0.001] in baseline data. In perioperative indicators, group A had a longer operation time [165 vs.135 min, P < 0.001], but group A had a shorter hospitalization time [10 vs.13 days, P = 0.002]. The overall complications were 7.3% (7/96) in group A and 12.5% (9/72) in group B. Postoperative bile leakage was less in group A [0% (0/96) vs. 5.6% (4/72), P = 0.032)]. There were no residual and recurrent stones in group A. And there were one residual stone and one recurrent stone in group B (all 1.4%). The median follow-up time was 12 months in group A and 6 months in group B. During the follow-up period, 2 (2.8%) patients in group B had a mild biliary stricture. At subgroup analysis, group A 1 had shorter operation time [150 vs. 182.5 min, P < 0.001], shorter hospitalization time [9 vs. 10 days, P = 0.002], and fewer patients with postoperative elevated pancreatic enzymes [32.6% (15/46) vs. 68% (34/50), P = 0.001]. Conclusion LC + LCBDE + IO-ENBD + PC is safer and more effective than LC + LCBDE + PC because it reduces hospitalization time and avoids postoperative bile leakage. In the IO-ENBD procedure, the antegrade placement of the nasobiliary drainage tube is more feasible and effective because it reduces the operation time and hospitalization time, and also reduces injury to the duodenal papilla.

Additional file 3. Differentlly expressed genes in ICC.

Tumor-associated macrophage (TAM) is a major component of tumor microenvironment (TME) and plays critical role in the progression of cancer metastasis. However, TAM-mediated regulation in gallbladder cancer (GBC) has not been fully characterized. Here, we found that exosomes derived from GBC cell polarized macrophage to M2 phenotype, which then facilitated the invasion and migration of GBC cells. We discovered that leptin was enriched in GBC cell-derived exosomes. Exosomal leptin levels promoted invasion and migration of GBC-SD cells. The inhibition of leptin not only attenuated M2 macrophage of polarization but also inhibited the invasive and migratory ability of GBC cell. In addition, GBC-SD cell-derived exosomal leptin induced M2 polarization of macrophage via activation of STAT3 signal pathway. Taken together, our results suggested that GBC cells secrete exosome-enclosed leptin facilitated cell invasion and migration via polarizing TAM.

目的 探究AK4对肝内胆管癌细胞HUCCT1增殖、迁移能力的影响.方法 采用小干扰RNA(siRNA)技术靶向沉默肝内胆管癌细胞HUCCT1中AK4的表达,采用免疫印迹法检测沉默效果以及筛选siRNA-AK4,通过EdU实验和细胞划痕实验检测该胆管癌细胞增殖、迁移能力.结果 通过免疫印迹法检测出siRNA-AK4-3沉默效果最好,EdU实验显示沉默AK4后,细胞增殖能力下降(P＜0.05),细胞划痕实验显示沉默AK4后,细胞迁移能力下降(P＜0.01).结论 沉默肝内胆管癌细胞HUCCT1中AK4的表达后,其增殖、迁移能力受到抑制.

Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor, which poses a serious threat to human health. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification involved in regulating a broad range of biological processes and has been considered as potential therapeutic target in types of cancer. However, there is limited research on investigating profiles of histone modification H3K9me3 in ICC patients. In this study, we applied the ChIP-seq technique to investigate the effect of H3K9me3 on ICC. Anti-H3K9me3 antibody was used for ChIP-seq in ICC (RBE cell lines) and HIBEpic (normal cell lines). MACS2 (peak-calling tools) was then used to identify the peaks recorded in RBE and HIBEpic cell lines. Gene expression, mutation and clinical data were downloaded from TCGA and cBioPortal databases. H3K9me3 exhibited abnormal methylation and influenced the process of abnormal gene expression in patients suffering from ICC. The Wnt/β-Catenin signaling pathway (also known as simply the WNT signaling pathway) was enriched in H3K9me3-regulated genes. We are the first to report that H3K9me3 may play an important role in the progression of ICC. It promotes the understanding of epigenetic molecular mechanisms for ICC.

The environmental safety and threats of graphene-based materials (GBMs) to the agroecosystem have attracted increasing attention in recent years. However, the mechanisms underlying the effects of GBMs on plants remain unclear. Here, we investigated the phytotoxicity of reduced graphene oxide (RGO), graphene oxide (GO) and amine-functionalized graphene (G-NH2) on Brassica napus L. The results revealed that RGO impaired photosynthesis mainly by decreasing the chlorophyll content and Rubisco activity. A further gene-level analysis suggested that this effect of RGO might be due to its toxicity on sulfate transmembrane transporter and nitrogen metabolism, which ultimately led to nutrient imbalance. However, GO directly damaged the photosystem by disrupting the chloroplast structure, and a decrease in Rubisco activity indicated that GO also inhibits carbon fixation. Further gene-level analysis demonstrated that GO has toxicity on the chloroplast membrane, photosystem, photosynthethic electron transport and F-type ATPase. In addition, G-NH2 at 10–1000 mg L−1 showed no significant toxicity. These findings shed light on the potential mechanism for the toxicity of GBMs on plants for risk assessment.