Systematic Characterization of DNA Methyltransferases Family in Tumor Progression and Antitumor Immunity.

Objective: DNA methylation is an essential epigenetic marker governed by DNA methyltransferases (DNMTs), which can influence cancer onset and progression. However, few studies have provided an integrated analysis of the relevance of DNMT family genes to cell stemness, the tumor microenvironment (TME), and immunotherapy biomarkers across diverse cancers. Methods: This study investigated the impact of five DNMTs on transcriptional profiles, prognosis, and their association with Ki67 expression, epithelial-mesenchymal transition signatures, stemness scores, the TME, and immunological markers across 31 cancer types from recognized public databases. Results: The results indicated that DNMT1/DNMT3B/DNMT3A expression increased, whereas TRDMT1/DNMT3L expression decreased in most cancer types. DNMT family genes were identified as prognostic risk factors for numerous cancers, as well as being prominently associated with immune, stromal, and ESTIMATE scores, as well as with immune-infiltrating cell levels. Expression of the well-known immune checkpoints, PDCD1 and CILA4, was noticeably related to DNMT1/DNMT3A/DNMT3B expression. Finally, we validated the role of DNMT1 in MCF-7 and HepG2-C3A cell lines through its knockdown, whereafter a decrease in cell proliferation and migration ability in vitro was observed. Conclusion: Our study comprehensively expounded that DNMT family genes not only behave as promising prognostic factors but also have the potential to serve as therapeutic targets in cancer immunotherapy for various types of cancer.

Influence of copper and aging on freely dissolved tetracycline concentration in soil.

Copper (Cu) and tetracyclines (TCs) often coexist in agricultural soils because of the use of manures on farmland; however, the influence of Cu on the bioavailability of TCs is still unclear, especially for cases with aging Cu. The freely dissolved concentrations (FDCs) of TCs are believed to be directly related to their bioavailability. In the present study, the FDCs of TCs were determined using organic-diffusive gradients in thin films (o-DGT), and the influence of Cu on the FDCs of TCs in soils was evaluated. The results showed that the FDCs of tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC) were 0.11-0.93, 0.28-1.02, and 0.24-0.53 µg/kg in the CK groups (no Cu added) and accounted for 0.09-0.58, 0.10-1.40, and 0.05-1.19‰ of their total concentrations which ranged from 0.2 to 10.0 mg/kg for TC, OTC, and CTC, respectively. The co-contamination of Cu reduced the FDCs of TCs in most cases, and aging increased the influence of Cu. The presence of Cu resulted in a decrease in the TC FDC by 35.48-95.04% in aged soils and 3.42-87.19% in newly prepared soils. FTIR analysis revealed that aging facilitated the bonding of Cu to soil particles via Cu-O, and Cu bonded to groups such as hydroxyl groups (-OH) in TCs. Our results suggested that the presence of Cu might reduce the bioavailability of TCs, and aging would enhance these effects. This is helpful for the bioavailability analysis of TCs under co-contamination of heavy metals.

Vimentin promotes glioma progression and maintains glioma cell resistance to oxidative phosphorylation inhibition.

PURPOSE: Glioma has been demonstrated as one of the most malignant intracranial tumors and currently there is no effective treatment. Based on our previous RNA-sequencing data for oxidative phosphorylation (OXPHOS)-inhibition resistant and OXPHOS-inhibition sensitive cancer cells, we found that vimentin (VIM) is highly expressed in the OXPHOS-inhibition resistant cancer cells, especially in glioma cancer cells. Further study of VIM in the literature indicates that it plays important roles in cancer progression, immunotherapy suppression, cancer stemness and drug resistance. However, its role in glioma remains elusive. This study aims to decipher the role of VIM in glioma, especially its role in OXPHOS-inhibition sensitivity, which may provide a promising therapeutic target for glioma treatment. METHODS: The expression of VIM in glioma and the normal tissue has been obtained from The Cancer Genome Atlas (TCGA) database, and further validated in Human Protein Atlas (HPA) and Chinese Glioma Genome Atlas (CGGA). And the single-cell sequencing data was obtained from TISCH2. The immune infiltration was calculated via Tumor Immune Estimation Resource (TIMER), Estimation of Stromal and Immune Cells in Malignant Tumors using Expression Data (ESTIMATE) and ssGSEA, and the Immunophenoscore (IPS) was calculated via R package. The differentiated expressed genes were analyzed including GO/KEGG and Gene Set Enrichment Analysis (GSEA) between the VIM-high and -low groups. The methylation of VIM was checked at the EWAS and Methsurv. The correlation between VIM expression and cancer stemness was obtained from SangerBox. We also employed DepMap data and verified the role of VIM by knocking down it in VIM-high glioma cell and over-expressing it in VIM-low glioma cells to check the cell viability. RESULTS: Vim is highly expressed in the glioma patients compared to normal samples and its high expression negatively correlates with patients' survival. The DNA methylation in VIM promoters in glioma patients is lower than that in the normal samples. High VIM expression positively correlates with the immune infiltration and tumor progression. Furthermore, Vim is expressed high in the OXPHOS-inhibition glioma cancer cells and low in the OXPHOS-inhibition sensitive ones and its expression maintains the OXPHOS-inhibition resistance. CONCLUSIONS: In conclusion, we comprehensively deciphered the role of VIM in the progression of glioma and its clinical outcomes. Thus provide new insights into targeting VIM in glioma cancer immunotherapy in combination with the current treatment.

Mechanistic insights into the allosteric inactivation mechanism of ZAP-70 induced by the hot spot W165C mutation.

Zeta chain-associated protein kinase 70 (ZAP-70) is a non-receptor tyrosine kinase that interacts with the activated T-cell receptor to transduce downstream signals, and thus plays an important role in the adaptive immune system. The biphosphorylated immunotyrosine-based activation motifs (ITAM-Y2P) binds to the N-SH2 and C-SH2 domains of ZAP-70 to promote the activation of ZAP-70. The present study explores molecular mechanisms of allosteric inactivation of ZAP-70 induced by the hot spot W165C mutation through atomically detailed molecular dynamics simulation approaches. We report microsecond-length simulations of two states of the tandem SH2 domains of ZAP-70 in complex with the ITAM-Y2P motif, including the wild-type and W165C mutant. Extensive analysis of local flexibility and dynamical correlated motions show that W165C mutation changes coupled motions of protein domains and community networks. The binding affinities of the ITAM-Y2P motif to the wild-type and W165C mutant of ZAP-70 are predicted using binding free energy calculations. The results suggest that the driving force to decrease the binding affinity in the W165C mutant derives from the difference in the protein-protein electrostatic interactions. Moreover, the per-residue free energy decomposition unravels that the contributions from residues in the phosphorylated Tyr315 (pY315) binding site, in particular pY315 of ITAM-Y2P, and Arg43, Tyr240 of ZAP-70, are the key determinants for the loss of binding affinity. This study may insights into our understanding of the pathological mechanism of ZAP-70.Communicated by Ramaswamy H. Sarma.

Surgical treatment of hilar cholangiocarcinoma: retrospective analysis.

BACKGROUND: Achieving a better prognosis for patients and reducing the risk of complications are primary considerations in surgical decisions for hilar cholangiocarcinoma. METHODS: A retrospective analysis of the authors' clinical practice outcomes in the surgical management of patients with hilar cholangiocarcinoma following the planned-hepatectomy surgical treatment programme between 2009 and 2018. RESULTS: Some 473 patients were included, of whom 127 (26.8 per cent) underwent bile duct tumour resection alone, 44 (9.3 per cent) underwent bile duct tumour resection combined with restrictive hepatectomy, and 302 (63.8 per cent) underwent bile duct tumour resection combined with extensive hepatectomy. R0 resection was achieved in 82.2 per cent and the postoperative complication rate was similar between the different operations. The 5-year survival rates after surgery were 37.0, 37.3, and 28.4 per cent in the bile duct tumour resection alone, restrictive hepatectomy, and extensive hepatectomy groups respectively, with no statistically significant differences. As TNM staging progressed, the 1-5-year cumulative survival rate for the patients in the three groups showed a significant downward trend. CONCLUSION: In the setting of a high-volume centre, a planned-hepatectomy surgical treatment programme helps to strike a better balance between achieving radical tumour resection for hilar cholangiocarcinoma and reasonable control of the extent of surgical damage.

N6-Methyladenosine-Mediated Up-Regulation of FZD10 Regulates Liver Cancer Stem Cells' Properties and Lenvatinib Resistance Through WNT/ß-Catenin and Hippo Signaling Pathways.

BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide, but there is a deficiency of early diagnosis biomarkers and therapeutic targets. Drug resistance accounts for most HCC-related deaths, yet the mechanisms underlying drug resistance remain poorly understood. METHODS: Expression of Frizzled-10 (FZD10) in liver cancer stem cells (CSCs) was identified by means of RNA sequencing and validated by means of real-time polymerase chain reaction and immunohistochemistry. In vitro and in vivo experiments were used to assess the effect of FZD10 on liver CSC expansion and lenvatinib resistance. RNA sequencing, RNA binding protein immunoprecipitation, and luciferase report assays were applied to explore the mechanism underlying FZD10-mediated liver CSCs expansion and lenvatinib resistance. RESULTS: Activation of FZD10 in liver CSCs was mediated by METTL3-dependent N6-methyladenosine methylation of FZD10 messenger RNA. Functional studies revealed that FZD10 promotes self-renewal, tumorigenicity, and metastasis of liver CSCs via activating ß-catenin and YAP1. The FZD10-ß-catenin/YAP1 axis is activated in liver CSCs and predicts poor prognosis. Moreover, FZD10-ß-catenin/c-Jun axis transcriptionally activates METTL3 expression, forming a positive feedback loop. Importantly, the FZD10/ß-catenin/c-Jun/MEK/ERK axis determines the responses of hepatoma cells to lenvatinib treatment. Analysis of patient cohort, patient-derived tumor organoids, and patient-derived xenografts further suggest that FZD10 might predict lenvatinib clinical benefit in patients with HCC. Furthermore, treatment of lenvatinib-resistant HCC with adeno-associated virus targeting FZD10 or a ß-catenin inhibitor restored lenvatinib response. CONCLUSIONS: Elevated FZD10 expression promotes expansion of liver CSCs and lenvatinib resistance, indicating that FZD10 expression is a novel prognostic biomarker and therapeutic target for human HCC.

Single-cell RNA sequencing highlights the functional role of human endogenous retroviruses in gallbladder cancer.

BACKGROUND: Gallbladder cancer (GBC), the most common malignancy of the biliary tract, shows late diagnosis and low survival rate and requires continued search for new diagnostic biomarkers and therapeutic targets. Human endogenous retroviruses (HERVs) are specifically prone to be reactivated in diverse cancers and are implicated in cancer progression and immunotherapy. METHODS: Single-cell RNA sequencing was performed on tumor tissues and paired adjacent tissues from 4 GBC patients. Dual-luciferase reporter assay was applied to measure enhancer activity of HERV sequences. FINDINGS: We dissected the cellular diversity and described the HERV transcriptomic landscape for GBC. We found that HERVs were transcribed in a cell type-specific manner and different HERV families were associated with diverse biological effects. HERVs could function as enhancers, presumably causing altered expression of neighboring genes. The transcription level of HERVH was gradually elevated with the malignant transformation of epithelial cells, suggesting HERVH may be a potential early diagnostic biomarker of GBC. HHLA2, a newly emerging immune checkpoint, was derived by HERVH, exhibited an expressional correlation with HERVH, and was identified as a promising target for immunotherapy. INTERPRETATION: Exploring the transcriptional landscape and potential functional impact of HERVs highlights the important role of HERVs in GBC and provides a fresh perspective on managing GBC. FUNDING: This study was supported by the National Natural Science Foundation of China (31970176, 81972256) and the research grants from the Innovation Capacity Building Project of Jiangsu province (BM2020019).

LncRNA MCF2L-AS1 aggravates the malignant development of colorectal cancer via targeting miR-105-5p/RAB22A axis.

BACKGROUND: Colorectal cancer (CRC) represents one of the major malignant cancers in the world. It has been demonstrated that long non-coding RNAs (lncRNAs) can cause great influences on various human cancers. Though MCF.2 cell line derived transforming sequence like antisense RNA 1 (MCF2L-AS1) and its carcinogenic effect in CRC has been elucidated by several previous researches, the underlying mechanism remains unknown. AIM: We aimed at exploring the function and regulatory mechanism of MCF2L-AS1 in CRC. METHODS: MCF2L-AS1 expression in CRC cells was tested via RT-qPCR assay. The effects of MCF2L-AS1 on the biological properties of CRC cells were testified through functional experiments. The molecular mechanism of MCF2L-AS1 was verified through mechanism experiments. RESULTS: MCF2L-AS1 was highly expressed in CRC cells, and it could enhance the proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) process of CRC cells. MiR-105-5p was sponged by MCF2L-AS1 in CRC cells and Ras-related protein Rab-22A (RAB22A) was verified to be the downstream target of miR-105-5p. It was verified through rescue assays that RAB22A overexpression or miR-105-5p silencing could reverse the repressive impact of MCF2L-AS1 silencing on CRC progression. CONCLUSION: MCF2L-AS1 accelerated the malignant development of CRC cells by targeting the miR-105-5p/RAB22A axis.

The Clinical Role of Preoperative Serum CA19-9 and Carcinoembryonic Antigen (CEA) Levels in Evaluating the Resectability of Advanced Gallbladder Cancer.

BACKGROUND The present study was designed to study the ability of preoperative serum concentrations of the tumor-associated biomarkers carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9) and adjusted CA19-9 to assess the resectability of advanced gallbladder cancer (GBC). MATERIAL AND METHODS This retrospective study included patients with potentially resectable stage II-IV (AJCC 8th) GBC examined at our institution between January 2012 and December 2016. Receiver operating characteristic (ROC) curve analysis was used to determine the predictive value and optimal cut-off point of tumor-associated biomarkers for curative resection. RESULTS Pathological examination of the 309 patients included in this study found that 169 (54.7%) underwent R0 (curative) resection, whereas 121 (39.2%) underwent R1/2 (non-curative) resection, and 19 (6.1%) were unresectable. The mean serum concentrations of CEA, CA19-9 and adjusted CA19-9 were significantly lower in patients who underwent R0 resection than in the other groups. ROC curve analysis showed that adjusted CA19-9 concentration was better able to predict resectability (area under the curve, 0.774; 95% confidence interval, 0.722-0.826; P<0.001) than total bilirubin, CEA, and CA19-9 concentrations. The optimal cut-off for adjusted CA19-9 concentration was 47.63 U/mL, which had a sensitivity of 69.82%, a specificity of 75%, a positive predictive value of 77.12% and a negative predictive value of 67.31%. CONCLUSIONS Adjusted CA19-9 concentration is an easily calculated parameter superior to CA19-9 and CEA concentrations in predicting the resectability of advanced gallbladder cancer.

RNA Sequencing Revealed Signals of Evolution From Gallbladder Stone to Gallbladder Carcinoma.

Gallbladder stone is a major risk factor for gallbladder carcinoma (GBC), while there is still a controversy whether period of follow-up since newly diagnoses of asymptomatic gallstones increases the risk of GBC. In this study, 10 GBC patients and 30 patients with gallstones were admitted to our hospital. Patients with gallstones were divided into 3 groups according to the follow-up time, involving 10 patients with follow-up period of 1-3 years (GS3 group), 10 patients with follow-up period of 5-10 years (GS5 group), and 10 patients with follow-up period of more than 10 years (GS10 group). Tumor and para-tumor tissues of GBC patients, and gallbladder tissues of gallstone patients were collected. RNA sequencing was performed on the 50 samples. Besides, 1,704 differentially expressed genes (DEGs) were identified in tumors compared with para-tumor tissues of 10 GBC patients, which were enriched into some well-known cancer-related pathways, such as PI3K-Akt, mitogen-activated protein kinase (MAPK), Ras, and Wnt signaling pathways, and the most significant pathway was neuroactive ligand-receptor interaction. Patients with gallstones with periods of follow-up equal to 1-3 and > 10 years showed to have higher cancer risk than those with 5-10 years. ALPP and GPR87 are potential biomarkers for predicting cancer risk in patients with gallstones. The in vitro results revealed that GPR-87 can promote the proliferation, migration, and invasion of GBC cells. Herein, we explored the relationship between GBC patients and patients with gallstones with different periods of follow-up in transcriptome level.

Assessment of Neutrophil-to-Lymphocyte Ratio and Platelet-to-Lymphocyte Ratio in Atopic Dermatitis Patients.

BACKGROUND To develop new strategies for identifying atopic dermatitis patients, a better understanding of the signs for chronic inflammatory status is needed. This study was designed to investigate whether neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) are related to the severity of atopic dermatitis (AD) assessed by the Scoring Atopic Dermatitis (SCORAD) index. MATERIAL AND METHODS A retrospective study involving 80 AD patients and 45 healthy control subjects was performed. NLR, PLR, and the number of peripheral blood eosinophils were compared between AD patients and healthy controls, and correlations between these indexes and clinical characteristics were analyzed. RESULTS NLR, PLR, and eosinophils in AD patients were all significantly higher than in healthy individuals. Among AD patients, NLR (p<0.001) and PLR (p<0.001), as contrasted with eosinophils (p=0.146), were correlated positively with SCORAD index. Additionally, an NLR level of 1.75 was determined as the predictive cut-off value of severe AD (SCORAD ≥51) (sensitivity 94.7%, specificity 58.6%, the area under the receiver-operating characteristic curve (AUROC) 0.778, p=0.001). For eosinophils, the sensitivity and specificity were 78.9% and 62.1%, respectively, and the AUROC was only 0.685 (p=0.032) in predicting high SCORAD. CONCLUSIONS NLR and PLR reflect inflammatory response and disease severity in AD patients.

Prognostic value of platelet to lymphocyte ratio in hepatocellular carcinoma: a meta-analysis.

This study was designed to evaluate the prognostic value of platelet to lymphocyte ratio (PLR) in hepatocellular carcinoma (HCC). A comprehensive literature search for relevant studies was performed in Web of science, Embase and Pubmed. A total of nine studies with 2017 patients were included in this meta-analysis, and combined hazard ratio (HR) or odds ratio (OR) and 95% confidence intervals (95%CIs) were served as effect measures. Pooled results showed that elevated PLR was associated with poor overall survival (OS) (HR = 1.63, 95%CI: 1.42-1.88, p = 0.000; I2 = 0.0%, Ph = 0.637) and poor disease-free survival (DFS)/recurrence-free survival (RFS) (HR=1.32, 95%CI: 1.15-1.52, p = 0.000; I2 = 19.3%, Ph = 0.287) in HCC patients. In addition, high PLR was not significantly correlated with the presence of vascular invasion, tumor multifocality, poor tumor grade or high level of serum AFP (>400 ng/ml). In conclusion, elevated PLR indicated a poor prognosis for patients with HCC. PLR may be a reliable, easily-obtained, and low cost biomarker with prognostic potential for HCC.