Background
Cancer-associated fibroblasts (CAFs) are involved in tumor growth, angiogenesis, metastasis, and resistance to therapy. We sought to explore the CAFs characteristics in hepatocellular ...carcinoma (HCC) and establish a CAF-based risk signature for predicting the prognosis of HCC patients.
Methods
The signal-cell RNA sequencing (scRNA-seq) data was obtained from the GEO database. Bulk RNA-seq data and microarray data of HCC were obtained from the TCGA and GEO databases respectively. Seurat R package was applied to process scRNA-seq data and identify CAF clusters according to the CAF markers. Differential expression analysis was performed to screen differentially expressed genes (DEGs) between normal and tumor samples in TCGA dataset. Then Pearson correlation analysis was used to determine the DEGs associated with CAF clusters, followed by the univariate Cox regression analysis to identify CAF-related prognostic genes. Lasso regression was implemented to construct a risk signature based on CAF-related prognostic genes. Finally, a nomogram model based on the risk signature and clinicopathological characteristics was developed.
Results
Based on scRNA-seq data, we identified 4 CAF clusters in HCC, 3 of which were associated with prognosis in HCC. A total of 423 genes were identified from 2811 DEGs to be significantly correlated with CAF clusters, and were narrowed down to generate a risk signature with 6 genes. These six genes were primarily connected with 39 pathways, such as angiogenesis, apoptosis, and hypoxia. Meanwhile, the risk signature was significantly associated with stromal and immune scores, as well as some immune cells. Multivariate analysis revealed that risk signature was an independent prognostic factor for HCC, and its value in predicting immunotherapeutic outcomes was confirmed. A novel nomogram integrating the stage and CAF-based risk signature was constructed, which exhibited favorable predictability and reliability in the prognosis prediction of HCC.
Conclusion
CAF-based risk signatures can effectively predict the prognosis of HCC, and comprehensive characterization of the CAF signature of HCC may help to interpret the response of HCC to immunotherapy and provide new strategies for cancer treatment.
Tissue sampling of biliary tract carcinomas (BTCs) for molecular characterization is challenging. The aim of this study was to investigate the possibility of identifying individual actionable ...mutations derived from bile cell‑free DNA (cfDNA) using targeted deep sequencing. Ten BTC patients, four with gallbladder carcinomas and six with cholangiocarcinomas, were enrolled in the present study. Using targeted deep sequencing with a panel of 150 tumor‑related genes, paired bile cfDNA and tumor DNA were analyzed for mutational variants individually and then compared. The present study, to the best of our knowledge, is the first to reveal that bile cfDNA is predominantly comprised of long DNA fragments, which is not the case for plasma cfDNA. Herein, paired bile cfDNA and tumors from ten BTC patients were examined using targeted deep sequencing. When comparing bile cfDNA and tumor DNA for single nucleotide variation (SNV)/insertion and deletion (Indel), the results using targeted deep sequencing revealed high sensitivity (94.7%) and specificity (99.9%). Additionally, the sensitivity of detecting a copy number variation (CNV) was 75.0%, with a specificity of 98.9%. When comparing two bile extraction methods, including percutaneous transhepatic cholangial drainage and operation, no significant difference in SNV/Indel or CNV detection sensitivity was noted. Moreover, when examining the tumor stage and incidence site, AJCC stage II and the distal bile duct both had significantly decreased CNV detection sensitivities. The present study revealed that targeted deep sequencing can reliably detect mutational variants within bile cfDNA obtained from BTC patients. These preliminary results may shed light on bile cfDNA as a promising liquid biopsy for BTC patients.
Cell-free DNA (cfDNA) exists in various types of bodily fluids, including plasma, urine, bile, and others. Bile cfDNA could serve as a promising liquid biopsy for biliary tract cancer (BTC) patients, ...as bile directly contacts tumors in the biliary tract system. However, there is no commercial kit or widely acknowledged method for bile cfDNA extraction. In this study, we established a silica-membrane-based method, namely 3D-BCF, for bile cfDNA isolation, exhibiting effective recovery of DNA fragments in the spike-in assay. We then compared the 3D-BCF method with four other commercial kits: the BIOG cfDNA Easy Kit (BIOG), QIAamp DNA Mini Kit (Qiagen), MagMAX
Cell-Free DNA Isolation Kit (Thermo Fisher), and NORGEN Urine Cell-Free Circulating DNA Purification Mini Kit (Norgen Biotek). The proposed 3D-BCF method exhibited the highest cfDNA isolation efficiency (p < 0.0001) from patient bile samples, and bile cfDNA of short, medium or long fragments could all be extracted effectively. To test whether the extracted bile cfDNA from patients carries tumor-related genomic information, we performed next-generation sequencing on the cfDNA and verified the gene-mutation results by polymerase chain reaction (PCR)-Sanger chromatograms and copy-number-variation (CNV) detection by fluorescence
hybridization (FISH) of tumor tissues. The 3D-BCF method could efficiently extract cfDNA from bile samples, providing technical support for bile cfDNA as a promising liquid biopsy for BTC patient diagnosis and prognosis.
In the last decade, circular RNAs (circRNAs) emerge as important regulators in multiple biological processes. Lately, it is reported hsa_circRNA_103809 could play vital parts in several types of ...cancers. Based on the analysis of GEO data (GSE97332), hsa_circRNA_103809 was found to be dysregulated in hepatocellular carcinoma (HCC). However, the biological function and underlying regulatory mechanisms of hsa_circRNA_103809 in HCC remain unclear. Our results suggested that hsa_circRNA_103809 was overexpressed in HCC patients, and hsa_circRNA_103809 knockdown remarkably inhibited the proliferation, cycle progression, and migration of HCC cells. The investigations of molecular showed that hsa_circRNA_103809 could elevate the protein expression of a miR‐377‐3p target, fibroblast growth factor receptor 1 (FGFR1), through interacting with miR‐377‐3p and decreasing its expression level. Additionally, in vivo assays revealed hsa_circRNA_103809 short hairpin RNA served as a tumor suppressor through downregulating FGFR1 in HCC. This study systematically investigated novel regulatory signaling of hsa_circRNA_103809/miR‐377‐3p/FGFR1 axis, providing insights into hepatocellular carcinoma treatment from bench to clinic.
In the last decade, circular RNAs (circRNAs) emerge as important regulators in multiple biological processes. Lately, it is reported hsa_circRNA_103809 could play vital parts in several types of cancers. Based on the analysis of GEO data (GSE97332), hsa_circRNA_103809 was found to be dysregulated in hepatocellular carcinoma (HCC). However, the biological function and underlying regulatory mechanisms of hsa_circRNA_103809 in HCC remain unclear. Our results suggested that hsa_circRNA_103809 was overexpressed in HCC patients, and hsa_circRNA_103809 knockdown remarkably inhibited the proliferation, cycle progression, and migration of HCC cells. The investigations of molecular showed that hsa_circRNA_103809 could elevate the protein expression of a miR‐377‐3p target, fibroblast growth factor receptor 1 (FGFR1), through interacting with miR‐377‐3p and decreasing its expression level. Additionally, in vivo assays revealed hsa_circRNA_103809 short hairpin RNA (shRNA) served as a tumor suppressor through downregulating FGFR1 in HCC. This study systematically investigated novel regulatory signaling of hsa_circRNA_103809/miR‐377‐3p/FGFR1 axis, providing insights into hepatocellular carcinoma treatment from bench to clinic.
Chinese solar greenhouse (CSG) is an important energy-saving building to ensure the winter production of crops, but it still faces the problem of unbalanced supply and demand between actual thermal ...performance and crop temperature demand. The purpose of this study is to establish the relationship between greenhouse thermal environment simulation and thermal performance design and to put forward specific thermal performance requirements for the main heat storage components (walls) in the greenhouse design stage. Therefore, this study proposed a method to construct the thermal environment fluctuation model of Chinese solar greenhouse based on temperature-wave interaction theory. The method used dimensional analysis method to comprehensively analyze the related physical quantities of greenhouse thermal environment, explored the temperature fluctuation interaction among indoor air, energy storage wall and outdoor air, and constructed the thermal environment fluctuation model of Chinese solar greenhouse. Finally, the thermal environment fluctuation equation of Chinese solar greenhouse was established under the external climatic conditions in Xi'an, Shaanxi Province, and verified by the measured data of the experimental greenhouse. The experimental results show that the mean absolute error (MAE) between the predicted and measured indoor air temperature is 0.66 °C, the root mean square error (RMSE) is 1.04 °C, and the determination coefficient (R2) is 0.9956 (n = 2822). The model and equation accurately described the interaction between greenhouse internal components and the external greenhouse environment. The study put forward specific thermal performance design requirements for the main heat storage components (walls) in greenhouse, and also provided a new research method for the thermal environment model of Chinese solar greenhouse.
Objectives
LncRNAs (long noncoding RNAs) have been reported to critically regulate colorectal cancer (CRC). We prospectively investigated effects and mechanisms of lncRNA LINC00858 on regulation of ...CRC progression.
Methods
Expression of LINC00858 and its target were analyzed by quantitative real-time polymerase chain reaction and in situ hybridization. MTT and bromodeoxyuridine/5-bromo-2′-deoxyuridine (BrdU) staining to assess cell proliferation ability. Flow cytometry, wound healing, and transwell assays were conducted to evaluate cell apoptosis, migration, and invasion, respectively. Interaction between LINC00858 and its target was confirmed by luciferase activity assay and RNA immunoprecipitation. Subcutaneous xenotransplanted tumor model was established and employed to detect tumorigenic functions of LINC00858, and further evaluated by qRT-PCR, western blot, immunohistochemistry, and hematoxylin and eosin staining.
Results
With a predicted poor prognosis, LINC00858 was upregulated in CRC patients. LINC00858 knockdown suppressed cell proliferation, invasion, and migration abilities, meanwhile induced cell apoptosis. Moreover, LINC00858 could target and inhibit the miR-4766-5p expression, thus promoting CRC progression. miR-4766-5p further suppressed serine/threonine kinase PAK2. Interestingly, interference of LINC00858 suppressed tumorigenic ability of CRC in vivo by downregulating PAK2.
Conclusions
LINC00858 promoted CRC progression by sponging miR-4766 to upregulate PAK2, shedding lights on LINC00858 as a potential therapeutic target candidate in CRC treatment from bench to clinic.
Despite stunning progress in single-atom catalysis (SAC), it remains a grand challenge to yield a high loading of single atoms (SAs) anchored on substrates. Herein, we report a one-step ...laser-planting strategy to craft SAs of interest under an atmospheric temperature and pressure on various substrates including carbon, metals, and oxides. Laser pulses render concurrent creation of defects on the substrate and decomposition of precursors into monolithic metal SAs, which are immobilized on the as-produced defects via electronic interactions. Laser planting enables a high defect density, leading to a record-high loading of SAs of 41.8 wt %. Our strategy can also synthesize high-entropy SAs (HESAs) with the coexistence of multiple metal SAs, regardless of their distinct characteristics. An integrated experimental and theoretical study reveals that superior catalytic activity can be achieved when the distribution of metal atom content in HESAs resembles the distribution of their catalytic performance in a volcano plot of electrocatalysis. The noble-metal mass activity for a hydrogen evolution reaction within HESAs is 11-fold over that of commercial Pt/C. The laser-planting strategy is robust, opening up a simple and general route to attaining an array of low-cost, high-density SAs on diverse substrates under ambient conditions for electrochemical energy conversion.
Long non-coding RNAs (lncRNA) have an essential role in progression and chemoresistance of hepatocellular carcinoma (HCC). In-depth study of specific regulatory mechanisms is of great value in ...providing potential therapeutic targets. The present study aimed to explore the regulatory functions and mechanisms of lncRNA TINCR in HCC progression and oxaliplatin response.
The expression of TINCR in HCC tissues and cell lines was detected by quantitative reverse transcription PCR (qRT-PCR). Cell proliferation, migration, invasion, and chemosensitivity were evaluated by cell counting kit 8 (CCK8), colony formation, transwell, and apoptosis assays. Luciferase reporter assays and RNA pulldown were used to identify the interaction between TINCR and ST6 beta-galactoside alpha-2,6-sialyltransferase 1 (ST6GAL1) via miR-195-3p. The corresponding functions were verified in the complementation test and in vivo animal experiment.
TINCR was upregulated in HCC and associated with poor patient prognosis. Silencing TINCR inhibited HCC proliferation, migration, invasion, and oxaliplatin resistance while overexpressing TINCR showed opposite above-mentioned functions. Mechanistically, TINCR acted as a competing endogenous (ceRNA) to sponge miR-195-3p, relieving its repression on ST6GAL1, and activated nuclear factor kappa B (NF-κB) signaling. The mouse xenograft experiment further verified that knockdown TINCR attenuated tumor progression and oxaliplatin resistance in vivo.
Our finding indicated that there existed a TINCR/miR-195-3p/ST6GAL1/NF-κB signaling regulatory axis that regulated tumor progression and oxaliplatin resistance, which might be exploited for anticancer therapy in HCC.
Colorectal cancer is one of the most common and leading malignancies globally. Long noncoding RNAs (lncRNAs) function as potentially critical regulator in colorectal cancer. LINC01234, a novel lncRNA ...in tumor biology, regulates the progression of various tumors. However, the tumorigenic mechanism of LINC01234 in colorectal cancer is still unclear. This study was performed with the aim to prospectively investigate clinical significance, effect, and mechanism of lncRNA LINC01234 in colorectal cancer. First, we found that LINC01234, localized in the cytoplasm, was increased in both colorectal cancer cell lines and tissues. Subsequent functional assays suggested LINC01234 knockdown suppressed cell proliferation, migration, and invasion of colorectal cancer cells, while blocked cell cycle and induced cell apoptosis. Moreover, we identified that miR‐1284 was target of LINC01234, we further demonstrated a negative correlation with LINC01234 in colorectal cancer tissues and cells. Furthermore, miR‐1284 targeted and suppressed tumor necrosis factor receptor–associated factor 6 (TRAF6). Loss‐of‐function assay revealed that LINC01234 silencing suppressed colorectal cancer progression through inhibition of miR‐1284. In vivo subcutaneous xenotransplanted tumor model indicated LINC01234 knockdown inhibited in vivo tumorigenic ability of colorectal cancer via downregulation of TRAF6. Collectively, this study clarified the biological significance of LINC01234/miR‐1284/TRAF6 axis in colorectal cancer progression, providing insights into LINC01234 as novel potential therapeutic target for colorectal cancer therapeutic from bench to clinic.
Long noncoding RNA, LINC01234, was upregulated in both colorectal cancer tissues and cell lines LINC01234 knockdown suppressed colorectal proliferation, migration, invasion, and induced cell apoptosis.
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