Immune profiling identifies CD8+ T-cell subset signatures as prognostic markers for recurrence in papillary thyroid cancer.

Background: Thyroid tissue has a special immune microenvironment that is not well characterized. Whether immune cells have a prognostic value in the recurrence of papillary thyroid cancer (PTC) needs further investigation. Methods: Multinodular non-toxic goiter (MNG) was taken as normal tissue for the difficulty in obtaining completely normal thyroid tissue (normal thyroid function, no thyroiditis, and no nodules). We compared the composition of mononuclear cells (MNCs) in peripheral blood and thyroid tissues from MNG and PTC patients by high-dimensional flow cytometry profiling and verified the results by multiplex immunohistochemistry. The recurrence rates of PTC patients with different CD8+T cell subset signatures were compared using TCGA database. Results: We observed that the immune cell composition of MNG was different from that in peripheral blood. Thyroid tissue contains higher percentages of T cells and NK cells. Moreover, the percentages of memory T cells and Treg cells were higher in thyroid than in peripheral blood and increased in PTC tumors. We further focused on the antitumoral CD8+T cells and found that the expression patterns of PD-1, CD39, and CD103 on CD8+T cells were different between MNG and PTC. Importantly, we found higher percentages of PD-1+CD39+CD103+CD8+T and PD-1+CD39+CD103-CD8+T cells in PTC tumor tissues from recurrent patients than non-recurrent patients. By analyzing PTC data from TCGA database, we found that the expression patterns of these molecules were associated with different pathologic types and genders among PTC patients. Moreover, patients with PD-1hiCD39loCD103hiCD8hi, PD-1hiCD39hiCD103loCD8hi, and PD-1loCD39hiCD103hiCD8hi expression patterns have a higher 10-year recurrence-free survival. Conclusion: The immune microenvironment in MNG tissue is distinct from that in peripheral blood and paratumor tissue. More memory CD8+T cells were detected in PTC, and expression patterns of PD-1, CD39, and CD103 on CD8+T cells were significantly different in physiology and gender and associated with the recurrence rate of PTC. These observations indicate that CD8+T cell signatures may be useful prognostic markers for PTC recurrence.

Prediction of Genetic Factors of Hyperthyroidism Based on Gene Interaction Network.

The number of hyperthyroidism patients is increasing these years. As a disease that can lead to cardiovascular disease, it brings great potential health risks to humans. Since hyperthyroidism can induce the occurrence of many diseases, studying its genetic factors will promote the early diagnosis and treatment of hyperthyroidism and its related diseases. Previous studies have used genome-wide association analysis (GWAS) to identify genes related to hyperthyroidism. However, these studies only identify significant sites related to the disease from a statistical point of view and ignore the complex regulation relationship between genes. In addition, mutation is not the only genetic factor of causing hyperthyroidism. Identifying hyperthyroidism-related genes from gene interactions would help researchers discover the disease mechanism. In this paper, we purposed a novel machine learning method for identifying hyperthyroidism-related genes based on gene interaction network. The method, which is called "RW-RVM," is a combination of Random Walk (RW) and Relevance Vector Machines (RVM). RW was implemented to encode the gene interaction network. The features of genes were the regulation relationship between genes and non-coding RNAs. Finally, multiple RVMs were applied to identify hyperthyroidism-related genes. The result of 10-cross validation shows that the area under the receiver operating characteristic curve (AUC) of our method reached 0.9, and area under the precision-recall curve (AUPR) was 0.87. Seventy-eight novel genes were found to be related to hyperthyroidism. We investigated two genes of these novel genes with existing literature, which proved the accuracy of our result and method.

Tumor Mutation Burden Predicts Relapse in Papillary Thyroid Carcinoma With Changes in Genes and Immune Microenvironment.

Background: The risk factors of papillary thyroid carcinoma (PTC) recurrence are meaningful for patients and clinicians. Tumor mutation burden (TMB) has been a biomarker for the effectiveness of immune checkpoint inhibitor (ICI) and prognosis in cancer. However, the role of TMB and its latent significance with immune cell infiltration in PTC are still unclear. Herein, we aimed to explore the effect of TMB on PTC prognosis. Material and Methods: RNA-seq and DNA-seq datasets of PTC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The Gene Ontology (GO) and gene set enrichment analysis (GSEA 4.0.1) were applied further to explore potential differences in PTC patients' biological functions. The differentially expressed genes (DEGs) and immune microenvironment between the high and low TMB groups were determined. Results: TMB had the highest AUC score than other clinical indicators in ROC analysis on recurrence-free survival, and a higher TMB score was related to a worse prognosis. Further, GSEA showed a higher level of oxidative phosphorylation (OXPHOS) in the high TMB group, and four genes correlated with recurrence-free survival rate were identified. The abundance of CD8+ T cells and M1 macrophages in the high TMB group was significantly lower than that in the low TMB group. Conclusions: Our study found that TMB was a better predictor variable at evaluating the risk of PTC recurrence. Moreover, TMB-related genes conferred dramatically correlated prognosis, which was worth exploring in guiding postoperative follow-up and predicting recurrence for PTC patients.

Identifying Thyroid Carcinoma-Related Genes by Integrating GWAS and eQTL Data.

Thyroid carcinoma (TC) is the most common endocrine malignancy. The incidence rate of thyroid cancer has increased rapidly in recent years. The occurrence and development of thyroid cancers are highly related to the massive genetic and epigenetic changes. Therefore, it is essential to explore the mechanism of thyroid cancer pathogenesis. Genome-Wide Association Studies (GWAS) have been widely used in various diseases. Researchers have found multiple single nucleotide polymorphisms (SNPs) are significantly related to TC. However, the biological mechanism of these SNPs is still unknown. In this paper, we used one GWAS dataset and two eQTL datasets, and integrated GWAS with expression quantitative trait loci (eQTL) in both thyroid and blood to explore the mechanism of mutations and causal genes of thyroid cancer. Finally, we found rs1912998 regulates the expression of IGFALS (P = 1.70E-06) and HAGH (P = 5.08E-07) in thyroid, which is significantly related to thyroid cancer. In addition, KEGG shows that these genes participate in multiple thyroid cancer-related pathways.

ALDH5A1 acts as a tumour promoter and has a prognostic impact in papillary thyroid carcinoma.

Thyroid cancer is the most common endocrine carcinoma, with papillary thyroid carcinoma (PTC) accounting for 80%-90% of thyroid cancers. Accumulating studies reported that mitochondria plays an important role in the regulation of cell proliferation. ALDH5A1, may function as an oncogene or tumour suppressor in various human cancers, and the role of ALDH5A1 in PTC is still unclear. The aim of this study was to investigate the clinical significance of ALDH5A1 expression and its functions in PTC. In this present study, we studied ALDH5A1 expression on primary papillary thyroid carcinoma (PTC) in The Cancer Genome Atlas (TCGA) database. Results showed that the levels of ALDH5A1 were found positively correlated with tumour stage, metastasis, lymph node stage, and higher levels of ALDH5A1 demonstrated poor disease-free survival (DFS). Immunohistochemistry (IHC) revealed that significantly higher expression of ALDH5A1 was found in PTC tissues. On the other hand, knockdown of ALDH5A1 significantly inhibited PTC cell proliferation, migration and invasion detection found the migration and invasion of cells also were hindered when ALDH5A1 level was reduced. The knockdown of ALDH5A1 inhibited the expression of Vimentin and promoted the expression of E-cadherin. In brief, knockdown of ALDH5A1may act as a novel molecular target for the prevention and treatment of PTC. SIGNIFICANCE OF THE STUDY: The present study focused on the role and the potential mechanism of ALDH5A1 in papillary thyroid carcinoma. We demonstrated that reduced expression of ALDH5A1 might inhibit the progression of TC by inhibiting cell proliferation, migration and invasion and reversing epithelial-mesenchymal transition (EMT). The findings ensured the interaction relation between ALDH5A1 and EMT in PTC, providing a novel biological marker for PTC and enriching the potential strategies for TC treatment.

Prognostic implications of the BRAF-V600E mutation in papillary thyroid carcinoma based on a new cut-off age stratification.

The BRAF-V600E mutation is the most common and specific oncogenic event known in papillary thyroid carcinoma (PTC). However, it remains controversial whether there is an association between the BRAF-V600E mutation and clinicopathologically aggressive characteristics of PTC. The purpose of the present retrospective study was to investigate the significance of the BRAF-V600E mutation in predicting prognostic and aggressive clinicopathological characteristics according to a new age-based stratification. Clinical data and the BRAF-V600E mutation status of 475 patients with PTC were downloaded from The Cancer Genome Atlas database. The association between BRAF-V600E status and clinicopathological characteristics was analyzed by χ2 test or Fisher's exact test. Recurrence-free survival rate (RFS) was analyzed using the Kaplan-Meier method. Aggressive clinicopathological factors associated with recurrence were analyzed by Cox multivariate regression. This study was conducted on 219 cases of patients with PTC with a known BRAF-V600E mutational status. In the ≥55 years age group, BRAF-V600E was found to be significantly associated with aggressive PTC characteristics, including tumor size, PTC subtype, radioactive iodine (RAI) dose, follow-up time, recurrence, recurrence risk stage, advanced T stage, advanced N stage and American Joint Committee on Cancer (III/IV) stage (all P<0.05). RFS was analyzed by the log-rank test and exhibited statistically significant differences in the ≥55 years group (P=0.041), but there was no significant difference in the <55 group (P=0.757), according to the BRAF-V600E mutation status. The BRAF-V600E gene was excluded from the recurrence Cox multivariate regression model. The BRAF-V600E mutation was found to better predict aggressive and recurrent PTC based on age stratification with the cut-off age of 55 years. The synergistic interaction between BRAF-V600E mutation and the new age stratification may help clinicians reach the optimal decision in terms of surgical approach and the extent of surgery.

Magnetically-mediated regeneration and reuse of core-shell Fe0@FeIII granules for in-situ hydrogen sulfide control in the river sediments.

A novel iron-cycling process based on core-shell iron granules, which contained zero-valent iron (Fe0) in the core and maghemite (γ-Fe2O3) on the shell (Fe0@FeIII granules), was proposed to in-situ control hydrogen sulfide in the sediments of the polluted urban rivers. The Fe0@FeIII granules added in the top sediment layer removed 97% of sulfide generated by sulfate-reducing bacteria in the sediments, and the sulfide removal capacity of virgin granules was 163 mg S/g Fe (114 mg S/g granule). The Fe0@FeIII granules removed the formed sulfide through the abiotic sulfide oxidation and precipitation, and they also stimulated the microbial iron reduction, which competitively consumed wastewater-derived organics and partially inhibited the sulfate reduction in the sediments. The used Fe0@FeIII granules were easily regenerated through magnetic separation from sediments and air exposure for 12 h, which enhanced the sulfide removal capacities of the regenerated granules by 12%-22%, compared to the virgin granules. During the air exposure, ferrous products (i.e., iron sulfide and surface-associated FeII) on the granule shell were completely oxidized to poorly ordered FeIII hydroxides (γ-FeOOH and amorphous FeOOH) having larger specific surface areas and higher reactivity to sulfide than γ-Fe2O3 on the virgin granules. Meanwhile, the Fe0 in the core was also partially oxidized through the indirect electron transfer, which was facilitated by the electrically conductive iron oxide minerals (Fe3O4 and Fe2O3) and the microbial electron carriers (e.g., Geobacter). The oxidation of Fe0 core contributed additional FeIII hydroxides to the sulfide control. The Fe0@FeIII granules were reused for four times in a 293-day trial, and their overall sulfide removal capacity was at least 920 mg S/g Fe. The proposed iron-cycling process can be a chemical-saving, energy-saving and cost-effective approach for the hydrogen sulfide control in the sediments of polluted urban rivers, as well as lakes, aquaculture ponds and marine.

Differentially expressed genes of HepG2 cells treated with gecko polypeptide mixture.

Gecko (Gekko japonicus) extracts have been used in traditional Chinese medicine for many years. It has been proven that the gecko polypeptide mixture (GPM) extracted from gecko can inhibit the growth of multiple types of tumor cells. In order to investigate the possible anti-tumor molecular mechanisms of GPM, we used RNA-seq technology to identify the differentially expressed genes (DEGs) of human hepatocellular carcinoma (HCC) HepG2 cells treated with or without GPM. MTT assay was used to detect the viability of HepG2 cells. DAPI fluorescence staining was performed to observe morphological changes in the nuclei of HepG2 cells. Western blot analysis was applied to observe the expressions of apoptosis-related and endoplasmic reticulum stress (ERS)-related proteins in HepG2 cells. Flow cytometry assay was performed to detect the apoptosis and reactive oxygen species (ROS) in HepG2 cells. Our results showed that GPM inhibited HepG2 cells proliferation and induced the apoptosis of HepG2 cells. RNA-seq analysis suggested that the ER-nucleus signaling pathway involved in the anti-cancer molecular mechanism of GPM. Therefore, GPM may induce apoptosis in HepG2 cells via the ERs pathway.

Association of CYP3A4*1B genotype with Cyclosporin A pharmacokinetics in renal transplant recipients: A meta-analysis.

OBJECTIVE: Cyclosporine (CsA) is a substrate of cytochrome P450 (CYP) 3A4 with a narrow therapeutic index and large individual difference. CYP3A4*1B is reported to be associated with CsA pharmacokinetics parameters, but the relevance is still in dispute. Therefore, a meta-analysis was employed to evaluate the influence of CYP3A4*1B on CsA pharmacokinetics at different post-transplantation times in adult renal transplant recipients. METHODS: Studies on evaluating the CYP3A4*1B genotype and CsA pharmacokinetics were retrieved through a systematical search of relevant database including PubMed, Emabase, Web of science, the Cochrane Library, Clinical Trials.gov and three Chinese literature databases (up to 15 October 2017). The pharmacokinetic parameters: weight-adjusted CsA daily dose (Dose), cyclosporine trough concentration (C0) and trough concentration/weight-adjusted CsA daily dose ratio (C0/Dose ratio) were extracted, and all statistical analysis were performed by using Review Manager 5.1.0. RESULTS: Four studies (involving 452 adult renal transplant recipients) were included in this meta-analysis. For the C0/Dose ratio, in all included renal transplant recipients, CYP3A4*1B carriers exhibited higher C0/Dose ratio than CYP3A4*1 (WMD 7.38, 95% CI 1.26-13.51; P = 0.02). The differences between CYP3A4*1B carriers and CYP3A4*1 in Dose (WMD 0.36, 95% CI 0.85-0.12; P = 0.14), C0 (WMD 10.81, 95% CI 77.72-99.34; P = 0.81) were not statistically significant. According to post-transplantation time, subgroup analysis also showed no significant statistical significance between CYP3A4*1B carriers and CYP3A4*1 carriers in Dose or C0. However, this result should be further explored because only four studies were included. CONCLUSIONS: CYP3A4*1B is associated with CsA C0/Dose ratio in renal transplant recipients which indicates patients with CYP3A4*1B allele require lower dose of CsA to reach target blood concentration compared with the CYP3A4*1 carriers.

Gecko crude peptides inhibit migration and lymphangiogenesis by down regulating the expression of VEGF-C in human hepatocellular carcinoma cells and human lymphatic endothelial cells / 中国药理学与毒理学杂志

OBJECTIVE To explore the role of gecko crude peptides (GCPs) in the proliferation, apoptosis, migration and lymphangiogenesis of human hepatocellular carcinoma cells (HepG2) and human lymphaticendothelial cells (HLECs) in vitro. METHODS The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was used to evaluate the anti- proliferative effect of GCPs and siRNA-VEGF-C on HepG2 cells, Hoechst 33258 staining and flow cytometry were performed to analyze cycle and apoptosis. The migration and invasion ability of cells were assayed by transwell chamber experiment and wound-healing assay. The protein and mRNA expressions of vascular endo?thelial growth factor-C (VEGF-C) and CXC chemokine receptor-4 (CXCR4) were detected by q-PCR, immunofluorescence, Western blot. The protein expressions of the extracellular signal regulated kinase (ERKI/2), c-Jun N-terminal kinase (JNK), p38-mitogen activated protein kinases (p38 MAPK), serine/threonine kinase (Akt) and phosphatidylinositol- 3- kinase (PI3K) were detected by western blot. The anti-lymphangiogenesis effect of GCPs on the HLECs was analyzed using an in vitro tube-formation assay. The protein and mRNA expressions of vascular endothelial growth factor receptor-3 (VEGFR-3) and stromal cell-derived factor-1 (SDF-1) were detected by q-PCR, Western blot. RESULTS GCPs and siRNA-VEGF-C inhibited HepG2 proliferation, invasion and migration, and the most obvious inhibitory effect was both synergistic effects. Thus, GCPs suppressed HLECs proliferation, migration and tube-like structure formationin a dose- dependent manner, and had inhibitory effect of tumor- induced lymphangiogenesis in vitro. Additionally, we found that GCPs and siRNA- VEGF- C decreased the expressions of MMP-2, MMP-9, VEGF-C, CXCR4, phospho-ERK1/2, phospho-P38, phospho-JNK and PI3K in HepG2 cells. Moreover, GCPs had a dose-dependent depressive effecton the expressions of VEGFR- 3, SDF- 1 in HLECs. CONCLUSION The low expression of VEGF- C mediated by siRNA-VEGF-C and GCPs inhibit tumor proliferation, invasion and migrationby suppressing the MAPK signaling pathway through reduced levels of VEGF-C, and GCPs inhibit tumor lymphangiogenesis by suppressing the CXCR4/SDF-1 signaling pathway through suppressed VEGF-C/VEGFR-3.

Differentially expressed genes of HepG2 cells treated with gecko polypeptide mixture / 中国药理学与毒理学杂志

OBJECTIVE In order to investigate the possible anti-tumor molecular mechanisms of gecko polypeptide mixture (GPM). METHODS RNA-seq technology was used to identify the differen?tially expressed genes of human hepatocellular carcinoma (HCC) HepG2 cells treated with or without GPM. The HepG2 cells were treated with different concentration of GPM (0, 0.1, 0.2, 0.3, 0.4 mg·mL-1) for 6 h, 12 h and 24 h, respectively. MTT assay was used to detect the viability of HepG2 cells. DAPI fluorescence staining was performed to observe nucleus morphological changes of HepG2 cells. Western blot analysis was applied to observe the expression of apoptosis-related proteins in HepG2 cells. RESULTS The results showed that GPM could induce HepG2 cells apoptosis and influence HepG2 cells proliferation in a dose-dependent manner. We applied many analysis methods, including differen?tially expressed genes analysis, Gene Ontology (GO) enrichment analysis, KEGG pathway enrichment analysis, protein- protein interaction network analysis to screen out possible molecular mechanisms. ER-nucleus signaling pathway, cellular response to stress and apoptotic processes were identified the potential anti-cancer molecular biological process of GPM. GPM may also induce apoptosis in HepG2 cells via endoplasmic reticulum stress pathway. The mechanism is closely related to ERs, which might be beneficial for clinical therapy of HCC. CONCLUSION GPM can inhibit cells proliferation and induce apoptosis in HepG2 cells. The gene expression profile of GPM in HepG2 cells was obtained. The present study revealed the potential anti-tumor mechanism of GPM.