Integrated transcriptome sequencing and weighted gene co-expression network analysis reveals key genes of papillary thyroid carcinomas.

Objective: Papillary thyroid carcinoma (PTC) accounts for the majority of thyroid cancers and has a high recurrence rate. We aimed to screen key genes involved in PTC to provide novel insights into the mechanisms of PTC. Methods: Seven microarray datasets of PTC were downloaded from gene expression omnibus database. Differentially expressed genes (DEGs) between PTC and normal samples were screened in the merged dataset. Then, protein-protein interaction (PPIs) functional modules analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify PTC-associated key genes. The identified key genes were then characterized from various aspects, including gene set enrichment analysis (GSEA) and the associations with immune infiltration, methylation levels and prognosis. Results: A large numbers of DEGs were identified, and these DEGs are involved in several cancer pathways. Nine key genes (including down-regulated genes GNA14, AVPR1A, and WFS1, and up-regulated genes LAMB3, PLAU, MET, MFGE8, PRSS23, and SERPINA1) were identified. Patients in the AVPR1A and GNA14 high expression groups had better disease-free survival (DFS) than those in the low expression group. Key genes were mainly involved in P53 pathway, estrogen response, apoptosis, glycolysis, NOTCH signaling, epithelial mesenchymal transition, WNT_beta catenin signaling, and inflammatory response. The expression of key genes was associated with immune cell infiltration and corresponding methylation levels. The verification results of key gene proteins and mRNA expression levels using external validation datasets were consistent with our expectations, implying the involvements of key genes in PTC. Conclusion: The key genes may serve as potential therapeutic targets for PTC. This study provides novel insights into the mechanisms underlying PTC development.

Immunosuppressive tumor microenvironment and immunotherapy of hepatocellular carcinoma: current status and prospectives.

Hepatocellular carcinoma (HCC) is a major health concern worldwide, with limited therapeutic options and poor prognosis. In recent years, immunotherapies such as immune checkpoint inhibitors (ICIs) have made great progress in the systemic treatment of HCC. The combination treatments based on ICIs have been the major trend in this area. Recently, dual immune checkpoint blockade with durvalumab plus tremelimumab has also emerged as an effective treatment for advanced HCC. However, the majority of HCC patients obtain limited benefits. Understanding the immunological rationale and exploring novel ways to improve the efficacy of immunotherapy has drawn much attention. In this review, we summarize the latest progress in this area, the ongoing clinical trials of immune-based combination therapies, as well as novel immunotherapy strategies such as chimeric antigen receptor T cells, personalized neoantigen vaccines, oncolytic viruses, and bispecific antibodies.

Alpha5 nicotine acetylcholine receptor subunit promotes intrahepatic cholangiocarcinoma metastasis.

Neurotransmitter-initiated signaling pathway were reported to play an important role in regulating the malignant phenotype of tumor cells. Cancer cells could exhibit a "neural addiction" property and build up local nerve networks to achieve an enhanced neurotransmitter-initiated signaling through nerve growth factor-mediated axonogenesis. Targeting the dysregulated nervous systems might represent a novel strategy for cancer treatment. However, whether intrahepatic cholangiocarcinoma (ICC) could build its own nerve networks and the role of neurotransmitters in the progression ICC remains largely unknown. Immunofluorescence staining and Enzyme-linked immunosorbent assay suggested that ICC cells and the infiltrated nerves could generate a tumor microenvironment rich in acetylcholine that promotes ICC metastasis by inducing epithelial-mesenchymal transition (EMT). Acetylcholine promoted ICC metastasis through interacting with its receptor, alpha 5 nicotine acetylcholine receptor subunits (CHRNA5). Furthermore, acetylcholine/CHRNA5 axis activated GSK3ß/ß-catenin signaling pathway partially through the influx of Ca2+-mediated activation of Ca/calmodulin-dependent protein kinases (CAMKII). In addition, acetylcholine signaling activation also expanded nerve infiltration through increasing the expression of Brain-Derived Neurotrophic Factor (BDNF), which formed a feedforward acetylcholine-BDNF axis to promote ICC progression. KN93, a small-molecule inhibitor of CAMKII, significantly inhibited the migration and enhanced the sensitivity to gemcitabine of ICC cells. Above all, Acetylcholine/CHRNA5 axis increased the expression of ß-catenin to promote the metastasis and resistance to gemcitabine of ICC via CAMKII/GSK3ß signaling, and the CAMKII inhibitor KN93 may be an effective therapeutic strategy for combating ICC metastasis.

Modulation of cellular metabolism by protein crotonylation regulates pancreatic cancer progression.

Protein lysine crotonylation has been recently identified as a vital posttranslational modification in cellular processes, particularly through the modification of histones. We show that lysine crotonylation is an important modification of the cytoplastic and mitochondria proteins. Enzymes in glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid metabolism, glutamine metabolism, glutathione metabolism, the urea cycle, one-carbon metabolism, and mitochondrial fusion/fission dynamics are found to be extensively crotonylated in pancreatic cancer cells. This modulation is mainly controlled by a pair of crotonylation writers and erasers including CBP/p300, HDAC1, and HDAC3. The dynamic crotonylation of metabolic enzymes is involved in metabolism regulation, which is linked with tumor progression. Interestingly, the activation of MTHFD1 by decrotonylation at Lys354 and Lys553 promotes the development of pancreatic cancer by increasing resistance to ferroptosis. Our study suggests that crotonylation represents a metabolic regulatory mechanism in pancreatic cancer progression.

The clinical and genetic features in patients coexisting primary breast and thyroid cancers.

Background: We attempted to examine the clinical characteristics in patients with breast cancer (BC) and thyroid cancer (TC); explore the potential mechanisms of tumorigenesis and progression. Methods: Using the Surveillance, Epidemiology, and End Result Program-9 (SEER-9) database, a retrospective study (1975-2017) was conducted on patients with BC and TC. We identified the common differentially expressed genes involved in BC and TC using the Gene Expression Omnibus database (GEO). Immunohistochemical staining (IHC) was performed to verify the expression of the hit gene in patients with co-occurrence of BC and TC. Using The Cancer Genome Atlas (TCGA) database, the relationship between gene expression and clinicopathological characters was determined. Gene set enrichment analysis (GSEA) was used to identify the pathways enriched in BC and TC. Results: BC patients had a higher predisposition to develop TC (standardized incidence ratio, SIR: 1.29) and vice-versa (SIR: 1.12). Most of these patients were differentiated thyroid carcinoma (DTC) and hormone receptor (HR) - positive BC. The mRNA expression of COMP (Cartilage oligomeric matrix protein) was significantly overexpressed in BC and TC by analyzing the GEO database. The protein expression of COMP was increased in both BC and TC tissues obtained from the same patients validated by IHC. COMP was correlated with worse OS in BC (stage II-IV) and TC; it was the independent factor for prognosis of BC. GSEA indicated that the estrogen response and epithelial-mesenchymal transition (EMT) pathways were significantly enriched in both TC- and BC- COMP overexpressed groups. Conclusion: The co-occurrence risk of BC and TC in the same individual is higher than in the general population. Overexpression of COMP could promote oncogenesis and progression in patients with BC and TC through estrogen signaling and EMT pathways.

An Angiogenic Gene Signature for Prediction of the Prognosis and Therapeutic Responses of Hepatocellular Carcinoma.

Among cancer-related deaths worldwide, hepatocellular carcinoma (HCC) ranks second. The hypervascular feature of most HCC underlines the importance of angiogenesis in therapy. This study aimed to identify the key genes which could characterize the angiogenic molecular features of HCC and further explore therapeutic targets to improve patients' prognosis. Public RNAseq and clinical data are from TCGA, ICGC, and GEO. Angiogenesis-associated genes were downloaded from the GeneCards database. Then, we used multi-regression analysis to generate a risk score model. This model was trained on the TCGA cohort (n = 343) and validated on the GEO cohort (n = 242). The predicting therapy in the model was further evaluated by the DEPMAP database. We developed a fourteen-angiogenesis-related gene signature that was distinctly associated with overall survival (OS). Through the nomograms, our signature was proven to possess a better predictive role in HCC prognosis. The patients in higher-risk groups displayed a higher tumor mutation burden (TMB). Interestingly, our model could group subsets of patients with different sensitivities to immune checkpoint inhibitors (ICIs) and Sorafenib. We also predicted that Crizotinib, an anti-angiogenic drug, might be more sensitive to these patients with high-risk scores by the DEPMAP. The inhibitory effect of Crizotinib in human vascular cells was obvious in vitro and in vivo. This work established a novel HCC classification based on the gene expression values of angiogenesis genes. Moreover, we predicted that Crizotinib might be more effective in the high-risk patients in our model.

Carbazole and polyhalogenated carbazoles in the marine environment around the Zhoushan Archipelago: Distribution characteristics, environmental behavior, and sources.

The distribution characteristics and drivers of carbazole (CZ) and polyhalogenated carbazoles are still poorly understood. In this study, 96 samples were collected around the Zhoushan Archipelago, and their distribution characteristics were assessed. The results showed that CZ, 36-CCZ, and 36-BCZ were the top three abundant congeners in most collected samples. The bioaccumulation analysis revealed that marine plants prefer to accumulate CZ and bromocarbazoles rather than chlorocarbazoles. Both the mean concentrations of total carbazole and its derivants (ΣCZDs), as well as individual congeners, are the highest in sediments around the berthing areas of cargo ships and oil tankers. Meanwhile, ΣCZDs of these sediments are significantly influenced by the geo-weighted displacement of ships (r = 0.61; p < 0.05), indicating the ballast water from these ships as potential contributor for marine CZDs. Moreover, the accumulation of CZ in plankton, planktonic origin of sedimentary organic matter, and relationship between CZ and C/N ratio (p < 0.05) in sediments support the scenario that plankton absorbs and takes CZ into the sediments. These findings will promote the understanding of the sources, environmental behaviors, and fates of marine CZDs.

Preoperative prognostic risk stratification model for papillary thyroid carcinoma based on clinical and ultrasound characteristics.

Background: The preoperative risk stratification for patients with papillary thyroid carcinoma (PTC) plays a crucial role in guiding individualized treatment. We aim to construct a predictive model that aids in distinguishing between patients with low-risk and high-risk PTC based on preoperative clinical and ultrasound characteristics. Materials and methods: Patients who underwent open surgery and were diagnosed with PTC via a postoperative pathological report between January 2020 and December 2020 were retrospectively reviewed. Data including basic information, preoperative ultrasound characteristics, thyroid function, and postoperative pathology characteristics were obtained. Univariate logistic regression analysis and least absolute shrinkage and selection operator regression analysis were performed to screen candidate variables. Finally, the preoperative predictive model for PTC was established based on the results of the multivariate logistic regression analysis. Results: A total of 1,875 patients with PTC were enrolled. Eight variables (sex, age, number of foci, maximum tumor diameter on ultrasound, calcification, capsule, lymph node status on ultrasound, and thyroid peroxidase (TPO) antibody level) significantly associated with risk stratification were included in the predictive model. A nomogram was constructed for clinical utility. The model showed good discrimination, and the area under the curve was 0.777 [95% confidence interval (CI): 0.752-0.803] and 0.769 (95% CI: 0.729-0.809) in the training set and validation set, respectively. The calibration curve exhibited a rather good consistency with the perfect prediction. Furthermore, decision curve analysis and clinical impact curve showed that the model had good efficacy in predicting the prognostic risk of PTC. Conclusions: The nomogram model based on preoperative indicators for predicting the prognostic stratification of PTC showed a good predictive value. This could aid surgeons in deciding on individualized precision treatments.

Evidence of association between single-nucleotide polymorphisms in lipid metabolism-related genes and type 2 diabetes mellitus in a Chinese population.

Background: Type 2 diabetes mellitus (T2DM) is a complex chronic metabolic disorder triggered by insulin resistance in peripheral tissues. Evidence has shown that lipid metabolism and related genetic factors lead to insulin resistance. Hence, it is meaningful to investigate the association between single-nucleotide polymorphisms (SNPs) in lipid metabolism-related genes and T2DM. Methods: A total of 1,194 subjects with T2DM and 1,274 Non-diabetic subjects (NDM) were enrolled. Five SNPs in three genes (rs864745 in JAZF1, rs35767 in IGF1, and rs4376068, rs4402960, and rs6769511 in IGF2BP2) that contribute to insulin resistance involving lipid metabolism were genotyped using the MassArray method in a Chinese population. Results: The allele and genotypes of rs6769511 in IGF2BP2 were associated with T2DM (P=0.009 and P=0.002, respectively). In inheritance model analysis, compared with the T/T-C/T genotype, the C/C genotype of rs6769511 in IGF2BP2 was a risk factor for the development of T2DM (P<0.001, odds ratio [OR] =1.76; 95% confidence interval [CI]: 1.29-2.42). Haplotype analysis revealed associations of the rs4376068-rs4402960-rs6769511 haplotypes in IGF2BP2 with the development of T2DM (P=0.015). Additionally, rs4376068C-rs4402960T-rs6769511C was a risk haplotype for T2DM (OR=1.179; 95% CI: 1.033-1.346). Conclusion: The rs6769511 in IGF2BP2 was associated with T2DM susceptibility, and the rs4376068-rs4402960-rs6769511 haplotypes in IGF2BP2 was associated with the development of T2DM in a Chinese population.

Identifying the association between single nucleotide polymorphisms in KCNQ1, ARAP1, and KCNJ11 and type 2 diabetes mellitus in a Chinese population.

Background: Type 2 diabetes mellitus (T2DM) has a high global prevalence, and insufficient insulin secretion is one of the major reasons for its development. Therefore, investigating the association between T2DM and the single nucleotide polymorphisms (SNPs) in genes associated with insulin secretion is necessary. Methods: T2DM (1,194) and nondiabetic (NDM) (1,292) subjects were enrolled and the ten single nucleotide polymorphisms (SNPs) in KCNQ1, ARAP1, and KCNJ11 associated with insulin secretion were genotyped in a Chinese population. Results: Our data revealed that the rs2237897T allele in KCNQ1 is the protective allele for T2DM (P<0.001, OR=0.793; 95%CI: 0.705-0.893). However, the A allele of rs1552224 in ARAP1 may be a risk factor for T2DM (P=0.002, OR=12.070; 95% CI: 1.578-92.337). The haplotype analysis revealed that rs151290-rs2237892CC and rs2237895-rs2237897CC in KCNQ1 constitute the risk haplotype in T2DM development (P=0.010, OR=1.160; 95% CI: 1.037-1.299 and P=0.004, OR=1.192; 95% CI: 1.057-1.344). Moreover, rs2237895-rs2237897AT in KCNQ1 constitutes the protective haplotype in T2DM (P=0.001, OR=0.819; 95% CI: 0.727-0.923). In the inheritance models analysis, the rs2283228 (C/A-C/C) genotype is the protective factor compared to the A/A genotype (P=0.005, OR=0.79; 95% CI: 0.68-0.93). For rs2237897, the C/T-T/T genotype is the protective factor compared to the C/C genotype (P<0.001, OR=0.74; 95% CI: 0.63-0.87). Furthermore, when compared with the rs2237897 (C/T-T/T) genotype, rs2237897C/C genotype showed higher HbA1C levels (8.731±2.697 vs 9.282±2.921, P=0.001). Conclusion: Our results revealed that genetic variations in KCNQ1 and ARAP1 were associated with T2DM susceptibility in a Chinese population.

Association Between Single Nucleotide Polymorphisms in CDKAL1 and HHEX and Type 2 Diabetes in Chinese Population.

PURPOSE: Type 2 diabetes mellitus (T2DM) has a high global prevalence, and the interaction of environmental factors and genetic factors may contribute to the risk of T2DM. We aimed to investigate the association between T2DM and the single nucleotide polymorphisms (SNPs) in genes (CDKAL1 and HHEX) associated with insulin secretion. SUBJECTS AND METHODS: T2DM (n=1,169) and nondiabetic (NDM) (n=1,277) subjects were enrolled and the eight SNPs in CDKAL1 and HHEX genes associated with insulin secretion were genotyped in a Chinese population using MassARRAY. Then, the association of these SNPs with T2DM was analyzed. RESULTS: Our results revealed that four SNPs (rs4712524, rs10946398, rs7754840 in CDKAL1, and rs5015480 in HHEX) showed significantly different distributions between the T2DM and NDM groups (P<0.00625). The G allele of rs4712524 (P=0.004, OR=1.184; 95% CI=1.057-1.327), C allele of rs10946398 (P<0.001, OR=1.247; 95% CI=1.112-1.398), and C allele of rs775480 in CDKAL1 (P<0.001, OR=1.229; 95% CI=1.096-1.387) functioned as risk alleles of T2DM. The C allele of rs5015480 in HHEX (P<0.001, OR=1.295; 95% CI=1.124-1.493) was also the risk factor for T2DM. The haplotype analysis revealed that CDKAL1 haplotype rs4712524G-rs10946398C-rs7754840C-rs9460546G (P=0.001, OR=1.210; 95% CI=1.076-1.360) and HHEX haplotype rs1111875C-rs5015480C (P<0.001, OR=1.364; 95% CI=1.180-1.576) were the risk factors of T2DM. CONCLUSION: Our results revealed that genetic variations in CDKAL1 and HHEX were associated with T2DM susceptibility in Chinese population.

Association of single nucleotide polymorphisms of miRNAs involved in the GLUT4 pathway in T2DM in a Chinese population.

BACKGROUND: The insulin/insulin receptor substrate (IRS)/phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/GLUT4 pathway plays a crucial role in insulin resistance and is closely associated with T2DM. Accumulating evidence indicates that miRNAs (such as miR-135a, let-7d, miR-107, miR-96, miR-29a, miR-23a, miR-126, miR-133a, and miR-106b) influence the GLUT4 pathway. METHODS: A total of 784 subjects with T2DM and 846 nondiabetic subjects were enrolled and 12 single nucleotide polymorphisms (SNPs) in miRNAs (rs10459194 in miR-135a-2, rs10993081 and rs7045890 in let-7d, rs2296616 in miR-107, rs2402959 and rs6965643 in miR-96, rs24168 in miR-29a, rs3745453 in miR-23a, rs4636297 in miR-126, rs8089787 and rs9948906 in miR-133a-1 and rs999885 in miR-106b) involved in the GLUT4 pathway were genotyped using the MassArray method in a Chinese population. RESULTS: Our data showed that the A allele of rs2402959 in miR-96 may increase the risk of developing T2DM (p = .002, OR = 1.266; 95% CI: 1.089-1.471). The genotypes of rs3745453 in miR-23a showed the difference between T2DM and control groups (p < .001). Moreover, for rs2402959, compared with the A/A genotype, the (G/A-G/G) genotype shows a protective effect in T2DM (p = .001, OR = 0.71; 95% CI: 0.58-0.87). For rs3745453, compared with the (A/A-A/G) genotype, the G/G genotype increases the risk of T2DM (p < .001, OR = 1.95; 95% CI: 1.38-2.77). In addition, we also found that rs4636297G/G genotype was associated with lower TC in T2DM group. CONCLUSION: Our results revealed that genetic variations in the miRNAs involved in the GLUT4 pathway were associated with T2DM susceptibility in a Chinese population, and these results emphasize the need to study the functional effects of these variations in the miRNAs involved in the GLUT4 pathway on the risk of developing T2DM.

Analysis of the oligopeptide transporter gene family in Ganoderma lucidum: structure, phylogeny, and expression patterns.

Oligopeptide transporters (OPTs) are believed to transport broad ranges of substrates across the plasma membrane from the extracellular environment into the cell and are thought to contribute to various biological processes. In the present study, 13 putative OPTs (Gl-OPT1 to Gl-OPT13) were identified through extensive search of Ganoderma lucidum genome database. Phylogenetic analysis with OPTs from other fungi and plants indicates that these genes can be further divided into five groups. Motif compositions of OPT members are highly conserved in each group, indicative of functional conservation. Expression profile analysis of the 13 Gl-OPT genes indicated that, with the exception of Gl-OPT7-Gl-OPT9, for which no transcripts were detected, all paralogues were differentially expressed, suggesting their potential involvement in stress response and functional development of fungi. Overall, the analyses in this study provide a starting point for elucidating the functions of OPT in G. lucidum, and for understanding the complexities of metabolic regulation.

[Simultaneous determination of 20 underivatized amino acids by high performance liquid chromatography-evaporative light-scattering detection].

An analytical method for the determination of underivatized amino acids was established with high performance liquid chromatography (HPLC) coupled with evaporative light-scattering detection (ELSD). A domestic evaporative light-scattering detector was used to determine underivatized amino acids. A BISCHOFF C18 AQ PLUS column and a solvent gradient elution with 0.2% heptafluorobutyric acid containing 0.1% trifluoroacetic acid as mobile phase A and methanol as mobile phase B were used. The temperature of the drift tube in ELSD was 40 degrees C and the flow rate of dry air was 2.5 L/min. The logarithm of the peak area and logarithm of the mass of each separated amino acid was in good linearity. The linear ranges of the 20 amino acids were from 30-300 mg/L. The limits of detection (S/N > 3) for the underivatized amino acids were from 24 ng to 100 ng. The average recoveries of the 20 amino acids were between 90.6% and 106.0%. This method and system are simple, rapid and accurate for the determination of underivatized amino acids. It can be used for the determination of underivatized amino acids in pharmaceutical, food and chemical industry fields.