Identification of Hypoxia-Related Prognostic Signature and Competing Endogenous RNA Regulatory Axes in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a common type of liver cancer and one of the highly lethal diseases worldwide. Hypoxia plays an important role in the development and prognosis of HCC. This study aimed to construct a new hypoxia-related prognosis signature and investigate its potential ceRNA axes in HCC. RNA profiles and hypoxia genes were downloaded, respectively, from the Cancer Genome Atlas hepatocellular carcinoma database and Gene Set Enrichment Analysis website. Cox regression analyses were performed to select the prognostic genes and construct the risk model. The ENCORI database was applied to build the lncRNA-miRNA-mRNA prognosis-related network. The TIMER and CellMiner databases were employed to analyze the association of gene expression in ceRNA with immune infiltration and drug sensitivity, respectively. Finally, the co-expression analysis was carried out to construct the potential lncRNA/miRNA/mRNA regulatory axes. We obtained a prognostic signature including eight hypoxia genes (ENO2, KDELR3, PFKP, SLC2A1, PGF, PPFIA4, SAP30, and TKTL1) and further established a hypoxia-related prognostic ceRNA network including 17 lncRNAs, six miRNAs, and seven mRNAs for hepatocellular carcinoma. Then, the analysis of immune infiltration and drug sensitivity showed that gene expression in the ceRNA network was significantly correlated with the infiltration abundance of multiple immune cells, the expression level of immune checkpoints, and drug sensitivity. Finally, we identified three ceRNA regulatory axes (SNHG1/miR-101-3p/PPFIA4, SNHG1/miR-101-3p/SAP30, and SNHG1/miR-101-3p/TKTL1) associated with the progression of HCC under hypoxia. Here, we constructed a prognosis gene signature and a ceRNA network related to hypoxia for hepatocellular carcinoma. Among the ceRNA network, six highly expressed lncRNAs (AC005540.1, AC012146.1, AC073529.1, AC090772.3, AC138150.2, AL390728.6) and one highly expressed mRNA (PPFIA4) were the potential biomarkers of hepatocellular carcinoma which we firstly reported. The three predicted hypoxia-related regulatory axes may play a vital role in the progression of hepatocellular carcinoma.

Construction of a 3-mRNA hypoxia prognostic model to evaluate immune microenvironment in hepatocellular carcinoma

BACKGROUND

Hypoxia is a key factor in the development of hepatocellular carcinoma (HCC), which is the most common primary liver cancer with poor prognosis. The current study aimed to identify the potential prognostic biomarkers of the hypoxia-associated gene signature in patients with HCC, and to further explore the relationship between hypoxia and immune infiltration.

METHODS

After the determination of differentially expressed genes (DEGs) using the HCC transcriptome data of The Cancer Genome Atlas database and hypoxia-related gene set, the prognosis-associated genes were identified using univariate Cox regression analysis. Then, the hypoxia prognosis model was established via multivariate Cox regression analysis, with functional annotation conducted using Gene Set Enrichment Analysis. CIBERSORT was utilized to analyze the degree of tumor immune invasion, and an International Cancer Genome Consortium cohort to verify the reliability of the prognosis model. Expression levels of hypoxia-associated genes were detected by real-time quantitative polymerase chain reaction in HCC samples.

RESULTS

3 genes (ENO1, SAP30, and STC2) constructed the hypoxia prognosis model. The patients were subdivided into 2 groups based on median risk score, with a high hypoxic score indicating poor prognosis of HCC. The hypoxia signature could be employed as an independent prognostic factor in HCC. In addition, the proportion of macrophages was higher in the high-risk group.

CONCLUSION

The hypoxia-associated signature could be a potential prognostic marker of HCC and provides a different perspective for immunotherapy of HCC.

SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens

Animals with muscle hypertrophy phenotype are targeted by the broiler industry to increase the meat production and the quality of the final product. Studies characterizing the molecular machinery involved with these processes, such as quantitative trait loci studies, have been carried out identifying several candidate genes related to this trait; however, validation studies of these candidate genes in cell culture is scarce. The aim of this study was to evaluate SAP30 as a candidate gene for muscle development and to validate its function in cell culture in vitro. The SAP30 gene was downregulated in C2C12 muscle cell culture using siRNA technology to evaluate its impact on morphometric traits and gene expression by RNA-seq analysis. Modulation of SAP30 expression increased C2C12 myotube area, indicating a role in muscle hypertrophy. RNA-seq analysis identified several upregulated genes annotated in muscle development in treated cells (SAP30-knockdown), corroborating the role of SAP30 gene in muscle development regulation. Here, we provide experimental evidence of the involvement of SAP30 gene as a regulator of muscle cell hypertrophy.

Neuropilin and tolloid-like 2 regulates the progression of osteosarcoma

Neuropilin and tolloid-like 2 (NETO2) is aberrantly expressed in various malignancies. However, its role in osteosarcoma (OS) remains to be elucidated. This study aimed to identify the function of NETO2 in OS cells. The expression of NETO2 in sarcoma tissues was determined using the GEPIA database, and the mRNA and protein expression of NETO2 in OS cells and OS tissue was also assessed. The biological effects of NETO2 on OS cells were determined by overexpressing and downregulating NETO2. Cell proliferation, invasion, migration, colony formation, and epithelial-mesenchymal transition in OS cells were evaluated. Consistent with the GEPIA database, expression of NETO2 was upregulated in human OS samples and cell lines. NETO2 overexpression not only promoted the proliferation, colony formation, invasion, and epithelial-mesenchymal transition of OS cells, but also activated the PI3K/AKT signaling. NETO2 downregulation resulted in opposite effects. Furthermore, after using an AKT inhibitor, the effects of NETO2 on OS cells were attenuated. In conclusion, this study showed that NETO2 functions as an oncogene of osteosarcomas by activating the PI3K/AKT pathway.

Pilot deep RNA sequencing of worker blood samples from Singapore printing industry for occupational risk assessment

Several engineered nanomaterials (ENMs) are used in toner-based printing equipment (TPE) including laser printers and photocopiers to improve toner performance. High concentration of airborne nanoparticles due to TPE emissions has been documented in copy centers and chamber studies. Recent animal inhalation studies by our group suggested exposure to laser printer-emitted nanoparticles (PEPs) increased cardiovascular risk by impairing ventricular performance and inducing hypertension and arrhythmia, consistent with global transcriptomic and metabolomic profiling results. There has been no genome-wide transcriptomic analysis of workers exposed to TPE emissions to systematically assess the occupational exposure health risks. In this pilot study, deep RNA sequencing of blood samples of workers in two printing companies in Singapore was performed. The genome-scale analysis of the blood samples from TPE exposed workers revealed perturbed transcriptional activities related to inflammatory and immune responses, metabolism, cardiovascular impairment, neurological diseases, oxidative stress, physical morphogenesis/deformation, and cancer, when compared with the control peers (office workers). Many of these disease risks associated with particle inhalation exposures in such work environments were consistent with the observation from the PEPs rat inhalation studies. In particular, the cell adhesion molecules (CAMs) was a top significantly perturbed pathway in blood samples from exposed workers compared with the office workers in both companies. The protein expression of sICAM was verified in plasma of exposed workers, showing a positive correlation with daily average nanoparticle concentration in indoor air measured in these two companies. Larger scale genomic and molecular epidemiology studies in copier operators are warranted in order to assess potential risks from such particulate matter exposures.

Differentially Expressed Genes Associated With Prognosis in Locally Advanced Lymph Node-Negative Prostate Cancer

Older age is one of the main risk factors for cancer development. The incidence of prostate cancer, as a multifactorial disease, also depends upon demographic factors, race, and genetic predisposition. Prostate cancer most frequently occurs in men over 60 years of age, indicating a clear association between older age and disease onset. Carcinogenesis is followed by the deregulation of many genes, and some of these changes could serve as biomarkers for diagnosis, prognosis, prediction of drug therapy efficacy, as well as possible therapeutic targets. We have performed a bioinformatic analysis of a The Cancer Genome Atlas (TCGA) data and RNA-Seq profiling of a Russian patient cohort to reveal prognostic markers of locally advanced lymph node-negative prostate cancer (lymph node-negative LAPC). We also aimed to identify markers of the most common molecular subtype of prostate cancer carrying a fusion transcript TMPRSS2-ERG. We have found several genes that were differently expressed between the favorable and unfavorable prognosis groups and involved in the enriched KEGG pathways based on the TCGA (B4GALNT4, PTK6, and CHAT) and Russian patient cohort data (AKR1C1 and AKR1C3). Additionally, we revealed such genes for the TMPRSS2-ERG prostate cancer molecular subtype (B4GALNT4, ASRGL1, MYBPC1, RGS11, SLC6A14, GALNT13, and ST6GALNAC1). Obtained results contribute to a better understanding of the molecular mechanisms behind prostate cancer progression and could be used for further development of the LAPC prognosis marker panel.

Reducing NETO2 expression prevents human nasopharyngeal carcinoma (NPC) progression by suppressing metastasis and inducing apoptosis

Nasopharyngeal carcinoma (NPC), the most common cancer in head and neck regions, is a serious health problem worldwide. Neuropilin and tolloid-like 2 (NETO2), a member of the subfamily of CUB domain and LDLa-containing proteins, has been suggested to be involved in tumor progression. Nevertheless, little is known about the function and molecular mechanism of NETO2 in NPC progression. In the study, NETO2 was found to be significantly up-regulated in clinical tissues and NPC cell lines. NETO2 expression was positively correlated with tumor size. NETO2 knockdown inhibited cell proliferation, migration and invasion in NPC cell lines. Significantly, NETO2 knockdown promoted the radiotherapy in vitro, as evidenced by the further reduced cell proliferation and metastasis in NPC cells using 3-[4, 5-dimethylthiazol-2-yl]-2, 5 diphenyl tetrazolium bromide (MTT), colony formation and transwell analysis. In addition, NETO2 inhibition markedly induced apoptosis in NPC cells through activating Caspase-3 signaling. Also, the knockdown of NETO2 obviously promoted the efficacy of radiotherapy in apoptosis induction, along with higher expression of cleaved Caspase-3. NETO2 knockdown-triggered apoptosis in NPC cells were considerably diminished by Caspase-3 inactivation, demonstrating the essential role of Caspase-3 in NETO2-regulated NPC development. Moreover, in vivo experiments suggested that NETO2 knockdown promoted radiation-induced tumor growth suppression in the absence of significant side effects. Collectively, reducing NETO2 expression might elevate the efficiency of radiotherapy in NPC patients.