Prediction of Gastric Cancer-Related Proteins Based on Graph Fusion Method.

Gastric cancer is a common malignant tumor of the digestive system with no specific symptoms. Due to the limited knowledge of pathogenesis, patients are usually diagnosed in advanced stage and do not have effective treatment methods. Proteome has unique tissue and time specificity and can reflect the influence of external factors that has become a potential biomarker for early diagnosis. Therefore, discovering gastric cancer-related proteins could greatly help researchers design drugs and develop an early diagnosis kit. However, identifying gastric cancer-related proteins by biological experiments is time- and money-consuming. With the high speed increase of data, it has become a hot issue to mine the knowledge of proteomics data on a large scale through computational methods. Based on the hypothesis that the stronger the association between the two proteins, the more likely they are to be associated with the same disease, in this paper, we constructed both disease similarity network and protein interaction network. Then, Graph Convolutional Networks (GCN) was applied to extract topological features of these networks. Finally, Xgboost was used to identify the relationship between proteins and gastric cancer. Results of 10-cross validation experiments show high area under the curve (AUC) (0.85) and area under the precision recall (AUPR) curve (0.76) of our method, which proves the effectiveness of our method.

Long noncoding RNA TMPO-AS1/miR-126-5p/BRCC3 axis accelerates gastric cancer progression and angiogenesis via activating PI3K/Akt/mTOR pathway.

BACKGROUND AND AIM: Gastric cancer (GC) is an aggressive tumor featured by uncontrolled cell proliferation and metastasis. In recent years, long noncoding RNAs (lncRNAs) act as crucial regulators and biological markers in multiple cancers. LncRNA TMPO-AS1 has been revealed to be an oncogene in some cancers. Nevertheless, there is little known about the biological role of TMPO-AS1 in GC. METHODS: Reverse transcription-quantitative polymerase chain reaction analysis was used to examine the expression level of TMPO-AS1 in GC tissues and cells. Cell Counting Kit-8, colony formation, wound healing assays, and western blot analysis were performed to determine the role of TMPO-AS1 in GC cells. RNA pull-down, luciferase reporter, and RNA immunoprecipitation assays were used to test the interaction among TMPO-AS1, miR-126-5p, and BRCC3. RESULTS: TMPO-AS1 was highly expressed in GC tissues and cells. Upregulated TMPO-AS1 was closely associated with adverse prognosis of GC patients. Functional assays showed that TMPO-AS1 promoted GC cell proliferation, migration, and angiogenesis. Furthermore, it was found that TMPO-AS1 acted as a competing endogenous RNA for miR-126-5p to upregulate BRCC3 expression. Rescue assays revealed that TMPO-AS1 facilitated cellular progression of GC by sponging miR-126-5p and upregulating BRCC3. In addition, we found that the effects of the TMPO-AS1/miR-126-5p/BRCC3 axis on GC cell progression were related to the PI3K/Akt/mTOR pathway. CONCLUSIONS: Our study demonstrated that the TMPO-AS1/miR-126-5p/BRCC3 axis was involved in GC progression via the regulation of PI3K/Akt/mTOR pathway, which might provide a potential therapeutic strategy for GC.

LncRNA LINC00511 Acts as an Oncogene in Colorectal Cancer via Sponging miR-29c-3p to Upregulate NFIA.

BACKGROUND: Colorectal cancer (CRC), characterized by high mortality and incidence rate, is one of the most common types of rectum tumors in the gastrointestinal tract worldwide. An increasing number of investigations indicated that long noncoding RNAs (lncRNAs) have been implicated in the growth of a wide range of cancers. Although it has obtained general acceptance that lncRNA LINC00511 plays a significant role in numerous cancers, the regulatory mechanism of LINC00511 in CRC still needs to be explored. MATERIALS AND METHODS: Bioinformatics analysis and a wide range of experiments of sphere formation assay, cell proliferation assay, RT-qPCR, colony formation assay, Transwell assay and Western blot assays investigated the function and mechanism of LINC00511 in CRC tissues and cells. RESULTS: Our results manifested that the expression level of LINC00511 was obviously upregulated in CRC tissues and cells and it accelerated CRC development through facilitating cell proliferation, metastasis and stemness. Molecular mechanism exploration uncovered that LINC00511 acted as a ceRNA competing with NFIA to bind with miR-29c-3p. Through rescue experiments, we discovered that NFIA upregulation partly counteracted the inhibitive effect induced by LINC00511 silencing on CRC progression. CONCLUSION: These results revealed that LINC00511 participated in the progression of CRC by targeting the LINC00511/miR-29c-3p/NFIA axis, indicating that LINC00511 may be a potential therapeutic target for CRC treatment.

MiR-566 mediates cell migration and invasion in colon cancer cells by direct targeting of PSKH1.

BACKGROUND: Colorectal cancer (CRC), a common malignancy worldwide, and microRNAs (miRs) have been suggested to play roles in the disease. MiR-566 expression has been shown to be reduced in CRC, but its functions and mechanisms are still unclear. METHODS: Cell viability was assessed by using the CellTiter 96 AQueous One Solution Cell Proliferation kit. Cell proliferation was measured with MTT assay. Cell metastasis were measured by transwell assay. Luciferase reporter assays was used to confirm the target of MiR-566. PSKH1 expression was measured by RT-PCR and western blot. RESULTS: In the present study, we first observed that miR-566 was expressed in several CRC cell lines (SW480, SW620, LoVo, HT29 and Caco-2) at low levels compared to control colon epithelial cell lines (FHC). Further study showed that miR-566 overexpression suppressed cell survival and impeded cell proliferation, whereas inhibition of its expression enhanced cell survival and proliferation. Transwell assays showed that cell invasion and migration were reduced in cells overexpressing miR-566 and increased in those with inhibition of miR-566. Further analysis confirmed that PSKH1 is a target of miR-566. MiR-566 overexpression significantly inhibited PSKH1 expression and reintroduction of PSKH1 partially reversed the effects of miR-566 on CRC cell growth and metastasis in SW480 and Caco-2 cells. CONCLUSIONS: Taken together, the data show that CRC cell growth and metastasis can be significantly suppressed by miR-566 through targeting PSKH1.

A novel circFMN2 promotes tumor proliferation in CRC by regulating the miR-1182/hTERT signaling pathways.

BACKGROUND: Circular RNAs (circRNAs) are a class of non-coding RNAs broadly expressed in cells of various species. However, the molecular mechanisms that link circRNAs with colorectal cancer (CRC) are not well understood. In the present study, we attempted to provide novel basis for targeted therapy for CRC from the aspect of circRNA-microRNA (miRNA)-mRNA interaction. METHODS: We investigated the expression of circRNAs in five paired CRC tissues and adjacent non-tumor tissues by microarray analysis. Differentially expressed circRNAs were identified between CRC tissues and non-cancerous matched tissues. We focused on hsa_circ_0005100, which is located on chromosome 1 and derived from FMN2, and thus we named it as circFMN2. The expression of circFMN2 was detected in 88 CRC tissues and cell lines by quantitative real-time PCR. Functional assays were performed to evaluate the effects of circFMN2 on proliferation in vitro, and on tumorigenesis in vivo. The relationship between circFMN2 and miR-1182 was confirmed by luciferase reporter assay. RESULTS: circFMN2 was found to be significantly up-regulated in CRC tissues and cell lines. Moreover, knockdown of circFMN2 significantly inhibited cell proliferation and migration in vitro. Bioinformatics analysis predicted that there is a circFMN2/miR-1182/hTERT axis in CRC progression. Dual-luciferase reporter system validated the direct interaction of circFMN2, miR-1182, hTERT. Western blot verified that inhibition of circFMN2 decreased hTERT expression. Importantly, we demonstrated that circFMN2 was up-regulated in serum exosomes from CRC patients. CONCLUSION: In conclusion, circFMN2 is a central component linking circRNAs to progression of CRC via an miR-1182/hTERT axis.

Annexin A3 depletion overcomes resistance to oxaliplatin in colorectal cancer via the MAPK signaling pathway.

Colorectal cancer (CRC) is a common disease with high mortality and morbidity. Annexin A3 (ANXA3) belongs to the structurally homologous family of Ca2+ and phospholipid-binding proteins. This study aimed to investigate the effects and potential mechanisms of ANXA3 on oxaliplatin (Ox) resistance in CRC. We generated two human CRC cell lines (HCT116/Ox and SW480/Ox) with acquired Ox resistance and determined their resistance properties. ANXA3 expression and cell apoptosis, migration and invasion also were evaluated. We found that cell viability of HCT116/Ox and SW480/Ox was higher than that in parental cells in the presence of Ox. ANXA3 was highly expressed in HCT116/Ox and SW480/Ox cells. ANXA3 downregulation diminished cell survival, migration and invasion, while increased the apoptosis of HCT116 and SW480 with or without Ox. Moreover, depletion of ANXA3 reduced cell viability and BrdU incorporation, increased cell apoptosis and c-caspase 3 expression in HCT116/Ox with or without Ox. A transwell assay determined that knockdown of ANXA3 impeded the migration and invasion of HCT116/Ox and SW480/Ox cells. Additionally, phosphorylation of extracellular signal-regulated kinase (ERK) and c-Jun N-terminal kinase (JNK) decreased upon ANXA3 depletion in HCT116/Ox cells, and ANXA3 silencing suppressed Ox-induced activation of ERK and JNK signaling pathway. ANXA3 downregulation reduced Ox resistance in CRC, and treatment with the ERK inhibitor PD098059 or JNK inhibitor SP600125 contributed to this process. These results indicate that silencing ANXA3 could overcome Ox resistance in CRC via the mitogen-activated protein kinase signaling pathway.

The protective effect of glutaredoxin 1/DJ-1/HSP70 signaling in renal tubular epithelial cells injury induced by ischemia.

AIMS: Gluaredoxin1 (GRX1) is an important protein of the cellular antioxidant defense system, but its role in renal epithelial cell injury caused by ischemia remains unclear. In this study, we aimed to gain insight into the role of GRX1 in HK-2 cells with oxygen glucose deprivation (OGD) injury, which served as an in vitro cell model of renal epithelial cell ischemic injury. We investigated the underlying regulation of GRX1, DJ-1, and HSP70 as well as the role of the GRX1/DJ-1/HSP70 signaling pathway in this model. MATERIALS AND METHODS: The protein and mRNA expressions were measured by Western blot and qRT-PCR assays, respectively. GRX1 was overexpressed by transfection of pcDNA.3.1-GRX1 and DJ-1 was inhibited by transfection with DJ-1 siRNA. Cell apoptosis, caspase-3 activity, lactate dehydrogenase (LDH) leakage, or superoxide dismutase (SOD) content was tested by the related detection kit. Reactive oxygen species (ROS) level was detected via carboxy-H2DCF-DA. KEY FINDINGS: We found that GRX1 was distinctly down-regulated in HK-2 cells after incubation under the OGD condition. GRX1 overexpression markedly constrained cell apoptosis, caspase-3 activity, LDH leakage, and the ROS level, while SOD content was elevated. GRX1 up-regulation increased DJ-1 and HSP70 protein expression, while DJ-1 inhibition significantly offset the effect of GRX1 overexpression on HSP70, indicating that GRX1 could regulate HSP70 via control of DJ-1. Moreover, we observed that HSP70 inhibition removed the constraints imposed by GRX1 overexpression on ROS level, LDH leakage, and caspase-3 activity. SIGNIFICANCE: Overall, this study showed that GRX1 minimizes cell injury and apoptosis in HK-2 cells under OGD conditions via regulation of DJ-1 and HSP70 expression.

Melatonin Attenuates Endothelial-to-Mesenchymal Transition of Glomerular Endothelial Cells via Regulating miR-497/ROCK in Diabetic Nephropathy.

BACKGROUND/AIMS: Endothelial-to-mesenchymal transition (EndMT) of glomerular endothelial cells (GEnCs) can induce albuminuria in diabetic nephropathy. Melatonin attenuates diabetic nephropathy, but its role and mechanism in EndMT of GEnCs in diabetic nephropathy remain unknown. METHODS: The effect of melatonin on EndMT induced by transforming growth factor (TGF)-ß2 in human renal GEnCs was determined by assaying the expression of endothelial marker cells (VE-cadherin and CD31) and mesenchymal cells (α-SMA and Snail), as well as monolayer permeability. The molecular mechanism of melatonin in these processes was focused on miR-497/ROCK signaling. Furthermore, the effect and mechanism of melatonin in EndMT were confirmed in glomeruli of rats with streptozotocin-induced diabetes. RESULTS: Melatonin increased expression of VE-cadherin and CD31 and inhibited α-SMA and Snail levels that were altered by TGF-ß2 in GEnCs. Melatonin treatment reduced expression and activity of ROCK1 and ROCK2, which suppressed TGF-ß2-induced hyperpermeability of GEnCs and EndMT of GEnCs. Melatonin reduced ROCK1 and ROCK2 expression and activity in TGF-ß2-stimulated GEnCs by enhancing expression of miR-497, which targets ROCK1 and ROCK2. Furthermore, we found that melatonin inhibited EndMT in glomeruli and albuminuria in rats with streptozotocin-induced diabetes. MiR-497 expression increased, whereas ROCK1 and ROCK2 expression and activity decreased in melatonin-treated diabetic rats. CONCLUSION: Melatonin attenuated EndMT of GEnCs via regulating miR-497/ROCK signaling in diabetic nephropathy. This study improves understanding of EndMT and the role of melatonin in diabetic nephropathy.

MiR-517a-3p accelerates lung cancer cell proliferation and invasion through inhibiting FOXJ3 expression.

AIMS: Aberrant expression of microRNAs (miRNAs) results in alterations of various biological processes (e.g., cell cycle, cell differentiation, and apoptosis) and cell transformation. Altered miRNAs expression was associated with lung carcinogenesis and tumor progression. This study aimed to investigate the function and underlying molecular events of miR-517a-3p on regulation of lung cancer cell proliferation and invasion. MAIN METHODS: Transfected miR-517a-3p mimics or inhibitors into 95D and 95C cells respectively, the effects of miR-517a-3p on lung cancer cell proliferation, migration, and invasion were detected. Bioinformatics software forecasted potential target genes of miR-517a-3p and dual luciferase reporter gene system and western blot verified whether miR-517a-3p regulates FOXJ3 expression directly. KEY FINDINGS: MiR-517a-3p was differentially expressed in lung cancer 95D and 95C cell lines that have different metastatic potential. Manipulation of miR-517a-3p expression changed lung cancer cell proliferation, migration and invasion capacity. MiR-517a-3p directly regulated FOXJ3 expression by binding to FOXJ3 promoter. SIGNIFICANCE: This study demonstrated that miR-517a-3p promoted lung cancer cell proliferation and invasion by targeting of FOXJ3 expression.

The tumor suppressor gene RhoBTB1 is a novel target of miR-31 in human colon cancer.

miRNAs are a class of endogenous non-coding RNA, which can regulate downstream target genes through binding to the 3'UTR of those genes. Numerous studies have indicated that abnormal expression of miRNAs is implicated in tumor development. Aberrant expression of miR-31 has been found in various cancers, including colorectal cancer. Here, we show that miR-31 is upregulated in human colon cancer tissues and cell lines, and that repression of miR-31 inhibited colon cancer cell proliferation and colony formation in soft agarose. To further elucidate the mechanism underlying the role of miR-31 in promoting colon cancer, we used online miRNA target prediction databases and found that the tumor suppressor RhoTBT1 may be a target of miR-31. Imunohistochemistry assay revealed that RhoBTB1 was significantly decreased in HT29 cells. In addition, ectopic expression of miR-31 reduced RhoBTB1 in the colon cancer cell line HT29. The results suggested that suppression of RhoBTB1 may be responsible for colon tumorigenesis, which was inhibited directly by miR-31. The results of MTT and soft agarose colony-formation assays showed that knockdown of RhoBTB1 by RNAi induced cell proliferation, and colony formation in soft agarose, which mimicked the function of miR-31. This further suggested that suppression of RhoBTB1 was responsible for colon tumorigenesis. In conclusion, we found that miR-31 acts as an oncogene in colon cancer and identified RhoBTB1 as a new target of miR-31 further study demonstrated that miR-31 contributed to the development of colon cancer at least partly by targeting RhoBTB1.