A novel prognostic biomarker SPC24 up-regulated in hepatocellular carcinoma

Elevated Shear Stress Modulates Heterogenous Cellular Subpopulations to Induce Vascular Remodeling

Rationale: Elevated shear stress (ESS) induces vascular remodeling in veins exposed to arterial blood flow, which can lead to arteriovenous (AV) fistula failure. The molecular mechanisms driving remodeling have not been comprehensively examined with a single-cell resolution before. Objective: Using an in vivo animal mode, single-cell RNA sequencing, and histopathology, we precisely manipulate blood flow to comprehensively characterize all cell subpopulations important during vascular remodeling. Methods: AV loops were created in saphenous vessels of rats using a contralateral saphenous vein interposition graft to promote ESS. Saphenous veins with no elevated shear stress (NSS) were anastomosed as controls. Findings: ESS promoted transcriptional homogeneity, and NSS promoted considerable heterogeneity. Specifically, ESS endothelial cells (ECs) showed a more homogeneous transcriptional response promoting angiogenesis and upregulating endothelial-to-mesenchymal transition inhibiting genes (Klf2). NSS ECs upregulated antiproliferation genes such as Cav1, Cst3, and Btg1. In macrophages, ESS promoted a large homogeneous subpopulation, creating a mechanically activated, proinflammatory and thus proangiogenic myeloid phenotype, whereas NSS myeloid cells expressed the anti-inflammatory and antiangiogenetic marker Mrc1. Conclusion: ESS activates unified gene expression profiles to induce adaption of the vessel wall to hemodynamic alterations. Targeted depletion of the identified cellular subpopulations may lead to novel therapies to prevent excessive venous remodeling, intimal hyperplasia, and AV fistula failure.

Coregulation of NDC80 Complex Subunits Determines the Fidelity of the Spindle-Assembly Checkpoint and Mitosis

NDC80 complex (NDC80C) is composed of four subunits (SPC24, SPC25, NDC80, and NUF2) and is vital for kinetochore-microtubule (KT-MT) attachment during mitosis. Paradoxically, NDC80C also functions in the activation of the spindle-assembly checkpoint (SAC). This raises an interesting question regarding how mitosis is regulated when NDC80C levels are compromised. Using a degron-mediated depletion system, we found that acute silencing of SPC24 triggered a transient mitotic arrest followed by mitotic slippage. SPC24-deficient cells were unable to sustain SAC activation despite the loss of KT-MT interaction. Intriguingly, our results revealed that other subunits of the NDC80C were co-downregulated with SPC24 at a posttranslational level. Silencing any individual subunit of NDC80C likewise reduced the expression of the entire complex. We found that the SPC24-SPC25 and NDC80-NUF2 subcomplexes could be individually stabilized using ectopically expressed subunits. The synergism of SPC24 downregulation with drugs that promote either mitotic arrest or mitotic slippage further underscored the dual roles of NDC80C in KT-MT interaction and SAC maintenance. The tight coordinated regulation of NDC80C subunits suggests that targeting individual subunits could disrupt mitotic progression and provide new avenues for therapeutic intervention.

IMPLICATIONS

These results highlight the tight coordinated regulation of NDC80C subunits and their potential as targets for antimitotic therapies.

Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics

Background

Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer.

Methods

In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR).

Results

In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics.

Conclusion

Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.

XYA-2: a marine-derived compound targeting apoptosis and multiple signaling pathways in pancreatic cancer

Background

Pancreatic cancer is a highly aggressive and fatal disease with limited treatment options and poor prognosis for patients. This study aimed to investigate the impact of XYA-2 {N-(3,7-dimethyl-2,6-octadienyl)-2-aza-2-deoxychaetoviridin A}, a nitrogenated azaphilon previously reported from a deep-sea-derived fungus on the progression of pancreatic cancer cells.

Methods

The inhibitory effects of XYA-2 on cell proliferation, clonogenic potential, cell cycle progression, apoptosis, migration, and invasion were assessed using various assays. The CCK-8 assay, clone formation assay, flow cytometry assay, wound healing assay, and transwell assay were employed to evaluate cell proliferation, clonogenic potential, cell cycle progression, apoptosis, migration, and invasion, respectively. Moreover, we employed RNA-seq and bioinformatics analyses to uncover the underlying mechanism by which XYA-2 influences pancreatic cancer cells. The revealed mechanism was subsequently validated through qRT-PCR.

Results

Our results demonstrated that XYA-2 dose-dependently inhibited the proliferation of pancreatic cancer cells and induced cell cycle arrest and apoptosis. Additionally, XYA-2 exerted a significant inhibitory effect on the invasion and migration of cancer cells. Moreover, XYA-2 was found to regulate the expression of genes involved in multiple cancer-related pathways based on our RNA-seq and bioinformatics analysis.

Conclusion

These findings highlight the potential of XYA-2 as a promising therapeutic option for the treatment of pancreatic cancer.

Cell Cycle-Related Gene SPC24: A Novel Potential Diagnostic and Prognostic Biomarker for Laryngeal Squamous Cell Cancer

Laryngeal squamous cell cancer (LSCC) is a common malignant tumor with a high degree of malignancy, and its etiology remains unclear. Therefore, screening potential biomarkers is necessary to facilitate the treatment and diagnosis of LSCC. Robust rank aggregation (RRA) analysis was used to integrate two gene expression datasets of LSCC patients from the Gene Expression Omnibus (GEO) database and identify differentially expressed genes (DEGs) between LSCC and nonneoplastic tissues. A gene coexpression network was constructed using weighted gene correlation network analysis (WGCNA) to explore potential associations between the module genes and clinical features of LSCC. Combining differential gene expression analysis and survival analysis, we screened potential hub genes, including CDK1, SPC24, HOXB7, and SELENBP1. Subsequently, western blotting and immunohistochemistry were used to test the protein levels in clinical specimens to verify our findings. Finally, four candidate diagnostic and prognostic biomarkers (CDK1, SPC24, HOXB7, and SELENBP1) were identified. We propose, for the first time, that SPC24 is a gene that may associate with LSCC malignancy and is a novel therapeutic target. These findings may provide important mechanistic insight of LSCC.

Spindle pole body component 24 homolog potentiates tumor progression via regulation of SRY-box transcription factor 2 in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of human kidney cancer with a high probability of metastasis. To understand the molecular processing essential for ccRCC tumorigenicity, we conducted an integrative in silico analysis of The Cancer Genome Atlas (TCGA) ccRCC dataset and clustered randomly interspersed short palindromic repeats (CRISPR) screening dataset of ccRCC cell lines from Depmap. We identified spindle pole body component 24 homolog (SPC24) as an essential gene for ccRCC cell lines with prognostic significance in the TCGA database. Targeting SPC24 by CRISPR/Cas9-mediated gene knockout attenuated ccRCC proliferation, metastasis, and in vivo tumor growth. Furthermore, we found that SPC24 regulates metastasis genes expression in a SRY-box transcription factor 2 (SOX2)-dependent manner. The anti-proliferative effects of SPC24 knockout were strengthened with SOX2 knockdown. Collectively, our findings suggest SPC24 has a pivotal function in promoting ccRCC progression, providing a new insight for the treatment of ccRCC.

Bioinformatics Analysis of Prognostic Value of SPC24 in ccRCC and Pan-Cancer

Purpose

Clear cell renal cell carcinoma (ccRCC) is one of the most common diseases in the world, with high morbidity and mortality. Recent studies have revealed the important role of SPC24, a subunit of the Ndc80 complex, in the occurrence and development of carcinoma. However, the latent effect of SPC24 in the progress of ccRCC remains to be further explored. The intent of this research is to investigate whether SPC24 can be used as an index to predict the progression of ccRCC and to explore its relationship with the immune microenvironment and pan-cancer.

Materials and Methods

Based on data from public databases, we determined the expression level and clinical value of SPC24 in ccRCC and human pan-cancer. RT-qPCR analysis was carried out to detect the expression level of SPC24 in the OSRC/786O (human ccRCC cells) cell lines and HK2 (human normal kidney cells) cell line. The signal transduction pathways activated by different levels of SPC24 expression were explored by Gene Set Enrichment Analysis (GSEA), and the CIBERSORT algorithm was applied to analyze the relationship between infiltrating immune cells and SPC24 expression in ccRCC and pan-cancer tissues.

Results

SPC24 is overexpressed in ccRCC and several types of tumors, which is associated with poor prognosis. GSEA and CIBERSORT algorithms suggested that the high expression group of SPC24 enriched various pathways including immune-related pathways, and the several infiltrated immunocytes were related to the expression of SPC24.

Conclusion

Our study revealed that SPC24 is a prognostic factor in ccRCC related to immunomodulation and has generalized value in pan-cancer.

Interferon Regulatory Factor 2 (IRF2) Inhibits the Invasion and Migration of Renal Clear Cell Carcinoma Cells by Downregulation of Spindle Pole Body Component 24 (SPC24)

It has been reported that the increased expression of SPC24 (spindle pole body component 24) was involved in the initiation and development of various cancers. However, the role of SPC24 in ccRCC (clear cell renal cell carcinoma) remains largely unknown. In the present study, the changes and correlation of SPC24 and IRF2 (interferon regulatory factor 2) with ccRCC were evaluated by using GEPIA, TCGA and GTEx database. Then the involvement of SPC24 and IRF2 in invasion and migration was investigated in CaKi-1 cells, a human renal adenocarcinoma cell line. The bioinformatics assay revealed that the expression of SPC24 and IRF2 in kidney tissue of patients with renal clear cell cancer was significantly increased, and the expression of SPC24 and IRF2 in kidney tissue was positively and negatively related to cancer phase and survival rate in patients with ccRCC respectively. Notably, in vitro experimental study demonstrated that SPC25 promoted the invasion and migration of CaKi-1 cells, a human renal adenocarcinoma cell line. Furthermore, IRF2 shows potential binding site with SPC24 promoter, IRF2 overexpression significantly decreased SPC24 mRNA level, whereas inhibition of IRF2 with specific small hairpin RNA (shRNA) significantly increased SPC24 mRNA level. Functionally, inhibition of SPC24 with specific shRNA reversed the stimulatory effect of IRF2 shRNA on the invasion and migration of cells, whereas SPC24 over-expression reversed the inhibitory effect of IRF2 overexpression on the invasion and migration of cells. Finally, ChIP (chromatin immunoprecipitation) assay shows that IRF2 could directly bind with SPC24 promoter. In conclusion, these results demonstrated that IRF2/SPC24 signaling pathway contributes to the increased invasion and migration in ccRCC.

RNA editing affects cis-regulatory elements and predicts adverse cancer survival

BACKGROUND

RNA editing exerts critical impacts on numerous biological processes and thus are implicated in crucial human phenotypes, including tumorigenesis and prognosis. While previous studies have analyzed aggregate RNA editing activity at the sample level and associated it with overall cancer survival, there is not yet a large-scale disease-specific survival study to examine genome-wide RNA editing sites' prognostic value taking into account the host gene expression and clinical variables.

METHODS

In this study, we solved comprehensive Cox proportional models of disease-specific survival on individual RNA-editing sites plus host gene expression and critical demographic covariates. This allowed us to interrogate the prognostic value of a large number of RNA-editing sites at single-nucleotide resolution.

RESULTS

As a result, we identified 402 gene-proximal RNA-editing sites that generally predict adverse cancer survival. For example, an RNA-editing site residing in ZNF264 indicates poor survival of uterine corpus endometrial carcinoma, with a hazard ratio of 2.13 and an adjusted p-value of 4.07 × 10-7 . Some of these prognostic RNA-editing sites mediate the binding of RNA binding proteins and microRNAs, thus propagating their impacts to extensive regulatory targets.

CONCLUSIONS

In conclusion, RNA editing affects cis-regulatory elements and predicts adverse cancer survival.

hsa-miR-7-5p suppresses proliferation, migration and promotes apoptosis in hepatocellular carcinoma cell lines by inhibiting SPC24 expression

Emerging evidence suggests that microRNAs (miRNAs) participate in hepatocellular carcinoma (HCC) progression. Nevertheless, the mechanism of miR-7-5p in HCC cells has not been researched. In the research, the underlying biological function of miR-7-5p and SPC24 in HCC was explored. qRT-PCR was performed to measure the miR-7-5p and SPC24 level in HCC tissues and cells. The effect of miR-7-5p on HCC progression was detected by performing CCK-8, BrdU, and transwell assay. The relationship between miR-7-5p and SPC24 was determined using luciferase and RNA pull-down assays. Our findings showed that miR-7-5p was downregulated in HCC whereas SPC24 was upregulated in HCC. It was also showed that miR-7-5p upregulation restricted malignant behaviors of HCC cells, but this inhibitory effect of miR-7-5p could be relieved by its target gene SPC24. In conclusion, this research suggested that by inhibiting SPC24, miR-7-5p could act as a tumor inhibitory factor in HCC.

Progression Risk Assessment of Post-surgical Papillary Thyroid Carcinoma Based on Circular RNA-Associated Competing Endogenous RNA Mechanisms

Background: Accurate risk assessment of post-surgical progression in papillary thyroid carcinoma (PTC) patients is critical. Exploring key differentially expressed mRNAs (DE-mRNAs) regulated by differentially expressed circular RNAs (circRNAs) via the ceRNA mechanism could help establish a novel assessment tool. Methods: ceRNA network was established based on differentially expressed RNAs and correlation analysis. DE-mRNAs within the ceRNA network associated with progression-free interval (PFI) of PTC were identified to construct a prognostic ceRNA regulatory subnetwork. least absolute shrinkage and selection operator (LASSO)-Cox regression was applied to identify hub DE-mRNAs and establish a novel DE-mRNA signature in predicting PFI of PTC. Results: Six hub DE-mRNAs, namely, CLCNKB, FXBO27, FXYD6, RIMS2, SPC24, and CDKN2A, were identified to be most significantly related to the PFI of PTC, and a prognostic DE-mRNA signature was proposed. A nomogram incorporating the DE-mRNA signature and clinical parameters was established to improve the progression risk assessment in post-surgical PTC, which was superior to the American Thyroid Association risk stratification system and distant Metastasis, patient Age, Completeness of resection, local Invasion, and tumor Size (MACIS) score American Joint Committee on Cancer staging system. Conclusions: Based on the circRNA-associated ceRNA RNA mechanism, a DE-mRNA signature and prognostic nomogram was established, which may improve the progression risk assessment in post-surgical PTC.

Identification of CDCA8, DSN1 and BIRC5 in Regulating Cell Cycle and Apoptosis in Osteosarcoma Using Bioinformatics and Cell Biology

Introduction:

Osteosarcoma is the most common primary tumor of bone, although some molecular markers have been identified, the detailed molecular mechanisms underlying osteosarcoma are currently not fully understood. In the present study, we attempted to identify the potential key genes and pathways in osteosarcoma using bioinformatics analysis.

Methods:

GSE14359 was downloaded from the GEO database, and analyzed using Limma package. Gene Ontology and pathway enrichment analyses of the DEGs were performed in the DAVID database, followed by the construction of a protein–protein interaction (PPI) network with software Cytoscape, subnetwork modules were subsequently identified and analyzed, and further validation in human osteosarcoma tissues and osteosarcoma cells line was performed.

Results:

964 Differentially expressed genes (DEGs) identified, of which 222 were up-regulated and 742 were down-regulated. Among them, 10 genes (including BIRC5, MAD2L1, Bub1, DSN1, SPC24, CDCA8, STAG2, CENPA, MLF1IP and Mis12) were identified as hub genes and they were mainly enriched in pathways, including mRNA surveillance, RNA transport and PI3K-Akt signaling pathways. Further validation indicated 6 gene (DSN1, BIRC5, CDCA8, MLF1IP, MAD2L1 and SPC24) is highly expressed in osteosarcoma tissues. Among them, CDCA8, DSN1 and BIRC5 significantly promoted the proliferation of osteosarcoma cells in vitro. In terms of mechanism, DSN1 and CDCA8 were mainly involved in cell cycle regulation, while BIRC5 was mainly involved in the regulation of apoptosis pathway.

Conclusions:

We identified some key genes and pathways in osteosarcoma, which might be used as molecular targets or diagnostic biomarker for the diagnosis and therapy of osteosarcoma.

Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer

Lapatinib, targeting the human epidermal growth factor receptor family members HER1 and HER2, has been approved by the US Food and Drug Administration for use in metastatic HER2-positive breast cancer. However, resistance to lapatinib remains a common challenge to HER2-positive metastatic breast cancer. Until now, the molecular mechanisms of acquired resistance to lapatinib (ALR) have remained unclear. With no definite biomarkers currently known, we aimed to screen for key biomarkers in ALR. In this research, we identified 55 differentially expressed genes (DEGs, 20 upregulated, 35 downregulated) through bioinformatic analysis using microarray datasets GSE16179, GSE38376, and GSE51889 from the Gene Expression Omnibus (GEO) database. The related gene function was explored using the Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. The protein-protein interaction (PPI) network was constructed with the Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape. The functional enrichment of the DEGs was analyzed, including negative regulation of the B cell apoptotic process, DNA replication, solute:proton symporter activity, synthesis, and degradation of ketone bodies, and metal sequestration by antimicrobial proteins. Analysis of seven hub genes revealed their concentration mainly in DNA replication and cell cycle. Survival analysis revealed that MCM10 and SPC24 may be related with poor prognosis in patients with ALR. Meanwhile, the prediction model of lapatinib sensitivity was constructed, and emerging role of the model was further analyzed using several webtools. In conclusion, hub genes are involved in the complex mechanisms underlying ALR in breast cancer and provide favorable support for treatment of ALR in future.

Potential therapeutic targets of the nuclear division cycle 80 (NDC80) complexes genes in lung adenocarcinoma

Background: Lung cancer is the most common cancer worldwide, both in terms of the incidence and mortality. NDC80 complex comprising of NDC80, NUF2, SPC24, and SPC25 is a heterotetrameric protein complex located in the outer layer of the kinetochore and plays a critical role in mitosis. This study focuses on the effects of NDC80 complex genes on clinical features and prognosis in lung adenocarcinoma (LUAD). Materials and methods: Expression of NDC80 complex in LUAD and related clinical information was extracted from the TCGA website. NDC80 complex gene functional analysis and correlation analysis was conducted by using DAVID, BiNGO, Gene MANIA, STRING and GSEA. Survival probability was predicted by nomogram. Statistical analysis was used to predict NDC80 complex gene expression on clinical features and prognosis in patients with LUAD. Results: Expression of NDC80, NUF2, SPC24 and SPC25 was significantly elevated in LUAD tumors compared with normal tissues (P < 0.05). These genes showed diagnostic values for LUAD (P < 0.001 for each; area under the curve (AUC), 0.958, 0.968, 0.951, and 0.932 respectively); combinatorial analysis of these genes was more advantageous than single analysis alone (P < 0.001; AUC > 0.900 for each). Expression of both NDC80 and SPC25 correlated with the prognosis of LUAD (P < 0.001; AUC > 0.600 for each). Higher expression of NDC80, NUF2, SPC24 and SPC25 was associated with low overall survival (OS) in univariate analysis. Higher expression of NDC80 and SPC25 was associated with low OS in multivariate analysis. High expression of NDC80 combined with high expression of SPC25 was predictive of poor OS in LUAD in joint analysis. Conclusion: NDC80 complex gene might be an early indicator of diagnosis and prognosis of LUAD. The combined detection of NDC80, NUF2, SPC24 and SPC25 may become a new research direction in LUAD diagnosis and a new target for tumor targeted gene therapy.

Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma

Anaplastic thyroid carcinoma (ATC) is the most aggressive type of thyroid cancer, with no effective treatment available. Identification of new anti-ATC drugs represents an urgent need. In this study, we find that ATC cells are highly sensitive to THZ531, a potent inhibitor of the transcriptional cyclin-dependent kinase (CDK), CDK12. Cell-based assays demonstrate that CDK12 inhibition significantly impedes cell cycle progression, induces apoptotic cell death, and impairs colony formation in ATC cells. THZ531 causes a loss of elongating RNA polymerase II and suppresses gene expression in ATC cells. An integrative analysis of gene expression profiles and super-enhancer landscape, combining with functional assays, leads to the discovery of two new ATC cancer genes, ZC3H4 and NEMP1. Furthermore, CDK12 inhibition enhances the sensitivity of ATC cells to doxorubicin-mediated chemotherapy. Thus, these findings indicate that CDK12 is a potential therapeutic target for ATC treatment and its inhibition may help to overcome the chemoresistance in patients with ATC.

Exploring the Molecular Mechanism of the Drug-Treated Breast Cancer Based on Gene Expression Microarray

: Breast cancer (BRCA) remains the leading cause of cancer morbidity and mortality worldwide. In the present study, we identified novel biomarkers expressed during estradiol and tamoxifen treatment of BRCA. The microarray dataset of E-MTAB-4975 from Array Express database was downloaded, and the differential expressed genes (DEGs) between estradiol-treated BRCA sample and tamoxifen-treated BRCA sample were identified by limma package. The pathway and gene ontology (GO) enrichment analysis, construction of protein-protein interaction (PPI) network, module analysis, construction of target genes-miRNA interaction network and target genes-transcription factor (TF) interaction network were performed using bioinformatics tools. The expression, prognostic values, and mutation of hub genes were validated by SurvExpress database, cBioPortal, and human protein atlas (HPA) database. A total of 856 genes (421 up-regulated genes and 435 down-regulated genes) were identified in T47D (overexpressing Split Ends (SPEN) + estradiol) samples compared to T47D (overexpressing Split Ends (SPEN) + tamoxifen) samples. Pathway and GO enrichment analysis revealed that the DEGs were mainly enriched in response to lysine degradation II (pipecolate pathway), cholesterol biosynthesis pathway, cell cycle pathway, and response to cytokine pathway. DEGs (MCM2, TCF4, OLR1, HSPA5, MAP1LC3B, SQSTM1, NEU1, HIST1H1B, RAD51, RFC3, MCM10, ISG15, TNFRSF10B, GBP2, IGFBP5, SOD2, DHF and MT1H) , which were significantly up- and down-regulated in estradiol and tamoxifen-treated BRCA samples, were selected as hub genes according to the results of protein-protein interaction (PPI) network, module analysis, target genes-miRNA interaction network and target genes-TF interaction network analysis. The SurvExpress database, cBioPortal, and Human Protein Atlas (HPA) database further confirmed that patients with higher expression levels of these hub genes experienced a shorter overall survival. A comprehensive bioinformatics analysis was performed, and potential therapeutic applications of estradiol and tamoxifen were predicted in BRCA samples. The data may unravel the future molecular mechanisms of BRCA.

Prognostic genes of hepatocellular carcinoma based on gene coexpression network analysis

Hepatocellular carcinoma (HCC) is the most common subtype in liver cancer whose prognosis is affected by malignant progression associated with complex gene interactions. However, there is currently no available biomarkers associated with HCC progression in clinical application. In our study, RNA sequencing expression data of 50 normal samples and 374 tumor samples was analyzed and 9225 differentially expressed genes were screened. Weighted gene coexpression network analysis was then conducted and the blue module we were interested was identified by calculating the correlations between 17 gene modules and clinical features. In the blue module, the calculation of topological overlap was applied to select the top 30 genes and these 30 genes were divided into the green group (11 genes) and the yellow group (19 genes) through searching whether these genes were validated by in vitro or in vivo experiments. The genes in the green group which had never been validated by any experiments were recognized as hub genes. These hub genes were subsequently validated by a new data set GSE76427 and KM Plotter Online Tool, and the results indicated that 10 genes (FBXO43, ARHGEF39, MXD3, VIPR1, DNASE1L3, PHLDA1, CSRNP1, ADR2B, C1RL, and CDC37L1) could act as prognosis and progression biomarkers of HCC. In summary, 10 genes who have never been mentioned in HCC were identified to be associated with malignant progression and prognosis of patients. These findings may contribute to the improvement of the therapeutic decision, risk stratification, and prognosis prediction for HCC patients.

A prognostic prediction system for hepatocellular carcinoma based on gene co-expression network

In the present study, gene expression data of hepatocellular carcinoma (HCC) were analyzed by using a multi-step Bioinformatics approach to establish a novel prognostic prediction system. Gene expression profiles were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The overlapping differentially expressed genes (DEGs) between these two datasets were identified using the limma package in R. Prognostic genes were further identified by Cox regression using the survival package. The significantly co-expressed gene pairs were selected using the R function cor to construct the co-expression network. Functional and module analyses were also performed. Next, a prognostic prediction system was established by Bayes discriminant analysis using the discriminant.bayes function in the e1071 package, which was further validated in another independent GEO dataset. A total of 177 overlapping DEGs were identified from TCGA and the GEO dataset (GSE36376). Furthermore, 161 prognostic genes were selected and the top six were stanniocalcin 2, carbonic anhydrase 12, cell division cycle (CDC) 20, deoxyribonuclease 1 like 3, glucosylceramidase β3 and metallothionein 1G. A gene co-expression network involving 41 upregulated and 52 downregulated genes was constructed. SPC24, endothelial cell specific molecule 1, CDC20, CDCA3, cyclin (CCN) E1 and chromatin licensing and DNA replication factor 1 were significantly associated with cell division, mitotic cell cycle and positive regulation of cell proliferation. CCNB1, CCNE1, CCNB2 and stratifin were clearly associated with the p53 signaling pathway. A prognostic prediction system containing 55 signature genes was established and then validated in the GEO dataset GSE20140. In conclusion, the present study identified a number of prognostic genes and established a prediction system to assess the prognosis of HCC patients.

Nuclear division cycle 80 complex is associated with malignancy and predicts poor survival of hepatocellular carcinoma

The NDC80 (nuclear division cycle 80) complex takes part in chromosome segregation by forming an outer kinetochore and providing a platform for the interaction between chromosomes and microtubules, thus impacting the progression of mitosis and the cell cycle. The clinical significance of its components, NDC80, nuf2, spc24, and spc25, were widely explored in various malignancies respectively, yet seldom were they studied from the perspective of a complex. This paper explores the clinical importance of the NDC80 kinetochore complex components in terms of their expression level, prognostic value, and therapeutic potential in HCC (hepatocellular carcinoma) patients. With the data from several paired HCC samples from Nanfang Hospital, HCC patients from the TCGA database and other cases from GSE89377, we analyzed the expression levels of the NDC80 complex components, NDC80/nuf2/spc24/spc25, along with the survival data as well as other clinical features using statistical methods and GSEA. The study found that a high expression of NDC80 complex predicts poor survival, and these components have the potential to be used as therapeutic targets.

The Y-linked proto-oncogene TSPY contributes to poor prognosis of the male hepatocellular carcinoma patients by promoting the pro-oncogenic and suppressing the anti-oncogenic gene expression

Background

Liver cancer is one of the major causes of cancer death worldwide, with significantly higher incidence and mortality among the male patients. Although sex hormones and their receptors could contribute to such sex differences, the story is incomplete. Genes on the male-specific region of the Y chromosome could play a role(s) in this cancer. TSPY is the putative gene for the gonadoblastoma locus on the Y chromosome (GBY) that is ectopically expressed in a subset of male hepatocellular carcinomas (HCCs). Although various studies showed that TSPY expression is associated with poor prognosis in the patients and its overexpression promotes cell proliferation of various cancer cell lines, it remains unclear how TSPY contributes to the clinical outcomes of the HCC patients. Identifying the downstream genes and pathways of TSPY actions would provide novel insights on its contribution(s) to male predominance in this deadly cancer.

Results

To determine the effects of TSPY on HCC, a TSPY transgene was introduced to the HCC cell line, HuH-7, and studied with RNA-Seq transcriptome analysis. The results showed that TSPY upregulates various genes associated with cell-cycle and cell-viability, and suppresses cell-death related genes. To correlate the experimental observations with those of clinical specimens, transcriptomes of male HCCs with high TSPY expression were analyzed with reference to those with silent TSPY expression from the Cancer Genome Atlas (TCGA). The comparative analysis identified 49 genes, which showed parallel expression patterns between HuH-7 cells overexpressing TSPY and clinical specimens with high TSPY expression. Among these 49 genes, 16 likely downstream genes could be associated with survival rates in HCC patients. The major upregulated targets were cell-cycle related genes and growth factor receptor genes, including CDC25B and HMMR, whose expression levels are negatively correlated with the patient survival rates. In contrast, PPARGC1A, SLC25A25 and SOCS2 were downregulated with TSPY expression, and possess favorable prognoses for HCC patients.

Conclusion

We demonstrate that TSPY could exacerbate the oncogenesis of HCC by differentially upregulate the expression of pro-oncogenic genes and downregulate those of anti-oncogenic genes in male HCC patients, thereby contributing to the male predominance in this deadly cancer.

Electronic supplementary material

The online version of this article (10.1186/s13578-019-0287-x) contains supplementary material, which is available to authorized users.

Identification of Five Genes as a Potential Biomarker for Predicting Progress and Prognosis in Adrenocortical Carcinoma

Background: Adrenocortical carcinoma (ACC) is a limited endocrine fatality with a minor diagnosis and rare remedial options. The progressive and predictive meaning of message RNA (mRNA) expression oddity in ACC has been studied extensively in recent years. However, differences in measurement platforms and lab protocols as well as small sample sizes can render gene expression levels incomparable.

Methods: An extensive study of GEO datasets was conducted to define potential mRNA biomarkers for ACC. The study compared the mRNA expression profiles of ACC tissues and neighboring noncancerous adrenal tissues in the pair. The study covered a sum of 165 tumors and 36 benign control samples. Hub genes were identified through a protein-protein interaction (PPI) network and Robust Rank Aggregation method. Then the Cancer Genome Atlas (TCGA) and Oncomine database were used to perform the validation of hub genes. 4 ACC tissues and 4 normal tissues were collected and then Polymerase Chain Reaction (PCR), Western-blot and immunofluorescence were conducted to validate the expression of five hub genes.

Results: We identified five statistically significant genes (TOP2A, NDC80, CEP55, CDKN3, CDK1) corrected with clinical features. The expression of five hub genes in TCGA and Oncomine database were significantly overexpressed in ACC compared with normal ones. Among all the TCGA ACC cases, the strong expression of TOP2A (logrank p=1.4e-04, HR=4.7), NDC80 (logrank p=8.8e-05, HR=4.9), CEP55 (logrank p=5.2e-07, HR=8.6), CDKN3 (log rank p=2.3e-06, HR=7.6) and CDK1 (logrank p=7e-08, HR=11) were correlated with low comprehensive survival, disease free survival (logrank p < 0.001), pathology stage and pathology T stage (FDR < 0.001). PCR results showed that the transcriptional levels of these five genes were significantly higher in ACC tissues than in normal tissues. The western blotting results also showed that the translational level of TOP2A was significantly higher in tumor tissues than in normal tissues. The results of immunofluorescence showed that TOP2A was abundantly observed in the adrenal cortical cell membrane and nucleus and its expression in ACC tissues was significantly higher than that in normal tissues.

Conclusions: The distinguished five genes may be utilized to form a board of progressive and predictive biomarkers for ACC for clinical purpose.

SPC24 Regulates breast cancer progression by PI3K/AKT signaling

Breast cancer is a heterogeneous disease, presenting as several diverse clinical and histologic varieties and it is now the most frequently diagnosed cancer and is the sixth leading cause of cancer-related death in Chinese women. SPC24 is an important component of the mitotic checkpoint machinery and its carcinogenic roles have been shown in several cancers, including anaplastic thyroid cancer, hepatocellular carcinoma, and osteosarcoma. However, the role of SPC24 in breast cancer is still unclear. Here, we show SPC24 is highly expressed in breast cancer compared with the normal tissues. In addition, we observe that SPC24 knockdown can lead to attenuated cell growth, increased cell apoptosis and cell cycle progression. Consistent with the breast cancer cell results, the in vivo growth of the SPC24-knocking down cells was significantly inhibited. Interestingly, molecular analysis indicates that SPC24 regulates PI3K/AKT kinase pathway, indicating the important of SPC24 for clinical treatment. In aggregate, our results provide an oncogenic functionality of SPC24 in breast cancer progression.

Exosomal neutral sphingomyelinase 1 suppresses hepatocellular carcinoma via decreasing the ratio of sphingomyelin/ceramide

Neutral sphingomyelinase 1 (NSMase1) mediates caspase-3 activation and apoptosis. However, the role of NSMase1, especially exosome-borne NSMase1 in hepatocellular carcinoma (HCC), remains unclear. We report that NSMase1, which converts sphingomyelin (SM) to ceramide, was significantly downregulated in HCC tissues. Low NSMase1 expression predicted poor long-term survival of HCC patients. NSMase1 downregulation in HCC resulted in increased SM and reduced ceramide (Cer) that led to an increased SM/Cer ratio. Interestingly, NSMase1 and NSMase activity were also decreased in exosomes isolated from HCC tissues and cell lines. Furthermore, NSMase activity increased in exosomes isolated from the culture medium of L02 cells transfected with pEGFP-C3-NSMase1 (NSMase1-Exo). NSMase1-Exo suppressed HCC cell growth and induced apoptosis via reduction of the SM/Cer ratio. Thus, NSMase1 in exosomes inhibits HCC growth by decreasing the SM/Cer ratio.

MiR-3613-3p affects cell proliferation and cell cycle in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common types of malignant tumors with poor sensitivity to chemotherapy drugs and poor prognosis among patients. In the present study, we downloaded the original data from the Gene Expression Omnibus and compared gene expression profiles of liver cancer cells in patients with HCC with those of colon epithelial cells of healthy controls to identify differentially expressed genes (DEGs). After filtering target microRNAs (miRNA) from core DEGs, we cultured HepG2 cells in vitro, knocked down the miRNA and core mRNAs, and analyzed the effects. We found 228 differentially expressed genes between liver cancer tissue and healthy control tissue. We also integrated the protein-proteininteraction network and module analysis to screen 13 core genes, consisting of 12 up-regulated genes and 1 down-regulated gene. Five core genes were regulated hsa-miR-3613-3p, therefor we hypothesized that hsa-miR-3613-3p was a critical miRNA. After the transfection procedure, we found that changes in hsa-miR-3613-3p were the most obvious. Therefore, we speculated that hsa-miR-3613-3p was a main target miRNA. In addition, we transfected with si (BIRC5, CDK1, NUF2, ZWINT and SPC24), to target genes that can be targeted by miR-3613-3p. Our data shows that BIRC5, NUF2, and SPC24 may be promising liver cancer biomarkers that may not only predict disease occurrence but also potential personalized treatment options.

SPC24 promotes osteosarcoma progression by increasing EGFR/MAPK signaling

In this study, we investigated the role of the spindle checkpoint protein SPC24 in osteosarcoma progression. SPC24 knockdown in 143B and U2OS osteosarcoma cells decreased cell growth, survival and invasiveness. The SPC24 knockdown cells also exhibited low EGFR, Ras and phospho-ERK levels and high E-cadherin levels, suggesting inhibition of EGFR/Ras/ERK signaling and epithelial-to-mesenchymal transitioning. Xenografted SPC24 knockdown osteosarcoma cells showed reduced tumor growth in nude mice with decreased EGFR and phospho-ERK levels and increased E-cadherin levels. By contrast, human osteosarcoma tissue samples showed high SPC24 and phospho-ERK levels and low E-cadherin levels. These results suggest SPC24 promotes osteosarcoma progression by increasing EGFR/Ras/ERK signaling.

SPC24 is critical for anaplastic thyroid cancer progression

In the past 2 decades, the incidence of thyroid cancer has been rapidly increasing worldwide. Anaplastic thyroid cancer (ATC) is the most lethal of all thyroid cancers and one of the most aggressive human carcinomas. SPC24 is an important component of the mitotic checkpoint machinery in the tumorigenesis and high levels of SPC24 have been found in colorectal and hepatocellular carcinomas, but its role in anaplastic thyroid cancer is still unclear. Our results showed that SPC24 was high expressed in human thyroid cancer samples. In addition, knockingdown endogenous SPC24 could repress cell growth, inhibit cell invasive ability and promote apoptosis in different ATC cells. Next, in vivo xenograft studies indicated that the SPC24 knockdown cells has decreased tumor size compared to the controls. This conclusion is also endorsed by our studies using human thyroid cancer samples. Taken together, our data demonstrates that SPC24 can serve as a promising prognostic biomarker of ATC cells and it is a novel strategy which could be developed by targeting SPC24 in future.

GFAPδ/GFAPα ratio directs astrocytoma gene expression towards a more malignant profile

Astrocytomas are the most common malignant brain tumours and are to date incurable. It is unclear how astrocytomas progress into higher malignant grades. The intermediate filament cytoskeleton is emerging as an important regulator of malignancy in several tumours. The majority of the astrocytomas express the intermediate filament protein Glial Fibrillary Acidic Protein (GFAP). Several GFAP splice variants have been identified and the main variants expressed in human astrocytoma are the GFAPα and GFAPδ isoforms. Here we show a significant downregulation of GFAPα in grade IV astrocytoma compared to grade II and III, resulting in an increased GFAPδ/α ratio. Mimicking this increase in GFAPδ/α ratio in astrocytoma cell lines and comparing the subsequent transcriptomic changes with the changes in the patient tumours, we have identified a set of GFAPδ/α ratio-regulated high-malignant and low-malignant genes. These genes are involved in cell proliferation and protein phosphorylation, and their expression correlated with patient survival. We additionally show that changing the ratio of GFAPδ/α, by targeting GFAP expression, affected expression of high-malignant genes. Our data imply that regulating GFAP expression and splicing are novel therapeutic targets that need to be considered as a treatment for astrocytoma.

Screening and identification of key biomarkers in hepatocellular carcinoma: Evidence from bioinformatic analysis

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the pathogeny, but the molecular mechanisms of HCC are still not well understood. To identify the candidate genes in the carcinogenesis and progression of HCC, microarray datasets GSE19665, GSE33006 and GSE41804 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified, and function enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape. A total of 273 DEGs were identified, consisting of 189 downregulated genes and 84 upregulated genes. The enriched functions and pathways of the DEGs include protein activation cascade, complement activation, carbohydrate binding, complement and coagulation cascades, mitotic cell cycle and oocyte meiosis. Sixteen hub genes were identified and biological process analysis revealed that these genes were mainly enriched in cell division, cell cycle and nuclear division. Survival analysis showed that BUB1, CDC20, KIF20A, RACGAP1 and CEP55 may be involved in the carcinogenesis, invasion or recurrence of HCC. In conclusion, DEGs and hub genes identified in the present study help us understand the molecular mechanisms underlying the carcinogenesis and progression of HCC, and provide candidate targets for diagnosis and treatment of HCC.

Clinical value and potential targets of miR-224-5p in hepatocellular carcinoma validated by a TCGA- and GEO- based study

OBJECTIVE

to explore clinical value and potential targets of MicroRNA-224-5p in the tumorigenesis and progression of hepatocellular carcinoma (HCC).

METHODS

We evaluated the clinical value of MicroRNA-224-5p from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Meanwhile, target genes of MicroRNA-224-5p were predicted by bioinformatics method. The target genes of MicroRNA-224-5p were finally analyzed in Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, and Protein-Protein Interaction (PPI) network annotation.

RESULTS

MicroRNA-224-5p expression level in HCC was higher than in non-tumor tissues (SMD=1.24; 95% CI, 0.68 to 1.81; P<0.0001) and MicroRNA-224-5p might represent a diagnostic marker (overall AUC=0.92; 95% CI, 0.90 to 0.94). 262 target genes were acquired by overlapping 4927 genes predicted by more than four computational prediction tools with 1,123 down-regulated DEGs in HCC. Furthermore, gene sets enrichment analysis of the 262 overlapping genes was implemented. The mostly significant GO terms within the overlapping target genes of MicroRNA-224-5p were cellular response to chemical stimulus, plasma membrane part and coenzyme binding. KEGG pathway annotation showed the overlapping genes mostly took part in metabolic pathways. In PPI analysis, one hub gene, GNA14, stood out cause for the significant negative correlation with MicroRNA-224.

CONCLUSION

MicroRNA-224-5p is upregulated in HCC and may be a prospective biomarker for diagnosis. Moreover, MicroRNA-224-5p might play an oncogenic role in HCC by targeting GNA14.

A potential prognostic biomarker SPC24 promotes tumorigenesis and metastasis in lung cancer

RESULTS

SPC24 is over-expressed in clinical lung adenocarcinoma samples, and high level of SPC24 is associated with advanced stages of lung tumors. Knocking down SPC24 repressed cell growth and promoted apoptosis. SPC24 deficiency reduced cancer cell migration as well. E-cadherin, one of the epithelial-mesenchymal transition markers, was up-regulated in the knockdown cells, along with down-regulation of N-cadherin and Vimentin. Oncomine expression analyses further confirmed that high level of SPC24 is associated with tumors from smokers, recurrent patients, or patients with shorter survivals.

PURPOSE AND METHODS

To reveal the role of SPC24, an important component of kinetochore, in the tumorigenesis of lung cancer, we performed Oncomine and immunohistochemistry (IHC) analyses for SPC24 in human lung adenocarcinoma tumors. We knocked down SPC24 in two non-small cell lung cancer (NSCLC) cell lines, PC9 and A549, by siRNA and evaluated cell proliferation, apoptosis, and migration in the SPC24-deficient cells. Using a mouse xenograft model, we compared in vivo tumor growth of the knockdown and control cells. We further performed multiple Oncomine expression analyses for SPC24 in various lung cancer datasets with important clinical characteristics and risk factors, including survival, recurrence, and smoking status.

CONCLUSIONS

SPC24 is a novel oncogene of lung cancer, and can serve as a promising prognostic biomarker to differentiate lung tumors that have various clinicopathological characteristics. The findings of the current study will benefit the diagnosis, management, and targeted therapy of lung cancer.

MicroRNA-500a promotes migration and invasion in hepatocellular carcinoma by activating the Wnt/β-catenin signaling pathway

Increased expression of microRNA-500a (miR-500a) has been reported in the serum of hepatocellular carcinoma (HCC) patients. However, the biological effects and mechanisms of miR-500a in hepatoma cells remain unclear. In this study, we found that miR-500a expression was up-regulated in HCC cell lines and tissues, and that high levels of miR-500a was associated with poor prognosis. We found that miR-500a upregulation promoted migration and invasion in two hepatoma cell lines, HCCLM3 and SMMC7721, while miR-500a downregulation had the opposite effect. We demonstrated that miR-500a activates the Wnt/β-catenin signaling pathway by directly binding to the 3'-untranslated region (UTR) of SFRP2 and GSK-3β mRNA. In conclusion, our results indicate miR-500a promotes HCC migration and invasion through activating Wnt/β-catenin signaling by directly binding to SFPR2 and GSK-3β.