Exome and transcriptome sequencing identifies loss of PDLIM2 in metastatic colorectal cancers

Knockdown of ADAMDEC1 ameliorates ox-LDL-induced endothelial cell injury and atherosclerosis progression

This study was designed to investigate the role of a disintegrin and metalloproteinase domain-like protein decysin 1 (ADAMDEC-1) in atherosclerosis (AS). The Gene Expression Omnibus (GEO) database was utilized to identify differentially expressed genes (DEGs) between carotid atheroma plaque and carotid tissue adjacent atheroma plaque obtained from AS patients. Gene functional enrichment analysis was conducted on DEGs using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). QRT-PCR was employed to quantify mRNAs expression. AS animal model was established using ApoE-/- mice; serum triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) levels were detected. Aortic sinus atherosclerotic lesions were observed using H&E staining and Oil Red O staining. ADAMDEC-1 was silenced using small interfering RNAs (siRNAs) in human vascular smooth muscle cells (HVSMCs). Cell proliferation, migration, and cell cycle progression were detected by cell count kit-8 (CCK8), 5-ethynyl-2'-deoxyuridine (EDU), wound scratch healing assay, transwell assay, and flow cytometry, respectively. Western blot was used to evaluate various protein expression levels. Our results showed that ADAMDEC-1 was highly expressed in the serum of AS patients, consistent with the in silico results. The elevated TG, LDL-C, and HDL-C levels along with H&E and Oil Red O staining confirmed the successful establishment of the AS mouse model. ADAMDEC-1 expression was also elevated in AS mice. ADAMDEC-1 knockdown in HVSMCs suppressed cell proliferation, inhibited the expression of proliferating cell nuclear antigen (PCNA), and reduced the levels of matrix metalloproteinases (MMP2 and MMP9) proteins. Protein-protein interaction (PPI) analysis indicated that ADAMDEC-1 was associated with CXCL9, CCR5, TNF-α, TNFR1, and NF-κB-p50. The expression levels of CXCL9, CCR5, TNF-α, TNFR1, and NF-κB-p50 increased, while ADAMDEC-1 knockdown attenuated the expression of these proteins. Our study findings substantiate that ADAMDEC-1 may represent a novel target for AS.

PDZ and LIM Domain-Encoding Genes: Their Role in Cancer Development

PDZ-LIM family proteins (PDLIMs) are a kind of scaffolding proteins that contain PDZ and LIM interaction domains. As protein-protein interacting molecules, PDZ and LIM domains function as scaffolds to bind to a variety of proteins. The PDLIMs are composed of evolutionarily conserved proteins found throughout different species. They can participate in cell signal transduction by mediating the interaction of signal molecules. They are involved in many important physiological processes, such as cell differentiation, proliferation, migration, and the maintenance of cellular structural integrity. Studies have shown that dysregulation of the PDLIMs leads to tumor formation and development. In this paper, we review and integrate the current knowledge on PDLIMs. The structure and function of the PDZ and LIM structural domains and the role of the PDLIMs in tumor development are described.

Differential Expression in the Tumor Microenvironment of mRNAs Closely Associated with Colorectal Cancer Metastasis

BACKGROUND

Metastasis of colorectal cancer (CRC) is a major cause of CRC-related mortality. However, the detailed molecular mechanism of CRC metastasis remains unknown. A recent study showed that the tumor microenvironment, which includes cancer cells and the surrounding stromal cells, plays a major role in tumor invasion and metastasis. Identification of altered messenger RNA (mRNA) expression in the tumor microenvironment is essential to elucidation of the mechanisms responsible for tumor progression. This study investigated the mRNA expression of genes closely associated with metastatic CRC compared with non-metastatic CRC.

METHODS

The samples examined were divided into cancer tissue and isolated cancer stromal tissue. The study examined altered mRNA expression in the cancer tissues using The Cancer Genome Atlas (TCGA) (377cases) and in 17 stromal tissues obtained from our laboratory via stromal isolation using an array-based analysis. In addition, 259 patients with CRC were enrolled to identify the association of the candidate markers identified with the prognosis of patients with stage 2 or 3 CRC. The study examined the enriched pathways identified by gene set enrichment analysis (GSEA) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) module in both the TCGA dataset and isolated stromal tissue.

RESULTS

As a result, whereas tenascin-C, secreted phosphoprotein 1 and laminin were expressed in metastatic CRC cells, olfactory receptors (ORs) 11H1 and OR11H4 were expressed in stromal tissue cells isolated from metastatic CRC cases. Finally, upregulated expression of tenascin-C and OR11H4 was correlated with the outcome for CRC patients.

CONCLUSION

The authors suggest that upregulated expression levels of tenascin-C and OR11H1 play an important role in CRC progression.

Evaluation of the Prognostic Relevance of Differential Claudin Gene Expression Highlights Claudin-4 as Being Suppressed by TGFβ1 Inhibitor in Colorectal Cancer

Background: Claudins (CLDNs) are a family of closely related transmembrane proteins that have been linked to oncogenic transformation and metastasis across a range of cancers, suggesting that they may be valuable diagnostic and/or prognostic biomarkers that can be used to evaluate patient outcomes. However, CLDN expression patterns associated with colorectal cancer (CRC) remain to be defined.

Methods: The mRNA levels of 21 different CLDN family genes were assessed across 20 tumor types using the Oncomine database. Correlations between these genes and patient clinical outcomes, immune cell infiltration, clinicopathological staging, lymph node metastasis, and mutational status were analyzed using the GEPIA, UALCAN, Human Protein Atlas, Tumor Immune Estimation Resource, STRING, Genenetwork, cBioportal, and DAVID databases in an effort to clarify the potential functional roles of different CLDN protein in CRC. Molecular docking analyses were used to probe potential interactions between CLDN4 and TGFβ1. Levels of CLDN4 and CLDN11 mRNA expression in clinical CRC patient samples and in the HT29 and HCT116 cell lines were assessed via qPCR. CLDN4 expression levels in these 2 cell lines were additionally assessed following TGFβ1 inhibitor treatment.

Results: These analyses revealed that COAD and READ tissues exhibited the upregulation of CLDN1, CLDN2, CLDN3, CLDN4, CLDN7, and CLDN12 as well as the downregulation of CLDN5 and CLDN11 relative to control tissues. Higher CLDN11 and CLDN14 expression as well as lower CLDN23 mRNA levels were associated with poorer overall survival (OS) outcomes. Moreover, CLDN2 and CLDN3 or CLDN11 mRNA levels were significantly associated with lymph node metastatic progression in COAD or READ lower in COAD and READ tissues. A positive correlation between the expression of CLDN11 and predicted macrophage, dendritic cell, and CD4+ T cell infiltration was identified in CRC, with CLDN12 expression further being positively correlated with CD4+ T cell infiltration whereas a negative correlation was observed between such infiltration and the expression of CLDN3 and CLDN15. A positive correlation between CLDN1, CLDN16, and neutrophil infiltration was additionally detected, whereas neutrophil levels were negatively correlated with the expression of CLDN3 and CLDN15. Molecular docking suggested that CLDN4 was able to directly bind via hydrogen bond with TGFβ1. Relative to paracancerous tissues, clinical CRC tumor tissue samples exhibited CLDN4 and CLDN11 upregulation and downregulation, respectively. LY364947 was able to suppress the expression of CLDN4 in both the HT29 and HCT116 cell lines.

Conclusion: Together, these results suggest that the expression of different CLDN family genes is closely associated with CRC tumor clinicopathological staging and immune cell infiltration. Moreover, CLDN4 expression is closely associated with TGFβ1 in CRC, suggesting that it and other CLDN family members may represent viable targets for antitumor therapeutic intervention.

PDLIM2: Signaling pathways and functions in cancer suppression and host immunity

PDZ and LIM domains-containing proteins play pivotal functions in cell cytoskeleton organization, cell polarization and differentiation. As a key member of the family, PDLIM2 regulates stability and activity of transcription factors such as NF-κB, STATs and β-catenin, and thus exert it functions in inflammation, immunity, and cancer. PDLIM2 functions as a tumor suppressor in multiple tissues and it is often genetically mutated or epigenetically silenced in human cancers derived from lung, breast, ovarian and other histologies. However, in certain types of cancers, PDLIM2 may promote cancer cell proliferation and metastases. Therefore, PDLIM2 is added to a long list of genes that can function as tumor suppressor or oncogenic protein. During tumorigenesis induced by oncogenic viruses, PDLIM2 is a key target. Through promotion of NF-κB/RelA and STAT3 degradation, PDLIM2 enhances expression of proteins involved in antigen presentation and promotes T-cell activation while repressing multidrug resistance genes, thereby rendering mutated cells susceptible to immune surveillance and cytotoxicity mediated by immune cells and chemotherapeutic drugs. Intriguingly, PDLIM2 in alveolar macrophages (AMs) plays key roles in monitoring lung tumorigenesis, as its selective genetic deletion leads to constitutive activation of STAT3, driving monocyte differentiation to AMs with pro-tumorigenic polarization and activation. PDLIM2 has also been explored as a therapeutic target for cancer therapy. At the end of this review, we provide perspectives on this important molecule and discuss the future directions of both basic and translational studies.

PDLIM2 Suppression Inhibit Proliferation and Metastasis in Kidney Cancer

Simple Summary

Kidney cancer is a common malignant tumor in both men and women and accounts for approximately 5% of all cancer incidences. Advances in imaging technology and the increasing use of health care facilities have led to the early detection of kidney cancer cases. However, many individuals are still diagnosed with metastatic kidney cancer. If the cancer is accompanied by metastases at the time of diagnosis, the 5-year survival rate is 12%. Despite the beneficial effects of anticancer drug treatment on the survival of patients with metastatic kidney cancer, survival may be less than a year. PDLIM2 plays an essential role in cancer formation and inhibition. To verify oncogenic function of the PDLIM2, we conducted several experiments and animal experiments. Our findings indicating that PDLIM2 may be a new therapeutic target for metastatic kidney cancer.

Abstract

We evaluated the expression of PDLIM2 in human kidney cancer cell lines from primary or metastatic origins and found that PDLIM2 expression was highly elevated in metastatic kidney cancers. We evaluated the effect of PDLIM2 inhibition by RNA interference method. PDLIM2 knockdown showed the decreased proliferation and metastatic character in human metastatic kidney cancer cells. By repeated round of orthotopic injection of RenCa mouse kidney cancer cell line, we obtained metastatic prone mouse kidney cancer cell lines. PDLIM2 expression was highly expressed in these metastatic prone cells comparing parental cells. In addition, we evaluated the in vivo efficacy of PDLIM2 knockout on the tumor formation and metastasis of kidney cancer cells using a PDLIM2 knockout mice. The experimental metastasis model with tail vein injection and orthotopic metastasis model injected into kidney all showed reduced lung metastasis cancer formation in PDLIM2 knockout mice comparing control Balb/c mice. Overall, our findings indicate that PDLIM2 is required for cancer formation and metastasis in metastatic kidney cancer, indicating that PDLIM2 may be a new therapeutic target for metastatic kidney cancer.

Distinguishing Rectal Cancer from Colon Cancer Based on the Support Vector Machine Method and RNA-sequencing Data

Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide. Several studies have indicated that rectal cancer is significantly different from colon cancer in terms of treatment, prognosis, and metastasis. Recently, the differential mRNA expression of colon cancer and rectal cancer has received a great deal of attention. The current study aimed to identify significant differences between colon cancer and rectal cancer based on RNA sequencing (RNA-seq) data via support vector machines (SVM). Here, 393 CRC samples from the The Cancer Genome Atlas (TCGA) database were investigated, including 298 patients with colon cancer and 95 with rectal cancer. Following the random forest (RF) analysis of the mRNA expression data, 96 genes such as HOXB13, PRAC, and BCLAF1 were identified and utilized to build the SVM classification model with the Leave-One-Out Cross-validation (LOOCV) algorithm. In the training (n=196) and the validation cohorts (n=197), the accuracy (82.1 % and 82.2 %, respectively) and the AUC (0.87 and 0.91, respectively) indicated that the established optimal SVM classification model distinguished colon cancer from rectal cancer reasonably. However, additional experiments are required to validate the predicted gene expression levels and functions.

PDLIM2 prevents the malignant phenotype of hepatocellular carcinoma cells by negatively regulating β-catenin

Hepatocellular carcinoma (HCC) is one of the most common malignancies and leading causes of cancer-related deaths globally. Despite significant advances in therapy, the molecular mechanisms underlying HCC development and progression remain unclear. Here, we aimed to explore the potential role of PDLIM2 in the development and epithelial-mesenchymal transition (EMT) of HCC via a possible modulation of β-catenin. We first confirmed that PDLIM2 was downregulated in HCC tissues and cells and found lower PDLIM2 expression was associated with worse prognosis in HCC patients. Loss- and gain- of function experiments were performed to evaluate the roles of PDLIM2 and β-catenin in HCC cell proliferation, migration, invasion, EMT, and colony formation. EMT was determined based on the levels of E-cadherin, zonula occludens-1, N-cadherin, and vimentin expression. In vivo, the roles of PDLIM2 and β-catenin in HCC were investigated by using a nude mouse xenograft model. It should be noted that PDLIM2 led to the inhibition of β-catenin activity and its downstream gene expression. Importantly, ectopic PDLIM2 expression inhibited the proliferation, migration, invasion, and EMT of HCC cells by reducing β-catenin expression both in vitro and in vivo, thereby suppressing the occurrence and progression of HCC. Taken together, our results demonstrated that overexpressed PDLIM2 exerts a tumor-suppressive role in HCC by regulating β-catenin. This study suggests that the PDLIM2 may be a promising target for the treatment of HCC.

LINC00294 negatively modulates cell proliferation in glioma through a neurofilament medium-mediated pathway via interacting with miR-1278

BACKGROUND

Accumulating long noncoding RNAs (lncRNAs) have been recognized to participate in glioma development. Nevertheless, knowledge of the role of linc00294 in glioma remains incomplete.

METHODS

Bioinformatics analysis predicted the differential expression of LINC00294 and neurofilament medium (NEFM) in tumors and normal tissues, as well as the binding between LINC00294 and miR-1278, miR-1278 and NEFM. Luciferase and RNA immunoprecipitation assays were used for the verification of interactions. The potential role of LINC00294 in glioma development was investigated using functional assays, singly and in parallel with its interplay with miR-1278 and NEFM. Cell counting kit-8 and EdU assays were applied to measure cellular proliferation, whereas the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) method was employed to detect apoptosis.

RESULTS

A new lncRNA, LINC00294, was highly expressed in normal brain tissues. However, it was markedly down-regulated in GBM tissues and glioma cell lines. Overexpression of LINC00294 abates glioma cell proliferation but induces apoptosis. Meanwhile, tumor suppressor NEFM was revealed to be distinctly diminished in cancerous conditions and enhanced in glioma cells by LINC00294 up-regulation. Interactions of miR-1278 with LINC00294 or NEFM occur, and the expression of NEFM is up-regulated by LINC00294 through their competition with respect to binding to miR-1278. Finally, the rescue assays further confirmed that LINC00294 inhibits glioma cell proliferation by absorbing miR-1278 to enhance NEFM.

CONCLUSIONS

Collectively, our observations demonstrate the tumor-suppressive function of LINC00294 in glioma development by sponging miR-1278 and promoting NEFM, suggesting a potential use in therapy for glioma.

Bioinformatics Analysis to Reveal Potential Differentially Expressed Long Non-Coding RNAs and Genes Associated with Tumour Metastasis in Lung Adenocarcinoma

Background

Due to the onset of metastases, the survival rate of lung adenocarcinoma (LUAD) is still low. In view of this, we performed this study to screen metastasis-associated genes and lncRNAs in LUAD.

Methods

The mRNA and lncRNA expression profiles of 185 metastatic LUAD and 217 non-metastatic LAUD samples were retrieved from the TCGA database and included in this study. The differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between metastatic samples and non-metastatic samples of LAUD, as well as the cis nearby-targeted DEmRNAs of DElncRNAs and the DElncRNA-DEmRNA co-expression network, were obtained. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression levels of selected DEmRNAs. Survival analysis of selected DElncRNAs and DEmRNAs was performed.

Results

In total, 1351 DEmRNAs and 627 DElncRNAs were screened between the LUAD primary tissue samples and metastatic samples. Then, 194 DElncRNA-nearby-targeted DEmRNA pairs and 191 DElncRNA-DEmRNA co-expression pairs were detected. Except for RHCG and KRT81, the expression of the other six DEmRNAs in the qRT-PCR results generally exhibited the same pattern as that in our integrated analysis. The expression of CRHR2, FAM83A-AS1, FAM83A and Z83843.1 was significantly correlated with the overall survival time of patients with metastatic LUAD.

Conclusion

We speculate that two interaction pairs (FAM83A-AS1-FAM83A and Z83843.1-MATR3) and four genes (CRHR2, UGT2B15, CHGB and NEFL) are closely associated with the metastasis of LUAD.

Electrochemical Biosensors for Determination of Colorectal Tumor Biomarkers

The accurate determination of specific tumor markers associated with cancer with non-invasive or minimally invasive procedures is the most promising approach to improve the long-term survival of cancer patients and fight against the high incidence and mortality of this disease. Quantification of biomarkers at different stages of the disease can lead to an appropriate and instantaneous therapeutic action. In this context, the determination of biomarkers by electrochemical biosensors is at the forefront of cancer diagnosis research because of their unique features such as their versatility, fast response, accurate quantification, and amenability for multiplexing and miniaturization. In this review, after briefly discussing the relevant aspects and current challenges in the determination of colorectal tumor markers, it will critically summarize the development of electrochemical biosensors to date to this aim, highlighting the enormous potential of these devices to be incorporated into the clinical practice. Finally, it will focus on the remaining challenges and opportunities to bring electrochemical biosensors to the point-of-care testing.

HCV and flaviviruses hijack cellular mechanisms for nuclear STAT2 degradation: Up-regulation of PDLIM2 suppresses the innate immune response

Host encounters with viruses lead to an innate immune response that must be rapid and broadly targeted but also tightly regulated to avoid the detrimental effects of unregulated interferon expression. Viral stimulation of host negative regulatory mechanisms is an alternate method of suppressing the host innate immune response. We examined three key mediators of the innate immune response: NF-KB, STAT1 and STAT2 during HCV infection in order to investigate the paradoxical induction of an innate immune response by HCV despite a multitude of mechanisms combating the host response. During infection, we find that all three are repressed only in HCV infected cells but not in uninfected bystander cells, both in vivo in chimeric mouse livers and in cultured Huh7.5 cells after IFNα treatment. We show here that HCV and Flaviviruses suppress the innate immune response by upregulation of PDLIM2, independent of the host interferon response. We show PDLIM2 is an E3 ubiquitin ligase that also acts to stimulate nuclear degradation of STAT2. Interferon dependent relocalization of STAT1/2 to the nucleus leads to PDLIM2 ubiquitination of STAT2 but not STAT1 and the proteasome-dependent degradation of STAT2, predominantly within the nucleus. CRISPR/Cas9 knockout of PDLIM2 results in increased levels of STAT2 following IFNα treatment, retention of STAT2 within the nucleus of HCV infected cells after IFNα stimulation, increased interferon response, and increased resistance to infection by several flaviviruses, indicating that PDLIM2 is a global regulator of the interferon response.

The response of cells to an invading pathogen must be swift and well controlled because of the detrimental effects of chronic inflammation. However, viruses often hijack host control mechanisms. HCV and flaviviruses are known to suppress the innate immune response in cells by a variety of mechanisms. This study clarifies and expands a specific cellular mechanism for global control of the antiviral response after the induction of interferon expression. It shows how several viruses hijack this control mechanism to suppress the innate interferon response.

Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC)

Till now, no appropriate biomarkers for high‐risk population screening and prognosis prediction have been identified for patients with oesophageal squamous cell carcinoma (ESCC). In this study, by the combined use of data from the Gene Expression Omnibus (GEO) datasets and The Cancer Genome Atlas (TCGA)‐oesophageal carcinoma (ESCA), we aimed to screen dysregulated genes with prognostic value in ESCC and the genetic and epigenetic alterations underlying the dysregulation. About 222 genes that had at least fourfold change in ESCC compared with adjacent normal tissues were identified using the microarray data in GDS3838. Among these genes, only PDLIM2 was associated with nodal invasion and overall survival (OS) at the same time. The high PDLIM2 expression group had significantly longer OS and its expression was independently associated with better OS (HR: 0.64, 95% CI: 0.43‐0.95, P = 0.03), after adjustment for gender and pathologic stages. The expression of its exon 7/8/9/10 had the highest AUC value (0.724) and better prognostic value (HR: 0.43, 95% CI: 0.22‐0.83, P = 0.01) than total PDLIM2 expression. PDLIM2 DNA copy deletion was common in ESCC and was associated with decreased gene expression. The methylation status of two CpG sites (cg23696886 and cg20449614) in the proximal promoter region of PDLIM2 showed a moderate negative correlation with the gene expression in PDLIM2 copy neutral/amplification group. In conclusion, we infer that PDLIM2 expression might be a novel prognostic indicator for ESCC patients. Its exon 7/8/9/10 expression had the best prognostic value. Its down‐regulation might be associated with gene‐level copy deletion and promoter hypermethylation.

OMICfpp: a fuzzy approach for paired RNA-Seq counts

BACKGROUND

RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. In addition, experimental design must be taken into account and few tools consider it.

RESULTS

We propose OMICfpp, a method for the statistical analysis of RNA-Seq paired design data. First, we obtain a p-value for each case-control pair using a binomial test. These p-values are aggregated using an ordered weighted average (OWA) with a given orness previously chosen. The aggregated p-value from the original data is compared with the aggregated p-value obtained using the same method applied to random pairs. These new pairs are generated using between-pairs and complete randomization distributions. This randomization p-value is used as a raw p-value to test the differential expression of each gene. The OMICfpp method is evaluated using public data sets of 68 sample pairs from patients with colorectal cancer. We validate our results through bibliographic search of the reported genes and using simulated data set. Furthermore, we compared our results with those obtained by the methods edgeR and DESeq2 for paired samples. Finally, we propose new target genes to validate these as gene expression signatures in colorectal cancer. OMICfpp is available at http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz .

CONCLUSIONS

Our study shows that OMICfpp is an accurate method for differential expression analysis in RNA-Seq data with paired design. In addition, we propose the use of randomized p-values pattern graphic as a powerful and robust method to select the target genes for experimental validation.

Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China

Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8x and 27.9x coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in‑frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China.