Two candidate tumor suppressor genes, MEOX2 and SOSTDC1, identified in a 7p21 homozygous deletion region in a Wilms tumor

Angiogenesis related gene signatures predict prognosis and guide therapeutic strategies in renal clear cell carcinoma

Kidney tumors are hypervascular tumors with crucial antiangiogenic effects in tumor therapy. This study aimed to develop a predictive model for kidney renal clear cell carcinoma (KIRC) by utilizing angiogenesis-related genes to formulate targeted therapy and immunotherapy strategies. Angiogenesis-related genes were screened via the GeneCard and Molecular Signatures Database (MSigDB). The KIRC data downloaded from The Cancer Genome Atlas (TCGA) were randomly divided into an experimental cohort and a validation cohort. In the experimental cohort, a risk score prediction model was constructed through successive analyses via univariate Cox regression, LASSO regression, and multivariate Cox regression. Receiver operating characteristic (ROC) curves were employed to assess the sensitivity of the model's predictions. The model's stability and generalizability were subsequently validated in both the validation cohort and the E-MTAB-1980 cohort. Subsequently, the TCGA-KIRC dataset was stratified into two distinct groups: a localized tumor cohort and a progression/metastasis cohort, based on tumor staging criteria. The efficacy of the prognostic prediction model was evaluated within each subgroup. A nomogram model was developed in conjunction with each independent prognostic factor to accurately predict patient outcomes. Additionally, single-cell and intercellular communication analyses were conducted via KIRC single-cell data obtained from the Gene Expression Omnibus (GEO) database. The effects of immunotherapy and targeted therapy on patients were predicted via prognostic modeling. A total of 260 angiogenesis-related genes were identified through screening in the GeneCards and Molecular Signatures Database(MSigDB). We subsequently developed a risk model comprising five genes: MEOX2, PLG, PROX1, TEK, and TIMP1. Survival analysis indicated that the prognosis for high-risk patients was significantly poorer than that for low-risk patients (P < 0.001), and the model demonstrated satisfactory accuracy in predicting 1-, 3-, and 5-year survival rates. This finding was further validated in both internal and external validation cohorts. The model demonstrated applicability for prognostic predictions in both the localized tumor cohort and the progression/metastasis cohort, with proficiency in forecasting the prognosis of patients diagnosed with metastatic renal cancer. The AUC values for 1, 3, and 5 years were recorded at 0.691, 0.709, and 0.773, respectively. We successfully constructed a nomogram model to facilitate accurate prognostic predictions for patients. Analysis of single-cell data revealed that PLG was expressed predominantly in tumor cell clusters, whereas TEK was highly expressed primarily in pericytes. TIMP1 was found to be highly expressed in vascular smooth muscle cells. In contrast, MEOX2 and PROX1 were highly expressed in specific cell clusters but presented low expression levels across the overall cell population. Cell communication analysis indicated that the modeling gene TEK was involved in the angiogenic pathway, with the interaction between the ligand ANGPT2 and the receptor ITGA5-ITGB1 being particularly prominent in this study. Furthermore, the immune dysfunction and rejection scores for high-risk patients within the non-localized renal cancer cohort were markedly elevated compared to those observed in the low-risk group. In terms of targeted pharmacological intervention, individuals classified in the low-risk group exhibited a heightened sensitivity to sorafenib. The KIRC prognostic prediction model, which is based on five angiogenesis-related genes, demonstrated reliable performance, indicating that high-risk patients have a significantly poorer prognosis than low-risk patients do. The developed nomogram model effectively visualizes and accurately predicts patient prognosis. It is essential to highlight that individuals diagnosed with low-risk metastatic KIRC may experience greater advantages from the administration of immunotherapy and sorafenib.

Deciphering the cellular and molecular landscapes of Wnt/β-catenin signaling in mouse embryonic kidney development

Background

The Wnt/β-catenin signaling pathway is critical in kidney development, yet its specific effects on gene expression in different embryonic kidney cell types are not fully understood.

Methods

Wnt/β-catenin signaling was activated in mouse E12.5 kidneys in vitro using CHIR99021, with RNA sequencing performed afterward, and the results were compared to DMSO controls (dataset GSE131240). Differential gene expression in ureteric buds and cap mesenchyme following pathway activation (datasets GSE20325 and GSE39583) was analyzed. Single-cell RNA-seq data from the Mouse Cell Atlas was used to link differentially expressed genes (DEGs) with kidney cell types. β-catenin ChIP-seq data (GSE39837) identified direct transcriptional targets.

Results

Activation of Wnt/β-catenin signaling led to 917 significant DEGs, including the upregulation of Notum and Apcdd1 and the downregulation of Crym and Six2. These DEGs were involved in kidney development and immune response. Single-cell analysis identified 787 DEGs across nineteen cell subtypes, with Macrophage_Apoe high cells showing the most pronounced enrichment of Wnt/β-catenin-activated genes. Gene expression profiles in ureteric buds and cap mesenchyme differed significantly upon β-catenin manipulation, with cap mesenchyme showing a unique set of DEGs. Analysis of β-catenin ChIP-seq data revealed 221 potential direct targets, including Dpp6 and Fgf12.

Conclusion

This study maps the complex gene expression driven by Wnt/β-catenin signaling in embryonic kidney cell types. The identified DEGs and β-catenin targets elucidate the molecular details of kidney development and the pathway's role in immune processes, providing a foundation for further research into Wnt/β-catenin signaling in kidney development and disease.

Low expression of MEOX2 is associated with poor survival in patients with breast cancer

Aim: To investigate associations of MEOX2 expression with clinicopathological features and survival of breast cancer patients. Materials & methods: We used a breast cancer tissue microarray for immunohistochemistry. Associations between MEOX2 expression and clinicopathological features were analyzed using the χ-square test. Survival analysis was determined using a Kaplan-Meier curve. Multivariate Cox regression was used to determine associations of MEOX2 expression with overall survival. Results: We found that 74.1% of patients (100/135) had expression of MEOX2 at varying levels. MEOX2 was associated with histological grade and negatively correlated with Ki67 expression. Lower MEOX2 expression was significantly associated with decreased overall survival (p = 0.0011). Conclusion: MEOX2 expression could be a novel diagnostic and prognostic biomarker of breast cancer.

Role of Sostdc1 in skeletal biology and cancer

Sclerostin domain-containing protein-1 (Sostdc1) is a member of the sclerostin family and encodes a secreted 28–32 kDa protein with a cystine knot-like domain and two N-linked glycosylation sites. Sostdc1 functions as an antagonist to bone morphogenetic protein (BMP), mediating BMP signaling. It also interacts with LRP6, mediating LRP6 and Wnt signaling, thus regulating cellular proliferation, differentiation, and programmed cell death. Sostdc1 plays various roles in the skin, intestines, brain, lungs, kidneys, and vasculature. Deletion of Sostdc1 gene in mice resulted in supernumerary teeth and improved the loss of renal function in Alport syndrome. In the skeletal system, Sostdc1 is essential for bone metabolism, bone density maintenance, and fracture healing. Recently, Sostdc1 has been found to be closely related to the development and progression of multiple cancer types, including breast, renal, gastric, and thyroid cancers. This article summarises the role of Sostdc1 in skeletal biology and related cancers to provide a theoretical basis for the treatment of related diseases.

SOSTDC1 acts as a tumor inhibitor in acute myeloid leukemia by downregulating the Wnt/β-catenin pathway

Sclerostin domain-containing 1 (SOSTDC1) has been documented as a key tumor-associated protein that is differentially expressed in multiple malignancies. However, the function of SOSTDC1 in acute myeloid leukemia (AML) is unexplored. The goal of this work was to assess the possible role of SOSTDC1 in AML. Our data showed decreased SOSTDC1 level in bone marrow from AML patients, and patients with low levels of SOSTDC1 had a reduced survival rate. SOSTC1 upregulation restrained the proliferative ability and promoted the apoptotic rate of AML cells. SOSTDC1 suppressed the activation of the Wnt/β-catenin pathway in AML cells. Reactivation of the Wnt/β-catenin pathway reversed SOSTDC1-mediated antitumor effects. SOSTDC1 upregulation weakened the tumorigenicity of AML cells in vivo. Collectively, our work demonstrates that SOSTDC1 has a tumor-inhibiting role in AML via downregulation of the Wnt/β-catenin pathway. This work underscores a key function for the SOSTDC1/Wnt/β-catenin pathway in AML.

Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1

The 10q24.33 locus is known to be associated with susceptibility to cutaneous malignant melanoma (CMM), but the mechanisms underlying this association have been not extensively investigated. We carried out an integrative genomic analysis of 10q24.33 using epigenomic annotations and in vitro reporter gene assays to identify regulatory variants. We found two putative functional single nucleotide polymorphisms (SNPs) in an enhancer and in the promoter of OBFC1, respectively, in neural crest and CMM cells, one, rs2995264, altering enhancer activity. The minor allele G of rs2995264 correlated with lower OBFC1 expression in 470 CMM tumors and was confirmed to increase the CMM risk in a cohort of 484 CMM cases and 1801 controls of Italian origin. Hi-C and chromosome conformation capture (3C) experiments showed the interaction between the enhancer-SNP region and the promoter of OBFC1 and an isogenic model characterized by CRISPR-Cas9 deletion of the enhancer-SNP region confirmed the potential regulatory effect of rs2995264 on OBFC1 transcription. Moreover, the presence of G-rs2995264 risk allele reduced the binding affinity of the transcription factor MEOX2. Biologic investigations showed significant cell viability upon depletion of OBFC1, specifically in CMM cells that were homozygous for the protective allele. Clinically, high levels of OBFC1 expression associated with histologically favorable CMM tumors. Finally, preliminary results suggested the potential effect of decreased OBFC1 expression on telomerase activity in tumorigenic conditions. Our results support the hypothesis that reduced expression of OBFC1 gene through functional heritable DNA variation can contribute to malignant transformation of normal melanocytes.

OUP accepted manuscript

BACKGROUND

Glioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10, and aberrantly activated receptor tyrosine kinase signaling pathways. Previously, we identified Mesenchyme Homeobox 2 (MEOX2), a gene located on chromosome 7, as an upregulated transcription factor in GBM. Overexpressed transcription factors can be involved in driving GBM. Here, we aimed to address the role of MEOX2 in GBM.

METHODS

Patient-derived GBM tumorspheres were used to constitutively knockdown or overexpress MEOX2 and subjected to in vitro assays including western blot to assess ERK phosphorylation. Cerebral organoid models were used to investigate the role of MEOX2 in growth initiation. Intracranial mouse implantation models were used to assess the tumorigenic potential of MEOX2. RNA-sequencing, ACT-seq, and CUT&amp;Tag were used to identify MEOX2 target genes.

RESULTS

MEOX2 enhanced ERK signaling through a feed-forward mechanism. We identified Ser155 as a putative ERK-dependent phosphorylation site upstream of the homeobox-domain of MEOX2. S155A substitution had a major effect on MEOX2 protein levels and altered its subnuclear localization. MEOX2 overexpression cooperated with p53 and PTEN loss in cerebral organoid models of human malignant gliomas to induce cell proliferation. Using high-throughput genomics, we identified putative transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor.

CONCLUSIONS

We identified MEOX2 as an oncogenic transcription regulator in GBM. MEOX2 increases proliferation in cerebral organoid models of GBM and feeds into ERK signaling that represents a core signaling pathway in GBM.

Failure to EGFR-TKI-based therapy and tumoural progression are promoted by MEOX2/GLI1-mediated epigenetic regulation of EGFR in the human lung cancer

BACKGROUND

Mesenchyme homeobox-2 (MEOX2)-mediated regulation of glioma-associated oncogene-1 (GLI1) has been associated with poor overall survival, conferring chemoresistance in lung cancer. However, the role of MEOX2/GLI1 in resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs)-based therapy remains unexplored in human lung cancer.

METHODS

Functional assays using genetic silencing strategy by short hairpin RNAs, as well as cytotoxic (tetrazolium dye MTT) and clonogenic assays, were performed to evaluate MEOX2/GLI1-induced malignancy capacity in lung cancer cells. Further analysis performed includes western blot, qPCR and ChIP-qPCR assays to identify whether MEOX2/GLI1 promote EGFR/AKT/ERK activation, as well as EGFR overexpression through epigenetic mechanisms. Finally, preclinical tumour progression in vivo and progression-free disease interval analyses in patients treated with EGFR-TKI were included.

RESULTS

Overexpressed MEOX2/GLI1 in both EGFR wild-type and EGFR/KRAS-mutated lung cancer cells were detected and involved in the activation/expression of EGFR/AKT/ERK biomarkers. In addition, MEOX2/GLI1 was shown to be involved in the increased proliferation of tumour cells and resistance capacity to cisplatin, EGFR-TKIs (erlotinib and AZD9291 'osimertinib'), AZD8542-SMO, and AZD6244-MEKK1/2. In addition, we identified that MEOX2/GLI1 promote lung tumour cells progression in vivo and are clinically associated with poorer progression-free disease intervals. Finally, both MEOX2 and GLI1 were detected to be epigenetically involved in EGFR expression by reducing both repressive markers polycomb-EZH2 and histone H3K27me3, but, particularly, increasing an activated histone profile H3K27Ac/H3K4me3 at EGFR-gene enhancer-promoter sequences that probably representing a novel EGFR-TKI-based therapy resistance mechanism.

CONCLUSION

MEOX2/GLI1 promote resistance to cisplatin and EGFR-TKI-based therapy in lung cancer cells, modulating EGFR/AKT/ERK signalling pathway activation, as well as inducing an aberrant epigenetic modulation of the EGFR-gene expression in human lung cancer.

MEOX2 Transcription Factor Is Involved in Survival and Adhesion of Glioma Stem-like Cells

Simple Summary

Glioblastoma is the most common and lethal primary brain tumor for which no curative treatment currently exists. In our previous work, we showed that MEOX2 was associated with a poor patient prognosis but its biological involvement in tumor development remains ill defined. To this purpose, the aim of our study was to investigate the role of MEOX2 in patient-derived glioblastoma cell cultures. We unraveled the MEOX2 contribution to cell viability and growth and its potential involvement in phenotype and adhesion properties of glioblastoma cells. This work paves the way toward a better understanding of the role of MEOX2 in the pathophysiology of primary brain tumors.

Abstract

The high expression of MEOX2 transcription factor is closely associated with poor overall survival in glioma. MEOX2 has recently been described as an interesting prognostic biomarker, especially for lower grade glioma. MEOX2 has never been studied in glioma stem-like cells (GSC), responsible for glioma recurrence. The aim of our study was to investigate the role of MEOX2 in GSC. Loss of function approach using siRNA was used to assess the impact of MEOX2 on GSC viability and stemness phenotype. MEOX2 was localized in the nucleus and its expression was heterogeneous between GSCs. MEOX2 expression depends on the methylation state of its promoter and is strongly associated with IDH mutations. MEOX2 is involved in cell proliferation and viability regulation through ERK/MAPK and PI3K/AKT pathways. MEOX2 loss of function correlated with GSC differentiation and acquisition of neuronal lineage characteristics. Besides, inhibition of MEOX2 is correlated with increased expression of CDH10 and decreased pFAK. In this study, we unraveled, for the first time, MEOX2 contribution to cell viability and proliferation through AKT/ERK pathway and its potential involvement in phenotype and adhesion properties of GSC.

MicroRNA-301a-3p promotes triple-negative breast cancer progression through downregulating MEOX2

Breast cancer is one of the most frequently diagnosed malignancies among women. Triple-negative breast cancer (TNBC) represents a significant challenge for breast oncologists, as the availability of effective therapies for this aggressive disease is limited. The molecular mechanisms underlying TNBC development are not fully understood. Previous studies have demonstrated that microRNAs (miRNAs/miRs) play important roles in the development of various types of cancer, including breast cancer; however, the role of miRNAs in TNBC remains undetermined. The results of the present study revealed that miR-301a-3p may function as an oncogenic miRNA in TNBC. Based on The Cancer Genome Atlas data, miR-301a-3p expression levels were found to be upregulated in breast cancer tissues. Reverse transcription-quantitative PCR analysis demonstrated that the expression levels of miR-301a-3p were upregulated in TNBC tissues compared with non-TNBC tissues, and in MDA-MB-231 cells compared with normal MCF-10A breast cells. miR-301a-3p mimics and inhibitors were subsequently used to overexpress and knock down miR-301a-3p expression, respectively, in MDA-MB-231 cells. Biological functional experiments demonstrated that miR-301a-3p overexpression increased the viability, and the migratory and invasive abilities of MDA-MB-231 cells. By contrast, miR-301a-3p knockdown exerted the opposite effects on MDA-MB-231 cells. Cell apoptosis was negatively regulated by miR-301a-3p. Moreover, overexpression of miR-301a-3p was found to downregulate the expression levels of mesenchyme homeobox 2 (MEOX2). The expression levels of miR-301a-3p were negatively correlated with the expression levels of MEOX2 in clinical tissue specimens from patients with TNBC. Subsequently, the knockdown of MEOX2 expression promoted the viability of MDA-MB-231 cells. In conclusion, the results of the present study suggested that miR-301a-3p may serve as an oncogenic miRNA in TNBC by regulating MEOX2 expression.

Prognostic significance of MEOX2 in gliomas

Gliomas are the most common malignant primary tumors in the central nervous system and have variable predictive clinical courses. Glioblastoma, the most aggressive form of glioma, is a complex disease with unsatisfactory therapeutic solutions and a very poor prognosis. Some processes at stake in gliomagenesis have been discovered but little is known about the role of homeobox genes, even though they are highly expressed in gliomas, particularly in glioblastoma. Among them, the transcription factor Mesenchyme Homeobox 2 (MEOX2) had previously been associated with malignant progression and clinical prognosis in lung cancer and hepatocarcinoma but never studied in glioma. The aim of our study was to investigate the clinical significance of MEOX2 in gliomas. We assessed the expression of MEOX2 according to IDH1/2 molecular profile and patient survival among three different public datasets: The Cancer Genome Atlas (TCGA), The Chinese Glioma Genome Atlas (CGGA) and the US National Cancer Institute Repository for Molecular Brain Neoplasia Data (Rembrandt). We then evaluated the prognostic significance of MEOX2 protein expression on 112 glioma clinical samples including; 56 IDH1 wildtype glioblastomas, 7 IDH1 wild-type lower grade gliomas, 49 IDH1 mutated lower grade gliomas. Survival rates were estimated by the Kaplan-Meier method followed by uni/multivariate analyses. We demonstrated that MEOX2 was one of the transcription factors most closely associated with overall survival in glioma. Moreover, MEOX2 expression was associated with IDH1/2 wildtype molecular subtype and was significantly correlated with overall survival of all gliomas and, more interestingly, in lower grade glioma. To conclude, our results may be the first to provide insight into the clinical significance of MEOX2 in gliomas, which is a factor closely related to patient outcome. MEOX2 could constitute an interesting prognostic biomarker, especially for lower grade glioma.

Down-regulation of SOSTDC1 promotes thyroid cancer cell proliferation via regulating cyclin A2 and cyclin E2

Sclerostin domain containing protein 1 (SOSTDC1) is down-regulated and acts as a tumor suppressor in some kinds of cancers. However, the expression pattern and biological significance of SOSTDC1 in thyroid cancer are largely unknown. We demonstrated that SOSTDC1 was significantly down-regulated in thyroid cancer. Ectopic over-expression of SOSTDC1 inhibited proliferation and induced G1/S arrest in thyroid cancer cells. Moreover, SOSTDC1 over-expression suppressed the growth of tumor xenografts in nude mice. We also found that elevated SOSTDC1 led to inhibition of cyclin A2 and cyclin E2. Together, our results demonstrate that SOSTDC1 is down-regulated in thyroid cancer and might be a potential therapeutic target in the treatment of thyroid cancer.

SOSTDC1 is down-regulated in non-small cell lung cancer and contributes to cancer cell proliferation

Background

Non-small cell lung cancer (NSCLC) is the most commonly diagnosed and fatal cancer worldwide. Sclerostin domain containing protein 1 (SOSTDC1) has been found to be tumor-suppressive in several types of cancers. However, the expression level and biological functions of SOSTDC1 in NSCLC remain unknown. Our current study aimed to identify the biological significance of SOSTDC1 in NSCLC.

Results

We found that SOSTDC1 was significantly down-regulated in NSCLC. Moreover, patients with higher expression of SOSTDC1 had a significant better prognosis than those with lower SOSTDC1 expression. Ectopic expression of SOSTDC1 in NSCLC cell lines A549 and NCI-H520 could inhibit proliferation as shown by MTT, colony formation, soft agar and EdU incorporation assays in vitro. Furthermore, A549 cells stably expressing ectopic SOSTDC1 grew more slowly and formed smaller tumors than vector-control cells in vivo. Mechanistic studies demonstrated that SOSTDC1 over-expression led to increased p21Cip and p27Kip levels, thereby decreasing Rb phosphorylation status and E2F transcription activity.

Conclusions

SOSTDC1 is down-regulated in NSCLC, and its expression level is indicative of clinical outcome of patients with the disease. SOSTDC1 might represent a tumor suppressor through inhibiting the proliferation of NSCLC cells by regulating p21Cip and p27Kip, which in turn affects Rb-E2F signaling.

Genetic variation frequencies in Wilms' tumor: A meta-analysis and systematic review

Over the last few decades, numerous biomarkers in Wilms' tumor have been confirmed and shown variations in prevalence. Most of these studies were based on small sample sizes. We carried out a meta-analysis of the research published from 1992 to 2015 to obtain more precise and comprehensive outcomes for genetic tests. In the present study, 70 out of 5175 published reports were eligible for the meta-analysis, which was carried out using Stata 12.0 software. Pooled prevalence for gene mutations WT1, WTX, CTNNB1, TP53, MYCN, DROSHA, and DGCR8 was 0.141 (0.104, 0.178), 0.147 (0.110, 0.184), 0.140 (0.100, 0.190), 0.410 (0.214, 0.605), 0.071 (0.041, 0.100), 0.082 (0.048, 0.116), and 0.036 (0.026, 0.046), respectively. Pooled prevalence of loss of heterozygosity at 1p, 11p, 11q, 16q, and 22q was 0.109 (0.084, 0.133), 0.334 (0.295, 0.373), 0.199 (0.146, 0.252), 0.151 (0.129, 0.172), and 0.148 (0.108, 0.189), respectively. Pooled prevalence of 1q and chromosome 12 gain was 0.218 (0.161, 0.275) and 0.273 (0.195, 0.350), respectively. The limited prevalence of currently known genetic alterations in Wilms' tumors indicates that significant drivers of initiation and progression remain to be discovered. Subgroup analyses indicated that ethnicity may be one of the sources of heterogeneity. However, in meta-regression analyses, no study-level characteristics of indicators were found to be significant. In addition, the findings of our sensitivity analysis and possible publication bias remind us to interpret results with caution.

Genomic imbalances pinpoint potential oncogenes and tumor suppressors in Wilms tumors

BACKGROUND

Wilms tumor (WT) has a not completely elucidated pathogenesis. DNA copy number alterations (CNAs) are common in cancer, and often define key pathogenic events. The aim of this work was to investigate CNAs in order to disclose new candidate genes for Wilms tumorigenesis.

RESULTS

Array-CGH of 50 primary WTs without pre-chemotherapy revealed a few recurrent CNAs not previously reported, such as 7q and 20q gains, and 7p loss. Genomic amplifications were exclusively detected in 3 cases of WTs that later relapsed, which also exhibited an increased frequency of gains affecting a 16.2 Mb 1q21.1-q23.2 region, losses at 11p, 11q distal, and 16q, and WT1 deletions. Conversely, aneuploidies of chromosomes 13 and 19 were found only in WTs without further relapse. The 1q21.1-q23.2 gain associated with WT relapse harbours genes such as CHD1L, CRABP2, GJA8, MEX3A and MLLT11 that were found to be over-expressed in WTs. In addition, down-regulation of genes encompassed by focal deletions highlighted new potential tumor suppressors such as CNKSR1, MAN1C1, PAQR7 (1p36), TWIST1, SOSTDC1 (7p14.1-p12.2), BBOX and FIBIN (11p13), and PLCG2 (16q).

CONCLUSION

This study confirmed the presence of CNAs previously related to WT and characterized new CNAs found only in few cases. The later were found in higher frequency in relapsed cases, suggesting that they could be associated with WT progression.

JNK-dependent gene regulatory circuitry governs mesenchymal fate

The epithelial to mesenchymal transition (EMT) is a biological process in which cells lose cell–cell contacts and become motile. EMT is used during development, for example, in triggering neural crest migration, and in cancer metastasis. Despite progress, the dynamics of JNK signaling, its role in genomewide transcriptional reprogramming, and involved downstream effectors during EMT remain largely unknown. Here, we show that JNK is not required for initiation, but progression of phenotypic changes associated with EMT. Such dependency resulted from JNK-driven transcriptional reprogramming of critical EMT genes and involved changes in their chromatin state. Furthermore, we identified eight novel JNK-induced transcription factors that were required for proper EMT. Three of these factors were also highly expressed in invasive cancer cells where they function in gene regulation to maintain mesenchymal identity. These factors were also induced during neuronal development and function in neuronal migration in vivo. These comprehensive findings uncovered a kinetically distinct role for the JNK pathway in defining the transcriptome that underlies mesenchymal identity and revealed novel transcription factors that mediate these responses during development and disease.

SOSTDC1 down-regulation of expression involves CpG methylation and is a potential prognostic marker in gastric cancer

Sclerostin domain containing 1 (SOSTDC1) is reportedly down-regulated in various cancers. Our purpose was to study whether epigenetic mechanisms were involved in the down-regulation of expression in gastric cancer. Expression analysis of SOSTDC1 in gastric cancer cell lines indicated mRNA down-regulation. Our reporter assays and gene reactivation studies using 5-aza-2'-deoxycytidine, a DNA demethylating agent, and trichostatin A (TSA), a histone deacetylase (HDAC) inhibitor, demonstrated that epigenetic mechanisms are involved in the down-regulation of SOSTC1 expression. Methylation analysis of the SOSTDC1 promoter CpGs using methylation-specific polymerase chain reaction analysis revealed methylation in gastric cancer cell lines and tissue samples. A majority of tumors (17 of 18) with observed methylation exhibited down-regulation of mRNA expression relative to apparently normal gastric tissues. Immunoreactivity for SOSTDC1 in gastric tumors (24 of 46, 52.1%) was down-regulated relative to normal tissues (36 of 38, 94.7%) (P = 0.00001). The difference in expression between gastric tumor subtypes, intestinal and diffuse, was significant (P = 0.040). Expression of SOSTDC1 in gastric tumors increased the probability of both overall and disease-free survival. When overexpressed in AGS cells, cell proliferation, cell cycle progression, and anchorage-independent growth was repressed. The present findings indicate SOSTDC1 down-regulation involves methylation; SOSTDC1 expression is a potential prognostic factor and tumor suppressor in gastric cancer.

Comparative genomic hybridization of Wilms' tumor

Cytogenetic analysis of solid tumors including Wilms' tumor is challenging due to poor chromosome morphology, complexity of abnormalities, and to the possibility of stromal cell overgrowth in tissue culture. Molecular cytogenetic techniques such as chromosomal comparative genomic hybridization (CGH) have improved the diagnosis of chromosomal aberrations in Wilms' tumor since they can provide results based on the analysis of DNA from nondividing cells. However, chromosomal CGH provides only a limited resolution across the whole genome, which is not different than routine cytogenetic analysis (gains or losses of less than one chromosome band or 10 Mb are not detectable by routine cytogenetics or chromosomal CGH). More recently, the development of genomic arrays opened the possibility of assessing the whole genome at a much higher resolution at a sub-microscopic or sub-band level. Based on the principle of chromosomal CGH, this approach, frequently termed array-CGH, opens the possibility to find invisible changes at the whole genome level not only in abnormal but also in normal tumor karyotypes. Here, we discuss the main technical features, benefits, and limitations of the above three techniques as applied to Wilms' tumor and summarize the main advances in our knowledge about the genetic changes of Wilms' tumor and their clinical relevance.

miR-301a is a candidate oncogene that targets the homeobox gene Gax in human hepatocellular carcinoma

BACKGROUND

MicroRNAs (miRNA) are a group of noncoding small RNAs that repress mRNA expression or induce mRNA degradation by binding to the 3'-untranslated regions of mRNAs. MiRNAs have been connected closely with the development of cancers such as hepatocellular carcinoma (HCC). However, the overexpression of microRNA-301a (miR-301a) has seldom been connected with tumorigenesis in HCC.

AIMS

This study aims to characterize the function of upregulated miR-301a in HCC and show how the downstream growth arrest-specific homeobox (Gax) is negatively regulated by miR-301a.

METHODS

The expression of miR-301a and Gax was detected using real-time PCR on HCC tissues and adjacent non-tumorous tissues. The luciferase reporter assay was used to assess Gax as a target of miR-301a. The nuclear factor κB (NF-κB) was measured by western blot after inhibiting miR-301a and enhancing Gax. The functions of miR-301a in vivo in HCC cells were measured by migration and invasion assays and flow cytometry.

RESULTS

MiR-301a was significantly upregulated and Gax was downregulated in HCC samples compared with in the matching nontumoral tissues. Inhibiting miR-301a expression caused the upregulation of Gax and repressed NF-κB expression. We have shown that miR-301a plays an important role in increasing proliferation, migration and invasion and in inhibiting apoptosis of HCC cells.

CONCLUSIONS

miR-301a is frequently upregulated in HCC and modulates NF-κB expression by negatively regulating Gax.

Genomic profiling by whole-genome single nucleotide polymorphism arrays in Wilms tumor and association with relapse

Despite the excellent survival rate of Wilms tumor (WT) patients, only approximately one-half of children who suffer tumor recurrence reach second durable remission. This underlines the need for novel markers to optimize initial treatment. We investigated 77 tumors using Illumina 370CNV-QUAD genotyping BeadChip arrays and compared their genomic profiles to detect copy number (CN) abnormalities and allelic ratio anomalies associated with the following clinicopathological variables: relapse (yes vs. no), age at diagnosis (≤ 24 months vs. >24 months), and disease stage (low stage, I and II, vs. high stage, III and IV). We found that CN gains at chromosome region 1q21.1-q31.3 were significantly associated with relapse. Additional genetic events, including allelic imbalances at chromosome arms 1p, 1q, 3p, 3q, and 14q were also found to occur at higher frequency in relapsing tumors. Interestingly, allelic imbalances at 1p and 14q also showed a borderline association with higher tumor stages. No genetic events were found to be associated with age at diagnosis. This is the first genome wide analysis with single nucleotide polymorphism (SNP) arrays specifically investigating the role of genetic anomalies in predicting WT relapse on cases prospectively enrolled in the same clinical trial. Our study, besides confirming the role of 1q gains, identified a number of additional candidate genetic markers, warranting further molecular investigations.

A curated database of genetic markers from the angiogenesis/VEGF pathway and their relation to clinical outcome in human cancers

INTRODUCTION

Angiogenesis causes local growth, aggressiveness and metastasis in solid tumors, and thus, is almost always associated with poor prognosis and survival in cancer patients. Because of this clinical importance, several chemotherapeutic agents targeting angiogenesis have also been developed. Genes and genetic variations in angiogenesis/VEGF pathway thus may be correlated with clinical outcome in cancer patients.

MATERIAL AND METHODS

Here, we describe a manually curated public database, dbANGIO, which posts the results of studies testing the possible correlation of genetic variations (polymorphisms and mutations) from the angiogenesis/VEGF pathway with demographic features, clinicopathological features, treatment response and toxicity, and prognosis and survival-related endpoints in human cancers. The scientific findings are retrieved from PUBMED and posted in the dbANGIO website in a summarized form.

RESULTS AND CONCLUSION

As of September 2011, dbANGIO includes 362 entries from 83 research articles encompassing 154 unique genetic variations from 39 genes investigated in several solid and hematological cancers. By curating the literature findings and making them freely available to researchers, dbANGIO will expedite the research on genetic factors from the angiogenesis pathway and will assist in their utility in clinical management of cancer patients. dbANGIO is freely available for non-profit institutions at http://www.med.mun.ca/angio.

SOSTDC1 differentially modulates Smad and beta-catenin activation and is down-regulated in breast cancer

Sclerostin domain containing 1 (SOSTDC1) protein regulates processes from development to cancer by modulating activity of bone morphogenetic protein (BMP) and wingless/int (Wnt) signaling pathways. As dysregulation of both BMP and Wnt signaling has been observed in breast cancer, we investigated whether disruption of SOSTDC1 signaling occurs in breast cancer. SOSTDC1 mRNA expression levels in breast tissue were examined using a dot blot. Affymetrix microarray data on SOSTDC1 levels were correlated with breast cancer patient survival using Kaplan-Meier plots. Correlations between SOSTDC1 protein levels and clinical parameters were assessed by immunohistochemistry of a breast cancer tissue microarray. SOSTDC1 secretion and BMP and Wnt signaling were investigated using immunoblotting. We found that SOSTDC1 is expressed in normal breast tissue and this expression is reduced in breast cancer. High levels of SOSTDC1 mRNA correlated with increased patient survival; conversely, SOSTDC1 protein levels decreased as tumor size and disease stage increased. Treatment of breast cancer cells with recombinant SOSTDC1 or Wise, a SOSTDC1 orthologue, demonstrated that SOSTDC1 selectively blocks BMP-7-induced Smad phosphorylation without diminishing BMP-2 or Wnt3a-induced signaling. In conclusion, SOSTDC1 mRNA and protein are reduced in breast cancer. High SOSTDC1 mRNA levels correlate with increased distant metastasis-free survival in breast cancer patients. SOSTDC1 differentially affects Wnt3a, BMP-2, and BMP-7 signaling in breast cancer cells. These results identify SOSTDC1 as a clinically important extracellular regulator of multiple signaling pathways in breast cancer.

Pathology, genetics and cytogenetics of Wilms' tumour

Wilms' tumour (WT) is an embryonal cancer of childhood and is thought to be derived from embryonic kidney precursor cells. The Knudson two hit model was initially thought to occur in WT, but findings emerging from genetic and cytogenetic studies in the past two decades have implicated several genetic events. Recent techniques in genetic analysis have improved our ability to characterise changes in genes involved in WT which include WT1, CTNNB1, IGF2 and WTX. These genetic events have not only provided insight into the pathobiology of this malignancy, but the recognition of these candidate genes may offer potential targets for novel therapies. In this review, we will provide an overview of the pathological, genetic and cytogenetic characteristics of WT.

Multiple genetic loci modulate lung adenocarcinoma clinical staging

PURPOSE

The main prognostic factor of lung cancer patient outcome is clinical stage, a parameter of tumor aggressiveness. Our study was conducted to test whether germ line variations modulate individual differences in clinical stage.

EXPERIMENTAL DESIGN

We conducted a case-only genome-wide association study (GWAS) using a 620,901 single-nucleotide polymorphism (SNP) array in a first series of 600 lung adenocarcinoma (ADCA) patients and in a replication series of 317 lung ADCA patients.

RESULTS

GWAS identified 54 putatively associated SNPs, 3 of which were confirmed in the replication series. Joint analysis of the two series pointed to 22 statistically associated (P < 0.01) genetic variants that together explained about 20% of the phenotypic variation in clinical staging (P < 2 × 10(-16)) and showed a statistically significant difference in overall survival (P = 8.0 × 10(-8)). The strongest statistical association was observed at rs10278557 (P = 1.1 × 10(-5)), located in the mesenchyme homeobox 2 (MEOX2) gene.

CONCLUSION

These data point to the role of germ line variations involving multiple loci in modulating clinical stage and, therefore, prognosis in lung ADCA patients.

Characteristics of highly polymorphic segmental copy-number variations observed in Japanese by BAC-array-CGH

Segmental copy-number variations (CNVs) may contribute to genetic variation in humans. Reports of the existence and characteristics of CNVs in a large Japanese cohort are quite limited. We report the data from a large Japanese population. We conducted population screening for 213 unrelated Japanese individuals using comparative genomic hybridization based on a bacterial artificial chromosome microarray (BAC-aCGH). We summarize the data by focusing on highly polymorphic CNVs in ≥5.0% of the individual, since they may be informative for demonstrating the relationships between genotypes and their phenotypes. We found a total of 680 CNVs at 16 different BAC-regions in the genome. The majority of the polymorphic CNVs presented on BAC-clones that overlapped with regions of segmental duplication, and the majority of the polymorphic CNVs observed in this population had been previously reported in other publications. Some of the CNVs contained genes which might be related to phenotypic heterogeneity among individuals.

Loss of heterozygosity and SOSTDC1 in adult and pediatric renal tumors

Background

Deletions within the short arm of chromosome 7 are observed in approximately 25% of adult and 10% of Wilms pediatric renal tumors. Within Wilms tumors, the region of interest has been delineated to a 2-Mb minimal region that includes ten known genes. Two of these ten candidate genes, SOSTDC1 and MEOX2, are particularly relevant to tumor development and maintenance. This finding, coupled with evidence that SOSTDC1 is frequently downregulated in adult renal cancer and regulates both Wingless-Int (Wnt)- and bone morphogenetic protein (BMP)-induced signaling, points to a role for SOSTDC1 as a potential tumor suppressor.

Methods

To investigate this hypothesis, we interrogated the Oncomine database to examine the SOSTDC1 levels in adult renal clear cell tumors and pediatric Wilms tumors. We then performed single nucleotide polymorphism (SNP) and sequencing analyses of SOSTDC1 in 25 pediatric and 36 adult renal tumors. Immunohistochemical staining of patient samples was utilized to examine the impact of SOSTDC1 genetic aberrations on SOSTDC1 protein levels and signaling.

Results

Within the Oncomine database, we found that SOSTDC1 levels were reduced in adult renal clear cell tumors and pediatric Wilms tumors. Through SNP and sequencing analyses of 25 Wilms tumors, we identified four with loss of heterozygosity (LOH) at 7p and three that affected SOSTDC1. Of 36 adult renal cancers, we found five with LOH at 7p, two of which affected SOSTDC1. Immunohistochemical analysis of SOSTDC1 protein levels within these tumors did not reveal a relationship between these instances of SOSTDC1 LOH and SOSTDC1 protein levels. Moreover, we could not discern any impact of these genetic alterations on Wnt signaling as measured by altered beta-catenin levels or localization.

Conclusions

This study shows that genetic aberrations near SOSTDC1 are not uncommon in renal cancer, and occur in adult as well as pediatric renal tumors. These observations of SOSTDC1 LOH, however, did not correspond with changes in SOSTDC1 protein levels or signaling regulation. Although our conclusions are limited by sample size, we suggest that an alternative mechanism such as epigenetic silencing of SOSTDC1 may be a key contributor to the reduced SOSTDC1 mRNA and protein levels observed in renal cancer.

Candidate genes and potential targets for therapeutics in Wilms' tumour

Wilms' tumour (WT) is the most common malignant renal tumour of childhood. During the past two decades or so, molecular studies carried out on biopsy specimens and tumour-derived cell lines have identified a multitude of chromosomal and epigenetic alterations in WT. In addition, a significant amount of evidence has been gathered to identify the genes and signalling pathways that play a defining role in its genesis, growth, survival and treatment responsiveness. As such, these molecules and mechanisms constitute potential targets for novel therapeutic strategies for refractory WT. In this report we aim to review some of the many candidate genes and intersecting pathways that underlie the complexities of WT biology.