Splice variants of zinc finger protein 695 mRNA associated to ovarian cancer

Promoter hypermethylation and comprehensive regulation of ncRNA lead to the down-regulation of ZNF880, providing a new insight for the therapeutics and research of colorectal cancer

The human genome encodes more than 350 kinds of Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), KRAB-type ZNF transcription factor family (KZNF) plays a vital role in gene regulatory networks. The KZNF family members include a large number of highly homologous genes, gene subtypes and pseudogenes, and their expression has a high degree of tissue specificity and precision. Due to the high complexity of its regulatory network, the KZNF gene family has not been researched in sufficient, and the role of its members in the occurrence of cancer is mostly unexplored. In this study, ZNF880 was significantly associated with overall survival (OS) and disease-free survival (DFS) in colorectal carcinoma (CRC) patients. Low ZNF880 expression resulted in shorter OS and DFS. Combined with Colon adenocarcinoma (COAD) and Rectum adenocarcinoma (READ) data collection in the TCGA database, we found that ZNF880 was significantly down-regulated in CRC. Further analysis of the sequence variation of ZNF880 in CRC showed that ZNF880 accumulated a large number of SNV in the C2H2 domain and KRAB domain, while promoter region of ZNF880 also showed high methylation in COAD and READ. Combined with the Cbioportal and TIMER databases, the expression of mutant ZNF880 was significantly lower in COAD compared to the wild type. Simultaneously, the lncRNA-miRNA-ZNF880 ceRNA regulatory network was constructed through co-expression and miRNAs target gene prediction, demonstrating the precision of the ZNF880 regulatory network. In addition, the decreased expression of ZNF880 caused the significant immune infiltration decreases of CD8 + cells in COAD. In contrast, the immune infiltration of CD4 + cells and macrophages in COAD is positively correlated with ZNF880. Finally, through protein-protein interaction (PPI) network analysis and transcription factor target gene prediction, we screened out the genes most likely to be related to the function of ZNF880. CENPK, IFNGR2, REC8 and ZBTB17 were identified as the most closely functioning genes with ZNF880, which may indicate that ZNF880 has important links with the formation of cell centromere, tumor immunity, cell cycle and other pathways closely related to the occurrence of CRC. These studies show that the down-regulation of ZNF880 gene is closely related to CRC, and the targeted change of the expression of its regulatory molecules (miRNA and lncRNA) may be a new perspective for CRC treatment.

Identification of hub genes and their correlation with infiltration of immune cells in MYCN positive neuroblastoma based on WGCNA and LASSO algorithm

Background

The prognosis of MYCN positive NB is poor, and there is no targeted drug for N-myc at present. This study aims to screen out hub genes closely related to MYCN, analyze the relationship between hub genes and NB microenvironment, and provide basis for molecular targeted therapy of MYCN positive NB.

Methods

We combined the microarray data of GSE45547 (n=649) and GSE49710 (n=498), screened the DEGs between MYCN positive (n=185) and MYCN negative NB (n=951), performed WGCNA, Lasso regression and Roc analyses on the merged matrix, and obtained the hub genes related to MYCN in the training group. We performed ssGSEA on the experimental group to calculate the infiltration level of 28 kinds of immune cells in each sample, compared the differences of immune cell infiltration between MYCN positive and MYCN negative group. The influences of hub genes on the distribution of each immune cell were also analyzed by ssGSEA. The expression differences of the three hub genes were verified in the E-MTAB-8248 cohort (n=223), and the correlation between hub genes and prognosis of NB was calculated by Kaplan-Meier method in GSE62564 (n=498) and the validation group. We also verified the expression differences of hub genes by qRT-PCR in SK-N-BE(2), SKNDZ, Kelly and SH-SY5Y cell lines.

Results

Here were 880 DEGs including 420 upregulated and 460 downregulated genes in MYCN positive NB in the training group. Overlap of the DEGs and WGCNA networks identified four shared genes, namely, ZNF695, CHEK1, C15ORF42 and EXO1, as candidate hub genes in MYCN positive NB. Three core genes, ZNF695, CHEK1 and C15ORF42, were finally identified by Lasso regression and Roc analyses. ZNF695, CHEK1 and C15ORF42 were highly expressed in MYCN positive NB tissues and cell lines. These three genes were closely related to the prognosis of children with NB. Except that Activated CD4 T cell and Type2 T helper cell increased, the infiltration levels of the other 26 cells decreased significantly in MYCN positive NB tissues. The infiltration levels of Type2 T helper cell and Activated CD4 T cell were also significantly positively correlated with the expression levels of the three hub genes.

Conclusion

ZNF695, CHEK1 and C15ORF42 are highly expressed in MYCN positive NB, and their expression levels are negatively correlated with the prognosis of children with NB. The infiltration levels of Activated CD4 T cell and Type2 T helper cell increased in the microenvironment of MYCN positive NB and were significantly positively correlated with the expression levels of the three hub genes. The results of this study provide that ZNF695, CHEK1 and C15ORF42 may be potential prognostic markers and immunotherapy targets for MYCN positive NB.

Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment

Alternative splicing (AS) events play a crucial role in the tumorigenesis and progression of cancer. Transcriptome data and Percent Spliced In (PSI) values of ovarian cancer patients were downloaded from TCGA database and TCGA SpliceSeq. Totally we identified 1472 AS events that were associated with survival of ovarian serous cystadenocarcinoma (OC) and exon skipping (ES) was the most important type. Univariate and multivariate Cox regression analysis were performed to identify survival-associated AS events and developed the prognostic model based on 11-AS events. The immune cells and different response to cytotoxic T lymphocyte associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1) blockers in low-risk and high-risk group of OC patients were analyzed. Ten kinds of immune cells were found up-regulated in low-risk group. Activated B cell, natural killer T cell, natural killer cell and regulatory T cell were associated with survival of OC. The patients in low-risk group had good response to CTLA-4 and PD-1 blockers treatment. Moreover, a regulatory network was established according to the correlation between AS events and splicing factors (SFs). The present study provided valuable insights into the underlying mechanisms of OC. AS events that were correlated with the immune system might be potential therapeutic targets.

Computational-based identification and analysis of globally expressed differential genes in high-grade serous ovarian carcinoma cell lines

Ovarian Cancer (OVCA) is the most occurring gynecological cancer worldwide, often diagnosed at a later stage and ultimate results in a high death rate. To overcome this serious health concern, it is important to understand the molecular mechanisms and equally significant to identify the putative biomarkers as well as the therapeutic drug targets for the early diagnosis and treatment of OVCA. In doing so, a strategy is designed to study the most frequently diagnosed cases of OVCA called as High-Grade Serous Ovarian Carcinoma (HGSOC) cell lines with the combination of computational biology, biostatistics and cancer informatics approaches. This study is directed to investigate the global gene expression profiling, and to perform the analyses of identified global Differently Expressed Genes (DEGs) of OVCA. The microarray dataset (GSE71524) is comprised of tumor and cell line samples of OVCA and it was used for the identification of DEGs in the current study. The STRING database was used to construct Protein-Protein Interaction (PPI) network of DEGs, and hub genes were identified by the CytoHubba. In addition, a functional enrichment analysis of up- and down-regulated DEGs was performed by a bioinformatics database called as DAVID. The microRNAs (miRNAs) and transcription factors (TFs) analyses were conducted with the aid of biological tools, MAGIA and GenCOdis3, respectively. As a result, the genes comprised of CSF1R, TYROBP, PLEK, FGR, ACLY, ACACA, LAPTM5, C1 or f162, IL10RA and CD163 were identified as hub genes. Additionally, miRNA analysis resulted in finding an association of zinc finger protein with OVCA comes out after implementing different algorithms. On the other hand, in the TFs analysis resulted in various DEGs that were enriched by NFAT, NF1 and GABP TFs. In this study, it was observed that ACACA, ACLY and CSF1R DEGs showed significant occurrence in different steps, and therefore, these genes were studied, precisely. Nevertheless, the results may help to discover the potential biomarkers with deep understanding of molecular mechanisms. However, further validation is required to explain the OVCA pathogenesis.

Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia

B-cell acute lymphoblastic leukemia is the most commonly diagnosed childhood malignancy worldwide; more than 50% of these cases are diagnosed in Mexico. Although the five-year survival rate is >80%, 30% of patients experience relapse with poor prognosis. Cancer-associated gene expression profiles have been identified in several malignancies, and some transcripts have been used to predict disease prognosis. The human transcriptome is incompletely elucidated; moreover, more than 80% of transcripts can be processed via alternative splicing (AS), which increases transcript and protein diversity. The human transcriptome is divided; coding RNA accounts for 2%, and the remaining 98% is noncoding RNA. Noncoding RNA can undergo AS, promoting the diversity of noncoding transcripts. We designed specific primers to amplify previously reported alternative transcript variants of ZNF695 and showed that six ZNF695 transcript variants are co-expressed in cancer cell lines. The amplicons were sequenced and identified. Additionally, we analyzed the expression of these six transcript variants in bone marrow from B-cell acute lymphoblastic leukemia patients and observed that ZNF695 transcript variants one and three were the predominant variants expressed in leukemia. Moreover, our results showed the co-expression of coding and long noncoding RNA. Finally, we observed that long noncoding RNA ZNF695 expression predicted survival rates.

Identification of promising prognostic genes for relapsed acute lymphoblastic leukemia

PURPOSE

The present study aimed to identify the molecular mechanism of acute lymphoblastic leukemia (ALL), and explore valuable prognostic biomarkers for relapsed ALL.

METHODS

Gene expression dataset including 59 samples from ALL survivals without recurrence (good group) and 114 samples from dead ALL patients died of recurrence (poor group) was downloaded from TCGA database. The differentially expressed genes (DEGs) were identified between good and poor groups, followed by pathway and functional enrichment analyses. Subsequently, logistic regression model and survival analysis were performed.

RESULTS

In total, 637 up- and 578 down-regulated DEGs were revealed between good and poor groups. These DEGs were mainly enriched in functions including transcription and pathways like focal adhesion. Genes including alpha-protein kinase 1 (ALPK1), zinc finger protein 695 (ZNF695), actinin alpha 4 (ACTN4), calreticulin (CALR), and F-Box and leucine rich repeat protein 5 (FBXL5) were outstanding in survival analysis.

CONCLUSION

Transcription and focal adhesion might play important roles in ALL progression. Furthermore, genes including ALPK1, ZNF695, ACTN4, CALR, and FBXL5 might be novel prognostic genes for relapsed ALL.

The expression signature of cancer-associated KRAB-ZNF factors identified in TCGA pan-cancer transcriptomic data

The KRAB-ZNF (Krüppel-associated box domain zinc finger) gene family is composed of a large number of highly homologous genes, gene isoforms, and pseudogenes. The proteins encoded by these genes, whose expression is often tissue-specific, act as epigenetic suppressors contributing to the addition of repressive chromatin marks and DNA methylation. Due to its high complexity, the KRAB-ZNF family has not been studied in sufficient detail, and the involvement of its members in carcinogenesis remains mostly unexplored. In this study, we aimed to provide a comprehensive description of cancer-associated KRAB-ZNFs using publicly available The Cancer Genome Atlas pan-cancer datasets. We analyzed 6727 tumor and normal tissue samples from 16 cancer types. Here, we showed that a small but distinctive cluster of 16 KRAB-ZNFs is commonly upregulated across multiple cancer cohorts in comparison to normal samples. We confirmed these observations in the independent panels of lung and breast cancer cell lines and tissues. This upregulation was also observed for most of the KRAB-ZNF splicing variants, whose expression is simultaneously upregulated in tumors compared to normal tissues. Finally, by analyzing the clinicopathological data for breast and lung cancers, we demonstrated that the expression of cancer-associated KRAB-ZNFs correlates with patient survival, tumor histology, and molecular subtyping. Altogether, our study allowed the identification and characterization of KRAB-ZNF factors that may have an essential function in cancer biology and thus potential to become novel oncologic biomarkers and treatment targets.

Centromere-associated protein E expresses a novel mRNA isoform in acute lymphoblastic leukemia

The alternative splicing plays an important role to generate protein diversity. Recent studies have shown alterations in alternative splicing, resulting in loss, gain or changes of functions in the resulting protein. Specific products of alternative splicing are known to contribute in cancer-related mechanisms, such as angiogenesis, migration, adhesion and cell proliferation, among others. We using high-density microarrays reported a CENP-E as a one of significant transcript expressed and potentially is alternatively spliced in cancer. We focus in validate alternative splicing of CENP-E transcript using RT-PCR and sequencing in different cancer cell lines. We performed RT-PCR using specific primers designed to delimit the non-reported alternative splicing in CENP-E transcript. Our results showed the co-expression of the variant one and two of CENP-E in all cell lines evaluated. We detected more expression of variant one than two. Moreover, we identify an alternative 5'splice site of CENP-E in the exon 38 and was observed in RoVa cell line. Additionally, we characterized alternative skipping from exon 20 (NAT-CENP-E), these alternative splicing was observed in all cell lines evaluated except RoVa. Finally, we corroborate alternative mRNA splicing in leukemia patients using quantitative RT-PCR, in 71.8% of the patients NAT-CENP-E is downregulated and 28.2% is overexpressed.

Systematic profiling of alternative splicing signature reveals prognostic predictor for ovarian cancer

OBJECTIVE

The majority of genes are alternatively spliced and growing evidence suggests that alternative splicing is modified in cancer and is associated with cancer progression. Systematic analysis of alternative splicing signature in ovarian cancer is lacking and greatly needed.

METHODS

We profiled genome-wide alternative splicing events in 408 ovarian serous cystadenocarcinoma (OV) patients in TCGA. Seven types of alternative splicing events were curated and prognostic analyses were performed with predictive models and splicing network built for OV patients.

RESULTS

Among 48,049 mRNA splicing events in 10,582 genes, we detected 2,611 alternative splicing events in 2,036 genes which were significant associated with overall survival of OV patients. Exon skip events were the most powerful prognostic factors among the seven types. The area under the curve of the receiver-operator characteristic curve for prognostic predictor, which was built with top significant alternative splicing events, was 0.937 at 2,000 days of overall survival, indicating powerful efficiency in distinguishing patient outcome. Interestingly, splicing correlation network suggested obvious trends in the role of splicing factors in OV.

CONCLUSIONS

In summary, we built powerful prognostic predictors for OV patients and uncovered interesting splicing networks which could be underlying mechanisms.

Data Mining for Identification of Molecular Targets in Ovarian Cancer

Ovarian cancer is possibly the sixth most common malignancy worldwide, in Mexico representing the fourth leading cause of gynecological cancer death more than 70% being diagnosed at an advanced stage and the survival being very poor. Ovarian tumors are classified according to histological characteristics, epithelial ovarian cancer as the most common (~80%). We here used high-density microarrays and a systems biology approach to identify tissue-associated deregulated genes. Non-malignant ovarian tumors showed a gene expression profile associated with immune mediated inflammatory responses (28 genes), whereas malignant tumors had a gene expression profile related to cell cycle regulation (1,329 genes) and ovarian cell lines to cell cycling and metabolism (1,664 genes).

Novel Candidate Biomarkers of Chemoradiosensitivity in Esophageal Squamous Cell Carcinoma: A Systematic Review

There is no doubt that, along with surgery, chemoradiotherapy is an important treatment for esophageal squamous cell carcinoma (ESCC). Patients who respond well to chemoradiotherapy obtain great benefits toward overcoming their cancer, and so a more favorable prognosis. On the other hand, patients who do not respond well have wasted valuable time and experienced severe toxicity and seriously diminished quality of life, only to have their cancer recur with an unfavorable prognosis. For this reason, a reliable biomarker of chemoradiosensitivity in ESCC has long been sought. In this review, we will enumerate recently reported candidate biomarkers of chemoradiosensitivity in ESCC that have the potential for future clinical application.

ZNF695 methylation predicts a response of esophageal squamous cell carcinoma to definitive chemoradiotherapy

PURPOSE

Definitive chemoradiotherapy (dCRT) is one of the standard treatments for esophageal squamous cell carcinoma. Patients with a response to dCRT have a better prognosis than those resistant to dCRT while survival benefits for patients with residual tumors are limited. Nevertheless, few molecular markers to predict the response to dCRT are currently available. Here, we aimed to establish a DNA methylation marker to predict the response to dCRT.

METHODS

A total of 104 patients were divided into screening (n = 43) and validation (n = 61) sets. A genome-wide DNA methylation analysis was performed using an Infinium HumanMethylation450 BeadChip array. Methylation levels were measured by quantitative methylation-specific PCR and normalized by the fraction of cancer cells in a sample.

RESULTS

The genome-wide methylation analysis of seven responders and eight non-responders identified 18 genomic regions specifically (un)methylated in the responders. Among these, methylation of the promoter CpG island of ZNF695 was significantly associated with the response to dCRT in the screening set (P = 0.004), and a cutoff value was determined. In the validation set, the association was successfully validated (P = 0.021), and a high specificity (90 %) for the prediction of responders was obtained using the prefixed cutoff value. In addition, a multivariate analysis showed that ZNF695 methylation was an independent predictive factor for the response to dCRT (OR 7.55, 95 % CI 2.12-26.9, P = 0.002).

CONCLUSION

ZNF695 methylation was significantly associated with the response to dCRT and is a promising predictive marker for the response to dCRT.

A case of cervical cancer expressed three mRNA variant of Hyaluronan-mediated motility receptor

Cervical cancer is the second malignancy in Mexico, little is known about the prognostic factors associated with this disease. Several cellular components are important in their transformation and progression. Alternative mRNA splice is an important mechanism for generating protein diversity, nevertheless, in cancer unknown mRNA diversity is expressed. Hyaluronan-mediated motility receptor (HMMR, RHAMM, CD168) is a family member of proteins, hyaluronan acid dependent, and has been associated with different malignant processes such as: angiogenesis, cell invasiveness, proliferation, metastasis and poor outcome in some tumors. In the present study we identified expression of HMMR in cervical cancer by means of RT-PCR and sequencing. Our results indicate co-expression of two HMMR variants in all samples, and one case expressed three alternative HMMR splice transcripts. These results showed the heterogeneity of mRNA transcripts of HMMR that could express in cancer and the expression of HMMR could be marker of malignancy in CC.