Down-Regulation of UNC5D in Bladder Cancer: UNC5D as a Possible Mediator of Cisplatin Induced Apoptosis in Bladder Cancer Cells

Molecular characterization analysis of PANoptosis-related genes in colorectal cancer based on bioinformatic analysis

Colorectal cancer (CRC) ranks as the third most prevalent cancer globally and stands as the second principal contributor to cancer-related fatalities. Recently, emerging research has emphasized the role of pan apoptosis (PANoptosis) in tumor development and anti-tumor therapy. In the course of this investigation, we meticulously identified and conducted a correlation analysis between differentially expressed genes associated with PANoptosis in CRC (CPAN_DEGs) and the proportion of immune cells. Subsequently, we formulated a prognostic score based on the CPAN_DEGs. Further our analysis revealed a noteworthy reduction in UNC5D mRNA expression within HCT116, HT29 and SW480 cells, as validated by qRT-PCR assay. Furthermore, scrutinizing the TCGA database unveiled a distinctive trend wherein individuals with the low UNC5D expression exhibited significantly reduced overall survival compared to their counterparts with the high UNC5D levels. The drug susceptibility analysis of UNC5D was further performed, which showed that UNC5D was corassociated with the sensitivity of CRC to 6-Thioguanine. The outcomes of our investigation underscore the mechanisms by which PANoptosis influences immune dysregulation as well as prognostic outcome in CRC.

Large-scale meta-genome-wide association study reveals common genetic factors linked to radiation-induced acute toxicities across cancer types

BACKGROUND

This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity across 4 cancer types (prostate, head and neck, breast, and lung).

METHODS

A genome-wide association study meta-analysis was performed using 19 cohorts totaling 12 042 patients. Acute standardized total average toxicity (STATacute) was modelled using a generalized linear regression model for additive effect of genetic variants, adjusted for demographic and clinical covariates (rSTATacute). Linkage disequilibrium score regression estimated shared single-nucleotide variation (SNV-formerly SNP)-based heritability of rSTATacute in all patients and for each cancer type.

RESULTS

Shared SNV-based heritability of STATacute among all cancer types was estimated at 10% (SE = 0.02) and was higher for prostate (17%, SE = 0.07), head and neck (27%, SE = 0.09), and breast (16%, SE = 0.09) cancers. We identified 130 suggestive associated SNVs with rSTATacute (5.0 × 10‒8 < P < 1.0 × 10‒5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size ‒0.17; P = 1.7 × 10‒7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 × 10‒6, P = .079 corrected) as the top gene set associated with rSTATacute among all patients. In silico gene expression analysis showed that the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed P = .004 corrected; sun exposed P = .026 corrected).

CONCLUSIONS

There is shared SNV-based heritability for acute radiation-induced toxicity across and within individual cancer sites. Future meta-genome-wide association studies among large radiation therapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types.

Promoter methylation-mediated repression of UNC5 receptors and the associated clinical significance in human colorectal cancer

Background

Deregulated methylation of tumor suppressor genes is a hallmark event in colorectal cancer (CRC) carcinogenesis. UNC5 receptors, down-regulated in various human malignancies due to epigenetic alterations, have been proposed as putative tumor suppressor genes. In this study, we focused on the methylation-mediated inhibition of UNC5 receptors and the associated clinical significance in CRC.

Methods

Methylation and expression analysis was performed in TCGA datasets. And the results were confirmed in vitro in CRC cell lines treated with 5-aza-deoxycytidine. Then, the expression and epigenetic alterations of UNC5 receptors were evaluated in clinical specimens. Moreover, the diagnostic and prognostic values of the methylation alterations were also analyzed.

Results

Methylation-mediated repression was observed in UNC5C and UNC5D, but not in UNC5A and UNC5B, which was confirmed in CRC cell lines. Except for UNC5B, significantly elevated methylation was observed in UNC5A, UNC5C, and UNC5D in CRC. The discrimination efficiency of the three receptors was comparable with that of SEPT9. Kaplan–Meier curve survival analysis showed that hypermethylation of UNC5A, UNC5C and UNC5D was associated with poor progression-free and overall survival. Moreover, methylation levels of UNC5C and UNC5D were independent predictors of CRC progression-free (P = 0.001, P = 0.003, respectively) and overall survival (P = 0.008, P = 0.004, respectively).

Conclusions

Hypermethylation of UNC5C and UNC5D mediates the repression and has promising diagnostic and prognostic values in CRC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-021-01211-5.

UNC5 dependence receptor family in human cancer: A controllable double-edged sword

UNC5 receptor family (UNC5A-D) have been identified as dependence receptors whose functions depend on the availability of their ligand netrin-1. Through binding to netrin-1, these receptors transmit signals for cell survival, migration and differentiation, and participate in diverse physiological and pathological processes. In the lack of netrin-1, however, these receptors initiate apoptosis-inducing signal. Accumulating evidence reveals that netrin-1 and its receptors play a role in tumorigenesis and tumor progression. The expression of UNC5 receptor family is down-regulated in a variety of human tumors. Expression aberrance of UNC5 receptor family in tumors is caused by diverse mechanisms including genomic, epigenetic, transcriptional and post-transcriptional regulation. Notably, blocking netrin-1 binding to its receptors induces apoptotic cell death in tumor cells. In this review, we describe the characters and roles of UNC5 family members in tumorigenesis and tumor progression, discussing the regulatory mechanisms underlying down-regulation of UNC5 family members as well as recent implications of targeting netrin-1/UNC5 on potential clinical application for cancer treatment.

Exome sequencing identifies somatic mutations in novel driver genes in non-small cell lung cancer

Lung cancer is the leading cause of cancer death worldwide and accounts for more than one-third of all newly diagnosed cancer cases in China. Therefore, it is of great clinical significance to explore new driver gene mutations in non-small-cell lung cancer (NSCLC). Using an initial bioinformatic analysis, we identified somatic gene mutations in 13 patients with NSCLC and confirmed these mutations by targeted sequencing in an extended validation group of 88 patients. Recurrent mutations were detected in UNC5D (7.9%), PREX1 (5.0%), HECW1 (4.0%), DACH1 (2.0%), and GPC5 (2.0%). A functional study was also performed in UNC5D mutants. Mutations in UNC5D promoted tumorigenesis by abolishing the tumor suppressor function of the encoded protein. Additionally, in ten patients with lung squamous cell carcinoma, we identified mutations in KEAP1/NFE2L2 that influenced the expression of target genes in vivo and in vitro. Overall, the results of our study expanded the known spectrum of driver mutations involved in the pathogenesis of NSCLC.

A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients

Background

This study aimed to construct prognostic model by screening prognostic miRNA signature of bladder cancer.

Methods

The miRNA expression profile data of bladder cancer (BC) in The Cancer Genome Atlas (TCGA) were obtained and randomly divided into the training set and the validation set. Differentially expressed miRNAs (DEMs) between BC and normal control samples in the training set were firstly identified, and DEMs related to prognosis were screened by Cox Regression analysis. Then, the MiR Score system was constructed using X-Tile based cutoff points and verified in the validation set. The prognostic clinical factors are selected out by univariate and multivariate Cox Regression analysis. Finally, the mRNAs related to prognosis were screened and the biological pathway analysis was carried out.

Results

We identified the 7-miRNA signature was significantly associated with the patient’s Overall Survival (OS). A prognostic model was constructed based on the prognostic 7-miRNA signature, and possessed a relative satisfying predicted ability both in the training set and validation set. In addition, univariate and multivariate Cox Regression analysis showed that age, lymphovascular invasion and MiR Score were considered as independent prognostic factors in BC patients. Furthermore, based on MiR Score prognostic model, several differentially expressed genes (DEGs), such as WISP3 and UNC5C, as well as their related biological pathway(s), including cell–cell adhesion and neuroactive ligand-receptor interaction, were considered to be related to BC prognosis.

Conclusion

The prognostic model which was constructed based on the prognostic 7-miRNA signature presented a high predictive ability for BC.

Explore prognostic marker of colorectal cancer based on ceRNA network

Colorectal cancer (CRC) is one of the most common malignant tumors in the world. With the deepening of people's understanding of CRC at the molecular level, the survival and prognosis of CRC have been significantly improved with the help of surgery, radiotherapy, and chemotherapy, molecular targeted biological therapy and early detection of diseases. The research of different disciplines and the development of multihistological analysis in recent years have proved that the occurrence and development of CRC is a complex biological process with the common action of multiple factors, which involves the huge changes of various histological levels such as the genome, transcriptome, and epigenome. At present, the abnormal expression of protein products in the transcription process has attracted more and more attention. Based on the sensitivity and timeliness of its changes, it has become a hot topic to study the occurrence and development mechanism of CRC through transcriptome changes, so as to provide markers for early diagnosis and prognosis. In recent years, competitive endogenous RNA (ceRNA) has become one of the hot topics in cancer research. The ceRNA hypothesis holds that transcripts such as long noncoding RNA can competitively bind microRNA (miRNA), thus preventing miRNA from binding to messenger RNA (mRNA) and thereby regulating the expression of mRNA. At present, the interaction mechanism of ceRNA in CRC is still unclear, and exploring its interaction relationship is of great significance to elucidate the occurrence and development mechanism of CRC. In this study, we used The Cancer Genome Atlas (TCGA) RNA - seq data of colorectal Cancer and microRnas - seq data to construct colorectal Cancer ceRNA topology network to mine key RNAs that influence the prognosis of colorectal cancer, providing potential RNA biomarkers.

UNC5D, suppressed by promoter hypermethylation, inhibits cell metastasis by activating death-associated protein kinase 1 in prostate cancer

Prostate cancer (PCa) death primarily occurs due to metastasis of the cells, but little is known about the underlying molecular mechanisms. This study aimed to evaluate the expression of UNC5D, a newly identified tumor suppressor gene, analyze its epigenetic alterations, and elucidate its functional relevance to PCa metastasis. Meta-analysis of publicly available microarray datasets revealed that UNC5D expression was frequently downregulated in PCa tissues and inversely associated with PCa metastasis. These results were verified in clinical specimens by real-time PCR and immunohistochemistry assays. Through methylation analysis, the downregulated expression of UNC5D in PCa tissues and cell lines was found to be attributable to the hypermethylation of the promoter. A negative correlation was observed between methylation and UNC5D mRNA expression in PCa samples. The ectopic expression of UNC5D in PCa cells effectively reduced their ability to migrate and invade both in vitro and in vivo, and siRNA-mediated knockdown of UNC5D yielded consistent results. UNC5D can recruit and activate death-associated protein kinase 1, which remained to be essential for its metastatic suppressor function. In conclusion, these results suggested that UNC5D as a novel putative metastatic suppressor gene that is commonly down-regulated by hypermethylation in PCa.

Copy number changes at 8p11-12 predict adverse clinical outcome and chemo- and radiotherapy response in breast cancer

Purpose

The short arm of chromosome 8 (8p) is a frequent target of loss of heterozygosity (LOH) in cancer, and 8p LOH is commonly associated with a more aggressive tumor phenotype. The 8p11-12 region is a recurrent breakpoint area characterized by a sharp decrease in gains/amplifications and increase in allelic loss towards 8pter. However, the clustering of genomic aberrations in this region, even in the absence of proximal amplifications or distal LOH, suggests that the 8p11-12 region could play a pivotal role in oncogenesis.

Results

Loss in the FGFR1 and ZNF703-containing 8p11 region was seen in 25% of patients, correlated with lower mRNA expression levels and independently predicted poor survival, particularly in systemic treatment-naïve patients and even without adjacent 8p12 loss. Amplification of FGFR1 at 8p11 and loss of DUSP26 and UNC5D, located in the 8p12 breakpoint region, independently predicted worse event free survival. Gains in the 8p12 region encompassing WRN, NRG1, DUSP26 and UNC5D, seen in 20-30% of patients, were associated with higher mRNA expression and independently predicted chemotherapy sensitivity. Losses at 8p12 independently predicted radiotherapy resistance.

Material and methods

Multiplex ligation-dependent probe amplification was used to investigate copy number aberrations at 8p11-12 in 234 female breast cancers. Alterations were correlated with clinicopathologic characteristics, survival and response to therapy. Results were validated using public METABRIC data.

Conclusion

Allelic loss and amplification in the 8p11-12 breakpoint region predict poor survival and chemo- and radiotherapy response. Assessment of 8p11-12 gene copy number status seems to augment existing prognostic and predictive tools.

Tumor-suppressive function of UNC5D in papillary thyroid cancer

Background

Studies have shown an association of the UNC5D gene with kidney and bladder cancer and neuroblastoma. We investigated whether UNC5D acts as a tumor suppressor in papillary thyroid carcinoma (PTC).

Methods

Primary PTC tumors and matched normal thyroid tissues were obtained from 112 patients to detect UNC5D mRNA by real-time PCR. Genomic DNA sequencing was performed to detect BRAF mutation in PTC tumors. The association between UNC5D expression and clinicopathological data from PTC patients was reviewed retrospectively. PTC-derived cancer cell lines TPC-1 and K1 with stable transfection of UNC5D were used to investigate the functions of UNC5D. Flow cytometry, CCK-8, Transwell assay and scratch tests were used to examine cell cycle distribution, proliferation and migration.

Results

The expression of UNC5D was significantly decreased in PTC compared with adjacent normal thyroid tissues. Lower UNC5D expression was significantly associated with aggressive tumor behaviors, such as lymph node metastasis and BRAF mutation. Overexpression of UNC5D significantly suppressed malignant cell behaviors, including cell proliferation and migration, as well as tumor growth in vivo.

Conclusions

These findings suggest a potential tumor suppressor role of UNC5D in PTC progression; and provide insight into potential clinical relevance for the prognosis of PTC.

Methylation of the UNC5C gene and its protein expression in colorectal cancer

UNC5C is a member of the UNC5H family of transmembrane receptors and functions as a dependence receptor. The expression of UNC5C is lost or markedly reduced in a large proportion of cancers at the messenger RNA level. However, there is little information available regarding the protein expression of UNC5C, the relationship between UNC5C protein expression and UNC5C methylation, and the correlation between patient clinical features and UNC5C protein expression in colorectal cancer. In this study, the methylation and protein expression of UNC5C were examined in 36 adenomatous polyps, 73 colorectal cancers, and 28 corresponding normal mucosa, and the correlation between the methylation, as well as protein expression status, and the clinicopathologic features was evaluated. Furthermore, the relationship between the methylation and protein expression of UNC5C, and correlation between UNC5C protein expression and overall survival were analyzed. The results showed that aberrant methylation of UNC5C was observed in colorectal cancers (78%) and adenomatous polyps (64%). The methylation-specific polymerase chain reaction results were confirmed by bisulfite sequencing of UNC5C promoter region. UNC5C methylation was significantly higher in early tumor, node, metastasis stage (I + II) of colorectal cancers. Compared with the corresponding normal tissues, protein expression of UNC5C was significantly lower in colorectal cancers (42%) and adenomatous polyps (81%). Protein expression of UNC5C was significantly higher in early tumor, node, metastasis stage (I + II) of colorectal cancers compared with advanced tumor, node, metastasis stage. Furthermore, patients with UNC5C-negative expression had a poorer prognosis than those with UNC5C-positive expression through Kaplan-Meier survival analysis ( p = 0.038), univariate ( p = 0.044) and multivariate analysis ( p = 0.045). According to Spearman rank correlation analysis, UNC5C methylation and protein expression were negatively correlated ( r = -0.461, p < 0.001). Together, these results suggest that UNC5C methylation may be an earlier event in the development of colorectal cancer, which was negatively correlated with protein expression. UNC5C may have a critical role in the pathogenesis of colorectal cancers and be a valuable prognostic factor of colorectal cancers patients. UNC5C may be identified as an attractive therapeutic target for the treatment of colorectal cancers in the further studies.

Whole-exome sequencing of muscle-invasive bladder cancer identifies recurrent mutations of UNC5C and prognostic importance of DNA repair gene mutations on survival

PURPOSE

Because of suboptimal outcomes in muscle-invasive bladder cancer even with multimodality therapy, determination of potential genetic drivers offers the possibility of improving therapeutic approaches and discovering novel prognostic indicators.

EXPERIMENTAL DESIGN

Using pTN staging, we case-matched 81 patients with resected ≥pT2 bladder cancers for whom perioperative chemotherapy use and disease recurrence status were known. Whole-exome sequencing was conducted in 43 cases to identify recurrent somatic mutations and targeted sequencing of 10 genes selected from the initial screening in an additional 38 cases was completed. Mutational profiles along with clinicopathologic information were correlated with recurrence-free survival (RFS) in the patients.

RESULTS

We identified recurrent novel somatic mutations in the gene UNC5C (9.9%), in addition to TP53 (40.7%), KDM6A (21.0%), and TSC1 (12.3%). Patients who were carriers of somatic mutations in DNA repair genes (one or more of ATM, ERCC2, FANCD2, PALB2, BRCA1, or BRCA2) had a higher overall number of somatic mutations (P = 0.011). Importantly, after a median follow-up of 40.4 months, carriers of somatic mutations (n = 25) in any of these six DNA repair genes had significantly enhanced RFS compared with noncarriers [median, 32.4 vs. 14.8 months; hazard ratio of 0.46, 95% confidence interval (CI), 0.22-0.98; P = 0.0435], after adjustment for pathologic pTN staging and independent of adjuvant chemotherapy usage.

CONCLUSION

Better prognostic outcomes of individuals carrying somatic mutations in DNA repair genes suggest these mutations as favorable prognostic events in muscle-invasive bladder cancer. Additional mechanistic investigation into the previously undiscovered role of UNC5C in bladder cancer is warranted.