In vitro biological characterization of DCUN1D5 in DNA damage response

Targeting GSK3β and signaling pathways in breast cancer: role of individual members of miR- 23/24/27 cluster

BACKGROUND

The high mortality rate of breast cancer and the difficulties associated with therapeutic resistance, especially in cases where targeted treatments are unavailable, make it a serious threat to women's health. This study examines the relationship between three mature microRNAs (miRNAs) that are clustered together, namely miR- 23a, miR- 27a, and miR- 24-2, as well as their potential correlation with breast cancer.

METHODS

We identified common gene targets of miR- 23a, miR- 27a, and miR- 24-2 using computational analysis. We also checked for the levels of miR- 23a, miR- 27a, and miR- 24-2 in 26 breast tumor tissues (with their matched control) as well as MCF7 and MDA-MB- 231 cell lines using qRT-PCR. Dual-luciferase reporter assay was conducted to validate the binding site of the microRNAs in their target gene. Western blot was performed to study the expression of various breast cancer related genes in the presence of the three microRNAs. In addition, the effect of microRNAs in cancer cell metastasis and cell division was carried out using invasion and cell cycle assay.

RESULTS

Computational analysis identified key genes, including GSK3β, NCOA1 and SP1, which are functionally linked to tumor progression and various other malignancies. All three microRNAs were found to be significantly downregulated in the breast cancer tissue samples in comparison to their respective controls. Kaplan-Meier plot analysis revealed that the expression levels of these genes and associated microRNAs correlates with breast cancer patient survival rates. Reduced SP1 and NCOA1 levels predicted a worse prognosis, but elevated levels of GSK3β were linked with decreased survival. Moreover, miR- 23a and miR- 24-2 specifically target GSK3β, potentially disrupting the Wnt/β-catenin pathway involved in breast cancer development. Functional tests showed that miR- 23a, miR- 27a and miR- 24-2 affect expression of EMT related genes, influencing cell invasion and migration, impacting ERK signaling and EMT, critical in the spread of breast cancer.

CONCLUSION

This study unlocks the potential of targeting the microRNA cluster as a therapeutic approach and emphasizes the complex regulatory roles of each individual members of the miR- 23a/27a/24-2 cluster in the pathogenesis of breast cancer.

DCUN1D5 is a prognostic biomarker and correlated immune infiltrates and glycolysis in lung adenocarcinoma

DCUN1D5 is up-regulated and promotes tumor progression in many cancers such as laryngeal squamous cell carcinoma and breast cancer, but the expression of DCUN1D5 in lung adenocarcinoma and its molecular mechanism are not clear. The differences of DCUN1D5 expression between lung adenocarcinoma and normal tissues were compared by TCGA, GEO and UALCAN databases, and the relationship between DCUN1D5 expression and clinicopathological features of patients was analyzed. The diagnostic and prognostic value of DCUN1D5 in patients with LUAD was analyzed by TCGA, GEPIA and Kaplan-Meier Plotter database. nomogram was constructed to predict the survival probability of patients. The GO, KEGG and GSEA enrichment analysis of DCUN1D5 co-expression genes were completed by R software. R software and GEPIA2 database were used to analyze the relationship between DCUN1D5 expression level and glycolysis-related genes and immune cell infiltration in patients with LUAD. The effects of interfering DCUN1D5 on the biological function and glycolysis level of lung adenocarcinoma cells were evaluated in vitro. The effect of down-regulation of DCUN1D5 on tumor formation in nude mice was studied in animal experiments. The expression of DCUN1D5 was increased in many kinds of tumors, and the expression in lung adenocarcinoma was significantly higher than that in normal tissues. The expression of DCUN1D5 was significantly correlated with TNM and pathological stage. DCUNN1D5 can play a diagnostic role in patients with LUAD and the prognosis of patients with high expression of DCUN1D5 is poor. Functional enrichment of DCUN1D5 co-expression genes involves a variety of biological processes. There is a strong correlation between DCUN1D5 and most glycolysis related genes. In addition, DCUN1D5 also affects tumor immune cell infiltration. In vitro experiments showed that the ability of cell proliferation, migration, invasion and glycolysis were significantly decreased and the ability of apoptosis was enhanced after down-regulation of DCUN1D5. Animal experiments showed that the tumor weight of nude mice decreased significantly after down-regulation of DCUN1D5. DCUN1D5 can be used as a biomarker for diagnosis and prognosis in lung adenocarcinoma. Down-regulation of DCUN1D5 can significantly affect the biological behavior of lung adenocarcinoma cells, which may be related to glycolysis and immune cell infiltration.

GHRH-stimulated pituitary small extracellular vesicles inhibit hepatocyte proliferation and IGF-1 expression by its cargo miR-375-3p

Small extracellular vesicles (sEV) have emerged as a novel mode of intercellular material transport and information transmission. It has been suggested hormones may regulate the production and function of sEV. However, the specific impact of growth hormone-releasing hormone (GHRH) on pituitary sEV production and the role of sEV in the regulation of the GHRH-GH-IGF axis has not been previously reported. The results of the present study demonstrated that GHRH increased the production of pituitary sEV by promoting the expression of Rab27a. More importantly, GHRH induced alterations in protein and miRNA levels within GH3-sEV components. Notably, GH3-sEV with GHRH treatment exhibited the enhanced ability to impede BRL 3A cell proliferation and the expression of IGF-1. Conclusively, for the first time, we corroborate the influence of GHRH on pituitary sEV, thereby presenting novel evidence for how sEV participates in the balance of the GHRH-GH-IGF axis. Importantly, this study provides new insight into a novel balance mechanism mediated by sEV within the endocrine system.

YY1 mediated DCUN1D5 transcriptional activation promotes triple-negative breast cancer progression by targeting FN1/PI3K/AKT pathway

Triple-negative breast cancer (TNBC) is more aggressive and has a higher metastasis rate compared with other subtypes of breast cancer. Due to the lack of drug-targetable receptors, chemotherapy is now the only available systemic treatment for TNBC. However, some patients might still develop drug resistance and have poor prognosis. Therefore, novel molecular biomarkers and new treatment targets are urgently needed for patients with TNBC. To provide molecular insights into TNBC progression, we investigated the function and the underlying mechanism of Defective in cullin neddylation 1 domain containing 5 (DCUN1D5) in the regulation of TNBC. By TCGA dataset and surgical specimens with immunohistochemical (IHC) staining method, DCUN1D5 was identified to be significantly upregulated in TNBC tumor tissues and negatively associated with prognosis. A series of in vitro and in vivo experiments were performed to confirm the oncogenic role of DCUN1D5 in TNBC. Overexpression of FN1 or PI3K/AKT activator IGF-1 could restore the proliferative and invasive ability induced by DCUN1D5 knockdown and DCUN1D5 could act as a novel transcriptional target of transcription factor Yin Yang 1 (YY1). In conclusion, YY1-enhanced DCUN1D5 expression could promote TNBC progression by FN1/PI3K/AKT pathway and DCUN1D5 might be a potential prognostic biomarker and therapeutic target for TNBC treatment.

Identifying common transcriptome signatures of cancer by interpreting deep learning models

Background

Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types.

Results

Here, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer.

Conclusions

Our results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types.

Supplementary Information

The online version contains supplementary material available at (10.1186/s13059-022-02681-3).

Widespread Alternative Splicing Changes in Metastatic Breast Cancer Cells

Aberrant alternative splicing (AS) is a hallmark of cancer and a potential target for novel anti-cancer therapeutics. Breast cancer-associated AS events are known to be linked to disease progression, metastasis, and survival of breast cancer patients. To identify altered AS programs occurring in metastatic breast cancer, we perform a global analysis of AS events by using RNA-mediated oligonucleotide annealing, selection, and ligation coupled with next-generation sequencing (RASL-seq). We demonstrate that, relative to low-metastatic, high-metastatic breast cancer cells show different AS choices in genes related to cancer progression. Supporting a global reshape of cancer-related splicing profiles in metastatic breast cancer we found an enrichment of RNA-binding motifs recognized by several splicing regulators, which have aberrant expression levels or activity during breast cancer progression, including SRSF1. Among SRSF1-regulated targets we found DCUN1D5, a gene for which skipping of exon 4 in its pre-mRNA introduces a premature termination codon (PTC), thus generating an unstable transcript degraded by nonsense-mediated mRNA decay (NMD). Significantly, distinct breast cancer subtypes show different DCUN1D5 isoform ratios with metastatic breast cancer expressing the highest level of the NMD-insensitive DCUN1D5 mRNA, thus showing high DCUN1D5 expression levels, which are ultimately associated with poor overall and relapse-free survival in breast cancer patients. Collectively, our results reveal global AS features of metastatic breast tumors, which open new possibilities for the treatment of these aggressive tumor types.

Transcriptome modifications in human gingival fibroblasts exposed to 2-hydroxyethyl methacrylate

2-Hydroxyethyl methacrylate (HEMA),a tooth filling material, was proven to have toxic effects on different cell types, including human gingival fibroblasts (HGFs), and to be able to influence odontoblast vitality. The aim of the present study was to assess the differential transcriptome modulation induced by low HEMA concentration in cultured HGFs. RNA extracted from cultured HGFs exposed to 3 mmol/l HEMA for 24 or 96 h underwent a whole genome microarray analysis. Data analysis showed the presence of two gene clusters, composed by 310 transcripts differentially expressed after 24- and 96-h HEMA treatment compared to controls. Functional analysis demonstrated that these transcripts are mainly involved in cellular survival and death, and inflammatory response. The study highlighted an overall damage induced by HEMA exposure at both 24 and 96 h, mainly leading to a proliferation impairment. Interestingly, 24-h HEMA treatment seems to induce the cells to trigger repair mechanisms, evidencing an early compensatory response, whereas 96-h incubation appears to cause the occurrence of apoptosis as a consequence of the chronic damage.

Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival

Oral squamous cell cancer of the oral cavity and oropharynx (OSCC) is associated with high case-fatality. For reasons that are largely unknown, patients with the same clinical and pathologic staging have heterogeneous response to treatment and different probability of recurrence and survival, with patients with Human Papillomavirus (HPV)-positive oropharyngeal tumors having the most favorable survival. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we used Affymtrix 6.0 SNP arrays to examine paired DNA from peripheral blood and tumor cell populations isolated by laser capture microdissection to assess genome-wide loss of heterozygosity (LOH) and DNA copy number aberration (CNA) and their associations with risk factors, tumor characteristics, and oral cancer-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p and 11q that seem to play an important role in oral cancer biology and survival from this disease. If confirmed, these findings could assist in designing personalized treatment or in the creation of models to predict survival in patients with HPV-negative OSCC.

Oncogenic function of SCCRO5/DCUN1D5 requires its Neddylation E3 activity and nuclear localization

PURPOSE

To determine mechanisms by which SCCRO5 (aka DCUN1D5) promotes oncogenesis.

EXPERIMENTAL DESIGN

SCCRO5 mRNA and protein expression were assessed in 203 randomly selected primary cancer tissue samples, matched histologically normal tissues, and cell lines by use of real-time PCR and Western blot analysis. SCCRO5 overexpression was correlated with survival. The effect of SCCRO5 knockdown on viability was assessed in selected cancer cell lines. Structure-function studies were performed to determine the SCCRO5 residues required for binding to the neddylation components, for neddylation-promoting activity, and for transformation.

RESULTS

In oral and lung squamous cell carcinomas, SCCRO5 mRNA levels corresponded with protein levels and overexpression correlated with decreased disease-specific survival. Knockdown of SCCRO5 by RNAi resulted in a selective decrease in the viability of cancer cells with high endogenous levels, suggesting the presence of oncogene addiction. SCCRO5 promoted cullin neddylation while maintaining conserved reaction processivity paradigms involved in ubiquitin and ubiquitin-like protein conjugation, establishing it as a component of the neddylation E3. Neddylation activities in vitro required the potentiating of neddylation (PONY) domain but not the nuclear localization sequence (NLS) domain. In contrast, both the NLS domain and the PONY domain were required for transformation of NIH-3T3 cells.

CONCLUSIONS

Our data suggest that SCCRO5 has oncogenic potential that requires its function as a component of the neddylation E3. Neddylation activity and nuclear localization of SCCRO5 are important for its in vivo function.