Identification of Long Noncoding RNA APOC1P1 as an Oncogene in Clear Cell Renal Cell Carcinoma

Comprehensive analysis of necroptosis-related lncRNA signature with potential implications in tumor heterogeneity and prediction of prognosis in clear cell renal cell carcinoma

BACKGROUND

Necroptosis has been reported to play a critical role in occurrence and progression of cancer. The dysregulation of long non-coding RNAs (lncRNAs) is associated with the progression and metastasis of clear cell renal cell carcinoma (CCRCC). However, research on necroptosis-related lncRNAs in the tumor heterogeneity and prognosis of CCRCC is not completely unclear. This study aimed to analysis the tumor heterogeneity among CCRCC subgroups and construct a CCRCC prognostic signature based on necroptosis-related lncRNAs.

METHODS

Weighted gene co-expression network analysis (WGCNA) was performed to identify necroptosis-related lncRNAs. A preliminary classification of molecular subgroups was performed by non-negative matrix factorization (NMF) consensus clustering analysis. Comprehensive analyses, including fraction genome altered (FGA), tumor mutational burden (TMB), DNA methylation alterations, copy number variations (CNVs), and single nucleotide polymorphisms (SNPs), were performed to explore the potential factors for tumor heterogeneity among the three subgroups. Subsequently, we constructed a predictive signature by multivariate Cox regression. Nomogram, calibration curves, decision curve analysis (DCA), and time-dependent receiver-operating characteristics (ROC) were used to validate and evaluate the signature. Finally, immune correlation analyses, including immune-related signaling pathways, immune cell infiltration status and immune checkpoint gene expression level, were also performed.

RESULTS

Seven necroptosis-related lncRNAs were screened out by WGCNA, and three subgroups were classified by NMF consensus clustering analysis. There were significant differences in survival prognosis, clinicopathological characteristics, enrichments of immune-related signaling pathway, degree of immune cell infiltration, and expression of immune checkpoint genes in the various subgroups. Most importantly, we found that 26 differentially expressed genes (DEGs) among the 3 subgroups were not affected by DNA methylation alterations, CNVs and SNPs. On the contrary, these DEGs were associated with the seven necroptosis-related lncRNAs. Subsequently, the identified RP11-133F8.2 and RP11-283G6.4 by multivariate Cox regression analysis were involved in the risk model, which could serve as an independent prognostic factor for CCRCC. Finally, qRT-PCR confirmed the differential expression of the two lncRNAs.

CONCLUSIONS

These findings contributed to understanding the function of necroptosis-related lncRNAs in CCRCC and provided new insights of prognostic evaluation and optimal therapeutic strategy for CCRCC.

Expression Level of lncRNA CYTOR in Iranian Cervical Cancer Patients

Background

A critical role has been known for lncRNAs in the initiation and development of cancers. Therefore, lncRNAs have been reported as the possible biomarkers in relation to the diagnosis and therapy of malignancies. This project examined the change in CYTOR lncRNA expression in human cervical cancer samples as compared with adjacent healthy ones.

Methods

We provided one hundred fifteen pairs of tumorous and adjacent healthy tissue specimens of cervical cancer patients. RNAs were isolated from tissue specimens and cDNAs were synthesized. We considered quantitative Real-time PCR (qRT-PCR) to examine the expression levels of CYTOR lncRNA. In addition, the biomarker activity of CYTOR and the associations between the lncRNA and clinicopathological characteristics were evaluated.

Results

The significant increased expression of CYTOR was obtained in cancerous samples as compared with non-cancerous ones (P< 0.0001). A significant correlation was indicated between CYTOR expression and the squamous subtype of cervical cancer (p=0.046). The receiver operating characteristic (ROC) curve-related AUC (area under the curve), specificity, and sensitivity were calculated 0.88, 81.74%, and 80%, respectively, which may introduce CYTOR as a potential biomarker.

Conclusion

CYTOR may be an effective oncogene and biomarker in cervical cancer cases given its increased expression in human cervical cancer tissues.

Alterations in the expression levels of long intergenic non-coding RNA APOC1P1-3 in cervical cancer tissue samples

lncRNAs play a crucial role in the carcinogenesis process. Thus, they have been recognized as the potential therapeutic and diagnostic biomarkers of cancers. This study assessed the alteration in the expression of APOC1P1-3 lncRNA in cancerous tissues compared to their adjacent non-tumorous tissues sampled from cervical cancer patients. one hundred fifteen pairs of cancerous and adjacent non-cancerous biopsy of cervical cancer specimens were collected. RNA isolation and cDNA synthesis were carried out. The qRT-PCR was used to assess the changes in the expression of APOC1P1-3 lncRNA. Moreover, the biomarker function of the lncRNA and the correlations between APOC1P1-3 and clinicopathological parameters were measured. The APOC1P1-3 expression was significantly increased in cervical cancer specimens as compared to adjacent non-tumorous specimens (p < 0.0001). A significant association was also observed between APOC1P1-3 expression and lymph node involvement (p = 0.031). Additionally, APOC1P1-3 expression demonstrated a significant association with the depth of tumor invasion (p = 0.035), and squamous type of cervical cancer (p = 0.019). The overexpression of APOC1P1-3 was significantly observed in patients younger than 50 years old as compared to another age group (p = 0.033). The results of ROC curve exhibited that APOC1P1-3 with area under the curve (AUC), specificity, and sensitivity of 0.96, 93.91%, and 78.26%, respectively can be considered as a potential biomarker. Regarding overexpression of APOC1P1-3 in human cervical cancer samples, this lncRNA may be considered as an oncogenic factor in cervical cancer patients. Besides, APOC1P1-3 may be a possible biomarker for the diagnosis and treatment of cervical cancer patients.

Expression of lncRNAs AK058003 and APOC1P1 in breast cancer patients

In the current study, the expression levels of two important lncRNAs, i.e., AK058003 and APOC1P1, in breast tumors were compared with adjacent non-tumor tissues to evaluate their diagnostic potential in a panel of 121 patients. Total RNA was extracted, cDNA was synthesized and expression of AK058003 and APOC1P1 was assessed using qRT-PCR. A significant overexpression and positive correlation between these two lncRNAs were observed in tumor tissues compared to marginal healthy tissues. In conclusion, the examined lncRNAs were overexpressed in tumor tissues, suggesting their significant diagnostic value in breast cancer.

Comprehensive analysis of lncRNA-mRNAs co-expression network identifies potential lncRNA biomarkers in cutaneous squamous cell carcinoma

Background

Cutaneous squamous cell carcinoma (cSCC) is the second most common type of skin cancer, the prognosis for patients with metastatic cSCC remains relatively poor. Thus, there is an urgent need to identify new diagnostic, prognostic, and therapeutic targets and pathways in cSCC.

Results

It detected a total of 37,507 lncRNA probes and 32,825 mRNA probes and found 3593 differentially expressed lncRNAs and 3236 differentially expressed mRNAs. It has been found that mRNAs ACY3, NR1D1, MZB1 has co-expression relationship with six lncRNAs, GXYLT1P3, LINC00348, LOC101928131, A-33-p3340852, A-21-p0003442 and LOC644838.

Conclusions

The aim of this study is to identify cSCC-specific lncRNAs and indicated that six unstudied lncRNAs may serve an important role in endoplasmic reticulum stress apoptosis, autophagy and the progression of cSCC by modulating ACY3, NR1D1 and MZB1.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08481-0.

Reversal of Radiotherapy Resistance of Ovarian Cancer Cell Strain CAOV3/R by Targeting lncRNA CRNDE

Radiotherapy resistance is one of the key factors of poor prognosis of ovarian cancer clinical treatment. The search for key targets of ovarian cancer radiotherapy resistance has become a high priority. Long noncoding RNA plays an important role in tumor development. However, the key lncRNA in ovarian cancer radiotherapy resistance is not identified. Our finding that lncRNA CRNDE is highly expressed in the radiotherapy resistance cell line CAOV3/R drew our attention. Therefore, in this study, we targeted lncRNA CRNDE to analyze whether it is a key factor of radiotherapy resistance in ovarian cancer. Ultimately, we found that silencing lncRNA CRNDE could reverse CAOV3/R radiotherapy resistance, which would be a boon to clinical treatment.

Nuclear Dishevelled targets gene regulatory regions and promotes tumor growth

Dishevelled (DVL) critically regulates Wnt signaling and contributes to a wide spectrum of diseases and is important in normal and pathophysiological settings. However, how it mediates diverse cellular functions remains poorly understood. Recent discoveries have revealed that constitutive Wnt pathway activation contributes to breast cancer malignancy, but the mechanisms by which this occurs are unknown and very few studies have examined the nuclear role of DVL. Here, we have performed DVL3 ChIP-seq analyses and identify novel target genes bound by DVL3. We show that DVL3 depletion alters KMT2D binding to novel targets and changes their epigenetic marks and mRNA levels. We further demonstrate that DVL3 inhibition leads to decreased tumor growth in two different breast cancer models in vivo. Our data uncover new DVL3 functions through its regulation of multiple genes involved in developmental biology, antigen presentation, metabolism, chromatin remodeling, and tumorigenesis. Overall, our study provides unique insight into the function of nuclear DVL, which helps to define its role in mediating aberrant Wnt signaling.

Long Non-Coding RNA PCED1B-AS1 Promotes the Progression of Clear Cell Renal Cell Carcinoma Through miR-484/ZEB1 Axis

Background

Long non-coding RNA (lncRNA) has been recognized as the new regulator and biomarker for cancers. However, in clear cell renal cell carcinoma (ccRCC), the functions of lncRNAs are not well characterized. This research aimed to probe the function of lncRNA PCED1B-AS1 in the progression of ccRCC.

Materials and Methods

Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to detect the expression levels of PCED1B-AS1, microRNA-484 (miR-484), and zinc finger E-box binding homeobox 1 (ZEB1) in 40 pairs of human ccRCC tissues and corresponding adjacent kidney tissue samples. Chi-square test was employed to evaluate the association between PCED1B-AS1 expression level and clinicopathological characteristics. The effects of PCED1B-AS1, miR-484 and ZEB1 on the cell proliferation, migration and epithelial-mesenchymal transition (EMT) process of ccRCC cells were studied by CCK-8 assay, EdU cell proliferation assay, wound healing test and Western blotting. The regulatory relationships among PCED1B-AS1, miR-484, ZEB1 were examined by luciferase reporter gene assay and RNA immunoprecipitation assay.

Results

PCED1B-AS1 was remarkably up-regulated in ccRCC tissues and cell lines. High expression of PCED1B-AS1 was associated with poor prognosis of the patients. Loss-of-function experiments showed that PCED1B-AS1 could regulate the proliferation, migration and EMT of ccRCC cells. PCED1B-AS1 sponged miR-484 to suppress its expression, and miR-484 targeted the 3ʹ-UTR of ZEB1 to repress the expression of ZEB1. MiR-484 counteracted the functions of PCED1B-AS1 in promoting the proliferation, migration and EMT of ccRCC cells, and PCED1B-AS1 promotes the expression of ZEB1 via repressing miR-484.

Conclusion

PCED1B-AS1/miR-484/ZEB1 axis is involved in regulating the progression of ccRCC.