Long non-coding RNA activated by TGF-β expression in cancer prognosis: A meta-analysis

The roles of LncRNA CARMN in cancers: biomarker potential, therapeutic targeting, and immune response

Long non-coding RNAs (LncRNAs) are crucial regulators of gene expression and cellular processes, with significant implications for cancer research. This review focuses on the role of LncRNA CARMN (Cardiac Arrest and Regulated Myocyte Nuclear Protein) in various cancers. CARMN, originally identified for its function in cardiac tissues, has shown dysregulated expression in several tumor types, including cervical, breast, colorectal, and esophageal cancers. Its altered expression often correlates with tumor progression, metastasis, and patient prognosis, suggesting its potential as both a biomarker and therapeutic target. In cervical cancer, CARMN's role as a tumor suppressor is highlighted by its ability to inhibit cell proliferation, migration, and invasion through interaction with the miR-92a-3p/BTG2 axis and modulation of the Wnt/β-catenin signaling pathway. In breast cancer, CARMN acts as an enhancer RNA, affecting epithelial-mesenchymal transition and metastasis by regulating MMP2 via DHX9. The downregulation of CARMN in triple-negative breast cancer is associated with enhanced sensitivity to chemotherapy. In colorectal cancer, CARMN's expression is regulated by m6A methylation and mutant p53, influencing tumor growth through miR-5683 and FGF2. Lastly, in esophageal cancer, genetic variations in CARMN affect cancer susceptibility, with certain SNPs and haplotypes associated with either increased or decreased risk. Additionally, the relationship between CARMN and immune cell dynamics highlights its potential role in cancer immune surveillance and therapy. Finally, we found that CARMN may regulate immune cell exhaustion in the tumor microenvironment by influencing the recruitment and activation of NK cells and T cells, as well as modulating macrophage polarization. This review emphasizes the diverse roles of CARMN across different cancers and its potential as a diagnostic and therapeutic tool. Future research should address the mechanistic details of CARMN's involvement in cancer, validate its clinical utility, and explore its therapeutic potential in combination with existing treatments.

The prognostic significance of lncRNA FGD5-AS1 in various malignancies: a meta-analysis

Background

Cancer is widely recognized as a prominent contributor to global mortality due to factors such as delayed diagnosis, unfavorable prognosis, and high likelihood of recurrence. FGD5 transcription factor G antisense RNA 1(FGD5-AS1), a newly identified long non-coding RNA, has emerged as a promising prognostic biomarker, for malignancy prognosis. This meta-analysis aimed to assess the prognostic significance of FGD5-AS1 in various carcinomas.

Methods

A systematic search was performed through five electronic databases to identify studies that investigating the role of FGD5-AS1 expression as a prognostic factor in carcinomas. The value of FGD5-AS1 in malignancies was estimated by odds ratios (ORs) and hazard ratios (HRs) with a corresponding 95% confidence intervals (CIs). Furthermore, the GEPIA database was used to further supplement our results.

Results

This analysis included 12 studies with 642 cases covering eight cancer types. High FGD5-AS1 expression exhibited a significant correlation with poor overall survival(OS) (HR = 2.04, 95%CI [1.72, 2.42], P < 0.00001), advanced tumor stage (OR = 3.47, 95%CI [2.34, 5.14], P < 0.00001), lymph node metastasis(LNM) (OR = 1.79, 95% CI [1.20,2.67], P = 0.004), and larger tumor size (OR= 5.25, 95%CI [2.68, 10.30], P < 0.00001). Furthermore, the FGD5-AS1 expression was notably upregulated in six types of malignancies as verified using the GEPIA online gene analysis tool.

Conclusions

The findings of this meta-analysis indicated that high FGD5-AS1 expression was significantly associated with poor prognosis in diverse cancer types, suggesting that FGD5-AS1 may be a promising biomarker for predicting cancer prognosis.

Systematic review registration

https://www.york.ac.uk/inst/crd, identifier CRD42024552582.

Exploring non-coding RNA mechanisms in hepatocellular carcinoma: implications for therapy and prognosis

Hepatocellular carcinoma (HCC) is a significant contributor to cancer-related deaths in the world. The development and progression of HCC are closely correlated with the abnormal regulation of non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Important biological pathways in cancer biology, such as cell proliferation, death, and metastasis, are impacted by these ncRNAs, which modulate gene expression. The abnormal expression of non-coding RNAs in HCC raises the possibility that they could be applied as new biomarkers for diagnosis, prognosis, and treatment targets. Furthermore, by controlling the expression of cancer-related genes, miRNAs can function as either tumor suppressors or oncogenes. On the other hand, lncRNAs play a role in the advancement of cancer by interacting with other molecules within the cell, which, in turn, affects processes such as chromatin remodeling, transcription, and post-transcriptional processes. The importance of ncRNA-driven regulatory systems in HCC is being highlighted by current research, which sheds light on tumor behavior and therapy response. This research highlights the great potential of ncRNAs to improve patient outcomes in this difficult disease landscape by augmenting the present methods of HCC care through the use of precision medicine approaches.

Prognostic effect of lncRNA BBOX1-AS1 in malignancies: a meta-analysis

Background: With the increasing number of new cancer cases and mortality rates, cancer has become a serious global health problem, but there are no ideal cancer biomarkers for effective diagnosis. Currently, mounting evidence demonstrates that lncRNAs play a fundamental role in cancer progression. BBOX1 anti-sense RNA 1 (BBOX1-AS1) is a recently clarified lncRNA and has been identified as dysregulated in various carcinomas, and it contributes to poor survival in cancer patients. Methods: We thoroughly searched six databases for eligible articles published as of 27, April 2023. The association of BBOX1-AS1 expression levels with prognostic and clinicopathological parameters was assessed by odds ratios (OR) and hazard ratios with 95% CIs. Additionally, we further validated our results utilizing the GEPIA online database. Results: Eight studies comprising 602 patients were included in this analysis. High BBOX1-AS1 expression indicated poor overall survival (OS) (hazard ratios = 2.30, 95% Cl [1.99, 2.67], p < 0.00001) when compared with low BBOX1-AS1 expression. Furthermore, BBOX1-AS1 expression was positively correlated with lymph node metastasis (OR = 3.00, 95% CI [1.71-5.28], p = 0.0001) and advanced tumor stage (OR = 3.74, 95% CI [2.63-5.32], p < 0.00001) for cancer patients. Moreover, BBOX1-AS1 was remarkably upregulated in 12 malignancies, and the elevated BBOX1-AS1 expression predicted poorer OS and worse disease-free survival (DFS) confirmed through the GEPIA online gene analysis tool. Conclusion: The findings highlight that BBOX1-AS1 was significantly associated with detrimental overall survival, disease-free survival, lymph node metastasis and tumor stage; thus, it could act as a novel promising biomarker to predict the clinicopathological characteristics and prognosis for various cancers.

Emerging role of transforming growth factor-β-regulated long non-coding RNAs in prostate cancer pathogenesis

Prostate cancer (PCa) is the most common malignancy in men. Despite aggressive therapy involving surgery and hormonal treatments, the recurrence and emergence of metastatic castration-resistant prostate cancer (CRPCa) remain a major challenge. Dysregulation of the transforming growth factor-β (TGF-β) signaling pathway is crucial to PCa development and progression. This also contributes to androgen receptor activation and the emergence of CRPC. In addition, TGF-β signaling regulates long non-coding RNA (lncRNA) expression in multiple cancers, including PCa. Here, we discuss the complex regulatory network of lncRNAs and TGF-β signaling in PCa and their potential applications in diagnosing, prognosis, and treating PCa. Further investigations on the role of lncRNAs in the TGF-β pathway will help to better understand PCa pathogenesis.

The function of LncRNA-ATB in cancer

Cancer as a progressive and complex disease is caused by early chromosomal changes and stimulated cellular transformation. Previous studies reported that long non-coding RNAs (lncRNAs) play pivotal roles in the initiation, maintenance, and progression of cancer cells. LncRNA activated by TGF-β (ATB) has been shown to be dysregulated in different types of cancer. Aberrant expression of lncRNA-ATB plays an important role in the progression of diverse malignancies. High expression of LncRNA-ATB is associated with cancer cell growth, proliferation, metastasis, and EMT. LncRNA-ATB by targeting various signaling pathways and microRNAs (miRNAs) can trigger cancer pathogenesis. Therefore, lncRNA-ATB can be a novel target for cancer prediction and diagnosis. In this review, we will focus on the function of lncRNA-ATB in various types of human cancers.

An immune-related lncRNA risk coefficient model to predict the outcomes in clear cell renal cell carcinoma

Objective: Using model algorithms, we constructed an immune-related long non-coding RNAs (lncRNAs) risk coefficient model to predict outcomes for patients with clear cell renal cell carcinoma (ccRCC) to understand the infiltration of tumor immune cells and the sensitivity to immune-targeted drugs.

Methods: Open genes data were downloaded from The Cancer Genome Atlas and The Immunology Database and Analysis Portal, and immune-related lncRNAs were obtained through Pearson correlation analysis. R language software was used to obtain differentially expressed immune-related lncRNAs and immune-related lncRNA pairs. The model was constructed using least absolute shrinkage and selector operation regression analysis, and receiver operator characteristic curves were drawn. The Akaike information criterion was used to distinguish the high-risk from the low-risk group. We also conducted correlation analysis for the high- and low-risk subgroups.

Results: We identified 27 immune-related lncRNAs pairs, 16 of which were included in the model construction. After merging clinical data, the areas under the curve of 1 -year, 3-year, and 5-year survival times of ccRCC patients were 0.867, 0.832, and 0.838, respectively. Subgroup analyses were conducted according to the cut-off value. We found that the high-risk group was associated with poor outcomes. The risk score and tumor stage were independent predictors of the outcome of ccRCC. The risk model predicted specific immune cell infiltration, immune checkpoint gene expression levels, and high-risk groups more sensitive to sunitinib targeted therapy.

Conclusion: We obtained prognostic-related novel ccRCC markers and risk model that predicts the outcome of patients with ccRCC and helps identify those who can benefit from sunitinib.

Progress in understanding the role of lncRNA in programmed cell death

Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but not translated into proteins. LncRNAs regulate gene expressions at multiple levels, such as chromatin, transcription, and post-transcription. Further, lncRNAs participate in various biological processes such as cell differentiation, cell cycle regulation, and maintenance of stem cell pluripotency. We have previously reported that lncRNAs are closely related to programmed cell death (PCD), which includes apoptosis, autophagy, necroptosis, and ferroptosis. Overexpression of lncRNA can suppress the extrinsic apoptosis pathway by downregulating of membrane receptors and protect tumor cells by inhibiting the expression of necroptosis-related proteins. Some lncRNAs can also act as competitive endogenous RNA to prevent oxidation, thereby inhibiting ferroptosis, while some are known to activate autophagy. The relationship between lncRNA and PCD has promising implications in clinical research, and reports have highlighted this relationship in various cancers such as non-small cell lung cancer and gastric cancer. This review systematically summarizes the advances in the understanding of the molecular mechanisms through which lncRNAs impact PCD.

Effects and mechanism of lncRNA-27785.1 that regulates TGF-β1 of Sika deer on antler cell proliferation

Transforming growth factor (TGF-β) plays an important role in the development of deer antlers. The purpose of this study was to investigate the role of long noncoding RNA in the transcriptional regulation of TGF-β1 and its relationship with the proliferation and differentiation of antler chondrocytes. High-throughput sequencing was used to screen lncRNAs related to TGF-β1. Next, the overexpression plasmid and interference sequence of target lncRNA27785.1 were constructed and transfected into chondrocytes. We found that lncRNA27785.1 inhibited the proliferation and migration of chondrocytes and delayed the transition of cells from G1 to S phase. qRT-PCR and Western blot analysis indicated that the overexpression of lncRNA27785.1 may downregulate mRNA and protein expression of TGF-BR2, Smad3, pSmad3, and Smad4. Our findings highlight lncRNA27785.1 as an inhibitor of chondrocytes proliferation and differentiation by negatively regulating the TGF-β/Smad signaling pathway; this implicates an important regulatory role for long noncoding RNA in the regeneration of antler.

The prognostic value of long noncoding RNA activated by TGF-β in digestive system cancers: A meta-analysis

BACKGROUND

To systematically evaluate whether the expression level of long non-coding RNA activated by transforming growth factor-β (lncRNA-ATB) is correlated with the prognosis of digestive system cancer (DSC) patients.

METHODS

PubMed, Embase, Cochrane Library, Web of Science, Springerlink, Nature, and Karger databases were searched up to April 20, 2019 by 2 experienced researchers independently. The quality of studies was assessed with the Newcastle-Ottawa scale. The Review Manager 5.2 and STATA 12.0 software were used for this meta-analysis.

RESULT

Eleven studies with 1227 DSC patients were included in the meta-analysis. Except for pancreatic cancer, high expression of lncRNA-ATB was associated with lymph node metastasis (risk ratio (RR) = 1.26, 95% confidence interval (CI): 1.12-1.42, P < .001), advanced clinical staging (RR = 1.44, 95%CI: 1.23-1.69, P < .001), reduced overall survival rate (OS) (hazard ratio (HR) = 2.33, 95%CI: 1.22-4.50, P = .01), and recurrence-free survival (RFS) (HR = 2.61, 95%CI: 1.46-4.65, P = .001) compared with low lncRNA-ATB expression in DSCs.

CONCLUSIONS

High expression of lncRNA-ATB was significantly correlated with poor prognosis for most DSCs. The expression level of lncRNA-ATB could be a promising prognostic biomarker for DSC patients.

Prognostic value of long non-coding RNA ATB in digestive system cancers: A meta-analysis

BACKGROUND

The present meta-analysis has evaluated the association between lncRNA ATB, prognosis and clinicopathological parameters in patients with digestive cancers.

METHODS

Eligible studies were gathered from Web of Science, PubMed, Embase, Cochrane Library, WanFang databases and China National Knowledge Infrastructure (up to October 15, 2019). Hazard ratios (HRs) and 95 % confidence intervals (CIs) were calculated to estimate the prognosis and clinicopathological parameters of lncRNA ATB in patients with digestive cancers.

RESULT

We divided this study into two groups, pancreatic cancer (PC, downregulation) and non-pancreatic cancer (non-PC, upregulation). In the non-PC group, high expression levels of lncRNA ATB were significantly related to poor OS (pooled HR = 2.19, 95 % CI 1.68-2.85, P＜0.00001). In contrast, increased levels of lncRNA ATB in pancreatic cancer tissue were favorable factors in OS (HR = 0.47, 95 % CI 0.32-0.69, P = 0.0001). The pooled data suggested that high expression levels of lncRNA ATB predicted a poor DFS in CRC and a poor RFS in HCC. Increased expression of lncRNA ATB was correlated with negative lymph node metastasis and TNM stage in the non-PC group. In contrast, lncRNA ATB were favorable factors for LNM and TNM stages in pancreatic cancer.

CONCLUSION

LncRNA ATBs, whether cancer promoters or suppressors, were potential biomarkers and therapeutic targets for digestive system cancers.

High Expression of TGF-β1 Predicting Tumor Progression in Skull Base Chordomas

OBJECTIVE

To investigate the expression characteristics and prognostic value of transforming growth factor β1 (TGF-β1) in primary skull base chordomas (SBCs).

METHODS

The mRNA expression levels of TGF-β1 were measured in 57 frozen samples from patients with primary SBCs. Clinical data collection, follow-up, correlations, and survival analyses were performed.

RESULTS

In the series of 57 patients (29 men and 28 women) with primary SBCs, the mean value of TGF-β1 mRNA was 1.713 with a median of 0.904. Twenty-four SBCs were soft type and 33 were hard type. The Mann-Whitney U test revealed that the expression level of TGF-β1 mRNA in hard type SBCs was significantly higher than the expression level found in the soft type (P = 0.03). The independent-samples median test suggested that the expression level of TGF-β1 mRNA in female patients' SBCs was significantly higher than that in male patients' SBCs (P = 0.01). Expression differences of TGF-β1 were not seen among different pathological subtypes, tumor blood supply, or degree of resection. The Spearman rank correlation coefficient clarified that TGF-β1 mRNA levels were not correlated with tumor diameter, preoperative Karnofsky Performance Status (KPS), postoperative KPS, follow-up KPS, age, or intraoperative blood loss. The multivariate Cox analysis revealed that pathological subtype (P = 0.008), expression level of TGF-β1 mRNA (P = 0.01), and tumor texture (P = 0.03) were all independent prognostic factors for tumor progression.

CONCLUSIONS

SBCs in female patients and SBCs with hard texture were prone to have high TGF-β1 mRNA expression. High expression of TGF-β1, hard tumor texture, and conventional subtype were all independent risk factors for tumor progression.

Roles and Regulation of Long Noncoding RNAs in Hepatocellular Carcinoma

Next-generation sequencing has uncovered thousands of long noncoding RNAs (lncRNA). Many are reported to be aberrantly expressed in various cancers, including hepatocellular carcinoma (HCC), and play key roles in tumorigenesis. This review provides an in-depth discussion of the oncogenic mechanisms reported to be associated with deregulated HCC-associated lncRNAs. Transcriptional expression of lncRNAs in HCC is modulated through transcription factors, or epigenetically by aberrant histone acetylation or DNA methylation, and posttranscriptionally by lncRNA transcript stability modulated by miRNAs and RNA-binding proteins. Seventy-four deregulated lncRNAs have been identified in HCC, of which, 52 are upregulated. This review maps the oncogenic roles of these deregulated lncRNAs by integrating diverse datasets including clinicopathologic features, affected cancer phenotypes, associated miRNA and/or protein-interacting partners as well as modulated gene/protein expression. Notably, 63 deregulated lncRNAs are significantly associated with clinicopathologic features of HCC. Twenty-three deregulated lncRNAs associated with both tumor and metastatic clinical features were also tumorigenic and prometastatic in experimental models of HCC, and eight of these mapped to known cancer pathways. Fifty-two upregulated lncRNAs exhibit oncogenic properties and are associated with prominent hallmarks of cancer, whereas 22 downregulated lncRNAs have tumor-suppressive properties. Aberrantly expressed lncRNAs in HCC exert pleiotropic effects on miRNAs, mRNAs, and proteins. They affect multiple cancer phenotypes by altering miRNA and mRNA expression and stability, as well as through effects on protein expression, degradation, structure, or interactions with transcriptional regulators. Hence, these insights reveal novel lncRNAs as potential biomarkers and may enable the design of precision therapy for HCC.