Comprehensive Analysis of Aberrantly Expressed Profiles of lncRNAs and miRNAs with Associated ceRNA Network in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma

Unraveling the role of miR-767 in tumor progression: Mechanisms and clinical implications

MicroRNAs (miRNAs), a distinctive class of small single-stranded non-coding RNA molecules typically spanning between 21 and 23 nucleotides, hold a pivotal position within the intricate regulatory network governing gene expression. Notably, miR-767, located on chromosome Xq28, has emerged as a significant player in tumor development, with its two mature products, miR-767-3p and miR-767-5p, garnering considerable attention in scientific inquiry. Extensive investigations reveal aberrant expression patterns of miR-767 across a spectrum of cancers affecting neurological, digestive, reproductive, urinary, and respiratory systems. Remarkably, miR-767 exhibits substantial upregulation in 13 distinct cancer types and demonstrates precise targeting of at least 14 pivotal protein-coding genes (PCGs) crucial for regulating cellular processes including the cell cycle, proliferation, epithelial-mesenchymal transition (EMT), invasion, and migration. Moreover, the expression level of miR-767 bears significant implications for cancer patient diagnosis, prognosis, and drug sensitivity, thus offering novel insights for clinical tumor management. At the mechanistic level, miR-767-5p and miR-767-3p intricately participate in the regulation of key signaling pathways, with miR-767-5p influencing JAK/STAT, EPK1/2, and PI3K/Akt pathways, while miR-767-3p predominantly affects TGF-β and PI3K/Akt pathways. Notably, both miRNAs converge on the PI3K/Akt pathway, underscoring its pivotal role in their joint regulation. This review provides a comprehensive analysis of the intricate mechanisms underlying miR-767-mediated tumor progression through the modulation of diverse target genes, and explores the potential correlation between host gene GABRA3 transcription and the expression of these miRNAs. Furthermore, the review systematically delineates the binding sites of miR-767-5p and miR-767-3p with circRNA and target genes, alongside the PCGs regulated by miR-767, offering profound insights into their multifaceted roles in tumor development. In essence, this review not only comprehensively elucidates the pivotal role of miR-767 in tumor progression but also provides valuable cues and avenues for future research, thereby fostering deeper scientific inquiry within the realm of cancer research.

High expression of miR-7974 predicts poor prognosis and is associated with autophagy in estrogen receptor-positive breast cancer

Estrogen receptor-positive (ER+) breast cancers (BC) cause death despite well-established treatments. MicroRNAs (miRNAs) have potential as biomarkers specific to cancer subtypes and tissues, therefore miRNA-based biomarkers could help improve patient survival. In this study, we investigated a relatively unknown miRNA, miR-7974. We utilized small RNA data from 204 breast tissue samples to study miR-7974 association with clinicopathological features and outcomes for BC patients. Additionally, in vitro and in ovo methods were used to identify miR-7974 role at molecular and cellular level in MCF-7 cells. Findings were validated using MDA-MB-453 cells. MiR-7974 was upregulated in many clinicopathological features of BC (P<0.05). Furthermore, the highest expression of miR-7974 was associated with poor relapse-free survival in ER+ BC patients [hazard ratio (HR)=8.70; 95% confidence interval (CI)=3.28-23.06; P=1.37x10-05] and poor BC-specific survival in patients receiving only surgical treatment (HR=8.36; 95% CI=1.01-69.06; P=0.049). Our studies revealed that miR-7974 targets autophagy gene, MAP1LC3B, identified as direct miR-7974 target (P<0.05) in MCF-7 cells. In vitro analyses indicated overexpressing miR-7974 had anti-proliferative effect in MCF7 and MDA-MB-453 cells. Overall, our results demonstrate potential prognostic role of miR-7974 in ER+ BC.

Hsa-miR-7974 Suppresses Epstein-Barr Virus Reactivation by Directly Targeting BZLF1 and BRLF1

Epstein-Barr virus (EBV) reactivation, a key factor in Epstein-Barr virus (EBV)-associated malignancies, is regulated by specific cellular microRNAs (miRNAs). This study investigated the role of Hsa-miR-7974 (miR-7974) in this process. miRNA sequencing revealed significant downregulation of miR-7974 in reactivated EBV-positive cell lines (Raji and C666-1). Bioinformatics prediction and dual-luciferase assays confirmed the direct targeting of the EBV immediate-early gene BRLF1 by miR-7974. Furthermore, miR-7974 mimics suppressed, whereas inhibitors increased, the expression of key EBV lytic genes (BZLF1, BRLF1, and BMRF1) and the viral load, as validated by RT-qPCR. Bioinformatics analyses revealed the involvement of miR-7974 in cellular pathways such as membrane dynamics and signal transduction (MAPK, NF-κB, and IL-10), and its association with Hodgkin's lymphoma, leukemia, and nasopharyngeal neoplasms. These findings establish that miR-7974 functions as a crucial negative regulator of EBV reactivation by directly targeting BRLF1, highlighting its potential significance in the pathogenesis of EBV-associated malignancies.

Identification of a Plasma Exosomal lncRNA- and circRNA-Based ceRNA Regulatory Network in Patients With Lung Adenocarcinoma

BACKGROUND

Exosomes have been established to be enriched with various long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) that exert various biological effects. However, the lncRNA- and circRNA-mediated coexpression competing endogenous RNA (ceRNA) regulatory network in exosomes derived from the plasma of patients with lung adenocarcinoma (LUAD) remains elusive.

METHODS AND RESULTS

This study enrolled nine patients with lung adenocarcinoma and three healthy individuals, and the differential expression of messenger RNAs (mRNAs), lncRNAs, and circRNAs was detected using microarray analysis, while microRNAs (miRNAs) were detected through RNA sequencing. Additionally, bioinformatics algorithms were applied to evaluate the lncRNA-miRNA-mRNAs/circRNA-miRNA-mRNA network. Differentially expressed cicRNAs were identified via quantitative reverse transcription polymerase chain reaction (RT-qPCR). A total of 1016 lncRNAs, 1396 circRNAs, 45 miRNAs, and 699 mRNAs were differentially expressed in the plasma exosomes of patients with LUAD compared with healthy controls. Among them, 881 lncRNAs were upregulated and 135 were downregulated, 916 circRNAs were upregulated while 480 were downregulated, 45 miRNAs were upregulated while none were downregulated, and 591 mRNAs were upregulated while 108 were downregulated (p ≤ 0.05, and fold change ≥ 2). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the biological functions of differentially expressed RNAs. Meanwhile, the RNA networks displayed the regulatory relationship between dysregulated RNAs. Finally, RT-qPCR validated that the expression of circ-0033861, circ-0043273, and circ-0011959 was upregulated in the plasma exosome of patients with LUAD compared to healthy controls (p = 0.0327, p = 0.0002, p = 0.0437, respectively).

CONCLUSION

This study proposed a newly discovered ncRNA-miRNA-mRNA/circRNA-miRNA-mRNA ceRNA network and identified that the expression of circulating circ-0033861, circ-0043273, and circ-0011959 was up-regulated in the plasma exosomes of patients with LUAD, offering valuable insights for exploring the potential function of exosomal noncoding RNA and identifying potential biomarkers for LUAD.

Circular RNA as new serum metabolic biomarkers in patients with premature ovarian insufficiency

OBJECTIVE

Quantitative real-time PCR (qPCR) is used to detect the differential expression of circular RNAs in patients of premature ovarian insufficiency (POI), to explore the new biomarkers of POI that can be detected from blood as soon as possible.

METHODS

The study collected plasma samples from 30 patients in POI group and 30 normal people group who meet the inclusion criteria, who visited the gynecology clinic of The First Affiliated Hospital of Guangzhou University of Chinese Medicine from July 2019 to December 2020. Then, circRNAs in plasma were extracted for qPCR validation.

RESULTS

1. qPCR technology was performed on hsa_circRNA_008901 and hsa_circRNA_403959, and it was found that the levels of both were considerably downregulated in POI group. Clinical evaluation showed that both hsa_circRNA_008901 and hsa_circRNA_403959 have good diagnostic value for POI. 2. According to miRNA Regulatory Element (MRE) analysis, the predicted target miRNAs of hsa_circRNA_008901 are: hsa-miR-548c-3p, hsa-miR-924, hsa-miR-4677-5p, hsa-miR-6786-3p and hsa-miR-7974; the predicted target miRNAs of hsa_circRNA_403959 are: hsa-miR-1207-5p, hsa-miR-4691-5p, hsa-miR-4763-3p, hsa-miR-6807-5p and hsa-miR-7160-5p.

CONCLUSION

Compared with the normal group, the expression levels of hsa_circRNA_008901 and hsa_circRNA_403959 in the POI group were downregulated, suggesting that these two circRNAs may be potential biomarkers of POI. Bioinformatics analysis indicated that hsa_circRNA_008901 and hsa_circRNA_403959 may regulate their binding miRNA through the action form of "molecular sponge", and then regulate the signaling pathway regulated by miRNA, and ultimately affect the disease progression of POI.

The Role of Long Non-Coding RNAs in Cardiovascular Diseases

Long non-coding RNAs (lncRNAs) are non-coding RNA molecules longer than 200 nucleotides that regulate gene expression at the transcriptional, post-transcriptional, and translational levels. Abnormal expression of lncRNAs has been identified in many human diseases. Future improvements in diagnostic, prognostic, and therapeutic techniques will be facilitated by a deeper understanding of disease etiology. Cardiovascular diseases (CVDs) are the main cause of death globally. Cardiac development involves lncRNAs, and their abnormalities are linked to many CVDs. This review examines the relationship and function of lncRNA in a variety of CVDs, including atherosclerosis, myocardial infarction, myocardial hypertrophy, and heart failure. Therein, the potential utilization of lncRNAs in clinical diagnostic, prognostic, and therapeutic applications will also be discussed.

Identification of a novel gene signature of lung adenocarcinoma based on epidermal growth factor receptor-tyrosine kinase inhibitor resistance

INTRODUCTION

Tyrosine kinase inhibitors (TKIs) that target epidermal growth factor receptor (EGFR) mutations are commonly administered to EGFR-positive lung cancer patients. However, resistance to EGFR-TKIs (mostly gefitinib and erlotinib) is presently a significant problem. Limited studies have focused on an EGFR-TKI resistance-related gene signature (ERS) in lung adenocarcinoma (LUAD).

METHODS

Gefitinib and erlotinib resistance-related genes were obtained through the differential analyses of three Gene Expression Omnibus datasets. These genes were investigated further in LUAD patients from The Cancer Genome Atlas (TCGA). Patients in the TCGA-LUAD cohort were split into two groups: one for training and one for testing. The training cohort was used to build the ERS, and the testing cohort was used to test it. GO and KEGG analyses were explored for the enriched pathways between the high-risk and low-risk groups. Various software, mainly CIBERSORT and ssGSEA, were used for immune infiltration profiles. Somatic mutation and drug sensitivity analyses were also explored.

RESULTS

An ERS based on five genes (FGD3, PCDH7, DEPDC1B, SATB2, and S100P) was constructed and validated using the TCGA-LUAD cohort, resulting in the significant stratification of LUAD patients into high-risk and low-risk groups. Multivariable Cox analyses confirmed that ERS had an independent prognostic value in LUAD. The pathway enrichment analyses showed that most of the genes that were different between the two risk groups were related to the immune system. Further immune infiltration results revealed that a lower immune infiltration score was observed in high-risk patients, and that various leukocytes were significantly related to the ERS. Importantly, samples from the high-risk group showed lower levels of PD-1, PD-L1, and CTLA-4, which are important biomarkers for immunotherapy responses. Patients in the high-risk group also had more gene mutation changes and were more sensitive to chemotherapy drugs like docetaxel and sorafenib. The ERS was also validated in the GSE30219, GSE11969 and GSE72094, and showed a favorable prognostic value for LUAD patients.

DISCUSSION

The ERS established during this study was able to predict a poor prognosis for LUAD patients and had great potential for predicting drug responses.

The AKT/mTOR Signaling Pathway Was Mediated through the LINC00514/miR-28-5p/TRIM44 Axis

Objective. Increasing evidence has demonstrated the essential role of lncRNAs in tumorigenesis. LINC00514, a novel lncRNA, was reported to be a promoter of malignant behaviors in cancer, but in pituitary adenoma (PA), its biological functions remain unclear. Methods. Herein, we measured LINC00514 expression by RT-qPCR analysis which indicated a significant elevation of LINC00514 expression in human PA tissues. Moreover, the effect of LINC00514 silencing on PA cell proliferation and invasion was, respectively, examined by CCK-8 and transwell assays. Results. The results showed that LINC00514 deletion markedly inhibited PA cell proliferation and invasion. Besides, investigation on the molecular mechanisms showed that LINC00514 might function as an endogenous RNA (ceRNA) to sponge miR-28-5p and TRIM44 was mediated by LINC00514-derived miR-28-5p in PA cells. Furthermore, the AKT/mTOR signaling pathway was mediated through the LINC00514/miR-28-5p/TRIM44 axis. Conclusion. To sum up, we suggested LINC00514 as a novel therapeutic target for PA treatment.

LncRNA PITPNA-AS1/miR-223-3p/PTN axis regulates malignant progression and stemness in lung squamous cell carcinoma

Background

Long noncoding RNAs (lncRNAs) are a kind of molecule that cannot code proteins, and their expression is dysregulated in diversified cancers. LncRNA PITPNA‐AS1 has been shown to act as a tumor promoter in a variety of malignancies, but its function and regulatory mechanisms in lung squamous cell carcinoma (LUSC) are yet unknown.

Methods

The mRNA and protein expression of genes were examined by RT‐qPCR, western blot, and IHC assay. The cell proliferation, migration, invasion, and stemness were detected through CCK‐8, colony formation, Transwell and spheroid formation assays. The CD44⁺ and CD166⁺‐positive cells were detected through flow cytometry. The binding ability among genes through luciferase reporter and RNA pull‐down assays. The tumor growth was detected through in vivo nude mice assay.

Results

The lncRNA PITPNA‐AS1 had increased expression in LUSC and was linked to a poor prognosis. In LUSC, PITPNA‐AS1 also enhanced cell proliferation, migration, invasion, and stemness. This mechanistic investigation showed that PITPNA‐AS1 absorbed miR‐223‐3p and that miR‐223‐3p targeted PTN. MiR‐223‐3p inhibition or PTN overexpression might reverse the inhibitory effects of PITPNA‐AS1 suppression on LUSC progression, as demonstrated by rescue experiments. In addition, the PITPNA‐AS1/miR‐223‐3p/PTN axis accelerated tumor development in vivo.

Conclusions

It is the first time we investigated the potential role and ceRNA regulatory mechanism of PITPNA‐AS1 in LUSC. The data disclosed that PITPNA‐AS1 upregulated PTN through sponging miR‐223‐3p to enhance the onset and progression of LUSC. These findings suggested the ceRNA axis may serve as a promising therapeutic biomarker for LUSC patients.

Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue

Background

Lung cancer is the leading cause of cancer death in both men and women. The most common lung cancer subtype is non-small cell lung carcinoma (NSCLC) comprising about 85% of all cases. NSCLC can be further divided into three subtypes: adenocarcinoma (LUAD), squamous cell carcinoma (LUSC), and large cell lung carcinoma. Specific genetic mutations and epigenetic aberrations play an important role in the developmental transition to a specific tumor subtype. The elucidation of normal lung versus lung tumor gene expression patterns and regulatory targets yields biomarker systems that discriminate lung phenotypes (i.e., biomarkers) and provide a foundation for the discovery of normal and aberrant gene regulatory mechanisms.

Results

We built condition-specific gene co-expression networks (csGCNs) for normal lung, LUAD, and LUSC conditions. Then, we integrated normal lung tissue-specific gene regulatory networks (tsGRNs) to elucidate control-target biomarker systems for normal and cancerous lung tissue. We characterized co-expressed gene edges, possibly under common regulatory control, for relevance in lung cancer.

Conclusions

Our approach demonstrates the ability to elucidate csGCN:tsGRN merged biomarker systems based on gene expression correlation and regulation. The biomarker systems we describe can be used to classify and further describe lung specimens. Our approach is generalizable and can be used to discover and interpret complex gene expression patterns for any condition or species.

Supplementary Information

The online version contains available at 10.1186/s12864-022-08591-9.

Role of Long Non-Coding RNA LINC00641 in Cancer

Long non-coding RNAs (lncRNAs) are non-protein coding RNAs with more than 200 nucleic acids in length. When lncRNAs are located in the nucleus, they regulate chromosome structure, participate in chromatin remodeling, and act as transcription regulators. When lncRNAs are exported to the cytoplasm, they regulate mRNA stability, regulate translation, and interfere with post-translational modification. In recent years, more and more evidences have shown that lncRNA can regulate the biological processes of tumor proliferation, apoptosis, invasion and metastasis, and can participate in a variety of tumor signaling pathways. Long-gene non-protein coding RNA641 (LINC00641), located on human chromosome 14q11.2, is differentially expressed in a variety of tumors and is related to overall survival and prognosis, etc. Interfering the expression of LINC00641 can lead to changes in tumor cell proliferation, invasion, metastasis, apoptosis and other biological behaviors. Therefore, LINC00641 is a promising new biomarker and potential clinical therapeutic target. In this review, the biological functions, related mechanisms and clinical significance of LINC00641 in many human cancers are described in detail.

A Signature of 14 Long Non-Coding RNAs (lncRNAs) as a Step towards Precision Diagnosis for NSCLC

LncRNAs have arisen as new players in the world of non-coding RNA. Disrupted expression of these molecules can be tightly linked to the onset, promotion and progression of cancer. The present study estimated the usefulness of 14 lncRNAs (HAGLR, ADAMTS9-AS2, LINC00261, MCM3AP-AS1, TP53TG1, C14orf132, LINC00968, LINC00312, TP73-AS1, LOC344887, LINC00673, SOX2-OT, AFAP1-AS1, LOC730101) for early detection of non-small-cell lung cancer (NSCLC). The total RNA was isolated from paired fresh-frozen cancerous and noncancerous lung tissue from 92 NSCLC patients diagnosed with either adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC). The expression level of lncRNAs was evaluated by a quantitative real-time PCR (qPCR). Based on Ct and delta Ct values, logistic regression and gradient boosting decision tree classifiers were built. The latter is a novel, advanced machine learning algorithm with great potential in medical science. The established predictive models showed that a set of 14 lncRNAs accurately discriminates cancerous from noncancerous lung tissues (AUC value of 0.98 ± 0.01) and NSCLC subtypes (AUC value of 0.84 ± 0.09), although the expression of a few molecules was statistically insignificant (SOX2-OT, AFAP1-AS1 and LOC730101 for tumor vs. normal tissue; and TP53TG1, C14orf132, LINC00968 and LOC730101 for LUAD vs. LUSC). However for subtypes discrimination, the simplified logistic regression model based on the four variables (delta Ct AFAP1-AS1, Ct SOX2-OT, Ct LINC00261, and delta Ct LINC00673) had even stronger diagnostic potential than the original one (AUC value of 0.88 ± 0.07). Our results demonstrate that the 14 lncRNA signature can be an auxiliary tool to endorse and complement the histological diagnosis of non-small-cell lung cancer.

Identification of Potential Long Non-coding RNA Expression Quantitative Trait Methylations in Lung Adenocarcinoma and Lung Squamous Carcinoma

There are associations between DNA methylation and the expression of long non-coding RNA (lncRNA), also known as lncRNA expression quantitative trait methylations (lnc-eQTMs). Lnc-eQTMs may induce a wide range of carcinogenesis pathways. However, lnc-eQTMs have not been globally identified and studied, and their roles in lung adenocarcinoma (LUAD) and lung squamous carcinoma (LUSC) are largely unknown. In the present study, we identified some differential methylation sites located in genes of long intergenic non-coding RNAs (lincRNAs) and other types of lncRNAs in LUAD and LUSC. An integrated pipeline was established to construct two global cancer-specific regulatory networks of lnc-eQTMs in LUAD and LUSC. The associations between eQTMs showed common and specific features between LUAD and LUSC. Some lnc-eQTMs were also related with survival in LUAD- and LUSC-specific regulatory networks. Lnc-eQTMs were associated with cancer-related functions, such as lung epithelium development and vasculogenesis by functional analysis. Drug repurposing analysis revealed that these lnc-eQTMs may mediate the effects of some anesthesia-related drugs in LUAD and LUSC. In summary, the present study elucidates the roles of lnc-eQTMs in LUAD and LUSC, which could improve our understanding of lung cancer pathogenesis and facilitate treatment.

Update on uveal melanoma: Translational research from biology to clinical practice (Review)

Uveal melanoma is the most common type of intraocular cancer with a low mean annual incidence of 5‑10 cases per million. Tumours are located in the choroid (90%), ciliary body (6%) or iris (4%) and of 85% are primary tumours. As in cutaneous melanoma, tumours arise in melanocytes; however, the characteristics of uveal melanoma differ, accounting for 3‑5% of melanocytic cancers. Among the numerous risk factors are age, sex, genetic and phenotypic predisposition, the work environment and dermatological conditions. Management is usually multidisciplinary, including several specialists such as ophthalmologists, oncologists and maxillofacial surgeons, who participate in the diagnosis, treatment and complex follow‑up of these patients, without excluding the management of the immense emotional burden. Clinically, uveal melanoma generates symptoms that depend as much on the affected ocular globe site as on the tumour size. The anatomopathological study of uveal melanoma has recently benefited from developments in molecular biology. In effect, disease classification or staging according to molecular profile is proving useful for the assessment of this type of tumour. Further, the improved knowledge of tumour biology is giving rise to a more targeted approach to diagnosis, prognosis and treatment development; for example, epigenetics driven by microRNAs as a target for disease control. In the present study, the main epidemiological, clinical, physiopathological and molecular features of this disease are reviewed, and the associations among all these factors are discussed.

Licochalcone A reverses NNK-induced ectopic miRNA expression to elicit in vitro and in vivo chemopreventive effects

BACKGROUND

Chemoprevention is the best cost-effective way regarding cancers. MicroRNAs (miRNAs) have been reported to be differentially expressed during the development of lung cancer. However, if lung cancer prevention can be achieved through modulating miRNAs expression so far remains unknown.

PURPOSE

To discover ectopically expressed miRNAs in NNK-induced lung cancer and clarify whether Licochalcone A (lico A) can prevent NNK-induced lung cancer by modulating miRNA expression.

STUDY DESIGN AND METHODS

A/J mice were used to construct a lung cancer model by intraperitoneal injection with physiological saline NNK (100 mg/kg). Chemopreventive effects of lico A against lung cancer at 2 mg/kg and 20 mg/kg doses were evaluated in vivo. MicroRNA array and RT-qPCR were used to assess the expression levels of miRNAs. MLE-12 cells were treated with 0.1 mg/ml NNK, stimulating the ectopic expression pattern of miR-144-3p, miR-20a-5p, miR-29c-3p, let-7d-3p, and miR-328-3p. miR-144-3p mimics and inhibitors were used to manipulate miR-144-3p levels. The effects of lico A (10 μM) on cell cycle distribution, apoptosis, and the expression of CK19, RASA1, miR-144-3p, miR-20a-5p, miR-29c-3p, let-7d-3p, and miR-328-3p in NNK-treated MLE-12 cells were studied.

RESULTS

The expression levels of miR-144-3p, miR-20a-5p, and miR-29c-3p increased, while those of let-7d-3p and miR-328-3p decreased in both NNK-induced A/J mice and MLE-12 cells. Lico A could reverse the NNK-induced ectopic miRNA (miR-144-3p, miR-20a-5p, miR-29c-3p, let-7d-3p, and miR-328-3p) expression both in vivo and in vitro and elicit in vivo lung cancer chemopreventive effect against NNK. In MLE-12 cells, the overexpression of miR-144-3p elicited the same effect as NNK regarding the expression of lung cancer biomarker CK19; the silencing of miR-144-3p reversed the effect of NNK on cell cycle distribution and apoptosis. Lico A could reverse the effect of NNK on the expression of miR-144-3p, CK19, and RASA1 (predicted target of miR-144-3p).

CONCLUSION

The present study suggests that miR-144-3p, miR-20a-5p, miR-29c-3p, let-7d-3p, and miR-328-3p were involved in the in vivo pathogenesis of NNK-induced lung cancer, and lico A could reverse the effect of NNK both in vivo and in vitro to elicit lung cancer chemopreventive effects through, at least partially, these five ectopically expressed miRNAs, especially miR-144-3p.