A novel mRNA-miRNA-lncRNA competing endogenous RNA triple sub-network associated with prognosis of pancreatic cancer

microRNA 21 and long non-coding RNAs interplays underlie cancer pathophysiology: A narrative review

Non-coding RNAs (ncRNAs) are a diverse group of functional RNA molecules that lack the ability to code for proteins. Despite missing this traditional role, ncRNAs have emerged as crucial regulators of various biological processes and have been implicated in the development and progression of many diseases, including cancer. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two prominent classes of ncRNAs that have emerged as key players in cancer pathophysiology. In particular, miR-21 has been reported to exhibit oncogenic roles in various forms of human cancer, including prostate, breast, lung, and colorectal cancer. In this context, miR-21 overexpression is closely associated with tumor proliferation, growth, invasion, angiogenesis, and chemoresistance, whereas miR-21 inactivation is linked to the regression of most tumor-related processes. Accordingly, miR-21 is a crucial modulator of various canonical oncogenic pathways such as PTEN/PI3K/Akt, Wnt/β-catenin, STAT, p53, MMP2, and MMP9. Moreover, interplays between lncRNA and miRNA further complicate the regulatory mechanisms underlying tumor development and progression. In this regard, several lncRNAs have been found to interact with miR-21 and, by functioning as competitive endogenous RNAs (ceRNAs) or miRNA sponges, can modulate cancer tumorigenesis. This work presents and discusses recent findings highlighting the roles and pathophysiological implications of the miR-21-lncRNA regulatory axis in cancer occurrence, development, and progression. The data collected indicate that specific lncRNAs, such as MEG3, CASC2, and GAS5, are strongly associated with miR-21 in various types of cancer, including gastric, cervical, lung, and glioma. Indeed, these lncRNAs are well-known tumor suppressors and are commonly downregulated in different types of tumors. Conversely, by modulating various mechanisms and oncogenic signaling pathways, their overexpression has been linked with preventing tumor formation and development. This review highlights the significance of these regulatory pathways in cancer and their potential for use in cancer therapy as diagnostic and prognostic markers.

The Role of lncRNA-miR-26a-mRNA Network in Cancer Progression and Treatment

The role of non-coding RNAs in regulating biological processes associated with cancer progression, such as proliferation, migration, and apoptosis, has been extensively studied. Long non-coding RNAs (lncRNAs) play a role in regulating these processes through various mechanisms, including transcriptional and post-transcriptional modifications. In post-transcriptional regulation, lncRNAs can bind to specific miRNAs and affect their function, which can either promote or inhibit cancer development. The interaction between lncRNAs, miRNAs, and mRNAs forms a network known as competitive endogenous RNA (ceRNA), which is involved in cancer progression or inhibition. One specific miRNA called miR-26a-5p has been identified as having tumor-suppressive properties. However, when lncRNAs bind to and inhibit miR-26a-5p, it can lead to cancer progression. Therefore, targeting this ceRNA network could be a promising strategy for preventing cancer development. This review will first discuss the anticancer effects of miR-26a-5p and then explore the involvement of the lncRNA-miR26a-5p-mRNA axis in cancer progression and potential targeted therapies.

Identification and validation of the TRHDE-AS1/hsa-miR-449a/ADAMTS5 axis as a novel prognostic biomarker in prostate cancer

Despite advancements in cancer research, the prognostic implications of competing endogenous RNA (ceRNA) networks in prostate cancer (PCa) remain incompletely understood. This study aimed to elucidate the prognostic relevance of ceRNA networks in PCa, utilizing a comprehensive bioinformatics approach alongside experimental validation. After searching The Cancer Genome Atlas (TCGA) database, RNA sequencing (RNA-Seq) data were extracted to identify differentially expressed RNAs (DERs) between 491 PCa samples and 51 normal prostate tissues, following which a comprehensive bioinformatics strategy was implemented to construct a ceRNA network. An optimal prognostic signature comprising these DERs was then established and validated using TCGA data. In addition, functional validation was performed through RNA pull-down, dual-luciferase reporter assays, quantitative real-time PCR, and western blot analysis conducted in PC-3 and DU145 cell lines, thereby complementing the bioinformatics analysis. A total of 613 DERs, comprising 103 long noncoding RNAs (lncRNAs), 60 microRNAs (miRNAs), and 450 messenger RNAs (mRNAs), were identified and utilized in constructing a ceRNA network, which encompassed 23 lncRNAs, 9 miRNAs, and 52 mRNAs. An optimal prognostic signature was established, including VPS9D1 antisense RNA 1 (VPS9D1-AS1), miR-449a, cyclin-dependent kinase 5 regulatory subunit 1 (CDK5R1), targeting protein for Xklp2 (TPX2), solute carrier family 7 member 11 (SLC7A11), copine7 (CPNE7), and maternal embryonic leucine zipper kinase (MELK), yielding area under the curve (AUC) values exceeding 0.8 across training, validation, and entire datasets. Our experiments results revealed an interaction between lncRNA TRHDE antisense RNA 1 (TRHDE-AS1) and miR-449a and that miR-449a could target the ADAM metallopeptidase with thrombospondin type 1 motif 5 (ADAMTS5) mRNA. Knockdown of miR-449a significantly impeded cell proliferation, G1/S transition, migration and invasion, and promoted apoptosis in PC-3 and DU145 cells. Furthermore, knockdown of miR-449a notably downregulated protein expression of CDK4, cyclin D1, N-cadherin and vimentin, while upregulating protein expression of cleaved caspase-3 and E-cadherin. This study contributes to a deeper understanding of the prognostic-linked ceRNA network in PCa, providing fundamental insights that could improve diagnostic and therapeutic approaches for PCa management.

Novel prognostic signature for lung adenocarcinoma based on immune-related mRNA pairs

Lung adenocarcinoma (LUAD) is a highly lethal malignant tumor. While the involvement of multiple mRNAs in the progression of LUAD is well established, the potential diagnostic value of immune-related mRNAs (irmRNAs) in LUAD remains largely unexplored. In this study, we utilized RNA-seq, clinical data, and immune-related gene information from LUAD patients to identify differentially expressed immune-related mRNAs (DEirmRNAs) and developed a predictive risk model based on specific DEirmRNA pairs closely linked with patient prognosis. We classified patients into high-risk and low-risk groups and analyzed factors such as survival rate, clinical characteristics, gene enrichment, immune cell infiltration, tumor mutation load, and drug susceptibility. We confirmed the expression levels of these DEirmRNAs in tumor tissues using qRT-PCR assay. Our results showed that the low-risk group had a longer survival time and lower tumor mutation burden (TMB) and microsatellite instability (MSI) compared to the high-risk group. The high-risk group also had a significant reduction in the number of certain immune cells and a lower half-maximum inhibitor concentration (IC50). We identified specific DEirmRNA pairs that were up-regulated or down-regulated in tumor tissues compared to adjacent tissues. Our prognostic risk model based on DEirmRNA pairs could be used to predict the prognosis of LUAD patients and provide reference for better treatment.

Silencing long noncoding RNA LINC01133 suppresses pancreatic cancer through regulation of microRNA-1299-dependent IGF2BP3

The deregulation of long noncoding RNAs (lncRNAs) holds great potential in the treatment of multiple cancers, including pancreatic cancer (PC). However, the specific molecular mechanisms by which LINC01133 contributes to pancreatic cancer remain unknown. Subsequent to bioinformatics analysis, we predicted and analyzed differentially expressed lncRNAs, microRNAs, and genes in pancreatic cancer. We determined the expression patterns of LINC01133, miR-1299, and insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) in pancreatic cancer cells, and validated their interactions through luciferase reporter and RNA immunoprecipitation assays. We implemented loss-of-function and gain-of-function experiments for LINC01133, miR-1299, and IGF2BP3 to assay their potential effects on pancreatic cancer cell functions. We observed high expression of LINC01133 and IGF2BP3, but low expression of miR-1299, in pancreatic cancer cells. Furthermore, we found that LINC01133 enhances IGF2BP3 through binding with miR-1299. Silencing LINC01133 or IGF2BP3 and/or overexpressing miR-1299 limited pancreatic cancer cell proliferation, invasion, epithelial-mesenchymal transition, and suppressed tumorigenic abilities in mice lacking T cells (nude mice). Overall, our findings identified that silencing LINC01133 downregulates IGF2BP3 by upregulating miR-1299 expression, ultimately leading to the prevention of pancreatic cancer.

MicroRNA 211-5p inhibits cancer cell proliferation and migration in pancreatic cancer by targeting BMP2

MicroRNAs (miRNAs) are essential to the tumour growth and metastasis of several cancers. However, the implied functions of miR-211-5p in pancreatic cancer (PC) remains poorly known. In the present study, we discovered that miR-211-5p was a significantly downregulated miRNA in PC tissues compared to adjacent non-tumour tissues. Moreover, we revealed that miR-211-5p overexpression suppressed the proliferation and metastasis of PC cells. Mechanistically, miR-211-5p directly bond to 3'UTR of bone morphogenetic protein-2 (BMP2) and negatively regulated its expression. Rescue experiments showed that the biological function of miR-211-5p was reversed by BMP-2 overexpression in PC cells. Clinical data indicated that BMP2 expression was negatively correlated with miR-211-5p levels in PC patients. Our study provided evidence that miR-211-5p served as a significant suppressor in PC, provided potential targets for prognosis and treatment of patients with PC.

High CTCF expression mediated by FGD5-AS1/miR-19a-3p axis is associated with immunosuppression and pancreatic cancer progression

The most common reason for cancer-related death globally is predicted to be pancreatic cancer (PC), one of the deadliest cancers. The CCCTC-binding factor (CTCF) regulates the three-dimensional structure of chromatin, was reported to be highly regulated in various malignancies. However, the underlying biological functions and possible pathways via which CTCF promotes PC progression remain unclear. Herein, we examined the CTCF function in PC and discovered that CTCF expression in PC tissues was significantly raised compared to neighboring healthy tissues. Additionally, Kaplan-Meier survival analysis demonstrated a strong connection between elevated CTCF expression and poor patient prognosis. A study of the ROC curve (receiver operating characteristic) revealed an AUC value for CTCF of 0.968. Subsequent correlation analysis exhibited a strong relationship between immunosuppression and CTCF expression in PC. CTCF knockdown significantly inhibited the malignant biological process of PC in vitro and in vivo, suggesting that CTCF may be a potential PC treatment target. We also identified the FGD5 antisense RNA 1 (FGD5-AS1)/miR-19a-3p axis as a possible upstream mechanism for CTCF overexpression. In conclusion, our data suggest that ceRNA-mediated CTCF overexpression contributes to the suppression of anti-tumor immune responses in PC and could be a predictive biomarker and potential PC treatment target.

Tumor cell-derived exosomes mediating hsa_circ_0001739/lncRNA AC159540.1 facilitate liver metastasis in colorectal cancer

BACKGROUND

The current study probed into how tumor cell-derived exosomes (Exos) mediated hsa_circ_0001739/lncRNA AC159540.1 to manipulate microRNA (miR)-218-5p/FTO-N6-methyladenosine (m6A)/MYC signal axis in liver metastasis in colorectal cancer (CRC).

METHODS

hsa_circ_0001739 and lncRNA AC159540.1 were identified as the upstream regulator of miR-218-5p using ENCORI and LncBase databases. Expression patterns of miR-218-5p, hsa_circ_0001739, lncRNA AC159540.1, FTO, and MYC were detected, accompanied by loss-and-gain-of function assays to examine their effects on CRC cell biological functions. SW480 cells-derived Exos were purified, followed by in vitro studies to uncover the effect of hsa_circ_0001739/lncRNA AC159540.

RESULTS

miR-218-5p was downregulated while hsa_circ_0001739/lncRNA AC159540.1 was upregulated in CRC tissues and cells. Silencing of hsa_circ_0001739/lncRNA AC159540.1 restrained the malignant phenotypes of CRC cells. Exos-mediated hsa_circ_0001739/lncRNA AC159540.1 competitively inhibited miR-218-5p to elevate FTO and MYC. The inducing role of Exos-mediated hsa_circ_0001739/lncRNA AC159540.1 in CRC was also validated in vivo.

CONCLUSION

Conclusively, Exos-mediated circ_0001739/lncRNA AC159540.1 regulatory network is critical for CRC, offering a theoretical basis for CRC treatment.

Long non-coding RNAs and pancreatic cancer: A multifaceted view

Pancreatic cancer (PC) is a highly malignant disease with a 5-year survival rate of only 10%. Families with PC are at greater risk, as are type 2 diabetes, pancreatitis, and other factors. Insufficient early detection methods make this cancer have a poor prognosis. Additionally, the molecular mechanisms underlying PC development remain unclear. Increasing evidence suggests that long non-coding RNAs (lncRNAs) contribute to PC pathology,which may control gene expression by recruiting histone modification complexes to chromatin and interacting with proteins and RNAs. In recent studies, abnormal regulation of lncRNAs has been implicated in PC proliferation, metastasis, invasion, angiogenesis, apoptosis, and chemotherapy resistance suggesting potential clinical implications. The paper reviews the progress of lncRNA research in PC about diabetes mellitus, pancreatitis, cancer metastasis, tumor microenvironment regulation, and chemoresistance. Furthermore, lncRNAs may serve as potential therapeutic targets and biomarkers for PC diagnosis and prognosis. This will help improve PC patients' survival rate from a lncRNA perspective.

BHLHE40, a potential immune therapy target, regulated by FGD5-AS1/miR-15a-5p in pancreatic cancer

Pancreatic cancer, as one of the neoplasms with the highest degree of malignancy, has become a main disease of concerns in recent years. BHLHE40, a critical transcription factor for remodeling of the tumor immune microenvironment, has been described to be substantially increased in a variety of tumor-associated immune cells. Nevertheless, the pro-cancer biological functions and underlying molecular mechanisms of BHLHE40 for pancreatic cancer and its unique microenvironment are unclear. Hereby, we investigated the pro-oncogenic role of BHLHE40 in the pancreatic cancer microenvironment by bioinformatics analysis and cell biology experiments and determined that the expression of BHLHE40 was obviously elevated in pancreatic cancer tissues than in adjacent normal tissues. In parallel, Kaplan-Meier survival analysis unveiled that lower expression of BHLHE40 was strongly associated with better prognosis of patients. Receiver operating characteristic (ROC) curve analysis confirmed the accuracy of the BHLHE40-related prediction model. Subsequent, spearman correlation analysis observed that higher expression of BHLHE40 might be involved in immunosuppression of pancreatic cancer. Silencing of BHLHE40 could inhibit proliferation, invasion, and apoptosis of pancreatic cancer in vitro and in vivo, implying that BHLHE40 is expected to be a potential therapeutic target for pancreatic cancer. In addition, we explored and validated the FGD5-AS1/miR-15a-5p axis as a potential upstream regulatory mode for high expression of BHLHE40 in pancreatic cancer. In summary, our data showed that ceRNA involved in the regulation of BHLHE40 contributes to the promotion of immunosuppressive response in pancreatic and is expected to be a diagnostic marker and potential immunotherapeutic target for pancreatic cancer.

A biomarker and molecular mechanism investigation for thyroid cancer

Introduction

This study aimed to reveal the potential molecular mechanism associated with thyroid cancer (THCA) prognosis, and investigate promising biomarkers for THCA.

Material and methods

Differentially expressed genes (DEGs) were compared between THCA samples (THCA group) and normal samples (N group). Then, enrichment analysis and protein-protein interaction (PPI) network analysis were performed, followed by prognostic hub gene exploration from the PPI network. Furthermore, the prognostic and mutation analysis was performed on these hub genes. Finally, the associations of the hub gene with immune cells were investigated.

Results

A total of 802 DEGs were obtained between the THCA group and the N group. These DEGs were mainly enriched in pathways such as lysine degradation. From the PPI network, 20 hub genes, including CD44, CCND1, SNAI1, and KIT, were investigated. The survival analysis showed that the up-regulation of CD44 and down-regulation of SNAI1 contributed to the favorable and unfavorable outcomes of patients with THCA, respectively. Meanwhile, the diagnostic analysis showed that the AUC of KIT in THCA was larger than 0.9. Furthermore, the gene mutation analysis showed that the alternated CCND1 participated in the cell cycle pathway. Finally, the correlation analysis showed that prognostic genes such as CD44 were positively correlated with immune cells such as M1 macrophages.

Conclusions

A total of 20 hub genes including CCND1, CD44, SNAI1, and KIT were revealed as potential biomarkers for the differential diagnosis, prognosis, and development of drug targets of THCA. The lysine degradation pathway and cell cycle pathway might take part in the progression of THCA.

Identification of MIR600HG/hsa-miR-342-3p/ANLN network as a potential prognosis biomarker associated with lmmune infiltrates in pancreatic cancer

Pancreatic cancer is one of the tumors with the worst prognosis, causing serious harm to human health. The RNA network and immune response play an important role in tumor progression. While a systematic RNA network linked to the tumor immune response remains to be further explored in pancreatic cancer. Based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, the MIR600HG/hsa-miR-342-3p/ANLN network was determined. WB and IHC were used to confirm the high expression of ANLN in pancreatic cancer. The prognostic model based on the RNA network could effectively predict the survival prognosis of patients. The analysis of immune infiltration showed that the MIR600HG/hsa-miR-342-3p/ANLN network altered the level of infiltration of T helper 2 (Th2) and effector memory T (Tem) cells. Furthermore, we found that the chemokines chemokine ligand (CCL) 5 and CCL14 may play a key role in immune cell infiltration mediated by the RNA network. In conclusion, this study constructed a prognostic model based on the MIR600HG/hsa-miR-342-3p/ANLN network and found that it may function in tumor immunity.

Differential miRNA expression of hypoxic MCF7 and PANC-1 cells

Background

Hypoxia plays a critical role in the tumor microenvironment by affecting cellular proliferation, metabolism, apoptosis, DNA repair, and chemoresistance. Since hypoxia provokes a distinct shift of microRNA, it is important to illustrate the relative contribution of each hypoxamiR to cancer progression.

Aims

The present study aims to shed light on the hypoxamiRs that are involved in pancreatic and breast cancer progression to highlight novel targets for the development of new therapies.

Methods

For 20 cycles, MCF7 breast cancer cells and PANC-1 pancreatic cancer cells were subjected to chronic cyclic hypoxia, which consisted of 72 hours of hypoxia followed by 24 hours of reoxygenation. After 10 and 20 cycles of hypoxia, miRNA expression alterations were profiled using RT-PCR array and further analyzed using a visual analytics platform. The MTT cell proliferation assay was used to determine hypoxic cells' chemoresistance to doxorubicin.

Results

Under chronic cyclic hypoxia, hypoxic PANC-1 cells have a comparable doubling time with their normoxic counterparts, whereas hypoxic MCF7 cells show a massive increase in doubling time when compared to their normoxic counterparts. Both hypoxic cell lines developed EMT-like phenotypes as well as doxorubicin resistance. According to the findings of miRNet, 6 and 10 miRNAs were shown to play an important role in enriching six hallmarks of pancreatic cancer in the 10th and 20th cycles of hypoxia, respectively, while 7 and 11 miRNAs were shown to play an important role in enriching the four hallmarks of breast cancer in the 10th and 20th cycles of hypoxia, respectively.

Conclusions

miR-221, miR-21, miR-155, and miR-34 were found to be involved in the potentiation of hypoxic PANC-1 hallmarks at both the 10th and 20th cycles, while miR-93, miR-20a, miR-15, and miR-17 were found to be involved in the potentiation of hypoxic MCF7 hallmarks at both the 10th and 20th cycles. This variation in miRNA expression was also connected to the emergence of an EMT-like phenotype, alterations in proliferation rates, and doxorubicin resistance. The chemosensitivity results revealed that chronic cyclic hypoxia is critical in the formation of chemoresistant phenotypes in pancreatic and breast cancer cells. miR-181a and let-7e expression disparities in PANC1, as well as miR-93, miR-34, and miR-27 expression disparities in MCF7, may be associated with the formation of chemoresistant MCF7 and PANC-1 cells following 20 cycles of chronic cyclic hypoxia. Indeed, further research is needed since the particular mechanisms that govern these processes are unknown.

Bifidobacterium infantis-Mediated Herpes Simplex Virus-TK/Ganciclovir Treatment Inhibits Cancer Metastasis in Mouse Model

Previous studies have found that Bifidobacterium infantis-mediated herpes simplex virus-TK/ganciclovir (BF-TK/GCV) reduces the expression of VEGF and CD146, implying tumor metastasis inhibition. However, the mechanism by which BF-TK/GCV inhibits tumor metastasis is not fully studied. Here, we comprehensively identified and quantified protein expression profiling for the first time in gastric cancer (GC) cells MKN-45 upon BF-TK/GCV treatment using quantitative proteomics. A total of 159 and 72 differential expression proteins (DEPs) were significantly changed in the BF-TK/GCV/BF-TK and BF-TK/GCV/BF/GCV comparative analysis. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis enriched some metastasis-related pathways such as gap junction and cell adhesion molecules pathways. Moreover, the transwell assay proved that BF-TK/GCV inhibited the invasion and migration of tumor cells. Furthermore, immunohistochemistry (IHC) demonstrated that BF-TK/GCV reduced the expression of HIF-1α, mTOR, NF-κB1-p105, VCAM1, MMP13, CXCL12, ATG16, and CEBPB, which were associated with tumor metastasis. In summary, BF-TK/GCV inhibited tumor metastasis, which deepened and expanded the understanding of the antitumor mechanism of BF-TK/GCV.

Construction of a novel nomogram based on competing endogenous RNAs and tumor-infiltrating immune cells for prognosis prediction in elderly patients with colorectal cancer

Competitive endogenous RNAs (ceRNAs) and tumor-infiltrating immune cells play essential roles in colorectal cancer (CRC) tumorigenesis. However, their prognostic role in elderly patients with CRC is unclear. Gene expression profiles and clinical information for elderly patients with CRC were downloaded from The Cancer Genome Atlas. Univariate, LASSO, and multivariate Cox regression analyses were utilized for screening key ceRNAs and prevent overfitting. A total of 265 elderly patients with CRC were included. We constructed a novel ceRNA network consisting of 17 lncRNAs, 35 miRNAs, and 5 mRNAs. We established three prognosis predictive nomograms based on four key ceRNAs (ceRNA nomogram), five key immune cells (immune cell nomogram), and their combination (ceRNA-immune cell nomogram). Among them, the ceRNA-immune cell nomogram had the best accuracy. Furthermore, the areas under the curve of the ceRNA-immune cell nomogram were also significantly greater than the TNM stage at 1 (0.818 vs. 0.693), 3 (0.865 vs. 0.674), and 5 (0.832 vs. 0.627) years. Co-expression analysis revealed that CBX6 was positively correlated with activated dendritic cells (R = 0.45, p < 0.01), whereas negatively correlated with activated mast cells (R =- 0.43, p < 0.01). In conclusion, our study constructed three nomograms to predict prognosis in elderly patients with CRC, among which the ceRNA-immune cell nomogram had the best prediction accuracy. We inferred that the mechanism underlying the regulation of activated dendritic cells and mast cells by CBX6 might play a crucial role in tumor development and prognosis of elderly patients with CRC.

LncRNA LZTS1-AS1 induces proliferation, metastasis and inhibits autophagy of pancreatic cancer cells through the miR-532 /TWIST1 signaling pathway

The 5 year survival rate after diagnosis of pancreatic cancer (PANC) is less than 5%, and it is one of the malignant tumors with the worst prognosis. Identification of novel oncogenes involved in the occurrence of pancreatic cancer is of great significance to improve the overall survival of PANC patients. Our previous study found that miR-532 is a key factor in PANC occurrence and development, and this study further explored its mechanism. We found that the expression of lncRNA LZTS1-AS1 was elevated in PANC tumor tissues and cells, and correlated with poor prognosis. In vitro experiments confirmed that LZTS1-AS1 could promote proliferation, oncogenicity, migration, and invasion of PANC cells, and inhibit apoptosis and autophagy. However, miR-532 had the completely opposite effect, and inhibition of miR-532 counteracted the effect of LZTS1-AS1 on PANC cells. Dual luciferase gene reporter assay and RNA immunoprecipitation assay confirmed the targeting relationship between LZTS1-AS1 and miR-532, and their expression levels were negatively correlated in PANC tissues. Overexpression of TWIST1 could counteract the effect of miR-532 in PANC cells, and the expression levels of both were negatively changed in PANC tissues and cells. Our results suggest that lncRNA LZTS1-AS1 acts as an oncogene to promote the metastasis of PANC and inhibit autophagy, and its mechanism may be to regulate TWIST1 through sponge miR-532. This study provides novel biomarkers and therapeutic targets for PANC.

Sparse Independence Component Analysis for Competitive Endogenous RNA Co-Module Identification in Liver Hepatocellular Carcinoma

OBJECTIVE

Long non-coding RNAs (lncRNAs) have been shown to be associated with the pathogenesis of different kinds of diseases and play important roles in various biological processes. Although numerous lncRNAs have been found, the functions of most lncRNAs and physiological/pathological significance are still in its infancy. Meanwhile, their expression patterns and regulation mechanisms are also far from being fully understood.

METHODS

In order to reveal functional lncRNAs and identify the key lncRNAs, we develop a new sparse independence component analysis (ICA) method to identify lncRNA-mRNA-miRNA expression co-modules based on the competitive endogenous RNA (ceRNA) theory using the sample-matched lncRNA, mRNA and miRNA expression profiles. The expression data of the three RNA combined together is approximated sparsely to obtain the corresponding sparsity coefficient, and then it is decomposed by using ICA constraint optimization to obtain the common basis and modules. Subsequently, affine propagation clustering is used to perform cluster analysis on the common basis under multiple running conditions to obtain the co-modules for the selection of different RNA elements.

RESULTS

We applied sparse ICA to Liver Hepatocellular Carcinoma (LIHC) dataset and the experiment results demonstrate that the proposed sparse ICA method can effectively discover biologically functional expression common modules.

CONCLUSION

It may provide insights into the function of lncRNAs and molecular mechanism of LIHC. Clinical and Translational Impact Statement-The results on LIHC dataset demonstrate that the proposed sparse ICA method can effectively discover biologically functional expression common modules, which may provide insights into the function of IncRNAs and molecular mechanism of LIHC.

The miR-183 Cluster: Biogenesis, Functions, and Cell Communication via Exosomes in Cancer

Cancer is one of the leading causes of human death. MicroRNAs have been found to be closely associated with cancer. The miR-183 cluster, comprising miR-183, miR-96, and miR-182, is transcribed as a polycistronic miRNA cluster. Importantly, in most cases, these clusters promote cancer development through different pathways. Exosomes, as extracellular vesicles, play an important role in cellular communication and the regulation of the tissue microenvironment. Interestingly, the miR-183 cluster can be detected in exosomes and plays a functional regulatory role in tumor development. Here, the biogenesis and functions of the miR-183 cluster in highly prevalent cancers and their relationship with other non-coding RNAs are summarized. In addition, the miR-183 cluster in exosomes has also been discussed. Finally, we discuss the miR-183 cluster as a promising target for cancer therapy. This review is expected to provide a new direction for cancer treatment.

Systematic analysis of circRNA-related ceRNA networks of black rockfish (Sebastes schlegelii) in response to Aeromonas salmonicides infection

Aeromonas salmonicides is a type of Gram-negative bacteria and has become the main fish pathogen in aquaculture because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. In the past years, studies have been focused to explore the regulatory roles of circRNA-miRNA-mRNA network in fish diseases. However, there are only few systematic studies linked to the anti-bacterial roles of circRNA-related ceRNA networks in the spleen immune system of black rockfish (Sebastes schlegelii). In this study, the whole-transcriptome sequencing (RNA-seq) was conducted in the black rockfish spleen with A. salmonicida challenging. The differentially expressed (DE) circRNAs were identified comprehensively for the following enrichment analysis. Interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted for the construction of circRNA-related ceRNA regulatory networks. Then, protein-protein interaction (PPI) analysis of mRNAs from these ceRNA networks were conducted. Finally, a total number of 39 circRNAs exhibited significantly differential expressions during A. salmonicida infection in the black rockfish spleen in 4338 identified circRNAs from 12 samples in 4 libraries. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Endocytosis, FoxO signaling pathway, Jak-STST signaling pathway, Herpes simplex infection, etc. Subsequently, 290 circRNA-miRNA-mRNA pathways (91 at 2 h, 142 at 12 h and 65 at 24 h) were constructed including 31 circRNAs, 50 miRNAs, and 156 mRNAs. In conclusion, the circRNA-related ceRNA networks were established, which will provide some novel insights in molecular mechanistic investigations of anti-bacterial immune response in teleost. Also, these findings will propose significant predictive values for the development of methods of treatment and prevention in black rockfish after bacterial infection in the future.

LncRNA HOXD-AS2 regulates miR-3681-5p/DCP1A axis to promote the progression of non-small cell lung cancer

Background

Non-small cell lung cancer (NSCLC) is the most common malignancy in lung cancer, with a low survival rate and unfavorable prognosis. Dysregulated long non-coding RNAs (lncRNAs) play vital functions in tumor progression. This study intended to probe the expression pattern and function of HOXD-AS2 in NSCLC.

Methods

Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze the expression of HOXD-AS2, miR-3681-5p, CCR1, mRNA-decapping enzyme 1A (DCP1A), and PPP3R1. Cell viability, migration, and invasion were separately examined via 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) and transwell experiments. Luciferase reporter assay was conducted to evaluate the binding of miR-3681-5p with HOXD-AS2 or DCP1A. Protein expression of DCP1A was assessed via Western blot. NSCLC animal models were constructed through injection of H1975 cells transfected with lentivirus (LV)-sh-HOXD-AS2 into nude mice, followed by hematoxylin and eosin (HE) staining and immunohistochemistry (IHC) analysis.

Results

In this study, HOXD-AS2 was upregulated in NSCLC tissues and cells, and high HOXD-AS2 predicted short overall survival (OS). Downregulation of HOXD-AS2 could impair the proliferation, migration, and invasion abilities of H1975 and A549 cells. MiR-3681-5p was shown to bind with HOXD-AS2 and be lowly expressed in NSCLC. Suppression of miR-3681-5p could abolish the inhibitory effect of HOXD-AS2 silencing on proliferation, migration, and invasion. DCP1A was screened as the target of miR-3681-5p and its overexpression could rescue miR-3681-5p upregulation-repressed proliferation, migration, and invasion activities. Moreover, animal experiments affirmed that HOXD-AS2 promoted tumor growth in vivo.

Conclusions

HOXD-AS2 modulates the miR-3681-5p/DCP1A axis to boost the progression of NSCLC, which founds the basis of HOXD-AS2 as a new diagnostic biomarker and molecular target for NSCLC therapy.

Long Noncoding RNA LINC01503 Silencing Suppresses KLK4 Expression to Impede Pancreatic Cancer Development as miR-1321 Sponge

Background

Long intergenic nonprotein coding RNA 1503 (LINC01503) was reportedly oncogenic in several malignancies, whereas whether it contributed to pancreatic cancer tumorigenesis and progression requires to be verified.

Methods

The expression pattern of LINC01503 was monitored via qRT-PCR assay in normal cells and cancerous pancreatic cancer cells. The introduction of silencing LINC01503 was to verify the relation between LINC01503 expression and cell growth. Then, the targeting relationship of LINC01503 to miR-1321 was confirmed by bioinformatics predication and luciferase reporter assay. In addition, luciferase reporter assays evaluated the binding of miR-1321 to the 3'-untranslated region of KLK4. Overexpressing KLK4 and inhibiting LINC01503 was introduced in tumor cells to investigate the corresponding impacts on pancreatic cancer cell proliferation and migration.

Results

LINC01503 and KLK4 were highly abundant in pancreatic cancer cells. Mechanistically, miR-1321 bound to LINC01503 and KLK4. Downregulating LINC01503 promoted the availability of miR-1321 in pancreatic cancer cells and thus repressed KLK4 expression. KLK4 overexpression abolished the impediment of LINC01503 depletion on cell proliferation and migration.

Conclusion

Oncogenic function of LINC01503 was dependent on KLK4 upregulation by sponging miR-1321. Revealing the tumor-promoting property of LINC01503 in pancreatic cancer may confer new biomarkers for this malignancy.

lncRNA GAS5 suppression of the malignant phenotype of ovarian cancer via the miR-23a-WT1 axis

Background

Growth arrest-specific 5 (GAS5) is a long noncoding RNA (lncRNA) that regulates cell viability. GAS5 lncRNA has been shown to decrease colorectal and breast cancer carcinogenesis. Although the function and mechanisms related to lncRNA GAS5 in the development of ovarian cancer (OC) remains unclear. The goal of this study was to clarify the essential functions of lncRNA GAS5 in regulating OC progression and its underlying mechanism.

Methods

Relative levels of lncRNA GAS5 in OC and normal ovarian tissues were identified by quantitative real-time polymerase chain reaction (qRT-PCR). The regulatory effects of lncRNA GAS5 on the proliferation and apoptosis of SK-OV-3 cells were evaluated. Moreover, bioinformatics tools were used to predict a novel target [microRNA (miRNA)] of lncRNA GAS5. To explore the key functions of the lncRNA GAS5/miRNA-23a/WT1 regulatory loop in mediating OC progression, we performed functional experiments and a dual-luciferase reporter (DLR) gene assessment.

Results

Downregulation of lncRNA GAS5 was found in tissues of OC, which was positively correlated with a poor prognosis. In addition, SK-OV-3 cells with a lower expression of lncRNA GAS5 and accelerated cancer cell migration demonstrated a lower percentage of apoptosis in in vitro experiments. It was demonstrated that lncRNA GAS5 acts as a molecular sponge for miR-23a in OC cells. Additionally, WT1 was detected as a miR-23a target gene in OC cells, and through sponging miR-23a, lncRNA GAS5 positively regulated WT1 expression. Rescue tests demonstrated that enhancing the outputs of the miR-23a-WT1 axis reversed the impacts of lncRNA GAS5 silencing on cell proliferation and apoptosis in OC.

Conclusions

The lncRNA GAS5/miR-23a/WT1 cascade was found participate in the progression of OC. lncRNA GAS5 also decreases OC progression by upregulating WT1 and attenuating miR-23a, suggesting that it could be an advantageous therapeutic target for OC intervention.

[Identification of key molecules in miRNA-mRNA regulatory network associated with high-grade serous ovarian cancer recurrence using bioinformatic analysis]

OBJECTIVE

To investigate the correlation of the potential functional microRNA (miRNA)-mRNA regulatory network with recurrence of high-grade serous ovarian carcinoma (HGSOC) and its biological significance.

METHODS

This study was performed based on the data of 354 patients with HGSOC from the Cancer Genome Atlas database. In these patients, HGSOC was divided into different subtypes based on the pathways identified by GO analysis, and the correlations of the subtypes with HGSOC recurrence and differentially expressed miRNAs and mRNAs were assessed. Two relapse-related datasets were identified using the Gene Set Enrichment (GSE) database, from which the differentially expressed miRNAs were identified by intersection with the TCGA data. The target genes of these miRNAs were predicted using miRWalk 2.0 database, and these common differentially expressed miRNAs and mRNAs were used to construct the key miRNA-mRNA network associated with HGSOC recurrence. The expression of miR-506-3p and SNAI2 in two ovarian cancer cell lines was detected using RT-qPCR and Western blotting, and their targeted binding was verified using a double luciferase assay. The effect of miR-506-3p expression modulation on ovarian cancer cell migration was detected using scratch assay and Transwell assay.

RESULTS

We screened 303 GO terms of HGSOC-related pathways and identified two HGSOC subtypes (C1 and C2). The subtype C1 was associated with a significantly higher recurrence rate than C2. The differentially expressed genes between C1 and C2 subtypes were mainly enriched in epithelial-mesenchymal transition (EMT). Five miRNAs were identified as potential regulators of EMT, and a total of 41 target genes were found to be involved in the differential expressions of EMT pathway between C1 and C2 subtypes. The key miRNA-mRNA network associated with HGSOC recurrence was constructed based on these 5 miRNAs and 41 mRNAs. MiR-506-3p was confirmed to bind to SNAI2, and up-regulation of miR-506-3p significantly inhibited SNAI2 expression and reduced migration and invasion of SKOV3 and CAOV3 cells (P < 0.05), while miR-506-3p knockdown produced the opposite effects (P < 0.05).

CONCLUSION

MiR-506-3p and SNAI2 are the key molecules associated with HGSOC recurrence. MiR-506-3p may affect EMT of ovarian cancer cells by regulating cell migration and invasion via SNAI2, and its expression level has predictive value for HGSOC recurrence.

Baicalin Blocks Colon Cancer Cell Cycle and Inhibits Cell Proliferation through miR-139-3p Upregulation by Targeting CDK16

Baicalin was reported to facilitate the apoptosis of colon cells and inhibit tumor growth in vivo. This study aimed to explore the specific mechanism and function of baicalin on colon cells. Relative mRNA levels were tested via qPCR. Cell proliferation, viability, and cell cycle phases were evaluated using MTT, colony formation, and flow cytometry assays, respectively. The interaction between miR-139-3p and cyclin-dependent kinase 16 (CDK16) was measured via a dual-luciferase reporter assay. Immunohistochemistry was used to count the positivity cells in tumor tissues collected from treated xenografted tumor mice. The results showed that baicalin increased miR-139-3p expression while also decreasing CDK16 levels, blocking the cell cycle, and inhibiting cell proliferation in colon cancer cells. miR-139-3p silencing or CDK16 overexpression abolished the inhibitory effects of baicalin on colon cancer proliferation. miR-139-3p directly targeted and interacted with CDK16 at the cellular level. The protective functions of miR-139-3p knockdown on tumor cells were abrogated by silencing CDK16. The combination of baicalin treatment and CDK16 knockdown further inhibited tumor growth of xenografted tumor mice compared with the groups injected with only sh-CDK16 or baicalin in vivo. In conclusion, baicalin inhibited colon cancer growth by modulating the miR-139-3p/CDK16 axis.

Discovery of metabolic markers for the discrimination of Helwingia species based on bioactivity evaluation, plant metabolomics, and network pharmacology

RATIONALE

Helwingia japonica (HJ), a traditional medicinal plant, is commonly used for the treatment of dysentery, blood in the stool, and scald burns. Three major HJ species, Helwingia japonica (Thunb.) Dietr. (QJY), Helwingia himalaica Hook. f. et Thoms. ex C. B. Clarke, and Helwingia chinensis Batal., share great similarities in both morphology and chemical constituents. The discrimination of medicinal plants directly affects their pharmacological and clinical effects. Here, we solved the taxonomy uncertainty of these three HJ species and explored the discrimination and study of other traditional medicines (TMs).

METHODS

First, the anti-inflammatory effects of the three HJ species were compared using lipopolysaccharide (LPS)-induced inflammatory responses in mouse leukemia cells of monocyte macrophage (RAW) 264.7 cells. Then, plant metabolomics were performed in 48 batches of samples to discover chemical markers for discriminating different HJ species. Finally, network pharmacology was applied to explore the linkages among constituents, targets, and signaling pathways.

RESULTS

In vitro experiments showed that the QJY exhibited the most potential anti-inflammatory activities. Meanwhile, 172 compounds were tentatively identified and eight metabolites with higher relative content in QJY were designated as chemical markers to distinguish QJY and the other two species. According to the property of absorbed in vivo, threonic acid, arginine, and tyrosine were selected to construct a component-target-pathway network. The network pharmacology analysis confirmed that the chemotaxonomy differentiation was consistent with the bioactive assessment.

CONCLUSIONS

The present study demonstrates that bioactivity evaluation integrated with plant metabolomics and network pharmacology could be used as an effective approach to discriminate different TMs and discover the active compounds.

Developing and validating a survival prediction model based on blood exosomal ceRNA network in patients with PAAD

BACKGROUND

Among the most lethal cancers, pancreatic adenocarcinoma (PAAD) is an essential component of digestive system malignancies that still lacks effective diagnosis and treatment methods. As exosomes and competing endogenous RNA (ceRNA) regulatory networks in tumors go deeper, we expect to construct a ceRNA regulatory network derived from blood exosomes of PAAD patients by bioinformatics methods and develop a survival prediction model based on it.

METHODS

Blood exosome sequencing data of PAAD patients and normal controls were downloaded from the exoRbase database, and the expression profiles of exosomal mRNA, lncRNA, and circRNA were differentially analyzed by R. The related mRNA, circRNA, lncRNA, and their corresponding miRNA prediction data were imported into Cytoscape software to visualize the ceRNA network. Then, we conducted GO and KEGG enrichment analysis of mRNA in the ceRNA network. Genes that express differently in pancreatic cancer tissues compared with normal tissues and associate with survival (P < 0.05) were determined as Hub genes by GEPIA. We identified optimal prognosis-related differentially expressed mRNAs (DEmRNAs) and generated a risk score model by performing univariate and multivariate Cox regression analyses.

RESULTS

205 DEmRNAs, 118 differentially expressed lncRNAs (DElncRNAs), and 98 differentially expressed circRNAs (DEcircRNAs) were screened out. We constructed the ceRNA network, and a total of 26 mRNA nodes, 7 lncRNA nodes, 6 circRNA nodes, and 16 miRNA nodes were identified. KEGG enrichment analysis showed that the DEmRNAs in the regulatory network were mainly enriched in Human papillomavirus infection, PI3K-Akt signaling pathway, Osteoclast differentiation, and ECM-receptor interaction. Next, six hub genes (S100A14, KRT8, KRT19, MAL2, MYO5B, PSCA) were determined through GEPIA. They all showed significantly increased expression in cancer tissues compared with control groups, and their high expression pointed to adverse survival. Two optimal prognostic-related DEmRNAs, MYO5B (HR = 1.41, P < 0.05) and PSCA (HR = 1.10, P < 0.05) were included to construct the survival prediction model.

CONCLUSION

In this study, we successfully constructed a ceRNA regulatory network in blood exosomes from PAAD patients and developed a two-gene survival prediction model that provided new targets which shall aid in diagnosing and treating PAAD.

lncRNA ACTA2-AS1 predicts malignancy and poor prognosis of triple-negative breast cancer and regulates tumor progression via modulating miR-532-5p

Background

Dysregulation of ACTA2-AS1 and miR-532-5p and their functions in various cancers have been widely reported. Their potential of serving as biomarkers in triple-negative breast cancer (TNBC) remains unknown. This study aimed to evaluate the function of ACTA2-AS1 and miR-532-5p and their potential of serving as biomarkers in TNBC.

Results

The TNBC tissues were collected from 119 patients, where the reduced level of ACTA2-AS1 and increased level of miR-532-5p were observed by PCR and showed a significantly negative correlation (P <  0.001). Both ACTA2-AS1 and miR-532-5p were closely associated with the malignant development and poor prognosis of TNBC patients. Moreover, in TNBC cell, overexpressing ACTA2-AS1 was found to suppress cell proliferation and metastasis, which was reversed by the upregulation of miR-532-5p.

Conclusions

ACTA2-AS1 and miR-532-5p could act as biomarkers of TNBC predicting the progression and prognosis of patients. ACTA2-AS1 served as a tumor suppressor of TNBC which was mediated by miR-532-5p.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12860-022-00432-7.

Comprehensive analysis to identify pseudogenes/lncRNAs-hsa-miR-200b-3p-COL5A2 network as a prognostic biomarker in gastric cancer

OBJECTIVE

Gastric cancer is one of the most common and deadly types of cancer. The molecular mechanism of gastric cancer progression remains unclear.

MATERIALS AND METHODS

Four hub genes were identified through GEO and TCGA database screening and analysis. Prognostic analysis revealed that COL5A2 was the most likely to affect the prognosis of gastric cancer among the four hub genes. The relationships between COL5A2 and clinical variables and immune cell infiltration were analyzed. Then, COL5A2 was analyzed for single-gene differences and related functional enrichment. Using the starBase database for prediction and analysis, miRNAs and pseudogenes/lncRNAs that might combine with COL5A2 were identified; thus, the ceRNA network was constructed. Finally, the network was verified by Cox analysis and qPCR, and a nomogram was constructed.

RESULTS

First, we found that COL5A2, COL12A1, BGN and THBS2 were highly expressed in gastric cancer. COL5A2 had statistical significance in overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) analysis. Immune infiltration analysis suggested that COL5A2 might influence the changes in the tumor immune microenvironment. The StarBase database was used to predict that 3 pseudogenes and 7 lncRNAs might inhibit the hsa-miR-200b-3p-COL5A2 axis in gastric cancer. The pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 ceRNA network was identified and verified using Cox regression analysis and PCR. Finally, we constructed a nomogram.

CONCLUSIONS

We elucidated the regulatory role of the pseudogenes/lncRNA-hsa-miR-200b-3p-COL5A2 network in gastric cancer progression and constructed a nomogram. These studies may provide effective treatments and potential prognostic biomarkers for gastric cancer.

Transcriptome Sequencing Reveals Tgf-β-Mediated Noncoding RNA Regulatory Mechanisms Involved in DNA Damage in the 661W Photoreceptor Cell Line

Transforming growth factor β (Tgf-β), a pleiotropic cytokine, can enhance DNA repair in various cells, including cancer cells and neurons. The noncoding regulatory system plays an important role in Tgf-β-mediated biological activities, whereas few studies have explored its role in DNA damage and repair. In this study, we suggested that Tgf-β improved while its inhibitor LSKL impaired DNA repair and cell viability in UV-irradiated 661W cells. Moreover, RNA-seq was carried out, and a total of 106 differentially expressed (DE)-mRNAs and 7 DE-lncRNAs were identified between UV/LSKL and UV/ctrl 661W cells. Gene ontology and Reactome analysis confirmed that the DE-mRNAs were enriched in multiple DNA damaged- and repair-related biological functions and pathways. We then constructed a ceRNA network that included 3 lncRNAs, 19 miRNAs, and 29 mRNAs with a bioinformatics prediction. Through RT-qPCR and further functional verification, 2 Tgf-β-mediated ceRNA axes (Gm20559-miR-361-5p-Oas2/Gbp7) were further identified. Gm20559 knockout or miR-361-5p mimics markedly impaired DNA repair and cell viability in UV-irradiated 661W cells, which confirms the bioinformatics results. In summary, this study revealed that Tgf-β could reduce DNA damage in 661W cells, provided a Tgf-β-associated ceRNA network for DNA damage and repair, and suggested that the molecular signatures may be useful candidates as targets of treatment for photoreceptor pathology.

Roles of H19/miR-29a-3p/COL1A1 axis in COE-induced lung cancer

Occupational lung cancer caused by coke oven emissions (COE) has attracted increasing attention, but the mechanism is not clear. Many evidences show ceRNA (competing endogenous RNA) networks play important regulatory roles in cancers. In this study, we aimed to construct and verify the ceRNA regulatory network in the occurrence of COE-induced lung squamous cell carcinoma (LUSC). We performed RNA sequencing with lung bronchial epithelial cell (16HBE) and COE induced malignant transformed cell (Rf). Furthermore, we analyzed RNA sequencing data of LUSC and adjacent tissues in the cancer genome atlas (TCGA) database. Combined our data and TCGA data to determine the differentially expressed lncRNAs, miRNAs, mRNAs. lncBASE, miRDB and miRTarBase were used to predict the binding relationship between lncRNA and miRNA, miRNA and mRNA. Based on these, we construct the ceRNA network. FREMSA, dual-luciferase reporter assay, quantitative real-time PCR (qRT-PCR), western-blot were used to verify the regulatory axis. CCK8 assay, phalloidin staining, p53 detection were used to explore the roles of this axis in the COE induced malignant transformation. Results showed 7 lncRNAs, 7 miRNAs and 146 mRNAs were identified. Among these, we constructed a ceRNA network including 1 lncRNA, 2 miRNAs and 9 mRNAs. Further verification confirmed the trend of lncRNA H19, miR-29a-3p and COL1A1 were consistent with sequencing results. H19 and COL1A1 were significantly higher in Rf than in 16HBE and miR-29a-3p was reverse. Regulatory investigation revealed H19 increased COL1A1 expression by sponging miR-29a-3p. Knockdown of H19, COL1A1 or overexpression of miR-29a-3p in Rf cells could inhibit cell proliferation, increased cell adhesion and p53 level. However, knockdown of H19 while suppressing the miR-29a-3p partially rescue the malignant phenotype of Rf caused by H19. In conclusion, all these indicated H19 functioned as a ceRNA to increase COL1A1 by sponging miR-29a-3p and promoted COE-induced cell malignant transformation.

A multi-omics machine learning framework in predicting the recurrence and metastasis of patients with pancreatic adenocarcinoma

Local recurrence and distant metastasis are the main causes of death in patients with pancreatic adenocarcinoma (PDAC). Microbial content in PDAC metastasis is still not well-characterized. Here, the tissue microbiome was comprehensively compared between metastatic and non-metastatic PDAC patients. We found that the pancreatic tissue microbiome of metastatic patients was significantly different from that of non-metastatic patients. Further, 10 potential bacterial biomarkers (Kurthia, Gulbenkiania, Acetobacterium and Planctomyces etc.) were identified by differential analysis. Meanwhile, significant differences in expression patterns across multiple omics (lncRNA, miRNA, and mRNA) of PDAC patients were found. The highest accuracy was achieved when these 10 bacterial biomarkers were used as features to predict recurrence or metastasis in PDAC patients, with an AUC of 0.815. Finally, the recurrence and metastasis in PDAC patients were associated with reduced survival and this association was potentially driven by the 10 biomarkers we identified. Our studies highlight the association between the tissue microbiome and recurrence or metastasis of pancreatic adenocarcioma patients, as well as the survival of patients.

Prognostic model and immunotherapy prediction based on molecular chaperone-related lncRNAs in lung adenocarcinoma

Introduction: Molecular chaperones and long non-coding RNAs (lncRNAs) have been confirmed to be closely related to the occurrence and development of tumors, especially lung cancer. Our study aimed to construct a kind of molecular chaperone-related long non-coding RNAs (MCRLncs) marker to accurately predict the prognosis of lung adenocarcinoma (LUAD) patients and find new immunotherapy targets.

Methods: In this study, we acquired molecular chaperone genes from two databases, Genecards and molecular signatures database (MsigDB). And then, we downloaded transcriptome data, clinical data, and mutation information of LUAD patients through the Cancer Genome Atlas (TCGA). MCRLncs were determined by Spearman correlation analysis. We used univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis to construct risk models. Kaplan-meier (KM) analysis was used to understand the difference in survival between high and low-risk groups. Nomogram, calibration curve, concordance index (C-index) curve, and receiver operating characteristic (ROC) curve were used to evaluate the accuracy of the risk model prediction. In addition, we used gene ontology (GO) enrichment analysis and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses to explore the potential biological functions of MCRLncs. Immune microenvironmental landscapes were constructed by using single-sample gene set enrichment analysis (ssGSEA), tumor immune dysfunction and exclusion (TIDE) algorithm, “pRRophetic” R package, and “IMvigor210” dataset. The stem cell index based on mRNAsi expression was used to further evaluate the patient’s prognosis.

Results: Sixteen MCRLncs were identified as independent prognostic indicators in patients with LUAD. Patients in the high-risk group had significantly worse overall survival (OS). ROC curve suggested that the prognostic features of MCRLncs had a good predictive ability for OS. Immune system activation was more pronounced in the high-risk group. Prognostic features of the high-risk group were strongly associated with exclusion and cancer-associated fibroblasts (CAF). According to this prognostic model, a total of 15 potential chemotherapeutic agents were screened for the treatment of LUAD. Immunotherapy analysis showed that the selected chemotherapeutic drugs had potential application value. Stem cell index mRNAsi correlates with prognosis in patients with LUAD.

Conclusion: Our study established a kind of novel MCRLncs marker that can effectively predict OS in LUAD patients and provided a new model for the application of immunotherapy in clinical practice.

MicroRNA-125a-3p, -4530, and -92a as a Potential Circulating MicroRNA Panel for Noninvasive Pancreatic Cancer Diagnosis

MicroRNA (miRNA) expression dysregulations in pancreatic ductal adenocarcinoma (PDAC) have been studied widely for their diagnostic and prognostic utility. By the use of bioinformatics-based methods, in our previous study, we identified some potential miRNA panels for diagnosis of pancreatic cancer patients from noncancerous controls (the screening stage). In this report, we used 142 plasma samples from people with and without pancreatic cancer (PC) to conduct RT-qPCR differential expression analysis to assess the strength of the first previously proposed diagnostic panel (consisting of miR-125a-3p, miR-4530, and miR-92a-2-5p). As the result, we identified significant upregulation for all the three considered miRNAs in the serum of PC patients. After that, a three-miRNA panel in serum was developed. The area under the receiver operating characteristic curves (AUC) for the panel were 0.850, 0.910, and 0.86, respectively, indicating that it had a higher diagnostic value than individual miRNAs. Therefore, we detected a promising three-miRNA panel in the plasma for noninvasive PC diagnosis (miR-125a-3p, miR-4530, and miR-92a-2-5p).

DPP10-AS1-Mediated Downregulation of MicroRNA-324-3p Is Conducive to the Malignancy of Pancreatic Cancer by Enhancing CLDN3 Expression

OBJECTIVES

Network of long noncoding RNA-microRNA (miRNA)-mRNA is becoming increasingly pivotal roles in carcinogenesis mechanism. Herein, we aim to delineate the mechanistic understanding of dipeptidyl peptidase like 10-antisense RNA 1 (DPP10-AS1)/miRNA-324-3p/claudin 3 (CLDN3) axis in the malignancy of pancreatic cancer (PC).

METHODS

Microarray profiling and other bioinformatics methods were adopted to predict differentially expressed long noncoding RNA-miRNA-mRNA in PC, followed by verification of expression of DPP10-AS1, microRNA-324-3p (miR-324-3p), and CLDN3 in PC cells. The relationship among DPP10-AS1, miR-324-3p, and CLDN3 were further assessed. The PC cell invasion and migration were evaluated by scratch test and transwell assay. Tumor formation and lymph node metastasis were assessed in nude mice.

RESULTS

Highly expressed DPP10-AS1 and CLDN3 and poorly expressed miR-324-3p were identified in PC cells. The competitively binding between DPP10-AS1 and miR-324-3p was identified, and CLDN3 was targeted and downregulated by miR-324-3p. In addition, DPP10-AS1 was found to sequester miR-324-3p to release CLDN3 expression. DPP10-AS1 knockdown or miR-324-3p restoration diminished migration, invasion, tumor formation, microvessel density, and lymph node metastasis of PC cells, which was associated with CLDN3 downregulation.

CONCLUSIONS

Taken together, the study identified the regulatory role of DPP10-AS1/miR-324-3p/CLDN3 axis in PC, offering a mechanistic basis suggesting DPP10-AS1 ablation as a therapeutic target against PC.

Diagnostic and Therapeutic Potential of Circulating-Free DNA and Cell-Free RNA in Cancer Management

Over time, molecular biology and genomics techniques have been developed to speed up the early diagnosis and clinical management of cancer. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. Important advances in applying molecular testing involve circulating-free DNA (cfDNA)- and cell-free RNA (cfRNA)-based liquid biopsies for the diagnosis, prognosis, prediction, and treatment of cancer. Both cfDNA and cfRNA are sensitive and specific biomarkers for cancer detection, which have been clinically proven through multiple randomized and prospective trials. These help in cancer management based on the noninvasive evaluation of size, quantity, and point mutations, as well as copy number alterations at the tumor site. Moreover, personalized detection of ctDNA helps in adjuvant therapeutics and predicts the chances of recurrence of cancer and resistance to cancer therapy. Despite the controversial diagnostic values of cfDNA and cfRNA, many clinical trials have been completed, and the Food and Drug Administration has approved many multigene assays to detect genetic alterations in the cfDNA of cancer patients. In this review, we underpin the recent advances in the physiological roles of cfDNA and cfRNA, as well as their roles in cancer detection by highlighting recent clinical trials and their roles as prognostic and predictive markers in cancer management.

LncRNA SCAMP1 disrupts the balance between miR-26a-5p and ZEB2 to promote osteosarcoma cell viability and invasion

Osteosarcoma often occurs in children and adolescents and affects their health. The survival rate of osteosarcoma patients is unsatisfactory due to the lack of early detection and metastasis development and drug resistance. Hence, dissection of molecular insight into osteosarcoma initiation and progression is pivotal to provide the new therapeutic strategy. In recent years, long noncoding RNAs (lncRNAs) have burst into stage in osteosarcoma development and malignant behaviors. LncRNA SCAMP1 has been discovered to play an essential role in carcinogenesis and progression. However, the mechanisms of lncRNA SCAMP1-involved tumorigenesis have not been reported in human osteosarcoma. In this study, we utilized multiple cellular biological approaches to determine the function of lncRNA SCAMP1 in osteosarcoma cells. Moreover, we performed several molecular biological approaches to define the mechanism by which lncRNA SCAMP1 regulated cell viability and invasion in osteosarcoma. We dissected that lncRNA SCAMP1 promoted progression of osteosarcoma via modulation of miR-26a-5p/ZEB2 axis. In conclusion, targeting lncRNA SCAMP1 and its downstream targets, miR-26a-5p and ZEB2, might be a useful approach for osteosarcoma therapy.

Identification of a dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in lung squamous cell carcinoma

Lung cancer is primarily responsive for cancer death, and its progression is aggressively affected by copy number variation (CNV). Through bioinformatics approach, a ceRNA network of CNV-driven lncRNAs in lung squamous cell carcinoma (LUSC) patients was constructed. Data on normal and LUSC tumor tissue from The Cancer Genome Atlas (TCGA)-LUSC dataset were subjected to differential analysis, and differentially expressed lncRNAs (DElncRNAs), DEmiRNAs, and DEmRNAs were obtained. Based on TCGA-LUSC, CNVs of normal and tumor tissue samples were then compared using a Chi-square test, and lncRNAs were intersected based on their CNVs and expression alternation. In combination with the Kruskal-Wallis test, CNV-driven lncRNAs were acquired. Afterwards, miRNAs and mRNAs that interacted with CNV-driven lncRNAs were obtained based on databases (LncBase, starBase, miRDB, mirDIP and TargetScan), DElncRNAs, DEmiRNAs and DEmRNAs, and correlation analysis. The acquired lncRNAs, miRNAs and mRNAs were subjected to Cytoscape software to construct a CNV-driven ceRNA network, which involved 5 lncRNAs (MIR143HG, LINC00702, MIR22HG, RP11-180 N14.1, RP11-473 M20.9), 6 miRNAs (miR-3200-3p, miR-1301-3p, miR-93-3p, miR-96-5p, miR-96-5p, miR-130b-5p, miR-205-5p) and 80 mRNAs. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses indicated that downstream mRNAs were mainly correlated with blood vessel development and T cell-mediated immunity. In summary, we devoted to analyzing CNV-related lncRNAs, mRNAs, and miRNAs in LUSC, thus clarifying 5 lncRNAs that may influence the malignant progression of LUSC. The ceRNA network regulated by these lncRNAs may be the novel pathogenesis of LUSC.

Methylated RNA Immunoprecipitation Sequencing Reveals the m6A Landscape in Oral Squamous Cell Carcinoma

N6-methyladenosine (m⁶A) is the most common epigenetic modification existing in eukaryocyte transcripts. However, genes related to m⁶A modification in oral squamous cell carcinoma (OSCC) are still unclear. Here, methylated RNA immunoprecipitation sequencing (MeRIP-Seq) was performed to map the m6A landscape in OSCC and corresponding controls. The m⁶A peaks are always distributed in the junction of the 3′-untranslated regions (3′-UTRs) and the coding sequences (CDS) of mRNAs, as well as the entire genome of long noncoding RNA (lncRNA). Furthermore, enrichment analysis showed that differentially methylated genes were significantly enriched in NF-kappa B signaling pathway, Hedgehog signaling pathway, etc. In summary, our findings reveal the landscape of m⁶A modification on mRNAs and lncRNAs in OSCC, which may provide key clues for the precision-targeted therapy of OSCC.

Pancreatic adenocarcinoma associated immune-gene signature as a novo risk factor for clinical prognosis prediction in hepatocellular carcinoma

Pancreatic adenocarcinoma (PAAD) has high mortality and a very poor prognosis. Both surgery and chemotherapy have a suboptimal therapeutic effect, and this caused a need to find new approaches such as immunotherapy. Therefore, it is essential to develop a new model to predict patient prognosis and facilitate early intervention. Our study screened out and validated the target molecules based on the TCGA-PAAD dataset. We established the risk signature using univariate and multivariate Cox regression analysis and used GSE62452 and GSE28735 to verify the accuracy and reliability of the model. Expanded application of PAAD-immune-related genes signature (-IRGS) on other datasets was conducted, and the corresponding nomograms were constructed. We also analyzed the correlation between immune-related cells/genes and potential treatments. Our research demonstrated that a high riskscore of PAAD-IRGS in patients with PAAD was correlated with poor overall survival, disease-specific survival and progression free interval. The same results were observed in patients with LIHC. The models constructed were confirmed to be accurate and reliable. We found various correlations between PAAD-IRGS and immune-related cells/genes, and the potential therapeutic agents. These findings indicate that PAAD-IRGS may be a promising indicator for prognosis and of the tumor-immune microenvironment status in PAAD.

Integrated Analysis Revealing the Senescence-Mediated Immune Heterogeneity of HCC and Construction of a Prognostic Model Based on Senescence-Related Non-Coding RNA Network

Background

Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality worldwide. Non-coding RNAs play an important role in HCC. This study aims to identify a senescence-related non-coding RNA network-based prognostic model for individualized therapies for HCC.

Methods

HCC subtypes with senescence status were identified on the basis of the senescence-related genes. Immune status of the subtypes was analyzed by CIBERSORT and ESTIMATE algorithm. The differentially expressed mRNAs, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) were identified between the two HCC subtypes. A senescence-based competing endogenous RNA (ceRNA) co-expression network in HCC was constructed. On the basis of the ceRNA network, Lasso Cox regression was used to construct the senescence-related prognostic model (S score). The prognosis potential of the S score was evaluated in the training dataset and four external validation datasets. Finally, the potential of the prognostic model in predicting immune features and response to immunotherapy was evaluated.

Results

The HCC samples were classified into senescence active and inactivate subtypes. The senescence active group showed an immune suppressive microenvironment compared to the senescence inactive group. A total of 2,902 mRNAs, 19 miRNAs, and 308 lncRNAs were identified between the two subtypes. A ceRNA network was constructed using these differentially expressed genes. On the basis of the ceRNA network, S score was constructed to predict the prognosis of patients with HCC. The S score was correlated with immune features and can predict response to immunotherapy of cancer.

Conclusion

The present study analyzed the biological heterogeneity across senescence-related subtypes and constructed a senescence-related ceRNA-network-based prognostic model for predicting prognosis and immunotherapy responsiveness.

An Independent Prognostic Model Based on Ten Autophagy-Related Long Noncoding RNAs in Pancreatic Cancer Patients

Purpose

Pancreatic cancer (PC) is a common, highly lethal cancer with a low survival rate. Autophagy is involved in the occurrence and progression of PC. This study aims to explore the feasibility of using an autophagy-related long noncoding RNA (lncRNA) signature for assessing PC patient survival.

Methods

We obtained RNA sequencing and clinical data of patients from the TCGA website. Autophagy genes were obtained from the Human Autophagy Database. The prognostic model, generated through univariate and multivariate Cox regression analyses, included 10 autophagy-related lncRNAs. Receiver operating characteristic (ROC) curves and forest plots were generated for univariate and multivariate Cox regression analyses, to examine the predictive feasibility of the risk model. Gene set enrichment analysis (GSEA) was used to screen enriched gene sets.

Results

Twenty-eight autophagy-related lncRNAs were filtered out through univariate Cox regression analysis (P < 0.001). Ten autophagy-related lncRNAs, including 4 poor prognosis factors and 6 beneficial prognosis factors, were further screened via multivariate Cox regression analysis. The AUC value of the ROC curve was 0.815. GSEA results demonstrated that cancer-related gene sets were significantly enriched.

Conclusion

A signature based on ten autophagy-related lncRNAs was identified. This signature could be potentially used for evaluating clinical prognosis and might be used for targeted therapy against PC.

miRNAs-mediated overexpression of Periostin is correlated with poor prognosis and immune infiltration in lung squamous cell carcinoma

Lung cancer is one of the most common malignancies with a high mortality rate worldwide. POSTN has been shown to be strongly correlated with the poor prognosis of lung cancer patients. However, the function and mechanism of action of POSTN in lung cancer remain unclear. Here, we carried out a pan-cancer analysis to assess the clinical prognostic value of POSTN based on the TCGA, TIMER, Oncomine, Kaplan-Meier, and UALCAN databases. We found that upregulated POSTN can be a promising biomarker to predict the prognosis of patients with lung cancer. High levels of POSTN correlated with immune cell infiltration in lung cancer, especially lung squamous cell carcinoma (LUSC), which was further confirmed based on the results from the TISIDB database. Moreover, the expression analysis, correlation analysis, and survival analysis revealed that POSTN-targeted miRNAs, downregulation of has-miR-144-3p and has-miR-30e-3p, were significantly linked to poor prognosis in patients with LUSC. Taken together, we identified that POSTN can act as a novel biomarker for determining the prognosis related to immune infiltration in patients with LUSC and deserves further research.

Identification of mRNA-miRNA-lncRNA regulatory network associated with the immune response to Aeromonas salmonicides infection in the black rockfish (Sebastes schlegelii)

In aquaculture, Aeromonas salmonicides (A. salmonicida) is a main fish pathogen because of its nearly worldwide distribution, and broad host range. Recently, an increasing number of evidences have uncovered the roles of mRNA-miRNA-lncRNA network in fish diseases. In current study, RNA-seq was conducted in the black rockfish spleen following A. salmonicida infection at 0 h (Sp0 or control) and three different post-infection time-points (2 h: Sp2, 12 h: Sp12 and 24 h: Sp24, respectively) to comprehensively identify differentially expressed (DE) mRNAs, miRNAs and lncRNAs. Enrichment analysis and protein-protein interaction (PPI) analysis of DE mRNAs were performed. Then, expression and correlation analysis for mRNAs and their upstream miRNAs and lncRNAs were conducted. Finally, a total of 1364 mRNAs, 17 miRNAs and 1584 lncRNAs exhibited significantly differential expressions during bacterial infection in the black rockfish spleen. Functional enrichment analysis suggested that they were significantly enriched in several immune-related pathways, including Amino sugar and nucleotide sugar metabolism, Cell adhesion molecules (CAMs), Neuroactive ligand-receptor interaction, Nicotinate and nicotinamide metabolism, Pentose and glucuronate interconversions, Phagosome, Proteasome, etc. Subsequently, 1091 lncRNA-miRNA-mRNA pathways (323 in Sp2, 609 in Sp12 and 207 in Sp24) were constructed including 400 lncRNAs, 69 miRNAs, and 70 mRNAs. Meanwhile, NLRC3/novel-264/LNC_00116154 pathway demonstrated important immune modulating function in the black rockfish against A. salmonicida infection. Finally, the novel mRNA-miRNA-lncRNA sub-networks were established, among which all mRNAs and ncRNAs possessed significant predictive values for further studies for immune responses in the black rockfish.

Long Non-Coding RNAs in Pancreatic Cancer: Biologic Functions, Mechanisms, and Clinical Significance

Despite tremendous efforts devoted to research in pancreatic cancer (PC), the mechanism underlying the tumorigenesis and progression of PC is still not completely clear. Additionally, ideal biomarkers and satisfactory therapeutic strategies for clinical application in PC are still lacking. Accumulating evidence suggests that long non-coding RNAs (lncRNAs) might participate in the pathogenesis of diverse cancers, including PC. The abnormal expression of lncRNAs in PC is considered a vital factor during tumorigenesis that affects tumor cell proliferation, migration, invasion, apoptosis, angiogenesis, and drug resistance. With this review of relevant articles published in recent years, we aimed to summarize the biogenesis mechanism, classifications, and modes of action of lncRNAs and to review the functions and mechanisms of lncRNAs in PC. Additionally, the clinical significance of lncRNAs in PC was discussed. Finally, we pointed out the questions remaining from recent studies and anticipated that further investigations would address these gaps in knowledge in this field.

Identification of a Prognostic Signature Composed of GPI, IL22RA1, CCT6A and SPOCK1 for Lung Adenocarcinoma Based on Bioinformatic Analysis of lncRNA-Mediated ceRNA Network and Sample Validation

Lung adenocarcinoma (LUAD) is one of the most common malignant tumors with high morbidity and mortality in China and worldwide. Long non-coding RNAs (lncRNAs) as the competing endogenous RNA (ceRNA) play an essential role in the occurrence and development of LUAD. However, identifying lncRNA-related biomarkers to improve the accuracy of LUAD prognosis remains to be determined. This study downloaded RNA sequence data from The Cancer Genome Atlas (TCGA) database and identified the differential RNAs by bioinformatics. A total of 214 lncRNA, 198 miRNA and 2989 mRNA were differentially identified between LUAD and adjacent nontumor samples. According to the ceRNA hypothesis, we constructed a lncRNA-miRNA-mRNA network including 95 protein-coding mRNAs, 7 lncRNAs and 15 miRNAs, and found 24 node genes in this network were significantly associated with the overall survival of LUAD patients. Subsequently, through LASSO regression and multivariate Cox regression analyses, a four-gene prognostic signature composed of GPI, IL22RA1, CCT6A and SPOCK1 was developed based on the node genes of the lncRNA-mediated ceRNA network, demonstrating high performance in predicting the survival and chemotherapeutic responses of low- and high-risk LUAD patients. Finally, independent prognostic factors were further analyzed and combined into a well-executed nomogram that showed strong potential for clinical applications. In summary, the data from the current study suggested that the four-gene signature obtained from analysis of lncRNA-mediated ceRNA could serve as a reliable biomarker for LUAD prognosis and evaluation of chemotherapeutic response.

Long noncoding RNA LINC00857 promotes pancreatic cancer proliferation and metastasis by regulating the miR-130b/RHOA axis

Dysregulation of long noncoding RNAs (lncRNAs) is involved in the pathogenesis and progression of pancreatic cancer (PC). In the current study, we investigated the role and molecular mechanism of LINC00857 in PC. The expression of LINC00857 in PC was analyzed by bioinformatics analysis and qRT-PCR, and the relationship between LINC00857 expression and clinical characteristics of patients of PC was analyzed by Fisher's exact test. Gain- and loss-of-function assays were performed to determine the biological function of LINC00857 in PC. The relationship between LINC00857, miR-130b, and RHOA were determined by RNA pull-down assay, luciferase assay, and qRT-PCR. Our results demonstrated that LINC00857 expression was elevated in PC, and high expression of LINC00857 was positively associated with tumor diameter, T stage, and lymph node metastasis. LINC00857 promoted the proliferation and mobility of PC cells in vitro and in vivo. Mechanistically, LINC00857 acts as a sponge for miR-130b and decreases its expression. miR-130b exhibits tumor suppressor functions in PC, and RHOA was identified as the key target gene of miR-130b. The functions induced by LINC00857 in PC cells were dependent on the miR-130b/RHOA axis. In conclusion, the current study indicated that LINC00857 promotes PC tumorigenesis and metastasis by modulating the miR-130b/RHOA axis, implying that LINC00857 might be a new therapeutic target for PC.

LINC00511 enhances LUAD malignancy by upregulating GCNT3 via miR-195-5p

Background

Accumulating evidence suggests that LINC00511 acts as an oncogenic long non-coding RNA (lncRNA) in various cancers, including lung adenocarcinoma (LUAD). Hence, we attempted to elucidate the potential role of LINC00511 in LUAD.

Methods

LINC00511, miR-195-5p, and GCNT3 expression in LUAD was detected by qRT-PCR. Changes in the proliferation, migration, and invasion of LUAD cells after abnormal regulation of LINC00511, miR-195-5p, or GCNT3 were detected by CCK-8, BrdU, wound healing, and transwell assays. Bax and Bcl-2 protein expression was measured by western blotting. Additionally, we identified the targeting effects of LINC00511, miR-195-5p, and GCNT3 using luciferase and RNA immunoprecipitation (RIP) assays.

Results

LINC00511 and GCNT3 were found to be upregulated in LUAD, while miR-195-5p was downregulated. Silencing LINC00511 or GCNT3 decreased the proliferation, migration, invasion, and Bcl-2 protein content in LUAD cells and increased the expression of Bax. Interference with miR-195-5p promoted malignant proliferation of cancer cells. miR-195-5p expression was affected by LINC00511and targeted GCNT3.

Conclusion

Silencing LINC00511 promotes GCNT3 expression by inhibiting miR-195-5p and ultimately stimulates the malignant progression of LUAD.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09459-7.

A noncoding regulatory RNA Gm31932 induces cell cycle arrest and differentiation in melanoma via the miR-344d-3-5p/Prc1 (and Nuf2) axis

Emerging evidence has shown that long non-coding RNAs (lncRNAs) play an important role in inhibiting tumor cell proliferation and inducing differentiation. In this study, integrative analysis of whole transcriptome sequencing data demonstrated that lncRNA-Gm31932 is significantly decreased in all-trans retinoic acid (ATRA)-induced and sodium 4-phenylbutanoate (PB-4)-induced mouse melanoma B16 cells. Silencing lncRNA-Gm31932 could inhibit B16 cell proliferation, with cell cycle arrest at the G0/G1 phase and obvious differentiation characteristics, e.g., increased cell volume, melanin content and tyrosinase (Tyr) activity. Furthermore, a series of experiments (luciferase reporter assay, RNA pull-down assay, and western blotting) showed that lncRNA-Gm3932 down-regulated Prc1 and Nuf2 by competitively sponging miR-344d-3-5p, which subsequently reduced the expression of cell cycle-related proteins CDK2, CDC2, and Cyclin B1, and increased the expression of P21 and P27. Moreover, silencing lncRNA-Gm31932 could significantly inhibit tumor growth in B16 melanoma-bearing mice. Taken together, these results indicate that as a possible signaling pathway for ATRA and PB-4, lncRNA-Gm31932 can induce cell cycle arrest and differentiation via miR-344d-3-5p/Prc1 (and Nuf2) axis.