LOC646329 long non-coding RNA sponges miR-29b-1 and regulates TGFβ signaling in colorectal cancer

A miRNA-disease association prediction model based on tree-path global feature extraction and fully connected artificial neural network with multi-head self-attention mechanism

BACKGROUND

MicroRNAs (miRNAs) emerge in various organisms, ranging from viruses to humans, and play crucial regulatory roles within cells, participating in a variety of biological processes. In numerous prediction methods for miRNA-disease associations, the issue of over-dependence on both similarity measurement data and the association matrix still hasn't been improved. In this paper, a miRNA-Disease association prediction model (called TP-MDA) based on tree path global feature extraction and fully connected artificial neural network (FANN) with multi-head self-attention mechanism is proposed. The TP-MDA model utilizes an association tree structure to represent the data relationships, multi-head self-attention mechanism for extracting feature vectors, and fully connected artificial neural network with 5-fold cross-validation for model training.

RESULTS

The experimental results indicate that the TP-MDA model outperforms the other comparative models, AUC is 0.9714. In the case studies of miRNAs associated with colorectal cancer and lung cancer, among the top 15 miRNAs predicted by the model, 12 in colorectal cancer and 15 in lung cancer were validated respectively, the accuracy is as high as 0.9227.

CONCLUSIONS

The model proposed in this paper can accurately predict the miRNA-disease association, and can serve as a valuable reference for data mining and association prediction in the fields of life sciences, biology, and disease genetics, among others.

The Role of the Transforming Growth Factor-β Signaling Pathway in Gastrointestinal Cancers

Transforming growth factor-β (TGF-β) has attracted attention as a tumor suppressor because of its potent growth-suppressive effect on epithelial cells. Dysregulation of the TGF-β signaling pathway is considered to be one of the key factors in carcinogenesis, and genetic alterations affecting TGF-β signaling are extraordinarily common in cancers of the gastrointestinal system, such as hereditary nonpolyposis colon cancer and pancreatic cancer. Accumulating evidence suggests that TGF-β is produced from various types of cells in the tumor microenvironment and mediates extracellular matrix deposition, tumor angiogenesis, the formation of CAFs, and suppression of the anti-tumor immune reaction. It is also being considered as a factor that promotes the malignant transformation of cancer, particularly the invasion and metastasis of cancer cells, including epithelial-mesenchymal transition. Therefore, elucidating the role of TGF-β signaling in carcinogenesis, cancer invasion, and metastasis will provide novel basic insight for diagnosis and prognosis and the development of new molecularly targeted therapies for gastrointestinal cancers. In this review, we outline an overview of the complex mechanisms and functions of TGF-β signaling. Furthermore, we discuss the therapeutic potentials of targeting the TGF-β signaling pathway for gastrointestinal cancer treatment and discuss the remaining challenges and future perspectives on targeting this pathway.

Roles of TGF‑β signalling pathway‑related lncRNAs in cancer (Review)

Long non-coding RNAs (lncRNAs) are a class of RNAs that are >200 nucleotides in length that do not have the ability to be translated into protein but are associated with numerous diseases, including cancer. The involvement of lncRNAs in the signalling of certain signalling pathways can promote tumour progression; these pathways include the transforming growth factor (TGF)-β signalling pathway, which is related to tumour development. The expression of lncRNAs in various tumour tissues is specific, and their interaction with the TGF-β signalling pathway indicates that they may serve as new tumour markers and therapeutic targets. The present review summarized the role of TGF-β pathway-associated lncRNAs in regulating tumorigenesis in different types of cancer and their effects on the TGF-β signalling pathway.

Targeting lncRNA/Wnt axis by flavonoids: A promising therapeutic approach for colorectal cancer

Despite the dramatic advances in our understanding of the etiology of colorectal cancer (CRC) in recent decades, effective therapeutic strategies are still urgently needed. Oncogenic mutations in the Wnt/β-Catenin pathway are hallmarks of CRC. Moreover, long non-coding RNAs (lncRNAs) as molecular managers are involved in the initiation, progression, and metastasis of CRC. Therefore, it is important to further explore the interaction between lncRNAs and Wnt/β-Catenin signaling pathway for targeted therapy of CRC. Natural phytochemicals have not toxicity and can target carcinogenesis-related pathways. Growing evidences suggest that flavonoids are inversely associated with CRC risk. These bioactive compounds could target carcinogenesis pathways of CRC and reduced the side effects of anti-cancer drugs. The review systematically summarized the progress of flavonoids targeting lncRNA/Wnt axis in the investigations of CRC, which will provide a promising therapeutic approach for CRC and develop nutrition-oriented preventive strategies for CRC based on epigenetic mechanisms. In the field, more epidemiological and clinical trials are required in the future to verify feasibility of targeting lncRNA/Wnt axis by flavonoids in the therapy and prevention of CRC.

Linc00883 affects colorectal cancer through miR-577/FKBP14 axis: a novel mechanism for regulating colorectal cancer cell proliferation, invasion, and migration

Long non-coding RNAs (lncRNAs) are relevant to the development of human cancers. Here, we aimed to investigate the role and mechanism of Linc00883 in the proliferation, invasion, and migration of colorectal cancer (CRC) cells. CRC cell lines SW480 and LoVo were applied as in vitro models in this study. Quantitative real-time PCR was applied to measure Linc00883, miR-577, and FKBP14 expressions. Cell Counting Kit-8, transwell, and wound-healing assays were carried out to confirm the function of Linc00883. Western blot was applied to detect the protein levels of the epithelial-mesenchymal transition-related proteins E-cadherin, vimentin, fibronectin, and α-SMA. RNA immunoprecipitation (RIP) and RNA pull-down experiments were performed to confirm the relationship between Linc00883 and miR-577. Linc00883 expression was elevated in CRC tissues and cells, and the patients with high expression of Linc00883 were related to a low survival rate and prone to distant metastasis. Moreover, we corroborated that Linc00883 and miR-577, miR-577 and FKBP14 are bound to each other. Linc00883 was negatively correlated with miR-577, and miR-577 was also negatively correlated with FKBP14. Furthermore, interference with Linc00883 restrained the proliferation, invasion, and migration of CRC cells through the miR-577/FKBP14 axis. In vivo studies also clarified that Linc00883 facilitated the growth of CRC tumors and the epithelial-mesenchymal transition (EMT) of CRC. Our results demonstrated that Linc00883 facilitated the proliferation, invasion, and migration of CRC cells by regulating the miR-577/FKBP14 axis.

TGFB3-AS1 promotes Hcy-induced inflammation of macrophages via inhibiting the maturity of miR-144 and upregulating Rap1a

It has been demonstrated that homocysteine (Hcy) can cause inflammatory diseases. Long noncoding RNAs (lncRNA) and microRNAs (miRNAs) are involved in this biological process, but the mechanism underlying Hcy-induced inflammation remains poorly understood. Here, we found that lncRNA TGFB3-AS1 was highly expressed in macrophages treated with Hcy and the peripheral blood monocytes from cystathionine beta-synthase heterozygous knockout (CBS^+/−) mice with a high-methionine diet using lncRNA microarray. In vivo and in vitro experiments further confirmed that TGFB3-AS1 accelerated Hcy-induced inflammation of macrophages through the Rap1a/wnt signaling pathway. Meanwhile, TGFB3-AS1 interacted with Rap1a and reduced degradation of Rap1a through inhibiting its ubiquitination in macrophages treated with Hcy. Rap1a mediated inflammation induced by Hcy and serves as a direct target of miR-144. Moreover, TGFB3-AS1 regulated miR-144 by binding to pri-miR-144 and inhibiting its maturation, which further regulated Rap1a expression. More importantly, we found that high expression of TGFB3-AS1 was positively correlated with the levels of Hcy and proinflammatory cytokines in serum of healthy individuals and patients with HHcy. Our study revealed a novel mechanism by which TGFB3-AS1 promoted inflammation of macrophages through inhibiting miR-144 maturation to stay miR-144 regulated inhibition of functional Rap1a expression.

miRNA Clusters with Up-Regulated Expression in Colorectal Cancer

Simple Summary

As miRNAs show the capacity to be used as CRC biomarkers, we analysed experimentally validated data about frequently up-regulated miRNA clusters in CRC tissue. We identified 15 clusters that showed increased expression in CRC: miR-106a/363, miR-106b/93/25, miR-17/92a-1, miR-181a-1/181b-1, miR-181a-2/181b-2, miR-181c/181d, miR-183/96/182, miR-191/425, miR-200c/141, miR-203a/203b, miR-222/221, mir-23a/27a/24-2, mir-29b-1/29a, mir-301b/130b and mir-452/224. Cluster positions in the genome are intronic or intergenic. Most clusters are regulated by several transcription factors, and by long non-coding RNAs. In some cases, co-expression of miRNA with other cluster members or host gene has been proven. miRNA expression patterns in cancer tissue, blood and faeces were compared. The members of the selected clusters target 181 genes. Their functions and corresponding pathways were revealed with the use of Panther analysis. Clusters miR-17/92a-1, miR-106a/363, miR-106b/93/25 and miR-183/96/182 showed the strongest association with metastasis occurrence and poor patient survival, implicating them as the most promising targets of translational research.

Abstract

Colorectal cancer (CRC) is one of the most common malignancies in Europe and North America. Early diagnosis is a key feature of efficient CRC treatment. As miRNAs can be used as CRC biomarkers, the aim of the present study was to analyse experimentally validated data on frequently up-regulated miRNA clusters in CRC tissue and investigate their members with respect to clinicopathological characteristics of patients. Based on available data, 15 up-regulated clusters, miR-106a/363, miR-106b/93/25, miR-17/92a-1, miR-181a-1/181b-1, miR-181a-2/181b-2, miR-181c/181d, miR-183/96/182, miR-191/425, miR-200c/141, miR-203a/203b, miR-222/221, mir-23a/27a/24-2, mir-29b-1/29a, mir-301b/130b and mir-452/224, were selected. The positions of such clusters in the genome can be intronic or intergenic. Most clusters are regulated by several transcription factors, and miRNAs are also sponged by specific long non-coding RNAs. In some cases, co-expression of miRNA with other cluster members or host gene has been proven. miRNA expression patterns in cancer tissue, blood and faeces were compared. Based on experimental evidence, 181 target genes of selected clusters were identified. Panther analysis was used to reveal the functions of the target genes and their corresponding pathways. Clusters miR-17/92a-1, miR-106a/363, miR-106b/93/25 and miR-183/96/182 showed the strongest association with metastasis occurrence and poor patient survival, implicating them as the most promising targets of translational research.

MicroRNAs as important contributors in the pathogenesis of colorectal cancer

Colorectal cancer (CRC) is the third most fatal and fourth most frequently diagnosed neoplasm in the world. Numerous non-coding RNAs have been shown to contribute in the development of CRC. MicroRNAs (miRNAs) are among the mostly assessed non-coding RNAs in CRC. These transcripts influence expression and activity of TGF-β, Wnt/β-catenin, MAPK, PI3K/AKT and other CRC-related pathways. In the context of CRC, miRNAs interact with long non-coding RNAs to influence CRC course. Stool and serum levels of miRNAs have been used to distinguish CRC patients from healthy controls, indicating diagnostic roles of these transcripts in CRC. Therapeutic application of miRNAs in CRC has been assessed in animal models, yet has not been verified in clinical settings. In the current review, we have provided a recent update on the role of miRNAs in CRC development as well as diagnostic and prognostic approaches.

The Role of non-coding RNAs in colorectal cancer, with a focus on its autophagy

Colorectal cancer (CRC) is one of malignant afflictions burdening people worldwide, mainly caused by shortages of effective medical intervention and poorly mechanistic understanding of the pathogenesis of CRC. Non-coding RNAs (ncRNAs) are a type of heterogeneous transcripts without the capability of coding protein, but have the potency of regulating protein-coding gene expression. Autophagy is an evolutionarily conserved catabolic process in which cytoplasmic contents are delivered to cellular lysosomes for degradation, resulting in the turnover of cellular components and producing energy for cell functions. A growing body of evidence reveals that ncRNAs, autophagy, and the crosstalks of ncRNAs and autophagy play intricate roles in the initiation, progression, metastasis, recurrence and therapeutic resistance of CRC, which confer ncRNAs and autophagy to serve as clinical biomarkers and therapeutic targets for CRC. In this review, we sought to delineate the complicated roles of ncRNAs, mainly including miRNAs, lncRNAs and circRNAs, in the pathogenesis of CRC, particularly focus on the regulatory role of ncRNAs in CRC-related autophagy, attempting to shed light on the complex pathological mechanisms, involving ncRNAs and autophagy, responsible for CRC tumorigenesis and development, so as to underpin the ncRNAs- and autophagy-based therapeutic strategies for CRC in clinical setting.

miRNA-independent function of long noncoding pri-miRNA loci

Among the large, diverse set of mammalian long noncoding RNAs (lncRNAs), long noncoding primary microRNAs (lnc-pri-miRNAs) are those that host miRNAs. Whether lnc-pri-miRNA loci have important biological function independent of their cognate miRNAs is poorly understood. From a genome-scale lncRNA screen, lnc-pri-miRNA loci were enriched for function in cell proliferation, and in glioblastoma (i.e., GBM) cells with DGCR8 or DROSHA knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied LOC646329 (also known as MIR29HG), which hosts the miR-29a/b1 cluster. In GBM cells, LOC646329 knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (LOC646329-miR29Δ) did not decrease cell growth, while knockdown of LOC646329-miR29Δ transcripts reduced cell proliferation. The miR-29a/b1-independent activity of LOC646329 corresponded to enhancer-like activation of a neighboring oncogene (MKLN1), regulating cell propagation. The LOC646329 locus interacts with the MKLN1 promoter, and antisense oligonucleotide knockdown of the lncRNA disrupts these interactions and reduces the enhancer-like activity. More broadly, analysis of genome-wide data from multiple human cell types showed that lnc-pri-miRNA loci are significantly enriched for DNA looping interactions with gene promoters as well as genomic and epigenetic characteristics of transcriptional enhancers. Functional studies of additional lnc-pri-miRNA loci demonstrated cognate miRNA-independent enhancer-like activity. Together, these data demonstrate that lnc-pri-miRNA loci can regulate cell biology via both miRNA-dependent and miRNA-independent mechanisms.

lncRNAS56464.1 as a ceRNA promotes the proliferation of fibroblast‑like synoviocytes in experimental arthritis via the Wnt signaling pathway and sponges miR‑152‑3p

Rheumatoid arthritis (RA) is an autoimmune disease that occurs in approximately 1.0% of the general population. In RA patients, physical disability and joint damage are the major prognostic factors, which are associated with a reduction in the quality of life and early mortality. At present, the exact molecular mechanism of RA remains elusive. Long noncoding RNAs (lncRNAs) have been revealed to play a regulatory role in the pathogenesis of RA. To reveal the function of lncRNAs in rheumatoid arthritis, lncRNAS56464.1 was screened to verify its targeting of the microRNA (miR)-152-3p/Wnt pathway and its effect on the proliferation of fibroblast-like synoviocytes (FLS). In the present study, based on the competing endogenous RNA (ceRNA) theory, siRNA was designed for transfection into FLS to calculate the lncRNAS56464.1 interference efficiency and then the effect of lncRNAS56464.1 interference on FLS proliferation was detected by MTT assay. Then, lncRNAS56464.1 targeting of the miR-152-3p/Wnt pathway was detected by a dual-luciferase reporter assay. In addition, RT-qPCR, immunofluorescence and western blotting techniques were employed to detect the expression of lncRNAS56464.1, miR-152-3p and some key genes of the Wnt signaling pathway in FLS after lncRNAS56464.1 interference. The results revealed that lncRNAS56464.1 could combine with miR-152-3p and promoted the proliferation of FLS. In addition, lncRNAS56464.1 interference could not only decrease the proliferation of FLS and the expression of Wnt1, β-catenin, c-Myc, cyclin D1, and p-GSK-3β/GSK-3β, but it also increased the expression of SFRP4. The present data indicated that lncRNAS56464.1 could target the miR-152-3p/Wnt pathway to induce synovial cell proliferation and then participate in the pathogenesis of RA.