Competing Endogenous RNAs, Non-Coding RNAs and Diseases: An Intertwined Story

Whole-transcriptome sequencing in neural and non-neural tissues of a mouse model identifies miR-34a as a key regulator in SMA pathogenesis

Spinal muscular atrophy (SMA) is a severe neurodegenerative disorder caused by deficiency of survival of motor neuron (SMN). While significant progress has been made in SMA therapy by rescuing SMN expression, limited knowledge about SMN downstream genes has hindered the development of alternative therapies. Here, we conducted whole-transcriptome sequencing of spinal cord, heart, and liver tissues of a severe SMA mouse model at early postnatal ages to explore critical coding and non-coding RNAs (ncRNAs). A large number of differentially expressed RNAs (DE-RNAs) were obtained, including 2,771 mRNAs, 382 microRNAs (miRNAs), 1,633 long ncRNAs, and 1,519 circular RNAs. Through in-depth data mining, we unveiled deregulation of miR-34a in all tissues. Analysis of competitive endogenous RNA networks of DE-RNAs identified multiple novel targets of miR-34a including Spag5 mRNA, lncRNA00138536, and circRNA007386. Further in vitro studies using mouse myoblast and human cardiomyocyte cell lines showed that knockdown of SMN upregulated miR-34a-5p and overexpression of miR-34a-5p alone disrupted cell-cycle progression through regulating its targets, recapitulating gene expression patterns observed in cardiac tissue of SMA mice. Our results identified a critical miRNA involved in SMA pathology, which sheds insights into the molecular basis of widespread tissue abnormalities observed in severe forms of SMA.

Interplay between LncRNAs and autophagy-related pathways in leukemia: mechanisms and clinical implications

Autophagy is a conserved catabolic process that removes protein clumps and defective organelles, thereby promoting cell equilibrium. Growing data suggest that dysregulation of the autophagic pathway is linked to several cancer hallmarks. Long non-coding RNAs (lncRNAs), which are key parts of gene transcription, are increasingly recognized for their significant roles in various biological processes. Recent studies have uncovered a strong connection between the mutational landscape and altered expression of lncRNAs in the tumor formation and development, including leukemia. Research over the past few years has emphasized the role of lncRNAs as important regulators of autophagy-related gene expression. These RNAs can influence key leukemia characteristics, such as apoptosis, proliferation, epithelial-mesenchymal transition (EMT), migration, and angiogenesis, by modulating autophagy-associated signaling pathways. With altered lncRNA expression observed in leukemia cells and tissues, they hold promise as diagnostic biomarkers and therapeutic targets. The current review focuses on the regulatory function of lncRNAs in autophagy and their involvement in leukemia, potentially uncovering valuable therapeutic targets for leukemia treatment.

Dysregulation of GAS5-miRNA-Mediated Signaling Pathways in Cancer Pathobiology: A Comprehensive Exploration of Pathways Influenced by this Axis

The long non-coding RNA Growth Arrest-Specific 5 (GAS5) is pivotal in modulating key signaling pathways by functioning as a molecular sponge for microRNAs (miRNAs). GAS5 is notably recognized for its antitumor properties, primarily through its ability to sequester oncogenic miRNAs, thereby influencing critical pathways such as p53, Wnt/β-catenin, and PI3K/Akt, all of which are integral to cell proliferation, apoptosis, and metastasis. The disruption of GAS5-miRNA interactions has been implicated in various malignancies, reinforcing its potential as both a biomarker and a therapeutic target. This paper delves into the intricate signaling cascades affected by GAS5-miRNA interactions and thoroughly investigates the diagnosis and treatment prospects associated with GAS5. Moreover, it addresses both the challenges and opportunities for translational applicability of these findings in clinical environments. The study emphasizes GAS5's significance within the cancer molecular landscape and posits that precise modulation of GAS5-miRNA interactions could catalyze transformative developments in cancer diagnostics and therapeutic approaches. This comprehensive review not only highlights the critical role of non-coding RNAs in cancer biology but also aims to lay the groundwork for future investigations aimed at harnessing these insights for therapeutic interventions.

Transcriptomic insights into early mechanisms underlying post-chikungunya chronic inflammatory joint disease

Chikungunya virus (CHIKV) infection often results in a chronic joint condition known as Post-Chikungunya Chronic Inflammatory Joint Disease (pCHIKV-CIJD). This condition disrupts individuals' daily lives and contributes to increased healthcare expenditure. This study investigated the molecular mechanisms underlying pCHIKV-CIJD development by analyzing RNA transcripts, including small RNAs, of whole blood from CHIKV-infected patients. By comparing patients who evolved to pCHIKV-CIJD with those who did not, we identified molecular signatures associated with chronification in acute and post-acute disease phases. These molecules were primarily associated with an altered immune response regulation. Notably, LIFR, an immune receptor that enhanced IL-6 transcription, was down-regulated in the acute phase of pCHIKV-CIJD patients, while its inhibitor, hsa-miR-98-5p, was up-regulated in these individuals. Other downregulated genes include members of immune mechanisms whose impairment can lead to a reduction in the first line of antiviral response, thereby promoting virus persistence for a longer period in these patients. Additionally, pCHIKV-CIJD patients exhibited reduced transcript levels of MMP8, LFT, and DDIT4, genes already implicated in the pathological process of other types of inflammatory arthritis and seemingly relevant for pCHIKV-CIJD development. Overall, our findings provide insights into the early molecular mechanisms involved in the chronification and highlight potential targets for further investigation.

The association between Clonorchis sinensis seropositivity and hepatocellular carcinoma in an endemic area: a study in Guangxi, China

BACKGROUND

Chronic infection with Clonorchis sinensis (C.sinensis) has been associated swith the development of intrahepatic cholangiocarcinoma (ICC); however, the relationship between C.sinensis and hepatocellular carcinoma (HCC) remains uncertain.

METHODS

This study examined 120 patients with liver cancer in the clonorchiasis endemic area of Hengzhou, Guangxi, China. The type of cancer, the differentiation grade according to Edmondson Steiner's classification, and the pathological characteristics of HCC were determined through postoperative tissue biopsy. C.sinensis infection was detected by measuring serum specific IgG antibody, and hepatitis B virus (HBV) infection was determined by detecting serum HBsAg and HBV DNA in HCC tissues. The C.sinensis infection rates in control groups were drawn from the local general population based on previous surveys. The association between C.sinensis infection and HCC was analyzed by comparing the differences in C.sinensis infection rates between the two groups.

RESULTS

Of the patients evaluated, 98 (81.7%) had HCC, 21 (17.5%) had ICC, and 1 (0.8%) had comorbidity of HCC/ICC. Among the HCC patients, 24 (24.5%) were solely infected with HBV, 71 (72.4%) were C. sinensis seropositive, and 3 (3.1%) showed no evidence of infection. C. sinensis seropositive rates in HCC patients are much higher than in general outpatient and non-liver cancer inpatients (χ2 = 141.92, p < 0.001), as well as in the local residents (χ2 = 82.61/21.38, p < 0.001). There were no significant differences in the pathological type, differentiation grade, and lesion composition between the tumor associated with C.sinensis/HBV mono- and co-infection (p > 0.05). Among the patients with C.sinensis-related HCC, 8 (8.2%) were solely C.sinensis seropositive, while 63 (64.3%) were co-infected with HBV. Infection with C. sinensis and HBV has a significant impact on the pathological types of liver cancer (χ2 = 22.86, p < 0.001).

CONCLUSIONS

These findings indicate that HCC still accounts for the majority of liver cancer in this region. In addition to being most commonly related with HBV infection, HCC may also be related to C. sinensis infection. Co-infection of C. sinensis and HBV may enhance the development of HCC in this area.

CLINICAL TRIAL

Not applicable.

N6-Methyladenosine (m6A)-Circular RNA Pappalysin 1 (circPAPPA) from Cashmere Goats: Identification, Regulatory Network and Expression Potentially Regulated by Methylation in Secondary Hair Follicles Within the First Intron of Its Host Gene

N6-methyladenosine (m6A) is one of the most abundant modifications in eukaryotic RNA molecules and mediates the functional exertion of RNA molecules. We characterized the circPAPPA and validated its potential m6A modification sites in secondary hair follicles (SHFs) of cashmere goats. Furthermore, we generated integrated regulatory networks of the circPAPPA along with enrichment analysis of signaling pathways. We also explored the potential relationship of circPAPPA expression with the first intron methylation of the PAPPA gene in SHFs of cashmere goats. Host source analysis revealed that circPAPPA is derived from the complete exon 2 of the PAPPA gene, spliced in reverse orientation, and predominantly localized in the cytoplasm of SHF stem cells in cashmere goats. The circPAPPA was verified to contain at least four m6A modification sites in SHFs of cashmere goats, including m6A-450/456, m6A-852, m6A-900, and m6A-963. The generated regulatory network indicated complex and diverse regulatory relationships of m6A-circPAPPA with its putative regulatory molecules, including miRNAs, mRNAs, and proteins. Enrichment analysis of signaling pathways showed that m6A-circPAPPA might play multiple functional roles in the growth and development of SHF in cashmere goats through the putative regulatory network mediated by its target miRNAs and regulatory proteins. The first intron methylation of the PAPPA gene most likely is significantly involved in the dynamic expression of m6A-circPAPPA in cashmere goat SHFs. Results from this study provided novel information to elucidate the biological roles and functional regulatory pathways of m6A-circPAPPA in SHF development and the growth of cashmere goat fiber.

Non-Coding RNAs in Cancer: Structure, Function, and Clinical Application

We are on the brink of a paradigm shift in both theoretical and clinical oncology. Genomic and transcriptomic profiling, alongside personalized approaches that account for individual patient variability, are increasingly shaping discourse. Discussions on the future of personalized cancer medicine are mainly dominated by the potential of non-coding RNAs (ncRNAs), which play a prominent role in cancer progression and metastasis formation by regulating the expression of oncogenic or tumor suppressor proteins at transcriptional and post-transcriptional levels; furthermore, their cell-free counterparts might be involved in intercellular communication. Non-coding RNAs are considered to be promising biomarker candidates for early diagnosis of cancer as well as potential therapeutic agents. This review aims to provide clarity amidst the vast body of literature by focusing on diverse species of ncRNAs, exploring the structure, origin, function, and potential clinical applications of miRNAs, siRNAs, lncRNAs, circRNAs, snRNAs, snoRNAs, eRNAs, paRNAs, YRNAs, vtRNAs, and piRNAs. We discuss molecular methods used for their detection or functional studies both in vitro and in vivo. We also address the challenges that must be overcome to enter a new era of cancer diagnosis and therapy that will reshape the future of oncology.

Anti-tumor effects of nanosecond pulsed electric fields in a murine model of pancreatic cancer

Nanosecond Pulsed Electric Fields (nsPEFs) treatment has demonstrated anti-tumor effects on various cancer cell lines. However, the use of this treatment in pancreatic cancer is limited. This study demonstrated that nsPEFs treatment effectively suppressed the proliferation and metastasis of pancreatic cancer cells, while also inducing DNA damage. Meanwhile, animal experiments have shown that nsPEFs effectively suppressed the growth of pancreatic cancer, even in cases where the tumor volume exceeded 500-600 mm3 at the initiation of treatment. Notably, a single treatment session was found to significantly inhibit tumor growth, while also showing no adverse effects on the main organs of the mice. RNA sequencing and bioinformatics revealed that seven key genes (CDK1, CENPA, UBE2C, CCNB2, PLK1, CCNA2, and CCNB14) were significantly correlated with the overall survival rate of patients with pancreatic cancer. Through the application of the competing endogenous RNA (ceRNA) hypothesis, two miRNAs (has-let-7b-5p and hsa-miR-193b-3p) and four lncRNAs (MIR4435-2HG, ZNF436-AS1, LINC01089, and MIR4435-2HG) were identified as significantly impacting the overall survival of pancreatic cancer patients. We have effectively developed an mRNA-miRNA-lncRNA network that has the potential to stimulate further investigation into the underlying mechanisms of nsPEFs on pancreatic cancer.

Nuclear factor I/B: Duality in action in cancer pathophysiology

The nuclear factor I (NFI) family of transcription factors plays a decisive role in organ development and maturation. Their deregulation has been linked with various diseases, most notably cancer. NFIB stands apart from the other NFI family members given its unique ability to drive both tumor suppressive and oncogenic programs. Thus, the ultimate impact of deregulated NFIB signaling is cancer-specific and strongly influenced by an intricate network of upstream regulators and downstream effectors. Deciphering the events that drive NFIB's paradoxical roles within these networks will enable us to not only understand how this critical transcription factor enacts its dual roles but also drive innovations to help us effectively target NFIB in different cancers. Here, we provide an in-depth review of NFIB. Starting with its defining role in the development of various organs, most notably the central nervous system, we highlight critical signaling pathways and the impact of deregulation on neoplastic transformation, contrasting it with the effect of silencing alone. We then provide examples of its dual roles in various cancers, identifying specific signaling networks associated with oncogenesis versus tumor suppression. We incorporate an example of a cancer type, osteosarcoma, wherein NFIB enacts its dual functions and explore which pathways influence each function. In this manner, we suggest plausible mechanisms for its role-switching from cancers sharing common triggering events in the setting of NFIB deregulation. We also review how NFIB enhances aggressiveness by driving metastasis, stemness, and chemoresistance. We conclude with a discussion on efficacious ways to target NFIB and pose some unanswered questions that may further help solidify our understanding of NFIB and facilitate clinical translation of NFIB targeting.

LncRNA C2orf27A Promotes Gastric Cancer by Sponging MiR-610 and Elevating NOX4 Expression

Long non-coding RNAs (lncRNAs) are crucial for gastric cancer (GC) progression. In this study, we aimed to investigate the function and molecular pathways of lncRNA C2orf27A in GC development. Bioinformatics databases, tissue cDNA microarrays, and cell lines were used to assess the expression of C2orf27A in GC. Cell proliferation was assessed using Cell Counting Kit-8, colony formation, cell cycle assays, whereas cell death using the Annexin V-APC/7-AAD assay. Subcutaneous xenograft mouse models were used to assess the effects of the C2orf27A knockdown on GC growth in vivo. The subcellular localization of C2orf27A in GC cells was verified using nucleocytoplasmic separation. Bioinformatics analysis predicted the binding of C2orf27A, miR-610, and NADPH oxidase 4 (NOX4), which was validated using dual luciferase reporter gene assay. We found that C2orf27A expression increased in GC tissues and cells. Furthermore, GC patients with increased C2orf27A expression levels had worse survival rates. Silencing of C2orf27A suppressed GC cell growth and induced GC cell death in vitro and in vivo. Further investigations into underlying mechanisms showed that C2orf27A functions as a competitive endogenous RNA against miR-610, leading to increased NOX4 expression levels in GC cells. Notably, blocking miR-610 and increasing NOX4 expression levels reversed the anticancer effects of reduced C2orf27A levels in GC cells. In summary, C2orf27A promotes cell proliferation and reduces cell death through the miR-610/NOX4 pathway in GC, which may provide a new perspective for further elucidation of the molecular mechanism underlying GC progression.

OTUD6B-AS1: a multifaceted regulator of cancer with critical clinical implications

OTU Deubiquitinase 6B-Antisense Transcript 1 (OTUD6B-AS1), a novel long non-coding RNA (lncRNA), has recently emerged as a critical regulator in various tumors. Current research underscores its dual functionality, acting either as an oncogene or a tumor suppressor depending on the tumor context. In this work, we compile and discuss findings from a range of studies investigating the expression patterns of OTUD6B-AS1 in different cancers and its consequent effects on tumor behavior, both in vitro and in vivo. We delve into the mechanisms through which OTUD6B-AS1 influences cancer initiation and progression, focusing on its role in regulating essential cellular processes such as cell growth, migration, invasion, angiogenesis, ferroptosis, and treatment resistance. Operating through complex interactions with microRNAs (miRNAs), proteins, and pivotal signaling pathways - most notably Wnt/β-catenin - OTUD6B-AS1 exhibits variable roles across cancer types and cellular environments. Additionally, we assess the clinical relevance of OTUD6B-AS1 expression levels, evaluating its potential as a biomarker for cancer prognosis and diagnosis, as well as a target for therapeutic intervention. By consolidating existing knowledge, this work aims to highlight the clinical implications of OTUD6B-AS1 and encourage further research in oncology, ultimately contributing to the advancement of targeted cancer therapies.

Construction of a potentially functional long noncoding RNA-microRNA-mRNA network in diabetic cardiomyopathy

Background

Diabetic cardiomyopathy (DCM) is a severe complication among patients with Type 2 diabetes, significantly increasing heart failure risk and mortality. Despite various implicated mechanisms, effective DCM treatments remain elusive. This study aimed to construct a comprehensive competing endogenous RNA (ceRNA) network in DCM using bioinformatics analysis.

Materials and Methods

Three expression profiles datasets (GSE161827, GSE161931, and GSE241166) were collected from gene expression omnibus database and then integrated for the identification of differentially expressed genes (DEGs). Gene Ontology, Kyoto Encyclopedia of Gene and Genome pathway analysis, and Gene set enrichment analysis (GSEA) were employed for functional analysis. Protein-protein interaction (PPI) network and hub genes were also identified. The ceRNA regulatory networks were constructed based on interaction between long noncoding RNA (lncRNA) and DEGs, microRNA (miRNA) and DEGs, as predicted by public available databases.

Results

A total of 105 DEGs, including 44 upregulated and 61 downregulated genes were identified to be associated with DCM. Functional enrichment analysis showed that fatty acid metabolism pathway and inflammatory responses were significantly enriched in DCM. A total of 56 interactions between miRNA with DEGs, and 27 interactions between lncRNA with miRNA was predicted. Besides, a ceRNA network includes 9 mRNA, 17 miRNA and 10 lncRNA was constructed, among which Cdh20 and Cacna2d2 were hub genes in PPI network.

Conclusion

The identified hub genes and ceRNA network components provide valuable insights into DCM biology and offer potential diagnostic biomarkers and therapeutic targets for further investigation. Further experimental validation and clinical studies are warranted to translate these findings into clinical applications.

Correlation between lncRNAs with human molecular chaperons in cancer immunopathogenesis and drug resistance

The development of cancer immunology heavily relies on the interaction between long non-coding RNAs (lncRNAs) and molecular chaperones. By participating in gene regulation, lncRNAs interact with molecular chaperones, which play a critical role in protein folding and stress responses, to influence oncogenic pathways. This interaction has an impact on both the immune cells within the tumor microenvironment and the tumor cells themselves. Understanding these mechanisms provides valuable insights into innovative approaches for diagnosis and treatment. Targeting the lncRNA-chaperone axis has the potential to strengthen anti-tumor immunity and enhance cancer treatment outcomes. Further research is necessary to uncover specific associations, identify biomarkers, and develop personalized therapies aimed at disrupting this axis, which could potentially revolutionize cancer diagnosis and treatment.

Immune checkpoints and ncRNAs: pioneering immunotherapy approaches for hematological malignancies

Hematological malignancies are typically treated with chemotherapy and radiotherapy as the first-line conventional therapies. However, non-coding RNAs (ncRNAs) are a rapidly expanding field of study in cancer biology that influences the growth, differentiation, and proliferation of tumors by targeting immunological checkpoints. This study reviews the results of studies (from 2012 to 2024) that consider the immune checkpoints and ncRNAs in relation to hematological malignancies receiving immunotherapy. This article provides a summary of the latest advancements in immunotherapy for treating hematological malignancies, focusing on the role of immune checkpoints and ncRNAs in the immune response and their capacity for innovative strategies. The paper also discusses the function of immune checkpoints in maintaining immune homeostasis and how their dysregulation can contribute to developing leukemia and lymphoma. Finally, this research concludes with a discussion on the obstacles and future directions in this rapidly evolving field, emphasizing the need for continued research to fully harness the capacity of immune checkpoints and ncRNAs in immunotherapy for hematological malignancies.

Bioinformatic analysis of neuropeptide related genes in patients diagnosed with invasive breast carcinoma

PURPOSE

Neuropeptide receptors are expressed in many malignancies. Effectors involved in the action mechanisms of HCRTR1, HCRTR2, NPY4R (PPYR1) may be related to breast cancer (BC). Genes encoding these receptors and PPY and PTPN11 genes were aimed to examine via bioinformatics tools in the BRCA cohort. To our knowledge, this is the first study in which these receptor genes and PP, which have not found much research in BC, are examined together with PTPN11 and analyzed comprehensively in large patient cohorts from public databases.

METHODS

cBioPortal was used for gene alteration analyses, GeneMania for association analyses with other genes, Kaplan-Meier Plotter for Overall Survival (OS) and Relapse Free Survival (RFS) analyses, UALCAN for methylation analyses, TIMER2.0 for expression analyses, The Human Protein Atlas database for expression validations, TIMER for immune infiltration analyses, WEKA 3.8.6 for diagnostic classification performances of the genes based on Random Forest Classifier and Enrichr-KG for Gene Ontology (GO) Biological Process (BP) and KEGG analysis.

RESULTS

19 (1.9 %) nucleotide changes were found in 996 cases. Missense mutation is most common. Decreased expression levels of the HCRTR1 gene were associated with shorter OS and RFS, but decreased expression levels of the PTPN11 gene were associated with longer OS and RFS. Decreased expression levels NPY4R (PPYR1) gene were associated with shorter RFS. Increased expression levels of HCRTR2 and PPY genes were associated with longer RFS. HCRTR1 and NPY4R (PPYR1) genes were statistically hypermethylated; conversely HCRTR2 and PPY genes were hypomethylated. There was no significant change in PTPN11 gene promoter methylation level. HCRTR1, NPY4R (PPYR1) and PTPN11 gene expressions were downregulated; conversely, HCRTR2 and PPY gene expressions upregulated. Weak correlations were observed between NPY4R (PPYR1) gene expression and CD4+ T Cell, Neutrophil, Dendritic Cell and between PTPN11 gene expression and CD8+ T Cell, Macrophage, Neutrophil, Dendritic Cell infiltrations. Area under the receiver operating characteristics curve values of the 10-fold cross-validation and by splitting the dataset in a ratio of 80:20 models were 0.930 and 0.963 respectively. HCRTR2 and HCRTR1 belong to regulation of cytosolic calcium ion concentration, cellular calcium ion homeostasis GO BPs.

CONCLUSION

In BC patients, increases in HCRTR2 and PPY gene expressions could be considered as positive prognostic factors. Decreases in HCRTR1 and NPY4R (PPYR1) gene expressions could be considered as negative prognostic factors. Decreased expression of PTPN11 gene may have a positive prognostic factor. Changes in existing genes are likely to be both a biomarker and therapeutic target for BC. However, experimental and clinical studies are needed to elucidate the mechanisms underlying these neuropeptide receptors in terms of breast carcinogenesis.

Construction of a cell cycle-specific lncRNA-miRNA-mRNA network reveals novel key lncRNAs in colorectal cancer

OBJECTIVE

The current study aimed to determine the roles of pivotal and novel lncRNAs associated with the cell cycle in the occurrence and development of Colorectal cancer (CRC).

METHODS

The TCGA-COAD project related to CRC was downloaded, and differential expression analysis was performed to identify differentially expressed lncRNAs, miRNAs, and mRNAs. A cell cycle-associated lncRNA-miRNA-mRNA regulatory network was constructed, and two novel lncRNAs were selected. Two subnetworks were constructed for selected lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were illustrated for the genes in each sub-network. qPCR analysis was used to validate the expression levels of the selected lncRNAs in CRC tissues compared to those adjacent normal tissues.

RESULTS

The differential expression analysis identified 416 lncRNAs, 317 miRNAs, and 117 mRNAs. The ceRNA subnetwork genes were associated with different pathways, including cellular senescence, DNA replication, human T-cell leukemia virus 1 infection, and oocyte meiosis. The bioinformatic results based on the TCGA project indicated the dysregulation of two novel lncRNAs, MIR29B2CHG and HELLPAR, in CRC tissues compared to adjacent normal tissues. Moreover, qPCR confirmed the dysregulation of lncRNAs in the CRC tissues. ROC curves revealed that both selected lncRNAs had acceptable specificity and sensitivity as biomarkers.

CONCLUSION

In conclusion, novel cell cycle-associated lncRNAs have the potential to be understood as the underlying molecular mechanisms that influence CRC. Therefore, these lncRNAs can be considered as promising biomarkers for the diagnosis and treatment of CRC.

A Comprehensive Analysis of the ceRNA Network and Hub Genes in Avian Leukosis Virus Subgroup J and Infectious Bursal Disease Virus Superinfection

In the realm of poultry production, viral superinfections pose significant challenges, causing substantial economic losses worldwide. Among these, avian leukosis virus subgroup J (ALV-J) and infectious bursal disease virus (IBDV) are particularly concerning as they frequently lead to superinfections in chicken, further exacerbating production losses and health complications. Our previous research delved into the pathogenicity and immunosuppressive effects of these superinfections through in vitro and in vivo analyses. Yet, the underlying key genes and pathways governing this phenomenon remained elusive. In this study, we randomly selected three chickens at 21 days post infection from each treatment group (ALV-J, IBDV, ALV-J+IBDV, and control group) to collect the bursa of Fabricius samples for full transcriptome analysis. Utilizing these data, we constructed a comprehensive circRNA/lncRNA-miRNA-mRNA network which elucidated both synergistic and specific activations during the superinfection. Notably, three pivotal genes (FILIP1L, DCX, and MYPN) were pinpointed in datasets reflecting synergistic activations. Conversely, four other genes (STAP, HKR6, XKR4, and TLR5) emerged in datasets associated with specific activations. Further exploration revealed diverse significant GO terms and pathways associated with both synergistic and distinct activation processes. These ceRNA network and core genes potentially wield substantial influence over the synergistic or specific activation of tumorigenesis and pathogenesis induced by ALV-J and IBDV. These findings could help develop targeted therapies and improve disease control in poultry, reducing economic losses.

In silico analysis and comprehensive review of circular-RNA regulatory roles in breast diseases; a step-toward non-coding RNA precision

In the current comprehensive review, we first highlighted circRNAs, which are key ncRNAs. Next, we discussed the relationships among circRNAs and breast cancer subtypes via in silico databases analysis and extensive literature search. CircRNAs, that sponge miRNA axes or act as silencers of oncogenic mRNAs, have been extensively addressed in the context of this review. During BC pathogenesis, the circRNA/microRNA/messenger RNA (mRNA) axis plays a major role in disease growth, progression, and survival/resistance and could be targeted for improved treatment options. This review also aimed to address oncogenic and tumor suppressor mRNAs, which are regulated by various circRNAs in BC. Moreover, we mentioned the relation of different circRNAs with cancer hallmarks, patient survival together with drug resistance. Additionally, we discussed circRNAs as vaccines and biomarkers in BC. Finally, we studied exosomal circRNAs as a hot interesting area in the research. REVIEW SIGNIFICANCE: Via using in silico databases, bioinformatics analysis, and a thorough literature search to first highlight circRNA as a crucial ncRNA and its biogenesis, and then we explored the connection between circRNA and breast illnesses. In the framework of the review, circRNA sponged-miRNAs axis or as silencers to oncogenic mRNAs were extensively discussed. In the pathophysiology of BC, the circular RNA/microRNA/messenger RNA axis is crucial for the propagation of the disease and resistance that may be targeted for more effective treatment options, in order to confront tumor suppressor and oncogenic mRNAs that are presently regulated by circRNAs in BC. For better patient results, we advised further mechanistic research to elucidate additional ncRNA axis that may be targeted for the therapy of BC and for prognosis/ or early diagnosis.

RUNX2 regulation in osteoblast differentiation: A possible therapeutic function of the lncRNA and miRNA-mediated network

Osteogenic differentiation is a crucial process in the formation of the skeleton and the remodeling of bones. It relies on a complex system of signaling pathways and transcription factors, including Runt-related transcription factor 2 (RUNX2). Non-coding RNAs (ncRNAs) control the bone-specific transcription factor RUNX2 through post-transcriptional mechanisms to regulate osteogenic differentiation. The most research has focused on microRNAs (miRNAs) and long ncRNAs (lncRNAs) in studying how they regulate RUNX2 for osteogenesis in both normal and pathological situations. This article provides a concise overview of the recent advancements in understanding the critical roles of lncRNA/miRNA/axes in controlling the expression of RUNX2 during bone formation. The possible application of miRNAs and lncRNAs as therapeutic agents for the treatment of disorders involving the bones and bones itself is also covered.

Emerging roles of noncoding RNAs in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, fibrotic lung disease with limited treatment options and efficacy. Evidence suggests that IPF arises from genetic, environmental, and aging-related factors. The pathogenic mechanisms of IPF primarily involve dysregulated repeated microinjuries to epithelial cells, abnormal fibroblast/myofibroblast activation, and extracellular matrix (ECM) deposition, but thus far, the exact etiology remains unclear. Noncoding RNAs (ncRNAs) play regulatory roles in various biological processes and have been implicated in the pathophysiology of multiple fibrotic diseases, including IPF. This review summarizes the roles of ncRNAs in the pathogenesis of IPF and their potential as diagnostic and therapeutic targets.

1,2-bis(2,4,6-tribromophenoxy) ethane induces necroptosis via the co-competition of GAS5 and NUAK1 for miR-743a-5p in rat hepatocytes

The brominated flame retardant 1,2-bis(2,4,6-tribromophenoxy) ethane (BTBPE) widely used in manufacturing is inevitably released into the environment, resulting in the exposure of organisms to BTBPE. Therefore, it is particularly important to explore its toxic mechanism. The liver is one of the main accumulating organs of BTBPE, but the mechanism underlying BTBPE hepatotoxicity has not been thoroughly investigated. In our study, BTBPE was administered to Sprague-Dawley (SD) rats and rat hepatocytes (BRL cells) in vivo and in vitro, respectively, and HE staining, AO/EB staining, fluorescent probes, qPCR, immunofluorescence, and dual-luciferase reporter assays were performed. We investigated the mechanism of action of growth arrest-specific 5 (GAS5), miR-743a-5p, and NUAK family kinase 1 (NUAK1) in BTBPE-induced necroptosis from the perspective of competing endogenous RNAs (ceRNAs) using NUAK1 inhibitors, siRNAs, mimics, and overexpression plasmids. Our study showed that exposure to BTBPE caused necroptosis in the liver and BRL cells, accompanied by an oxidation-reduction imbalance and an inflammatory response. It is worth noting that NUAK1 is a newly discovered upstream regulatory target for necroptosis. In addition, miR-743a-5p was shown to inhibit necroptosis by targeting NUAK1 and down-regulating NUAK1. GAS5 upregulates NUAK1 expression by competitively binding to miR-743a-5p, thereby inducing necroptosis. This study demonstrated, for the first time, that the GAS5-miR-743a-5p-NUAK1 axis is involved in the regulation of necroptosis via ceRNAs. Thus, GAS5 and NUAK1 induce necroptosis by competitively binding to miR-743a-5p.

LncRNA MIAT suppresses inflammation in LPS-induced J774A.1 macrophages by promoting autophagy through miR-30a-5p/SOCS1 axi

Accumulated data implicate that long noncoding RNA (lncRNA) plays a pivotal role in rheumatoid arthritis (RA), potentially serving as a competitive endogenous RNA (ceRNA) for microRNAs (miRNAs). The lncRNA myocardial infarction-associated transcript (MIAT) has been demonstrated to regulate inflammation. However, the role of MIAT in the inflammation of RA remains inadequately explored. This study aims to elucidate MIAT's role in the inflammation of lipopolysaccharide (LPS)-induced macrophages and to uncover the underlying molecular mechanisms. We observed heightened MIAT expression in LPS-induced J774A.1 cells and collagen-induced arthritis mouse models, in contrast to the expression pattern of miR-30a-5p. Silencing MIAT resulted in increased expression of the inflammatory cytokines IL-1β and TNF-α. Simultaneously, MIAT interference significantly impeded macrophage autophagy, evidenced by decreased expression of autophagy-related markers LC3-II and Beclin-1, alongside increased levels of p62 in LPS-induced J774A.1 cells. Notably, MIAT functioned as a ceRNA, sponging miR-30a-5p and exerting a negative regulatory influence on its expression. SOCS1 emerged as a target of miR-30a-5p, modulated by MIAT. Mechanistically, inhibiting miR-30a-5p reversed the impact of MIAT deficiency in promoting LPS-induced inflammation, while SOCS1 knockdown countered the cytokine inhibitory effect induced by silencing miR-30a-5p. In summary, this study indicates that lncRNA MIAT suppresses inflammation in LPS-induced J774A.1 macrophages by stimulating autophagy through the miR-30a-5p/SOCS1 axis. This suggests that MIAT holds promise as a potential therapeutic target for RA inflammation.

The importance of the circRNA/Wnt axis in gliomas: Biological functions and clinical opportunities

Gliomas are among the most common cancers in the central nervous system, arising through various signaling pathways. One significant pathway is Wnt signaling, a tightly regulated process that plays a crucial role in gliomagenesis and development. The current study aims to explore the relationship between circular RNAs (circRNAs) and the Wnt/β-catenin signaling pathway in gliomas, considering the growing recognition of circRNAs in disease pathogenesis. A comprehensive review of recent research was conducted to investigate the roles of circRNAs in gliomas, focusing on their expression patterns and interactions with the Wnt signaling pathway. The analysis included studies examining circRNAs' function as microRNA sponges and their impact on glioma biology. The findings reveal that circRNAs are differentially expressed in gliomas and significantly influence the occurrence, growth, and metastasis of these tumors. Specifically, circRNAs interact with the Wnt signaling pathway, affecting glioma development and progression. This interaction highlights the importance of circRNAs in glioma pathophysiology. Understanding the regulatory network involving circRNAs and Wnt signaling offers valuable insights into glioma pathophysiology. CircRNAs hold promise as diagnostic and prognostic biomarkers and may serve as targets for novel therapeutic strategies in glioma treatment.

Unveiling the role of microRNAs in metabolic dysregulation of Gestational Diabetes Mellitus

Gestational Diabetes Mellitus (GDM) presents a significant health concern globally, necessitating a comprehensive understanding of its metabolic intricacies for effective management. MicroRNAs (miRNAs) have emerged as pivotal regulators in GDM pathogenesis, influencing glucose metabolism, insulin signaling, and lipid homeostasis during pregnancy. Dysregulated miRNA expression, both upregulated and downregulated, contributes to GDM-associated metabolic abnormalities. Ethnic and temporal variations in miRNA expression underscore the multifaceted nature of GDM susceptibility. This review examines the dysregulation of miRNAs in GDM and their regulatory functions in metabolic disorders. We discuss the involvement of specific miRNAs in modulating key pathways implicated in GDM pathogenesis, such as glucose metabolism, insulin signaling, and lipid homeostasis. Furthermore, we explore the potential diagnostic and therapeutic implications of miRNAs in GDM management, highlighting the promise of miRNA-based interventions for mitigating the adverse consequences of GDM on maternal and offspring health.

SexAnnoDB, a knowledgebase of sex-specific regulations from multi-omics data of human cancers

BACKGROUND

Sexual differences across molecular levels profoundly impact cancer biology and outcomes. Patient gender significantly influences drug responses, with divergent reactions between men and women to the same drugs. Despite databases on sex differences in human tissues, understanding regulations of sex disparities in cancer is limited. These resources lack detailed mechanistic studies on sex-biased molecules.

METHODS

In this study, we conducted a comprehensive examination of molecular distinctions and regulatory networks across 27 cancer types, delving into sex-biased effects. Our analyses encompassed sex-biased competitive endogenous RNA networks, regulatory networks involving sex-biased RNA binding protein-exon skipping events, sex-biased transcription factor-gene regulatory networks, as well as sex-biased expression quantitative trait loci, sex-biased expression quantitative trait methylation, sex-biased splicing quantitative trait loci, and the identification of sex-biased cancer therapeutic drug target genes. All findings from these analyses are accessible on SexAnnoDB ( https://ccsm.uth.edu/SexAnnoDB/ ).

RESULTS

From these analyses, we defined 126 cancer therapeutic target sex-associated genes. Among them, 9 genes showed sex-biased at both the mRNA and protein levels. Specifically, S100A9 was the target of five drugs, of which calcium has been approved by the FDA for the treatment of colon and rectal cancers. Transcription factor (TF)-gene regulatory network analysis suggested that four TFs in the SARC male group targeted S100A9 and upregulated the expression of S100A9 in these patients. Promoter region methylation status was only associated with S100A9 expression in KIRP female patients. Hypermethylation inhibited S100A9 expression and was responsible for the downregulation of S100A9 in these female patients.

CONCLUSIONS

Comprehensive network and association analyses indicated that the sex differences at the transcriptome level were partially the result of corresponding sex-biased epigenetic and genetic molecules. Overall, SexAnnoDB offers a discipline-specific search platform that could potentially assist basic experimental researchers or physicians in developing personalized treatment plans.

Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network

Background

Ulcerative colitis (UC) is a common chronic disease associated with inflammation and oxidative stress. This study aimed to construct a long noncoding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) network based on bioinformatics analysis and to explore oxidative stress-related genes underlying the pathogenesis of UC.

Methods

The GSE75214, GSE48959, and GSE114603 datasets were downloaded from the Gene Expression Omnibus database. Following differentially expressed (DE) analysis, the regulatory relationships among these DERNAs were identified through miRDB, miRTarBase, and TargetScan; then, the lncRNA-miRNA-mRNA network was established. The Molecular Signatures Database (MSigDB) was used to search oxidative stress-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for functional annotation and enrichment analyses. Based on the drug gene interaction database DGIdb, drugs that interact with oxidative stress-associated genes were explored. A dextran sulfate sodium (DSS)-induced UC mouse model was used for experimental validation.

Results

A total of 30 DE-lncRNAs, 3 DE-miRNAs, and 19 DE-mRNAs were used to construct a lncRNA-miRNA-mRNA network. By comparing these 19 DE-mRNAs with oxidative stress-related genes in MSigDB, three oxidative stress-related genes (CAV1, SLC7A11, and SLC7A5) were found in the 19 DEM sets, which were all negatively associated with miR-194. GO and KEGG analyses showed that CAV1, SLC7A11, and SLC7A5 were associated with immune inflammation and steroid hormone synthesis. In animal experiments, the results showed that dexamethasone, a well-known glucocorticoid drug, could significantly decrease the expression of CAV1, SLC7A11, and SLC7A5 as well as improve UC histology, restore antioxidant activities, inhibit inflammation, and decrease myeloperoxidase activity.

Conclusion

SLC7A5 was identified as a representative gene associated with glucocorticoid therapy resistance and thus may be a new therapeutic target for the treatment of UC in the clinic.

ST8SIA6-AS1, a novel lncRNA star in liver cancer

Liver cancer is one of the most lethal gastrointestinal malignancies. Emerging evidence has underscored the pivotal role of long non-coding RNAs (lncRNAs) in tumorigenesis, with ST8SIA6-AS1 identified as a novel oncogenic lncRNA contributing to liver cancer progression. ST8SIA6-AS1 is consistently upregulated in hepatic cancer tissues and is strongly associated with unfavorable prognosis. Moreover, it demonstrates high diagnostic efficacy in detecting HCC. ST8SIA6-AS1 is involved in various cellular processes including proliferation, migration, and invasion, primarily through its function as a competing endogenous RNA (ceRNA), thereby facilitating hepatocarcinogenesis and disease advancement. This review provides a detailed examination of the molecular functions and regulatory mechanisms of ST8SIA6-AS1 in hepatocellular carcinoma (HCC) and highlights its potential as a promising biomarker for liver cancer, aiming to propel the development of innovative therapeutic strategies for HCC management.

Cuproptosis related ceRNA axis AC008083.2/miR-142-3p promotes the malignant progression of nasopharyngeal carcinoma through STRN3

Background

CeRNA axis is an important way to regulate the occurrence and development of Nasopharyngeal carcinoma (NPC). Although the research on inducing cuproptosis of tumor cells is in the early stage of clinical practice, its mechanism of action is still of great significance for tumor treatment, including NPC. However, the regulation mechanism of cuproptosis in NPC by ceRNA network remains unclear.

Methods

The ceRNA network related to the survival of nasopharyngeal carcinoma related genes was constructed by bioinformatics. Dual-luciferase reporter assay and other experiments were used to prove the conclusion.

Results

Our findings indicate that the AC008083.2/miR-142-3p axis drives STRN3 to promote the malignant progression of NPC. By performing enrichment analysis and phenotypic assays, we demonstrated that the changes in the expressions of AC008083.2/miR-142-3p/NPC can affect the proliferation of NPC. Mechanistically, luciferase reporter gene assays suggested that AC008083.2 acts as a ceRNA of miR-142-3p to regulate the content of STRN3. Furthermore, the regulations of STRN3 and the malignant progression of NPC by AC008083.2 depends on miR-142-3p to some extent.

Conclusions

Our study reveals an innovative ceRNA regulatory network in NPC, which can be considered a new potential target for diagnosing and treating NPC.

Bta-miR-200a Regulates Milk Fat Biosynthesis by Targeting IRS2 to Inhibit the PI3K/Akt Signal Pathway in Bovine Mammary Epithelial Cells

Milk fat synthesis has garnered significant attention due to its influence on the quality of milk. Recently, an increasing amount of proofs have elucidated that microRNAs (miRNAs) are important post-transcriptional factor involved in regulating gene expression and play a significant role in milk fat synthesis. MiR-200a was differentially expressed in the mammary gland tissue of dairy cows during different lactation periods, which indicated that miR-200a was a candidate miRNA involved in regulating milk fat synthesis. In our research, we investigated the potential function of miR-200a in regulating milk fat biosynthesis in bovine mammary epithelial cells (BMECs). We discovered that miR-200a inhibited cellular triacylglycerol (TAG) synthesis and suppressed lipid droplet formation; at the same time, miR-200a overexpression suppressed the mRNA and protein expression of milk fat metabolism-related genes, such as fatty acid synthase (FASN), peroxisome proliferator-activated receptor gamma (PPARγ), sterol regulatory element-binding protein 1 (SREBP1), CCAAT enhancer binding protein alpha (CEBPα), etc. However, knocking down miR-200a displayed the opposite results. We uncovered that insulin receptor substrate 2 (IRS2) was a candidate target gene of miR-200a through the bioinformatics online program TargetScan. Subsequently, it was confirmed that miR-200a directly targeted the 3'-untranslated region (3'-UTR) of IRS2 via real-time fluorescence quantitative PCR (RT-qPCR), western blot analysis, and dual-luciferase reporter gene assay. Additionally, IRS2 knockdown in BMECs has similar effects to miR-200a overexpression. Our research set up the mechanism by which miR-200a interacted with IRS2 and discovered that miR-200a targeted IRS2 and modulated the activity of the PI3K/Akt signaling pathway, thereby taking part in regulating milk fat synthesis in BMECs. Our research results provided valuable information on the molecular mechanisms for enhancing milk quality from the view of miRNA-mRNA regulatory networks.

Regulation potential of transcribed simple repeated sequences in developing neurons

Simple repeated sequences (SRSs), defined as tandem iterations of microsatellite- to satellite-sized DNA units, occupy a substantial part of the human genome. Some of these elements are known to be transcribed in the context of repeat expansion disorders. Mounting evidence suggests that the transcription of SRSs may also contribute to normal cellular functions. Here, we used genome-wide bioinformatics approaches to systematically examine SRS transcriptional activity in cells undergoing neuronal differentiation. We identified thousands of long noncoding RNAs containing >200-nucleotide-long SRSs (SRS-lncRNAs), with hundreds of these transcripts significantly upregulated in the neural lineage. We show that SRS-lncRNAs often originate from telomere-proximal regions and that they have a strong potential to form multivalent contacts with a wide range of RNA-binding proteins. Our analyses also uncovered a cluster of neurally upregulated SRS-lncRNAs encoded in a centromere-proximal part of chromosome 9, which underwent an evolutionarily recent segmental duplication. Using a newly established in vitro system for rapid neuronal differentiation of induced pluripotent stem cells, we demonstrate that at least some of the bioinformatically predicted SRS-lncRNAs, including those encoded in the segmentally duplicated part of chromosome 9, indeed increase their expression in developing neurons to readily detectable levels. These and other lines of evidence suggest that many SRSs may be expressed in a cell type and developmental stage-specific manner, providing a valuable resource for further studies focused on the functional consequences of SRS-lncRNAs in the normal development of the human brain, as well as in the context of neurodevelopmental disorders.

Exploring the Regulatory Landscape of Dementia: Insights from Non-Coding RNAs

Dementia, a multifaceted neurological syndrome characterized by cognitive decline, poses significant challenges to daily functioning. The main causes of dementia, including Alzheimer's disease (AD), frontotemporal dementia (FTD), Lewy body dementia (LBD), and vascular dementia (VD), have different symptoms and etiologies. Genetic regulators, specifically non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are known to play important roles in dementia pathogenesis. MiRNAs, small non-coding RNAs, regulate gene expression by binding to the 3' untranslated regions of target messenger RNAs (mRNAs), while lncRNAs and circRNAs act as molecular sponges for miRNAs, thereby regulating gene expression. The emerging concept of competing endogenous RNA (ceRNA) interactions, involving lncRNAs and circRNAs as competitors for miRNA binding, has gained attention as potential biomarkers and therapeutic targets in dementia-related disorders. This review explores the regulatory roles of ncRNAs, particularly miRNAs, and the intricate dynamics of ceRNA interactions, providing insights into dementia pathogenesis and potential therapeutic avenues.

Circular RNA circEfnb2 promotes cell injury after cerebral infarction by sponging miR-202-5p and regulating TRAF3 expression

BACKGROUND

Exogenous neural cell transplantation may be therapeutic for stroke, cerebral ischemic injury. Among other mechanisms, increasing findings indicated circular RNAs (circRNAs) regulate the pathogenesis progression of cerebral ischemia. Mmu_circ_0015034 (circEfnb2) was upregulated in focal cortical infarction established by middle cerebral artery occlusion (MCAO) in mice. Our study was designed to probe the molecular mechanism of circEfnb2 in the oxygen-glucose deprivation/reperfusion (OGD/R)-induced neuronal damage in cerebral ischemia.

METHODS

We established an in vitro OGD/R cell model. CircEfnb2 and microRNA-202-5p (miR-202-5p) levels were detected using real-time quantitative polymerase chain reaction (RT-qPCR). Lactate dehydrogenase (LDH), malondialdehyde (MDA), and reactive oxygen species (ROS) levels were assessed using specific kits. Tumor necrosis factor-α (TNF-α) and Interleukin-1β (IL-1β) levels were examined using an Enzyme-linked immunosorbent assay (ELISA). Flow cytometry analysis evaluated cell apoptosis. Protein levels of B-cell lymphoma-2 (Bcl-2), Bcl-2 related X protein (Bax), cleaved caspase 3, and Tumor necrosis factor receptor-associated factor 3 (TRAF3) were determined using Western blot assay.

RESULTS

Overall, circEfnb2 was highly expressed whereas miR-202-5p was decreased in OGD/R-treated mouse hippocampal neuronal HT22 cells compared to normal controls (both p > 0.05). From an in vitro functional perspective, circEfnb2 knockdown attenuated an OGD/R-triggered neuronal injury compared to controls (p > 0.05). Mechanically, circEfnb2 acted as a sponge of miR-202-5p; downregulation of miR-202-5p annulled the inhibitory roles of circEfnb2 silencing in an OGD/R-caused neuronal injury model. Our analysis showed that miR-202-5p directly targeted TRAF3 as enhanced TRAF3 abolished the effects of miR-202-5p in the OGD/R-induced neuronal injury. In vivo, lentivirus with a short hairpin (sh)-circEfnb2 inhibited cerebral injury, when injected into cerebral cortex in MCAO mice (p > 0.05).

CONCLUSION

Our results suggest that circEfnb2 deficiency may decrease OGD/R-induced HT22 cell damage by modulating the miR-202-5p/TRAF3 axis. This explanation may provide a new direction for cerebral infarction potential therapeutic targets.

WTAP-mediated m6A modification of lncRNA Snhg1 improves myocardial ischemia-reperfusion injury via miR-361-5p/OPA1-dependent mitochondrial fusion

BACKGROUND

Myocardial ischemia-reperfusion injury (MIRI) is caused by reperfusion after ischemic heart disease. LncRNA Snhg1 regulates the progression of various diseases. N6-methyladenosine (m6A) is the frequent RNA modification and plays a critical role in MIRI. However, it is unclear whether lncRNA Snhg1 regulates MIRI progression and whether the lncRNA Snhg1 was modified by m6A methylation.

METHODS

Mouse cardiomyocytes HL-1 cells were utilized to construct the hypoxia/reoxygenation (H/R) injury model. HL-1 cell viability was evaluated utilizing CCK-8 method. Cell apoptosis, mitochondrial reactive oxygen species (ROS), and mitochondrial membrane potential (MMP) were quantitated utilizing flow cytometry. RNA immunoprecipitation and dual-luciferase reporter assays were applied to measure the m6A methylation and the interactions between lncRNA Snhg1 and targeted miRNA or target miRNAs and its target gene. The I/R mouse model was constructed with adenovirus expressing lncRNA Snhg1. HE and TUNEL staining were used to evaluate myocardial tissue damage and apoptosis.

RESULTS

LncRNA Snhg1 was down-regulated after H/R injury, and overexpressed lncRNA Snhg1 suppressed H/R-stimulated cell apoptosis, mitochondrial ROS level and polarization. Besides, lncRNA Snhg1 could target miR-361-5p, and miR-361-5p targeted OPA1. Overexpressed lncRNA Snhg1 suppressed H/R-stimulated cell apoptosis, mitochondrial ROS level and polarization though the miR-361-5p/OPA1 axis. Furthermore, WTAP induced lncRNA Snhg1 m6A modification in H/R-stimulated HL-1 cells. Moreover, enforced lncRNA Snhg1 repressed I/R-stimulated myocardial tissue damage and apoptosis and regulated the miR-361-5p and OPA1 levels.

CONCLUSION

WTAP-mediated m6A modification of lncRNA Snhg1 regulated MIRI progression through modulating myocardial apoptosis, mitochondrial ROS production, and mitochondrial polarization via miR-361-5p/OPA1 axis, providing the evidence for lncRNA as the prospective target for alleviating MIRI progression.

Construction of competing endogenous RNA networks in systemic lupus erythematosus by integrated analysis

Objective

Systemic lupus erythematosus (SLE) is a disease characterised by immune inflammation and damage to multiple organs. Recent investigations have linked competing endogenous RNAs (ceRNAs) to lupus. However, the exact mechanism through which the ceRNAs network affects SLE is still unclear. This study aims to investigate the regulatory functions of the ceRNAs network, which are important pathways that control the pathophysiological processes of SLE.

Methods

CircRNA microarray for our tested assays were derived from bone marrow samples from three healthy individuals and three SLE patients in our hospital. The other sequencing data of circRNA, miRNA and mRNA were obtained from Gene Expression Omnibus (GEO) datasets. Using the limma package of R program, the differential expression of mRNA and miRNA in the GEO database was discovered. Then predicted miRNA-mRNA and circRNA-miRNA were established using miRMap, miRanda, miRDB, TargetScan, and miTarBase. CircRNA-miRNA-mRNA ceRNA network was constructed using Cytoscape, and hub genes were screened using a protein-protein interaction network. Immune infiltration analysis of the hub gene was also performed by CIBERSORT and GSEA.

Results

230 overlapped circRNAs, 86 DEmiRNAs and 2083 DEmRNAs were identified in SLE patients as compared to healthy controls. We constructed a circRNA-miRNA-mRNA ceRNAs network contained 11 overlapped circRNAs, 9 miRNAs and 51 mRNAs. ESR1 and SIRT1 were the most frequently associated protein-protein interactions in the PPI network. KEGG analysis showed that DEGs was enriched in FoxO signaling pathway as well as lipids and atherosclerosis. We constructed a novel circRNA-miRNA-mRNA ceRNA network (HSA circ 0000345- HSA miR-22-3-P-ESR1/SIRT1) that may have a major impact on SLE.

Conclusion

Through this bioinformatics and integrated analysis, we suggest a regulatory role for ceRNA network in the pathogenesis and treatment of SLE.

Visfatin Facilitates VEGF-D-Induced Lymphangiogenesis through Activating HIF-1α and Suppressing miR-2277-3p in Human Chondrosarcoma

Chondrosarcoma is a malignant bone tumor that arises from abnormalities in cartilaginous tissue and is associated with lung metastases. Lymphangiogenesis plays an essential role in cancer metastasis. Visfatin is an adipokine reported to enhance tumor metastasis, but its relationship with VEGF-D generation and lymphangiogenesis in chondrosarcoma remains undetermined. Our results from clinical samples reveal that VEGF-D levels are markedly higher in chondrosarcoma patients than in normal individuals. Visfatin stimulation promotes VEGF-D-dependent lymphatic endothelial cell lymphangiogenesis. We also found that visfatin induces VEGF-D production by activating HIF-1α and reducing miR-2277-3p generation through the Raf/MEK/ERK signaling cascade. Importantly, visfatin controls chondrosarcoma-related lymphangiogenesis in vivo. Therefore, visfatin is a promising target in the treatment of chondrosarcoma lymphangiogenesis.

Regulatory and therapeutic implications of competing endogenous RNA network in breast cancer progression and metastasis: A review

Breast cancer (BC) is a global health concern, and development of diagnostic tools and targeted treatments for BC remains challenging. Therapeutic approaches for BC often involve a combination of surgery, radiation therapy, chemotherapy, targeted therapy, and hormone therapy. In recent years, there has been a growing interest in the role of noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRNAs), in BC and their therapeutic implications. Various biological processes such as cell proliferation, migration, and apoptosis rely on the activities of these ncRNAs, and their dysregulation has been implicated in BC progression. The regulatory function of the competitive endogenous RNA (ceRNA) network, which comprises lncRNAs, miRNAs, and mRNAs, has been the subject of extensive pathophysiological research. Most lncRNAs serve as molecular sponges for miRNAs and sequester their activities, thereby regulating the expression of target mRNAs and contributing to the promotion or inhibition of BC progression. This review summarizes recent findings on the role of ceRNA networks in BC progression, metastasis, and therapeutic resistance, and highlights the association of ceRNA networks with transcription factors and signaling pathways. Understanding the ceRNA network can lead to the discovery of biomarkers and targeted treatment methods to prevent the spread and metastasis of BC.

Exploring the Key Signaling Pathways and ncRNAs in Colorectal Cancer

Colorectal cancer (CRC) is the third most prevalent cancer to be diagnosed, and it has a substantial mortality rate. Despite numerous studies being conducted on CRC, it remains a significant health concern. The disease-free survival rates notably decrease as CRC progresses, emphasizing the urgency for effective diagnostic and therapeutic approaches. CRC development is caused by environmental factors, which mostly lead to the disruption of signaling pathways. Among these pathways, the Wingless/Integrated (Wnt) signaling pathway, Phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway, Mitogen-Activated Protein Kinase (MAPK) signaling pathway, Transforming Growth Factor-β (TGF-β) signaling pathway, and p53 signaling pathway are considered to be important. These signaling pathways are also regulated by non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). They have emerged as crucial regulators of gene expression in CRC by changing their expression levels. The altered expression patterns of these ncRNAs have been implicated in CRC progression and development, suggesting their potential as diagnostic and therapeutic targets. This review provides an overview of the five key signaling pathways and regulation of ncRNAs involved in CRC pathogenesis that are studied to identify promising avenues for diagnosis and treatment strategies.

Bioinformatics analysis of a disease-specific lncRNA-miRNA-mRNA regulatory network in recurrent spontaneous abortion (RSA)

BACKGROUND

This study investigated the molecular mechanisms of long non-coding RNAs (lncRNAs) in RSA using the lncRNA-miRNA-mRNA regulatory network.

METHODS

The present study obtained expression datasets of long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), and microRNAs (miRNAs) from blood samples of individuals with unexplained recurrent spontaneous abortion (RSA) and healthy controls. Differentially expressed lncRNAs (DELs), mRNAs (DEMs), and miRNAs (DEmiRs) were identified. A regulatory network comprising lncRNA, miRNA, and mRNA was constructed, and Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to analyze the biological functions of DEM. Also, a protein-protein interaction (PPI) network was made and key genes were identified.

RESULTS

A total of 57 DELs, 212 DEmiRs, and 301 DEMs regarding RSA were identified. Later analysis revealed a lncRNA-miRNA-mRNA network comprising nine lncRNAs, 14 miRNAs, and 65 mRNAs. Then, the ceRNA network genes were subjected to functional enrichment and pathway analysis, which showed their association with various processes, such as cortisol and thyroid hormone synthesis and secretion, human cytomegalovirus infection, and parathyroid hormone synthesis. In addition, ten hub genes (ITGB3, GNAI2, GNAS, SRC, PLEC, CDC42, RHOA, RAC1, CTNND1, and FN1) were identified based on the PPI network results.

CONCLUSION

In summary, the outcomes of our study provided some data regarding the alteration genes involved in RSA pathogenic mechanism via the lncRNA-miRNA-mRNA network and reveal the possibility of identifying new lncRNAs and miRNAs as promising molecular biomarkers.

InflammamiRs in focus: Delivery strategies and therapeutic approaches

microRNAs (miRNAs) are small non-protein-coding RNAs which are essential regulators of host genome expression at the post-transcriptional level. There is evidence of dysregulated miRNA expression patterns in a wide variety of diseases, such as autoimmune and inflammatory conditions. These miRNAs have been termed "inflammamiRs." When working with miRNAs, the method followed, the approach to treat or diagnosis, and the selected biological material are very crucial. Demonstration of the role of miRNAs in particular disease phenotypes facilitates their evaluation as potential and effective therapeutic tools. A growing number of reports suggest the significant utility of miRNAs and other small RNA drugs in clinical medicine. Most miRNAs seem promising therapeutic options, but some features associated with miRNA therapy like off-target effect, effective dosage, or differential delivery methods, mainly caused by the short target's sequence, make miRNA therapies challenging. In this review, we aim to discuss some of the inflammamiRs in diseases associated with inflammatory pathways and the challenge of identifying the most potent therapeutic candidates and provide a perspective on achieving safe and targeted delivery of miRNA therapeutics. We also discuss the status of inflammamiRs in clinical trials.

LncRNA NEAT1/miR-146a-5p Axis Restores Normal Angiogenesis in Diabetic Foot Ulcers by Targeting mafG

Non-healing lesions in diabetic foot ulcers are a significant effect of poor angiogenesis. Epigenetic regulators, mainly lncRNA and miRNA, are recognized for their important roles in disease progression. We deciphered the regulation of lncRNA NEAT1 through the miR-146a-5p/mafG axis in the progression of DFU. A lowered expression of lncRNA NEAT1 was associated with dysregulated angiogenesis through the reduced expression of mafG, SDF-1α, and VEGF in chronic ulcer subjects compared to acute DFU. This was validated by silencing NEAT1 by SiRNA in the endothelial cells which resulted in the transcriptional repression of target genes. Our in silico analysis identified miR-146a-5p as a potential target of lncRNA NEAT1. Further, silencing NEAT1 led to an increase in the levels of miR-146a-5p in chronic DFU subjects. This research presents the role of the lncRNA NEAT1/miR-146a-5p/mafG axis in enhancing angiogenesis in DFU.

Angio-Long Noncoding RNA MALAT1 (rs3200401) and MIAT (rs1061540) Gene Variants in Ovarian Cancer

The genotyping of long non-coding RNA (lncRNA)-related single-nucleotide polymorphisms (SNPs) could be associated with cancer risk and/or progression. This study aimed to analyze the angiogenesis-related lncRNAs MALAT1 (rs3200401) and MIAT (rs1061540) variants in patients with ovarian cancer (OC) using "Real-Time allelic discrimination polymerase chain reaction" in 182 formalin-fixed paraffin-embedded (FFPE) samples of benign, borderline, and primary malignant ovarian tissues. Differences in the genotype frequencies between low-grade ovarian epithelial tumors (benign/borderline) and malignant tumors and between high-grade malignant epithelial tumors and malignant epithelial tumors other than high-grade serous carcinomas were compared. Odds ratios (ORs)/95% confidence intervals were calculated as measures of the association strength. Additionally, associations of the genotypes with the available pathological data were analyzed. The heterozygosity of MALAT1 rs3200401 was the most common genotype (47.8%), followed by C/C (36.3%). Comparing the study groups, no significant differences were observed regarding this variant. In contrast, the malignant epithelial tumors had a higher frequency of the MIAT rs1061540 C/C genotype compared to the low-grade epithelial tumor cohorts (56.7% vs. 37.6, p = 0.031). The same genotype was significantly higher in high-grade serous carcinoma than its counterparts (69.4% vs. 43.8%, p = 0.038). Multivariate Cox regression analysis showed that the age at diagnosis was significantly associated with the risk of OC development. In contrast, the MIAT T/T genotype was associated with a low risk of malignant epithelial tumors under the homozygote comparison model (OR = 0.37 (0.16-0.83), p = 0.017). Also, MIAT T allele carriers were less likely to develop high-grade serous carcinoma under heterozygote (CT vs. CC; OR = 0.33 (0.12-0.88), p = 0.027) and homozygote (TT vs. CC; OR = 0.26 (0.07-0.90), p = 0.034) comparison models. In conclusion, our data provide novel evidence for a potential association between the lncRNA MIAT rs1061540 and the malignant condition of ovarian cancer, suggesting the involvement of such lncRNAs in OC development.

Long non-coding RNA MEG3 acts as a suppressor in breast cancer by regulating miR-330/CNN1

BACKGROUND

The current study aimed to investigate the molecular mechanism of long non-coding RNA (lncRNA) MEG3 in the development of breast cancer.

METHODS

The regulating relationships among lncRNA MEG3, miRNA-330 and CNN1 were predicted by bioinformatics analysis of breast cancer samples in the Cancer Genome Atlas database. The differential expression of lncRNA MEG3, miRNA-330 and CNN1 was first validated in breast cancer tissues and cells. The effects of lncRNA MEG3 on breast cancer malignant properties were evaluated by manipulating its expression in MCF-7 and BT-474 cells. Rescue experiments, dual-luciferase assays, and RNA immunoprecipitation (RIP) experiments were further used to validate the relationships among lncRNA MEG3, miRNA-330 and CNN1.

RESULTS

Bioinformatics analysis showed that lncRNA MEGs and CNN1 were significantly downregulated in breast cancer tissues, while miR-330 was upregulated. These differential expressions were further validated in our cohort of breast cancer samples. High expression levels of lncRNA MEG3 and CNN1 as well as low expression of miR-330 were significantly associated with favorable overall survival. Overexpression of lncRNA MEG3 significantly inhibited cell viability, migration and invasion, decreased cells in S stage and promoted cell apoptosis. Dual-luciferase reporter gene assay and RIP experiments showed that lncRNA MEG3 could directly bind to miR-330. Moreover, miR-330 mimics on the basis of lncRNA MEG3 overexpression ameliorated the tumor-suppressing effects of lncRNA MEG3 in breast cancer malignant properties by decreasing CNN1 expression.

CONCLUSION

Our study indicated lncRNA MEG3 is a breast cancer suppressor by regulating miR-330/CNN1 axis.

Relationship between long non-coding RNAs and Hippo signaling pathway in gastrointestinal cancers; molecular mechanisms and clinical significance

Long non-coding RNAs (lncRNAs) play a significant biological role in the regulation of various cellular processes such as cell proliferation, differentiation, apoptosis and migration. In various malignancies, lncRNAs interplay with some main cancer-associated signaling pathways, including the Hippo signaling pathway to regulate the various cellular processes. It has been revealed that the cross-talking between lncRNAs and Hippo signaling pathway involves in gastrointestinal (GI) cancers development and progression. Considering the clinical significance of these lncRNAs, they have also been introduced as potential biomarkers in diagnostic, prognostic and therapeutic strategies in GI cancers. Herein, we review the mechanisms of lncRNA-mediated regulation of Hippo signaling pathway and focus on the corresponding molecular mechanisms and clinical significance of these non-coding RNAs in GI cancers.

Introduction of LPIN1 as a potential diagnostic and prognostic biomarker for gastric cancer via integrative bioinformatics analysis of a competing endogenous RNA network and experimental validation

Objectives

Identification of effective biomarkers is crucial for the heterogeneous disease of gastric cancer (GC). Recent studies have focused on the role of pseudogenes regulating gene expression through competing endogenous RNA (ceRNA) networks, however, the pseudogene-associated ceRNA networks in GC remain largely unknown. The current study aimed to construct and analyze a three-component ceRNA network in GC and experimentally validate a ceRNA.

Materials and Methods

A comprehensive analysis was conducted on the RNA-seq and miRNA-seq data of The Cancer Genome Atlas (TCGA) stomach adenocarcinoma (STAD) dataset to identify differentially-expressed mRNAs (DEMs), pseudogenes (DEPs), and miRNAs (DEMis). Pseudogene-associated ceRNA and protein-protein interaction (PPI) networks were constructed, and functional enrichment analyses were performed. DEMs and DEPs with degree centralities≥2 were selected for survival analysis. A ceRNA was further selected for experimental validation.

Results

10,145 DEMs, 3576 DEPs, and 66 DEMis were retrieved and a ceRNA network was then constructed by including DEMis with concurrent interactions with at least a DEM and a DEP. Functional enrichment analysis demonstrated that DEMs of the ceRNA network were significantly enriched in cancer-associated pathways. LPIN1 and WBP1L were two mRNAs showing an association with STAD patients overall survival. Expression analysis of LPIN1 showed a significant decrease in GC tumors compared to non-tumor tissues (P=0.003).

Conclusion

Our research emphasizes the significant implications of ceRNA networks in the development of new biomarkers for the detection and prognosis of cancer. Further examination is necessary to explore the functional roles of LPIN1 in the pathogenesis of GC.

Molecular Biomarkers and Signaling Pathways of Cancer Stem Cells in Colorectal Cancer

Colorectal cancer (CRC) is the third most frequently found cancer in the world, and it is frequently discovered when it is already far along in its development. About 20% of cases of CRC are metastatic and incurable. There is more and more evidence that colorectal cancer stem cells (CCSCs), which are in charge of tumor growth, recurrence, and resistance to treatment, are what make CRC so different. Because we know more about stem cell biology, we quickly learned about the molecular processes and possible cross-talk between signaling pathways that affect the balance of cells in the gut and cancer. Wnt, Notch, TGF-β, and Hedgehog are examples of signaling pathway members whose genes may change to produce CCSCs. These genes control self-renewal and pluripotency in SCs and then decide the function and phenotype of CCSCs. However, in terms of their ability to create tumors and susceptibility to chemotherapeutic drugs, CSCs differ from normal stem cells and the bulk of tumor cells. This may be the reason for the higher rate of cancer recurrence in patients who underwent both surgery and chemotherapy treatment. Scientists have found that a group of uncontrolled miRNAs related to CCSCs affect stemness properties. These miRNAs control CCSC functions like changing the expression of cell cycle genes, metastasis, and drug resistance mechanisms. CCSC-related miRNAs mostly control signal pathways that are known to be important for CCSC biology. The biomarkers (CD markers and miRNA) for CCSCs and their diagnostic roles are the main topics of this review study.

Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention

Antisense transcription, a prevalent occurrence in mammalian genomes, gives rise to natural antisense transcripts (NATs) as RNA molecules. These NATs serve as agents of diverse transcriptional and post-transcriptional regulatory mechanisms, playing crucial roles in various biological processes vital for cell function and immune response. However, when their normal functions are disrupted, they can contribute to human diseases. This comprehensive review aims to establish the molecular foundation linking NATs to the development of disorders like cancer, neurodegenerative conditions, and cardiovascular ailments. Additionally, we evaluate the potential of oligonucleotide-based therapies targeting NATs, presenting both their advantages and limitations, while also highlighting the latest advancements in this promising realm of clinical investigation.Abbreviations: NATs- Natural antisense transcripts, PRC1- Polycomb Repressive Complex 1, PRC2- Polycomb Repressive Complex 2, ADARs- Adenosine deaminases acting on RNA, BDNF-AS- Brain-derived neurotrophic factor antisense transcript, ASOs- Antisense oligonucleotides, SINEUPs- Inverted SINEB2 sequence-mediated upregulating molecules, PTBP1- Polypyrimidine tract binding protein-1, HNRNPK- heterogeneous nuclear ribonucleoprotein K, MAPT-AS1- microtubule-associated protein tau antisense 1, KCNQ1OT- (KCNQ1 opposite strand/antisense transcript 1, ERK- extracellular signal-regulated kinase 1, USP14- ubiquitin-specific protease 14, EGF- Epidermal growth factor, LSD1- Lysine Specific Demethylase 1, ANRIL- Antisense Noncoding RNA in the INK4 Locus, BWS- Beckwith-Wiedemann syndrome, VEGFA- Vascular Endothelial Growth component A.

Two lncRNA signatures with cuproptosis as a novel prognostic model and clinicopathological value for endometrioid endometrial adenocarcinoma

OBJECTIVE

Cuproptosis may contribute to tumorigenesis. However, the predictive value and therapeutic significance of cuproptosis-related lncRNAs (CRLs) in endometrioid endometrial adenocarcinoma (EEA) remains unknown.

METHODS

We obtained RNA-seq data from TCGA database and searched the Literature to identify cuproptosis-related genes. Using machine learning models, we identified prognostic lncRNAs for cuproptosis. Immune properties and drug sensitivity were investigated based on these signatures. Further, a ceRNA network was constructed by bioinformatics and in vitro experiments were performed.

RESULTS

We determined two cuproptosis-related signatures to build the prognostic model in EEA. Afterward, the risk scores of two cuproptosis-related signatures were associated with clinicopathological molecular typing and as independent prognostic factors for EEA. In addition, we observed significant differences in immune function, checkpoints, and CD8+ T lymphocyte infiltration between the two risk groups. Furthermore, chemotherapy drugs such as AKT inhibitors exhibited lower IC50 values in the high-risk group. We speculate that ACOXL-AS1 can be served as an endogenous 'sponge' to regulate the expression of MTF1 by miR-421. Through in vitro experiments, we preliminarily validated the ceRNA network relationship in the cellular model.

CONCLUSION

In EEAs, this study proposed a broad molecular signature of CRLs are promising biomarkers for predicting clinical outcomes and therapeutic responses.

ceRNA networks in gynecological cancers progression and resistance

Gynecological cancers are the second most common types of cancer in women. Clinical diagnosis of these cancers is often delayed or misdiagnosed due to lack of insight into their tumorigenesis mechanism and specific diagnostic biomarkers. Many studies have demonstrated that competing endogenous RNAs (ceRNAs) modulate the progression and resistance of gynecological cancer through microRNA (miRNA)-mediated mechanisms, which affect gene expression in multiple cancer-related pathways. Here we review studies on the involvement of the ceRNA hypothesis in the progression and resistance of gynaecological cancers to validate some ceRNAs as therapeutic targets and predictive biomarkers.

CXCL8 as a Potential Biomarker for Crohn's Disease is Associated with Immune Infiltration and RNA Methylation

TRP channels have an important role in regulating the function of gastrointestinal epithelial cells. The aim of this study was to investigate the molecular mechanisms of genes associated with TRP channels in Crohn's disease (CD) by bioinformatics approach and to identify potential key biomarkers. In our study, we identified TRP channel-related differentially expressed genes (DEGs) based on the GSE95095 dataset and the TRP channel-related gene set from the GeneCards database. Hub genes (CXCL8, HIF1A, NGF, JUN, IL1A) were identified by the PPI network and validated by the external GSE52746 dataset. Immune infiltration analysis revealed that CXCL8 was significantly correlated with B cells memory, NK cells activated, Mast cells resting, Mast cells activated, and Neutrophils. GSEA of CXCL8 results showed inositol phosphate metabolism, RNA polymerase, propanoate metabolism, MAPK signaling pathway, base excision repair, and Calcium signaling pathway. In addition, we constructed a lncRNA-miRNA-mRNA ceRNA network and a drug-gene interaction network. Finally, we performed in vitro experiments to verify that LPS induced CXCL8 expression in HT-29 cells and that knockdown of CXCL8 inhibited the inflammatory stimulatory effects of LPS. This study reveals that CXCL8 plays an important role in the pathogenesis of Crohn's disease and is expected to be a novel biomarker.

The lncRNA DLX6-AS1/miR-16-5p axis regulates autophagy and apoptosis in non-small cell lung cancer: A Boolean model of cell death

Long non-coding RNA (lncRNA) distal-less homeobox 6 antisense RNA 1 (DLX6-AS1) is elevated in a variety of cancers, including non-small cell lung cancer (NSCLC) and cervical cancer. Although it was found that the microRNA-16-5p (miR-16), which is known to regulate autophagy and apoptosis, had been downregulated in similar cancers. Recent research has shown that in tumors with similar characteristics, DLX6-AS1 acts as a sponge for miR-16 expression. However, the cell death-related molecular mechanism of the DLX6-AS1/miR-16 axis has yet to be investigated. Therefore, we propose a dynamic Boolean model to investigate gene regulation in cell death processes via the DLX6-AS1/miR-16 axis. We found the finest concordance when we compared our model to many experimental investigations including gain-of-function genes in NSCLC and cervical cancer. A unique positive circuit involving BMI1/ATM/miR-16 is also something we predict. Our results suggest that this circuit is essential for regulating autophagy and apoptosis under stress signals. Thus, our Boolean network enables an evident cell-death process coupled with NSCLC and cervical cancer. Therefore, our results suggest that DLX6-AS1 targeting may boost miR-16 activity and thereby restrict tumor growth in these cancers by triggering autophagy and apoptosis.