LncRNA BRCAT54 inhibits the tumorigenesis of non-small cell lung cancer by binding to RPS9 to transcriptionally regulate JAK-STAT and calcium pathway genes

Lung cancer cell derived sEVs enhance the metastasis of non-small cell lung cancer via SNHG12/miR-326/SLC7A11 axis

Abnormally expressed long non-coding (lnc)RNAs are closely associated with the pathogenesis of non-small cell lung cancer (NSCLC); thus, the present study aimed to investigate the potential role of SNHG12 in NSCLC. Transmission electron microscopy and nanoparticle tracking analysis were conducted to verify NSCLC cell-derived small extracellular vesicles (sEVs). MicroRNA (miRNA/miR) and mRNA expression levels were determined using reverse transcription-quantitative PCR, while protein expression levels were determined using western blot analysis and immunofluorescence. In addition, potential binding sites between miR-326 and SNHG12/SLC7A11 were verified using a dual-luciferase reporter assay. Cell behavior was detected using flow cytometry, colony formation, wound healing and Transwell assays, and xenograft experiments were conducted to confirm the roles of SNHG12 in NSCLC. H&E staining was used for histological analysis, and each experiment was repeated three times. Results of the present study demonstrated that NSCLC-derived SNHG12 promoted type-2 tumor-associated macrophage (TAM2) polarization. However, the decrease of SNHG12 expression in EVs reduced TAM2 polarization, weakened NSCLC cell proliferation, migration and invasion, and promoted tumor cell ferroptosis. Moreover, results of the present study revealed that SNHG12 knockdown markedly suppressed tumor growth and the metastasis of NSCLC. In addition, SNHG12 upregulated SLC7A11 expression via binding to miR-326. Overexpressed SLC7A11 promoted tumor aggressiveness and suppressed the ferroptosis of NSCLC cells. Collectively, results of the present study revealed that SNHG12 suppressed ferroptosis and promoted the metastasis of NSCLC, further demonstrating that high SNHG12 expression levels may be indicative of poor clinical outcomes for patients with NSCLC. Thus, the present study highlighted that the SNHG12/miR-326/SLC7A11 axis may exhibit potential as a novel target for the treatment of NSCLC.

Cuproptosis genes in predicting the occurrence of allergic rhinitis and pharmacological treatment

BACKGROUND

While drug therapy and allergen immunotherapy are useful for alleviating symptoms of seasonal allergic rhinitis (AR), existing therapeutic options remain limited. Cuproptosis is a novel form of programmed cell death, and its role in allergic rhinitis has not yet been explored. Researching the interaction between cuproptosis and allergic rhinitis will likely pave the way for future treatment of this disease.

METHODS

A microarray dataset of AR patients and normal controls (GSE43523) were obtained from the Gene Expression Omnibus (GEO) database for differential gene analysis. Cuproptosis related genes were extracted from the differentially expressed genes (DEGs) to form the AR/cuprotosis-gene set and analyzed by the GO and KEGG databases. Intersection analysis further defined the AR signature genes (AR-sg). Consensus cluster analyses were used to define the AR/cuprotosis-genes into subsets. Finally, AR signature genes were used as targets for drug prediction and molecular docking to identify candidate drugs that may affect SAR.

RESULTS

Four AR signature genes (MRPS30, CLPX, MRPL13, and MRPL53) were selected by the MCC, EPC, BottleNeck, and Closeness algorithms. Correlation analysis of the AR signature genes and immune genes showed strong interactions; xCell analysis identified multiple immune cell types and supported these cells' importance in the AR pathogenesis. Finally, drug target analysis suggests that 1,5-isoquinolinediol and gefitinib have the potential to become future AR treatments.

CONCLUSION

Our study analyzed allergic rhinitis and cuproptosis related genes by the bioinformatics approach and predicted 1,5-isoquinolinediol and gefitinib as potentially useful drugs for treating AR patients in the future.

Non-coding RNA in infantile hemangioma

Infantile hemangioma (IH) is the most common benign vascular tumor of infancy, but its pathogenesis has not been fully discovered. From the cellular perspective, CD133+ stem cells orchestrate the proliferation and development of IH. Regarding molecular mechanisms, hypoxia inducible factor-1α, renin-angiotensin system, and vascular endothelial growth factor are current study hotspots, while non-coding RNAs (ncRNAs) might be essential factors participating in this network. Therefore, this article reviewed published studies concerning the roles of ncRNAs in IH and listed noted miRNAs, lncRNAs, and circRNAs. Other ncRNAs, such as snRNAs, snoRNAs, and tsRNAs, though have not been examined in IH, are mentioned as well to discuss their potential functions. Due to the continuous development of sequencing technologies and computational pipelines for ncRNAs annotation, relevant studies will provide evidence to gradually enhance acknowledgments of ncRNAs' role in IH. The pathogenesis of IH might be revealed and the treatment protocol would be optimized in the future. IMPACT: Non-coding RNAs (ncRNAs) play critical roles in infantile hemangioma. This article thoroughly reviewed all ncRNAs (miRNAs, lncRNAs, and circRNAs) mentioned in previous studies regarding the pathogenesis of infantile hemangioma. Other ncRNAs are promising subjects for further investigation. This review introduced the emerging ncRNAs that need to be explored in IH.

In silico identification and in vitro evaluation of MRPS30-DT lncRNA and MRPS30 gene expression in breast cancer

BACKGROUND

It has been reported that long non-coding RNAs (lncRNAs) can play important roles in a variety of biological processes and cancer regulatory networks, including breast cancer.

AIMS

This study aimed to identify a novel upregulated lncRNA in breast cancer and its associated gene using bioinformatics analysis, and then evaluate their potential roles in breast cancer.

METHODS AND RESULTS

Extensive in silico studies were performed using various bioinformatics databases and tools to identify a potential upregulated breast cancer-associated lncRNA and its co-expressed gene, and to predict their potential roles, functions, and interactions. The expression level of MRPS30-DT lncRNA and MRPS30 was assessed in both BC tissues and cell lines using qRT-PCR technology. MRPS30-DT lncRNA and MRPS30 were selected as target genes using bioinformatics analysis. We found that MRPS30-DT and MRPS30 were significantly overexpressed in BC tissues compared with normal tissues. Also, MRPS30 showed upregulation in all three BC cell lines compared with HDF. On the other hand, MRPS30-DT significantly increased in MDA-MB-231 compared with HDF. While the expression of MRPS30-DT was significantly dropped in the resistance cell line MCF/MX compared to HDF and MCF7. Moreover, bioinformatics analysis suggested that MRPS30-DT and MRPS30 may play a potential role in BC through their involvement in some cancer signaling pathways and processes, as well as through their interaction with TFs, genes, miRNAs, and proteins related to carcinogenesis.

CONCLUSIONS

Overall, our findings showed the dysregulation of MRPS30-DT lncRNA and MRPS30 may provide clues for exploring new therapeutic targets or molecular biomarkers in BC.

Decoding long non‑coding RNAs: Friends and foes in cancer development (Review)

Cancer remains a formidable adversary, challenging medical advancements with its dismal prognosis, low cure rates and high mortality rates. Within this intricate landscape, long non‑coding RNAs (lncRNAs) emerge as pivotal players, orchestrating proliferation and migration of cancer cells. Harnessing the potential of lncRNAs as therapeutic targets and prognostic markers holds immense promise. The present comprehensive review delved into the molecular mechanisms underlying the involvement of lncRNAs in the onset and progression of the top five types of cancer. By meticulously examining lncRNAs across diverse types of cancer, it also uncovered their distinctive roles, highlighting their exclusive oncogenic effects or tumor suppressor properties. Notably, certain lncRNAs demonstrate diverse functions across different cancers, confounding the conventional understanding of their roles. Furthermore, the present study identified lncRNAs exhibiting aberrant expression patterns in numerous types of cancer, presenting them as potential indicators for cancer screening and diagnosis. Conversely, a subset of lncRNAs manifests tissue‑specific expression, hinting at their specialized nature and untapped significance in diagnosing and treating specific types of cancer. The present comprehensive review not only shed light on the intricate network of lncRNAs but also paved the way for further research and clinical applications. The unraveled molecular mechanisms offer a promising avenue for targeted therapeutics and personalized medicine, combating cancer proliferation, invasion and metastasis.

Functional impact of multi-omic interactions in lung cancer

Lung tumors are a leading cause of cancer-related death worldwide. Lung cancers are highly heterogeneous on their phenotypes, both at the cellular and molecular levels. Efforts to better understand the biological origins and outcomes of lung cancer in terms of this enormous variability often require of high-throughput experimental techniques paired with advanced data analytics. Anticipated advancements in multi-omic methodologies hold potential to reveal a broader molecular perspective of these tumors. This study introduces a theoretical and computational framework for generating network models depicting regulatory constraints on biological functions in a semi-automated way. The approach successfully identifies enriched functions in analyzed omics data, focusing on Adenocarcinoma (LUAD) and Squamous cell carcinoma (LUSC, a type of NSCLC) in the lung. Valuable information about novel regulatory characteristics, supported by robust biological reasoning, is illustrated, for instance by considering the role of genes, miRNAs and CpG sites associated with NSCLC, both novel and previously reported. Utilizing multi-omic regulatory networks, we constructed robust models elucidating omics data interconnectedness, enabling systematic generation of mechanistic hypotheses. These findings offer insights into complex regulatory mechanisms underlying these cancer types, paving the way for further exploring their molecular complexity.

LncRNA BRCAT54 is downregulated and inhibits cancer cell proliferation by downregulating miR-130b-3p through methylation in prostate cancer

BRCAT54 and miR-130b-3p are two recently characterized critical players in cancer biology, while their functions in prostate cancer (PC) are unknown. From preliminary sequencing analysis, we observed altered expression of BRCAT54 and miR-130b-3p in PC and an inverse correlation between them. This study was conducted to explore their involvement in PC. A total of 64 PC patients were enrolled to collect paired PC and nontumor tissues. The expression of BRCAT54 and miR-130b-3p were determined by RT-qPCR. Overexpression of BRCAT54 and miR-130b-3p was achieved in PC cells to explore their roles in regulating the expression of each other. Methylation-specific PCR (MSP) was conducted to explore the role of BRCAT54 in regulating promoter methylation of miR-130b-3p. BrdU assay was used to evaluate the role of BRCAT54 and miR-130b-3p in regulating PC cell proliferation. The results showed that PC tissues exhibited downregulation of BRCAT54 and upreglation of miR-130b-3p compared to that in nontumor tissues. They were inversely correlated across PC tissue samples. Overexpression of BRCAT54 decreased RNA accumulation of miR-130b-3p in PC cells. In addition, overexpression of BRCAT54 increased promoter methylation of miR-130b-3p. Moreover, BRCAT54 suppressed the role of miR-130b-3p in promoting PC cell proliferation. In conclusion, BRCAT54 is downregulated in PC and it may inhibit cancer cell proliferation by downregulating miR-130b-3p through methylation.

Comprehensive landscape and future perspective of long noncoding RNAs in non-small cell lung cancer: it takes a village

Long noncoding RNAs (lncRNAs) are a distinct subtype of RNA that lack protein-coding capacity but exert significant influence on various cellular processes. In non-small cell lung cancer (NSCLC), dysregulated lncRNAs act as either oncogenes or tumor suppressors, contributing to tumorigenesis and tumor progression. LncRNAs directly modulate gene expression, act as competitive endogenous RNAs by interacting with microRNAs or proteins, and associate with RNA binding proteins. Moreover, lncRNAs can reshape the tumor immune microenvironment and influence cellular metabolism, cancer cell stemness, and angiogenesis by engaging various signaling pathways. Notably, lncRNAs have shown great potential as diagnostic or prognostic biomarkers in liquid biopsies and therapeutic strategies for NSCLC. This comprehensive review elucidates the significant roles and diverse mechanisms of lncRNAs in NSCLC. Furthermore, we provide insights into the clinical relevance, current research progress, limitations, innovative research approaches, and future perspectives for targeting lncRNAs in NSCLC. By summarizing the existing knowledge and advancements, we aim to enhance the understanding of the pivotal roles played by lncRNAs in NSCLC and stimulate further research in this field. Ultimately, unraveling the complex network of lncRNA-mediated regulatory mechanisms in NSCLC could potentially lead to the development of novel diagnostic tools and therapeutic strategies.

LINC02489 with m6a modification increase paclitaxel sensitivity by inhibiting migration and invasion of ovarian cancer cells

The long non-coding RNA LINC02489 has been shown to be significantly downregulated in advanced ovarian cancer (OC). However, the function of LINC02489 remains unknown. This study aims to explain the role and mechanism of LINC02489 in OC. The expression of LINC02489 was examined by qRT-PCR in primary OC tissues. Additionally, MTT, wound healing, transwell, and flow cytometry assays were used to analyze the function of LINC02489. The mechanism of LINC02489 in OC was investigated by high-throughput RNA-sequencing, qRT-PCR, western blot, and N6-methyladenosine (m6A) meRIP. A total of 1101 and 827 genes are significantly down-regulated and up-regulated in metastatic and chemoresistant OC tissues. The expression of LINC02489 is decreased in metastatic and chemoresistant OC tissues compared with the primary OC tissues (p < 0.05). Overexpression of LINC02489 inhibits proliferation, invasion, and migration of drug-resistant OC cells. In the LINC02489 overexpressed chemoresistant SKOV3 cells, the m6A modified LINC02489 is significantly up-regulated. Furthermore, the expression of PKNOX2 is increased during overexpression of LINC02489, while the expression of PTEN and mTOR plummets. This study demonstrates that LINC02489 can inhibit the invasion and migration of chemoresistant OC cells by increasing its m6A modification and up-regulating PKNOX2 expression. In addition, LINC02489 regulates the invasion ability of OC cells through the PTEN/mTOR signaling pathway, thereby regulating the sensitivity of SKOV3 cells to paclitaxel. This result provides a potential therapeutic target for chemoresistant OC.

The cross-talk between LncRNAs and JAK-STAT signaling pathway in cancer

Long non-coding RNAs (lncRNAs) are non-coding RNAs that were transcribed from the human genome and have become important regulators in a number of cellular activities, mostly via controlling gene expression. A growing body of evidence shows that lncRNAs regulate various factors to impact various biological activities that are related to tumorigenesis, including the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway. lncRNAs influence the JAK-STAT signaling pathway either by directly targeting or via indirectly modulating other upstream or downstream pathways' components like members of the suppressor of cytokine signaling (SOCS) family, and other genes that regulate cell proliferation, apoptosis, migration, invasion, and epithelial-mesenchymal transition. Furthermore, lncRNAs can act as downstream effectors of the JAK-STAT pathway and mediates tumorigenesis. The relationship between JAK-STAT signaling and lncRNAs differs among various types of cancers. Besides, lncRNAs, as biological molecules, have been shown to play a dual role in either tumorigenesis or tumor suppression in various cancers. In this review, we focus on the reciprocated regulation and functions of lncRNAs and the JAK-STAT signaling pathway in cancer, as well as narrate the latest research progress on this association. A deeper understanding of this correlation may simplify the recognition of potential targets for clinical therapeutics.

CircTBX5 knockdown modulates the miR-558/MyD88 axis to alleviate IL-1β-induced inflammation, apoptosis and extracellular matrix degradation in chondrocytes via inactivating the NF-κB signaling

BACKGROUND

It has been widely shared that the dysregulation of circular RNA (circRNA) may contribute to the progression of osteoarthritis (OA). OA is characterized by persistent chondrocyte injury. We aimed to clarify the role of circTBX5 in IL-1β-induced chondrocyte injury.

METHODS

The expression of circTBX5, miR-558 and MyD88 mRNA was measured using quantitative real-time PCR (qPCR). Cell viability, proliferation and apoptosis were assessed by CCK-8, EdU or flow cytometry assay. The protein levels of extracellular matrix (ECM)-associated markers, MyD88, IkBα, p65 and phosphorylated IkBα were measured by western blot. The release of inflammatory factors was assessed by ELISA. The targets of circTBX5 were screened by RIP and pull-down assay. The putative binding between miR-558 and circTBX5 or MyD88 was validated by dual-luciferase reporter assay.

RESULTS

CircTBX5 and MyD88 were enhanced, while miR-558 was downregulated in OA cartilage tissues and IL-1β-treated C28/I2 cells. IL-1β induced C28/I2 cell injury by impairing cell viability and proliferation and promoting cell apoptosis, ECM degradation and inflammatory response, while circTBX5 knockdown alleviated IL-1β induced injury. CircTBX5 bound to miR-558 to regulate IL-1β induced cell injury. In addition, MyD88 was a target of miR-558, and circTBX5 targeted miR-558 to positively regulate MyD88 expression. MiR-558 enrichment attenuated IL-1β induced injury by sequestering MyD88 expression. Moreover, circTBX5 knockdown weakened the activity of NF-κB signaling, while miR-558 inhibition or MyD88 overexpression recovered the activity of NF-κB signaling.

CONCLUSION

CircTBX5 knockdown modulated the miR-558/MyD88 axis to alleviate IL-1β induced chondrocyte apoptosis, ECM degradation and inflammation via inactivating the NF-кB signaling pathway.

Pan-cancer analysis of PCAT6 and its effect on oesophageal squamous cell carcinoma cell proliferation and migration

Bioinformatics methods were used to analyze the role of PCAT6 in a variety of tumors and verify its role in oesophageal squamous cell carcinoma (ESCC) EC109 cells. The pan-cancer dataset was downloaded from the University of California Santa Cruz (UCSC) database to analyze the expression of PCAT6 in pan-cancer and its relationship with prognosis, clinical features, and immune infiltration. The expression and prognosis of PCAT6 in ESCC were verified by Gene Expression Omnibus (GEO) and Kaplan-Meier database. CCK8, colony formation, wound healing, Transwell cell invasion (CI), and cell migration (CM) assays were used to detect the effect of PCAT6 knockdown on the ability of ESCC cell proliferation (CP), CI and CM. Gene Set Enrichment Analysis was used to analyze the signaling pathways involved in the regulation of PCAT6. Quantitative real-time PCR and western blotting were used to examine the expression of cancer stem cell-related markers and the activation of JAK/STAT pathway in ESCC after PCAT6 knockdown. PCAT6 is significantly up-regulated in a variety of tumor tissues, and its expression is closely related to prognosis, clinical features and immune infiltration. High expression of PCAT6 leads to poor prognosis in ESCC patients. In ESCC EC109 cells, PCAT6 knockdown inhibited the ability of CP, CI, CM, and stemness, and inhibited the activation of JAK/STAT signaling pathway. PCAT6 expression is elevated in a variety of tumors. PCAT6 plays an oncogene role in ESCC by activating the JAK/STAT signaling pathway.

LAPTM4B promotes AML progression through regulating RPS9/STAT3 axis

Acute myeloid leukemia (AML) is a heterogeneous disorder with high morbidity and mortality under the existing treatment strategy. Here, we found that lysosome-associated protein transmembrane 4 beta (LAPTM4B) was frequently upregulated in AML, and high LAPTM4B was associated with poor outcome. Moreover, LAPTM4B promoted leukemia progression in vitro and in vivo. Mechanically, LAPTM4B interacted with RPS9, and positively regulated RPS9 protein stability, which enhanced leukemia cell progression via activating STAT3. Our findings indicate for the first time that LAPTM4B contributes to leukemia progression in a RPS9/STAT3-dependent manner, suggesting that LAPTM4B may serve as a promising target for treatment of AML.

Janus kinase/signal transducers and activator of transcription (JAK/STAT) and its role in Lung inflammatory disease

A key signaling channel for the signal transduction of several crucial cytokines implicated in sepsis is the JAK/STAT system. Once cytokines attach to the proper receptors, JAK kinases linked to them are activated and can selectively phosphorylate STATs. Activated STATs subsequently go to the nucleus, where they play a key role in the transcription of the target genes. Various biological activities use the JAK/STAT pathway, including hematopoiesis, immunological modulation, cell differentiation, and apoptosis. Inflammatory lung illnesses affect people worldwide and are a serious public health concern. Numerous common respiratory conditions, such as asthma, bronchiectasis, chronic obstructive pulmonary disease (COPD), and acute respiratory distress syndrome, are strongly influenced by inflammation. Microorganism infections or the destruction or demise of host cells are the causes of inflammation and the factors that perpetuate it. This review discusses the main elements of severe lung inflammation and how the JAK/STAT signaling pathway is essential for lung inflammation.

LncRNA34977 promotes the proliferation, migration, and invasion and inhibits the apoptosis of canine mammary tumors by regulating the expression of miR-8881/ELAVL4

Long-stranded noncoding RNAs (lncRNAs) play different roles in various diseases. lncRNA34977 has been shown to play a relevant role the development of canine mammary tumors (CMTs). However, the mechanism of lncRNA34977 in canine mammary tumors has not been fully investigated. The aim of this study was to investigate the effects of lncRNA34977 on the proliferation, migration, invasion, and apoptosis of canine mammary tumor (CMT) cells through the regulation of miR-8881/ELAVL4 expression. The apoptosis was detected by an in situ fluorescence assay and flow cytometry. The expression levels were analyzed by RT-qPCR. CCK-8, colony formation, wound healing, and Transwell assays were used to assess the proliferation, migration, and invasion. The expression of protein was detected by western blot. The siRNA-induced silencing of lncRNA34977 promoted the apoptosis of CHMp cells, and in overexpression of lncRNA34977, the result is the opposite. LncRNA34977 has a direct targeting relationship with miR-8881 and that miR-8881 is correlated with ELAVL4. Transfection of miR-8881 mimics inhibited the proliferation, migration, invasion, and promoted the apoptosis of CHMp cells of CHMp cells. In the transfection with miR-8881 inhibitors, the result is the opposite. Co-transfected with lncRNA34977, miR-8881, or ELAVL4, we found that lncRNA34977 could regulate the expression of miR-8881 or ELAVL4. Our study shows that lncRNA34977 promotes the proliferation, migration, and invasion and suppresses the apoptosis of CMT cells by regulating the expression of miR-8881/ELAVL4.

Genetic polymorphisms of MRPS30-DT and NINJ2 may influence lung cancer risk

Lung cancer is one of the malignant tumors, and genetic background is a risk factor in lung cancer that cannot be neglected. In this study, we aimed to find out the effect of MRPS30-DT and NINJ2 variants on lung cancer risk. In this study, the seven selected single-nucleotide polymorphisms (SNPs) of MRPS30-DT and NINJ2 were genotyped in 509 lung cancer patients and 501 healthy controls based on the Agena MassARRAY platform. Odds ratios and 95% confidence intervals were calculated by logistic regression analysis to evaluate association between gene polymorphisms and lung cancer risk. False-positive report probability was also used to assess false-positive results. Furthermore, the interaction between SNPs was analyzed by multifactor dimensionality reduction to predict lung cancer risk. We identified the genotype TA of rs16901963 (T < A) in MRPS30-DT as a protective factor against lung cancer, while rs16901963-TT was significantly associated with an increased risk of lung cancer. We also revealed that the effect of MRPS30-DT and NINJ2 variants on the risk of lung cancer was dependent on age, gender, smoking, and drinking status. In conclusion, this study first proved that MRPS30-DT and NINJ2 variants played important roles in affecting the susceptibility to lung cancer.

Potential anticancer activities of securinine and its molecular targets

BACKGROUND

Securinine is an alkaloid identified from the roots and leaves of the shrub Flueggea suffruticosa (Pall.) Baill. The molecular structure of securinine consists of four rings, including three chiral centers. It has been suggested that securinine can be chemically synthesized from tyrosine and lysine. Securinine has long been used to treat central nervous system diseases. In recent years, more and more evidence shows that securinine also has anticancer activity, which has not been systematically discussed and analyzed.

PURPOSE

This study aims to propose an overall framework to describe the molecular targets of securinine in different signal pathways, and discuss the current status and prospects of each pathway, so as to provide a theoretical basis for the development securinine as an effective anticancer drug.

METHODS

The research databases on the anticancer activity of securinine from PubMed, Scopus, Web of Science and ScienceDirect to 2021 were systematically searched. This paper follows the Preferred Reporting Items and Meta-Analysis guidelines.

RESULTS

Securinine has the ability to kill a variety of human cancer cells, including, leukemia as well as prostate, cervical, breast, lung, and colon cancer cells. It can regulate the signal pathways of phosphatidylinositol-3-kinase/protein kinase B/mammalian target of rapamycin, Wnt and Janus kinase-signal transducer and activator of transcription, promote cancer cell apoptosis and autophagy, and inhibit cancer cell metastasis. Securinine also has the activity of inducing leukemia cell differentiation.

CONCLUSION

Although there has been some experimental evidence indicating the anticancer effect of securinine and its possible pharmacology, in order to design more effective anticancer drugs, it is necessary to study the synergy of intracellular signaling pathways. More in vivo experiments and even clinical studies are needed, and the synergy between securinine and other drugs is also worth studying.

Current treatments for non-small cell lung cancer

Despite improved methods of diagnosis and the development of different treatments, mortality from lung cancer remains surprisingly high. Non-small cell lung cancer (NSCLC) accounts for the large majority of lung cancer cases. Therefore, it is important to review current methods of diagnosis and treatments of NSCLC in the clinic and preclinic. In this review, we describe, as a guide for clinicians, current diagnostic methods and therapies (such as chemotherapy, chemoradiotherapy, targeted therapy, antiangiogenic therapy, immunotherapy, and combination therapy) for NSCLC.

Long non-coding RNAs and exosomal lncRNAs: Potential functions in lung cancer progression, drug resistance and tumor microenvironment remodeling

Among the different kinds of tumors threatening human life, lung cancer is one that is commonly observed in both males and females. The aggressive behavior of lung cancer and interactions occurring in tumor microenvironment enhances the malignancy of this tumor. The lung tumor cells have demonstrated capacity in developing chemo- and radio-resistance. LncRNAs are a category of non-coding RNAs that do not encode proteins, but their aberrant expression is responsible for tumor development, especially lung cancer. In the present review, we focus on both lncRNAs and exosomal lncRNAs in lung cancer, and their ability in regulating proliferation and metastasis. Cell cycle progression and molecular mechanisms related to lung cancer metastasis such as EMT and MMPs are regulated by lncRNAs. LncRNAs interact with miRNAs, STAT, Wnt, EZH2, PTEN and PI3K/Akt signaling pathways to affect progression of lung cancer cells. LncRNAs demonstrate both tumor-suppressor and tumor-promoting functions in lung cancer. They can be considered as biomarkers in lung cancer and especially exosomal lncRNAs present in body fluids are potential tools for minimally invasive diagnosis. Furthermore, we discuss regulation of lncRNAs by anti-cancer drugs and genetic tools as well as the role of these factors in therapy response of lung cancer cells.

Long non-coding RNA breast cancer-associated transcript 54 sponges microRNA-1269b to suppress the proliferation of hemangioma-derived endothelial cells

Long non-coding RNA (lncRNA) breast cancer-associated transcript 54 (BRCAT54) and microRNA-1269b (miR-1269b) are two critical ncRNAs in cancer biology, while their roles in hemangioma are unknown. Our preliminary sequencing data revealed their altered expression in hemangioma and predicted they could interact with each other. This study was therefore carried out to investigate the roles of BRCAT54 and miR-1269b in hemangioma, with a focus on their interaction. In this study, hemangioma samples donated by 20 infantile hemangioma patients at proliferating-phase and 20 infantile hemangioma patients at involuting-phase were used. The expression of BRCAT54 and miR-1269b in hemangioma samples, as well as hemangioma-derived endothelial cells (HDECs) and human umbilical vein endothelial cells (HUVECs) were detected by RT-qPCR. IntaRNA 2.0 was applied to predict the interaction between BRCAT54 and miR-1269b, which was then confirmed by RNA-RNA pulldown assay. Accumulation of BRCAT54 in the subcellular location of HDECs was detected by subcellular fractionation assay. The role of BRCAT54 and miR-1269b in cell proliferation has been explored by the BrdU assay. Compared to proliferating-phase tissues, involuting-phase tissues exhibited decreased expression levels of BRCAT54 and increased expression levels of miR-1269b. HDECs had decreased expression levels of BRCAT54 and increased expression levels of miR-1269b compared to that of HUVECs. In HDECs, BRCAT54, which was detected in both nuclear and cytoplasm fractions, directly interacted with miR-1269b. BRCAT54 and miR-1269b did not affect the expression of each other, while BRCAT54 suppressed the role of miR-1269b in enhancing the proliferation of HDECs. BRCAT54 may sponge miR-1269b to suppress the proliferation of HDECs.

Long non-coding RNA MRPS30 divergent transcript can be detected in the cytoplasm of triple-negative breast cancer cells and is targeted by microRNA-130b

Long non-coding RNA (lncRNA) MRPS30 divergent transcript (also known as BRCAT54) is recently reported to promote lung cancer. The involvement of BRCAT54 in triple-negative breast cancer (TNBC) is unknown. This study investigated the role of BRCAT54 in TNBC. The expression of BRCAT54 and microRNA(miR)-130b was detected by RT-qPCR. The subcellular location of BRCAT54 in TNBC cells was analyzed by nuclear fractionation assay. Overexpression of BRCAT54 and miR-130b was achieved in TNBC cells to explore the interaction between then. The role of BRCAT54 and miR-130b in TNBC cell proliferation was evaluated by BrdU assay. BRCAT54 was downregulated in TNBC, while miR-130b was upregulated in TNBC tissues. BRCAT54 and miR-130b were inversely correlated across both TNBC and normal tissues. BRCAT54 was detected in cytoplasm and was predicted to be targeted by miR-130b. In TNBC cells, downregulation of BRCAT54 was observed after the overexpression of miR-130b. Moreover, BRCAT54 decreased cell proliferation and miR-130b increased cell proliferation. Besides, BRCAT54 suppressed the role of miR-130b in increasing cell proliferation. Therefore, BRCAT54 can be detected in cytoplasm and was targeted by miR-130b to increase cell proliferation.

LncRNA Expression Profiles in Canine Mammary Tumors Identify lnc34977 as a Promoter of Proliferation, Migration and Invasion of Canine Mammary Tumor Cells

Canine mammary tumor (CMT) is the most common tumor in canines after skin tumors. Long noncoding RNAs (lncRNAs) have crucial roles in human breast tumor initiation and progression, but the role of lncRNAs in canine mammary tumors is unclear. We analyzed the expression profiles of canine mammary tumors and their adjacent non-neoplastic tissue to explore abnormally expressed lncRNAs. LncRNA expression was detected by qRT–PCR. After overexpression of lnc40589 and knockdown of lnc34977 in CMT cells, CCK-8, colony formation, wound healing and Transwell assays were used to assess the proliferation, migration and invasive ability of canine mammary tumor cells. We also established a mammary tumor-bearing nude mouse model. GO analysis and KEGG pathway analysis demonstrated that the differentially expressed lncRNAs were closely related to the mammary tumor. lnc40589 was significantly upregulated and lnc34977 was significantly downregulated in CMTs. In addition, lnc40589 inhibits cell proliferation, migration and invasion, while lnc34977 promotes cell proliferation, migration and invasion. In addition, lnc34977 promotes the development of mammary tumors in animals. Taken together, our study results reveal the lncRNA expression profiles in CMTs and indicate that lnc34977 promotes the development of CMT both in cell culture and in vivo.

RNA recovery from specimens of duct-washing cytology performed contemporaneously with mammary ductoscopy

Objective

Conventional cytological diagnosis including duct-washing cytology (DWC) is sometimes performed using ductal epithelial cells collected during mammary ductoscopy; it is useful for detection of early-stage breast cancer such as ductal carcinoma in situ (DCIS). However, conventional cytological diagnosis focuses exclusively on cellular morphology; false negatives and false positives may be caused by inadequate specimen preparation (triggering cell degeneration) or poor examiner diagnostic skills. Molecular diagnosis using RNA biomarkers is expected to compensate for the weaknesses of cytological diagnosis. We previously employed microarray analysis to identify highly expressed genes in DCIS, suggesting that they may be useful for DCIS diagnosis. Here, we explored whether DWC samples yielded RNA of sufficient quantity and quality for RNA biomarker-based diagnosis.

Results

We extracted RNAs from 37 DWC samples. RNA from 12 samples exhibited RNA integrities of  ≥ 6, indicative of moderate-to-high quality. We then showed that cocaine and amphetamine regulated transcript prepropeptide (CARTPT) and breast cancer-associated transcript 54 (BRCAT54) mRNA—previously shown by microarray analysis to be highly expressed in DCIS—were detectable in these samples. Therefore, DWC samples may be useful for molecular diagnosis involving RNA biomarkers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-022-05928-1.

Long non-coding RNA BRCAT54 sponges microRNA-21 in vestibular schwannoma to suppress cell proliferation

BRCAT54 (also known as MRPS30 divergent transcript) is an anti-tumor long non-coding RNA (lncRNA) in lung cancer, while its role in vestibular schwannoma (VS) is unclear. We predicted that BRCAT54 could interact with microRNA (miR)-21, which suppresses VS cell proliferation. This study was then carried out to study the interaction between BRCAT54 and miR-21 in VS. A total of 56 VS samples and 42 normal vestibular nerve (VN) samples were included in this study. The expression of BRCAT54 and miR-21 in these samples were analyzed with RT-qPCR. Subcellular location of BRCAT54 in primary VS cells was analyzed by subcellular fractionation assay. The direct interaction between BRCAT54 and miR-21 was analyzed through RNA pull-down assay. Overexpression assay was performed to explore the interaction between BRCAT54 and miR-21. The role of BRCAT54 and miR-21 in primary VS cell proliferation was analyzed using BrdU assay. We found that BRCAT54 was downregulated in VS samples than that in VN samples, while miR-21 was upregulated in VS samples. BRCAT54 and miR-21 were not closely correlated. BRCAT54 was detected in both nuclear and cytoplasm samples, and BRCAT54 directly interacted with miR-21. However, BRCAT54 and miR-21 did not affect the expression of each other. BRCAT54 suppressed primary VS cell proliferation and inhibited the role of miR-21 in promoting cell proliferation. Therefore, BRCAT54 may sponge miR-21 to suppress cell proliferation in VS.

Regulatory Networks of Prognostic mRNAs in Pediatric Acute Myeloid Leukemia

Acute myeloid leukemia (AML) in children refers to a malignant tumor caused by the abnormal proliferation of immature myeloid cells in the bone marrow and peripheral blood. The prognosis of patients with pediatric acute myeloid leukemia (AML) remains poor, highlighting the need for improved targeted therapy. The expression data of lncRNAs, mRNAs, and miRNAs and survival information of pediatric AML patients were collected from The Cancer Genome Atlas (TCGA) database. Cox regression analysis was used to screen the lncRNAs, mRNAs, and miRNAs that significantly affect the overall survival (OS) of patients as OS-related genes (included lncRNAs, mRNAs, and miRNAs). Enrichment analysis and protein-protein interaction (PPI) network construction were performed for the OS-related mRNAs. We further established a ceRNAs regulatory network. In addition, the potential prognostic role of genes was further evaluated by risk score. We have identified 5275 lncRNAs, 176 miRNAs, and 6221 mRNAs that significantly affect the prognosis of pediatric AML patients. It is worth noting that OS-related mRNAs are mainly involved in ribosome, RNA transport, and spliceosome. We identified the top 10 most connected mRNAs in the PPI network as important mRNAs and constructed a ceRNAs regulatory network (including NCBP2, RPLP0, UBC, RPS2, and RPS9). The risk score and nomogram results suggest that NCBP2 may be a risk factor for pediatric AML, while RPLP0, UBC, RPS2, and RPS9 may be protective factors. Our results construct 5 gene signals as new prognostic indicators for predicting the survival of pediatric AML patients. Our research has demonstrated the ceRNAs regulatory network may become a new target for pediatric AML treatment.

DNA-methylation-induced silencing of DIO3OS drives non-small cell lung cancer progression via activating hnRNPK-MYC-CDC25A axis

DNA methylation is a class of epigenetic modification manner, which is responsible for the inactivation of various tumor suppressors. Recently, long non-coding RNAs (lncRNAs) were revealed to be implicated in a variety of malignancies, including non-small cell lung cancer (NSCLC). However, the contributions of lncRNAs to DNA-methylation-induced oncogenic effects in NSCLC remain largely unknown. In this study, we identified a DNA-methylation-repressed lncRNA DIO3 opposite strand upstream RNA (DIO3OS) in NSCLC. DIO3OS is downregulated in NSCLC, and its low expression is related to poor prognosis. Ectopic expression of DIO3OS repressed NSCLC cell growth and motility and promoted NSCLC cell apoptosis in vitro. DIO3OS also repressed NSCLC tumorigenesis and metastasis in vivo. DIO3OS knockdown exhibited opposite biological effects. DIO3OS competitively bound heterogeneous nuclear ribonucleoprotein K (hnRNPK), repressed the binding of hnRNPK to MYC DNA and MYC mRNA, reduced the promoting roles of hnRNPK on MYC transcription and translation, led to the repression of MYC transcription and translation, and therefore remarkably decreased the expression of MYC and CDC25A, a downstream target of MYC. Additionally, depletion of hnRNPK blocked the tumor-suppressive roles of DIO3OS in NSCLC. In conclusion, these findings identified DIO3OS as an important protective factor against NSCLC via modulating hnRNPK-MYC-CDC25A axis.

WGCNA Identification of Genes and Pathways Involved in the Pathogenesis of Postmenopausal Osteoporosis

Purpose

Postmenopausal osteoporosis (PMO) patients may suffer from chronic pain and increased fractures due to brittle bones that seriously affect their normal work and life. Exploring the pathogenesis of PMO can help clinicians construct individualized therapeutic targets.

Methods

Differentially expressed genes (DEGs) were identified by analyzing the microarray assays of monocytes from 20 PMO and 20 control samples. Weighted correlation network analysis (WGCNA) and gene set enrichment analysis (GAEA) were performed. Genes associated with PMO were identified in the Comparative Toxicogenomics Database (CTD). miRNAs associated with osteoporosis were found in miRNet, and target genes were predicted. Hub genes and functional pathways associated with PMO were also identified. miRNA-mRNA networks were constructed. The association between hub genes and PMO was analyzed in the CTD.

Results

A total of 1055 genes were up-regulated, and 694 genes were down-regulated in PMO samples (P<0.01). Five modules were identified by WGCNA. The blue module was significantly associated with PMO and selected for further analysis (P < 0.05). A total of 229 genes were significantly associated with PMO gene significance and module membership. Pathway variations were predominantly enriched in mRNA metabolic process, RNA splicing, Notch signaling pathway, apoptosis, cytokine-cytokine receptor interaction and so on. We identified 10 hub genes associated with PMO with different inference scores.

Conclusion

We identified genes, miRNAs, and pathways associated with PMO. These molecules may participate in the pathogenesis of PMO and serve as therapeutic targets.

The role of ceRNA-mediated diagnosis and therapy in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death worldwide due to its high degree of malignancy, high incidence, and low survival rate. However, the underlying mechanisms of hepatocarcinogenesis remain unclear. Long non coding RNA (lncRNA) has been shown as a novel type of RNA. lncRNA by acting as ceRNA can participate in various biological processes of HCC cells, such as tumor cell proliferation, migration, invasion, apoptosis and drug resistance by regulating downstream target gene expression and cancer-related signaling pathways. Meanwhile, lncRNA can predict the efficacy of treatment strategies for HCC and serve as a potential target for the diagnosis and treatment of HCC. Therefore, lncRNA serving as ceRNA may become a vital candidate biomarker for clinical diagnosis and treatment. In this review, the epidemiology of HCC, including morbidity, mortality, regional distribution, risk factors, and current treatment advances, was briefly discussed, and some biological functions of lncRNA in HCC were summarized with emphasis on the molecular mechanism and clinical application of lncRNA-mediated ceRNA regulatory network in HCC. This paper can contribute to the better understanding of the mechanism of the influence of lncRNA-mediated ceRNA networks (ceRNETs) on HCC and provide directions and strategies for future studies.

Identification of Epithelial-Mesenchymal Transition- (EMT-) Related LncRNA for Prognostic Prediction and Risk Stratification in Esophageal Squamous Cell Carcinoma

Background

Epithelial-mesenchymal transition (EMT) is significantly associated with the invasion and development of esophageal squamous cell carcinoma (ESCC). However, the importance of EMT-related long noncoding RNA (lncRNA) is little known in ESCC.

Methods

GSE53624 (N = 119) and GSE53622 (N = 60) datasets retrieved from the Gene Expression Omnibus (GEO) database were used as training and external validation cohorts, respectively. GSE53624 and GSE53622 datasets were all sampled from China. Then, the prognostic value of EMT-related lncRNA was comprehensively investigated by weighted coexpression network analysis (WGCNA) and COX regression model.

Results

High expression of PLA2G4E-AS1, AC063976.1, and LINC01592 significantly correlated with the favorable overall survival (OS) of ESCC patients, and LINC01592 had the greatest contribution to OS. Importantly, ESCC patients were divided into low- and high-risk groups based on the optimal cut-off value of risk score estimated by the multivariate COX regression model of these three lncRNA. Patients with high risk had a shorter OS rate and restricted mean survival time (RMST) than those with low risk. Moreover, univariate and multivariate COX regression revealed that risk stratification, age, and TNM were independent prognostic predictors, which were used to construct a nomogram model for individualized and visualized prognosis prediction of ESCC patients. The calibration curves and time-dependent ROC curves in the training and validation cohorts suggested that the nomogram model had a good performance. Interestingly, clear trends indicated that risk score positively correlated with tumor microenvironment (TME) scores and immune checkpoints TIGIT, CTLA4, and BTLA. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that PLA2G4E-AS1, AC063976.1, and LINC01592 were primarily associated with TNF signaling pathway, NF-kappa B signaling pathway, and ECM-receptor interaction.

Conclusion

We developed EMT-related lncRNA PLA2G4E-AS1, AC063976.1, and LINC01592 for prognostic prediction and risk stratification of Chinese ESCC patients, which might provide deep insight for personalized prognosis prediction in Chinese ESCC patients and be potential biomarkers for designing novel therapy.

Regulatory role of long non-coding RNA UCA1 in signaling pathways and its clinical applications

Long non-coding RNA metastasis-associated urothelial carcinoma associated 1 (UCA1) plays a pivotal role in various human diseases. Its gene expression is regulated by several factors, including transcription factors, chromatin remodeling and epigenetic modification. UCA1 is involved in the regulation of the PI3K/AKT, Wnt/β-catenin, MAPK, NF-κB and JAK/STAT signaling pathways, affecting a series of cellular biological functions, such as cell proliferation, apoptosis, migration, invasion and tumor drug resistance. Furthermore, UCA1 is used as a novel potential biomarker for disease diagnosis and prognosis, as well as a target for clinical gene therapy. The present review systematically summarizes and elucidates the mechanisms of upstream transcriptional regulation of UCA1, the regulatory role of UCA1 in multiple signaling pathways in the occurrence and development of several diseases, and its potential applications in clinical treatment.

ITGB1-DT Facilitates Lung Adenocarcinoma Progression via Forming a Positive Feedback Loop With ITGB1/Wnt/β-Catenin/MYC

Lung adenocarcinoma (LUAD) is the main histological type of lung cancer, which is the leading cause of cancer-related deaths. Long non-coding RNAs (lncRNAs) were recently revealed to be involved in various cancers. However, the clinical relevance and potential biological roles of most lncRNAs in LUAD remain unclear. Here, we identified a prognosis-related lncRNA ITGB1-DT in LUAD. ITGB1-DT was upregulated in LUAD and high expression of ITGB1-DT was correlated with advanced clinical stages and poor overall survival and disease-free survival. Enhanced expression of ITGB1-DT facilitated LUAD cellular proliferation, migration, and invasion, and also lung metastasis in vivo. Knockdown of ITGB1-DT repressed LUAD cellular proliferation, migration, and invasion. ITGB1-DT interacted with EZH2, repressed the binding of EZH2 to ITGB1 promoter, reduced H3K27me3 levels at ITGB1 promoter region, and therefore activated ITGB1 expression. Through upregulating ITGB1, ITGB1-DT activated Wnt/β-catenin pathway and its downstream target MYC in LUAD. The expressions of ITGB1-DT, ITGB1, and MYC were positively correlated with each other in LUAD tissues. Intriguingly, ITGB1-DT was found as a transcriptional target of MYC. MYC directly transcriptionally activated ITGB1-DT expression. Thus, ITGB1-DT formed a positive feedback loop with ITGB1/Wnt/β-catenin/MYC. The oncogenic roles of ITGB1-DT were reversed by depletion of ITGB1 or inhibition of Wnt/β-catenin pathway. In summary, these findings revealed ITGB1-DT as a prognosis-related and oncogenic lncRNA in LUAD via activating the ITGB1-DT/ITGB1/Wnt/β-catenin/MYC positive feedback loop. These results implicated ITGB1-DT as a potential prognostic biomarker and therapeutic target for LUAD.