LncRNA LINC00472 regulates cell stiffness and inhibits the migration and invasion of lung adenocarcinoma by binding to YBX1

The genomic and immunogenomic landscape of mechanics pathway informs clinical prognosis and response to mechanotherapy

Mechanics shape cell and tissue plasticity and maintain their homeostasis. In cancers, mechanical signals regulate cancer hallmarks via mechanotransduction pathways, such as proliferation, metastasis and metabolic reprogramming. However, comprehensive characterization of mechanotransduction pathway genes and their clinical relevance across different cancer types remains untouched. Herein, we systematically portrayed the alterations of mechanotransduction pathway genes across 31 cancer types using The Cancer Genome Atlas (TCGA) databases. All the cancer types could be categorized into 6 subtypes based upon the transcriptional pattern of mechanics pathway genes. Each subtype has its own unique molecular expression pattern, mutation landscapes, immune infiltrates, and patient clinical outcome. We further found that the responses of two subtypes of cancers, one with the optimal outcome and the other with the worst prognosis, to a classical mechanotherapeutic agent (Fasudil, RhoA/ROCK inhibitor) were totally different, indicating that our cancer stratification system based upon mechanotransduction pathway genes could inform clinical responses of patients to mechanotherapeutic agents. Collectively, our study provides a novel pan-cancer landscape of the mechanotransduction pathways and underscores its potential clinical significance in the prediction of clinical prognosis and therapeutic responses to mechanotherapy among cancer patients.

PRELP reduce cell stiffness and adhesion to promote the growth and metastasis of colorectal cancer cells by binding to integrin α5

PRELP is thought to be an inhibitor of the development and progression of a variety of malignancies. Metastasis is a major cause of death in patients with colorectal cancer, but the mechanism underlying the role of PRELP in colorectal cancer metastasis remains poorly understood. In this study, we found that PRELP was significantly higher in metastatic tissues than in non-metastatic tissues of colorectal cancer and was closely associated with poor prognosis of colorectal cancer patients. PRELP promotes growth and metastasis of colorectal cancer cells. PRELP reduces cell stiffness and adhesion. PRELP promoted EMT in colorectal cancer cells and that PRELP bind to integrin α5 to activate the integrin α5/FAK/AKT signaling pathway. In conclusion, we demonstrate that PRELP is upregulated in metastatic colorectal cancer, providing a potential prognostic marker and therapeutic target for the clinical management of metastatic colorectal cancer from a biomechanical perspective.

Readers of RNA Modification in Cancer and Their Anticancer Inhibitors

Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.

KCNK1 promotes proliferation and metastasis of breast cancer cells by activating lactate dehydrogenase A (LDHA) and up-regulating H3K18 lactylation

Breast cancer is the most prevalent malignancy and the most significant contributor to mortality in female oncology patients. Potassium Two Pore Domain Channel Subfamily K Member 1 (KCNK1) is differentially expressed in a variety of tumors, but the mechanism of its function in breast cancer is unknown. In this study, we found for the first time that KCNK1 was significantly up-regulated in human breast cancer and was correlated with poor prognosis in breast cancer patients. KCNK1 promoted breast cancer proliferation, invasion, and metastasis in vitro and vivo. Further studies unexpectedly revealed that KCNK1 increased the glycolysis and lactate production in breast cancer cells by binding to and activating lactate dehydrogenase A (LDHA), which promoted histones lysine lactylation to induce the expression of a series of downstream genes and LDHA itself. Notably, increased expression of LDHA served as a vicious positive feedback to reduce tumor cell stiffness and adhesion, which eventually resulted in the proliferation, invasion, and metastasis of breast cancer. In conclusion, our results suggest that KCNK1 may serve as a potential breast cancer biomarker, and deeper insight into the cancer-promoting mechanism of KCNK1 may uncover a novel therapeutic target for breast cancer treatment.

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.

Dysregulated microRNAs and long non-coding RNAs associated with extracellular matrix stiffness

Extracellular matrix (ECM) stiffness regulates development and homeostasis in vivo and affects both physiological and pathological processes. A variety of studies have demonstrated that mRNAs, such as Piezo1, integrin β1, and Yes-associated protein (YAP)/tafazzin (TAZ), can sense the mechanical signals induced by ECM stiffness and transmit them from the extracellular space into the cytoplasm. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have been reported to play important roles in various cellular processes. Therefore, the interactions between ncRNAs and ECM stiffness, as well as the underlying molecular mechanisms, have become intriguing. In this review, we summarize recent findings on miRNAs and lncRNAs that interact with ECM stiffness. Several miRNAs and lncRNAs are involved in the progression of liver cancer, breast cancer, osteosarcoma, and cardiovascular diseases under the regulation of ECM stiffness. Through these ncRNAs, cellular behaviors including cell differentiation, proliferation, adhesion, migration, invasion, and epithelial-mesenchymal transition (EMT) are affected by ECM stiffness. We also integrate the ncRNA signaling pathways associated with ECM stiffness, in which typical signaling pathways like integrin β1/TGFβ1, phosphatidylinositol-3 kinase (PI3K)/AKT, and EMT are involved. Although our understanding of the relationships between ncRNAs and ECM stiffness is still limited, further investigations may provide new insights for disease treatment. ECM-associated ncRNAs may serve as disease biomarkers or be targeted by drugs.

Biological functions and clinical significance of tRNA-derived small fragment (tsRNA) in tumors: Current state and future perspectives

A new class of noncoding RNAs, tsRNAs are not only abundant in humans but also have high tissue specificity. Recently, an increasing number of studies have explored the correlations between tsRNAs and tumors, showing that tsRNAs can affect biological behaviors of tumor cells, such as proliferation, apoptosis and metastasis, by modulating protein translation, RNA transcription or posttranscriptional regulation. In addition, tsRNAs are widely distributed and stably expressed, which endows them with broad application prospects in diagnosing and predicting the prognosis of tumors, and they are expected to become new biomarkers. However, notably, the current research on tsRNAs still faces problems that need to be solved. In this review, we describe the characteristics of tsRNAs as well as their unique features and functions in tumors. Moreover, we also discuss the potential opportunities and challenges in clinical applications and research of tsRNAs.

LINC00472 Regulates Ferroptosis of Neurons in Alzheimer's Disease via FOXO1

INTRODUCTION

The objective of the study was to explore the molecular mechanism of long noncoding RNA (lncRNA) LINC00472 in Alzheimer's disease (AD) and identify potential novel targets for AD therapy.

METHOD

Ferroptosis-related lncRNAs were screened by GEO database. AD mouse model was constructed for in vivo experiments. The content of Aβ protein and tau protein hyperphosphorylation were examined in hippocampal tissue samples of mice. Subsequently, HT22 cells were induced with Aβ25-35 to establish a neuronal injury model of AD in vitro. The expression of FOXO1, a key gene for ferroptosis, was verified by overexpressing/knocking down the LINC00472. The effects of LINC00472 on ROS and lipid peroxidation content, GPX4, and tau protein in AD model cells were examined by ROS assay, MDA assay, Western blot, and qRT-PCR. Subsequently, the expression of iron ion, FTH, TfRC, and Fpn protein were detected in AD cells.

RESULTS

The level of FOXO1 was positively correlated with the degree of AD. In vivo experiments showed that the expression of Aβ and tau hyperphosphorylated were significantly reduced in the inhibitor group and iron was significantly reduced relative to the AD group. In the AD cell model, the content of lipid peroxide was upregulated, GPX4 protein and mRNA were decreased, and phosphorylation of tau protein was enhanced in the AD cell model relative to the control group. Whereas knocking down LINC00472 inhibited the upregulation of lipid peroxide, decreased the level of GPX4, and enhanced tau protein phosphorylation, and reduced iron accumulation in AD cells.

CONCLUSIONS

LINC00472 affects ferroptosis in AD by regulating iron accumulation in neuronal cells.

YB-1 Targeted by miR-509-3-5p Affects Migration and Invasion of Triple‑Negative Breast Cancer by Regulating Cellular Epithelial‑Mesenchymal Transition

The epithelial-mesenchymal transition (EMT) process is closely linked to metastasis of breast cancer. This article elucidates the role of Y-box binding protein-1 (YB-1) on the migration and invasion of triple-negative breast cancer (TNBC) cells by regulating EMT, and the related mechanism. The expression data of YB-1 and miR-509-3-5p in TNBC samples and normal samples were downloaded from the GEO database. The proliferation, migration, invasion, and EMT of TNBC cells were detected by CCK-8 assay, colony formation assay, wound-healing assay, transwell assay, and immunoblotting analyses. The targeted binding of YB-1 and miR-509-3-5p was validated by luciferase reporter experiment. A xenograft mouse model was constructed to investigate the influence of the miR-509-3-5p/YB-1 axis on TNBC tumor growth in vivo. YB-1 was overexpressed, while miR-509-3-5p was underexpressed in TNBC tumor tissues and various cell lines. Silencing YB-1 depressed cell viability, proliferation, motility, and EMT in vitro, and miR-509-3-5p upregulation exerted the same effects. YB-1 was targeted by miR-509-3-5p. The suppressive effects on the phenotypes of TNBC cells caused by overexpressed miR-509-3-5p were attenuated by YB-1 upregulation. In addition, miR-509-3-5p overexpression restrained TNBC tumor growth and downregulated the YB-1-mediated EMT process in vivo. YB-1 targeted by miR-509-3-5p affects motility of TNBC cells by regulating cellular EMT.

A Novel High-Dimensional Kernel Joint Non-Negative Matrix Factorization With Multimodal Information for Lung Cancer Study

Judging and identifying biological activities and biomarkers inside tissues from imaging features of diseases is challenging, so correlating pathological image data with genes inside organisms is of great significance for clinical diagnosis. This paper proposes a high-dimensional kernel non-negative matrix factorization (NMF) method based on muti-modal information fusion. This algorithm can project RNA gene expression data and pathological images (WSI) into a common feature space, where the heterogeneous variables with the largest coefficient in the same projection direction form a co-module. In addition, the miRNA-mRNA and miRNA-lncRNA interaction networks in the ceRNA network are added to the algorithm as a priori information to explore the relationship between the images and the internal activities of the gene. Furthermore, the radial basis kernel function is used to calculate the feature proportion between different kinds of genes mapped in the high-dimensional feature space and projected into the common feature space to explore the gene interaction in the high-dimensional situation. The original feature matrix is regularized to improve biological correlation, and the feature factors are sparse by orthogonal constraints to reduce redundancy. Experimental results show that the proposed NMF method is better than the traditional NMF method in stability, decomposition accuracy, and robustness. Through data analysis applied to lung cancer, genes related to tissue morphology are found, such as COL7A1, CENPF and BIRC5. In addition, gene pairs with a correlation degree exceeding 0.8 are found, and potential biomarkers of significant correlation with survival are obtained such as CAPN8. It has potential application value for the clinical diagnosis of lung cancer.

PIWI-interacting RNA-YBX1 inhibits proliferation and metastasis by the MAPK signaling pathway via YBX1 in triple-negative breast cancer

Breast cancer is the second leading cause of death in women worldwide, with triple-negative breast cancer (TNBC) having the worst prognosis. Although there are numerous studies on TNBC, there is no effective treatment for it, and it is still a major problem today. Studies on PIWI-interacting RNAs (piRNAs) are increasing and investigating the mechanism of piRNAs in the proliferation and metastasis of TNBC may lead to new potential treatment targets. Here, we identified a novel piRNA, piR-YBX1, which was downregulated in TNBC compared to matched normal breast tissue. Overexpression of piR-YBX1 significantly inhibited the proliferation, migration, invasion ability of TNBC cells both in vivo and in vitro. Mechanistically, piR-YBX1 could bind directly to mRNA of Y-box binding protein 1 (YBX1) and overexpression of piR-YBX1 downregulated YBX1 in both mRNA and protein levels, while the function of piR-YBX1 could be partly rescued by overexpression of YBX1. In addition, YBX1 could bind to RAF1 which is the key molecule in the MAPK signaling pathway, and overexpression of piR-YBX1 inhibited the p-MEK and p-ERK1/2, which can be reverted by YBX1. In conclusion, our findings discovered that the piR-YBX1/YBX1/MAPK axis suppresses the proliferation and metastasis of TNBC and therefore piR-YBX1 has the potential to be an effective therapeutic agent for breast cancer.

Y-Box Binding Protein 1: Unraveling the Multifaceted Role in Cancer Development and Therapeutic Potential

Y-box binding protein 1 (YBX1), a member of the Cold Shock Domain protein family, is overexpressed in various human cancers and is recognized as an oncogenic gene associated with poor prognosis. YBX1's functional diversity arises from its capacity to interact with a broad range of DNA and RNA molecules, implicating its involvement in diverse cellular processes. Independent investigations have unveiled specific facets of YBX1's contribution to cancer development. This comprehensive review elucidates YBX1's multifaceted role in cancer across cancer hallmarks, both in cancer cell itself and the tumor microenvironment. Based on this, we proposed YBX1 as a potential target for cancer treatment. Notably, ongoing clinical trials addressing YBX1 as a target in breast cancer and lung cancer have showcased its promise for cancer therapy. The ramp up in in vitro research on targeting YBX1 compounds also underscores its growing appeal. Moreover, the emerging role of YBX1 as a neural input is also proposed where the high level of YBX1 was strongly associated with nerve cancer and neurodegenerative diseases. This review also summarized the up-to-date advanced research on the involvement of YBX1 in pancreatic cancer.

Modulation of ferroptosis by non‑coding RNAs in cancers: Potential biomarkers for cancer diagnose and therapy

Ferroptosis is a recently discovered cell programmed death. Extensive researches have indicated that ferroptosis plays an essential role in tumorigenesis, development, migration and chemotherapy drugs resistance, which makes it become a new target for tumor therapy. Non-coding RNAs (ncRNAs) are considered to control a wide range of cellular processes by modulating gene expression. Recent studies have indicated that ncRNAs regulate the process of ferroptosis via various pathway to affect the development of cancer. However, the regulation network remains ambiguous. In this review, we outlined the major metabolic processes of ferroptosis and concluded the relationship between ferroptosis-related ncRNAs and cancer progression. In addition, the prospect of ncRNAs being new therapeutic targets and early diagnosis biomarkers for cancer by regulating ferroptosis were presented, and the possible obstacles were also predicted. This could help in discovering novel cancer early diagnostic methods and therapeutic approaches.

Promotion of colorectal cancer progression by immune-related lnc-SOX9-4 via suppression of YBX1 poly-ubiquitination and degradation

BACKGROUND

Recent research has highlighted the versatile functions of long non-coding RNAs (lncRNAs) in the onset and progression of various malignancies. Still, insufficient knowledge is available on how lnc-SOX9-4 functions in colorectal cancer (CRC) progression.

METHODS

Bioinformatics analysis was used to identify a novel lncRNA (lnc-SOX9-4), and the expression pattern of the RNA in CRC was verified using qRT-PCR. Gene ontology (GO) term analysis and Gene set enrichment analysis (GSEA) were implemented for the identification of the related mechanisms and roles of lnc-SOX9-4. Immune infiltration analysis was conducted for assessment of how lnc-SOX9-4 is linked to tumor immune cell infiltration level. Both in vitro and in vivo phenotype analyses were conducted for scrutinizing how lnc-SOX9-4 impacts the proliferation and metastasis of CRC. RNA pulldown, mass spectrometry analysis, fluorescent in situ hybridization (FISH), western blotting, and RIP assay aided in verifying lnc-SOX9-4 mechanisms linked to CRC progression.

RESULTS

An upregulation of lnc-SOX9-4 was observed in the sample CRC cells and tissues. Elevated lnc-SOX9-4 levels showed a positive association with poor clinical prognosis. Lnc-SOX9-4 was closely correlated to several types of immune infiltrating cells. Functionally, the knockdown of lnc-SOX9-4 significantly inhibited CRC cell proliferation, migration, and invasion abilities. Mechanistically, YBX1 was identified as lnc-SOX9-4, specifically interacting protein in the nucleus. Lnc-SOX9-4 could stabilize YBX1 protein levels by inhibiting poly-ubiquitination and degradation of YBX1. Furthermore, phenotype rescue experiments reveal that lnc-SOX9-4 enhanced the CRC cellular potential to proliferate and metastasize by regulating YBX1 levels.

CONCLUSIONS

Lnc-SOX9-4 promoted CRC progression by suppressing cytoplasmic translocation and promoting protein levels of YBX1 can serve as novel treatment targets for diagnosing and treating CRC.

LncRNAs and PTEN/PI3K signaling: A symphony of regulation in cancer biology

The Emergence of Long Non-coding RNAs (lncRNAs) as Key Regulators in Diverse Biological Processes: A Paradigm Shift in Understanding Gene Expression and its Impact on Cancer. The PTEN/PI3K pathway, a pivotal signaling cascade involved in cancer progression, orchestrates critical cellular functions such as survival, proliferation, and growth. In light of these advances, our investigation delves into the intricate and multifaceted interplay between lncRNAs and the PTEN/PI3K signaling pathway, unearthing previously undisclosed mechanisms that underpin cancer growth and advancement. These elusive lncRNAs exert their influence through direct targeting of the PTEN/PI3K pathway or by skillfully regulating the expression and activity of specific lncRNAs. This comprehensive review underscores the paramount significance of the interaction between lncRNAs and the PTEN/PI3K signaling pathway in cancer biology, unveiling an auspicious avenue for novel diagnostic tools and targeted therapeutic interventions. In this review, we navigate through the functional roles of specific lncRNAs in modulating PTEN/PI3K expression and activity. Additionally, we scrutinize their consequential effects on downstream components of the PTEN/PI3K pathway, unraveling the intricacies of their mutual regulation. By advancing our understanding of this complex regulatory network, this study holds the potential to revolutionize the landscape of cancer research, paving the way for tailored and efficacious treatments to combat this devastating disease.

Unveiling the connection: Long-chain non-coding RNAs and critical signaling pathways in breast cancer

Breast cancer is a complex and diverse condition that disrupts multiple signaling pathways essential for cell proliferation, survival, and differentiation. Recently, the significant involvement of long-chain non-coding RNAs (lncRNAs) in controlling key signaling pathways associated with breast cancer development has been discovered. This review aims to explore the interaction between lncRNAs and various pathways, including the AKT/PI3K/mTOR, Wnt/β-catenin, Notch, DNA damage response, TGF-β, Hedgehog, and NF-κB signaling pathways, to gain a comprehensive understanding of their roles in breast cancer. The AKT/PI3K/mTOR pathway regulates cell growth, survival, and metabolic function. Recent data suggests that specific lncRNAs can influence the functioning of this pathway, acting as either oncogenes or tumor suppressors. Dysregulation of this pathway is commonly observed in breast cancer cases. Moreover, breast cancer development has been associated with other pathways such as Wnt/β-catenin, Notch, TGF-β, Hedgehog, and NF-κB. Emerging studies have identified lncRNAs that modulate breast cancer's growth, progression, and metastasis by interacting with these pathways. To advance the development of innovative diagnostic tools and targeted treatment options, it is crucial to comprehend the intricate relationship between lncRNAs and vital signaling pathways in breast cancer. By fully harnessing the therapeutic potential of lncRNAs, there is a possibility of developing more effective and personalized therapy choices for breast cancer patients. Further investigation is necessary to comprehensively understand the role of lncRNAs within breast cancer signaling pathways and fully exploit their therapeutic potential.

Circular RNA circRILPL1 promotes nasopharyngeal carcinoma malignant progression by activating the Hippo-YAP signaling pathway

Circular RNAs (circRNAs) play an important regulatory role in the pathogenesis and progression of nasopharyngeal carcinoma (NPC), which have not been thoroughly elucidated. In this study, we revealed for the first time that circRILPL1 was upregulated in NPC, weakened adhesion and decreased stiffness of NPC cells, and promoted NPC proliferation and metastasis in vitro and in vivo. Mechanistically, circRILPL1 inhibited the LATS1-YAP kinase cascade by binding to and activating ROCK1, resulting in decrease of YAP phosphorylation. Binding and cooperating with transport receptor IPO7, circRILPL1 promoted the translocation of YAP from the cytoplasm to the nucleus, where YAP enhanced the transcription of cytoskeleton remodeling genes CAPN2 and PXN. By which, circRILPL1 contributed to the pathogenesis of NPC. Our results demonstrated that circRILPL1 promoted the proliferation and metastasis of NPC through activating the Hippo-YAP signaling pathway by binding to both ROCK1 and IPO7. Highly expressed circRILPL1 in NPC may serve as an important biomarker for tumor diagnosis and may also be a potential therapeutic target.

LINC00943 regulates miR-1252-5p/YWHAH axis to promote tumor proliferation and metastasis in lung adenocarcinoma

Lung cancer is the most common malignant tumor worldwide. In recent years, the incidence of lung adenocarcinoma (LAD) has increased significantly, with an unfavorable 5-year survival rate. Long non-coding RNAs (lncRNAs) have been shown to play a significant role in the emergence, growth, and metastasis of tumors. However, the functional role and mechanism of LINC00943 in LAD progression have not yet been investigated. Aberrant expressions of LINC00943, miR-1252-5p, and YWHAH were determined by RT-qPCR and Western blot analyses. The binding relationship between miR-1252-5p and LINC00943 or YWHAH was examined by Pearson's correlation analysis, RNA pull-down, and dual-luciferase reporter assays. MTT assay was conducted to measure cell viability and colony formation assay was performed to evaluate cell proliferation potential. Transwell assay was used to investigate cell migration and invasion and flow cytometry was applied to evaluate cell apoptosis. We found that LINC00943 was highly expressed in LAD tissue samples and cell lines and was a reliable biomarker with high sensitivity, and specificity (P < 0.0001; AUC: 0.8966) for LAD detection. LINC00943 was mainly localized in the cytoplasm. In vitro, LINC00943 promoted LAD cell proliferation, migration, and invasion; however, silencing LINC00943 inhibited LAD tumor metastasis. Mechanistically, LINC00943 was competitively bound with miR-1252-5p to enhance YWHAH expression. Moreover, LINC00943 silencing sponged miR-1252-5p to inhibit YWHAH, thereby retraining LAD cell malignant behaviors. In summary, LINC00943 facilitates LAD cell malignancy through sponging miR-1252-5p to upregulate YWHAH. LINC00943 is a novel lncRNA that serves as an oncogene and might be used as a prognostic biomarker for LAD.

Tropomyosin 2 exerts anti-tumor effects in lung adenocarcinoma and is a novel prognostic biomarker

BACKGROUND

Tropomyosin 2 (TPM2), a member of the actin filament binding protein family, plays distinct roles in the progression of different cancer types. Until now, there has been no study reporting TPM2 expression nor its function in lung adenocarcinoma (LUAD).

METHODS

In the present study, we examined the expression profile of TPM2 by immunohistochemistry (IHC). The clinical significance of TPM2 was assessed by univariate and multivariate analyses. Function of TPM2 in LUAD was evaluated by knockdown and overexpression strategies in three LUAD cell lines, followed by proliferation and invasion assays. Xenografts were conducted in nude mice to further validate the tumor-related role of TPM2.

RESULTS

Our results showed that TPM2 was downregulated in LUAD specimens and the low expression of TPM2 was associated with poor outcomes of LUAD patients. Overexpressing TPM2 inhibited cell proliferation and invasion of LUAD cell lines, while silencing TPM2 exerted the opposite effects. The effects of TPM2 in LUAD were further confirmed by xenograft assays.

CONCLUSIONS

Our results indicated that TPM2 exerted an anti-oncogenic role in LUAD via inhibiting tumor progression, thus providing a novel direction for the prognostic prediction and disease treatment.

A review on the role of LINC00472 in malignant and non-malignant disorders

Long intergenic non-protein coding RNA 472 (LINC00472) has been shown to regulate diverse cellular functions and contribute to the etiology of human disorders. LINC00472 gene is located on 6q13 and has different alternatively spliced transcripts. Expression pattern and function of LINC00472 have been evaluated in different types of cancers and some other disorders, including atherosclerosis, sepsis-induced acute hepatic injury, atrial fibrillation, neuropathic pain, primary biliary cholangitis and sepsis-induced cardiac dysfunction. This lincRNA can serve as a sponge for miR-24-3p, miR-196b-5p, miR-23a-3p, miR-93-5p, miR-4311, miR-455-3p and a number of other miRNAs. LINC00472 is able to regulate several pathways, including MEK/ERK, NF-kB, PTEN/PI3K/AKT, and STAT3 signaling pathways. This raises some concerning aspects that need to be investigated further and clarified in relation to diseases. Increasing our understanding of LINC00472's crucial roles will open new doors for creating effective therapeutic approaches against cancer and related diseases. The current study aims at providing an overview of functions of LINC00472 in malignant and non-malignant disorders.

Long noncoding RNAs induced control of ferroptosis: Implications in cancer progression and treatment

A novel kind of nonapoptotic, iron-dependent cell death brought on by lipid peroxidation is known as ferroptosis. Numerous pathological processes, including neurotoxicity, neurological disorders, ischemia-reperfusion damage, and particularly cancer, have been demonstrated to be influenced by changes in the ferroptosis-regulating network. Recent studies have established the critical roles that ferroptosis can play in cancer development and the evolution of resistance to standard chemoradiotherapy, thus suggesting that ferroptosis may be a feasible therapeutic strategy for cancer management. Gene expression may be regulated at the transcriptional and posttranscriptional levels by long noncoding RNAs (lncRNAs). They have been implicated in tumorigenesis. Some lncRNAs participate in the biological process of ferroptosis, which represents an exciting alternative to regulate ferroptosis as a means of cancer therapy. Even though there is evidence that lncRNAs have a mechanistic role in the ferroptosis of cancer cells, research on the mechanism and potential treatments for these lncRNAs is still lacking. We elucidate the potential mechanisms by which lncRNAs modulate ferroptosis in cancer and examine the promise and challenges of employing lncRNAs as novel therapeutic targets in cancer.

The lncRNA epigenetics: The significance of m6A and m5C lncRNA modifications in cancer

Most of our transcribed RNAs are represented by non-coding sequences. Long non-coding RNAs (lncRNAs) are transcripts with no or very limited protein coding ability and a length &gt;200nt. They can be epigenetically modified. N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G) and 2’-O-methylation (Nm) are some of the lncRNAs epigenetic modifications. The epigenetic modifications of RNA are controlled by three classes of enzymes, each playing a role in a specific phase of the modification. These enzymes are defined as “writers”, “readers” and “erasers”. m6A and m5C are the most studied epigenetic modifications in RNA. These modifications alter the structure and properties, thus modulating the functions and interactions of lncRNAs. The aberrant expression of several lncRNAs is linked to the development of a variety of cancers and the epigenetic signatures of m6A- or m5C-related lncRNAs are increasingly recognized as potential biomarkers of prognosis, predictors of disease stage and overall survival. In the present manuscript, the most up to date literature is reviewed with the focus on m6A and m5C modifications of lncRNAs and their significance in cancer.

Identification and integration analysis of a novel prognostic signature associated with cuproptosis-related ferroptosis genes and relevant lncRNA regulatory axis in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is a highly prevalent malignancy worldwide, and its clinical prognosis assessment and treatment is a major research direction. Both ferroptosis and cuproptosis are novel forms of cell death and are considered to be important factors involved in cancer progression. To further understand the correlation between the cuproptosis-related ferroptosis genes (CRFGs) and the prognosis of LUAD, we explore the molecular mechanisms related to the development of the disease. We constructed a prognostic signature containing 13 CRFGs, which, after grouping based on risk score, revealed that the LUAD high-risk group exhibited poor prognosis. Nomogram confirmed that it could be an independent risk factor for LUAD, and ROC curves and DCA validated the validity of the model. Further analysis showed that the three prognostic biomarkers (LIFR, CAV1, TFAP2A) were significantly correlated with immunization. Meanwhile, we found that a LINC00324/miR-200c-3p/TFAP2A regulatory axis could be involved in the progression of LUAD. In conclusion, our report reveals that CRFGs are well correlated with LUAD and provide new ideas for the construction of clinical prognostic tools, immunotherapy, and targeted therapy for LUAD.

IGF2BP3 Worsens Lung Cancer through Modifying Long Non-coding RNA CERS6-AS1/microRNA-1202 Axis

BACKGROUND

Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) can epigenetically regulate lung cancer progression, but its regulatory mechanism in the disease lacks sufficient exploration.

OBJECTIVE

The study was conducted to probe the regulatory function of IGF2BP3 in lung cancer via modulating the long non-coding RNA CERS6-AS1/microRNA-1202 (CERS6- AS1/miR-1202) axis.

METHODS

Clinical samples were collected to evaluate IGF2BP3, CERS6-AS1, miR-1202 and glycerophosphodiester phosphodiesterase domain containing 5 (GDPD5) levels. The interactions among IGF2BP3, CERS6-AS1, miR-1202 and GDPD5 were assessed. IGF2BP3-, CERS6-AS1-, and miR-1202-related constructs were transfected into lung cancer cells to determine cell biological functions. Cell tumor formation ability was further detected in vivo.

RESULTS

High expression of IGF2BP3, CERS6-AS1 and GDPD5, and low expression of miR-1202 levels were witnessed in lung cancer tissues. Suppression of IGF2BP3 restrained lung cancer progression. IGF2BP3 positively modulated CERS6-AS1 to regulate miR-1202-targeted GDPD5. Inhibition of CERS6-AS1 or promotion of miR-1202 depressed lung cancer aggravation. CERS6-AS1 silencing or miR-1202 overexpression reversed the impacts induced by IGF2BP3 on lung cancer.

CONCLUSION

IGF2BP3 facilitates the development of lung cancer cells via binding to the CERS6-AS1 promoter and down-regulating miR-1202, which may be related to GDPD5 upregulation.

Development and validation of an endoplasmic reticulum stress long non-coding RNA signature for the prognosis and immune landscape prediction of patients with lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD), the most common histotype of lung cancer, may have variable prognosis due to molecular variations. This work investigated long non-coding RNA (lncRNA) related to endoplasmic reticulum stress (ERS) to predict the prognosis and immune landscape for LUAD patients. Methods: RNA data and clinical data from 497 LUAD patients were collected in the Cancer Genome Atlas database. Pearson correlation analysis, univariate Cox regression, least absolute shrinkage and selection operator regression analyses, as well as the Kaplan-Meier method, were used to screen for ERS-related lncRNAs associated with prognosis. The risk score model was developed using multivariate Cox analysis to separate patients into high- and low-risk groups and a nomogram was constructed and evaluated. Finally, we explore the potential functions and compared the immune landscapes of two groups. Quantitative real-time PCR was used to verify the expression of these lncRNAs. Results: Five ERS-related lncRNAs were shown to be strongly linked to patients' prognosis. A risk score model was built by using these lncRNAs to categorize patients based on their median risk scores. For LUAD patients, the model was found to be an independent prognostic predictor (p < 0.001). The signature and clinical variables were then used to construct a nomogram. With 3-year and 5-year OS' AUC of 0.725 and 0.740, respectively, the nomogram's prediction performance is excellent. The 5-lncRNA signature was associated with DNA replication, epithelial-mesenchymal transition, and the pathway of cell cycle, P53 signaling. Between the two risk groups, immune responses, immune cells, and immunological checkpoints were found to be considerably different. Conclusion: Overall, our findings indicate that the 5 ERS-related lncRNA signature was an excellent prognostic indicator and helped to predict the immunotherapy response for patients with LUAD.

Decreased Expression of a Novel lncRNA FAM181A-AS1 is Associated with Poor Prognosis and Immune Infiltration in Lung Adenocarcinoma

BACKGROUND

There is no clear information regarding the role of FAM181A antisense RNA 1 (FAM181A-AS1) in lung adenocarcinoma (LUAD). We explored the relationship between FAM181A-AS1 and LUAD using bioinformatics analysis and experimental validation in this study.

METHODS

Statistics and databases were used to evaluate the relationship between clinical features in LUAD patients and FAM181A-AS1 expression, prognostic factors, regulation network, and immune infiltration of FAM181A-AS1 in function. LUAD cell lines were tested for FAM181A-AS1 expression using qRT-PCR.

RESULTS

FAM181A-AS1 showed significantly low expression in LUAD patients. Low FAM181A-AS1 expression predicted a poorer overall survival (OS) (HR: 0.66; 95% CI: 0.49-0.88; P=0.005) and disease specific survival (DSS) (HR: 0.64; 95% CI: 0.44-0.92; P=0.017) of LUAD patients. There was also an independent correlation between low FAM181A-AS1 expression (HR: 0.547; 95% CI: 0.350-0.857; P=0.008) and OS in LUAD patients. The FAM181A-AS1 high-expression phenotype was differentially enriched for M phase, cellular senescence, cell cycle checkpoints, chromatin modifying enzymes, ESR-mediated signaling, DNA repair, G2/M checkpoints, HCMV infection, and DNA double-strand break repair. A correlation was found between the expression of FAM181A-AS1 and immune infiltrating cells. A significant decrease in FAM181A-AS1 expression was observed in LUAD cell lines compared to Beas-2B.

CONCLUSION

There was a significant association between low FAM181A-AS1 expression in LUAD patients and poor survival and immune infiltration. The FAM181A-AS1 gene may provide a useful biomarker for LUAD prognosis and immunotherapy response.

Extracellular Vesicles Derived from Lung Cancer Cells Induce Transformation of Normal Fibroblasts into Lung Cancer-Associated Fibroblasts and Promote Metastasis of Lung Cancer by Delivering lncRNA HOTAIR

Human lung cancer (LC) cells A549/H358, normal lung epithelial cells BEAS-2B, and lung normal fibroblasts (NFs) were cultured, followed by transfection of H358 cells with HOTAIR shRNA. Extracellular vesicles (EVs) extracted from H358 cells were identified. The internalization of Dil-labeled-EVs by NFs was tested, and protein levels of cancer-associated fibroblast (CAF) surface markers, inflammatory cytokines, cell proliferation, invasion, and migration, and lncRNA HOTAIR levels were determined. A549 cells were cultured in an H358-EVs-treated conditioned medium of NFs (NFCM), followed by intravenous injection of A549 cells into nude mice. The lesions and Ki-67-positive cells in lung tissues were measured. The results showed that tumor cell-derived EVs (T-EVs) motivated the transformation of NFs into CAFs. Specifically, EVs can be internalized by NFs, and the protein levels of CAF surface markers and inflammation levels were elevated in H358-EVs-treated NFs. The proliferation, invasion, and migration of A549 cells cultured in T-EVs-treated NFCM were increased. H358-EVs carried HOTAIR into NFs and promoted the transformation of NFs into CAFs. Inhibition of HOTAIR partially reversed the promoting effect of H358-EVs on the transformation of NFs into CAFs and invasion and migration of LC cells. T-EVs promoted metastasis of LC in vivo by transforming NFs into CAFs.

A cuproptosis-related long non-coding RNA signature to predict the prognosis and immune microenvironment characterization for lung adenocarcinoma

BACKGROUND

Cuproptosis or copper-dependent cell death is a newly identified non-apoptotic cell death pathway which plays a critical role in the development of multiple cancers. Long non-coding RNAs (lncRNAs) are increasingly recognized as crucial regulators of programmed cell death and lung adenocarcinoma (LUAD) development, and a comprehensive understanding of cuproptosis-related lncRNAs may improve prognosis prediction of LUAD. However, few studies have explored the association of cuproptosis-related lncRNAs with the prognosis of LUAD.

METHODS

The RNA sequencing data and corresponding clinical information of patients were extracted from The Cancer Genome Atlas (TCGA) database. Five hundred LUAD patients were randomly divided into a training (n=250) and a testing cohort (n=250). Pearson correlations were performed to identify cuproptosis-related lncRNAs, and univariate Cox regression was performed to screen prognostic lncRNAs. A cuproptosis-related lncRNAs prognostic signature (CLPS) was constructed by the least absolute shrinkage and selection operator Cox regression. Kaplan-Meier analysis, receiver operating characteristic curves, and multivariate Cox regression were performed to verify the prognostic performance of CLPS. Additionally, immune cell infiltration was estimated using the single-sample gene-set enrichment analysis. pRRophetic algorithm and Tumor Immune Dysfunction and Exclusion algorithm were used to assess the immunotherapy and chemotherapy response, respectively.

RESULTS

CLPS was established based on 61 cuproptosis-related prognostic lncRNAs and exhibited a satisfactory performance predicting LUAD patients' survival (area under the curve at 1, 3, 5 years was 0.784, 0.749, 0.775, respectively). multivariate Cox analysis confirmed the independent prognostic effect of CLPS (hazard ratio: 1.128; 95% confidence interval: 1.071-1.189; P<0.001), and a nomogram containing it exhibited robust validity in prognostic prediction. We further demonstrated a higher CLPS-risk score was associated with lower levels of signatures including immune cell infiltration, immune activation, and immune checkpoints.

CONCLUSIONS

The CLPS serves as an effective predictor for the prognosis and therapeutic responses of LUAD patients. Our findings provide promising novel biomarkers and therapeutic targets for LUAD.

lncRNA MANCR Inhibits NK Cell Killing Effect on Lung Adenocarcinoma by Targeting miRNA-30d-5p

Background. NK cells are imperative in spontaneous antitumor response of various cancers. Currently, lncRNAs are considered important modulators of the tumor microenvironment. This study investigated the molecular mechanism by which mitotically associated long noncoding RNA (MANCR) controls killing effect of NK cells on lung adenocarcinoma (LUAD) in the tumor microenvironment. Methods. The interplay between MANCR and miRNA-30d-5p was analyzed by bioinformatics. Expression of MANCR mRNA and miRNA-30d-5p was examined using qRT-PCR. Dual-luciferase reporter and RIP assays were utilized to verify the targeted relationship between MANCR and miRNA-30d-5p. To investigate regulation of MANCR/miRNA-30d-5p axis in NK cell killing effect on LUAD cells, western blot tested the protein level of perforin and granzyme B. ELISA determined the level of IFN-γ. CytoTox 96 Non-Radioactive Cytotoxicity Assay kit was applied for cytotoxicity detection of NK cells. Perforin and granzyme B fluorescence intensity was measured via immunofluorescence, and cell apoptosis levels were also revealed via flow cytometry. Results. MANCR was found to be upregulated, while miRNA-30d-5p expression was downregulated in LUAD tissues. Overexpression of MANCR in LUAD cells significantly reduced NK cell IFN-γ secretion, expression of granzyme B and perforin, and NK cell killing effect. In addition, MANCR could target and downregulate miRNA-30d-5p expression, and miRNA-30d-5p overexpression reversed the inhibition of NK cell killing effect caused by MANCR overexpression. Conclusion. MANCR inhibited the killing effect of NK cells on LUAD via targeting and downregulating miRNA-30d-5p and provided new ideas for antitumor therapy based on tumor microenvironment.

LINC01094/SPI1/CCL7 Axis Promotes Macrophage Accumulation in Lung Adenocarcinoma and Tumor Cell Dissemination

Objective

Infiltration of tumor-associated macrophages is closely linked to the malignant development of human cancers. This research studies the function of C-C motif chemokine ligand 7 (CCL7) in the macrophage accumulation in lung adenocarcinoma (LUAD) and the underpinning mechanism.

Methods

The expression profile of CCL7 in LUAD and its correlations with patient's prognosis and macrophage infiltration were predicted via bioinformatics systems. Artificial up- or downregulation of CCL7 was induced in LUAD cells to explore its function in the mobility, EMT of cancer cells, and migration of M2 macrophages. Cancer cells were implanted in NOD/SCID mice to induce xenograft tumors. The CCL7-related transcription factors or factors were predicted by bioinformatic tools, and the molecular interactions were confirmed by immunoprecipitation or luciferase assays.

Results

CCL7 was highly expressed in LUAD and linked to increased TAM infiltration. Knockdown of CCL7 suppressed the chemotaxis and M2 skewing of macrophages, and it blocked the EMT and mobility of LUAD cells. CCL7 downregulation also suppressed macrophage infiltration in xenograft tumors in mice. Spi-1 proto-oncogene (SPI1) was confirmed as an upstream factor activating CCL7 transcription, and LINC01094 was found to bind to SPI1 to promote its nuclear translocation. Upregulation of SPI1 restored the chemotactic migration and M2 polarization of macrophages in LUAD cells.

Conclusion

This paper reveals that LINC01094 binds to SPI1 to promote its nuclear translocation, which further activates CCL7 transcription by binding to its promoter, leading to M2 macrophage accumulation and dissemination of tumor cells.

Identification of Novel Multi-Omics Expression Landscapes and Meta-Analysis of Landscape-Based Competitive Endogenous RNA Networks in ALDH+ Lung Adenocarcinoma Stem Cells

ALDH+ H1975 lung adenocarcinoma stem cells (LSCs) are a rare cell population identified in lung adenocarcinoma (LUAD). LSCs can self-renew, drive tumor initiation, growth, metastasis, and recurrence and are also the predominant cause of poor prognosis due to their intrinsic resistance to drugs and chemotherapy. Consequently, LSCs are a promising target for LUAD therapy. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), exert many significant regulatory functions in the pathogenesis of human cancers, showing the necessity for a comprehensive understanding of the mechanisms that underlie lung carcinogenesis. Nonetheless, research on many known transcripts and messenger RNAs (mRNAs) has already generated new information. Unknown biomarkers in ncRNAs and systematic and comprehensive interrelation with unknown ncRNAs and mRNAs may provide further insights into the biology of LUAD. Herein, a set of novel ncRNAs that include miRNAs, lncRNAs, and circRNAs were identified, and differentially expressed patterns of ncRNAs and mRNAs in LSCs and ALDH-H1975 LUAD tumor cells (LTCs) were obtained using stringent bioinformatics pipelines. Through a meta-analysis of the identified landscapes, novel competitive endogenous RNA (ceRNA) networks were constructed to reveal the potential molecular mechanisms that regulate the hallmarks of LSCs and LTCs. This study presents a summary of novel ncRNAs and the fundamental roles of differentially expressed ncRNAs implicated in the activity of LSCs and LTCs. In addition, the study also provides a comprehensive resource for the future identification of diagnostic, therapeutic, and prognostic biomarkers in LUAD.

LINC00365 inhibited lung adenocarcinoma progression and glycolysis via sponging miR-429/KCTD12 axis

This study researched the function of long non-coding RNA LINC00365 in lung adenocarcinoma (LAD) progression. LINC00365, miR-429, and KCTD12 expression in the LAD clinical tissues and cells were detcetd by qRT-PCR and Western blot. LINC00365, miR-429, and KCTD12 effects on H1975 cells malignant phenotype were detected by cell counting kit-8 assay, clone formation experiment, Transwell experiment, and glycolysis. Dual luciferase reporter gene assay and RNA pull-down assay were implemented. LINC00365 effect on H1975 cells in vivo growth was detected. LINC00365 was low expressed in the LAD patients and cells, associating with poor outcome. LINC00365 up-regulation attenuated H1975 cells proliferation, migration, invasion, glycolysis and in vivo growth. LINC00365 inhibited KCTD12 expression by sponging miR-429. miR-429 up-regulation and KCTD12 down-regulation partial reversed LINC00365 inhibition on H1975 cells malignant phenotype. Thus, LINC00365 inhibited LAD progression and glycolysis via targeting miR-429/KCTD12 axis. LINC00365 might be a potential candidate for LAD target treatment clinically.

A novel cuproptosis-related prognostic lncRNA signature and lncRNA MIR31HG/miR-193a-3p/TNFRSF21 regulatory axis in lung adenocarcinoma

Lung adenocarcinoma (LUAD) remains the most common subtype of lung malignancy. Cuproptosis is a newly identified cell death which could regulate tumor cell proliferation and progression. Long non-coding RNAs (lncRNAs) are key molecules and potential biomarkers for diagnosing and treating various diseases. However, the effects of cuproptosis-related lncRNAs on LUAD are still unclear. In our study, 7 cuproptosis-related lncRNAs were selected to establish a prognostic model using univariate Cox regression analysis, LASSO algorithm, and multivariate analysis. Furthermore, we evaluated AC008764.2, AL022323.1, ELN-AS1, and LINC00578, which were identified as protective lncRNAs, while AL031667.3, AL606489.1, and MIR31HG were identified as risk lncRNAs. The risk score calculated by the prognostic model proved to be an effective independent factor compared with other clinical features by Cox regression analyses [univariate analysis: hazard ratio (HR) = 1.065, 95% confidence interval (CI) = 1.043–1.087, P < 0.001; multivariate analysis: HR = 1.067, 95% CI = 1.044–1.091, P < 0.001]. In addition, both analyses (ROC and nomogram) were used to corroborate the accuracy and reliability of this signature. The correlation between cuproptosis-related lncRNAs and immune microenvironment was elucidated, where 7 immune cells and 8 immune-correlated pathways were found to be differentially expressed between two risk groups. Furthermore, our results also identified and verified the ceRNA of cuproptosis-related lncRNA MIR31HG/miR-193a-3p/TNFRSF21 regulatory axis using bioinformatics tools. MIR31HG was highly expressed in LUAD specimens and some LUAD cell lines. Inhibition of MIR31HG clearly reduced the proliferation, migration, and invasion of the LUAD cells. MIR31HG showed oncogenic features via sponging miR-193a-3p and tended to positively regulate TNFRSF21 expression. In a word, lncRNA MIR31HG acts as an oncogene in LUAD by targeting miR-193a-3p to modulate TNFRSF21, which may be beneficial to the gene therapy of LUAD.

LncRNA LINC00511 promotes COL1A1-mediated proliferation and metastasis by sponging miR-126-5p/miR-218-5p in lung adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is currently the leading cause of cancer-related death worldwide. Long noncoding RNAs (lncRNAs) play key roles in tumor occurrence and development as crucial cancer regulators. The present study aimed to explore the molecular mechanism and regulatory network of Linc00511 in LUAD and to identify new potential therapeutic targets for LUAD.

Methods

Real-time quantitative polymerase chain reaction (RT–qPCR) was performed to determine the relative Linc00511 levels in LUAD tissues and cells. The proliferation, apoptosis, migration, and invasion abilities of LUAD cells were assessed by a Cell Counting Kit-8 (CCK-8) assay, a colony formation assay, flow cytometry, and a Transwell assay. Changes in hsa_miR-126-5p, hsa_miR-218-5p, and COL1A1 expression were analyzed using western blotting and RT–qPCR. Targeted binding between miR-126-5p/miR-218-5p and Linc00511 or COL1A1 was verified with a luciferase reporter system and confirmed by an RNA pulldown assay. The participation of the PI3K/AKT signaling pathway was confirmed via western blotting. Xenograft animal experiments were performed to detect the impact of Linc00511 on LUAD tumor growth in vivo.

Results

In the present work, we observed that Linc00511 was upregulated in LUAD tissues and cells. Loss/gain-of-function experiments indicated that knockdown of Linc00511 significantly inhibited LUAD cell proliferation, migration and invasion and promoted LUAD cell apoptosis, whereas overexpression of Linc00511 showed the opposite effects. In addition, we determined that Linc00511 promoted COL1A1-mediated cell proliferation and cell motility by sponging miR-126-5p and miR-218-5p. Moreover, Linc00511 activated the PI3K/AKT signaling pathway through upregulation of COL1A1. Finally, silencing of Linc00511 inhibited LUAD tumor growth in vivo.

Conclusions

Linc00511 acts as a competing endogenous RNA to regulate COL1A1 by targeting miR-126-5p and miR-218-5p, thereby promoting the proliferation and invasion of LUAD cells.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-022-02070-3.

Risk coefficient model of necroptosis-related lncRNA in predicting the prognosis of patients with lung adenocarcinoma

Model algorithms were used in constructing the risk coefficient model of necroptosis-related long non-coding RNA in identifying novel potential biomarkers in the prediction of the sensitivity to chemotherapeutic agents and prognosis of patients with lung adenocarcinoma (LUAD). Clinic and transcriptomic data of LUAD were obtained from The Cancer Genome Atlas. Differently expressed necroptosis-related long non-coding RNAs got identified by performing both the univariate and co-expression Cox regression analyses. Subsequently, the least absolute shrinkage and selection operator technique was adopted in constructing the nrlncRNA model. We made a comparison of the areas under the curve, did the count of the values of Akaike information criterion of 1-year, 2-year, as well as 3-year receiver operating characteristic curves, after which the cut-off value was determined for the construction of an optimal model to be used in identifying high risk and low risk patients. Genes, tumor-infiltrating immune cells, clinical correlation analysis, and chemotherapeutic agents data of both the high-risk and low-risk subgroups were also performed. We identified 26 DEnrlncRNA pairs, which were involved in the Cox regression model constructed. The curve areas under survival periods of 1 year, 2 years, and 3 years of patients with LUAD were 0.834, 0.790, and 0.821, respectively. The cut-off value set was 2.031, which was used in the identification of either the high-risk or low-risk patients. Poor outcomes were observed in patients belonging to the high-risk group. The risk score was the independent predictor of the LUAD outcome (p < 0.001). The expression levels of immune checkpoint and infiltration of specific immune cells were anticipated by the gene risk model. The high-risk group was found to be highly sensitive to docetaxel, erlotinib, cisplatin, and paclitaxel. The model established through nrlncRNA pairs irrespective of the levels of expression could give a prediction on the LUAD patients’ prognosis and assist in identifying the patients who might gain more benefit from chemotherapeutic agents.

Identification and Validation of lncRNA-AC087588.2 in Lung Adenocarcinoma: A Novel Prognostic and Diagnostic Indicator

Lung adenocarcinoma (LUAD) is the most common histological lung cancer, and it is the leading cause of cancer-related deaths worldwide. Long non-coding RNAs (lncRNAs) have been implicated in the initiation and progression of various cancers. LncRNA-AC087588.2 (ENSG00000274976) is a novel lncRNA that is abnormally expressed in diverse cancer types, including LUAD. However, the clinical significance, prognostic value, diagnostic value, immune role, and the potential biological function of AC087588.2 LUAD remain elusive. In this study, we found that AC087588.2 was upregulated and associated with a poor prognosis in LUAD. In addition, univariate and multivariate Cox regression analysis indicated that AC087588.2 could be an independent prognostic factor for LUAD. Functionally, the knockdown of AC087588.2 restrained LUAD cell proliferation and migration in vitro. Finally, we constructed a ceRNA network that included hsa-miR-30a-5p and four mRNAs (ANLN, POLR3G, EHBP1, and ERO1A) specific to AC087588.2 in LUAD. The Kaplan–Meier survival analysis showed that lower expression of hsa-miR-30a-5p and higher expression of ANLN, POLR3G, EHBP1, and ERO1A were associated with adverse clinical outcomes in patients with LUAD. This finding provided a comprehensive view of the AC087588.2-mediated ceRNA network in LUAD, thereby highlighting its potential role in the diagnosis and prognosis of LUAD.

Characterizing the landscape of cervical squamous cell carcinoma immune microenvironment by integrating the single-cell transcriptomics and RNA-Seq

Background

Cervical squamous cell carcinoma (CSCC), caused by the infection of high‐risk human papillomavirus, is one of the most common malignancies in women worldwide.

Methods

RNA expression data, including those from the Cancer Genome Atlas, Gene Expression Omnibus, and Genotype‐Tissue Expression databases, were used to identify the expression of RNAs in normal and tumor tissue. Correlation analysis was performed to identify the immune‐related long noncoding RNAs (IRLs) and hypoxia‐related genes (IRHs) that can influence the activity of the immune system. Prognosis models of immune‐related RNAs (IRRs) were used to construct a coexpression network of the immune system. We identified the role of IRRs in immunotherapy by correlation analysis with immune checkpoint genes (ICGs). We then validated the expression data by integrating two single‐cell sequencing data sets of CSCC to identify the key immune features.

Results

In total, six immune‐related gene (IRG), four IRL, and five IRH signatures that can significantly influence the characteristics of the tumor immune microenvironment (TIME) were selected using machine learning methods. The expression level of ICGs was significantly upregulated in GZMB⁺CD8⁺ T‐cells and tumor‐associated macrophages (TAMs) in tumor tissues. TGFBI⁺ TAMs are a kind of blood‐derived monocyte‐derived M0‐like TAM linked to hypoxia and a poor prognosis. IFI30⁺ M1‐like TAMs participate in the process of immune‐regulation and showed a role in the promotion of CD8⁺ T‐cells and Type 1 T helper (Th1)/Th2 cells in the coexpression network, together with several IRLs, IRGs, and ICGs.

Conclusions

CD16⁺ monocyte‐derived IFI30⁺ TAMs participated in our coexpression network to regulate the TIME, showing the potential to be a novel immunotherapy target. The enrichment of M0‐like TAMs was associated with a worse prognosis in the high‐risk score group with IRH signatures. Remarkably, M0‐like TAMs in tumor tissues overexpressed TGFBI and were associated with several well‐known tumor‐proliferation pathways.

Non-coding RNAs and ferroptosis: potential implications for cancer therapy

Ferroptosis is a recently defined form of regulated cell death, which is biochemically and morphologically distinct from traditional forms of programmed cell death such as apoptosis or necrosis. It is driven by iron, reactive oxygen species, and phospholipids that are oxidatively damaged, ultimately resulting in mitochondrial damage and breakdown of membrane integrity. Numerous cellular signaling pathways and molecules are involved in the regulation of ferroptosis, including enzymes that control the cellular redox status. Alterations in the ferroptosis-regulating network can contribute to the development of various diseases, including cancer. Evidence suggests that ferroptosis is commonly suppressed in cancer cells, allowing them to survive and progress. However, cancer cells which are resistant to common chemotherapeutic drugs seem to be highly susceptible to ferroptosis inducers, highlighting the great potential of pharmacologic modulation of ferroptosis for cancer treatment. Non-coding RNAs (ncRNAs) are considered master regulators of various cellular processes, particularly in cancer where they have been implicated in all hallmarks of cancer. Recent work also demonstrated their involvement in the molecular control of ferroptosis. Hence, ncRNA-based therapeutics represent an exciting alternative to modulate ferroptosis for cancer therapy. This review summarizes the ncRNAs implicated in the regulation of ferroptosis in cancer and highlights their underlying molecular mechanisms in the light of potential therapeutic applications.

Long non-coding RNAs are involved in alternative splicing and promote cancer progression

Alternative splicing (AS) is a key process in which precursor RNAs produce different mature RNAs, and the disorder of AS is a key factor in promoting cancer development. Compared with coding RNA, studies on the functions of long non-coding RNAs (lncRNAs) are far from enough. In fact, lncRNA is an important participant and regulator in the process of AS. On the one hand, lncRNAs regulate cancer progression as AS products of precursor messenger RNA (mRNA), but on the other hand, precursor lncRNA generates cancer-related abnormal splicing variants through AS. In addition, lncRNAs directly or indirectly regulate the AS events of downstream target genes, thus affecting the occurrence and development of cancer. Here, we reviewed how lncRNAs regulate AS and influence oncogenesis in different ways.

YB-1 as an Oncoprotein: Functions, Regulation, Post-Translational Modifications, and Targeted Therapy

Y box binding protein 1 (YB-1) is a protein with a highly conserved cold shock domain (CSD) that also belongs to the family of DNA- and RNA-binding proteins. YB-1 is present in both the nucleus and cytoplasm and plays versatile roles in gene transcription, RNA splicing, DNA damage repair, cell cycle progression, and immunity. Cumulative evidence suggests that YB-1 promotes the progression of multiple tumor types and serves as a potential tumor biomarker and therapeutic target. This review comprehensively summarizes the emerging functions, mechanisms, and regulation of YB-1 in cancers, and further discusses targeted strategies.

circ_0020123 promotes cell proliferation and migration in lung adenocarcinoma via PDZD8

High circ_0020123 expression is associated with poor prognosis in patients with non-small cell lung cancer (NSCLC) as previously reported. Whether circ_0020123 also plays an oncogenic role in lung adenocarcinoma (LUAD) is still unknown. Additionally, circ_0020123 is derived from part of exon (1312–3851) from its host gene PDZ domain-containing protein 8 (PDZD8). We hypothesized that circ_0020123 might affect malignant behaviors of LUAD cells by regulating PDZD8. Reverse transcription quantitative polymerase chain reaction revealed that PDZD8 was highly expressed in LUAD tissues and cells. PDZD8 knockdown suppressed LUAD cell proliferation and migration as shown by colony formation assays, Ethynyl deoxyuridine incorporation assays, Transwell assays, and wound healing assays. circ_0020123 was also found to be upregulated in LUAD tissues and cells. Moreover, circ_0020123 positively regulated PDZD8 expression in LUAD cells but exerted no significant effect on the transcriptional level of PDZD8. Mechanistically, circ_0020123 act as a competing endogenous RNA (ceRNA) to interact with miR-1283, thereby releasing the repression on PDZD8. Moreover, PDZD8 overexpression rescued the suppressive effect of circ_0020123 knockdown on LUAD cell proliferation and migration. In conclusion, circ_0020123 interacts with miR-1283 as a ceRNA to regulate PDZD8 expression, thus promoting the proliferation and migration of LUAD cells. The study might provide new biomarkers for future LUAD investigation.

Long non-coding RNA LINC00472 inhibits oral squamous cell carcinoma via miR-4311/GNG7 axis

Emerging studies indicate that long non-coding RNAs play important roles in oral squamous cell carcinoma (OSCC). However, the function of the majority of long non-coding RNAs is still unclear. Recently, LINC00472 has been reported to play crucial roles in multiple cancers. However, the role of LINC00472 in oral squamous cell carcinoma (OSCC) is still not clear. This study found that LncRNA LINC00472 was significantly down-regulated in several squamous cell carcinoma cancer tissues and OSCC cell lines. Over-expression of LINC00472 in OSCC cells inhibited OSCC progression and alleviated OSCC immune responses. Additionally, we confirmed that LINC00472 functioned as an hsa-miR-4311 sponge and regulated the expression of GNG7 (guanine nucleotide-binding protein, gamma 7). Also, we found that LINC00472 over-expression could suppress xenograft tumor growth in vivo. Our study provides evidence that LINC00472 plays an essential role in inhibiting oral squamous cell carcinoma progression and affecting immune responses by directly binding to hsa-miR-4311 to regulate the expression of GNG7 positively.

Long non-coding RNA HIF1A-AS2 modulates the proliferation, migration, and phenotypic switch of aortic smooth muscle cells in aortic dissection via sponging microRNA-33b

Aortic dissection (AD), also known as aortic dissecting aneurysm, is one of the most common and dangerous cardiovascular diseases with high morbidity and mortality. This study was aimed to investigate the functional role of long non-coding RNA Hypoxia-inducible factor 1 alpha-antisense RNA 2 (lncRNA HIF1A-AS2) in AD. An in vitro model of AD was established by platelet-derived growth factor-BB (PDGF-BB)-mediated human aortic Smooth Muscle Cells (SMCs). HIF1A-AS2 expression in human AD tissues was determined by quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH) assays, followed by investigation of biological roles of HIF1A-AS2 in AD development by Cell Counting Kit-8 (CCK-8), immunofluorescence, and transwell assays. Additionally, the correlation between HIF1A-AS2, miR-33b, and high mobility group AT-hook2 (HMGA2) were identified by RNA immunoprecipitation (RIP), RNA pull-down and luciferase reporter assays. Results showed that HIF1A-AS2 was obviously increased, while the contractile-phenotype markers of vascular SMCs were significantly decreased in human AD tissues, when compared to normal tissues. Inhibition of HIF1A-AS2 attenuated SMCs proliferation and migration, whereas enhanced the phenotypic switch under the stimulation of PDGF-BB. Results from RIP, RNA pull-down and luciferase reporter assays demonstrated that miR-33b directly bound with HIF1A-AS2, and HIF1A-AS2 silencing suppressed the expression of HMGA2, which was induced by miR-33b inhibitor. In conclusion, knockdown of HIF1A-AS2 suppressed the proliferation and migration, while promoted the phenotypic switching of SMCs through miR-33b/HMGA2 axis, which laid a theoretical foundation for understanding the development of AD and shed light on a potential target for AD treatment.

LINC00472 suppresses oral squamous cell carcinoma growth by targeting miR-455-3p/ELF3 axis

LINC00472 is reported to play a role in suppressing tumors in cancers such as lung cancer and hepatocellular carcinoma, among others. We made investigations into the effects of LINC00472 in oral squamous cell carcinoma (OSCC) progression to explore the underlying molecular mechanisms. By qRT-PCR, we assessed the LINC00472 expression in OSCC tissues and cells and performed functional analysis to investigate how LINC00472/miR-455-3p/ELF3 impacts OSCC cell proliferation, apoptosis, and cell cycle. The role that LINC00472 plays in OSCC tumor growth was examined by establishing a xenograft model. Down-regulation of LINC00472 occurred in tissues and cells of an OSCC tumor. LINC00472 overexpression caused OSCC cell proliferation to be inhibited, cell apoptosis to be promoted, and cell cycle arrest to be induced. As a competing endogenous RNA (ceRNA), LINC00472 can block miR-455-3p function and further promote ELF3 expression. The overexpression of miR-455-3p or ELF3 knockdown was shown to be capable of reversing the anti-tumor effects of LINC00472 in OSCC. In vivo experiments confirmed the tumor-suppressing role of LINC00472 in the progression of OSCC. In short, we found that the novel LINC00472 inhibits OSCC growth via the miR-455-3p/ELF3 axis. LINC00472 and its targeted miR-455-3p/ELF3 axis may represent valuable targets for treating OSCC.

Long Noncoding RNA 00472: A Novel Biomarker in Human Diseases

Long non-coding RNAs (lncRNAs) play important roles in human diseases. They control gene expression levels and influence various biological processes through multiple mechanisms. Functional abnormalities in lncRNAs are strongly associated with occurrence and development of various diseases. LINC00472, which is located on chromosome 6q13, is involved in several human diseases, particularly cancers of the breast, lung, liver, osteosarcoma, bladder, colorectal, ovarian, pancreatic and stomach. Importantly, LINC00472 can be used as a biomarker for breast cancer cell sensitivity to chemotherapeutic regimens, including doxorubicin. LINC00472 is regulated by microRNAs and several signaling pathways. However, the significance of LINC00472 in human diseases has not been clearly established. In this review, we elucidate on the significance of LINC00472 in various human diseases, indicating that LINC00472 may be a diagnostic, prognostic as well as therapeutic target for these diseases.

Computational detection of a genome instability-derived lncRNA signature for predicting the clinical outcome of lung adenocarcinoma

Evidence has been emerging of the importance of long non-coding RNAs (lncRNAs) in genome instability. However, no study has established how to classify such lncRNAs linked to genomic instability, and whether that connection poses a therapeutic significance. Here, we established a computational frame derived from mutator hypothesis by combining profiles of lncRNA expression and those of somatic mutations in a tumor genome, and identified 185 candidate lncRNAs associated with genomic instability in lung adenocarcinoma (LUAD). Through further studies, we established a six lncRNA-based signature, which assigned patients to the high- and low-risk groups with different prognosis. Further validation of this signature was performed in a number of separate cohorts of LUAD patients. In addition, the signature was found closely linked to genomic mutation rates in patients, indicating it could be a useful way to quantify genomic instability. In summary, this research offered a novel method by through which more studies may explore the function of lncRNAs and presented a possible new way for detecting biomarkers associated with genomic instability in cancers.

Substrate Stiffness Drives Epithelial to Mesenchymal Transition and Proliferation through the NEAT1-Wnt/β-Catenin Pathway in Liver Cancer

Background: Extracellular matrix (ECM)-derived mechanical stimuli regulate many cellular processes and phenotypes through mechanotransduction signaling pathways. Substrate stiffness changes cell phenotypes and promotes angiogenesis, epithelial to mesenchymal transition (EMT), and metastasis in tumors. Enhanced liver tissue matrix stiffness plays a crucial role in the tumorigenesis and malignant development of liver cancer and is associated with unfavorable survival outcomes. However, how liver cancer cells sense changes in ECM stiffness and the underlying molecular mechanisms are largely unknown. Methods: Seeding HepG2 cells on the micropillar gels, HepG2 cells were assessed for responsiveness to mechanotransduction using Western blot and immunofluorescence. Conclusions: We found that higher substrate stiffness dramatically enhanced malignant cell phenotypes and promoted G1/S transition in HepG2 cells. Furthermore, nuclear paraspeckle assembly transcript 1 (NEAT1) was identified as a matrix stiffness-responsive long non-coding RNA (lncRNA) regulating proliferation and EMT in response to increasing matrix stiffness during the progression of HepG2 cells towards liver cancer phenotypes. Higher matrix stiffness contributed to enhancing NEAT1 expression, which activated the WNT/β-catenin pathway. β-catenin translocates and enters the nucleus and the EMT transcription factor zinc finger E-box binding homeobox 1 (ZEB1) was upregulated to trigger EMT. Additionally, the proteins required for matrix stiffness-induced proliferation and resistance were strikingly upregulated in HepG2 cells. Therefore, our findings provide evidence that ECM-derived mechanical signals regulate cell proliferation and drive EMT through a NEAT1/WNT/β-catenin mechanotransduction pathway in the tumor microenvironment of liver cancer.

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.

Construction of a Novel Lung Adenocarcinoma Immune-Related lncRNA Pair Signature

Background

A growing number of studies have demonstrated that immune-related long noncoding ribonucleic acids (irlncRNAs) are potential prognostic factors for lung adenocarcinoma. Two-gene combination patterns could improve the sensitivity of prognostic models, providing us a novel signature construction concept that we applied to lung adenocarcinoma.

Methods

Gene expression and clinical data were downloaded from the Lung Adenocarcinoma project of The Cancer Genome Atlas (TCGA) database. We applied a co-expression analysis with immune genes obtained from the ImmPort database to recognize irlncRNA. The matrix of irlncRNA pairs was established by a cyclic comparison of each lncRNA pair expression level. Univariate and multivariate Cox regressions and Lasso penalized regression analysis were applied to construct the risk model. Patients with lung adenocarcinoma were divided into high- and low-risk groups, according to the Akaike Information Criterion (AIC) values of the receiver operating characteristic (ROC) curve. Then, we evaluated our signature under various clinical settings: clinical-pathological characteristics, tumor-infiltrating immune cells, checkpoint-related biomarkers, targeted therapy, and chemotherapy.

Results

Based on the 239 differently expressed irlncRNAs, we constructed an 11-irlncRNA pair signature. The area under the curve (AUC) of the ROC curve for the signature to predict the 4-year survival rate was 0.819, and the cut-off point was recognized as 1.003. Subsequent analysis showed that our signature can effectively distinguish unfavorable survival outcomes, prognostic clinic-pathological characteristics, and specify tumor infiltration status. Highly expressed immune checkpoint-related genes, as well as higher chemosensitivity, were correlated to the low-risk group.

Conclusion

We constructed a novel lung adenocarcinoma irlncRNA signature with promising prognostic value using the TCGA database, based on paired irlncRNAs and not relying on lncRNAs special expression levels.

Keep your eyes peeled for long noncoding RNAs: Explaining their boundless role in cancer metastasis, drug resistance, and clinical application

Cancer metastasis and drug resistance are two major obstacles in the treatment of cancer and therefore, the leading cause of cancer-associated mortalities worldwide. Hence, an in-depth understanding of these processes and identification of the underlying key players could help design a better therapeutic regimen to treat cancer. Earlier thought to be merely transcriptional junk and having passive or secondary function, recent advances in the genomic research have unravelled that long noncoding RNAs (lncRNAs) play pivotal roles in diverse physiological as well as pathological processes including cancer metastasis and drug resistance. LncRNAs can regulate various steps of the complex metastatic cascade such as epithelial-mesenchymal transition (EMT), invasion, migration and metastatic colonization, and also affect the sensitivity of cancer cells to various chemotherapeutic drugs. A substantial body of literature for more than a decade of research evince that lncRNAs can regulate gene expression at different levels such as epigenetic, transcriptional, posttranscriptional, translational and posttranslational levels, depending on their subcellular localization and through their ability to interact with DNA, RNA and proteins. In this review, we mainly focus on how lncRNAs affect cancer metastasis by modulating expression of key metastasis-associated genes at various levels of gene regulation. We also discuss how lncRNAs confer cancer cells either sensitivity or resistance to various chemo-therapeutic drugs via different mechanisms. Finally, we highlight the immense potential of lncRNAs as prognostic and diagnostic biomarkers as well as therapeutic targets in cancer.