DUSP5 regulated by YTHDF1-mediated m6A modification promotes epithelial-mesenchymal transition and EGFR-TKI resistance via the TGF-ß/Smad signaling pathway in lung adenocarcinoma.

BACKGROUND: Lung adenocarcinoma (LUAD) patients have a dismal survival rate because of cancer metastasis and drug resistance. The study aims to identify the genes that concurrently modulate EMT, metastasis and EGFR-TKI resistance, and to investigate the underlying regulatory mechanisms. METHODS: Cox regression and Kaplan-Meier analyses were applied to identify prognostic oncogenes in LUAD. Gene set enrichment analysis (GSEA) was used to indicate the biological functions of the gene. Wound-healing and Transwell assays were used to detect migratory and invasive ability. EGFR-TKI sensitivity was evaluated by assessing the proliferation, clonogenic survival and metastatic capability of cancer cells with treatment with gefitinib. Methylated RNA immunoprecipitation (MeRIP) and RNA immunoprecipitation (RIP) analyses established the level of m6A modification present on the target gene and the protein's capability to interact with RNA, respectively. Single-sample gene set enrichment (ssGSEA) algorithm used to investigate levels of immune cell infiltration. RESULTS: Our study identified dual-specificity phosphatase 5 (DUSP5) as a novel and powerful predictor of adverse outcomes for LUAD by using public datasets. Functional enrichment analysis found that DUSP5 was positively enriched in EMT and transforming growth factor-beta (TGF-ß) signaling pathway, a prevailing pathway involved in the induction of EMT. As expected, DUSP5 knockdown suppressed EMT via inhibiting the canonical TGF-ß/Smad signaling pathway in in vitro experiments. Consistently, knockdown of DUSP5 was first found to inhibit migratory ability and invasiveness of LUAD cells in in vitro and prevent lung metastasis in in vivo. DUSP5 knockdown re-sensitized gefitinib-resistant LUAD cells to gefitinib, accompanying reversion of EMT progress. In LUAD tissue samples, we found 14 cytosine-phosphate-guanine (CpG) sites of DUSP5 that were negatively associated with DUSP5 gene expression. Importantly, 5'Azacytidine (AZA), an FDA-approved DNA methyltransferase inhibitor, restored DUSP5 expression. Moreover, RIP experiments confirmed that YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), a m6A reader protein, could bind DUSP5 mRNA. YTHDF1 promoted DUSP5 expression and the malignant phenotype of LUAD cells. In addition, the DUSP5-derived genomic model revealed the two clusters with distinguishable immune features and tumor mutational burden (TMB). CONCLUSIONS: Briefly, our study discovered DUSP5 which was regulated by epigenetic modification, might be a potential therapeutic target, especially in LUAD patients with acquired EGFR-TKI resistance.

Bioinformatics analysis of the prognostic and immunotherapeutic significance of NPRL2 in stomach adenocarcinoma.

Background: Stomach adenocarcinoma (STAD) is a major type of gastric cancer with high morbidity and mortality. NPRL2, a candidate cancer suppressor gene, has been shown to have anti-cancer effects in various types of cancers. Therefore, comprehensive analyses of NPRL2 in STAD may provide a potential prognostic marker and clinical target for the management of gastric cancer. Methods: Genomic expression and methylation were analysed based on data from the Human Protein Atlas, Gene Expression Omnibus and Oncomine database. Survival analyses were conducted with the Kaplan-Meier method, using data from The Cancer Genome Atlas database. Immune correlation analyses and prediction of response to immunotherapy were performed using the online Immune Cell Abundance Identifier. Co-expression analyses, functional clustering analyses and construction of a prognostic risk model were conducted in R, with the clinical covariates balanced by the inverse probability treatment weighting method. Results: NPRL2 was abnormally downregulated in STAD (P<0.05). Survival analysis highlighted a positive association between the expression of NPRL2 and clinical outcomes for patients (P<0.05). Based on co-expression analyses, we found that NPRL2 may be involved in epithelial-mesenchymal transition, gastric cancer stem cells, and responsiveness to chemotherapeutic agents in STAD (P<0.05). Furthermore, functional clustering analysis revealed that NPRL2 was involved in the mTOR signalling pathway, autophagy, and the amino acid starvation response (adjust P<0.05). In addition, NPRL2 was negatively associated with tumour-infiltrating immune cells while positively associated with immunotherapeutic biomarkers in STAD (P<0.05). Meanwhile, patients with high NPRL2 expression were predicted to have a better response to immunotherapy (P<0.05). Finally, a prognostic model constructed based on NPRL2-related genes could predict the prognosis of STAD patients (AUC =0.641), and the risk score was an independent prognostic factor for STAD patients (HR =4.855, 95% CI: 2.683-8.785, P<0.001). Conclusions: The present study provided a comprehensive analysis of the role and potential mechanisms of NPRL2 in STAD, suggesting that NPRL2 is a potential biomarker for the survival and prediction of immunotherapy response in STAD.

TRIM44 promotes BRCA1 functions in HR repair to induce Cisplatin Chemoresistance in Lung Adenocarcinoma by Deubiquitinating FLNA.

Tripartite motif-containing 44 (TRIM44) has recently been implicated in various pathological processes in numerous cancers, including lung adenocarcinoma (LUAD); however, its functional roles in chemoresistance are poorly understood. Herein, TRIM44 knockdown sensitized LUAD cells to cisplatin and enhanced cisplatin-induced apoptosis. Microarray analysis indicated that the "Role of BRCA1 in DNA damage" and the BRCA1 gene expression were positively regulated by TRIM44, which was further verified by immunofluorescence, qRT-PCR, and Western blotting. BRCA1 depletion effectively abolished TRIM44-modulated cisplatin resistance and regulation of homologous recombination (HR) repair. Interestingly, TRIM44 interacted with FLNA, an upstream regulator of BRCA1 as specified by STRING V 11.5, and facilitated its stability and deubiquitination. FLNA was also found to be required for the functions of TRIM44 in drug resistance. Using animal models, overexpression of TRIM44 was shown to confer resistance to cisplatin in a BRCA1- and FLNA-dependent manner. TRIM44 expression levels in tissues from cisplatin-resistant LUAD patients were significantly higher than those in tissues from cisplatin-sensitive LUAD patients. Collectively, our study results demonstrate that the TRIM44/FLNA/BRCA1 axis is involved in cisplatin chemoresistance, providing potential therapeutic targets for LUAD patients with cisplatin resistance.

A novel EHD1/CD44/Hippo/SP1 positive feedback loop potentiates stemness and metastasis in lung adenocarcinoma.

BACKGROUND: There is growing evidence that endocytosis plays a pivotal role in cancer metastasis. In this study, we first identified endocytic and metastasis-associated genes (EMGs) and then investigated the biological functions and mechanisms of EMGs. METHODS: Cancer stem cells (CSCs)-like characteristics were evaluated by tumour limiting dilution assays, three-dimensional (3D) spheroid cancer models. Microarray analysis was used to identify the pathways significantly regulated by mammalian Eps15 homology domain protein 1 (EHD1) knockdown. Mass spectrometry (MS) was performed to identify EHD1-interacting proteins. The function of EHD1 as a regulator of cluster of differentiation 44 (CD44) endocytic recycling and lysosomal degradation was determined by CD44 biotinylation and recycling assays. RESULTS: EHD1 was identified as a significant EMG. Knockdown of EHD1 suppressed CSCs-like characteristics, epithelial-mesenchymal transition (EMT), migration and invasion of lung adenocarcinoma (LUAD) cells by increasing Hippo kinase cascade activation. Conversely, EHD1 overexpression inhibited the Hippo pathway to promote cancer stemness and metastasis. Notably, utilising MS analysis, the CD44 protein was identified as a potential binding partner of EHD1. Furthermore, EHD1 enhanced CD44 recycling and stability. Indeed, silencing of CD44 or disruption of the EHD1/CD44 interaction enhanced Hippo pathway activity and reduced CSCs-like traits, EMT and metastasis. Interestingly, specificity protein 1 (SP1), a known downstream target gene of the Hippo-TEA-domain family members 1 (TEAD1) pathway, was found to directly bind to the EHD1 promoter region and induce its expression. Among clinical specimens, the EHD1 expression level in LUAD tissues of metastatic patients was higher than that of non-metastatic patients. CONCLUSIONS: Our findings emphasise that EHD1 might be a potent anti-metastatic target and present a novel regulatory mechanism by which the EHD1/CD44/Hippo/SP1 positive feedback circuit plays pivotal roles in coupling modules of CSCs-like properties and EMT in LUAD. Targeting this loop may serve as a remedy for patients with advanced metastatic LUAD.

Effectiveness of Resilience Interventions on Psychosocial Outcomes for Persons With Neurocognitive Disorders: A Systematic Review and Meta-Analysis.

Background: Neurocognitive disorders, such as mild cognitive impairment (MCI), dementia, and Alzheimer's disease, not only harm people's cognitive function but also lead to negative emotions, poor quality of life (QOL), and unsatisfactory level of well-being. Resilience can be defined as a dynamic and amendable process, which maintains or improves life satisfaction and quick recovery from own dilemma. However, no meta-analysis of randomized controlled trials (RCTs) has thus far examined the effectiveness of resilience interventions among persons with neurocognitive disorders, and the results of RCTs were inconsistent. This systematic review aimed to assess the effectiveness of resilience interventions on psychosocial outcomes among persons with neurocognitive disorders. Methods: Nine electronic Chinese and English databases (the Cochrane Library, PsycINFO, Web of Science, PubMed, Medline, Eric, JSTOR, CNKI, and WANGFANG) were searched through April 2021. Only RCTs were included, and the quality of the included studies was assessed by the Cochrane "Risk of Bias" tool. Meta-analysis was carried out on psychosocial outcomes, and heterogeneity was investigated by subgroup and sensitivity analysis. RevMan 5.4 was used for meta-analysis. Results: Fourteen RCT studies were identified, representing a total of 2,442 participants with neurocognitive disorders. The risk of bias was high or unclear for most included studies in the domains of allocation concealment, blinding participants, and interventionists. Meta-analysis showed that heterogeneity was low or moderate. There were significant differences in favor of resilience interventions compared with control on the outcome of QOL, using the Quality of Life-Alzheimer Disease scale (QOL-AD) [I 2 = 36%, standardized mean difference (SMD) = 0.14, 95% CI (0.02, 0.26), p = 0.02], and no significant differences on depression, using the Cornell Scale for Depression in Dementia (CSDD) [I 2 = 41%, SMD = -0.14, 95% CI (-0.34, 0.05), p = 0.16], and neuropsychiatric symptoms using the Neuropsychiatric Inventory Questionnaire (NPI-Q) [I 2 = 62%, SMD = -0.10, 95% CI (-0.37, -0.16), p ≤ 0.46]. Conclusions: Resilience interventions had a significant benefit on QOL but no significant benefit on depression and neuropsychiatric behavioral symptoms. More evidence is needed to answer questions about how to implement resilience interventions and how to evaluate their effectiveness.

LINC02678 as a Novel Prognostic Marker Promotes Aggressive Non-small-cell Lung Cancer.

Non-small-cell lung carcinoma (NSCLC) is considered to be a fatal disease and characterized by a poor prognosis. Long non-coding RNAs (lncRNAs) have been reported to act as biomarkers and therapeutic targets in solid tumors. However, the expression of lncRNAs and their clinical relevance in NSCLC remain undetermined. The gene expression data profiled in The Cancer Genome Atlas and Gene Expression Omnibus (GSE81089) were employed to screen differentially expressed lncRNAs in NSCLC. LINC02678 was found to be upregulated in NSCLC and exhibited hypomethylation of the promoter region in NSCLC tissues. LINC02678 (also called RP11-336A10.5) was associated with poorer overall survival and relapse-free survival in NSCLC patients. In vitro models of gain- and loss-of-function demonstrated that LINC02678 promotes NSCLC progression by promoting NSCLC cell proliferation and cell cycle progression, as well as inducing NSCLC cell migration, invasion and epithelial-mesenchymal transition. LINC02678 was primarily located in the nucleus and could bind with the enhancer of zeste homolog 2 (EZH2). Moreover, we found that LINC02678 knockdown impaired the occupancy capacity of EZH2 and trimethylation of lysine 27 on histone 3 (H3K27me3) at the promoter region of cyclin dependent kinase inhibitor 1B (CDKN1B) and E-cadherin, as confirmed by ChIP-qPCR. A mouse transplantation model further demonstrated that LINC02678 could promote the tumorigenic and metastatic capacities of NSCLC cells. We identified LINC02678 as a tumor promoter in NSCLC, which enhanced the growth and metastasis of NSCLC cells by binding with EZH2, indicating that LINC02678 may serve as a potential biomarker for cancer diagnosis and treatment.

Identification of Differentially Expressed and Prognostic lncRNAs for the Construction of ceRNA Networks in Lung Adenocarcinoma.

BACKGROUND: Long noncoding RNAs (lncRNAs) could function as competitive endogenous RNAs (ceRNAs) to competitively adsorb microRNAs (miRNAs), thereby regulating the expression of their target protein-coding mRNAs. In this study, we aim to identify more effective diagnostic and prognostic markers for lung adenocarcinoma (LUAD). METHODS: We obtained differentially expressed lncRNAs (DElncRNAs), miRNAs (DEmiRNAs), and mRNAs (DEmRNAs) for LUAD by using The Cancer Genomes Atlas (TCGA) portal. Weighted gene coexpression network analysis (WGCNA) was performed to unveil core gene modules associated with LUAD. The Cox proportional hazards model was performed to determine the prognostic significance of DElncRNAs. The diagnostic and prognostic significance of DElncRNAs was further verified based on the receiver operating characteristic curve (ROC). Cytoscape was used to construct the ceRNA networks comprising the lncRNAs-miRNAs-mRNAs axis based on the correlation obtained from the miRcode, miRDB, and TargetScan. RESULTS: Compared with normal lung tissues, 2355 DElncRNAs, 820 DEmiRNAs, and 17289 DEmRNAs were identified in LUAD tissues. We generated 8 WGCNA core modules in the lncRNAs coexpression network, 5 modules in the miRNAs, and 12 modules in the mRNAs coexpression network, respectively. One lncRNA module (blue) consisting of 441 lncRNAs, two miRNA modules (blue and turquoise) containing 563 miRNAs, and one mRNA module (turquoise), which consisted of 15162 mRNAs, were mostly significantly related to LUAD status. Furthermore, 67 DEmRNAs were found to be tumor-associated as well as the target genes of the DElncRNAs-DEmiRNAs axis. Survival analyses showed that 6 lncRNAs (LINC01447, WWC2-AS2, OGFRP1, LINC00942, LINC01168, and AC005863.1) were significantly correlated with the prognosis of LUAD patients. Ultimately, the potential ceRNA networks including 6 DElncRNAs, 4 DEmiRNAs, and 22 DEmRNAs were constructed. CONCLUSION: Our study indicated that 6 DElncRNAs had the possibilities as diagnostic and prognostic biomarkers for LUAD. The lncRNA-mediated ceRNA networks might provide novel insights into the molecular mechanisms of LUAD progression.

Identification and Validation of the Immune Subtypes of Lung Adenocarcinoma: Implications for Immunotherapy.

Lung adenocarcinoma (LUAD) is a devastating disease with poor patient survival. Cancer immunotherapy has revolutionized the treatment of LUAD, but only a limited number of patients effectively respond to this treatment. Thus, the work to elucidate the LUAD immune heterogeneity could be crucial in developing new immunotherapeutic strategies with better efficacy. Non-negative matrix factorization-based deconvolution was performed to identify robust clusters of 489 LUAD patients in The Cancer Genome Atlas (TCGA) and verify their reproducibility and stability in an independent LUAD cohort of 439 patients from the Gene Expression Omnibus (GEO). We used the graph learning-based dimensionality reduction to visualize the distribution of individual patients. In this study, four reproducible immune subtypes, Clusters 1-4 (C1-C4) associated with distinct gene module signatures, clinicopathological features, molecular and cellular characteristics were identified and validated. The immune-cold subtype, C3, was associated with the Dead event, the most advanced T stage, N stage, TNM stage and the worst prognosis for LUAD patients. Moreover, C3 exhibited the lowest infiltrating levels of B cells, T cell receptor (TCR) repertoire diversity and the highest level of neoantigen and mutation rate among C1-C4. On the other hand, the immune-hot subtype (C4) exhibited the highest infiltration of six types of infiltrating immune cells as well as the greatest leukocyte fraction, TCR and B cell receptor (BCR) repertoire diversity. C1 and C2 subtypes showed diverse clinicopathological and immunological features. Finally, our investigations discovered a complex immune landscape with a scattered immune subtype profile. This work may help inform immunotherapeutic decision-making and design advanced immunotherapy strategies for the treatment of lung cancer.