Identification and validation of an autophagy-related long non-coding RNA signature as a prognostic biomarker for patients with lung adenocarcinoma

BackgroundLung adenocarcinoma (LUAD) is the most predominant pathological subtype of lung cancer, accounting for 40–70% of all lung cancer cases. Although significant improvements have been made in the screening, diagnosis, and precise management in recent years, the prognosis of LUAD remains bleak. This study aimed to investigate the prognostic significance of autophagy-related long non-coding RNAs (lncRNAs) and construct an autophagy-related lncRNA prognostic model in LUAD.MethodsThe gene expression data of LUAD patients were obtained from The Cancer Genome Atlas (TCGA) database. All autophagy-related genes were downloaded from the Human Autophagy Database (HADb). Spearman’s correlation test was exploited to identify potential autophagy-related lncRNAs. The multivariate Cox regression analysis was used to construct the prognostic signature, which divided LUAD patients into high-risk and low-risk groups. Subsequently, the receiver operating characteristic (ROC) curves were generated to assess the predictive ability of this prognostic model for overall survival (OS) in these individuals. Then, the Gene set enrichment analysis (GSEA) was conducted to execute pathway enrichment analysis. Finally, a multidimensional validation was exploited to verify our findings.ResultsA total of 1,144 autophagy-related lncRNAs were identified to construct the co-expression network via Spearman’s correlation test (|R²| >0.4 and P≤0.001). Ultimately, a 16 autophagy-related lncRNAs prognostic model was constructed, and the area under the ROC curve (AUC) was 0.775. The results of GSEA enrichment analysis showed that the genes in the high-risk group were mainly enriched in cell cycle and p53 signaling pathways. The results of the multidimensional database validation indicated that the expression level of BIRC5 was significantly correlated with the expression level of TMPO-AS1. Furthermore, both TMPO-AS1 and BIRC5 had a higher expression level in LUAD samples. LUAD patients with high expression levels of TMPO-AS1 and BIRC5 were correlated with advanced disease stage and poor OS.ConclusionsIn summary, our results suggested that the prognostic signature of the 16 autophagy-related lncRNAs has significant prognostic value for LUAD patients. Furthermore, TMPO-AS1 and BIRC5 are potential predictors and therapeutic targets in these individuals.     

Cationic Albumin‐Conjugated Chelating Agent as a Novel Brain Drug Delivery System in Neurodegeneration

The critical role of metal ions and in particular iron in oxidative stress and protein aggregation offers chelation therapy as a sensible pharmaceutical strategy in oxidative stress‐induced neuronal damages. In this research, we conjugated an iron‐chelating agent, deferasirox, to cationized human serum albumin molecules in order to develop a novel brain delivery system for the management of neurodegenerative disorders due to the significant role of oxidative stress‐induced neuronal injury in such diseases. Cationized albumin is known to be able to transport to brain tissue via adsorptive‐mediated transcytosis. The developed structures were molecularly characterized, and their conjugation ratio was determined. PC12 cell line was utilized to evaluate the neuroprotective features of these newly developed molecules in the presence of hydrogen peroxide neuronal damage and to identify the mechanisms behind the observed neuronal protection including apoptotic and autophagic pathways. Furthermore, a rat model of Alzheimer's disease was utilized to evaluate the impact of conjugated structures in vivo. Data analysis revealed that the conjugated species were able to hinder apoptotic cell death while enhancing autophagic process. The developed conjugated species were also able to attenuate amyloid beta‐induced learning deficits when administered peripherally.     

Antiaging effects of bioactive molecules isolated from plants and fungi

Aging is influenced by many lifestyle choices that are under human control, including nutrition and exercise. The most effective known antiaging intervention consists of calorie restriction (CR), which increases lifespan in yeasts, worms, fruit flies, mice, and nonhuman primates. CR also improves healthspan by preventing the development of various aging-related diseases such as cancer, cardiovascular disease, diabetes, and neurodegeneration. Many compounds isolated from plants and fungi prolong lifespan and prevent age-related diseases in model organisms. These plant and fungal compounds modulate the same cellular and physiological pathways as CR, including those involving insulin and insulin-like growth factor-1, mammalian target of rapamycin, and sirtuins. Modulation of these aging-related pathways results in the activation of various cellular processes such as autophagy, DNA repair, and neutralization of reactive oxygen species. Together, these cellular processes are believed to delay aging and prevent chronic diseases by improving bodily functions and stress resistance. We review here the mechanisms of action of plant and fungal molecules possessing antiaging properties and discuss the possibilities and challenges associated with the development of antiaging compounds isolated from natural products.     

Endolysosomal trafficking of viral G protein-coupled receptor functions in innate immunity and control of viral oncogenesis

The ubiquitin-proteasome system degrades viral oncoproteins and other microbial virulence factors; however, the role of endolysosomal degradation pathways in these processes is unclear. Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma, and a constitutively active viral G protein-coupled receptor (vGPCR) contributes to the pathogenesis of KSHV-induced tumors. We report that a recently discovered autophagy-related protein, Beclin 2, interacts with KSHV GPCR, facilitates its endolysosomal degradation, and inhibits vGPCR-driven oncogenic signaling. Furthermore, monoallelic loss of Becn2 in mice accelerates the progression of vGPCR-induced lesions that resemble human Kaposi’s sarcoma. Taken together, these findings indicate that Beclin 2 is a host antiviral molecule that protects against the pathogenic effects of KSHV GPCR by facilitating its endolysosomal degradation. More broadly, our data suggest a role for host endolysosomal trafficking pathways in regulating viral pathogenesis and oncogenic signaling.Phagocytosis and autophagy are two processes that deliver microbes and their constituent proteins to the lysosome for degradation, thereby contributing to the clearance of pathogens and to the presentation of peptide antigens to T cells (1, 2). However, it is not known whether endocytic internalization and lysosomal targeting of virus-encoded cell-surface receptors contributes to the control of viral infection and disease.Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of AIDS-related and other forms of Kaposi’s sarcoma (KS), primary effusion lymphoma, and multicentric Castleman’s disease (3–5). KS is a multifocal tumor characterized by proliferating spindle cells (possibly of endothelial origin), angiogenesis, vascular slits, erythrocyte extravasation, and inflammatory cells. Proinflammatory signaling by the dominant KS cell, the spindle cell, is considered the driving force in KS lesions (6). The risk of KSHV-associated malignancies increases with increased lytic viral replication (7–9), suggesting that KSHV-induced oncogenesis may be related to the levels of expression of viral oncoproteins.The oncogenic KSHV G protein-coupled receptor (vGPCR), encoded by the KSHV ORF74 lytic gene, is a constitutively active chemokine receptor expressed in patients with KSHV-associated tumors (10). At least in animal studies, there are strong data that vGPCR substantially contributes to the onset and progression of KSHV-associated neoplasia in vivo (11–19). Although only a small proportion of tumor cells express vGPCR (10), they are both sufficient and necessary for KSHV-induced sarcomagenesis. The endothelial-specific expression of vGPCR (but of neither KSHV latent genes, such as vCyclin, vFlip, and Kaposin, nor other KSHV lytic genes, such as vBcl-2 or vIRF1) or injection of murine endothelial cells stably expressing vGPCR (but not other KSHV genes, such as vCyclin, vFlip, Kaposin, LANA, vIL-6, vBcl-2, and K1) causes multifocal KS-like tumors in mice (15, 18). Furthermore, injection of a small number of endothelial cells expressing vGPCR increases the tumorigenic potential, in a paracrine fashion, of endothelial cells expressing other KSHV latent genes (vCyclin and vFlip), whereas eradication of the small number of vGPCR-expressing cells in established mix-cell tumors induces tumor regression (15, 18). Moreover, in a nude mouse model of KS driven by transfection of a KSHV bacterial artificial chromosome into bone marrow endothelial-lineage cells, siRNA interference (RNAi)-mediated suppression of vGPCR expression dramatically reduces angiogenesis and tumor formation (19). In addition, immunocompetent mice that transgenically express doxycycline (DOX)-inducible KSHV GPCR in endothelial cells (hereafter referred to as ikGPCR⁺) manifest lesions that strongly resemble human Kaposi’s sarcoma (16, 17). Importantly, the progression of lesions in ikGPCR⁺ mice is reversible because DOX withdrawal leads to significant regression of vGPCR-induced lesions (17), suggesting that vGPCR-driven oncogenesis is highly dependent on sustained vGPCR expression and signaling.Based on these previous observations in animal models regarding KSHV GPCR and oncogenesis, we developed the hypothesis that cell-intrinsic mechanisms that decrease vGPCR protein levels may function as an important host defense mechanism for controlling viral oncogenesis. Recently, we showed that the autophagy protein, Beclin 2 (but not the related autophagy protein Beclin 1) is essential for the endolysosomal degradation of certain cellular GPCRs that are regulated by GASP1 rather than by ubiquitination and the endosomal sorting complexes required for the transport pathway (20). This function of Beclin 2, but not Beclin 1, regulates mouse brain cannabinoid receptor levels and metabolism in vivo (20). Therefore, we investigated whether Beclin 2 may play a role in the endolysosomal degradation of viral GPCRs and thereby represent an important host defense mechanism against KSHV GPCR-induced oncogenic effects. Our results demonstrate a crucial role for Beclin 2 in KSHV GPCR trafficking, proinflammatory signaling, and in vivo tumorigenicity, and thus represent a previously undescribed role for endolysosomal trafficking in innate immunity and the control of viral GPCR-driven oncogenesis.     

Conditional destabilization of the TPLATE complex impairs endocytic internalization

In plants, endocytosis is essential for many developmental and physiological processes, including regulation of growth and development, hormone perception, nutrient uptake, and defense against pathogens. Our toolbox to modulate this process is, however, rather limited. Here, we report a conditional tool to impair endocytosis. We generated a partially functional TPLATE allele by substituting the most conserved domain of the TPLATE subunit of the endocytic TPLATE complex (TPC). This substitution destabilizes TPC and dampens the efficiency of endocytosis. Short-term heat treatment increases TPC destabilization and reversibly delocalizes TPLATE from the plasma membrane to aggregates in the cytoplasm. This blocks FM uptake and causes accumulation of various known endocytic cargoes at the plasma membrane. Short-term heat treatment therefore transforms the partially functional TPLATE allele into an effective conditional tool to impair endocytosis. Next to their role in endocytosis, several TPC subunits are also implicated in actin-regulated autophagosomal degradation. Inactivating TPC via the WDX mutation, however, does not impair autophagy, thus enabling specific and reversible modulation of endocytosis in planta.

Endocytosis is an evolutionarily conserved eukaryotic pathway by which extracellular material and plasma membrane (PM) components are internalized via vesicles (1, 2). Clathrin-mediated endocytosis (CME), relying on the scaffolding protein clathrin, is the most prominent and the most studied endocytic pathway (3–5). As clathrin does not interact directly with the PM, nor does it recognize cargoes, adaptor proteins are required to act as essential links between the clathrin coat and the PM (6). In plant cells, material selected for CME is recognized by two adaptor complexes, the adaptor complex 2 (AP-2) and the TPLATE complex (TPC) (7–9). In contrast to TPC, single subunit mutants of AP-2 are viable (7, 8, 10–13) and AP-2 recruitment and dynamics appear to rely on TPC function (8, 14).TPC represents an ancestral adaptor complex, which is however absent in present-day metazoans and yeasts. It was experimentally identified as an octameric complex in Arabidopsis and as a hexametric complex in Dictyostelium (8, 15). Plants, however, are the only eukaryotic supergroup identified so far where TPC is essential for life (8, 15), as knockout or severe knockdown of single subunits of TPC in Arabidopsis leads to pollen or seedling lethality, respectively (8, 13). Two TPC subunits, AtEH1/Pan1 and AtEH2/Pan1, were not associated with the other TPC core components when the complex was forced into the cytoplasm by truncating the TML subunit and did not copurify with the other TSET components in Dictyostelium. This indicates that they may be auxiliary components to the core TPC (8, 15). These AtEH/Pan1 proteins were recently identified as important players in actin-regulated autophagy in plants. AtEH/Pan1 proteins recruit several components of the endocytic machinery to the autophagosomes, and are degraded together with them under stress conditions (16). However, whether this pathway serves to degrade specific cargoes or to regulate the endocytic machinery itself (17), and whether the whole TPC is required for this degradation pathway, remains unclear.Genetic and chemical tools to manipulate endocytosis have been extensively investigated via interfering with the functions of endocytic players, such as clathrin (18–22), adaptor proteins (7, 10–12, 14, 23–25), and dynamin-related proteins (26–30). The chemical inhibitors originally used to affect CME in plants have recently been described to possess undesirable side effects (31) or to affect proteins that are not only specific for endocytosis: for example, clathrin itself, as it is also involved in TGN trafficking (19, 22). The same is true for several genetic tools currently available to affect CME in plants (18, 21, 22, 30). Manipulation of TPC, functioning exclusively at the PM, represents a very good candidate to affect CME more specifically. So far however, there are no chemical tools to target TPC functions or dominant-negative mutants available. Inducible silencing works, but causes seedling lethality and takes several days to become effective (8). The only tools to manipulate TPC function in viable plants consist of knock-down mutants with very mild reduction of expression and consequently similar mild effects on CME (8, 14, 16, 32).     

Neuroprotective Effects of Lithium: Implications for the Treatment of Alzheimer’s Disease and Related Neurodegenerative Disorders

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Lithium,Inositol and Mitochondria

Our recent DNA-microarray and proteomics studies searching for pathways affected both by chronic lithium treatment and by knockout of each of two genes (IMPA1 or Slc5a3) encoding for proteins related to inositol metabolism, indicated up-regulation of mitochondria-related genes and autophagy-related proteins in the frontal cortex. Differently from previously reported observations of aberrant mitochondrial function in bipolar patients which leave a causality relationship between mitochondrial dysfunction and bipolar disorder an open question, the behavioral results of our recent report following rotenone treatment tempt us to speculate that mitochondrial dysfunction predisposes manic behavior and that drugs targeted to ameliorate mitochondrial function are potential preventers of bursting manic episodes. However, the promiscuity of the involvement of mitochondrial dysfunction and impaired autophagy in the pathophysiology of psychiatric and neurodegenerative disorders raises questions regarding the credibility and relevance of these findings.     

自噬与前列腺癌

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巨噬源性泡沫细胞中p62蛋白上调作用和机制的研究

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氧化苦参碱介导细胞自噬减轻溃疡性结肠炎小鼠结肠黏膜氧化性损伤的作用机制研究

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