Understanding Of Autophagy Research Articles

Biogenesis of omegasomes and autophagosomes in mammalian autophagy.

Autophagy is a highly conserved catabolic pathway that maintains cellular homeostasis by promoting the degradation of damaged or superfluous cytoplasmic material. A hallmark of autophagy is the generation of membrane cisternae that sequester autophagic cargo. Expansion of these structures allows cargo to be engulfed in a highly selective and exclusive manner. Cytotoxic stress or starvation induces the formation of autophagosomes that sequester bulk cytoplasm instead of selected cargo. This rather nonselective pathway is essential for maintaining vital cellular functions during adverse conditions and is thus a major stress response pathway. Both selective and nonselective autophagy rely on the same molecular machinery. However, due to the different nature of cargo to be sequestered, the involved molecular mechanisms are fundamentally different. Although intense research over the past decades has advanced our understanding of autophagy, fundamental questions remain to be addressed. This review will focus on molecular principles and open questions regarding the formation of omegasomes and phagophores in nonselective mammalian autophagy.

Assessing Autophagy Flux in Glioblastoma Temozolomide Resistant Cells.

Autophagy is a critical cellular process involved in the degradation and recycling of cytoplasmic components, playing a dual role in cancer by either promoting cell survival or facilitating cell death. In glioblastoma (GB), autophagy has been implicated in resistance to the chemotherapeutic agent temozolomide (TMZ). This study presents a novel method to accurately measure autophagy flux in TMZ-resistant glioblastoma cells, combining advanced imaging techniques with biochemical assays. By quantifying key autophagy markers such as LC3-II and SQSTM1, our approach provides detailed insights into the dynamic processes of autophagosome formation and clearance under therapeutic stress. This method advances our understanding of autophagy in GB chemoresistance and has significant implications for the development of autophagy-targeted therapies. The ability to monitor and manipulate autophagy flux in real time offers a promising avenue for monitoring and understanding TMZ resistance and improving patient outcomes in glioblastoma treatment.

Mitophagy: From the dark into the spotlight

Despite the generally placid appearance of plants, many dynamic processes take place inside a plant cell. One such process that has garnered attention in recent years is termed 'autophagy'. While originally discovered in yeast, our understanding of autophagy in plants has improved significantly. Autophagy is considered a cellular recycling system in which cellular components or even entire organelles can be encapsulated by a membrane structure (autophagosome) and then transported to the vacuole (in plants) for degradation and re-use. One example of components degraded by autophagy are the mitochondria ('mitophagy'). Only a few years ago there was almost no information about plant mitophagy available, but lately several important studies have been published. A recent study identified an ATG8-FLZ-SnRK1 regulatory axis that connects carbon starvation signaling to mitophagy. In this Spotlight article, we focus on the function of mitochondrial FLZ proteins and SnRK1, and discuss them in context of current knowledge on the regulation of mitophagy in plants.

Unlocking the potential of Mesenchymal stem cells in liver Fibrosis: Insights into the impact of autophagy and aging.

Liver fibrosis is a chronic liver disease characterized by extracellular matrix protein accumulation, potentially leading to cirrhosis or hepatocellular carcinoma. Liver cell damage, inflammatory responses, and apoptosis due to various reasons induce liver fibrosis. Although several treatments, such as antiviral drugs and immunosuppressive therapies, are available for liver fibrosis, they only provide limited efficacy. Mesenchymal stem cells (MSCs) have become a promising therapeutic option for liver fibrosis, because they can modulate the immune response, promote liver regeneration, and inhibit the activation of hepatic stellate cells that contribute to disease development. Recent studies have suggested that the mechanisms through which MSCs gain their antifibrotic properties involve autophagy and senescence. Autophagy, a vital cellular self-degradation process, is critical for maintaining homeostasis and protecting against nutritional, metabolic, and infection-mediated stress. The therapeutic effects of MSCs depend on appropriate autophagy levels, which can improve the fibrotic process. Nonetheless, aging-related autophagic damage is associated with a decline in MSC number and function, which play a crucial role in liver fibrosis development. This review summarizes the recent advancements in the understanding of autophagy and senescence in MSC-based liver fibrosis treatment, presenting the key findings from relevant studies.

Autophagy in Crohn's Disease: Converging on Dysfunctional Innate Immunity.

Crohn's disease (CD) is a chronic inflammatory bowel disease marked by relapsing, transmural intestinal inflammation driven by innate and adaptive immune responses. Autophagy is a multi-step process that plays a critical role in maintaining cellular homeostasis by degrading intracellular components, such as damaged organelles and invading bacteria. Dysregulation of autophagy in CD is revealed by the identification of several susceptibility genes, including ATG16L1, IRGM, NOD2, LRRK2, ULK1, ATG4, and TCF4, that are involved in autophagy. In this review, the role of altered autophagy in the mucosal innate immune response in the context of CD is discussed, with a specific focus on dendritic cells, macrophages, Paneth cells, and goblet cells. Selective autophagy, such as xenophagy, ERphagy, and mitophagy, that play crucial roles in maintaining intestinal homeostasis in these innate immune cells, are discussed. As our understanding of autophagy in CD pathogenesis evolves, the development of autophagy-targeted therapeutics may benefit subsets of patients harboring impaired autophagy.

The role of lysosomal membrane proteins in autophagy and related diseases.

As a self-degrading and highly conserved survival mechanism, autophagy plays an important role in maintaining cell survival and recycling. The discovery of autophagy-related (ATG) genes has revolutionized our understanding of autophagy. Lysosomal membrane proteins (LMPs) are important executors of lysosomal function, and increasing evidence has demonstrated their role in the induction and regulation of autophagy. In addition, the functional dysregulation of the process mediated by LMPs at all stages of autophagy is closely related to neurodegenerative diseases and cancer. Here, we review the role of LMPs in autophagy, focusing on their roles in vesicle nucleation, vesicle elongation and completion, the fusion of autophagosomes and lysosomes, and degradation, as well as their broad association with related diseases.

Constant Conversion Rate of Endolysosomes Revealed by a pH-Sensitive Fluorescent Probe.

Endolysosome dynamics plays an important role in autophagosome biogenesis. Hence, imaging the subcellular dynamics of endolysosomes using high-resolution fluorescent imaging techniques would deepen our understanding of autophagy and benefit the development of pharmaceuticals against endosome-related diseases. Taking advantage of the intramolecular charge-transfer mechanism, herein we report a cationic quinolinium-based fluorescent probe (PyQPMe) that exhibits excellent pH-sensitive fluorescence in endolysosomes at different stages of interest. A systematic photophysical and computational study on PyQPMe was carried out to rationalize its highly pH-dependent absorption and emission spectra. The large Stokes shift and strong fluorescence intensity of PyQPMe can effectively reduce the background noise caused by excitation light and microenvironments and provide a high signal-to-noise ratio for high-resolution imaging of endolysosomes. By applying PyQPMe as a small molecular probe in live cells, we were able to reveal a constant conversion rate from early endosomes to late endosomes/lysosomes during autophagy at the submicron level.

The world’s first (and probably last) autophagy video game

ABSTRACT Macroautophagy/autophagy is the process by which portions of the cytoplasm are sequestered within a transient compartment and delivered to the degradative organelle of the cell, the vacuole or lysosome. Autophagy is a fundamental cytoprotective mechanism, and defects in this process are associated with many diseases. For example, the inability to degrade certain cargo such as mitochondria may lead to neurodegenerative disorders such as Parkinson disease. Autophagic cargo can be many different things including organelles, but also proteins and protein aggregates, nucleic acids, and lipids. Much of our understanding of autophagy comes from studies in baker’s yeast, Saccharomyces cerevisiae. In that organism, autophagy begins at the phagophore assembly site (PAS), which nucleates the initial sequestering compartment, referred to as a phagophore. With the help of autophagy-related (Atg) proteins and lipid addition, the phagophore membrane expands to enclose damaged or superfluous cytoplasmic components, eventually closing into a completed double-membrane vesicle called the autophagosome. The autophagosome is delivered to the degradative organelle where it fuses, releasing the encapsulated cargo into the interior of the organelle where it is broken down into macromolecular building blocks. The resulting building blocks are released back into the cytosol for reuse. Video games are modern expressions of art incorporating illustration, animation, and mechanistic design. While often underappreciated as a scientific art form, video games can beautifully express scientific topics in a way that is both intuitive and engaging, especially to a younger audience.

Emerging roles of mitotic autophagy.

Lysosomes exert pleiotropic functions to maintain cellular homeostasis and degrade autophagy cargo. Despite the great advances that have boosted our understanding of autophagy and lysosomes in both physiology and pathology, their function in mitosis is still controversial. During mitosis, most organelles are reshaped or repurposed to allow the correct distribution of chromosomes. Mitotic entry is accompanied by a reduction in sites of autophagy initiation, supporting the idea of an inhibition of autophagy to protect the genetic material against harmful degradation. However, there is accumulating evidence revealing the requirement of selective autophagy and functional lysosomes for a faithful chromosome segregation. Degradation is the most-studied lysosomal activity, but recently described alternative functions that operate in mitosis highlight the lysosomes as guardians of mitotic progression. Because the involvement of autophagy in mitosis remains controversial, it is important to consider the specific contribution of signalling cascades, the functions of autophagic proteins and the multiple roles of lysosomes, as three entangled, but independent, factors controlling genomic stability. In this Review, we discuss the latest advances in this area and highlight the therapeutic potential of targeting autophagy for drug development.

Establishment and validation of five autophagy-related signatures for predicting survival and immune microenvironment in glioma.

Gliomas, especially Glioblastoma multiforme, are the most frequent type of primary tumors in central nervous system. Increasing researches have revealed the relationship between autophagy and tumor, while the molecular mechanism of autophagy in glioma is still rarely reported. Our research aims to conform the autophagy-related genes (ARGs) implicated in the development and progression of glioma and improve our understanding of autophagy in glioma. 20 candidate ARGs were screened through the protein-protein interaction network. We also downloaded the publicly accessible glioma data for 665 individuals from TCGA and 970 individuals from CGGA with RNA sequences and clinicopathological information. Subsequently, univariate and multivariate Cox regression analysis identified 5 key ARGs among the 20 candidate genes as key prognostic genes for survival, GSEA and immune response analysis. ATG5, BCL2L1, CASP3, CASP8, GAPDH were identified as key ARGs in our research. Further studies showed that the high-risk population was linked to a dismal prognosis and suggested an immune-inhibitory microenvironment. GSEA results demonstrated that high risk population was closely related to DNA repair, hypoxia pathways, implicated in immunosuppression and carcinogenesis. Through CMap, we finally identified 14 candidate drugs for the ARG high risk population. This study established and verified an ARG risk model, which can serve as an independent predictor for prognosis, reflect on the strength of the immune response and predict the potential drugs in glioma. Our findings offer new understandings of ARG molecular mechanism and promising therapeutic targets for glioma treatment.

Autophagy in liver diseases: A review

The liver is a highly dynamic metabolic organ that plays critical roles in plasma protein synthesis, gluconeogenesis and glycogen storage, cholesterol metabolism and bile acid synthesis as well as drug/xenobiotic metabolism and detoxification. Research from the past decades indicate that autophagy, the cellular catabolic process mediated by lysosomes, plays an important role in maintaining cellular and metabolic homeostasis in the liver. Hepatic autophagy fluctuates with hormonal cues and the availability of nutrients that respond to fed and fasting states as well as circadian activities. Dysfunction of autophagy in liver parenchymal and non-parenchymal cells can lead to various liver diseases including non-alcoholic fatty liver diseases, alcohol associated liver disease, drug-induced liver injury, cholestasis, viral hepatitis and hepatocellular carcinoma. Therefore, targeting autophagy may be a potential strategy for treating these various liver diseases. In this review, we will discuss the current progress on the understanding of autophagy in liver physiology. We will also discuss several forms of selective autophagy in the liver and the molecular signaling pathways in regulating autophagy of different cell types and their implications in various liver diseases.

Friend or Foe: Paradoxical Roles of Autophagy in Gliomagenesis.

Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain tumor in adults, with a poor median survival of approximately 15 months after diagnosis. Despite several decades of intensive research on its cancer biology, treatment for GBM remains a challenge. Autophagy, a fundamental homeostatic mechanism, is responsible for degrading and recycling damaged or defective cellular components. It plays a paradoxical role in GBM by either promoting or suppressing tumor growth depending on the cellular context. A thorough understanding of autophagy’s pleiotropic roles is needed to develop potential therapeutic strategies for GBM. In this paper, we discussed molecular mechanisms and biphasic functions of autophagy in gliomagenesis. We also provided a summary of treatments for GBM, emphasizing the importance of autophagy as a promising molecular target for treating GBM.

Proteomics for Autophagy Receptor and Cargo Identification in Plants.

Autophagy is a catabolic process facilitating the degradation of cytoplasmic proteins and organelles in a lysosome- or vacuole-dependent manner in plants, animals, and fungi. Proteomic studies have demonstrated that autophagy controls and shapes the proteome and has identified both receptor and cargo proteins inside autophagosomes. In a smaller selection of studies, proteomics has been used for the analysis of post-translational modifications that target proteins for elimination and protein-protein interactions between receptors and cargo, providing a better understanding of the complex regulatory processes controlling autophagy. In this perspective, we highlight how proteomic studies have contributed to our understanding of autophagy in plants against the backdrop of yeast and animal studies. We then provide a framework for how the future application of proteomics in plant autophagy can uncover the mechanisms and outcomes of sculpting organelles during plant development, particularly through the identification of autophagy receptors and cargo in plants.

Hypoxia Helps Maintain Nucleus Pulposus Homeostasis by Balancing Autophagy and Apoptosis.

Intervertebral disc degeneration (IVDD) is a common cause of lower back pain. Programmed cell death (PCD) including apoptosis and autophagy is known to play key mechanistic roles in the development of IVDD. We hypothesized that the nucleus pulposus cells that make up the center of the IVD can be affected by aging and environmental oxygen concentration, thus affecting the development of IVDD. Here, we evaluated the phenotype changes and PCD signaling in nucleus pulposus cells in two different oxygen percentages (5% (hypoxia) and 20% (normoxia)) up to serial passage 20. NP cells were isolated from the lumbar discs of rats, and the chondrogenic, autophagic, and apoptotic gene expressions were analyzed during cell culture up to serial passage 20. Hypoxia significantly increased the number of autophagosomes, as determined by monodansylcadaverine staining and transmission electron microscopy. Furthermore, hypoxia triggered the activation of autophagic flux (beclin-1, LC3-II/LC3-I ratio, and SIRT1) with a concomitant decrease in the expression of apoptotic proteins (Bax and caspase-3). Despite injury and age differences, no significant differences were observed between the ex vivo lumbar disc cultures of groups incubated in the hypoxic chamber. Our study provides a better understanding of autophagy- and apoptosis-related senescence in NP cells. These results also provide insight into the effects of aging on NP cells and their PCD levels during aging.

Autophagy Inhibits Grass Carp Reovirus (GCRV) Replication and Protects Ctenopharyngodon idella Kidney (CIK) Cells from Excessive Inflammatory Responses after GCRV Infection.

Autophagy is an essential and highly conserved process in mammals, which is critical to maintaining physiological homeostasis, including cell growth, development, repair, and survival. However, the understanding of autophagy in fish virus replication is limited. In this study, we found that grass carp reovirus (GCRV) infection stimulated autophagy in the spleen of grass carp (Ctenopharyngodon idella). Moreover, both Western blot (WB) analysis and fluorescent tracer tests showed that GCRV infection induced the enhancement of autophagy activation in Ctenopharyngodon idella kidney (CIK) cells. Autophagy inducer rapamycin and autophagy inhibitor 3-MA pretreatment can inhibit and promote the proliferation of GCRV, respectively. In addition, grass carp autophagy-related gene 5 (CiATG5)-induced autophagy, as well as rapamycin, showed effects on GCRV replication in CIK cells. Transcriptome analysis revealed that the total number of differentially expressed genes (DEGs) in CiATG5 overexpression groups was less than that of the control during GCRV infection. Enrichment analysis showed that CiATG5 overexpression induced the enhancement of autophagy, lysosome, phagosome, and apoptosis in the early stage of GCRV infection, which led to the clearance of viruses. In the late stage, steroid biosynthesis, DNA replication, terpenoid backbone biosynthesis, and carbon metabolism were upregulated, which contributed to cell survival. Moreover, signaling pathways involved in the immune response and cell death were downregulated in CiATG5 overexpression groups. Further study showed that CiATG5 repressed the expression of inflammatory response genes, including cytokines and type I interferons. Taken together, the results demonstrate that autophagy represses virus replication and attenuates acute inflammatory responses to protect cells.

An autophagy-related model of 4 key genes for predicting prognosis of patients with laryngeal cancer.

Autophagy, a major cause of cancer-related death, is correlated with the pathogenesis of various diseases including cancers. Our study aimed to develop an autophagy-related model for predicting prognosis of patients with laryngeal cancer.We analyzed the correlation between expression profiles of autophagy-related genes (ARGs) and clinical outcomes in 111 laryngeal cancer patients from The Cancer Genome Atlas (TCGA). Afterward, gene functional enrichment analyses of gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed to find the major biological attributes. Univariate Cox regression analyses and multivariate Cox regression analyses were performed to screen ARGs whose expression profiles were significantly associated with laryngeal cancer patients overall survival (OS). Furthermore, to provide the doctors and patients with a quantitative method to perform an individualized survival prediction, we constructed a prognostic nomogram.Thirty eight differentially expressed ARGs were screened out in laryngeal cancer patients through the TCGA database. Related functional enrichments may act as tumor-suppressive roles in the tumorigenesis of laryngeal cancer. Subsequently, 4 key prognostic ARGs (IKBKB, ST13, TSC2, and MAP2K7) were identified from all ARGs by the Cox regression model, which significantly correlated with OS in laryngeal cancer. Furthermore, the risk score was constructed, which significantly divided laryngeal cancer patients into high- and low-risk groups. Integrated with clinical characteristics, gender, N and the risk score are very likely associated with patients OS. A prognostic nomogram of ARGs was constructed using the Cox regression model.Our study could provide a valuable prognostic model for predicting the prognosis of laryngeal cancer patients and a new understanding of autophagy in laryngeal cancer.

Autophagy and the potential linkage with the human oral diseases

Autophagy is a cell survival mechanism that has a key role in both physiologic and pathologic conditions. In this cellular ‘clearance’ process, damaged organelles and macromolecules are transported to the lysosomes for degradation. With autophagy, a protection mechanism occurs in the cell under difficult conditions including oxidative stress and lack of growth factor. Paradoxically, in autophagy under some conditions, non-apoptotic cell death can be observed via a caspase-independent pathway. Recent, studies indicated that there is a strong correlation between the composition of the oral microbiota and the pathogenesis of oral diseases, and autophagy plays a crucial role in the development of this process. This review is focused on the molecular mechanism of autophagy and its relationship with human oral diseases. In this review, the importance of the autophagy mechanism in the maintenance of oral tissue health is emphasized. After examining the studies, we observed the importance of autophagy in response to a variety of oral diseases and aimed to present this awareness. Thus, a better understanding of autophagy will be the basis for developing new therapeutic strategies in the treatment of oral diseases.

The identification of tick autophagy-related genes in Ixodes scapularis responding to amino acid starvation

Ticks are obligate hematophagous arthropods and must tolerate starvation during off‐host periods. Macroautophagy (hereafter autophagy) is a well-conserved self-eating mechanism of cell survival and is essential for recycling cellular contents during periods of starvation, stress, and injury in organisms. Although the genome sequence of Ixodes scapularis (Say) is available, the characteristics and functions of autophagy-related gene families remain largely unknown. To advance our understanding of autophagy in I. scapularis, we used comprehensive genomic approaches to identify Atg genes. Homologues of 14 Atg genes were identified, and their protein motif compositions were predicted. Phylogenetic analysis indicated that ATGs in I. scapularis were evolutionarily closely related to their homologues in Haemaphysalis longicornis and Rhipicephalus microplus ticks. Expression patterns of Atg genes differed across tick developmental stages. Immunofluorescence results by monodansylcadaverine (MDC) staining indicated that autophagy was activated after amino acid starvation treatments in I. scapularis embryo-derived cell lines ISE6 and IDE8. Subsequently, the expression of key Atg genes involved in autophagy pathway in both cell lines were examined. In ISE6 cells, the expression levels of three Atg genes (Atg4B, Atg6 and Atg8A) increased significantly after amino acid starvation; similarly, four Atg genes (Atg4A, Atg4B, Atg6 and Atg8B) were upregulated in IDE8 cells in response to starvation. In parallel, the MDC and lysotracker staining results indicated that autophagy was triggered after amino acid starvation treatments in R. microplus embryo-derived cell line BME26. Our observations showed that Atg family genes are highly conserved in ticks and function in autophagy pathway induced by amino acid starvation. These results also provide valuable insight for further autophagy-related research as a new strategy for blocking the transmission of tick-borne pathogens.

Autophagy and Diabetic Nephropathy.

In recent years, diabetic kidney disease has been the main cause of end-stage renal disease; more and more people have faced this serious public health problem worldwide. Autophagy is a conserved multistep pathway that degrades and recycles damaged organelles and macromolecules to maintain intracellular homeostasis. Autophagy plays key roles in several diseases, including kidney diseases. It has been suggested that dysregulated autophagy plays a vital role in both glomerular and tubulointerstitial pathologies in kidneys under diabetic conditions. The advances in our understanding of autophagy in diabetic kidney disease will be helpful for us to discover a new therapeutic target for the prevention and treatment of this life-threatening diabetes complication.

MiRNA-211 triggers an autophagy-dependent apoptosis in cervical cancer cells: regulation of Bcl-2.

Cervical cancer is a significant cause of morbidity and mortality in gynecological malignancies. Although autophagy plays a critical role in affecting cell apoptosis and proliferation, the role of hsa-miR-211-5p (miR-211) in modulating autophagy of cervical cancer cells remains unclear. In the current study, the level of miR-211 was downregulated in cervical cancer specimens, compared to the paired para-carcinoma tissues. While Bcl-2 was upregulated, LC3-II/I was decreased in the tumors, indicating inhibited apoptosis and autophagy. The forced expression of miR-211 inhibited proliferation, and promoted apoptosis in SiHa cervical cancer cells, evidenced by increased expression of apoptotic proteins, caspase-3, and PARP. While the miR-211 inhibitor exerted reverse effects on C-33A cervical cancer cells. Further, miR-211 induced autophagy in cervical cancer cells, as manifested by the presence of LC3 puncta, increased LC3-II/I and Beclin1 levels, and decreased p62 level. The miR-211-induced apoptosis was alleviated by an autophagy inhibitor 3-methyladenine (3-MA). In addition, Bcl-2 was identified as a target of miR-211. Besides, the apoptosis and autophagy triggered by miR-211 were attenuated by Bcl-2 in SiHa cells. In summary, our work indicates that miR-211 induced autophagy and autophagy-dependent apoptosis by regulating Bcl-2 in cervical cancer cells, which provided further understanding of autophagy in cervical carcinogenesis.