ATG7-mediated autophagy involves in miR-138-5p regulated self-renewal and invasion of lung cancer stem-like cells derived from A549 cells

DGNMDA: Dual Heterogeneous Graph Neural Network Encoder for miRNA-Disease Association Prediction

In recent years, numerous studies have highlighted the pivotal importance of miRNAs in personalized healthcare, showcasing broad application prospects. miRNAs hold significant potential in disease diagnosis, prognosis assessment, and therapeutic target discovery, making them an integral part of precision medicine. They are expected to enable precise disease subtyping and risk prediction, thereby advancing the development of precision medicine. GNNs, a class of deep learning architectures tailored for graph data analysis, have greatly facilitated the advancement of miRNA-disease association prediction algorithms. However, current methods often fall short in leveraging network node information, particularly in utilizing global information while neglecting the importance of local information. Effectively harnessing both local and global information remains a pressing challenge. To tackle this challenge, we propose an innovative model named DGNMDA. Initially, we constructed various miRNA and disease similarity networks based on authoritative databases. Subsequently, we creatively design a dual heterogeneous graph neural network encoder capable of efficiently learning feature information between adjacent nodes and similarity information across the entire graph. Additionally, we develop a specialized fine-grained multi-layer feature interaction gating mechanism to integrate outputs from the neural network encoders to identify novel associations connecting miRNAs with diseases. We evaluate our model using 5-fold cross-validation and real-world disease case studies, based on the HMDD V3.2 dataset. Our method demonstrates superior performance compared to existing approaches in various tasks, confirming the effectiveness and potential of DGNMDA as a robust method for predicting miRNA-disease associations.

Hotspots and frontiers of autophagy and chemotherapy in lung cancer: a bibliometric and visualization analysis from 2003 to 2023

Autophagy was considered to induce resistance in chemotherapy, which was significantly associated with proliferation of cancer; however, few bibliometric studies on the relation between autophagy and chemotherapy in lung cancer are available. The aim of the present study was to provide a comprehensive overview of the knowledge structure and research hotspots of autophagy and chemotherapy in lung cancer by bibliometric analysis. Publications related to autophagy and chemotherapy in lung cancer from 2003 to 2023 were searched on the Web of Science Core Collection (WoSCC) database. The bibliometric analysis was conducted by using VOSviewers, CiteSpace, and the R package "bibliometrix." A total of 675 articles from 70 countries, led by China and the United States, were included in the analysis. The number of publications related to autophagy and chemotherapy in lung cancer is increasing year by year. Nanjing Medical University, Zhejiang University, China Medical University, and Sichuan University are among the main research institutions contributing to this field. The journal Cancers is the most popular publication in this area, with Autophagy being the most co-cited journal. These publications involve 4481 authors, with Chiu Chien-chih and Gewirtz David having published the most papers, and Noboru Mizushima being the most frequently co-cited author. Studying the relation between autophagy and chemotherapy in the occurrence and development of lung cancer, and exploring therapeutic strategies involving autophagy and chemotherapy in lung cancer, are the primary topics in this research field. "Tumor stem cells," "microRNA," and "EGFR" emerge as the primary keywords in the emerging research hotspots. Indeed, this bibliometric study provides valuable insights into the research trends and developments concerning autophagy and chemotherapy in lung cancer. By identifying recent research frontiers and highlighting hot directions, this study serves as a valuable reference for scholars interested in understanding the relationship between autophagy and chemotherapy in lung cancer. The comprehensive summary of findings offers a foundation for further exploration and advancement in this critical area of cancer research.

Insights on E1-like enzyme ATG7: functional regulation and relationships with aging-related diseases

Autophagy is a dynamic self-renovation biological process that maintains cell homeostasis and is responsible for the quality control of proteins, organelles, and energy metabolism. The E1-like ubiquitin-activating enzyme autophagy-related gene 7 (ATG7) is a critical factor that initiates classic autophagy reactions by promoting the formation and extension of autophagosome membranes. Recent studies have identified the key functions of ATG7 in regulating the cell cycle, apoptosis, and metabolism associated with the occurrence and development of multiple diseases. This review summarizes how ATG7 is precisely programmed by genetic, transcriptional, and epigenetic modifications in cells and the relationship between ATG7 and aging-related diseases.

DAEMDA: A Method with Dual-Channel Attention Encoding for miRNA-Disease Association Prediction

A growing number of studies have shown that aberrant microRNA (miRNA) expression is closely associated with the evolution and development of various complex human diseases. These key biomarkers' identification and observation are significant for gaining a deeper understanding of disease pathogenesis and therapeutic mechanisms. Consequently, pinpointing potential miRNA-disease associations (MDA) has become a prominent bioinformatics subject, encouraging several new computational methods given the advances in graph neural networks (GNN). Nevertheless, these existing methods commonly fail to exploit the network nodes' global feature information, leaving the generation of high-quality embedding representations using graph properties as a critical unsolved issue. Addressing these challenges, we introduce the DAEMDA, a computational method designed to optimize the current models' efficacy. First, we construct similarity and heterogeneous networks involving miRNAs and diseases, relying on experimentally corroborated miRNA-disease association data and analogous information. Then, a newly-fashioned parallel dual-channel feature encoder, designed to better comprehend the global information within the heterogeneous network and generate varying embedding representations, follows this. Ultimately, employing a neural network classifier, we merge the dual-channel embedding representations and undertake association predictions between miRNA and disease nodes. The experimental results of five-fold cross-validation and case studies of major diseases based on the HMDD v3.2 database show that this method can generate high-quality embedded representations and effectively improve the accuracy of MDA prediction.

A miRNome analysis at the early postmortem interval

The postmortem interval (PMI) is the time elapsing since the death of an individual until the body is examined. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI as they can better support degradation. In the present work, we analyzed the miRNome at early PMI in rats' skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 microarrays. We found 156 dysregulated miRNAs in rats' skeletal muscle at 24 h of PMI, out of which 84 were downregulated, and 72 upregulated. The miRNA most significantly downregulated was miR-139-5p (FC = -160, p = 9.97 × 10^-11), while the most upregulated was rno-miR-92b-5p (FC = 241.18, p = 2.39 × 10^-6). Regarding the targets of these dysregulated miRNAs, the rno-miR-125b-5p and rno-miR-138-5p were the miRNAs with more mRNA targets. The mRNA targets that we found in the present study participate in several biological processes such as interleukin secretion regulation, translation regulation, cell growth, or low oxygen response. In addition, we found a downregulation of SIRT1 mRNA and an upregulation of TGFBR2 mRNA at 24 h of PMI. These results suggest there is an active participation of miRNAs at early PMI which could be further explored to identify potential biomarkers for PMI estimation.

Current and potential roles of RNA modification-mediated autophagy dysregulation in cancer

Autophagy, a cellular lysosomal degradation and survival pathway, supports nutrient recycling and adaptation to metabolic stress and participates in various stages of tumor development, including tumorigenesis, metastasis, and malignant state maintenance. Among the various factors contributing to the dysregulation of autophagy in cancer, RNA modification can regulate autophagy by directly affecting the expression of core autophagy proteins. We propose that autophagy disorder mediated by RNA modification is an important mechanism for cancer development. Therefore, this review mainly discusses the role of RNA modification-mediated autophagy regulation in tumorigenesis. We summarize the molecular basis of autophagy and the core proteins and complexes at different stages of autophagy, especially those involved in cancer development. Moreover, we describe the crosstalk of RNA modification and autophagy and review the recent advances and potential role of the RNA modification/autophagy axis in the development of multiple cancers. Furthermore, the dual role of the RNA modification/autophagy axis in cancer drug resistance is discussed. A comprehensive understanding and extensive exploration of the molecular crosstalk of RNA modifications with autophagy will provide important insights into tumor pathophysiology and provide more options for cancer therapeutic strategies.

Upregulation of nuclear division cycle 80 contributes to therapeutic resistance via the promotion of autophagy-related protein-7-dependent autophagy in lung cancer

Lung cancer remains the leading cause of malignant mortality worldwide. Hence, the discovery of novel targets that can improve therapeutic effects in lung cancer patients is an urgent need. In this study, we screened differentially expressed genes using isobaric tags for relative and absolute quantitation (iTRAQ) analysis and datasets from the cancer genome atlas database, and found that nuclear division cycle 80 (NDC80) might act as a novel prognostic indicator of lung cancer. The expression of NDC80 was significantly increased in lung cancer tissues, as compared to normal tissues, and high expression levels of NDC80 were correlated with unfavorable survival rates. Furthermore, an in vitro analysis showed that the stable knockdown of NDC80 decreased the cell viability and increased therapeutic sensitivity in two lung cancer cell lines, A549-IRR and H1246-IRR. Moreover, gene set enrichment analysis results showed that NDC80 was enriched in autophagy-related pathways. The downregulation of NDC80 inhibited the formation of autophagosomes, and reduced the expression of autophagy-related proteins such as LC3II, Beclin-1, and p62 in lung cancer cells. To further clarify the role of NDC80 as a downstream regulator of autophagy, we validated autophagic mediators through iTRAQ analysis and real-time polymerase chain reaction arrays. Autophagy-related protein7 (ATG7) was observed to be downregulated after the knockdown of NDC80 in lung cancer cells. Immunohistochemistry assay results revealed that both NDC80 and ATG7 were upregulated in an array of lung adenocarcinoma samples, compared to normal tissues, and the expression of NDC80 was identified to be positively associated with the levels of ATG7. Our findings suggest that NDC80 promotes the development of lung cancer by regulating autophagy, and might serve as a potential target for increasing the therapeutic sensitivity of lung cancer.

Recent Advances of Autophagy in Non-Small Cell Lung Cancer: From Basic Mechanisms to Clinical Application

Lung cancer is characterized by the most common oncological disease and leading cause of cancer death worldwide, of which a group of subtypes known as non-small cell lung cancer (NSCLC) accounts for approximately 85%. In the past few decades, important progression in the therapies of NSCLC has enhanced our understanding of the biology and progression mechanisms of tumor. The application of immunotherapy and small molecule tyrosine kinase inhibitors has brought significant clinical benefits in certain patients. However, early metastasis and the emergence of resistance to antitumor therapy have resulted in the relatively low overall cure and survival rates for NSCLC. Autophagy is a conserved process that allows cells to recycle unused or damaged organelles and cellular components. It has been reported to be related to the progression of NSCLC and resistance to targeted therapy and cytotoxic chemotherapy. Therefore, autophagy is considered as a potential therapeutic target for NSCLC. Mounting results have been reported about the combination of tyrosine kinase inhibitors and inhibitors of autophagy in models of NSCLC. This review aims to provide a comprehensive review on the roles of autophagy in NSCLC, focusing on related clinical data of agents that regulate autophagy in NSCLC. Furthermore, this study will provide a theoretical basis for further improvement of autophagy-based cancer therapy.

MiR-7-5p suppresses invasion via downregulation of the autophagy-related gene ATG7 and increases chemoresistance to cisplatin in BCa

Bladder cancer (BCa) is one of the most common cancers in men and is a major threat to the lives and health of older men. Many studies have shown that miR-7, as an important tumor suppressor gene, could directly inhibit some pathways involved in the development of cancer. MiR-7-5p, which was assessed in this study, consists of one arm of miR-7 and acts as a cancer suppressor gene in multiple cancer types. Autophagy, as a common biological process, plays dual roles in the process of cancer. Chemotherapy resistance is a problem in the treatment of BCa. In this study, the data showed that miR-7-5p was obviously down-regulated in BCa tissues and cells compared to their respective controls. In addition, miR-7-5p mimic effectively inhibited migration, invasion and autophagy both in vitro and in vivo. In the mechanistic study, miR-7-5p targeted autophagy-related gene ATG7 to inhibit its expression, which in turn inhibited autophagy. Finally, the migration of BCa cells was inhibited, and chemosensitivity was improved. Overall, our results provide evidence of the role of miR-7-5p as a cancer suppressor gene in BCa and provide new opportunities for the treatment of BCa.

Autophagy Regulation on Cancer Stem Cell Maintenance, Metastasis, and Therapy Resistance

Simple Summary

Certain types of cancer have higher relapse rates compared to others, and cancer stem cells (CSCs) have been shown as the main drivers of cancer relapse and cancer severity. This subpopulation of cells displays stem-like characteristics which bolster tumorigenesis along with metastasis and lead to poorer prognoses. Autophagy has been studied as a mechanism by which CSCs maintain stemness and acquire resistance to chemotherapy and radiation. The aim of this review is to condense and organize what has been recently published on the connection between cancer stem cells (CSCs) and autophagy. Multiple studies on autophagy have suggested that the pathway is a double-edged sword, which can either undermine or enhance CSC characteristics depending on interactions with different pathways. Thus, future research should investigate regulation of autophagy in combination with traditional cancer therapies as a possible method to effectively eliminate CSCs and minimize cancer relapse.

Abstract

Cancer stem cells (CSCs) are a subset of the tumor population that play critical roles in tumorigenicity, metastasis, and relapse. A key feature of CSCs is their resistance to numerous therapeutic strategies which include chemotherapy, radiation, and immune checkpoint inhibitors. In recent years, there is a growing body of literature that suggests a link between CSC maintenance and autophagy, a mechanism to recycle intracellular components during moments of environmental stress, especially since CSCs thrive in a tumor microenvironment that is plagued with hypoxia, acidosis, and lack of nutrients. Autophagy activation has been shown to aid in the upkeep of a stemness state along with bolstering resistance to cancer treatment. However, recent studies have also suggested that autophagy is a double-edged sword with anti-tumorigenic properties under certain circumstances. This review summarizes and integrates what has been published in the literature in terms of what role autophagy plays in stemness maintenance of CSCs and suggests that there is a more complex interplay between autophagy and apoptosis which involves multiple pathways of regulation. Future cancer therapy strategies are needed to eradicate this resistant subset of the cell population through autophagy regulation.

Non-coding RNAs as new autophagy regulators in cancer progression

Recent advances highlight that non-coding RNAs (ncRNAs) are emerging as fundamental regulators in various physiological as well as pathological processes by regulating macro-autophagy. Studies have disclosed that macro-autophagy, which is a highly conserved process involving cellular nutrients, components, and recycling of organelles, can be either selective or non-selective and ncRNAs show their regulation on selective autophagy as well as non-selective autophagy. The abnormal expression of ncRNAs will result in the impairment of autophagy and contribute to carcinogenesis and cancer progression by regulating both selective autophagy as well as non-selective autophagy. This review focuses on the regulatory roles of ncRNAs in autophagy and their involvement in cancer which may provide valuable therapeutic targets for cancer management.

Mechanisms of Survival of Cytomegalovirus-Infected Tumor Cells

Human cytomegalovirus (HCMV) DNA and proteins are often detected in malignant tumors, warranting studies of the role that HCMV plays in carcinogenesis and tumor progression. HCMV proteins were shown to regulate the key processes involved in tumorigenesis. While HCMV as an oncogenic factor just came into focus, its ability to promote tumor progression is generally recognized. The review discusses the viral factors and cell molecular pathways that affect the resistance of cancer cells to therapy. CMV inhibits apoptosis of tumor cells, that not only promotes tumor progression, but also reduces the sensitivity of cells to antitumor therapy. Autophagy was found to facilitate either cell survival or cell death in different tumor cells. In leukemia cells, HCMV induces a "protective" autophagy that suppresses apoptosis. Viral factors that mediate drug resistance and their interactions with key cell death pathways are necessary to further investigate in order to develop agents that can restore the tumor sensitivity to anticancer drugs.

Autophagy Regulation by Crosstalk between miRNAs and Ubiquitination System

MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules encoded by endogenous genes with ~22 nucleotides which are involved in the regulation of post-transcriptional gene expression. Ubiquitination and deubiquitination are common post-translational modifications in eukaryotic cells and important pathways in regulating protein degradation and signal transduction, in which E3 ubiquitin ligases and deubiquitinases (DUBs) play a decisive role. MiRNA and ubiquitination are involved in the regulation of most biological processes, including autophagy. Furthermore, in recent years, the direct interaction between miRNA and E3 ubiquitin ligases or deubiquitinases has attracted much attention, and the cross-talk between miRNA and ubiquitination system has been proved to play key regulatory roles in a variety of diseases. In this review, we summarized the advances in autophagy regulation by crosstalk between miRNA and E3 ubiquitin ligases or deubiquitinases.

Targeting Cancer Stem Cells by Dietary Agents: An Important Therapeutic Strategy against Human Malignancies

As a multifactorial disease, treatment of cancer depends on understanding unique mechanisms involved in its progression. The cancer stem cells (CSCs) are responsible for tumor stemness and by enhancing colony formation, proliferation as well as metastasis, and these cells can also mediate resistance to therapy. Furthermore, the presence of CSCs leads to cancer recurrence and therefore their complete eradication can have immense therapeutic benefits. The present review focuses on targeting CSCs by natural products in cancer therapy. The growth and colony formation capacities of CSCs have been reported can be attenuated by the dietary agents. These compounds can induce apoptosis in CSCs and reduce tumor migration and invasion via EMT inhibition. A variety of molecular pathways including STAT3, Wnt/β-catenin, Sonic Hedgehog, Gli1 and NF-κB undergo down-regulation by dietary agents in suppressing CSC features. Upon exposure to natural agents, a significant decrease occurs in levels of CSC markers including CD44, CD133, ALDH1, Oct4 and Nanog to impair cancer stemness. Furthermore, CSC suppression by dietary agents can enhance sensitivity of tumors to chemotherapy and radiotherapy. In addition to in vitro studies, as well as experiments on the different preclinical models have shown capacity of natural products in suppressing cancer stemness. Furthermore, use of nanostructures for improving therapeutic impact of dietary agents is recommended to rapidly translate preclinical findings for clinical use.

Recent progress of autophagy signaling in tumor microenvironment and its targeting for possible cancer therapeutics

Autophagy, a lysosomal catabolic process, involves degradation of cellular materials, protein aggregate, and dysfunctional organelles to maintain cellular homeostasis. Strikingly, autophagy exhibits a dual-sided role in cancer; on the one hand, it promotes clearance of transformed cells and inhibits tumorigenesis, while cytoprotective autophagy has a role in sustaining cancer. The autophagy signaling in the tumor microenvironment (TME) during cancer growth and therapy is not adequately understood. The review highlights the role of autophagy signaling pathways to support cancer growth and progression in adaptation to the oxidative and hypoxic context of TME. Furthermore, autophagy contributes to regulating the metabolic switch for generating sufficient levels of high-energy metabolites, including amino acids, ketones, glutamine, and free fatty acids for cancer cell survival. Interestingly, autophagy has a critical role in modulating the tumor-associated fibroblast resulting in different cytokines and paracrine signaling mediated angiogenesis and invasion of pre-metastatic niches to secondary tumor sites. Moreover, autophagy promotes immune evasion to inhibit antitumor immunity, and autophagy inhibitors enhance response to immunotherapy with infiltration of immune cells to the TME niche. Furthermore, autophagy in TME maintains and supports the survival of cancer stem cells resulting in chemoresistance and therapy recurrence. Presently, drug repurposing has enabled the use of lysosomal inhibitor-based antimalarial drugs like chloroquine and hydroxychloroquine as clinically available autophagy inhibitors in cancer therapy. We focus on the recent developments of multiple autophagy modulators from pre-clinical trials and the challenges in developing autophagy-based cancer therapy.