Deciphering the Rules of in Silico Autophagy Methods for Expediting Medicinal Research

Multi-omics approaches identify novel prognostic biomarkers of autophagy in uveal melanoma

PURPOSE

Uveal melanoma (UVM) is a rare yet malignant ocular tumor that metastases in approximately half of all patients, with the majority of those developing metastasis typically succumbing to the disease within a year. Hitherto, no effective treatment for UVM has been identified. Autophagy is a cellular mechanism that has been suggested as an emerging regulatory process for cancer-targeted therapy. Thus, identifying novel prognostic biomarkers of autophagy may help improve future treatment.

METHODS

Consensus clustering and similarity network fusion approaches were performed for classifying UVM patient subgroups. Weighted correlation network analysis was performed for gene module screening and network construction. Gene set variation analysis was used to evaluate the autophagy activity of the UVM subgroups. Kaplan-Meier survival curves (Log-rank test) were performed to analyze patient prognosis. Gene set cancer analysis was used to estimate the level of immune cell infiltration.

RESULTS

In this study, we employed multi-omics approaches to classify UVM patient subgroups by molecular and clinical characteristics, ultimately identifying HTR2B, EEF1A2, FEZ1, GRID1, HAP1, and SPHK1 as potential prognostic biomarkers of autophagy in UVM. High expression levels of these markers were associated with poorer patient prognosis and led to reshaping the tumor microenvironment (TME) that promotes tumor progression.

CONCLUSION

We identified six novel potential prognostic biomarkers in UVM, all of which are associated with autophagy and TME. These findings will shed new light on UVM therapy with inhibitors targeting these biomarkers expected to regulate autophagy and reshape the TME, significantly improving UVM treatment outcomes.

Application of Novel Degraders Employing Autophagy for Expediting Medicinal Research

Targeted protein degradation (TPD) technology is based on a unique pharmacological mechanism that has profoundly revolutionized medicinal research by overcoming limitations associated with traditional small-molecule drugs. Autophagy, a mechanism for intracellular waste disposal and recovery, is an important biological process in medicinal research. Recently, studies have demonstrated that several emerging autophagic degraders can treat human diseases. Herein we summarize the progress in medicinal research on autophagic degraders, including autophagosome-tethering compounds (ATTEC), autophagy-targeting chimeras (AUTAC), and AUTOphagy-TArgeting chimeras (AUTOTAC), for treating human diseases. These autophagic degraders exhibit excellent potential for treating neurodegenerative diseases. Our research on autophagic degraders provides a new avenue for medicinal research on TPD via autophagy.

Targeting regulated cell death with plant natural compounds for cancer therapy: A revisited review of apoptosis, autophagy-dependent cell death, and necroptosis

Regulated cell death (RCD) refers to programmed cell death regulated by various protein molecules, such as apoptosis, autophagy-dependent cell death, and necroptosis. Accumulating evidence has recently revealed that RCD subroutines have several links to many types of human cancer; therefore, targeting RCD with pharmacological small-molecule compounds would be a promising therapeutic strategy. Moreover, plant natural compounds, small-molecule compounds synthesized from plant sources, and their derivatives have been widely reported to regulate different RCD subroutines to improve potential cancer therapy. Thus, in this review, we focus on updating the intricate mechanisms of apoptosis, autophagy-dependent cell death, and necroptosis in cancer. Moreover, we further discuss several representative plant natural compounds and their derivatives that regulate the above-mentioned three subroutines of RCD, and their potential as candidate small-molecule drugs for the future cancer treatment.

Unravelling the roles of Autophagy in OSCC: A renewed perspective from mechanisms to potential applications

Oral squamous cell carcinoma (OSCC) is associated with a low survival rate and a high disability rate, making it a serious health burden, particularly in Southeast Asian countries. Therefore, improvements in the diagnosis, treatment, and prognosis prediction of OSCC are highly warranted. Autophagy has a significant impact on cancer development. Studies on autophagy in various human cancers have made outstanding contributions; however, the relationship between autophagy and OSCC remains to be explored. This review highlights the roles of autophagy in OSCC and discusses the relationship between autophagy and Epithelial–mesenchymal transition. Considering the lack of OSCC biomarkers, we focus on the studies involving OSCC-related bioinformatics analysis and molecular targets. Based on some classical targets, we summarize several key autophagy-related biomarkers with a considerable potential for clinical application, which may become the hotspot of OSCC research. In conclusion, we elaborate on the interrelationship between autophagy and OSCC and highlight the shortcomings of current studies to provide insights into the potential clinical strategies.

Multi-omics approaches identify SF3B3 and SIRT3 as candidate autophagic regulators and druggable targets in invasive breast carcinoma

Autophagy is a critical cellular homeostatic mechanism, and its dysfunction is linked to invasive breast carcinoma (BRCA). Recently, several omics methods have been applied to explore autophagic regulators in BRCA; however, more reliable and robust approaches for identifying crucial regulators and druggable targets remain to be discovered. Thus, we report here the results of multi-omics approaches to identify potential autophagic regulators in BRCA, including gene expression (EXP), DNA methylation (MET) and copy number alterations (CNAs) from The Cancer Genome Atlas (TCGA). Newly identified candidate genes, such as SF3B3, TRAPPC10, SIRT3, MTERFD1, and FBXO5, were confirmed to be involved in the positive or negative regulation of autophagy in BRCA. SF3B3 was identified firstly as a negative autophagic regulator, and siRNA/shRNA-SF3B3 were shown to induce autophagy-associated cell death in in vitro and in vivo breast cancer models. Moreover, a novel small-molecule activator of SIRT3, 1-methylbenzylamino amiodarone, was discovered to induce autophagy in vitro and in vivo. Together, these results provide multi-omics approaches to identify some key candidate autophagic regulators, such as the negative regulator SF3B3 and positive regulator SIRT3 in BRCA, and highlight SF3B3 and SIRT3 as new druggable targets that could be used to fill the gap between autophagy and cancer drug development.

Autophagy modulators for the treatment of oral and esophageal squamous cell carcinomas

Oral squamous cell carcinomas (OSCC) and esophageal squamous cell carcinomas (ESCC) exhibit a survival rate of less than 60% and 40%, respectively. Late-stage diagnosis and lack of effective treatment strategies make both OSCC and ESCC a significant health burden. Autophagy, a lysosome-dependent catabolic process, involves the degradation of intracellular components to maintain cell homeostasis. Targeting autophagy has been highlighted as a feasible therapeutic strategy with clinical utility in cancer treatment, although its associated regulatory mechanisms remain elusive. The detection of relevant biomarkers in biological fluids has been anticipated to facilitate early diagnosis and/or prognosis for these tumors. In this context, recent studies have indicated the presence of specific proteins and small RNAs, detectable in circulating plasma and serum, as biomarkers. Interestingly, the interplay between biomarkers (eg, exosomal microRNAs) and autophagic processes could be exploited in the quest for targeted and more effective therapies for OSCC and ESCC. In this review, we give an overview of the available biomarkers and innovative targeted therapeutic strategies, including the application of autophagy modulators in OSCC and ESCC. Additionally, we provide a viewpoint on the state of the art and on future therapeutic perspectives combining the early detection of relevant biomarkers with drug discovery for the treatment of OSCC and ESCC.