Regulation of autophagy by microRNAs in human breast cancer

Chong, Zhi Xiong; Yeap, Swee Keong; Ho, Wan Yong

doi:10.1186/s12929-021-00715-9

Cited by 16 publications

(7 citation statements)

References 102 publications

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“…While initially it was thought that autophagy is solely regulated at the protein level, a seminal report in 1999 showed that gene regulatory changes affect autophagy at a transcriptional level [64]. Moreover, autophagy regulation on the post-transcriptional level by non-coding RNAs has also been described, but less studied [65][66][67]. Although the knowledge on autophagy regulation has been expanded significantly, data on post-translational and (post-)transcriptional regulations are scattered across many resources -making it difficult to find and integrate highquality and relevant data.…”

Section: Discussionmentioning

confidence: 99%

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

Csabai

Bohár

Türei

et al. 2023

Preprint

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Autophagy is a highly-conserved catabolic process eliminating dysfunctional cellular components and invading pathogens. Autophagy malfunction contributes to disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy regulation in health and disease has been the focus of the last decades. We previously provided an integrated database for autophagy research, the Autophagy Regulatory Network (ARN). For the last seven years, this resource has been used by thousands of users. Here, we present a new and upgraded resource, AutophagyNet. It builds on the previous database but contains major improvements to address user feedback and novel needs due to the advancement in omics data availability. AutophagyNet contains updated interaction curation and integration of over 280,000 experimentally verified interactions between core autophagy proteins and their protein, transcriptional and post-transcriptional regulators as well as their potential upstream pathway connections. AutophagyNet provides annotations for each core protein about their role: 1) in different types of autophagy (mitophagy, xenophagy, etc.); 2) in distinct stages of autophagy (initiation, elongation, termination, etc); 3) with subcellular and tissue-specific localization. These annotations can be used to filter the dataset, providing customizable download options tailored to the users needs. The resource is available in various file formats (e.g., CSV, BioPAX and PSI-MI), and data can be analyzed and visualized directly in Cytoscape. The multi-layered regulation of autophagy can be analyzed by combining AutophagyNet with tissue- or cell type-specific using (multi-)omics datasets (e.g. transcriptomic or proteomic data). The resource is publicly accessible at http://autophagynet.org.

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Section: Discussionmentioning

confidence: 99%

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

Csabai

Bohár

Türei

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…While initially it was thought that autophagy is solely regulated at the protein level, a seminal report in 1999 showed that gene regulatory changes affect autophagy at a transcriptional level [ 65 ]. Moreover, autophagy regulation on the post-transcriptional level by non-coding RNAs has also been described, but less studied [ 66 , 67 ]. Although the knowledge on autophagy regulation has been expanded significantly, data on post-translational and (post-)transcriptional regulations are scattered across many resources – making it difficult to find and integrate high-quality and relevant data.…”

Section: Discussionmentioning

confidence: 99%

AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation

Csabai,

Bohár,

Türei

et al. 2023

Autophagy

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Macroautophagy/autophagy is a highly-conserved catabolic procss eliminating dysfunctional cellular components and invading pathogens. Autophagy malfunction contributes to disorders such as cancer, neurodegenerative and inflammatory diseases. Understanding autophagy regulation in health and disease has been the focus of the last decades. We previously provided an integrated database for autophagy research, the Autophagy Regulatory Network (ARN). For the last eight years, this resource has been used by thousands of users. Here, we present a new and upgraded resource, AutophagyNet. It builds on the previous database but contains major improvements to address user feedback and novel needs due to the advancement in omics data availability. AutophagyNet contains updated interaction curation and integration of over 280,000 experimentally verified interactions between core autophagy proteins and their protein, transcriptional and post-transcriptional regulators as well as their potential upstream pathway connections. AutophagyNet provides annotations for each core protein about their role: 1) in different types of autophagy (mitophagy, xenophagy, etc.); 2) in distinct stages of autophagy (initiation, expansion, termination, etc.); 3) with subcellular and tissue-specific localization. These annotations can be used to filter the dataset, providing customizable download options tailored to the user’s needs. The resource is available in various file formats (e.g. CSV, BioPAX and PSI-MI), and data can be analyzed and visualized directly in Cytoscape. The multi-layered regulation of autophagy can be analyzed by combining AutophagyNet with tissue- or cell type-specific (multi-)omics datasets (e.g. transcriptomic or proteomic data). The resource is publicly accessible at http://autophagynet.org . Abbreviations : ARN: Autophagy Regulatory Network; ATG: autophagy related; BCR: B cell receptor pathway; BECN1: beclin 1; GABARAP: GABA type A receptor-associated protein; IIP: innate immune pathway; LIR: LC3-interacting region; lncRNA: long non-coding RNA; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; miRNA: microRNA; NHR: nuclear hormone receptor; PTM: post-translational modification; RTK: receptor tyrosine kinase; TCR: T cell receptor; TLR: toll like receptor.

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“…Recent research has shown that autophagy is a ‘two‐edged sword’; it inhibits malignant development. In the early stages of cancer, it reduces chromatin instability, tissue damage, and inflammation mostly related to cancer growth (Arun et al, 2015; Chong et al, 2021). Autophagy may perform a complicated role throughout later phases depending on internal and external circumstances.…”

Section: Signaling Pathways In Pathogenesis Of Bcmentioning

confidence: 99%

Role of Medicinal plant‐derived Nutraceuticals as a potential target for the treatment of breast cancer

Alharbi

Almalki

Makeen

et al. 2022

Journal of Food Biochemistry

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Breast cancer (BC) is one of the most challenging cancers to treat, accounting for many cancer‐related deaths. Over some years, chemotherapy, hormone treatment, radiation, and surgeries have been used to treat cancer. Unfortunately, these treatment options are unsuccessful due to crucial adverse reactions and multidrug tolerance/resistance. Although it is clear that substances in the nutraceuticals category have a lot of anti‐cancer activity, using a supplementary therapy strategy, in this case, could be very beneficial. Nutraceuticals are therapeutic agents, which are nutrients that have drug‐like characteristics and can be used to treat diseases. Plant nutraceuticals categorized into polyphenols, terpenoids, vitamins, alkaloids, and flavonoids are part of health food products, that have great potential for combating BC. Nutraceuticals can reduce BC's severity, limit malignant cell growth, and modify cancer‐related mechanisms. Nutraceuticals acting by attenuating Hedgehog, Nuclear factor kappa‐light‐chain‐enhancer of activated B cells (NF‐κB), Notch, and Wnt/β‐catenin signaling are the main pathways in controlling the self‐renewal of breast cancer stem cells (BCSCs). This article reviews some important nutraceuticals and their modes of action, which can be very powerful versus BC. Practical applications Nutraceuticals' importance to the control and diagnosis of breast cancer is undeniable and cannot be overlooked. Natural dietary compounds have a wide range of uses and have been used in traditional medicine. In addition, these natural chemicals can enhance the effectiveness of other traditional medicines. They may also be used as a treatment process independently because of their capacity to affect several cancer pathways. This study highlights a variety of natural chemicals, and their mechanisms of action, routes, synergistic effects, and future potentials are all examined.

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Regulation of autophagy by microRNAs in human breast cancer

Cited by 16 publications

References 102 publications

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

AutophagyNet: High-resolution data source for the analysis of autophagy and its regulation

AutophagyNet: high-resolution data source for the analysis of autophagy and its regulation

Role of Medicinal plant‐derived Nutraceuticals as a potential target for the treatment of breast cancer

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