Differential gene co-expression network analyses reveal novel molecules associated with transcriptional dysregulation of key biological processes in osteoarthritis knee cartilage

Buzzatto-Leite, I.; Afonso, Juliana; Silva-Vignato, Bárbara; Coutinho, Luiz Lehmann; Alvares, L.E.

doi:10.1016/j.ocarto.2022.100316

Cited by 2 publications

(1 citation statement)

References 49 publications

(64 reference statements)

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“…This helps further confirm key biological characteristics and molecular mechanisms involved in OA development. Bioinformatics analysis, utilizing DEGs, enhances our understanding of gene regulatory changes in OA and aids in uncovering associated signaling pathways and biological processes [ [24] , [25] , [26] ]. A gene expression profiling study has found significant alterations in gene expression related to chondrocyte differentiation and inflammatory response in OA cartilage tissue [ 27 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of diagnostic biomarkers for osteoarthritis through bioinformatics and machine learning

Wang,

Li,

Lin

2024

Heliyon

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Section: Discussionmentioning

confidence: 99%

Identification of diagnostic biomarkers for osteoarthritis through bioinformatics and machine learning

Wang,

Li,

Lin

2024

Heliyon

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Pleiotropic Roles of a KEAP1-Associated Deubiquitinase, OTUD1

Oikawa¹,

Shimizu²,

Tokunaga³

2023

Antioxidants

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Protein ubiquitination, which is catalyzed by ubiquitin-activating enzymes, ubiquitin-conjugating enzymes, and ubiquitin ligases, is a crucial post-translational modification to regulate numerous cellular functions in a spatio–temporal-specific manner. The human genome encodes ~100 deubiquitinating enzymes (DUBs), which antagonistically regulate the ubiquitin system. OTUD1, an ovarian tumor protease (OTU) family DUB, has an N-terminal-disordered alanine-, proline-, glycine-rich region (APGR), a catalytic OTU domain, and a ubiquitin-interacting motif (UIM). OTUD1 preferentially hydrolyzes lysine-63-linked ubiquitin chains in vitro; however, recent studies indicate that OTUD1 cleaves various ubiquitin linkages, and is involved in the regulation of multiple cellular functions. Thus, OTUD1 predominantly functions as a tumor suppressor by targeting p53, SMAD7, PTEN, AKT, IREB2, YAP, MCL1, and AIF. Furthermore, OTUD1 regulates antiviral signaling, innate and acquired immune responses, and cell death pathways. Similar to Nrf2, OTUD1 contains a KEAP1-binding ETGE motif in its APGR and regulates the reactive oxygen species (ROS)-mediated oxidative stress response and cell death. Importantly, in addition to its association with various cancers, including multiple myeloma, OTUD1 is involved in acute graft-versus-host disease and autoimmune diseases such as systemic lupus erythematosus, rheumatoid arthritis, and ulcerative colitis. Thus, OTUD1 is an important DUB as a therapeutic target for a variety of diseases.

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Differential gene co-expression network analyses reveal novel molecules associated with transcriptional dysregulation of key biological processes in osteoarthritis knee cartilage

Cited by 2 publications

References 49 publications

Identification of diagnostic biomarkers for osteoarthritis through bioinformatics and machine learning

Identification of diagnostic biomarkers for osteoarthritis through bioinformatics and machine learning

Pleiotropic Roles of a KEAP1-Associated Deubiquitinase, OTUD1

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