Characterization of immune microenvironment infiltration and m6A regulator-mediated RNA methylation modification patterns in osteoarthritis

Ouyang, Yulong; Tu, Yuanqing; Chen, Shuilin; Min, Huan; Wen, Zhexu; Zheng, Guihao; Wan, Ting; Fan, Hao; Yang, Wenzhao; Sun, Guicai

doi:10.3389/fimmu.2022.1018701

Cited by 3 publications

(3 citation statements)

References 44 publications

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“…ssGSEA calculates the individual enrichment scores of samples and gene sets through the "GSVA" and "GSEABase" R packages. The gene set of in ltrating immune cells included both immune-enhancing and immunosuppressive cells 21,22 . The CIBERSORT algorithm (https://cibersort.stanford.edu/) was used to estimate the relative abundance of immune cells in each sample 23 .…”

Section: Methodsmentioning

confidence: 99%

Cuproptosis-related gene signatures and immunological characterization in sepsis- associated acute lung injury

Zhu

Tang

et al. 2023

Preprint

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Sepsis is a common cause of acute lung injury (ALI), often accompanied by immune disorders and a high mortality rate. Cuproptosis is a recently discovered form of cell death that participates in the progression of various diseases. There is no information on the role of cuproptosis in sepsis-associated ALI. Data from the Gene Expression Omnibus (GEO) database were used for a comprehensive analysis of the transcriptional changes and role of cuproptosis-related genes (CRGs) in sepsis-associated ALI. Gene enrichment analysis, the WGCNA and CIBERSORT algorithms, and consensus clustering were used to explore the relationships between CRGs and immune cells, as well as the underlying mechanisms. We found that fourteen CRGs that showed significant differences in expression between sepsis-associated ALI and healthy controls. Two different CRG subtypes were identified. The scores of the CRG and gene clusters were consistent, and the expression of immune-related factors in the two clusters was similar. Infiltration of immune cells differed between the subgroups, indicating an association between the subgroups and immune cell. A CRG-scoring model was constructed, and was effective in predicting the incidence of sepsis-associated ALI through the expression of CRGs. Real-time PCR analysis showed that the expression of CRGs in the sepsis-associated ALI cell model was similar to that seen in CRG cluster B. CRGs were found to be significantly associated with the occurrence, immune characteristics, and biological processes of sepsis-associated ALI. These findings provide new insights into the mechanisms underlying sepsis-associated ALI.

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Section: Methodsmentioning

confidence: 99%

Cuproptosis-related gene signatures and immunological characterization in sepsis- associated acute lung injury

Zhu

Tang

et al. 2023

Preprint

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“…Recently study revealed that m6A was proved involved in OA progression by regulating immune responses [ 88 ]. Evidence found that IGFBP1 and RBM15B were strongly correlated with infiltrating immunocytes [ 89 ], YTHDF2 was positively related with regulatory T cells, IGFBP2 was negatively associated with dendritic cells [ 90 ], and IGF2BP3 upregulation promoted macrophage M1 polarization in OA [ 91 ].…”

Section: M6a and Skeletal System Diseasementioning

confidence: 99%

Recent advances of m6A methylation in skeletal system disease

Liang,

Yi,

Liu

et al. 2024

J Transl Med

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Skeletal system disease (SSD) is defined as a class of chronic disorders of skeletal system with poor prognosis and causes heavy economic burden. m6A, methylation at the N6 position of adenosine in RNA, is a reversible and dynamic modification in posttranscriptional mRNA. Evidences suggest that m6A modifications play a crucial role in regulating biological processes of all kinds of diseases, such as malignancy. Recently studies have revealed that as the most abundant epigentic modification, m6A is involved in the progression of SSD. However, the function of m6A modification in SSD is not fully illustrated. Therefore, make clear the relationship between m6A modification and SSD pathogenesis might provide novel sights for prevention and targeted treatment of SSD. This article will summarize the recent advances of m6A regulation in the biological processes of SSD, including osteoporosis, osteosarcoma, rheumatoid arthritis and osteoarthritis, and discuss the potential clinical value, research challenge and future prospect of m6A modification in SSD.

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“…Alterations in RNA methylation are also observed in age-related diseases and, interestingly, m 6 A modifications have been implicated in the regulation of different biological processes associated with ageing, including inflammation ( 117 ). Often, these alterations derive from a misbalanced regulation of m 6 A regulatory factors.…”

Section: Metabolism and Epigenetics Deregulation In Diseasementioning

confidence: 99%

Metabolo-epigenetic interplay provides targeted nutritional interventions in chronic diseases and ageing

Gómez de Cedrón,

Moreno Palomares,

Ramírez de Molina

2023

Front. Oncol.

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Epigenetic modifications are chemical modifications that affect gene expression without altering DNA sequences. In particular, epigenetic chemical modifications can occur on histone proteins -mainly acetylation, methylation-, and on DNA and RNA molecules -mainly methylation-. Additional mechanisms, such as RNA-mediated regulation of gene expression and determinants of the genomic architecture can also affect gene expression. Importantly, depending on the cellular context and environment, epigenetic processes can drive developmental programs as well as functional plasticity. However, misbalanced epigenetic regulation can result in disease, particularly in the context of metabolic diseases, cancer, and ageing. Non-communicable chronic diseases (NCCD) and ageing share common features including altered metabolism, systemic meta-inflammation, dysfunctional immune system responses, and oxidative stress, among others. In this scenario, unbalanced diets, such as high sugar and high saturated fatty acids consumption, together with sedentary habits, are risk factors implicated in the development of NCCD and premature ageing. The nutritional and metabolic status of individuals interact with epigenetics at different levels. Thus, it is crucial to understand how we can modulate epigenetic marks through both lifestyle habits and targeted clinical interventions -including fasting mimicking diets, nutraceuticals, and bioactive compounds- which will contribute to restore the metabolic homeostasis in NCCD. Here, we first describe key metabolites from cellular metabolic pathways used as substrates to “write” the epigenetic marks; and cofactors that modulate the activity of the epigenetic enzymes; then, we briefly show how metabolic and epigenetic imbalances may result in disease; and, finally, we show several examples of nutritional interventions - diet based interventions, bioactive compounds, and nutraceuticals- and exercise to counteract epigenetic alterations.

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Characterization of immune microenvironment infiltration and m6A regulator-mediated RNA methylation modification patterns in osteoarthritis

Cited by 3 publications

References 44 publications

Cuproptosis-related gene signatures and immunological characterization in sepsis- associated acute lung injury

Cuproptosis-related gene signatures and immunological characterization in sepsis- associated acute lung injury

Recent advances of m6A methylation in skeletal system disease

Metabolo-epigenetic interplay provides targeted nutritional interventions in chronic diseases and ageing

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