A genome-wide association analysis: m6A-SNP related to the onset of oral ulcers

Wu, Zhuoxuan; Lin, Weimin; Yuan, Quan; Lyu, Mingyue

doi:10.3389/fimmu.2022.931408

Cited by 4 publications

(5 citation statements)

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“…m6A methylation plays a crucial role in post-transcriptional gene regulation, exerting major impacts on diverse cellular functions. Multiple studies have established a link between its dysregulation and a diverse array of diseases, such as cancer and neurological disorders (4,(14)(15)(16)(17)84). The significance of m6A in the progression of diseases not only demonstrates its vital functions but also presents opportunities for developing therapeutic and diagnostic tools (85).…”

Section: Discussionmentioning

confidence: 99%

“…The types of specific regions include exons, 5’-UTR, coding sequences (CDS), introns, and 3’-UTR. Varying the number of fragments (8, 16, 32, and 64) enables the generation of features at different levels of detail. It allows the model to recognise the local information of each fragment and its relative position within the transcripts.…”

Section: Methodsmentioning

confidence: 99%

“…Several experiments have conclusively shown a substantial association between m6A methylations and the development of various diseases, such as cancers, neurological disorders, and cardiovascular diseases (4,(14)(15)(16). Genetic studies known as genome-wide association studies (GWAS) have revealed an array of single nucleotide polymorphisms (SNPs) that interfere with the deposition of m6A, resulting in cellular changes and disease progression (16,17). Understanding the m6A deposition mechanism provides valuable insights into the pathogenesis of diseases, thereby facilitating the investigation of innovative therapeutic and diagnostic approaches.…”

Section: Introductionmentioning

confidence: 99%

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AI-m6ARS: Machine learning-driven m6A RNA methylation site discovery with integrated sequence, conservation, and geographical descriptors

Uthayopas,

de Sá,

Ascher

2024

Preprint

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N6-Methyladenosine (m6A) is a predominant type of human RNA methylation, regulating diverse biochemical processes and being associated with the development of several diseases. Despite its significance, an extensive experimental examination across diverse cellular and transcriptome contexts is still lacking due to time and cost constraints. Computational models have been proposed to prioritise potential m6A methylation sites, although having limited predictive performance due to inadequate characterisation and modelling of m6A sites. This work presents AI-m6ARS, a novel model that utilises integrated sequence, conservation, and geographical descriptive features to predict human m6A methylation sites. The model was trained using the Light Gradient Boosting Machine (LightGBM) algorithm, which was coupled with comprehensive feature selection to improve the data quality. AI-m6RS demonstrates strong predictive capabilities, achieving an impressive area under the receiver operating characteristic curve of 0.87 on cross-validation. Consistent results on unseen transcripts in a blind test highlight the AI-m6ARS generalisability. AI-m6ARS also demonstrates comparable performance to state-of-the-art models, but offers two significant benefits: the model interpretability and the availability of a user-friendly web server. The AI-m6ARS web server offers valuable insights into the distribution of m6A sites within the human genome, thereby facilitating progress in medical applications.GRAPHICAL ABSTRACT

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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AI-m6ARS: Machine learning-driven m6A RNA methylation site discovery with integrated sequence, conservation, and geographical descriptors

Uthayopas,

de Sá,

Ascher

2024

Preprint

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“…A number of studies have identified some genes related to various diseases or traits based on the combined analysis of GWAS and other public data (Table I) (41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57). Firstly, disease-associated m 6 A-SNPs were selected from GWAS according to the m6Avar database.…”

Section: Data Mining Of Genome-wide Association Studiesmentioning

confidence: 99%

m6A‑SNP: From genetics to epigenetics (Review)

Niu

Zhou

2022

Int J Epigen

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N 6 -methyladenosine (m 6 A), the most abundant RNA modification, can participate in various physiological functions and pathological processes by regulating the expression or structure of genes due to its involvement in all aspects of RNA metabolism. Thus, the genetic variant that influences m 6 A, such as m 6 A-associated single nucleotide polymorphism (m 6 A-SNP), which is in close proximity to or in the methylation site, may be related to various pathological processes by increasing or decreasing the m 6 A methylation level due to the alteration of the nucleotide. The present review summarizes the recent advances made in m 6 A-SNPs. Both the mining of genome-wide association studies and the combined analysis of the m6Avar database with expression quantitative trait loci datasets have identified functional variants and causal genes associated with various diseases and have provided new direction for future studies on disease pathogenesis. In particular, some studies have indicated that base change in m 6 A-sNps lead to alterations in m 6 A modification levels, a conversion from genetics to epigenetics, and the expression variation of corresponding genes, which may affect the biological behavior of cells and explain the association of m 6 A-SNPs with the risk or prognosis of diseases. In bladder cancer, colorectal cancer, coeliac disease, and pancreatic ductal adenocarcinoma, the overexpression of a specific allele alone can significantly modify the function of corresponding genes. On the whole, m 6 A-SNPs play a pivotal role in all stages of diseases. In the future, the identification of m 6 A-SNPs as disease biomarkers and ascertaining the functions of these m 6 A-SNPs may prove beneficial. This would help to identify susceptible individuals in a timely manner and clarify the roles of corresponding genes in the occurrence and progression of diseases, and would also aid in the development of novel treatment strategies, ultimately improving patients' survival. Contents 1. Introduction 2. Data mining of genome-wide association studies 3. Combined analysis of the m6Avar database and eQTLs 4. Effects and mechanisms of m 6 A sNps 5. Conclusion

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“… 6 Oral ulcers are characterized by inflammatory and ulcerative lesions involving the stimulation of various inflammatory cells, metabolic enzymes, and cytokines. 7 Taylor et al studied the peripheral blood of patients with RAU during attacks and intermittent periods and found that the content of TNF-α produced by white blood cells in patients was significantly increased during attacks. 8 Shen et al also found that the levels of IL-6 and TNF-α in serum of RAS patients were significantly increased, indicating that the occurrence and development of oral ulcers were related to the level of inflammatory response.…”

Section: Introductionmentioning

confidence: 99%

Recombinant Humanized Collagen Type XVII Promotes Oral Ulcer Healing via Anti-Inflammation and Accelerate Tissue Healing

Hao,

Zhao,

et al. 2024

JIR

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Introduction Recombinant humanized collagen, as a novel biomaterial, exhibits multiple excellent biological functions, such as inhibition of inflammation, promotion of cell proliferation and vascular proliferation, and promotion of tissue healing. However, there is a lack of conclusive evidence regarding the specific role of recombinant humanized collagen type 17 (rhCol 17) in oral ulcer healing. This study explored whether rhCol 17 could promote the proliferation of human gingival fibroblasts (HGFs) and inhibit its inflammation, and whether it could promote the healing of oral ulcers in rats by inhibiting inflammation and accelerating tissue healing. Methods At the cellular level, we investigated the effect of rhCol 17 on the proliferation of (HGFs) by CCK8; HGFs were mixed with lipopolysaccharide (LPS) to investigate the effect of rhCol 17 on HGFs in an inflammatory state. Eighteen adult male Sprague-Dawley rats were randomly distributed into three groups: blank control group, carbomer group (carbomer sprayed only), and rhCol 17 group (carbomer containing rhCol 17 sprayed), 1 time/day. The samples were collected at D3 and D5. At completion, histological staining and PCR were carried out to study its effect on the healing of oral ulcers in rats. Results Through cellular experiments, we found that rhCol 17 possesses good biocompatibility and anti-inflammatory properties, and can effectively promote the proliferation and migration of HGFs, as well as significantly reduce the inflammation level of the cells. The animal experimental results showed that rhCol 17 could significantly reduce the inflammation level, promote collagen deposition and angiogenesis at the ulcer site, thus effectively accelerating the healing of oral ulcers in rats. Conclusion In summary, the collagen sprays containing rhCol 17 have excellent anti-inflammatory effects and could accelerate tissue healing and are expected to provide a new effective treatment for patients with recurrent oral ulcers.

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A genome-wide association analysis: m6A-SNP related to the onset of oral ulcers

Cited by 4 publications

References 55 publications

AI-m6ARS: Machine learning-driven m6A RNA methylation site discovery with integrated sequence, conservation, and geographical descriptors

AI-m6ARS: Machine learning-driven m6A RNA methylation site discovery with integrated sequence, conservation, and geographical descriptors

m6A‑SNP: From genetics to epigenetics (Review)

Recombinant Humanized Collagen Type XVII Promotes Oral Ulcer Healing via Anti-Inflammation and Accelerate Tissue Healing

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