Analysis and prognostic significance of tumour immune infiltrates and immune microenvironment of m6A-related lncRNAs in patients with gastric cancer

Huang, Jingmin; Song, Jinxuan; Li, xiangyu; Liu, Shuangfei; Huang, Wentao; Shen, Ziyi; Cheng, Yan; Kou, Shien; Gao, Zhenguo; Tian, Yunhong; Hu, Jiani

doi:10.1186/s12920-022-01318-5

Cited by 8 publications

(3 citation statements)

References 38 publications

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“…In our data neither miRNA was present the common regulators of the protein-coding transcripts of the radiation-responsive modules, very well keeping in mind that we examined healthy tissues, these patterns might be cancer-specific. Additionally, TYMSOS was used in a prognostic model as one of thirteen lncRNAs related to M6A regulators, a certain type of mRNA modification, that is also of importance in cancer ( 64 ), as one of 18 immune-related lncRNAs for clinical prediction in head and neck squamous cell carcinoma due to its potential to modulate tumor microenvironment ( 65 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

et al. 2023

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IntroductionLong non-coding ribonucleic acids (lncRNAs) are involved in the cellular damage response following exposure to ionizing radiation as applied in radiotherapy. However, the role of lncRNAs in radiation response concerning intrinsic susceptibility to late effects of radiation exposure has not been examined in general or in long-term survivors of childhood cancer with and without potentially radiotherapy-related second primary cancers, in particular.MethodsPrimary skin fibroblasts (n=52 each) of long-term childhood cancer survivors with a first primary cancer only (N1), at least one second primary neoplasm (N2+), as well as tumor-free controls (N0) from the KiKme case-control study were matched by sex, age, and additionally by year of diagnosis and entity of the first primary cancer. Fibroblasts were exposed to 0.05 and 2 Gray (Gy) X-rays. Differentially expressed lncRNAs were identified with and without interaction terms for donor group and dose. Weighted co-expression networks of lncRNA and mRNA were constructed using WGCNA. Resulting gene sets (modules) were correlated to the radiation doses and analyzed for biological function.ResultsAfter irradiation with 0.05Gy, few lncRNAs were differentially expressed (N0: AC004801.4; N1: PCCA-DT, AF129075.3, LINC00691, AL158206.1; N2+: LINC02315). In reaction to 2 Gy, the number of differentially expressed lncRNAs was higher (N0: 152, N1: 169, N2+: 146). After 2 Gy, AL109976.1 and AL158206.1 were prominently upregulated in all donor groups. The co-expression analysis identified two modules containing lncRNAs that were associated with 2 Gy (module1: 102 mRNAs and 4 lncRNAs: AL158206.1, AL109976.1, AC092171.5, TYMSOS, associated with p53-mediated reaction to DNA damage; module2: 390 mRNAs, 7 lncRNAs: AC004943.2, AC012073.1, AC026401.3, AC092718.4, MIR31HG, STXBP5-AS1, TMPO-AS1, associated with cell cycle regulation).DiscussionFor the first time, we identified the lncRNAs AL158206.1 and AL109976.1 as involved in the radiation response in primary fibroblasts by differential expression analysis. The co-expression analysis revealed a role of these lncRNAs in the DNA damage response and cell cycle regulation post-IR. These transcripts may be targets in cancer therapy against radiosensitivity, as well as provide grounds for the identification of at-risk patients for immediate adverse reactions in healthy tissues. With this work we deliver a broad basis and new leads for the examination of lncRNAs in the radiation response.

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Section: Discussionmentioning

confidence: 99%

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

et al. 2023

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“…The heatmap of the correlation between the model genes and immune cells in this study showed a significant positive correlation between disulfidptosis PLS3 and resting mast cells ( P < 0.001). Indeed, previous studies have found a correlation between resting mast cells and GC[ 104 , 105 ], and it has been suggested that PLS3 [ 106 ] may also be related to GC. Through the analysis of TME differences in the prognosis model, we found differences in the Stromal Score and ESTIMATE Score in the high- and low-risk groups, with both scores found to be upregulated in the high-risk group, indicating that the risk score of the prognosis model is related to the TME of GC.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive analysis of disulfidptosis related genes and prognosis of gastric cancer

Li,

Yin

2023

World J Clin Oncol

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BACKGROUND Gastric cancer (GC) is a common malignant tumor of the digestive system. Disulfidptosis is a new programmed cell death mechanism, although its specific mechanism in GC is incompletely understood. AIM In this study, we used bioinformatics analysis to explore a disulfidptosis-based predictive model related to GC prognosis and to identify potential therapeutic targets and sensitive drugs for GC. METHODS We extracted GC-related data from The Cancer Genome Atlas and Gene Expression Omnibus databases. R software (version 4.2.1) was used for correlation analysis. RESULTS Through the above analysis, we found that the disulfidptosis related gene may be related to the prognosis of GC. Six genes, namely, PLS3 , GRP , APOD , SGCE , COL8A1 , and VAMP7 , were found to constitute a predictive model for GC prognosis. APOD is a potential therapeutic target for treating GC. Bosutinib and other drugs are sensitive for the treatment of GC. CONCLUSION The results of this study indicate that disulfidptosis is related to the prognosis and treatment of GC, while APOD represents a potential therapeutic target for GC.

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“…m6A controls cellular proliferation and maturation, both of which are linked to cancer genesis ( 13 ). Evidence shows that abnormal m6A methylation may promote cancer development by upregulating oncogenes and suppressing tumor suppressor genes and that m6A RNA methylation can be altered by the expression of m6A regulators and the activity of m6A enzymes, further impacting tumor progression ( 25 ). Based on the interactions of m6A regulators in STAD, the tendencies of m6A readers, writers, and erasers were determined.…”

Section: Discussionmentioning

confidence: 99%

Constructing and validating of m6a-related genes prognostic signature for stomach adenocarcinoma and immune infiltration: Potential biomarkers for predicting the overall survival

Yang

et al. 2022

Front. Oncol.

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BackgroundStomach adenocarcinoma (STAD) arises from the mutations of stomach cells and has poor overall survival. Chemotherapy is commonly indicated for patients with stomach cancer following surgical resection. The most prevalent alteration that affects cancer growth is N6-methyladenosine methylation (m6A), although the possible function of m6A in STAD prognosis is not recognized.MethodThe research measured predictive FRGs in BLCA samples from the TCGA and GEO datasets. Data on the stemness indices (mRNAsi), gene mutations, copy number variations (CNV), tumor mutation burden (TMB), and corresponding clinical characteristics were obtained from TCGA and GEO. STAD from TCGA and GEO at 24 m6A was investigated. Lasso regression was used to construct the prediction model to assess the m6A prognostic signals in STAD. In addition, the correlation between m6a and immune infiltration in STAD patients was discussed using GSVA and ssGSEA analysis. Based on these genes, GO and KEGG analyses were performed to identify key biological functions and key pathways.ResultA significant relationship was discovered between numerous m6A clusters and the tumor immune microenvironment, as well as three m6A alteration patterns with different clinical outcomes. Furthermore, GSVA and ssGSEA showed that m6A clusters were significantly associated with immune infiltration in the STAD. The low-m6Ascore group had a lower immunotherapeutic response than the high-m6Ascore group. ICIs therapy was more effective in the group with a higher m6Ascore. Three writers (VIRMA, ZC3H13, and METTL3) showed significantly lower expression, whereas five authors (METTL14, METTL16, WTAP, RBM15, and RBM15B) showed considerably higher expression. Three readers (YTHDC2, YTHDF2, and LRPPRC) had higher levels of expression, whereas eleven readers (YTHDC1, YTHDF1, YTHDF3, HNRNPC, FMR1, HNRNPA2B1, IGFBP1, IGFBP2, IGFBP3, and RBMX) had lower levels. As can be observed, the various types of m6 encoders have varied ramifications for STAD control.ConclusionSTAD occurrence and progression are linked to m6A-genes. Corresponding prognostic models help forecast the prognosis of STAD patients. m6A-genes and associated immune cell infiltration in the tumor microenvironment (TME) may serve as potential therapeutic targets in STAD, which requires further trials. In addition, the m6a-related gene signature offers a viable alternative to predict bladder cancer, and these m6A-genes show a prospective research area for STAD targeted treatment in the future.

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Analysis and prognostic significance of tumour immune infiltrates and immune microenvironment of m6A-related lncRNAs in patients with gastric cancer

Cited by 8 publications

References 38 publications

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

Identification of lncRNAs involved in response to ionizing radiation in fibroblasts of long-term survivors of childhood cancer and cancer-free controls

Comprehensive analysis of disulfidptosis related genes and prognosis of gastric cancer

Constructing and validating of m6a-related genes prognostic signature for stomach adenocarcinoma and immune infiltration: Potential biomarkers for predicting the overall survival

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