Identifying tumor antigens and immune subtypes of gastrointestinal MALT lymphoma for immunotherapy development

Jiang, Xinlu; Zhang, Huanhuan; Ni, Jinju; Zhang, Xu; Ding, Kaiyang

doi:10.3389/fonc.2022.1060496

Cited by 11 publications

(9 citation statements)

References 27 publications

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“…In recent years, multiple studies have applied the bioinformatics analysis to evaluate the correlation between environmental toxicity and cancers. As is shown in the previous study, phthalates have been associated with potential negative effects on prostate cancer, and a pharmacological method has been proposed to predict harmful effects ( 27 ). In addition, a former study also discovered that multiple water pollutants were considered to be closely associated with the human diseases, such as colon tumors, breast tumors, hepatitis B, bladder cancer, and human cytomegalovirus infection ( 28 ).…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of triphenyl phosphate: contextual interpretation of bladder cancer cohort

Zhang,

Huang,

Huang

et al. 2023

Front. Oncol.

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In recent years, organophosphate ester flame retardants (OPFRs) have emerged as preferred alternatives to brominated flame retardants (BFRs) in materials such as building supplies, textiles, and furnishings. Simultaneously, a notable surge in bladder cancer incidences has been observed globally, particularly in developed nations, placing it as the 10th most prevalent cancer type. Among the extensive OPFRs, the linkage between triphenyl phosphate (TPP) and bladder cancer remains inadequately investigated. Hence, our study endeavors to elucidate this potential association. We sourced transcriptome profiles and TPP-related data from The Cancer Genome Atlas and Comparative Toxicogenomics databases. Using the ssGSEA algorithm, we established TPP-correlated scores within the bladder cancer cohort. Differentially expressed analysis enabled us to identify key genes in bladder cancer patients. We utilized the LASSO regression analysis, along with univariate and multivariate COX regression analyses to construct a prognostic prediction model. To uncover critical pathways involving key genes, we employed GSEA and GSVA enrichment analyses. Molecular docking analysis was performed to determine the binding capability between TPP and proteins. Our findings reveal that the TPP-centric risk model offers valuable prediction for bladder cancer cohorts. Furthermore, the reliability of this TPP-influenced risk model was verified through ROC curve analysis and survival studies. Intriguingly, TPP exposure appears to bolster the proliferation and invasiveness of bladder cancer cells. This study furnishes new insights into the possible benefits of minimizing TPP exposure for hindering bladder cancer progression.

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Section: Discussionmentioning

confidence: 99%

Integrative analysis of triphenyl phosphate: contextual interpretation of bladder cancer cohort

Zhang,

Huang,

Huang

et al. 2023

Front. Oncol.

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“…In a previous study, pharmacological techniques and omics databases were used to predict the potentially harmful effects of hazardous substances The effects of dibutyl phthalate on prostate cancer are possibly androgen-independent at low concentrations, so androgen-deprivation therapy patients may be exposed to this chemical ( 20 ). In another study, an online database provided a rationale for mRNA vaccine development and suggested that KLHL14 might serve as an antigen for the development of mRNA vaccines in MALT lymphoma patients ( 21 ).…”

Section: Discussionmentioning

confidence: 99%

“…Firstly, the different methods used in the bioinformatics analysis may lead to the bias ( 27 ). In addition, the application of the biomarkers in the clinical diagnosis, treatment and diagnosis requires the further validation ( 20 , 21 ). Also, multiple studies are also very important to further validate the role of risk model in the OCSS cohort ( 28 , 29 ).…”

Section: Discussionmentioning

confidence: 99%

Single-cell RNA sequencing and traditional RNA sequencing reveals the role of cancer-associated fibroblasts in oral squamous cell carcinoma cohort

Yang

She

et al. 2023

Front. Oncol.

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Chronic inflammation of the alveolar bones and connective tissues supporting teeth causes periodontal disease, one of the most prevalent infectious diseases in humans. It was previously reported that oral cancer was the sixth most common cancer in the world, followed by squamous cell carcinoma. Periodontal disease has been linked to an increased risk for oral cancer in some studies, and these studies have found a positive relationship between oral cancer and periodontal disease. In this work, we aimed to explore the potential correlation between oral squamous cell carcinoma (OSCC) and Periodontal disease. The single-cell RNA sequence analysis was applied to explore the genes that were closely associated with cancer-associated fibroblasts (CAFs). the head and neck squamous cell carcinoma. The Single sample Gene Set Enrichment Analysis (ssGSEA) algorithm was applied to explore the scores of CAFs. Subsequently, the differentially expressed analysis was applied to explore the CAFs-related genes that play a key role in the OSCC cohort. The LASSO regression analysis and the COX regression analysis were applied to construct the CAFs-based periodontal disease-related risk model. In addition, the correlation analysis was used to explore the correlation between the risk model and clinical features, immune-related cells, and immune-related genes. By using the single-cell RNA sequence analysis, we successfully obtained the biomarkers for the CAFs. Finally, we successfully obtained a six-CAFs-related genes risk model. The ROC curve and survival analysis revealed that the risk model showed good predictive value in OSCC patients. Our analysis successfully provided a new direction for the treatment and prognosis of OSCC patients.

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“…Based on the molecular signatures database (version 7.0), gene sets were retrieved. In order to evaluate potential biological function changes, various samples were evaluated using the GSVA algorithm [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

“…In recent years, with the quick development of bioinformatics analysis, in silico analysis has been widely taken into consideration for the analysis of the etiology, prevention, and prognostic prediction [13][14][15]. In this work, the aim is to explore the genes that play a key role in the occurrence of OA.…”

Section: Introductionmentioning

confidence: 99%

The Identification of Immune-Related Biomarkers for Osteoarthritis Immunotherapy Based on Single-Cell RNA Sequencing Analysis

et al. 2023

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Osteoarthritis (OA) is a chronic musculoskeletal disease affecting approximately 500 million people worldwide. Globally, OA is one of the most common and leading causes of disability. Several genetic factors are involved in OA, including inherited genes, genetic susceptibility, and genetic predisposition. As the pathogenesis of OA is unknown, there are almost no effective treatments available to prevent the onset or progression of the disease. In recent years, many researchers focused on bioinformatics analysis to explore new biomarkers for the diagnosis, treatment, and prognosis of human diseases. In this work, we obtain the traditional RNA sequencing data of OA patients from the GEO database. By performing the differentially expressed analysis, we successfully obtain the genes that are closely associated with the OA. In addition, the Venn diagram was applied to evaluate the genes that are involved in OA and immune-related genes. The protein-protein interaction analysis was further conducted to explore the hub genes. The single-cell RNA sequencing analysis was used to evaluate the expression distribution of the MMP, VEGFA, SPI1, and IRF8 in synovial tissues of patients with osteoarthritis. Finally, the GSVA enrichment analysis discovered the potential pathways involved in OA patients. Our analysis provides a new direction for the exploration of the process of OA patients. In addition, VEGFA may be considered a promising biomarker in OA.

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Identifying tumor antigens and immune subtypes of gastrointestinal MALT lymphoma for immunotherapy development

Cited by 11 publications

References 27 publications

Integrative analysis of triphenyl phosphate: contextual interpretation of bladder cancer cohort

Integrative analysis of triphenyl phosphate: contextual interpretation of bladder cancer cohort

Single-cell RNA sequencing and traditional RNA sequencing reveals the role of cancer-associated fibroblasts in oral squamous cell carcinoma cohort

The Identification of Immune-Related Biomarkers for Osteoarthritis Immunotherapy Based on Single-Cell RNA Sequencing Analysis

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