Identification of angiogenesis-related genes and molecular subtypes for psoriasis based on random forest algorithm.

IF 3.4 3区 医学 Q3 IMMUNOLOGY Clinical and experimental immunology Pub Date : 2024-10-16 DOI:10.1093/cei/uxae052
Meng-Jie Zhang, Ting-Ting Xue, Xiao-Ya Fei, Ying Zhang, Ying Luo, Yi Ru, Jing-Si Jiang, Jian-Kun Song, Le Kuai, Yue Luo, Rui-Ping Wang, Bin Li
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Abstract

Psoriasis is a chronic immune-mediated recurrent skin disease causing systemic damage. Increased angiogenesis has been reported to participate in the progression of psoriasis. However, angiogenesis-related genes (ARGs) in psoriasis have not been systematically elucidated. Therefore, we aim to identify potential biomarkers and subtypes using two algorithmsr. Transcriptome sequencing data of patients with psoriasis were obtained, in which differentially expressed genes were assessed by principal component analysis. A diagnostic model was developed using random forest algorithm and validated by receiver operating characteristic (ROC) curves. Subsequently, we performed consensus clustering to calculate angiogenesis-associated molecular subtypes of psoriasis. Additionally, a correlation analysis was conducted between ARGs and immune cell infiltration. Finally, validation of potential ARG genes was performed by quantitative real-time PCR (qRT-PCR). We identified 29 differentially expressed ARGs, including 13 increased and 16 decreased. Ten ARGs, CXCL8, ANG, EGF, HTATIP2, ANGPTL4, TNFSF12, RHOB, PML, FOXO4, and EMCN were subsequently sifted by the diagnostic model based on a random forest algorithm. Analysis of the ROC curve (area under the curve [AUC] = 1.0) indicated high diagnostic performance in internal validation. The correlation analysis suggested that CXCL8 has a high positive correlation with neutrophil (R =0.8, P < 0.0001) and interleukins pathway (R = 0.79, P < 0.0001). Furthermore, two ARG-mediated subtypes were obtained, indicating potential heterogeneity. Finally, the qRT-PCR demonstrated that the mRNA expression levels of CXCL8 and ANGPTL4 were elevated in psoriasis patients, with a reduced expression of EMCN observed. The current paper indicated potential ARG-related biomarkers of psoriasis, including CXCL8, ANGPTL4, and EMCN, with two molecular subtypes.

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基于随机森林算法的银屑病血管生成相关基因和分子亚型鉴定
银屑病是一种由免疫介导的慢性复发性皮肤病,会造成全身性损害。据报道,血管生成增加参与了银屑病的进展。然而,银屑病中的血管生成相关基因(ARGs)尚未得到系统阐明。因此,我们旨在利用两种算法确定潜在的生物标志物和亚型。我们获得了银屑病患者的转录组测序数据,并通过主成分分析(PCA)对其中的差异表达基因进行了评估。使用随机森林算法(ntree=400)建立了诊断模型,并通过 ROC 曲线进行了验证。随后,我们进行了共识聚类,计算出与血管生成相关的银屑病分子亚型。此外,我们还进行了 ARG 与免疫细胞浸润之间的相关性分析。最后,通过 qRT-PCR 对潜在的 ARG 基因进行了验证。我们确定了 29 个差异表达的 ARGs,包括 13 个增加的 ARGs 和 16 个减少的 ARGs。随后,基于随机森林算法的诊断模型筛选出了 10 个 ARGs,即 CXCL8、ANG、EGF、HTATIP2、ANGPTL4、TNFSF12、RHOB、PML、FOXO4 和 EMCN。ROC 曲线分析(曲线下面积 [AUC] = 1.0)表明,内部验证的诊断性能很高。相关性分析表明,CXCL8 与中性粒细胞呈高度正相关(R =0.8,P<0.05)。
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来源期刊
CiteScore
8.40
自引率
2.20%
发文量
101
审稿时长
3-8 weeks
期刊介绍: Clinical & Experimental Immunology (established in 1966) is an authoritative international journal publishing high-quality research studies in translational and clinical immunology that have the potential to transform our understanding of the immunopathology of human disease and/or change clinical practice. The journal is focused on translational and clinical immunology and is among the foremost journals in this field, attracting high-quality papers from across the world. Translation is viewed as a process of applying ideas, insights and discoveries generated through scientific studies to the treatment, prevention or diagnosis of human disease. Clinical immunology has evolved as a field to encompass the application of state-of-the-art technologies such as next-generation sequencing, metagenomics and high-dimensional phenotyping to understand mechanisms that govern the outcomes of clinical trials.
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