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pmid:36816541
A prognostic 15-gene model based on differentially expressed genes among metabolic subtypes in diffuse large B-cell lymphoma.
Jun Hou · Peng Guo · Yujiao Lu · Xiaokang Jin · Ke Liang · Na Zhao · Shunxu Xue · Chengmin Zhou · Guoqiang Wang · Xin Zhu · Huangming Hong · Yungchang Chen · Huafei Lu · Wenxian Wang · Chunwei Xu · Yusheng Han · Shangli Cai · Yang Liu
Pathology oncology research : POR · 2023 doi:10.3389/pore.2023.1610819
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Complete file
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Here, we aim to construct a prognostic model based on the genetic signature of metabolic heterogeneity of DLBCL to explore therapeutic strategies for DLBCL patients. Clinical and transcriptomic data of one training and four validation cohorts of DLBCL were obtained from the GEO database. Metabolic subtypes were identified by PAM clustering of 1,916 metabolic genes in the 7 major metabolic pathways in the training cohort. DEGs among the metabolic clusters were then analyzed. In total, 108 prognosis-related DEGs were identified. Through univariable Cox and LASSO regression analyses, 15 DEGs were used to construct a risk score model. The overall survival (OS) and progression-free survival (PFS) of patients with high risk were significantly worse than those with low risk (OS: HR 2.86, 95%CI 2.04-4.01, p < 0.001; PFS: HR 2.42, 95% CI 1.77-3.31, p < 0.001). This model was also associated with OS in the four independent validation datasets (GSE10846: HR 1.65, p = 0.002; GSE53786: HR 2.05, p = 0.02; GSE87371: HR 1.85, p = 0.027; GSE23051: HR 6.16, p = 0.007) and PFS in the two validation datasets (GSE87371: HR 1.67, p = 0.033; GSE23051: HR 2.74, p = 0.049). Multivariable Cox analysis showed that in all datasets, the risk model could predict OS independent of clinical prognosis factors (p < 0.05). Compared with the high-risk group, patients in the low-risk group predictively respond to R-CHOP (p = 0.0042), PI3K inhibitor (p < 0.05), and proteasome inhibitor (p < 0.05). 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"basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: mann_whitney."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE31312", "GSE10846", "GSE53786", "GSE87371", "GSE23501", "GSE23051"], "resolved_accessions": ["GSE31312", "GSE10846", "GSE53786", "GSE87371", "GSE23501", "GSE23051"], "statements": ["The datasets generated and analyzed in the present study are available in the public data repository, GEO: https://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE31312, GSE10846, GSE53786, GSE87371, GSE23501, GSE23051 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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