OSdlbcl: An online consensus survival analysis web server based on gene expression profiles of diffuse large B‐cell lymphoma

Abstract

Diffuse large B‐cell lymphoma (DLBCL) is the most common subtype of non‐Hodgkin lymphoma (NHL) and is a clinical, pathological, and molecular heterogeneous disease with highly variable clinical outcomes. Currently, valid prognostic biomarkers in DLBCL are still lacking. To optimize targeted therapy and improve the prognosis of DLBCL, the performance of proposed biomarkers needs to be evaluated in multiple cohorts, and new biomarkers need to be investigated in large datasets. Here, we developed a consensus Online Survival analysis web server for Diffuse Large B‐Cell Lymphoma, abbreviated OSdlbcl, to assess the prognostic value of individual gene. To build OSdlbcl, we collected 1100 samples with gene expression profiles and clinical follow‐up information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. In addition, DNA mutation data were also collected from the TCGA database. Overall survival (OS), progression‐free survival (PFS), disease‐specific survival (DSS), disease‐free interval (DFI), and progression‐free interval (PFI) are important endpoints to reflect the survival rate in OSdlbcl. Moreover, clinical features were integrated into OSdlbcl to allow data stratifications according to the user's special needs. By inputting an official gene symbol and selecting desired criteria, the survival analysis results can be graphically presented by the Kaplan‐Meier (KM) plot with hazard ratio (HR) and log‐rank p value. As a proof‐of‐concept demonstration, the prognostic value of 23 previously reported survival associated biomarkers, such as transcription factors FOXP1 and BCL2, was evaluated in OSdlbcl and found to be significantly associated with survival as reported (HR = 1.73, P < .01; HR = 1.47, P = .03, respectively). In conclusion, OSdlbcl is a new web server that integrates public gene expression, gene mutation data, and clinical follow‐up information to provide prognosis evaluations for biomarker development for DLBCL. The OSdlbcl web server is available at https://bioinfo.henu.edu.cn/DLBCL/DLBCLList.jsp.

The dual role of CD70 in B‐cell lymphomagenesis

“…The impact of CD70 expression on DLBCL survival was further explored in the gene expression omnibus (GEO) and TCGA databases. High CD70 mRNA expression was also associated with shorter OS in a rituximab‐containing regimen‐treated DLBCL cohort (GSE117556) 38 and TCGA DLBCL cohort (dbGaP Study Accession: phs000178 39 ; figure generated by online OSDLBCL tool 40 ) (Figure 6F,G ).…”

Fbxl8 suppresses lymphoma growth and hematopoietic transformation through degradation of cyclin D3

“…Patient samples with low, medium, or high expression of cyclin D3 have high, medium, or low expression of Fbxl8, respectively, underscoring Fbxl8 negatively regulates cyclin D3 expression in human lymphomas in a dose dependent manner. We further used a recently developed online tool to assess the lymphoma patients’ overall survival with gene expression [ 23 ], and observed that the low expression of Fbxl8 mRNA significantly correlated with reduced overall survival for lymphoma patients while the expression of cyclin D3 mRNA does not (Fig. 7c ).…”

Ubiquitylation of unphosphorylated c-myc by novel E3 ligase SCFFbxl8

“… 29 Kaplan–Meier analysis wsas derived from the TCGA database for DLBCL and generated by the OSdlbcl webserver. 30 Kaplan–Meier analysis for UCEC was derived from the TCGA database and generated by the UALCAN web platform. 31 Alterations of Cyclin D3 in UCEC data were derived from TCGA database and generated by the cBio Cancer Genomics Portal platform.…”