Reproducibility of Gene Expression Signatures in Diffuse Large B-Cell Lymphoma

• Published in: Cancers Vol. 14; no. 5; p. 1346
• Main Authors: Plaça, Jessica Rodrigues, Diepstra, Arjan, Los, Tjitske, Mendeville, Matías, Seitz, Annika, Lugtenburg, Pieternella J, Zijlstra, Josée, Lam, King, da Silva, Jr, Wilson Araújo, Ylstra, Bauke, de Jong, Daphne, van den Berg, Anke, Nijland, Marcel
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 05-03-2022; MDPI
• Subjects: Algorithms; B-cell lymphoma; B-cell receptor; Biopsy; Chemotherapy; Classification; Clinical trials; Gene expression; Immune response; Lymphocytes B; Lymphoma; Myc protein; Oxidative phosphorylation; Patients; Phosphorylation; Reproducibility; United States > US; reproducibility; gene expression profiles; diffuse large B-cell lymphoma
• ISSN: 2072-6694; 2072-6694
• DOI: 10.3390/cancers14051346

Multiple gene expression profiles have been identified in diffuse large B-cell lymphoma (DLBCL). Besides the cell of origin (COO) classifier, no signatures have been reproduced in independent studies or evaluated for capturing distinct aspects of DLBCL biology. We reproduced 4 signatures in 175 samples of the HOVON-84 trial on a panel of 117 genes using the NanoString platform. The four gene signatures capture the COO, MYC activity, B-cell receptor signaling, oxidative phosphorylation, and immune response. Performance of our classification algorithms were confirmed in the original datasets. We were able to validate three of the four GEP signatures. The COO algorithm resulted in 94 (54%) germinal center B-cell (GCB) type, 58 (33%) activated B-cell (ABC) type, and 23 (13%) unclassified cases. The MYC-classifier revealed 77 cases with a high MYC-activity score (44%) and this MYC-high signature was observed more frequently in ABC as compared to GCB DLBCL (68% vs. 32%, p < 0.00001). The host response (HR) signature of the consensus clustering was present in 55 (31%) patients, while the B-cell receptor signaling, and oxidative phosphorylation clusters could not be reproduced. The overlap of COO, consensus cluster and MYC activity score differentiated six gene expression clusters: GCB/MYC-high (12%), GCB/HR (16%), GCB/non-HR (27%), COO-Unclassified (13%), ABC/MYC-high (25%), and ABC/MYC-low (7%). In conclusion, the three validated signatures identify distinct subgroups based on different aspects of DLBCL biology, emphasizing that each classifier captures distinct molecular profiles.