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N. Oishi et al.
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Figure 4. Gene signatures associated with hypoxia and CA9 expression in breast implant-associated anaplastic large cell lymphoma cells. (A) CA9 mRNA expres- sion is induced by hypoxia and inhibited by CA9 siRNA in TLBR-2 breast implant-associated (BIA) anaplastic large cell lymphoma (ALCL) cells. RPKM: reads per kilo- base per million mapped reads; ****P<0.0001. (B) Heatmap showing relative gene expression in TLBR-2 for each of the three conditions shown in panel A. RNA sequencing was performed in triplicate for each condition. (C) Top panel: TLBR-2 cells cultured under hypoxic conditions show significant enrichment for the set of genes overexpressed in BIA- versus non-BIA-ALCL tissue samples (“tissue-derived gene set,” defined as log2FC >1 and FDR ≤0.05; cf. Figure 1A). Middle panel: the HALLMARK HYPOXIA gene set identified by gene set enrichment analysis in BIA- versus non-BIA-ALCL tissue samples is also significantly enriched in hypoxic TLBR- 2 cells. See also Online Supplementary Table S2. Bottom panel: hypoxic TLBR-2 cells treated with CA9 siRNA show marked depletion of REACTOME S PHASE and other gene sets related to cell cycle and MYC targets. See also Online Supplementary Table S3. FC: fold change; NES: normalized enrichment score; FDR: false dis- covery rate.
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haematologica | 2021; 106(6)