The RNA sequencing (RNASeq) data for U937 cells deposited in Gene Expression Omnibus (accession number GSE229032) contained a BCR::ABL1 translocation characteristic of K562 cells. The authors researched the issue and found that the U937 RNA sample in question had derived from an older ATCC-derived stock that was contaminated with K562 cells. The RNASeq deposit has been corrected to replace the contaminated sample of U937 cells with an uncontaminated sample.
Page 1138: In the right column, the sentence “For the cell lines and primary samples with sphingolipidomics, we identified 734 increased transcripts in HexlowSMhigh and 1125 increased transcripts in HexhighSMlow (Figure 2C; supplemental Table 7), including 6 enzymes with complex roles in sphingolipid metabolism (UGCG, FUT4, NAGA, SMPD3, GANC, and B3GALT1 are discussed in supplemental Table 8)” should read “For the cell lines and primary samples with sphingolipidomics, we identified 708 increased transcripts in HexlowSMhigh and 1127 increased transcripts in HexhighSMlow (Figure 2C; supplemental Table 7), including 5 enzymes with complex roles in sphingolipid metabolism (UGCG, FUT4, NAGA, SMPD3, and FUT1 are discussed in supplemental Table 8).”
The HexlowSMhigh and HexhighSMlow AML subtypes differ in gene expression and survival outcome. (C) Volcano plot of differentially expressed genes between the HexlowSMhigh and HexhighSMlow subtypes. Purple genes are upregulated in the HexlowSMhigh cluster whereas green genes are upregulated in the HexhighSMlow cluster (−log10Padj >1). (D) The HexlowSMhigh subtype is enriched for the LSC program. Gene set enrichment analysis score plot for an LSC signature of 104 genes.14 The y-axis is the running enrichment score along the ranked gene list. The enrichment score is the maximum deviation from 0 encountered along the list and represents the degree to which a gene set is overrepresented at the top or the bottom of the ranked gene list. The normalized enrichment score (NES) is the enrichment score normalized for variation in gene set sizes. The adjusted P-value (Padj) for the NES is shown. (I) An RNASeq-based classifier accurately distinguishes sphingolipidomic subtypes. Receiver operating characteristics curve for a 284-gene support vector machine classifier applied to test data that includes both primary AML samples and cell lines with paired RNASeq and sphingolipidomic data. The area under the curve (AUC), its 95% confidence interval in brackets, and the 1-sided binomial test P-value (Pbinom) of the classifier are shown.
The HexlowSMhigh and HexhighSMlow AML subtypes differ in gene expression and survival outcome. (C) Volcano plot of differentially expressed genes between the HexlowSMhigh and HexhighSMlow subtypes. Purple genes are upregulated in the HexlowSMhigh cluster whereas green genes are upregulated in the HexhighSMlow cluster (−log10Padj >1). (D) The HexlowSMhigh subtype is enriched for the LSC program. Gene set enrichment analysis score plot for an LSC signature of 104 genes.14 The y-axis is the running enrichment score along the ranked gene list. The enrichment score is the maximum deviation from 0 encountered along the list and represents the degree to which a gene set is overrepresented at the top or the bottom of the ranked gene list. The normalized enrichment score (NES) is the enrichment score normalized for variation in gene set sizes. The adjusted P-value (Padj) for the NES is shown. (I) An RNASeq-based classifier accurately distinguishes sphingolipidomic subtypes. Receiver operating characteristics curve for a 284-gene support vector machine classifier applied to test data that includes both primary AML samples and cell lines with paired RNASeq and sphingolipidomic data. The area under the curve (AUC), its 95% confidence interval in brackets, and the 1-sided binomial test P-value (Pbinom) of the classifier are shown.
Page 1139: In Figure 2, panels C, D, and I needed revision to reflect the change in GSE229032. The corrected Figure 2C, D, and I are shown below.
Supplemental Data: Supplemental Figure 3C-H and supplemental Tables 7 and 8 are revised to reflect the change in GSE229032. In addition, the resolution of supplemental Figures 1, 3, and 4 has been improved. The corrected supplemental files are available in the online version of this erratum.
None of these changes impact the conclusions or scientific validity of the study.
