Figure 2.
Novel subtype with high expression of CDX2. (A) Volcano plot comparing expression profiles of cases with CDX2-high subtype (n = 11) and other B-ALL cases (n = 316; including 4 Ph+ ALL). Genes with twofold or greater changes in expression and -log10 (q value) >5 are shown in red. (B) Box plot comparing fragments per kilobase of transcript per million (FPKM) of CDX2 in CDX2-high (n = 11), KMT2A (n = 14), ZNF384 (n = 73), Ph-like (n = 51), TCF3-PBX1 (n = 29), DUX4 (n = 24), MEF2D (n = 17) subtypes, other B-ALL cases (n = 108; including 4 Ph+ ALL), and normal B/T cells (n = 6). P values were calculated using the Wilcoxon rank-sum test. (C) CDX2 mRNA expression normalized to that of ACTB was determined using TaqMan reverse transcription-polymerase chain reaction analysis for CDX2-high ALL (n = 11), AML (n = 9; 3 clinical specimens and 6 cell lines [MV4-11, OCI-AML2, OCI-AML3, MOLM-13, THP-1, and NOMO1]), T-ALL (n = 16), and normal tissues (n = 8; colon, small intestine, brain, thymocytes, kidneys, lungs, liver, and heart). The abundance of CDX2 was further normalized to that of a normal colon. Data are shown as means from 3 independent experiments. (D) Sections of bone marrow (BM) clots immunostained with a CDX2 antibody to determine the expression levels of CDX2. Representative micrographs from specimens derived from 2 cases with CDX2-high subtype (202O-203 [left panel] and 202O-236 [right panel]) at the time of both initial diagnoses and either relapse (202O-203) or complete remission (202O-236) are shown (original magnification ×400). (E) The 323 cases of Ph– B-ALL plus 4 Ph+ ALL cases were clustered according to expression levels of CDX2, HOXA family genes (n = 11), HOXB family genes (n = 10), and MEIS1 using Ward’s correlation algorithms. Information on disease subtypes is shown at the top of the panel. (F) Methylation status of CpG dinucleotides of CDX2 promoter regions from 3 CDX2-high and 3 other B-ALL samples assessed by bisulfite sequencing. Each column represents sequenced clones. Methylated alleles (pink) and unmethylated alleles (blue) at 5 cytosine residues are indicated. HCT116 DKO and HCT116 gDNA were used as controls of unmethylated and methylated DNA, respectively. P values were calculated using Fisher’s exact test.

Novel subtype with high expression of CDX2. (A) Volcano plot comparing expression profiles of cases with CDX2-high subtype (n = 11) and other B-ALL cases (n = 316; including 4 Ph+ ALL). Genes with twofold or greater changes in expression and -log10 (q value) >5 are shown in red. (B) Box plot comparing fragments per kilobase of transcript per million (FPKM) of CDX2 in CDX2-high (n = 11), KMT2A (n = 14), ZNF384 (n = 73), Ph-like (n = 51), TCF3-PBX1 (n = 29), DUX4 (n = 24), MEF2D (n = 17) subtypes, other B-ALL cases (n = 108; including 4 Ph+ ALL), and normal B/T cells (n = 6). P values were calculated using the Wilcoxon rank-sum test. (C) CDX2 mRNA expression normalized to that of ACTB was determined using TaqMan reverse transcription-polymerase chain reaction analysis for CDX2-high ALL (n = 11), AML (n = 9; 3 clinical specimens and 6 cell lines [MV4-11, OCI-AML2, OCI-AML3, MOLM-13, THP-1, and NOMO1]), T-ALL (n = 16), and normal tissues (n = 8; colon, small intestine, brain, thymocytes, kidneys, lungs, liver, and heart). The abundance of CDX2 was further normalized to that of a normal colon. Data are shown as means from 3 independent experiments. (D) Sections of bone marrow (BM) clots immunostained with a CDX2 antibody to determine the expression levels of CDX2. Representative micrographs from specimens derived from 2 cases with CDX2-high subtype (202O-203 [left panel] and 202O-236 [right panel]) at the time of both initial diagnoses and either relapse (202O-203) or complete remission (202O-236) are shown (original magnification ×400). (E) The 323 cases of Ph– B-ALL plus 4 Ph+ ALL cases were clustered according to expression levels of CDX2, HOXA family genes (n = 11), HOXB family genes (n = 10), and MEIS1 using Ward’s correlation algorithms. Information on disease subtypes is shown at the top of the panel. (F) Methylation status of CpG dinucleotides of CDX2 promoter regions from 3 CDX2-high and 3 other B-ALL samples assessed by bisulfite sequencing. Each column represents sequenced clones. Methylated alleles (pink) and unmethylated alleles (blue) at 5 cytosine residues are indicated. HCT116 DKO and HCT116 gDNA were used as controls of unmethylated and methylated DNA, respectively. P values were calculated using Fisher’s exact test.

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