Most B cell precursor acute lymphoblastic leukemia (BCP ALL) can be classified into known major genetic subtypes, while a substantial proportion of BCP ALL remains poorly characterized in relation to its underlying genomic abnormalities. We therefore initiated a large-scale international study to reanalyze and delineate the transcriptome landscape of 1,223 BCP ALL cases using RNA sequencing. Fourteen BCP ALL gene expression subgroups (G1 to G14) were identified. Apart from extending eight previously described subgroups (G1 to G8 associated with MEF2D fusions, TCF3–PBX1 fusions, ETV6–RUNX1–positive/ETV6–RUNX1–like, DUX4 fusions, ZNF384 fusions, BCR–ABL1/Ph–like, high hyperdiploidy, and KMT2A fusions), we defined six additional gene expression subgroups: G9 was associated with both PAX5 and CRLF2 fusions; G10 and G11 with mutations in PAX5 (p.P80R) and IKZF1 (p.N159Y), respectively; G12 with IGH–CEBPE fusion and mutations in ZEB2 (p.H1038R); and G13 and G14 with TCF3/4–HLF and NUTM1 fusions, respectively. In pediatric BCP ALL, subgroups G2 to G5 and G7 (51 to 65/67 chromosomes) were associated with low-risk, G7 (with ≤50 chromosomes) and G9 were intermediate-risk, whereas G1, G6, and G8 were defined as high-risk subgroups. In adult BCP ALL, G1, G2, G6, and G8 were associated with high risk, while G4, G5, and G7 had relatively favorable outcomes. This large-scale transcriptome sequence analysis of BCP ALL revealed distinct molecular subgroups that reflect discrete pathways of BCP ALL, informing disease classification and prognostic stratification. The combined results strongly advocate that RNA sequencing be introduced into the clinical diagnostic workup of BCP ALL.

Understanding the complexity and dynamics of cancer cells in response to effective therapy requires hypothesis-driven, quantitative, and high-throughput measurement of genes and proteins at both spatial and temporal levels. This study was designed to gain insights into molecular networks underlying the clinical synergy between retinoic acid (RA) and arsenic trioxide (ATO) in acute promyelocytic leukemia (APL), which results in a high-quality disease-free survival in most patients after consolidation with conventional chemotherapy. We have applied an approach integrating cDNA microarray, 2D gel electrophoresis with MS, and methods of computational biology to study the effects on APL cell line NB4 treated with RA, ATO, and the combination of the two agents and collected in a time series. Numerous features were revealed that indicated the coordinated regulation of molecular networks from various aspects of granulocytic differentiation and apoptosis at the transcriptome and proteome levels. These features include an array of transcription factors and cofactors, activation of calcium signaling, stimulation of the IFN pathway, activation of the proteasome system, degradation of the PML-RAR␣ oncoprotein, restoration of the nuclear body, cell-cycle arrest, and gain of apoptotic potential. Hence, this investigation has provided not only a detailed understanding of the combined therapeutic effects of RA͞ATO in APL but also a road map to approach hematopoietic malignancies at the systems level.systems biology ͉ self-organizing map A cute promyelocytic leukemia (APL) is a form of acute myeloid leukemia that responds remarkably to the effect of differentiation-induction by all-trans-retinoic acid and the differentiation͞ apoptosis-inducing effect of arsenic trioxide (ATO). Cytogenetically, a translocation t(15;17)(q22;q21) is found in most APL patients, resulting in the formation of the promyelocytic leukemiaretinoic acid receptor ␣ (PML-RAR␣) fusion gene (1). The chimeric protein encoded by the fusion gene oligomerizes with retinoid-X receptor (RXR) and disrupts the retinoic acid (RA) signal pathway, which is essential for granulocytic differentiation. PML-RAR␣ can also form a homodimer that competes with RAR␣ for binding to the RA-response elements of target genes and binds to the corepressor (CoR) complex with a much higher affinity than does the wild-type RAR␣͞RXR. This change leads to transcriptional repression under physiological concentrations of RA and, thus, blocks cell differentiation. Pharmacological concentrations of RA can convert the PML-RAR␣ fusion protein from a transcription repressor to a transcription activator, resulting in the release of the CoR and the recruitment of a coactivator (CoA) complex. The RA treatment can also trigger degradation of the PML-RAR␣ protein via the ubiquitin͞proteasome (U͞P) pathway and, thus, trigger reassembly of the nuclear body (NB) (2). On the other hand, ATO induces partial differentiation and͞or apoptosis of APL cells in a dose-dependent manner. Importantly, cellular and m...