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Supplementary Fig. 5. Kaplan-Meier analysis of the survival of patients with different mutations.

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Current standard of care for patients with pediatric acute lymphoblastic leukemia (ALL) is mainly effective, with high remission rates after treatment. However, the genetic perturbations that give rise to this disease remain largely undefined, limiting the ability to address resistant tumors or develop less toxic targeted therapies. Here, we report the use of next-generation sequencing to interrogate the genetic and pathogenic mechanisms of 240 pediatric ALL cases with their matched remission samples. Commonly mutated genes fell into several categories, including RAS/receptor tyrosine kinases, epigenetic regulators, transcription factors involved in lineage commitment, and the p53/cell-cycle pathway. Unique recurrent mutational hotspots were observed in epigenetic regulators CREBBP (R1446C/H), WHSC1 (E1099K), and the tyrosine kinase FLT3 (K663R, N676K). The mutant WHSC1 was established as a gain-of-function oncogene, while the epigenetic regulator ARID1A and transcription factor CTCF were functionally identified as potential tumor suppressors. Analysis of 28 diagnosis/relapse trio patients plus 10 relapse cases revealed four evolutionary paths and uncovered the ordering of acquisition of mutations in these patients. This study provides a detailed mutational portrait of pediatric ALL and gives insights into the molecular pathogenesis of this disease. Cancer Res; 77(2); 390–400. ©2016 AACR.

Supplementary Fig. 4. p53 pathway is dysregulated in ALL.

Supplementary Fig. 2. Mutations found in the ASXL family of genes.

Supplementary Fig. 1. Mutational spectrum of pediatric ALL.

Supplementary Table 1. Samples used for whole exome and targeted sequencing. Supplementary Table 2. Clinical information of patients. Supplementary Table 3. 560 Genes screened in the targeted sequencing. Supplementary Table 4. Sequences of shRNA or CRISPR-Cas9 sgRNA used in this study. Supplementary Table 5. Sequences of real-time PCR primers used in this study. Supplementary Table 6. Sequences of primers used for Sanger validation of CRISPR-Cas9 indel. Supplementary Table 7. Mutations of KRAS identified in this study have been found in a variety of cancers. Supplementary Table 8. Mutations of PTPN11 in other cancers occurring in the same location as in our ALL cohort. Supplementary Table 9. Recurrent mutation sites of FLT3 in different cancers. Supplementary Table 10. Cell lines or cancer samples harboring either E1099K or T1150A hotspot mutation of WHSC1. Supplementary Table 11. R1446 mutations of CREBBP recurrently occurred in a variety of cancers. Supplementary Table 12. Mutational hotspot (D1399) of EP300 occurring in other cancers occurring in the same location as in our ALL cohort.Supplementary Table 13. Rare mutations occurring in our ALL cohort (mutated in one individual each), but these mutations have been recurrently documented in the COSMIC cancer mutations database. Supplementary Table 14. Mutations of genes involved in DNA repair pathway in relapse samples.

Current standard of care for patients with pediatric acute lymphoblastic leukemia (ALL) is mainly effective, with high remission rates after treatment. However, the genetic perturbations that give rise to this disease remain largely undefined, limiting the ability to address resistant tumors or develop less toxic targeted therapies. Here, we report the use of next-generation sequencing to interrogate the genetic and pathogenic mechanisms of 240 pediatric ALL cases with their matched remission samples. Commonly mutated genes fell into several categories, including RAS/receptor tyrosine kinases, epigenetic regulators, transcription factors involved in lineage commitment, and the p53/cell-cycle pathway. Unique recurrent mutational hotspots were observed in epigenetic regulators CREBBP (R1446C/H), WHSC1 (E1099K), and the tyrosine kinase FLT3 (K663R, N676K). The mutant WHSC1 was established as a gain-of-function oncogene, while the epigenetic regulator ARID1A and transcription factor CTCF were functionally identified as potential tumor suppressors. Analysis of 28 diagnosis/relapse trio patients plus 10 relapse cases revealed four evolutionary paths and uncovered the ordering of acquisition of mutations in these patients. This study provides a detailed mutational portrait of pediatric ALL and gives insights into the molecular pathogenesis of this disease. Cancer Res; 77(2); 390–400. ©2016 AACR.

Background Glioblastoma multiforme (GBM) is one of the most aggressive cancers in humans. Identification and characterization of the GBM-promoting factors is imperative for the development of novel and effective clinical interventions. We recently discovered that the expression of B-cell lymphoma 6 (BCL6), a gene involved in the development of B cell lymphoma, is up-regulated in GBM. This study aims to explore the functional implications of BCL6 in this disease. Methods We analysed the transcriptional level of BCL6 in primary glioma samples, and screened the protein expression in a panel of human GBM cell lines as well as primary GBM explants. cDNA microarray analysis was conducted to identify the potential downstream targets of BCL6 in GBM. Small-interfering RNA (siRNA), small hairpin RNA (shRNA), and CRISPR-mediated gene silencing strategies were applied to examine the biological function of BCL6. Finally, inhibitors targeting BCL6 were tested in glioma cells. Results In silico analysis revealed elevated BCL6 mRNA levels in both primary GBM samples and cell lines when compared with neural stem cell or non-tumor brain tissues. Western blot confirmed the prevalent expression of BCL6 in GBM cell lines as well as primary GBM explants. Functional studies showed that BCL6 played an important role in promoting cell growth. Depletion of endogenous BCL6 through siRNA, shRNA or CRISPR in GBM cells led to marked inhibition of cell proliferation both in vitro and in vivo. Transcriptome analysis showed that BCL6 is an important regulator of TP53 signaling pathway. Knockdown of BCL6 increased the expression of p53, p21CIP and p27KIP. CHIP-qPCR further confirmed that BCL6 interacted directly to the TP53 promoter and suppressed its expression. Moreover, BCL6 negatively regulated MEK-ERK activation in GBM cells. BCL6 depletion reduced the phosphorylation levels of both MEK1/2 and ERK1/2, but had little effect on AKT phosphorylation. Our further investigations uncovered that BCL6 modulated the expression of several key regulators of MEK-ERK pathway, such as SPRY1, SPRY2 and AXL. Finally, BCL6 inhibitor showed marked anti-proliferation activity in GBM cells, suggesting that targeting BCL6 may serve as a new strategy to treat GBM. Conclusion Our data suggest that BCL6 is involved in glioma tumorigenesis through regulating both the TP53 and MEK-ERK pathways, and that BCL6 is a potential therapeutic target for glioma treatment. Citation Format: Ye Chen, Liang Xu, Masaharu Hazawa, Anand M. Thippeswamy, Henry Yang, Markus Müschen, De-Chen Lin, Phillip Koeffler. Identification of B-cell lymphoma 6 as a novel therapeutic target in glioblastoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4944. doi:10.1158/1538-7445.AM2015-4944