Rabbit Anti-Human PAX5 Monoclonal Antibody, clone CQ7251

Background: To understand the changes of gene regulation in carcinogenesis, we explored signals of DNA methylation -a stable epigenetic mark of gene regulatory elements - and designed a computational model to profile loss and gain of regulatory elements (REs) during carcinogenesis. We also utilized sequencing data to analyze the allele frequency of single nucleotide polymorphisms (SNPs) and detected the cancer-associated SNPs, i. e., the SNPs displaying the significant allele frequency difference between cancer and normal samples. Results: After applying this model to chronic lymphocytic leukemia (CLL) data, we identified REs differentially activated (dREs) between normal and CLL cells, consisting of 6,802 dREs gained and 4,606 dREs lost in CLL. The identified regulatory perturbations coincide with changes in the expression of target genes. In particular, the genes encoding DNA methyltransferases harbor multiple lost-in-cancer dREs and zero gained-in-cancer dREs, indicating that the damaged regulation of these genes might be one of the key causes of tumor formation. dREs display a significantly elevated density of the genome-wide association study (GWAS) SNPs associated with CLL and CLLrelated traits. We observed that most of dRE GWAS SNPs associated with CLL and CLL-related traits (83%) display a significant haplotype association among the identified cancer-associated alleles and the risk alleles that have been reported in GWAS. Also dREs are enriched for the binding sites of the well-established B-cell and CLL transcription factors (TFs) NF-kB, AP2, P53, E2F1, PAX5, and SP1. We also identified CLL-associated SNPs and demonstrated that the mutations at these SNPs change the binding sites of key TFs much more frequently than expected. Conclusions: Through exploring sequencing data measuring DNA methylation, we identified the epigenetic alterations (more specifically, DNA methylation) and genetic mutations along non-coding genomic regions CLL, and demonstrated that these changes play a critical role in carcinogenesis through damaging the regulation of key genes and alternating the binding of key TFs in B and CLL cells.

Oncogenic MYC activation promotes proliferation in Burkitt lymphoma, but also induces cell-cycle arrest and apoptosis mediated by p53, a tumor suppressor that is mutated in 40% of Burkitt lymphoma cases. To identify molecular dependencies in Burkitt lymphoma, we performed RNAi-based, loss-of-function screening in eight Burkitt lymphoma cell lines and integrated non-Burkitt lymphoma RNAi screens and genetic data. We identified 76 genes essential to Burkitt lymphoma, including genes associated with hematopoietic cell differentiation (FLI1, BCL11A) or B-cell development and activation (PAX5, CDKN1B, JAK2, CARD11) and found a number of context-specific dependencies including oncogene addiction in cell lines with TCF3/ID3 or MYD88 mutation. The strongest genotype-phenotype association was seen for TP53. MDM4, a negative regulator of TP53, was essential in TP53 wild-type (TP53wt) Burkitt lymphoma cell lines. MDM4 knockdown activated p53, induced cell-cycle arrest, and decreased tumor growth in a xenograft model in a p53-dependent manner. Small molecule inhibition of the MDM4-p53 interaction was effective only in TP53wt Burkitt lymphoma cell lines. Moreover, primary TP53wt Burkitt lymphoma samples frequently acquired gains of chromosome 1q, which includes the MDM4 locus, and showed elevated MDM4 mRNA levels. 1q gain was associated with TP53wt across 789 cancer cell lines and MDM4 was essential in the TP53wt-context in 216 cell lines representing 19 cancer entities from the Achilles Project. Our findings highlight the critical role of p53 as a tumor suppressor in Burkitt lymphoma and identify MDM4 as a functional target of 1q gain in a wide range of cancers that is therapeutically targetable. Significance: Targeting MDM4 to alleviate degradation of p53 can be exploited therapeutically across Burkitt lymphoma and other cancers with wild-type p53 harboring 1q gain, the most frequent copy number alteration in cancer.