The Staudt laboratory has conducted RNA interference genetic screens for genes required for the proliferation and/or survival of human cell lines representing various subtypes of lymphoma and multiple myeloma. In diffuse large B cell lymphoma (DLBCL), previous work in the Staudt laboratory demonstrated that the anti-apoptotic NF-kB pathway is constitutively active in the activated B cell-like (ABC) subtypes of DLBCL but not the germinal center B cell-like (GCB) subtype of DLBCL, but the mechanisms underlying this abnormal signaling were enigmatic. The laboratory therefore conducted an RNAi screen in ABC and GCB DLBCL cell lines, searching for shRNAs that were selectively toxic for ABC DLBCL cells. This effort revealed that a signaling complex comprised of CARD11, MALT1, and BCL10 is required for the survival of ABC but not GCB DLBCL cell lines. In normal lymphocytes, this CARD11 complex engages the NF-kB pathway during antigen receptor signaling. The Staudt laboratory demonstrated that this signaling complex is responsible for the constitutive activation of the NF-kB pathway in ABC DLBCLs. An RNAi screen uncovered a crucial dependency of multiple myeloma cells on IRF4, a lymphoid-restricted transcriptional factor that is required for both lymphocyte activation and for plasmacytic differentiation. IRF4 knockdown by RNAi was toxic to 10 different myeloma cell lines representing many of the known genetic subtypes of this cancer. Of note, IRF4 is not translocated, amplified or mutated in most cases of multiple myeloma, and thus the dependency of myeloma cells on IRF4 exemplifies a new concept in cancer biology known as non-oncogene addiction. These results establish IRF4 as an important new therapeutic target in this lethal cancer. Most recently, our Achilles heel screens allowed us to define a chronic active form of B cell receptor (BCR) signaling that activates NF-kB in ABC DLBCLs with wild type CARD11. Such ABC DLBCLs die upon knockdown of BCR signaling components, including subunits of the B cell receptor itself. ABC DLBCLs have prominent clusters of the BCR in the plasma membrane, similar to antigen-stimulated normal B cells. Cancer gene resequencing revealed that over one fifth of ABC DLBCLs have mutations in the CD79B or CD79A subunits of the BCR. The most common mutations, present in 18% of ABC DLBCLs, involved a single tyrosine of the BCR signaling subunit, CD79B. These mutations affect the critical ITAM signaling motif, generating BCRs that avoid negative autoregulation by the LYN tyrosine kinase. Importantly, the BCR pathway offers a wealth of targets that can be exploited therapeutically, including several protein kinases (SRC-family kinases, SYK, BTK, PKCbeta) as well as PI(3) kinase. Dasatinib, a clinically available kinase inhibitor that targets BTK and SRC-family kinases, kills ABC DLBCL cells by blocking their chronic active BCR signaling. An important new initiative in the past year was the construction of a new RNAi library that targets each gene with 12 shRNAs. This approach allows us to identify effective shRNAs that do not have appreciable off-target effects. This library targets all protein kinases, PI(3) kinase pathway component, and other regulatory proteins relevant to lymphoid malignancies. Using this new library we have embarked on an ambitious project to screen more than 50 cell line models of various lymphoid malignancies, searching for pathways that are selectively required for the proliferation and survival of particular cancer subtypes. A recent success was the identification of the MYD88 signaling pathway as essential for the survival of ABC DLBCL cells. MYD88 is a key adapter protein in the signaling pathway downstream of Toll-like receptors in innate immune cells. The RNAi screen identified shRNAs targeting MYD88 and its assocatiated kinase IRAK1 as toxic for ABC DLBCL cells but not for cell line models of other lymphoma subtypes. This led us to discover recurrent mutations in MYD88 that create mutant isoforms that spontaneously activate the NF-kB pathway and are oncogenic. We investigated a recurrent amplicon in primary mediastinal large B cell lymphoma (PMBL) and Hodgkin lymphoma on chromosome 9p24 using RNAi screens. We uncovered three essential genes using an RNAi screen: JAK2, JMJD2C, and RANBP6. We showed that the kinase activity of JAK2 is activated in these lymphomas by autocrine IL-13 signaling. Surprisingly, JAK2 cooperated with JMJD2C in promoting survival of these lymphoma cells. JMJD2C is a histone H3K9 demethylase, which activates gene expression by removing this histone mark, thereby preventing the recruitment of the heterochromatin protein HP-1 alpha. We traced the synergism between JAK2 and JMJD2C to cooperative epigenetic modification of chromatin. JAK2 acts in the nucleus of these lymphoma cells to phosphorylate the histone H3 tail on tyrosine 41, which also blocks recruitment of HP-1 alpha. A major target of epigenetic modication by JAK2 and JMJD2C is MYC, but in addition, these two proteins modify the chromatin structure of several hundred protein-coding genes. Importantly, drugs that target JAK2 kill these lymphoma cells. RNA interference screening has proven highly successful in unraveling the key survival pathways in Burkitt lymphoma. We discovered that knockdown of the transcription factor TCF3 was lethal to Burkitt lymphoma cell lines, but not to cell line models of other aggressive lymphomas. By RNA resequencing, we found that TCF3 and its negative regulator are mutated in 70% of cases of sporadic Burkitt lymphoma, leading to TCF3 dependency. Our RNA interference screens also demonstrated that about two thirds of Burkitt lymphoma cell lines depend upon tonic signaling from the B cell receptor (BCR). Further, we discovered that TCF3 amplifies this tonic BCR signaling. Finally, we discovered that Burkitt lymphoma cell lines require cyclin D3/CDK6 for cell cycle progression. RNA resequencing revealed oncogenic activating mutations in cyclin D3 in 38% of cases. Surprisingly, pharmacologic inhibition of CDK6 causes apoptotis of Burkitt lymphoma cell lines and induced regression of established Burkitt lymphoma xenografts. Recent RNAi efforts have identified new vulnerabilities in multiple myeloma. In particular, we showed that caspase-10 is required for the survival of all multiple myeloma cell lines. Caspase-10 prevents autophagic cell death and represents a new therapeutic target in this disease. We have embarked on two new large functional genomics initiatives to enhance our ability to discover cancer vulnerabilities. First, we have amplififed a whole-genome lentiviral shRNA library constiting of over 150,000 independent vectors targeting each gene with 5-15 shRNAs. Second, we have adopted the Cas9/CRISPR technology, which is an alternative way to inactivate genes. In this system, a short guide RNA (sgRNA) is used to direct the Cas9 endonuclease precise genomic locations. If the sgRNA targets the beginning of the coding region of a gene, the gene can be inactivated as a result of repeated cutting and deletion events. We have begun to use bar-coded lentiviral libraries expressing sgRNAs to identify essential genes in lymphoid malignancies.
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