Support for UNRWA's survival

The United Nations Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) provides life-saving humanitarian aid for 5·4 million Palestine refugees now entering their eighth decade of statelessness and conflict. About a third of Palestine refugees still live in 58 recognised camps. UNRWA operates 702 schools and 144 health centres, some of which are affected by the ongoing humanitarian disasters in Syria and the Gaza Strip. It has dramatically reduced the prevalence of infectious diseases, mortality, and illiteracy. Its social services include rebuilding infrastructure and homes that have been destroyed by conflict and providing cash assistance and micro-finance loans for Palestinians whose rights are curtailed and who are denied the right of return to their homeland

The genetic landscape of mutations in Burkitt lymphoma

Burkitt lymphoma is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. Here, we describe the first completely sequenced genome from a Burkitt lymphoma tumor and germline DNA from the same affected individual. We further sequenced the exomes of 59 Burkitt lymphoma tumors and compared them to sequenced exomes from 94 diffuse large B-cell lymphoma (DLBCL) tumors. We identified 70 genes that were recurrently mutated in Burkitt lymphomas, including ID3, GNA13, RET, PIK3R1 and the SWI/SNF genes ARID1A and SMARCA4. Our data implicate a number of genes in cancer for the first time, including CCT6B, SALL3, FTCD and PC. ID3 mutations occurred in 34% of Burkitt lymphomas and not in DLBCLs. We show experimentally that ID3 mutations promote cell cycle progression and proliferation. Our work thus elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a new tumor suppressor gene

Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis

<p>Lymphomas comprise a diverse group of malignancies derived from immune cells. High throughput sequencing has recently emerged as a powerful and versatile method for analysis of the cancer genome and transcriptome. As these data continue to emerge, the crucial work lies in sorting through the wealth of information to hone in on the critical aspects that will give us a better understanding of biology and new insight for how to treat disease. Finding the important signals within these large data sets is one of the major challenges of next generation sequencing.</p><p>In this dissertation, I have developed several complementary strategies to describe the genetic underpinnings of lymphomas. I begin with developing a better method for RNA sequencing that enables strand-specific total RNA sequencing and alternative splicing profiling in the same analysis. I then combine this RNA sequencing technique with whole exome sequencing to better understand the global landscape of aberrations in these diseases. Finally, I use traditional cell and molecular biology techniques to define the consequences of major genetic alterations in lymphoma.</p><p>Through this analysis, I find recurrent silencing mutations in the G alpha binding protein GNA13 and associated focal adhesion proteins. I aim to describe how loss-of-function mutations in GNA13 can be oncogenic in the context of germinal center B cell biology. Using in vitro techniques including liquid chromatography-mass spectrometry and knockdown and overexpression of genes in B cell lymphoma cell lines, I determine protein binding partners and downstream effectors of GNA13. I also develop a transgenic mouse model to study the role of GNA13 in the germinal center in vivo to determine effects of GNA13 deletion on germinal center structure and cell migration.</p><p>Thus, I have developed complementary approaches that span the spectrum from discovery to context-dependent gene models that afford a better understanding of the biological function of aberrant events and ultimately result in a better understanding of disease.</p>Dissertatio

Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis within the Germinal Center Niche

Abstract Nonhodgkin Lymphoma (NHL) is among the most common cancer subtypes, with approximately >350,000 new cases diagnosed annually worldwide. The vast majority of NHLs arise from germinal center (GC) B cells. We and others have identified GNA13 as one of the most frequently mutated genes in GC-derived lymphomas, including ~30% of Burkitt Lymphoma and ~25% of Germinal Center B Cell-like (GCB) Diffuse Large B cell Lymphoma. Despite this association, the role of GNA13 in lymphomagenesis remains elusive. In human breast and prostate cancer, GNA13 behaves as an oncogene, with increased expression linked to cellular invasion and metastasis. Intriguingly, GNA13 mutations in GCB DLBCL and Burkitt Lymphoma are frequently inactivating, possessing a high number of nonsense and missense mutations in conserved domains. This suggests that GNA13 may function as a tumor suppressor in the context of lymphoma, in contrast to its role in solid tumors. The purpose of this study is to define the role of GNA13 in GC B cells and to clarify how GNA13 loss may contribute to lymphoma within the germinal center niche. We first investigated the expression pattern of GNA13 in lymphocyte populations from normal human tonsil. Our data demonstrated that GNA13 is enriched in GC B cells by quantitative PCR and immunohistochemistry. To determine the effect of GNA13 abundance on global mRNA expression patterns, we performed RNA sequencing on lymphoma derived cell lines. Using this method, we found that GNA13 knockdown and overexpression was highly correlated with GC dark and light zone gene signatures, respectively. We next devised a proteomics approach to identify potential GNA13 binding partners in GCs. Lysates from lymphoma-derived cell lines overexpressing FLAG-tagged GNA13 were subjected to immunoprecipitation with M2-antibody bound magnetic beads, followed by LC-MS/MS. Our results demonstrated an enrichment of proteins involved in focal adhesion, consistent with the known involvement of GNA13 in processes of cytoskeletal reorganization and cell migration. We next explored the role of GNA13 in vivo. Since GNA13 mutations are a unique feature of GC-derived lymphomas, we developed mouse models that would allow us study GNA13 exclusively in the germinal center context. We generated B cell and GC specific GNA13 knockout mice by crossing GNA13fl/fl mice with MB1-Cre and AID-Cre strains. After immunization with sheep red blood cells, both B cell and GC specific GNA13 deficient mice possessed normal levels of B, T and GC cells within secondary lymphoid sites including Peyer’s patches and spleen, suggesting that GNA13 is not essential for GC formation. GC B cells from both GNA13 deficient strains demonstrated enhanced cellular motility toward GC directed chemokines CXCL12, CXCL13 and S1P using in vitro transwell migration assays. Furthermore, B cells isolated from GNA13 deficient animals showed enhanced RhoA activity. These data suggested that GNA13 inhibits GC B cell migration and RhoA mediated cell motility in normal conditions. Loss of GNA13 may then deregulate normal chemokine gradient signaling, resulting in global increases in GC migration. We also demonstrated that GNA13 deficient B cells possess elevated levels of phosphorylated AKT, an effect potentiated by the addition of CXCL12 and S1P. AKT signaling is known to promote cell survival in a variety of cell types, which may further promote oncogenesis. In this study, we have synthesized the complementary approaches of next generation sequencing, proteomics and genetic mouse models to gain novel insight into the biological function of GNA13, a gene that is mutated in a high proportion of GC-derived lymphomas. As a whole, our work suggests that GNA13 serves as a tumor suppressor during the germinal center reaction. The acquisition of inactivating GNA13 mutations may promote lymphoma by allowing cells to physically escape the germinal center niche and evade apoptosis while continuing to express GC signature genes. Affected cells may be subjected to persistent somatic hypermutation, which, over time, could result in the accumulation of additional oncogenic mutations, culminating in development of GC-derived lymphoma. Disclosures No relevant conflicts of interest to declare

The genetic landscape of mutations in Burkitt lymphoma

Burkitt lymphoma is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. Here, we describe the first completely sequenced genome from a Burkitt lymphoma tumor and germline DNA from the same affected individual. We further sequenced the exomes of 59 Burkitt lymphoma tumors and compared them to sequenced exomes from 94 diffuse large B-cell lymphoma (DLBCL) tumors. We identified 70 genes that were recurrently mutated in Burkitt lymphomas, including ID3, GNA13, RET, PIK3R1 and the SWI/SNF genes ARID1A and SMARCA4. Our data implicate a number of genes in cancer for the first time, including CCT6B, SALL3, FTCD and PC. ID3 mutations occurred in 34% of Burkitt lymphomas and not in DLBCLs. We show experimentally that ID3 mutations promote cell cycle progression and proliferation. Our work thus elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a new tumor suppressor gene