Carla Danussi

The integrated landscape of driver genomic alterations in glioblastoma

Glioblastoma is one of the most challenging forms of cancer to treat. Here we describe a computational platform that integrates the analysis of copy number variations and somatic mutations and unravels the landscape of in-frame gene fusions in glioblastoma. We found mutations with loss of heterozygosity in LZTR1, encoding an adaptor of CUL3-containing E3 ligase complexes. Mutations and deletions disrupt LZTR1 function, which restrains the self renewal and growth of glioma spheres that retain stem cell features. Loss-of-function mutations in CTNND2 target a neural-specific gene and are associated with the transformation of glioma cells along the very aggressive mesenchymal phenotype. We also report recurrent translocations that fuse the coding sequence of EGFR to several partners, with EGFR-SEPT14 being the most frequent functional gene fusion in human glioblastoma. EGFR-SEPT14 fusions activate STAT3 signaling and confer mitogen independence and sensitivity to EGFR inhibition. These results provide insights into the pathogenesis of glioblastoma and highlight new targets for therapeutic intervention.

Emilin1 Deficiency Causes Structural and Functional Defects of Lymphatic Vasculature

ABSTRACT Lymphatic-vasculature function critically depends on extracellular matrix (ECM) and on its connections with lymphatic endothelial cells (LECs). However, the composition and the architecture of ECM have not been fully taken into consideration in studying the biology and the pathology of the lymphatic system. EMILIN1, an elastic microfibril-associated protein, is highly expressed by LECs in vitro and colocalizes with lymphatic vessels in several mouse tissues. A comparative study between WT and Emilin1−/− mice highlighted the fact that Emilin1 deficiency in both CD1 and C57BL/6 backgrounds results in hyperplasia, enlargement, and frequently an irregular pattern of superficial and visceral lymphatic vessels and in a significant reduction of anchoring filaments. Emilin1-deficient mice also develop larger lymphangiomas than WT mice. Lymphatic vascular morphological alterations are accompanied by functional defects, such as mild lymphedema, a highly significant drop in lymph drainage, and enhanced lymph leakage. Our findings demonstrate that EMILIN1 is involved in the regulation of the growth and in the maintenance of the integrity of lymphatic vessels, a fundamental requirement for efficient function. The phenotype displayed by Emilin1−/− mice is the first abnormal lymphatic phenotype associated with the deficiency of an ECM protein and identifies EMILIN1 as a novel local regulator of lymphangiogenesis.

EMILIN1 represents a major stromal element determining human trophoblast invasion of the uterine wall

The detection of EMILIN1, a connective tissue glycoprotein associated with elastic fibers, at the level of the ectoplacental cone and trophoblast giant cells of developing mouse embryos (Braghetta et al., 2002) favored the idea of a structural as well as a functional role for this protein in the process of placentation. During the establishment of human placenta, a highly migratory subpopulation of extravillous trophoblasts (EVT), originating from anchoring chorionic villi, penetrate and invade the uterine wall. In this study we show that EMILIN1, produced by decidual stromal and smooth muscle uterine cells, is expressed in the stroma and in some instances as a gradient of increasing concentration in the perivascular region of modified vessels. This distribution pattern is consistent with the haptotactic directional migration observed in in vitro functional studies of freshly isolated EVT and of the immortalized HTR-8/SVneo cell line of trophoblasts. Function-blocking monoclonal antibodies against α4-integrin chain and against EMILIN1 as well as the use of EMILIN1-specific short interfering RNA confirmed that trophoblasts interact with EMILIN1 and/or its functional gC1q1 domain via α4β1 integrin. Finally, membrane type I-matrix metalloproteinase (MT1-MMP) and MMP-2 were upregulated in co-cultures of trophoblast cells and stromal cells, suggesting a contributing role in the haptotactic process towards EMILIN1.

EMILIN1–α4/α9 integrin interaction inhibits dermal fibroblast and keratinocyte proliferation

The α4/α9 integrins directly engage the ECM glycoprotein EMILIN1 to inhibit skin cell proliferation upstream of TGF-β signaling.

EMILIN1/α9β1 integrin interaction is crucial in lymphatic valve formation and maintenance.

ABSTRACT Lymphatic vasculature plays a crucial role in the maintenance of tissue interstitial fluid balance. The role of functional collecting lymphatic vessels in lymph transport has been recently highlighted in pathologies leading to lymphedema, for which treatments are currently unavailable. Intraluminal valves are of paramount importance in this process. However, valve formation and maturation have not been entirely elucidated yet, in particular, the role played by the extracellular matrix (ECM). We hypothesized that EMILIN1, an ECM multidomain glycoprotein, regulates lymphatic valve formation and maintenance. Using a mouse knockout model, we show that in the absence of EMILIN1, mice exhibit defects in lymphatic valve structure and in lymph flow. By applying morphometric in vitro and in vivo functional assays, we conclude that this impaired phenotype depends on the lack of α9β1 integrin engagement, the specific lymphatic endothelial cell receptor for EMILIN1, and the ensuing derangement of cell proliferation and migration. Our data demonstrate a fundamental role for EMILIN1-integrin α9 interaction in lymphatic vasculature, especially in lymphatic valve formation and maintenance, and underline the importance of this ECM component in displaying a regulatory function in proliferation and acting as a “guiding” molecule in migration of lymphatic endothelial cells.

RHPN2 Drives Mesenchymal Transformation in Malignant Glioma by Triggering RhoA Activation

Mesenchymal transformation is a hallmark of aggressive glioblastoma (GBM). Here, we report the development of an unbiased method for computational integration of copy number variation, expression, and mutation data from large datasets. Using this method, we identified rhophilin 2 (RHPN2) as a central genetic determinant of the mesenchymal phenotype of human GBM. Notably, amplification of the human RHPN2 gene on chromosome 19 correlates with a dramatic decrease in the survival of patients with glioma. Ectopic expression of RHPN2 in neural stem cells and astrocytes triggered the expression of mesenchymal genes and promoted an invasive phenotype without impacting cell proliferation. Mechanistically, these effects were implemented through RHPN2-mediated activation of RhoA, a master regulator of cell migration and invasion. Our results define RHPN2 amplification as a central genetic determinant of a highly aggressive phenotype that directs the worst clinical outcomes in patients with GBM.

An EMILIN1-negative microenvironment promotes tumor cell proliferation and lymph node invasion.

The evidence that EMILIN1 (Elastic Microfibril Interface Located proteIN) deficiency in Emilin1−/− mice caused dermal and epidermal hyperproliferation and an abnormal lymphatic phenotype prompted us to hypothesize the involvement of this extracellular matrix component in tumor development and in lymphatic metastasis. Using the 12-dimethylbenz(α)anthracene/12-O-tetradecanoylphorbol-13-acetate (DMBA/TPA) two-stage model of skin carcinogenesis, we found that Emilin1−/− mice presented an accelerated formation, a higher incidence, and the development of a larger number of tumors compared with their wild-type littermates. EMILIN1-negative tumors showed more Ki67-positive proliferating cells and higher levels of pErk1/2. In these tumors, PTEN expression was lower. Emilin1−/− mice displayed enhanced lymphangiogenesis both in the tumor and in the sentinel lymph nodes. Accordingly, tumor growth and lymph node metastasis of transplanted syngenic tumors were also increased in Emilin1−/− mice. In vitro transmigration assays through lymphatic endothelial cells showed that EMILIN1 deficiency greatly facilitated tumor cell trafficking. Overall, these data established that EMILIN1 exerts a protective role in tumor growth, in tumor lymphatic vessel formation, as well as in metastatic spread to lymph nodes and reinforced the importance of its presence in the microenvironment to determine the tumor phenotype. Cancer Prev Res; 5(9); 1131–43. ©2012 AACR.

Neutrophil elastase-dependent cleavage compromises the tumor suppressor role of EMILIN1

Proteolysis of the extracellular matrix (ECM) is a key event in tumor growth and progression. The breakdown of ECM can lead to the generation of bioactive fragments that promote cell growth and spread. EMILIN1, a multidomain glycoprotein expressed in several tissues, exerts a crucial regulatory function through the engagement of α4/α9 integrins. Unlike the majority of ECM molecules that elicit a proliferative program, the signals emitting from EMILIN1 engaged by α4/α9β1 integrins are antiproliferative. In this study, aimed to demonstrate if the suppressor role of EMILIN1 was related to its structural integrity, we tested the possibility that EMILIN1 could be specifically cleaved. Among the proteolytic enzymes released in the tumor microenvironment we showed that neutrophil elastase cleaved EMILIN1 in three/four major fragments. The consequence of this proteolytic process was the impairment of its anti-proliferative role. Accordingly, EMILIN1 was digested in sarcomas and ovarian cancers. Sarcoma specimens were infiltrated by neutrophils (PMNs) and stained positively for elastase. The present findings highlight the peculiar activity of PMN elastase in disabling EMILIN1 suppressor function.

Cancer Stem Cells and the Microenvironment

The traditional interpretation of cancer progression is that tumor cells accumulate multiple genetic alterations, resulting in the capability to surmount a variety of obstacles including detachment from the primary tumor, intravasation into blood or lymphatic vessels, survival into circulation, extravasation and growth at a secondary site, lymph node and/or distant organ (Vogelstein and Kinzler, Nat Med 10:789–799, 2004). The hypothesis of a hierarchical organization of cells within at least certain tumors in which a subset of tumor cells has the property to self-renew, hence defined “stem-like” or cancer stem cells (CSC), and to generate and sustain the wide heterogeneity comprising the tumor is very attractive. However, the tumor cell-centered view of cancer progression ignores the contribution of the tumor microenvironment to the malignant phenotype. A tumor should be viewed as a complex dynamically evolving ecosystem where minor alterations may cause dramatic reorganization of the whole system and of the malignant versus benign behavior of cells. In fact, the tumor microenvironment is constantly changing and cancer cells, either CSC or more differentiated tumor cells, adapt, evolve, and survive during this process. Tumors grow in conducive microenvironments reminiscent of the normal stem cells niche concept. The tumor microenvironment is implicated in the transition from preinvasive to invasive growth and is regarded as a crucial participant in tumorigenesis promoting a more aggressive phenotype and has relevance also for therapeutical approaches.

Abstract A26: Multi-Reg: An integrative parallel approach to uncover drivers of cancer

Tumor samples harbor a vast number of genomic alterations of various kinds, and it is not easy to distinguish driver alterations that contribute to oncogenesis from passenger alterations. Most computational methods attempt to identify driver alternations by focusing on the most frequent alterations. Previous work in our lab has led to the development of CONEXIC, a Bayesian framework for integrating copy number and gene expression to identify candidate driver genes in cancer and to link them to gene expression signatures they regulate (Akavia et al, Cell, 2010). This framework was applied to data from melanoma cell lines, where it correctly identified known drivers (MITF) and connected them to their known targets. In addition, it predicted novel tumor dependencies not previously implicated in melanoma, which were confirmed experimentally. In general, current algorithms identify only one driver (the strongest) controlling a gene expression signature. However, drivers may act in parallel, where not only the strongest one is important. For example, either PTEN deletion or AKT activation can lead to a similar expression signature and phenotype. Therefore, we developed a new algorithm, based on the same principles as CONEXIC with multiple improvements. The new algorithm (called Multi-Reg) is capable of detecting multiple candidate regulators that can all act in parallel to regulate an expression signature. This algorithm can integrate mutations in addition to copy number and expression. Finally, we have designed Multi-Reg to be easier and quicker to run and more robust. We applied Multi-Reg to glioblastoma data from The Cancer Genome Atlas (TCGA). This data includes copy number, gene expression and mutations for hundreds of primary tumor samples. We found 84 candidate regulators that were missed by CONEXIC, but discovered by Multi-Reg. Because of Multi-Reg9s ability to search for genes working in parallel, it identified FGFR3, PDGFRA and NF1, in addition to EGFR & MET (identified by CONEXIC), as important candidate drivers. Additionally, Multi-Reg results identified RHPN2 as a novel oncogenic factor controlling a gene expression signature related to invasion and migration. Validation has shown that RHPN2 has limited effect on cell proliferation but induces invasiveness in glioblastoma cell lines. Our results correctly identify known drivers of glioblastoma progression, including oncogenes such as EGFR, MET, CEBPB and tumor suppressors such as p16 and NF1. Multi-Reg also has the capability to identify more regulators than CONEXIC, and has correctly linked RHPN2 to the oncogenic phenomena it controls. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A26.