Patient-specific modeling of diffuse large B-cell lymphoma

Personalized medicine aims to tailor treatment to patients based on their individual genetic or molecular background. Especially in diseases with a large molecular heterogeneity, such as diffuse large B-cell lymphoma (DLBCL), personalized medicine has the potential to improve outcome and/or to reduce resistance towards treatment. However, integration of patient-specific information into a computational model is challenging and has not been achieved for DLBCL. Here, we developed a computational model describing signaling pathways and expression of critical germinal center markers. The model integrates the regulatory mechanism of the signaling and gene expression network and covers more than 50 components, many carrying genetic lesions common in DLBCL. Using clinical and genomic data of 164 primary DLBCL patients, we implemented mutations, structural variants and copy number alterations as perturbations in the model using the CoLoMoTo notebook. Leveraging patient-specific genotypes and simulation of the expression of marker genes in specific germinal center conditions allows us to predict the consequence of the modeled pathways for each patient. Finally, besides modeling how genetic perturbations alter physiological signaling, we also predicted for each patient model the effect of rational inhibitors, such as Ibrutinib, that are currently discussed as possible DLBCL treatments, showing patient-dependent variations in effectiveness and synergies

SH2 domain-containing inositol 5-phosphatases support the survival of Burkitt lymphoma cells by promoting energy metabolism

Burkitt lymphoma cells (BL) exploit antigen-independent tonic signals transduced by the B-cell antigen receptor (BCR) for their survival, but the molecular details of the rewired BL-specific BCR signal network remain unclear. A loss of function screen revealed the SH2 domain-containing 5`-inositol phosphatase 2 (SHIP2) as a potential modulator of BL fitness. We characterized the role of SHIP2 in BL survival in several BL cell models and show that perturbing SHIP2 function renders cells more susceptible to apoptosis, while attenuating proliferation in a BCR-dependent manner. Unexpectedly, SHIP2 deficiency did neither affect PI3K survival signals nor MAPK activity, but attenuated ATP production. We found that an efficient energy metabolism in BL cells requires phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2), which is the enzymatic product of SHIP proteins. Consistently, interference with the function of SHIP1 and SHIP2 augments BL cell susceptibility to PI3K inhibition. Notably, we provide here a molecular basis of how tonic BCR signals are connected to energy supply, which is particularly important for such an aggressively growing neoplasia. These findings may help to improve therapies for the treatment of BL by limiting energy metabolism through the inhibition of SHIP proteins, which renders BL cells more susceptible to the targeting of survival signals

Molecular and functional profiling identifies therapeutically targetable vulnerabilities in plasmablastic lymphoma

Plasmablastic lymphoma (PBL) represents a rare and aggressive lymphoma subtype frequently associated with immunosuppression. Clinically, patients with PBL are characterized by poor outcome. The current understanding of the molecular pathogenesis is limited. A hallmark of PBL represents its plasmacytic differentiation with loss of B-cell markers and, in 60% of cases, its association with Epstein-Barr virus (EBV). Roughly 50% of PBLs harbor a MYC translocation. Here, we provide a comprehensive integrated genomic analysis using whole exome sequencing (WES) and genome-wide copy number determination in a large cohort of 96 primary PBL samples. We identify alterations activating the RAS-RAF, JAK-STAT, and NOTCH pathways as well as frequent high-level amplifications in MCL1 and IRF4. The functional impact of these alterations is assessed using an unbiased shRNA screen in a PBL model. These analyses identify the IRF4 and JAK-STAT pathways as promising molecular targets to improve outcome of PBL patients

Analysis of the putative AP-3 fuction for vesicle formation at the transgolgi network.

Analyse der putativen AP-3-Funktion für die Vesikelbildung am Trans-Golgi-NetzwerkDer gerichtete Transport von Membranproteinen in der Zelle geschieht durch Transportvesikel. Obwohl den heterotetrameren Adaptorproteinkomplexen eine zentrale Funktion bei der Bildung dieser Transportvesikel zugesprochen wird, ist über deren subzellulären Wirkort wenig bekannt. Von den vier identifizierten Adaptorproteinkomplexen AP-1, AP-2, AP-3 und AP-4 ist lediglich für AP-2 eine Beteiligung bei der Rezeptor-vermittelten Endozytose an der Plasmamembran gut belegt. Während für AP-1 schon verschiedentlich eine Sortierfunktion von Membranproteinen am Trans-Golgi-Netzwerk (TGN) gezeigt wurde, steht der direkte experimentelle Nachweis einer möglichen Funktion am TGN für AP-3 noch aus. In dieser Arbeit konnte durch die Etablierung eines in-vitro-Golgi/TGN-Budding-Assays gezeigt werden, dass neben AP-1 auch AP-3 eine Sortierfunktion am TGN für lysosomale und melanosomale Membranproteine zukommt. Unter Verwendung von Adaptor-defizienten Zytosolen konnte belegt werden, dass AP-1 erwartungsgemäß für die Sortierung von MPR46 essentiell ist. Für TRP-1 konnte erstmals eine Sortierung am TGN ebenfalls in Abhängigikeit von AP-1- nachgewiesen werden. Ebenso wurde gezeigt, dass AP-3 für die korrekte Verpackung (Sortierung) von Tyrosinase und Lamp-1 in Transportvesikel am TGN einen essentiellen Faktor darstelllt, womit durch diese Arbeit der erste direkte experimentelle Nachweis einer Funktion von AP-3 beim Golgi/TGN-Export vorliegt.Basierend auf dem etablierten Assay ist nun die Untersuchung weiterer Membranproteine bezüglich des Sortierverhaltens am TGN möglich. Außerdem wird mit dem Assay die Analyse von distinkten Transport-Vesikelpopulationen des Golgi/TGN-Exports hinsichtlich ihrer Membrankomposition zugänglich