ALBERT

Description: Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/ .

Description: Le Bris, A., Fréchet, A., Galbraith, P. S., and Wroblewski, J. S. 2013. Evidence for alternative migratory behaviours in the northern Gulf of St Lawrence population of Atlantic cod ( Gadus morhua L.). – ICES Journal of Marine Science, 70: 793–804. Inter-individual variation in migration propensity affects population dynamics and connectivity. The diversity of migratory behaviours of Atlantic cod (fork length 〉40 cm) in the northern Gulf of St Lawrence was studied using data-storage tags that record depth and temperature. Movement patterns of Atlantic cod equipped with data-storage tags were reconstructed using a geolocation model based on daily maximum depth and bottom temperature. Reconstructed migration routes revealed the previously undocumented coexistence of resident and migratory individuals in the population. Migratory cod overwintered in relatively deep (300–500 m) and warm (5°C) waters, while residents displayed a prolonged period of immobility in shallow (〈100 m) and near-freezing (–1.5°C) coastal waters of western Newfoundland. In the spring, migratory cod displayed extensive diel vertical migration suggestive of spawning behaviour. The presence of alternative migratory behaviours should be considered in the spatiotemporal management of the collapsed population.

Description: Background: Daratumumab is a human IgGκ monoclonal antibody targeting CD38 with a direct on-tumor and immunomodulatory mechanism of action. The intravenous (IV) formulation of daratumumab is approved in many countries for use as monotherapy in relapsed/refractory multiple myeloma (RRMM), and in combination with standard-of-care regimens in RRMM and patients with NDMM who are transplant ineligible. A subcutaneous (SC) formulation of daratumumab is currently under investigation in several ongoing studies. In the phase 3 COLUMBA study, daratumumab SC was shown to be non-inferior to daratumumab IV, demonstrating similar efficacy and pharmacokinetics, with a significantly decreased rate of infusion-related reactions and reduced administration time. The randomized phase 2 LYNX (MMY2065) study will evaluate the efficacy and safety of retreatment with subcutaneous daratumumab in patients with RRMM who were previously exposed to daratumumab IV therapy. Study Design and Methods: In this ongoing, multicenter, open-label, randomized phase 2 study, approximately 230 patients with prior exposure to daratumumab will be randomized 1:1 to receive daratumumab plus carfilzomib and dexamethasone (D-Kd) or carfilzomib and dexamethasone (Kd) alone. Patients must have received 1 to 2 prior lines of therapy (at least one of which included daratumumab IV) with the daratumumab-based therapy completed ≥3 months prior to randomization. Eligible patients must have achieved a partial response or better (as defined by International Myeloma Working Group [IMWG] criteria) to daratumumab-based therapy, with a duration of response of ≥4 months. Patients must not have discontinued daratumumab due to a daratumumab-related adverse event or received prior treatment with carfilzomib. All patients will receive 20 mg/m2 carfilzomib IV on Day 1 of Cycle 1, escalated to 70 mg/m2 on Days 8 and 15; carfilzomib 70 mg/m2 will be administered on Days 1, 8, and 15 of each 28-day cycle thereafter. Dexamethasone 40 mg will be administered (IV or PO) QW for Cycles 1-9 and then on Days 1, 8, and 15 from Cycle 10 onwards. Patients in the D-Kd group will also receive daratumumab SC (1,800 mg co-formulated with recombinant human hyaluronidase PH20 [rHuPH20; 2,000 U/mL; ENHANZE® drug delivery technology, Halozyme, Inc.]) QW in Cycles 1-2, Q2W in Cycles 3-6, and Q4W thereafter. The primary endpoint is the rate of patients achieving a very good partial response or better. Secondary endpoints include overall response rate, rate of patients achieving complete response or better, progression-free survival, overall survival, overall MRD-negativity rate, time to next treatment, pharmacokinetics, and safety. The ClinicalTrials.gov identifier is NCT03871829. Disclosures Bahlis: Janssen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria; Amgen: Consultancy, Honoraria. Zonder:Celgene Corporation: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Intellia: Consultancy, Membership on an entity's Board of Directors or advisory committees; Caelum: Consultancy, Membership on an entity's Board of Directors or advisory committees; Alnylam: Consultancy, Membership on an entity's Board of Directors or advisory committees; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Oncopeptides: Consultancy, Membership on an entity's Board of Directors or advisory committees. Wroblewski:Janssen: Employment, Equity Ownership. Qi:Janssen: Employment. Renaud:Janssen: Employment, Equity Ownership. Jackson:Janssen: Employment, Equity Ownership. Facon:Celgene: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Janssen: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Sanofi: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Amgen: Membership on an entity's Board of Directors or advisory committees. OffLabel Disclosure: This presentation/paper includes information/discussion of a subcutaneous formulation of daratumumab, which is currently under investigation in several clinical trials, but has not yet been approved. The intravenous formulation of daratumumab is approved as monotherapy and in combination with standard-of-care regimens for the treatment of MM.

Description: When performed under strict conditions of temperature and pH, Perchloric acid (PCA) extraction is claimed to be a reliable method of providing cytosolic composition without quantitative or qualitative changes. We applied this technique to human lymphocytes, and obtained 31P-NMR spectra of both infected and uninfected cell extracts. Our studies show that the phosphomonoester (PME) to phosphodiester (PDE) ratio in uninfected cell extracts is up to three times higher than in extracts of HIV-1 infected cells. While PME signals include mainly phosphocholine and phosphoethanolamine, the PDE was identified mainly as glycerophosphorylcholine. Changes are clearly visible within 8–12 hours after infection. We conducted our initial studies on cells infected in vitro with HIV-1. We used the cell lines U87, MAGI, SupT1 and CEM, and primary lymphocytes isolated from blood of healthy donors (obtained from Bergen Community Regional Blood Center, Paramus, NJ) infected in vitro with HIV-1 type IIIB (X4-type) or 89.6 (X4/R5-type) at an M.O.I. of 0.01. The infection of these cells was confirmed by PCR analysis. The mean PDE/PME ratio of 30 uninfected lymphocyte samples was 0.482 ± 0.094 while the mean PDE/PME ratio of 30 infected samples was 0.206±0.056. Prior to extraction all cells were isolated from dead ones using Ficoll procedure, then cell pellets containing at least 5×106 cells were placed on ice and extracted with PCA. Subsequently, the KHCO3 neutralized extract was analyzed using phosphorus NMR spectroscopy. The mechanisms that determine the content of phosphodiesters and their modulation by the presence of HIV-1 comprise another target for future investigation, but its analytical value is clearly visible. Lastly, to determine whether the observation of reduced PDE/PME ratio was applicable in the analysis of HIV-1 sero-positive patients, we analyzed, in a blinded fashion, the 31P-NMR spectra of lymphocyte extracts obtained from six HIV-1 infected individuals. HIV-1 infected cells and plasma were isolated from subjects enrolled in the AIDS clinic at the University of Durban, South Africa. These individuals constitute both HIV-1 infected asymptomatic and AIDS patients, and were previously untreated by any regimen for HIV-1 infection. This population was confined to individuals aged 18–50 and consisted of ∼50% male participants, of which 100% were Black. The mean PDE/PME ratio for these samples was 0.203 ± 0.076, and again all six samples fell below the mean PDE/PME ratio of uninfected cells minus Standard Deviation. Statistical analysis was then conducted among all of these groups: uninfected (group 1), in-vitro infected (group 2) and in-vivo infected (group 3), using the Student t-test for unpaired samples. For group 1 vs. group 2 the t = 5.34, probability = 0.000040, for group 2 vs. group 3 the t = 0.142, probability = 0.89, and for group 1 vs. group 3 the t = 4.88, probability = 0.00011. The method developed here is self-calibrating (thus it measures the ratio of two blood extract components), easy to implement, and allows for measurements to be done automatically, using methods which are much more sensitive than NMR spectroscopy- for example HPLC. This technology is also much faster and cheaper than any currently used screening technique.

Description: BCR-ABL1 inhibitors have revolutionized the treatment of CML patients. However several drawbacks remain, including clinical resistance of T315I-mutated CML. Further, the clinical success of ponatinib, a selective inhibitor of T315I-mutated BCR-ABL1 is hampered by vascular side effects. Therefore, novel treatment strategies are warranted especially in T315I-mutated CML. We investigated the relevance of the Gas6-Axl axis in CML patients and the therapeutic potential of the clinically applicable small molecule Axl inhibitor BGB324 in primary CML (stem cell) samples, cell lines and preclinical models. We previously found that Gas6 and Axl represent potential novel targets in this disease and that BGB324 inhibits CML growth in vitro and in vivo (Erdmann et al., ASH meeting 2013, New Orleans, #1469). We next wished to confirm Axl as specific therapeutic target and therefore down regulated its expression in KCL-22 and K562 cells by means of shRNA. In these experiments blockade of Axl inhibited CML cell proliferation in comparison to control-transduced cells, thereby confirming that Axl promotes CML growth. Subsequently, we added BGB324 to shAxl- and shcontrol-transduced cells. Surprisingly BGB324 inhibited cell growth significantly more in shAxl-transduced cells in comparison to control-treated shAxl-transduced cells (p