ALBERT

Description: Article DNA may be used to fabricate functional nanostructures with various possible geometries, but first being able to predict these structures is a challenging task. Here, the authors use coarse-grained modelling to predict the shape of artificial DNA nanostructures in solution. Nature Communications doi: 10.1038/ncomms6578 Authors: Keyao Pan, Do-Nyun Kim, Fei Zhang, Matthew R. Adendorff, Hao Yan, Mark Bathe

Description: Oligosaccharyltransferases (OSTs) N-glycosylate proteins by transferring oligosaccharides from lipid-linked oligosaccharides (LLOs) to asparaginyl residues of Asn-Xaa-Ser/Thr acceptor sequons. Mammals have OST isoforms with STT3A or STT3B catalytic subunits for cotranslational or posttranslational N-glycosylation, respectively. OSTs also hydrolyze LLOs, forming free oligosaccharides (fOSs). It has been unclear whether hydrolysis is due...

Description: Geosciences, Vol. 8, Pages 182: HF/VHF Radar Sounding of Ice from Manned and Unmanned Airborne Platforms Geosciences doi: 10.3390/geosciences8050182 Authors: Emily Arnold Fernando Rodriguez-Morales John Paden Carl Leuschen Shawn Keshmiri Stephen Yan Mark Ewing Rick Hale Ali Mahmood Aaron Blevins Akhilesh Mishra Teja Karidi Bailey Miller John Sonntag Ice thickness and bed topography of fast-flowing outlet glaciers are large sources of uncertainty for the current ice sheet models used to predict future contributions to sea-level rise. Due to a lack of coverage and difficulty in sounding and imaging with ice-penetrating radars, these regions remain poorly constrained in models. Increases in off-nadir scattering due to the highly crevassed surfaces, volumetric scattering (due to debris and/or pockets of liquid water), and signal attenuation (due to warmer ice near the bottom) are all impediments in detecting bed-echoes. A set of high-frequency (HF)/very high-frequency (VHF) radars operating at 14 MHz and 30–35 MHz were developed at the University of Kansas to sound temperate ice and outlet glaciers. We have deployed these radars on a small unmanned aircraft system (UAS) and a DHC-6 Twin Otter. For both installations, the system utilized a dipole antenna oriented in the cross-track direction, providing some performance advantages over other temperate ice sounders operating at lower frequencies. In this paper, we describe the platform-sensor systems, field operations, data-processing techniques, and preliminary results. We also compare our results with data from other ice-sounding radars that operate at frequencies both above (Center for Remote Sensing of Ice Sheets (CReSIS) Multichannel Coherent Depth Sounder (MCoRDS)) and below (Jet Propulsion Laboratory (JPL) Warm Ice Sounding Explorer (WISE)) our HF/VHF system. During field campaigns, both unmanned and manned platforms flew closely spaced parallel and repeat flight lines. We examine these data sets to determine image coherency between flight lines and discuss the feasibility of forming 2D synthetic apertures by using such a mission approach.

Description: Noroviruses (NoVs) have high levels of genetic sequence diversities, which lead to difficulties in designing robust universal primers to efficiently amplify specific viral genomes for molecular analysis. We here described the practicality of sequence-independent amplification combined with DNA microarray analysis for simultaneous detection and genotyping of human NoVs in fecal specimens. We showed that single primer isothermal linear amplification (Ribo-SPIA) of genogroup I (GI) and genogroup II (GII) NoVs could be run through the same amplification protocol without the need to design and use any virus-specific primers. Related virus could be subtyped by the unique pattern of hybridization with the amplified product to the microarray. By testing 22 clinical fecal specimens obtained from acute gastroenteritis cases as blinded samples, 2 were GI positive and 18 were GII positive as well as 2 negative for NoVs. A NoV GII positive specimen was also identified as having co-occurrence of hepatitis A virus. The study showed that there was 100 % concordance for positive NoV detection at genogroup level between the results of Ribo-SPIA/microarray and the phylogenetic analysis of viral sequences of the capsid gene. In addition, 85 % genotype agreement was observed for the new assay compared to the results of phylogenetic analysis.

Description: Inflammasomes are cytosolic multiprotein complexes that initiate host defense against bacterial pathogens by activating caspase-1–dependent cytokine secretion and cell death. In mice, specific nucleotide-binding domain, leucine-rich repeat-containing family, apoptosis inhibitory proteins (NAIPs) activate the nucleotide-binding domain, leucine-rich repeat-containing family, CARD domain-containing protein 4 (NLRC4) inflammasome upon sensing components of the...

Description: Introduction: Patients (pts) with higher-risk myelodysplastic syndrome (HR-MDS) and those who fail to respond to or relapse/progress after treatment with hypomethylating agents (HMA) have limited therapeutic options and poor prognosis. PD-L1 expression is upregulated in HR-MDS pts (compared with lower-risk MDS pts) and in those who fail HMA therapy. Combining inhibition of the PD-L1/PD-1 pathway with azacitidine may improve outcomes in MDS. Methods: We conducted a Phase Ib trial of the anti-PD-L1 monoclonal antibody atezolizumab, with or without azacitidine, in HMA-failure and HMA-naive MDS pts (NCT02508870). The primary objective was to determine the safety and tolerability of atezolizumab as a single agent or in combination with azacitidine. An initial safety evaluation was performed in three cohorts. Cohort A1 (10 pts) consisted of HMA-failure HR-MDS pts treated with atezolizumab alone (1200mg IV q3w). Cohort B1 (11 pts) consisted of HMA-failure HR-MDS pts treated with atezolizumab (840mg IV q2w) in combination with azacitidine (75mg/m2 qd for 7 days q4w) for 6 cycles, followed by atezolizumab maintenance alone (1200mg IV q3w). Cohort C1 (6 pts) consisted of HMA-naive HR-MDS pts treated with atezolizumab (840mg IV q2w) in combination with azacitidine (75mg/m2 qd for 7 days q4w). If atezolizumab alone or in combination with azacitidine was deemed safe and tolerable in Cohorts A1 and B1, an additional 1:1 randomization into two cohorts of 30 pts each (Cohorts A2 and B2) was planned. If the combination of atezolizumab and azacitidine was found to be safe and tolerable in Cohort C1, an additional expansion cohort (Cohort C2) of 14 pts with HMA-naive HR-MDS was planned. Primary endpoints included determining the safety and tolerability of atezolizumab-based regimens in HR-MDS and defining the recommended Phase II dose for the combination. Results: As of January 2018, 42 HR-MDS pts had been treated with atezolizumab-based regimens: Cohort A, 10 pts; Cohort B, 11 pts; Cohort C, 21 pts. Median age for the entire pt cohort was 76 years (range: 63−89). Median treatment duration for Cohorts A, B, and C was 4.2, 5.5, and 5.8 months, respectively. The overall response rate for Cohorts A, B, and C was 0%, 9% (hematologic improvement [HI]: 9%), and 62% (CR, 14%; mCR, 19%; mCR + HI, 10%; HI, 19%), respectively. All pts in Cohorts A and B have discontinued therapy, with a median overall survival (OS) of 5.9 months and 10.7 months, respectively. For pts in Cohort C, 8/21 pts remain on therapy, and median OS has not been reached. Grade 3−5 adverse events (AEs) in 〉10% of pts were primarily hematologic; grade 3−5 febrile neutropenia occurred in 29% of all pts and was particularly common in pts receiving the atezolizumab-azacitidine combination (Cohorts B [36%] and C [33%] compared with Cohort A [10%]; Table 1). In Cohort A, 70% (7/10) of pts died, as did 64% (7/11) of pts in Cohort B and 29% (6/21) of pts in Cohort C. Median time to death was 160 days (Cohort A), 299 days (Cohort B), and 53 days (Cohort C). Timing and causes of death were different in the three cohorts. Causes of death were more commonly from disease progression in Cohorts A and B, while serious AEs accounted for all deaths in Cohort C (Table 2). In addition, deaths within 3 months occurred in 10%, 18%, and 29% of pts in Cohorts A, B, and C, respectively. The high early death rate compared with historical controls observed in HMA-naive HR-MDS patients (Cohort C) led to early termination of the study prior to completing recruitment. Biomarker assessment demonstrated PD-L1 expression on variable proportions of AML blasts in samples from all pts analyzed. However, PD-L1 expression was not associated with clinical response (Figure). Conclusions: Combination of atezolizumab plus azacitidine in HMA-naive HR-MDS pts had an unfavorable safety profile, which led to early termination. Limited responses were observed with atezo-based regimens (with or without azacitidine) in HMA-failure HR-MDS pts, without excessive or unexpected toxicity. Better understanding of the reasons associated with the differential toxicity profile observed between HMA-naive versus HMA-failure HR-MDS pts will be crucial for potential future developments of this combination. Disclosures Gerds: Incyte: Consultancy; Celgene: Consultancy; CTI Biopharma: Consultancy; Apexx Oncology: Consultancy. Khaled:Daiichi: Consultancy; Alexion: Consultancy, Speakers Bureau; Juno: Other: Travel Funding. Lin:Jazz Pharmaceuticals: Honoraria. Pollyea:AbbVie: Consultancy, Research Funding; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Curis: Membership on an entity's Board of Directors or advisory committees; Gilead: Consultancy; Agios: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Argenx: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Celyad: Consultancy, Membership on an entity's Board of Directors or advisory committees. Dail:Genentech: Employment, Equity Ownership. Green:Genentech: Employment. Ma:Genentech: Employment. Medeiros:Genentech: Employment, Equity Ownership. Phuong:Genentech Inc: Employment, Equity Ownership, Other: Ownership interests PLC. Wenger:F. Hoffmann-La Roche Ltd: Employment, Equity Ownership, Other: Ownership interests PLC. Yan:Roche: Employment.

Description: Introduction: Immune checkpoint inhibition targeting the PD-1/PD-L1 pathway is insufficient to induce clinical response in relapsed or refractory (R/R) multiple myeloma (MM). We postulated that combining atezolizumab (A; anti-PD-L1) with daratumumab (D; anti-CD38), which targets myeloma cells and has immunomodulatory activity, may alter the tumor microenvironment (TME) to favor cytotoxic T-cell activation and clinical activity. To assess the immunologic efficacy of this combination, we studied changes in CD8+ T cells in D-naïve and D-refractory pts from a Phase Ib study (GO29695; NCT02431208). Methods: Flow cytometry was performed using longitudinal peripheral blood (PB) and bone marrow aspirates (BMA) to characterize CD8+ cytotoxic T cells using 8 color flow panels. RNA sequencing (RNAseq) and dual-plex immunohistochemistry (IHC) (CD138/CD8, CD8/Ki-67, CD138/osteoclast) were performed using longitudinal CD138+ fraction and bone biopsies, respectively. For IHC, CD138+ cell masses of 〉5000μm2 were defined as tumor clusters. Osteoclasts were enumerated based on TRAP positivity and morphology. Table 1 shows on-treatment changes in Cohorts D1-D3. Table 2 shows baseline data in Cohorts A, B, D1-D3, and E. The median (bootstrap 95% CI) is used to describe the data. Results: 9/36 (25%) pts in cohorts D1-3 showed clinical efficacy (partial response or better); all were D-naïve. We studied CD8+ T-cell activation and proliferation (%CD8+HLA-DR+Ki-67+), the pharmacodynamic marker for A (Herbst et al. Nature 2014), in PB. All D-naive pts showed on-treatment increase in %CD8+HLA-DR+Ki-67+ cells in the periphery (C1D15-C2D1) compared to baseline, which was not observed in D-refractory pts (Table 1). In BMA, the increase in %CD8+HLA-DR+Ki-67+ (C2D15-C4D1) was observed in D-naïve pts with clinical response to A-D (sensitive), but not in non-responders (resistant) or D-refractory pts (all resistant), suggesting that sensitive pts have an immune-supportive TME. Preliminary IHC staining also showed an increase in CD8+Ki-67+ T cells in two responders after treatment. Gene enrichment analysis (RNAseq data, n=20) showed upregulation of an innate immune response signature, which appeared to be driven by a 'macrophage activation' gene signature post-treatment, in the CD138+ fraction of responders. To understand the mechanisms regulating sensitivity to treatment, we studied the spatial localization of CD8+ T cells with respect to CD138+ tumor cells by IHC. A higher density of CD8+ T cells within tumor clusters was seen at baseline in sensitive versus resistant pts, but this was not observed outside of tumor clusters (Table 1). In addition, the number of osteoclasts in the tumor region was higher in resistant pts, suggesting that these cells may contribute to the inhibition of T-cell function as reported(An et al. Blood 2016). This hypothesis was further supported by higher osteoclast numbers in D-refractory pts at baseline (Table 2), for whom an on-treatment increase in %CD8+HLA-DR+Ki-67+ cells was not observed in PB or BMA. Interestingly, higher median fluorescence intensity of PD-1 on CD8+ T-effector cells and on CD8+ T-effector memory cells was observed at baseline in D-naïve relative to D-refractory pts, while the level of PD-L1 expression on tumor cells was similar. An increase in activated proliferating T cells (%CD8+HLA-DR+Ki-67+) observed after treatment in D-naïve responders suggests that high PD-1 expression in this subset is not a marker of CD8+ T-cell exhaustion, but of functional capability. Conclusions: Clinical efficacy of A-D therapy in R/R MM pts is associated with higher CD8+ cell density in tumor clusters and lower osteoclast numbers in the tumor region at baseline, and an on-treatment increase in activated CD8+ T-cell populations in the bone marrow. The lack of a D-monotherapy arm in this study makes it difficult to assess the individual contribution of A to T-cell activation. The data presented, albeit a small number of samples from a Phase Ib study, support the hypothesis that the TME, including CD8+ T cells, tumor cells, and cells of myeloid lineage such as osteoclasts, has significant impact on the immunologic and clinical efficacy of combination therapy. A better understanding of the complex interplay between myeloma cells and their immune environment should pave the way for designing better immunotherapies with the potential for long-term disease control. Disclosures Raval: Roche: Employment, Equity Ownership. Cho:Agenus: Research Funding; Genentech: Honoraria, Research Funding; Takeda: Research Funding; BMS: Consultancy; The Multiple Myeloma Research Foundation: Employment; Celgene: Honoraria, Research Funding; GSK: Consultancy. Green:Genentech Inc.: Employment. Wassner Fritsch:F. Hoffmann-La Roche Ltd: Employment, Equity Ownership. Ma:Genentech: Employment. Chang:Roche Canada: Employment. Yan:F. Hoffmann-La Roche Ltd, Mississauga, Canada: Employment. Kockx:HistoGeneX: Equity Ownership. Shen:Genentech, Inc.: Employment. Huw:Roche/ Genentech: Employment, Equity Ownership. Balestiere:Genentech: Employment. Lipkind:Roche/Genentech: Employment. Huang:F. Hoffmann-La Roche Ltd: Employment. Byrtek:Genentech: Employment; Roche: Equity Ownership. Colburn:Genentech: Employment; Roche: Equity Ownership. Wong:Celgene Corporation: Research Funding; Genentech: Research Funding; Janssen: Research Funding; Fortis: Research Funding; Juno: Research Funding. Venstrom:F. Hoffmann-La Roche Ltd: Employment. Adamkewicz:F. Hoffmann-La Roche Ltd: Equity Ownership; Genentech, Inc.: Employment. OffLabel Disclosure: Atezolizumab (atezo) is a programmed death-ligand 1 (PD-L1) blocking antibody. In the United States, atezo is approved for treatment of pts with locally advanced or metastatic urothelial carcinoma who are not eligible for cisplatin-containing chemotherapy (chemo) and whose tumors express PDââ‚â'¬Ã'ÂL1, or are not eligible for any platinumââ‚â'¬Ã'Âcontaining chemo regardless of PDââ‚â'¬Ã'ÂL1 status, or have disease progression during or following any platinum-containing chemo, or within 12 months of neoadjuvant or adjuvant chemo. Atezo is also approved: in combination with bevacizumab, paclitaxel and carboplatin for first-line treatment of pts with metastatic non-squamous non-small-cell lung carcinoma (NSCLC) with no EGFR or ALK genomic tumor aberrations, and for pts with metastatic NSCLC who have disease progression during or following platinum-containing chemo; in combination with paclitaxel protein-bound for the treatment of adults with unresectable locally advanced or metastatic triple-negative breast cancer whose tumors express PD-L1; and in combination with carboplatin and etoposide, for the first-line treatment of adults with extensive-stage small cell lung cancer. Atezo is not approved for treatment of pts with multiple myeloma.

Description: Introduction: The lymphoma microenvironment is increasingly recognized as crucial to sustaining lymphoma cell growth and an important contributor to treatment outcome, especially in the context of immunotherapies. CD20-targeted monoclonal antibodies (e.g. obinutuzumab [G] and rituximab [R]) function by several mechanisms, including antibody-dependent cellular cytotoxicity/phagocytosis (ADCC/ADCP). Immune effector cells, such as natural killer (NK) cells and phagocytes (i.e. macrophages and dendritic cells), and the Fc gamma receptor (FcγR) found on the surface of these cells, are critical to antibody treatment efficacy. Here we evaluated how the lymphoma microenvironment may affect clinical outcome in patients (pts) with previously untreated diffuse large B-cell lymphoma (DLBCL) receiving immunochemotherapy. Methods: We leveraged two large Phase III clinical trials of pts with previously untreated DLBCL (GOYA [NCT01287741] and MAIN [NCT00486759]) to produce comprehensive lymphoma immune microenvironment profiles from 604 tissue biopsies from pts treated with R plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP) or G plus CHOP (G-CHOP) using the RNA-Seq deconvolution and marker gene methods: quanTIseq and xCell. The infiltration scores in each pt for various immune and stromal cell types were assessed, and their contribution to disease biology and treatment outcome was examined. Results: The extent of lymphoma microenvironment heterogeneity highlighted by the deconvolution analyses was consistent with previous studies (Figure A). Of the infiltrating cell types analyzed, the M1 macrophage signature quantified by either quanTIseq or xCell was most strongly associated with lower risk of progression (progression-free survival [PFS]; quanTIseq: HR, 0.596; 95% CI: 0.441-0.805; 24-month PFS: 82% [M1 high] vs 68% [M1 low] and xCell: HR, 0.627; 95% CI: 0.465-0.844; 24-month PFS: 80% [M1 high] vs 70% [M1 Low]; Figure B, C, D) and improved overall survival (OS; quanTIseq: HR, 0.465; 95% CI: 0.318-0.679; and xCell: HR, 0.527; 95% CI: 0.365-0.762). This finding was confirmed by both algorithms. This prognostic trend was stronger amongst G-treated pts than R-treated pts, consistent with the previous finding that G exhibits higher ADCC versus R (Mössner, et al. Blood 2010). Pts with PFS 〉24 months had significantly higher levels of M1 macrophage scores than pts with PFS