Presentation1_Practices for running a research-oriented shared cryo-EM facility.pdf

The Harvard Cryo-Electron Microscopy Center for Structural Biology, which was formed as a consortium between Harvard Medical School, Boston Children’s Hospital, Dana-Farber Cancer Institute, and Massachusetts General Hospital, serves both academic and commercial users in the greater Harvard community. The facility strives to optimize research productivity while training users to become expert electron microscopists. These two tasks may be at odds and require careful balance to keep research projects moving forward while still allowing trainees to develop independence and expertise. This article presents the model developed at Harvard Medical School for running a research-oriented cryo-EM facility. Being a research-oriented facility begins with training in cryo-sample preparation on a trainee’s own sample, ideally producing grids that can be screened and optimized on the Talos Arctica via multiple established pipelines. The first option, staff assisted screening, requires no user experience and a staff member provides instant feedback about the suitability of the sample for cryo-EM investigation and discusses potential strategies for sample optimization. Another option, rapid access, allows users short sessions to screen samples and introductory training for basic microscope operation. Once a sample reaches the stage where data collection is warranted, new users are trained on setting up data collection for themselves on either the Talos Arctica or Titan Krios microscope until independence is established. By providing incremental training and screening pipelines, the bottleneck of sample preparation can be overcome in parallel with developing skills as an electron microscopist. This approach allows for the development of expertise without hindering breakthroughs in key research areas.</p

Evidence of Kinetic Cooperativity in Dimeric Ketopantoate Reductase from <i>Staphylococcus aureus</i>

Ketopantoate reductase (KPR) catalyzes the NADPH-dependent production of pantoate, an essential precursor in the biosynthesis of coenzyme A. Previous structural studies have been limited to <i>Escherichia coli</i> KPR, a monomeric enzyme that follows a sequential ordered mechanism. Here we report the crystal structure of the <i>Staphylococcus aureus</i> enzyme at 1.8 Å resolution, the first description of a dimeric KPR. Using sedimentation velocity analysis, we show that the <i>S. aureus</i> KPR dimer is stable in solution. In fact, our structural analysis shows that the dimeric assembly we identify is present in the majority of KPR crystal structures. Steady state analysis of <i>S. aureus</i> KPR reveals strong positive cooperativity with respect to NADPH (Hill coefficient of 2.5). In contrast, high concentrations of the substrate ketopantoate (KP) inhibit the activity of the enzyme. These observations are consistent with a random addition mechanism in which the initial binding of NADPH is the kinetically preferred path. In fact, Förster resonance energy transfer studies of the equilibrium binding of NADPH show only a small degree of cooperativity between subunits (Hill coefficient of 1.3). Thus, the apparently strong cooperativity observed in substrate saturation curves is due to a kinetic process that favors NADPH binding first. This interpretation is consistent with our analysis of the A181L substitution, which increases the <i>K</i>_m of ketopantoate 844-fold, without affecting <i>k</i>_cat. The crystal structure of KPR_A181L shows that the substitution displaces Ser239, which is known to be important for the binding affinity of KP. The decrease in KP affinity would enhance the already kinetically preferred NADPH binding path, making the random mechanism appear to be sequentially ordered and reducing the kinetic cooperativity. Consistent with this interpretation, the NADPH saturation curve for KPR_A181L is hyperbolic

Imprime PGG-Mediated Anti-Cancer Immune Activation Requires Immune Complex Formation

<div><p>Imprime PGG (Imprime), an intravenously-administered, soluble β-glucan, has shown compelling efficacy in multiple phase 2 clinical trials with tumor targeting or anti-angiogenic antibodies. Mechanistically, Imprime acts as pathogen-associated molecular pattern (PAMP) directly activating innate immune effector cells, triggering a coordinated anti-cancer immune response. Herein, using whole blood from healthy human subjects, we show that Imprime-induced anti-cancer functionality is dependent on immune complex formation with naturally-occurring, anti-β glucan antibodies (ABA). The formation of Imprime-ABA complexes activates complement, primarily via the classical complement pathway, and is opsonized by iC3b. Immune complex binding depends upon Complement Receptor 3 and Fcg Receptor IIa, eliciting phenotypic activation of, and enhanced chemokine production by, neutrophils and monocytes, enabling these effector cells to kill antibody-opsonized tumor cells via the generation of reactive oxygen species and antibody-dependent cellular phagocytosis. Importantly, these innate immune cell changes were not evident in subjects with low ABA levels but could be rescued with exogenous ABA supplementation. Together, these data indicate that pre-existing ABA are essential for Imprime-mediated anti-cancer immune activation and suggest that pre-treatment ABA levels may provide a plausible patient selection biomarker to delineate patients most likely to benefit from Imprime-based therapy.</p></div

ABA are critical for Imprime function.

<p>(A) The generation of C5a in WB plasma (14 LB and 18 HB) after incubation with Imprime for 30 mins, and IL-8 (21 LB and 11 HB) in WB after incubation with Imprime for 24 hrs were measured by ELISA. The amounts of C5a or IL-8 produced by Imprime—treated WB are presented as fold increase for individual HB and LB relative to the vehicle control. CD11b expression on neutrophils (11 LB and 12 HB) and monocytes (8 LB and 10 HB) after incubation with Imprime for 30 mins were assessed by flow cytometry. The % increase of CD11b was calculated using the MFI of Imprime-treated cells compared with vehicle-treated cells as baseline. ROS and ADCP assays were performed as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165909#pone.0165909.g006" target="_blank">Fig 6</a>. The amount of ROS activity is presented as fold increase of AUC relative to that of the vehicle-treated neutrophils. The insets show the representative ROS activity of neutrophils from a LB or a HB over a 60-mins time period. The ADCP is presented as average fold increase relative to the vehicle control. Results for ADCP and ROS are from 3 HB and 3 LB. Data represent mean ± SEM of triplicates for each treatment condition. IL-8 and MCP-1 production (B) and neutrophil ROS activity (C) were assessed in LB after exogenous addition of ABA to Imprime-treated WB. Results presented are representative of at least 3 independent experiments performed with different donors.</p

List of antibodies used in the study.

<p>List of antibodies used in the study.</p

Imprime binding requires ABA.

<p>(A) Imprime binding (10 μg/mL) was measured in WB from 143 healthy donors. The serum from the same blood donation was used to measure relative ABA concentrations by ELISA with RAU/mL as the reportable value. The Pearson’s correlation (r) and <i>P</i>-value of Imprime binding to neutrophils and monocytes binding and ABA IgG and IgM concentrations are shown. (B) The IgG and IgM ABA level of each of the 143 healthy subjects identified as HB (>5% binding) and LB (≤ 5% binding) are shown in the scatter plot with the mean IgG or IgM ABA concentration of each group indicated. Imprime binding in a LB was evaluated by (C) adding increasing amount of HB serum and increasing concentration of ABA. (D) Imprime binding in a HB was evaluated in ABA-depleted serum (FT; flow through from the Imprime-conjugated bead column) and subsequently rescued binding by exogenous supplementation of ABA. MFI and percentages of BfD IV-positive cells are indicated on the contour plots. Data presented in (C) and (D) are representative of at least 3 independent experiments performed with different donors.</p

Imprime interacts with endogenous IgG and IgM ABA in human serum.

<p>(A) The surface IgG and IgM ABA on vehicle- or Imprime-treated neutrophils and monocytes were detected by flow cytometry using rabbit anti-human IgG- and IgM-specific Abs, respectively, after Imprime was incubated with WB at 37°C for 30 mins. The MFI and percentage of IgG- or IgM-positive cells are indicated on the contour plots. Data shown are representative of 3 independent experiments. (B) The ability of an Imprime-conjugated bead column to selectively bind and retain IgG (filled bar) and IgM (empty bar) ABA from human serum is shown. The percentage of ABA in the flow-through (FT) and the eluate was measured based on the serum ABA concentration pre-loaded on the column. The ABA eluted off the Imprime-conjugated bead column along with purified IgG and IgM controls were resolved by SDS-PAGE under reducing conditions. Protein bands corresponding to the heavy and light chain of IgG and IgM were observed by Coomassie staining (left panel), or detected by immunoblotting with an anti-IgG Ab (middle panel) or anti-IgM heavy chain Ab (right panel).</p

Imprime binding to neutrophils and monocytes in whole blood is complement-dependent.

<p>(A) Binding of increasing concentration of Imprime (0, 0.1, 1, 10, and 25 μg/mL) to human neutrophils and monocytes was measured by flow cytometry after incubation of WB with Imprime or vehicle at 37°C for 30 mins. (B) Imprime binding in the absence of serum (serum removed), heat-inactivated serum (HI serum), presence of anti-C3 peptide, compstatin (100 μM) or α-CR1 mAb (10 μg/mL) (right column in each respective row) are compared to the binding to vehicle or Imprime of untreated WB (left and middle column in each respective row). For compstatin and α-CR1 mAb treatment, WB was pre-treated with the blocking agents at 4°C for 30 mins prior to the incubation with 10 μg/mL Imprime at 37°C for 30 mins. (C) The role of classical pathway in Imprime binding to neutrophils and monocytes was evaluated by blocking with the anti-C1q mAb (50 μg/mL) at 4°C for 30 mins prior to the incubation with Imprime or vehicle. (D) Imprime binding to enriched human neutrophils and monocytes in 20% serum, 20% C1q-depleted serum (C1q-dep serum), or 20% C1q-depleted serum replenished with 100 μg/mL purified human C1q protein (C1q-dep serum + C1q protein) was determined by flow cytometry. The MFI and percentage of BfD IV positive cells are indicated on the contour plots. Data shown for each part are representative of 3–5 independent experiments performed with different donors.</p

Structure of Imprime.

<p>Imprime is composed of a β-(1–3)-linked glucopyranose backbone with periodic β-(1–3)-linked glucopyranose side chains linked to the backbone via β-(1–6) glycosidic linkages.</p

Imprime activates innate immune functions.

<p>(A) Complement activation proteins C4a, C5a, SC5b-9 in the plasma of WB treated with 10 μg/mL Imprime or vehicle for 30 mins at 37°C was measured by ELISA. Data represent mean ± SEM of triplicates for each treatment condition. (B) Modulation of CD11b, CD62L, CD88 and CXCR2 expression on neutrophils and monocytes post Imprime binding in WB was determined by flow cytometry. (C) Chemokine, IL-8 and MCP-1, production in the plasma of WB treated with Imprime or vehicle for 24 h at 37°C was measured by Luminex. Data represent mean ± SEM of duplicates from 3 independent experiments. (D) ROS production in 25:1 co-cultures of neutrophils (isolated from WB treated with 25 μg/mL Imprime or vehicle for 2 hrs at 37°C) and Raji cells treated with or without 1 μg/mL rituximab was measured by luminescence-based assay. Macrophage-mediated ADCP was measured by flow cytometry after 1:1 co-incubation of macrophages (differentiated from monocytes isolated from WB treated with 25 μg/mL Imprime or vehicle for 2 hrs at 37°C) with Raji cells treated with or without 1 μg/mL rituximab. Representative results are shown here from at least 3 independent experiments performed with three different donors.</p