Achievement of Target Gain Larger than Unity in an Inertial Fusion Experiment

On December 5, 2022, an indirect drive fusion implosion on the National Ignition Facility (NIF) achieved a target gain G_{target} of 1.5. This is the first laboratory demonstration of exceeding "scientific breakeven" (or G_{target}>1) where 2.05 MJ of 351 nm laser light produced 3.1 MJ of total fusion yield, a result which significantly exceeds the Lawson criterion for fusion ignition as reported in a previous NIF implosion [H. Abu-Shawareb et al. (Indirect Drive ICF Collaboration), Phys. Rev. Lett. 129, 075001 (2022)PRLTAO0031-900710.1103/PhysRevLett.129.075001]. This achievement is the culmination of more than five decades of research and gives proof that laboratory fusion, based on fundamental physics principles, is possible. This Letter reports on the target, laser, design, and experimental advancements that led to this result.

Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens

The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.

Global detection of human variants and isoforms by deep proteome sequencing

An average shotgun proteomics experiment detects approximately 10,000 human proteins from a single sample. However, individual proteins are typically identified by peptide sequences representing a small fraction of their total amino acids. Hence, an average shotgun experiment fails to distinguish different protein variants and isoforms. Deeper proteome sequencing is therefore required for the global discovery of protein isoforms. Using six different human cell lines, six proteases, deep fractionation and three tandem mass spectrometry fragmentation methods, we identify a million unique peptides from 17,717 protein groups, with a median sequence coverage of approximately 80%. Direct comparison with RNA expression data provides evidence for the translation of most nonsynonymous variants. We have also hypothesized that undetected variants likely arise from mutation-induced protein instability. We further observe comparable detection rates for exon-exon junction peptides representing constitutive and alternative splicing events. Our dataset represents a resource for proteoform discovery and provides direct evidence that most frame-preserving alternatively spliced isoforms are translated.

Mycobacterial formation of intracellular lipid inclusions is a dynamic process associated with rapid replication

Intracellular lipid inclusions (ILI) are triacylglyceride rich organelles produced by mycobacteria thought to serve as energy reservoirs. It is believed that ILI are formed as a result of a dosR mediated transition from replicative growth to non-replicating persistence (NRP). ILI rich Mycobacterium tuberculosis (Mtb) bacilli have been reported during infection and in sputum, establishing their importance in Mtb pathogenesis. Studies conducted in mycobacteria such as Mycobacterium smegmatis, Mycobacterium abscessus, or lab Mtb strains have demonstrated ILI formation in the presence of hypoxic, nitric oxide, nutrient limitation, or low nitrogen stress, conditions believed to emulate the host environment within which Mtb resides. Here, we show that M. marinum and clinical Mtb isolates make ILI during active replication in axenic culture independent of environmental stressors. By tracking ILI formation dynamics we demonstrate that ILI are quickly formed in the presence of fresh media or exogenous fatty acids but are rapidly depleted while bacteria are still actively replicating. We also show that the cell envelope is an alternate site for neutral lipid accumulation observed during stationary phase. In addition, we screen a panel of 60 clinical isolates and observe variation in ILI production during early log phase growth between and among Mtb lineages. Finally, we show that dosR expression level does not strictly correlate with ILI accumulation in fresh clinical isolates. Taken together, our data provide evidence of an active ILI formation pathway in replicating mycobacteria cultured in the absence of stressors, suggesting a decoupling of ILI formation from NRP.

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics

Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth of protein quantification, especially for proteins and modifications of biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus increasing proteome depth. These strategies increased the sensitivity, data completeness and proteome coverage over twofold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport, similarly across both treatment conditions. This covariation is coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at http://scp.slavovlab.net/pSCoPE .

A79 THE RELATIONSHIP BETWEEN VISCERAL ADIPOSITY AND NONALCOHOLIC FATTY LIVER DISEASE DIAGNOSED BY CONTROLLED ATTENUATION PARAMETER IN PEOPLE WITH HIV: A PILOT STUDY

Background

Aging people with HIV (PWH) on antiretroviral therapy face high rates of metabolic dysfunction and nonalcoholic fatty liver disease (NAFLD). Fat alterations are frequent in PWH and predict worse cardiometabolic outcomes. Visceral adipose tissue (VAT) is an important compartment of body fat tissue releasing bioactive molecules. As a hormonally active tissue, VAT critically contributes to obesity-related disorders and is associated with ectopic fat accumulation in the liver.

Purpose

We aimed to investigate NAFLD diagnosed by controlled attenuation parameter (CAP) as a marker of visceral adiposity in PWH.

Method

We conducted a prospective pilot study (ClinicalTrials.gov 2021-6656) of HIV mono-infected patients undergoing metabolic characterization and paired CAP by transient elastography with dual-energy X-ray absorptiometry (DEXA) scan. NAFLD was defined as CAP ≥285 dB/m, in absence of alcohol abuse. Excess visceral adiposity was defined as VAT>1.32 Kg. Pairwise correlation, area under the curve (AUC) and logistic regression analysis were employed to study the association between VAT and CAP.

Result(s)

30 patients (90% male, mean age 48.5, mean BMI 29.9, mean waist circumference 100.9, 50% with NAFLD) were included. When compared to those without excess VAT, PWH with excess VAT were older (53+12 vs 43+13 years, p=0.035), had longer duration of HIV infection (20+13 vs. 9+9 years, p=0.021), had higher BMI (32+4 vs 27+4 Kg/m², p=0.002) and waist circumference (107+11 vs. 93+12 cm, p=0.004). They also had more history of cardiovascular events (29% vs. 0, p=0.032) and higher lipid accumulation product, a marker of lipid accumulation based on waist circumference and triglycerides (112+53 vs. 38+27, p<0.001). CAP was higher in PWH with excess VAT (319+52 vs. 213+52 dB/m, p<0.001). CAP positively correlated with all visceral fat measurements by DEXA, including VAT (r=0.650, p<0.001), VAT/body weight ratio (r=0.565, p=0.001) and fat mass (r=0.390, p=0.033). Both BMI and waist circumference showed correlation with VAT and fat mass, but not with VAT/body weight ratio (see Figure). After adjusting for duration of HIV infection (aOR 1.01 per year, 95% CI 0.91-1.12; p=0.921), BMI (aOR 1.77, 95% CI 0.74-4.23; p=0.202) and waist circumference (aOR 0.91 per cm, 95% 0.68-1.21; p=0.509), CAP remained the only independent predictor of excess VAT (aOR 1.05 per dB/m, 95% CI 1.01-1.10; p=0.036). The AUC analysis determined CAP had excellent performance to diagnose excess VAT (AUC 0.92, 95% CI 0.81-1.00), higher than BMI (AUC 0.83, 95% CI 0.68-0.99) and waist circumference (AUC 0.81, 95% CI 0.65-0.97). The optimized CAP cut-off to diagnose excess VAT was 266 dB/m, with a sensitivity of 88.3% and a specificity of 84.6%.

Image

Conclusion(s)

NAFLD diagnosed by CAP is associated with VAT in PWH independently of anthropometric measures of obesity. CAP could be used as a diagnostic marker of visceral adiposity in the practice of HIV medicine

Please acknowledge all funding agencies by checking the applicable boxes below

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Please indicate your source of funding;

CanHepC

Disclosure of Interest

W. Elgretli Grant / Research support from: CanHepC, N. Paisible: None Declared, C. Costiniuk: None Declared, J. Cox: None Declared, D. Kablawi: None Declared, M. Klein: None Declared, N. Kronfli: None Declared, J.-P. Routy: None Declared, J. Falutz: None Declared, B. Lebouche: None Declared, G. Guaraldi: None Declared, G. Sebastiani: None Declared

Prediction of peptide mass spectral libraries with machine learning

The recent development of machine learning methods to identify peptides in complex mass spectrometric data constitutes a major breakthrough in proteomics. Longstanding methods for peptide identification, such as search engines and experimental spectral libraries, are being superseded by deep learning models that allow the fragmentation spectra of peptides to be predicted from their amino acid sequence. These new approaches, including recurrent neural networks and convolutional neural networks, use predicted in silico spectral libraries rather than experimental libraries to achieve higher sensitivity and/or specificity in the analysis of proteomics data. Machine learning is galvanizing applications that involve large search spaces, such as immunopeptidomics and proteogenomics. Current challenges in the field include the prediction of spectra for peptides with post-translational modifications and for cross-linked pairs of peptides. Permeation of machine-learning-based spectral prediction into search engines and spectrum-centric data-independent acquisition workflows for diverse peptide classes and measurement conditions will continue to push sensitivity and dynamic range in proteomics applications in the coming years.

Diagnosis of venous thromboembolism in pregnancy: a review of current guidelines

Venous thromboembolic disease (VTE) is the leading cause of maternal death throughout the developed world. International and national guidance for the diagnosis and management of VTE in pregnancy is varied and limited, which can result in problems in clinical practice. The imaging challenges of VTE in the general population are challenging but become more complex in pregnancy due to the physiological changes in the circulatory system, which alter clinical judgment and test performance. As an additional factor, the relative radiation risks to the mother and fetus arising from diagnostic tests need to be assessed and communicated to the patient in a clear and understandable way. The purpose of this review is fourfold. We propose to review and summarise the current imaging guidelines available for this condition; critically review the evidence base within the current literature; address the issues of test performance of imaging examinations used for VTE in pregnancy; and address the question of radiation risk and how to communicate this information to patients.

Lawson Criterion for Ignition Exceeded in an Inertial Fusion Experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion.

P-698 Pituitary functioning gonadotroph adenomas (FGA)-induced ovarian hyperstimulation syndrome (OHSS): results from tertiary neuroendocrine centres in the UK

Study question

There are no published series of OHSS due to FGA. What FGA features should clinicians look for during OHSS, and what treatments are effective?

Summary answer

FGA tumour size is always &gt;10mm. Other pituitary hormones may be deficient. Surgical resection of FGA is an effective treatment for OHSS.

What is known already

Pituitary adenomas affect 1:1000 adults and are classified as functioning or non-functioning. Non-functioning pituitary adenomas do not secrete hormones, but most commonly stain histologically gonadotroph cells. Functional pituitary adenomas secrete hormones such as prolactin causing prolactinoma. However, it is rare for a pituitary tumour to cause clinical features of excessive gonadotrophins (functioning gonadotroph adenoma; FGA).

Single case reports, but no case series, have been published on the presentation of FGA-induced OHSS in women.

Surgical excision of adenomas has been reported to cause remission of symptoms, though systematic data are lacking owing to rarity of these tumours.

Study design, size, duration

National case series from tertiary neuroendocrine units in England, Wales and Scotland.

Participants/materials, setting, methods

Eight high-volume pituitary endocrine tertiary units within England, Wales and Scotland audited their records for any cases of FGA-induced OHSS; only seven patients have been identified to date. In all cases, there had been no recent exposure to assisted reproductive technologies (ART) or drugs known to induce OHSS including gonadotrophins or selective oestrogen receptor modulators (SERMS).

Main results and the role of chance

Seven cases of FGA were identified with mean age 31.6 years (range 16-48) at diagnosis. Two-of-seven women presented acutely unwell with abdominal pain, distention and palpable mass requiring oophorectomy for ovarian torsion/ruptured ovarian cyst. The remaining five women presented with abdominal pain (n = 2), thyrotoxicosis (n = 1), menstrual irregularities/galactorrhoea (n = 1) and visual disturbances (n = 1). All women experienced intermittent pelvic pain during medical attendance. Pelvic ultrasound demonstrated enlarged multiseptated ovaries (volume ranging 27-442cm3). Ascites was noted in one woman. Six women had visual field defects due to optic chiasm compression on formal assessment. Median FSH was 26.10 u/L (8.3-33), but LH was &lt;2.5 u/L in all cases. Estradiol (E2) far exceeded the reference range in 5/7 women (2990 to &gt; 18000pmol/L);E2 was at the upper limit of normal in the remaining 2/7 women (960-1450pmol/L). Hyperprolactinaemia, hyperthyroidism and other pituitary hormones deficiency were noted in 6/7, 1/7 and 4/7 women respectively. All FGAs were macroadenomas with diameters ranging 16-48mm. Two patients were administered a somatostatin analogue prior to surgery, but FSH, E2 and tumour size did not change. Transsphenoidal surgery was performed in 6/7 women, and always improved symptomatic and biochemical features of OHSS; however, residual FGA tumour was present post-operatively in all cases studied.

Limitations, reasons for caution

It is possible that some ‘non-functioning’ gonadotroph adenomas cause subclinical problems including menstrual irregularity and mild OHSS which were never diagnosed.

We have insufficient data to determine the prognosis for future pregnancy after FGA-induced OHSS.

This study utilised historical case-notes, so some data is missing.

Wider implications of the findings

The ‘spontaneous’ presentation of OHSS may be confusing for clinicians. We report that FGA is an important cause of spontaneous OHSS which has well-defined biochemical and radiological characteristics, which may be treated effectively in the short-to-medium with pituitary surgery. Results of this study may provide greater awareness of FGA-induced OHSS.

Trial registration number

N/A

AB0060 SYSTEMIC INFLAMMATORY EFFECT ON HIPPOCAMPAL VOLUME IN RHEUMATOID ARTHRITIS AND ULCERATIVE COLITIS

Background

Autoimmune diseases represent a large and heterogeneous group of disorders that afflict specific target organs. However, multiple factors point to common links between the differing presentations of autoimmune disorders.

With increased interest in further understanding the neuro-immune axis, autoimmune diseases represent an important opportunity to explore whether systemic inflammation from these autoimmune pathways has a central effect and, if so, whether there is a common or discrete central effect caused by different autoimmune diseases.

Objectives

The present study aimed to analyse hippocampal volume in patients with rheumatoid arthritis (RA) and ulcerative colitis (UC) as compared to healthy control groups. The hippocampus was chosen as a region of interest given the regulatory role it exhibits in the hypothalamic–pituitary–adrenal (HPA) axis2. Additionally, the hippocampus has been identified as a region that is affected in other autoimmune diseases such as systemic lupus erythematosus (SLE).

Methods

Data from 1,040 individuals in the UKBiobank Imaging sub-study were included in the present study. This was divided into two separate patient populations with separate control groups. Data from 267 individuals (mean age ± SD =65.52 ± 7.02, 70.8% females) were included in the RA patient group with 267 age and sex matched controls (mean age ± SD = 65.51 ± 7, 70.8% females). Data from 253 individuals (mean age ± SD = 64.09 ± 7.03, 51.6% females) were included in the UC patient group with 253 age and sex matched controls (mean age ± SD = 63.4 ± 7.02, 51.6% females).

The UKBiobank is a prospective observational study with a proposed cohort of 500,000 participants. The imaging substudy is planned to scan 100,000 of those participants with a standardised scanning protocol including MRI of the brain. Multi-modal images were acquired on a 3T scanner3. From the T1w data, volumetric imaging derived phenotypes (IDPs) are provided using the FMRIB Integrated Registration and Segmentation Tool (FIRST); http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST. This study utilised the right and left hippocampal volume outputs from that tool.

Results

We observed a smaller hippocampal volume in UC patients when compared to healthy controls (difference right: 99.78 mm3, SD ± 38.97, p = 0.01; left: 74.30 mm3, SD ± 39.41, p = 0.06). The Cohen’s effect size was d = -0.24 [95% CI -0.43, -0.05] for right hippocampal volume and d = -0.18 [95% CI -0.36, 0.00] for left hippocampal volume.

Figure 1.

Right and left hippocampal volume in UC patients versus controls and right and left hippocampal volume in RA patients versus controls.

There was no significant difference seen in hippocampal volume in RA patients compared to controls (difference right: 61.32 mm3, SD ± 40.33, p = 0.13; left: 39.00 mm3, SD ± 38.19, p = 0.31). The Cohen’s effect size was d = -0.12 [95% CI -0.30, 0.06] for right hippocampal volume and d = -0.08 [95% CI -0.27, 0.10] for left hippocampal volume.

Conclusion

This study provides evidence of moderate reduction in hippocampal volumes in patients with ulcerative colitis as compared to age and sex matched healthy controls. This same effect was not seen in a similarly matched rheumatoid arthritis patient population. Further analysis of additional subcortical regions could provide further context for whether there are alternative regions affected in both RA and UC.

References

[1]Bellavance, M.A, Rivest, S., (2014), ‘The HPA – immune axis and the immunomodulatory actions of glucocorticoids in the brain’, Frontiers in Immunology, vol, 5, pp 136.

[2]Miller, K.L., Alfaro-Almagro, F., Bangerter, N.K. et al. (2016), ‘Multimodal Multimodal population brain imaging in the UK Biobank prospective epidemiological study’, Nature Neuroscience, vol. 19, pp. 1523-1536.

Disclosure of Interests

Jennifer Cox Grant/research support from: PhD funded by GlaxoSmithKline, Employee of: Former employee of GlaxoSmithKline, Marius de Groot Shareholder of: Employee of GlaxoSmithKline, Employee of: Employee of GlaxoSmithKline, James Cole: None declared, Steven Williams: None declared

Deubiquitinating enzymes and the proteasome regulate preferential sets of ubiquitin substrates

The ubiquitin-proteasome axis has been extensively explored at a system-wide level, but the impact of deubiquitinating enzymes (DUBs) on the ubiquitinome remains largely unknown. Here, we compare the contributions of the proteasome and DUBs on the global ubiquitinome, using UbiSite technology, inhibitors and mass spectrometry. We uncover large dynamic ubiquitin signalling networks with substrates and sites preferentially regulated by DUBs or by the proteasome, highlighting the role of DUBs in degradation-independent ubiquitination. DUBs regulate substrates via at least 40,000 unique sites. Regulated networks of ubiquitin substrates are involved in autophagy, apoptosis, genome integrity, telomere integrity, cell cycle progression, mitochondrial function, vesicle transport, signal transduction, transcription, pre-mRNA splicing and many other cellular processes. Moreover, we show that ubiquitin conjugated to SUMO2/3 forms a strong proteasomal degradation signal. Interestingly, PARP1 is hyper-ubiquitinated in response to DUB inhibition, which increases its enzymatic activity. Our study uncovers key regulatory roles of DUBs and provides a resource of endogenous ubiquitination sites to aid the analysis of substrate specific ubiquitin signalling.

Perseus plugin "Metis" for metabolic-pathway-centered quantitative multi-omics data analysis for static and time-series experimental designs

We introduce Metis, a new plugin for the Perseus software aimed at analyzing quantitative multi-omics data based on metabolic pathways. Data from different omics types are connected through reactions of a genome-scale metabolic-pathway reconstruction. Metabolite concentrations connect through the reactants, while transcript, protein, and protein post-translational modification (PTM) data are associated through the enzymes catalyzing the reactions. Supported experimental designs include static comparative studies and time-series data. As an example for the latter, we combine circadian mouse liver multi-omics data and study the contribution of cycles of phosphoproteome and metabolome to enzyme activity regulation. Our analysis resulted in 52 pairs of cycling phosphosites and metabolites connected through a reaction. The time lags between phosphorylation and metabolite peak show non-uniform behavior, indicating a major contribution of phosphorylation in the modulation of enzymatic activity.

Benchmarking differential expression, imputation and quantification methods for proteomics data

Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools for protein quantification, imputation and differential expression (DE) analysis were generated in the past decade and the search for optimal tools is still going on. Moreover, due to the rapid development of RNA sequencing (RNA-seq) technology, a vast number of DE analysis methods were created for that purpose. The applicability of these newly developed RNA-seq-oriented tools to proteomics data remains in doubt. In order to benchmark these analysis methods, a proteomics dataset consisting of proteins derived from humans, yeast and drosophila, in defined ratios, was generated in this study. Based on this dataset, DE analysis tools, including microarray- and RNA-seq-based ones, imputation algorithms and protein quantification methods were compared and benchmarked. Furthermore, applying these approaches to two public datasets showed that RNA-seq-based DE tools achieved higher accuracy (ACC) in identifying DEPs. This study provides useful guidelines for analyzing quantitative proteomics datasets. All the methods used in this study were integrated into the Perseus software, version 2.0.3.0, which is available at https://www.maxquant.org/perseus.

The proteogenomic subtypes of acute myeloid leukemia

Acute myeloid leukemia (AML) is an aggressive blood cancer with a poor prognosis. We report a comprehensive proteogenomic analysis of bone marrow biopsies from 252 uniformly treated AML patients to elucidate the molecular pathophysiology of AML in order to inform future diagnostic and therapeutic approaches. In addition to in-depth quantitative proteomics, our analysis includes cytogenetic profiling and DNA/RNA sequencing. We identify five proteomic AML subtypes, each reflecting specific biological features spanning genomic boundaries. Two of these proteomic subtypes correlate with patient outcome, but none is exclusively associated with specific genomic aberrations. Remarkably, one subtype (Mito-AML), which is captured only in the proteome, is characterized by high expression of mitochondrial proteins and confers poor outcome, with reduced remission rate and shorter overall survival on treatment with intensive induction chemotherapy. Functional analyses reveal that Mito-AML is metabolically wired toward stronger complex I-dependent respiration and is more responsive to treatment with the BCL2 inhibitor venetoclax.

Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx

Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the three-dimensional (3D) structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to noncleavable and MS-cleavable cross-linkers. For both, we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For noncleavable peptides, we implemented a novel dipeptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the dipeptide individually. A posterior error probability (PEP) based on total and partial scores is used to control false discovery rates (FDRs). For MS-cleavable cross-linkers, a score of signature peaks is combined with the conventional Andromeda score on the cleavage products. The MaxQuant 3D peak detection was improved to ensure more accurate determination of the monoisotopic peak of isotope patterns for heavy molecules, which cross-linked peptides typically are. A wide selection of filtering parameters can replace the manual filtering of identifications, which is often necessary when using other pipelines. On benchmark data sets of synthetic peptides, MaxLynx outperforms all other tested software on data for both types of cross-linkers and on a proteome-wide data set of cross-linked Drosophila melanogaster cell lysate. The workflow also supports ion mobility-enhanced MS data. MaxLynx runs on Windows and Linux, contains an interactive viewer for displaying annotated cross-linked spectra, and is freely available at https://www.maxquant.org/.

MaxQuant Module for the Identification of Genomic Variants Propagated into Peptides

Standard shotgun proteomics data analysis pipelines usually only identify peptides that are encoded in the reference genome. In many situations, it is desirable to identify peptides resulting from non-synonymous variations as well. Here, we present a new module in the MaxQuant software that takes both DNA and RNA based next-generation sequencing (NGS) data as well as raw proteomics data as input. This allows for the identification of variant peptides that are otherwise missed.

Human papillomavirus (HPV) vaccination across a cascade of knowledge, willingness, and uptake among gay, bisexual, and other men who have sex with men in Canada's three largest cities

BACKGROUND

Some Canadian jurisdictions offer publicly funded HPV vaccine to gay, bisexual, and other men who have sex with men (GBM) aged ≤26 years. We characterized factors associated with being in different stages of HPV vaccination.

METHODS

Engage is a sexual health study of GBM in the three largest Canadian cities recruited via respondent driven sampling (RDS). We categorized participants as: (1) unaware of HPV vaccine, (2) undecided/unwilling to get vaccinated, (3) willing to get vaccinated, (4) vaccinated with one or more doses. Our RDS-II weighted analyses used multinomial logistic regression to identify factors associated with being in earlier stages of the cascade compared to Stage 4.

RESULTS

Across the cities, 26-40%, 7-14%, 33-39%, and 13-28% were in Stages 1 to 4, respectively. Compared to Stage 4, being in earlier stages of the cascade was associated with bisexual-identification (Stage 1: adjusted odds ratio[aOR] = 2.84, 95% confidence interval[CI] = 1.06-7.62; Stage 2: aOR = 3.09, 95%CI = 1.19-8.05), having immigrated to Canada (Stage 1: aOR = 1.79, 95%CI 1.07-2.99), preference to keep same-sex romantic relationships private (Stage 1: aOR = 1.25, 95% CI = 1.05-1.48; Stage 2: aOR = 1.24, 95%CI = 1.05-1.46), not receiving sexual health information (Stage 1: aOR = 0.31, 95% CI = 0.13-0.71; Stage 2: aOR = 0.27, 95%CI = 0.12-0.64), not accessing a health-care provider (Stage 2: aOR = 0.36, 95%CI = 0.15-0.83), and no past hepatitis A/B vaccination (Stage 1: aOR = 0.16, 95% CI = 0.09-0.30; Stage 2: aOR = 0.18, 95%CI = 0.09-0.35; Stage 3: aOR = 0.38, 95%CI = 0.21-0.61).

DISCUSSION

Interventions are needed to reduce social and financial barriers, increase sexual health knowledge, and improve GBM-competent health-care access to increase vaccine uptake among GBM.

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins

The Perseus software provides a comprehensive framework for the statistical analysis of large-scale quantitative proteomics data, also in combination with other omics dimensions. Rapid developments in proteomics technology and the ever-growing diversity of biological studies increasingly require the flexibility to incorporate computational methods designed by the user. Here, we present the new functionality of Perseus to integrate self-made plugins written in C#, R, or Python. The user-written codes will be fully integrated into the Perseus data analysis workflow as custom activities. This also makes language-specific R and Python libraries from CRAN (cran.r-project.org), Bioconductor (bioconductor.org), PyPI (pypi.org), and Anaconda (anaconda.org) accessible in Perseus. The different available approaches are explained in detail in this article. To facilitate the distribution of user-developed plugins among users, we have created a plugin repository for community sharing and filled it with the examples provided in this article and a collection of already existing and more extensive plugins. © 2020 The Authors. Basic Protocol 1: Basic steps for R plugins Support Protocol 1: R plugins with additional arguments Basic Protocol 2: Basic steps for python plugins Support Protocol 2: Python plugins with additional arguments Basic Protocol 3: Basic steps and construction of C# plugins Basic Protocol 4: Basic steps of construction and connection for R plugins with C# interface Support Protocol 4: Advanced example of R Plugin with C# interface: UMAP Basic Protocol 5: Basic steps of construction and connection for python plugins with C# interface Support Protocol 5: Advanced example of python plugin with C# interface: UMAP Support Protocol 6: A basic workflow for the analysis of label-free quantification proteomics data using perseus.

Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons

Tet3 is the main α-ketoglutarate (αKG)-dependent dioxygenase in neurons that converts 5-methyl-dC into 5-hydroxymethyl-dC and further on to 5-formyl- and 5-carboxy-dC. Neurons possess high levels of 5-hydroxymethyl-dC that further increase during neural activity to establish transcriptional plasticity required for learning and memory functions. How αKG, which is mainly generated in mitochondria as an intermediate of the tricarboxylic acid cycle, is made available in the nucleus has remained an unresolved question in the connection between metabolism and epigenetics. We show that in neurons the mitochondrial enzyme glutamate dehydrogenase, which converts glutamate into αKG in an NAD⁺-dependent manner, is redirected to the nucleus by the αKG-consumer protein Tet3, suggesting on-site production of αKG. Further, glutamate dehydrogenase has a stimulatory effect on Tet3 demethylation activity in neurons, and neuronal activation increases the levels of αKG. Overall, the glutamate dehydrogenase-Tet3 interaction might have a role in epigenetic changes during neural plasticity.

α-ketoglutarate (αKG) is an intermediate in the tricarboxylic acid cycle that is required in the nucleus for genomic DNA demethylation by Tet3. Here, the authors show that the enzyme glutamate dehydrogenase, which converts glutamate to αKG, is redirected from the mitochondria to the nucleus.

Human papillomavirus (HPV) vaccine uptake among a community-recruited sample of gay, bisexual, and other men who have sex with men in the three largest cities in Canada from 2017 to 2019

INTRODUCTION

In 2015/2016, Canada's largest provinces implemented publicly-funded human papillomavirus (HPV) vaccination programs for gay, bisexual, and other men who have sex with men (GBM) ≤ 26 years old. We sought to describe HPV vaccine uptake among GBM and determine barriers and facilitators to vaccine initiation with a focus on healthcare access and utilization.

METHODS

Engage is a cohort study among GBM aged 16 + years in three Canadian cities recruited from 2017 to 2019 via respondent driven sampling (RDS). Men completed a comprehensive questionnaire at baseline. By publicly-funded vaccine eligibility (≤26 years old = eligible for vaccination, ≥27 years old = ineligible), we described HPV vaccine uptake (initiation = 1 + dose, completion = 3 doses) and explored factors associated with vaccine initiation using Poisson regression. All analyses were weighted with the RDS-II Volz-Heckathorn estimator.

RESULTS

Across the three cities, 26-35% and 14-21% of men ≤ 26 years and 7-26% and 2-9% of men ≥ 27 years initiated and completed HPV vaccination, respectively. Vaccine initiation was significantly associated with STI/HIV testing or visiting a HIV care specialist in the past six months (≤26: prevalence ratio[PR] = 2.15, 95% confidence interval[CI] 1.06-4.36; ≥27: PR = 2.73, 95%CI 1.14-6.51) and past hepatitis A or B vaccination (≤26: PR = 2.88, 95%CI 1.64-5.05; ≥27: PR = 2.03, 95%CI 1.07-3.86). Among men ≥ 27 years old, vaccine initiation was also positively associated with accessing PrEP, living in Vancouver or Toronto, but negatively associated with identifying as Latin American and increasing age. Vaccine initiation was twice as likely among men ≥ 27 years with private insurance versus no insurance.

CONCLUSIONS

Sixty-five to 74% of men eligible for publicly-funded vaccine across the three cities remained unvaccinated against HPV by 2019. High vaccine cost may partly explain even lower uptake among men ≥ 27 years old. Men seeking sexual health care were more likely to initiate vaccination; bundling vaccination with these services may help improve HPV vaccine uptake.

Defining the Adult Neural Stem Cell Niche Proteome Identifies Key Regulators of Adult Neurogenesis

The mammalian brain contains few niches for neural stem cells (NSCs) capable of generating new neurons, whereas other regions are primarily gliogenic. Here we leverage the spatial separation of the sub-ependymal zone NSC niche and the olfactory bulb, the region to which newly generated neurons from the sub-ependymal zone migrate and integrate, and present a comprehensive proteomic characterization of these regions in comparison to the cerebral cortex, which is not conducive to neurogenesis and integration of new neurons. We find differing compositions of regulatory extracellular matrix (ECM) components in the neurogenic niche. We further show that quiescent NSCs are the main source of their local ECM, including the multi-functional enzyme transglutaminase 2, which we show is crucial for neurogenesis. Atomic force microscopy corroborated indications from the proteomic analyses that neurogenic niches are significantly stiffer than non-neurogenic parenchyma. Together these findings provide a powerful resource for unraveling unique compositions of neurogenic niches.

A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English primary schools with application of structured expert judgement

Personal contacts drive COVID-19 infections. After being closed (23 March 2020) UK primary schools partially re-opened on 1 June 2020 with social distancing and new risk mitigation strategies. We conducted a structured expert elicitation of teachers to quantify primary school contact patterns and how contact rates changed upon re-opening with risk mitigation measures in place. These rates, with uncertainties, were determined using a performance-based algorithm. We report mean number of contacts per day for four cohorts within schools, with associated 90% confidence ranges. Prior to lockdown, younger children (Reception and Year 1) made 15 contacts per day [range 8.35] within school, older children (Year 6) 18 contacts [range 5.55], teaching staff 25 contacts [range 4.55] and non-classroom staff 11 contacts [range 2.27]. After re-opening, the mean number of contacts was reduced by 53% for young children, 62% for older children, 60% for classroom staff and 64% for other staff. Contacts between teaching and non-teaching staff reduced by 80%. The distributions of contacts per person are asymmetric with heavy tail reflecting a few individuals with high contact numbers. Questions on risk mitigation and supplementary structured interviews elucidated how new measures reduced daily contacts in-school and contribute to infection risk reduction.

MaxDIA enables library-based and library-free data-independent acquisition proteomics

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.

The effect of computer decision support on optimizing appropriate dosing of novel oral anticoagulant therapy in the IMPACT-AF study

Background

Guidelines favour use of the non-vitamin K oral anticoagulants (NOACs) over vitamin-K antagonists for stroke prevention in atrial fibrillation (AF). However, studies have shown these agents are being under-dosed relative to the doses recommended in the product labels.

Purpose

To assess the ability of a CDS tool, employed to support management of patients with AF in primary care, to optimize NOAC prescribing.

Methods

The Integrated Management Program Advancing Community Treatment of Atrial Fibrillation (IMPACT-AF) study was a cluster randomized controlled trial that assessed the ability of a CDS tool to optimize care of community-based AF patients. Between September 2014 and December 2016, 203 primary care providers (104 randomized to CDS use, 99 to usual care [UC]) and 1133 of their patients (n=597 CDS, n=548 UC) were enrolled. Among other functions, 9 CDS program rules provided recommendations on NOAC prescribing based upon a given patient's clinical profile, as per product labels. Appropriate NOAC prescribing within the IMPACT-AF study population was compared between patients managed with the CDS versus UC at baseline and 12-months.

Results

Of those patients prescribed a NOAC, a high proportion (approximately 70%) were managed as per NOAC prescribing recommendations at baseline (Fig. 1). At 12 months, this proportion did not appreciably change in the UC arm (Fig. 1). In the CDS arm, an 8.2% absolute/11.8% relative improvement in appropriate NOAC prescribing over baseline was seen at 12-months (Fig. 1).

A comparison of patients at baseline and 12-months within each arm revealed a non-significant decline in the level of appropriate NOAC prescribing in the UC group (p=0.53). In the CDS arm, a significant improvement was observed in appropriate NOAC prescribing over time (p&lt;0.001).

Conclusion

Even prior to any quality improvement efforts, appropriate NOAC prescribing was higher than anticipated in this contemporary cohort of community-based AF patients. At 12-months, significant further improvements were seen in the CDS but not the UC arm. These findings suggest that physician decision support can help enhance appropriate NOAC prescribing in the primary care setting.

Figure 1. Appropriate NOAC prescribing

Funding Acknowledgement

Type of funding source: Private grant(s) and/or Sponsorship. Main funding source(s): Bayer Inc.

Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification

Isobaric labeling has the promise of combining high sample multiplexing with precise quantification. However, normalization issues and the missing value problem of complete n-plexes hamper quantification across more than one n-plex. Here, we introduce two novel algorithms implemented in MaxQuant that substantially improve the data analysis with multiple n-plexes. First, isobaric matching between runs makes use of the three-dimensional MS1 features to transfer identifications from identified to unidentified MS/MS spectra between liquid chromatography–mass spectrometry runs in order to utilize reporter ion intensities in unidentified spectra for quantification. On typical datasets, we observe a significant gain in MS/MS spectra that can be used for quantification. Second, we introduce a novel PSM-level normalization, applicable to data with and without the common reference channel. It is a weighted median-based method, in which the weights reflect the number of ions that were used for fragmentation. On a typical dataset, we observe complete removal of batch effects and dominance of the biological sample grouping after normalization. Furthermore, we provide many novel processing and normalization options in Perseus, the companion software for the downstream analysis of quantitative proteomics results. All novel tools and algorithms are available with the regular MaxQuant and Perseus releases, which are downloadable at http://maxquant.org.

Author Correction: The dental proteome of Homo antecessor

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The effects of waste sorting in environmental microbiome, THP-1 cell viability and inflammatory responses

Workers in the waste sorting industry are exposed to diverse bioaerosols. Characterization of these bioaerosols is necessary to more accurately assess the health risks of exposure. The use of high-throughput DNA sequencing for improved analysis of microbial composition of bioaerosols, in combination with their in vitro study in relevant cell cultures, represents an important opportunity to find answers on the biological effects of bioaerosols. This study aimed to characterize by high-throughput sequencing the biodiversity present in complex aerosol mixtures retained in forklift air conditioning filters of a waste-sorting industry and its effects on cytotoxicity and secretion of proinflammatory cytokines in vitro using human macrophages derived from monocytic THP-1 cells. Seventeen filters from the filtration system from forklifts operating in one waste sorting facility and one control filter (similar filter without prior use) were analyzed using high-throughput sequencing and toxicological tests in vitro. A trend of positive correlation was seen between the number of bacterial and fungal OTUs (r = 0.47, p = 0.06). Seven filters (39%) exhibited low or moderate cytotoxicity (p < 0.05). The highest cytotoxic responses had a reduction in cell viability between 17 and 22%. Filter samples evoked proinflammatory responses, especially the production of TNFα. No significant correlation was found between fungal richness and inflammatory responses in vitro. The data obtained stress the need of thorough exposure assessment in waste-sorting industry and to take immunomodulatory properties into consideration for bioaerosols hazard characterization. The broad spectrum of microbial contamination detected in this study demonstrates that adequate monitoring of bioaerosol exposure is necessary to evaluate and minimize risks. The combined techniques can support the implementation of effective environmental monitoring programs of public and occupational health importance.

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range. Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.

The PRIDE database and related tools and resources in 2019: improving support for quantification data

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.

Care for adult non-ICU Covid-19 patients: early experiences from a Belgian tertiary care centre

The current Covid-19 outbreak poses many challenges on hospital organisation and patient care. Our hospital lies at the epicentre of the Belgian epidemic. On April 1st, a total of 235 Covid-19 patients had been admitted to our hospital. This demanded an unprecedented adaptation of our hospital organisation, and we have met many clinical issues in the care for Covid-19 patients. In this article, we share our experience in the handling of some of the practical and organisational issues in the care for Covid-19 patients.

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation

The circadian clock drives daily changes of physiology, including sleep-wake cycles, through regulation of transcription, protein abundance, and function. Circadian phosphorylation controls cellular processes in peripheral organs, but little is known about its role in brain function and synaptic activity. We applied advanced quantitative phosphoproteomics to mouse forebrain synaptoneurosomes isolated across 24 hours, accurately quantifying almost 8000 phosphopeptides. Half of the synaptic phosphoproteins, including numerous kinases, had large-amplitude rhythms peaking at rest-activity and activity-rest transitions. Bioinformatic analyses revealed global temporal control of synaptic function through phosphorylation, including synaptic transmission, cytoskeleton reorganization, and excitatory/inhibitory balance. Sleep deprivation abolished 98% of all phosphorylation cycles in synaptoneurosomes, indicating that sleep-wake cycles rather than circadian signals are main drivers of synaptic phosphorylation, responding to both sleep and wake pressures.

The nucleolus functions as a phase-separated protein quality control compartment

The nuclear proteome is rich in stress-sensitive proteins, which suggests that effective protein quality control mechanisms are in place to ensure conformational maintenance. We investigated the role of the nucleolus in this process. In mammalian tissue culture cells under stress conditions, misfolded proteins entered the granular component (GC) phase of the nucleolus. Transient associations with nucleolar proteins such as NPM1 conferred low mobility to misfolded proteins within the liquid-like GC phase, avoiding irreversible aggregation. Refolding and extraction of proteins from the nucleolus during recovery from stress was Hsp70-dependent. The capacity of the nucleolus to store misfolded proteins was limited, and prolonged stress led to a transition of the nucleolar matrix from liquid-like to solid, with loss of reversibility and dysfunction in quality control. Thus, we suggest that the nucleolus has chaperone-like properties and can promote nuclear protein maintenance under stress.

High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis

Peptide fragmentation spectra are routinely predicted in the interpretation of mass-spectrometry-based proteomics data. However, the generation of fragment ions has not been understood well enough for scientists to estimate fragment ion intensities accurately. Here, we demonstrate that machine learning can predict peptide fragmentation patterns in mass spectrometers with accuracy within the uncertainty of measurement. Moreover, analysis of our models reveals that peptide fragmentation depends on long-range interactions within a peptide sequence. We illustrate the utility of our models by applying them to the analysis of both data-dependent and data-independent acquisition datasets. In the former case, we observe a q-value-dependent increase in the total number of peptide identifications. In the latter case, we confirm that the use of predicted tandem mass spectrometry spectra is nearly equivalent to the use of spectra from experimental libraries.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis

Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affinity purification experiments, but networks are also used to explore proteomics data. PerseusNet supports the biomedical researcher for both modes of data analysis with a multitude of activities. For affinity purification, a volcano-plot-based statistical analysis method for network generation is featured which is scalable to large numbers of baits. For posttranslational modifications of proteins, such as phosphorylation, a collection of dedicated network analysis tools helps in elucidating cellular signaling events. Co-expression network analysis of proteomics data adopts established tools from transcriptome co-expression analysis. PerseusNet is extensible through a plugin architecture in a multi-lingual way, integrating analyses in C#, Python, and R, and is freely available at http://www.perseus-framework.org .

Abstract P2-09-08: Imprime PGG, a novel innate immune modulator, combined with pembrolizumab in a phase 2 multicenter, open label study in chemotherapy-resistant metastatic triple negative breast cancer (TNBC)

Background: CPI monotherapy provides substantial clinical benefit to patients (pts) in multiple cancers, yet response rates are limited (˜15-30%) and fails to benefit the majority. In these pts there is limited or no ongoing T cell-based immune response. Imprime PGG (Imprime), a novel beta glucan derived from Saccharomyces, may expand the clinical benefit of CPI therapy by stimulating an anti-cancer immune response. Acting as a pathogen-associated molecularpattern (PAMP), Imprime enlists innate immune functions including cytotoxic effector mechanisms, reversal of immunosuppression and cross-talk with the adaptive immune system.Imprime-mediated innate immune activation requires formation of an immune complex with naturally-occurring anti-beta glucan antibodies (ABA); sufficient ABA levels is required for complex formation. Imprime is now being studied in combination with pembrolizumab (KEYTRUDA®,Pembro), a humanized mAb against PD-1 which has been previously studied in TNBC pts.

Methods: In this study of patients who previously failed chemotherapy for metastatic TNBC, Imprime is being used in combination with Pembro in a Simon 2 stage design. Asample size of 12 evaluable pts in Stage 1 was planned.Evaluable pts received at least one dose of study treatment (tx), had measurable disease at baseline per RECIST v1.1, had at least one post-baseline scan or discontinued tx as a result of progressive disease, death, or a tx-related adverse event before the first post-baseline scan.Pts received Imprime (4 mg/kg IV days 1, 8, 15 of each 3-week cycle) + Pembro 200 mg on D1 of each cycle. Criteria to advance to Stage 2 were ≤4 grade 3/4 AEs during the first tx cycle (other than infusion reactions) and ≥1 objective response. Study primary endpoints are ORR and safety; secondary endpoints are TTR, CRR, DoR, PFS, and OS. Exploratory endpoints include ORR and PFS per irRECIST. Biopsies and blood samples are being collected to assess tx impact on immune activating events at the tumor site and in the periphery.

Results: A review of efficacy and safety data was conducted at the end of Stage 1. Thirteen pts (12 evaluable) were enrolled into Stage 1. Safety review noted 2 grade 3 adverse events that met protocol definition of Stage 1 events (1 pt: cellulitis and 1 pt: pleural infusion; both unrelated to treatment). Two events lead to 2 pts discontinuing treatment (infusion reaction and pancreatitis) and only 1 autoimmune event was observed (pancreatitis). Observed efficacy responses in the evaluable pts included 1 complete response (CR; ongoing) and 2 partial responses (PR; ongoing). Secondary efficacy endpoints have not been assessed. Early translational results support proposed MOA and analysis of Stage 1 translational data is ongoing.

Conclusion: The use of Imprime with Pembro was well tolerated and met both safety and efficacy requirements to move forward with Stage 2 of the study. No significant safety concerns were identified in Stage 1. Further investigation is thus warranted and enrollment into Stage 2 is ongoing. Updated data will be presented.

Citation Format: O'Day S, Borges V, Chmielowski B, Rao R, Abu-Khalaf M, Stopeck A, Lowe J, Mattson P, Breuer K, Gargano M, Bose N, Uhlik M, Graff J, Chisamore M, Cox J, Osterwalder B. Imprime PGG, a novel innate immune modulator, combined with pembrolizumab in a phase 2 multicenter, open label study in chemotherapy-resistant metastatic triple negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-09-08.