Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors

We sought to better understand the immune response during the immediate post-diagnosis phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. In lymphocytes, the CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. These early stage observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. BACKGROUND: Much of the literature on immune response post-SARS-CoV-2 infection has been in the acute and post-acute phases of infection. TRANSLATIONAL SIGNIFICANCE: We found differences at early time points of infection in approximately 160 participants. We compared multi-omic signatures in immune cells between individuals progressing to needing more significant medical intervention and non-progressors. We observed widespread evidence of a state of increased inflammation associated with progression, supported by a range of epigenomic, transcriptomic, and proteomic signatures. The signatures we identified support other findings at later time points and serve as the basis for prognostic biomarker development or to inform interventional strategies.

Gaseous polycyclic aromatic hydrocarbons over the South China Sea: Implications for atmospheric transport under monsoon influences

The seasonal monsoon variations have significant impact on the atmospheric transport of semi-volatile organic pollutants over the South China Sea (SCS). We analyzed polycyclic aromatic hydrocarbons (PAHs) over the basin and island areas (Yongxing Island and Yongshu Island) in 2017. Gaseous PAHs (0.17-1.4 ng m^-3) showed spatio-temporal distinctions in their composition and sources among the basin and island areas. Mixed combustion sources of PAHs were identified over the SCS, including a petroleum source near the island areas. The transport routes of PAHs were inferred by the air mass back trajectories and potential source contribution factor analysis, identifying strong biomass burning signals from the Indochina Peninsula and other Southeast Asian countries. Emissions from approximately 90 % of the combustion sources were transported to basin areas by monsoons, whereas the island areas were dominated by local emissions. This study emphasizes the main potential terrestrial source of PAHs over the SCS under monsoon influences.

Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a rapid response by the scientific community to further understand and combat its associated pathologic etiology. A focal point has been on the immune responses mounted during the acute and post-acute phases of infection, but the immediate post-diagnosis phase remains relatively understudied. We sought to better understand the immediate post-diagnosis phase by collecting blood from study participants soon after a positive test and identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. Additionally, in the lymphocyte compartment, CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. Importantly, the identification of these cellular and molecular immune changes occurred at the early stages of COVID-19 disease. These observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19.

Dynamic phosphatase-recruitment controls B-cell selection and oncogenic signaling

Initiation of B-cell receptor (BCR) ¹ signaling, and subsequent antigen-encounter in germinal centers ^2,3 represent milestones of B-lymphocyte development that are both marked by sharp increases of CD25 surface-expression. Oncogenic signaling in B-cell leukemia (B-ALL) ⁴ and lymphoma ⁵ also induced CD25-surface expression. While CD25 is known as an IL2-receptor chain on T- and NK-cells ^6-9 , the significance of its expression on B-cells was unclear. Our experiments based on genetic mouse models and engineered patient-derived xenografts revealed that, rather than functioning as an IL2-receptor chain, CD25 expressed on B-cells assembled an inhibitory complex including PKCδ and SHIP1 and SHP1 phosphatases for feedback control of BCR-signaling or its oncogenic mimics. Recapitulating phenotypes of genetic ablation of PKCδ ¹⁰ - ¹² , SHIP1 ^13,14 and SHP1 ^{14, 15,16} , conditional CD25-deletion decimated early B-cell subsets but expanded mature B-cell populations and induced autoimmunity. In B-cell malignancies arising from early (B-ALL) and late (lymphoma) stages of B-cell development, CD25-loss induced cell death in the former and accelerated proliferation in the latter. Clinical outcome annotations mirrored opposite effects of CD25-deletion: high CD25 expression levels predicted poor clinical outcomes for patients with B-ALL, in contrast to favorable outcomes for lymphoma-patients. Biochemical and interactome studies revealed a critical role of CD25 in BCR-feedback regulation: BCR-signaling induced PKCδ-mediated phosphorylation of CD25 on its cytoplasmic tail (S ²⁶⁸ ). Genetic rescue experiments identified CD25-S ²⁶⁸ tail-phosphorylation as central structural requirement to recruit SHIP1 and SHP1 phosphatases to curb BCR-signaling. A single point mutation CD25 ^S268A abolished recruitment and activation of SHIP1 and SHP1 to limit duration and strength of BCR-signaling. Loss of phosphatase-function, autonomous BCR-signaling and Ca ²⁺ -oscillations induced anergy and negative selection during early B-cell development, as opposed to excessive proliferation and autoantibody production in mature B-cells. These findings highlight the previously unrecognized role of CD25 in assembling inhibitory phosphatases to control oncogenic signaling in B-cell malignancies and negative selection to prevent autoimmune disease.

Concurrent IRF4 Rearrangements in a Patient with B Cell and T Cell Disorders

Introduction/Objective

IRF4 is a regulatory protein which required at several stages of B and T cell development and differentiation. Rearrangements of the IRF4 chromosomal region have been detected in various B and T cell neoplasms including a distinct entity in the WHO tumor classification for diffuse large B cell lymphoma (DLBCL) with IRF4 rearrangement and another for an IRF4 rearranged subtype of the CD30-positive T cell lymphoproliferative disorder, lymphomatoid papulosis (LyP).

Methods/Case Report

We present the case of a 52-year-old man with a past medical history of treated Hodgkin disease in remission who now presents with a DLBCL of the tonsil as well a cutaneous LyP, both of which demonstrate the IRF4 gene rearrangement. Immunohistochemical stains support the morphologic diagnoses and the rearrangement is detected in both cases using fluorescence in situ hybridization (FISH).

Results (if a Case Study enter NA)

NA.

Conclusion

The detection of IRF4 translocation in two separate cell lineages may result from one of a handful of possible explanations that we explore. First, a mutation in a multipotent hematopoietic progenitor cell may give rise to common lymphoid progenitors which pass the mutation on to subsequent B and T differentiated lymphocytes. Second, de novo mutations may be occurring in both B and T cell lines leading to the mature lesions. Finally, it may be possible that one of the two lesions is not truly positive for IRF4 rearrangement, but rather the background B cells in the skin or T cells in the tonsil are the cells positive for the aberration. This is a unique case of a B and T cell lesion in the same patient which both possess the same rare genetic rearrangement. The implications on our understanding of the genetic development of such lesions is significant and may subsequently impact diagnosis and therapy going forward.

A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation

Noncanonical inflammasome activation by cytosolic lipopolysaccharide (LPS) is a critical component of the host response to Gram-negative bacteria. Cytosolic LPS recognition in macrophages is preceded by a Toll-like receptor (TLR) priming signal required to induce transcription of inflammasome components and facilitate the metabolic reprograming that fuels the inflammatory response. Using a genome-scale arrayed siRNA screen to find inflammasome regulators in mouse macrophages, we identified the mitochondrial enzyme nucleoside diphosphate kinase D (NDPK-D) as a regulator of both noncanonical and canonical inflammasomes. NDPK-D was required for both mitochondrial DNA synthesis and cardiolipin exposure on the mitochondrial surface in response to inflammasome priming signals mediated by TLRs, and macrophages deficient in NDPK-D had multiple defects in LPS-induced inflammasome activation. In addition, NDPK-D was required for the recruitment of TNF receptor-associated factor 6 (TRAF6) to mitochondria, which was critical for reactive oxygen species (ROS) production and the metabolic reprogramming that supported the TLR-induced gene program. NDPK-D knockout mice were protected from LPS-induced shock, consistent with decreased ROS production and attenuated glycolytic commitment during priming. Our findings suggest that, in response to microbial challenge, NDPK-D-dependent TRAF6 mitochondrial recruitment triggers an energetic fitness checkpoint required to engage and maintain the transcriptional program necessary for inflammasome activation.

InterCarb: A Community Effort to Improve Interlaboratory Standardization of the Carbonate Clumped Isotope Thermometer Using Carbonate Standards

Increased use and improved methodology of carbonate clumped isotope thermometry has greatly enhanced our ability to interrogate a suite of Earth-system processes. However, interlaboratory discrepancies in quantifying carbonate clumped isotope (Δ47) measurements persist, and their specific sources remain unclear. To address interlaboratory differences, we first provide consensus values from the clumped isotope community for four carbonate standards relative to heated and equilibrated gases with 1,819 individual analyses from 10 laboratories. Then we analyzed the four carbonate standards along with three additional standards, spanning a broad range of δ47 and Δ47 values, for a total of 5,329 analyses on 25 individual mass spectrometers from 22 different laboratories. Treating three of the materials as known standards and the other four as unknowns, we find that the use of carbonate reference materials is a robust method for standardization that yields interlaboratory discrepancies entirely consistent with intralaboratory analytical uncertainties. Carbonate reference materials, along with measurement and data processing practices described herein, provide the carbonate clumped isotope community with a robust approach to achieve interlaboratory agreement as we continue to use and improve this powerful geochemical tool. We propose that carbonate clumped isotope data normalized to the carbonate reference materials described in this publication should be reported as Δ47 (I-CDES) values for Intercarb-Carbon Dioxide Equilibrium Scale.

TurboID biotin-tagging mass spectrometry identifies specific caspase-11-associated proteins regulating non-canonical inflammasome activation

While it has been demonstrated that cytosolic LPS can directly activate caspase11, the cellular processes regulating the non-canonical inflammasome response remain poorly defined. Caspase11 and caspase1 show substantial structural similarity, however, unlike the activation of caspase1 by NLR inflammasomes, there are no sensor or adaptor proteins known to be involved in transmitting cytosolic LPS signal to caspase11. Also, while caspase11 has been shown to associate with LPS, it lacks a characteristic LPS binding domain as observed in many other LPS binding proteins such as MD2 and LBP. Thus, we hypothesized that other effectors may be required to facilitate cytosolic LPS recognition. Moreover, the pathway is likely to be tightly regulated as caspase11 activation leads to highly inflammatory cell death.

To identify novel regulators of caspase11, we generated immortalized macrophages expressing a caspase11-TurboID-DHFR chimeric protein. The destabilizing domain was included to avoid cell death induced by caspase11 over-expression. We used a TurboID biotin-tagging MS assay to detect proteins in close proximity to caspase11 pre and post cytosolic LPS introduction. Importantly, the TurboID assay permits recognition of transient interactions, typically missed by traditional IP. To validate relevance of putative hits, we used siRNA knockdown in BMDM.

We’ve identified novel regulators specific for cytosolic LPS triggering. Several proteins interact with caspase11 only in the resting state, suggesting negative regulation to prevent pyroptosis. Among the identified regulators are kinases and proteins with pyrin and LRR domains, both common NLR features.

This work was supported by the Intramural Research Program of NIAID, NIH.

SIGNAL: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from genome-scale assays

Hit selection from high-throughput assays remains a critical bottleneck in realizing the potential of omic-scale studies in biology. Widely used methods such as setting of cutoffs, prioritizing pathway enrichments, or incorporating predicted network interactions offer divergent solutions yet are associated with critical analytical trade-offs. The specific limitations of these individual approaches and the lack of a systematic way by which to integrate their rankings have contributed to limited overlap in the reported results from comparable genome-wide studies and costly inefficiencies in secondary validation efforts. Using comparative analysis of parallel independent studies as a benchmark, we characterize the specific complementary contributions of each approach and demonstrate an optimal framework to integrate these methods. We describe selection by iterative pathway group and network analysis looping (SIGNAL), an integrated, iterative approach that uses both pathway and network methods to optimize gene prioritization. SIGNAL is accessible as a rapid user-friendly web-based application (https://signal.niaid.nih.gov). A record of this paper's transparent peer review is included in the Supplemental information.

Dynamic ADP-Ribosylome, Phosphoproteome, and Interactome in LPS-Activated Macrophages

We have used mass spectrometry (MS) to characterize protein signaling in lipopolysaccharide (LPS)-stimulated macrophages from human blood, human THP1 cells, mouse bone marrow, and mouse Raw264.7 cells. Protein ADP-ribosylation was truncated down to phosphoribose, allowing for enrichment and identification of the resulting phosphoribosylated peptides alongside phosphopeptides. Size exclusion chromatography-MS (SEC-MS) was used to separate proteoforms by size; protein complexes were then identified by weighted correlation network analysis (WGCNA) based on their correlated movement into or out of SEC fractions following stimulation, presenting an analysis method for SEC-MS that does not rely on established databases. We highlight two modules of interest: one linked to the apoptosis signal-regulating kinase (ASK) signalosome and the other containing poly(ADP-ribose) polymerase 9 (PARP9). Finally, PARP inhibition was used to perturb the characterized systems, demonstrating the importance of ADP-ribosylation for the global interactome. All post-translational modification (PTM) and interactome data have been aggregated into a meta-database of 6729 proteins, with ADP-ribosylation characterized on 2905 proteins and phosphorylation characterized on 2669 proteins. This database-titled MAPCD, for Macrophage ADP-ribosylation, Phosphorylation, and Complex Dynamics-serves as an invaluable resource for studying crosstalk between the ADP-ribosylome, phosphoproteome, and interactome.

Glucocorticoid-induced osteoporosis preventive care in rheumatology patients

Glucocorticoid-induced osteoporosis (GIOP) is common in patients prescribed with long-term glucocorticoids. Guidelines suggest patients receiving moderate-dose glucocorticoid therapy receive GIOP preventive care. Previous studies have shown preventive care rates are not optimal. We look at GIOP preventive care rates in rheumatology patients and predictors of various components of care.

PURPOSE

Glucocorticoid-induced osteoporosis (GIOP) is a common concern in patients prescribed with long-term glucocorticoids. Studies have shown GIOP preventive care is not provided optimally in the general population; however, little is published on GIOP preventive care among patients with rheumatic disease. The objective of this study is to determine the proportion of rheumatology patients who received GIOP preventive care.

METHODS

A population-based retrospective quality assurance study of adults seen at the University of Alberta Rheumatology Clinic was performed using the electronic outpatient medical record. Records of adult patients prescribed with prednisone from January 1st to December 31st, 2016 by a rheumatologist were initially included for review. Those who had been prescribed ≥ 7.5 mg/day for ≥ 3 months were assessed for concurrent GIOP preventive care.

RESULTS

A total of 745 discreet courses of prednisone were prescribed in 433 patients with 113 meeting the above inclusion criteria. Following the prednisone prescription, 79% were taking vitamin D, 86% were taking calcium, and 50% were prescribed with osteoporosis pharmacotherapy. Twenty-five percent of patients had DXA imaging ordered by the rheumatologist within the first 6 months; of these, 86% of patients completed the DXA.

CONCLUSIONS

Overall, our study shows that patients under the care of rheumatologists receive better GIOP preventative care than previously reported care in the general population. However, there is still room for improvement. In particular, men, younger patients, and rural patients seem to be at the most at risk of not receiving optimal GIOP prevention.

Reversible light-dependent molecular switches on Ag/AgCl nanostructures

Nanostructured Ag/AgCl substrates were used to generate reversible and highly efficient light-dependent chemical switches based on adsorbed 4,4'-dimercaptoazobenzene (DMAB). DMAB was formed in situ via laser-induced dimerization either from 4-nitrothiophenol (4-NTP) or 4-aminothiophenol (4-ATP). The subsequent reaction pathways of DMAB, however, were quite different as monitored by surface enhanced Raman spectroscopy. In the 4-NTP/DMAB system, AgCl catalyses the reversal of the dimerization. Conversely, irradiation of adsorbed 4-ATP first generated cis-DMAB attached to the surface via two Ag-S bonds, followed by AgCl-catalysed cleavage of one Ag-S bond and cis → trans photoisomerisation of DMAB. In the dark, the trans-isomer thermally reverts to cis-DMAB. The here presented light-dark chemical switches, which work without changing other parameters (e.g., pH, anaerobic vs. aerobic), are based on the (photo)catalytic properties of the Ag/AgCl substrate and do not function on pure metal surfaces.

Genome-wide siRNA screen of genes regulating the LPS-induced TNF-α response in human macrophages

The mammalian innate immune system senses many bacterial stimuli through the toll-like receptor (TLR) family. Activation of the TLR4 receptor by bacterial lipopolysaccharide (LPS) is the most widely studied TLR pathway due to its central role in host responses to gram-negative bacterial infection and its contribution to endotoxemia and sepsis. Here we describe a genome-wide siRNA screen to identify genes regulating the human macrophage TNF-α response to LPS. We include a secondary validation screen conducted with six independent siRNAs per gene to facilitate removal of off-target screen hits. We also provide microarray data from the same LPS-treated macrophage cells to facilitate downstream data analysis. Tertiary screening with multiple TLR ligands and a microbial extract demonstrate that novel screen hits have broad effects on the innate inflammatory response to microbial stimuli. These data provide a resource for analyzing gene function in the predominant pathway driving inflammatory cytokine expression in human macrophages.

Vibrational spectroscopy reveals the initial steps of biological hydrogen evolution

[FeFe] hydrogenases are biocatalytic model systems for the exploitation and investigation of catalytic hydrogen evolution. Here, we used vibrational spectroscopic techniques to characterize, in detail, redox transformations of the [FeFe] and [4Fe4S] sub-sites of the catalytic centre (H-cluster) in a monomeric [FeFe] hydrogenase. Through the application of low-temperature resonance Raman spectroscopy, we discovered a novel metastable intermediate that is characterized by an oxidized [FeIFeII] centre and a reduced [4Fe4S]1+ cluster. Based on this unusual configuration, this species is assigned to the first, deprotonated H-cluster intermediate of the [FeFe] hydrogenase catalytic cycle. Providing insights into the sequence of initial reaction steps, the identification of this species represents a key finding towards the mechanistic understanding of biological hydrogen evolution.