Trypanolytic variants in APOL1, which encodes apolipoprotein L1, associate with kidney disease in African Americans, but whether APOL1-associated glomerular disease has a distinct clinical phenotype ...is unknown. Here we determined APOL1 genotypes for 271 African American cases, 168 European American cases, and 939 control subjects. In a recessive model, APOL1 variants conferred seventeenfold higher odds (95% CI 11 to 26) for focal segmental glomerulosclerosis (FSGS) and twenty-nine-fold higher odds (95% CI 13 to 68) for HIV-associated nephropathy (HIVAN). FSGS associated with two APOL1 risk alleles associated with earlier age of onset (P = 0.01) and faster progression to ESRD (P < 0.01) but similar sensitivity to steroids compared with other subjects. Individuals with two APOL1 risk alleles have an estimated 4% lifetime risk for developing FSGS, and untreated HIV-infected individuals have a 50% risk for developing HIVAN. The effect of carrying two APOL1 risk alleles explains 18% of FSGS and 35% of HIVAN; alternatively, eliminating this effect would reduce FSGS and HIVAN by 67%. A survey of world populations indicated that the APOL1 kidney risk alleles are present only on African chromosomes. In summary, African Americans carrying two APOL1 risk alleles have a greatly increased risk for glomerular disease, and APOL1-associated FSGS occurs earlier and progresses to ESRD more rapidly. These data add to the evidence base required to determine whether genetic testing for APOL1 has a use in clinical practice.
Although oncogene-targeted therapy often elicits profound initial tumor responses in patients, responses are generally incomplete because some tumor cells survive initial therapy as residual disease ...that enables eventual acquired resistance. The mechanisms underlying tumor cell adaptation and survival during initial therapy are incompletely understood. Here, through the study of EGFR mutant lung adenocarcinoma, we show that NF-κB signaling is rapidly engaged upon initial EGFR inhibitor treatment to promote tumor cell survival and residual disease. EGFR oncogene inhibition induced an EGFR-TRAF2-RIP1-IKK complex that stimulated an NF-κB-mediated transcriptional survival program. The direct NF-κB inhibitor PBS-1086 suppressed this adaptive survival program and increased the magnitude and duration of initial EGFR inhibitor response in multiple NSCLC models, including a patient-derived xenograft. These findings unveil NF-κB activation as a critical adaptive survival mechanism engaged by EGFR oncogene inhibition and provide rationale for EGFR and NF-κB co-inhibition to eliminate residual disease and enhance patient responses.
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•NF-κB is activated early in response to EGFR oncogene-targeted therapy•EGFR inhibition adaptively promotes formation of an NF-κB-activating complex•Adaptive NF-κB signaling drives tumor cell survival and residual disease•NF-κB inhibition via PBS-1086 combats tumor cell survival and residual disease
Blakely et al. reveal that NF-κB signaling is acutely activated in response to EGFR oncogene inhibition in lung cancer via a complex that promotes tumor cell survival and residual disease. They uncover a direct pharmacologic NF-κB inhibitor that overrides this adaptive survival mechanism and may enhance patient outcomes.
Mapping host-pathogen interactions has proven instrumental for understanding how viruses manipulate host machinery and how numerous cellular processes are regulated. DNA viruses such as herpesviruses ...have relatively large coding capacity and thus can target an extensive network of cellular proteins. To identify the host proteins hijacked by this pathogen, we systematically affinity tagged and purified all 89 proteins of Kaposi’s sarcoma-associated herpesvirus (KSHV) from human cells. Mass spectrometry of this material identified over 500 virus-host interactions. KSHV causes AIDS-associated cancers, and its interaction network is enriched for proteins linked to cancer and overlaps with proteins that are also targeted by HIV-1. We found that the conserved KSHV protein ORF24 binds to RNA polymerase II and brings it to viral late promoters by mimicking and replacing cellular TATA-box-binding protein (TBP). This is required for herpesviral late gene expression, a complex and poorly understood phase of the viral lifecycle.
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•A herpesvirus-human protein interactome was systematically assembled in human cells•The KSHV interaction network is a tool for predicting viral protein functions•KSHV ORF24 recruits RNA polymerase II and replaces human TBP at late promoters
Kaposi’s sarcoma-associated herpesvirus (KSHV) is a major AIDS-associated pathogen. Davis et al. assemble a KSHV-host protein-protein interaction network that suggests herpesvirus-host evolutionary interplay. Using the network, they describe a hybrid KSHV-human transcription complex that activates viral late genes.
Several systems-level datasets designed to dissect host-pathogen interactions during influenza A infection have been reported. However, apparent discordance among these data has hampered their full ...utility toward advancing mechanistic and therapeutic knowledge. To collectively reconcile these datasets, we performed a meta-analysis of data from eight published RNAi screens and integrated these data with three protein interaction datasets, including one generated within the context of this study. Further integration of these data with global virus-host interaction analyses revealed a functionally validated biochemical landscape of the influenza-host interface, which can be queried through a simplified and customizable web portal (http://www.metascape.org/IAV). Follow-up studies revealed that the putative ubiquitin ligase UBR4 associates with the viral M2 protein and promotes apical transport of viral proteins. Taken together, the integrative analysis of influenza OMICs datasets illuminates a viral-host network of high-confidence human proteins that are essential for influenza A virus replication.
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•Meta-analysis of influenza OMICs datasets reveals high-confidence virus-host interactions•Integration of orthogonal data exposes unique host and restriction factor activities•Experimental validation of virus-host circuits supports robustness of approach•The host E3 ligase UBR4 is identified as essential for virus budding and pathogenesis
Tripathi et al. have reconciled and integrated divergent influenza “OMICs” studies to reveal a functionally validated virus-host interaction network of high-confidence human proteins essential for influenza A virus replication. The authors leverage this approach to identify UBR4 as a host protein essential for virus budding and pathogenesis.
Objective
To provide guidance to rheumatology providers on the use of coronavirus disease 2019 (COVID‐19) vaccines for patients with rheumatic and musculoskeletal diseases (RMDs).
Methods
A task ...force was assembled that included 9 rheumatologists/immunologists, 2 infectious disease specialists, and 2 public health physicians. After agreeing on scoping questions, an evidence report was created that summarized the published literature and publicly available data regarding COVID‐19 vaccine efficacy and safety, as well as literature for other vaccines in RMD patients. Task force members rated their agreement with draft consensus statements on a 9‐point numerical scoring system, using a modified Delphi process and the RAND/University of California Los Angeles Appropriateness Method, with refinement and iteration over 2 sessions. Consensus was determined based on the distribution of ratings.
Results
Despite a paucity of direct evidence, 74 draft guidance statements were developed by the task force and agreed upon with consensus to provide guidance for use of the COVID‐19 vaccines in RMD patients and to offer recommendations regarding the use and timing of immunomodulatory therapies around the time of vaccination.
Conclusion
These guidance statements, made in the context of limited clinical data, are intended to provide direction to rheumatology health care providers on how to best use COVID‐19 vaccines and to facilitate implementation of vaccination strategies for RMD patients.
Small-molecule BET bromodomain inhibitors (BETis) are actively being pursued in clinical trials for the treatment of a variety of cancers, but the mechanisms of resistance to BETis remain poorly ...understood. Using a mass spectrometry approach that globally measures kinase signaling at the proteomic level, we evaluated the response of the kinome to targeted BETi treatment in a panel of BRD4-dependent ovarian carcinoma (OC) cell lines. Despite initial inhibitory effects of BETi, OC cells acquired resistance following sustained treatment with the BETi JQ1. Through application of multiplexed inhibitor beads (MIBs) and mass spectrometry, we demonstrate that BETi resistance is mediated by adaptive kinome reprogramming, where activation of compensatory pro-survival kinase networks overcomes BET protein inhibition. Furthermore, drug combinations blocking these kinases may prevent or delay the development of drug resistance and enhance the efficacy of BETi therapy.
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•Inhibition of BET proteins reprograms kinome activity in ovarian cancer cells•Receptor tyrosine kinase activation overcomes BET inhibition, causing resistance•Elevated PI3K/ERK activity stabilizes MYC/FOSL1 proteins in JQ1-resistant cells•Co-targeting BET proteins and RTK or PI3K signaling enhances BET inhibitor therapy
BET inhibitors are currently being evaluated in clinical trials for a number of cancers, including ovarian cancer. Kurimchak et al. demonstrate that BET inhibitors may have limited success as single agents in ovarian cancer due to adaptive kinome reprogramming and will require combination therapies targeting kinases and BET bromodomain proteins
The National Aeronautics and Space Administration's (NASA) Soil Moisture Active and Passive (SMAP) mission, which was launched on January 31, 2015, is providing global measurements of soil moisture ...and freeze/thaw state. The SMAP radiometer operates within the protected Earth Exploration Satellite Service passive frequency allocation of 1400-1427 MHz. However, unauthorized in-band transmitters and out-of-band emissions from transmitters operating at frequencies adjacent to this allocated spectrum are known to cause interference to microwave radiometry in this band. Because measurement corruption by these terrestrial transmissions, which is referred to as radio-frequency interference (RFI), threatens mission success, the SMAP radiometer includes special flight hardware to enable the detection and filtering of RFI. Results from the first year of SMAP data show the presence of RFI with frequent occurrence over Asia and Europe. During the calibration/validation stage of the mission, the RFI detection and mitigation algorithms were modified to provide enhanced performance. Analysis of the L1B_TB products indicates good algorithmic performance with respect to RFI detection and removal. However, some regions of the globe (e.g., Japan) continue to experience complete data loss. This paper summarizes updates to the SMAP RFI processing algorithms based on prelaunch tests and on-orbit measurements, as well as RFI information obtained in SMAP's first year on orbit.
Objective
To provide guidance to rheumatology providers on the use of coronavirus disease 2019 (COVID‐19) vaccines for patients with rheumatic and musculoskeletal diseases (RMDs).
Methods
A task ...force was assembled that included 9 rheumatologists/immunologists, 2 infectious disease specialists, and 2 public health physicians. After agreeing on scoping questions, an evidence report was created that summarized the published literature and publicly available data regarding COVID‐19 vaccine efficacy and safety, as well as literature for other vaccines in RMD patients. Task force members rated their agreement with draft consensus statements on a 9‐point numerical scoring system, using a modified Delphi process and the RAND/University of California Los Angeles Appropriateness Method, with refinement and iteration over 2 sessions. Consensus was determined based on the distribution of ratings.
Results
Despite a paucity of direct evidence, 74 draft guidance statements were developed by the task force and agreed upon with consensus to provide guidance for use of the COVID‐19 vaccines in RMD patients and to offer recommendations regarding the use and timing of immunomodulatory therapies around the time of vaccination.
Conclusion
These guidance statements, made in the context of limited clinical data, are intended to provide direction to rheumatology health care providers on how to best use COVID‐19 vaccines and to facilitate implementation of vaccination strategies for RMD patients.
Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interactions remains limited. We systematically used affinity purification/mass spectrometry to define the ...host interactions of all ten HCV proteins in hepatoma cells. We combined these studies with RNAi knockdown of corresponding genes using a two-step scoring approach to generate a map of 139 high-confidence HCV-host protein-protein interactions. We found mitochondrial proteins highly involved in HCV infection and characterized an interaction between the viral core protein and host protein within bgcn homolog (WIBG). Expression of core prevents WIBG from binding its regular interaction partners Y14 and Magoh, two known mediators of the nonsense-mediated mRNA decay pathway. We discovered that this surveillance pathway is disrupted in HCV-infected cells, causing potentially harmful transcripts to accumulate. Our study provides a comprehensive view of HCV-host interactions and uncovers mechanisms for how HCV perturbs host functions during infection.
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•Combined AP-MS and RNAi approaches identify key HCV-human protein interactions•Mitochondrial proteins interact with viral proteins core, p7, and NS4B•VAP proteins bind the NS4A cofactor within the NS3/4A protease•HCV infection disrupts the nonsense-mediated mRNA decay pathway
Ramage et al. report a hepatitis C virus (HCV)-host protein-protein interactome that identifies host factors and pathways implicated in HCV pathogenesis. They show that HCV blocks nonsense-mediated mRNA surveillance, a potential host restriction pathway, in infected hepatoma cells.
By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, ...we discuss how to use data obtained in affinity purification-mass spectrometry (AP-MS) experiments to generate meaningful interaction networks and effective figures. We begin with an overview of common epitope tagging, expression and AP practices, followed by liquid chromatography-MS (LC-MS) data collection. We then provide a detailed procedure covering a pipeline approach to (i) pre-processing the data by filtering against contaminant lists such as the Contaminant Repository for Affinity Purification (CRAPome) and normalization using the spectral index (SIN) or normalized spectral abundance factor (NSAF); (ii) scoring via methods such as MiST, SAInt and CompPASS; and (iii) testing the resulting scores. Data formats familiar to MS practitioners are then transformed to those most useful for network-based analyses. The protocol also explores methods available in Cytoscape to visualize and analyze these types of interaction data. The scoring pipeline can take anywhere from 1 d to 1 week, depending on one's familiarity with the tools and data peculiarities. Similarly, the network analysis and visualization protocol in Cytoscape takes 2-4 h to complete with the provided sample data, but we recommend taking days or even weeks to explore one's data and find the right questions.
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