PubMed

Recent Publications

A survey of the kinome pharmacopeia reveals multiple scaffolds and targets for the development of novel anthelmintics

Sci Rep. 2021 Apr 28;11(1):9161. doi: 10.1038/s41598-021-88150-6.

ABSTRACT

Over one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to the anthelmintics currently used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-selective manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematode Caenorhabditis elegans. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant in C. elegans, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-selective inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.

PMID:33911106 | PMC:PMC8080662 | DOI:10.1038/s41598-021-88150-6



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SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma

Sci Transl Med. 2021 Apr 28;13(591):eabe7378. doi: 10.1126/scitranslmed.abe7378.

ABSTRACT

Treatment of solid cancers with chimeric antigen receptor (CAR) T cells is plagued by the lack of ideal target antigens that are both absolutely tumor specific and homogeneously expressed. We show that multi-antigen prime-and-kill recognition circuits provide flexibility and precision to overcome these challenges in the context of glioblastoma. A synNotch receptor that recognizes a specific priming antigen, such as the heterogeneous but tumor-specific glioblastoma neoantigen epidermal growth factor receptor splice variant III (EGFRvIII) or the central nervous system (CNS) tissue-specific antigen myelin oligodendrocyte glycoprotein (MOG), can be used to locally induce expression of a CAR. This enables thorough but controlled tumor cell killing by targeting antigens that are homogeneous but not absolutely tumor specific. Moreover, synNotch-regulated CAR expression averts tonic signaling and exhaustion, maintaining a higher fraction of the T cells in a naïve/stem cell memory state. In immunodeficient mice bearing intracerebral patient-derived xenografts (PDXs) with heterogeneous expression of EGFRvIII, a single intravenous infusion of EGFRvIII synNotch-CAR T cells demonstrated higher antitumor efficacy and T cell durability than conventional constitutively expressed CAR T cells, without off-tumor killing. T cells transduced with a synNotch-CAR circuit primed by the CNS-specific antigen MOG also exhibited precise and potent control of intracerebral PDX without evidence of priming outside of the brain. In summary, by using circuits that integrate recognition of multiple imperfect but complementary antigens, we improve the specificity, completeness, and persistence of T cells directed against glioblastoma, providing a general recognition strategy applicable to other solid tumors.

PMID:33910979 | DOI:10.1126/scitranslmed.abe7378



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How workers respond to social rewards: evidence from community health workers in Uganda

Health Policy Plan. 2021 Apr 21;36(3):239-248. doi: 10.1093/heapol/czaa162.

ABSTRACT

This paper investigates the effect of a non-financial incentive-a competitive annual award-on community health workers' (CHWs) performance, an issue in the public health literature that has not been explored to its potential. Combining data on a competitive social 'Best CHW' award with the monthly performance of 4050 CHWs across Uganda, we examined if introducing social recognition awards improved the performance of CHWs. In contrast to predominant explanations about the effect of awards on motivation, our first multilevel mixed-effect models found that an award within a branch (consisting of ∼30 CHWs) was negatively associated with the performance of the local peers of the winning CHW. Models focused on non-winning branch offices revealed two additional findings. First, a branch showed underperformance if a CHW from any of the three neighbouring branches won an award in the previous year, with average monthly performance scores dropping by 27 percentage points. Second, this negative association was seen only in the top 50th percentile of CHWs. The bottom 50th percentile of CHWs exhibited increased performance by 13 percentage points. These counter-intuitive results suggest that the negative response from high performers might be explained by their frustration of not winning the award or by emotions such as envy and jealousy generated by negative social comparisons. Our results suggest that more fine-grained examination of data pertaining to motivators for CHWs in low-income countries is needed. Motivational incentives like awards may need to be customized for higher- and lower-performing CHWs.

PMID:33881139 | PMC:PMC8058949 | DOI:10.1093/heapol/czaa162



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Setting molecular traps in yeast for identification of anticancer drug targets

Proc Natl Acad Sci U S A. 2021 May 4;118(18):e2105547118. doi: 10.1073/pnas.2105547118.

NO ABSTRACT

PMID:33853860 | PMC:PMC8106309 | DOI:10.1073/pnas.2105547118



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Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2

Commun Biol. 2021 Apr 12;4(1):475. doi: 10.1038/s42003-021-02030-3.

ABSTRACT

COVID-19 is a respiratory illness caused by a novel coronavirus called SARS-CoV-2. The viral spike (S) protein engages the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells with ~10-15-fold higher affinity compared to SARS-CoV S-protein, making it highly infectious. Here, we assessed if ACE2 polymorphisms can alter host susceptibility to SARS-CoV-2 by affecting this interaction. We analyzed over 290,000 samples representing >400 population groups from public genomic datasets and identified multiple ACE2 protein-altering variants. Using reported structural data, we identified natural ACE2 variants that could potentially affect virus-host interaction and thereby alter host susceptibility. These include variants S19P, I21V, E23K, K26R, T27A, N64K, T92I, Q102P and H378R that were predicted to increase susceptibility, while variants K31R, N33I, H34R, E35K, E37K, D38V, Y50F, N51S, M62V, K68E, F72V, Y83H, G326E, G352V, D355N, Q388L and D509Y were predicted to be protective variants that show decreased binding to S-protein. Using biochemical assays, we confirmed that K31R and E37K had decreased affinity, and K26R and T92I variants showed increased affinity for S-protein when compared to wildtype ACE2. Consistent with this, soluble ACE2 K26R and T92I were more effective in blocking entry of S-protein pseudotyped virus suggesting that ACE2 variants can modulate susceptibility to SARS-CoV-2.

PMID:33846513 | PMC:PMC8041869 | DOI:10.1038/s42003-021-02030-3



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Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Cell. 2021 Apr 15;184(8):2239-2254.e39. doi: 10.1016/j.cell.2021.03.009. Epub 2021 Apr 7.

ABSTRACT

Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.

PMID:33831375 | PMC:PMC8054914 | DOI:10.1016/j.cell.2021.03.009



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Toward the discovery of biological functions associated with the mechanosensor Mtl1p of Saccharomyces cerevisiae via integrative multi-OMICs analysis

Sci Rep. 2021 Apr 1;11(1):7411. doi: 10.1038/s41598-021-86671-8.

ABSTRACT

Functional analysis of the Mtl1 protein in Saccharomyces cerevisiae has revealed that this transmembrane sensor endows yeast cells with resistance to oxidative stress through a signaling mechanism called the cell wall integrity pathway (CWI). We observed upregulation of multiple heat shock proteins (HSPs), proteins associated with the formation of stress granules, and the phosphatase subunit of trehalose 6-phosphate synthase which suggests that mtl1Δ strains undergo intrinsic activation of a non-lethal heat stress response. Furthermore, quantitative global proteomic analysis conducted on TMT-labeled proteins combined with metabolome analysis revealed that mtl1Δ strains exhibit decreased levels of metabolites of carboxylic acid metabolism, decreased expression of anabolic enzymes and increased expression of catabolic enzymes involved in the metabolism of amino acids, with enhanced expression of mitochondrial respirasome proteins. These observations support the idea that Mtl1 protein controls the suppression of a non-lethal heat stress response under normal conditions while it plays an important role in metabolic regulatory mechanisms linked to TORC1 signaling that are required to maintain cellular homeostasis and optimal mitochondrial function.

PMID:33795741 | PMC:PMC8016984 | DOI:10.1038/s41598-021-86671-8



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MaveRegistry: a collaboration platform for multiplexed assays of variant effect

Bioinformatics. 2021 Mar 27:btab215. doi: 10.1093/bioinformatics/btab215. Online ahead of print.

ABSTRACT

SUMMARY: Multiplexed assays of variant effect (MAVEs) are capable of experimentally testing all possible single nucleotide or amino acid variants in selected genomic regions, generating 'variant effect maps', which provide biochemical insight and functional evidence to enable more rapid and accurate clinical interpretation of human variation. Because the international community applying MAVE approaches is growing rapidly, we developed the online MaveRegistry platform to catalyze collaboration, reduce redundant efforts, allow stakeholders to nominate targets, and enable tracking and sharing of progress on ongoing MAVE projects.

AVAILABILITY AND IMPLEMENTATION: MaveRegistry service: https://registry.varianteffect.org. MaveRegistry source code: https://github.com/kvnkuang/maveregistry-front-end.

SUPPLEMENTARY INFORMATION: no Supplementary data.

PMID:33774657 | DOI:10.1093/bioinformatics/btab215



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Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection

Sci Rep. 2021 Mar 24;11(1):6777. doi: 10.1038/s41598-021-86087-4.

ABSTRACT

Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost. Here, we present a novel microdroplet-based, one-step reverse-transcriptase polymerase chain reaction (RT-PCR) platform and demonstrate the detection of three targets simultaneously in over 100,000 single cells in a single experiment with a rapid read-out. Our customized reagent cocktail incorporates the bacteriophage T7 gene 2.5 protein to overcome cell lysate-mediated inhibition and allows for one-step RT-PCR of single cells encapsulated in nanoliter droplets. Fluorescent signals indicative of gene expressions are analyzed using a probabilistic deconvolution method to account for ambient RNA and cell doublets and produce single-cell gene signature profiles, as well as predict cell frequencies within heterogeneous samples. We also developed a simulation model to guide experimental design and optimize the accuracy and precision of the assay. Using mixtures of in vitro transcripts and murine cell lines, we demonstrated the detection of single RNA molecules and rare cell populations at a frequency of 0.1%. This low cost, sensitive, and adaptable technique will provide an accessible platform for high throughput single-cell analysis and enable a wide range of research and clinical applications.

PMID:33762663 | PMC:PMC7990930 | DOI:10.1038/s41598-021-86087-4



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Inhibition of HECT E3 ligases as potential therapy for COVID-19

Cell Death Dis. 2021 Mar 24;12(4):310. doi: 10.1038/s41419-021-03513-1.

ABSTRACT

SARS-CoV-2 is responsible for the ongoing world-wide pandemic which has already taken more than two million lives. Effective treatments are urgently needed. The enzymatic activity of the HECT-E3 ligase family members has been implicated in the cell egression phase of deadly RNA viruses such as Ebola through direct interaction of its VP40 Protein. Here we report that HECT-E3 ligase family members such as NEDD4 and WWP1 interact with and ubiquitylate the SARS-CoV-2 Spike protein. Furthermore, we find that HECT family members are overexpressed in primary samples derived from COVID-19 infected patients and COVID-19 mouse models. Importantly, rare germline activating variants in the NEDD4 and WWP1 genes are associated with severe COVID-19 cases. Critically, I3C, a natural NEDD4 and WWP1 inhibitor from Brassicaceae, displays potent antiviral effects and inhibits viral egression. In conclusion, we identify the HECT family members of E3 ligases as likely novel biomarkers for COVID-19, as well as new potential targets of therapeutic strategy easily testable in clinical trials in view of the established well-tolerated nature of the Brassicaceae natural compounds.

PMID:33762578 | PMC:PMC7987752 | DOI:10.1038/s41419-021-03513-1



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