Article
|
Open Access
Featured
-
-
Article
| Open AccessA small-molecule inhibitor of SOD1-Derlin-1 interaction ameliorates pathology in an ALS mouse model
Amyotrophic lateral sclerosis (ALS) is a neurological disease that leads to loss of voluntary muscle movement. Here, the authors screen for molecules that disrupt interaction between SOD1, a protein linked to ALS, and Derlin-1, and find an inhibitor that reduces pathology in an ALS mouse model.
- Naomi Tsuburaya
- , Kengo Homma
- & Hidenori Ichijo
-
Article
| Open AccessGlobal pairwise RNA interaction landscapes reveal core features of protein recognition
RNA–protein interactions often depend on the recognition of extended RNA elements but the identification of these motifs is challenging. Here, the authors present a global integrated approach to analyze RNA–protein binding landscapes, mapping extended RNA interaction motifs for four RNA-binding proteins.
- Qin Zhou
- , Nikesh Kunder
- & Zachary T. Campbell
-
Article
| Open AccessPooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance
Systemic investigation of the bacterial genome is essential for both basic microbiology and bioengineering. Here the authors demonstrate CRISPRi pooled screening as a high-throughput tool for identifying gene and phenotype associations in bacteria.
- Tianmin Wang
- , Changge Guan
- & Xin-Hui Xing
-
Article
| Open AccessProfiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity
Epithelial subpopulations are present in the human breast but how these differentiate or form is unclear. Here, the authors use single-cell RNA sequencing of primary human breast epithelial cells to define previously undescribed luminal, basal epithelial subpopulations and ZEB1-positive basal cells.
- Quy H. Nguyen
- , Nicholas Pervolarakis
- & Kai Kessenbrock
-
Article
| Open AccessTargeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes
Spinal muscular atrophy (SMA) is an autosomal recessive disorder with no present cure. Here the authors perform an in vitro screening leading to the identification of a small molecule that alters the conformational dynamics of the TSL2 RNA structure and acts as a modulator of SMN exon 7 splicing.
- Amparo Garcia-Lopez
- , Francesca Tessaro
- & Leonardo Scapozza
-
Article
| Open AccessA comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum
Currently available platforms to study liver stage of Plasmodium species have limitations. Here, the authors show that primary human hepatocyte cultures in 384-well format support hypnozoite and other liver stage development and are suitable for drug and antibody screens.
- Alison Roth
- , Steven P. Maher
- & John H. Adams
-
Article
| Open AccessSystematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact
The internal organization of the cell has been enriched by the discovery that organelles establish membrane contact sites, however the entire repertoire of these contacts is still being explored. Here the authors systematically identify the landscape of cellular contact sites in yeast, discovering four potential novel contact sites and two tether proteins for the peroxisome-mitochondria contact site.
- Nadav Shai
- , Eden Yifrach
- & Einat Zalckvar
-
Article
| Open AccessAggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target
Aggressive natural killer-cell leukemia (ANKL) has few targeted therapies. Here ANKL patients are reported to harbor STAT3, RAS-MAPK pathway, DDX3X and epigenetic modifier mutations; and drug sensitivity profiling uncovers the importance of the JAK-STAT pathway, revealing potential ANKL therapeutic targets.
- Olli Dufva
- , Matti Kankainen
- & Satu Mustjoki
-
Article
| Open AccessIn silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design
Antimicrobial peptides are considered promising alternatives to antibiotics. Here the authors developed a computational algorithm that starts with peptides naturally occurring in plants and optimizes this starting material to yield new variants which are highly distinct from the parent peptide.
- William F. Porto
- , Luz Irazazabal
- & Octavio L. Franco
-
Article
| Open AccessHow single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin
Influenza A virus can escape antibodies, but it is unclear how the ease of escape depends on the epitope targeted by an antibody. Here, the authors show that neutralization breadth is an imperfect indicator of the ease of viral escape by single mutations, and that antibodies targeting the stalk of hemagglutinin are harder to escape.
- Michael B. Doud
- , Juhye M. Lee
- & Jesse D. Bloom
-
Article
| Open AccessJMJD5 is a human arginyl C-3 hydroxylase
Jumonji-C domain containing protein 5 (JMJD5) is essential for animal development but its catalytic activity has remained elusive so far. Here the authors show that human JMJD5 is an arginyl-hydroxylase and present the cofactor, substrate and product bound JMJD5 crystal structures.
- Sarah E. Wilkins
- , Md. Saiful Islam
- & Rasheduzzaman Chowdhury
-
Article
| Open AccessEfficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform
Optimizing an enzyme usually requires testing thousands of variants, thus consuming large amounts of material and time. Here, the authors present a method that allows for measuring two different activities of the same enzyme simultaneously instead of doing two consecutive rounds of screening.
- Fuqiang Ma
- , Meng Ting Chung
- & Guang-Yu Yang
-
Article
| Open AccessA human endothelial cell-based recycling assay for screening of FcRn targeted molecules
The development of IgG and albumin-based therapeutics with increased half-lives needs more efficient screening procedures. Here the authors report a human endothelial cell-based recycling assay enabling screening of IgG and albumin variants without chemical labelling and prior to animal testing.
- Algirdas Grevys
- , Jeannette Nilsen
- & Jan Terje Andersen
-
Article
| Open AccessSingle-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs
Total RNA sequencing has been used to profile poly(A) and non-poly(A) RNA expression, processing and the activity of enhancers. Here the authors develop RamDA-seq, a method for full-length total RNA sequencing in single cells.
- Tetsutaro Hayashi
- , Haruka Ozaki
- & Itoshi Nikaido
-
Article
| Open AccessLeucine-rich repeat receptor-like gene screen reveals that Nicotiana RXEG1 regulates glycoside hydrolase 12 MAMP detection
The role of most plant leucine-rich repeat (LRR) receptors in innate immunity is unknown. Here, the authors develop virus-based constructs to silence LRR receptor-like genes in the Nicotiana benthamiana genome and identify Response to XEG1 that specifically recognizes the glycoside hydrolase 12 protein XEG1.
- Yan Wang
- , Yuanpeng Xu
- & Yuanchao Wang
-
Article
| Open AccessA printable hydrogel microarray for drug screening avoids false positives associated with promiscuous aggregating inhibitors
False positive results significantly slow down the drug discovery process. Here, the authors developed a gel serving as a screening platform in which enzymes can be stored, stabilized, and protected from most of the compounds that typically cause these misleading results.
- Rabia Mateen
- , M. Monsur Ali
- & Todd Hoare
-
Correspondence
| Open AccessCorrespondence: Reply to ‘Compound 17b and formyl peptide receptor biased agonism in relation to cardioprotective effects in ischaemia-reperfusion injury’
- Cheng Xue Qin
- , Lauren T. May
- & Rebecca H. Ritchie
-
Article
| Open AccessMultiplex glycan bead array for high throughput and high content analyses of glycan binding proteins
The low throughput or content of current methods for the analysis of glycans-glycan binding proteins (GBPs) interactions hampers their clinical applications. Here, the authors conjugate synthesized glycans to Luminex beads to detect GBPs and apply it for the discovery of ovarian cancer biomarkers.
- Sharad Purohit
- , Tiehai Li
- & Jin-Xiong She
-
Article
| Open AccessBrain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects
One challenge in drug screening for neurological disorders is how to accurately capture disease pathology and side effects. Here, the authors developed a multi-channel recording platform based on a zebrafish genetic model of epilepsy to screen for antiepileptic drugs.
- Peter M. Eimon
- , Mostafa Ghannad-Rezaie
- & Mehmet Fatih Yanik
-
Article
| Open AccessMammalian display screening of diverse cystine-dense peptides for difficult to drug targets
Pathologies related to protein:protein interaction are hard to treat but cystine-dense peptides have the potential to disrupt such interactions. Here the authors develop a high-diversity mammalian cell screen for cystine-dense peptides with drug potential and use it to identify a YAP:TEAD inhibitor.
- Zachary R. Crook
- , Gregory P. Sevilla
- & James M. Olson
-
Article
| Open AccessSystematic screening of generic drugs for progressive multiple sclerosis identifies clomipramine as a promising therapeutic
Progressive multiple sclerosis is an inflammatory and degenerative disease of the central nervous system, for which effective treatment is lacking. The authors carry out a screen to identify orally available generic medications, and show that the antidepressant clomipramine reduces pathology in mouse models.
- Simon Faissner
- , Manoj Mishra
- & V. Wee Yong
-
Article
| Open AccessCellular microRNA networks regulate host dependency of hepatitis C virus infection
Using genome-wide miRNA mimic and hairpin inhibitor screens, Li et al. identify 31 miRNAs that either inhibit or promote hepatitis C virus (HCV) replication at different steps of the viral life cycle. Furthermore, human liver biopsies show that HCV down-regulates identified miRNAs with antiviral function.
- Qisheng Li
- , Brianna Lowey
- & T. Jake Liang
-
Article
| Open AccessAssay interference and off-target liabilities of reported histone acetyltransferase inhibitors
A substantial obstacle in basic research is the use of poorly validated tool compounds with purported useful biological functions. Here, the authors systematically profile widely used histone acetyltransferase inhibitors and find that the majority are nonselective interference compounds.
- Jayme L. Dahlin
- , Kathryn M. Nelson
- & Michael A. Walters
-
Article
| Open AccessPhage display and selection of lanthipeptides on the carboxy-terminus of the gene-3 minor coat protein
Lanthipeptides are a class of cyclic post-translationally modified peptides with potential drug-like properties. Here the authors develop a phage display system by expressing lanthipeptide precursors as C-terminal fusions to the phage M13 coat protein pIII in E. coli along with the heterologous modifying enzymes.
- Johannes H. Urban
- , Markus A. Moosmeier
- & Josef Prassler
-
Article
| Open AccessGenome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding
During cell division animal cells generate intracellular pressure and round against their environment, but the genes responsible for this are largely unknown. Here the authors use a microcantilever- and RNAi-based assay to screen > 1000 genes and identify 49 genes involved in mitotic cell rounding; many are novel to this process.
- Yusuke Toyoda
- , Cedric J. Cattin
- & Daniel J. Müller
-
Article
| Open AccessParallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia
Fanconi anemia is a complex disease affecting multiple DNA repair proteins that resolve DNA crosslinks which can block vital processes. Here the authors use parallel genome-wide screens that identify the BLM helicase complex as a suppressor of Fanconi anemia phenotypes.
- Martin Moder
- , Georgia Velimezi
- & Joanna I. Loizou
-
Article
| Open AccessA novel Fer/FerT targeting compound selectively evokes metabolic stress and necrotic death in malignant cells
The tyrosine-kinases Fer/FerT associate with the mitochondrial electron transport chain in cancer cells supporting their metabolic reprogramming. Here the authors discover a compound that disrupts Fer /FerT activity and selectively induces cell death of cancer cell lines displaying anti-tumor activity in vivo.
- Yoav Elkis
- , Moshe Cohen
- & Uri Nir
-
Article
| Open AccessHigh-throughput screens using photo-highlighting discover BMP signaling in mitochondrial lipid oxidation
High-throughput genetic screens in animals could benefit from an easy way to mark positive hits. Here the authors introduce photo-highlighting using a photoconvertible fluorescent protein, and in combination with stimulated Raman scattering (SRS) microscopy, define a role for BMP signaling in lipid metabolism in C. elegans.
- Yong Yu
- , Ayse Sena Mutlu
- & Meng C. Wang
-
Article
| Open AccessMicrofluidics with fluid walls
The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.
- Edmond J. Walsh
- , Alexander Feuerborn
- & Peter R. Cook
-
Article
| Open AccessSmall molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice
Upon DNA binding cyclic GMP-AMP synthase (cGAS) produces a cyclic dinucleotide, which leads to the upregulation of inflammatory genes. Here the authors develop small molecule cGAS inhibitors, functionally characterize them and present the inhibitor and DNA bound cGAS crystal structures, which will facilitate drug development.
- Jessica Vincent
- , Carolina Adura
- & Manuel Ascano
-
Article
| Open AccessCheckpoint blockade immunotherapy reshapes the high-dimensional phenotypic heterogeneity of murine intratumoural neoantigen-specific CD8+ T cells
Immune checkpoint blockade (ICB) therapies can unleash anti-tumour T-cell responses. Here the authors show, by integrating MHC tetramer multiplexing, mass cytometry and high-dimensional analyses, that neoantigen-specific, tumour-infiltrating T cells are highly heterogeneous and are subjected to ICB modulations.
- M. Fehlings
- , Y. Simoni
- & E. W. Newell
-
Article
| Open AccessMultiscale cytometry and regulation of 3D cell cultures on a chip
3D cell culture is more relevant than the two-dimensional format, but methods for parallel analysis and temporal regulation of the microenvironment are limited. Here the authors develop a droplet microfluidics system to perform long-term culture of 3D spheroids, enabling multiscale cytometry of individual cells within the spheroid.
- Sébastien Sart
- , Raphaël F.-X. Tomasi
- & Charles N. Baroud
-
Article
| Open AccessMultivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation
Multivariate analysis methods can uncover the relationship between phenotypic measures characterised by modern omic techniques. Here the authors conduct a multivariate GWAS on IgG N-glycosylation phenotypes and identify 5 novel loci enriched in immune system genes.
- Xia Shen
- , Lucija Klarić
- & Yurii S. Aulchenko
-
Article
| Open AccessIdentification of HSP90 inhibitors as a novel class of senolytics
The accumulation of senescent cells is thought to contribute to the age-associated decline in tissue function. Here, the authors identify HSP90 inhibitors as a new class of senolytic compounds in an in vitro screening and show that administration of a HSP90 inhibitor reduces age-related symptoms in progeroid mice.
- Heike Fuhrmann-Stroissnigg
- , Yuan Yuan Ling
- & Paul D. Robbins
-
Article
| Open AccessRNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes
Screening libraries of genetically engineered microbes for secreted products is limited by the available assay throughput. Here the authors combine aptamer-based fluorescent detection with droplet microfluidics to achieve high throughput screening of yeast strains engineered for enhanced tyrosine or streptavidin production.
- Joseph Abatemarco
- , Maen F. Sarhan
- & Adam R. Abate
-
Article
| Open AccessPLATE-Seq for genome-wide regulatory network analysis of high-throughput screens
Despite the importance of pharmacological and functional genomic screens the readouts are of low complexity. Here the authors introduce PLATE-Seq, a low-cost genome-wide mRNA profiling method to complement high-throughput screening.
- Erin C. Bush
- , Forest Ray
- & Peter A. Sims
-
Article
| Open AccessSingle-cell profiling reveals heterogeneity and functional patterning of GPCR expression in the vascular system
GPCRs are key regulators of vascular functions. By analysing single-cell GPCRs expression in vascular smooth muscle and endothelial cells from healthy and diseased murine vessels, Kauret al. show that GPCR expression is highly heterogeneous in all cell types and that disease causes GPCR repertoire changes depending on cell type and vascular localization.
- H. Kaur
- , J. Carvalho
- & N. Wettschureck
-
Article
| Open AccessBlood-brain-barrier spheroids as an in vitro screening platform for brain-penetrating agents
In vitroblood-brain barrier (BBB) models are crucial tools for screening brain-penetrating compounds. Here the authors develop a self-assembling BBB spheroid model with superior performance to the standard transwell BBB model, and use their platform to identify cell-penetrating peptides that can cross the BBB.
- Choi-Fong Cho
- , Justin M. Wolfe
- & Sean E. Lawler
-
Article
| Open AccessA scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions
Protein-protein interactions (PPIs) play a major role in defining biological functions. Here, the authors present PPiSeq, a method to quantitatively score dynamic PPIs in yeast combining fragment complementation assays, genomic double-barcoding, and an analytical framework to precisely call fitness from barcode lineage trajectories.
- Ulrich Schlecht
- , Zhimin Liu
- & Sasha F. Levy
-
Article
| Open AccessHundreds of dual-stage antimalarial molecules discovered by a functional gametocyte screen
There is a need forPlasmodium transmission blocking drugs for malaria elimination. Here, Miguel-Blanco et al. screen >10,000 compounds against stage V female gametocytes, identify active compounds belonging to 57 chemotypes and confirm transmission blocking activity of four selected compounds in vitro.
- Celia Miguel-Blanco
- , Irene Molina
- & Esperanza Herreros
-
Article
| Open AccessTradict enables accurate prediction of eukaryotic transcriptional states from 100 marker genes
Global patterns of gene transcription can be represented with reduced dimensionality. Here, the authors devise a method called Tradict that learns and uses 100 marker genes to predict transcriptome-wide pathway expression levels and patterns that reflect cell activity and state.
- Surojit Biswas
- , Konstantin Kerner
- & Philip A. Wigge
-
Article
| Open AccessGenome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens
CRISPR-Cas9 screens are powerful high-throughput tools but can be confounded by nuclease toxicity. Here the authors design a library of variable length gRNAs with thousands of negative controls, including the targeting of ‘safe’ loci to account for on-target site DNA damage toxicity.
- David W. Morgens
- , Michael Wainberg
- & Michael C. Bassik
-
Article
| Open AccessMacrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases
River blindness, a disease affecting millions throughout the tropics, is caused by parasitic worms. Here, Yuet al. report the discovery and structural characterization of potent macrocyclic peptide inhibitors of iPGM, a nematode-specific phosphoglycerate mutase, as potential leads for novel antimicrobial agents.
- Hao Yu
- , Patricia Dranchak
- & James Inglese
-
Article
| Open AccessInhibition of delta-secretase improves cognitive functions in mouse models of Alzheimer’s disease
Delta-secretases are associated with Alzheimer’s disease (AD) as they cleave both amyloid precursor protein and tau. Here the authors develop a series of orally bioactive small molecule delta-secretase inhibitors and report its therapeutic effects in mouse models of AD.
- Zhentao Zhang
- , Obiamaka Obianyo
- & Keqiang Ye
-
Article
| Open AccessA genome-wide screen identifies YAP/WBP2 interplay conferring growth advantage on human epidermal stem cells
Individual human epidermal cells differ in their self-renewal ability. Here the authors perform genome-wide pooled RNAi screens to uncover the molecular basis for this heterogeneity, and identify genes conferring a clonal growth advantage on normal and neoplastic human epidermal cells.
- Gernot Walko
- , Samuel Woodhouse
- & Fiona M. Watt
-
Article
| Open AccessThe OncoPPi network of cancer-focused protein–protein interactions to inform biological insights and therapeutic strategies
Understanding of dysregulation in cancers requires knowledge, beyond cancer genomes, of the interactions of cancer-associated proteins. Here, the authors use high-throughput, time-resolved FRET to map protein–protein interactions to establish a lung cancer protein network, and demonstrate its utility in revealing new oncogenic pathways and connectivity of tumour suppressors with druggable targets.
- Zenggang Li
- , Andrei A. Ivanov
- & Haian Fu
-
Article
| Open AccessDissection of goadsporin biosynthesis by in vitro reconstitution leading to designer analogues expressed in vivo
Goadsporin is an antibacterial peptide highly customized by multiple post-translational modifying enzymes. Here, the authors dissect its biosynthetic pathway byin vitro reconstitution and use their insights to produce goadsporin analogues in vitro and in vivo.
- Taro Ozaki
- , Kona Yamashita
- & Hiroyasu Onaka
-
Article
| Open AccessDeep phenotyping unveils hidden traits and genetic relations in subtle mutants
Experimenter scoring of cellular imaging data can be biased. This study describes an automated and unbiased multidimensional phenotyping method that relies on machine learning and complex feature computation of imaging data, and identifies weak alleles affecting synapse morphology in live C. elegans.
- Adriana San-Miguel
- , Peri T. Kurshan
- & Hang Lu
-
Article
| Open AccessRapid construction of a whole-genome transposon insertion collection for Shewanella oneidensis by Knockout Sudoku
Knockout collections provide a valuable tool to explore gene function, yet are expensive and technically challenging to produce at a genome-wide scale. Here Baym et al. devise a cost-effective transposon-based method to quickly develop a knockout collection for the electroactive microbe Shewanella oneidensis.
- Michael Baym
- , Lev Shaket
- & Buz Barstow