101 Citations
SummaryBACH is a transcriptional regulator that modulates various cytoprotective pathways Among these pathways BACH regulates the cellular oxidative stress responses by suppressing the expression of cytoprotective genes Dysregulated BACH activity has been implicated in a range of pathologies including chronic inflammatory diseases fibrosis and cancer making it a promising therapeutic target However BACH remains an underexploited drug target with limited pharmacological inhibitors available We have developed a novel luciferase-based reporter cell line enabling quantitative high-throughput assessment of BACH inhibition Using this platform we rigorously screened two small-molecule libraries with compounds and identified four structurally distinct compounds that robustly inhibit BACH ... More
SummaryBACH1 is a transcriptional regulator that modulates various cytoprotective pathways. Among these pathways BACH1 regulates the cellular oxidative stress responses by suppressing the expression of cytoprotective genes. Dysregulated BACH1 activity has been implicated in a range of pathologies, including chronic inflammatory diseases, fibrosis, and cancer, making it a promising therapeutic target. However, BACH1 remains an underexploited drug target, with limited pharmacological inhibitors available. We have developed a novel luciferase-based reporter cell line enabling quantitative, high-throughput assessment of BACH1 inhibition. Using this platform, we rigorously screened two small-molecule libraries with 2,046 compounds and identified four structurally distinct compounds that robustly inhibit BACH1 function. Notably, these compounds simultaneously activate transcription factor NRF2, suggesting the potential for a broader modulation of oxidative stress pathways.Importantly, we demonstrate that commonly used 2D migration assays may fail to detect phenotypes consistent with BACH1 inhibition, resulting in false negatives. In contrast, we establish that 3D invasion assays more robustly capture anti-invasive effects of BACH1 functional inhibition. Using this 3D system, we validate the identified compounds as potent suppressors of lung cancer cell invasion in vitro.This study delivers a novel screening platform for BACH1-targeted drug discovery, and challenges current in vitro standards by establishing 3D invasion assays as a more accurate functional readout for BACH1-targeting compounds. Additionally, it identifies new dual functional BACH1 inhibitors/NRF2 activators, offering novel chemical scaffolds for the development of anti-metastatic therapies and potentially treatments for diseases driven by oxidative stress and inflammation. Less
The PD- PD-L immune checkpoint is a pivotal target for cancer immunotherapy Monoclonal antibodies mAbs targeting the PD- PD-L interaction have achieved clinical success but face limitations including high production costs suboptimal tumor penetration and potential immunogenicity To address these challenges we present the DNA-linked Inhibitor Antibody Assay DIANA a robust high-throughput screening platform optimized for identifying and characterizing low-molecular-weight inhibitors of human PD-L DIANA integrates competitive binding with qPCR detection enabling single-well determination of dissociation constants Kd and rapid screening of thousands of compounds The assay was validated using three FDA-approved mAbs atezolizumab avelumab and durvalumab the PD-L -binding ... More
The PD-1/PD-L1 immune checkpoint is a pivotal target for cancer immunotherapy. Monoclonal antibodies (mAbs) targeting the PD-1/PD-L1 interaction have achieved clinical success but face limitations, including high production costs, suboptimal tumor penetration, and potential immunogenicity. To address these challenges, we present the DNA-linked Inhibitor Antibody Assay (DIANA)─a robust, high-throughput screening platform optimized for identifying and characterizing low-molecular-weight inhibitors of human PD-L1. DIANA integrates competitive binding with qPCR detection, enabling single-well determination of dissociation constants (Kd) and rapid screening of thousands of compounds. The assay was validated using three FDA-approved mAbs (atezolizumab, avelumab, and durvalumab), the PD-L1-binding macrocyclic peptide WL12, and the native PD-1 receptor, yielding Kd values consistent with the literature. DIANA demonstrated a broad dynamic range spanning more than 4 orders of magnitude, excellent robustness (Z′-factor = 0.94), and high tolerance to DMSO (up to 10%). We applied DIANA to screen two libraries: a 5,280-compound in-house library (pooled format) and a 1,298-compound commercial peptidomimetic library (individual format). While very weak initial hits were detected, none were confirmed in follow-up manual (non-HTS) experiments or in an orthogonal cell-based assay. Nonetheless, DIANA’s sensitivity, scalability, and minimal sample requirements establish it as a powerful tool for accelerating the discovery of next-generation PD-1/PD-L1 inhibitors and overcoming key limitations of conventional screening methods. Less
Imidazolium LipidBrick cationic lipid nanoparticles LNPs provide a pH-independent alternative to conventional ionizable systems for nucleic acid delivery Through a high-throughput screen of formulations spanning eight imidazolium cores three helper lipids and varying PEG densities we found that more than half of the library outperformed the clinical ionizable benchmark ALC- in multiple representative mammalian cell types Top-performing candidates showed robust cellular uptake efficient endosomal escape and strong transgene expression both in vitro and following intramuscular administration A lead formulation C LNP incorporating an imidazolium lipid core bearing a hydroxyethyl substituent with mol DOPE achieved comparable intramuscular luciferase expression and antibody ... More
Imidazolium LipidBrick® cationic lipid nanoparticles (LNPs) provide a pH-independent alternative to conventional ionizable systems for nucleic acid delivery. Through a high-throughput screen of 1,944 formulations spanning eight imidazolium cores, three helper lipids, and varying PEG densities, we found that more than half of the library outperformed the clinical ionizable benchmark ALC-0315 in multiple representative mammalian cell types. Top-performing candidates showed robust cellular uptake, efficient endosomal escape, and strong transgene expression both in vitro and following intramuscular administration. A lead formulation (C3 LNP), incorporating an imidazolium lipid core bearing a hydroxyethyl substituent, with 30 mol% DOPE, achieved comparable intramuscular luciferase expression and antibody titers to ALC-0315, while eliciting ∼ 3-fold stronger ovalbumin-specific IFN-γ+ T-cell responses and maintaining low cytotoxicity. Machine-learning analysis of the dataset further distilled transferable design rules to inform future formulation strategies. Collectively, these findings establish cationic LipidBrick® LNPs as a versatile platform for mRNA delivery, offering a generalizable framework for the high-throughput discovery of ionization-independent systems that effectively prime adaptive immune responses. Less
Tankyrases are poly-ADP-ribosyltransferases that orchestrate numerous biological processes involved in disease Their established regulatory roles particularly within the WNT -catenin pathway have driven notable drug discovery efforts aimed at inhibiting their catalytic activity Targeting tankyrases interaction with proteins through their ARC domains represents an alternative strategy to be explored as a therapeutic approach against specific protein-protein interactions In this article we employed a pre-established FRET-based assay to screen the EU-OPENSCREEN libraries for identification of ARC inhibitors We discovered a series of pyrrolone-based compounds and we synthesized compound S ARCher- which binds selectively to ARC with a potency of M NMR ... More
Tankyrases are poly-ADP-ribosyltransferases that orchestrate numerous biological processes involved in disease. Their established regulatory roles, particularly within the WNT/β-catenin pathway, have driven notable drug discovery efforts aimed at inhibiting their catalytic activity. Targeting tankyrases’ interaction with proteins through their ARC domains represents an alternative strategy to be explored as a therapeutic approach against specific protein-protein interactions. In this article, we employed a pre-established FRET-based assay to screen the EU-OPENSCREEN libraries for identification of ARC4 inhibitors. We discovered a series of pyrrolone-based compounds, and we synthesized compound S8 (ARCher-142), which binds selectively to ARC4 with a potency of 8 μM. NMR analysis and X-ray crystallography allowed us to identify the binding site and to rationalize the observed selectivity. Despite binding exclusively to ARC4, the inhibitor can attenuate the WNT/β-catenin signaling pathway in cells. Our work demonstrates that targeting single ARC domains is possible, offering an inhibition approach tailored to tankyrase ARC4. Less
Insulin resistance drives cardiometabolic disease yet its molecular signatures and tissue origins remain incompletely characterized and scalable assessment methods are lacking Here we apply Multi-Workflow Proteomics on plasma from individuals spanning the metabolic spectrum defined by hyperinsulinemic euglycemic clamp derived insulin sensitivity We identify proteins associated with insulin sensitivity revealing contributions from liver adipose tissue and immune cells alongside underappreciated roles for brain and heart An exercise intervention demonstrated these signatures are modifiable We developed a model combining proteins including IGFBP LEP GDF PON and LDLR with clinical variables sex HbA c TG HDL ratio that estimates hyperinsulinemic euglycemic clamp-derived ... More
Insulin resistance drives cardiometabolic disease, yet its molecular signatures and tissue origins remain incompletely characterized, and scalable assessment methods are lacking. Here, we apply Multi-Workflow Proteomics on plasma from 161 individuals spanning the metabolic spectrum defined by hyperinsulinemic–euglycemic clamp–derived insulin sensitivity. We identify 488 proteins associated with insulin sensitivity, revealing contributions from liver, adipose tissue, and immune cells alongside underappreciated roles for brain and heart. An exercise intervention demonstrated these signatures are modifiable. We developed a model combining 13 proteins, including IGFBP1, LEP, GDF15, PON3, and LDLR, with clinical variables (sex, HbA1c, TG/HDL ratio) that estimates hyperinsulinemic–euglycemic clamp-derived insulin sensitivity (R² = 0.73). Applied to ~20,000 UK Biobank participants, estimated insulin sensitivity outperformed TG/HDL in predicting type 2 diabetes (c-index 0.86 vs. 0.71) and other cardiometabolic outcomes, including obesity, cardiovascular disease, and chronic kidney disease. This proteomic atlas enables scalable insulin resistance assessment and precision risk stratification. Less
Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing chromatography and MS acquisition Here we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients and samples per day along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer We found that tissue type was as important as gradient length and sample amount in determining proteome coverage Moreover the benefit of increased tissue sampling was gradient- and dynamic range-dependent Analyzing mouse liver a high dynamic range tissue over tenfold more tissue sampling led to only ... More
Achieving high-resolution spatial tissue proteomes requires careful balancing and integration of optimized sample processing, chromatography, and MS acquisition. Here, we present an advanced cellenONE protocol for loss-reduced tissue processing and compare all Evosep ONE Whisper Zoom gradients (20, 40, 80, and 120 samples per day), along with three common DIA acquisition schemes on a timsUltra AIP mass spectrometer. We found that tissue type was as important as gradient length and sample amount in determining proteome coverage. Moreover, the benefit of increased tissue sampling was gradient- and dynamic range-dependent. Analyzing mouse liver, a high dynamic range tissue, over tenfold more tissue sampling led to only ~30% gain in protein identification for short gradients (120 SPD and 80 SPD). However, even the lowest tested tissue amount (0.04 nL, 40,000 µm3) yielded 3,200 reproducibly quantified proteins for the 120 SPD method. Longer gradients (40 SPD and 20 SPD) instead significantly benefited from more tissue sampling, quantifying over 7,500 proteins from 0.5 nL of tonsil T-cell niches. Finally, we applied our workflow to a rare squamous cell carcinoma of the oral cavity, uncovering disease-associated pathways and region-specific protein level changes. Our study demonstrates that more than 100 high-quality spatial tissue proteomes can be prepared and acquired daily, laying a strong foundation for cohort-size spatial tissue proteomics in translational research. Less
Prophages dormant bacteriophage genomes integrated within the bacterial chromosome play pivotal roles in shaping microbial communities when awakened Our current understanding of prophage activation is largely shaped by a narrow set of traditional DNA-damaging inducers such as mitomycin C and ciprofloxacin which trigger the bacterial SOS response This study employed high-throughput screening of compounds to identify novel prophage inducers using model lambdoid prophage HK We identified multiple new inducers across diverse pharmacological classes including dietary supplements and therapeutics Despite the variety in compounds all acted through SOS-dependent pathways However bleomycin an antineoplastic antibiotic demonstrated broad-spectrum and potent prophage induction exceeding ... More
Prophages, dormant bacteriophage genomes integrated within the bacterial chromosome, play pivotal roles in shaping microbial communities when awakened. Our current understanding of prophage activation is largely shaped by a narrow set of traditional DNA-damaging inducers, such as mitomycin C and ciprofloxacin, which trigger the bacterial SOS response. This study employed high-throughput screening of 3,921 compounds to identify novel prophage inducers using model lambdoid prophage HK97. We identified multiple new inducers across diverse pharmacological classes, including dietary supplements and therapeutics. Despite the variety in compounds, all acted through SOS-dependent pathways. However, bleomycin, an antineoplastic antibiotic, demonstrated broad-spectrum and potent prophage induction exceeding standard inducers, with activity validated across multiple phage-host pairings. These findings expand the repertoire of prophage inducers into commonly ingested xenobiotics and introduce bleomycin as a powerful, cost-effective tool for prophage research.
Around 75% of bacteria carry within them dormant viruses (prophages), which can awaken when the bacterium is stressed, killing the bacterium. Historically, this has been done using DNA-damaging antibiotics, but increasingly, more such signals have been discovered. Here, through a high-throughput screen, we identify phage-waking activity in several commonly consumed compounds, such as the SSRI Prozac, as well as a new DNA-damaging agent that is much more effective in waking phages than the previous gold standard. Less
Around 75% of bacteria carry within them dormant viruses (prophages), which can awaken when the bacterium is stressed, killing the bacterium. Historically, this has been done using DNA-damaging antibiotics, but increasingly, more such signals have been discovered. Here, through a high-throughput screen, we identify phage-waking activity in several commonly consumed compounds, such as the SSRI Prozac, as well as a new DNA-damaging agent that is much more effective in waking phages than the previous gold standard. Less
ADP-ribosylation is an enzymatic process where an ADP-ribose moiety is transferred from NAD to an acceptor molecule While ADP-ribosylation is well-established as a post-translational modification of proteins rifamycin antibiotics are its only known small-molecule targets ADP-ribosylation of rifampicin was first identified in Mycolicibacterium smegmatis whose Arr enzyme transfers the ADP-ribose moiety to the -hydroxy group of rifampicin preventing its interaction with the bacterial RNA polymerase thereby inactivating the antibiotic Arr homologues are widely spread among bacterial species and present in several pathogenic species often associated with mobile genetic elements Inhibition of Arr enzymes offers a promising strategy to overcome ADP-ribosylation ... More
ADP-ribosylation is an enzymatic process where an ADP-ribose moiety is transferred from NAD+ to an acceptor molecule. While ADP-ribosylation is well-established as a post-translational modification of proteins, rifamycin antibiotics are its only known small-molecule targets. ADP-ribosylation of rifampicin was first identified in Mycolicibacterium smegmatis, whose Arr enzyme transfers the ADP-ribose moiety to the 23-hydroxy group of rifampicin preventing its interaction with the bacterial RNA polymerase thereby inactivating the antibiotic. Arr homologues are widely spread among bacterial species and present in several pathogenic species often associated with mobile genetic elements. Inhibition of Arr enzymes offers a promising strategy to overcome ADP-ribosylation mediated rifamycin resistance. We developed a high-throughput activity assay, which was applied to screen an in-house library of human ADP-ribosyltransferase-targeted compounds. We identified 15 inhibitors with IC50 values below 5 µM against four Arr enzymes from M. smegmatis, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Mycobacteroides abscessus. The observed overall selectivity of the hit compounds over the other homologues indicated structural differences between the proteins. We crystallized M. smegmatis and P. aeruginosa Arr enzymes, the former in complex with its most potent hit compound with an IC50 value of 1.3 µM. We observed structural differences in the NAD+ binding pockets of the two Arr homologues explaining the selectivity. Although the Arr inhibitors did not sensitize M. smegmatis to rifampicin in a growth inhibition assay, the structural information and the collection of inhibitors provide a foundation for rational modifications and further development of the compounds. Less
Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering DNA synthesis and genomic editing However to access the massive potential of microbial production a vast parametric space remains to be investigated to optimize these biobased processes for a robust bioeconomy Here we review the current state of the art some key challenges and possible solutions We see a critical role of automation high-throughput technologies self-driving and cloud labs and data management to enable Artificial Intelligence Machine Learning and mechanistic models to overcome the design space challenges and accelerate the development of novel ... More
Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering, DNA synthesis, and genomic editing. However, to access the massive potential of microbial production, a vast parametric space remains to be investigated to optimize these biobased processes for a robust bioeconomy. Here, we review the current state of the art, some key challenges and possible solutions. We see a critical role of automation, high-throughput technologies, self-driving and cloud labs, and data management to enable Artificial Intelligence/Machine Learning and mechanistic models to overcome the design space challenges and accelerate the development of novel bio-based solutions. Accurate models will expedite the development and scale-up of engineered microbes for a range of final products from many starting materials. Less
Physical activity improves health yet the molecular mechanisms remain partially understood This study presents a high-resolution time-resolved atlas profiling proteins across plasma saliva and urine from healthy adults post-acute exercise Exercise regulated over proteins revealing distinct fluid-specific temporal dynamics By integrating fluid-specific exercise signatures with tissue and disease atlases we delineated the contribution of tissues and associations to various diseases Network analysis across body fluids elucidated coordinated remodeling in the extracellular matrix and immune activation orchestrating exercise-induced networks Many exercise-responsive plasma proteins were robust across age sex and exercise modalities indicating a conserved systemic signature Integration with genetic data established ... More
Physical activity improves health, yet the molecular mechanisms remain partially understood.
This study presents a high-resolution, time-resolved atlas profiling 10,127 proteins across
plasma, saliva, and urine from healthy adults post-acute exercise. Exercise regulated over
3,000 proteins, revealing distinct, fluid-specific temporal dynamics. By integrating fluid-specific
exercise signatures with tissue and disease atlases, we delineated the contribution of tissues
and associations to various diseases. Network analysis across body fluids elucidated
coordinated remodeling in the extracellular matrix and immune activation orchestrating
exercise-induced networks. Many exercise-responsive plasma proteins were robust across
age, sex, and exercise modalities, indicating a conserved systemic signature. Integration with
genetic data established exercise-regulated proteins as modulators of metabolic traits and
identified over 200 targeted by approved drugs, highlighting their impact on disease-relevant
pathways. This comprehensive atlas, available as an open-access resource
https://cbmr.ku.dk/research/research-groups/deshmukh-group/shiny-apps/, advances our
molecular insight into exercise adaptations and enables exerkine discovery, biomarker
development, and pharmacological exercise-mimetic strategies. Less
This study presents a high-resolution, time-resolved atlas profiling 10,127 proteins across
plasma, saliva, and urine from healthy adults post-acute exercise. Exercise regulated over
3,000 proteins, revealing distinct, fluid-specific temporal dynamics. By integrating fluid-specific
exercise signatures with tissue and disease atlases, we delineated the contribution of tissues
and associations to various diseases. Network analysis across body fluids elucidated
coordinated remodeling in the extracellular matrix and immune activation orchestrating
exercise-induced networks. Many exercise-responsive plasma proteins were robust across
age, sex, and exercise modalities, indicating a conserved systemic signature. Integration with
genetic data established exercise-regulated proteins as modulators of metabolic traits and
identified over 200 targeted by approved drugs, highlighting their impact on disease-relevant
pathways. This comprehensive atlas, available as an open-access resource
https://cbmr.ku.dk/research/research-groups/deshmukh-group/shiny-apps/, advances our
molecular insight into exercise adaptations and enables exerkine discovery, biomarker
development, and pharmacological exercise-mimetic strategies. Less
Mobile phones contaminated with pathogenic microorganisms have the potential to act as trojan horses The microbial signatures present on their surfaces most probably vary across different geographical regions As a result mobile phones belonging to international conference attendees may serve as a model for global microbial dissemination posing potential risks to public health and biosecurity This study aimed to profile the microbes present on mobile phones belonging to delegates attending an international scientific conference through use of metagenomic shotgun DNA sequencing Results A total of microbial hits were accumulated across mobile phones inclusive of bacteria viruses fungi and protozoa Of ... More
Mobile phones, contaminated with pathogenic microorganisms, have
the potential to act as “trojan horses”. The microbial signatures present on their surfaces most probably vary across different geographical regions. As a result, mobile phones belonging to
international conference attendees may serve as a model for global microbial dissemination,
posing potential risks to public health and biosecurity. This study aimed to profile the microbes present on mobile phones belonging to delegates
attending an international scientific conference through use of metagenomic shotgun DNA
sequencing. Results: A total of 2204 microbial hits were accumulated across 20 mobile phones inclusive of
882 bacteria, 1229 viruses, 88 fungi and 5 protozoa. Of particular concern was the identification of 65 distinct antibiotic resistance genes and 86 virulence genes. Plant, animal and human
pathogens, including ESKAPE and HACEK bacteria were found on mobile phones Less
the potential to act as “trojan horses”. The microbial signatures present on their surfaces most probably vary across different geographical regions. As a result, mobile phones belonging to
international conference attendees may serve as a model for global microbial dissemination,
posing potential risks to public health and biosecurity. This study aimed to profile the microbes present on mobile phones belonging to delegates
attending an international scientific conference through use of metagenomic shotgun DNA
sequencing. Results: A total of 2204 microbial hits were accumulated across 20 mobile phones inclusive of
882 bacteria, 1229 viruses, 88 fungi and 5 protozoa. Of particular concern was the identification of 65 distinct antibiotic resistance genes and 86 virulence genes. Plant, animal and human
pathogens, including ESKAPE and HACEK bacteria were found on mobile phones Less
Personalised cell therapies utilising T cell receptors TCRs show tremendous clinical promise though TCR synthesis and validation techniques lag far behind current TCR repertoire sequencing capacity To address this gap we developed makeTCR a modular TCR cloning system that enables rapid single-step fidelity assembly of human or murine TCR sequences into diverse expression vectors We provide pre-cloned modules for and TCRs as well as many native and engineered constant regions We show how implementing cell-free manufacturing both facilitates the propagation of precloned modules and allows testable TCR material to be synthesised in hours enabling patient-derived TCRs to be prototyped prior ... More
Personalised cell therapies utilising T cell receptors (TCRs) show tremendous clinical promise, though TCR synthesis and validation techniques lag far behind current TCR repertoire sequencing capacity. To address this gap we developed makeTCR: a modular TCR cloning system that enables rapid, single-step, 100% fidelity assembly of human or murine TCR sequences into diverse expression vectors. We provide pre-cloned modules for αβ and γδ TCRs, as well as many native and engineered constant regions. We show how implementing cell-free manufacturing both facilitates the propagation of precloned modules, and allows testable TCR material to be synthesised in 24 hours, enabling patient-derived TCRs to be prototyped prior to use in personalised cell therapies. makeTCR scales to making thousands of TCRs, at high fidelity and at substantially reduced cost. makeTCR is facilitated by a free, open-source, extensible, graphical platform to simplify, standardise, and accelerate TCR functionality testing for personalised medicine and beyond. Less
High-throughput experimentation HTE is a critical tool in modern pharmaceutical discovery and development The ability to perform multiple parallel experiments in miniaturized plate-based formats has revolutionized how chemical reactions are optimized HTE has been especially enabling for catalytic reactions where the complexity of factors influencing the outcome makes the HTE approach especially suitable We detail AstraZeneca s -year journey with HTE from early beginnings to a global community of HTE specialists that are critical to the delivery of our complex portfolio with reduced environmental impact With an emphasis on catalytic reactions we provide relevant case study examples from across discovery ... More
High-throughput experimentation (HTE) is a critical tool in modern pharmaceutical discovery and development. The ability to perform multiple parallel experiments in miniaturized plate-based formats has revolutionized how chemical reactions are optimized. HTE has been especially enabling for catalytic reactions, where the complexity of factors influencing the outcome makes the HTE approach especially suitable. We detail AstraZeneca’s 20-year journey with HTE, from early beginnings to a global community of HTE specialists that are critical to the delivery of our complex portfolio with reduced environmental impact. With an emphasis on catalytic reactions, we provide relevant case study examples from across discovery and development, discuss current technology, data science and workflows, and provide insights into where we see future advances in HTE. Less
The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds Advances in molecular engineering tools such as CRISPR have provided some access to the metabolic potential of Streptomyces but efficient genetic engineering of strains is hindered by laborious and slow manual transformation protocols In this paper we present a semi-automated medium-throughput workflow for the introduction of recombinant DNA into Streptomyces spp using the affordable and open-sourced Opentrons OT- robotics platform To increase the accessibility of the workflow we provide an open-source protocol-creator ActinoMation ActinoMation is a literate programming environment using Python in Jupyter Notebook We validated ... More
The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, have provided some access to the metabolic potential of Streptomyces, but efficient genetic engineering of strains is hindered by laborious and slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for the introduction of recombinant DNA into Streptomyces spp. using the affordable and open-sourced Opentrons (OT-2) robotics platform. To increase the accessibility of the workflow we provide an open-source protocol-creator, ActinoMation. ActinoMation is a literate programming environment using Python in Jupyter Notebook. We validated the method by transforming Streptomyces coelicolor (M1152 and M1146), S. albidoflavus (J1047), and S. venezuelae (DSM40230) with the plasmids pSETGUS and pIJ12551. We demonstrate conjugation efficiencies of 3.33*10-3/0.33% for M1152 with pSETGUS and pIJ12551; 2.96*10-3/0.29%for M1146 with pSETGUS and pIJ12551; 1.21*10-5/0.0012% for J1047 with pSETGUS and 4.70*10-4/0.047% with pIJ12551, and 4.97*10-2/4.97% for DSM40230 with pSETGUS and 6.13*10-2 /6.13% with pIJ12551 with a false positive rate between 8.33% and 54.54%. Automation of the conjugation workflow facilitates a streamlined workflow on a larger scale without any evident loss of conjugation efficiency. Less
Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms Its potential for elucidating the ecological roles of microeukaryotes especially non-model ones remains largely unexplored This study employed the Smart-seq protocol on Ochromonas triangulata a microeukaryote lacking a reference genome showcasing how transcriptional states align with two distinct growth phases a fast-growing phase and a slow-growing phase Besides the two expected expression clusters each corresponding to either growth phase a third transcriptional state was identified across both growth phases Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth ... More
Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics. Less
Non-alcoholic fatty liver disease NAFLD - characterized by excess accumulation of fat in the liver - now affects one third of the world s population As NAFLD progresses extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis a major determinant of disease severity and mortality To identify transcriptional regulators of fibrosis we computationally inferred the activity of transcription factors TFs relevant to fibrosis by profiling the matched transcriptomes and epigenomes of human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD CRISPR-based genetic knockout of the top TFs identified ZNF as ... More
Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world’s population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis. Less
ackground The Safety and Immunogenicity of COVID- Vaccines in Systemic Autoimmune-Mediated Inflammatory Diseases SUCCEED study was created to better understand COVID- vaccination in immune-mediated inflammatory disease IMID Knowing the frequency of COVID- breakthrough infections is important particularly in IMID Our objective was to assess these events in IMID Methods We prospectively studied IMID participants who had received three COVID- vaccine doses Individuals provided saliva samples monthly September to August These were evaluated by polymerase chain reaction PCR for SARS-CoV- We also assessed antibodies against SARS-CoV- anti-spike SmT receptor binding domain RBD and nucleocapsid NP based on dried blood spots Multivariable ... More
ackground: The Safety and Immunogenicity of COVID-19 Vaccines in Systemic Autoimmune-Mediated Inflammatory Diseases (SUCCEED) study was created to better understand COVID-19 vaccination in immune-mediated inflammatory disease (IMID). Knowing the frequency of COVID-19 breakthrough infections is important, particularly in IMID. Our objective was to assess these events in IMID. Methods: We prospectively studied IMID participants who had received ≥three COVID-19 vaccine doses. Individuals provided saliva samples monthly (September 2022 to August 2023). These were evaluated by polymerase chain reaction (PCR) for SARS-CoV-2. We also assessed antibodies against SARS-CoV-2 (anti-spike, SmT1, receptor binding domain, RBD, and nucleocapsid, NP) based on dried blood spots. Multivariable general estimating equation regression produced odd ratios (OR) for PCR SARS-CoV-2 positivity, related to demographics, immunosuppressives, and antibody levels. Results: Diagnoses included rheumatoid arthritis RA (N = 161, 44% of the total), systemic lupus, psoriatic arthritis, spondylarthritis, vasculitis, systemic sclerosis, and inflammatory bowel disease. Of the 366 participants, most were taking immunosuppressive medication. Of 1266 saliva samples, 56 (5.1%) were positive for SARS-CoV-2 on PCR. Higher anti-SmT1 antibodies were inversely associated with SARS-CoV-2 detection on PCR (adjusted OR 0.66, 95% confidence interval 0.45–0.97). Antibodies to SmT1, RBD, and NP were correlated and thus could not be included in a single model, but when anti-RBD was used in place of anti-SmT1, the results were similar. No other factor (including prior COVID-19 infection) was clearly associated with SARS-CoV-2 detection. Conclusions: This is the first study of SARS-CoV-2 in a large prospective cohort of triple (or more) vaccinated individuals with IMIDs. Anti-SmT1 antibodies appeared to be protective against later SARS-CoV-2 positivity, although recent past infection was not clearly related. This suggests the importance of maintaining robust vaccine-induced immunity through vaccination in IMID. Less
The rise of drug-resistant fungal pathogens including Candida auris highlights the urgent need for novel antifungal therapies We developed a cost-effective platform combining microbial extract prefractionation with rapid MS MS-bioinformatics-based dereplication to efficiently prioritize new antifungal scaffolds Screening C auris and C albicans revealed novel lipopeptaibiotics coniotins from Coniochaeta hoffmannii WAC which were undetectable in crude extracts Coniotins exhibited potent activity against critical fungal pathogens on the WHO Fungal Priority Pathogens List including C albicans C neoformans multidrug-resistant C auris and Aspergillus fumigatus with high selectivity and low resistance potential Coniotin A targets -glucan compromising fungal cell wall integrity remodelling ... More
The rise of drug-resistant fungal pathogens, including Candida auris, highlights the urgent need for novel antifungal therapies. We developed a cost-effective platform combining microbial extract prefractionation with rapid MS/MS-bioinformatics-based dereplication to efficiently prioritize new antifungal scaffolds. Screening C. auris and C. albicans revealed novel lipopeptaibiotics, coniotins, from Coniochaeta hoffmannii WAC11161, which were undetectable in crude extracts. Coniotins exhibited potent activity against critical fungal pathogens on the WHO Fungal Priority Pathogens List, including C. albicans, C. neoformans, multidrug-resistant C. auris, and Aspergillus fumigatus, with high selectivity and low resistance potential. Coniotin A targets β-glucan, compromising fungal cell wall integrity, remodelling, and sensitizing C. auris to caspofungin. Identification of a PKS-NRPS biosynthetic gene cluster further enables the discovery of related clusters encoding potential novel lipopeptaibiotics. This study demonstrates the power of natural product prefractionation in uncovering bioactive scaffolds and introduces coniotins as promising candidates for combating multidrug-resistant fungal pathogens. Less
Transcription factors of the bHLH-PAS family play vital roles in animal development physiology and disease Two members of the family require binding of low-molecular weight ligands for their activity the vertebrate aryl hydrocarbon receptor AHR and the insect juvenile hormone receptor JHR In the fly Drosophila melanogaster the paralogous proteins GCE and MET constitute the ligand-binding component of JHR complexes Whilst GCE MET and AHR are phylogenetically heterologous their mode of action is similar JHR is targeted by several synthetic agonists that serve as insecticides disrupting the insect endocrine system AHR is an important regulator of human endocrine homeostasis and ... More
Transcription factors of the bHLH-PAS family play vital roles in animal development, physiology, and disease. Two members of the family require binding of low-molecular weight ligands for their activity: the vertebrate aryl hydrocarbon receptor (AHR) and the insect juvenile hormone receptor (JHR). In the fly Drosophila melanogaster, the paralogous proteins GCE and MET constitute the ligand-binding component of JHR complexes. Whilst GCE/MET and AHR are phylogenetically heterologous, their mode of action is similar. JHR is targeted by several synthetic agonists that serve as insecticides disrupting the insect endocrine system. AHR is an important regulator of human endocrine homeostasis and it responds to environmental pollutants and endocrine disruptors. Whether AHR signaling is affected by compounds that can activate JHR has not been reported. To address this question, we screened a chemical library of 50,000 compounds to identify 93 novel JHR agonists in a reporter system based on Drosophila cells. Of these compounds, 26% modulated AHR signaling in an analogous reporter assay in a human cell line, indicating a significant overlap in the agonist repertoires of the two receptors. To explore the structural features of agonist-dependent activation of JHR and AHR, we compared the ligand-binding cavities and their interactions with selective and common ligands of AHR and GCE. Molecular dynamics modeling revealed ligand-specific as well as conserved side chains within the respective cavities. Significance of predicted interactions was supported through site-directed mutagenesis. The results have indicated that synthetic insect juvenile hormone agonists might interfere with AHR signaling in human cells. Less
T cells are key players in adaptive immunity The specificity of T cells is determined by the sequences of the hypervariable T cell receptor TCR and chains Although bulk TCR sequencing offers a cost-effective approach for in-depth TCR repertoire profiling it does not provide chain pairings which are essential for determining T cell specificity In contrast single-cell TCR sequencing technologies produce paired chain data but are limited in throughput to thousands of cells and are cost-prohibitive for cohort-scale studies Here we present TIRTL-seq Throughput-Intensive Rapid TCR Library sequencing a novel approach that generates ready-to-sequence TCR libraries from live cells in ... More
ɑ/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) ɑ and β chains. Although bulk TCR sequencing offers a cost-effective approach for in-depth TCR repertoire profiling, it does not provide chain pairings, which are essential for determining T cell specificity. In contrast, single-cell TCR sequencing technologies produce paired chain data, but are limited in throughput to thousands of cells and are cost-prohibitive for cohort-scale studies. Here, we present TIRTL-seq (Throughput-Intensive Rapid TCR Library sequencing), a novel approach that generates ready-to-sequence TCR libraries from live cells in less than 7 hours. The protocol is optimized for use with non-contact liquid handlers in an automation-friendly 384-well plate format. Reaction volume miniaturization reduces library preparation costs to <$0.50 per well. The core principle of TIRTL-seq is the parallel generation of hundreds of libraries providing multiple biological replicates from a single sample that allows precise inference of both frequencies of individual clones and TCR chain pairings from well-occurrence patterns. We demonstrate scalability of our approach up to 1 million unique paired αβTCR clonotypes corresponding to over 30 million T cells per sample at a cost of less than $2000. For a sample of 10 million cells the cost is ~$200. We benchmarked TIRTL-seq against state-of-the-art 5'RACE bulk TCR-seq and 10x Genomics Chromium technologies on longitudinal samples. We show that TIRTL-seq is able to quantitatively identify expanding and contracting clonotypes between timepoints while providing accurate TCR chain pairings, including distinct temporal dynamics of SARS-CoV-2-specific and EBV-specific CD8+ T cell responses after infection. While clonal expansion was followed by sharp contraction for SARS-CoV-2 specific TCRs, EBV-specific TCRs remained stable once established. The sequences of both ɑ and β TCR chains are essential for determining T cell specificity. As the field moves towards greater applications in diagnostics and immunotherapy that rely on TCR specificity, we anticipate that our scalable paired TCR sequencing methodology will be instrumental for collecting large paired-chain datasets and ultimately extracting therapeutically relevant information from the TCR repertoire. Less
The SARS-CoV- main protease Mpro is essential for viral replication because it is responsible for the processing of most of the non-structural proteins encoded by the virus Inhibition of Mpro prevents viral replication and therefore constitutes an attractive antiviral strategy We set out to develop a high-throughput Mpro enzymatic activity assay using fluorescently labeled peptide substrates A library of fluorogenic substrates of various lengths sequences and dye quencher positions was prepared and tested against full length SARS-CoV- Mpro enzyme for optimal activity The addition of buffers containing strongly hydrated kosmotropic anion salts such as citrate from the Hofmeister series significantly ... More
The SARS-CoV-2 main protease (Mpro) is essential for viral replication because it is responsible for the processing of most of the non-structural proteins encoded by the virus. Inhibition of Mpro prevents viral replication and therefore constitutes an attractive antiviral strategy. We set out to develop a high-throughput Mpro enzymatic activity assay using fluorescently labeled peptide substrates. A library of fluorogenic substrates of various lengths, sequences and dye/quencher positions was prepared and tested against full length SARS-CoV-2 Mpro enzyme for optimal activity. The addition of buffers containing strongly hydrated kosmotropic anion salts, such as citrate, from the Hofmeister series significantly boosted the enzyme activity and enhanced the assay detection limit, enabling the ranking of sub-nanomolar inhibitors without relying on the low-throughput Morrison equation method. By comparing cooperativity in citrate or non-citrate buffer while titrating the Mpro enzyme concentration, we found full positive cooperativity of Mpro with citrate buffer at less than one nanomolar (nM), but at a much higher enzyme concentration (∼320 nM) with non-citrate buffer. In addition, using a tight binding Mpro inhibitor, we confirmed there was only one active catalytical site in each Mpro monomer. Since cooperativity requires at least two binding sites, we hypothesized that citrate facilitates dimerization of Mpro at sub-nanomolar concentration as one of the mechanisms enhances Mpro catalytic efficiency. This assay has been used in high-throughput screening and structure activity relationship (SAR) studies to support medicinal chemistry efforts. IC50 values determined in this assay correlates well with EC50 values generated by a SARS-CoV-2 antiviral assay after adjusted for cell penetration. Less
Menstrual toxic shock syndrome mTSS is a rare but severe disorder associated with the use of menstrual products such as high-absorbency tampons and is caused by Staphylococcus aureus strains that produce the toxic shock syndrome toxin- TSST- superantigen Herein we screened a library of small bioactive molecules for the ability to inhibit transcription of the TSST- gene without inhibiting the growth of S aureus The dominant positive regulator of TSST- is the SaeRS two-component system TCS and we identified phenazopyridine hydrochloride PP-HCl that repressed the production of TSST- by inhibiting the kinase function of SaeS PP-HCl competed with ATP for ... More
Menstrual toxic shock syndrome (mTSS) is a rare but severe disorder associated with the use of menstrual products such as high-absorbency tampons and is caused by Staphylococcus aureus strains that produce the toxic shock syndrome toxin-1 (TSST-1) superantigen. Herein, we screened a library of 3920 small bioactive molecules for the ability to inhibit transcription of the TSST-1 gene without inhibiting the growth of S. aureus. The dominant positive regulator of TSST-1 is the SaeRS two-component system (TCS), and we identified phenazopyridine hydrochloride (PP-HCl) that repressed the production of TSST-1 by inhibiting the kinase function of SaeS. PP-HCl competed with ATP for binding of the kinase SaeS leading to decreased phosphorylation of SaeR and reduced expression of TSST-1 as well as several other secreted virulence factors known to be regulated by SaeRS. PP-HCl targets the virulence of S. aureus, and it also decreases the impact of TSST-1 on human lymphocytes without affecting the healthy vaginal microbiota. Our findings demonstrate the promising potential of PP-HCl as a therapeutic strategy against mTSS. Less
Background Neutrophils the most abundant white blood cells in humans play pivotal roles in innate immunity rapidly migrating to sites of infection and inflammation to phagocytose neutralize and eliminate invading pathogens Neutrophil extracellular trap NET formation is increasingly recognized as an essential rapid innate immune response but when dysregulated it contributes to pathogenesis of sepsis and immunothrombotic disease Objectives Current NETosis models are limited routinely employing nonphysiological triggers that can bypass natural NET regulatory pathways Models utilizing isolated neutrophils and immortalized cell lines do not reflect the complex biology underlying neutrophil activation and NETosis that occurs in whole blood To ... More
Background
Neutrophils, the most abundant white blood cells in humans, play pivotal roles in innate immunity, rapidly migrating to sites of infection and inflammation to phagocytose, neutralize, and eliminate invading pathogens. Neutrophil extracellular trap (NET) formation is increasingly recognized as an essential rapid innate immune response, but when dysregulated, it contributes to pathogenesis of sepsis and immunothrombotic disease.
Objectives
Current NETosis models are limited, routinely employing nonphysiological triggers that can bypass natural NET regulatory pathways. Models utilizing isolated neutrophils and immortalized cell lines do not reflect the complex biology underlying neutrophil activation and NETosis that occurs in whole blood. To our knowledge, we report the first human ex vivo model utilizing naturally occurring molecules to induce NETosis in whole blood. This approach could be used for drug screening and, importantly, inadvertent activators of NETosis.
Methods
Here we describe a novel, high-throughput ex vivo whole blood–induced NETosis model using combinatorial pooling of native NETosis-inducing factors in a more biologically relevant Synthetic-Sepsis model.
Results
We found different combinations of factors evoked distinct neutrophil responses in the rate of NET generation and/or magnitude of NETosis. Despite interdonor variability, similar sets of proinflammatory molecules induced consistent responses across donors. We found that at least 3 biological triggers were necessary to induce NETosis in our system including either tumor necrosis factor-α or lymphotoxin-α.
Conclusion
These findings emphasize the importance of investigating neutrophil physiology in a biologically relevant context to enable a better understanding of disease pathology, risk factors, and therapeutic targets, potentially providing novel strategies for disease intervention and treatment. Less
Neutrophils, the most abundant white blood cells in humans, play pivotal roles in innate immunity, rapidly migrating to sites of infection and inflammation to phagocytose, neutralize, and eliminate invading pathogens. Neutrophil extracellular trap (NET) formation is increasingly recognized as an essential rapid innate immune response, but when dysregulated, it contributes to pathogenesis of sepsis and immunothrombotic disease.
Objectives
Current NETosis models are limited, routinely employing nonphysiological triggers that can bypass natural NET regulatory pathways. Models utilizing isolated neutrophils and immortalized cell lines do not reflect the complex biology underlying neutrophil activation and NETosis that occurs in whole blood. To our knowledge, we report the first human ex vivo model utilizing naturally occurring molecules to induce NETosis in whole blood. This approach could be used for drug screening and, importantly, inadvertent activators of NETosis.
Methods
Here we describe a novel, high-throughput ex vivo whole blood–induced NETosis model using combinatorial pooling of native NETosis-inducing factors in a more biologically relevant Synthetic-Sepsis model.
Results
We found different combinations of factors evoked distinct neutrophil responses in the rate of NET generation and/or magnitude of NETosis. Despite interdonor variability, similar sets of proinflammatory molecules induced consistent responses across donors. We found that at least 3 biological triggers were necessary to induce NETosis in our system including either tumor necrosis factor-α or lymphotoxin-α.
Conclusion
These findings emphasize the importance of investigating neutrophil physiology in a biologically relevant context to enable a better understanding of disease pathology, risk factors, and therapeutic targets, potentially providing novel strategies for disease intervention and treatment. Less
Drug sensitivity testing of patient-derived tumor organoids PDTOs is a promising tool for personalizing cancer treatment Here we present a protocol for generation of and high-throughput drug testing with PDTOs We describe detailed steps for PDTO establishment from colorectal cancer tissues preparation of PDTOs for high-throughput drug testing and quantification of drug testing results using image analysis This protocol provides a standardized workflow for PDTO testing of standard-of-care therapies along with exploring the activity of new agents for translational research
Methods of studying eukaryotic cell responses to a perturbation or of stratifying eukaryotic cells or cell lines into one or more subgroups are described The methods involve perturbing a library of cells or cell lines in the same manner and observing how the cells respond to the same perturbation The observation may be via a high throughput screening method for example cell painting and the perturbation may be for example exposure to a therapeutic agent The methods may be used for grouping cells or cell lines that respond similarly to a given therapeutic agent which may be useful for identifying ... More
Methods of studying eukaryotic cell responses to a perturbation, or of stratifying eukaryotic cells or cell lines into one or more subgroups are described. The methods involve perturbing a library of cells or cell lines in the same manner, and observing how the cells respond to the same perturbation. The observation may be via a high throughput screening method, for example, cell painting; and the perturbation may be, for example, exposure to a therapeutic agent.The methods may be used for grouping cells or cell lines that respond similarly to a given therapeutic agent, which may be useful for identifying patient groups and selecting appropriate treatments. Less
Nowadays an efficient and robust virtual screening procedure is crucial in the drug discovery process especially when performed on large and chemically diverse databases Virtual screening methods like molecular docking and classic QSAR models are limited in their ability to handle vast numbers of compounds and to learn from scarce data respectively In this study we introduce a universal methodology that uses a machine learning-based approach to predict docking scores without the need for time-consuming molecular docking procedures The developed protocol yielded times faster binding energy predictions than classical docking-based screening The proposed predictive model learns from docking results allowing ... More
Nowadays, an efficient and robust virtual screening procedure is crucial in the drug discovery process, especially when performed on large and chemically diverse databases. Virtual screening methods, like molecular docking and classic QSAR models, are limited in their ability to handle vast numbers of compounds and to learn from scarce data, respectively. In this study, we introduce a universal methodology that uses a machine learning-based approach to predict docking scores without the need for time-consuming molecular docking procedures. The developed protocol yielded 1000 times faster binding energy predictions than classical docking-based screening. The proposed predictive model learns from docking results, allowing users to choose their preferred docking software without relying on insufficient and incoherent experimental activity data. The methodology described employs multiple types of molecular fingerprints and descriptors to construct an ensemble model that further reduces prediction errors and is capable of delivering highly precise docking score values for monoamine oxidase ligands, enabling faster identification of promising compounds. An extensive pharmacophore-constrained screening of the ZINC database resulted in a selection of 24 compounds that were synthesized and evaluated for their biological activity. A preliminary screen discovered weak inhibitors of MAO-A with a percentage efficiency index close to a known drug at the lowest tested concentration. The approach presented here can be successfully applied to other biological targets as target-specific knowledge is not incorporated at the screening phase. Less
The activities of the phospholipase C gamma PLC and enzymes are essential for numerous cellular processes Unsurprisingly dysregulation of PLC or PLC activity is associated with multiple maladies including immune disorders cancers and neurodegenerative diseases Therefore the modulation of either of these two enzymes has been suggested as a therapeutic strategy to combat these diseases To aid in the discovery of PLC family enzyme modulators that could be developed into therapeutic agents we have synthesized a high-throughput screening-amenable micellular fluorogenic substrate called C CF -coumarin Herein the ability of PLC and PLC to enzymatically process C CF -coumarin was confirmed ... More
The activities of the phospholipase C gamma (PLCγ) 1 and 2 enzymes are essential for numerous cellular processes. Unsurprisingly, dysregulation of PLCγ1 or PLCγ2 activity is associated with multiple maladies including immune disorders, cancers, and neurodegenerative diseases. Therefore, the modulation of either of these two enzymes has been suggested as a therapeutic strategy to combat these diseases. To aid in the discovery of PLCγ family enzyme modulators that could be developed into therapeutic agents, we have synthesized a high-throughput screening-amenable micellular fluorogenic substrate called C16CF3-coumarin. Herein, the ability of PLCγ1 and PLCγ2 to enzymatically process C16CF3-coumarin was confirmed, the micellular assay conditions were optimized, and the kinetics of the reaction were determined. A proof-of-principle pilot screen of the Library of Pharmacologically Active Compounds 1280 (LOPAC1280) was performed. This new substrate allows for an additional screening methodology to identify modulators of the PLCγ family of enzymes. Less
ADP-ribosyltransferases PARP and PARP play a major role in DNA repair mechanism by detecting the DNA damage and inducing poly-ADP-ribosylation dependent chromatin relaxation and recruitment of repair proteins Catalytic PARP inhibitors are used as anticancer drugs especially in the case of tumors arising from sensitizing mutations Recently a study showed that Histone PARylation Factor HPF forms a joint active site with PARP The interaction of HPF with PARP alters the modification site from Aspartate Glutamate to Serine which has been shown to be a key ADP-ribosylation event in the context of DNA damage Therefore disruption of PARP -HPF interaction could ... More
ADP-ribosyltransferases PARP1 and PARP2 play a major role in DNA repair mechanism by detecting the DNA damage and inducing poly-ADP-ribosylation dependent chromatin relaxation and recruitment of repair proteins. Catalytic PARP inhibitors are used as anticancer drugs especially in the case of tumors arising from sensitizing mutations. Recently, a study showed that Histone PARylation Factor (HPF1) forms a joint active site with PARP1/2. The interaction of HPF1 with PARP1/2 alters the modification site from Aspartate/Glutamate to Serine, which has been shown to be a key ADP-ribosylation event in the context of DNA damage. Therefore, disruption of PARP1/2-HPF1 interaction could be an alternative strategy for drug development to block the PARP1/2 activity. In this study, we describe a FRET based high-throughput screening assay to screen inhibitor libraries against PARP-HPF1 interaction. We optimized the conditions for FRET signal and verified the interaction by competing the FRET pair in multiple ways. The assay is robust and easy to automate. Validatory screening showed the robust performance of the assay, and we discovered two compounds Dimethylacrylshikonin and Alkannin, with µM inhibition potency against PARP1/2-HPF1 interaction. The assay will facilitate the discovery of inhibitors against HPF1-PARP1/2 complex and to develop potentially new effective anticancer agents. Less
Exposure to environmental pollutants is linked to numerous toxic outcomes warranting concern about the effect of pollutants on human health To assess the threat of pollutant exposure it is essential to understand their biological activity Unfortunately gaps remain for many pollutants specific biological activity and molecular targets A superfamily of signaling proteins G-protein-coupled receptors GPCRs has been shown as potential targets for pollutant activity However research investigating the pollutant activity at the GPCRome is scarce This work explores pollutant activity across a library of human GPCRs by leveraging modern high-throughput screening techniques devised for drug discovery and pharmacology We designed ... More
Exposure to environmental pollutants is linked to numerous toxic outcomes, warranting concern about the effect of pollutants on human health. To assess the threat of pollutant exposure, it is essential to understand their biological activity. Unfortunately, gaps remain for many pollutants’ specific biological activity and molecular targets. A superfamily of signaling proteins, G-protein-coupled receptors (GPCRs), has been shown as potential targets for pollutant activity. However, research investigating the pollutant activity at the GPCRome is scarce. This work explores pollutant activity across a library of human GPCRs by leveraging modern high-throughput screening techniques devised for drug discovery and pharmacology. We designed and implemented a pilot screen of eight pollutants at 314 human GPCRs and discovered specific polychlorinated biphenyl (PCB) activity at sphingosine-1-phosphate and melatonin receptors. The method utilizes open-source resources available to academic and governmental institutions to enable future campaigns that screen large numbers of pollutants. Thus, we present a novel high-throughput approach to assess the biological activity and specific targets of pollutants. Less
We herein describe the development and application of a modular technology platform which incorporates recent advances in plate-based microscale chemistry automated purification in situ quantification and robotic liquid handling to enable rapid access to high-quality chemical matter already formatted for assays In using microscale chemistry and thus consuming minimal chemical matter the platform is not only efficient but also follows green chemistry principles By reorienting existing high-throughput assay technology the platform can generate a full package of relevant data on each set of compounds in every learning cycle The multiparameter exploration of chemical and property space is hereby driven by ... More
We herein describe the development and application of a modular technology platform which incorporates recent advances in plate-based microscale chemistry, automated purification, in situ quantification, and robotic liquid handling to enable rapid access to high-quality chemical matter already formatted for assays. In using microscale chemistry and thus consuming minimal chemical matter, the platform is not only efficient but also follows green chemistry principles. By reorienting existing high-throughput assay technology, the platform can generate a full package of relevant data on each set of compounds in every learning cycle. The multiparameter exploration of chemical and property space is hereby driven by active learning models. The enhanced compound optimization process is generating knowledge for drug discovery projects in a time frame never before possible. Less
Predictive drug testing of patient-derived tumor organoids PDTOs holds promise for personalizing treatment of metastatic colorectal cancer mCRC but prospective data are limited to chemotherapy regimens with conflicting results We describe a unified framework for PDTO-based predictive testing across standard-of-care chemotherapy and biologic and targeted therapy options In an Australian community cohort PDTO predictions based on treatment-naive patients n and response rates from first-line mCRC clinical trials achieve accuracy for forecasting responses in patients receiving palliative treatments patients treatments Similar assay accuracy is achieved in a prospective study of third-line or later mCRC treatment AGITG FORECAST- n patients Resistant predictions ... More
Predictive drug testing of patient-derived tumor organoids (PDTOs) holds promise for personalizing treatment of metastatic colorectal cancer (mCRC), but prospective data are limited to chemotherapy regimens with conflicting results. We describe a unified framework for PDTO-based predictive testing across standard-of-care chemotherapy and biologic and targeted therapy options. In an Australian community cohort, PDTO predictions based on treatment-naive patients (n = 56) and response rates from first-line mCRC clinical trials achieve 83% accuracy for forecasting responses in patients receiving palliative treatments (18 patients, 29 treatments). Similar assay accuracy is achieved in a prospective study of third-line or later mCRC treatment, AGITG FORECAST-1 (n = 30 patients). “Resistant” predictions are associated with inferior progression-free survival; misclassification rates are similar by regimen. Liver metastases are the optimal site for sampling, with testing achievable within 7 weeks for 68.8% cases. Our findings indicate that PDTO drug panel testing can provide predictive information for multifarious standard-of-care therapies for mCRC. Less
Microbial natural products are specialized metabolites that are sources of many bioactive compounds including antibiotics antifungals antiparasitics anticancer agents and probes of biology The assembly of libraries of producers of natural products has traditionally been the province of the pharmaceutical industry This sector has gathered significant historical collections of bacteria and fungi to identify new drug leads with outstanding outcomes - upwards of of drug scaffolds originate from such libraries Despite this success the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds ... More
Microbial natural products are specialized metabolites that are sources of many bioactive
compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of
biology. The assembly of libraries of producers of natural products has traditionally been the
province of the pharmaceutical industry. This sector has gathered significant historical
collections of bacteria and fungi to identify new drug leads with outstanding outcomes - upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we
report a perspective on our efforts to assemble a library of natural product-producing microbes
and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds. Less
compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of
biology. The assembly of libraries of producers of natural products has traditionally been the
province of the pharmaceutical industry. This sector has gathered significant historical
collections of bacteria and fungi to identify new drug leads with outstanding outcomes - upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we
report a perspective on our efforts to assemble a library of natural product-producing microbes
and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds. Less
Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection It is responsible for US deaths annually Neutrophils are an integral part of the innate immune response and rapidly clear pathogens from circulation using neutrophil extracellular traps NETs which are released through a process called NETosis NETs prevent dissemination of pathogens by entrapment in externalized chromatin containing deactivating enzymes While we have learned much about the mechanisms underlying NETosis we are yet to translate it to improved therapies or patient outcomes This gap may be attributable to the models used to study NETosis Current models used ... More
Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection (1). It is responsible for ~370,000 US deaths annually (2). Neutrophils are an integral part of the innate immune response and rapidly clear pathogens from circulation using neutrophil extracellular traps (NETs), which are released through a process called NETosis (3). NETs prevent dissemination of pathogens by entrapment in externalized chromatin containing deactivating enzymes. While we have learned much about the mechanisms underlying NETosis, we are yet to translate it to improved therapies or patient outcomes. This gap may be attributable to the models used to study NETosis. Current models used to investigate NETosis are limited and routinely employ unnatural triggers such as phorbol 12-myristate 13-acetate (PMA). PMA is not a physiological trigger present in the immune system and may bypass the natural pathways that regulate NETs production. Mouse models that use isolated neutrophils and neutrophil-like cells induced from immortalized cell lines do not completely reflect the complex cellular and molecular biology underlying neutrophil activation and NETosis, especially in a whole-blood environment. Therefore, it is crucial to study how specific factors, known to be upregulated in disease, interact and potentially induce NETosis. Here we use high-throughput screening and natural NETosis triggers to develop a more biologically relevant ex vivo NETosis (Synthetic-Sepsis™) model.
Whole blood was collected from healthy donors and aliquoted into a 384 well plate using a Formulatrix Mantis liquid handler. This plate contained small molecules associated with neutrophils or NETosis activation, such as interleukins: Il-1b, IL-5, IL-6, IL-8, IL-15, IL-17, IL-18 and other molecules TNF- α, LT-α, IFN-γ, G-CSF, GM-CSF, E-selectin, PAF-16, CXCL1, CXCL2, LTB4, CXCL5, CCL2, CCL3, fMLP, Ferritin, HMGB1, C5a and LPS. We used a combinatorial pooling strategy designed using JMP software to identify which combinations of small molecules could stimulate NET formation. NETosis was assessed using Sytox green intercalation at 5 minute intervals for up to 24 hours using a Molecular Devices plate reader. PMA was utilized as a positive control for NETosis induction at varying concentrations.
Using our combinatorial pooling approach of the various factors, we successfully induced NETosis in an ex vivo whole blood system using naturally occurring cytokines and chemokines at physiologically relevant concentrations. We found that different combinations of factors evoke distinct neutrophil responses both in the time of NET generation and/or magnitude of NET-associated intercalation signal. We observed inter-donor variability in response time and amplitude however, similar small molecule pools induced consistent responses across donors. Furthermore, our findings suggest that at least four naturally occurring factors are necessary to induce NETosis in our system. Although some factors activate similar pathways, they are unable to induce a signal alone and as the number of factors increased beyond four, there was an enhanced NET response. Interestingly, we found either TNF-α or LT-α was required to cause a NETosis response, underlining the potentially significant roles these factors play in inflammatory disease. These results suggest an underlying master regulatory mechanism, such that certain factors are essential but not individually sufficient to trigger NETosis.
To our knowledge, we report the first ex-vivo model using naturally occurring cytokines and chemokines to induce NETosis in whole blood. These findings emphasize the importance of expanding our understanding of neutrophil physiology in a biologically relevant context with physiological triggers to induce NETosis. This approach could reveal new dimensions in our understanding of disease pathology and risk factors and might unearth potential therapeutic targets providing novel strategies for disease intervention and treatment. Further investigation of these factors is underway to further understand the release of NETs in natural and pathological states. Less
Whole blood was collected from healthy donors and aliquoted into a 384 well plate using a Formulatrix Mantis liquid handler. This plate contained small molecules associated with neutrophils or NETosis activation, such as interleukins: Il-1b, IL-5, IL-6, IL-8, IL-15, IL-17, IL-18 and other molecules TNF- α, LT-α, IFN-γ, G-CSF, GM-CSF, E-selectin, PAF-16, CXCL1, CXCL2, LTB4, CXCL5, CCL2, CCL3, fMLP, Ferritin, HMGB1, C5a and LPS. We used a combinatorial pooling strategy designed using JMP software to identify which combinations of small molecules could stimulate NET formation. NETosis was assessed using Sytox green intercalation at 5 minute intervals for up to 24 hours using a Molecular Devices plate reader. PMA was utilized as a positive control for NETosis induction at varying concentrations.
Using our combinatorial pooling approach of the various factors, we successfully induced NETosis in an ex vivo whole blood system using naturally occurring cytokines and chemokines at physiologically relevant concentrations. We found that different combinations of factors evoke distinct neutrophil responses both in the time of NET generation and/or magnitude of NET-associated intercalation signal. We observed inter-donor variability in response time and amplitude however, similar small molecule pools induced consistent responses across donors. Furthermore, our findings suggest that at least four naturally occurring factors are necessary to induce NETosis in our system. Although some factors activate similar pathways, they are unable to induce a signal alone and as the number of factors increased beyond four, there was an enhanced NET response. Interestingly, we found either TNF-α or LT-α was required to cause a NETosis response, underlining the potentially significant roles these factors play in inflammatory disease. These results suggest an underlying master regulatory mechanism, such that certain factors are essential but not individually sufficient to trigger NETosis.
To our knowledge, we report the first ex-vivo model using naturally occurring cytokines and chemokines to induce NETosis in whole blood. These findings emphasize the importance of expanding our understanding of neutrophil physiology in a biologically relevant context with physiological triggers to induce NETosis. This approach could reveal new dimensions in our understanding of disease pathology and risk factors and might unearth potential therapeutic targets providing novel strategies for disease intervention and treatment. Further investigation of these factors is underway to further understand the release of NETs in natural and pathological states. Less
The efficacy of aminoglycoside antibiotics is waning due to the acquisition of diverse resistance mechanisms by bacteria Among the most prevalent are aminoglycoside acetyltransferases AACs that inactivate the antibiotics through acetyl coenzyme A-mediated modification Most AACs are members of the GCN superfamily of acyltransferases which lack conserved active site residues that participate in catalysis ApmA is the first reported AAC belonging to the left-handed -helix superfamily These enzymes are characterized by an essential active site histidine that acts as an active site base Here we show that ApmA confers broad-spectrum aminoglycoside resistance with a molecular mechanism that diverges from other ... More
The efficacy of aminoglycoside antibiotics is waning due to the acquisition of diverse resistance mechanisms by bacteria. Among the most prevalent are aminoglycoside acetyltransferases (AACs) that inactivate the antibiotics through acetyl coenzyme A-mediated modification. Most AACs are members of the GCN5 superfamily of acyltransferases which lack conserved active site residues that participate in catalysis. ApmA is the first reported AAC belonging to the left-handed β-helix superfamily. These enzymes are characterized by an essential active site histidine that acts as an active site base. Here we show that ApmA confers broad-spectrum aminoglycoside resistance with a molecular mechanism that diverges from other detoxifying left-handed β-helix superfamily enzymes and canonical GCN5 AACs. We find that the active site histidine plays different functions depending on the acetyl-accepting aminoglycoside substrate. This flexibility in the mechanism of a single enzyme underscores the plasticity of antibiotic resistance elements to co-opt protein catalysts in the evolution of drug detoxification. Less
This study aimed to identify inhibitors of the translocated intimin receptor Tir of enteropathogenic Escherichia coli EPEC EPEC is an intestinal pathogen that causes diarrhea and is a major health concern worldwide Because Tir is a key virulence factor involved in EPEC pathogenesis inhibiting its function is a potential strategy for controlling EPEC infections Virtual screening was applied to chemical libraries to search for compounds that inhibit Tir-mediated bacterial adherence to host cells Three sites were targeted using the cocrystal structure published earlier A selection of compounds was then assessed in a cell-based infection model and fluorescence microscopy assay The ... More
This study aimed to identify inhibitors of the translocated intimin receptor (Tir) of enteropathogenic Escherichia coli (EPEC). EPEC is an intestinal pathogen that causes diarrhea and is a major health concern worldwide. Because Tir is a key virulence factor involved in EPEC pathogenesis, inhibiting its function is a potential strategy for controlling EPEC infections. Virtual screening was applied to chemical libraries to search for compounds that inhibit Tir-mediated bacterial adherence to host cells. Three sites were targeted using the cocrystal structure published earlier. A selection of compounds was then assessed in a cell-based infection model and fluorescence microscopy assay. The results of this study provide a basis for further optimization and testing of Tir inhibitors as potential therapeutic agents for EPEC infections. Less
Transglutaminases TGases are a family of calcium-dependent enzymes primarily known for their ability to cross-link proteins Transglutaminase TG is one isozyme in this family whose role is multifaceted TG can act not only as a typical transamidase through its catalytic core but also as a G-protein via its GTP binding site These two discrete activities are tightly regulated by both environmental stimuli and redox reactions Ubiquitously expressed in humans TG has been implicated in numerous disease pathologies that require extensive investigation The catalytic activity of TG can be monitored through various mechanisms including hydrolysis transamidation or cleavage of isopeptide bonds ... More
Transglutaminases (TGases) are a family of calcium-dependent enzymes primarily known for their ability to cross-link proteins. Transglutaminase 2 (TG2) is one isozyme in this family whose role is multifaceted. TG2 can act not only as a typical transamidase through its catalytic core but also as a G-protein via its GTP binding site. These two discrete activities are tightly regulated by both environmental stimuli and redox reactions. Ubiquitously expressed in humans, TG2 has been implicated in numerous disease pathologies that require extensive investigation. The catalytic activity of TG2 can be monitored through various mechanisms, including hydrolysis, transamidation, or cleavage of isopeptide bonds. Activity assays are required to monitor the activity of this isozyme not only for studying its transamidation reaction but also for validation of therapeutics designed to abolish this activity. Herein, we present the design, synthesis, and evaluation of a new TG2 activity substrate based on a previously optimized inhibitor scaffold. The substrate APH7 exhibits excellent affinity, selectivity, and reactivity with TG2 (KM = 3.0 μM). Furthermore, its application also allowed the discovery of unique hysteresis at play within the catalytic activity and inhibition reactivity of TG2. Less
We have adapted the cell painting assay developed by Carpenter and colleagues on cultured U OS cells to human spermatozoa In Sperm Cell Painting SCP we assemble an image-based quantitative fingerprint of the functional state of sperm We use this assay to gain insight into the mechanism of action of compounds that modify sperm function and as a platform for contraceptive discovery
The COVID- pandemic caused by severe acute respiratory syndrome coronavirus SARS-CoV- virus has made it clear that further development of antiviral therapies will be needed to combat additional SARS-CoV- variants or novel CoVs Here we describe small molecule inhibitors for SARS-CoV- Mac which counters ADP-ribosylation mediated innate immune responses The compounds inhibiting Mac were discovered through high-throughput screening HTS using a protein FRET-based competition assay and the best hit compound had an IC of M Three validated HTS hits have the same -amide- -methylester thiophene scaffold and the scaffold was selected for structure-activity relationship SAR studies through commercial and synthesized ... More
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed to combat additional SARS-CoV-2 variants or novel CoVs. Here, we describe small molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation mediated innate immune responses. The compounds inhibiting Mac1 were discovered through high-throughput screening (HTS) using a protein FRET-based competition assay and the best hit compound had an IC50 of 14 µM. Three validated HTS hits have the same 2-amide-3-methylester thiophene scaffold and the scaffold was selected for structure-activity relationship (SAR) studies through commercial and synthesized analogs. We studied the compound binding mode in detail using X-ray crystallography and this allowed us to focus on specific features of the compound and design analogs. Compound 27 (MDOLL-0229) had an IC50 of 2.1 µM and was generally selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human ADP-ribose binding proteins. The improved potency allowed testing of its effect on virus replication and indeed, 27 inhibited replication of a mouse hepatitis virus, a prototype CoV. Compound 27 is the first Mac1 targeted small molecule demonstrated to inhibit coronavirus replication in a cell model. This, together with its well-defined binding mode, makes 27 a good candidate for further hit/lead-optimization efforts. Less
Wastewater-based SARS-CoV- epidemiology WBE has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants However for a timely transmission of results sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis comparative quality control of the analytical procedures is essential to report reliable and comparable results In this study we performed an interlaboratory comparison at laboratories ... More
Wastewater-based SARS-CoV-2 epidemiology (WBE) has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies. WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants. However, for a timely transmission of results, sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required. Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis, comparative quality control of the analytical procedures is essential to report reliable and comparable results.In this study, we performed an interlaboratory comparison at laboratories specialized for PCR and high-throughput-sequencing (HTS)-based WBE analysis. Frozen reserve samples from low COVID-19 incidence periods were spiked with different inactivated authentic SARS-CoV-2 variants in graduated concentrations and ratios. Samples were sent to the participating laboratories for analysis using laboratory specific methods and the reported viral genome copy numbers and the detection of viral variants were compared with the expected values.Despite the different procedures, a high concordance regarding the SARS-CoV-2 PCR quantification could be achieved with low variation between the workflows. PCR-based genotyping was, in dependence of the underlying PCR-assay performance, able to predict the relative amount of variant specific substitutions even in samples with low spike-in amount. The identification of variants by HTS, however, required >100 copies/mL wastewater and had limited predictive value when analyzing at a genome coverage below 60%.This interlaboratory test demonstrates that despite different extraction and analysis methods, a high agreement of the SARS-CoV-2 genome copy equivalents could be achieved. Hence, decentralized SARS-CoV-2 wastewater monitoring is feasible to generate comparable analysis results. However, since not all assays detected the correct variant, prior evaluation of PCR and sequencing workflows as well as sustained quality control such as interlaboratory comparisons are mandatory for correct variant detection. Less
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells including their types states transitions trajectories and spatial position Scientific methods such as fluorescence labeling nanoscale super-resolution microscopy advances in single cell RNAseq and proteomics technologies provide more detailed information about biological processes which were not evident with the analysis of bulk material This new era of single-cell biology provides a better understanding of such complex biological systems as cancer inflammation immunity mechanism and aging processes and opens the door into the field of drug ... More
Single-cell analysis has clearly established itself in biology and biomedical fields as an invaluable tool that allows one to comprehensively understand the relationship between cells, including their types, states, transitions, trajectories, and spatial position. Scientific methods such as fluorescence labeling, nanoscale super-resolution microscopy, advances in single cell RNAseq and proteomics technologies, provide more detailed information about biological processes which were not evident with the analysis of bulk material. This new era of single-cell biology provides a better understanding of such complex biological systems as cancer, inflammation, immunity mechanism and aging processes, and opens the door into the field of drug response heterogeneity. The latest discoveries of cellular heterogeneity gives us an unique understanding of complex biological processes, such as disease mechanism, and will lead to new strategies for better and personalized treatment strategies. Recently, single-cell proteomics techniques that allow quantification of thousands of proteins from single mammalian cells have been introduced. Here we present an improved single-cell mass spectrometry-based proteomics platform called SCREEN (Single Cell pRotEomE aNalysis) for deep and high-throughput single-cell proteome coverage with high efficiency, less turnaround time and with an improved ability for protein quantitation across more cells than previously achieved. We applied this new platform to analyze the single-cell proteomic landscape under different drug treatment over time to uncover heterogeneity in cancer cell response, which for the first time, to our knowledge, has been achieved by mass spectrometry based analytical methods. We discuss challenges in single-cell proteomics, future improvements and general trends with the goal to encourage forthcoming technical developments. Less
We have used a cohort of human induced pluripotent stem cell hiPSC lines to develop a laboratory-based drug screening platform to predict variable drug responses of potential clinical relevance Our approach is based on the findings that hiPSC lines reflect the genetic identity of the donor and that pluripotent hiPSC lines express a broad repertoire of gene transcripts and proteins We demonstrate that a cohort of hiPSC lines from different donors can be screened efficiently in their pluripotent state using high-throughput cell painting assays allowing detection of variable phenotypic responses to a wide range of clinically approved drugs across multiple ... More
We have used a cohort of human induced pluripotent stem cell (hiPSC) lines to develop a laboratory-based drug screening platform to predict variable drug responses of potential clinical relevance. Our approach is based on the findings that hiPSC lines reflect the genetic identity of the donor and that pluripotent hiPSC lines express a broad repertoire of gene transcripts and proteins. We demonstrate that a cohort of hiPSC lines from different donors can be screened efficiently in their pluripotent state using high-throughput cell painting assays, allowing detection of variable phenotypic responses to a wide range of clinically approved drugs, across multiple disease areas. Furthermore, we provide information on mechanisms of drug-cell interactions underlying the observed variable responses by using quantitative proteomic analysis to compare sets of hiPSC lines that had been stratified objectively using cell painting data. We propose that information derived from comparative drug screening using curated libraries of hiPSC lines can help to increase the success rate of drug development pipelines and improve the delivery of safe new drugs suitable for a broader ethnic and gender diversity within human populations. Less
Training artificial intelligence AI systems to perform autonomous experiments would vastly increase the throughput of microbiology however few microbes have large enough datasets for training such a system In the present study we introduce BacterAI an automated science platform that maps microbial metabolism but requires no prior knowledge BacterAI learns by converting scientific questions into simple games that it plays with laboratory robots The agent then distils its findings into logical rules that can be interpreted by human scientists We use BacterAI to learn the amino acid requirements for two oral streptococci Streptococcus gordonii and Streptococcus sanguinis We then show ... More
Training artificial intelligence (AI) systems to perform autonomous experiments would vastly increase the throughput of microbiology; however, few microbes have large enough datasets for training such a system. In the present study, we introduce BacterAI, an automated science platform that maps microbial metabolism but requires no prior knowledge. BacterAI learns by converting scientific questions into simple games that it plays with laboratory robots. The agent then distils its findings into logical rules that can be interpreted by human scientists. We use BacterAI to learn the amino acid requirements for two oral streptococci: Streptococcus gordonii and Streptococcus sanguinis. We then show how transfer learning can accelerate BacterAI when investigating new environments or larger media with up to 39 ingredients. Scientific gameplay and BacterAI enable the unbiased, autonomous study of organisms for which no training data exist. Less
A rare coding variant in PLC P R expressed in microglia induces a mild activation of enzymatic activity when compared to wild-type This mutation is reported to be protective against the cognitive decline associated with late-onset Alzheimer's disease LOAD and therefore activation of wild-type PLC has been suggested as a potential therapeutic target for the prevention and treatment of LOAD Additionally PLC has been associated with other diseases such as cancer and some autoimmune disorders where mutations with much greater increases in PLC activity have been identified Here pharmacological inhibition may provide a therapeutic effect In order to facilitate our ... More
A rare coding variant in PLCγ2 (P522R) expressed in microglia induces a mild activation of enzymatic activity when compared to wild-type. This mutation is reported to be protective against the cognitive decline associated with late-onset Alzheimer's disease (LOAD) and therefore, activation of wild-type PLCγ2 has been suggested as a potential therapeutic target for the prevention and treatment of LOAD. Additionally, PLCγ2 has been associated with other diseases such as cancer and some autoimmune disorders where mutations with much greater increases in PLCγ2 activity have been identified. Here, pharmacological inhibition may provide a therapeutic effect. In order to facilitate our investigation of the activity of PLCγ2, we developed an optimized fluorogenic substrate to monitor enzymatic activity in aqueous solution. This was accomplished by first exploring the spectral properties of various “turn-on” fluorophores. The most promising turn-on fluorophore was incorporated into a water-soluble PLCγ2 reporter substrate, which we named C8CF3-coumarin. The ability of PLCγ2 to enzymatically process C8CF3-coumarin was confirmed, and the kinetics of the reaction were determined. Reaction conditions were optimized to identify small molecule activators, and a pilot screen of the Library of Pharmacologically Active Compounds 1280 (LOPAC1280) was performed with the goal of identifying small molecule activators of PLCγ2. The optimized screening conditions allowed identification of potential PLCγ2 activators and inhibitors, thus demonstrating the feasibility of this approach for high-throughput screening. Less
Ubiquitination is a complex and reversible protein post-translational modification in which the subsequent action of enzymes belonging to three different families broadly referred to as E E and E results in the covalent linking of ubiquitin to a target protein While this linkage is canonically an isopeptide bond between the C-terminus of ubiquitin and the lysine residue of the target protein Ser Thr and Tyr can also be susceptible to ubiquitination through an oxyester bond Once ubiquitinated multiple units of ubiquitin can be attached to the initial ubiquitin thus extending it to a chain of ubiquitins Ubiquitination regulates multiple cellular ... More
Ubiquitination is a complex and reversible protein post-translational modification in which the subsequent action of enzymes belonging to three different families, broadly referred to as E1, E2 and E3, results in the covalent linking of ubiquitin to a target protein. While this linkage is canonically an isopeptide bond between the C-terminus of ubiquitin and the lysine residue of the target protein, Ser, Thr, and Tyr can also be susceptible to ubiquitination through an oxyester bond. Once ubiquitinated, multiple units of ubiquitin can be attached to the initial ubiquitin thus extending it to a chain of ubiquitins. Ubiquitination regulates multiple cellular processes, but it is best known as a modification that targets proteins for proteasomal degradation following the formation poly-ubiquitin chains linked through lysine 48 or 63 of ubiquitin. Dysregulation of ubiquitination has been associated with multiple types of cancer and efforts have been carried out to develop technologies that lead to the identification of inhibitors of the enzymes involved in the ubiquitination cascade. Herein, we present the development of a FRET-based assay that allows us to monitor auto-ubiquitination of DTX3L, a RING-type E3 ubiquitin ligase. Our method shows a robust signal window with a robust average Z’ factor of 0.76. From a validatory screening experiment we have identified the first molecules that inhibit DTX3L with potencies in the low micromolar range. Additionally, we have expanded the system to study deubiquitinases such as USP28 that lead to reduction of FRET due to hydrolysis of fluorescent poly-Ub chains. Less
Analyzing proteins from single cells by tandem mass spectrometry MS has recently become technically feasible While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design sample preparation data acquisition and data analysis We expect that broadly accepted community guidelines and standardized metrics will enhance rigor data quality and alignment between laboratories Here we propose best practices quality controls and data-reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics
Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication DNA repair and telomere maintenance Due to their essential role they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited Here we present a simple and versatile real-time exonuclease assay based on -aminopurine an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both and DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor ... More
Exonucleases are essential enzymes that remove nucleotides from free DNA ends during DNA replication, DNA repair, and telomere maintenance. Due to their essential role, they are potential targets for novel anticancer and antimicrobial drugs but have so far been little exploited. Here, we present a simple and versatile real-time exonuclease assay based on 2-aminopurine, an intrinsically fluorescent nucleotide that is quenched by neighboring bases when embedded in DNA. We show that our assay is applicable to different eukaryotic and bacterial exonucleases acting on both 3′ and 5′ DNA ends over a wide range of protein activities and suitable for a high-throughput inhibitor screening campaign. Using our assay, we discover a novel inhibitor of the Mycobacterium tuberculosis PHP-exonuclease that is part of the replicative DNA polymerase DnaE1. Hence, our novel assay will be a useful tool for high-throughput screening for novel exonuclease inhibitors that may interfere with DNA replication or DNA maintenance. Less
This high-throughput protocol details the steps to extract protein from Gram-negative bacteria Gram-positive bacteria or non-filamentous fungi in -well plate format for quantitative proteomic workflows This protocol uses a bench-top automated liquid dispenser but the volumes and times also apply to manual and multi-channel pipetter use This protocol is designed for lab-based culture conditions and synthetic community experiments where complex sample matrices are minimized Additional sample preservation and or protein extraction methods may be required for environmental samples e g feces soil to minimize protein degradation and maintain sample integrity
The recent discovery of comammox complete ammonia oxidation Nitrospira has upended the long-held nitrification paradigm Although comammox Nitrospira have been identified in wastewater treatment systems the conditions for their dominance over canonical ammonia oxidizers remain unclear Here we report the dominance of comammox Nitrospira in a moving bed biofilm reactor MBBR fed with synthetic mainstream wastewater Integrated S rRNA gene amplicon sequencing fluorescence in situ hybridization FISH and metagenomic sequencing methods demonstrated the selective enrichment of comammox bacteria when the MBBR was operated at a dissolved oxygen DO concentration above mg O L The dominance of comammox Nitrospira over canonical ... More
The recent discovery of comammox (complete ammonia oxidation) Nitrospira has upended the long-held nitrification paradigm. Although comammox Nitrospira have been identified in wastewater treatment systems, the conditions for their dominance over canonical ammonia oxidizers remain unclear. Here, we report the dominance of comammox Nitrospira in a moving bed biofilm reactor (MBBR) fed with synthetic mainstream wastewater. Integrated 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization (FISH), and metagenomic sequencing methods demonstrated the selective enrichment of comammox bacteria when the MBBR was operated at a dissolved oxygen (DO) concentration above 6 mg O2/L. The dominance of comammox Nitrospira over canonical ammonia oxidizers (i.e., Nitrosomonas) was attributed to the low residual ammonium concentration (0.02–0.52 mg N/L) formed in the high-DO MBBR. Two clade A comammox Nitrospira were identified, which are phylogenetically close to Candidatus Nitrospira nitrosa. Interestingly, cryosectioning-FISH showed these two comammox species spatially distributed on the surface of the biofilm. Moreover, the ammonia-oxidizing activity of comammox Nitrospira-dominated biofilms was susceptible to the oxygen supply, which dropped by half with the DO concentration decrease from 6 to 2 mg O2/L. These features collectively suggest a low apparent oxygen affinity for the comammox Nitrospira-dominated biofilms in the high-DO nitrifying MBBR. Less
Polyurethane-based hydrogels are relatively inexpensive and mechanically robust biomaterials with ideal properties for various applications including drug delivery prosthetics implant coatings soft robotics and tissue engineering In this report we present a simple method for synthesizing and casting biocompatible polyurethane-poly ethylene glycol PU-PEG hydrogels with tunable mechanical properties non-fouling characteristics and sustained tolerability as an implantable material or coating The hydrogels are synthesized via a simple one-pot method using commercially available precursors and low toxicity solvents and reagents yielding a consistent and biocompatible gel platform primed for long-term biomaterial applications The mechanical and physical properties of the gels are easily ... More
Polyurethane-based hydrogels are relatively inexpensive and mechanically robust biomaterials with ideal properties for various applications, including drug delivery, prosthetics, implant coatings, soft robotics, and tissue engineering. In this report, we present a simple method for synthesizing and casting biocompatible polyurethane-poly(ethylene glycol) (PU-PEG) hydrogels with tunable mechanical properties, non-fouling characteristics, and sustained tolerability as an implantable material or coating. The hydrogels are synthesized via a simple one-pot method using commercially available precursors and low toxicity solvents and reagents, yielding a consistent and biocompatible gel platform primed for long-term biomaterial applications. The mechanical and physical properties of the gels are easily controlled by varying the curing concentration, producing networks with complex shear moduli of 0.82 kPa – 190 kPa, similar to a range of human soft tissues. When evaluated against a mechanically-matched PDMS formulation the PU-PEG hydrogels demonstrated favorable non-fouling characteristics including comparable adsorption of plasma proteins (albumin and fibrinogen) and significantly reduced cellular adhesion. Moreover, preliminary murine implant studies reveal a mild foreign body response after 41 days. Due to the tunable mechanical properties, excellent biocompatibility, and sustained in vivo tolerability of these hydrogels, we propose that this method offers a simplified platform for fabricating soft PU-based biomaterials for a variety of applications. Less
Clonogenic assays evaluate the ability of single cells to proliferate and form colonies This process approximates the regrowth and recurrence of tumors after treatment with radiation or chemotherapy and thereby provides a drug discovery platform for compounds that block this process However because of their labor-intensive and cumbersome nature adapting canonical clonogenic assays for high throughput screening HTS has been challenging We overcame these barriers by developing an integrated system that automates cell- and liquid-handling irradiation dosimetry drug administration and incubation Further we developed a fluorescent live-cell based automated colony scoring methodology that identifies and counts colonies precisely based upon ... More
Clonogenic assays evaluate the ability of single cells to proliferate and form colonies. This process approximates the regrowth and recurrence of tumors after treatment with radiation or chemotherapy, and thereby provides a drug discovery platform for compounds that block this process. However, because of their labor-intensive and cumbersome nature, adapting canonical clonogenic assays for high throughput screening (HTS) has been challenging. We overcame these barriers by developing an integrated system that automates cell- and liquid-handling, irradiation, dosimetry, drug administration, and incubation. Further, we developed a fluorescent live-cell based automated colony scoring methodology that identifies and counts colonies precisely based upon actual nuclei number rather than colony area, thereby eliminating errors in colony counts caused by radiation induced changes in colony morphology. We identified 13 cell lines from 7 cancer types, where radiation is a standard treatment module, that exhibit identical radiation and chemoradiation response regardless of well format and are amenable to miniaturization into small-well HTS formats. We performed pilot screens through a 1584 compound NCI Diversity Set library using two cell lines representing different cancer indications. Radiation modulators identified in the pilot screens were validated in traditional clonogenic assays, providing proof-of-concept for the screen. The integrated methodology, hereafter ‘clonogenic HTS’, exhibits excellent robustness (Z’ values >0.5) and shows high reproducibility (>95%). We propose that clonogenic HTS we developed can function as a drug discovery platform to identify compounds that inhibit tumor regrowth following radiation therapy, to identify new efficacious pair-wise combinations of known oncologic therapies, or to identify novel modulators of approved therapies. Less