Biology subjects

Bader, J.

Publications and source records attributed to Bader, J..

8 recordsLinked to original sources

bioRxiv2024

Loading of extracellular vesicles with nucleic acids via hybridization with sponge-like lipid nanoparticles

The translation of cell-derived extracellular vesicles (EVs) into biogenic gene delivery systems is limited by relatively inefficient loading strategies. In this work, we describe the loading of various nucleic acids into small EVs via their spontaneous hybridization with preloaded non-lamellar liquid crystalline lipid nanoparticles (LCNPs) under physiological conditions, forming hybrid EVs (HEVs). We correlate LCNPs topological characteristics with their propensity to fuse/aggregate with EVs and found that sponge (L3) phases at pH 7.4 were particularly suitable to induce a controlled hybridization process. State-of-the-art single-particle analysis techniques revealed that L3-based LCNPs interact with various EV subpopulations and that around 40% of HEVs were loaded with the genetic cargo. Importantly, this study demonstrates that EV membrane proteins remain accessible on HEV surfaces, with their intrinsic enzymatic activity unaffected after the hybridization process. Finally, HEVs showed in vitro improved transfection efficiencies compared to unhybridized LCNPs. In summary, this versatile platform holds potential for loading various nucleic acid molecules into native EVs and may help developing EV-based therapeutics. TeaserTopology of lipid nanoparticles influences their hybridization behavior with extracellular vesicles and produces novel biogenic gene delivery systems.

bioengineering↗

bioRxiv2023

Functional whole genome screen of nutrient-starved Mycobacterium tuberculosis identifies genes involved in antibiotic tolerance

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), poses a global health challenge and is responsible for over a million deaths each year. Current treatment is lengthy and complex, and new, abbreviated regimens are urgently needed. Mtb adapts to nutrient starvation, a condition experienced during host infection, by shifting its metabolism and becoming tolerant to the killing activity of bactericidal antibiotics. An improved understanding of the mechanisms mediating antibiotic tolerance in Mtb can serve as the basis for developing more effective therapies. We performed a forward genetic screen to identify candidate Mtb genes involved in tolerance to the two key first-line antibiotics, rifampin and isoniazid, under nutrient-rich and nutrient-starved conditions. In nutrient-rich conditions, we found 220 mutants with differential antibiotic susceptibility (218 in the rifampin screen and 2 in the isoniazid screen). Following Mtb adaptation to nutrient starvation, 82 mutants showed differential antibiotic susceptibility (80 in the rifampin screen and 2 in the isoniazid screen). Using targeted mutagenesis, we validated the rifampin-hypersusceptible phenotype under nutrient starvation in Mtb mutants lacking the following genes: ercc3, moeA1, rv0049, and rv2179c. These findings shed light on potential therapeutic targets, which could help shorten the duration and complexity of antitubercular regimens. ImportanceTreatment of Mtb infection requires a long course of combination antibiotics, likely due to subpopulations of tolerant bacteria exhibiting decreased susceptibility to antibiotics. Identifying and characterizing the genetic pathways involved in antibiotic tolerance is expected to yield therapeutic targets for the development of novel TB treatment-shortening regimens.

microbiology↗

bioRxiv2022

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE system to the newly synthesized Sc2.0 megabase chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by i) removing most of the chromosome content, or ii) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic yeast resource opens new paradigms in studying aneuploidy. In briefUse of SCRaMbLE and newly synthesized Mb-scale Sc2.0 chromosome VII enables insights into genotype/phenotype relationships associated with aneuploidy HighlightsO_LIDe novo design and synthesis of a Mb-scale synthetic yeast chromosome VII, carrying 11.8% sequence modifications and representing nearly 10% of the yeast genome. C_LIO_LIA disomic yeast (n + synVII) is constructed for dissecting the aneuploidy phenotype C_LIO_LISCRaMbLE enables systematic exploration of regions causing aneuploidy phenotypes C_LIO_LIChromosomal copy number and content both contribute to aneuploidy phenotypes C_LIO_LIA 20 Kb deletion on the right arm of synVII leads to fitness improvement linked to up-regulation of protein synthesis C_LI

synthetic biology↗

bioRxiv2021

Gel-like inclusions of C-terminal fragments of TDP-43 sequester and inhibit proteasomes in neurons

TDP-43 inclusions enriched in C-terminal fragments of ~25kDa ("TDP-25") are associated with neurodegeneration in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here, we analyzed gain-of-function mechanisms of TDP-25 combining cryo-electron tomography, proteomics and functional assays. TDP-25 inclusions are amorphous with gel-like biophysical properties and sequester proteasomes adopting exclusively substrate-processing conformations. This leads to proteostasis impairment, further enhanced by pathogenic mutations. These findings bolster the importance of proteasome dysfunction in ALS/FTD.

neuroscience↗

bioRxiv2021

Genetic determinants of intrinsic antibiotic tolerance in Mycobacterium avium

Mycobacterium avium complex (MAC) is one of the most prevalent causes of nontuberculous mycobacteria pulmonary infection in the United States, yet it remains understudied. Current MAC treatment requires more than a year of intermittent to daily combination antibiotic therapy, depending on disease severity. In order to shorten and simplify curative regimens, it is important to identify the innate bacterial factors contributing to reduced antibiotic susceptibility, namely antibiotic tolerance genes. In this study, we performed a genome-wide transposon screen to elucidate M. avium genes that play a role in the bacteriums tolerance to first- and second-line antibiotics. We identified a total of 193 unique M. avium mutants with significantly altered susceptibility to at least one of the four clinically used antibiotics we tested, including two mutants (in DFS55_00905 and DFS55_12730) with panhypersusceptibility. The products of the antibiotic tolerance genes we have identified may represent novel targets for future drug development studies aimed at shortening the duration of therapy for MAC infections. ImportanceThe prolonged treatment required to eradicate Mycobacterium avium complex (MAC) infection is likely due to the presence of subpopulations of antibiotic-tolerant bacteria with reduced susceptibility to currently available drugs. However, little is known about the genes and pathways responsible for antibiotic tolerance in MAC. In this study, we performed a forward genetic screen to identify M. avium antibiotic tolerance genes, whose products may represent attractive targets for the development of novel adjunctive drugs capable of shortening curative treatment for MAC infections.

microbiology↗

bioRxiv2019

Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure.

Mycobacterium avium (Mav) is increasingly recognized as a significant cause of morbidity, particularly in elderly patients or those with immune deficiency or underlying structural lung disease. Generally, Mav infection is treated with 2-3 antimicrobial drugs for at least 12 months. Identification of genes essential for Mav growth may yield novel strategies for improving curative therapy. We have generated saturating genome-wide transposon mutant pools in a commonly used laboratory strain of Mycobacterium avium subsp. hominissuis (MAC109) and developed a computational technique for classifying annotated genomic features as essential (ES), growth defect (GD), growth advantage (GA), or no-effect (NE) based on the in vitro effect of disruption by transposon. We identified 270 features as ES with 230 of these overlapping with ES features in Mycobacterium tuberculosis. These results may be useful for identifying drug targets or for informing studies requiring genetic manipulation of Mycobacterium avium, which should seek to avoid disrupting ES features to ensure bacterial viability.\n\nImportanceMycobacterium avium subsp. hominissuis is an emerging cause of morbidity in vulnerable populations in many countries. It is known to be particularly difficult to treat, often requiring years of antibiotic therapy. In this study we report the genes of Mycobacterium avium subsp. hominissuis that are required for the organism to grow in vitro. Our findings may help guide future research into identifying new drugs to improve the treatment of this serious infection.

microbiology↗

bioRxiv2018

Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies

Plasma and serum are rich sources of information regarding an individuals health state and protein tests inform medical decision making. Despite major investments, few new biomarkers have reached the clinic. Mass spectrometry (MS)-based proteomics now allows highly specific and quantitative read-out of the plasma proteome. Here we employ Plasma Proteome Profiling to define contamination marker panels to assess plasma samples and the likelihood that suggested biomarkers are instead artifacts related to sample handling and processing. We acquire deep reference proteomes of erythrocytes, platelets, plasma and whole blood of 20 individuals (>6000 proteins), and compare serum and plasma proteomes. Based on spike-in experiments we determine contamination-associated proteins, many of which have been reported as biomarker candidates as revealed by a comprehensive literature survey. We provide sample preparation guidelines and an online resource (www.plasmaproteomeprofiling.org) to assess overall sample-related bias in clinical studies and to prevent costly miss-assignment of biomarker candidates.

epidemiology↗

bioRxiv2017

Temporal expression divergence of network modules

Here we propose new module-based approaches to identify differentially regulated network sub-modules combining temporal trajectories of expression profiles with static network skeletons. Starting from modules identified by network clustering of static networks, our analysis refines pre-defined genesets by partitioning them into smaller homogeneous sets by non-paramettric Bayesian methods. Especially for case-control time series data we developed multi-time point discriminative models and identified each network module as a mixture or admixture of dynamic discriminative functions. Our results shows that our proposed approach outperformed existing geneset enrichment methods in simulation studies. Moreover we applied the methods to neural stem cell differentiation data, and discovered novel modules differentially perturbed in different developmental stages.

bioinformatics↗