Biology subjects

Wegner, F.

Publications and source records attributed to Wegner, F..

7 recordsLinked to original sources

bioRxiv2024

Chlamydia trachomatis genomes from rectal samples: description of new clade comprising ompA-genotype L4 from Argentina

Whole genome analysis has provided us with insights into the evolution of Chlamydia trachomatis and recently into circulating strains which cause lymphogranuloma venereum (LGV). A large LGV outbreak of a new ompA-genotype, L2b, was first reported in Europe in the early 2000s, primarily affecting men who have sex with men (MSM), and then expanded globally. More recent work shows this outbreak diversifying into variants of described ompA-genotypes, with the same L2b genomic backbone. This study extends the investigation of LGV cases to Argentina and Finland. In 2017, an LGV outbreak was described in Argentina characterized by distinct genomic features shown by both ompA-genotyping and MLST analysis. We have obtained whole genome sequences from cultured isolates and clinical samples via SureSelect (Agilent) target enrichment. Based on ompA and phylogenetic analyses, we describe further diversity within the ompA-genotype L2b clade, illustrating the transmission dynamics in both Argentina and Finland. A key finding is that of a novel clade of Argentinian samples, characterised by a proposed new ompA-genotype L4. Additionally, we present the genome sequence of a non-LGV strain associated with anorectal proctitis. These findings contribute to the investigation of LGV evolution, particularly with the presence of the novel L4 lineage, and provide insights into genomic diversity and transmission dynamics of C. trachomatis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/624510v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@3bd641org.highwire.dtl.DTLVardef@6f6866org.highwire.dtl.DTLVardef@2f1b6eorg.highwire.dtl.DTLVardef@b2137a_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementThe phylogeny of C. trachomatis has been described in several publications and has been clear for a decade. The evolution of this STI in the intervening years also informs a great deal about the transmission opportunities and selective pressures that the intracellular bacterium is under. Through genome sequencing, also directly from clinical samples, we provide the first LGV genomes from Argentina and Finland, and describe further evidence of global circulation of the ompA-genotype L2b lineage. We describe a fully novel lineage of LGV C. trachomatis, from Argentina, proposed as ompA-genotype L4. We also find evidence of a strain causing proctitis from the urogenital lineage. Together, these provide significant new findings in the investigation of C. trachomatis. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.

microbiology↗

bioRxiv2024

The challenge of sequencing Chlamydia trachomatis and other bacterial STI genomes directly from clinical swabs: the optimum solution

Rates of bacterial sexually transmitted infections (STIs) are rising and accessing their genomes provides information on strain evolution, circulating strains, and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasma genitalium (MG) is also a bacterial STI which is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole genome sequences, and evaluated four approaches using clinical samples from Argentina (39), Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies (ONT), which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP, and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT positive samples; from 36% of NG positive samples, and from 60% of TP positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. This data can be utilized to examine circulating strains, genotypic resistance, and guide public health strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/624631v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@578aeborg.highwire.dtl.DTLVardef@16185f9org.highwire.dtl.DTLVardef@1a2ae87org.highwire.dtl.DTLVardef@1703fa7_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementGenome data on circulating sexually transmitted infections (STIs) is important to better understand transmission networks, antimicrobial resistance and to guide treatment decisions. For many bacterial STIs, this information is difficult to obtain, as the bacteria are fastidious, in some cases intracellular, and often recalcitrant to culture. We have developed and tested a target enrichment STI panel of baits to capture whole genomes of Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, and Mycoplasma genitalium with approximately 50% success in genome sequencing for the first three pathogens. We compare this against other sequencing and enrichment methods, which did not provide sufficient data for genome analysis. This panel approach shows potential for clinical samples carrying these pathogens and can potentially also be developed for further pathogen groups. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.

microbiology↗

bioRxiv2023

DJ-1 products glycolic acid and D-lactate restore deficient axonal trafficking and DNA damage response in FUS and SOD1-associated amyotrophic lateral sclerosis

Amyotrophic Lateral Sclerosis (ALS) is the most common motor neuron disease leading to death within 2-5 years. Currently available drugs can only slightly prolong survival. Despite the progress that has been achieved in unravelling the molecular mechanisms of the disease so far, the underlying pathophysiology is not fully understood. We present novel insights into the pathophysiology of Superoxide Dismutase 1 (SOD1)- and in particular Fused In Sarcoma (FUS)-ALS by revealing a putatively central role of the Parkinsons disease (PD) associated glyoxylase DJ-1 and its products glycolic acid (GA) and D-lactic acid (DL). Combined, but not single, treatment with GA and DL restored axonal trafficking deficits of mitochondria and lysosomes in FUS- and SOD1-ALS patient-derived motoneurons (MNs). This was accompanied by restoration of mitochondrial membrane potential as well as mitochondrial fragmentation (FUS-ALS) or elongation (SOD1-ALS). Furthermore, GA and DL restored cytoplasmic mislocalization of FUS and FUS recruitment to DNA damage sites. We further show that despite presenting an early axonal transport deficiency as well, TDP-43 patient-derived MNs did not share this mechanism. While this points towards the necessity of individualized (gene-) specific therapy stratification, it also suggests common therapeutic targets across different gene variants of ALS. Thus, we introduce a putative novel treatment for ALS based on a combination of the two substances GA and DL which might be not only an interesting novel drug candidate in subsets of ALS cases but also in other neurodegenerative diseases characterized by mitochondrial depolarization.

neuroscience↗

bioRxiv2022

Innate immune response to SARS-1 CoV-2 infection contributes to neuronal damage in human iPSC-derived peripheral neurons

Severe acute respiratory coronavirus 2 (SARS-CoV-2) infection causes neurological disease in some patients suggesting that infection can affect both the peripheral and central nervous system (PNS and CNS, respectively). It is not clear whether the outcome of SARS-CoV-2 infection of PNS and CNS neurons is similar, and which are the key factors that cause neurological disease: SARS-CoV-2 infection or the subsequent immune response. Here, we addressed these questions by infecting human induced-pluripotent stem cell-derived CNS and PNS neurons with the {beta} strain of SARS-CoV-2. Our results show that SARS-CoV-2 infects PNS neurons more efficiently than CNS neurons, despite lower expression levels of angiotensin converting enzyme 2. Infected PNS neurons produced interferon {lambda}1, several interferon stimulated genes and proinflammatory cytokines. They also displayed neurodegenerative-like alterations, as indicated by increased levels of sterile alpha and Toll/interleukin receptor motif-containing protein 1, amyloid precursor protein and -synuclein and lower levels of nicotinamide mononucleotide adenylyltransferase 2 and {beta}-III-tubulin. Interestingly, blockade of the Janus kinase and signal transducer and activator of transcription pathway by Ruxolitinib did not increase SARS-CoV-2 infection, but reduced neurodegeneration, suggesting that an exacerbated neuronal innate immune response contributes to pathogenesis in the PNS.

microbiology↗

bioRxiv2021

Retention Time Prediction Using Neural Networks Increases Identifications in Crosslinking Mass Spectrometry

Crosslinking mass spectrometry (Crosslinking MS) has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the spectra limits the numbers of protein-protein interactions (PPIs) that can be confidently identified. Here, we successfully leveraged chromatographic retention time (RT) information to aid the identification of crosslinked peptides from spectra. Our Siamese machine learning model xiRT achieved highly accurate RT predictions of crosslinked peptides in a multi-dimensional separation of crosslinked E. coli lysate. We combined strong cation exchange (SCX), hydrophilic strong anion exchange (hSAX) and reversed-phase (RP) chromatography and reached R2 0.94 in RP and a margin of error of 1 fraction for hSAX in 94%, and SCX in 85% of the predictions. Importantly, supplementing the search engine score with retention time features led to a 1.4-fold increase in PPIs at a 1% false discovery rate. We also demonstrate the value of this approach for the more routine analysis of a crosslinked multiprotein complexes. An increase of 1.7-fold in heteromeric crosslinked residue-pairs was achieved at 1% residue-pair FDR for Fanconi anaemia monoubiquitin ligase complex, solely using reversed-phase RT. Retention times are a powerful complement to mass spectrometric information to increase the sensitivity of Crosslinking MS analyses.

bioinformatics↗

bioRxiv2020

Reliable identification of protein-protein interactions by crosslinking mass spectrometry

Crosslinking mass spectrometry is widening its scope from structural analyzes of purified multi-protein complexes towards systems-wide analyzes of protein-protein interactions. Assessing the error in these large datasets is currently a challenge. Using a controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate a reliable false-discovery rate estimation procedure for protein-protein interactions identified by crosslinking mass spectrometry.

systems biology↗

bioRxiv2017

Age-dependent neurodegeneration and organelle transport deficiencies in mutant TDP43 patient-derived neurons are independent of TDP43 aggregation

TAR DNA-binding protein 43 (TDP43) is a cause of familiar and sporadic amyotrophic lateral sclerosis (ALS). The diverse postulated mechanisms by which TDP43 mutations cause the disease are not fully understood. Human wildtype and TDP43 S393L and G294V mutant spinal motor neuron cultures were differentiated from patient-derived iPSCs. Mutant hTDP43 and wildtype motor neuron cultures did not differ in neuron differentiation capacity during early maturation stage. During aging we detected a dramatic neurodegeneration including neuron loss and pathological neurofilament abnormalities in TDP43 mutant cultures only. Additionally mitochondria and lysosomes of aging spinal motor neurons revealed robust TDP43 mutation dependent abnormal phenotypes in size, shape, speed and motility which all appeared without TDP43 mislocalization or aggregation formation. Furthermore, D-sorbitol - known to induce stress granules and cytoplasmic mislocalization of TDP43 - rescued axonal trafficking phenotypes without any signs of TDP43 mislocalization or aggregation formation. Our data indicate TDP43 mutation-dependent but cytosolic aggregation-independent mechanisms of motor neuron degeneration in TDP43 ALS.

neuroscience↗