Biology subjects

Beck, C.

Publications and source records attributed to Beck, C..

10 recordsLinked to original sources

bioRxiv2024

Human Topoisomerase IIα Promotes Chromatin Condensation Via a Phase Transition

Topoisomerase II (topo II) enzymes are essential enzymes known to resolve topological entanglements during DNA processing. Curiously, while yeast expresses a single topo II, humans express two topo II isozymes, topo II and topo II{beta}, which share a similar catalytic domain but differ in their intrinsically disordered C-terminal domains (CTDs). During mitosis, topo II and condensin I constitute the most abundant chromosome scaffolding proteins essential for chromosome condensation. However, how topo II enables this function is poorly understood. Here, we discovered a new and functionally distinct role for human topo II - it condenses DNA and chromatin at a low topo II concentration (100 pM or less) during a polymer-collapse phase transition. The removal of the topo II CTDs effectively abolishes its condensation ability, indicating that the condensation is mediated by the CTDs. Although topo II{beta} can also perform condensation, it is about 4-fold less effective. During the condensation, topo II-DNA condensates form along DNA, working against a DNA tension of up to 1.5 pN, greater than that previously reported for yeast condensin. In addition, this condensation does not require ATP and thus is independent of topo IIs catalytic activity. We also found that condensation and catalysis can concurrently proceed with minimal mutual interference. Our findings suggest topo II may directly participate in chromosome condensation during mitosis.

biophysics↗

bioRxiv2024

Systematic classification of phage receptor-binding proteins predicts surface glycopolymer structure in Staphylococcus pathogens

Wall teichoic acids (WTAs) are major surface polymers of staphylococcal pathogens and commensals, whose variable structure governs interaction with host receptors, immunoglobulins, and bacteriophages. The ribitol phosphate (RboP) WTA type contributes to virulence, for instance in Staphylococcus aureus, but we lack comprehensive knowledge of WTA types and cognate phages. We developed a computational pipeline to identify the receptor-binding proteins (RBPs) in 335 Staphylococcus phage genomes, yielding multiple distinct RBP clusters. Notably, many phages had two separate RBPs with in part different WTA preferences. RBP representatives differed in specificity for RboP WTA glycosylation types, recapitulating the specificity of the corresponding phage. Based on these results, we created a publicly available bioinformatic tool to predict phage host specificity based on RBP similarity. The RboP WTA specific {Phi}13-RBP also revealed that the presence of RboP WTA on non-aureus staphylococci is more common than previously thought. Our approach facilitates the characterization of opportunistic Staphylococcus pathogens according to WTA types, which has major implications for phage-mediated interspecies horizontal gene transfer and future phage therapies.

microbiology↗

bioRxiv2022

From empirical to data-driven host selection: a broad-host-range expression platform to facilitate chassis screening

Nature has provided a vast landscape of organisms through evolution, each with unique phenotypic traits adapted to varying environments. Nevertheless, host selection in biotechnological research is exceedingly dominated by empirical preference, where the endogenous physiology of the selected host is often not suited to the desired application. Considering that large parts of cellular regulation and metabolism remain obscure, empirical selection of a preferred model organism may lead to undue caveats in further engineering attempts, arising from intrinsic metabolism. One reason for the empirical host selection is the lack of engineering tools for screening novel organisms. In this study, we provide a modular, single vector-based expression platform, compatible with a wide range of prokaryotes. It centers around a tight and titratable promoter system, inducible by anhydrotetracyclin within an 84-fold dynamic range. It enables easy screening of recombinant proteins and pathways in both mesophilic and thermophilic Gram-negative and Gram-positive hosts. Overall, this platform enables simple screening of heterologous expression and production in a variety of hosts, including the exploration of previously unconsidered hosts thereby aiding the transition from empirical to data-driven host selection.

synthetic biology↗

bioRxiv2021

Usutu virus uses langerin as a receptor to productively infect Langerhans cells more efficiently than West Nile virus.

Usutu virus (USUV) and West Nile virus (WNV) are phylogenetically close emerging arboviruses transmitted by mosquitoes, and constitute a global public health threat. Since USUV and WNV enter the body through the skin, the first immune cells they encounter are skin-resident dendritic cells, the most peripheral outpost of immune defense. This unique network is composed of Langerhans cells (LCs) and dermal DCs, which reside in the epidermis and the dermis, respectively. Using human skin explants, we show that while both viruses can replicate in keratinocytes, they can also infect resident DCs with distinct tropism, since WNV preferentially infects DCs in the dermis, whereas USUV has a greater propensity to infect LCs. Using both purified human epidermal LCs (eLCs) and monocyte derived LCs (MoLCs), we confirm that LCs sustain a faster and more efficient replication of USUV compared with WNV and that this correlates with a more intense innate immune response to USUV compared with WNV. Next, we show that ectopic expression of the LC-specific C-type lectin receptor (CLR), langerin, in HEK293T cells allows WNV and USUV to bind and enter, but supports the subsequent replication of USUV only. Conversely, blocking or silencing langerin in MoLCs or eLCs made them resistant to USUV infection, thus demonstrating that USUV uses langerin to enter and replicate in LCs. Altogether, our results demonstrate that LCs constitute privileged target cells for USUV in human skin, because langerin favors its entry and replication. Intriguingly, this suggests that USUV efficiently escapes the antiviral functions of langerin, which normally safeguards LCs from most viral infections.

microbiology↗

bioRxiv2021

SvAnna: efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to limitations of existing technology. Recent technological advances such as long-read sequencing (LRS) enable more comprehensive detection of SVs, but approaches for clinical prioritization of candidate SVs are needed. Existing computational approaches do not specifically target LRS data, thereby missing a substantial proportion of candidate SVs, and do not provide a unified computational model for assessing all types of SVs. Structural Variant Annotation and Analysis (SvAnna) assesses all classes of SV and their intersection with transcripts and regulatory sequences in the context of topologically associating domains, relating predicted effects on gene function with clinical phenotype data. We show with a collection of 182 published case reports with pathogenic SVs that SvAnna places over 90% of pathogenic SVs in the top ten ranks. The interpretable prioritizations provided by SvAnna will facilitate the widespread adoption of LRS in diagnostic genomics.

bioinformatics↗

bioRxiv2021

A genetic shift in an escaped transmitted/founder virus guides combinatorial vaccine design against HIV-1

A productive HIV-1 infection in humans is often established by transmission and propagation of a single transmitted/founder (T/F) virus, which then evolves into a complex mixture of variants during the lifetime of infection. An effective HIV-1 vaccine should elicit broad immune responses in order to block the entry of diverse T/F viruses. Currently, no such vaccine exists. An in-depth study of escape variants emerging under host immune pressure during very early stages of infection might provide insights into such a HIV-1 vaccine design. Here, in a rare longitudinal study involving HIV-1 infected individuals just days after infection in the absence of antiretroviral therapy, we discovered a remarkable genetic shift that resulted in near complete disappearance of the original T/F virus and appearance of a variant with H173Y mutation in the variable V2 domain of the HIV-1 envelope protein. This coincided with the disappearance of the first wave of strictly H173-specific antibodies and emergence of a second wave of Y173-specific antibodies with increased breadth. Structural analyses indicated conformational dynamism of the envelope protein which likely allowed selection of escape variants with a conformational switch in the V2 domain from an -helix (H173) to a {beta}-strand (Y173) and induction of broadly reactive antibody responses. This differential breadth due to a single mutational change was also recapitulated in a mouse model. Rationally designed combinatorial libraries containing 54 conformational variants of V2 domain around position 173 further demonstrated increased breadth of antibody responses elicited to diverse HIV-1 envelope proteins. These results offer new insights into designing broadly effective HIV-1 vaccines.

microbiology↗

bioRxiv2020

JARID2 and AEBP2 regulate PRC2 activity in the presence of H2A ubiquitination or other histone modifications

The Polycomb repressive complexes PRC1 and PRC2 functionally interact to coordinate cell type identity by the epigenetic regulation of gene expression. It has been proposed that PRC2 is recruited to genomic loci via the recognition of PRC1-mediated mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub1), but the mechanism of this process remains poorly understood. Here, we report the cryo-EM structure of human PRC2 with cofactors JARID2 and AEBP2 bound to a nucleosome substrate containing H2AK119ub1. We find that JARID2 and AEBP2 each interact with one of the two ubiquitin molecules in the nucleosome. A ubiquitin-interaction motif (UIM) in JARID2 is sandwiched between ubiquitin and the histone H2A-H2B acidic patch. Simultaneously, the tandem zinc-fingers of AEBP2 interact with the second ubiquitin and the histone H2A-H2B surface on the opposite side of the nucleosome. JARID2 plays a dual role in the H2AK119ub1 dependent stimulation of PRC2 through interactions with both EED via its K116 trimethylation and with the H2AK119-ubiquitin. AEBP2, on the other hand, appears to primarily serve as a scaffold contributing to the interaction between PRC2 and the H2AK119ub1 nucleosome. Our structure also provides a detailed visualization of the EZH2-nucleosome interface, revealing a segment of EZH2 (named "bridge helix") that is stabilized as it bridges the EZH2(SET) domain, the H3 tail and the nucleosomal DNA. In addition to the role played by AEBP2 and JARID2 in PRC2 regulation by H2AK119ub1 recognition, we also observe that the presence of these cofactors partially overcomes the inhibitory effect that H3K4- and H3K36-trimethylation have on core PRC2. Together, our results reveal the central role played by cofactors JARID2 and AEBP2 in orchestrating the crosstalk between histone post-translational modifications and PRC2 methyltransferase activity.

biophysics↗

bioRxiv2019

Frequent extrachromosomal oncogene amplification drives aggressive tumors

Extrachromosomal DNA (ecDNA) amplification promotes high oncogene copy number, intratumoral genetic heterogeneity, and accelerated tumor evolution1-3, but its frequency and clinical impact are not well understood. Here we show, using computational analysis of whole-genome sequencing data from 1,979 cancer patients, that ecDNA amplification occurs in at least 26% of human cancers, of a wide variety of histological types, but not in whole blood or normal tissue. We demonstrate a highly significant enrichment for oncogenes on amplified ecDNA and that the most common recurrent oncogene amplifications arise on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number matched linear DNA, coupled with enhanced chromatin accessibility. Patients whose tumors have ecDNA-based oncogene amplification showed increase of cell proliferation signature activity, greater likelihood of lymph node spread at initial diagnosis, and significantly shorter survival, even when controlled for tissue type, than do patients whose cancers are not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification plays a central role in driving the poor outcome for patients with some of the most aggressive forms of cancers.

cancer biology↗

bioRxiv2019

A post-processing algorithm for building longitudinal medication dose data from extracted medication information using natural language processing from electronic health records

ObjectiveWe developed a post-processing algorithm to convert raw natural language processing (NLP) output from electronic health records (EHRs) into a usable format for analysis. This algorithm was specifically developed for creating datasets for use in medication-based studies. Materials and MethodsThe algorithm was developed using output from two NLP systems, MedXN and medExtractR. We extracted medication information from deidentified clinical notes from Vanderbilts EHR system for two medications, tacrolimus and lamotrigine. The algorithm consists of two parts. Part I parses the raw NLP output and connects entities together. Part II removes redundancies and calculates dose intake and daily dose. We evaluated each part by comparing to human-determined gold standards that were generated using approximately 300 records from 10 subjects for each medication and each NLP system. ResultsThe algorithm performed well. For MedXN, the F-measures were at or above 0.99 for Part I and at or above 0.97 for Part II. For medExtractR, the F-measures for Part I were 1.00 and for Part II they were at or above 0.98. DiscussionOur post-processing algorithm was developed separately from an NLP system, making it easier to modify and generalize to other systems. It performed well to convert NLP output to analyzable data, but it cannot perform well in certain cases, such as when incorrect information is extracted by the NLP system. ConclusionOur post-processing algorithm provides a way to convert raw NLP output to a form that is useful for medication-based studies, leading to more opportunities to use EHR data for diverse studies.

bioinformatics↗

bioRxiv2017

Modules Of Co-Occurrence In The Cyanobacterial Pan-Genome

The increasing availability of fully sequenced cyanobacterial genomes opens unprecedented opportunities to investigate the manifold adaptations and functional relationships that determine the genetic content of individual bacterial species. Here, we use comparative genome analysis to investigate the cyanobacterial pan-genome based on 77 strains whose complete genome sequence is available. Our focus is the co-occurrence of likely ortholog genes, denoted as CLOGs. We conjecture that co-occurrence CLOGs is indicative of functional relationships between the respective genes. Going beyond the analysis of pair-wise co-occurrences, we introduce a novel network approach to identify modules of co-occurring ortholog genes. Our results demonstrate that these modules exhibit a high degree of functional coherence and reveal known as well as previously unknown functional relationships. We argue that the high functional coherence observed for the extracted modules is a consequence of the similar-yet-diverse nature of the cyanobacterial phylum. We provide a simple toolbox that facilitates further analysis of our results with respect to specific cyanobacterial genes of interest.

bioinformatics↗