Biology subjects

Danis, C.

Publications and source records attributed to Danis, C..

3 recordsLinked to original sources

bioRxiv2025

SVCROWS: A User-Defined Tool for Delineating Biologically Significant Structural Variants in Heterogeneous Datasets

Genomic structural variants (SVs) are pervasive and can impose major phenotypic impacts. However, it is difficult to appreciate the individual significance of SVs when they are heterogeneously positioned across a genomic neighborhood. Further, ubiquitous variance in SV calling accuracy complicates SV counting and downstream analysis. Tools exist to simplify SV datasets but they are not suited for all applications. Here, we present a new SV merger, SVCROWS: Structural Variation Consensus with Reciprocal Overlap and Weighted Sizes. This option-rich merger summarizes SV regions using a size-weighted reciprocal overlap framework, accounting for skewed impacts of variable-length SVs. User input directs stringency, enabling various levels of resolution in complex genome regions that harbor a spectrum of SV sizes. Further, by optimizing SVCROWS parameters, the user can tailor results to their study system. When compared to other SV merging programs, SVCROWS maintained accuracy and conserved rare genotypes from both simulated and real-world datasets. Visualization of merger output was critical for identifying how some algorithms derived erroneous conclusions while SVCROWS remained reliable, especially in complex regions. Overall, the novel SVCROWS algorithm presents an improved framework for SV interpretation; its intuitive nature and generalizability facilitates its application to virtually any workflow. Graphical AbstractSVCROWS (Structural Variation Consensus with Reciprocal Overlap and Weighted Sizes) is a structural variant merger that leverages option-rich, size-weighted comparisons to better resolve complex inputs and separate out regions of meaningful biological differences. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/634734v3_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1658d18org.highwire.dtl.DTLVardef@1239f0org.highwire.dtl.DTLVardef@99efeaorg.highwire.dtl.DTLVardef@5607a7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Strategy of selection and optimization of single domain antibodies targeting the PHF6 linear peptide within the Tau intrinsically disordered protein

The use of VHHs (Variable domain of the Heavy-chain of the Heavy-chain-only antibodies) as disease-modifying biomolecules in neurodegenerative disorders holds promises including to target aggregation-sensitive proteins. Exploitation of their clinical values dependents however on the capacity to deliver VHHs with optimal physico-chemical properties for their specific context of use. We described previously a VHH with high therapeutic potential in a family of neurodegenerative diseases called tauopathies. The activity of this promising parent VHH named Z70 relies on its binding within the central region of the Tau protein. Accordingly, we carried out random mutagenesis followed by yeast two-hybrid screening to obtain optimized variants. The VHHs selected from this initial screen targeted the same epitope as VHH Z70 as shown using nuclear magnetic resonance spectroscopy and had indeed improved binding affinities according to dissociation constant values obtained by surface plasmon resonance spectroscopy. The improved affinities can be partially rationalized based on three-dimensional structures of three complexes consisting of an optimized VHH and a peptide containing the Tau epitope. Interestingly, the ability of the VHH variants to inhibit Tau aggregation and seeding could not be predicted from their affinity alone. We indeed showed that the in vitro and in cellulo VHH stabilities are other limiting key factors to their efficacy. Our results demonstrate that only a complete pipeline of experiments, here described, permits a rational selection of optimized VHH variants, resulting in our capacity to propose two VHH variants derived from the parent Z70 for their next development steps.

biochemistry↗

bioRxiv2021

Inhibition of Tau seeding by targeting Tau nucleation core within neurons with a single domain antibody fragment

Tau proteins aggregate into filaments in brain cells in Alzheimers disease and related disorders referred to as tauopathies. Here, we used fragments of camelid heavy-chain-only antibodies (VHHs or single domain antibody fragments) targeting Tau as immuno-modulators of its pathologic seeding. A VHH issued from the screen against Tau of a synthetic phage-display library of humanized VHHs was selected for its capacity to bind Tau microtubule-binding domain, composing the core of Tau fibrils. This lead VHH was optimized to improve its biochemical properties and to act in the intracellular compartment, resulting in VHH Z70. VHH Z70 was more efficient than the lead to inhibit in vitro Tau aggregation in heparin-induced assays. Expression of VHH Z70 in a cellular model of Tau seeding also decreased the fluorescence-reported aggregation. Finally, intracellular expression of VHH Z70 in the brain of an established tauopathy mouse seeding model demonstrated its capacity to mitigate accumulation of pathological Tau. VHH Z70, by targeting Tau inside brain neurons, where most of the pathological Tau resides, provides a new tool to explore the optimal strategies of immunotherapy in tauopathies.

biochemistry↗