Biology subjects

Hildebrand, S.

Publications and source records attributed to Hildebrand, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Activation of perivascular thermogenic fat improves aortic stenosis

Aim: Aortic stenosis (AS) is a common condition with exponential increases in incidence in aging populations. Perivascular adipose tissue (PVAT) forms the outer layer of the aortic wall and has - especially in the thoracic area - characteristics of thermogenic adipose tissue, which dissipates energy and releases endocrine factors. Here, we set out to investigate the role of thermogenic PVAT in AS. Methods and results: We studied the role of (PVAT) in the development of AS in a murine model of AS. To specifically delineate the role of PVAT activity in AS, we used a pharmacological {beta}3-adrenergic agonist as well as cold exposure in combination with a genetic mouse model with deficient PVAT development. To investigate the role of thermogenic adipose tissue in human AS, we used 18F-FDG PET-CT imaging. We found that pharmacological activation of thermogenic adipose tissue resulted in an improvement of AS, but not in mice genetically deficient in PVAT. Similarly, PVAT was found to be protective against AS during physiological stimulation of PVAT using cold exposure. Mechanistically, PVAT activation resulted in enhanced aortic distensibility and cellular remodeling of the aortic wall, possibly via release of polyunsaturated fatty acids and oxylipins from perivascular adipocytes. Finally, analysis of thermogenic fat activity in humans revealed that mediastinal thermogenic fat activity correlated negatively with diagnostic criteria of AS severity, suggesting an important role for PVAT activity in human AS. Conclusion: Our data indicate that PVAT activation reduces aortic stenosis and supports aortic remodeling to improve ascending aorta hemodynamics. PVAT activation might be a novel therapeutic target to ameliorate AS progression. Translational perspective: Currently, there are no effective strategies for treating AS other than valve replacement. Since the molecular mechanisms underlying the disease progression remain unclear, there are no pharmacological agents approved for either treatment or prevention of this disease. Furthermore, AS development cannot currently be predicted and is often only diagnosed when patients develop symptoms, which may be 10-20 years after disease onset. Therefore, identifying novel mechanisms that improve aortic valve function and prevent AS is of high medical need. This study identifies activation of PVAT-dependent aortic remodeling as a potential new therapeutic approach to improve or prevent AS.

physiology↗

bioRxiv2026

Endothelial CXCL12 is dispensable for adipose tissue function

Background/Objectives: The adipose tissue endothelium plays a critical role for tissue function in acting as an interface between circulating blood and the various tissue-resident cells. Proper endothelial function ensures, among other things, well-regulated adipose tissue lipid in- and efflux, immune cell diapedesis, and oxygen supply. Dysregulated lipid flux, inflammation, and adipose tissue hypoxia are hallmarks of adipose tissue dysfunction and metaflammation. Additionally, lipid uptake and oxygen supply are important processes enabling heat production in active brown adipose tissue (BAT), which is associated with cardiometabolic health in humans. However, so far, little is known about the role of adipose tissue endothelial cells (ECs) and their intercellular communication with other adipose tissue cell compartments. Particularly, how this communication changes during thermogenic stimuli such as cold exposure is largely unknown. Methods: We used transcriptome analysis of adipose tissue ECs to identify EC Cxcl12 as a potential regulator of adipose tissue function. In vitro experiments were performed on primary sympathetic neurons and immortalized ECs. The role of EC Cxcl12 in adipose tissue function was analyzed in vivo using conditional knock-out mice. Results: Cxcl12 expression was induced in BAT ECs upon exposure to cold. Recombinant CXCL12 increased axon outgrowth in primary sympathetic neurons and angiogenesis in ECs. Conditional knock-out of Cxcl12 in ECs did not yield a discernable phenotype in mice either in normal housing or during cold adaption. Additionally, we could show that EC-derived CXCL12 does not play a role in adipose tissue dysfunction during obesity. Conclusions: Cxcl12 is highly expressed in the adipose tissue endothelium, but appears to be dispensable for adipose tissue function.

physiology↗

bioRxiv2026

Mismatch repair dissection by in vivo RNAi reveals dose-dependent modulators of somatic instability and proteome remodeling in Huntingtons disease

Human and mouse genetics have established mismatch repair (MMR) as a central mediator of somatic repeat expansion, a key pathogenic process in Huntingtons disease (HD) and related disorders. How individual MMR components function within the intact mammalian brain and interact with broader cellular networks remains poorly understood. We screened more than 500 chemically stabilized siRNAs targeting 10 MMR genes and used interventional RNAi in the Q111 HD mouse model to systematically dissect MMR function in vivo. MSH3 and PMS1 emerged as the most dose-sensitive regulators of somatic expansion but displayed markedly different effects on proteome stability. Quantitative proteomics generated an in vivo atlas of MMR component abundance and cross-regulation in the mammalian CNS, uncovering extensive connectivity between DNA repair, transcriptional regulation, chromatin remodeling, and mitochondrial biology. Together, these findings establish a systems-level framework linking MMR biology to neuronal function and offer mechanistic insight into selective neuronal vulnerability in HD.

neuroscience↗

bioRxiv2026

C57BL/6 BAC-CAG Huntingtons disease mice show somatic CAG expansion and responses to small interfering RNAs comparable to the FVB strain

Huntingtons disease (HD) is a neurodegenerative disorder caused by CAG repeat expansion in the huntingtin (HTT) gene, with longer repeats linked to earlier onset. Somatic CAG expansion, particularly in the striatum, contributes to disease progression and is influenced by HTT biology and genetic modifiers. Modulating somatic expansion is emerging as a promising approach to slow or prevent HD, and mouse models have been crucial for preclinical testing of different therapeutic strategies. The BAC-CAG model, developed on the FVB strain, has been used to study somatic expansion of human expanded HTT. However, comparisons with other key HD mouse models have been limited by differences in genetic background, as many other models are on the C57BL/6 strain. The BAC-CAG model has now been developed on a C57BL/6 background. To determine whether the C57BL/6 BAC-CAG model can be used to study and modulate somatic expansion, we compared CAG expansion in mice on C57BL/6 or FVB backgrounds, with and without intraventricular divalent small interfering RNAs (siRNA) targeting HD modifiers MutS homolog 3 (MSH3) and HTT. Both strains exhibited robust, comparable somatic expansion over two months, which was blocked by MSH3-, but not HTT-, targeted siRNA. RNA sequencing identified gene expression differences primarily in pseudogenes, with no differences in endogenous Htt, human HTT, or mismatch repair genes. These results demonstrate that BAC-CAG mice on a C57BL/6 background exhibit somatic CAG expansion comparable to the validated FVB strain, providing a model to study and preclinically test therapies targeting somatic expansion in HD.

neuroscience↗

bioRxiv2026

Organyl 5'-Phosphates in siRNA Guide Strands: Structure-Function Relationships Governing Anchoring in Argonaute 2 and Metabolic Stability

Efficient siRNA loading into Argonaute2 (AGO2) requires a 5'-phosphate (5'-P) on the guide strand, yet this group is vulnerable to metabolic degradation in vivo. Although numerous chemical mimics of 5'-P have been reported, structural principles governing AGO2 interactions with organyl substituents on the 5'-P remain unclear. Moreover, structural determinants of 5'-P mimic recognition by known degradative enzymes (principally phosphatases and 5'-exonucleases) are also poorly understood. The 5'-P binding site of the AGO2 MID domain contains a stack of aromatic residues (Y527/F811/Y815), presenting a structural basis for augmenting canonical anchoring interactions. Herein, we systematically synthesized and characterized a diverse panel of organyl 5'-phosphates (5'-POR; R = 35 variable substituents) as guide strand 5'-P mimics designed to engage this unique hydrophobic pocket. Among the compounds evaluated, 5'-POR guide strands bearing methyl (Me) or phenylpropargyl (PhPrp) substituents are well-tolerated by AGO2 in cells. Previously uncharacterized 5'-P mimics, including 5'-phosphorothioate (5'-PS), phenylpropargyl 5'-phosphorothioate (5'-PS-PhPrp), and 5'-mesylphosphoramidate (5'-MsPA), maintain comparable AGO2 compatibility. All examined 5'-P mimics are markedly resistant to phosphatase, while 5'-POR variants and 5'-PS-PhPrp are also resistant to 5'-exonuclease degradation due to masking a negative charge of 5'-P. A crystal structure of a 5'-PO-PhPrp guide strand loaded into AGO2 reveals an unexpected network of {pi}-{pi} interactions between the rigid phenylpropargyl group and the targeted hydrophobic pocket of the MID domain. Collectively, these findings expand the functional chemical space of 5'-P mimics and define new modes for metabolically stabilizing the guide strand 5'-end while augmenting AGO2 MID anchoring. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/705631v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@e6f88forg.highwire.dtl.DTLVardef@1c87dfaorg.highwire.dtl.DTLVardef@1c6e68corg.highwire.dtl.DTLVardef@14a1f60_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Two-photon volumetric study of cleared, invasive ductal carcinoma breast tissue samples and associated axillary lymph nodes

BackgroundBreast cancer remains the most frequently diagnosed cancer among women worldwide, with invasive ductal carcinoma (IDC) representing the most common subtype. Despite its high prevalence, current diagnostic workflows rely on 5 {micro}m-thin haematoxylin and eosin-stained (H&E) sections, inherently limiting spatial insight into tumor architecture and extracellular matrix (ECM) organization. As the interest in studying intratumoral heterogeneity increases, three-dimensional (3D) imaging is becoming an increasingly valuable tool. MethodsThis study applied a tissue clearing and imaging pipeline to large formalin-fixed paraffin-embedded (FFPE) breast and lymph node tissue using IDC samples from Maastricht University Medical Centre+. Deparaffinized samples were processed using a modified MASH protocol. Tissues were labelled with Neutral Red, Eosin Y, Methyl Green, and DAPI. Tissue shrinkage was analysed across all processed samples. Two-photon (2P) microscopy was used to image malignant and non-malignant breast tissue, and matched axillary lymph nodes from a patient with grade I IDC to depths of up to 1000 {micro}m via DAPI and second harmonic generation (SHG) channels. Image analysis included assessments of dye penetration, nuclear and collagen content, and fiber orientation using FIJI software. ResultsClearing and staining preserved tissue structure and achieved high transparency across millimetre-scale volumes. 2D surface shrinkage averaged 6.7% (p < 0.001). DAPI signal penetration was consistent with SHG signal profiles up to approximately 600 {micro}m of tissue depth. Structures such as terminal ductal lobular units, adipocytes, vasculature, and lymphoid follicles were clearly visualized in 3D. Quantitative and qualitative analysis in grade I IDC tissue revealed regional differences in cell size and shape, collagen content, and fiber coherency, indicating localized early-stage ECM remodelling. ConclusionThis is the first study to apply 2P microscopy with MASH clearing to large FFPE IDC breast and lymph node samples. The protocol enables reproducible high-resolution volumetric imaging and lays the groundwork for future research applications, leading to potential diagnostic applications.

cancer biology↗

bioRxiv2025

Endothelial deletion of ADGRF5 (GPR116) promotes fibro-inflammatory EndMT and impairs adaptive thermogenesis in brown adipose tissue

ObjectiveBrown adipose tissue (BAT) dissipates energy via non-shivering thermogenesis, and it is a promising therapeutic target for metabolic disease. While most research focuses on thermogenic adipocytes, emerging data point to critical contributions from the surrounding stromal niche. Here, we investigated the role of adhesion G protein-coupled receptors (aGPCRs) in BAT function, focusing on Adgrf5 (Gpr116), a receptor enriched in endothelial cells. MethodsWe used single-nuclei RNA sequencing to map aGPCRs expression across mouse and human BAT. We then examined the consequences of Adgrf5(Gpr116) loss using global, brown adipocyte, and endothelial-specific knockout mouse models under acute and prolonged cold exposure. ResultsInducible endothelial deletion of Adgrf5(Gpr116) impaired the maintenance of thermogenic capacity during prolonged--but not acute--cold exposure. This was not associated with defective angiogenesis, but rather with endothelial fibro-inflammatory reprogramming. Single-nuclei RNA sequencing analysis revealed endothelial-to- mesenchymal transition (EndMT) features, including induction of mesenchymal markers, collagens, and metalloproteinases, and loss of barrier genes. Adgrf5(Gpr116)-deficient endothelial cells also exhibited cytoskeletal remodeling and activation of stress fiber pathways, implicating Adgrf5(Gpr116) as a mechanosensory safeguard of endothelial identity. ConclusionEndothelial Adgrf5(Gpr116) preserves thermogenic competence in BAT by suppressing EndMT and maladaptive matrix remodeling. Our findings establish vascular mechanosensing as a critical determinant of thermogenic tissue homeostasis. HighlightsO_LIAdhesion GPCRs are the second most abundant GPCR family in mouse and human brown fat C_LIO_LIAdhesion GPCRs are enriched in non-adipocyte cell types in brown fat and participate in cell-cell contact signaling C_LIO_LIEndothelial Adgrf5(Gpr116) is required for thermogenic adaptation during prolonged cold exposure C_LIO_LILoss of Adgrf5(Gpr116) induces fibro-inflammatory reprogramming and endothelial-to-mesenchymal transition (EndMT) C_LI

molecular biology↗

bioRxiv2025

From Brown to White: Brown Adipose Tissue Endothelial Cells whiten in Culture Conditions

Endothelial cells (ECs) are central regulators of vascular and metabolic homeostasis, yet their organ- and depot-specific diversity remains underexplored. Two major types of adipose tissue (AT) can be distinguished that differ substantially in their physiological function and vascularization: white AT (WAT), which is the major energy storage and brown AT (BAT), which is highly vascularized and dissipates energy [1-5]. While ECs from these depots likely contribute to adipose function, their characterization has been hindered by technical limitations in isolation and culture. Here, we establish a protocol for isolating and expanding ECs from murine BAT and WAT, enabling transcriptomic and functional analyses across depots. We demonstrate that freshly isolated BAT-ECs express depot-specific gene signatures, including Rgcc, Cdkn1c, Tcf15, Meox2, and Efnb1, several of which are dynamically regulated during cold-induced BAT activation. These findings reveal novel BAT-EC markers and highlight specialized endothelial programs that may support thermogenesis. However, we also uncover that culturing BAT-ECs profoundly remodels EC identity. Transcriptomic profiling shows that BAT-ECs rapidly downregulate BAT-specific markers and acquire features resembling WAT- and lymphatic ECs. This dedifferentiation is accompanied by signatures of proliferation, adhesion remodeling, and endothelial-to-mesenchymal transition. While these changes present challenges for maintaining depot-specific identity in culture, they also provide a framework to better interpret experimental outcomes and to investigate EC plasticity. Taken together, our study delivers a novel isolation and culture protocol for adipose ECs, defines BAT-EC markers, and demonstrates how culture conditions reshape their identity. These insights build the foundation for future research of AT vasculature. HighlightsO_LIFast method to purify endothelial cells (ECs) for direct RNA or protein extraction. C_LIO_LIEasy method to isolate and culture ECs specifically from thermogenic adipose tissue. C_LIO_LINovel signature of BAT-ECs regulated upon browning and lost in culture. C_LIO_LIRGC-32, p57kip2, TCF15/MEOX2 and EFNB1 as novel BAT-EC-specific markers. C_LI

cell biology↗

bioRxiv2025

Blocking somatic repeat expansion and lowering huntingtin via RNA interference synergize to prevent Huntingtons disease pathogenesis in mice

Huntingtons disease (HD) is a progressive neurodegenerative disorder with no approved therapies. Two major molecular drivers--somatic expansion of inherited CAG repeats and toxic mutant HTT (mHTT) variants--lead to neuronal dysfunction. Despite multiple trials, HTT-lowering strategies have not shown meaningful clinical benefit. Using therapeutic divalent siRNAs, we assessed the long-term impact of silencing MSH3 (a key regulator of somatic expansion), HTT, or both. In Q111 HD mice (>110 CAGs), which exhibit robust expansion, mHTT inclusions, and transcriptional dysregulation by 12 months, long-term MSH3 silencing blocked expansion, reduced inclusions, and reversed gene expression changes. HTT silencing alone had limited effect, but combined MSH3/HTT targeting synergistically eliminated inclusions and restored transcriptomic profiles. Parallel treatment in wild-type mice showed no toxicity, supporting the safety of long-term intervention. These findings position somatic expansion as a promising therapeutic target and demonstrate the potential of RNAi-based co-silencing of MSH3 and HTT as a disease-modifying strategy for HD.

neuroscience↗

bioRxiv2025

Single-dose administration of therapeutic divalent siRNA targeting MECP2 prevents lethality for one year in an MECP2 duplication mouse model

AbstractMECP2 duplication syndrome (MDS) is a rare X-linked neurodevelopmental disorder caused by duplications of the dosage-sensitive methyl-CpG-binding protein 2 (MECP2) gene. Developing effective therapies for MDS is particularly challenging due to the variability in MECP2 expression among patients and the potential risk of inducing Rett syndrome through excessive pharmacological intervention. Reducing dosage to optimize silencing levels often compromises durability and necessitates increased dosing frequency. We present here a series of fully chemically modified small interfering RNAs (siRNAs) designed for both isoform-selective and total MECP2 silencing. Among these, we identify six lead siRNA candidates across two distinct chemical scaffolds, achieving targeted total MECP2 expression reductions ranging from 25% to 75%, sustained for at least four months following a single administration. The efficacy and safety of human ortholog silencing were evaluated using two mouse models with distinct levels of human MECP2 transgene expression. In the severe duplication model, a single dose of the total isoform-silencing siRNA fully rescued early mortality and behavioral impairments. Additionally, we show that the isoform-selective targeting strategy may be safer in mild cases of MDS where exaggerated pharmacology may lead to Rett Syndrome. Overall, this study introduces a series of preclinical candidates with the capacity to address the varying levels of MECP2 duplication encountered in clinical settings. Furthermore, it establishes a target selection strategy that may be applied to other dosage-sensitive gene imbalances. One Sentence SummaryTherapeutic siRNAs provide safe and durable modulation of MECP2 for the treatment of mild and severe MECP2 Duplication Syndrome.

neuroscience↗

bioRxiv2024

Investigating microscopic angioarchitecture in the human visual cortex in 3D with angioMASH tissue clearing and labelling

Non-invasive imaging techniques, such as ultra-high field fMRI, are intricately connected to the underlying vasculature and are approaching ever higher resolutions. For the analysis of fMRI signals over cortical depth at such high resolutions, microvascular differences might have to be taken into account. Therefore, a better understanding of the laminar distribution and interareal differences in the cortical vasculature is becoming more important. However, in comparison to cyto- and myeloarchitecture, the study of angioarchitecture has received far less attention and relatively few methods have been described to visualise the vascular network in the human brain. Here we present angioMASH, a method for double labelling angioarchitecture and cytoarchitecture in archival human brain tissue, based on the recently published MASH protocol. The double labelling and optical clearing of thick human brain slices can be accomplished within 16 days. We use this method to acquire multi-resolution 3D datasets of combined cyto- and angioarchitecture in large ([~]30 mm x 10 mm x 3 mm) volumes of human samples covering visual areas V1 and V2. We demonstrate for the first time, that classical angioarchitectonic features can be visualised in the human cortex and in 3D using tissue clearing and light-sheet microscopy. Lastly, we show differences in the vessel density and orientation over cortical depth within and between the two areas. Especially in V1, the vascular density is not homogeneous over cortical depth but shows distinct layering. These layers are also determined by changes in the orientation of the blood vessels from a predominantly radial to a more tangential distribution. In V2, differences in vascular density are less pronounced, but orientation profiles follow a similar trend over cortical depth. We discuss potential consequences of these differences for the interpretation of non-invasive functional imaging modalities such as fMRI or fNIRS. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/609648v2_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@f9f841org.highwire.dtl.DTLVardef@1197e29org.highwire.dtl.DTLVardef@a9c9ccorg.highwire.dtl.DTLVardef@ffaefe_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Efficient targeting of heart lesions with cardiac myofibroblasts: Combined gene and cell therapy enhanced by magnetic steering

1The cardiac scar is a collagen-rich area, which is populated by myofibroblasts and has proven little amenable for therapeutic interventions. Herein, we have established an efficient targeting strategy for cardiac lesions by genetically manipulating embryonic cardiac myofibroblasts (mFB) in vitro, load the cells with magnetic nanoparticles and inject these into infarcted mouse hearts using magnetic steering. This yields strongly increased numbers ([~]4 fold compared to other cell types) of engrafted mFB. The injected mFB and endogenous myofibroblast (endoFB) population remain separate in the scar, but grafted mFB enhance the proliferation rate of endoFB by [~]4 fold. We also tested the functional impact of this approach by grafting lentiviral (LV)-transduced Connexin43 (Cx43) overexpressing mFB into the cardiac lesion. Prominent engraftment of Cx43+ mFB provides strong protection against post-infarct ventricular tachycardia (VT) in vivo, as VT incidence is reduced by [~]50 % at two and eight weeks after cell injection. Thus, ex vivo gene and subsequent in vivo cell therapy combined with magnetic steering of cardiac mFB enable efficient functional targeting of the cardiac scar.

physiology↗

bioRxiv2024

From Planning Stage To FAIR Data: A Practical Metadatasheet For Biomedical Scientists

Datasets consist of measurement data and metadata. Metadata provides context, essential for understanding and (re-)using data. Various metadata standards exist for different methods, systems and contexts. However, relevant information resides at differing stages across the data-lifecycle. Often, this information is defined and standardized only at publication stage, which can lead to data loss and workload increase. In this study, we developed Metadatasheet, a metadata standard based on interviews with members of two biomedical consortia and systematic screening of data repositories. It aligns with the data-lifecycle allowing synchronous metadata recording within Microsoft Excel, a widespread data recording software. Additionally, we provide an implementation, the Metadata Workbook, that offers user-friendly features like automation, dynamic adaption, metadata integrity checks, and export options for various metadata standards. By design and due to its extensive documentation, the proposed metadata standard simplifies recording and structuring of metadata for biomedical scientists, promoting practicality and convenience in data management. This framework can accelerate scientific progress by enhancing collaboration and knowledge transfer throughout the intermediate steps of data creation.

bioinformatics↗

bioRxiv2023

A programmable dual-targeting di-valent siRNA scaffold supports potent multi-gene modulation in the central nervous system

Di-valent short interfering RNA (siRNA) is a promising therapeutic modality that enables sequence-specific modulation of a single target gene in the central nervous system (CNS). To treat complex neurodegenerative disorders, where pathogenesis is driven by multiple genes or pathways, di-valent siRNA must be able to silence multiple target genes simultaneously. Here we present a framework for designing unimolecular "dual-targeting" di-valent siRNAs capable of co-silencing two genes in the CNS. We reconfigured di-valent siRNA - in which two identical, linked siRNAs are made concurrently - to create linear di-valent siRNA - where two siRNAs are made sequentially attached by a covalent linker. This linear configuration, synthesized using commercially available reagents, enables incorporation of two different siRNAs to silence two different targets. We demonstrate that this dual-targeting di-valent siRNA is fully functional in the CNS of mice, supporting at least two months of maximal target silencing. Dual-targeting di-valent siRNA is highly programmable, enabling simultaneous modulation of two different disease-relevant gene pairs (e.g., Huntingtons disease: MSH3 and HTT; Alzheimers disease: APOE and JAK1) with similar potency to a mixture of single-targeting di-valent siRNAs against each gene. This work potentiates CNS modulation of virtually any pair of disease-related targets using a simple unimolecular siRNA.

molecular biology↗

bioRxiv2023

The Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples

In 2015, we launched the mesoSPIM initiative (www.mesospim.org), an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at higher speed and resolution has increased, requiring major improvements in the capabilities of light-sheet microscopy. Here, we introduce the next-generation mesoSPIM ("Benchtop") with significantly increased field of view, improved resolution, higher throughput, more affordable cost and simpler assembly compared to the original version. We developed a new method for testing objectives, enabling us to select detection objectives optimal for light-sheet imaging with large-sensor sCMOS cameras. The new mesoSPIM achieves high spatial resolution (1.5 {micro}m laterally, 3.3 {micro}m axially) across the entire field of view, a magnification up to 20x, and supports sample sizes ranging from sub-mm up to several centimetres, while being compatible with multiple clearing techniques. The new microscope serves a broad range of applications in neuroscience, developmental biology, and even physics.

neuroscience↗

bioRxiv2023

Extended Nucleic Acid (exNA): A Novel, Biologically Compatible Backbone that Significantly Enhances Oligonucleotide Efficacy in vivo

Metabolic stabilization of therapeutic oligonucleotides requires both sugar and backbone modifications, where phosphorothioate (PS) is the only backbone chemistry used in the clinic. Here, we describe the discovery, synthesis, and characterization of a novel biologically compatible backbone, extended nucleic acid (exNA). Upon exNA precursor scale up, exNA incorporation is fully compatible with common nucleic acid synthetic protocols. The novel backbone is orthogonal to PS and shows profound stabilization against 3- and 5-exonucleases. Using small interfering RNAs (siRNAs) as an example, we show exNA is tolerated at most nucleotide positions and profoundly improves in vivo efficacy. A combined exNA-PS backbone enhances siRNA resistance to serum 3-exonuclease by [~]32-fold over PS backbone and >1000-fold over the natural phosphodiester backbone, thereby enhancing tissue exposure ([~]6-fold), tissues accumulation (4- to 20-fold), and potency both systemically and in brain. The improved potency and durability imparted by exNA opens more tissues and indications to oligonucleotide-driven therapeutic interventions.

biochemistry↗

bioRxiv2022

Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors

Pre-adenylated single-stranded DNA ligation adaptors are essential reagents in many next generation RNA sequencing library preparation protocols. These oligonucleotides can be adenylated enzymatically or chemically. Enzymatic adenylation reactions have high yield but are not amendable to scale up. In chemical adenylation, Adenosine 5{square}-phosphorimidazolide (ImpA) reacts with 5' phosphorylated DNA. It is easily scalable but gives poor yields, requiring labor-intensive cleanup steps. Here, we describe an improved chemical adenylation method using 95% formamide as the solvent, which results in the adenylation of oligonucleotides with >90% yield. In standard conditions, with water as the solvent, hydrolysis of the starting material to adenosine monophosphate limits the yields. To our surprise, we find that rather than increasing adenylation yields by decreasing the rate of ImpA hydrolysis, formamide does so by increasing the reaction rate between ImpA and 5'-phosphorylated DNA by [~]10 fold. The method described here enables straightforward preparation of chemically adenylated adapters with higher than 90% yield, simplifying reagent preparation for NGS.

molecular biology↗

bioRxiv2022

Reflective multi-immersion microscope objectives inspired by the Schmidt telescope

Rapid advances in tissue clearing protocols have begun to outpace the capabilities of existing microscope objectives: High-resolution imaging inside cm-sized cleared samples is often not possible as it requires multi-immersion objectives with high numerical aperture (NA > 0.7), long working distance (WD > 10 mm) and a large field-of-view (FOV > 1 mm). Here, we introduce a novel mirror-based optical design, the "Schmidt objective", which meets all these criteria despite containing only two optical elements. It consists of a spherical mirror in contact with the immersion medium and an aspherical correction plate. We showcase a multi-photon variant of a Schmidt objective that reaches NA 1.08 at an refractive index of 1.56 and demonstrate its versatility by imaging fixed samples in a wide range of immersion media ranging from air and water to BABB, DBE, and ECI. In addition, we demonstrate in vivo imaging by recording neuronal activity in larval zebrafish.

neuroscience↗