Targeting AAV vectors to the central nervous system by engineering capsid-receptor interactions that enable crossing of the blood-brain barrier.

Viruses have evolved the ability to bind and enter cells through interactions with a wide variety of cell macromolecules. We engineered peptide-modified adeno-associated virus (AAV) capsids that transduce the brain through the introduction of de novo interactions with 2 proteins expressed on the mouse blood-brain barrier (BBB), LY6A or LY6C1. The in vivo tropisms of these capsids are predictable as they are dependent on the cell- and strain-specific expression of their target protein. This approach generated hundreds of capsids with dramatically enhanced central nervous system (CNS) tropisms within a single round of screening in vitro and secondary validation in vivo thereby reducing the use of animals in comparison to conventional multi-round in vivo selections. The reproducible and quantitative data derived via this method enabled both saturation mutagenesis and machine learning (ML)-guided exploration of the capsid sequence space. Notably, during our validation process, we determined that nearly all published AAV capsids that were selected for their ability to cross the BBB in mice leverage either the LY6A or LY6C1 protein, which are not present in primates. This work demonstrates that AAV capsids can be directly targeted to specific proteins to generate potent gene delivery vectors with known mechanisms of action and predictable tropisms.

An AAV capsid reprogrammed to bind human transferrin receptor mediates brain-wide gene delivery.

Developing vehicles that efficiently deliver genes throughout the human central nervous system (CNS) will broaden the range of treatable genetic diseases. We engineered an adeno-associated virus (AAV) capsid, BI-hTFR1, that binds human transferrin receptor (TfR1), a protein expressed on the blood-brain barrier. BI-hTFR1 was actively transported across human brain endothelial cells and, relative to AAV9, provided 40 to 50 times greater reporter expression in the CNS of human TFRC knockin mice. The enhanced tropism was CNS-specific and absent in wild-type mice. When used to deliver GBA1, mutations of which cause Gaucher disease and are linked to Parkinson's disease, BI-hTFR1 substantially increased brain and cerebrospinal fluid glucocerebrosidase activity compared with AAV9. These findings establish BI-hTFR1 as a potential vector for human CNS gene therapy.

Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia.

We sequenced all protein-coding regions of the genome (the "exome") in two family members with combined hypolipidemia, marked by extremely low plasma levels of low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and triglycerides. These two participants were compound heterozygotes for two distinct nonsense mutations in ANGPTL3 (encoding the angiopoietin-like 3 protein). ANGPTL3 has been reported to inhibit lipoprotein lipase and endothelial lipase, thereby increasing plasma triglyceride and HDL cholesterol levels in rodents. Our finding of ANGPTL3 mutations highlights a role for the gene in LDL cholesterol metabolism in humans and shows the usefulness of exome sequencing for identification of novel genetic causes of inherited disorders. (Funded by the National Human Genome Research Institute and others.).

An AAV capsid reprogrammed to bind human Transferrin Receptor mediates brain-wide gene delivery.

Developing vehicles that efficiently deliver genes throughout the human central nervous system (CNS) will broaden the range of treatable genetic diseases. We engineered an AAV capsid, BI-hTFR1, that binds human Transferrin Receptor (TfR1), a protein expressed on the blood-brain barrier (BBB). BI-hTFR1 was actively transported across a human brain endothelial cell layer and, relative to AAV9, provided 40-50 times greater reporter expression in the CNS of human TFRC knock-in mice. The enhanced tropism was CNS-specific and absent in wild type mice. When used to deliver GBA1, mutations of which cause Gaucher disease and are linked to Parkinson's disease, BI-hTFR1 substantially increased brain and cerebrospinal fluid glucocerebrosidase activity compared to AAV9. These findings establish BI-hTFR1 as a promising vector for human CNS gene therapy.

Alzheimer's disease brain-derived amyloid-ß-mediated inhibition of LTP in vivo is prevented by immunotargeting cellular prion protein.

Synthetic amyloid-ß protein (Aß) oligomers bind with high affinity to cellular prion protein (PrP(C)), but the role of this interaction in mediating the disruption of synaptic plasticity by such soluble Aß in vitro is controversial. Here we report that intracerebroventricular injection of Aß-containing aqueous extracts of Alzheimer's disease (AD) brain robustly inhibits long-term potentiation (LTP) without significantly affecting baseline excitatory synaptic transmission in the rat hippocampus in vivo. Moreover, the disruption of LTP was abrogated by immunodepletion of Aß. Importantly, intracerebroventricular administration of antigen-binding antibody fragment D13, directed to a putative Aß-binding site on PrP(C), prevented the inhibition of LTP by AD brain-derived Aß. In contrast, R1, a Fab directed to the C terminus of PrP(C), a region not implicated in binding of Aß, did not significantly affect the Aß-mediated inhibition of LTP. These data support the pathophysiological significance of SDS-stable Aß dimer and the role of PrP(C) in mediating synaptic plasticity disruption by soluble Aß.

A monoclonal antibody against synthetic Aß dimer assemblies neutralizes brain-derived synaptic plasticity-disrupting Aß.

Diverse lines of evidence indicate that pre-fibrillar, diffusible assemblies of the amyloid ß-protein (Aß) play an important role in Alzheimer's disease pathogenesis. Although the precise molecular identity of these soluble toxins remains unsettled, recent experiments suggest that sodium dodecyl sulfate (SDS)-stable Aß dimers may be the basic building blocks of Alzheimer's disease-associated synaptotoxic assemblies and as such present an attractive target for therapeutic intervention. In the absence of sufficient amounts of highly pure cerebral Aß dimers, we have used synthetic disulfide cross-linked dimers (free of Aß monomer or fibrils) to generate conformation-specific monoclonal antibodies. These dimers aggregate to form kinetically trapped protofibrils, but do not readily form fibrils. We identified two antibodies, 3C6 and 4B5, which preferentially bind assemblies formed from covalent Aß dimers, but do not bind to Aß monomer, amyloid precursor protein, or aggregates formed by other amyloidogenic proteins. Monoclonal antibody 3C6, but not an IgM isotype-matched control antibody, ameliorated the plasticity-disrupting effects of Aß extracted from the aqueous phase of Alzheimer's disease brain, thus suggesting that 3C6 targets pathogenically relevant Aß assemblies. These data prove the usefulness of covalent dimers and their assemblies as immunogens and recommend further investigation of the therapeutic and diagnostic utility of monoclonal antibodies raised to such assemblies.

Metamorphosis in Insect Muscle: Insights for Engineering Muscle-Based Actuators.

One of the major limitations to advancing the development of soft robots is the absence of lightweight, effective soft actuators. While synthetic systems, such as pneumatics and shape memory alloys, have created important breakthroughs in soft actuation, they typically rely on large external power sources and some rigid components. Muscles provide an ideal actuator for soft constructs, as they are lightweight, deformable, biodegradable, silent, and powered by energy-dense hydrocarbons such as glucose. Vertebrate cell lines and embryonic cultures have allowed critical foundational work to this end, but progress there is limited by the difficulty of identifying individual pathways in embryonic development, and the divergence of immortal cell lines from these normal developmental programs. An alternative to culturing muscles from embryonic cells is to exploit the advantages of species with metamorphic stages. In these animals, muscles develop from a predefined pool of myoblasts with well-characterized contacts to other tissues. In addition, the endocrine triggers for development into adult muscles are often known and tractable for experimental manipulation. This is particularly true for metamorphic muscle development in holometabolous insects, which provide exciting new avenues for tissue engineering. Using insect tissues for actuator development confers additional benefits; insect muscles are more robust to varying pH, temperature, and oxygenation than are vertebrate cells. Given that biohybrid robots are likely to be used in ambient conditions and changing environments, this sort of hardiness is likely to be required for practical use. In this study, we summarize key processes and signals in metamorphic muscle development, drawing attention to those pathways that offer entry points for manipulation. By focusing on lessons learned from in vivo insect development, we propose that future culture designs will be able to use more systematic, hypothesis-driven approaches to optimizing engineered muscle. Impact statement This review summarizes our current understanding of metamorphic muscle development in insects. It provides a framework for engineering muscle-based actuators that can be used in robotic applications in a wide range of ambient conditions. The focus is on identifying key processes that might be manipulated to solve current challenges in controlling tissue development such as myoblast proliferation, myotube formation and fusion, cytoskeletal alignment, myotendinous attachment and full differentiation. An important goal is to gather findings that cross disciplinary boundaries and to promote the development of better bioactuators for nonclinical applications.

Metal or muscle? The future of biologically inspired robots.

Biology has inspired the development of agile robots, and it is now teaching us how to grow machines from living cells.

Enhancing colorimetric loop-mediated isothermal amplification speed and sensitivity with guanidine chloride.

Loop-mediated isothermal amplification (LAMP) is a versatile technique for detection of target DNA and RNA, enabling rapid molecular diagnostic assays with minimal equipment. The global SARS-CoV-2 pandemic has presented an urgent need for new and better diagnostic methods, with colorimetric LAMP utilized in numerous studies for SARS-CoV-2 detection. However, the sensitivity of colorimetric LAMP in early reports has been below that of the standard RT-qPCR tests, and we sought to improve performance. Here we report the use of guanidine hydrochloride and combined primer sets to increase speed and sensitivity in colorimetric LAMP, bringing this simple method up to the standards of sophisticated techniques and enabling accurate, high-throughput diagnostics.

NEBNext Direct: A Novel, Rapid, Hybridization-Based Approach for the Capture and Library Conversion of Genomic Regions of Interest.

Next-generation sequencing (NGS) is a powerful tool for genomic studies, translational research, and clinical diagnostics that enables the detection of single nucleotide polymorphisms, insertions and deletions, copy number variations, and other genetic variations. Target enrichment technologies improve the efficiency of NGS by only sequencing regions of interest, which reduces sequencing costs while increasing coverage of the selected targets. Here we present NEBNext Direct® , a hybridization-based, target-enrichment approach that addresses many of the shortcomings of traditional target-enrichment methods. This approach features a simple, 7-hr workflow that uses enzymatic removal of off-target sequences to achieve a high specificity for regions of interest. Additionally, unique molecular identifiers are incorporated for the identification and filtering of PCR duplicates. The same protocol can be used across a wide range of input amounts, input types, and panel sizes, enabling NEBNext Direct to be broadly applicable across a wide variety of research and diagnostic needs. © 2017 by John Wiley & Sons, Inc.

Automated small-scale protein purification and analysis for accelerated development of protein therapeutics.

Small-scale protein purification presents opportunities for accelerated process development of biotherapeutic molecules. Miniaturization of purification conditions reduces time and allows for parallel processing of samples, thus offering increased statistical significance and greater breadth of variables. The ability of the miniaturized platform to be predictive of larger scale purification schemes is of critical importance. The PerkinElmer JANUS BioTx Pro and Pro-Plus workstations were developed as intuitive, flexible, and automated devices capable of performing parallel small-scale analytical protein purification. Preprogrammed methods automate a variety of commercially available ion exchange and affinity chromatography solutions, including miniaturized chromatography columns, resin-packed pipette tips, and resin-filled microtiter vacuum filtration plates. Here, we present a comparison of microscale chromatography versus standard fast protein LC (FPLC) methods for process optimization. In this study, we evaluated the capabilities of the JANUS BioTx Pro-Plus robotic platform for miniaturized chromatographic purification of proteins with the GE ӒKTA Express system. We were able to demonstrate predictive analysis similar to that of larger scale purification platforms, while offering advantages in speed and number of samples processed. This approach is predictive of scale-up conditions, resulting in shorter biotherapeutic development cycles and less consumed material than traditional FPLC methods, thus reducing time-to-market from discovery to manufacturing.

Determination of carotenoids, total phenolic content, and antioxidant activity of Arazá (Eugenia stipitata McVaugh), an Amazonian fruit.

The fruit of Arazá (Eugenia stipitata McVaugh) native to the Colombian Amazon is considered a potentially economically valuable fruit for the Andean economy due to its novel and unique taste. The fruit has an intense yellow color, but its chemical composition and properties have not been well studied. Here we report the identification and quantitation of carotenoids in the ripe fruit using high performance liquid chromatography (HPLC) with photodiode array detector (PDA) and atmospheric pressure chemical ionization (APcI) mass spectrometry (MS/MS). The qualitative carotenoid profile of the fruit according to maturity stage was also observed. Furthermore, antioxidant activity of the peel and pulp were assessed using the ferric reducing ability of plasma (FRAP), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and 1,1-diphenyl-2-picrylhydrazyl (DPPH) methods, in addition to chemical indexes and total phenolic content. Multiple carotenoids were identified in the peel and pulp including four xanthophylls (free and esterified as their mono and diesters) and two carotenes. One of the xanthophylls was tentatively identified as zeinoxanthin, while the others were identified as lutein, zeaxanthin, and ß-cryptoxanthin. Carotenes included α-carotene and ß-carotene. The total carotenoid content was significantly higher in the peel (2484 ± 421 µg/100 g FW) than in the pulp (806 ± 348 µg/100 g FW) with lutein, ß-cryptoxanthin, and zeinoxanthin as the major carotenoid components. The unique carotenoid composition of this fruit can differentiate it from other carotenoid-rich fruits and perhaps be useful in authentication procedures. Overall, results from this study suggest that Colombian Arazá may be a good edible source of carotenoids important in retinal health as well as carotenoids with provitamin A activity. Therefore, Arazá fruit can be used as a nutraceutical ingredient and in production of functional foods in the Colombian diet.

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries.

Genome targeting methods enable cost-effective capture of specific subsets of the genome for sequencing. We present here an automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced. Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol.

Alzheimer's disease amyloid beta-protein and synaptic function.

Alzheimer's disease (AD) is characterized neuropathologically by the deposition of different forms of amyloid beta-protein (A beta) including variable amounts of soluble species that correlate with severity of dementia. The extent of synaptic loss in the brain provides the best morphological correlate of cognitive impairment in clinical AD. Animal research on the pathophysiology of AD has therefore focussed on how soluble A beta disrupts synaptic mechanisms in vulnerable brain regions such as the hippocampus. Synaptic plasticity in the form of persistent activity-dependent increases or decreases in synaptic strength provide a neurophysiological substrate for hippocampal-dependent learning and memory. Acute treatment with human-derived or chemically prepared soluble A beta that contains certain oligomeric assemblies, potently and selectively disrupts synaptic plasticity causing inhibition of long-term potentiation (LTP) and enhancement of long-term depression (LTD) of glutamatergic transmission. Over time these and related actions of A beta have been implicated in reducing synaptic integrity. This review addresses the involvement of neurotransmitter intercellular signaling in mediating or modulating the synaptic plasticity disrupting actions of soluble A beta, with particular emphasis on the different roles of glutamatergic and cholinergic mechanisms. There is growing evidence to support the view that NMDA and possibly nicotinic receptors are critically involved in mediating the disruptive effect of A beta and that targeting muscarinic receptors can indirectly modulate A beta's actions. Such studies should help inform ongoing and future clinical trials of drugs acting through the glutamatergic and cholinergic systems.

Targeted exon sequencing by in-solution hybrid selection.

This unit describes a protocol for the targeted enrichment of exons from randomly sheared genomic DNA libraries using an in-solution hybrid selection approach for sequencing on an Illumina Genome Analyzer II. The steps for designing and ordering a hybrid selection oligo pool are reviewed, as are critical steps for performing the preparation and hybrid selection of an Illumina paired-end library. Critical parameters, performance metrics, and analysis workflow are discussed.

A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.

We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA barcoding of constructs. Automation-friendly magnetic bead-based size selection and cleanup steps have been devised, eliminating major bottlenecks and significant sources of error. Using this methodology, one technician can create 96 sequence-ready 454 libraries in 2 days, a dramatic improvement over the standard method.

Antisense inhibition of neuronal nicotinic receptors in the tobacco-feeding insect, Manduca sexta.

Acetylcholine is the predominant excitatory transmitter in the insect central nervous system with many of its effects mediated by nicotinic acetylcholine receptors. These receptors are present at very high density and are structurally heterogeneous, although little is known about functional distinctions between them. An interesting system for examining these receptors is the larval stage of Manduca sexta, a nicotine-resistant tobacco-feeding insect. The nicotinic responses of cultured neurons were found to be blocked by mecamylamine and curare but highly resistant to alpha-bungarotoxin. The responses were also unaffected by the reducing agent dithiothreitol and the alkylating agent bromoacetylcholine suggesting that the alpha-subunit dicysteine agonist binding site is protected. To begin determining the functional roles of different subunits in these receptors, cultured neurons were treated with oligonucleotides based on the gene sequence of the alpha subunit, MARA1. Antisense DNA caused a significant downward shift in the amplitude distribution of nicotinic responses compared to sense or reverse antisense treatments. These treatments did not affect currents mediated by the application of GABA. The reduction in the nicotinic depolarization and inward currents did not affect the rate of current onset or recovery, suggesting that antisense MARA1 causes a partial block of all nicotinic responses in these neurons. These results demonstrate that receptor gene expression in insect neurons can be manipulated in a sequence-specific manner by antisense treatment and they provide evidence that MARA1 is important for normal nicotinic responses in Manduca.