Biology subjects

Garton, M.

Publications and source records attributed to Garton, M..

6 recordsLinked to original sources

bioRxiv2026

Generative design of de novo AAV vectors with unique serological profiles

More than 5000 monogenic diseases are potentially curable by replacing a single defective gene with one that functions normally. Currently, the only clinically approved vector able to effectively deliver a therapeutic gene to a target tissue is Adeno-Associated Viruses (AAVs). However, despite decades of work, only a handful of gene replacement therapies have been approved, and many patients remain ineligible for even those. A major barrier to broad adoption of AAV therapies is pre-existing immunity to AAVs, mediated by neutralizing antibodies (nAbs). It is potentially possible to change exposed capsid surfaces in AAV capsids to avoid nAb recognition. However, traditional techniques such as rational design and directed evolution only allow modest changes. AAV function becomes compromised long before full nAb avoidance is achieved. Recent advances in protein design by generative modelling provide a new way to overcome this problem by learning AAV design constraints from natural sequences. We built a variational autoencoder that could learn these sequence constraints and generate functional AAV capsid proteins de novo. More than 255 designs were synthesized and tested in vitro in two design sets, with one set dedicated to exploring uncertain regions of the sequence space. Between the two campaigns, seven designs transduced human cells with >50% efficiency, of which four avoided nAb neutralization (NT50 < 1:50) in all human sera that were reactive to AAV. In one of these designs, sequence identity to the nearest natural AAV sequence was 18% divergent. Given the radical sequence diversity and its unique serological profile, this new capsid design would represent the first ever AAV serotype designed de novo.

bioengineering↗

bioRxiv2026

ARCHIVE: Machine-Guided Design of an Efficient Open-Ended DNA Recording Device to Increase Resolution of Multiplexed Cell History Tracking

Engineering cell-based devices to record events into DNA has potential both as a non-ablative research tool and in the clinic for enacting gene-circuit-based logic of cell therapies conditional on cell history. Whether as a means of understanding interactions on the single-cell level, or reconstructing histories of cellular events, a cellular DNA recording device has widespread utility, with prime editing-based methods at the forefront of this endeavor - notably peCHYRON. Yet, the resolution of such open-ended recording tools are inherently constrained by edit insertion efficiency and cannot yet capture RNA-polymerase II-transcribed signals, which represent a large segment of functionally-defined endogenous gene-regulatory architectures. Here we present ARCHIVE (Amplified Recording of Cellular Histories into Information-dense Vectors of Events), capable of integrating RNA-encoded signals into a predefined genomic recording locus with high efficiency. By utilizing deep-learning assisted prediction of prime-editing efficiency as a surrogate fitness model for generative in silico pegRNA evolution, we developed a recording device with an order-of-magnitude improvement in temporal resolution (efficiency of iterative message integration steps) compared to the state of the art - a capability we establish here at the level of constitutive promoter tracking. We expect ARCHIVE to serve as a launching point for more advanced mammalian synthetic-biology recording devices for both functional genomics and therapeutics research.

synthetic biology↗

bioRxiv2025

Inorganic pyrophosphate disrupts amorphous hydrated bone mineral interfaces in hypophosphatasia

Bone mineral molecular architecture is tightly regulated by the kinetics of calcium phosphate phase transformations. In the rare skeletal disease hypophosphatasia (HPP), caused by inactivating mutations in the ALPL gene encoding tissue-nonspecific alkaline phosphatase (TNSALP), accumulation of inorganic pyrophosphate (PPi) alters these phase dynamics. Using solid-state nuclear magnetic resonance spectroscopy and high-resolution electron microscopy, in patient samples we show that bone mineral from compound heterozygous HPP patients exhibits a loss of hydrated amorphous interfacial phases and instead contains highly crystalline hydroxyapatite (HAP), correlating with abnormally high bone mineral density and brittle atypical femoral fractures. Synthetic and cellular models demonstrate that elevated PPi impedes normal phase transitions from amorphous calcium phosphate precursors, bypassing intermediate states and driving ordered HAP nucleation. These findings link disrupted mineral phase kinetics to pathological bone mineral molecular structure, emphasising the critical importance of the hydrated amorphous shell around bone mineral for its material properties and redefining HPP as a molecular mineralization disorder. Our findings also illustrate how biochemical cues regulate non-equilibrium crystallization pathways in biomineralization.

biophysics↗

bioRxiv2023

ProteinVAE: Variational AutoEncoder forTranslational Protein Design

There have recently been rapid advances in deep learning models for protein design. To demonstrate proof-of-concept, these advancements have focused on small proteins with lots of data for training. This means that they are often not suitable for generating proteins with the most potential for high clinical impact -due to the additional challenges of sparse data and large size many therapeutically relevant proteins have. One major application that fits this category is gene therapy delivery. Viral vectors such as Adenoviruses and AAVs are a common delivery vehicle for gene therapy. However, environmental exposure means that most people exhibit potent pre-existing immune responses to many serotypes. This response, primarily driven by neutralizing antibodies, also precludes repeated administration with the same serotype. Rare serotypes, serotypes targeting other species, and capsid engineering, have all been deployed in the service of reducing neutralization by pre-existing antibodies. However, progress has been very limited using conventional methods and a new approach is urgently needed. To address this, we developed a variational autoencoder that can generate synthetic viral vector serotypes without epitopes for pre-existing neutralizing antibodies. A compact generative computational model was constructed, with only 12.4 million parameters that could be efficiently trained on the limited natural sequences (e.g., 711 natural Adenovirus hexon sequences with average length of 938 amino acids). In contrast to the current state-of-the-art, the model was able to generate high-quality Adenovirus hexon sequences that were folded with high confidence by Alphafold2 to produce structures essentially identical to natural hexon structures. Molecular dynamics simulations confirmed that the structures are stable and protein-protein interfaces are intact. Local secondary structure and local mobility is also comparable with natural serotype behavior. Our model could be used to generate a broad range of synthetic adenovirus serotype sequences without epitopes for pre-existing neutralizing antibodies in the human population. It could be used more broadly to generate different types of viral vector, and any large, therapeutically valuable proteins, where available data is sparse.

synthetic biology↗

bioRxiv2023

A Flexible Transgene Integration Landing-Pad Toolkit in Human Induced Pluripotent Stem Cells Enables Facile Cellular Engineering, Gene Zygosity Control, and Parallel Transgene Integration

Development of a repeatable method for delivering transgene payloads to human induced pluripotent stem cells (hiPSCs) without risking unintended off-target effects is not fully realized. Yet, such methods are indispensable to fully unlocking the potential for applying synthetic biological approaches to regenerative medicine, delivering quantum impacts to cell-based therapeutics development. Here we present a toolkit for engineering hiPSCs centred on the development of two core landing-pad cell-lines, facilitating rapid high-efficiency delivery of transgenes to the AAVS1 safe-harbour locus using the Bxb1 large-serine recombinase. We developed two landing-pad cell lines expressing green and red fluorescent reporters respectively, both retaining stemness whilst fully capable of differentiation into all three germ layers. A fully selected hiPSC population can be isolated within 1-2 weeks after landing-pad recombinase-mediated cassette exchange. We demonstrate the capability for investigator-controlled homozygous or heterozygous transgene configurations in these cells. As such, the toolkit of vectors and protocols associated with this landing-pad hiPSC system has the potential to accelerate engineering workflows for researchers in a variety of disciplines.

synthetic biology↗

bioRxiv2023

Systematically testing human HMBS missense variants to reveal mechanism and pathogenic variation

Defects in hydroxymethylbilane synthase (HMBS) can cause Acute Intermittent Porphyria (AIP), an acute neurological disease. Although sequencing-based diagnosis can be definitive, ~[1/3] of clinical HMBS variants are missense variants, and most clinically-reported HMBS missense variants are designated as "variants of uncertain significance" (VUS). Using saturation mutagenesis, en masse selection, and sequencing, we applied a multiplexed validated assay to both the erythroid-specific and ubiquitous isoforms of HMBS, obtaining confident functional impact scores for >84% of all possible amino-acid substitutions. The resulting variant effect maps generally agreed with biochemical expectation. However, the maps showed variants at the dimerization interface to be unexpectedly well tolerated, and suggested residue roles in active site dynamics that were supported by molecular dynamics simulations. Most importantly, these HMBS variant effect maps can help discriminate pathogenic from benign variants, proactively providing evidence even for yet-to-be-observed clinical missense variants.

molecular biology↗