Biology subjects

McNeill, M.

Publications and source records attributed to McNeill, M..

3 recordsLinked to original sources

bioRxiv2025

UNCOVERseq Enables Sensitive and Controlled Gene Editing Off-Target Nomination Across CRISPR-Cas Modalities and Systems

The rapid development of CRISPR-Cas gene editing technologies has revolutionized genetic medicine, offering unprecedented precision and potential for treating a wide array of genetic disorders. However, assessing the risks of unintended gene editing effects remains critical, and is complicated by new editing modalities and unclear analytical guidelines. We present UNCOVERseq (Unbiased Nomination of CRISPR Off-target Variants using Enhanced RhPCR), an improved in cellulo off-target nomination workflow designed to sensitively nominate off-target sites (<0.01% editing) with defined input requirements and analytical process controls to provide empirical performance evidence across diverse circumstances. Using this workflow, we nominated off-targets across 192 guide RNAs (gRNAs) and demonstrated superior performance compared to existing methodologies. We identified a subset of six gRNAs with a dynamic range of specificity and confirmed the relevance and high true positive rate of our nomination method, providing relative risk assessments for multiple modalities (S.p. Cas9 and derived high-fidelity variants / base editors) in a translational system involving hematopoietic stem and progenitor cells (HSPCs). Additionally, we established that double-strand break (DSB) editing retains a strong, positive rank correlation to single-strand break (SSB)-mediated base editing, highlighting the importance of DSB nomination sites as candidate loci for base editing. Overall, UNCOVERseq improves informed risk assessment of gene editing in translational systems by enhancing the quality of off-target nomination.

molecular biology↗

bioRxiv2024

Exploring mechanisms of change in a Southern Ocean fishery with a co-produced network model

A key challenge in planning long-term fisheries sustainability is overcoming uncertainties in predicted changes in target populations and catch rates in response to climate change and fishery trends. We combine transdisciplinary knowledge co-production and qualitative network modelling to advance system understanding and elucidate likely responses of a Patagonian toothfish fishery to future change. We co-developed a model of the Kerguelen Plateau biophysical-socioeconomic system with knowledge holders from industry and science; the first whole-of-system qualitative network model of intermediate complexity for this region. We present new approaches for dealing with uncertainty in network structure, and for investigating how perturbations propagate through a network. Using these tools, we found multiple potential pathways of decline for toothfish population and catch, but also some possible mechanisms of increase dependent on magnitude of certain effects. Our results highlight critical information gaps, including the potential role of scavenging benthos in fishery-ecosystem interactions and likely changes in the prey-field in response to warmer water, that require filling to improve predictions for toothfish populations and catch and forward planning for the fishery.

ecology↗

bioRxiv2018

In vivo selection for corrected β-globin alleles after CRISPR/Cas9 editing in human sickle hematopoietic stem cells enhances therapeutic potential

Sickle Cell Disease (SCD), one of the worlds most common genetic disorders, causes anemia and progressive multiorgan damage that typically shortens lifespan by decades; currently there is no broadly applicable curative therapy. Here we show that Cas9 RNP-mediated gene editing with an ssDNA oligonucleotide donor yields markerless correction of the sickle mutation in more than 30% of long-term engrafting human hematopoietic stem cells (HSCs), using a selection-free protocol that is directly applicable to a clinical setting. We further find that in vivo erythroid differentiation markedly enriches for corrected {beta}-globin alleles. Adoption of a high-fidelity Cas9 variant demonstrates that this approach can yield efficient editing with almost no off-target events. These findings indicate that the sickle mutation can be corrected in human HSCs at curative levels with a streamlined protocol that is ready to be translated into a therapy.\n\nONE SENTENCE SUMMARYCas9-mediated correction of the sickle mutation in human hematopoietic stem cells can be accomplished at curative levels.

genetics↗