Biology subjects

Snell, D. M.

Publications and source records attributed to Snell, D. M..

7 recordsLinked to original sources

bioRxiv2026

Genome editing of marsupial RSX reveals conserved and divergent principles in mammalian X-inactivation

X-chromosome inactivation balances X-gene dosage between the sexes in eutherians and marsupials. The lncRNA Xist mediates X-inactivation in eutherians but is absent from marsupials. An evolutionarily unrelated lncRNA, RSX, has been identified in marsupials, but its role in X-inactivation is unresolved because genome editing in these mammals has only recently become feasible. Using CRISPR-Cas9 in the opossum, we show that RSX is required for the initiation of X-inactivation in marsupial embryos. RSX deletion later, in differentiated cells, causes modest X-gene de-repression, with repressive chromatin marks H3K27me3 and H3K9me3 retained. H2AK119ub is not enriched on the opossum inactive X, revealing divergent Polycomb-mediated regulation in therians. Our findings reveal stage-specific roles of RSX in marsupial X-inactivation and identify conserved and divergent features of X-dosage compensation in mammals.

genomics↗

bioRxiv2025

Autoantibody origins in lupus and in relapse post CAR-T therapy

Anti-CD19 chimeric antigen receptor (CAR)-T therapy induces profound remissions in lupus by depleting B cells, challenging the longstanding view that treatment-resistant disease is sustained by long-lived plasma cells. Additionally, emerging relapses highlight the need to understand how pathogenic autoantibodies arise. Using molecular antibody tagging in mice with human monogenic lupus variants, we reveal that autoantibody-producing cell cohorts are long-lived but plasma cells are short-lived, requiring continuous replenishment from proliferating precursors. The spleen acts as a major plasma cell reservoir, with perivascular localization conserved in mice and lupus patients. Relapse after anti-CD19 CAR-T occurred through newly-generated B cells rather than treatment-resistant clones. Plasma cell depletion by anti-BCMA CAR-T failed to eliminate some precursors that become autoantibody-secreting. These findings demonstrate that continuous B cell-to-plasma cell differentiation, not intrinsic plasma cell longevity, sustains pathogenic antibody responses in lupus, supporting a potential benefit of adjunctive therapies after CAR-T, particularly in genetically predisposed patients.

immunology↗

bioRxiv2025

SLFN11 restricts escape from telomere crisis to prevent alternative lengthening of telomeres

The tRNA nuclease SLFN11 is epigenetically silenced in [~]50% of treatment-naive tumours and is the strongest predictor of chemoresistance but why it is frequently inactivated in cancer is unknown. To acquire immortality, cancer cells can activate alternative lengthening of telomeres (ALT), typically accompanied by ATRX loss. Here, we implicate SLFN11 in sensing telomere replication stress, triggering eradication of ATRX deficient cells prior to ALT establishment. Whereas progressive telomere shortening of cells lacking telomerase and ATRX leads to telomere crisis and cell death, SLFN11 loss confers tolerance to PML-BLM dependent ALT intermediates, permitting emergence of ALT survivors. We propose that during tumorigenesis SLFN11 inactivation is selected as means to tolerate endogenous replication stress following telomere crisis, leading to the development of therapy resistant tumours before treatment.

molecular biology↗

bioRxiv2024

Sex chromosomes shape the transcriptional landscape of the preimplantation mouseembryo

Sex chromosomes are emerging as key regulators of adult health and disease in males (XY) and females (XX), but their impact on embryo development is poorly understood. Using single-cell RNA sequencing (scRNA-seq) on wild type and aneuploid mouse embryos, we show that sex chromosomes significantly shape the preimplantation embryo transcriptional landscape. A hierarchy of effects are identified, distinctly mediated by the Y chromosome, the dosage of X chromosomes, X-chromosome imprinting, and by Xist, the non-coding RNA that initiates X-inactivation. The sex chromosomes have strong trans effects on autosomal gene expression throughout preimplantation development. The Y chromosome has an unexpectedly pronounced impact on the trophectoderm, the precursor of the placenta, and this property is shared with genes expressed from the inactive X chromosome. The paternal and maternal X chromosomes differentially promote preimplantation growth, and we identify multiple novel candidate X-linked imprinted genes mediating this effect. Our findings show that sex chromosomes impact the embryo from the beginning of life, long before the appearance of overt sex differences.

developmental biology↗

bioRxiv2023

Deep dynamical modelling of developmental trajectories with temporal transcriptomics

Developmental cell fate decisions are dynamic processes driven by the complex behaviour of gene regulatory networks. A challenge in studying these processes using single-cell genomics is that the data provides only a static snapshot with no detail of dynamics. Metabolic labelling and splicing can provide time-resolved information, but current methods have limitations. Here, we present experimental and computational methods that overcome these limitations to allow dynamical modelling of gene expression from single-cell data. We developed sci-FATE2, an optimised metabolic labelling method that substantially increases data quality, and profiled approximately 45,000 embryonic stem cells differentiating into multiple neural tube identities. To recover dynamics, we developed velvet, a deep learning framework that extends beyond instantaneous velocity estimation by modelling gene expression dynamics through a neural stochastic differential equation system within a variational autoencoder. Velvet outperforms current velocity tools across quantitative benchmarks, and predicts trajectory distributions that accurately recapitulate underlying dataset distributions while conserving known biology. Velvet trajectory distributions capture dynamical aspects such as decision boundaries between alternative fates and correlative gene regulatory structure. Using velvet to provide a dynamical description of in vitro neural patterning, we highlight a process of sequential decision making and fate-specific patterns of developmental signalling. Together, these experimental and computational methods recast single-cell analyses from descriptions of observed data distributions to models of the dynamics that generated them, providing a new framework for investigating developmental gene regulation and cell fate decisions.

bioinformatics↗

bioRxiv2022

Emergence of new subgenomic mRNAs in SARS-CoV-2

Two mutations occurred in SARS-CoV-2 early during the COVID-19 pandemic that have come to define circulating virus lineages1: first a change in the spike protein (D614G) that defines the B.1 lineage and second, a double substitution in the nucleocapsid protein (R203K, G204R) that defines the B.1.1 lineage, which has subsequently given rise to three Variants of Concern: Alpha, Gamma and Omicron. While the latter mutations appear unremarkable at the protein level, there are dramatic implications at the nucleotide level: the GGG[->]AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. We find that N.iORF3 also emerged independently within the Iota variant, and further show that additional TRS motifs have convergently evolved to express novel sgmRNAs; notably upstream of Spike within the nsp16 coding region of ORF1b, which is expressed during human infection. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. Greater attention to this aspect in the assessment of emerging strains of SARS-CoV-2 is warranted.

microbiology↗

bioRxiv2020

Generating single-sex litters: development of CRISPR-Cas9 genetic tools to produce all-male offspring

Animals are extremely useful genetic tools in science and global resources in agriculture. However, a single sex is often required in surplus, and current genetic methods for producing all-female or all-male litters are inefficient. Using the mouse as a model, we developed a synthetic, two-part bicomponent strategy for generating all-male litters. We achieved this using CRISPR-Cas9 genome editing technology to generate large stable knock-ins on the autosomes and X chromosome. The bicomponent system functions via the sex-specific co-inheritance of a Cas9 transgene and an sgRNA transgene targeting the essential Topoisomerase 1 gene. This technology proved to be highly efficient in generating on-target mutations, resulting in embryonic lethality of the target sex. Our study is the first to successfully generate all-male mammalian litters using a CRISPR-Cas9 bicomponent system and provides great strides towards generating single-sex litters for laboratory or agricultural research.

genetics↗