Biology subjects

Watson, R. A.

Publications and source records attributed to Watson, R. A..

14 recordsLinked to original sources

bioRxiv2026

Reconstructing donor genotypes from scRNA-seq for downstream eQTL and HLA-TCR analysis

Single-cell eQTL studies can reveal heterogeneous genetic effects on gene expression that vary with cell type, but their wider application has been constrained by the frequent absence of matched genotype data. Here, we present single-cell Transcriptome Allelic Prediction and Association Studies (scTAPAS), a bioinformatic framework for reconstructing donor genotypes directly from single-cell RNA-sequencing reads and downstream genetic analysis. Applying scTAPAS to 5' single-cell RNA-sequencing data from the COVID-19 Multi-omic Blood Atlas (COMBAT), we show that reference-based imputation of sparse RNA-derived genetic information generates genotype dosages sufficiently accurate for association testing. Despite testing only 18.0% of the variants available from conventional array-based genotyping and imputation, scTAPAS recovers 68.6% of cell type-eGene pairs identified using conventional array-based genotypes, with strong concordance in effect sizes. We further show that scTAPAS-derived variants can support imputation of classical HLA alleles and enable HLA-aware QTL analyses, including associations between HLA variation and TCR repertoire at single-cell resolution. Using matched single-cell TCR-sequencing data, we identify CD4+ T cell-specific associations between HLA class II alleles and T-cell receptor (TCR) Va; gene segment usage, highlighting the potential of analyses that complement TCR sequencing at single-cell resolution with HLA types. These results show that genetic information recovered from single-cell RNA sequencing data can support both regulatory and immunogenetic association analyses, expanding the discovery potential of single-cell cohorts for which conventional genotyping or HLA typing is unavailable.

bioinformatics↗

bioRxiv2026

Beneficial microbes may have favoured the evolution of adaptive immunity

Vertebrate adaptive immunity has long been considered uniquely advantageous for its capacity to recognise and remember a wide diversity of molecular targets, potentially conferring lasting defence from any threatening microbe. However, over the last two decades, results from comparative immunology have called into question the relative benefits of vertebrate adaptive immunity as a defence mechanism, raising the possibility of alternative evolutionary explanations. For instance, the hypothesis that managing the diverse and often beneficial host-microbiota associations characteristic of the vertebrate gut may have favoured the evolution of adaptive immunity. Here, we use individual-based simulations to investigate co-evolutionary interactions between hosts and their microbiota and the implication for the evolution of adaptive immunity. We focus on the capacity of adaptive immunity to produce and modify a diverse repertoire of immune receptors by using somatic variation and selective clonal reinforcement, in combination with a reinforcement bias from the innate immune system. Strikingly, we find that a high diversity of rapidly evolving parasites is insufficient to favour the evolution of adaptive immunity. Instead, our findings suggest that neutral and beneficial microbes can play a crucial role in weakening selection on innate immune defence against parasites, in favour of the exploitation of beneficial microbes. In turn, this facilitates the emergence of adaptive immunity as a mechanism reducing the risk associated with infrequent parasite infections while exploiting beneficial microbes. In addition, we show that adaptive immunity can subsequently alter selection affecting both innate immune defence and microbe evolution, such that its loss becomes increasingly unlikely with evolutionary time. Together, these results suggest that simultaneous interactions with diverse mutualists and parasites is a compelling selective explanation for the emergence and maintenance of adaptive immunity.

evolutionary biology↗

bioRxiv2025

Formation of chromosomal rearrangements in Saccharomyces cerevisiae diploids through regionally-biased non-allelic homologous recombination

In earlier studies, we optimized an assay system for the genome-wide detection of copy number variation (CNV) in diploid Saccharomyces cerevisiae cells, based on selection for formaldehyde plus copper (FA+Cu) resistance conferred by the amplification of a dosage-dependent reporter cassette, SFA1-CUP1. Our analyses identified a robust bias for terminal deletions of the right arm of Chr7 (Chr7R) associated with unbalanced translocations. This bias was observed at approximately constant strength across all three sites where the amplification reporter cassette was inserted, in CNV-carrying yeast clones derived both spontaneously and from mutagen-induced recombinogenic conditions. We conducted allelic mitotic recombination experiments to investigate the possibility of the presence of a fragile site on Chr7R, but the results disfavored this model, and instead indicated that the Chr7R bias applies only to non-allelic rearrangements. We validated the existence of a CNV formation bias at Chr7R through an orthologous NAHR competition approach that was independent of selection for FA+Cu resistance. Finally, we showed the in contrast to its high participation in NAHR as a recipient sequence, Chr7R becomes amplified as a translocation donor less frequently than other comparable regions of the genome. To begin unraveling the cause of this unusual behavior, we evaluated the effect of a set of candidate genes involved in chromatin mobility and sister chromatid cohesion on the rearrangement spectra involving Chr7R. We found that deletion mutations in some of these genes, particularly SAP30, attenuated the biased NAHR behavior. Taken together, our results suggested that although Chr7R is not inherently more prone to DNA breakage than other regions, once a DNA lesion is formed there, it has a higher propensity to undergo inappropriate repair leading to a chromosomal rearrangement.

genetics↗

bioRxiv2024

Defining the genetic determinants of CD8+ T cell receptor repertoire in the context of immune checkpoint blockade

CD8+ T cells play a central role in the cancer response to immune checkpoint blockade (ICB) treatment, with activity predicated upon antigen recognition by the associated T cell receptor (TCR) repertoire. The contribution of genetic variation to this in cancer treatment is under-explored. We have conducted a genome-wide and human leukocyte antigen (HLA)-focused analysis of CD8+ T cell TCR repertoire to identify genetic determinants of variable gene (V-gene) and CDR3 K-mer usage from samples taken prior to and after ICB treatment (n=250). We find 11 genome-wide significant cis associations and 10 trans associations, primarily to the HLA, with V-gene usage meeting permuted P-value thresholds. Notably, TCR clones containing V-genes associated with HLA were less likely to be persistent across treatment. In a single-cell experiment, we find cells with HLA-matched TCR clones have increased tumor reactivity expression profiles and patients with HLA-matched TCR clones have improved overall survival. Our work indicates a complex relationship between genotype and TCR repertoire in the context of treatment with ICB, which has novel implications for understanding determinants of treatment response and patient outcomes. One Sentence SummaryTCR repertoire is strongly associated with specific HLA alleles in cancer patients, but immune checkpoint blockade influences this association.

genetics↗

bioRxiv2024

Natural Induction: Spontaneous adaptive organisation without natural selection

Evolution by natural selection is believed to be the only possible source of spontaneous adaptive organisation in the natural world. This places strict limits on the kinds of systems that can exhibit adaptation spontaneously, i.e. without design. Physical systems can show some properties relevant to adaptation without natural selection or design. 1) The relaxation, or local energy minimisation, of a physical system constitutes a natural form of optimisation insomuch as it finds locally optimal solutions to the frustrated forces acting on it or between its components. 2) When internal structure gives way or accommodates to a pattern of forcing on a system this constitutes learning insomuch as it can store, recall and generalise past configurations. Both these effects are quite natural and general, but in themselves insufficient to constitute non-trivial adaptation. However, here we show that the recurrent interaction of physical optimisation and physical learning together results in significant spontaneous adaptive organisation. We call this adaptation by natural induction. The effect occurs in dynamical systems described by a network of viscoelastic connections subject to occasional disturbances. When the internal structure of such a system accommodates slowly across many disturbances and relaxations, it spontaneously learns to preferentially visit solutions of increasingly greater quality (exceptionally low energy). We show that adaptation by natural induction thus produces network organisations that improve problem-solving competency with experience. We note that the conditions for adaptation by natural induction, and its adaptive competency, are different from those of natural selection. We therefore suggest that natural selection is not the only possible source of spontaneous adaptive organisation in the natural world.

evolutionary biology↗

bioRxiv2024

An ability to respond begins with inner alignment: How phase synchronisation effects transitions to higher levels of agency

How do multiple active components at one level of organisation create agential wholes at higher levels of organisation? For example, in organismic development, how does the multi-scale autonomy of the organism arise from the interactions of the molecules, cells and tissues that an organism contains? And, in the major evolutionary transitions, how does a multicellular organism, for example, arise as an evolutionary unit from the selective interests of its unicellular ancestors? We utilise computational models as a way to think about this general question. We take a deliberately minimalistic notion of an agent: a competency to take one of two possible actions to minimise stress. Helping ourselves to this behaviour at the microscale, we focus on conditions where this same type of agency appears spontaneously at a higher level of organisation. We find that a simple process of positive feedback on the timing of individual responses, loosely analogous to the natural phase synchronisation of weakly coupled oscillators, causes such a transition in behaviour. The emergent collectives that arise become, quite suddenly, able to respond to their external stresses in the same (minimal) sense as the original microscale units. This effects a dramatic rescaling of the system behaviour, and a quantifiable increase in problem-solving competency, serving as a model of how higher-level agency emerges from a pool of lower-level agents or active matter. We discuss how this dynamical waking-up of higher-level collectives, through the alignment of their internal dynamics, might relate to reproductive/cell-cycle synchronisation in evolutionary transitions and development.

evolutionary biology↗

bioRxiv2023

Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability

Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Pol{delta}-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.

genetics↗

bioRxiv2023

Deep sequencing of the T cell Receptor reveals common and reproducible CD8+ signatures of response to checkpoint immunotherapy

Immune checkpoint blockade (ICB) has markedly improved outcomes across a range of tumours, including metastatic melanoma (MM). However, peripheral biomarkers of response remain lacking and underlying mechanisms of action incompletely described. A number of studies have demonstrated the value of T cell receptor (TCR) repertoire analysis in determining associations with response, however identifying key groups of T cells based on their TCR usage has remained elusive. Here we performed deep sequencing of the TCR of CD8+ T cells isolated from peripheral blood of patients receiving ICB for MM (n=91) at multiple time points, along with healthy control samples (n=42) and resected tumour specimens (from n=7 patients). Using the GLIPH2 algorithm to cluster TCR based on putative shared antigen specificity, we describe groups of TCR which expand post-ICB in responding patients which we term Emergent Responder (ER) clones. We find that these ER clones are typically large and of a memory phenotype, with increased expression of genes encoding cytotoxic proteins. Analysis of tumours resected in advance of ICB demonstrates ER clones are enriched and expanded within the tumour compared to the periphery at pre-treatment. Significantly, we note the proportion of the peripheral repertoire occupied by ER clones strongly correlates with long-term clinical response. Clinical outcome further associated with HLA type and, crucially, can be validated across replication and independent datasets. This work provides the first-in-kind description of TCR-defined CD8+ T cells that mediate the response to ICB in MM, demonstrating the prognostic utility of the peripheral immune repertoire with potential widespread therapeutic and prognostic applications.

immunology↗

bioRxiv2020

Immune Checkpoint Blockade induces peripheral cytotoxicity and persistence of large effector CD8+ T cell clones

Immune checkpoint blockers (ICB) exert their anti-cancer effects via CD8+ T cells, although how responses vary over sub-populations and across clones is incompletely understood. We performed single-cell RNA-sequencing of CD8+ T cells and their receptors pre- and post-ICB across eight patients, integrating results with bulk-sequencing data (n=209). We identify seven subsets with divergent responses to ICB, finding the effector cluster demonstrates the most pronounced changes. Likewise, transcriptomic response to ICB relates to clone size, with large clones demonstrating increased numbers of regulated genes of higher immunological pertinence. Cytotoxic effector clones were more likely to persist long-term following ICB and overlapped with public tumour-infiltrating lymphocyte clonotypes. Notably, pre-treatment CD8+ cytotoxicity associated with progression-free survival, highlighting the importance of the baseline CD8+ immune landscape in long-term response. This work further advances understanding of the molecular determinants of ICB response and assists in the search for peripheral prognostic biomarkers. ONE SENTENCE SUMMARYUsing single-cell and bulk RNA sequencing we explore checkpoint immunotherapy activity on peripheral CD8+ T cells in metastatic melanoma; demonstrating that cell subset and clone size determine gene expression responses to treatment, and that pre-treatment cytotoxicity and clonality of peripheral CD8+ T cells is clinically prognostic.

immunology↗

bioRxiv2020

Identifying causes of social evolution: The Price approach, contextual analysis, and multilevel selection

Kin selection theory and multilevel selection theory are different approaches to explaining the evolution of social traits. The latter claims that it is useful to regard selection as a process that can occur on multiple levels of organisation such as the level of individuals and the level of groups. This is reflected in a decomposition of fitness into an individual component and a group component. However, the two major statistical tools to determine the coefficients of such a decomposition, the multilevel Price equation and contextual analysis, are inconsistent and may disagree on whether group selection is present. Here we show that the reason for the discrepancies is that underlying the multilevel Price equation and contextual analysis are two nonequivalent causal models for the generation of individual fitness effects (thus leaving different remainders explained by group effects). While the multilevel Price equation assumes that the individual effect of a trait determines an individuals relative success within a group, contextual analysis posits that the individual effect is context-independent. Since these different assumptions reflect claims about the causal structure of the system, the correct approach cannot be determined on general theoretical or statistical grounds but must be identified by experimental intervention. We outline interventions that reveal the underlying causal structure and thus facilitate choosing the appropriate approach. We note that the reductionist viewpoint of kin selection theory with its focus on the individual is immune to such inconsistency because it does not address causal structure with respect to levels of organisation. In contrast, our analysis of the two approaches to measuring group selection demonstrates that multilevel selection theory adds meaningful (falsifiable) causal structure to explain the sources of individual fitness and thereby constitutes a proper refinement of kin selection theory.

evolutionary biology↗

bioRxiv2020

Developmental models reveal the role of phenotypic plasticity in explaining genetic evolvability

Biological evolution exhibits an extraordinary capability to adapt organisms to their environments. The explanation for this often takes for granted that random genetic variation produces at least some beneficial phenotypic variation for natural selection to act on. Such genetic evolvability could itself be a product of evolution, but it is widely acknowledged that the immediate selective gains of evolvability are small on short timescales. So how do biological systems come to exhibit such extraordinary capacity to evolve? One suggestion is that adaptive phenotypic plasticity makes genetic evolution find adaptations faster. However, the need to explain the origin of adaptive plasticity puts genetic evolution back in the driving seat, and genetic evolvability remains unexplained. To better understand the interaction between plasticity and genetic evolvability, we simulate the evolution of phenotypes produced by gene-regulation network-based models of development. First, we show that the phenotypic variation resulting from genetic and environmental change are highly concordant. This is because phenotypic variation, regardless of its cause, occurs within the relatively specific space of possibilities allowed by development. Second, we show that selection for genetic evolvability results in the evolution of adaptive plasticity and vice versa. This linkage is essentially symmetric but, unlike genetic evolvability, the selective gains of plasticity are often substantial on short, including within-lifetime, timescales. Accordingly, we show that selection for phenotypic plasticity is, in general, the most efficient and results in the rapid evolution of high genetic evolvability. Thus, without overlooking the fact that adaptive plasticity is itself a product of genetic evolution, this shows how plasticity can influence adaptive evolution and helps explain the genetic evolvability observed in biological systems.

evolutionary biology↗

bioRxiv2020

Characterization of systemic genomic instability in budding yeast

Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) in Saccharomyces cerevisiae, providing support for an additional non-independent and faster mode of mutation accumulation. We initially characterized a yeast clone isolated for carrying an LOH event at a specific chromosome site, and surprisingly, found that it also carried multiple unselected rearrangements elsewhere in its genome. Whole genome analysis of over 100 additional clones selected for carrying primary LOH tracts revealed that they too contained unselected structural alterations more often than control clones obtained without any selection. We also measured the rates of coincident LOH at two different chromosomes and found that double LOH formed at rates 14-150 fold higher than expected if the two underlying single LOH events occurred independently of each other. These results were consistent across different strain backgrounds, and in mutants incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population can experience discrete episodes of systemic genomic instability, when the entire genome becomes vulnerable and multiple chromosomal alterations can form over a narrow time window. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in the cancer and genomic disorder contexts. The experimental model we describe provides a system to further dissect the fundamental biological processes responsible for punctuated bursts of structural genomic variation. SIGNIFICANCE STATEMENTMutations are generally thought to accumulate independently and gradually over many generations. Here, we combined complementary experimental approaches in budding yeast to track the appearance of chromosomal changes resulting in loss-of-heterozygosity (LOH). In contrast to the prevailing model, our results provide evidence for the existence of a path for non-independent accumulation of multiple chromosomal alteration events over few generations. These results are analogous to recent reports of bursts of genomic instability in human cells. The experimental model we describe provides a system to further dissect the fundamental biological processes underlying such punctuated bursts of mutation accumulation.

genetics↗

bioRxiv2020

Punctuated Aneuploidization of the Budding Yeast Genome

Remarkably complex patterns of aneuploidy have been observed in the genomes of many eukaryotic cell types, ranging from brewing yeasts to tumor cells (1, 2). Such aberrant karyotypes are generally thought to take shape progressively over many generations, but evidence also suggests that genomes may undergo faster modes of evolution (2, 3). Here, we used diploid Saccharomyces cerevisiae cells to investigate the dynamics with which aneuploidies arise. We found that cells selected for the loss of a single chromosome often acquired additional unselected aneuploidies concomitantly. The degrees to which these genomes were altered fell along a spectrum, ranging from simple events affecting just a single chromosome, to systemic events involving many. The striking complexity of karyotypes arising from systemic events, combined with the high frequency at which we detected them, demonstrates that cells can rapidly achieve highly altered genomic configurations during temporally restricted episodes of genomic instability.

genomics↗

bioRxiv2018

How adaptive plasticity evolves when selected against

Adaptive plasticity allows organisms to cope with environmental change, thereby increasing the populations long-term fitness. However, individual selection can only compare the fitness of individuals within each generation: if the environment changes more slowly than the generation time (i.e., a coarse-grained environment) a population will not experience selection for plasticity even if it is adaptive in the long-term. How does adaptive plasticity then evolve? One explanation is that, if competing alleles conferring different degrees of plasticity persist across multiple environments, natural selection between lineages carrying those alleles could select for adaptive plasticity (lineage selection).\n\nWe show that adaptive plasticity can evolve even in the absence of such lineage selection. Instead, we propose that adaptive plasticity in coarse-grained environments evolves as a by-product of inefficient short-term natural selection. In our simulations, populations that can efficiently respond to selective pressures follow short-term, local, optima and have lower long-term fitness. Conversely, populations that accumulate limited genetic change within each environment evolve long-term adaptive plasticity even when plasticity incurs short-term costs. These results remain qualitatively similar regardless of whether we decrease the efficiency of natural selection by increasing the rate of environmental change or decreasing mutation rate, demonstrating that both factors act via the same mechanism. We demonstrate how this mechanism can be understood through the concept of learning rate.\n\nOur work shows how plastic responses that are costly in the short term, yet adaptive in the long term, can evolve as a by-product of inefficient short-term selection, without selection for plasticity at either the individual or lineage level.

evolutionary biology↗