Biology subjects

Blundell, J. R.

Publications and source records attributed to Blundell, J. R..

11 recordsLinked to original sources

bioRxiv2026

In vivo lineage tracing across human tissues using methylation barcodes in the protocadherin gene cluster

Resolving the lineage history of human cells is fundamental to understanding ageing and cancer but remains hampered by a lack of native, high-resolution markers. Here, we identify the protocadherin (PCDH) gene cluster as a naturally occurring, highly diverse methylation barcode. While PCDH methylation creates neuronal diversity in the brain, we show that stochastic methylation patterns in this region are maintained as heritable, evolvable lineage markers across multiple non-neuronal tissues, including blood, kidney, prostate, and bladder. By tracking these barcodes in serial samples over a decade, we reveal clonal dynamics with high fidelity, quantitatively recapitulating genetic clone sizes. Crucially, PCDH barcodes identify "cryptic" clonal expansions invisible to standard driver-mutation sequencing and resolve subclonal architectures via continuous epimutation. This native barcoding system provides a scalable, driver-agnostic framework for reconstructing somatic evolution in humans.

genomics↗

bioRxiv2025

Methylation dynamics in the decades preceding acute myeloid leukaemia

DNA methylation is emerging as a highly sensitive and specific marker of cancer initiation and progression. How these cancer-specific methylation changes are established in the decades before cancer, however, remains largely unknown. Here, we use a unique collection of longitudinal blood samples collected annually up to 15 years prior to a diagnosis of acute myeloid leukaemia to sensitively track the dynamics of DNA methylation changes at high temporal resolution. We identify thousands of differentially methylated regions (DMRs) that exhibit altered patterns of methylation up to 10 years before acute myeloid leukaemia (AML) diagnosis. Most of these DMRs are strongly associated with expanding clones carrying somatic driver mutations. We identify a subset of epigenetic driver DMRs characterised by recurrent CpG alterations that are highly shared across pre-AML cases. These are likely to reflect early epigenetic reprogramming associated with AML development. We also reveal large numbers of stochastic passenger CpGs whose differential methylation results from hitch-hiking with clonal expansions driven by somatically acquired genetic events. These passenger CpGs can be exploited for lineage tracing to discover clonal expansions driven by missing driver mutations. Our findings show widespread changes in methylation patterns during the early stages of cancer development which could be utilised for risk prediction and therapeutic intervention.

genomics↗

bioRxiv2024

No evidence of immunosurveillance in mutation-hotspot driven clonal haematopoiesis

The theory of immunosurveillance posits that T-cells can selectively eliminate clones harbouring non-self antigens generated by somatic mutations. There is considerable evidence supporting the role of immune surveillance in cancer. Whether immunosurveillance imposes a negative selective pressure on pre-cancerous clones, however, is not well established. Here, we studied the association between MHC-variant binding and risk of clonal haematopoiesis (CH), a pre-cancer state in the blood driven by expansions of mutant haematopoietic stem cells (HSCs). We predicted MHC binding affinity towards 40 known CH hotspot variants in 380,000 UK Biobank participants, and examined the relationship between predicted binding to each variant and risk of its expansion in the blood. Despite being well powered to detect subtle differences in selective pressure, we did not find associations between predicted MHC binding and CH prevalence for any of the hotspot variants. In individuals in whom we identified CH, there was no relationship between predicted binding affinity to the variant and size of the clone. Overall, we do not find evidence for the MHC genotype to be a factor that affects which somatic variants expand in CH, suggesting a limited role for immunosurveillance in shaping the genetic diversity of the blood.

genomics↗

bioRxiv2024

Evolutionary dynamics in the decades preceding acute myeloid leukaemia

Somatic evolution in ageing tissues underlies many cancers. However, our quantitive understanding of the rules governing this pre-cancerous evolution remains incomplete. Here we exploit a unique collection of serial blood samples collected annually up to 15 years prior to diagnosis of acute myeloid leukaemia (AML) to provide a quantitative description of pre-cancerous evolutionary dynamics. Using deep duplex sequencing and evolutionary theory, we quantify the acquisition ages and fitness effects of the key driver events in AML development. The first driver mutations are typically acquired in the first few decades of life when the blood remains highly polyclonal. These early slow-growing clones subsequently acquire multiple further driver mutations which confer selective advantages up to 100-fold larger than the early drivers. These faster-growing clones harbouring multiple driver mutations can cause complete somatic sweeps of the blood decades before diagnosis, a feature strongly associated with future AML. Once established in the blood, the dynamics of driver mutations are highly predictable. Trajectories are shaped by strong clonal competition between lineages with limited evidence of other extrinsic factors playing a major role. Our data show that the clonal dynamics of blood are consistent with a set of remarkably simple evolutionary rules which strike a balance between chance and determinism.

cancer biology↗

bioRxiv2023

Modelling the age-related deceleration of clonal haematopoiesis in UK Biobank

Somatic mutations acquired in haematopoietic stem cells can drive clonal expansions, a phenomenon known as clonal haematopoiesis (CH). CH has been associated with higher risk of haematological cancer, cardiovascular disease and lower life expectancy and is strongly age-dependent, becoming almost ubiquitous in older adults. However, the dynamics of CH are not yet fully understood, and an accurate quantitative model of clonal expansion in healthy people could inform strategies for risk stratification and early detection of haematological malignancy. Here, we analyse the age-dependence of the variant allele frequency (VAF) distributions of CH driver variants from blood-derived whole exomes in 420,000 cancer-free UK Biobank participants. Across a number of CH driver genes (including DNMT3A, TP53 and TET2) we find evidence of a substantial deceleration of clonal expansion with age, while other drivers (including SRSF2, SF3B1, and IDH2) display more consistent growth throughout life. We find that this deceleration occurs consistently across the population and happens mostly before the age of 40. Using evolutionary models of clonal dynamics we assess the validity of alternative mechanisms of clonal deceleration. We find that variation in fitness among individuals (e.g. due to genetic susceptibility) is not sufficient to explain the deceleration. We also consider a clonal competition model in which clonal expansion later in life is inhibited by interference with a background of other expanding clones, and find this model inconsistent with the data given established estimates of the prevalence of hidden selection in blood. Our results imply that the intrinsic selection landscape in blood is substantially different in early life compared with middle age.

genetics↗

bioRxiv2023

Preleukemic clonal evolution revealed using single-cell DNA sequencing and computational modelling

The representation of driver mutations in preleukemic haematopoietic stem cells (pHSCs) provides a window into the somatic evolution that precedes Acute Myeloid Leukemia (AML). Here, we isolate pHSCs from the bone marrow of 16 patients diagnosed with AML and perform single-cell DNA sequencing on thousands of cells to reconstruct phylogenetic trees of the major driver clones in each patient. We develop a computational framework that can infer levels of positive selection operating during preleukemic evolution from the statistical properties of these phylogenetic trees. Combining these data with 67 previously published phylogenetic trees, we find that the highly variable structures of preleukemic trees emerge naturally from a simple model of somatic evolution in which there is pervasive positive selection acting throughout the disease trajectory. We infer that selective advantages of preleukemic clones are typically in the range of 9%-24% per year, but vary considerably between individuals. At these level of positive selection, we show that the identification of early multiple-mutant clones identifies individuals at risk of future AML.

cancer biology↗

bioRxiv2022

Dynamics of TCRβ repertoires from serial sampling of healthy individuals

T-cell receptor (TCR) repertoires provide a historical record of antigen exposure. However, the dynamics of TCR repertoires in healthy individuals remain largely uncharacterised. How much of the repertoire is under immune selection in healthy individuals? Do groups of sequences under immune selection share similar dynamics due to convergent specificity? What is the relationship between dynamic similarity and sequence similarity of TCRs? Here we develop a statistical framework for identifying clonotypes under immune selection in time series repertoire data. Applying this framework to serially sampled repertoires collected over the course of a year from 3 healthy volunteers, we are able to detect hundreds of TCRs undergoing strong immune selection whereby clonotype frequencies can change by orders of magnitude over timescales as short as a month. Clonotypes under immune selection belong to a handful of distinct dynamic clusters each of which show highly coordinated temporal behaviour suggesting a common immunogenic stimulus. Whilst a subset of clonotypes within dynamic clusters show shared amino acid motif usage, most do not, suggesting the same immunogenic stimulus elicits a diverse TCR response. Conversely, shared amino acid motif usage alone identifies far fewer clonotypes under immune selection and these clonotypes do not routinely exhibit correlated temporal behaviour. These results highlight the potential of using information contained in the dynamics of TCR repertoires for identifying clonotypes responding to the same immunogenic stimulus in a sequence agnostic way.

immunology↗

bioRxiv2022

Mutation rates and fitness consequences of mosaic chromosomal alterations in blood

Mosaic chromosomal alterations (mCAs) are commonly detected in many cancers and have been found to arise decades before diagnosis. A quantitative understanding of the rate at which these events occur and their functional consequences could improve cancer risk prediction and yet they remain poorly characterised. Here we use clone size estimates of mCAs from the blood of 500,000 participants in the UK Biobank to estimate the mutation rates and fitness consequences of acquired gain, loss and copy-neutral loss of heterozygosity (CN-LOH) events at the chromosomal arm level. Most mCAs have moderate to high fitness effects, but occur at a low rate, being over 10-fold less common than equivalently fit SNVs. While the majority of mCAs increase in prevalence with age in a way that is consistent with a constant growth rate, we find specific examples of mCAs whose behaviour deviates from this suggesting fitness effects for these mCAs may depend on inherited variants or be influenced by extrinsic factors. We find an association between mCA fitness effect and future blood cancer risk, highlighting the important role mCAs may play in risk stratification.

genomics↗

bioRxiv2020

Synonymous mutations reveal genome-wide driver mutation rates in healthy tissues

Genetic alterations that drive clonal expansions in ostensibly healthy tissues have implications for cancer risk. However, the total rate at which clonal expansions occur in healthy tissues remains unknown. Synonymous passenger mutations that hitchhike to high variant allele frequency due to a linked driver mutation can be used to estimate the total rate of positive selection across the genome. Because these synonymous hitchhikers are influenced by all mutations under selection, regardless of type or location, they can be used to estimate how many driver mutations are missed by narrow gene-focused sequencing panels. Here we analyse the variant allele frequency spectrum of synonymous passenger mutations to estimate the total rate at which mutations driving clonal expansions occur in healthy tissues. By applying our framework to data from physiologically healthy blood, we find that a large fraction of mutations driving clonal expansions occur outside of canonical cancer driver genes. In contrast, analysis of data from healthy oesophagus reveals little evidence for many driver mutations outside of those in NOTCH1 and TP53. Our framework, which generalizes to other tissues, sheds light on the fraction of drivers mutations that remain undiscovered and has implications for cancer risk prediction.

evolutionary biology↗

bioRxiv2019

The Evolutionary Dynamics and Fitness Landscape of Clonal Haematopoiesis

Somatic mutations acquired in healthy tissues as we age are major determinants of cancer risk. Whether variants confer a fitness advantage or rise to detectable frequencies by chance, however, remains largely unknown. Here, by combining blood sequencing data from [~]50,000 individuals, we reveal how mutation, genetic drift and fitness differences combine to shape the genetic diversity of healthy blood ( clonal haematopoiesis). By analysing the spectrum of variant allele frequencies we quantify fitness advantages for key pathogenic variants and genes and provide bounds on the number of haematopoietic stem cells. Positive selection, not drift, is the major force shaping clonal haematopoiesis. The remarkably wide variation in variant allele frequencies observed across individuals is driven by chance differences in the timing of mutation acquisition combined with differences in the cell-intrinsic fitness effect of variants. Contrary to the widely held view that clonal haematopoiesis is driven by ageing-related alterations in the stem cell niche, the data are consistent with the age dependence being driven simply by continuing risk of mutations and subsequent clonal expansions that lead to increased detectability at older ages.

genomics↗

bioRxiv2017

The dynamics of adaptive genetic diversity during the early stages of clonal evolution

The dynamics of genetic diversity in large clonally-evolving cell populations are poorly understood, despite having implications for the treatment of cancer and microbial infections. Here, we combine barcode lineage tracking, sequencing of adaptive clones, and mathematical modelling of mutational dynamics to understand diversity changes during experimental evolution. We find that, despite differences in beneficial mutational mechanisms and fitness effects between two environments, early adaptive genetic diversity increases predictably, driven by the expansion of many single-mutant lineages. However, a crash in diversity follows, caused by highly-fit double-mutants fed from exponentially growing single-mutants, a process closely related to the classic Luria-Delbruck experiment. The diversity crash is likely to be a general feature of clonal evolution, however its timing and magnitude is stochastic and depends on the population size, the distribution of beneficial fitness effects, and patterns of epistasis.

evolutionary biology↗