Speaker
Description
Human intestinal epithelium is organised into test-tube-like structures called “crypts” or “glands”. These crypts are maintained by a small pool of stem cells that undergo a process of selectively-neutral replacement, leading each crypt to inevitably drift towards monoclonality \cite{lopez-garcia2010}. We previously discovered fluctuating CpGs (fCpGs), endogenous CpG sites that undergo stochastic changes in methylation state and therefore record lineage \cite{gabbutt2022}. We used these fCpGs to infer the intra-crypt stem cell dynamics of individual human crypts.
Here, we built upon our previous work adapting phylogenetics to somatic evolution \cite{martinez2018} to develop PHYFUM: a Bayesian phylogenetic approach to jointly infer the intra-crypt replacement dynamics and the inter-crypt fission lineage relationships using fCpGs. We validated PHYFUM using simulations, confirming that it improves recovery of the correct topology and branch lengths than our previously published discretised binary approach \cite{gabbutt2025}. In patient data, we consistently observed that the last universal common ancestor (LUCA) in intestinal samples occurred in early life, in contrast to endometrial samples where the LUCA occurred notably later. We implemented different models of crypt fission, and found strong evidence against the hypothesis that crypts fission via budding of a single stem cell.
Bibliography
@article{lopez-garcia2010,
title = {Intestinal stem cell replacement follows a pattern of neutral drift},
volume = {330},
issn = {00368075},
doi = {10.1126/science.1196236},
abstract = {With the capacity for rapid self-renewal and regeneration, the intestinal epithelium is stereotypical of stem cell-supported tissues. Yet the pattern of stem cell turnover remains in question. Applying analytical methods from population dynamics and statistical physics to an inducible genetic labeling system, we showed that clone size distributions conform to a distinctive scaling behavior at short times. This result demonstrates that intestinal stem cells form an equipotent population in which the loss of a stem cell is compensated by the multiplication of a neighbor, leading to neutral drift dynamics in which clones expand and contract at random until they either take over the crypt or they are lost. Combined with long-term clonal fate data, we show that the rate of stemcell replacement is comparable to the cell division rate, implying that neutral drift and symmetrical cell divisions are central to stem cell homeostasis.},
number = {6005},
urldate = {2020-02-26},
journal = {Science},
publisher = {American Association for the Advancement of Science},
author = {Lopez-Garcia, Carlos and Klein, Allon M. and Simons, Benjamin D. and Winton, Douglas J.},
month = nov,
year = {2010},
pages = {822--825},
file = {PDF:/Users/cgabbutt/Zotero/storage/ZGDTEPKH/full-text.pdf:application/pdf},
}
@article{gabbutt2022,
title = {Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues},
issn = {1546-1696},
url = {https://www.nature.com/articles/s41587-021-01109-w},
doi = {10.1038/s41587-021-01109-w},
abstract = {Molecular clocks that record cell ancestry mutate too slowly to measure the short-timescale dynamics of cell renewal in adult tissues. Here, we show that fluctuating DNA methylation marks can be used as clocks in cells where ongoing methylation and demethylation cause repeated ‘flip–flops’ between methylated and unmethylated states. We identify endogenous fluctuating CpG (fCpG) sites using standard methylation arrays and develop a mathematical model to quantitatively measure human adult stem cell dynamics from these data. Small intestinal crypts were inferred to contain slightly more stem cells than the colon, with slower stem cell replacement in the small intestine. Germline APC mutation increased the number of replacements per crypt. In blood, we measured rapid expansion of acute leukemia and slower growth of chronic disease. Thus, the patterns of human somatic cell birth and death are measurable with fluctuating methylation clocks (FMCs). Lineage tracing of human stem cells is achieved by measuring fluctuating DNA methylation.},
urldate = {2022-01-04},
journal = {Nature Biotechnology 2022},
publisher = {Nature Publishing Group},
author = {Gabbutt, Calum and Schenck, Ryan O. and Weisenberger, Daniel J. and Kimberley, Christopher and Berner, Alison and Househam, Jacob and Lakatos, Eszter and Robertson-Tessi, Mark and Martin, Isabel and Patel, Roshani and Clark, Susan K. and Latchford, Andrew and Barnes, Chris P. and Leedham, Simon J. and Anderson, Alexander R. A. and Graham, Trevor A. and Shibata, Darryl},
month = jan,
year = {2022},
keywords = {Intestinal stem cells, Bioinformatics, Computational models},
pages = {1--11},
file = {full-text.pdf:/Users/cgabbutt/Zotero/storage/28AG9BJ9/full-text.pdf:application/pdf;s41587-021-01109-w.pdf:/Users/cgabbutt/Zotero/storage/A7H5TP5M/s41587-021-01109-w.pdf:application/pdf},
}
@article{martinez2018,
title = {Evolution of {Barrett}’s esophagus through space and time at single-crypt and whole-biopsy levels},
volume = {9},
issn = {2041-1723},
url = {https://www.nature.com/articles/s41467-017-02621-x},
doi = {10.1038/s41467-017-02621-x},
abstract = {The low risk of progression of Barrett’s esophagus (BE) to esophageal adenocarcinoma can lead to over-diagnosis and over-treatment of BE patients. This may be addressed through a better understanding of the dynamics surrounding BE malignant progression. Although genetic diversity has been characterized as a marker of malignant development, it is still unclear how BE arises and develops. Here we uncover the evolutionary dynamics of BE at crypt and biopsy levels in eight individuals, including four patients that experienced malignant progression. We assay eight individual crypts and the remaining epithelium by SNP array for each of 6–11 biopsies over 2 time points per patient (358 samples in total). Our results indicate that most Barrett’s segments are clonal, with similar number and inferred rates of alterations observed for crypts and biopsies. Divergence correlates with geographical location, being higher near the gastro-esophageal junction. Relaxed clock analyses show that genomic instability precedes and is enhanced by genome doubling. These results shed light on the clinically relevant evolutionary dynamics of BE. Clonal dynamics of Barrett’s esophagus (BE) leading to cancer are poorly understood. Here, they report BE segments are clonal, have frequent mutations at the gastro-esophageal junction, genomic instability precedes genome doubling/clonal expansion, and a correlation between inter-\ and intra-biopsy genetic diversity.},
number = {1},
urldate = {2023-07-18},
journal = {Nature Communications 2018 9:1},
publisher = {Nature Publishing Group},
author = {Martinez, Pierre and Mallo, Diego and Paulson, Thomas G. and Li, Xiaohong and Sanchez, Carissa A. and Reid, Brian J. and Graham, Trevor A. and Kuhner, Mary K. and Maley, Carlo C.},
month = feb,
year = {2018},
keywords = {Cancer genomics, Tumour heterogeneity, Oesophageal cancer, Phylogenetics},
pages = {1--12},
file = {PDF:/Users/cgabbutt/Zotero/storage/FE5Y2UCQ/full-text.pdf:application/pdf},
}
@article{gabbutt2025,
title = {Fluctuating {DNA} methylation tracks cancer evolution at clinical scale},
volume = {645},
issn = {0028-0836, 1476-4687},
url = {https://www.nature.com/articles/s41586-025-09374-4},
doi = {10.1038/s41586-025-09374-4},
language = {en},
number = {8081},
urldate = {2025-10-24},
journal = {Nature},
author = {Gabbutt, Calum and Duran-Ferrer, Martí and Grant, Heather E. and Mallo, Diego and Nadeu, Ferran and Househam, Jacob and Villamor, Neus and Müller, Madlen and Heath, Simon and Raineri, Emanuele and Krali, Olga and Nordlund, Jessica and Zenz, Thorsten and Gut, Ivo G. and Campo, Elias and Lopez-Guillermo, Armando and Fitzgibbon, Jude and Barnes, Chris P. and Shibata, Darryl and Martin-Subero, José I. and Graham, Trevor A.},
month = sep,
year = {2025},
pages = {764--773},
}
