Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine

Islam, M.; Bechard, M. E.; Yang, Y.; Simmons, A. J.; Xu, Y.; Higginbotham, J. N.; Zhao, P.; Cao, Z.; Tasneem, N.; Glass, S. E.; Markham, N. O.; Revetta, F.; Ramirez-Solano, M. A.; Liu, Q.; Franklin, J. L.; Lau, K.; Coffey, R. J.

doi:10.1101/2025.06.10.658707

bioRxiv · 10.1101/2025.06.10.658707

Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine

Islam, M.·Bechard, M. E.·Yang, Y.·Simmons, A. J.·Xu, Y.·Higginbotham, J. N.·Zhao, P.·Cao, Z.·Tasneem, N.·Glass, S. E.·Markham, N. O.·Revetta, F.·Ramirez-Solano, M. A.·Liu, Q.·Franklin, J. L.·Lau, K.·Coffey, R. J.

View original source ↗Export metadata ↓

Abstract

The mammalian intestine regenerates rapidly after damage, yet the clonal dynamics and species-specific regulation of different populations remain poorly understood. Here we used synthetic or naturally occurring DNA alterations to reconstruct clonal histories of the mouse and human intestinal epithelium at single-cell resolution. In mice, we uncovered the clonal architecture of different cell types and their roles in regeneration, supporting a hierarchical regenerative response model. We identified a rare embryonic precursor population that persisted in the adult and was crucial for regeneration after irradiation. This population was marked by Tob2, which is required for nuclear transport of Ascl2. A parallel clonal analysis of 65 human colonic biopsies revealed secretory lineage bias and an age-associated decline in clonal diversity in the distal colon. Unlike highly proliferative murine Lgr5+ stem cells, human LGR5+ cells were found largely quiescent, revealing species-specific difference in clonal potency, and suggesting a distinct regulation of intestinal stemness.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Islam, M., Bechard, M. E., Yang, Y., Simmons, A. J., Xu, Y., Higginbotham, J. N., Zhao, P., Cao, Z., Tasneem, N., Glass, S. E., Markham, N. O., Revetta, F., Ramirez-Solano, M. A., Liu, Q., Franklin, J. L., Lau, K., Coffey, R. J.. 2025-06-12. Unbiased recording of clonal potency reveals species-specific regulation of mammalian intestine. https://doi.org/10.1101/2025.06.10.658707

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Reconstruction of the Prox gene family evolution in vertebrates reveals multiple lineage-specific gene losses

Prospero-related homeobox (Prox) genes encode a family of transcription factors that play essential roles in the development of several organs and systems, including the central nervous system, lymphatic endothelium, musculature, and liver. Despite their developmental importance, the evolutionary history of the vertebrate Prox gene family remains poorly understood. In this study we combined phylogenetic and synteny analysis to characterise the evolution of the Prox family in vertebrates. Our results reveal that two to three Prox subfamilies were already present in the last common ancestor of jawed vertebrates. We clarify the identity and evolutionary relationships of well-studied members of this family and identify multiple independent losses of Prox2 and Prox3 genes in specific vertebrate lineages. Furthermore, we uncover evidence for the existence of a fourth Prox gene in the ancestral vertebrate genome, which was subsequently lost. Overall, this study provides the first comprehensive analysis of the evolutionary history of the vertebrate Prox gene family and establishes a foundations for future studies on the functional roles of these genes.

genomics↗

bioRxiv2026

Gene flux shapes diversity and evolution of the ancient 17q21.31 inversion polymorphism

A hallmark of chromosomal inversions is that they suppress recombination between haplotypes, allowing inversion haplotypes to persist as single co-inherited units. To determine the extent to which inversions nevertheless permit genetic exchange, we investigated a common 979-kb inversion polymorphism at the human 17q21.31 locus. This locus exhibits deep divergence between the reference (H1) and inverted (H2) haplotypes, extensive segmental duplications (SDs) flanking the inversion, and association with neurodegenerative diseases, developmental disorders, and fertility-related phenotypes. Using single-cell sperm genome sequencing data, we directly measured recombination rates between H1 and H2 haplotypes and found near-complete suppression of single-crossover events between the haplotypes. The rare single crossovers that did occur were mediated by non-allelic homologous recombination between shared H1 and H2 SDs, generating novel duplication architectures. In contrast, two-switch events consistent with gene conversion or double crossovers, spanning 17-150 kb, occurred throughout the inversion at rates exceeding genome-wide estimates for events of comparable size. Consistent with recurring genetic exchange, we identified 99 distinct H1-H2 recombinant haplotypes segregating in All of Us genomes, including 26 with combinations of H1 and H2 SDs. These recombinant haplotypes facilitated dissection of the inversion's effects on fertility-related phenotypes; using a large parent-embryo dataset, we found that H2 additively increases female crossover rates across chromosomes and that KANSL1 duplications do not explain this effect. Finally, ancestral recombination graphs dated H1-H2 gene flux (the exchange of genetic material between alternative arrangements) to approximately 100-500 thousand years ago, revealing that H1 and H2 haplotypes have co-segregated for at least half a million years. Together, these results demonstrate that inversions can be permeable barriers to recombination, with ongoing gene flux influencing the diversity and evolution of inversion polymorphisms.

genomics↗

bioRxiv2026

Genomic correlates of metastatic competence and progression in human melanoma

Genomic events and their timing that grant a primary tumour the competence to disseminate remain poorly defined. We performed sequencing of 247 stage I/II primary cutaneous melanomas (CMs) and 60 matched metastases without intervening therapy from a prospectively followed registry cohort with a median followup of 92 months, integrating copy-number, mutational, protein and spatial-transcriptomic analyses. Relapse was not distinguished by oncogenic point mutations, which were largely shared between primaries and metastases, but by somatic copy-number alterations (SCNAs) and global chromosomal instability. We defined OncoCycle, a six-gene copy-number signature (amplification of CDK4, MCL1 and CD276; biallelic loss of CDKN2A, CDKN2B and TP53BP1) that predicted relapse independently of established clinicopathological features in melanoma, and a pan-cancer analysis. In matched pairs, metastatic progression was driven by continued copy-number evolution and reduction in intra-tumoural heterogeneity, rather than by acquired point mutations, and OncoCycle alterations from primary tumours were preserved in metastasis seeding clones. Clonal reconstruction revealed both monoclonal and polyclonal metastasis seeding, and spatial transcriptomics resolved copy-number-defined metastatic subclones occupying and programming distinct immune and stromal niches. Thus, metastatic competence was primed early by focal SCNAs on a background of chromosomal instability, elaborated by continued copy-number evolution during dissemination and spatio-temporal interactions with the tumour-microenvironment.

genomics↗