Biology subjects

Loubet-Senear, K.

Publications and source records attributed to Loubet-Senear, K..

5 recordsLinked to original sources

bioRxiv2024

Regeneration recapitulates many embryonic processes, including reuse of developmental regulatory regions

The wide distribution of regenerative capacity across the animal tree of life raises the question of how regeneration has evolved in distantly-related animals. Given that whole-body regeneration shares the same end-point - formation of a functional body plan - as embryonic development, it has been proposed that regeneration likely recapitulates developmental processes to some extent. Therefore, understanding how developmental processes are reactivated during regeneration is important for uncovering the evolutionary history of regeneration. Comparative transcriptomic studies in some species have revealed shared gene expression between development and regeneration, but it is not known whether these shared expression profiles correspond to shared functions, and which mechanisms activate expression of developmental genes during regeneration. We sought to address these questions using the acoel Hofstenia miamia, which is amenable to studies of both embryonic development and whole-body regeneration. By examining functionally validated regeneration processes during development at single-cell resolution, we found that whereas patterning and cellular differentiation are largely similar, wound response programs have distinct dynamics between development and regeneration. Chromatin accessibility analyses revealed that regardless of playing concordant or divergent roles during regeneration and development, genes expressed in both processes are frequently controlled by the same regulatory regions, potentially via utilization of distinct transcription factor binding sites. This study extends the known correspondence of development and regeneration from broad transcriptomic similarity to include patterning and differentiation processes. Further, our work provides a catalog of regulatory regions and binding sites that potentially regulate developmental genes during regeneration, fueling comparative studies of regeneration.

developmental biology↗

bioRxiv2023

Chromatin profiling data indicate regulatory mechanisms for differentiation during development in the acoel Hofstenia miamia

Chromatin profiling data can corroborate and generate hypotheses for regulatory events that underlie the control of gene expression in any biological process. Here, we applied the Assay for Transposase Accessible Chromatin (ATAC) sequencing to build a catalog of putative regulatory DNA during the process of embryonic development in an acoel. Acoels represent an enigmatic phylum-level lineage of animals, the Xenacoelomorpha, which is placed either as a sister-group to all other animals with bilateral symmetry or as an early-diverging ambulacrarian, two alternative phylogenetic placements that both position acoels equally well to inform the evolution of developmental mechanisms. We focused on the acoel Hofstenia miamia, a.k.a. the three-banded panther worm, which has emerged as a new laboratory research organism for whole-body regeneration that also enables the study of development from zygote to hatching. We profiled chromatin landscapes over a time course encompassing many major morphological events, including gastrulation, axial patterning, and differentiation of tissues such as epidermis and muscle. Broad patterns of chromatin accessibility and predicted binding of various transcription factor (TF) motifs identified major biological processes and their putative regulators, and we noted that differential accessibility tended to precede major developmental transitions in embryogenesis. Focused analysis of TF binding combined with single-cell RNA-seq data provided regulatory linkages for genes in a previously hypothesized differentiation trajectory for epidermis and generated new hypotheses for gene regulatory networks associated with the formation of muscle. This work provides a platform for the identification of developmental mechanisms in Hofstenia and enables comparisons of embryogenesis in acoels to other animals as well as comparisons of embryogenesis to regeneration.

developmental biology↗

bioRxiv2020

A regulatory program for initiation of Wnt signaling during posterior regeneration

Whole-body regeneration requires the re-establishment of body axes for appropriate patterning of new and old tissue. Wnt signaling has been utilized to correctly regenerate tissues along the primary axis in many animals. However, the causal molecular mechanisms that first launch Wnt signaling during regeneration are poorly characterized. We used the acoel worm Hofstenia miamia to identify processes that initiate Wnt signaling. Transcriptome profiling, in situ hybridization, and functional studies revealed a Wnt ligand, wnt-3, as an early wound-induced gene specifically activated in posterior-facing wound sites and was required for establishing posterior identity during regeneration. wnt-3 was upregulated upon amputation in stem cells, and its inhibition affected stem cell proliferation. Ectopic expression of anterior markers in wnt-3 RNAi head fragments was stem cell dependent. Chromatin accessibility data revealed that wnt-3 activation during regeneration required input from the general wound response. Additionally, the expression of a different Wnt ligand, wnt-1, prior to amputation was required for activation of wound-induced wnt-3 expression. Our study establishes a gene regulatory network for initiating Wnt signaling in posterior tissues in a bilaterian.

developmental biology↗

bioRxiv2018

Ultra-sensitive sequencing for cancer detection reveals progressive clonal selection in normal tissue over a century of human lifespan

High accuracy next-generation DNA sequencing promises a paradigm shift in early cancer detection by enabling the identification of mutant cancer molecules in minimally-invasive body fluid samples. We demonstrate 80% sensitivity for ovarian cancer detection using ultra-accurate Duplex Sequencing to identify TP53 mutations in uterine lavage. However, in addition to tumor DNA, we also detect low frequency TP53 mutations in nearly all lavages from women with and without cancer. These mutations increase with age and share the selection traits of clonal TP53 mutations commonly found in human tumors. We show that low frequency TP53 mutations exist in multiple healthy tissues, from newborn to centenarian, and progressively increase in abundance and pathogenicity with older age across tissue types. Our results illustrate that subclonal cancer evolutionary processes are a ubiquitous part of normal human aging and great care must be taken to distinguish tumor-derived, from age-associated mutations in high sensitivity clinical cancer diagnostics.

cancer biology↗

bioRxiv2017

CRISPR-DS: An efficient, low DNA input method for ultra-accurate sequencing

Current next-generation sequencing techniques suffer from inefficient target enrichment and frequent errors. To address these issues, we have developed a targeted genome fragmentation approach based on CRISPR/Cas9 digestion. By designing all fragments to similar lengths, regions of interest can be size-selected prior to library preparation, increasing hybridization capture efficiency. Additionally, homogenous length fragments reduce PCR bias and maximize read usability. We combine this novel target enrichment approach with ultra-accurate Duplex Sequencing. The result, termed CRISPR-DS, is a robust targeted sequencing technique that overcomes the inherent challenges of small target enrichment and enables the detection of ultra-low frequency mutations with small DNA inputs.

genomics↗