Biology subjects

Ellis, S. J.

Publications and source records attributed to Ellis, S. J..

6 recordsLinked to original sources

bioRxiv2026

Inflammation-driven cellular selection impacts X-linked mosaicism in the epidermis

In eutherian females, the choice of which X chromosome gets embryonically inactivated is thought to be random. Somatic tissues are thus assumed to comprise cells with a 50:50 ratio of maternal:paternal X active. However, a phenomenon known as X-skewing has been observed, wherein tissue composition shifts to be dominated by cells expressing one X or the other. On a gross level, such X-skewing is phenotypically silent except in the case where one X-chromosome carries a disease mutation. Here, by leveraging a mouse model of an X-linked disease called Incontinentia Pigmenti, caused by heterozygous mutations in the NF-kB effector, Nemo, we explore how X-linked cellular dynamics shape progenitor biology in the epidermis. Lineage tracing with X-linked reporters shows that at birth, the epidermis is unexpectedly skewed toward mutant cells. Within a week, as inflammation emerges, these dynamics reverse leaving surviving animals with almost entirely wild-type epithelium. The shift is driven by loss rather than growth since mutant cells adopt an aberrant fate and die at higher rates than their wild-type neighbours; proliferation rises in both populations. Notably, wild-type proliferation scales with local tissue composition, suggesting these cells calibrate their response to the extent of the mutant burden to compensate appropriately for tissue loss. Depleting macrophages, the principal TNF- source, attenuates inflammation, mutant cell death and ultimately is expected to preserve the mutant population. Altogether, our results identify inflammation as a selective force capable of resolving deleterious mosaicism, not only in the context of an X-linked disease, but within any dynamic, clonally heterogeneous epithelium.

cell biology↗

bioRxiv2026

E-cadherin-mediated neighborhood surveillance dictates pre-malignant outcomes

Stratified epithelia accumulate oncogenic mutations throughout life, yet overgrowths are rare. How epithelia detect and eliminate aberrant clones remains poorly understood. Using a mouse model of oncogenic clonal mosaicism in the skin, we find that pre-malignant epidermal cells redistribute E-cadherin to interfaces shared with wild-type neighbors, generating local tension heterogeneity that triggers elimination by cell competition. We show that gain or loss of E-cadherin can each drive competitive elimination, and although mechanical routes differ, both establish tension heterogeneity between neighbors, rather than any absolute adhesion state, as the critical determinant of epidermal fitness. This mechanism carries the seeds of its own failure: these tension differentials precipitate clonal sorting, depleting the wild-type contacts that surveillance requires. Pre-malignant cells then become supercompetitors, eliminating wild-type neighbors and expanding hyperplastically. Mechanical heterogeneity therefore endows tissues with an active, yet inherently fragile error-correction system whose collapse initiates a switch in competitive status, increasing tumorigenesis susceptibility.

cell biology↗

bioRxiv2025

In vivo single-cell CRISPR screening for microproteins identifies a critical ribosomal component

The dark proteome includes a rapidly expanding catalog of microproteins with unknown functions that have been historically ignored in genome annotations. Here, we exploit an in vivo single-cell CRISPR screening strategy in the mouse epidermis to systematically investigate the tissue-wide function of microproteins. We document the global and cell-type-specific roles of microproteins during epidermal development and homeostasis at single-cell transcriptomic resolution. Focusing on select candidates, we identify a novel microprotein on Gm10076, identical to the ribosomal intersubunit bridge protein RPL41, whose perturbation strongly impairs proliferation and protein synthesis. Employing ribosome profiling and RNA sequencing, we show that Gm10076 perturbation profoundly reshapes the translational landscape. Contrary to its prior classification as nonessential, we find that the ribosomal protein RPL41 is essential for cellular proliferation, warranting further investigation into its role as an intersubunit bridge in the translational machinery. Together, our study comprehensively charts the tissue-wide functional landscape of the dark proteome, uncovers a second Rpl41 gene critical for ribosome function and establishes a basis for exploring the impact of microproteins on disease pathogenesis.

genetics↗

bioRxiv2024

In vivo single-cell ribosome profiling reveals cell-type-specific translational programs during aging

Somatic stem cells are characterized by their low overall protein synthesis rates, a feature implicated in driving their stemness. However, how aging reshapes the translational landscape of stem cells and how these changes impact their regenerative capacity remains poorly understood. Here, we present an in vivo single-cell ribosome profiling strategy to monitor tissue-wide translational landscapes of the young and aged mouse epidermis. By implementing ribosomal elongation-inhibited cell isolation and switching to RNase I ribonuclease for generating ribosomal footprints, we expand the applicability of single-cell ribosome profiling to in vivo systems and facilitate the evaluation of triplet periodicity, a hallmark of high-quality ribosome profiling data. Leveraging this strategy and integrating ribosome profiling with single-cell RNA sequencing, we document the in vivo translational landscapes of the major epidermal cell types, outline cell-type-specific translational efficiencies and capture heterogeneity in differentiation commitment within stem cell populations. Notably, we identify a pronounced translational reprogramming of AP-1 subunits specifically in aged epidermal stem cells, with functional consequences for keratinocyte behavior. Our study illustrates the power of in vivo single-cell ribosome profiling to map cell-type-specific translational programs and offers a scalable strategy for tissue-wide interrogation of translational landscapes at single-cell resolution.

genomics↗

bioRxiv2023

In vivo single-cell CRISPR uncovers distinct TNF-alphaprograms in clonal expansion and tumorigenesis

The tumor evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions occur frequently in human epithelia and can remodel almost entire tissues, the mechanisms behind why only a small number of clones transform into malignant tumors remain enigmatic. Here, we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing, guide capture and spatial transcriptomics to longitudinally monitor cell type-specific clonal expansions, document their underlying gene programs and contrast clonal expansions from tumor initiation. We uncover a TNF- signaling module that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF- signaling module is downregulated, and instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF- gene program. By analyzing clonally expanded perturbations and their frequency in tumors, we demonstrate that the autocrine TNF- gene program is associated with epithelial-mesenchymal transition (EMT) and is preexistent in a subpopulation of expanded epidermal stem cells, contributing to the predisposition for tumor initiation. Finally, we provide in vivo evidence that the epithelial TNF- gene program is sufficient to mediate invasive properties of epidermal stem cells and show that the TNF- signature correlates with shorter overall survival in human squamous cell carcinoma patients. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues and unveils distinct TNF- programs in tumor evolution. Understanding the biology of clonal expansions in phenotypically normal epithelia and the mechanisms governing their transformation will guide the development of novel strategies for early cancer detection and therapy.

cancer biology↗

bioRxiv2017

GEOracle: Mining perturbation experiments using free text metadata in Gene Expression Omnibus

There exists over 2.5 million publicly available gene expression samples across 101,000 data series in NCBIs Gene Expression Omnibus (GEO) database. Due to the lack of the use of standardised ontology terms in GEOs free text metadata to annotate the experimental type and sample type, this database remains di[ffi]cult to harness computationally without significant manual intervention.\n\nIn this work, we present an interactive R/Shiny tool called GEOracle that utilises text mining and machine learning techniques to automatically identify perturbation experiments, group treatment and control samples and perform differential expression. We present applications of GEOracle to discover conserved signalling pathway target genes and identify an organ specific gene regulatory network.\n\nGEOracle is effective in discovering perturbation gene targets in GEO by harnessing its free text metadata. Its effectiveness and applicability has been demonstrated by cross validation and two real-life case studies. It opens up new avenues to unlock the gene regulatory information embedded inside large biological databases such as GEO. GEOracle is available at https://github.com/VCCRI/GEOracle.

bioinformatics↗