Biology subjects

Bell, A.

Publications and source records attributed to Bell, A..

At least 19 recordsLinked to original sources

bioRxiv2026

The genome of the coral model sea anemone Exaiptasia diaphana (Aiptasia) strain F003

We present a genome assembly of Aiptasia strain F003, a broadly used laboratory strain of the sea anemone and coral model organism Exaiptasia diaphana (Cnidaria; Anthozoa; Hexacorallia; Actiniaria; Aiptasiidae; Exaiptasia). The genome assembly spans 237.34 Mb across 12,480 contigs with a contig N50 of 76.47 kb (12,423 scaffolds with a scaffold N50 of 77.93 kb), including a single-contig mitochondrial genome with a length of 19.79 kb. The assembly is highly complete with a BUSCO completeness of 96.50% based on the metazoa dataset, including 94.80% single-copy, 1.70% duplicated, 1.70% fragmented, and 1.80% missing BUSCO genes. Genome annotation identified 29,589 protein-coding genes (including 2 pseudogenes) and a repeat content of 32.89%. The genome of the female Aiptasia strain F003 enhances the utility of a key cnidarian model organism by enabling comparisons among Aiptasia strains in studies of symbiosis, microbiomes, and thermal stress. It thereby strengthens the value of Aiptasia as a model for investigating the mechanisms underlying coral holobiont function, response, and resilience to environmental change.

genomics↗

bioRxiv2026

Immune checkpoint inhibitors amplify type 2 immune mediated repair bypro-regenerative scaffolds

Extracellular matrix (ECM) scaffolds induce type 2 immunity to promote repair. Here, we show that immune cells recruited to ECM-treated murine muscle injuries and clinical soft tissue defects express immune checkpoints. Specifically, TH2 cells and regulatory T cells (Tregs) increase LAG3 expression, while macrophages express PDL2. TCR analysis and a triple-reporter strain for interleukin (IL)-13 and Treg fate-mapping suggest that Tregs in ECM-treated wounds transition into TH2-like exTregs that express LAG3. Immune checkpoint inhibition (ICI) significantly stimulated type 2 immunity in ECM-treated wounds, including increased TH2 cells, Treg transition to TH2-like exTregs, and pro-regenerative macrophages. Moreover, ICI enhanced muscle repair and reduced fibrosis in ECM-treated wounds. Collectively, these findings show Treg/TH2 plasticity in wound healing and introduce a novel ICI application to enhance immune-mediated regeneration.

bioengineering↗

bioRxiv2026

Cannibalism as a mechanism to offset reproductive costs in three-spined sticklebacks

Parents often go to great lengths to promote the survival of their offspring, yet in many species parents may abandon or cannibalize offspring under their care. Using three-spined sticklebacks, where males are the sole providers of energetically costly parental care, we investigated the factors driving patterns of cannibalism in two natural populations in the field. Cannibalism was prevalent in both populations: more than 70% of parenting males contained embryos in their stomach. Neither standard length nor body condition predicted the number of embryos eaten, suggesting that males are not cannibalizing based on energetic need alone. However, males cannibalized significantly more embryos from large compared to small broods, suggesting that greater access to embryos is driving high levels of cannibalism. Using microsatellites to determine parentage, we investigated whether males cannibalize embryos fertilized by other males (heterocannibalism) to mitigate the costs of parental care. In both populations males engaged in both filial and heterocannibalism, but the two populations significantly differed in the relative amount of filial versus heterocannibalism, suggesting that males in these two populations face different reproductive costs. Combined, results from this study help disentangle the complex factors contributing to cannibalism, providing insight into how animals balance reproductive costs and benefits.

ecology↗

bioRxiv2026

Building neuroanatomical resources for three-spined sticklebacks: Brain areas important for social behavior

IntroductionThree-spined stickleback fish are famous for their diversity and charismatic social behavior. However, there are few neuroanatomical resources for studying the neural and brain mechanisms underlying their fascinating behavior. Methods and ResultsWe identify 11 brain areas important for social behavior by referencing brain atlases for six other teleost fishes. Brain regions were identified via neuroanatomical landmarks and we characterized the presence / absence of tyrosine hydroxylase (TH), a key gene product of the dopaminergic system, in those regions. Comparing the neuroanatomical location of these regions in the stickleback brain and the expression of TH therein to that of other fish species highlights similarities and differences and the need for a brain atlas specific to sticklebacks. This resource serves as a map of the location of regions important for social behavior in the stickleback brain. ConclusionThis resource will help guide future studies connecting gene function to social behavior through the brain and will enable future work to understand the evolution of neural mechanisms that contribute to the diversity of social behavior in this emerging model organism.

neuroscience↗

bioRxiv2025

Microglia are not required for normal postnatal brain development and cognitive function in the rat.

The development, maintenance and survival of microglia, the brains resident immune cells, requires signalling via the colony stimulating factor 1 receptor (CSF1R). In mice, the Fms intronic regulatory element (FIRE), a highly conserved super enhancer, is required for CSF1R expression in microglia and germ-line deletion of FIRE leads to microglial deficiency. We have generated Csf1r{Delta}FIRE/{Delta}FIRE (Fireko) rats using CRISPR/Cas9. Fireko rats are born at expected Mendelian frequency, grow normally and survive to adulthood. Like Fireko mice, they lack microglia and subpopulations of resident macrophages in kidney and heart, but retain the other brain associated macrophages and resident populations in the liver, spleen and lungs. In contrast to mutant mice, macrophages in the peritoneum are unaffected and CSF1R expression is not completely abolished in the blood. Aside from the loss of microglia-specific transcripts, the Fireko has no effect on expression of genes associated with neurons, oligodendrocytes or astrocytes in adult rats but is associated with detectable calcification in the thalamus. Despite the absence of microglia, we detected no significant differences in ethologically relevant behaviours compared to littermates. The results suggest that microglia are not essential for normal cognitive development. Fireko rats provide an alternative to mice as a model for human microglial deficiency and the functions of microglia in development and homeostasis in the brain.

immunology↗

bioRxiv2024

The probability and duration of immigration in microbial communities

Immigration is a fundamental feature of microbial communities. We propose a method to determine the probability (Pi) that a number of immigrants (i) can attain an abundance N using the ratio of the probabilities of death q and division or "birth" p and the gamblers ruin equation: Pi= (1-(q/p)i/(1-(q/p)N). We estimate the probability of successful bioaugmentation or transplantation, the fate of a mutation infection and extinction. For example, an inoculum of 108 bacteria with a q/p of 1.00000001 has a 10-43 chance of attaining an abundance of 1010. The immigration parameter used in neutral models, m is 1/(1-q/p). We calculated the long-term average value of m and q/p in a wastewater treatment plant. The value of m varies by >5 orders of magnitude, with a curious bimodal distribution. However, all the values of q/p are very close to, but greater than, 1. We expect the long-term average value of q/p to be [~]1 in all stable microbial communities. In the absence of migration, bacterial populations with a q/p [≥]1 will go extinct with probability 1. The link between q/p and infectious dose is known and we demonstrate that, in principle, the gamblers ruin equation can estimate the infectious dose in naturally occurring infections, using Vibrio cholerae "carriers" to illustrate the point. We use the ratio q/p to estimate the time (measured in events or solar time) for a given change in abundance to happen. When q/p=1, extinction in even a small microbial population will take thousands of years.

microbiology↗

bioRxiv2024

Namibian fairy circles: Hostile territory for soil nematodes

Fairy circles are rings of grass with centers of bare soil that are found in some arid grasslands. Above- and belowground chemical and biological attributes of fairy circles have been explored in an ongoing debate about the ultimate causes of this pattern. We studied the soil nematode communities associated with Stipagrostis fairy circles along a 900-km range in the Namib Desert of Namibia in southern Africa. Nematode abundance and diversity were highest in soils along the vegetation rings that define fairy circles and in soils in the vegetated matrix surrounding the bare circles, demonstrating the positive impact of plant-derived resources on nematode communities. In contrast, soils from the bare centers of fairy circles had lower organic matter content and were nearly defaunated, averaging only 9.9 {+/-} 1.7 nematodes 100 g-1 soil. Bacterial-feeding Acrobeloides nematodes were the only taxa over-represented in center soils in comparison to ring soils. Our results indicate that nematode communities are influenced by the unique soil environments that the fairy circle vegetation pattern generates and suggest that the soils at the centers of fairy circles are uniquely hostile habitat for soil organisms as well as plants. Co-occurrence network analysis of nematode communities elucidated relationships among the taxa. For example, the abundances of dorylaims and Nothacrobeles were positively correlated across all soil positions, suggesting they have overlapping ecological niches. In ring soils, the abundances of fungal-feeding Aphelenchoides, Ditylenchus, and Hexatylus were positively correlated, likely due to enhanced fungal communities in these plant-influenced soils. Panagrobelus demonstrated niche specialization by being negatively correlated to two other bacterial-feeding taxa (Elaphonema in matrix soils and Acrobeloides in ring soils). The co-occurrence patterns revealed by these relatively low diversity communities provide insights into the potential roles of nematode interactions as well as environmental factors in community assembly.

ecology↗

bioRxiv2024

Exploring the PET in vivo generator 134Ce as a theranostic match for 225Ac

PurposeThe radionuclide pair cerium-134/lanthanum-134 (134Ce/134La) was recently proposed as a suitable diagnostic counterpart for the therapeutic alpha-emitter actinium-225 (225Ac). The unique properties of 134Ce offer perspectives for developing innovative in vivo investigations not possible with 225Ac. In this work, 225Ac- and 134Ce-labeled tracers were directly compared using internalizing and slow-internalizing cancer models to evaluate their in vivo comparability, progeny meandering, and potential as a matched theranostic pair for clinical translation. Despite being an excellent chemical match, 134Ce/134La has limitations to the setting of quantitative positron emission tomography imaging. MethodsThe precursor PSMA-617 and a macropa-based tetrazine-conjugate (mcp-PEG8-Tz) were radiolabelled with 225Ac or 134Ce and compared in vitro and in vivo using standard (radio)chemical methods. Employing biodistribution studies and positron emission tomography (PET) imaging in athymic nude mice, the radiolabelled PSMA-617 tracers were evaluated in a PC3/PIP (PC3 engineered to express a high level of prostate-specific membrane antigen) prostate cancer mouse model. The 225Ac and 134Ce-labeled mcp-PEG8-Tz were investigated in a BxPC-3 pancreatic tumour model harnessing the pretargeting strategy based on a trans-cyclooctene-modified 5B1 monoclonal antibody. ResultsIn vitro and in vivo studies with both 225Ac and 134Ce-labelled tracers led to comparable results, confirming the matching pharmacokinetics of this theranostic pair. However, PET imaging of the 134Ce-labelled precursors indicated that quantification is highly dependent on tracer internalization due to the redistribution of 134Ces PET-compatible daughter 134La. Consequently, radiotracers based on internalizing vectors like PSMA-617 are suited for this theranostic pair, while slow-internalizing 225Ac-labelled tracers are not quantitatively represented by 134Ce PET imaging. ConclusionWhen employing slow-internalizing vectors, 134Ce might not be an ideal match for 225Ac due to the underestimation of tumour uptake caused by the in vivo redistribution of 134La. However, this same characteristic makes it possible to estimate the redistribution of 225Acs progeny noninvasively. In future studies, this unique PET in vivo generator will further be harnessed to study tracer internalization, trafficking of receptors, and the progression of the tumour microenvironment. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/591165v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@ca3cb6org.highwire.dtl.DTLVardef@157eac6org.highwire.dtl.DTLVardef@f6ac6dorg.highwire.dtl.DTLVardef@b24d87_HPS_FORMAT_FIGEXP M_FIG C_FIG Redistribution of progeny. Investigating the 225Ac and 134Ce decay chain. This figure was created with BioRender.

pharmacology and toxicology↗

bioRxiv2024

Characterisation of anhydro-sialic acid transporters from mucosa-associated bacteria

Sialic acid (Sia) transporters are critical to the capacity of host-associated bacteria to utilise sialic acid for growth and/or cell-surface modification. While N-acetyl-neuraminic acid (Neu5Ac)-specific transporters have been studied extensively, little is known on transporters dedicated to anhydro-sialic acid forms such as 2,7-anhydro-Neu5Ac (2,7-AN) or 2,3-dehydro-2-deoxy-Neu5Ac (Neu5Ac2en). Here, we used a Sia-transport-null strain of Escherichia coli to investigate the function of members of anhydro-Sia transporter families previously identified by computational studies. First, we showed that the transporter NanG, from the Glycoside-Pentoside-Hexuronide:cation symporter family, is a specific 2,7-AN transporter, and identified by mutagenesis a crucial functional residue within the putative substrate-binding site. We then demonstrated that NanX transporters, of the Major Facilitator Superfamily, also only transport 2,7-AN and not Neu5Ac2en nor Neu5Ac. Finally, we provided evidence that SiaX transporters, of the Sodium-Solute Symporter superfamily, are promiscuous Neu5Ac/Neu5Ac2en transporters able to acquire either substrate equally well. The characterisation of anhydro-Sia transporters expands our current understanding of prokaryotic Sia metabolism within host-associated microbial communities.

microbiology↗

bioRxiv2022

A spatial atlas of Wnt and Frizzled receptor expression in adult mouse liver

Hepatic zonation is critical for most metabolic functions in liver. Wnt signaling plays an important role in establishing and maintaining liver zonation. Yet, the anatomic expression of Wnt signaling components, including all 10 Frizzled receptors (Fzds), has not been characterized in adult liver. To address this, we quantitatively mapped the spatial expression of Wnt/Fzd pathway components in adult mouse liver via multiplex fluorescent in situ hybridization. While all 10 Fzds are expressed within a metabolic unit, Fzds 1, 4, and 6 are the highest expressed. Though the majority of Wnt signaling occurs in zone 3, expression of most Fzds is not zonated. In contrast, Fzd6 is preferentially expressed in zone 1. We also discovered that Wnt2 and Wnt9b expression is highly zonated and primarily found in zone 3. Therefore, our results suggest that zonated Wnt expression is critical for zonation maintenance in healthy adult liver. Finally, we showed that Fzds and Wnts are not uniformly expressed by all hepatic cell types. Rather, there is broad distribution among both hepatocytes and non-parenchymal cells, including endothelial cells. Overall, our establishment of a definitive mRNA expression atlas of Wnt/Fzd pathway components opens the door to future functional characterization in healthy and disease states.

cell biology↗

bioRxiv2022

Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

In the summer months, the waters of the Sargasso Sea are nutrient-limited and strongly stratified, serving as a model system for the predicted warmer and nutrient-limited oceans of the Anthropocene. The dominant microorganisms of surface waters are key drivers of the global carbon cycle. However, the viruses of the Sargasso Sea that shape these host communities and influence host biogeochemical function are not well understood. Here, we apply a hybrid sequencing approach that combines short- and long reads to survey Sargasso Sea phage communities via metagenomics at the viral maximum (80m) and mesopelagic (200m) depths. Taxonomically, we identified 2,301 Sargasso Sea phage populations (~species-level taxonomy) across 186 genera. Over half of the phage populations lacked representation in other global ocean viral metagenomes, whilst 177 phage genera lacked representation in phage isolate databases. Viral fraction and cell-associated viral communities captured in short-read data were distinct and decoupled at both depths, possibly indicating low active lytic viral replication in the Sargasso Sea, with viral turnover occurring across periods longer than the sampling period of three days. Inclusion of long read data was critical for (1) the identification of 79 ecologically important and common viral genomes; (2) capturing the extent of viral genome microdiversity; and (3) enabling the recovery of hypervariable regions in viral genomes predicted to encode proteins involved in host recognition, DNA synthesis and DNA packaging. Host prediction was only possible for ~4% of viral populations. Genomes of phages known to infect Prochlorococcus and Pelagibacter were poorly represented in our data, supporting recent evidence of low infection levels in the dominant bacterial taxa of oligotrophic regions. SubjectsBioinformatics, Genomics, Marine Biology, Microbiology, Virology Sequence data accession numbersPRJNA767318

microbiology↗

bioRxiv2022

Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces

Recent advances in spatial transcriptomics (ST) enable gene expression measurements from a tissue sample while retaining its spatial context. This technology enables unprecedented in situ resolution of the regulatory pathways that underlie the heterogeneity in the tumor and its microenvironment (TME). The direct characterization of cellular co-localization with spatial technologies facilities quantification of the molecular changes resulting from direct cell-cell interaction, as occurs in tumor-immune interactions. We present SpaceMarkers, a novel bioinformatics algorithm to infer molecular changes from cell-cell interaction from latent space analysis of ST data. We apply this approach to infer molecular changes from tumor-immune interactions in Visium spatial transcriptomics data of metastasis, invasive and precursor lesions, and immunotherapy treatment. Further transfer learning in matched scRNA-seq data enabled further quantification of the specific cell types in which SpaceMarkers are enriched. Altogether, SpaceMarkers can identify the location and context-specific molecular interactions within the TME from ST data.

bioinformatics↗

bioRxiv2022

Dynamic control of metabolic zonation and liver repair by endothelial cell Wnt2 and Wnt9b revealed by single cell spatial transcriptomics using Molecular Cartography

The conclusive identity of Wnt proteins regulating liver zonation (LZ) and regeneration (LR) remains unclear despite an undisputed role of {beta}-catenin. Using single-cell analysis of liver cells from various species, a conserved Wnt2 and Wnt9b expression in endothelial cells (ECs) in zone 3 shown to be the major Wnt cell source, was identified. Conditional EC-elimination of Wnt2 and Wnt9b led to perturbation of LZ with not only loss of {beta}-catenin targets in zone 3, but also re-appearance of zone 1 genes in zone 3, unraveling dynamicity as revealed by single-cell spatial transcriptomics using Molecular Cartography. Defective LR observed in the knockouts phenocopied other models of defective hepatic Wnt signaling. Administration of a tetravalent antibody to activate Wnt signaling rescued LZ and LR in the knockouts. Molecular Cartography on the livers of the agonist-treated animal revealed changes in LZ. Administration of the agonist also promoted LR in acetaminophen overdose acute liver failure (ALF) fulfilling an unmet clinical need. Overall, we report an unequivocal role of EC-Wnt2 and Wnt9b in LZ and LR and show the role of Wnt activators as regenerative therapy for ALF.

pathology↗

bioRxiv2021

β-Catenin-NFκB-CFTR interactions in cholangiocytes regulate inflammation and fibrosis during ductular reaction

Expansion of biliary epithelial cells (BECs) during ductular reaction (DR) is observed in liver diseases including cystic fibrosis (CF), and associated with inflammation and fibrosis, albeit without complete understanding of underlying mechanism. Using two different genetic knockouts of {beta}-catenin, one with {beta}-catenin loss is hepatocytes and BECs (KO1), and another with loss in only hepatocytes (KO2), we demonstrate disparate long-term repair after an initial injury by 2-week choline-deficient ethionine- supplemented diet. KO2 show gradual liver repopulation with BEC-derived {beta}-catenin- positive hepatocytes, and resolution of injury. KO1 showed persistent loss of {beta}-catenin, NF-{kappa}B activation in BECs, progressive DR and fibrosis, reminiscent of CF histology. We identify interactions of {beta}-catenin, NF{kappa}B and CF transmembranous conductance regulator (CFTR) in BECs. Loss of CFTR or {beta}-catenin led to NF-{kappa}B activation, DR and inflammation. Thus, we report a novel {beta}-catenin-NF{kappa}B-CFTR interactome in BECs, and its disruption may contribute to hepatic pathology of CF.

pathology↗

bioRxiv2021

Differential expression of glycosyltransferases identified through comprehensive pan-cancer analysis

Despite accumulating evidence supporting a role for glycosylation in cancer progression and prognosis, the complexity of the human glycome and glycoproteome poses many challenges to understanding glycosylation-related events in cancer. In this study, a multifaceted genomics approach was applied to analyze the impact of differential expression of glycosyltransferases (GTs) in 16 cancers. An enzyme list was compiled and curated from numerous resources to create a consensus set of GTs. Resulting enzymes were analyzed for differential expression in cancer, and findings were integrated with experimental evidence from other analyses, including: similarity of healthy expression patterns across orthologous genes, miRNA expression, automatically-mined literature, curation of known cancer biomarkers, N-glycosylation impact, and survival analysis. The resulting list of GTs comprises 222 human enzymes based on annotations from five databases, 84 of which were differentially expressed in more than five cancers, and 14 of which were observed with the same direction of expression change across all implicated cancers. 25 high-value GT candidates were identified by cross-referencing multimodal analysis results, including PYGM, FUT6 and additional fucosyltransferases, several UDP-glucuronosyltransferases, and others, and are suggested for prioritization in future cancer biomarker studies. Relevant findings are available through OncoMX at https://data.oncomx.org, and the overarching pipeline can be used as a framework for similarly analysis across diverse evidence types in cancer. This work is expected to improve the understanding of glycosylation in cancer by transparently defining the space of glycosyltransferase enzymes and harmonizing variable experimental data to enable improved generation of data-driven cancer biomarker hypotheses.

genomics↗

bioRxiv2021

Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonisation potential of bacterial pathogens and commensals.

Located at the tip of cell surface glycoconjugates, sialic acids are at the forefront of host-microbe interactions and, being easily liberated by sialidase enzymes, are used as metabolites by numerous bacteria, particularly by pathogens and commensals living on or near diverse mucosal surfaces. These bacteria rely on specific transporters for the acquisition of host-derived sialic acids. Here, we present the first comprehensive genomic and phylogenetic analysis of bacterial sialic acid transporters, leading to the identification of multiple new families and subfamilies. Our phylogenetic analysis suggests that sialic acid-specific transport has evolved independently at least 8 times during the evolution of bacteria, from within 4 of the major families/superfamilies of bacterial transporters, and we propose a robust classification scheme to bring together a myriad of different nomenclatures that exist to date. The new transporters discovered occur in diverse bacteria including Spirochaetes, Bacteroidetes, Planctomycetes, and Verrucomicrobia, many of which are species that have not been previously recognised to have sialometabolic capacities. Two subfamilies of transporters stand out in being fused to the sialic acid mutarotase enzyme, NanM, and these transporter fusions are enriched in bacteria present in gut microbial communities. We also provide evidence for a possible function of a sialic acid transporter component in chemotaxis that is independent of transport. Our analysis supports the increasing experimental evidence that competition for host-derived sialic acid is a key phenotype for successful colonisation of complex mucosal microbiomes, such that a strong evolutionary selection has occurred for the emergence of sialic acid specificity within existing transporter architectures.

microbiology↗

bioRxiv2020

NOTCH-YAP1/TEAD-DNMT1 axis regulates hepatocytereprogramming into intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC), a disease of poor prognosis, has increased in incidence. It is challenging to treat due to intra- and inter-tumoral heterogeneity, which in part is attributed to diverse cellular origin. Indeed, co-expression of AKT and NICD in hepatocytes (HCs) yielded ICC, with similarity to proliferative, Notch-activated, and stem cell-like subclasses of clinical ICC. NICD regulated SOX9 and YAP1 during ICC development. Yap1 deletion or TEAD inhibition impaired HC-to-biliary epithelial cell (BEC) reprogramming and ICC proliferation; Sox9 loss repressed tumor growth; and Yap1-Sox9 combined loss abolished ICC development in AKT-NICD model. DNMT1 was discovered as a novel downstream effector of YAP1-TEAD complex that directed HC-to-BEC/ICC fate-switch. DNMT1 loss prevented Notch-dependent HC-to-ICC development, and DNMT1 re-expression restored ICC development following TEAD repression. Coexpression of DNMT1 with AKT was sufficient to induce hepatic tumor development including ICC. Thus, we have identified a novel NOTCH-YAP1/TEAD-DNMT1 axis essential for HC-driven ICC development. SIGNIFICANCEWe evaluated the clinical relevance of hepatocyte-driven ICC model and revealed critical but distinct roles of YAP1 and SOX9 in AKT-NICD-driven hepatocyte-derived ICC. We also identified NOTCH-YAP1/TEAD-DNMT1 axis as a critical driver for hepatocyte-to-ICC reprogramming, which might have biological and therapeutic implications in ICC subsets.

cancer biology↗

bioRxiv2020

Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors

YAP1 regulates cell plasticity during liver injury, regeneration and cancer, but its role in liver development is unknown. YAP1 activity was detected in biliary cells and in cells at the hepato-biliary bifurcation in single-cell RNA-sequencing analysis of developing livers. Hepatoblast deletion of Yap1 led to no impairment in Notch-driven SOX9+ ductal plate formation, but prevented the formation of the abutting second layer of SOX9+ ductal cells, blocking the formation of a patent intrahepatic biliary tree. Intriguingly, the mice survived for 8 months with severe cholestatic injury and without any hepatocyte-to-biliary transdifferentiation. Ductular reaction in the perihilar region suggested extrahepatic biliary proliferation likely seeking the missing intrahepatic biliary network. Long-term survival of these mice occurred through hepatocyte adaptation via reduced metabolic and synthetic function including altered bile acid metabolism and transport. Overall, we show YAP1 as a key regulator of bile duct development while highlighting a profound adaptive capability of hepatocytes.

pathology↗