Biology subjects

Fish, M.

Publications and source records attributed to Fish, M..

14 recordsLinked to original sources

bioRxiv2025

Innate antiviral readiness drives the expansion of protective T stem cell memory against influenza

The development of T-cell-based influenza vaccines relies on eliciting broad CD8+ T-cell immunity, wherein T stem cell-like memory (TSCM) cells serve as the ultimate long-lived reservoir for immune memory, thereby unlocking the potential for durable protection against viral drift and shift. However, the specific immunological cues that drive the robust expansion and functional preservation of this self-renewing, multipotent subset remain unknown. Here, utilizing multi-omic systems immunology in a pediatric cohort immunized with live attenuated influenza vaccine, we identified the determinants governing the expansion of influenza virus-reactive TSCM cells. We show that a pre-existing state of innate antiviral readiness, defined by a plasmacytoid dendritic cell-associated type I interferon signature, is the requisite condition for a robust TSCM expansion. Mechanistically, this baseline innate state enhances antigen priming and enforces a qualitative divergence in T-cell fate, driving responders toward a functionally poised, Th1-dominant phenotype while non-responders default to a dysfunctional, hyper-proliferative state. To determine the clinical relevance of this cellular subset, we analyzed an independent controlled human influenza challenge study. This validation revealed a critical functional division of labor in host defense: whereas pre-existing antibodies primarily mitigated symptom severity, the baseline frequency of influenza virus-reactive TSCM cells was the strongest predictor of rapid viral load clearance. These findings establish that the expansion of durable cellular memory is not stochastic but is predetermined by the innate cytokine environment, providing a predictive biomarker for patient stratification and a validated target for adjuvants designed to expand the TSCM reservoir deliberately.

immunology↗

bioRxiv2025

A regulatory region that controls Wnt gene expression following tissue injury is required for proper muscle regeneration

The capacity to detect and respond to injury is critical for the recovery and long-term survival of many organisms. Wnts are commonly induced by tissue damage but how they become activated transcriptionally is not well understood. Here, we report that mouse Wnt1 and Wnt10b are induced following injury in both lung and muscle. These Wnts occupy the same chromosome and are transcribed in opposite directions with 12kb between them. We identified a highly conserved cis-acting regulatory region (enhancer) residing between Wnt1 and Wnt10b that, when fused to a LacZ reporter, is activated post-injury. This enhancer harbors putative AP-1 binding sites that are required for reporter activity, a feature observed in other injury-responsive enhancers. Injured muscles in mice carrying a germ-line deletion of the enhancer region display reduced Wnt1 and Wnt10b expression and show elevated intramuscular adipogenesis--a hallmark of impaired regenerative capacity--revealing a requirement of this enhancer for proper regeneration. Enhancer redundancy is common in development, but our in vivo analysis shows that loss of a single injury-responsive regulatory region in adult tissues can produce a detectable regenerative phenotype. SummaryA new, previously unknown shared regulatory region residing between two Wnts, Wnt1 and Wnt10b, is induced by tissue damage and required for muscle regeneration.

developmental biology↗

bioRxiv2025

Foxh1 is a locus-specific PRC2 recruiter governing germ layer silencing

Polycomb Repressive Complex 2 (PRC2) establishes H3K27me3 marks to shape spatiotemporal gene expression during embryogenesis. While its dysregulation is linked to developmental disorders, cancer, and aging, the mechanisms guiding PRC2 to specific genomic loci remain a subject of ongoing debate. A prevailing model proposes that PRC2 recruitment occurs via its intrinsic affinity for chromatin rather than through sequence-specific transcription factors. Here, we provide evidence that the maternally deposited pioneer transcription factor Foxh1 plays a critical role in directing PRC2 to specific genomic loci during zygotic genome activation in Xenopus. Foxh1 is a critical transcription factor mediating Nodal signaling, but it also plays an earlier role by pre-binding enhancers prior to signaling activation. This pre-binding is essential for forming enhanceosome complexes that trigger mesendodermal gene expression and drive gastrulation, in cooperation with other maternal transcription factors. Using maternal Foxh1-null embryos, we demonstrate that Foxh1 directly recruits Ezh2, the catalytic subunit of PRC2, to Foxh1-bound loci. Loss of Foxh1 impairs Ezh2 recruitment, leading to a global reduction in H3K27me3. These findings support a dual-function model in which Foxh1 not only activates endodermal gene expression in endoderm, but also recruits PRC2 to silence the same genes in ectoderm. This dual activity of Foxh1 allows the spatially coordinated epigenetic states of the endodermal gene regulatory program during early embryogenesis. HighlightsO_LIFoxh1 recruits Ezh2 to deposit H3K27me3 at specific loci in early embryos C_LIO_LIMaternal Foxh1 loss reduces H3K27me3 and disrupts lineage segregation C_LIO_LIFoxh1 both activates and represses endoderm genes in a context-specific way C_LI

developmental biology↗

bioRxiv2024

AtTOC159 Receptors are Targeted to the Chloroplast Outer Membrane by a β-Signal and Galactolipid-Specific Transit Peptide-Like Sequence at the C-Terminus

Chloroplasts, the essential organelles responsible for photosynthesis, rely on the coordinated import of nuclear-encoded proteins for their biogenesis and function. TOC159 receptors are critical components of the translocon at the outer membrane of chloroplasts (TOC complex), responsible for recognizing and importing preproteins. However, the mechanisms by which TOC159 itself is targeted and integrated into the chloroplast outer envelope are only partially understood. In this study, we explore the structural aspects of the C-terminal membrane (M) domain of Arabidopsis thaliana TOC159, with a focus on its role in chloroplast outer envelope targeting and TOC complex integration. Structural predictions using AlphaFold and far-UV circular dichroism (CD) spectroscopy experiments suggested that the M domain forms an integral {beta}-barrel that fuses with the {beta}-barrel of TOC75, forming a hybrid channel at the chloroplast outer envelope. We identified a novel bi-partite targeting signal within the M domain, composed of a C-terminal {beta}-signal with the consensus sequence G-Q-{Phi}-[ST]-{Phi}-[RK]-X-[SN]-[ST] and a transit peptide (TP)-like sequence. Using fluorescence microscopy and mutational analyses, we demonstrated that the {beta}-signal is essential for chloroplast targeting, while the TP-like sequence enhances targeting ejiciency. Furthermore, CD spectroscopy and Langmuir-Blodgett trough experiments revealed that the TP-like sequence preferentially interacts with galactolipids unique to the chloroplast outer membrane, particularly sulfoquinovosyl diacylglycerol (SQDG), facilitating chloroplast outer envelope targeting specificity. Overall, our findings provide a deeper understanding of TOC159 receptor targeting mechanisms, TOC complex biogenesis and highlight the broader significance of lipid-mediated targeting in intracellular protein trajicking. These results pave the way for future studies on the role of TP-like sequences in chloroplast outer membrane protein targeting and other novel targeting pathways more generally.

plant biology↗

bioRxiv2024

NeuroFold: A Multimodal Approach to Generating Novel Protein Variants in silico

The generation of high-performance enzyme variants with desired physicochemical and functional properties presents a formidable challenge in the field of protein engineering. Existing in silico design methods are limited by inadequate training data, insufficient diversity within datasets, and suboptimal sampling techniques. Here, we introduce a novel approach that addresses these limitations and significantly improves the efficiency of generating functional enzyme variants. Using a multimodal approach, NeuroFold can leverage sequence, structural, and homology data during both sampling and discrimination phases, thereby enabling more diverse and informed sampling of the sequence space. Our model demonstrated a 40-fold increase in Spearman rank correlation as compared to large language models (LLMs) such as ESM-1v and empowers the rapid creation of high-quality enzyme variants, such as the {beta}-lactamase variants generated by NeuroFold in this study, which demonstrated increased thermostability and varying levels of activity. This pipeline represents a promising advancement in the field of enzyme engineering, offering a valuable tool for the development of novel enzymes with enhanced performance and desired chemical properties. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/584504v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@6d8137org.highwire.dtl.DTLVardef@13e6c28org.highwire.dtl.DTLVardef@12ebff6org.highwire.dtl.DTLVardef@3ce466_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Liver size is predetermined in the neonate by adding lobules at the periphery

Organs vary in size between and within species to match organismal needs1,2. Decades-old theoretical work has proposed that scaling of organs and body parts relative to the body relies on the features of energy-transport systems, the vascular system in mammals3. Yet, experimental studies on whether or how vascularization helps determine organ size have lagged behind. The mammalian liver is a remarkable example, as liver size scales proportionally with high precision between individuals4. Here, we use quantitative clonal mapping, volumetric imaging, and genetic perturbations combined with novel molecular and genetic tools to identify the temporal and spatial constraints that establish mouse liver size. We find that adult liver size is predetermined during a neonatal period when new functional units, termed lobules, are added to the organ. New lobules are vascularized by prominent sprouting angiogenesis of the hepatic vein, restricted to the periphery of the organ. When Wnt signals are ablated in the single cell-layered mesothelium at the periphery, lobule growth fails, and the organ adopts a compromised size set point. Remarkably, within a week after birth and well before hepatocyte division stops, vein sprouting rapidly declines and lobule addition concludes, setting a limit on the final liver size. These findings posit that vascularization in the neonate constrains and helps determine adult liver size. Together, these results propose a novel, vasculature-centric experimental framework for studying organ size control and scaling in mammals.

developmental biology↗

bioRxiv2023

Cholangiocytic differentiation drives cell proliferation in hepatoblastoma through Wnt-dependent FGF19 signaling

Cancers evolve not only through the acquisition and clonal transmission of somatic mutations but also by non-genetic mechanisms that modify cell phenotype. Here, we describe how transcriptional heterogeneity arises within human hepatoblastoma, one of the cancers with the lowest mutational burden, characterized by activating mutations in the Wnt pathway. Histology-guided RNA sequencing and evaluation of spatial gene expression in primary hepatoblastomas identified foci of tumor cells within the highly proliferative embryonal histology that express the growth factor FGF19, colocalizing with markedly increased expression of Wnt target genes and cholangiocyte markers. In patient-derived tumoroids, FGF19 provided a required growth signal for FGF19-negative cells, and its expression depended on both Wnt/-catenin and the biliary transcription factor SOX4. Our results reveal that a biliary lineage program induces FGF19 as a paracrine signal for tumor growth, thereby modulating the transcriptional outcome of constitutive Wnt activation and tumor cell proliferation.

cancer biology↗

bioRxiv2021

Hepatocyte Cell Cycle Progression Depends on a Transcriptional Repressor Cascade Downstream of Wnt Signaling

Cell proliferation is tightly controlled by inhibitors that block cell cycle progression until growth signals relieve this inhibition. In several tissues including the liver, transcriptional repressors such as E2F7 and E2F8 function as inhibitors of mitosis and promote polyploidy, but how growth factors release these mitotic inhibitors to facilitate cell cycle progression is unknown. We describe here a newly identified mechanism of cell division control in which Wnt/{beta}catenin signaling in the postnatal liver maintains active hepatocyte proliferation through Tbx3, a Wnt target gene. TBX3 directly represses transcription of E2f7 and E2f8, promoting a low ploidy state and cell cycle progression. This sequential transcriptional repressor cascade, initiated by Wnts, provides a new paradigm for exploring how a commonly active developmental signal impacts cell cycle completion.

cell biology↗

bioRxiv2021

Intermittent fasting induces rapid hepatocyte proliferation

Nutrient availability fluctuates in most natural populations, forcing organisms to undergo periods of fasting and re-feeding. It is unknown how dietary changes influence liver homeostasis. Here, we show that a switch from ad libitum feeding to intermittent fasting, IF, promotes rapid hepatocyte proliferation. Mechanistically, IF-induced hepatocyte proliferation is driven by the combined action of intestinally produced, systemic endocrine FGF15 and localized WNT signaling. Hepatocyte proliferation during periods of fasting and re-feeding re-establishes a constant liver-to-body-mass ratio, thus maintaining the hepatostat. This study provides the first example of dietary influence on adult hepatocyte proliferation and challenges the widely held view that liver tissue is mostly quiescent unless chemically or mechanically injured.

cell biology↗

bioRxiv2020

Uncovering the mesendoderm gene regulatory network through multi-omic data integration

Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low-throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data comprised of more than two data types is challenging. Here, we use linked self-organizing maps to combine ChIP-seq/ATAC-seq with temporal, spatial and perturbation RNA-seq data from Xenopus tropicalis mesendoderm development to build a high resolution genome scale mechanistic GRN. We recovered both known and previously unsuspected TF-DNA/TF-TF interactions and validated through reporter assays. Our analysis provides new insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly-dimensional multi-omic data sets. HighlightsO_LIBuilt a generally applicable pipeline to creating GRNs using highly-dimensional multi-omic data sets C_LIO_LIPredicted new TF-DNA/TF-TF interactions during mesendoderm development C_LIO_LIGenerate the first genome scale GRN for vertebrate mesendoderm and expanded the core mesendodermal developmental network with high fidelity C_LIO_LIDeveloped a resource to visualize hundreds of RNA-seq and ChIP-seq data using 2D SOM metaclusters. C_LI

genomics↗

bioRxiv2020

Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic

The COVID-19 pandemic spread very fast around the world. A few days after the first detected case in South Africa, an infection started a large hospital outbreak in Durban, KwaZulu-Natal. Phylogenetic analysis of SARS-CoV-2 genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. In this manuscript, we outline the obstacles we encountered in order to genotype SARS-CoV-2 in real-time during an urgent outbreak investigation. In this process, we encountered problems with the length of the original genotyping protocol, reagent stockout and sample degradation and storage. However, we managed to set up three different library preparation methods for sequencing in Illumina. We also managed to decrease the hands on library preparation time from twelve to three hours, which allowed us to complete the outbreak investigation in just a few weeks. We also fine-tuned a simple bioinformatics workflow for the assembly of high-quality genomes in real-time. In order to allow other laboratories to learn from our experience, we released all of the library preparation and bioinformatics protocols publicly and distributed them to other laboratories of the South African Network for Genomics Surveillance (SANGS) consortium.

genomics↗

bioRxiv2020

Pituitary stem cells produce paracrine WNT signals to control the expansion of their descendant progenitor cells

In response to physiological demand, the pituitary gland generates new hormone-secreting cells from committed progenitor cells throughout life. It remains unclear to what extent pituitary stem cells (PSCs), which uniquely express SOX2, contribute to pituitary growth and renewal. Moreover, neither the signals that drive proliferation nor their sources have been elucidated. We have used genetic approaches in the mouse, showing that the WNT pathway is essential for proliferation of all lineages in the gland. We reveal that SOX2+ stem cells are a key source of WNT ligands. By blocking secretion of WNTs from SOX2+ PSCs in vivo, we demonstrate that proliferation of neighbouring committed progenitor cells declines, demonstrating that progenitor multiplication depends on the paracrine WNT secretion from SOX2+ PSCs. Our results indicate that stem cells can hold additional roles in tissue expansion and homeostasis, acting as paracrine signalling centres to coordinate the proliferation of neighbouring cells.

developmental biology↗

bioRxiv2018

Tissue repair in the mouse liver following acute carbon tetrachloride depends on injury-induced Wnt/β-catenin signaling

In the liver, Wnt/{beta}-catenin signaling is involved in regulating zonation and hepatocyte proliferation during homeostasis. We have examined Wnt gene expression and signaling after injury and we show by in situ hybridization that Wnts are activated by acute carbon tetrachloride (CCl4) toxicity. Following injury, peri-injury hepatocytes become Wnt-responsive, expressing the Wnt target gene Axin2. Lineage tracing of peri-injury Axin2+ hepatocytes shows that during recovery, the injured parenchyma becomes repopulated and repaired by Axin2+ descendants. Using single cell RNA sequencing (scRNA-seq), we show that endothelial cells are the major source of Wnts following acute CCl4 toxicity. Induced loss of {beta}-catenin in peri-injury hepatocytes results in delayed repair and ultimately to injury-induced lethality, while loss of Wnt production from endothelial cells leads to a delay in the proliferative response after injury.\n\nConclusionOur Pindings highlight the importance of the Wnt/{beta}-catenin signaling pathway in restoring tissue integrity following acute liver toxicity and establishes a role of endothelial cells as an important Wnt-producing regulator of liver tissue repair following localized liver injury.

developmental biology↗

bioRxiv2018

The role of matrix-oriented salt-bridge on the proton transport in a multimeric uncoupling protein 2

Uncoupling proteins (UCPs) are members of the mitochondrial carrier family (MCF) that transport protons across the inner mitochondrial membrane, thereby uncoupling electron transport from ATP synthesis. The stoichiometry of UCPs, and the possibility of co-existence of this protein as mono-meric and associated forms in lipid membranes remain an intriguing open question. In the current study, the tertiary structure of UCP2 was analyzed both experimentally and through molecular dynamics (MD) simulations. After recombinant expression of UCP2 in the inner membrane of E. coli, the protein was directly extracted from the bacterial membranes with a non-denaturing detergent and purified both as a pure monomer and as a mixture of monomers, dimers and tetramers. Both protein preparations were re-constituted in egg yolk lipid vesicles. Gel electrophoresis, circular dichroism spectroscopy and fluorescence methods were used to characterize the structure and the proton transport function of protein. UCP2 showed unique stable tetrameric forms in lipid bilayers. MD simulations using membrane lipids and principal component analysis support the experimental results and provided new molecular insights into the nature of noncovalent interactions in oligomeric UCP2. MD simulations indicate that UCP2 tetramers are asymmetric dimers of dimers, in which the interactions between the monomers forming the dimer are stronger than the interactions between the dimers within the tetramer. It is also shown that UCP2 has a specific tendency to form functional tetramers in lipid bilayers, capable of proton transport. The asymmetric nature of the UCP2 tetramer could act as a scaffold for regulating the activity of the monomeric units through cooperative intercommunication between these subunits. Under similar experimental conditions, the structurally comparable ADP/ATP carrier protein did not form tetramers in vesicles, implying that spontaneous tetramerization cannot be generalized to all MCF members.\n\nSTATEMENT OF SIGNIFICANCESelf-assembly of membrane proteins plays a significant role in their biological function. In this article, both experimental and computational evidence are provided for spontaneous tetramerization of one of the mitochondrial uncoupling proteins (UCP2) in model lipid membranes. It is also shown that the tetrameric form of UCP2 is capable of proton transport, which leads to regulation of ATP synthesis in mitochondrion. Molecular dynamics simulations confirm the presence of asymmetric UCP2 tetramers as a potential scaffold for regulating the activity of the monomeric units through mutual intercommunication. The outcome of this study provides a solid ground for potential co-existence of monomeric and multimeric functional forms of UCPs that contributes to a deeper molecular insight into their structure and function.

biophysics↗