Biology subjects

Hoppe, C.

Publications and source records attributed to Hoppe, C..

8 recordsLinked to original sources

bioRxiv2026

Lamin A/C directs nucleosome-scale chromatin remodeling to define early lineage segregation in mammals

Chromatin organization underlies gene regulation and cell fate specification, yet how nucleosome-scale chromatin structure contributes to lineage segregation during early development remains unknown. Here, we resolved chromatin ultrastructure during the first lineage decision in mouse and human, which forms the pluripotent inner cell mass (ICM) and trophectoderm (TE). To achieve this, we developed dual-tilt chromatin electron tomography (2T-ChromEMT) that allows multiscale visualization of chromatin architecture. Our analysis reveals that TE cells of both species display denser chromatin with nucleosome aggregation at the nuclear periphery. We show upregulation of the nuclear matrix protein Lamin A/C within the TE lineage across mouse, human, and opossum embryos, indicating that its regulatory role is conserved across eutherian and marsupial species. Loss of Lamin A/C reduces heterochromatin at the nuclear lamina in TE cells, reactivates pluripotency genes, and impairs mouse blastocyst expansion and human blastoid formation. These findings define the nucleosome-resolution chromatin signatures of early mammalian lineages and establish Lamin A/C-mediated chromatin organization as a conserved mechanism in the exit from pluripotency and maintenance of trophectoderm identity.

developmental biology↗

bioRxiv2025

Extrahepatic effects of thyroid hormone and resmetirom override their beneficial hepatic effects in alcohol-associated liver disease in mice

BackgroundAlcohol-associated liver disease (ALD) is a common type of liver disease worldwide. Excessive consumption of ethanol (EtOH) causes fat accumulation leading to hepatic steatosis. Hepatic thyroid hormone (TH) action or liver-specific thyromimetics, e.g. resmetirom, can reduce hepatic triglycerides. We therefore hypothesized that TH treatment could ameliorate ALD. MethodsTo induce ALD, mice were treated with either EtOH or liquid control diet for 10 days followed by a single EtOH or maltose control gavage on day 11. The liquid diets were supplemented with solvent, T3 or Resmetirom. We studied WT and hepatocyte-specific TR{beta} KO mice (hepTR{beta}KO). Effects were measured by clinical chemistry, liver staining, hepatic triglyceride content, and RNA-sequencing. ResultsSurprisingly, resmetirom had no beneficial effect and T3 treatment even aggravated EtOH-induced steatosis (increased liver weight and hepatic triglycerides). The liver phenotype was worsened in hepTR{beta}KO mice, which still suggested beneficial effects of hepatic TR{beta} signaling in WT mice. These seemingly paradoxical results could be explained by extrahepatic effects in WAT: WAT weight and adipocyte size were reduced by EtOH, T3 and resmetirom. These data indicate lipolysis and subsequent fatty acid accumulation in the liver, explaining the more severe ALD phenotype with T3 and attenuated effect of resmetirom. As WAT loss was reduced in hepTR{beta}KO mice, the hepatic TR{beta} mediated the extrahepatic effects of T3 and resmetirom on WAT. ConclusionWe conclude that extrahepatic TH effects in WAT were detrimental in ALD and counteracted beneficial local hepatic TH/TR{beta} action. As WAT loss appeared to originate from the hepatic TR{beta}, this also applied to resmetirom.

pathology↗

bioRxiv2025

ALK Inhibition Prolongs Survival in a Mouse Model of ALK-positive Anaplastic Thyroid Cancer

BackgroundAnaplastic thyroid cancer (ATC) is the most aggressive thyroid cancer with a median survival of about 6 months. So far, no therapies offering a survival benefit are established. Thus, new therapeutic approaches are urgently needed. In general, genetic alterations leading to ATC increase PI3K and MAPK/ERK signalling and include mutations in receptor tyrosine kinases and tumour suppressor genes. They often occur together with the loss of P53, the most prevalent mutation in human ATC. Among such mutations are mutations and rearrangements of the anaplastic lymphoma kinase (ALK) gene. MethodsTo study ATC and potential treatment options, we generated a mouse model with inducible thyrocyte-specific expression of constitutively active mutant ALKF1174L and homozygous deletion of Trp53 due to a Cre recombinase under control of the thyroglobulin promoter (Tg-CreERT2+/0;LSL-ALKF1174L/+;Trp53LoxP/LoxP mice, here referred to as Trp53KO/ALKF1174L mice). Moreover, we established several primary thyroid cancer cell lines harbouring ALKF1174L and Trp53KO and investigated the effects of ALK inhibition in vitro and in vivo. ResultsMedian survival of Trp53KO/ALKF1174L mice was severely reduced and the mice showed massively enlarged thyroids. Histopathology confirmed development of locally invasive and metastatic ATC. Treatment of primary Trp53KO/ALKF1174L ATC cells with the ALK inhibitor TAE-684 decreased AKT and ERK phosphorylation and induced a dose-dependent cytotoxicity. Trp53KO/ALKF1174L mice treated with TAE-684 showed significantly extended median survival compared to the solvent group (66 days vs. 18 days, p < 0.0001). ConclusionOur data demonstrate that the combination of ALKF1174L mutation with Trp53 loss leads to the development of ATC. This study provides first functional data supporting the use of ALK inhibitors in patients with ALK-driven ATC. Our novel ATC mouse model and the derived cell lines offer valuable tools to explore the molecular characteristics of ATC, especially signalling pathway activation and tumour microenvironment, and to test novel therapeutics for the treatment of advanced thyroid cancers.

cancer biology↗

bioRxiv2024

Novel cell states arise in embryonic cells devoid of key reprogramming factors

The capacity for embryonic cells to differentiate relies on a large-scale reprogramming of the oocyte and sperm nucleus into a transient totipotent state. In zebrafish, this reprogramming step is achieved by the pioneer factors Nanog, Pou5f3, and Sox19b (NPS). Yet, it remains unclear whether cells lacking this reprogramming step are directed towards wild type states or towards novel developmental canals in the Waddington landscape of embryonic development. Here we investigate the developmental fate of embryonic cells mutant for NPS by analyzing their single-cell gene expression profiles. We find that cells lacking the first developmental reprogramming steps can acquire distinct cell states. These states are manifested by gene expression modules that result from a failure of nuclear reprogramming, the persistence of the maternal program, and the activation of somatic compensatory programs. As a result, most mutant cells follow new developmental canals and acquire new mixed cell states in development. In contrast, a group of mutant cells acquire primordial germ cell-like states, suggesting that NPS-dependent reprogramming is dispensable for these cell states. Together, these results demonstrate that developmental reprogramming after fertilization is required to differentiate most canonical developmental programs, and loss of the transient totipotent state canalizes embryonic cells into new developmental states in vivo.

developmental biology↗

bioRxiv2023

Genetically encoded affinity reagents (GEARs): A toolkit for visualizing and manipulating endogenous protein function in vivo.

Probing endogenous protein localization and function in vivo remains challenging due to laborious gene targeting and monofunctional alleles. Here, we develop a multifunctional, universal, and adaptable toolkit based on genetically encoded affinity reagents (GEARs). GEARs use nanobodies and single chain variable fragments (scFv), which recognize small epitopes, enabling fluorescent visualization and selective degradation of protein targets in vivo. Furthermore, we delineate a CRISPR/Cas9-based epitope tagging pipeline to demonstrate its utility for producing knock-in alleles that have broad multifunctionality. We use GEARs to examine the native behaviour of the pioneer transcription factor Nanog and the planar cell polarity protein Vangl2 during early zebrafish development. Together, this toolkit provides a versatile system for probing and perturbing endogenous protein function while circumventing challenges associated with conventional gene targeting and is broadly available to the model organism community.

developmental biology↗

bioRxiv2021

Dynamics of hunchback translation in real time and at single mRNA resolution in the Drosophila embryo

The Hunchback (Hb) transcription factor is critical for anterior-posterior patterning of the Drosophila embryo. Despite the maternal hb mRNA acting as a paradigm for translational regulation, due to its repression in the posterior of the embryo, little is known about the translatability of zygotically transcribed hb mRNAs. Here we adapt the SunTag system, developed for imaging translation at single mRNA resolution in tissue culture cells, to the Drosophila embryo to study the translation dynamics of zygotic hb mRNAs. Using singlemolecule imaging in fixed and live embryos, we provide evidence for translational repression of zygotic SunTag-hb mRNAs. While the proportion of SunTag-hb mRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulated hb mRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation in Drosophila.

developmental biology↗

bioRxiv2020

Scalable inference of transcriptional kinetic parameters from MS2 time series data

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSThe MS2-McP (MS2 coat protein) live imaging system allows for visualisation of transcription dynamics through the introduction of hairpin stem-loop sequences into a gene. A fluorescent signal at the site of nascent transcription in the nucleus quantifies mRNA production. computational modelling can be used to infer the promoter states along with the kinetic parameters governing transcription, such as promoter switching frequency and polymerase loading rate. However, modelling of the fluorescent trace presents a challenge due its persistence; the observed fluorescence at a given time point depends on both current and previous promoter states. A memory-adjusted Hidden Markov Model (mHMM) was recently introduced to allow inference of promoter activity from MS2-McP data. However, the computational time for inference scales exponentially with gene length and the mHMM is therefore not currently practical for application to many eukaryotic genes. ResultsWe present a scalable implementation of the mHMM for fast inference of promoter activity and transcriptional kinetic parameters. This new method can model genes of arbitrary length through the use of a time-adaptive truncated compound state space. The truncated state space provides a good approximation to the full state space by retaining the most likely set of states at each time during the forward pass of the algorithm. Testing on MS2-MCP fluorescent data collected from early Drosophila melanogaster embryos indicates that the method provides accurate inference of kinetic parameters within a computationally feasible timeframe. The inferred promoter traces generated by the model can also be used to infer single-cell transcriptional parameters. AvailabilityPython implementation available at https://github.com/ManchesterBioinference/burstInfer, along with code to reproduce the examples presented here.

bioinformatics↗

bioRxiv2019

Modulation of promoter occupancy dictates the transcriptional response to graded BMP signalling levels in the Drosophila embryo

SUMMARYMorphogen gradients specify cell fates during development, with a classic example being the BMP gradient’s conserved role in embryonic dorsal-ventral axis patterning. Here we elucidate how the BMP gradient is interpreted in the Drosophila embryo, by combining live imaging with computational modelling to infer transcriptional burst parameters at single cell resolution. By comparing burst kinetics in cells receiving different levels of BMP signaling, we show that BMP signaling controls burst frequency by regulating the promoter activation rate. We provide evidence that the promoter activation rate is influenced by both enhancer and promoter sequences, whereas Pol II loading rate is primarily modulated by the enhancer. Consistent with BMP-dependent regulation of burst frequency, the numbers of BMP target gene transcripts per cell are graded across their expression domains. We suggest that graded mRNA output is a general feature of morphogen gradient interpretation and discuss how this can impact on cell fate decisions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗