Biology subjects

Ratcliffe, C. D. H.

Publications and source records attributed to Ratcliffe, C. D. H..

4 recordsLinked to original sources

bioRxiv2026

Intravital imaging uncovers remodelling of humanised bone marrow-like niches

The bone marrow haematopoietic niche is composed of a diverse array of cell types and extracellular matrix components that together support healthy haematopoiesis. However, live imaging of the bone marrow microenvironment is hampered by tissue accessibility limitations. Using intravital imaging through a titanium imaging window, we investigated the dynamics of human haematopoietic cells and mesenchymal stromal cells within an ectopically implanted humanised scaffold in an immunodeficient murine host. These cell populations expand and differentiate over time, accompanied by progressive remodelling of the scaffold. We observe migration of murine endothelial cells into the scaffold, leading to the formation of a vascular network during the initial development of the humanised niche. Subsequently, the dense collagen matrix that makes up the implanted niche is altered and larger gaps form in regions populated by mesenchymal stroma cells. Collectively, our findings demonstrate dynamic remodelling of the extracellular milieu that supports haematopoietic cell development and establish a platform for longitudinal, in vivo investigation of these processes. Altogether, we describe a novel model that aligns with the 3R guiding principles and enables real-time assessment of bone marrow cell dynamics in vivo. Summary statementRatcliffe and Mian et al. image in vivo dynamics of a bone marrow haematopoietic niche model.

cell biology↗

bioRxiv2025

VISIBLE: An imaging-driven system for sampling, biofabrication, and manipulation of complex biological models

Complex in vitro models (CIVMs), including organoids, spheroids, and bioprinted constructs, have emerged as powerful platforms for recapitulating human tissue architecture and function. However, their inherent heterogeneity and dynamic nature pose significant challenges for standardization, reproducibility, and real-time manipulation. Here, we present VISIBLE (Versatile Imaging-Based Interactive Sampling and Bioprinting System), a modular, imaging-guided platform that integrates real-time monitoring with automated manipulation and 3D bioprinting that addresses these challenges. VISIBLE employs a dual-axis system comprising independently controlled tool-heads and microscope stages, enabling precise spatiotemporal interventions within live cultures. We demonstrate the system capabilities across a range of applications, including morphology- and function-based sampling of organoids and neurospheres, interactive 3D bioprinting, serial scratch assays, and real-time cell-cell interaction studies. Furthermore, we illustrate the system utility in translational contexts through the selective sampling and implantation of patient-derived xenograft organoids. VISIBLE supports long-term culture within an integrated incubation environment and accommodates interchangeable tool-heads for scalable, high-throughput workflows. By enabling closed-loop, feedback-controlled experimentation, VISIBLE addresses some of the critical limitations in existing CIVM platforms and offers a new versatile solution for a wide range of biomedical research applications. This work represents a significant step toward the development of autonomous experimental systems for complex tissue modelling and preclinical investigation.

bioengineering↗

bioRxiv2025

Multimodal profiling unveils a reversible basal-like breast cancer cell state resistant to AKT inhibition

The PI3K/AKT/mTOR pathway is central to cell metabolism and growth. However, pharmacological inhibition of the pathway is not uniformly effective across cancer types, or even within a single cancer model. In this study, we leverage oblique plane microscopy of triple negative breast cancer organoids, as well as lineage tracing to uncover a source of heterogeneity. Non-genetic resistance to AKT inhibition is associated with basal cell features of normal breast epithelium and the master transcription factor of basal cell state, {Delta}Np63, is sufficient to confer resistance. Cells can transition between states within four weeks and therefore, AKT inhibition only delays tumour growth, with tumours rich in KRT14+ cells resulting. Thus, under selection, triple negative breast cancer exploits a repertoire of cell states inherent to the breast.

cancer biology↗

bioRxiv2020

EphB6 regulates TFEB-lysosomal pathway and survival of disseminated indolent breast cancer cells

Late relapse of disseminated cancer cells is a common feature of some types of tumors. Several intrinsic and extrinsic factors have been shown to affect reawakening of disseminated dormant cancer cells (DDCCs); however, the signals and processes sustaining survival of DDCCs in a foreign environment are still poorly understood. We have recently shown that crosstalk with lung epithelial cells promotes persistence of DDCCs from estrogen receptor positive (ER+) breast tumors. Here we show that TFEB-lysosomal axis is activated in DDCCs and that it is modulated by the pro-survival ephrin receptor EphB6. TFEB lysosomal direct targets are enriched in DDCCs in vivo and correlate with relapse in ER+ breast cancer patients. Direct contact of DDCCs with alveolar type I-like lung epithelial cells drives lysosomal accumulation and EphB6 induction. EphB6 contributes to TFEB transcriptional activity and lysosome formation in DDCCs in vitro and in vivo, and supports survival of DDCCs in coculture and in vivo. Furthermore, signaling from EphB6 promotes the proliferative response of surrounding lung parenchymal cells in vivo.

cancer biology↗