Biology subjects

Hosny, N.

Publications and source records attributed to Hosny, N..

4 recordsLinked to original sources

bioRxiv2026

LYNX: a deep generative model for linking spatial dynamics and cellinteractions in multimodal spatial data

Tissues are spatially organized systems in which cell states, functions and interactions vary across spatial coordinates, forming compartments or gradients shaped by local microenvironments. Understanding how molecular features and cell-cell interactions change across space and time is central to studying development, homeostasis and disease. Addressing these questions increasingly requires the integration of multi-modal spatial data, which provides complementary views of cellular and structural organization. However, existing computational approaches typically combine modalities by weighting them equally, overlooking domain-specific technical artifacts, differences in spatial resolution and non-overlapping feature spaces. In addition, methods for spatial cell-cell communication analysis are largely developed for single-modality settings and do not model how interactions vary across the tissue. To address these gaps, we introduce LYNX, a deep generative framework that learns a shared latent representation of spatial dynamics from joint-measured modalities in the 2D or 3D domain, to provide a unified coordinate system for modeling how cell-cell interactions, phenotypes, and molecular programs vary along continuous spatial gradients. LYNX identifies spatial programs difficult to resolve with existing approaches, including metabolically coupled porto-central interaction remodeling in liver, recovery of degraded proteomic signals along the cortico-medullary axis in thymus, and branching trajectories towards DCIS and invasive niches marked by distinct stromal activation-states and immune-tumor crosstalk in breast tumor microenvironment. We demonstrate that LYNX robustly infers spatially resolved gradients, maps functional compartments and cell-cell interactions along spatial axes and is compatible across diverse spatial profiling technologies, modalities, and resolution disparities. LYNX provides a foundational and scalable framework to advance our understanding of healthy tissue physiology and to decode temporal evolution of complex diseases.

bioengineering↗

bioRxiv2025

HIF-1α and RhoA Drive Enhanced Motility and Aerotaxis of Polyaneuploid Prostate Cancer Cells in Hypoxia

Most cancer deaths result from metastasis, yet only a rare subset of tumor cells can complete this process. Among these, polyaneuploid cancer cells (PACCs), which arise via endoreplication under stressors such as hypoxia, are implicated as metastatic drivers, but how they acquire this potential is poorly understood. Here, we show that prostate cancer-derived PACCs exhibit features predictive of invasion and intravasation. Time-lapse fluorescence microscopy and single-cell tracking under hypoxia revealed that PACCs migrated significantly farther than Non-PACCs, consistent with local invasion. PACC trajectories showed a strong tendency to migrate toward oxygen, consistent with aerotaxis and predictive of intravasation. siRNA-mediated knockdown demonstrated that the enhanced motility and aerotaxis of hypoxic PACCs require both HIF-1and RhoA, with RhoA expression suppressed upon HIF-1 inhibition. Altogether, we propose a HIF-1[->] RhoA [->] motility/aerotaxis mechanism enabling PACCs to escape hypoxic cores, invade tissue, and access vasculature, highlighting them as a uniquely invasive subpopulation with implications for anti-metastatic therapies.

cancer biology↗

bioRxiv2025

Elucidating cancer cachexia-mediated aberrant cardiac wasting signaling in human iPSC-derived cardiac muscle

Cancer cachexia is a highly debilitating clinical syndrome of involuntary body mass loss featuring profound muscle wasting leading to high mortality. Notably, cardiac wasting is prominent in cancer patients and cancer survivors. Cachexia studies present significant challenges due to the absence of human models and mainly short-term animal studies. To address this translational gap, we have developed a robust human-based cachexia experimental approach characterized by marked cardiac muscle wasting and contractile dysfunction, with increased expression of protein degradation markers. Using human iPSC-derived cardiac muscle, we investigated morphological, functional, and metabolic alterations in the key stages of cachexia and in the post-cachexia phase. C26 and HCT116 tumor cell lines were used to induce cachexia by two methods, pulse addition of cancer cell conditioned media or in transwell-adapted co-culture. Cachectic cardiac myocytes exhibited reduced contraction amplitude, prolonged relaxation time, and increased oxygen consumption rate (OCR), as assessed by video-based and Seahorse analyses. Mechanistic investigations centered on the Atrogin-1/Calcineurin A/NFAT axis revealed this signaling pathway as a central driver of cachexia-induced cardiac atrophy. Cachectic cardiac myocytes exhibited significant upregulation of Atrogin-1, leading to a marked decrease in Calcineurin A protein levels. This, in turn, impaired nuclear translocation of NFAT, thereby suppressing its transcriptional activity and downstream cell growth signaling. These molecular changes were accompanied by increased autophagic flux, as indicated by elevated LC3BII/LC3BI ratios. Furthermore, withdrawal of cachexia-inducing stimuli followed by regular media changes for one week led to normalization of Atrogin-1 and autophagy markers; however, functional impairments and metabolic dysregulation persisted, highlighting delayed recovery. Our new findings establish the Atrogin-1/Calcineurin A/NFAT axis as a key regulatory mechanism in cardiac muscle wasting and suggest this aberrant signaling axis may serve as a targetable mechanism for treatment of cachexia-induced cardiac dysfunction. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC="FIGDIR/small/670675v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@12e9borg.highwire.dtl.DTLVardef@19ad494org.highwire.dtl.DTLVardef@1fa664corg.highwire.dtl.DTLVardef@5232a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Application of Airy beam Light sheet microscopy to examine early neurodevelopmental structures in 3D hiPSC-derived human cortical spheroids

BackgroundThe inability to observe relevant biological processes in vivo significantly restricts human neurodevelopmental research. Advances in appropriate in vitro model systems, including patient-specific human brain organoids and human Cortical Spheroids (hCSs) offer a pragmatic solution to this issue. In particular, hCSs are an accessible method of generating homogenous organoids of dorsal telencephalic fate, which recapitulate key aspects of human corticogenesis, including the formation of neural rosettes. These neurogeneic niches give rise to neural progenitors that subsequently differentiate into neurons. Atypical formation of these structures has been associated with neurodevelopmental disorders such as autism spectrum conditions, from studies of patient-specific human induced pluripotent stem cells grown as 2D cultures. Thus far however, conventional methods of tissue preparation in this field limit the ability to image these structures in three-dimensions within intact hSC or other 3D preparations. To overcome this limitation, we have sought to optimise a methodological approach to process hCSs to maximise the utility of a novel Airy-beam light sheet microscope (ALSM) to acquire high resolution volumetric images of internal structures within hCS representative of early developmental time points. ResultsConventional approaches to imaging hCS by confocal microscopy were limited in their ability to image effectively into intact spheroids. Conversely, volumetric acquisition by ALSM offered superior imaging through intact, non-clarified, in vitro tissues, in both speed and resolution as compared to conventional confocal imaging systems. Furthermore, optimised immunohistochemistry and optical clearing of hCSs afforded improved imaging at depth. This permitted visualization of the morphology of the inner lumen of neural rosettes. ConclusionWe present an optimized methodology that takes advantage of an ALSM system that can rapidly image intact 3D brain organoids at high resolution while retaining a large field of view. This imaging modality can be applied to both non-cleared and cleared in vitro human brain spheroids derived from hiPSCs for precise examination of their internal 3D structures. Furthermore, this process represents a rapid, highly efficient method to examine and quantify in 3D the formation of key structures required for the coordination of neurodevelopmental processes in both health and disease states. We posit that this approach would facilitate investigation of human neurodevelopmental processes.

neuroscience↗