Biology subjects

Najera, J.

Publications and source records attributed to Najera, J..

6 recordsLinked to original sources

bioRxiv2026

Multi-omics and spatial analysis of microgravity-grown glioblastoma organoids reveals superior modeling of advanced disease after long-term spaceflight

Glioblastoma (GBM) is an incurable brain cancer characterized by its highly immunosuppressive tumor microenvironment and aggressive malignant features that resist treatment. To overcome limitations of Earth-based models (sedimentation and disaggregation) and leverage the unique biological effects of space (accelerated disease progression and immune dysregulation), we developed a panel of GBM-myeloid organoids for extended culture on the International Space Station. After 40 days, the spaceflight-grown organoids had more uniform and reproducible morphology compared to identical ground controls. Organoids containing GBM cells + monocytes had increased expression of chronic innate inflammation, adaptive immune activation, and tissue and vascular remodeling-associated genes. There was an increase in organization of gene expression patterns, with mesenchymal-related genes enriched in the core and inflammation-related genes enriched at the periphery, mimicking GBM tumor architecture. Secretomics confirmed the generation of more immunosuppressive organoids, with enrichment of proteins associated with more aggressive disease, including CXCL12 and LOX-1. GBM co-culture organoids thus had enhanced transcriptomic, proteomic, and architectural features when grown in microgravity that are associated with worse patient outcomes from retrospective data. Infrared laser scanning microscopy confirmed spatial chemical gradients for DNA, protein, and lipid species in both space- and terrestrially-grown organoids. In summary, we present not only a novel and superior model of glioblastoma for more relevant basic, mechanistic, and translational research, but also demonstrate methods to acquire high-quality and diverse data from organoids compatible with the unique experimental constraints of biological research in space to help establish a working model for orbital oncology.

cancer biology↗

bioRxiv2025

Instant fluorescence lifetime imaging microscopy reveals mechano-metabolic reprogramming of stromal cells in breast cancer peritumoral microenvironments

The breast peritumor microenvironment (pTME) is increasingly recognized as a mediator of breast cancer progression and treatment resistance. However, if and how growth-induced tumor compressive forces (i.e., solid stresses) influence the breast pTME remains unclear. Here we show using instant fluorescence lifetime imaging microscopy (FLIM)--a frequency-domain FLIM system capable of simultaneous image acquisition and instantaneous data processing--that breast tumor-mimicking in vitro compression promotes metabolic changes in stromal cells found in the breast pTME. Namely, compression shifts NIH3T3 fibroblasts and differentiated 3T3-L1 (d3T3-L1) adipocytes toward a more glycolytic state, while it promotes increased oxidative phosphorylation in 3T3-L1 undifferentiated adipocytes. The gold-standard Seahorse extracellular flux assay fails to capture these changes, underscoring the superior sensitivity of instant FLIM in detecting metabolic shifts. We validate these phenotypic findings at the transcriptomic level via RNA sequencing, confirming that compressed fibroblasts downregulate oxidative phosphorylation and upregulate glycolysis compared to uncompressed controls. We further demonstrate that compression induces mitochondrial dysregulation in undifferentiated adipocytes, driven in part by upregulated mitophagy and disrupted fusion dynamics. Finally, we confirm that these stromal cell types recapitulate these distinct metabolic states in human breast cancer patient samples, consistent with our in vitro findings. By elucidating mechano-metabolic interactions occurring at the tumor-host interface, these results will inform the development of innovative mechano-metabolic reprogramming treatment strategies to improve breast cancer patient survival.

biochemistry↗

bioRxiv2025

Mechanical compression induces neuronal apoptosis, reduces synaptic activity, and promotes glial neuroinflammation in mice and humans

Mass effect, characterized by the compression and deformation of neural tissue from space-occupying lesions, can lead to debilitating neurological symptoms and poses a significant clinical challenge. In the primary brain tumor glioblastoma (GBM), we have shown previously that compressive solid stress originating from the growing tumor reduces cerebral blood flow, leads to neuronal loss, increased functional impairment, and poor clinical outcomes. However, the direct effects of compression on neurons and the underlying biophysical mechanisms are poorly understood. Here, using multi-scale compression systems and physiologically relevant in vitro and in vivo models, we find that mechanical compression induces neuronal apoptosis and synapse loss, leading to disrupted neural network activity. This is accompanied by increased HIF-1 signaling and upregulation of downstream stress-adaptive genes in neurons. We further show that compression triggers AP-1-driven gene expression in glial cells, promoting a neuroinflammatory response. Together, these findings reveal that solid stress directly contributes to neuronal dysfunction and inflammation caused by GBM by activating distinct pathways that can be targeted in future studies for neuroprotection. SIGNIFICANCE STATEMENTGlioblastoma (GBM), the deadliest primary brain tumor in adults, exerts physical forces on surrounding brain tissue as it grows, leading to neuronal damage. However, the molecular mechanisms underlying this process are not well understood. In the present study, by applying multiple model systems, we show that mechanical compression triggers neuronal apoptosis, disrupts synaptic communication between neurons, and reduces neural network activity. We also find that compression activates inflammatory pathways in both neurons and glia, further contributing to neuronal damage. These findings reveal how compression exerted by space-occupying lesions may contribute to patients cognitive and motor impairments and suggest new directions for treatment. This work lays the groundwork for therapies that protect neurons from mechanical injury, with relevance not only to GBM but also other neurological diseases that present with mass effect.

neuroscience↗

bioRxiv2025

Chronic compression drives macrophages toward a pathological pro-tumor state

Macrophages comprise a significant portion of the glioblastoma tumor microenvironment and are essential in promoting immunosuppression and tumor progression. Solid tumors such as glioblastoma generate solid stress as they expand, creating a compressive microenvironment for mechanosensitive immune cells including macrophages. Macrophages are known to respond to various mechanical stimuli but have not yet been studied in the context of chronic compression observed in growing tumors. Here, we used a custom in vitro compression system to elucidate the effects of compressive solid stress on murine macrophages. We found that macrophages have significant morphological, transcriptional, metabolic, and functional responses to compression. These changes corresponded to both canonical pro- and anti-inflammatory macrophage states. The gene expression signatures of compressed macrophages more closely resembled those of glioma-associated macrophages known to be associated with worse patient outcomes. These results indicate that compression alone, independent from tumor cell-derived biochemical factors, may contribute to the pathological tumor-associated macrophage phenotype. This could represent a vicious cycle of tumor immunomechanics and mechano-immunology. Targeting solid stress in tumors or the response to solid stress by macrophages may interrupt this feedback loop to help normalize the tumor immune microenvironment and improve glioblastoma response to immunotherapy.

immunology↗

bioRxiv2023

Single-cell mechanical analysis reveals viscoelastic similarities between normal and neoplastic brain cells

Understanding cancer cell mechanics allows for the identification of novel disease mechanisms, diagnostic biomarkers, and targeted therapies. In this study, we utilized our previously established fluid shear stress assay to investigate and compare the viscoelastic properties of normal immortalized human astrocytes (IHAs) and invasive human glioblastoma (GBM) cells when subjected to physiological levels of shear stress that are present in the brain microenvironment. We used a parallel-flow microfluidic shear system and a camera-coupled optical microscope to expose single cells to fluid shear stress and monitor the resulting deformation in real-time, respectively. From the video-rate imaging, we fed cell deformation information from digital image correlation into a three-parameter generalized Maxwell model to quantify the nuclear and cytoplasmic viscoelastic properties of single cells. We further quantified actin cytoskeleton density and alignment in IHAs and GBM cells via immunofluorescence microscopy and image analysis techniques. Results from our study show that contrary to the behavior of many extracranial cells, normal and cancerous brain cells do not exhibit significant differences in their viscoelastic behavior. Moreover, we also found that the viscoelastic properties of the nucleus and cytoplasm as well as the actin cytoskeletal densities of both brain cell types are similar. Our work suggests that malignant GBM cells exhibit unique mechanical behaviors not seen in other cancer cell types. These results warrant future study to elucidate the distinct biophysical characteristics of the brain and reveal novel mechanical attributes of GBM and other primary brain tumors.

bioengineering↗

bioRxiv2020

Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration

AO_SCPLOWBSTRACTC_SCPLOWHuman Milk Oligosaccharides (HMOs) are abundant carbohydrates fundamental to infant health and development. Although these oligosaccharides were discovered more than half a century ago, their biosynthesis in the mammary gland remains largely uncharacterized. Here, we used a systems biology framework that integrated glycan and RNA expression data to construct an HMO biosynthetic network and predict glycosyltransferases involved. To accomplish this, we constructed models describing the most likely pathways for the synthesis of the oligosaccharides accounting for >95% of the HMO content in human milk. Through our models, we propose candidate genes for elongation, branching, fucosylation, and sialylation of HMOs. We further explored selected enzyme activities through kinetic assay and their co-regulation through transcription factor analysis. These results provide the molecular basis of HMO biosynthesis necessary to guide progress in HMO research and application with the ultimate goal of understanding and improving infant health and development. SO_SCPLOWIGNIFICANCEC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWSTATEMENTC_SCPLOWWith the HMO biosynthesis network resolved, we can begin to connect genotypes with milk types and thereby connect clinical infant, child and even adult outcomes to specific HMOs and HMO modifications. Knowledge of these pathways can simplify the work of synthetic reproduction of these HMOs providing a roadmap for improving infant, child, and overall human health with the specific application of a newly limitless source of nutraceuticals for infants and people of all ages.

systems biology↗