Biology subjects

Amruz Cerna, K.

Publications and source records attributed to Amruz Cerna, K..

4 recordsLinked to original sources

bioRxiv2026

From Patient to Tumor Organoid: Culture Protocol Choice Controls Glioblastoma Tumor Architecture and Identity

BackgroundPatient-derived tumor organoids are widely used in cancer research, yet the biological impact of tissue processing during model generation remains unclear. Fragment-based and dissociation-based approaches are commonly assumed to trade fidelity for uniformity, but their molecular consequences remain incompletely defined. MethodsWe performed a proteome-wide comparison of fragment-based (CUT) and dissociation-based (DIS) glioblastoma organoid protocols using quantitative mass spectrometry. Organoids from multiple patient tumors were cultured under growth factor-free or growth factor-supplemented conditions and compared with matched primary tissue. ResultsBoth protocols produced technically robust glioblastoma organoids when maintained in their native media. However, CUT organoids matched the reproducibility of DIS cultures while preserving a broader extracellular matrix repertoire and networks linked to collagen assembly, vascular support, and cell-matrix signaling. DIS cultures were biased toward exogenous basement membrane components and proliferative, growth factor-responsive states. Across tumors, CUT organoids consistently showed greater proteomic similarity to matched primary tissue, retaining neural, glial, stromal, and extracellular features largely absent from DIS models. ConclusionsFragment-based glioblastoma organoids can be both reproducible and biologically faithful. Tissue dissociation acts as a major perturbation that reshapes extracellular matrix organization, cellular states, and tumor identity, making protocol choice a critical determinant of model fidelity and translational relevance.

cancer biology↗

bioRxiv2026

Patient-Derived PSEN1 Cerebral Organoids Revealed Parallel Development of Amyloid-β Accumulation and Network Dysfunction

Alzheimers disease (AD) is a neurodegenerative disorder characterised by progressive dementia, brain atrophy, and ultimately death. Using cerebral organoids derived from human induced pluripotent stem cells (hiPSCs) carrying the familial PSEN1 A246E variant, we investigated the temporal relationship between amyloid-{beta} (A{beta}) dysregulation and spontaneous neuronal activity. Multielectrode array recordings from the differentiation day 60 (DD60) to at least DD130 revealed that AD organoids exhibited transient hyperexcitability and hypersynchrony compared with wild-type (WT) controls, followed by a gradual decline in activity. During the enhanced excitability stage, both elevated A{beta}42/40 and A{beta} aggregate size showed positive correlations with the percentage of active electrodes and the global synchrony index (GSI) in AD organoids. These findings indicate that A{beta} dysregulation might contribute to transient network hyperexcitability in early AD. The results also suggest that patient-derived cerebral organoids may serve as a translational model to examine early network dysfunction and inform future investigations of potential A{beta}-induced changes in excitability during the preclinical stages of AD.

neuroscience↗

bioRxiv2025

The Alzheimer's-Associated SORL1 p.Y1816C Variant Impairs APP Sorting, Axonal Trafficking, and Neuronal Activity in iPSC-Derived Brain Models

BackgroundSORL1, encoding the sorting receptor SORLA, is now recognized as the fourth autosomal dominant Alzheimers disease (AD) gene. Loss of SORLA function is known to disrupt endosomal trafficking and enhance amyloidogenic APP processing, two key aspects of the onset and progression of AD. However, the pathogenic consequences of disrupted endolysosomal pathways, deregulated protein sorting, as well as the effects of specific SORL1 missense variants on human neuronal function, still remain understudied. MethodsOur investigations were performed using two complementary human iPSC-derived models: 2D NGN2-induced neurons and 3D cerebral organoids established from isogenic wild-type (WT), SORL1 p.Y1816C (KI) missense variant, and SORL1 knock-out (KO) cells. We analyzed SORLA maturation and ectodomain shedding, APP localization, and amyloid-{beta} secretion. Endosomal morphology and neuritic swellings were assessed via electron microscopy, while axonal transport of APP and Rab5+ endosomes was evaluated through live-cell imaging. Neuronal network activity was measured using multielectrode array recordings. ResultsOur results demonstrate that the p.Y1816C variant leads to impaired SORLA maturation and reduced shedding, without affecting neuronal or organoid differentiation. Notably, we show an ultrastructure of endosomes, including their content, and demonstrate that both KO and KI models exhibit early endosome enlargement, increased APP retention in endosomes, elevated A{beta}40/42 secretion, and amyloid-{beta} deposition in 3D organoids. Importantly, we identified previously uncharacterized functional consequences of abolished SORLA activity, including axonal swellings and significantly impaired transport of Rab5+ endosomes and APP, characterized by deregulated velocities, directionality of transport, and increased stalling. Additionally, we discovered that both KO and p.Y1816C KI neurons exhibit abnormal electrophysiological activity, including increased spontaneous firing, burst frequency, and network synchrony. ConclusionsOur study defines the mechanistic consequences of the SORL1 p.Y1816C variant and demonstrates its pathogenicity in human neurons. Importantly, we also identify novel roles for SORLA in maintaining axonal transport homeostasis and regulating neuronal excitability, expanding its functional relevance beyond endosomal APP processing. These findings reinforce the central role of endosomal trafficking disruption in AD and support the use of isogenic human models for evaluating AD risk variants.

neuroscience↗

bioRxiv2025

Viral Infection Induces Alzheimer's Disease-Related Pathways and Senescence in iPSC-Derived Neuronal Models

Structured AbstractO_ST_ABSINTRODUCTIONC_ST_ABSThe Pathogen Infection Hypothesis proposes that {beta}-Amyloid (A{beta}) functions as an antimicrobial peptide, with pathogen-induced aggregation potentially contributing to Alzheimers disease (AD) pathology. METHODSWe used human iPSC-derived 2D neurons and 3D cerebral organoids from wild-type and familial AD (PSEN1/2 mutant) lines to model acute infections with HSV-1 and TBEV and A{beta} aggregation. Transcriptomic and proteomic analyses were conducted to assess molecular responses. RESULTSHSV-1, but not TBEV, induced robust A{beta} clustering, which was, however, dependent on extracellular amyloid peptides. Transcriptomic profiling revealed widespread HSV-1-induced changes, including activation of neurodegeneration-related pathways. Proteomic profiling confirmed enrichment of neurodegeneration- and senescence-associated secretome signatures. PSEN1/2 mutations did not alter the acute infection response. Reanalysis of independent datasets confirmed our findings and revealed a limited protective effect of acyclovir. DISCUSSIONResults directly support the Pathogen Infection Hypothesis and suggest that preventing viral infections via vaccinations may represent a feasible approach to reducing AD risk.

neuroscience↗