Biology subjects

Cuda, G.

Publications and source records attributed to Cuda, G..

7 recordsLinked to original sources

bioRxiv2026

ClonoDynamics enables replicate-resolved inference of longitudinal T cell receptor repertoire dynamics

Longitudinal T cell receptor repertoire analysis can confound biological change with measurement noise and estimator-induced structure. We developed ClonoDynamics, a framework integrating latent abundance inference with replicate-decoupled estimates of directional change and cross-replicate displacement covariance. Pseudo longitudinal series assembled from 12 independently processed technical measurements of one biological sample revealed apparent restoring dynamics caused by reusing measurements for conditioning and change estimation. Separating these roles between replicates largely removed this artifact. Synthetic controls preserving empirical detection patterns showed dose-dependent recovery of temporal accumulation, resolving the two larger imposed effects but not the smallest. Applied to TCR{beta} repertoires from ten healthy adults sampled weekly for six weeks, ClonoDynamics identified abundance-dependent directional change and shared fluctuations exceeding the technical reference. Within the analyzed abundance domain, these fluctuations showed no consistent positive accumulation over 1 to 5 weeks. ClonoDynamics provides an experimentally benchmarked framework for distinguishing estimator-induced patterns, replicate-consistent longitudinal variation, and temporal accumulation.

immunology↗

bioRxiv2026

Motor Neuron Dysfunction in SORD Deficiency: Implications for Therapeutic Development in Peripheral Neuropathies

Biallelic mutations in the sorbitol dehydrogenase (SORD) gene have been identified as one of the most common causes of autosomal-recessive Charcot-Marie-Tooth disease type 2 (CMT2) and distal hereditary neuropathy, collectively referred to as SORD deficiency. These mutations result in loss of sorbitol dehydrogenase activity, a key enzyme in the polyol pathway that metabolizes glucose, leading to marked accumulation of sorbitol in patient-derived fibroblasts. However, the mechanisms by which SORD dysfunction drives axonal degeneration remain poorly understood, and robust in vitro models of human SORD-deficient motor neurons (MNs) are still lacking. To address this gap, we established a human in vitro model of SORD deficiency by generating induced pluripotent stem cells (iPSCs) from fibroblasts affected individual carrying biallelic SORD mutations (SORDc.757delG/c.316_425+165del), and unaffected heterozygous carriers (SORDc.757delG/wt and SORDwt/c.316_425+165del). These iPSCs were subsequently differentiated into motor neuron progenitors (MNPs) and MNs. Comprehensive analysis of SORD-deficient human cells--including fibroblasts, MNPs, and MNs--revealed pronounced structural and functional abnormalities in the mitochondrial compartment, characterized by mitochondrial fragmentation and increased proton leak. Importantly, fibroblasts derived from two additional unrelated patients carrying the SORD mutation (SORDc.757delG/ c.757delG) further confirmed that SORD deficiency is associated with a mitochondrial phenotype. At the molecular level, SORD deficiency led to upregulation of aldose reductase (AR), another key enzyme of the polyol pathway, resulting in disruption of cellular redox homeostasis and increased oxidative stress. Consistent with these alterations, MNs derived from CMT2/SORD patients exhibited clear neurodegenerative features, including severe defects in neurite branching and synaptic architecture, ultimately impairing neuronal connectivity. Notably, pharmacological inhibition of AR effectively rescued both mitochondrial dysfunction and neuronal structural defects, supporting the targeting of AR as a promising therapeutic strategy for polyol pathway-associated neuropathies as CMT2/SORD and diabetic neuropathy.

cell biology↗

bioRxiv2025

Non-neuronal, TGF-β- extracellular matrix restructuring promotes neurodegeneration in a PSP-Richardson syndrome model

Progressive supranuclear palsy-Richardson syndrome (PSP-RS) is a rapidly progressive tauopathy lacking effective therapies. Although tau aggregation is a defining feature, the initiating mechanisms remain elusive. Here we used patient-derived induced pluripotent stem cell midbrain organoids, integrating single-cell transcriptomics, bulk RNA profiling, and quantitative proteomics, to dissect early pathogenic events. We identified vascular leptomeningeal-like cells (VLMCs) as the first altered population, exhibiting TGF-{beta}-driven extracellular matrix (ECM) remodeling enriched in collagens, integrins, and TGFBI. The resulting pathological ECM increased stiffness, induced integrin clustering, and activated RhoA-ROCK-mediated cytoskeletal disorganization. These changes sustained PI3K-AKT and MAPK-ERK signaling, suppressed PP2A, hyperactivated mTOR, and impaired autophagy, culminating in tau hyperphosphorylation and mislocalization. Pharmacological inhibition of TGF-{beta}, AKT, ERK, or mTORC1 restored autophagic flux, reduced tau burden, and rescued neuronal architecture. Our findings establish non-neuronal, matrix-producing niche cells as upstream drivers of tauopathy and reveal TGF-{beta}-mediated ECM restructuring as a mechanochemical trigger of neurodegeneration, opening multiple therapeutic avenues for PSP-RS and related tauopathies.

neuroscience↗

bioRxiv2024

Mosaic midbrain organoids: a new tool to study Progressive Supranuclear Palsy and advancing clinical neurology research

Progressive supranuclear palsy (PSP) is a severe neurodegenerative disease pathologically characterized by intracellular tangles of hyperphosphorylated tau protein, widely distributed across the neocortex, basal ganglia, and midbrain. Developing effective drugs for PSP presents challenges due to its complex underpinning mechanism and the absence of robust human models that accurately recapitulate biochemical and pathological features of the disease phenotype. Brain organoids have recently emerged as a three-dimensional tissue culture platform to study brain development and pathology. Here, we present a novel induced pluripotent stem cell (iPSC)-derived mosaic midbrain organoid (mMOs) system from four patients with progressive supranuclear palsy-Richardson syndrome (PSP-RS), aimed at reproducing key molecular disease features while reducing variability across organoids derived from different iPSC donors. The PSP-RS 3D model exhibited accumulation of hyperphosphorylated tau protein, predominance of 4R-tau, increased GFAP-positive cells, and PSP-associated histological alterations compared to organoids derived from healthy donors. Pathologically, diseased mMOs showed typical neurofibrillary tangles and tufted-shaped astrocytes, and poorly branched processes of Tyrosine Hydroxylase-immunoreactive cells with thin terminal branches. Our results suggest that mMOs represent a valuable experimental model for PSP research and hold great promise for future identification of new therapeutic targets for progressive supranuclear palsy. O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/597136v1_unfig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@8b2942org.highwire.dtl.DTLVardef@41e3baorg.highwire.dtl.DTLVardef@1cddaeeorg.highwire.dtl.DTLVardef@1e0716c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2023

ZZZ3 protects human embryonic stem cells from nucleolar stress by boosting mTOR/ribosome pathway.

Embryonic stem cells (ESCs) are defined as stem cells with self-renewing and differentiation capabilities. These unique properties are tightly regulated and controlled by complex genetic and molecular mechanisms whose understanding is essential for both basic and translational research. A large number of studies have mostly focused on understanding the molecular mechanisms governing pluripotency and differentiation of ESCs, while the regulation of proliferation has received comparably less attention. In mouse ESCs, pluripotency and proliferation can be independent processes meaning that it is possible for mouse ESCs to maintain their pluripotent state without actively proliferating. Here, we investigate the role of ZZZ3 (Zinc Finger ZZ-Type Containing 3) function in human ESCs homeostasis. We found that knockdown of ZZZ3 strongly decreases ribosome biogenesis, translation, and mTOR signaling leading to nucleolar stress and significant reduction of cell proliferation. This process occurs without affecting pluripotency, suggesting that ZZZ3-depleted ESCs enter a dormant-like state and that proliferation and pluripotency can be uncoupled also in human ESCs.

molecular biology↗

bioRxiv2020

Primate heart regeneration via migration and fibroblast repulsion by human heart progenitors

SUMMARYHuman heart regeneration is one of the most critical unmet clinical needs at a global level1. Muscular regeneration is hampered both by the limited renewing capacity of adult cardiomyocytes2-4 and the onset of cardiac fibrosis5,6, resulting in reduced compliance of the tissue. Primate have proven to be ideal models for pluripotent stem cell strategies for heart regeneration, but unravelling specific approaches to drive cell migration to the site of injury and inhibition of subsequent fibrosis have been elusive. Herein, by combining human cardiac progenitor lineage tracing and single-cell transcriptomics in injured non-human primate heart bio-mimics, we uncover the coordinated muscular regeneration of the primate heart via directed migration of human ventricular progenitors to sites of injury, subsequent fibroblast repulsion targeting fibrosis, and ultimate functional replacement of damaged cardiac muscle by differentiation and electromechanical integration. Single-cell RNAseq captured distinct modes of action, uncovering chemoattraction mediated by CXCL12/CXCR4 signalling and fibroblast repulsion regulated by SLIT2/ROBO1 guidance in organizing cytoskeletal dynamics. Moreover, transplantation of human cardiac progenitors into hypo-immunogenic CAG-LEA29Y transgenic porcine hearts following injury proved their chemotactic response and their ability to generate a remuscularized scar without the risk of arrhythmogenesis in vivo. Our study demonstrates that inherent developmental programs within cardiac progenitors are sequentially activated in the context of disease, allowing the cells to sense and counteract injury. As such, they may represent an ideal bio-therapeutic for functional heart rejuvenation.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2017

3’UTR Remodelling of Axonal Transcripts in Sympathetic Neurons

The 3 untranslated regions (3UTRs) of messenger RNAs (mRNA) are non-coding sequences that regulate several aspects of mRNA metabolism, including intracellular localisation and translation. Here, we show that in sympathetic neuron axons, the 3UTRs of many transcripts undergo cleavage, generating both translatable isoforms expressing a shorter 3UTR, and 3UTR fragments. 3end RNA sequencing indicated that 3UTR cleavage is a potentially widespread event in axons, which is mediated by a protein complex containing the endonuclease Ago2 and the RNA binding protein HuD. Analysis of the Inositol monophosphatase 1 (Impa1) mRNA revealed that a stem loop structure within the 3UTR is necessary for Ago2 cleavage. Thus, remodeling of the 3UTR provides an alternative mechanism that simultaneously regulates local protein synthesis and generates a new class of 3UTR RNAs with yet unknown functions.

neuroscience↗