Biology subjects

Serra, M.

Publications and source records attributed to Serra, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Recipient-driven metabolic and epigenetic remodeling of donor hematopoietic cells after transplantation in Fanconi Anemia.

Background Haematopoietic cell transplantation (HCT) restores donor-derived haematopoiesis in Fanconi anaemia (FA) but leaves recipient stromal and other non-haematopoietic cells genetically uncorrected. We investigated to what extent the persistent FA recipient environment influences the metabolic, redox, inflammatory and epigenetic phenotype of donor-derived haematopoietic cells after HCT. Methods Peripheral blood and, when available, bone marrow samples were analysed from healthy donors, patients with FA before and after HCT, and severe aplastic anaemia (SAA) patients after HCT as transplant controls. Mitochondrial function, cellular energy status, oxidative damage, antioxidant responses and circulating cytokines were assessed. Healthy donor mononuclear cells were exposed to conditioned media from FANCA-deficient mesenchymal stromal cells or FA fibroblasts, with FANCA-corrected fibroblasts as controls. DNA methylation profiling, acute inflammatory stimulation and pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress were also performed. Results Despite stable full donor chimerism, FA recipients retained a pro-inflammatory and pro-oxidative circulating environment after HCT that was not observed in SAA transplant controls. Donor-derived mononuclear cells exposed to this environment acquired a distinct dysfunctional phenotype characterized by impaired mitochondrial oxidative phosphorylation and energy homeostasis, compensatory antioxidant and stress-response activation, and persistent lipid and protein oxidation. These alterations remained detectable after 96 h of ex vivo culture, suggesting relatively stable cellular remodelling, and were accompanied by a DNA methylation profile that, although globally shifted toward the donor state, retained an intermediate FA-associated episignature. Mechanistically, conditioned media from FANCA-deficient stromal cells and FA fibroblasts reproduced mitochondrial and oxidative abnormalities in healthy donor cells, whereas FANCA-corrected fibroblasts did not. Pharmacological targeting of inflammatory pathways or mitochondrial oxidative stress improved energy homeostasis and reduced oxidative damage, supporting a contributory role for chronic inflammation and oxidative stress in the microenvironment-driven phenotype acquired by donor-derived cells. Conclusions HCT corrects FA haematopoiesis without fully normalising the recipient environment. Persistent exposure to the FA milieu promotes metabolic, redox, signalling and epigenetic remodelling of donor-derived haematopoietic cells after transplantation. These findings identify the recipient environment as a determinant of post-HCT cell biology and highlight chronic inflammation and oxidative stress as mechanisms contributing to donor-cell remodelling in FA.

cell biology↗

bioRxiv2026

APLNR regulates directed migration to spatially pattern mesoderm in human gastruloids

During human gastrulation, mesoderm progenitors migrate while acquiring distinct identities. Whether this movement contributes to subsequent patterning remains unclear. Here, we identify the apelin receptor (APLNR) as a regulator of directed migration of mesoderm in human gastruloids. TBXT+ cells ingress basally and disperse from the PS-like region toward epiblast-like cells. Tracking reveals that this dispersal reflects a directional bias rather than increased speed. APLNR is enriched in nascent mesoderm, while its ligand APELA is expressed in adjacent epithelial cells. Control gastruloids exhibit fourfold greater dispersal than APLNR-depleted gastruloids despite modest speed differences, consistent with a model of chemotaxis by an epithelial ligand field. Paraxial and lateral mesoderm differentiation competence is preserved following APLNR depletion, while signaling programs and central FOXC2+ paraxial organization are altered. These findings support a role for APLNR-dependent guidance in positioning competent mesoderm progenitors for subsequent patterning.

developmental biology↗

bioRxiv2026

Pdk1-dependent metabolic heterogeneity promotes aggressive colorectal cancer through cell-intrinsic interferon signaling

Tumor heterogeneity is a major determinant of tumor progression and therapeutic resistance, yet the contribution of metabolism to intratumoral heterogeneity still remains poorly explored. Here, we find that pyruvate dehydrogenase kinase-1 (Pdk1) expression defines metabolically distinct cancer cell populations in colorectal tumors. Image-based spatial single-cell phenotyping shows that Pdk1-high cells are associated with tumor progression in orthotopic models of colorectal cancer (CRC). Genetic ablation experiments demonstrate the role of Pdk1-high cells in tumor growth, 5-fluorouracil chemoresistance and tumor relapse. Mechanistically, we identify a link between Pdk1-driven metabolic states and specific cell phenotypes, where Pdk1-high cancer cells exhibit an EMT, stem cell-like phenotype characterized by increased interferon (IFN) signaling. Mitochondrial remodeling in Pdk1-high cells leads to the release of mitochondrial DNA to the cytosol and activation of IFN pathways, promoting Pdk1-driven phenotypes. Inhibition of IFN signaling impairs the tumorigenic and aggressive features of Pdk1-high cancer cells, thus establishing a functional connection between metabolic heterogeneity, cell-intrinsic IFN signaling and aggressive CRC.

cancer biology↗

bioRxiv2026

Sex-specific effects of prenatal delta-9-tetrahydrocannabinol exposure on repetitive behavior and prefrontal cortex neuronal excitability in preadolescent rats

Cannabis is the most common illicit drug abused worldwide, and its consumption has substantially increased among pregnant women. We previously demonstrated that male preadolescent offspring prenatally exposed to {Delta}9-tetrahydrocannabinol (THC), a model of prenatal cannabinoid exposure (PCE), exhibit a mesolimbic dopamine (DA) neuron dysfunction contributing to at-risk psychotic-like (endo)phenotypes that are unmasked by acute THC exposure at preadolescence. Dysregulation of mesocortical DA signaling along with prefrontal cortex (PFC) function is also a central feature of psychotic disorders. Furthermore, studies investigating the impact of PCE on PFC in the offspring at preadolescence, a window of heightened plasticity and vulnerability, are limited. To fill this gap, we applied a multiscale analysis of mesocortical DA transmission and PFC function in PCE preadolescent offspring by integrating behavioral, neurochemical, electrophysiological, and molecular approaches. PCE enhanced spontaneous repetitive behaviors in a male-specific manner. PCE also abolished sex differences in the intrinsic excitability of PFC pyramidal neurons and Netrin-1 expression. In addition, PCE altered the expression of genes associated with endocannabinoid signaling without changing basal and THC-induced extracellular levels of DA in the PFC. Collectively, these findings demonstrate that prenatal THC exposure disrupts both proper maturation and sexual differentiation of PFC circuitry, thus extending the impact of PCE from previously described mesolimbic abnormalities to mesocortical pathway. Finally, our data identify early cortical molecular and cellular alterations that may contribute to neuropsychiatric vulnerability later in life. Highlights* Preadolescent male rats exposed in utero to THC display repetitive behavior * Prenatal cannabinoid exposure (PCE) does not alter dopamine transmission in the PFC * PCE potentiates AMPA-mediated transmission in male pyramidal cells * PCE abolishes sex differences in Netrin-1 expression levels in the PFC

neuroscience↗

bioRxiv2026

Achiral Odd Mechanics in Cell Monolayers

Cell monolayers are active, orientationally ordered materials whose mechanics can depart from near-equilibrium behavior. Existing continuum theories often inherit assumptions from equilibrium liquid-crystal physics, motivating explicit nonequilibrium formulations. Here, we develop a minimal continuum model of two-dimensional monolayers based on odd mechanics, accounting for broken symmetries and nonequilibrium dynamics. We show that nematic order can support an odd viscous modulus generated by broken time-reversal symmetry and spatial anisotropy, without chirality. The model reproduces half-integer defect motion and stress profiles in Madin-Darby canine kidney (MDCK) monolayers, as well as defect-associated cell accumulation and depletion in neural progenitor and ovarian mesothelium systems. Finally, we estimate the viscous-moduli tensor from measured stress, velocity, and orientation fields in MDCK monolayers and identify a nonzero odd modulus. Our results show that odd mechanics provides a minimal framework for nonequilibrium cell monolayers, complementing conventional active-nematic theories.

cell biology↗

bioRxiv2026

Safety Transparency in Animal Cell-Cultured Ingredients for Pet Food: A Case Study Establishing the Standard for Public Disclosure

Animal cell-cultured ingredients are entering the EU and UK pet food markets under frameworks that do not require pre-market, ingredient-level safety assessments, creating an ethical need for transparent safety disclosure. We present the first public safety dossier for this sector, describing the proprietary mouse embryonic stem cell line PE25 and its derived, non-viable cellular and conditioned media ingredient produced in food and feed-grade media. PE25 characterization confirmed Mus musculus identity, sterility, absence of mycoplasma and replication-competent retroviruses, and stable growth. Doxorubicin-induced p53 stress testing, CD44/BMI1 profiling, and soft agar assays showed no cancer-like traits and a non-tumorigenic profile; the final ingredient contains no viable cells. Independent OECD TG 471 and 487 assays confirmed non-genotoxicity. Heavy metals, biogenic amines, solvents, and chemical residues were below regulatory limits. Given process variability, we recommend case-by-case safety evaluation and propose this dossier as a model for responsible commercialization.

cell biology↗

bioRxiv2026

Nitazoxanide activates BMP9-ALK1-SMAD signaling cascade and improves HHT vascular pathology

ObjectiveHereditary hemorrhagic telangiectasia (HHT) is a vascular genetic disorder caused by endothelial cell dysfunction and characterized by telangiectasias and arteriovenous malformations (AVMs). HHT results primarily from loss-of-function mutations affecting components of the BMP9-ALK1-ENG-SMAD signaling cascade, a pathway essential for endothelial quiescence and vascular homeostasis, and currently lacks a cure. Here, we investigated whether nitazoxanide, an orally bioavailable drug with extensive clinical use, can modulate endothelial signaling relevant to HHT. Approach and ResultsNitazoxanide treatment activated SMAD1/5/8 signaling and increased expression of the downstream target ID1 in endothelial cells, while concurrently inhibiting mTOR signaling, indicating a dual modulatory effect on pathways implicated in HHT pathogenesis. In vivo, nitazoxanide activated SMAD signaling in BMP9/10-immunoblocked mice and significantly reduced AVM formation and hypervascularization. Importantly, nitazoxanide restored SMAD1/5/8 activation and ID1 expression in patient-derived blood outgrowth endothelial cells harboring loss-of-function mutations in ALK1 or SMAD4, which exhibit impaired BMP signaling. ConclusionThese findings identify nitazoxanide as a pharmacological modulator capable of activating BMP-SMAD signaling while restraining mTOR activity, thereby overcoming key signaling defects in HHT endothelial cells. Collectively, our results highlight nitazoxanide as a promising therapeutic candidate to target endothelial dysfunction in HHT.

cell biology↗

bioRxiv2026

Mapping binding landscape of allosteric inhibitor G6PDi-1 on human G6PD

Targeting the oxidative pentose phosphate pathway by inhibiting glucose-6-phosphate dehydrogenase (G6PD), is a promising anticancer strategy, yet clinically useful inhibitors remain unavailable. A key limitation is the lack of molecular insight into how allosteric and non-competitive inhibitors perturb enzymatic activity, limiting rational optimization. Here, we investigated the mechanism of G6PDi-1, a potent, reversible, non-competitive G6PD inhibitor, by combining biochemical assays with molecular dynamics simulations, Markov state model and MM/PBSA binding energy calculations. Experimentally, G6PDi-1 reduced active dimer formation in hepatoblastoma HepG2 cells and increased the inactive monomer fraction, linking inhibition to disrupted oligomerization. Computationally, we identified multiple sites on the enzyme surface, with preferential binding at dimer interface that sterically blocks oligomerization. Importantly, additional distal sites showed enhanced inter-residue correlations, suggesting secondary allosteric effects that shift G6PD toward monomeric states less competent for oligomerization. These findings provide a molecular basis for structure-based development of improved strategies for G6PD inhibition suited for cancer therapy.

biophysics↗

bioRxiv2026

Positional information and information flows in dynamic tissues

During development, embryos store, transmit, and transform information to generate spatial patterns. Positional information (PI) quantifies how precisely cells form patterns at a given time, but cell motion has limited its application to static tissues. We introduce a framework for PI in dynamic tissues by decomposing mutual information between cells positions and properties over time into information flows contributing to PI preservation, loss and generation. These reveal information-theoretic signatures of ubiquitous developmental processes, including instruction, sorting and mixing, directly from data. Applying this framework to whole-embryo cell trajectories in Drosophila, mouse and zebrafish gastrulation, we provide local and global information-theoretic quantification of cell mixing and derive bounds on PI preservation imposed by tissue dynamics. Analyzing tissue flows as dynamical systems, we further show that morphogenesis structures mixing, preferentially preserving specific patterns. Finally, we derive inequality conditions for tracing generated PI to candidate information sources and distinguishing among alternative pattern-formation mechanisms, from programmed extracellular cues to self-organizing intercellular interactions.

biophysics↗

bioRxiv2026

A new therapeutic approach for Parkinson's disease: dual targeting of alpha-Synuclein aggregation and microglial function by the novel immunomodulator 3-Monothiopomalidomide

Background-Synuclein (-Syn) plays a central role in Parkinsons disease (PD). Under pathological conditions, -Syn aggregates into toxic oligomers and fibrils that act as damage-associated molecular patterns (DAMPs), stimulating microglial reactivity. This -Syn-microglia axis creates a self-perpetuating cycle of neuroinflammation and neurodegeneration, accelerating dopaminergic neuron loss in the substantia nigra pars compacta (SNpc) and contributing to motor deficits. Moreover, -Syn pathology spreads through the brain, disrupting synaptic plasticity in cognitive regions like the cortex and hippocampus, leading to early cognitive decline. Thus, targeting -Syn aggregation and its inflammatory consequences presents a promising dual-hit therapeutic strategy for PD. MethodsThis study investigates the therapeutic potential of 3-monothiopomalidomide (3MP), a novel thalidomide derivative designed to reduce neuroinflammation with a potentially better safety profile than Pomalidomide (POM). The neuroprotective and anti-inflammatory effects of 3MP were evaluated in rat primary mesencephalic mixed neuron-microglia cultures exposed to human -Syn oligomers (H-SynOs). Anti-aggregation activity was assessed via Thioflavin T (ThT) assays and Thioflavin S (ThS) staining in SH-SY5Y cells. Finally, the anti-aggregation, anti-inflammatory, and neuroprotective effects of 3MP were evaluated in vivo in a rat model of PD induced by intracerebral infusion of H-SynOs. ResultsIn primary cell cultures, 3MP dose-dependently reduced -Syn-induced neuronal death and microglial inflammatory responses. It also significantly inhibited -Syn aggregation in vitro in the ThT assay and in SH-SY5Y cells exposed to -Syn protofibrils, outperforming POM. When chronically administered in vivo, 3MP preserved dopaminergic neurons within the SNpc and yielded functional benefits on motor and cognitive readouts. Notably, 3MP markedly attenuated -Syn aggregates induced by the H-SynOs infusion in the SNpc more efficiently than POM, as shown by reduced intraneuronal staining for pSer129--Syn+ and reduced pSer129-Syn in both cytoplasmic and phagolysosomal compartments of microglia. In addition, mesencephalic and cortical inflammatory microgliosis that followed to intranigral H-SynOs-infusion, were significantly dampened by 3MP. ConclusionsOverall, 3MP emerges as a dual-action drug candidate capable of modulating neuroinflammation and -Syn aggregation and thereby disrupting the -Syn-driven inflammatory cycle. Its neuroprotective effects and favourable safety profile support its potential as a disease-modifying therapy for PD, with promising implications for clinical translation.

neuroscience↗

bioRxiv2026

Corticospinal propagation of full-length TDP-43 toxicity drives brain-to-muscle pathology

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive degeneration of upper and lower motor neurons. Cytoplasmic inclusions containing TAR DNA-binding protein 43 (TDP-43), a key regulator of RNA metabolism, represent a pathological hallmark of all sporadic (sALS) and most familial (fALS) forms, underscoring its central role in disease pathophysiology. In affected neurons, full-length (FL) TDP-43 undergoes nuclear-to-cytoplasmic mislocalization, leading to aggregation and cellular dysfunction, and can be released to propagate pathology across neural and non-neural circuits. However, the in vivo toxicity and spreading capacity of FL TDP-43 remain poorly defined. Here, we show that purified, stable human FL TDP-43 was readily internalized by neuronal cells, where it induced aggregation and significantly reduced cell viability. In vivo, an acute unilateral stereotaxic infusion of FL TDP-43 into the rat primary motor cortex was sufficient to trigger a robust centrifugal propagation of pathology along the corticospinal axis and beyond the central nervous system (CNS). TDP-43 pathology spread from the motor cortex to the spinal cord and reached skeletal muscle. At the cellular level, propagated pathology was characterized by intraneuronal phosphorylated TDP-43 (pTDP-43) inclusions, accumulation of high-molecular-weight TDP-43 species, region-specific neurodegeneration, and pronounced mitochondrial vulnerability. Notably, skeletal muscle displayed impaired mitochondrial bioenergetics, accompanied by both motor and non-motor behavioral deficits. Collectively, our findings demonstrate neuron-to-neuron, brain-to-spinal cord and brain-to-muscle spreading of FL TDP-43 toxicity in vivo, establishing a mechanistic link between central TDP-43 pathology and peripheral dysfunction. This work identifies FL TDP-43 as an active driver of disease spreading in ALS and provides the basis for a non-transgenic, TDP-43-driven rat model of disease propagation.

neuroscience↗

bioRxiv2025

CDK4/6 Inhibition Uncovers Subtype-Specific Vulnerabilities and Immune-Related Responses in Esophageal Squamous Cell Carcinoma.

Esophageal squamous cell carcinoma (eSCC) is a highly aggressive malignancy with poor prognosis and limited therapeutic options. Although immune checkpoint inhibitors such as nivolumab, have shown clinical benefit, particularly in patients with high PD-L1 expression, this subgroup represents only a small fraction of eSCC cases. CDK4/6 inhibitors such as palbociclib have only been tested as second-line agents in eSCC, often in combination with EGFR inhibitors, with minimal benefit. Our study evaluates palbociclib as a first-line therapy in treatment-naive eSCC models. Using a panel of 22 eSCC cell lines with integrated multi-omics and phenotypic assays, we identified three response subtypes, resistant, delayed and arrested, correlated to Rb-pathway status. Interestingly, in delayed responders, palbociclib induced replication stress, DNA damage, and unprotected micronuclei enriched for cGAS, triggering activation of interferon-stimulated genes. Consistent with this, palbociclib enhanced immune cell infiltration in delayed eSCC spheroids within a preclinical vascularized 3D microfluidic system. Our study demonstrates that first-line palbociclib treatment unmasks intrinsic vulnerabilities in the CDK4/6-Rb axis and triggers innate immune activation in molecularly defined eSCC. Using a translationally relevant 3D vascularized microfluidic system, we provide evidence that early CDK4/6 inhibition not only stall cancer cell growth but also promotes immune cells recruitment. In conclusion, our study identifies palbociclib as a viable first-line therapeutic candidate in selected eSCC patients and uncover its immunomodulatory potential. SignificanceThese findings support further research into CDK4/6 inhibition as first-line treatment for eSCC and highlight its potential to influence the tumor immune microenvironment in ways that could improve responses to combination therapies.

cancer biology↗

bioRxiv2025

Tissue geometry and mechanochemical feedback initiate rotational migration in Drosophila

Collective migration of epithelial cells drives diverse tissue remodeling processes. In many cases, a free tissue edge polarizes the cells to promote directed motion, but how edge-free or closed epithelia initiate migration remains unclear. Here, we show that the rotational migration of follicular epithelial cells in the Drosophila egg chamber is a self-organizing process. Combining experiments and theoretical modeling, we identify a positive feedback loop in which the mechanosensitive behavior of the atypical cadherin Fat2 synergizes with the rigid-body dynamics of the egg chamber to both initiate and sustain rotation. Mechanical constraints arising from cell-cell interactions and tissue geometry further align this motion around the egg chambers anterior-posterior axis. Our findings reveal a biophysical mechanism -- combining Fat2-mediated velocity-polarity alignment, rigid-body dynamics, and tissue geometry -- by which a closed epithelial tissue self-organizes into persistent, large-scale rotational migration in vivo, expanding current flocking theories.

cell biology↗

bioRxiv2025

Deep Brain Stimulation rescues the homeostasis disruption of circulating D- and L-amino acids level in men with Parkinson's Disease.

Recent evidence indicates a marked downregulation of circulating D- and L-amino acids involved in regulating glutamatergic NMDAR function in Parkinsons disease (PD) patients compared with matched controls. However, the extent to which disease progression and antiparkinsonian therapies contribute to this dysregulation remains unclear. To address these issues, in the present study we measured by High Performance Liquid Chromatography the concentrations of glutamatergic system-related D- and L-amino acids and their precursors in the plasma of male and female healthy controls (HC) and PD patients across three distinct clinical stages and treatment conditions: (1) early stage L-DOPA naive patients treated with MAO-B inhibitors; (2) mid-stage patients treated with L-DOPA; and (3) advanced stage patients receiving Deep Brain Stimulation in the subthalamic nucleus (STN-DBS) plus L-DOPA. Our results reveal notable reduction of circulating neuroactive D- and L-amino acids exclusively in male PD patients, while female patients exhibit a similar directional trend. In male patients, this dysregulation manifests early, with L-DOPA-naive individuals showing decreased plasma levels of L-glutamate and L-aspartate. In mid-stage L-DOPA-treated PD patients, amino acid reductions extend to L-alanine, L-serine, L-glutamine, L-asparagine, and L-threonine. Remarkably, in advanced PD patients, with a median disease duration of [~] 23 years, STN-DBS normalizes the blood concentrations of these amino acids to those observed in HC. In conclusion, our study highlights the potential of circulating D- and L-amino acid dysregulation as an early biomarker of PD and demonstrates that, in contrast to L-DOPA therapy, the STN-DBS confers systemic metabolic benefits even at advanced stages of the disease.

neuroscience↗

bioRxiv2025

Ultra-performance liquid chromatography-mass spectrometry analysis of post-mortem brain tissue reveals specific amino acid profile dysregulation in Parkinson's Disease and Alzheimer's Disease patients

BackgroundCombined metabolomic and HPLC-based analyses have identified significant metabolic alterations in serum and plasma amino acid levels of Parkinsons disease (PD) patients, underscoring their potential as biomarkers. However, it remains unclear whether these biochemical changes also manifest within the central nervous system or are confined to peripheral metabolism, reflecting systemic metabolic disturbances. MethodsTo address this issue, here we measured the levels of 44 different amino acids in post-mortem brain samples from MPTP-intoxicated, L-DOPA-treated monkeys and PD patients at different Braak Lewy body (LB) stages, compared to their respective controls, through targeted Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). ResultsIn MPTP-intoxicated monkeys, UPLC-MS revealed significant elevations in GABA, citrulline, threonine, isoleucine, phenylalanine, valine, glycine, and serine in the putamen, whereas we failed to detect alterations in the superior frontal gyrus (SFG). In PD patients, caudate-putamen (CPu) analysis demonstrated consistent serine upregulation across Braak LB stages 3-4 and 6, with stage 6 specifically showing additional proline increases and phosphoethanolamine decreases. Notably, serine was the sole amino acid significantly altered in both the putamen of MPTP-intoxicated monkeys and the CPu of PD patients. No significant amino acid alterations were observed in the SFG of PD patients, mirroring the findings in monkeys. In contrast, Alzheimers disease (AD) patient SFG samples showed significant increases in tryptophan, phenylalanine, threonine, tyrosine, and methionine relative to controls. ConclusionsThese findings demonstrate that cerebral amino acid alterations in PD are region-specific and primarily localized to brain areas receiving nigrostriatal dopaminergic innervation. Moreover, the cortical amino acid profile in AD differs substantially from that in PD, suggesting disease-specific metabolic signatures in distinct neurodegenerative conditions.

neuroscience↗

bioRxiv2025

Coherent Structures in Active Flows on Dynamic Surfaces

Coherent structures--flow features that organize material transport and deformation--are central to analyzing complex flows in fluids, plasmas, and active matter. Yet, identifying such structures on dynamic surfaces remains an open challenge, limiting their application to many living and synthetic systems. Here, we introduce a geometric framework to extract Lagrangian and Eulerian coherent structures from velocity data on arbitrarily shaped, time-evolving surfaces. Our method operates directly on triangulated meshes, avoiding global parametrizations while preserving objectivity and robustness to noise. Applying this framework to active nematic vesicles, collectively migrating epithelial spheroids, and beating zebrafish hearts, we uncover hidden transport barriers and Lagrangian deformation patterns--such as dynamic attractors, repellers, isotropic and anisotropic strain--missed by conventional Eulerian analyses. This approach offers a new perspective on soft and living matter, revealing how geometry and activity can be harnessed to program synthetic materials, and how Lagrangian strain and principal deformation directions can help uncover mechanosensitive processes and directional cues in morphogenesis.

biophysics↗

bioRxiv2025

miR-29a-3p and TGF-beta Axis in Fanconi Anemia: Mechanisms Driving Metabolic Dysfunction and Genome Stability

Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure and cancer susceptibility due to defective DNA double-strand break repair. However, FA cells are also characterized by mitochondrial dysfunction and redox imbalance. To identify a common factor among these alterations, we focused on miR-29a-3p, a microRNA involved in hematopoiesis. Our data show that miR-29a-3p is downregulated in lymphoblasts and fibroblasts mutated for the FANC-A gene, causing the overexpression of its target genes, FOXO3, SGK1, and IGF1, which results in PI3K/AKT pathway hyperactivation, altered mitochondrial metabolism and insufficient antioxidant response. Furthermore, miR-29a-3p downregulation appears associated with hyperactivation of the TGF-{beta} signal. However, restoring miR-29a-3p expression improves mitochondrial metabolism, oxidative stress response, and DNA damage repair by inhibiting the PI3K/AKT pathway and modulating TGF-{beta} signaling by a feedback mechanism. Based on these findings, miR-29a-3p appears as a promising molecular target to address several mechanisms based on FA pathogenesis.

cell biology↗

bioRxiv2025

Morphogen Patterning in Dynamic Tissues

Embryogenesis integrates morphogenesis--coordinated cell movements--with morphogen patterning and cell differentiation. While largely studied independently, morphogenesis and patterning often unfold simultaneously in early embryos. Yet, how cell movements affect patterning remains unclear, as most pattern formation models assume static tissues. We address this gap by developing a mathematical framework for morphogen patterning in dynamic tissues, reformulating advection-reaction-diffusion models in cells reference frames--the most natural for signal interpretation and fate decisions. This framework (i) elucidates how morphogenesis mediates morphogen transport and compartmentalization: multicellular attractors enhance cell-cell diffusive transport, while repellers act as barriers, affecting cell fate induction and bifurcations. (ii) It formalizes cell-cell signaling ranges in dynamic tissues, deconfounding morphogenetic movements and identifying which cells can communicate. (iii) It provides two nondimensional numbers--typically distinct from the Peclet number--to assess when and where morphogenesis is relevant for patterning. (iv) It elucidates the generative role of cell density dynamics in patterning. We apply this framework to classic patterning models, morphogenetic motifs, and avian gastrulation data. Broadly, our work provides a quantitative perspective to rationalize dynamic tissue patterning in natural and synthetic embryos.

developmental biology↗