Biology subjects

Blum, N.

Publications and source records attributed to Blum, N..

7 recordsLinked to original sources

bioRxiv2026

A Nerve-Dependent NGF Receptor Switch Controls Corneal Epithelial Renewal In Neurotrophic Keratopathy

Corneal epithelial integrity depends on continuous epithelial renewal by limbal epithelial stem cells (LESCs), a process tightly linked to sensory innervation. Loss or impairment of innervation causes neurotrophic keratopathy (NK), a sight-threatening degenerative disease for which rhNGF, the only FDA-approved pharmacologic therapy, often has limited efficacy in advanced or refractory disease. The mechanistic basis for this limited response remains unclear. Using surgical, genetic, and pharmacologic approaches in a rodent model of NK with corneal Schwann cell ablation or structural and functional denervation, together with primary human LESCs, we examined how denervation alters NGF receptor signaling during epithelial repair. In innervated corneas, NGF promoted epithelial regeneration through TrkA. Denervation, however, increased expression of a second NGF receptor, anti-regenerative p75NTR, and activation of its effector JNK, and reduced the activity of the TrkA effector AKT in LESCs. In this altered receptor context, denervation-induced elevation of endogenous NGF amplified p75NTR signaling, thereby explaining the failure of topical rhNGF to rescue severely denervated NK phenotype corneas. Conversely, selective TrkA activation, either with the clinical-stage agonist tavilermide, or pharmacologic or genetic inhibition/ablation of p75NTR, restored AKT signaling and rescued epithelial healing in denervated corneas independent of reinnervation. These findings identify a nerve-dependent NGF receptor switch as a key regulator of corneal epithelial renewal and establish receptor-selective modulation as a mechanistically rational therapeutic strategy for treating NK. One Sentence SummaryCorneal denervation shifts limbal epithelial stem cell signaling from pro-regenerative TrkA-AKT toward anti-regenerative p75NTR-JNK, explaining the limited efficacy of recombinant human nerve growth factor (rhNGF; cenegermin), the only approved pharmacologic therapy for neurotrophic keratopathy, in severely denervated corneas and identifying receptor-selective modulation as a mechanistically distinct therapeutic strategy.

cell biology↗

bioRxiv2026

Mitochondrial malate metabolism acts as a control hub for photosynthesis and carbon-nitrogen balance in Arabidopsis

Malate is a central metabolite in plant energy metabolism and biosynthesis and serves as a major carrier of carbon and reducing equivalents between chloroplasts, the cytosol, and mitochondria. However, how individual malate-converting systems contribute to physiology in specific subcellular compartments remains incompletely understood. Here, we investigated the impact of combined loss of mitochondrial malate dehydrogenase (MDH) and NAD-dependent malic enzyme (NAD-ME) activity in Arabidopsis thaliana by integrating reverse genetics, physiological analyses, transcriptomics, quantitative proteomics, and metabolite profiling. Specifically, we generated triple mutants (mdh1xme1xme2) lacking the predominant mitochondrial isoform MDH1 together with both NAD-ME subunits, thereby reducing overall mitochondrial malate conversion capacity. By growing plants under contrasting photoperiod and irradiance regimes to vary photosynthetic demand on malate-linked fluxes, we uncovered a conditional phenotype that was most pronounced under short-day/low-light conditions. Under these conditions, mdh1xme1xme2 exhibited impaired growth and photosynthetic performance, accompanied by cytosolic redox imbalance and altered chloroplast ultrastructure. Transcriptomic profiling revealed that low light unmasks a dawn-phase bottleneck in establishing photosynthetic and redox homeostasis. Consistent with this, the low-light plastid proteome revealed a reallocation away from chloroplast translation and photosynthetic capacity toward proteome maintenance, photoprotection/repair, and iron/ROS management, consistent with a protective acclimation state that nevertheless constrains carbon gain under energy limitation. Low light also triggered C/N imbalance and ammonium accumulation in the mutants. In contrast, increasing irradiance or extending the photoperiod largely alleviated these defects. Together, our results identified mitochondrial malate conversion capacity as a key control point coupling respiratory energy supply and redox homeostasis to photosynthetic metabolism when photosynthetic energy input is limiting.

plant biology↗

bioRxiv2025

Effects of Pesticide Exposure on Neuroinflammation and Microglial Gene Expression: Relevance to Mechanisms of Alzheimer's Disease Risk

BackgroundAlzheimers disease (AD) is characterized by the presence of amyloid-{beta} plaques, neurofibrillary tangles, and neuroinflammation. Previously, we reported serum levels of dichlorodiphenyldichloroethylene (DDE), the primary metabolite of the pesticide dichlorodiphenyltrichloroethane (DDT), were significantly higher in AD patients compared to age-matched controls and that DDT exposure worsened AD pathology in animal models. ObjectiveHere, we investigated the effect of DDT on neuroinflammation in primary mouse microglia (PMG) and C57BL/6J mice. MethodsEffects of DDT on inflammation and disease-associated microglia were determined in primary mouse microglia and C57BL/6J mice. ResultsPMG exposed to DDT (0.5-5.0 {micro}M) elicited a [~]2-3-fold increase in Il-1b mRNA levels, with similar concentration-dependent upregulation in Il-6, Nos2, and Tnfa. These effects were blocked by the sodium channel antagonist tetrodotoxin, demonstrating the role of DDT-microglial sodium channel interactions in mediating this response. Additionally, NOS2 protein levels increased by [~]1.5-2-fold, while TNFa was elevated by 2-4-fold. C57BL/6J male and female mice exposed to DDT (30 mg/kg) demonstrated significantly increased mRNA levels of Nos2, Il-1b, and Il-6 in the frontal cortex (1.5-2.3-fold), and Nos2, Il-1b, and Tnfa (1.5-1.8-fold) in the hippocampus. Furthermore, microglial homeostatic genes, Cx3cr1, P2ry12, and Tmem119, were downregulated, while stage 1 disease-associated microglia genes were upregulated both in vitro and in vivo. Notably, Apoe and Trem2 were only upregulated in the frontal cortex and hippocampus of females. ConclusionThese data indicate that DDT increases neuroinflammation, which may result from direct actions of DDT on microglia, providing a novel pathway by which DDT may contribute to AD risk.

neuroscience↗

bioRxiv2024

Relating GPCR domains with functionality: receptor helix-bundle and C-terminus differentially influence GRK-specific functions and β-arrestin-mediated regulation

G protein-coupled receptors (GPCRs) orchestrate diverse physiological responses via intracellular signaling through G proteins, GPCR kinases (GRKs), and arrestins. While the role of G proteins in receptor signaling is well-established, the contributions of GRKs and arrestins remain incompletely understood. Here, we investigate the influence of arrestin-interacting GPCR domains (helix-bundle/C-terminus) on {beta}-arrestin conformations and functions using refined biosensors and advanced cellular knockout systems. By focusing on prototypical class A (b2AR) and B (V2R) receptors and their chimeras (b2V2/V2b2), we can now characterize differential {beta}-arrestin conformational changes as primarily mediated by the receptor C-terminus or helix-bundle. Moreover, we demonstrate that some {beta}-arrestin-supported processes are governed by distinct receptor domains, such as ERK1/2 activation (helix-bundle) and arrestin co-internalization (C-terminus), while others depend on the overall GPCR configuration, such as receptor internalization. Our findings elucidate how individual GPCR domains dictate downstream signaling events, shedding light on the structural basis of receptor-specific signaling and regulation.

pharmacology and toxicology↗

bioRxiv2023

A genomic and structural bioinformatic pipeline identifies candidate type VI secretion antibacterial effector-immunity pairs

Type VI secretion systems (T6SS) are common bacterial contractile injection systems that inject toxic "effector" proteins into neighboring cells. We bioinformatically investigated T6SS core proteins in 11,832 genomes of Gram negative bacteria. Comparison of T6SS core proteins that are covalently attached to toxic T6SS effector proteins (T6Es) versus those that are not revealed differences in phylogenetic distribution, physical properties, and genomic position. Using the data generated from our bioinformatic analysis, we developed a new genomic- and Alphafold2-based pipeline for discovery of putative T6Es. We experimentally validated the toxic and immunity activities of four putative antibacterial T6SS effector proteins and four cognate immunity genes from diverse species, respectively. We used Foldseek to predict possible mechanisms of action of the putative T6Es, which was much more effective than sequence-based methods. Evidence of the possible mechanisms of action of the putative T6Es was explored through fluorescence microscopy, where we observed cell wall-targeting, DNA degradation, and cell filamentation. This study shows how combining genomic data mining with new structure-based bioinformatic tools can facilitate identification of novel antibacterial toxins.

microbiology↗

bioRxiv2022

Localized heterochrony integrates overgrowth potential of oncogenic clones

Somatic oncogenic mutations are frequent and can occur early during development. The result is the formation of a patchwork of mutant clones. Such mosaicism has been implicated in a broad range of developmental anomalies however their etiology is poorly understood. Patients carrying a common somatic oncogenic mutation in either PIK3CA or AKT1, can present with disproportionally large digits or limbs. How mutant clones, carrying an oncogenic mutation that often drives unchecked proliferation leads to controlled and coordinated overgrowth is unknown. We use the zebrafish to explore growth dynamics of oncogenic clones during development. In subset of clones, we observe a local increase in proportion of the fin skeleton closely resembling patient overgrowth phenotypes. We unravel the cellular and developmental mechanisms of these overgrowths and pinpoint the cell type and timing of clonal expansion. Coordinated overgrowth is associated with rapid clone expansion during early pre-chondrogenic phase of bone development inducing a heterochronic shift that drives the change in bone size. Our study details how development integrates and translates growth potential of oncogenic clones, thereby shaping the phenotypic consequences of somatic mutations.

developmental biology↗

bioRxiv2021

Novel regulators of growth identified in the evolution of fin proportion in flying fish

Identifying the genetic foundations of trait variation and evolution is challenging as it is often difficult to parse meaningful signals from confounding signatures such as drift and epistasis. However, identification of the genetic loci underlying morphological and physiological traits can be honed through the use of comparative and complementary genetic approaches, whereby shared sets of genes that are repeatedly implicated across large evolutionary time periods as under selection can illuminate important pathways and epistatic relationships that function as novel regulators of trait development. Here we intersect comparative genomic analyses with unbiased mutagenesis screens in distantly related species to define the control of proportional growth, as changes in the size and relative proportions of tissues underlie a large degree of the variant forms seen in nature. Through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors, key innovations for flying fishes and flying halfbeaks. To refine our analysis, we intersected convergent phylogenomic signatures with mutants identified in distantly related zebrafish with altered fin size. Through these paired approaches, we identify a surprising role for an L-type amino acid transporter, lat4a, and the potassium channel, kcnh2a, in the regulation of fin proportion. We show that specific epistatic interaction between these genetic loci in zebrafish closely phenocopies the observed fin proportions of flying fishes. The congruence of experimental and phylogenomic findings point to a conserved, non-canonical signaling interaction that integrates bioelectric cues and amino acid transport in the establishment of relative size in development and evolution.

developmental biology↗