Biology subjects

Mueller, S.

Publications and source records attributed to Mueller, S..

At least 19 recordsLinked to original sources

bioRxiv2026

A harmonized phantom MRI quality control framework identifies sources of longitudinal and multi-site variability

The shift towards open science in preclinical research requires high-quality, comparable data adhering to FAIR principles, yet rigorous quality assurance (QA) and quality control (QC) frameworks remain less established in preclinical magnetic resonance imaging (MRI) than in clinical imaging. To address this limitation, a multicenter study was conducted across 21 international laboratories using standardized commercial liquid phantoms for mouse and rat MRI setups and a harmonized acquisition protocol. Data processing was centralized using AIDAqc, an automated pipeline extracting quantitative metrics including signal-to-noise ratio (SNR), temporal SNR (tSNR), ghost-to-signal ratio (GSR), and motion-equivalent temporal instability, combined with five complementary outlier-detection algorithms. The evaluated datasets encompassed magnetic field strengths from 3.0 to 16.4 T and heterogeneous coil and acquisition configurations. In mouse phantom data, SNR and tSNR were significantly lower at 3 T than at 7 and 9.4 T, whereas artifact-related metrics did not differ significantly between field-strength groups. In rat phantom data, differences between field strengths were less pronounced. At 7 T, substantial dataset-specific differences were observed in anatomical and functional quality metrics, also among datasets using the similar coil configuration. Multicenter reference values for frequently represented 7 T configurations were established, including SNR/tSNR of 48 {+/-} 3/48 {+/-} 1 dB for mouse surface-coil datasets and 49 {+/-} 3/44 {+/-} 4 dB for rat array-coil datasets. Longitudinal anatomical SNR showed generally low variability, whereas ghosting was more variable across time. Automated outlier detection additionally identified transient acquisition instabilities that were not always apparent by visual inspection. Together, these findings show that field strength and nominal coil configuration alone do not adequately characterize MRI performance and support standardized, longitudinal phantom-based QC combined with automated analysis as a practical approach for improving the reliability, transparency, and interoperability of multicenter preclinical MRI data.

bioengineering↗

bioRxiv2026

From TD50 to Benchmark Dose in Nitrosamine Risk Assessment: Evidence from N-Nitrosotrimetazidine Carcinogenicity and TGR Mutation Data.

The presence of N-nitrosamine drug substance-related impurities (NDSRIs) in pharmaceuticals represents a significant regulatory and safety challenge due to their classification as "cohort of concern" compounds. This paper describes the toxicological evaluation of N-Nitrosotrimetazidine (NTMZ), performed to refine the initial default acceptable intake (AI) limits of 18 to 26.5 ng/day established by regulatory authorities. The evaluation followed a tiered approach: NTMZ was first confirmed as mutagenic in vitro via the standard Ames test. To further investigate its genotoxic potential, two in vivo studies were conducted in Wistar and transgenic rats. Detection of DNA strand breaks in the liver and duodenum (comet assay) together with positive results in the cII mutation assay confirmed an in vivo mutagenic mode of action. Benchmark Dose (BMD) analysis of the transgenic rat data yielded a BMDL50 of 7 mg/kg/day in the male liver. To characterize long-term carcinogenic risk, a GLP-compliant 2-year carcinogenicity study was conducted in Wistar rats. Chronic exposure induced dose-dependent increases in liver tumors (hemangiosarcomas, hepatocellular carcinomas and adenomas) and intestinal tumors (adenomas and adenocarcinomas), leading to a Tumor Dose 50 (TD50) of 23 mg/kg/day in male rats. Benchmark dose analysis of tumor incidence identified a lowest BMDL10 of 2.6 mg/kg/day in females, which served as the basis for deriving an AI of 13 microg/day. This assessment demonstrates a strong predictive correlation between the BMD derived from the in vivo transgenic model, the BMDL10 and the final TD50 values obtained in the 2-year carcinogenicity study. These findings provided the scientific basis for establishing a conservative AI of 13 microg/person/day based on the BMDL10 and further support the regulatory acceptance and use of BMD-derived approaches for the evaluation of nitrosamine impurities.

pharmacology and toxicology↗

bioRxiv2026

Image-based Disease-wide Association Study via Self-supervised Learning links Abdominal MRI Features to 158 Diseases

Medical images contain rich phenotypic information that is often not fully captured by manual clinical assessment. Here, we present a systematic framework for extracting such information and conducting image-based disease-wide association studies (iDWAS) using self-supervised learning (SSL). We applied this framework to abdominal MRI data from the UK Biobank and evaluated associations between MRI-derived features and 562 diseases. Features were learned using a VICReg-based SSL model and tested for disease associations using logistic regression models. We identified 158 diseases that were significantly associated with the MRI-derived features, including the ones which are not directly linked to abdominal anatomy. Focusing on Metabolic dysfunction-associated steatohepatitis (MASH), we showed that the MRI-derived features captured disease-relevant information and separated MASH cases from controls better than established biomarkers such as PDFF and Iron-cT1. These findings highlight the ability of SSL to uncover clinically meaningful signals from routine imaging data. The proposed framework is broadly applicable to other imaging datasets and modalities, enabling more systematic approaches to incidental and early disease detection. The trained model and analysis pipeline are publicly available at https://github.com/srm2022/iDWAS. BackgroundMedical images, often analyzed manually by clinicians, contain valuable information that may not be fully captured by the human eye. Machine Learning (ML) has demonstrated significant potential in extracting this information, allowing us to enhance our understanding of underlying pathologies. We present a systematic framework for extracting such information and performing image-based disease-wide association studies (iDWAS) using self-supervised learning. We then applied the framework to abdominal Magnetic Resonance Imaging (MRI) from UK Biobank (UKB) and investigated the associations between MRI-derived features and 562 diseases. Finally, we delved deeper into the observed associations for Metabolic dysfunction-associated steatohepatitis (MASH), a prevalent yet underdiagnosed condition with a high unmet need for non-invasive diagnostic tools. MethodsWe extracted features from MRI images using VICReg-based self-supervised learning and modeled the associations of the extracted features with 562 diseases using logistic regression. Using the likelihood ratio (LR) test, we then assessed how much additional variance can be explained by the MRI-derived features relative to the variance explained by a null model including only common confounders such as age, gender, and BMI. ResultsOf these 562 diseases, we identified 158 diseases to be significantly associated with the MRI-derived features. While many of them (e.g. MASH) are known to primarily emerge in the abdomen, others (e.g. neuropsychiatric diseases) are not. Taking MASH as a use-case and adjusting for MASH-specific confounding, we then showed that our MRI-derived features captured additional MASH-relevant information compared to standard MRI-derived biomarkers of liver health such as proton density fat fraction (PDFF) and iron-corrected T1 (Iron-cT1). The trained SSL model and analysis pipeline are available at https://github.com/srm2022/iDWAS. ConclusionsOur results illustrate (1) how MRIs from one organ of the body can inform about the diseases primarily rooted in other organs of the body, reflecting patients overall health status, and (2) how SSL can extract more information relevant for specific diseases compared to current state-of-the-art biomarkers. Our framework can be applied to other MRI datasets as well as other imaging modalities with minimal adjustment, providing opportunities for the development of more systematic approaches to incidental diagnosing, i.e. (early) detection of diseases falling outside the scope of the original imaging procedure.

bioinformatics↗

bioRxiv2026

The plant specific VPS2.2/HYADE of the ESCRT-III protein sorting machinery localizes to a secretory compartment and is required for cell division plane determination in Arabidopsis

Positioning of the division plane is a critical step during cellular development. While in animal cells the plane of cell division is defined during metaphase, in plants this decision is made before mitosis and includes the formation of a cytoskeletal structure termed the preprophase band (PPB). Although not essential, the PPB constitutes the earliest mark for the plane of cell division and coincides with the sites where the cell plate fuses with the parental plasma membrane during cytokinesis. Recent studies indicate that endo- and exocytosis are involved in remodelling of the cortical division zone. Here we show that PPBs, phragmoplasts, cell plates and cell walls are misplaced in Arabidopsis mutants of Atvps2.2/hyade (hya), a plant-specific component of the Endosomal Sorting Complex Required for Transport (ESCRT)-III. We demonstrate that the amino acid substitution Q71P of the hya-3 allele abolishes the homo- and heteromerization with other ESCRT-III components. Functional HYA-GFP fusion proteins are excluded from the canonical location of ESCRT-III complexes at multivesicular bodies (MVBs) and are absent from Brefeldin A (BFA) and Wortmannin (WM) sensitive compartments in Arabidopsis. HYA-GFP neither localize to early nor late endosomes but colocalizes with markers of secretory compartments such as the Qc-SNARE, SYP61 and with trans-Golgi-network (TGN) derived secretory Rab-A3 vesicles. Moreover, HYA-GFP locates to the extracellular space indicating that VPS2.2/HYA is involved in secretion. These results are consistent with a novel, non-canonical function of ESCRT-III in the establishment and maintenance of the cortical division zone via secretion.

plant biology↗

bioRxiv2026

Mitochondrial turnover at central GABAergic synapses governs vulnerability to epileptic seizures

Mitochondrial dysfunction has long been known to underlie neurodegeneration, yet the contribution of mitochondrial turnover dynamics to functional aspects of defined synaptic circuits remains poorly understood. Here, we show that the mitochondrial proteome and turnover rates of hippocampal glutamatergic and GABAergic neurons is differentially remodelled by experience, with distal axon terminals of somatostatin-positive neurons exhibiting most dramatic changes, suggesting a form of metabolic plasticity at GABAergic synapses coupled to circuit activity. Conditional ablation of the mitochondrial transport proteins MIRO1 or TRAK1 (whose human mutations cause congenital epilepsy) stalled turnover at axon terminals driving loss of cristae, without affecting synapse or neuron integrity. The resulting reduction in synaptic GABA levels destabilized network oscillations and led to hyperexcitability, culminating in recurrent seizures and premature death. Post-weaning gene therapy efficiently reversed mitochondrial alterations and ameliorated the epileptic phenotype, underscoring the crucial role of mitochondrial turnover at central GABAergic synapses for balancing network excitability.

neuroscience↗

bioRxiv2026

Patterns of Typical and Atypical Age-related Brainstem Volume losses

BackgroundThe brainstem and its different sub-systems control essential functions such as motor agility etc. that worsen with age. The purpose of this study was: 1. To assess the impact of age-related volume loss within three brainstem sub-systems on functions supported by them. 2. To use data-driven machine learning to identify different volume loss patterns or subtypes and investigate how they are associated with function. MethodsStructural MRI and behavioral data from 674 Human Connectome Project Aging (HCA) participants was used in this project. The brainstem was extracted, internal brainstem structures segmented and the segmentations warped onto a probabilistic population atlas on which the nuclei of interest had been labeled. Jacobian deformation maps were calculated, each rois mean Jacobians extracted and converted into z-scores with and without correction for age. Linear regression analyses were used to assess volume - function (cognition, motor agility, autonomic control) associations for each roi belonging to the sub-system supporting these functions. Subtype and Stage Inference (SuStaIn) was used to identify different volume loss patterns in each sub-system. ResultsAge explained larger percentage of the variation of the behavioral variables than brainstem volumes. SuStaIn identified up to 4 subtypes, one representing typical aging and the remainder atypical aging. The subtypes did not significantly differ behaviorally with the exception of grip strength and diastolic blood pressure. ConclusionAging affects brainstem systems which contributes to the worsening of these functions with increasing age. SuStaIn detected different patterns of volume loss or subtypes within each of the brainstem systems.

neuroscience↗

bioRxiv2026

H3K27M-driven hypertranscription leads to a new targetable dependency in diffuse midline gliomas

Diffuse midline gliomas (DMGs) are driven by the H3K27M oncohistone--a challenging therapeutic target. However, conventional therapeutic modalities are never curative. Against this backdrop, we address an important unresolved question--are there H3K27M-induced oncogenic vulnerabilities that can be exploited for therapeutic benefit. We show that H3K27M induces hypertranscription, thus identifying hypertranscription as a new molecular feature of H3K27M-driven DMGs. We demonstrate this finding in genetic mouse models, human DMG cells, and primary tumor specimens. We further demonstrate that H3K27M-induced hypertranscription perturbs replication, heightens basal replication stress, and enhances sensitivity to ATR inhibition. In exploring therapeutic implications of these findings, we document brain penetrance, target engagement, and therapeutic efficacy of a clinical-stage ATR inhibitor (alnodesertib) in vitro and in intracranial DMG xenografts. We further demonstrate synergistic activity of alnodesertib with radiotherapy--the current standard of care for DMGs. These findings provide the mechanistic underpinning and preclinical rationale for including alnodesertib as monotherapy and in combination with radiation in clinical trials for children with H3K27M DMGs. The broad implications of our studies highlight ATR inhibition as a therapy for aggressive human cancers displaying hypertranscription.

cancer biology↗

bioRxiv2026

High throughput single-cell RNA sequencing of intact adult cardiomyocytes and non-myocytes using a split-pool approach

MOTIVATIONAdult cardiomyocytes are difficult to profile by whole-cell single-cell RNA sequencing because of their large size and fragility, which make them poorly compatible with standard workflows. Current approaches for adult cardiomyocyte transcriptomics often require a trade-off between data quality and throughput, thus, studies instead rely heavily on sequencing of nuclei alone. Therefore, we set out to develop a high-quality and scalable workflow for adult heart cells using in-cell ligation and split-pool barcoding strategies to address this methodological gap. This workflow may be further generalisable to other large cell types or samples containing cell populations with highly unequal RNA content. SUMMARYAdult cardiomyocytes are difficult to profile by whole-cell single-cell RNA sequencing (scRNA-seq). Here, we developed a high-quality and scalable workflow for adult heart cells using in-cell ligation and split-pool barcoding. We identified per-cell RNA content as a significant variable that must be accounted for. Separation of cardiomyocytes (large cells) and non-cardiomyocytes (small cells) before library construction, and allocation of deeper sequencing to cardiomyocytes, produced high-quality whole-cell datasets for both compartments. Compared with single-nucleus RNA sequencing, whole-cell cardiomyocyte profiling better recovered metabolic, mitochondrial, cytoplasmic translational, and contractile gene programs. This workflow provides a practical method for scalable, high-quality cardiomyocyte whole-cell scRNA-seq and offers general strategies for other large cell types or samples containing cell populations with highly unequal RNA content.

cell biology↗

bioRxiv2026

Macrocyclization of Broad-Spectrum Kinase Inhibitor Bosutinib leads to Potent and Selective Quinoline-based HIPK4 Inhibitor AZ137

Homeodomain-interacting protein kinase 4 (HIPK4) remains an understudied member of the dark kinome. While genetic knockout studies suggest roles for HIPK4 in spermiogenesis and cutaneous squamous cell carcinoma, whether these cellular functions can be recapitulated by pharmacological inhibition remains to be determined. However, such investigations have been hampered by a lack of high-quality chemical tools. To address this, we employed a rational design strategy utilizing macrocyclization of a bosutinib-based scaffold. Systematic optimization led to the discovery of AZ137 (28e), a potent and selective HIPK4 inhibitor (IC50 = 11 nM; cellular EC50 = 76 nM). AZ137 exhibits exceptional selectivity across three comprehensive orthogonal panels, high solubility, and no detectable cytotoxicity. Its cellular activity was confirmed in cell-based assays of HIPK4-dependent F-actin remodeling. Together with a negative control compound, this probe set provides a foundational framework for the validating HIPK4 as a therapeutic target and a high-quality resource to elucidate its roles in normal physiology and disease.

biochemistry↗

bioRxiv2026

KLRG1 identifies circulating cytotoxic CD4 T cells with selective anti-tumor function in human cancer

Given the critical role of CD4 T cells in anti-tumor immunity, strategies to harness these cells for cancer immunotherapy are gaining increasing interest. Historically overshadowed by CD8 T cells, cytotoxic CD4 T cells can directly kill MHC class II-expressing tumor cells. However, the defining molecular signature and the mechanisms underlying their cytolytic activity remain poorly understood, particularly in cancer patients. Here, using ex vivo single-cell transcriptomic and spatial analyses of CD4 T cells from paired blood and tumor samples of melanoma patients, we identified Killer Cell Lectin-Like Receptor G1 (KLRG1) as a defining surface marker of cytotoxic CD4 T cells. The CD4+ KLRG1+ T cell subset was notably enriched among circulating cells compared with tumor-infiltrating populations, which were instead enriched in T follicular helper (Tfh) states. Functionally, KLRG1+ CD4 T cells expressed elevated levels of cytotoxic genes and exhibited superior tumor-killing capacity compared with their KLRG1- counterparts. We demonstrated that their cytotoxicity is granulysin-dependent, as confirmed by CRISPR/Cas9-mediated gene deletion. Mechanistically, CD4 T cells spared MHC class II+ cells lacking the KLRG1 ligands CD324 and CD325, such as professional antigen-presenting cells (APCs), indicating that cytotoxicity was selectively directed towards tumor cells while preserving immune cells. Finally, by investigating how the tumor microenvironment may impair CD4 T cell cytotoxicity, we showed that tumor-derived factors, including interleukin-6 (IL-6), are key drivers promoting the transition of cytotoxic CD4 T cells toward a Tfh phenotype. In summary, our findings define KLRG1 as a defining cell surface marker of cytotoxic CD4 T cells in cancer patients, as well as a key regulator that protects MHC class II+ APCs. Moreover, targeting the IL-6 signalling pathway may enhance CD4 T cell anti-tumor cytotoxicity, offering new avenues for cancer immunotherapy.

immunology↗

bioRxiv2026

System-Wide Proteomic Remodeling in Spinal Muscular Atrophy Reveals Tissue-Specific Responses and Partial Rescue by SMN Restoration

Spinal muscular atrophy (SMA), traditionally defined as a neuromuscular disorder characterized by degeneration of lower motor neurons, is increasingly recognized as a multi-organ disease. SMA is caused by deficiency of the survival motor neuron (SMN) protein below a critical threshold required for cellular homeostasis. While motor neurons are particularly vulnerable, the ubiquitous expression and fundamental functions of SMN result in widespread perturbations across multiple tissues. Here, we generated a label-free quantitative proteomics atlas of spinal cord, heart, and gastrocnemius muscle from wild-type, heterozygous, and SMA mice at the symptomatic stage, including cohorts treated, at postnatal day 1 (P1), with a systemic suboptimal dose of SMN antisense oligonucleotides (SMN-ASOs), resulting in partial SMN restoration. SMN deficiency induced pronounced, tissue-specific proteome remodeling, with peripheral tissues exhibiting broader molecular alterations than spinal cord. Cross-tissue analyses revealed limited overlap, although heart and muscle showed partial convergence in metabolic and mitochondrial-associated pathways. SMN-ASO treatment partially repositioned these proteomes toward control states; however, restoration was incomplete and strongly tissue-dependent, with persistent dysregulation of mitochondrial and metabolic pathways. These findings demonstrate that SMN deficiency drives systemic yet heterogeneous proteome remodeling and that partial SMN restoration does not fully reverse established molecular alterations. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/715402v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@114d73borg.highwire.dtl.DTLVardef@13e8c13org.highwire.dtl.DTLVardef@15e4ba0org.highwire.dtl.DTLVardef@1b70fb8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Bivalent bispecific CD28 antibodies reinforce T-cell responsiveness and revert anergy/quiescence in patients treated with bispecific CD3 antibodies

Bispecific T-cell engagers stimulating CD3 (TCEs) rapidly gain momentum in oncological therapy. We report that single-agent TCE-treatment of cancer patients induces T cell hyporesponsiveness including abolished proliferative and lytic capacity. Single-cell RNA-sequencing identified transcriptional features of anergy/quiescence like upregulation of CBLB and BACH2, and suppression of AP 1-dependent activation programs due to isolated provision of T cell signal-1. To restore T cell functionality, we engineered bispecific costimulators (BiCos) which deliver signal-2 via highly efficient bivalent CD28-binding yet maintain strictly target-restricted activity after binding antigens expressed not only by tumor cells but also the extracellular matrix. Preclinical analyses documented that BiCos potentiate efficacy of single-agent TCE treatment with activity exceeding that of univalent Knob-into-Hole CD28-costimulators and revert T cell hyporesponsiveness. In humanized mice, BiCos induced elimination of established tumors in combination with very low doses of TCE. Finally, BiCos reversed molecular hallmark features of quiescence such as high expression of BACH2 and KLF2 in T cells of TCE-treated patients resulting in complete restoration of cellular function, thereby reinstating durable antitumor immunity.

immunology↗

bioRxiv2026

A high-throughput cost-efficient in vitro platform for the screening of immune senomodulators

With advancing age, the immune systems capacity to effectively combat pathogens diminishes. This decline of the overall immune function impacts both the innate and adaptive compartments, contributing in many cases to a systemic state of chronic inflammation which further increases the risk of the most prevalent non-communicable diseases and severe infections. Given the increase in median life expectancy with a demographic development towards a larger number of elderly people, identifying interceptive strategies to mitigate the individual and societal impact of diseases related to immune aging is of paramount importance. We developed a molecularly defined strategy to guide interventions with the aim to reduce immune aging. We introduce an omics-based drug screening platform to identify and characterize the pharmacological profile of immune senomodulators applicable to cross-age human cohorts using human-derived peripheral immune cells. To this aim we developed a robust experimental approach to screen for effective anti-aging compounds directly on human cells. This methodology allows us to quickly screen for drug candidates at different scales: from cost-effective bulk transcriptomics for a broader high-throughput overview of cellular responses, down to single-cell resolution approaches for a more detailed look at gene expression and other molecular data. This in vitro screening method is designed to maximize the clinical relevance of our findings, providing a direct link between preclinical research and patient care. By analyzing how different compounds affect the immune cells of individual persons, we can identify treatments that are most likely to be effective against aging in a subject-specific manner--a key step toward personalized medicine. In short, our approach enables a faster translation of anti-aging immune treatments from the lab to the clinic, tailoring them to each individuals unique biological makeup.

systems biology↗

bioRxiv2026

Transcriptome-wide association study and fly experiments uncover the role of CoA synthase in ageing across species.

While significant progress has been made in understanding the genetic architecture of ageing in model organisms, our understanding of human ageing remains limited. We performed a multi-tissue Transcriptome-wide association study (TWAS) on human lifespan, integrating GWAS data from >1 million parental lifespans with gene expression prediction models derived from reference transcriptomic datasets; followed by replication using healthspan and longevity phenotypes as additional readouts of ageing. The TWAS uncovered 563 significant gene associations, of which 139 replicated. TOMM40, encoding a component of the mitochondrial outer membrane translocase that is fundamental for mitochondrial function, had the strongest association with parental lifespan and longevity and was fine-mapped as a putatively causal lifespan gene at the APOE-TOMM40 region. Uniquely in our study, we identified fly orthologues of replicating genes and examined if modulating their expression impacts Drosophila longevity. The nine novel associations with all three ageing outcomes included COASY, encoding Coenzyme A synthase. Knocking down its fly orthologue, Ppat-dpck, resulted in significant lifespan extension in flies. Hence, in addition to discovering new genes associated with human ageing, by combining human TWAS with experimental Drosophila work, we provide evidence for the role of COASY (Ppat-dpck) in ageing across species. Significance statementExtensive research on ageing has been conducted in Drosophila and C.elegans due to their short lifespan and experimental tractability. However, in human genetic research, only a few loci have been consistently replicated. To bridge this gap, we conducted a transcriptome-wide association study (TWAS) followed by experimental validation in Drosophila. TWAS revealed 139 significant and replicating gene associations, including COASY. Knockdown of its fly orthologue (Ppat-dpck) significantly extended fly lifespan, validating its roles in ageing across species. Thus, integrating multiple ageing outcomes through TWAS in human genetic research can uncover robust associations and highlight genes involved in fundamental ageing mechanisms.

genetics↗

bioRxiv2026

SMN deficiency disrupts hepatic mitochondrial iron homeostasis and NRF2-dependent redox control in spinal muscular atrophy

Spinal muscular atrophy (SMA), classically defined as a motor neuron disorder caused by deficiency of the survival motor neuron (SMN) protein, is increasingly recognized as a multi-system disease. Among peripheral organs, the liver, essential for metabolic regulation and xenobiotic processing, remains underexplored despite growing evidence of dysfunction. Defining hepatic contributions may be critical for understanding systemic disease progression and optimizing therapeutic strategies. Here, we performed integrative profiling of liver pathology in SMA by combining unbiased proteomics from wild-type (WT), heterozygous (HET), and SMA mice at the late symptomatic stage (postnatal day 10; P10) with targeted analyses of mitochondrial function, iron metabolism, and redox homeostasis. To resolve temporal dynamics, key pathways were examined at early symptomatic disease (P5), and the reversibility of identified defects was evaluated following SMN-restoring antisense oligonucleotide (ASO) therapy. We uncover early (P5) activation of the heme biosynthetic pathway, marked by increased ferrochelatase (FECH), preceding overt metabolic disruption. By P10, SMA liver shows a coordinated loss of mitochondrial Complex II integrity, pathological mitochondrial iron accumulation, disruption of the NRF2-KEAP1 antioxidant axis, and heightened susceptibility to ferroptotic redox stress. ASO treatment robustly restored mitochondrial and redox phenotypes, yet FECH remained elevated, indicating sustained heme pathway activation despite SMN rescue. HET mice displayed mild redox abnormalities, revealing a dosage-sensitive hepatic phenotype. Collectively, these findings delineate a mitochondrial-iron-redox axis uniquely vulnerable in SMA liver, identify ferroptotic sensitivity as an early and therapeutically responsive feature, and highlight persistent heme biosynthesis activation as a target to complement SMN-directed therapies.

cell biology↗

bioRxiv2025

Network Adaptability Governs Resilience and Susceptibility to Social Defeat

Stress resilience is defined as the ability to maintain mental health after adversity. In humans, resilience is marked by threat-safety discrimination and extinction of fear, whereas susceptibility involves fear generalization and extinction resistance. Using a translational mouse model of chronic social defeat stress combined with preregistered multimodal brain imaging, we investigated structural and network-level markers of resilience, susceptibility, and threat learning. Resilience was characterized by preserved dentate gyrus integrity, greater microstructural complexity in prefrontal regions, and signatures consistent with enhanced inhibitory gating within amygdalar circuits. Susceptibility, in contrast, involved reduced dentate gyrus complexity and diminished microstructural flexibility, with a weaker but parallel pattern in the basolateral amygdala. Impaired threat learning was linked to compromised CA1/CA2 integrity and reduced pons connectivity, highlighting hippocampal-brainstem interactions in memory consolidation. Overall, these findings show that resilience emerges from adaptive network reorganization, whereas susceptibility and impaired learning reflect distinct dysfunctions, underscoring individual coping differences even among genetically identical animals.

neuroscience↗

bioRxiv2025

Dynamic Epigenetic Changes During Antidepressant Pharmacotherapy in Major Depressive Disorder

Although antidepressants remain the main pharmacological treatment for major depressive disorder (MDD), therapeutic response varies, highlighting the need for molecular markers that predict treatment response, as well as insights into the biological processes underlying antidepressant efficacy. Candidate-gene and cross-sectional epigenome-wide association studies (EWAS) have reported DNA methylation signatures associated with antidepressant response; however, findings remain inconsistent. To date, no longitudinal EWAS has examined methylation trajectories across multiple time points during antidepressant treatment in MDD. Within the Early Medication Change trial, DNA methylation data was generated for 162 patients with MDD (81 responders, 81 non-responders) and 48 matched healthy controls. Patients were assessed at four times across eight-weeks of standardized antidepressant treatment, while controls were assessed twice. Differentially methylated positions (DMPs) and regions (DMRs) were identified using longitudinal EWAS models and the comb-p algorithm. Baseline methylation levels were associated with depressive symptom severity at day 28 and day 56 through two and six DMRs, respectively (e.g., TNRC6C, CAT), whereas no single DMP reached significance. Longitudinal analyses identified one DMP associated with improvement in depressive symptoms (YLMP1) and three DMRs showing methylation changes over time (e.g., GPR126, PM20D1). Combined patient-control analyses revealed additional DMPs and DMRs associated with diagnosis and temporal effects. This study provides first longitudinal evidence of regionally coordinated DNA methylation changes during antidepressant pharmacotherapy, revealing alterations in genes involved in neuroplasticity and inflammatory processes that are associated with clinical response. Replication and functional validation will be essential to determine their relevance for personalized antidepressant treatment.

genomics↗

bioRxiv2025

Neuronal compartmentalization results in impoverished axonal mitochondria

Mitochondria differ depending on their location within a neuron. Morphological heterogeneity between somatic, dendritic, and axonal mitochondria is well established. Emerging evidence suggests that further specialization is needed to meet the unique demands of different neuronal compartments. However, the molecular and functional diversity of mitochondria within a neuron remains poorly understood. Here, we utilized proteomics in MitoTag mice to profile somatodendritic and axonal mitochondria across four distinct neuron types, thereby generating a compendium of intracellular mitochondrial diversity. Combining proteomics, functional, and immunofluorescence analyses, we demonstrated that axonal mitochondria are not defined by the presence of unique proteins, but rather by the selective loss or preservation of specific pathways compared to their somatodendritic counterparts. This results in "impoverished" axonal mitochondria, which are characterized by diminished mtDNA expression and impaired oxidative phosphorylation yet retain other pathways, such as fatty acid metabolism. Bioinformatic analyses of multiomic data identified local translation as one mechanism underlying compartment-specific diversity. Together, these findings provide a comprehensive in vivo framework for understanding mitochondrial specialization across neuronal compartments.

neuroscience↗