Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney

Trim, W. V.; Oh, S.; Diakova, M.; Petrova, K.; Ichimura, T.; Takakura, A.; Karmakar, R.; Norrelykke, S. F. F.; Peshkin, L.; Bonventre, J. V.; Kirschner, M. W.

doi:10.1101/2025.10.12.681746

bioRxiv · 10.1101/2025.10.12.681746

Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney

Trim, W. V.·Oh, S.·Diakova, M.·Petrova, K.·Ichimura, T.·Takakura, A.·Karmakar, R.·Norrelykke, S. F. F.·Peshkin, L.·Bonventre, J. V.·Kirschner, M. W.

View original source ↗Export metadata ↓

Abstract

Conventional histological relies on fixation, embedding, sectioning, and staining methods that distort cellular architecture, extract lipids, and introduces variability, limiting reproducibility. We present Normalized Stimulated Raman Imaging (NoRI) that enables quantitative, label-free protein and lipid measurements at high-spatial resolution. NoRI computationally corrects protein, lipid, and water Raman signals, allowing quantitative biomass measurements while preserving tissue architecture, facilitating analysis by convolutional neural networks. Applied to mouse kidney, NoRI accurately classified tubule types (F1-[harmonic mean of precision and recall against manual annotation]=0.93), anatomical regions (F1=0.91), and biological sex (F1=0.97), revealing greater cytoplasmic lipid (+6.9mg/mL; p=0.028) and nuclear protein (+26.3mg/mL; p<0.001) in female tubules. In acute kidney injury, NoRI captured dynamic lipid and protein organization and quantified brush border remodelling and lipid droplet changes over 25 days. Spatial lipid quantification was central for feature classification in AKI (F1=1.0). These results establish NoRI as a reproducible, quantitative method for diagnostics, histopathology, and feature discovery.

Explore related subjects

physiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Trim, W. V., Oh, S., Diakova, M., Petrova, K., Ichimura, T., Takakura, A., Karmakar, R., Norrelykke, S. F. F., Peshkin, L., Bonventre, J. V., Kirschner, M. W.. 2025-10-14. Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney. https://doi.org/10.1101/2025.10.12.681746

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Stress-induced Metabolic Remodeling of Adipose and Brain Tissue revealed by Positron Emission Tomography

Stress impacts our health and triggers physiological adaptations, yet the metabolic programs engaged during stress remain incompletely understood. To fill this knowledge gap, we utilized total-body positron emission tomography (PET), multi-OMICS, and endocrine profiling to assess how various murine stress models affect systemic metabolic remodeling. We found that acute immobilization and surgery activate brown adipose tissue as part of the stress response, independently of hypothermia, thereby acting as a highly stress-sensitive metabolic hub. Additionally, we identified stress-specific hypo- and hypermetabolic signatures in different brain regions, and distinguished networks between brain and adipose tissue depots across the different stress groups. Our work presents a novel perspective on stress and its mobilization of metabolic resources and identifies PET imaging of brain and adipose tissue as a valuable, minimally invasive technique for tracking metabolic stress responses in mice, with relevance for animal welfare and disease models, and translational impact for mental health studies and preventive medicine.

physiology↗

bioRxiv2026

Multiparametric in vivo mapping reveals tissue-specific mitochondrial aging trajectories

Mitochondrial dysfunction is a hallmark of aging, yet how mitochondrial states are remodeled across tissues and subcellular compartments in vivo remains elusive. Progress has been limited, in part, because mitochondrial physiology is highly sensitive to experimental perturbations, underscoring the need for minimally disruptive measurement strategies. Here, we establish a tissue-resolved, in vivo framework for the quantitative analysis of mitochondrial states in live, intact Caenorhabditis elegans without confounding effects from mounting-induced hypoxia. This platform couples two-photon fluorescence lifetime imaging microscopy (2p-FLIM) with a custom segmentation pipeline, MitoSLIT, to track functional and structural features across multiple tissues and single neurons. By integrating membrane potential-associated TMRM intensity, lifetime-based microenvironmental metrics, and morphological descriptors, we uncover localized metabolic heterogeneity masked by conventional intensity analysis. Leveraging this framework, we mapped physiological aging against mitochondrial shifts induced by acute stress and fission-fusion mutations. Our analyses reveal that mitochondrial aging is highly tissue-specific, executing distinct trajectories across cell types. Extending the framework to genetically identified neurons revealed age-dependent divergence between somatic and axonal mitochondrial states, accompanied by structural remodeling and a late shift in optical redox ratio. Together, our findings demonstrate that mitochondrial populations do not converge on a uniform bioenergetic endpoint during aging, but rather follow highly compartmentalized, tissue-specific spatiotemporal trajectories in vivo.

physiology↗

bioRxiv2026

Arginine methyltransferase signalling is hyperactive in conditions of neuromuscular junction instability and muscle atrophy

Background: The neuromuscular junction (NMJ) is the site of communication between myofibers and a-motor neurons. Cellular and molecular mechanisms that determine, maintain, and remodel the neuromuscular synapse are poorly understood. Coactivator-associated arginine methyltransferase 1 (CARM1) post-translationally modifies target proteins by methylating arginine residues and has emerged as a key determinant of skeletal muscle biology. Methylarginine signalling is required for the maintenance and repair of the NMJ, but the direct role of CARM1 on the NMJ in health and disease remains unexplored, particularly in humans. Methods: We generated Carm1 skeletal muscle-specific knockout-out (mKO) mice to gain a basic understanding for the role of the enzyme in NMJ biology under homeostatic and denervated conditions. Additionally, we investigated CARM1 activity in severe mouse models of neuromuscular disorders (NMDs) including D2.mdx and Smn2B/- mice, which replicate Duchenne's muscular dystrophy (DMD) and spinal muscular atrophy (SMA), respectively, and exhibit chronic remodelling of the NMJ. Lastly, to evaluate if methylarginine signalling is implicated during NMJ instability in human skeletal muscle, we obtained samples from healthy volunteers before and after 14 days of single leg immobilization as well as from patients with myotonic dystrophy type 1. Results: Our results demonstrated that Carm1 mRNA expression and activity are elevated (P<0.05) in NMJ-enriched regions of healthy murine skeletal muscle. Carm1 muscle-specific deletion reduced NMJ compactness (-9.3%; P<0.05), increased fragmentation (+33%; P<0.05), and disrupted the expression of synapse-specific transcripts basally and following sciatic nerve transection. In skeletal muscle from pre-clinical models of NMDs, we observed a compensatory upregulation in CARM1-dependent arginine methylation as evident by +54% and +71 increases (P<0.05) in asymmetric dimethylarginine (ADMA)-marked CARM1 substrates in DMD and SMA mice, respectively. Similarly, muscle CARM1 was hyperactive with increased NMJ instability during neuromuscular disuse (+22%; P<0.05), and disease (+30%; P<0.05), in humans. In a cohort of muscular dystrophy patients and healthy volunteers, elevated CARM1 signalling was negatively correlated with clinical metrics of skeletal muscle health including grip strength (r = -0.583; P<0.05) as well as positively correlated with mRNA expression of NMJ machinery such as CHRNA1 (r = 0.578; P<0.05). Conclusion: In summary, we highlight that muscle-specific CARM1 is required for maintaining NMJ morphology and transcriptional regulation. Insults to NMJ stability during muscle disuse or in myopathic conditions were associated with enhanced CARM1-mediated methylarginine signalling in mice and humans. Collectively, our findings demonstrate CARM1 as a key mediator of NMJ biology and plasticity in health and disease.

physiology↗