Biology subjects

Hofmann, J. W.

Publications and source records attributed to Hofmann, J. W..

3 recordsLinked to original sources

bioRxiv2026

Soma-seq links intracellular protein states to transcriptional programs in the human brain

Neurodegenerative disease is largely driven by pathological protein states, which cannot be fully inferred from transcript levels. Yet, joint measurement of cytoplasmic proteins and RNA in single cells from archival human brain tissue remains challenging. Here we present Soma-seq, a method integrating transcriptome and antibody-based intracellular protein measurements in single cells from frozen human brain tissue. Applying Soma-seq to Alzheimers disease cortex, we quantified multiple intracellular proteins, including hyperphosphorylated Tau, alongside RNA. Soma-seq resolves a continuous trajectory of pathological progression based on multiplexed protein measurements and reveals associated gene programs. CRISPR perturbation in human iPSC-derived neurons validates Soma-seq-derived candidates and identifies protective factors to Tau aggregation.

neuroscience↗

bioRxiv2025

Evaluating Flavoprotein Fluorescence Imaging as a Biomarker of Early Retinal Ganglion Cell Mitochondrial Stress

PurposeRetinal neurodegeneration is difficult to monitor due to insensitive disease endpoints. Mitochondrial dysfunction and oxidative stress are promising early biomarkers of retinal ganglion cell (RGC) degeneration. This study investigates dynamics of flavoprotein fluorescence (FPF), a non-invasive mitochondrial oxidative stress measure, and sensitivity to early neurodegeneration and neuroprotection in vitro and in vivo. MethodsFPF activity in response to neurodegeneration and neuroprotection were characterized in vitro in wild-type (WT) and SARM1 knockout (SARMKO) human embryonic stem cell-derived RGCs with and without Vacor treatment over 24 hours and confirmed with mitochondrial reactive oxygen species (ROS) measures. Further FPF evaluation was explored in vivo using the optic nerve crush (ONC) model in WT and SARMKO mice to compare early RGC stress detection within rodent retinas. ResultsIn vitro FPF intensities in WT RGCs increased within 8 hours of degeneration induction, preceding significant mitochondrial ROS production. Neuroprotective SARMKO RGCs maintained comparable FPF and ROS levels following insult. In vivo FPF changes were not observed in WT and SARMKO mice over 4 days following ONC, while only early retinal thickening was observed from OCT. Early FPF and OCT changes were not reflective of late RGC survival observed from ex vivo RGC soma and axon counts. ConclusionsThese findings highlight differences in FPF sensitivity to mitochondrial stress between simplified in vitro systems and complex in vivo rodent retinas. This study demonstrates the potential of FPF as an early neurodegeneration and neuroprotection endpoint in vitro while identifying limitations and areas of development for its translatability to preclinical in vivo assessment.

bioengineering↗

bioRxiv2024

TDP43 proteinopathy exhibits disease, tissue, and context-specific cryptic splicing signatures

Mislocalization of the nuclear TAR DNA-binding protein 43 (TDP43) is a hallmark of ALS and FTD which leads to de-repression and inclusion of cryptic exons (CEs), promising biomarkers of TDP43 pathology in a spectrum of neurodegenerative diseases. However, most CEs to date have been identified from in vitro models or a single cortical FTD dataset, and little is known about cryptic splicing in the spinal cord, or within different neuronal subtypes. We meta-analyzed published bulk RNAseq datasets representing 1,778 RNAseq profiles of ALS and FTD post-mortem tissue, and in vitro models with experimentally depleted TDP43. We identified 142 cryptic splices, including 68 novel events. We found divergent cryptic splicing primarily between the spinal cord and cortex, validated in an independent ALS cohort by qPCR and supported by in situ hybridization (ISH). We also identified a set of cryptic splices observed in tissue but not in vitro, and, being present in either SOD1-ALS or MAPT-FTD subjects, likely TDP43 independent. Finally, leveraging multiple public single-nucleus RNAseq datasets of ALS and FTD motor and frontal cortex, we confirmed the elevation of cortical-enriched splices in disease and localized them to layer-specific neuronal populations. We provide a web interface to browse the meta-analysis results at https://go.roche.com/CrypticSplicingLandscape. This catalog of cryptic splices will inform efforts to develop biomarkers for tissue-specific and cell type-specific TDP43 pathology.

neuroscience↗