Biology subjects

Kofler, J. K.

Publications and source records attributed to Kofler, J. K..

7 recordsLinked to original sources

bioRxiv2026

An open-source stereotaxic container with an integrated cutting guide for human brain fixation during magnetic resonance imaging and sectioning for histology

IntroductionPostmortem imaging at ultrahigh field strengths, such as 7 Tesla (7T) magnetic resonance imaging (MRI), enables unprecedented visualization of fine brain structures and pathology. However, precise registration between MRI and histology is often compromised by tissue deformation and lack of standardized tools for preserving anatomical orientation. A reliable, high-resolution MRI-to-histology workflow is essential for MRI-guided sampling to investigate neurodegenerative diseases. MethodsWe developed a human postmortem brain container composed of stereotaxic enclosure and cutting guide system using iterative 3D printing. The final design is constructed from Victrex AM 200, a polyaryletherketone material engineered with MRI compatibility, high mechanical strength, and high resistance to fixatives. Human brains were embedded in an agar/sucrose mixture within the container and scanned at 7T using high-contrast and high-resolution imaging sequences. The cutting guide enables reproducible sectioning at defined tissue coronal slab thicknesses (9.2 {+/-} 0.6 mm). Block face photographs of each coronal slab were then co-registered with MRI for targeted tissue sampling. ResultsTo date, 215 human postmortem brains have been imaged ex vivo using this container. The container maintains consistent spatial orientation from imaging through sectioning, supporting correlation between MR-visible features and histological findings. Imaging-visible abnormalities, such as white matter hyperintensities and cerebral microbleeds, were localized and sampled with minimal deformation. The container enables single-scan workflows, avoiding custom cutting templates or repeat imaging. It supports deep learning-based lesion segmentation and MRI-guided histology registration, facilitating large-scale neuropathological investigations. ConclusionThe stereotaxic cutting guide system addresses a critical gap in postmortem imaging by integrating MRI-compatible materials, precision-guided sectioning, and high-throughput imaging. It has enabled multimodal studies of aging and neurodegeneration and is being adopted in neuropathological workflows. This platform provides a reproducible, scalable, and anatomically precise solution for aligning ultrahigh field MRI with histology, enhancing both clinical research and digital pathology efforts.

bioengineering↗

bioRxiv2025

Proteomic Analysis in Alzheimer's Disease with Psychosis Reveals Separate Molecular Signatures for Core AD Proteinopathy and Postsynaptic Density Disruption

Background and Hypothesis: Alzheimers disease with psychosis (AD+P) is a subgroup of AD patients with more rapid cognitive deterioration. While our previous study showed that AD+P is associated with loss of prefrontal cortex postsynaptic density (PSD) proteins, identifying proteins in the broader cellular environment that influence PSD loss addresses a critical knowledge gap about synaptic dysfunction mechanisms in early disease stages. Study Design: We conducted a proteomic analysis comparing prefrontal grey matter cortex tissue homogenates from elderly normal controls (n=18), individuals with AD+P (n=61), and individuals with AD-P (n=48), all with Braak stages 3-5. Study Results: AD+P showed the most pronounced alterations relative to controls (178 proteins with q<0.05), although alterations in AD-P and AD+P relative to controls were highly similar (R{superscript 2}=0.965, p<0.001). Weighted-gene correlation network analysis (WGCNA) identified four modules significantly associated with disease status comparing AD subjects to controls, but none differed significantly between AD+P and AD-P. We identified 15 proteins significantly correlated with PSD yield across all samples, including ENPP6, linked to AD+P by GWAS. Additionally, PSD yield-associated proteins showed minimal overlap with altered AD proteins (1 of 137). WGCNA revealed one module significantly correlated with PSD yield across all samples, enriched for inflammatory terms. Conclusions: Our findings suggest a model in which AD+P arises from the combination of quantitative alterations within a shared AD proteome profile and a superimposed set of protein alterations correlated with PSD yield that are largely independent of the shared AD proteome, conferring distinct mechanisms of synaptic vulnerability and psychosis risk.

neuroscience↗

bioRxiv2025

Cellular and Regional Vulnerability Shapes the Molecular Landscape of Psychosis in Alzheimers Disease

Approximately 40 percent of Alzheimers disease patients develop psychosis (AD+P), yet the molecular and cellular basis of these symptoms remains poorly understood. Here we profiled single-nucleus transcriptomes and epigenomes from 48 postmortem Alzheimers brains stratified by psychiatric diagnosis. Across cell types, AD+P was distinguished by transcriptional programs in upper-layer cortical pyramidal neurons consistent with re-engagement of developmental and structural plasticity pathways. These neurons exhibited greater loss in AD+P cortex, indicating that such programs emerge in a context of heightened vulnerability. Integrating these findings with functional perturbation screens in stem-cell-derived brain organoids, we found that activation of these programs alters cortico-cortical network connectivity and can exacerbate network dysfunction. Our data suggest that compensatory neuronal plasticity, shaped by glial inflammatory responses, may paradoxically contribute to circuit instability and selective vulnerability underlying neuropsychiatric symptoms in dementia. HighlightsO_LICell-type- and brain-region-specific transcriptional changes in AD with psychosis (AD+P) C_LIO_LIUpper-layer pyramidal dysfunction and metabolic vulnerability marks the pathophysiology of AD+P C_LIO_LICircuit wiring programs are evoked in AD+P as maladaptive compensatory responses C_LIO_LIAD+P-associated IL-6 signaling impairs neuronal network function in brain organoids C_LI

neuroscience↗

bioRxiv2023

Circulating senescent myeloid cells drive blood brain barrier breakdown and neurodegeneration

Neurodegenerative diseases (ND) are characterized by progressive loss of neuronal function. Mechanisms of ND pathogenesis are incompletely understood, hampering the development of effective therapies. Langerhans cell histiocytosis (LCH) is an inflammatory neoplastic disorder caused by hematopoietic progenitors expressing MAPK activating mutations that differentiate into senescent myeloid cells that drive lesion formation. Some patients with LCH subsequently develop progressive and incurable neurodegeneration (LCH-ND). Here, we show that LCH-ND is caused by myeloid cells that are clonal with peripheral LCH cells. We discovered that circulating BRAFV600E+ myeloid cells cause the breakdown of the blood-brain barrier (BBB), enhancing migration into the brain parenchyma where they differentiate into senescent, inflammatory CD11a+ macrophages that accumulate in the brainstem and cerebellum. Blocking MAPK activity and senescence programs reduced parenchymal infiltration, neuroinflammation, neuronal damage and improved neurological outcome in preclinical LCH-ND. MAPK activation and senescence programs in circulating myeloid cells represent novel and targetable mechanisms of ND.

cell biology↗

bioRxiv2021

Predictors of cognitive impairment in primary age-related tauopathy: an autopsy study

Primary age-related tauopathy (PART) is a form of Alzheimer-type neurofibrillary degeneration occurring in the absence of amyloid-beta (A{beta}) plaques. While PART shares some features with Alzheimer disease (AD), such as progressive accumulation of neurofibrillary tangle pathology in the medial temporal lobe and other brain regions, it does not progress extensively to neocortical regions. Given this restricted pathoanatomical pattern and variable symptomatology, there is a need to reexamine and improve upon how PART is neuropathologically assessed and staged. We performed a retrospective autopsy study in a collection (n=174) of post-mortem PART brains and used logistic regression to determine the extent to which a set of clinical and neuropathological features predict cognitive impairment. We compared Braak staging, which focuses on hierarchical neuroanatomical progression of AD tau and A{beta} pathology, with quantitative assessments of neurofibrillary burden using computer-derived positive pixel counts on digitized whole slide images of sections stained immunohistochemically with antibodies targeting abnormal hyperphosphorylated tau (p-tau) in the entorhinal region and hippocampus. We also assessed other factors affecting cognition, including aging-related tau astrogliopathy (ARTAG) and atrophy. We found no association between Braak stage and cognitive impairment when controlling for age (p=0.76). In contrast, p-tau burden was significantly correlated with cognitive impairment even when adjusting for age (p=0.03). The strongest correlate of cognitive impairment was cerebrovascular disease, a well-known risk factor (p<0.0001), but other features including ARTAG (p=0.03) and hippocampal atrophy (p=0.04) were also associated. In contrast, sex, APOE, psychiatric illness, education, argyrophilic grains, and incidental Lewy bodies were not. These findings support the hypothesis that comorbid pathologies contribute to cognitive impairment in subjects with PART. Quantitative approaches beyond Braak staging are critical for advancing our understanding of the extent to which age-related tauopathy changes impact cognitive function.

pathology↗

bioRxiv2021

Neuronal NADPH oxidase in Parkinson disease pathogenesis

Mitochondrial dysfunction and oxidative stress are strongly implicated in the pathogenesis of Parkinsons disease (PD) and there is evidence that mitochondrially-generated superoxide can activate NADPH oxidase 2 (NOX2), which is a major enzymatic generator of superoxide. Although NOX2 has been examined in the context of PD, previous studies have focused on microglial function; the role of neuronal NOX2 in PD pathogenesis remains to be defined. Here we devised and validated a proximity ligation assay for NOX2 activity and demonstrated that in human PD and 2 models thereof, neuronal NOX2 is highly active in substantia nigra dopamine neurons. Further, NOX2 activity is responsible for accumulation, post-translational modification and oligomerization of -synuclein as well as activation of leucine-rich repeat kinase 2 (LRRK2). Administration of a brain-penetrant, specific NOX2 inhibitor prevented NOX2 activation and its downstream effects in vivo in a rat model of PD. We conclude that neuronal NOX2 is a major contributor to oxidative stress in PD, to -synuclein pathology and to LRRK2 activation in idiopathic PD. In this context, NOX2 inhibitors hold potential as a disease-modifying therapy in PD. SummaryIn dopamine neuron, NADPH oxidase isoform 2 amplifies the oxidative stress-related pathogenic cascade in Parkinsons disease

neuroscience↗

bioRxiv2021

Deep learning from multiple experts improves identification of amyloid neuropathologies

Pathologists can label pathologies differently, making it challenging to yield consistent assessments in the absence of one ground truth. To address this problem, we present a DL approach that draws on a cohort of experts, weighs each contribution, and is robust to noisy labels. We collected 100,495 annotations on 20,099 candidate amyloid beta neuropathologies (cerebral amyloid angiopathy (CAA), and cored and diffuse plaques) from three institutions, independently annotated by five experts. DL methods trained on a consensus-of-two strategy yielded 12.6-26% improvements by area under the precision recall curve (AUPRC) when compared to those that learned individualized annotations. This strategy surpassed individual-expert models, even when unfairly assessed on benchmarks favoring them. Moreover, ensembling over individual models was robust to hidden random annotators. In blind prospective tests of 52,555 subsequent expert-annotated images, the models labeled pathologies like their human counterparts (consensus model AUPRC=0.74 cored; 0.69 CAA). This study demonstrates a means to combine multiple ground truths into a common-ground DL model that yields consistent diagnoses informed by multiple and potentially variable expert opinion.

pathology↗