Biology subjects

Rosenberg, A.

Publications and source records attributed to Rosenberg, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Manifolds for the neural representation of 3D spatial experience

The precision with which animals navigate and interact with objects depends in part on how their brains represent position and orientation in three dimensions. A central challenge is to explain within a common framework how neural systems ranging from insects to primates represent three-dimensional (3D) pose. Here we develop a framework based on the hypothesis that neural representations of pose lie on manifolds derived from the Special Euclidean Group, SE(3), which describes the full space of rigid-body positions and orientations in three dimensions. The framework shows how movement constraints, object geometry, and visual features jointly determine the topology of the resulting pose manifold, yielding a taxonomy that guides experimental tests. We apply the framework to derive low-dimensional manifolds for neural representations of 3D object orientation in macaque parietal cortex and head direction in the limbic systems of fruit bats, mice, and monkeys. This analysis also guides the construction of neuronal tuning functions that respect the topology determined by experimental conditions. Together, these results provide a common approach for linking the geometry of 3D pose to neural coding across species and brain systems.

neuroscience↗

bioRxiv2026

Reassessing Choice Probability: What 59 Macaque Studies Tell Us About Decision-Related Activity in Visual Cortex

Choice probability (CP) quantifies the trial-by-trial covariation between a sensory neurons response and perceptual reports. Despite extensive interest in CP as a window into how perception is linked to the activity of sensory neurons, the usefulness of CP remains debated. On one hand, reported CP magnitudes vary widely across seemingly equivalent studies, questioning its utility as a metric. On the other hand, the absence of clear patterns in CP variability has made it difficult to use it to adjudicate between competing models of visual perception. Here, we performed a meta-analysis of 150 CP estimates from 59 macaque neurophysiology studies to identify factors that systematically influence CP. We confirmed the positive relationship between CP and neuronal sensitivity both across and within individual studies. When controlled for sensitivity, we found remarkable consistency in CP across varying tasks and brain regions with two notable exceptions. First, CPs were higher in tasks involving bistable percepts, reinforcing the link between CP magnitude and subjective perception. Second, CPs were smaller in area V1, supporting prior suggestions about V1s special role in visual processing. We further found a significant effect of stimulus duration on CP, providing evidence against strictly feedforward models and favoring models with substantial feedback and recurrent processing. Finally, we offer recommendations for future studies to enhance the cross-study comparability and theoretical utility of choice signals as the field transitions to large-scale population recordings. More broadly, our findings demonstrate the benefits of meta-studies that expose patterns across many different tasks and animals - yielding insights that complement large-scale population recordings.

neuroscience↗

bioRxiv2026

Jump-starting the T cell response in established tumors

Checkpoint blockade only works in 10-20% of patients. Consequently, investigators are testing checkpoint inhibitors in combination with drugs like the class I histone deacetylase inhibitor, entinostat (ENT). Unfortunately, the combination of ENT and checkpoint blockade fared poorly in patients with breast or ovarian cancer, despite promising pre-clinical results. Here we show that ENT enhances CD8+ T cell responses by maintaining a progenitor-like population of CD8+ T cells that supplies activated effector T cells to tumors for prolonged periods. Surprisingly, the anti-tumor effects of ENT are only experienced when delivered during a narrow window that occurs after T cell activation and before T cell exhaustion--a window that is likely closed in most patients. However, by first "jump-starting" the T cell response using an oncolytic virus, the anti-tumor activity of ENT and PD1 blockade is restored. These data establish a general paradigm, independent of tumor type, to rationally manipulate anti-tumor immunity.

immunology↗

bioRxiv2026

Statistical signals indicate a dependence between amino acid backbone conformation and the translated synonymous codon

Synonymous codons encode the same amino acid but can differ in their usage and translational properties. In previous work we reported statistical differences in backbone dihedral angle distributions associated with synonymous codons in the Escherichia coli proteome. This finding has been questioned due to concerns regarding the statistical methodology used. Here we revisit the dataset using corrected statistical procedures and alternative statistical tests. Across multiple frameworks, the real dataset consistently shows an excess of small p-values relative to randomized controls, indicating detectable codon-associated differences in backbone conformation.

bioinformatics↗

bioRxiv2026

A Suite of Eight Toxoplasma gondii Effectors Cooperates to Activate the Non-canonical NF-κB Pathway

As a master of host-cell reprogramming, Toxoplasma gondii (T. gondii) tachyzoites manipulate diverse signaling networks to establish a niche permissive for long-term infection. While the parasites subversion of canonical NF-{kappa}B signaling (p65/p50) is well established, how infection impacts the non-canonical NF-{kappa}B pathway has been largely unexplored. Here, we report that T. gondii infection induces robust nuclear accumulation of the non-canonical NF-{kappa}B subunits RelB and p52 in both human and murine cells. This activation follows a gradual kinetic profile and is conserved across both Type I and Type II parasite genetic backgrounds. We demonstrate that this reprogramming is strictly dependent on the MYR1-dependent export of dense granule effectors. Mechanistically, T. gondii infection drives the depletion of the negative regulator TRAF3, leading to the stabilization of NF-{kappa}B-inducing kinase (NIK), phosphorylation of p100, and its subsequent processing into p52. Utilizing a panel of combinatorial knockout parasites, we reveal that no single effector is responsible for this phenotype. Instead, a suite of eight MYR1-dependent effectors, IST, NSM, HCE1/TEEGR, GRA16, GRA18, GRA24, GRA28, and GRA84, functions through a collaborative, additive network to trigger the non-canonical response. These findings highlight a distributed regulatory strategy used by the parasite to overcome host transcriptional robustness and shape host signaling. ImportanceToxoplasma gondii infects nearly one-third of the global population and establishes infection by extensively rewiring host immune signaling. While decades of work have focused on how the parasite modulates canonical NF-{kappa}B activity, whether it also engages the alternative, non-canonical arm of this pathway has remained unclear. Here, we show that T. gondii tachyzoites activate non-canonical NF-{kappa}B signaling, driving nuclear accumulation of RelB/p52 through MYR1-dependent effector export. Unexpectedly, no single effector is responsible. Instead, eight secreted proteins act cooperatively to enable NIK stabilization and engage the alternative NF-{kappa}B cascade, revealing a networked mode of immune control. This discovery highlights a regulatory logic evolved by the parasite to overcome host transcriptional robustness. Together, these findings identify non-canonical NF-{kappa}B activation as a new axis of host-parasite interaction and expand our understanding of how T. gondii reprograms central immune signaling circuits through multi-effector networks.

microbiology↗

bioRxiv2025

Sphingolipid Homeostasis, Mitochondrial Activity, and PKA Signaling Drive an Azole-Tolerant State

Antifungal therapies frequently fail, resulting in persistent infections caused by the important opportunistic pathogen, Candida albicans, which is highly tolerant to azole drugs. Tolerance arises from a subpopulation of cells that survive prolonged drug exposure, yet the underlying mechanisms remain poorly defined. Here, transcription factor mutant library screens identified Mnl1 as a key repressor of tolerance. Loss of MNL1 elevated cAMP levels and activated the PKA pathway, linking Mnl1 to growth control and stress responses. Additionally, mnl1 cells exhibited altered sphingolipid composition, implicating Mnl1 in regulating membrane permeability, a key determinant of drug efflux and membrane integrity. Increased tolerance in mnl1 cells was also linked to increased mitochondrial function. Thus, Mnl1 regulates tolerance through coordinated control of sphingolipid metabolism, mitochondrial activity, and PKA signaling, highlighting that tolerant cells adopt a distinct physiological state primed to withstand antifungal stress.

microbiology↗

bioRxiv2025

Impaired perception of isoluminant contrast modulation stimuli: Evidence for a magnocellular pathway mechanism

Contrast modulation (CM) stimuli have been previously used to reveal nonlinear contributions of Y-like retinal ganglion cells (RGCs) such as parasol cells to cortical responses and perception. To test whether CMs are selectively processed within the magnocellular pathway, we assessed envelope motion discrimination and detection for achromatic (yellow-black) and chromatic (red-green) CMs in the presence of luminance masking noise to disrupt luminance-based mechanisms of motion processing. Compared to achromatic CMs, perception of chromatic CMs was more sensitive to luminance masking noise, suggesting that CM envelope motion perception relied predominantly on luminance signals. Specifically, envelope motion discrimination performance was better maintained for achromatic CMs than chromatic CMs, even at high masking noise levels. Notably, luminance masking noise greatly impaired envelope direction discrimination for chromatic CMs but had minimal impact on their detection, suggesting that chromatic aberrations may enhance envelope motion perception for chromatic CMs by introducing luminance signals. These findings collectively emphasize that CM stimuli selectively activate Y-like/parasol RGCs of the retino-geniculate magnocellular pathway, underscoring their potential to specifically target this pathway. This might have clinical advantages for early diagnosis in disorders such as glaucoma or dyslexia, where magnocellular pathway dysfunction is predominant.

neuroscience↗

bioRxiv2025

CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images

Image-based machine learning tools have emerged as powerful resources for analyzing medical images, with deep learning-based semantic segmentation commonly utilized to enable spatial quantification of structures in images. However, customization and training of segmentation algorithms requires advanced programming skills and intricate workflows, limiting their accessibility to many investigators. Here, we present a protocol and software for automatic segmentation of medical images guided by a graphical user interface (GUI) using the CODAvision algorithm. This workflow simplifies the process of semantic segmentation of microanatomical structures by enabling users to train highly customizable deep learning models without extensive coding expertise. The protocol outlines best practices for creating robust training datasets, configuring model parameters, and optimizing performance across diverse biomedical image modalities. CODAvision enhances the usability of the CODA algorithm (Nature Methods, 2022) by streamlining parameter configuration, model training, and performance evaluation, automatically generating quantitative results and comprehensive reports. We expand beyond the original implementation of CODA to serial histology by demonstrating robust performance across numerous medical image modalities and diverse biological questions. We provide sample results in data types including histology, magnetic resonance imaging (MRI), and computed tomography (CT). We demonstrate the diverse use of this tool in applications including quantification of metastatic burden in in vivo models and deconvolution of spot-based spatial transcriptomics datasets. This protocol is designed for researchers with interest in rapid design of highly customizable semantic segmentation algorithms and a basic understanding of programming and anatomy.

bioinformatics↗

bioRxiv2025

Tahoe-100M: A Giga-Scale Single-Cell Perturbation Atlas for Context-Dependent Gene Function and Cellular Modeling

Building predictive models of the cell requires systematically mapping how perturbations reshape each cells state, function, and behavior. Here, we present Tahoe-100M, a giga-scale single-cell atlas of 100 million transcriptomic profiles measuring how each of 1,100 small-molecule perturbations impact cells across 50 cancer cell lines. Our high-throughput Mosaic platform, composed of a highly diverse and optimally balanced "cell village", reduces batch effects and enables parallel profiling of thousands of conditions at single-cell resolution at an unprecedented scale. As the largest single-cell dataset to date, Tahoe-100M enables artificial-intelligence (AI)-driven models to learn context-dependent functions, capturing fundamental principles of gene regulation and network dynamics. Although we leverage cancer models and pharmacological compounds to create this resource, Tahoe-100M is fundamentally designed as a broadly applicable perturbation atlas and supports deeper insights into cell biology across multiple tissues and contexts. By publicly releasing this atlas, we aim to accelerate the creation and development of robust AI frameworks for systems biology, ultimately improving our ability to predict and manipulate cellular behaviors across a wide range of applications.

genomics↗

bioRxiv2025

A Semi-Automated MEA Spike sorting (SAMS) method for high throughput assessment of cultured neurons

Neurons derived from human pluripotent stem cells (hPSCs) are valuable models for studying brain development and developing therapies for brain disorders. Evaluating human-derived neurons requires assessing their electrical activity, which can be achieved using multi-electrode arrays (MEAs) for extracellular recordings. Because each electrode channel generally detects activity from multiple neurons, resolving the activity of single neurons requires a process called spike sorting. However, currently available spike sorting methods are not optimized for the analysis of hPSC-derived neurons, and require complex workflows and time-consuming manual intervention. Here, we introduce a Semi-Automated MEA Spike sorting software (SAMS) designed specifically for low-density MEA recordings of cultured neurons. SAMS outperforms commercially available automated spike sorting algorithms in terms of accuracy and greatly reduces computational and human processing time. By providing an accessible, efficient, and integrated platform for spike sorting, SAMS enhances the resolution and utility of MEA in disease modeling and drug development using human-derived neurons. HighlightsO_LISAMS is designed and optimized for high throughput analysis of hPSC-derived neurons. C_LIO_LISAMS is more efficient and accurate compared to recommended spike-sorting software. C_LIO_LISAMS resolves phenotypic differences previously not observed without spike sorting. C_LIO_LISAMS is an open-source software. C_LI

neuroscience↗

bioRxiv2024

Inflammation in Areas of Fibrosis Precedes Loss of Kidney Function in Lupus Nephritis

BackgroundInterstitial fibrosis in lupus nephritis (LN) is often infiltrated by immune cells but typically regarded as nonspecific "scar reaction." This study aimed to investigate the relationship between inflammatory fibrosis and kidney disease progression in LN. MethodsInterstitial fibrosis and tubular atrophy (IFTA) were scored in 124 LN kidney biopsies. Inflammation in areas of IFTA (i-IFTA) was graded 0-3 according to the Banff Classification of Allograft Pathology. Significant glomerular filtration rate (GFR) loss was defined as a decline of >15 ml/min at 3 years from biopsy. Immune cell phenotype was defined by serial immunohistochemistry (13-plex). ResultsIFTA was observed in 88/124 (71%) biopsies, and i-IFTA was identified in 76/88 (86%) cases. The distribution of i-IFTA grades was heterogenous across all IFTA grades. In patients with moderate-to-severe IFTA (>25%), the degree of i-IFTA was associated with a higher risk of significant GFR loss: 0/2 (0%), 1/3 (33%), 3/4 (75%), and 7/9 (78%) for i-IFTA grades 0, 1, 2, and 3, respectively (p = 0.028). Multiplexed histology revealed that i-IFTA was mostly composed of CD163+ macrophages and CD4 T cells, followed by CD8 T cells and granulocytes. ConclusionI-IFTA is frequently observed in LN and is dominated by macrophages and T cells. For patients with baseline IFTA >25%, the degree of i-IFTA emerged as a predictor of GFR loss. These data support the routine scoring of i-IFTA in LN due to its prognostic implications and nominate i-IFTA as a potential therapeutic target. LAY SUMMARYScar tissue often contains immune cells, but we still do not fully understand their role. In lupus nephritis (LN), this is typically dismissed as "nonspecific inflammation". However, our study analyzed kidney biopsies from 124 people with LN and found that inflammation in scarred areas may predict future kidney function loss. Specifically, we identified a type of immune cell, CD163+ macrophages, that may contribute to scarring and kidney damage. Our findings suggest that routinely assessing inflammation in scarred areas could help predict kidney health in LN patients and highlight a possible new target for therapies to prevent kidney damage.

immunology↗

bioRxiv2024

Functional localization of visual motion area FST in humans

The fundus of the superior temporal sulcus (FST) in macaques is implicated in the processing of complex motion signals, yet a human homolog remains elusive. Here we considered potential localizers and evaluated their effectiveness in delineating putative FST (pFST), from hMT and MST, two nearby motion-sensitive areas in humans. Nine healthy participants underwent scanning sessions with 2D and 3D motion localizers, as well as population receptive field (pRF) mapping. We observed consistent anterior and inferior activation relative to hMT and MST in response to stimuli that contained coherent 3D, but not 2D, motion. Motion opponency and myelination measures further validated the functional and structural distinction between pFST and hMT/MST. At the same time, standard pRF mapping techniques that reveal the visual field organization of hMT/MST proved suboptimal for delineating pFST. Our findings provide a robust framework for localizing pFST in humans, and underscore its distinct functional role in motion processing.

neuroscience↗

bioRxiv2024

ComPRePS: An Automated Cloud-based Image Analysis tool to democratize AI in Digital Pathology

Digital pathology using whole slide imaging (WSI) and artificial intelligence (AI) has the potential to transform diagnostic workflows, but adoption remains limited by technical complexity and scalability. We developed the Computational Renal Pathology Suite (ComPRePS), a scalable cloud-based platform that automates WSI ingestion, compartmental segmentation, feature extraction, and AI-assisted interpretation through an integrated high-performance architecture. ComPRePS was evaluated in two use cases. First, using 213 procurement biopsies, we compared conventional assessments with automated AI analyses and a hybrid AI-assisted expert workflow. ComPRePS AI-assisted methods achieved higher precision and significantly improved interobserver agreement for key lesions, including global glomerulosclerosis, interstitial fibrosis and tubular atrophy, and arterial intimal thickening. Second, ComPRePS enabled high-throughput quantitative profiling of glomerular and tubular features across minimal change disease, diabetic nephropathy, and amyloid nephropathy revealing disease-specific phenotypic patterns inaccessible to manual evaluation. Overall, ComPRePS improves reproducibility, interpretability, and objectivity in renal pathology, bridging computation with clinical practice.

pathology↗

bioRxiv2023

A Combination of Four Nuclear Targeted Effectors Protects Toxoplasma Against Interferon Gamma Driven Human Host Cell Death During Acute Infection.

In both mice and humans, Type II interferon-gamma (IFN{gamma}) is crucial for regulation of Toxoplasma gondii (T. gondii) infection, during acute or chronic phases. To thwart this defense, T. gondii secretes protein effectors hindering the hosts immune response. For example, T. gondii relies on the MYR translocon complex to deploy soluble dense granule effectors (GRAs) into the host cell cytosol or nucleus. Recent genome-wide loss-of-function screens in IFN{gamma}-primed primary human fibroblasts identified MYR translocon components as crucial for parasite resistance against IFN{gamma} driven vacuole clearance. However, these screens did not pinpoint specific MYR-dependent GRA proteins responsible for IFN{gamma} signaling blockade, suggesting potential functional redundancy. Our study reveals that T. gondii depends on the MYR translocon complex to prevent host cell death and parasite premature egress in human cells stimulated with IFN{gamma} post-infection, a unique phenotype observed in various human cell lines but not in murine cells. Intriguingly, inhibiting parasite egress did not prevent host cell death, indicating this mechanism is distinct from those described previously. Genome-wide loss-of-function screens uncovered TgIST, GRA16, GRA24, and GRA28 as effectors necessary for a complete block of IFN{gamma} response. GRA24 and GRA28 directly influenced IFN{gamma} driven transcription, GRA24s action depended on its interaction with p38 MAPK, while GRA28 disrupted histone acetyltransferase activity of CBP/p300. Given the intricate nature of the immune response to T. gondii, it appears that the parasite has evolved equally elaborate mechanisms to subvert IFN{gamma} signaling, extending beyond direct interference with the JAK/STAT1 pathway, to encompass other signaling pathways as well.

microbiology↗

bioRxiv2023

Three-dimensional reconstruction of fetal rhesus macaque kidneys at single-cell resolution reveals complex inter-relation of structures

Kidneys are among the most structurally complex organs in the body. Their architecture is critical to ensure proper function and is often impacted by diseases such as diabetes and hypertension. Understanding the spatial interplay between the different structures of the nephron and renal vasculature is crucial. Recent efforts have demonstrated the value of three-dimensional (3D) imaging in revealing new insights into the various components of the kidney; however, these studies used antibodies or autofluorescence to detect structures and so were limited in their ability to compare the many subtle structures of the kidney at once. Here, through 3D reconstruction of fetal rhesus macaque kidneys at cellular resolution, we demonstrate the power of deep learning in exhaustively labelling seventeen microstructures of the kidney. Using these tissue maps, we interrogate the spatial distribution and spatial correlation of the glomeruli, renal arteries, and the nephron. This work demonstrates the power of deep learning applied to 3D tissue images to improve our ability to compare many microanatomical structures at once, paving the way for further works investigating renal pathologies.

developmental biology↗

bioRxiv2023

Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury

Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression. Translational StatementThe manuscript describes innovation, application and discovery that impact clinical care in kidney disease. First, the approach to maximize use of remnant frozen clinical biopsies to inform on clinically relevant molecular features can augment existing pathological workflow for any frozen tissue without much change in the protocol. Second, this approach is transformational in medical crises such as pandemics where mechanistic insights are needed to evaluate organ injury, targets for drug therapy and diagnostic and prognostic markers. Third, the cell type specific and soluble markers identified and validated can be used for diagnoses or prognoses in AKI due to different etiologies and in multiorgan injury.

genetics↗

bioRxiv2023

High-resolution tracking of unconfined zebrafish behavior reveals stimulatory and anxiolytic effects of psilocybin

Serotonergic psychedelics are emerging therapeutics for psychiatric disorders, yet their underlying mechanisms of action in the brain remain largely elusive. Zebrafish have evolutionarily conserved serotonergic circuits and subcortical targets such as the brainstem regions and the cerebellum, providing a promising model for studying the subcortical effects of serotonergic drugs. Here, we developed a wide-field behavioral tracking system for larval zebrafish and investigated the effects of psilocybin, a psychedelic serotonin receptor agonist. Machine learning analyses of precise body kinematics identified latent behavioral states reflecting spontaneous exploration, visually-driven rapid swimming, and irregular swim patterns following stress exposure. Using this method, we identified two main behavioral effects of acute psilocybin treatment: [i] increased rapid swimming in the absence of visual stimuli and [ii] prevention of irregular swim patterns following stress exposure. Together, these effects indicate that psilocybin induces a brain state that is both stimulatory and anxiolytic. These findings pave the way for using larval zebrafish to elucidate subcortical mechanisms underlying the behavioral effects of serotonergic psychedelics.

neuroscience↗

bioRxiv2022

Alzheimer's disease biomarker profiling in a memory clinic cohort without common comorbidities

Alzheimers disease is a multifactorial disorder with a heterogeneous patient population. Comorbidities such as hypertension, hypercholesterolemia and diabetes are known contributors to the disease progression. Indeed, therapies targeting these disorders have been shown efficient in dementia prevention. However, their mechanistic contribution to Alzheimers pathology and neurodegeneration has not been fully clarified. In the current study, we used CSF samples from a memory clinic cohort of 90 patients without diagnosed hypertension, hypercholesterolemia, or diabetes nor other neurodegenerative disorder, to investigate 13 molecular markers representing key mechanisms underlying Alzheimers pathogenesis. Levels were compared between clinical groups of subjective cognitive decline, mild cognitive impairment, and Alzheimers disease. Associations between markers and groups of markers were analyzed by linear regression. Two-step cluster analysis was used to determine patient clusters. Two key markers were further analyzed by immunofluorescence staining in hippocampus from control and AD individuals without hypertension, hypercholesterolemia nor diabetes. CSF angiotensinogen, thioredoxin-1, and interleukin-15 were the biomarkers with the most prominent associations with Alzheimers pathology, synaptic and axonal damage. Synaptosomal-associated protein 25 kDa and neurofilament light chain were increased in mild cognitive impairment and Alzheimer cases. When we grouped biomarkers by biological function, we found that inflammatory and survival components were associated with Alzheimers pathology, synaptic dysfunction and axonal damage. Moreover, a vascular/metabolic component was associated with synaptic dysfunction. In data-driven analysis, two patient clusters were identified; Older participants with increased CSF markers of oxidative stress, vascular pathology and neuroinflammation were assigned to cluster 1, that was also smaller and characterized by increased synaptic and axonal damage, compared to individuals in cluster 2. Clinical groups were evenly distributed between the clusters. Analysis of post-mortem hippocampal tissue, showed that, compared to controls, angiotensinogen staining was higher in Alzheimers disease and was also found to co-localize with phosphorylated-tau. In a population free of common comorbidities, we could still find associations between Alzheimers disease biomarkers and markers of pathways associated with increased risk for Alzheimers disease (i.e., neuroinflammation, vascular function, oxidative stress and cholesterol homeostasis), suggesting that these pathways are contributing to Alzheimers disease mechanisms even in absence of clinically diagnosed comorbidities. The identification of distinct biomarker-driven endophenotypes of cognitive disorder patients, further highlights the biological heterogeneity of Alzheimers disease and the importance of developing tailored prevention and treatment strategies.

neuroscience↗