Biology subjects

Diks, I. F.

Publications and source records attributed to Diks, I. F..

6 recordsLinked to original sources

bioRxiv2025

Angiopoietin signalling is a central axis of amyloid-driven vascular dysfunction in Alzheimer's disease

The neurovascular unit is critical for brain health, and its dysfunction has been linked to Alzheimers disease (AD). However, a cell-type-resolved understanding of how diverse vascular cells become dysfunctional and contribute to disease has been missing. Here, we applied Vessel Isolation and Nuclei Extraction for Sequencing (VINE-seq) to build a comprehensive transcriptomic atlas from 101 individuals along AD progression. Our analysis of over 842,646 parenchymal and vascular nuclei reveals that vascular dysfunction in AD is driven by transcriptional changes rather than shifts in cell proportions, with brain endothelial cells (BECs) and smooth muscle cells (SMCs) most affected. Strikingly, these molecular signatures emerge early at the mild cognitive impairment (MCI) stage, implicating vascular dysfunction early in AD pathogenesis. Stratifying by pathology reveals distinct vascular responses to {beta}-amyloid and tau: {beta}-amyloid burden primarily perturbs BECs and SMCs, while tau pathology predominantly impacts glial cells. We identify dysregulated angiopoietin signaling across multiple vascular cell types as a key axis, with antagonistic ANGPT2 in vascular cells and ANGPT1 in astrocytes becoming progressively dysregulated with AD. Together, this work provides a foundational resource that reveals early and pathology-specific pathways of vascular dysfunction in AD. Key MessagesO_LIVINE-seq analysis from 101 individuals creates a comprehensive human brain vascular atlas across Alzheimers disease (AD) progression. C_LIO_LIAD vascular dysfunction is driven by transcriptional changes rather than shifts in cell proportions, with BECs and SMCs most affected. C_LIO_LITranscriptional signatures of vascular dysfunction emerge early at the mild cognitive impairment (MCI) stage, preceding severe cognitive symptoms and aligning more closely with AD than cognitively normal individuals. C_LIO_LIA{beta} and tau associate with distinct vascular changes: A{beta} mainly perturbs endothelial and smooth muscle cells, while tau impacts microglia and astrocytes. C_LIO_LIAngiopoietin signaling (antagonistic ANGPT2 in vascular cells vs. ANGPT1 in astrocytes) becomes progressively dysregulated during AD progression. C_LI

neuroscience↗

bioRxiv2025

ROSMAP-Compass: A data-harmonised, AI-ready atlas of 22 million single nuclei from the ROSMAP cohort

The Religious Orders Study and Memory and Aging Project (ROSMAP) cohort has generated the worlds most comprehensive single-cell transcriptomic resource for Alzheimers disease research. Naturally, in a project spanning multiple years with dozens of research groups involved, the resulting data landscape shows fragmentation across sequencing chemistries, protocols, and pipelines. This presents both a challenge and a unique opportunity for harmonized, collaborative analysis. Following an early data integration strategy and complete realignment of all single nucleus RNA sequencing data, we generated a fully harmonized resource: ROSMAP-Compass, comprising more than 22 million high-quality nuclei from 2,058 donors in multiple brain regions from the ROSMAP and Neuro Psychiatric Symptoms (NPS-AD) cohorts. Through systematic curation and unified reprocessing, we addressed substantial technical challenges including chemistry-specific biases, cross-study batch effects, and sample redundancies across multiple studies spanning different time periods and research groups. ROSMAP-Compass demonstrates the critical importance of systematic data harmonization when integrating large-scale single-cell datasets from multiple sources. By combining open science principles with cutting-edge AI integration, we provide both a critical resource for understanding Alzheimers disease heterogeneity and a blueprint for making complex biomedical data accessible to the global research community. The full resource, interactive web portal, and LLM compatible API are freely available, empowering researchers worldwide to accelerate discovery in neurodegenerative diseases.

neuroscience↗

bioRxiv2025

PBMCpedia: A Harmonized PBMC scRNA-seq Database With Unified Mapping and Enhanced Celltype Annotation

Reproducibility in single-cell transcriptomics remains limited by inconsistent preprocessing, heterogeneous cell type annotations, and study-specific batch effects. This challenge is particularly pronounced in peripheral blood mononuclear cell (PBMC) datasets, which are central to immunological research but rarely harmonized across studies. We present PBMCpedia, a unified PBMC atlas comprising over 4.3 million single cells from 519 samples across 24 publicly available scRNA-seq studies. Unlike prior efforts, PBMCpedia reprocesses all raw sequencing data using a single, standardized pipeline with consistent quality control, batch correction, and multi-resolution cell type annotation. The dataset spans 14 diseases, including autoimmune, infectious, and neurodegenerative conditions, alongside healthy controls, enabling reproducible, metadata-aware comparisons across biological contexts. In addition to transcriptomes, PBMCpedia includes TCR/BCR repertoire data for 75 samples and surface protein measurements for 56 samples, supporting integrative immune profiling at the transcriptomic and proteogenomic levels. To support exploration and accessibility, we provide an interactive web interface (https://web.ccb.uni-saarland.de/pbmcpedia/) for querying gene expression, marker genes, and pathway enrichment across cell types, conditions, sexes, and age groups. PBMCpedia fills a critical gap by offering a transparent, harmonized, and disease-diverse PBMC resource designed for cross-study immune profiling and discovery.

bioinformatics↗

bioRxiv2025

SingleRust: A High-Performance Toolkit for Single-Cell Data Analysis at Scale

Single-cell RNA sequencing studies increasingly generate datasets exceeding 10 million cells, surpassing the memory capacity of standard analytical tools on typical institutional infrastructure. Here we introduce SingleRust, a computational framework that addresses these constraints through systematic algorithmic optimizations and systems-level design. Key improvements include sparse masked principal component analysis that reduces memory footprint while preserving biological signal, lock-free parallel implementations for differential expression testing, and adaptive k-nearest neighbor algorithms that automatically select optimal data structures based on dataset size. These optimizations achieve 2.4-25.5-fold performance improvements and 1.3-3.0-fold memory reduction compared to Scanpy, enabling routine analysis of 30 million cells on our representative test system with 512 GB RAM. Comprehensive validation confirms numerical equivalence with established methods while maintaining biological interpretation fidelity. SingleRust maintains full compatibility with the AnnData ecosystem while providing researchers immediate access to population-scale analyses on existing infrastructure, addressing a critical bottleneck in single-cell genomics workflows.

bioinformatics↗

bioRxiv2025

Single-cell Spatial Transcriptomics Reveals Disease-specificMicroenvironmental Niches in Neurodegeneration and COVID-19

Neurodegenerative diseases and infections can produce lasting effects on brain function, yet the spatial molecular mechanisms underlying these changes remain poorly understood. Here, we present high-resolution spatial transcriptomics of 40 postmortem brain samples from patients with Parkinsons disease, frontotemporal dementia, dementia with Lewy bodies, and severe COVID-19. Analyzing over 1.5 million spatially resolved cells across dorsolateral prefrontal cortex and anterior cingulate cortex revealed disease-specific transcriptional signatures with pronounced layer-and region-specificity. In Parkinsons disease, we identified stressed neurons creating distinctive microenvironmental gradients where metabolic and protein degradation pathways are elevated near stress epicenters, while regenerative processes increase with distance. COVID-19 brains displayed extensive peripheral immune cell infiltration, particularly in the subcortical white matter, accompanied by compromised blood-brain barrier and coordinated neuroinflammatory responses from microglia, astrocytes, and endothelial cells. Integration of miRNA sequencing with spatial transcriptomics uncovered layer-specific regulatory patterns, including neuroinflammation-associated miR-155. This atlas provides unprecedented insights into disease pathology and highlights the critical importance of spatial molecular context in understanding brain disorders. Key Messages[1] A high-resolution single-cell spatial transcriptomics atlas of the dorsolateral prefrontal cortex and anterior cingulate cortex across neurodegenerative conditions and severe COVID-19 [2] Region-and layer-specific transcriptional dysregulation across disease comparisons reveals disease-specific differential vulnerability [3] Metabolically stressed cells found selectively in the anterior cingulate cortex of Parkinsons disease patients but not in dementia with Lewy bodies, along with detailed characterization of their spatial microenvironment [4] Peripheral immune cell clusters identified in the white matter of the cerebral cortex of COVID-19 patients, with detailed characterization of their spatial microenvironment [5] Integration of bulk miRNA sequencing reveals cortical layer-specific miRNA regulatory patterns

neuroscience↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗