Biology subjects

Heck, A.

Publications and source records attributed to Heck, A..

6 recordsLinked to original sources

bioRxiv2025

Single-cell Spatial Transcriptional Profiling Uncovers Heterogeneous Cellular Responses to Pathogenic Tau in a Mouse Model of Neurodegeneration

Intracellular tau accumulation contributes to neurodegeneration and systemic dysfunction. Although tau primarily aggregates in neurons as neurofibrillary tangles (NFTs), it also affects other cell types through poorly understood mechanisms. To define the molecular characteristics of tangle-bearing neurons and their influence on surrounding cells, we used CosMx SMI to evaluate the expression of 950 genes in more than 265,000 cells from rTg(tauP301L)4510 tauopathy and control mouse brains. In the cerebral cortex, tau pathology disrupted the excitatory-inhibitory neuron balance and altered pathways critical for myelination, similar myelin changes were observed in postmortem brain tissue from patients with progressive supranuclear palsy. In the hypothalamus, tau accumulation was associated with transcriptional changes linked to pathways involved in body weight and metabolic regulation. These findings reveal molecular mechanisms underlying both cell-autonomous and non-autonomous effects of tauopathy and identify targets for further investigation into tau pathogenesis and its systemic impact.

neuroscience↗

bioRxiv2025

Tracing colorectal malignancy transformation from cell to tissue scale

The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remains poorly resolved. Here, we survey colorectal tumorigenesis by combining whole-transcriptome spatial molecular imaging (WTx CosMx SMI) with single-nucleus RNA-sequencing (snPATHO-seq) and digital histopathology on colon samples containing reference mucosa, adenomas and carcinomas, as well as a metastatic lymph node. Leveraging (discrete) histological annotations and (continuous) data-driven trajectories, we quantify the dynamics of cellular density, heterogeneity, function and signaling along the reference-adenoma-carcinoma axis, which is concordant in its spatial and molecular definition. This combination of analytical approaches across different data views let us chart tissue transformation across dimensions (physical/transcriptional) and scales (cell/tissue). We resolve [~]3.5 million cells into 43 epithelial, immune, and stromal subpopulations that exhibit a bi-furcating tumor evolution: On the one hand, LGR5+ stem-like epithelial cells are enriched in highly homogeneous proliferative tumor cores. On the other hand, MMP7+ fetal-like states are restricted to immunosuppressive invasive fronts, rich in cancer-associated fibroblasts (CAFs) and tumor-associated macrophages. These subpopulations form concentric spatial layers that organize transformed regions, and their compound aligns with histological malignancy. We further define transition crypts - single colonic crypts with divided histological and transcriptional makeup - that arise from rare crypt fusion or abrupt transformation events. Finally, we trace MMP7+ fetal-like tumor cell states and concomitant myofibroblast-like FAP+ CAFs to lymphovascular invasion sites and matched lymph node metastases, thereby recapitulating invasive programs at single-cell resolution and across sites. In all, we present single cell- and WTx-resolved spatial data that are among the first of their kind. These open up spatial-centric, out-of-the-box analytical avenues to resolve the molecular, cellular and architectural dynamics that attend tissue transformation during CRC onset, progression and dissemination.

cancer biology↗

bioRxiv2025

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

The Spatial Atlas of Human Anatomy (SAHA) represents the first multimodal, subcellular- resolution reference of healthy adult human tissues across multiple organ systems. Integrating spatial transcriptomics, proteomics, and histological features across over 15 million cells from more than 100 donors, SAHA maps conserved and organ-specific cellular niches in gastrointestinal and immune tissues. High-resolution profiling using CosMx SMI, 10x Xenium, RNAscope, GeoMx DSP, and single-nucleus RNA-seq reveals spatially organized cell states, rare adaptive immune populations, and tissue-specific cell-cell interactions and ligand-receptor pairs. Comparative analyses with colorectal cancer and inflammatory bowel disease demonstrate the power of SAHA to detect disease-associated spatial disruptions, including crypt dedifferentiation, perineural invasion, and therapy-resistant immune remodeling. All data are openly accessible through a FAIR-compliant interactive portal to support exploration, benchmarking, and machine learning model training. Through SAHA, we provide a foundational framework for spatial diagnostics and next-generation precision medicine grounded in a comprehensive human tissue atlas, enabling the development of context-aware models that simulate tissue behavior, decode complex pathologies, and accelerate therapeutic innovation at unprecedented scale.

systems biology↗

bioRxiv2023

Olfactory and neuropeptide inputs to appetite neurons in the arcuate nucleus

The sense of smell has potent effects on appetite, but the underlying neural pathways remain undefined. Here we investigated how olfactory signals reach two subsets of appetite-linked neurons in the hypothalamic arcuate nucleus: AgRP (agouti-related peptide) neurons, which stimulate appetite, and POMC (pro-opiomelanocortin) neurons, which suppress it. Using polysynaptic viral tracing, we show that AgRP and POMC neurons receive indirect input from partially overlapping but distinct areas of the olfactory cortex, indicating that they process different sets of olfactory information. We also identify different complements of neurons directly upstream of AgRP and POMC neurons that can relay olfactory cortical signals to the appetite neurons. Single cell transcriptomics shows heterogeneous expression of neuromodulator receptors among AgRP neurons, suggesting variations in the signals they receive. Integrated viral tracing and RNA localization further reveals selected brain areas where upstream neurons express cognate receptor ligands. Together, these findings outline multiple pathways by which distinct olfactory and modulatory signals are differentially routed to neurons that promote versus inhibit appetite.

neuroscience↗

bioRxiv2022

Unraveling the intricate microtubule inner protein networks that reinforce mammalian sperm flagella

To find and fuse with the egg, mammalian sperm must complete an arduous voyage through the female reproductive tract. The sperm cells remarkable odyssey is powered by its flagellum, a microtubule-based molecular machine ornamented with accessory structures that stabilize the sperm tail in viscous media. Recently, cryo-electron tomography (cryo-ET) revealed that mammalian sperm flagella are further reinforced at the molecular scale with sperm-specific microtubule inner proteins (sperm-MIPs), but the identities of these sperm-MIPs are unknown. Here, we use cryo-electron microscopy to resolve structures of native bovine sperm doublet microtubules, thus identifying most sperm-MIPs. In the A-tubule, several copies of testis-specific Tektin-5 contribute to an extended protein network spanning nearly the entire microtubule lumen. Different copies of Tektin-5 adopt a range of conformations and organizations based on their local interactions with other MIPs. The B-tubule is in turn stabilized by sperm-MIPs that bind longitudinally along and laterally across protofilaments. We further resolve structures of endpiece singlet microtubules, revealing MIPs shared between singlets and doublets. Our structures shed light on the molecular diversity of cilia across different cell types of the vertebrate body and provide a structural framework for understanding the molecular underpinnings of male infertility.

cell biology↗

bioRxiv2021

Multipotent progenitors and hematopoietic stem cells arise independently during the endothelial to hematopoietic transition in the early mouse embryo

During embryogenesis, waves of hematopoietic progenitors develop from hemogenic endothelium (HE) prior to the emergence of self-renewing hematopoietic stem cells (HSC). Although previous studies have shown that yolk sac-derived erythromyeloid progenitors and HSC emerge from distinct populations of HE, it remains unknown whether the earliest lymphoid-competent progenitors, multipotent progenitors, and HSC originate from common HE. Here we demonstrate by clonal assays and single cell transcriptomics that rare HE with functional HSC potential in the early murine embryo are distinct from more abundant HE with multilineage hematopoietic potential that fail to generate HSC. Specifically, HSC-competent HE are characterized by expression of CXCR4 surface marker and by higher expression of genes tied to arterial programs regulating HSC dormancy and self-renewal. Together, these findings suggest a revised model of developmental hematopoiesis in which the initial populations of multipotent progenitors and HSC arise independently from HE with distinct phenotypic and transcriptional properties.

developmental biology↗