Biology subjects

Andrews, T. S.

Publications and source records attributed to Andrews, T. S..

8 recordsLinked to original sources

bioRxiv2026

An anatomically distinct dopaminergic cell population of the zona incerta as evidence for the human A13 nucleus

The zona incerta (ZI) is a functionally and molecularly diverse deep brain region increasingly recognized as an integrative hub. The rodent ZI contains the dopaminergic A13 nucleus, with studies supporting a central role in modulating sensorimotor integration, nociception, and confers resilience in models of neurodegeneration; however, to date, no clear human homologue has been identified. Here, we identified a tyrosine hydroxylase-positive subregion in the human ZI consistent with the A13, and refined its borders using ex vivo MRI and histology. We translate these findings to in vivo MRI, demonstrating the A13 is distinguishable from surrounding regions by elevated T1 and T2* values. We further revealed a principal rostral-caudal axis of molecular and structural connectivity variation in the ZI, and identified the A13 as a localized molecular specialization. Altogether, we report a distinct ZI subregion corresponding to the A13 nucleus, providing an anatomical foundation for further mechanistic and translational investigation.

neuroscience↗

bioRxiv2026

Characterizing and Mitigating Protocol-Dependent Gene Expression Bias in 3' and 5' Single-Cell RNA Sequencing

Single-cell RNA sequencing (scRNA-seq) has enabled large-scale characterization of cellular heterogeneity; yet, integrating datasets generated through different library preparation protocols remains challenging. For instance, comparisons between 10X Genomics 3' and 5' chemistries are complicated by protocol-dependent technical biases imposed by differences in transcript end capture and amplification. While normalization, and often batch correction, is an integral step in preprocessing scRNA-seq datasets, it remains unclear which correction is most appropriate, or even necessary, for reliable cross-protocol comparisons. Here, we systematically characterize protocol-related expression differences using 35 matched donors across six tissues profiled with both 3' and 5' scRNA-seq approaches. We find that gene expression discrepancies are not pervasive across the whole transcriptome, but driven instead by a relatively small, reproducible subset of protocol-biased genes. Excluding these genes improves cross-protocol concordance, indicating that most genes are directly comparable without aggressive correction. We then benchmark commonly employed normalization approaches and show that while several methods, such as fastMNN, improve statistical alignment when cell populations are well matched, they can distort gene-level signals and inflate differential expression in biologically realistic settings with incomplete cell-type overlap. Taken together, our results demonstrate that protocol bias between 3' and 5' scRNA-seq is limited in scope and that targeted handling of a small set of biased genes presents an alternative approach to normalization or batch correction strategies. This work provides a practical guideline for integrating 3' and 5' scRNA-seq data and highlights the importance of matching normalization strategies to the structure of technical variation and the intended downstream analyses.

bioinformatics↗

bioRxiv2025

Cholinergic synaptic plasticity shapes resilience and vulnerability to tau

Synaptic dysfunction is a hallmark of Alzheimers disease (AD). Yet due to their plasticity, synapses may also adapt to early AD pathology. Here, we demonstrate that cholinergic neurons mount a presynaptic response to tau pathology in the living human brain. Using multi-tracer positron emission tomography in cognitively normal older adults at risk for AD, we observe that cholinergic neurons increase presynaptic vesicular acetylcholine transporter (VAChT) protein levels when colocalized to tau, but not amyloid. Notably, stronger VAChT responses were associated with cognitive resilience over a decade. Whole-brain single-nucleus RNA sequencing in human and mouse tissue reveal that cholinergic neurons are enriched for a plasticity gene-network anchored to the microtubule-associated protein tau (MAPT) gene. In mice, forebrain-specific deletion of VAChT impairs cortical plasticity and hippocampal structural integrity. Overall, our findings identify cholinergic synaptic plasticity, and its failure, as a fundamental mechanism of resilience and vulnerability to tau in presymptomatic AD.

neuroscience↗

bioRxiv2025

CycleMix: Gaussian Mixture Modeling of the Cell Cycle

The cell cycle is a crucial component of many biological processes, including cancer, tissue repair, and inflammation. However, due to the heterogeneity of this cycle it has been difficult to assess the extent of proliferation in clinical tissues. Single-cell RNAseq (scRNAseq) and spatial transcriptomics enables high resolution measurement of gene expression enabling the classification of individual cells into their cycling state. The most widely used method for cell-cycle assignment is Seurat, however their approach is limited to classifying cells into only 3 states: G1, S, G2M and frequently incorrectly labels fully mature non-cycling cells (e.g. neurons) as S/G2M. Here we propose CycleMix, an alternative cell-cycle assignment algorithm that can flexibly assign cells into any number of states provided sufficient marker genes as well as being capable of identifying when cells are not cycling.

bioinformatics↗

bioRxiv2023

Single-cell and spatial transcriptomics reveals the human liver immunological landscape and myeloid dysfunction in PSC.

BackgroundPrimary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease characterized by bile retention, biliary tree destruction, and progressive fibrosis leading to end stage liver disease and transplantation. There is an unmet need to understand the cellular composition of the PSC liver and how it underlies disease pathogenesis. As such, we generated a comprehensive atlas of the PSC liver and a reference healthy liver dataset using multiple multi-omic modalities and functional validation. MethodsIn this work, we employed single-cell (12,000 cells), single-nuclei (23,000 nuclei), and spatial transcriptomics (1 sample by 10x Visium and 3 samples with multi-region profiling by Nanostring GeoMx DSP) to profile the cellular ecosystem in 5 patients with PSC. Transcriptomic profiles were compared to 100k single cell transcriptomes and spatial transcriptomics controls from 24 healthy neurologically deceased donor (NDD) livers. Flow cytometry and intracellular cytokine staining was performed to validate PSC-specific differences in immune phenotype and function. ResultsPSC explants with cirrhosis of the liver parenchyma and prominent periductal fibrosis were associated with a unique population of hepatocytes which transformed to a cholangiocyte-like phenotype. These hepatocytes were surrounded by diverse immune cell populations, including monocyte-like macrophages, liver-resident and circulating natural killer (NK) cells. Inflamed cholangiocytes, fibrosis-resident hepatic stellate cells, and endothelial cells released cytokines that recruited CD4+T-cells, dendritic cells, and neutrophils to the PSC liver. Tissue-resident macrophages, by contrast, were reduced in number and exhibited a dysfunctional inflammatory response to LPS and IFN-{gamma} stimulation. ConclusionsWe present the first comprehensive atlas of the PSC liver and demonstrate hyper-activation and exhaustion-like phenotypes of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. Lay SummaryPrimary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.

cell biology↗

bioRxiv2022

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.

genomics↗

bioRxiv2021

Single Cell, Single Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity

The critical functions of the human liver are coordinated through the interactions of hepatic parenchymal and non-parenchymal cells. Recent advances in single cell transcriptional approaches have enabled an examination of the human liver with unprecedented resolution. However, dissociation related cell perturbation can limit the ability to fully capture the human livers parenchymal cell fraction, which limits the ability to comprehensively profile this organ. Here, we report the transcriptional landscape of 73,295 cells from the human liver using matched single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The addition of snRNA-seq enabled the characterization of interzonal hepatocytes at single-cell resolution, revealed the presence of rare subtypes of hepatic stellate cells previously only seen in disease, and detection of cholangiocyte progenitors that had only been observed during in vitro differentiation experiments. However, T and B lymphocytes and NK cells were only distinguishable using scRNA-seq, highlighting the importance of applying both technologies to obtain a complete map of tissue-resident cell-types. We validated the distinct spatial distribution of the hepatocyte, cholangiocyte and stellate cell populations by an independent spatial transcriptomics dataset and immunohistochemistry. Our study provides a systematic comparison of the transcriptomes captured by scRNA-seq and snRNA-seq and delivers a high-resolution map of the parenchymal cell populations in the healthy human liver.

cell biology↗

bioRxiv2021

Pro-inflammatory alveolar macrophages associated with allograft dysfunction after lung transplantation

PurposeLung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells of stable and ALAD patients to determine key cellular elements in dysfunctional lung allografts. Our particular focus here is on studying alveolar macrophages (AMs) as scRNAseq enables us to elucidate their heterogeneity and possible association with ALAD where our knowledge from cytometry-based assays is very limited. MethodsFresh bronchoalveolar lavage (BAL) cells from 6 LT patients, 3 with stable lung function (3044 {+/-} 1519 cells) and 3 undergoing an episode of ALAD (2593 {+/-} 904 cells) were used for scRNAseq. R Bioconductor and Seurat were used to perform QC, dimensionality reduction, annotation, pathway analysis, and trajectory. Donor and recipient deconvolution was performed using single nucleotide variations. ResultsOur data revealed that AMs are highly heterogeneous (12 transcriptionally distinct subsets in stable). We identified two AM subsets uniquely represented in ALAD. Based on pathway analysis and the top differentially expressed genes in BAL we annotated them as pro-inflammatory interferon-stimulated genes (ISG) and metallothioneins-mediated inflammatory (MT). Pseudotime analysis suggested that ISG AMs represent an earlier stage of differentiation which may suggest them as monocyte drive macrophages. Our functional analysis on an independent set of BAL samples shows that ALAD samples have significantly higher expression of CXCL10, a marker of ISG AM, as we as higher secretion of pro-inflammatory cytokines. Single nucleotide variation calling algorithm has allowed us to identify macrophages of donor origin and demonstrated that donor AMs are lost with time post-transplant. ConclusionUsing scRNAseq, we observed AMs heterogeneity and identified specific subsets that may be associated with allograft dysfunction. Further exploration with scRNAseq will shed light on LT immunobiology and the role of AMs in allograft injury and dysfunction.

immunology↗