Biology subjects

Lund, A.

Publications and source records attributed to Lund, A..

9 recordsLinked to original sources

bioRxiv2026

Surrogate variables and the risk of overfitting in neuropsychiatric gene expression analyses

The reproducibility crisis in biomedical research calls for re-evaluation of how common analytic approaches affect results. One such approach, surrogate variable analysis (SVA), is widely used to adjust for unmeasured drivers of variation in transcriptomic differential expression analyses. We systematically quantified the impact of SVA using synthetic data with known ground truth and fourteen brain RNA-seq and microarray datasets spanning Alzheimer's disease, autism spectrum disorder, bipolar disorder, schizophrenia, and Parkinson's disease. In synthetic data, SVA usage frequently led to high false positive rates. This issue was not revealed by standard diagnostics nor resolved by strategies such as maximizing cross-dataset signal correlation. In real data, using SVA reduced cross-cohort reproducibility of differential expression signatures regardless of the number of surrogate variables included. These findings show that SVA risks inducing overfitting at realistic signal levels, advocating for a cautious, case-by-case application, with a preference for modeling known covariates.

bioinformatics↗

bioRxiv2026

Cross-species spatial profiling links progranulin to an immune suppressive niche in brain metastasis

Immune checkpoint inhibitors (ICI) have revolutionized the treatment of brain metastasis (BM), demonstrating intracranial response rates and durability not previously seen with other therapies. However, approximately 50% of patients do not respond to ICI, and the brain-specific interactions that shape anti-tumor immunity remain poorly understood. We profiled five syngeneic BM models using spatial transcriptomics, identifying myeloid-rich niches enriched for interferon-responsive and disease-associated microglia (DAM)-like programs. Ligand-receptor colocalization analyses identified progranulin (PGRN) as a candidate mediator of these niches. Host- or tumor-cell Grn loss reduced BM burden, and Grn-deficient macrophages exhibited altered metabolic programs and tumor-cell engulfment in vitro. Across independent human BM datasets, GRN expression was associated with conserved lysosomal and DAM-like myeloid programs, and GRN-high myeloid regions colocalized with immunosuppressive signatures and dysfunctional CD8+ T cell states. These cross-species findings identify PGRN as a candidate mediator of the BM immune niche and support further investigation of its therapeutic relevance.

cancer biology↗

bioRxiv2024

Quiescent cell re-entry is limited by macroautophagy-induced lysosomal damage

To maintain tissue homeostasis, many cells are kept in a quiescent state until prompted to divide. The re-activation of quiescent cells is perturbed with aging and may underlie declining tissue homeostasis and resiliency. The unfolded protein response regulators IRE-1 and XBP-1 are required for the re-activation of quiescent cells in developmentally L1 arrested C. elegans. Utilizing a forward genetic screen in C. elegans, we discovered that macroautophagy targets protein aggregates to lysosomes in quiescent cells, leading to lysosome damage that prevents cell cycle re-entry in the absence of IRE-1/XBP-1. Genetic inhibition of macroautophagy and stimulation of lysosomes via the overexpression of HLH-30 (TFEB/TFE3) synergistically reduces lysosome damage. Protein aggregates are also targeted to lysosomes by macroautophagy in quiescent cultured mammalian cells, causing lysosome damage that is associated with reduced re-activation. Thus, lysosome damage is a hallmark of quiescent cells and limiting lysosome damage by restraining macroautophagy can stimulate their re-activation.

cell biology↗

bioRxiv2023

A Distinct Phenotype of Polarized Memory B cell holds IgE Memory

Allergen-specific IgE antibodies mediate allergic pathology in diseases such as allergic rhinitis and food allergy. Memory B cells (MBCs) contribute to circulating IgE by regenerating IgE-producing plasma cells upon allergen encounter. We report a population of type 2 polarized MBCs defined as CD23hi, IL-4Rhi, CD32low at the transcriptional and surface protein levels. These "MBC2s" are enriched in IgG1 and IgG4-expressing cells, while constitutively expressing germline transcripts for IgE. Allergen-specific B cells from patients with allergic rhinitis and food allergy were enriched in MBC2s. MBC2s generated allergen specific-IgE during sublingual immunotherapy, thereby identifying these cells as the primary reservoir of IgE. The identification of MBC2s provides insights into the maintenance of IgE memory, which is detrimental in allergic diseases, but which could be beneficial in protection against venoms and helminths. One-Sentence SummaryIdentification of a novel memory B cell subset which holds allergen specific IgE memory.

immunology↗

bioRxiv2022

In-silico and in-vitro morphometric analysis of intestinal organoids

Organoids offer a powerful model to study cellular self-organisation, the growth of specific tissue morphologies in-vitro, and to assess potential medical therapies. However, the intrinsic mechanisms of these systems are not entirely understood yet, which can result in variability of organoids due to differences in culture conditions and basement membrane extracts used. Improving the standardisation of organoid cultures is essential for their implementation in clinical protocols. Developing tools to assess and predict the behaviour of these systems may produce a more robust and standardised biological model to perform accurate clinical studies. Here we developed an algorithm to automate crypt-like structure counting on intestinal organoids in both in-vitro and in-silico images. In addition, we modified an existing two-dimensional agent-based mathematical model of intestinal organoids to better describe the system physiology, and evaluated its ability to replicate budding structures compared to new experimental data we generated. The crypt-counting algorithm proved useful in approximating the average budding structures found in our in-vitro intestinal organoid culture images on days 3 and 7 after seeding. Our changes to the in-silico model maintain the potential to produce simulations that replicate the number of budding structures found on days 5 and 7 of in-vitro data. The present study aims to aid in quantifying key morphological structures and provide a method to compare both in-vitro and in-silico experiments. Our results could be extended later to 3D in-silico models.

systems biology↗

bioRxiv2022

Mitochondrial TFAM in the Regulation of FOXP3+ T cell Mediated Maintenance of CD4+ T Cell Landscapes

Foxp3 regulatory T cells (Tregs) maintain immune homeostasis, yet the process that preserves their stability during aging remain unclear. Mechanistic progress has been hindered by models that ablate Tregs or delete Foxp3, which induce acute autoimmunity and prevent longitudinal study of physiological regulatory drift. Here, we establish a dose-dependent mitochondrial framework that preserves Treg lineage survival while permitting gradual metabolic attenuation. Using Treg-restricted TFAM modulation, a complementary haploinsufficient model, and whole-spleen single-cell profiling. We identify lineage-selective immune remodeling characterized by contraction of naive CD8 and follicular B-cell pools, alteration of CD4 states, expansion of activated Tregs, and emergence of neuroimmune stress linked transcriptional modules that parallel physiological aging. Mechanistically, mitochondrial insufficiency is associated with functional loss of FOXP3-centered chromatin coordination and enrichment of NF-{kappa}B/NFAT/AP-1 inflammatory and senescence programs while lineage identity remains detectable. Partial mitochondrial attenuation within Tregs alone is sufficient to drive chronic low-grade systemic inflammation, neuromuscular decline, gut microbial restructuring, and elevated microglial responsiveness without Treg depletion. Pharmacologic and microbiota-directed interventions partially reduce inflammatory tone and improve functional metrics. Together, our findings identify TFAM as a key regulator of immune aging and reveal that healthy mitochondrial function in Tregs is essential for protecting against inflammaging and age-associated functional decline.

immunology↗

bioRxiv2021

Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment

While genetic tumor heterogeneity has long been recognized, recent work has revealed significant variation among cancer cells at the epigenetic and transcriptional levels. Profiling tumors at the single-cell level in individual cancer types has shown that transcriptional heterogeneity is organized into cancer cell states, implying that diverse cell states may represent stable and functional units with complementary roles in tumor maintenance and progression. However, it remains unclear to what extent these states span tumor types, constituting general features of cancer. Furthermore, the role of cancer cell states in tumor progression and their specific interactions with cells of the tumor microenvironment remain to be elucidated. Here, we perform a pan-cancer single-cell RNA-Seq analysis across 15 cancer types and identify a catalog of 16 gene modules whose expression defines recurrent cancer cell states, including stress, interferon response, epithelial-mesenchymal transition, metal response, basal and ciliated. Using mouse models, we find that induction of the interferon response module varies by tumor location and is diminished upon elimination of lymphocytes. Moreover, spatial transcriptomic analysis further links the interferon response in cancer cells to T cells and macrophages in the tumor microenvironment. Our work provides a framework for studying how cancer cell states interact with the tumor microenvironment to form organized systems capable of immune evasion, drug resistance, and metastasis.

cancer biology↗

bioRxiv2021

Defining dysfunction due to loss of MECP2 in Rett Patient Brain

Rett Syndrome is characterized by a postnatal loss of neurophysiological function and regression of childhood development. Because the syndrome is X-linked and males with MECP2 mutations generally do not survive birth, the study of this syndrome has been complicated by the fact that in female brain, a portion of neurons express wild type MECP2, and another portion express a non-functional allele of MECP2. Therefore, bulk-RNA-sequencing of Rett brain is confounded by the presence of chimerism of neurons for functional MECP2 in neurons. We developed an approach that allows for single-nuclei transcriptional profiling of individual neurons and a direct comparison between neurons that express functional MECP2 with those that express the disease-causing allele. We found that mutant neurons from Rett brain show patterns of aberrant expression of synaptic and metabolic genes, both of which can be detected in in vitro models of Rett Syndrome. We used these resources to identify a role for POU2F1/OCT1 transcription factor in mediating the response to stress due to loss of MECP2, highlighting a potential key molecular regulator of stress in Rett neurons. Together, our new sorting approach enables us to highlight defective molecular and metabolic pathways in Rett brain neurons and suggests that in vitro models could serve as valuable tools to further study this syndrome and potentially for development of novel therapeutics.

molecular biology↗

bioRxiv2020

Publicly available hiPSC lines with extreme polygenic risk scores for modeling schizophrenia

Schizophrenia (SZ) is a common and debilitating psychiatric disorder with limited effective treatment options. Although highly heritable, risk for this polygenic disorder depends on the complex interplay of hundreds of common and rare variants. Translating the growing list of genetic loci significantly associated with disease into medically actionable information remains an important challenge. Thus, establishing platforms with which to validate the impact of risk variants in cell-type-specific and donor-dependent contexts is critical. Towards this, we selected and characterize a collection of twelve human induced pluripotent stem cell (hiPSC) lines derived from control donors with extremely low and high SZ polygenic risk scores (PRS). These hiPSC lines are publicly available at the California Institute for Regenerative Medicine (CIRM). The suitability of these extreme PRS hiPSCs for CRISPR-based isogenic comparisons of neurons and glia was evaluated across three independent laboratories, identifying 9 out of 12 meeting our criteria. We report a standardized resource of publicly available hiPSCs, with which we collectively commit to conducting future CRISPR-engineering, in order to facilitate comparison and integration of functional validation studies across the field of psychiatric genetics.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗