Biology subjects

Vanderlinden, L. A.

Publications and source records attributed to Vanderlinden, L. A..

5 recordsLinked to original sources

bioRxiv2026

scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies

Longitudinal single-cell clinical studies enable tracking within-individual cellular dynamics, but methods for modeling temporal phenotypic changes and estimating power remain limited. We present scLASER, a framework detecting time-dependent cellular neighborhood dynamics and simulating longitudinal single-cell datasets for power estimation. Across benchmark experiments, scLASER shows consistently higher sensitivity than traditional cluster--based approaches, with particularly pronounced gains in rare cell types and non-linear temporal patterns. Applications to inflammatory bowel disease (95,813 cells, 38 patients) reveal treatment-responsive NOTCH3+ stromal trajectories with high cell type discrimination (AUC > 0.92), while analysis of COVID-19 data (188,181 cells, 84 patients) identifies three distinct axes of T cell activity (cytotoxic effector, NK immunoreceptor signaling, and interferon-stimulated gene programs) over disease progression. scLASER enables robust longitudinal single-cell analysis and optimization of study design. TeaserA new framework detects time-dependent cellular dynamics and enables power estimation for longitudinal clinical single-cell studies.

bioinformatics↗

bioRxiv2025

Differences in immune cell profiles around the time of islet autoimmunity seroconversion in children with and without type 1 diabetes

Seroconversion (SV) marks the initiation of islet autoimmunity (IA) and pre-clinical phase of type 1 diabetes, yet the contributions of immune cells beyond cytotoxic T cells remain unclear. We applied high-resolution immune cell-type deconvolution using peripheral blood DNA methylation data from nested case-control samples of the Diabetes Autoimmunity Study in the Young (DAISY; n=151) and The Environmental Determinants of Diabetes in the Young (TEDDY; n=166) to estimate immune cell proportions across pre-SV and SV timepoints and construct functional ratios, such as the neutrophil-to-lymphocyte ratio (NLR). Using linear models, we evaluated differences between type 1 diabetes cases and controls at pre-SV, SV, and the change across timepoints. Pre-SV, cases had higher NLR and lower CD4T/CD8T cell ratios. At SV, the combined B-CD4T-CD8T memory/naive ratio was reduced in cases. From pre-SV to SV, cases showed attenuations in NLR, B-memory/naive, and B-CD4T-CD8T memory/naive ratios. These patterns may reflect delayed or disrupted immune maturation with the persistence or expansion of naive cells or impaired transition to memory subsets following antigen exposure. Our findings highlight early shifts in innate and adaptive immune cell dynamics during type 1 diabetes pathogenesis and support immune cell ratios as potential biomarkers for risk stratification and mechanistic insight. Article HighlightsO_LIWe sought to examine immune cells around the time of IA seroconversion in children at higher risk for type 1 diabetes. C_LIO_LIWe wanted to answer whether immune cell ratio differences exist between type 1 diabetes cases and controls around IA at pre-SV, SV, and the change pre-SV to SV. C_LIO_LIWe found immune cell ratio differences between type 1 diabetes cases and controls before, during, and across SV timepoints, suggesting potential etiological and pathophysiological roles. C_LIO_LIOur findings highlight the complexity of immunodynamics around IA seroconversion and potential role for immune cell ratios in type 1 diabetes risk stratification and intervention. C_LI

immunology↗

bioRxiv2024

Genome-Wide Association Study and transcriptome analysis reveals a complex gene network that regulates opsin gene expression and cell fate determination in Drosophila R7 photoreceptor cells.

BackgroundAn animals ability to discriminate between differing wavelengths of light (i.e., color vision) is mediated, in part, by a subset of photoreceptor cells that express opsins with distinct absorption spectra. In Drosophila R7 photoreceptors, expression of the rhodopsin molecules, Rh3 or Rh4, is determined by a stochastic process mediated by the transcription factor spineless. The goal of this study was to identify additional factors that regulate R7 cell fate and opsin choice using a Genome Wide Association Study (GWAS) paired with transcriptome analysis via RNA-Seq. ResultsWe examined Rh3 and Rh4 expression in a subset of fully-sequenced inbred strains from the Drosophila Genetic Reference Panel and performed a GWAS to identify 42 naturally-occurring polymorphisms--in proximity to 28 candidate genes--that significantly influence R7 opsin expression. Network analysis revealed multiple potential interactions between the associated candidate genes, spineless and its partners. GWAS candidates were further validated in a secondary RNAi screen which identified 12 lines that significantly reduce the proportion of Rh3 expressing R7 photoreceptors. Finally, using RNA-Seq, we demonstrated that all but four of the GWAS candidates are expressed in the pupal retina at a critical developmental time point and that five are among the 917 differentially expressed genes in sevenless mutants, which lack R7 cells. ConclusionsCollectively, these results suggest that the relatively simple, binary cell fate decision underlying R7 opsin expression is modulated by a larger, more complex network of regulatory factors. Of particular interest are a subset of candidate genes with previously characterized neuronal functions including neurogenesis, neurodegeneration, photoreceptor development, axon growth and guidance, synaptogenesis, and synaptic function.

genomics↗

bioRxiv2022

Power and precision: Evaluation and recommendations of quantitative trait analysis methods for RNA expression levels in the Hybrid Rat Diversity Panel

The Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of various plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power.

systems biology↗

bioRxiv2019

Identification of genes involved in the differentiation of R7y and R7p photoreceptor cells in Drosophila

The R7 and R8 photoreceptor cells of the Drosophila compound eye mediate color vision. Throughout the majority of the eye, these cells occur in two principal types of ommatidia. Approximately 35% of ommatidia are of the pale type and express Rh3 in R7 cells and Rh5 in R8 cells. The remaining 65% are of the yellow type and express Rh4 in R7 cells and Rh6 in R8 cells. The specification of an R8 cell in a pale or yellow ommatidium depends on the fate of the adjacent R7 cell. However, pale and yellow R7 cells are specified by a stochastic process that requires the genes spineless, tango and klumpfuss. To identify additional genes involved in this process we performed a genetic screen using a collection of 480 P{EP} transposon insertion strains. We identified genes that when inactivated and/or ectopically expressed in R7 cells resulted in a significantly altered percentage of Rh3 expressing R7 cells (Rh3%) from wild-type. 53 strains resulted in altered Rh3% in the heterozygous inactivation arm of the screen. 36 strains resulted in altered Rh3% in the ectopic expression arm of the screen, where the P{EP} insertion strains were crossed to a sevEP-GAL4 driver line. 4 strains showed differential effects between the two screens. Analyses of these results suggest that R7 cell fate specification is sensitive to perturbations in transcription, growth inhibition, glycoprotein ligand binding, WNT signaling, ubiquitin protease activity and Ser/Thr kinase activity, among other diverse signaling and cell biological processes.

genetics↗