Biology subjects

Tegtmeyer, M.

Publications and source records attributed to Tegtmeyer, M..

14 recordsLinked to original sources

bioRxiv2026

Cellular morphology emerges from polygenic, distributed transcriptional variation

Height and disease risk are canonical polygenic traits, but whether an analogous architecture governs cellular phenotypes remains unclear. Here, we show that cellular morphology behaves as a polygenic systems phenotype by integrating cross-modal modeling, perturbation profiling, and human genetic variation. An adversarially aligned autoencoder trained on four perturbation datasets predicted morphology from gene expression and generalized without retraining to matched RNA-seq and Cell Painting profiles from 100 genetically diverse iPSC donors. Seventeen morphological features were strongly predicted, particularly those capturing organelle distribution and cytoskeletal architecture. Predictive signal was broadly distributed across genes, with weak individual gene-morphology correlations. Independent CRISPR perturbations supported model-prioritized genes including TIAM1, RAB31, and ABCC5, while genetic analyses identified variant-gene-morphology associations involving PDHX, SLC11A2, and MAPKAPK5. These findings extend polygenic models of complex traits to cellular architecture and provide a framework for interpreting cross-modal prediction in functional genomics.

genetics↗

bioRxiv2025

Gene editing in "cell villages" enables exploring disease-relevant mutations in many genetic backgrounds

Understanding how individual genetic backgrounds shape the effects of disease-associated mutations is central to elucidating the biology of complex psychiatric disorders. We developed a scalable village editing strategy that enables simultaneous genome editing across multiple induced pluripotent stem cell (iPSC) lines, allowing systematic assessment of how polygenic context modulates the impact of specific mutations. Using pooled CRISPR editing in 15 iPSC lines spanning a range of schizophrenia (SCZ) polygenic risk scores, we generated homozygous and heterozygous knockouts in two known SCZ-associated genes: LRP1, involved in cholesterol import, and NRXN1, a presynaptic adhesion molecule. By mixing all lines prior to editing and de-multiplexing them afterward, we efficiently produced multi-donor knockout neurons at scale. Transcriptomic profiling revealed that LRP1 and NRXN1 loss produce both shared and donor-specific effects on neuronal gene expression, with variable perturbation of neurotransmitter transport and cholesterol biosynthesis pathways across genetic backgrounds. These results demonstrate that village editing enables systematic dissection of gene-background interactions in human neurons, offering a powerful framework for studying the polygenic architecture of psychiatric disease.

cell biology↗

bioRxiv2025

Human genetic variation shapes the response of neurons to interferons

Inflammation is increasingly recognized as important to neuropathology, including more classic neuroimmune disease as well as neurodegenerative and neuropsychiatric disorders. Interferons (IFN) are important mediators of central nervous system inflammation. Individuals appear to vary in susceptibility to neuroinflammatory pathology, suggesting that identifying human genetic modifiers of the neuronal IFN response might provide insight into disease pathophysiology. To identify potential modifiers, we stimulated neuronal "cellular villages" of iPSC-derived neurons from over one hundred donors with IFN-alpha (IFNa) or IFN-gamma (IFNg). We then correlated allele states of common variable SNPs to gene expression to identify hundreds of expression quantitative trait loci (eQTLs), many of which emerged specifically upon IFN treatment. We characterized the distinct but overlapping neuronal transcriptional responses to IFNa and IFNg, and identified specific response QTLs. Functional annotation of STAT1 binding to the genome in response to IFN stimulus identified STAT1 binding sites as enriched for response-regulating human genetic variation and also enabled identification of loci with IFN-dependent allele-specific binding of STAT1. These results demonstrate how human genetic variation can influence IFN-dependent mechanisms in neurons in disease-relevant ways.

molecular biology↗

bioRxiv2025

Abnormal Lipid Metabolism and Altered Neuronal Support by Astrocytes Lacking Akap11, a Risk Gene for Schizophrenia and Bipolar Disorder

A-Kinase Anchoring Protein 11 (AKAP11) is a shared genetic risk factor for schizophrenia and bipolar disorder, yet its role in the brain remains poorly understood. Through multi-omic analysis of Akap11 mutant mouse brains and cultured astrocytes, we identified significant transcriptomic, proteomic, and metabolomic alterations. Key findings include the upregulation of cholesterol and fatty acid metabolic pathways, accumulation of lipid species such as cholesteryl esters, triacylglycerols, ceramides, and glycerophospholipids, and elevated levels of 3,5-cyclic AMP and protein kinase A (PKA) signaling. These metabolic perturbations manifested as increased lipid droplet accumulation in Akap11 mutant astrocytes, highlighting AKAP11s critical role in regulating intracellular lipid homeostasis. Mechanistically, AKAP11 functions as an autophagy receptor mediating PKA degradation and interacts with endoplasmic reticulum-resident proteins VAP-A and VAP-B through its FFAT motif, providing possible molecular insight into AKAP11s regulation of lipid metabolism. Co-culture experiments with mouse astrocytes and human induced pluripotent stem cell-derived neurons demonstrated that loss of Akap11 in astrocytes, relative to wild-type, increases excitatory neurotransmission and neuronal activity. Collectively, these findings link AKAP11-mediated lipid and synaptic dysregulation to psychiatric disease risk and highlight the potential role of astrocytes in these disorders.

cell biology↗

bioRxiv2025

Astrocytic-supplied cholesterol drives synaptic gene expression programs in developing neurons and downstream astrocytic transcriptional programs

Astrocytes participate in neuronal synaptic programs that are enriched for genetic associations in schizophrenia and autism spectrum disorders (ASD). To better understand how these co-regulated cellular programs are induced during early neuronal development, we studied astrocytes and iPSC-derived neurons in co-cultures and mono-cultures at 16 time points spanning 0.5 hours to 8 days. We found that upregulation in astrocytes of genes involved in cholesterol biosynthesis preceded the activation of synaptic gene programs in neurons and upregulation of the astrocytic Nrxn1. Neuronal knockdown of key cholesterol receptors led to downregulation of neuronal synaptic genes and induced a robust transcriptional response in the astrocytes, including further upregulation of Nrxn1. This suggests that astrocyte-supplied cholesterol drives these neuronal changes and that bi-directional signalling is occuring. The genes upregulated in neurons were enriched for deleterious variants in schizophrenia and neurodevelopmental disorders, suggesting that their pathogenic effect may be, in part, mediated by reduced buffering capacity for changes in the astrocyte cholesterol supply to neurons. These findings highlight the critical role of astrocyte-neuron interactions in psychiatric and neurodevelopmental disorders, particularly in relation to lipid metabolism and synaptic plasticity.

molecular biology↗

bioRxiv2024

Combining NeuroPainting with transcriptomics reveals cell-type-specific morphological and molecular signatures of the 22q11.2 deletion

Neuropsychiatric conditions pose substantial challenges for therapeutic development due to their complex and poorly understood underlying mechanisms. High-throughput, unbiased phenotypic assays present a promising path for advancing therapeutic discovery, especially within disease-relevant neural tissues. Here, we introduce NeuroPainting, a novel adaptation of the Cell Painting assay, optimized for high-dimensional morphological phenotyping of neural cell types, including neurons, neuronal progenitor cells, and astrocytes derived from human stem cells. Using NeuroPainting, we quantified cell structure and organelle behavior across various brain cell types, creating a public dataset of over 4,000 cellular traits. This extensive dataset not only sets a new benchmark for phenotypic screening in neuropsychiatric research but also serves as a gold standard for the research community, enabling comparisons and validation of results. We then applied NeuroPainting to identify morphological signatures associated with the 22q11.2 deletion, a major genetic risk factor for schizophrenia. We observed profound cell-type-specific effects of the 22q11.2 deletion, with significant alterations in mitochondrial structure, endoplasmic reticulum organization, and cytoskeletal dynamics, particularly in astrocytes. Transcriptomic analysis revealed reduced expression of cell adhesion genes in 22q11.2 deletion astrocytes, consistent with recent post-mortem findings. Integrating the RNA sequencing data and morphological profiles uncovered a novel biological link between altered expression of specific cell adhesion molecules and observed changes in mitochondrial morphology in 22q11.2 deletion astrocytes. These findings underscore the power of combined phenomic and transcriptomic analyses to reveal mechanistic insights associated with human genetic variants of neuropsychiatric conditions.

neuroscience↗

bioRxiv2024

Modeling interpretable correspondence between cell state and perturbation response with CellCap

Single-cell transcriptomics, in conjunction with genetic and compound perturbations, offers a robust approach for exploring cellular behaviors in diverse contexts. Such experiments allow un-covering cell-state-specific responses to perturbations, a crucial aspect in unraveling the intricate molecular mechanisms governing cellular behavior and potentially discovering novel regulatory pathways and therapeutic targets. However, prevailing computational methods predominantly focus on predicting average cellular responses, disregarding the inherent response heterogeneity associated with cell state diversity. In this study, we present CellCap, a deep generative model designed for the end-to-end analysis of single-cell perturbation experiments. CellCap employs sparse dictionary learning in a latent space to deconstruct cell-state-specific perturbation responses into a set of transcriptional response programs. These programs are then utilized by each perturbation condition and each cell at varying degrees. The incorporation of specific model design choices, such as dot-product cross-attention between cell states and response programs, along with a linearly-decoded latent space, underlay the interpretation power of CellCap. We evaluate CellCaps model interpretability through multiple simulated scenarios and apply it to two real single-cell perturbation datasets. These datasets feature either heterogeneous cellular populations or a complex experimental setup. Our results demonstrate that CellCap successfully uncovers the relationship between cell state and perturbation response, unveiling novel insights overlooked in previous analyses. The models interpretability, coupled with its effectiveness in capturing heterogeneous responses, positions CellCap as a valuable tool for advancing our understanding of cellular behaviors in the context of perturbation experiments.

bioinformatics↗

bioRxiv2023

Multi-donor human cortical Chimeroids reveal individual susceptibility to neurotoxic triggers

Inter-individual genetic variation affects the susceptibility to and progression of many diseases. Efforts to study the molecular mechanisms mediating the impact of human genetic variation on normal development and disease phenotypes are limited, however, by the paucity of faithful cellular human models, and the difficulty of scaling current systems to represent multiple individuals. Here, we present human brain "Chimeroids", a highly reproducible, multi-donor human brain cortical organoid model generated by the co-development of cells from a panel of individual donors in a single organoid, while maintaining fidelity to endogenous tissue. By reaggregating cells from multiple single-donor organoids at the neural stem or committed progenitor cell stage, we generate Chimeroids in which each donor produces all cell lineages of the cerebral cortex, even when using pluripotent stem cell lines with notable growth biases. We leveraged Chimeroids to investigate inter-individual variation in susceptibility to neurotoxic stressors that exhibit high clinical phenotypic variability: ethanol and the anti-epileptic drug valproic acid. Individual donors varied in both the penetrance of the effect on target cell types, and the molecular phenotype within each affected cell type. Our results show that human genetic background may be an important mediator of neurotoxin susceptibility and introduce Chimeroids as a scalable system for high-throughput investigation of the contribution of human genetic variation to brain development and disease.

neuroscience↗

bioRxiv2023

Early Alzheimer's disease pathology in human cortex is associated with a transient phase of distinct cell states

Cellular perturbations underlying Alzheimers disease are primarily studied in human postmortem samples and model organisms. Here we generated a single-nucleus atlas from a rare cohort of cortical biopsies from living individuals with varying degrees of Alzheimers disease pathology. We next performed a systematic cross-disease and cross-species integrative analysis to identify a set of cell states that are specific to early AD pathology. These changes-which we refer to as the Early Cortical Amyloid Response--were prominent in neurons, wherein we identified a transient state of hyperactivity preceding loss of excitatory neurons, which correlated with the selective loss of layer 1 inhibitory neurons. Microglia overexpressing neuroinflammatory-related processes also expanded as AD pathological burden increased. Lastly, both oligodendrocytes and pyramidal neurons upregulated genes associated with amyloid beta production and processing during this early hyperactive phase. Our integrative analysis provides an organizing framework for targeting circuit dysfunction, neuroinflammation, and amyloid production early in AD pathogenesis.

genomics↗

bioRxiv2023

High-dimensional phenotyping to define the genetic basis of cellular morphology

The morphology of cells is dynamic and mediated by genetic and environmental factors. Characterizing how genetic variation impacts cell morphology can provide an important link between disease association and cellular function. Here, we combined genomic and high-content imaging approaches on iPSCs from 297 unique donors to investigate the relationship between genetic variants and cellular morphology to map what we term cell morphological quantitative trait loci (cmQTLs). We identified novel associations between rare protein altering variants in WASF2, TSPAN15, and PRLR with several morphological traits related to cell shape, nucleic granularity, and mitochondrial distribution. Knockdown of these genes by CRISPRi confirmed their role in cell morphology. Analysis of common variants yielded one significant association and nominated over 300 variants with suggestive evidence (P<10-6) of association with one or more morphology traits. Our results showed that, similar to other molecular phenotypes, morphological profiling can yield insight about the function of genes and variants.

genomics↗

bioRxiv2022

Robust induction of functional astrocytes using NGN2 expression in human pluripotent stem cells

Astrocytes play essential roles in normal brain function, with dysfunction implicated in diverse developmental and degenerative disease processes. Emerging evidence of profound species divergent features of astrocytes coupled with the relative inaccessibility of human brain tissue underscore the utility of human pluripotent stem cell (hPSC) technologies for the generation and study of human astrocytes. However, existing approaches for hPSC-astrocyte generation are typically lengthy, incompletely characterized, or require intermediate purification steps, limiting their utility for multi-cell line, adequately powered functional studies. Here, we establish a rapid and highly scalable method for generating functional human induced astrocytes (hiAs) based upon transient Neurogenin 2 (NGN2) induction of neural progenitor-like cells followed by maturation in astrocyte media, which demonstrate remarkable homogeneity within the population and across 11 independent cell lines in the absence of additional purification steps. These hiAs express canonical astrocyte markers, respond to pro-inflammatory stimuli, exhibit ATP-induced calcium transients and support neuronal maturation in vitro. Moreover, single-cell transcriptomic analyses reveal the generation of highly reproducible cell populations across individual donors, most closely resembling human fetal astrocytes, and highly similar to hPSC-derived astrocytes generated using more complex approaches. Finally, the hiAs capture key molecular hallmarks in a trisomy 21 disease model. Thus, hiAs provide a valuable and practical resource well-suited for study of basic human astrocyte function and dysfunction in disease.

neuroscience↗

bioRxiv2021

Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells

Variation in the human genome contributes to abundant diversity in human traits and vulnerabilities, but the underlying molecular and cellular mechanisms are not yet known, and will need scalable approaches to accelerate their recognition. Here, we advanced and applied an experimental platform that analyzes genetic, molecular, and phenotypic heterogeneity across cells from very many human donors cultured in a single, shared in vitro environment, with algorithms (Dropulation and Census-seq) for assigning phenotypes to individual donors. We used natural genetic variation and synthetic (CRISPR-Cas9) genetic perturbations to analyze the vulnerability of neural progenitor cells to infection with Zika virus. These analyses identified a common variant in the antiviral IFITM3 gene that regulated IFITM3 expression and explained most inter-individual variation in NPCs susceptibility to Zika virus infectivity. These and other approaches could provide scalable ways to recognize the impact of genes and genetic variation on cellular phenotypes. HIGHLIGHTSO_LIMeasuring cellular phenotypes in iPSCs and hPSC-derived NPCs from many donors C_LIO_LIEffects of donor sex, cell source, genetic and other variables on hPSC RNA expression C_LIO_LINatural genetic variation and synthetic perturbation screens both identify IFITM3 in NPC susceptibility to Zika virus C_LIO_LIA common genetic variant in IFITM3 explains most inter-individual variation in NPC susceptibility to Zika virus C_LI

genomics↗

bioRxiv2021

The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia

To study how the 22q11.2 deletion predisposes to psychiatric disease, we generated induced pluripotent stem cells from deletion carriers and controls, as well as utilized CRISPR/Cas9 to introduce the heterozygous deletion into a control cell line. Upon differentiation into neural progenitor cells, we found the deletion acted in trans to alter the abundance of transcripts associated with risk for neurodevelopmental disorders including Autism Spectrum Disorder. In more differentiated excitatory neurons, altered transcripts encoded presynaptic factors and were associated with genetic risk for schizophrenia, including common (per-SNP heritability p ({tau}c)= 4.2 x 10-6) and rare, loss of function variants (p = 1.29x10-12). These findings suggest a potential relationship between cellular states, developmental windows and susceptibility to psychiatric conditions with different ages of onset. To understand how the deletion contributed to these observed changes in gene expression, we developed and applied PPItools, which identifies the minimal protein-protein interaction network that best explains an observed set of gene expression alterations. We found that many of the genes in the 22q11.2 interval interact in presynaptic, proteasome, and JUN/FOS transcriptional pathways that underlie the broader alterations in psychiatric risk gene expression we identified. Our findings suggest that the 22q11.2 deletion impacts genes and pathways that may converge with risk loci implicated by psychiatric genetic studies to influence disease manifestation in each deletion carrier.

neuroscience↗

bioRxiv2020

Mapping genetic effects on cellular phenotypes with "cell villages"

Tens of thousands of genetic variants shape human phenotypes, mostly by unknown cellular mechanisms. Here we describe Census-seq, a way to measure cellular phenotypes in cells from many people simultaneously. Analogous to pooled CRISPR screens but for natural variation, Census-seq associates cellular phenotypes to donors genotypes by quantifying the presence of each donors DNA in cell "villages" before and after sorting or selection for cellular traits of interest. Census-seq enables population-scale cell-biological phenotyping with low cost and high internal control. We demonstrate Census-seq through investigation of genetic effects on the SMN protein whose deficiency underlies spinal muscular atrophy (SMA). Census-seq quantified and mapped effects of many common alleles on SMN protein levels and response to SMN-targeted therapeutics, including a common, cryptic non-responder allele. We provide tools enabling population-scale cell experiments and explain how Census-seq can be used to map genetic effects on diverse cell phenotypes. O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/174383v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@169bf4borg.highwire.dtl.DTLVardef@18dd9c0org.highwire.dtl.DTLVardef@1d30ca5org.highwire.dtl.DTLVardef@e35bf0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICensus-seq reveals how inherited genetic variation affects cell phenotypes C_LIO_LIGenetic analysis of cellular traits in cell villages of >100 donors C_LIO_LICharacterizing human alleles that shape SMN protein expression and drug responses C_LIO_LIDevelopment of protocols and software to enable cellular population genetics C_LI

genetics↗