Biology subjects

Schaefer, N. K.

Publications and source records attributed to Schaefer, N. K..

6 recordsLinked to original sources

bioRxiv2026

Developmental signaling reveals functionally enriched human-specific gene regulation in telencephalic progenitors

Comparative transcriptomic studies of neural progenitors implicated in human brain expansion have identified extensive baseline gene expression divergence, yet these differences are weakly enriched for functions relevant to development and disease. This suggests that functionally important regulatory divergence may emerge only under specific developmental signaling conditions. Here, we profiled morphogen-dependent gene expression responses in matched telencephalic neuroepithelial cells (telNECs) from human, chimpanzee, and orangutan at the onset of cortical neurogenesis. Baseline interspecies differences were extensive but functionally diffuse. In contrast, a distinct set of genes exhibited species-divergent responses to morphogen stimulation despite conserved baseline expression. These response genes were strongly enriched for regulators of progenitor proliferation and differentiation, neurodevelopmental disorder risk genes, and loci harboring human-lineage sequence changes. Together, these findings show that developmental signaling exposes a functionally enriched class of regulatory divergence beyond baseline comparisons and provide a framework for identifying evolutionarily relevant gene regulation during human brain development.

evolutionary biology↗

bioRxiv2025

CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities

Pooled processing, in which cells from multiple sources are cultured or captured together, is an increasingly popular strategy for droplet-based single cell sequencing studies. This design allows efficient scaling of experiments, isolation of cell-intrinsic differences, and mitigation of batch effects. We present CellBouncer, a computational toolkit for demultiplexing and analyzing single-cell sequencing data from pooled experiments. We demonstrate that CellBouncer can separate and quantify multi-species and multi-individual cell mixtures, identify unknown mitochondrial haplotypes in cells, assign treatments from lipid-conjugated barcodes or CRISPR sgRNAs, and infer pool composition, outperforming existing methods. We also introduce methods to quantify ambient RNA contamination per cell, infer individual donors contributions to the ambient RNA pool, and determine a consensus doublet rate harmonized across data types. Applying these tools to tetraploid composite cells, we identify a competitive advantage of human over chimpanzee mitochondria across 10 cell fusion lines and provide evidence for inter-mitochondrial incompatibility and mito-nuclear incompatibility between species.

genomics↗

bioRxiv2024

Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability

The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite the central role of dopaminergic neurons in human-enriched disorders, molecular specializations associated with human-specific features and vulnerabilities of the dopaminergic system remain unexplored. Here, we establish a phylogeny-in-a-dish approach to examine gene regulatory evolution by differentiating pools of human, chimpanzee, orangutan, and macaque pluripotent stem cells into ventral midbrain organoids capable of forming long-range projections, spontaneous activity, and dopamine release. We identify human-specific gene expression changes related to axonal transport of mitochondria and reactive oxygen species buffering and candidate cis- and trans-regulatory mechanisms underlying gene expression divergence. Our findings are consistent with a model of evolved neuroprotection in response to tradeoffs related to brain expansion and could contribute to the discovery of therapeutic targets and strategies for treating disorders involving the dopaminergic system.

evolutionary biology↗

bioRxiv2023

Mapping cis- and trans-regulatory target genes of human-specific deletions

Deletion of functional sequence is predicted to represent a fundamental mechanism of molecular evolution1,2. Comparative genetic studies of primates2,3 have identified thousands of human-specific deletions (hDels), and the cis-regulatory potential of short ([≤]31 base pairs) hDels has been assessed using reporter assays4. However, how structural variant-sized ([≥]50 base pairs) hDels influence molecular and cellular processes in their native genomic contexts remains unexplored. Here, we design genome-scale libraries of single-guide RNAs targeting 7.2 megabases of sequence in 6,358 hDels and present a systematic CRISPR interference (CRISPRi) screening approach to identify hDels that modify cellular proliferation in chimpanzee pluripotent stem cells. By intersecting hDels with chromatin state features and performing single-cell CRISPRi (Perturb-seq) to identify their cis- and trans-regulatory target genes, we discovered 20 hDels controlling gene expression. We highlight two hDels, hDel_2247 and hDel_585, with tissue-specific activity in the brain. Our findings reveal a molecular and cellular role for sequences lost in the human lineage and establish a framework for functionally interrogating human-specific genetic variants.

genetics↗

bioRxiv2023

Comparative landscape of genetic dependencies in human and chimpanzee stem cells

Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether changes in human cells alter requirements for essential genes. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells, providing support for the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells can reshape the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.

evolutionary biology↗

bioRxiv2017

Natural selection shaped the rise and fall of passenger pigeon genomic diversity

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. While theory predicts that large populations will be more genetically diverse and respond more efficiently to selection, passenger pigeon genetic diversity was surprisingly low. To investigate this we analysed 41 mitochondrial and 4 nuclear genomes from passenger pigeons, and 2 genomes from band-tailed pigeons, passenger pigeons closest living relatives. We find that passenger pigeons large population size allowed for faster adaptive evolution and removal of harmful mutations, but that this drove a huge loss in neutral genetic diversity. These results demonstrate how great an impact selection can have on a vertebrate genome, and invalidate previous results that suggested population instability contributed to this species surprisingly rapid extinction.

genomics↗