Biology subjects

Lee, C. E.

Publications and source records attributed to Lee, C. E..

11 recordsLinked to original sources

bioRxiv2026

Climate warming reduces the speed and predictability of polygenic adaptation to salinity decline

Climate change exposes populations to multiple stressors simultaneously, yet our understanding of how the addition of one stressor alters adaptation to another remains poor. As a result of climate change, high-latitude coastal habitats are experiencing rapid salinity decline, resulting in serious impacts on food webs and ocean circulation. Here, we examine how temperature increase impacts adaptation to salinity decline, in terms of the speed, genomic response, and repeatability of adaptation. We performed replicated Evolve-and-Resequence experiments over 20 to 25 generations in the model copepod Eurytemora carolleeae (Atlantic clade of the E. affinis species complex). Under salinity decline alone, replicate selection lines exhibited a polygenic response involving 66 selected haplotype blocks, with increasing parallelism among the replicate lines through Generation 20. Fitness (egg number) declined sharply over the first four generations but underwent full Evolutionary Rescue, recovering to ancestral levels by Generation 10. In contrast, imposing temperature increase on the salinity decline lines resulted in significantly lower parallelism among the selection lines, along with delayed and incomplete Evolutionary Rescue. Only 14% of selected SNPs were shared between the two selection regimes, and Gene Ontology analyses revealed largely distinct functional categories of genes under selection. These results show that adding warming to salinity decline can alter the genomic trajectory of salinity adaptation, slowing and impeding Evolutionary Rescue, and reducing the repeatability of polygenic responses. Our findings have direct implications for predicting evolutionary responses to realistic, multi-stressor climate change in high-latitude coastal ecosystems experiencing simultaneous ocean freshening and warming.

evolutionary biology↗

bioRxiv2026

Impacts of genome architecture on the repeatability of polygenic adaptation

A central but poorly resolved question regards how genome architecture shapes the selection response and repeatability of polygenic adaptation. We addressed this question using Evolve-and-Resequence experiments under rapid salinity decline in two sibling species (clades) of the invasive copepod Eurytemora affinis complex that differ strikingly in chromosome number (15 versus 4). The 4-chromosome genome arose from chromosomal fusions of the ancestral 15-chromosome genome, bringing together coadapted alleles at fusion sites. Across 10-20 generations of selection, both clades adapted to low salinity but followed divergent evolutionary trajectories. The selection lines of the 15-chromosome clade exhibited highly parallel genomic responses, whereas the 4-chromosome clade lines showed delayed and less repeatable responses. Forward genetic simulations revealed that strong synergistic epistasis among beneficial alleles best explained elevated parallelism in the 15-chromosome clade. Additional simulations varying chromosome number and epistasis revealed that strong positive epistasis, combined with high chromosome numbers, enhances parallelism by enabling recombination to assemble coadapted allelic combinations. In contrast, the high starting frequency of beneficial alleles in the 4-chromosome clade lines indicated selection on standing variation, likely acting on alternative linked haplotypes. These findings demonstrate that genome architecture and gene-gene interactions jointly determine the dynamics and predictability of polygenic adaptation.

evolutionary biology↗

bioRxiv2026

A rare human TNFAIP3 variant reveals how A20 abundance is regulated by TAX1BP1

Variants in TNFAIP3 (encoding A20) are among the most consistent non-MHC genetic associations with human autoimmune disease. Moreover, TNFAIP3 haploinsufficiency confers an autosomal dominant autoinflammatory and autoimmune disease. Whilst these findings strongly suggest that quantitative changes in A20 predispose to pathology, there is currently no evidence that post-transcriptional modifications regulate A20 abundance. We used human reverse genetics approach to investigate this question. From a cohort of patients with complex immune diseases, we identified an ultrarare hypomorphic TNFAIP3 variant (A20S254R) that is both hypomorphic and prone to phosphorylation. One of five carriers of this variant was distinguished by autoimmunity and an NF-kB gain-of-function transcriptional signature. A search for modifiers identified a variant in TAX1BP1 (p.Leu207Ile). We discovered that TAX1BP1 normally retrains A20 phosphorylation. Furthermore, TAX1BP1 preferentially binds phospho-A20, which explains the enhanced interaction between TAX1BP1L207I and A20S254R. A20 phosphorylation regulates its abundance, not by MALT1-mediated degradation, but probably via autophagy. Thus, while A20 phosphorylation has been implicated in A20 protease activity, an epistatic interaction between rare human genetic variants reveals how phosphorylation also regulates A20 abundance.

immunology↗

bioRxiv2025

FCHo2, instead of talin, enables inside-out activation of integrin αvβ5 in curved adhesions

Inside-out activation of integrins is crucial for transducing mechanical forces through the extracellular ligand-integrin-talin-F-actin axis. Extensive studies have shown that talin is the essential player in this process by binding to the intracellular tail of {beta} integrins. Here, we show that, while talin binding is essential for inside-out integrin activation in focal adhesions, it is dispensable in curved adhesions - a distinct adhesion architecture that is exclusively mediated by integrin v{beta}5 and selectively formed at curved membranes. Instead, a curvature-sensing protein FCHo2 binds to the HDRRE motif in the cytoplasmic tail of integrin {beta}5 (ITG{beta}5) and inside-out activates integrin v{beta}5 in curved adhesions. Intriguingly, FCHo2 does not bind to a similar motif in the homologous integrin {beta}3 tail. Through truncations and mutations, we identified a pivotal tryptophan (W) in the {beta}3 tail, which is conserved in all homologous integrin {beta} isoforms except {beta}5, where it is replaced by a tyrosine (Y766). This tyrosine substitution is crucial for integrin {beta}5s unique capability in forming curved adhesions. A Y766W mutation abolishes integrin {beta}5s capacity to form curved adhesions, without affecting its ability to form focal adhesions. Furthermore, our studies suggest that the phosphorylation state of Y766 regulates whether integrin v{beta}5 forms curved adhesions or focal adhesions, providing a cellular mechanism governing different adhesion types. Overall, our work unveils distinct molecular interactions and regulatory mechanisms between curved adhesions and focal adhesions, and establishes a molecular basis for the formation of curved adhesions by integrin v{beta}5. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/691229v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@eb4addorg.highwire.dtl.DTLVardef@1802a01org.highwire.dtl.DTLVardef@145e805org.highwire.dtl.DTLVardef@83d641_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Evolutionary history of the α-Carbonic Anhydrase (αCA) gene family in the phylum Arthropoda, with a focus on the copepod Eurytemora affinis species complex

The -Carbonic Anhydrase (CA) gene family encodes an abundant and ancient metalloenzyme present in all animals. Found in both eukaryotes and prokaryotes, members of this gene family play vital roles in ionic regulation, acid-base regulation, and respiration. However, little is known regarding the evolutionary history and patterns of molecular evolution of this gene family in the phylum Arthropoda. Through phylogenetic reconstruction and subcellular localization prediction, we discovered that arthropod CA genes could be classified into three clades based on phylogenetic topology and predicted subcellular localization, as has been found in chordate CA. Within the three distinct arthropod CA clades, the Extracellular & Membrane-bound CA clade exhibited the highest rates of evolution, variation in predicted subcellular localization, and number of homologs. Intriguingly, while we found that the majority of arthropod CA homologs were classified in the Extracellular & Membrane-bound CA clade, the majority of chordate CA were within the Cytosolic CA clade. This result indicates divergence in CA expansion patterns between the two phyla. In addition, we found that CA12, a paralog that showed salinity-associated signatures of selection in the copepod Eurytemora affinis species complex in previous studies, also shows signatures of positive selection (based on dN/dS) in two of the three sister species of the copepod Eurytemora affinis species complex (E. carolleeae and E. gulfia), compared to the general arthropod CA background. Overall, our results indicate that the CA gene family shows signatures of selection at the macroevolutionary scale, across phyla, and between closely related sister species. Significance statementAlpha Carbonic Anhydrase (CA) is an essential enzyme that is particularly well-studied among certain metazoan lineages, such as chordates and poriferans, but not in arthropods. Here, we provide the first comprehensive analysis of the evolutionary history of CA, and uncover the signatures of selection across phylum and between species. Through phylogenetic reconstruction, predicted subcellular localization, and dN/dS-based selection tests, our study shed light on how the CA gene family has and continues to evolve in the largest animal phylum Arthropoda.

evolutionary biology↗

bioRxiv2025

Microtubule anchoring and coupling of CD20 to the RhoA/Rock1 pathway

CD20 is a B cell-specific four-helix transmembrane protein and a prominent target of therapeutic anti-CD20 antibodies. CD20 is localized within a membrane nanocluster harboring the IgD class B cell antigen receptor (IgD-BCR) where it functions as a gatekeeper for the resting state of naive B lymphocytes. How CD20 exerts its gatekeeper function is not yet known. Using Ramos and human peripheral blood B cells, we show here that the serine/threonine kinase PKC{delta}, constitutively phosphorylates serine residues at the cytosolic tails of CD20. The phosphorylated CD20 becomes a target for 14-3-3 adaptor proteins that link CD20 to the RhoA GDP/GTP exchange factor GEF-H1 and the microtubule (MT) network controlling the stability of the IgD-BCR nanocluster. The binding of anti-CD20 antibodies results in MT disassembly and the replacement of the GEF-H1/CD20 complex by a RhoA-GTP/ROCK1/CD20 complex which drives actomyosin contractility. Our study suggests that CD20 not only maintains the resting state, but also orchestrates the MT/actin switch in active B lymphocytes. This could have implications for treatment with anti-CD20 antibodies and may help to optimize therapeutic protocols. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/656301v2_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1cfe15aorg.highwire.dtl.DTLVardef@d3ee14org.highwire.dtl.DTLVardef@1b375eforg.highwire.dtl.DTLVardef@103c9dd_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Systemic Metabolic and Mitochondrial Defects in Rett Syndrome Models

Genes mutated in monogenic neurodevelopmental disorders are broadly expressed. This observation supports the concept that monogenic neurodevelopmental disorders are systemic diseases that profoundly impact neurodevelopment. We tested the systemic disease model focusing on Rett syndrome, which is caused by mutations in MECP2. Transcriptomes and proteomes of organs and brain regions from Mecp2-null mice as well as diverse MECP2-null male and female human cells were assessed. Widespread changes in the steady-state transcriptome and proteome were identified in brain regions and organs of presymptomatic Mecp2-null male mice as well as mutant human cell lines. The extent of these transcriptome and proteome modifications was similar in cortex, liver, kidney, and skeletal muscle and more pronounced than in the hippocampus and striatum. In particular, Mecp2- and MECP2-sensitive proteomes were enriched in synaptic and metabolic annotated gene products, the latter encompassing lipid metabolism and mitochondrial pathways. MECP2 mutations altered pyruvate-dependent mitochondrial respiration while maintaining the capacity to use glutamine as a mitochondrial carbon source. We conclude that mutations in Mecp2/MECP2 perturb lipid and mitochondrial metabolism systemically limiting cellular flexibility to utilize mitochondrial fuels.

neuroscience↗

bioRxiv2023

Curved adhesions mediate cell attachment to soft matrix fibres in 3D

Mammalian cells adhere to the extracellular matrix (ECM) and sense mechanical cues through integrin-mediated adhesions1, 2. Focal adhesions and related structures are the primary architectures that transmit forces between the ECM and the actin cytoskeleton. Although focal adhesions are abundant when cells are cultured on rigid substrates, they are sparse in soft environments that cannot support high mechanical tensions3. Here, we report a new class of integrin-mediated adhesions, curved adhesions, whose formation is regulated by membrane curvature instead of mechanical tension. In soft matrices made of protein fibres, curved adhesions are induced by membrane curvatures imposed by the fibre geometry. Curved adhesions are mediated by integrin [a]V{beta}5 and are molecularly distinct from focal adhesions and clathrin lattices. The molecular mechanism involves a previously unknown interaction between integrin {beta}5 and a curvature-sensing protein FCHo2. We find that curved adhesions are prevalent in physiologically relevant environments. Disruption of curved adhesions by knocking down integrin {beta}5 or FCHo2 abolishes the migration of multiple cancer cell lines in 3D matrices. These findings provide a mechanism of cell anchorage to natural protein fibres that are too soft to support the formation of focal adhesions. Given their functional importance for 3D cell migration, curved adhesions may serve as a therapeutic target for future development.

cell biology↗

bioRxiv2023

Piconewton forces mediate GAIN domain dissociation of the latrophilin-3 adhesion GPCR

Latrophilins are adhesion G-protein coupled receptors (aGPCRs) that control excitatory synapse formation. aGPCRs, including latrophilins, are autoproteolytically cleaved at their GPCR-Autoproteolysis Inducing (GAIN) domain, but the two resulting fragments remain associated on the cell surface. It is thought that force-mediated dissociation of the fragments exposes a peptide that activates G-protein signaling of aGPCRs, but whether GAIN domain dissociation can occur on biologically relevant timescales and at physiological forces is unknown. Here, we show using magnetic tweezers that physiological forces dramatically accelerate the dissociation of the latrophilin-3 GAIN domain. Forces in the 1-10 pN range were sufficient to dissociate the GAIN domain on a seconds-to-minutes timescale, and the GAIN domain fragments reversibly reassociated after dissociation. Thus, mechanical force may be a key driver of latrophilin signaling during synapse formation, suggesting a physiological mechanism by which aGPCRs may mediate mechanically-induced signal transduction.

biophysics↗

bioRxiv2020

Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus that are Necessary for Synapse Function

Eukaryotic cells maintain proteostasis through mechanisms that require cytoplasmic and mitochondrial translation. Genetic defects affecting cytoplasmic translation perturb synapse development, neurotransmission, and are causative of neurodevelopmental disorders such as Fragile X syndrome. In contrast, there is little indication that mitochondrial proteostasis, either in the form of mitochondrial protein translation and/or degradation, is required for synapse development and function. Here we focus on two genes deleted in a recurrent copy number variation causing neurodevelopmental disorders, the 22q11.2 microdeletion syndrome. We demonstrate that SLC25A1 and MRPL40, two genes present in this microdeleted segment and whose products localize to mitochondria, interact and are necessary for mitochondrial protein translation and proteostasis. Our Drosophila studies show that mitochondrial ribosome function is necessary for synapse neurodevelopment, function, and behavior. We propose that mitochondrial proteostasis perturbations, either by genetic or environmental factors, are a novel pathogenic mechanism for neurodevelopmental disorders.

neuroscience↗

bioRxiv2018

The Genomic Basis of Arthropod Diversity

BackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.\n\nResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality and chemoperception.\n\nConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

genomics↗