Biology subjects

Okamoto, A. S.

Publications and source records attributed to Okamoto, A. S..

6 recordsLinked to original sources

bioRxiv2026

Evolutionary trade-offs between growth and reproduction under obesogenic conditions: sex-biased skeletal and gonadal maturation in mice

Adolescence is a brief period during which finite energy resources are reallocated from linear growth toward reproductive maturation. Rising childhood obesity and earlier onset of puberty suggest that modern, energy rich diets may distort these evolved energy allocation rules, but causal mechanisms remain unclear. Here, we expose male and female wild-type and leptin receptor deficient (Db/Db) to either high fat or normal chow diets. We longitudinally analyze metabolic, skeletal, gonadal, endocrine and insulin-receptor phenotypes from 4-10 weeks of age (sexual maturation window in mice). In WT males, HFDs increased adiposity and impaired glucose tolerance, and selectively remodeled joint morphology, advanced gonadal maturation, and shifted insulin receptor expression from growth plates to testes. Together, these changes indicate a rebalancing of energy use toward reproduction at the expense of skeletal and metabolic health. WT females showed subtler systemic metabolic disruption but clear diet-responsive changes in growth plate and ovarian maturation. Our findings indicate that energy-rich diets during adolescence shift evolved allocation rules to prioritize reproductive readiness over skeletal robustness in a sex-dependent manner, with potential consequences for precocious puberty and bone health in humans.

evolutionary biology↗

bioRxiv2026

Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements

Immortalized cell lines are widely used in biological research despite their known differences from their tissues and cell types of origin. Such cell lines are especially popular for testing hypotheses regarding the activity of cis-regulatory elements (CREs) that regulate gene expression. Previous investigations of blood and skin cell lines revealed many differences between the transcriptional regulatory networks of the cell lines and the associated primary cells. Similar comparisons for other tissues have been limited. Here, we used ATAC-seq to profile CREs in four immortalized liver cell lines and found many differences between each cell lines CREs and primary liver tissue, including differences in the transcription factors that are likely to bind them and differences in the genes that they are likely to regulate. Modifying cell culture conditions based on recommendations in the literature did not improve the similarity with primary liver tissue. Our results suggest that differences between the transcriptional regulatory networks in cell lines and primary tissue should be considered when designing and interpreting cell line experiments.

genomics↗

bioRxiv2025

Massively parallel functional screen identifies thousands of regulatory differences in human versus chimpanzee postcranial skeletal development

Every element of the human skeleton exhibits some differences in comparison to our closest living relatives, chimpanzees. Many of these skeletal modifications underpin key events in human evolution, enabling our species to walk upright, manipulate tools with precision, and support enlarged brains. Identifying the genomic changes that underlie these features remains an outstanding challenge due to the substantial number of differences between the human and chimpanzee genomes. To identify human-chimp sequence differences that modulate gene expression in the developing postcranial skeleton, we used a massively parallel reporter assay (MPRA) to screen the human and chimp versions of 70,000 regulatory elements present in the prenatal skeletal template for differential activity. After testing our library in two cartilage and one bone marrow-derived lymphoblast line, we identify 30,736 regions (45.2%) with activity in our assay. Of the active regions, we find that 11,542 (37.6%; or 17% of the entire pool) regions exhibited differential activity between the human and chimpanzee. We find that human ancestor quickly evolved regions (HAQERs) were predictive of differential activity while Human Accelerated Regions were not and both sets failed to predict the magnitude of effect, unlike the total number of base pair differences between species, which was weakly correlated with effect size. These findings reveal that human skeletal evolution involves widespread regulatory changes distributed across thousands of elements rather than concentrated effects at a few key loci, supporting a polygenic model for the evolution of complex morphological traits.

evolutionary biology↗

bioRxiv2025

Combined ADAMTS10 and ADAMTS17 inactivation exacerbates bone shortening and skin phenotypes

Weill-Marchesani syndrome (WMS) is characterized by severe short stature, short hands and feet (brachydactyly), joint contractures, tight skin, and heart valve, eye, and skin anomalies. Whereas recessive WMS is caused by mutations in ADAMTS10, ADAMTS17, or LTBP2, dominant WMS is caused by mutations in FBN1 (encoding fibrillin-1). Since bone growth is driven by chondrocyte proliferation and hypertrophy in the growth plates, the genetics of WMS suggests that the affected ECM proteins act within the same pathway to regulate chondrocyte and growth plate function. Here, we investigated the role of the secreted ADAMTS proteases ADAMTS10 and ADAMTS17 in growth plate function and ECM formation. We generated Adamts10;Adamts17 double knockout (DKO) mice, which showed significant postnatal lethality compared to single Adamts10 or Adamts17 KO mice. Importantly, we observed severe bone shortening DKO mice, which correlated with a narrower hypertrophic zone in their growth plates. ADAMTS17 substrates identified by N-terminomics and yeast two-hybrid screening identified the ECM proteins fibronectin and collagen VI (COL6). However, validation experiments did not reveal direct proteolysis of either fibronectin or COL6 by ADAMTS17. We then investigated ECM formation in primary ADAMTS10- and ADAMTS17-deficient skin fibroblasts and observed compromised fibronectin deposition concomitant with aberrant intracellular accumulation of fibrillin-1. These findings support a role for ADAMTS17 in ECM protein secretion and assembly. Collectively, our data suggest that ADAMTS10 and ADAMTS17 regulate bone growth by regulating chondrocyte hypertrophy or hypertrophic chondrocyte turnover. Mechanistically, ADAMTS17 appears to be a critical regulator of ECM protein secretion or pericellular matrix assembly, whereas ADAMTS10 likely modulates ECM formation at later stages, possibly regulating the spatio-temporal deposition of fibrillin isoforms.

cell biology↗

bioRxiv2024

Parallel evolution at the regulatory base-pair level contributes to mammalian inter-specific differences in polygenic traits.

Parallel evolution occurs when distinct lineages with similar ancestral states converge on a new phenotype. Parallel evolution has been well documented at the organ, gene pathway, and amino-acid sequence level but in theory it can also occur at individual nucleotides within non-coding regions. To examine the role of parallel evolution in shaping the biology of mammalian complex traits, we used data on single nucleotide polymorphisms (SNPs) influencing human intraspecific variation to predict trait values in other species for eleven complex traits. We found that the alleles at SNP positions associated with human intraspecific height and red blood cell count variation are associated with interspecific variation in the corresponding traits across mammals. These associations hold for deeper branches of mammalian evolution as well as between strains of collaborative cross mice. While variation in red blood cell count between primates uses both ancient and more recently evolved genomic regions, we found that only primate-specific elements were correlated with primate body size. We show that the SNP positions driving these signals are flanked by conserved sequences, maintain synteny with target genes, and overlap transcription factor binding sites. This work highlights the potential of conserved but tunable regulatory elements to be reused in parallel to facilitate evolutionary adaptation in mammals.

evolutionary biology↗

bioRxiv2020

Intergenerational microbial transmission in the little skate (Leucoraja erinacea)

BackgroundMicrobial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate, Leucoraja erinacea, a common North Atlantic species and popular system for chondrichthyan biology. MethodsTo assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST. ResultsWe identify site-specific and stage-specific microbiota dominated by the bacterial phyla Proteobacteria and Bacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community-particularly on the internal surface of the capsule-and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. ConclusionsOur study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

microbiology↗