Mikita Suyama

A recent study showed that female medaka lacking the estrogen receptor gene esr2b are unreceptive to male courtship and instead court other females. In this study, we investigated the brain transcriptome of esr2b ‐deficient females to explore the underlying mechanisms of this behavioral phenotype, and identified npyb , one of the two neuropeptide Y (NPY) genes in teleosts, as substantially downregulated. Follow‐up analyses revealed that npyb is expressed in a markedly female‐biased manner, dependent on estrogen/Esr2b signaling, in a ventral telencephalic nucleus implicated in mating behavior. These findings led us to hypothesize that npyb may mediate the phenotypic consequence of esr2b deficiency. To test this, we generated npyb ‐deficient medaka and assessed their mating behavior; however, no notable abnormalities were observed. Given that npya , the other NPY gene in teleosts, is also expressed in the same brain nucleus, we considered the possibility that npya compensates for the loss of npyb function. Nevertheless, even medaka lacking both npya and npyb showed no discernible deficits in mating behavior. While the precise physiological roles of NPY in medaka remain elusive, our findings establish npyb as a downstream target of estrogen/Esr2b signaling and demonstrate its female‐biased expression in a behaviorally relevant brain region.

The sequence of the human genome provides a foundation for understanding cellular processes in health and disease. The organisation of this primary genetic information into cell-specific structure and function is critical to understanding the cell type-specific interpretation and execution of the genome. Epigenetic processes are essential for packaging and higher-level functional organisation of the genome, and changes therein are increasingly recognised as contributors to human disease. Building on primary data generated by multinational consortia, the International Human Epigenome Consortium (IHEC) has uniformly processed a collection of more than 2000 comprehensive human reference epigenomes, collectively referred to as EpiATLAS. This effort involved the development of standardised molecular and bioinformatics protocols, metadata models, and analytical tools to manage, integrate, display, and share vast amounts of epigenomic data. This includes the creation of a publicly available Epigenome Reference Registry, which provides a system for accessing protected human subject datasets and facilitates open searching of de-identified samples and experimental data. The integrated EpiATLAS ecosystem and its comprehensive human reference epigenome maps provide an unprecedented resource for the biosciences, expanding the annotated epigenomic landscape while uncovering previously unappreciated relationships among regulatory layers and revealing how epigenetic inputs underpin fundamental cellular functions and disease associations.

Trophoblasts are multifunctional cells in the placenta and essential for normal pregnancy. Although trophoblast dysfunction can cause pregnancy complications, the underlying mechanisms remain unclear, and effective treatments are limited, partly because of the scarcity of appropriate experimental models. We previously reported the derivation of human trophoblast stem cells (hTSCs) from 1st-trimester placentas and blastocysts, providing a powerful tool to investigate human trophoblast development and function. However, the difficulty in deriving hTSCs from late-gestation placentas has limited their application to pregnancy complication research. Here we report a robust technique to derive hTSCs from term placentas based on the transient expression of a p53 dominant negative mutant, SALL4, and shRNAs against cyclin-dependent kinase inhibitors. Using this technique, we derived and characterized hTSCs from placentas obtained from patients with early-onset preeclampsia (PE). PE-derived hTSCs exhibit impaired trophoblast invasion and reduced placental growth factor secretion, consistent with trophoblast abnormalities reported in PE. Therefore, this study provides a technological basis for investigating pregnancy complications associated with trophoblast dysfunction.

Bone marrow (BM) is the primary site of postnatal hematopoiesis, yet how it is established during embryogenesis remains poorly understood. BM formation is initiated by the invasion of vascular and mesenchymal cells into a preformed cartilage template, generating the primary ossification center (POC). Here, we identify CD55⁺CD90⁺ mesenchymal cells as early regulators of osteoclastogenesis within the POC. These cells share a matrix-degrading transcriptional program with FABP5⁺ septoclasts that localize to the chondro-osseous interface of developing bone. Fate-mapping analyses reveal that CD55⁺CD90⁺ cells transiently give rise to septoclasts during perinatal development, whereas osteoclast-supporting activity is subsequently assumed by LepR⁺ bone marrow stromal cells (BMSCs). During fracture repair, FABP5⁺ septoclasts and LepR⁺ BMSCs are redeployed within the callus, indicating reactivation of a developmental osteogenic program. Together, our findings uncover a conserved mechanism that links skeletal remodeling to the establishment of the BM microenvironment required for hematopoiesis.

Acidic-environment targeting peptides (AEPs), which insert into cell membranes under acidic conditions, have been gaining attention as potential targeting ligands for acidic tissues such as tumors. Conventional AEPs have been taken from archaea or designed rationally; therefore, they have a risk of antigenicity. Here, we propose screening for AEPs from the human proteome. AEP candidates were screened from more than 20000 human proteome transmembrane peptides based on 4 conditions AEPs should fulfill. Twenty-seven peptides were found to satisfy the four conditions. The same number of candidate peptides were identified in the mouse membrane proteome, most of which originated from the orthologous membrane proteins identified in the human proteome. Four of the 27 peptides selected from the human proteome were synthesized with a fluorescence label attached or expressed as fusion proteins with green fluorescent protein to examine their acid-responsive accumulation in vitro and in vivo. We found that 1 of the 4 peptides performed similarly to the pH-low insertion peptide, the first reported AEP.

Variants generating premature termination codons (PTCs) are a major cause of human genetic disease, and it is crucial to accurately assess their impact. Nonsense-mediated mRNA decay (NMD) is a surveillance system that degrades mRNAs containing PTCs to prevent the production of truncated proteins. Prior studies have shown that PTC position-dependent rules are major contributors to NMD efficiency, though they leave a portion of the variability unexplained. To improve the coverage of current NMD escape rules, we used matched human genome and transcriptome data from 1086 individuals and re-evaluated NMD efficiency by considering multi-nucleotide variants (MNVs), translation status, and RNA isoform expression as part of an accurate annotation. Integrated data assessment and accurate annotation resulted in a 12.0% improvement in the explanatory power of NMD efficiency. Furthermore, we found that variants with high allele frequency or occurring in regions of low genomic conservation escape NMD due to the presence of MNVs or the absence of translation by ribosomes. Our results emphasize the importance of accurate annotation in assessing the impact of nonsense variants.

The APOBEC3 (A3) genes encoding cytidine deaminases evolved in mammals to restrict retroviral replication. The MUC1 gene appeared in mammals to protect barrier tissues from viral infections. There is no known involvement of the MUC1 encoded MUC1-C/M1C protein in the regulation of A3s. We found that induction of MUC1-C in NSCLC cells treated with EGFR inhibitors integrates activation of an inflammatory memory response with the type I interferon (IFN) STAT1/STAT2/IRF9 (U-ISGF3) pathway. In turn, MUC1-C drives expression of A3 genes by activating their U-ISGF3-stimulated response elements (ISREs). We also report that MUC1-C-mediated induction of type II IFN STAT1 homodimer (U-GAF) complexes and the gamma-associated signaling (GAS) pathway drives human endogenous retrovirus HERV-K102/K108 expression. Our results in NSCLC cell line and patient-derived models further demonstrate that MUC1-C activates A3 and HERV-K expression by a common MUC1-C→STAT1 auto-inductive pathway. These previously unrecognized findings demonstrate that a MUC1-C-driven inflammatory pathway coordinates activation of APOBEC3 and HERV-K expression.

Type 2 diabetes (T2D) is a multifactorial disease caused by insulin resistance and impaired insulin secretion from pancreatic β-cells, but the precise mechanisms remain to be elucidated. To identify primary genetic factors of T2D in a rat model, we performed comparative transcriptome and mutation analyses of the pancreatic islets between the obese Zucker fatty rat and the Zucker fatty rat-derived T2D model Zucker fatty diabetes mellitus (ZFDM) rat. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identified a nonsense mutation, c.409C > T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. We examined the relevance of the Lcn2 mutation with T2D in the ZFDM rat by using genome editing and genetic linkage analysis and confirmed that the Lcn2 mutation exhibits no significant association with the onset of T2D. Interestingly, we found that the Lcn2 mutation is distributed widely in rat species, such as commonly used DA and F344 strains. Our data indicate that several rat strains would serve as Lcn2 deficient models, contributing to elucidate the pathophysiological roles of Lcn2 in a wide variety of phenotypes.

The root of asthma can be linked to early life, with prenatal environments influencing risk. We investigate the effects of maternal asthma on the offspring’s lungs during fetal and adult life. Adult offspring of asthmatic mothers show an increase in lung group 2 innate lymphoid cell (ILC2) number and function with allergen-induced lung inflammation. Offspring of asthmatic mothers show phenotypic alteration of their lung ILC2s during fetal life, with increased expression of genes related to activation and glucocorticoid signaling. Furthermore, these offspring carry overlapping chromatin-accessible altered regions, including glucocorticoid receptor-binding regions in their lung ILC2s both at the fetal stage and adulthood, suggesting persistent prenatal epigenetic changes. Moreover, maternal exposure to glucocorticoids has similar effects on fetal lung ILC2s and contributes to allergen-induced lung inflammation during adulthood. Thus, asthma during pregnancy may have long-term effects on lung ILC2s in the offspring from the embryonic period, contributing to an increased risk of developing asthma.

The placenta is essential for nutrient exchange and hormone production between the mother and the developing fetus and serves as an invaluable model for epigenetic research. Most epigenetic studies of the human placenta have used whole placentas from term pregnancies and have identified the presence of partially methylated domains (PMDs). However, the origin of these domains, which are typically absent in most somatic cells, remains unclear in the placental context. Using whole-genome bisulfite sequencing and analysis of histone H3 modifications, we generated epigenetic profiles of human cytotrophoblasts during the first trimester and at term, as well as human trophoblast stem cells. Our study focused specifically on PMDs. We found that genomic regions likely to form PMDs are resistant to global DNA demethylation during trophectoderm reprogramming, and that PMDs arise through a slow methylation process within condensed chromatin near the nuclear lamina. In addition, we found significant differences in histone H3 modifications between PMDs in cytotrophoblasts and trophoblast stem cells. Our findings suggest that spatiotemporal genomic features shape megabase-scale DNA methylation patterns, including PMDs, in the human placenta and highlight distinct differences in PMDs between human cytotrophoblasts and trophoblast stem cells. These findings advance our understanding of placental biology and provide a basis for further research into human development and related diseases.