Summary: Microbial metabolites affect host physiology, but how they link genetic defects to abnormal stem cell behavior is unclear. In Drosophila , losing Atg4 in progenitors changes the gut microbiota and raises short-chain fatty acids (SCFAs), such as acetate and propionate. These SCFAs increase intracellular acetyl-CoA, which boosts acetylation by inhibiting histone deacetylases (HDACs) and activating multiple histone acetyltransferases. Chromatin immunoprecipitation identifies Socs36E as a direct acetylation target. Socs36E upregulation serves as a feedback brake on EGFR signaling. However, this brake is too weak to stop sustained proliferation, causing intestinal stem cell overgrowth. These phenotypes are abolished in a germ-free niche and can be recapitulated by SCFA-producing bacteria. Our results support a model where niche-derived metabolites drive locus-specific acetylation of Socs36E, modulating a key homeostatic node and influencing stem cell fate decisions.
Peroxisomes are metabolic organelles that undergo fission to maintain peroxisome number for lipid homeostasis and cellular function. The peroxisomal fission machinery is shared with mitochondria, and although mitochondrial fission regulates neural cell fate decisions during human neurogenesis, it remains unclear whether peroxisomal fission independently influences human neural development. PEX11j3 selectively regulates peroxisomal fission by promoting membrane deformation, elongation, and downstream fission factor recruitment. To uncouple mitochondrial and peroxisomal fission in early human neurogenesis, we generated PEX11j3 knockout iPSCs and tracked differentiation into neural progenitors and neural rosettes. At the cellular level, perturbing PEX11j3 selectively impaired peroxisomal lipid metabolism, characterized by reduced ether-linked phospholipids. At the tissue level, PEX11j3 deficiency altered neural rosette architecture, resulting in enlarged central lumens and expanded neural progenitor populations. This human neural model uncouples mitochondrial and peroxisomal fission and positions PEX11j3 as a distinct regulator of lipid metabolism and neural progenitor fate during human neurogenesis.
Human induced pluripotent stem cells (hiPSCs), together with CRISPR editing, are commonly used for studying neurodevelopmental disorders. Female iPSCs gradually lose the expression of the noncoding X chromosome inactive-specific transcript (XIST), leading to random X chromosome inactivation (XCI) erosion that affects both X-linked and autosomal gene expression. However, the effects of CRISPR editing and neural differentiation on XCI erosion and how this may confound a real-world analysis of differentially expressed genes (DEGs) are poorly understood. Here, we analyzed hundreds of RNA sequencing (RNA-seq) samples of CRISPR-edited iPSC lines for 66 genes and the matched single-neuron RNA-seq data. We found variable XCI in CRISPR-edited female iPSCs, which was largely preserved in iPSC-derived neurons and predominantly influenced X-linked genes. Mechanistically, XIST mediates allele-specific epigenetic regulation of both X-linked and autosomal genes, with the former showing stronger allele-specific expression (ASE) bias that affects neurodevelopmental genes. These results have significant implications in hiPSC-based modeling of neurodevelopmental disorders.
Metabotropic glutamate receptor 6 (mGluR6), encoded by GRM6, is a core component of the ON-bipolar signaling cascade in the retina, but its role in human retinal development remains unclear. Here, we used temporally controlled CRISPR-based genetic ablation in human-induced pluripotent stem cell-derived retinal organoids to define the developmental functions of mGluR6. Unexpectedly, we found that mGluR6 is expressed not only in ON-bipolar cells but also transiently in cone photoreceptors during human retinal development, a pattern not observed in the mouse retina. Early loss of GRM6 before synaptogenesis disrupted cone pedicle architecture, leading to mislocalization of synaptic proteins including Bassoon, ELFN2, and TRPM1, and ultimately resulting in widening or duplication of the outer plexiform layer. In contrast, deletion after synapse formation did not alter retinal architecture. These findings uncover a previously unrecognized, temporally restricted role for mGluR6 in cone terminal targeting and synaptic layer assembly during human retinal development.
