Yuin-Han Loh

Human diseases are complex and arise from the coordinated action of multiple genes and their protein products. Genes’ behaviors extend beyond genetic variants, mutations, and differential expressions. Their coordinated activity across biological scales (molecules, cells, tissues, organs) produces emergent behaviors that shape health and disease. These emergent behaviors span time and space and are often hard to measure directly from observation when using standard experimental measurements. Yet these “hidden” or latent gene characteristics can be powerful drivers of disease. We propose a Mini-Galaxy Model (MGM), a systems-level AI-driven network framework that models cells as “mini-galaxies” composed of multilayered biological information, with each layer encoding a different dimension of genes’ behavior. Here, we delineate a strategy on how to construct and compare MGMs across health and disease and map their etiological relatedness. We also operationalize the MGM as a discovery platform for translational medicine, offering modules to allow target prioritization and editing. By reframing human diseases as the result of emergent behavior of multilayered multimode biological networks and their perturbations, the MGM yields actionable rules to streamline biomarker discovery, guide target selection and enable rational design of combinatorial interventions, and accelerate drug repurposing.

The thymus is the primary site for T cell maturation. While transcriptional profiling of human thymi has been reported, a high-resolution spatial atlas is needed. Here we use Stereo-seq spatial transcriptomics to generate a spatial atlas of the human fetal (13, 14, 17 or 18 weeks post-conception) and pediatric (7 weeks, and 2, 5 or 6 years old) thymi. The architecture of the thymus comprises regions such as the outer cortex, inner medulla, and septa, and contains multiple cell types, including thymic epithelial cells (TEC), thymocytes, dendritic cells, macrophages, and B cells. Utilising this spatial transcriptomics and proteomics information, we further describe lineage-defining transcription factors (TF) that govern molecular signatures of rare mimetic TEC regulation. Our study thus establishes a high-resolution spatial atlas of the human fetal and pediatric thymi to uncover distinct architectural features and TFs regulating these rare cell types, and serves as a resource for further studies.

Very low efficiency limits the application of interspecies somatic cell nuclear transfer (iSCNT) on preserving endangered species. Our study demonstrated when taxonomical distance increased from intra-species to inter-species to inter-subfamily, the blastocyst rates decreased gradually (27.8% to 12.4% to 0). Scriptaid treatment significantly improved blastocyst rate of Bearded pig iSCNT embryos, accelerated the division timing and enhanced the level of H3K9ac at earlier stages. Transcriptome analysis revealed that half of the comparison groups based on taxonomical relations or Scriptaid treatment, displayed high proportion of enriched GO terms related to mitochondrion structure and/or function. Inter-subfamily or inter-species comparison groups reflected in downregulated differentially expressed genes (DEGs) or upregulated DEGs, contrarily. Accordingly, all these comparison groups displayed KEGG pathway enrichment to oxidative phosphorylation under their top pathways. The key genes related to the GO terms were identified for taxonomical relations or Scriptaid treatment, which are mainly from the NADH-ubiquinone oxidoreductase (NDUF) or ND gene family, separately. These findings suggest that taxonomical distance or Scriptaid treatment is closely associated with development fate of iSCNT embryos in Suidae through regulating the expression of mitochondrion-related genes. Our distinct contribution is identifying specific dysregulation in the NDUF (nuclear-encoded) and ND (mitochondrially encoded) gene families as a potential molecular basis for the "taxonomic wall," specifically showing how Scriptaid partially rescues this uncoupling.

Impaired neural stem cell (NSC) proliferation/activation is associated with brain aging, but the underlying mechanisms remain poorly understood. Here, we unexpectedly find that DMTF1, a transcription factor that regulates the Arf/p53 axis in cancer, is down-regulated in the NSCs of a premature aging model driven by telomerase deficiency. DMTF1 up-regulation was able to rescue the impaired proliferation of telomere dysfunctional NSCs. Mechanistically, DMTF1 regulates the transcription of Arid2 and Ss18 genes, two subunits of the SWI/SNF complexes that mediate H3K27ac at E2F gene promoters to promote NSC proliferation. Accordingly, Arid2 or Ss18 depletion phenocopies DMTF1 loss in reducing H3K27ac levels, expression of E2F target genes, and NSC proliferation. Thus, our study has identified DMTF1 as a potential therapeutic target to reverse the proliferation defect of aged NSC that is modeled by telomere attrition and unearthed a distinct genetic program controlled by DMTF1 in NSC.

Understanding early primate embryogenesis remains limited by ethical and technical constraints. To address this, we established a stem cell-based embryo model from the North Bornean orangutan ( Pongo pygmaeus pygmaeus ). Using integration-free induced pluripotent stem cells (iPSCs), we generated blastoids that self-organized into structures resembling human blastocysts in morphology, lineage composition, and transcriptomic identity. Initial aggregation of primed iPSCs produced blastoids with organized lineage segregation. We enhanced this approach by combining isogenic iPSCs maintained under different culture conditions at optimized ratios, generating "bi-blastoids" with high formation efficiency, balanced lineage specification, and dimensions matching human blastocysts. Single-cell RNA sequencing revealed epiblast-, trophectoderm-, and hypoblast-like populations with transcriptomic profiles closely resembling human E6-7 blastocysts. Comparative analysis demonstrated that orangutan blastoids exhibited stronger transcriptional fidelity to human embryos than existing macaque models, establishing their unique value for developmental studies. Functional validation confirmed that orangutan blastoids could generate embryonic stem cell-like and trophectoderm stem cell-like lines, recapitulate trophoblast differentiation and secrete chorionic gonadotropin. However, primitive endoderm/hypoblast-like cells failed to form a distinct compartment, mirroring limitations observed across other primate models. This orangutan blastoid system provides a less ethically restrictive platform for studying human-relevant embryogenesis while maintaining high developmental fidelity. Beyond developmental insights into primate development, this model may inform future reproductive interventions for critically endangered great apes as conservation technologies advance.

Human mesenchymal stem cells (MSCs) have been studied in over 1500 clinical trials to treat over 30 diseases. However, the understanding towards MSC stemness remains under studied. So far, little is known about how MSCs maintain undifferentiated state or commit to specific lineages under different microenvironmental cues. The lack of comprehensive understanding regarding MSC stemness greatly hampers the translation of research findings into successful clinical application due to unclear mechanism of action. Emerging evidence shows that a variety of genetic factors delicately regulate MSC self-renewal and differentiation. In this review, we summarize the role of transcriptional factors, cell cycle regulators, genomic stability genes, cellular quality control, epigenetic regulators, non-coding RNAs, mitochondrial function, growth factors and m6A modification in regulating the stemness of MSCs. Strategies to maintain MSC stemness during ex-vivo expansion are also discussed. This review will deepen understanding of MSC stemness for advancing clinical applications and provide insights into future directions for research aimed at improving MSC-based therapies.

Tissue macrophages reside in anatomically distinct subtissular niches that shape their identity and function. In white adipose tissue (WAT), we identified three macrophage populations with distinct localization, turnover, and phenotypes. Septal adipose tissue macrophages (sATMs), marked by CD209b and lymphatic vessel endothelial hyaluronan receptor 1, were long-lived and positioned in close proximity to adipocyte stem cells (ASCs) within the WAT septum. Within this shared niche, sATMs instructed the differentiation of ASCs into white adipocytes through transforming growth factor–β1 (TGFβ1). Depletion of sATMs, or the selective loss of TGFβ1 within tissue-resident macrophages, redirected ASC fate toward thermogenic adipocytes, enhancing WAT beiging and protecting against diet-induced obesity. These findings highlight the role of a discrete, anatomically defined macrophage population that governs ASC fate and orchestrates adipose tissue expansion.

The interplay between 3D genomic structure and transposable elements (TE) in regulating cell state-specific gene expression program is largely unknown. Here, we explore the utilization of TE-derived enhancers in naïve and expanded pluripotent states by integrative analysis of genome-wide Hi-C-defined enhancer interactions, H3K27ac HiChIP profiling and CRISPR-guided TE proteomics landscape. We find that short interspersed nuclear elements (SINEs) are the more involved TEs in the active chromatin and 3D genome architecture. In particular, mammalian-wide interspersed repeat (MIR), a SINE family member, is highly associated with naïve-specific genomic interactions compared to the expanded state. Primarily, in the naïve pluripotent state, MIR enhancer is co-opted by ESRRB for naïve-specific gene expression program. This ESRRB and MIR enhancer interaction is crucial for the formation of loops that build a network of enhancers and super-enhancers regulating pluripotency genes. We demonstrate that loss of a ESRRB-bound MIR enhancer impairs self-renewal. We also find that MIR is co-bound by structural protein complex, ESRRB-YY1, in the naïve pluripotent state. Altogether, our study highlights the topological regulation of ESRRB on MIR in the naïve potency state.

A time-lapse live embryo monitoring system provides a powerful approach to recording dynamic developmental events of cultured embryos in detail. By obtaining continuous short-interval images, blastocyst formation can be predicted and embryos can be selected. The objective of this study was to investigate the morphokinetic parameters of fishing cat–domestic cat interspecies somatic cell nuclear transfer (iSCNT) embryos from one-cell to blastocyst stages, and in particular, the cleavage patterns of the first division in iSCNT and IVF embryos, as these play a central role in euploidy. Domestic cat in vitro fertilization (IVF) embryos were set up as controls. The results show that morula and blastocyst development rates were significantly lower in the iSCNT embryos compared to their IVF counterparts. All earlier time points of embryonic development before the onset of blastulation in the iSCNT embryos were significantly delayed when compared with their IVF counterparts. In iSCNT, normal embryos (defined as those that developed to the blastocyst stage) took a longer time to reach the morula stage, and these morulas were more likely to undergo compaction, compared to their arrested embryo counterparts. Direct cleavage in the first division is a morphological aberration, and was seen with greater prevalence in iSCNT embryos than control IVF embryos; these aberrant embryos displayed a significantly lower blastocyst development rate than embryos that had undergone normal cleavage. In conclusion, the morphokinetic parameters of fishing cat–domestic cat iSCNT embryos at early stages could be used to predict their potential for development to the blastocyst stage. A time-lapse imaging system is potentially a powerful tool for selecting early embryos with developmental potential for transfer, and hence, for improving feline iSCNT efficiency.