Jiahao Jiang

Elevated circulating low‐density lipoprotein cholesterol (LDL‐C) is a key risk factor for coronary artery disease (CAD). The pathogenesis of CAD is multifactorial, driven by heritable and lifestyle‐related risk factors. Although CD4 ⁺ T cells are one of the main cell types in atherosclerotic lesions, their interaction with atherogenic oxidized LDL (ox‐LDL) remains poorly understood. Therefore, we sought to characterize the transcriptomic and epigenomic consequences of ox‐LDL on activated human CD4 ⁺ T cells. We find that ox‐LDL causes a shift towards a pro‐inflammatory, cytokine‐producing CD4 ⁺ T cell transcriptomic state. Concurrently, ox‐LDL induces genome‐wide changes in chromatin accessibility, notably in promoter regions. By integrating our multiomic data, we identify the NRF1 and SP1 transcription factors as likely mediators of ox‐LDL‐induced changes in gene expression. In contrast, the influence of AP‐1 related factors over CD4 ⁺ T cell gene expression decreases following ox‐LDL stimulation. We leveraged our multiomic data to investigate the disease relevance of ox‐LDL exposure, by investigating genomic locations where CAD‐associated single nucleotide polymorphisms were found within dynamic ox‐LDL‐regulated accessible chromatin regions. Together, we demonstrate a disease‐relevant role for ox‐LDL in atherogenic conditioning of CD4 ⁺ T cells. Understanding such cell‐type specific interactions with CAD risk factors may facilitate the development of targeted therapies for CAD.

Transcript diversity including splicing and alternative 3′ end usage is crucial for cellular identity and adaptation, yet its spatial coordination remains poorly understood. Here we present SPLISOSM (spatial isoform statistical modeling), a method for detecting isoform-resolution patterns from spatial transcriptomics data. SPLISOSM uses multivariate testing with nonparametric kernels to account for spot-level and isoform-level dependencies, achieving high statistical power on sparse data. In the mouse brain, we identify over 1,000 spatially variable transcript diversity events, primarily in synaptic signaling pathways linked to neuropsychiatric disorders, and uncover both known and previously unknown regulatory relationships with region-specific RNA binding proteins. We further show that these patterns are evolutionarily conserved between mouse and human prefrontal cortex. Analysis of human glioblastoma highlights pervasive transcript diversity in antigen presentation and adhesion genes associated with specific microenvironmental conditions. Together, we present a comprehensive spatial splicing analysis in the brain under normal and neoplastic conditions.

Transcript diversity including splicing and alternative 3’end usage is crucial for cellular identity and adaptation, yet its spatial coordination remains poorly understood. Here, we present SPLISOSM (SpatiaL ISOform Statistical Modeling), a computational framework for detecting isoform-resolution patterns from spatial transcriptomics data. SPLISOSM leverages multivariate testing to account for spot- and isoform-level dependencies, demonstrating robust and theoretically grounded performance on sparse data. In the mouse brain, we identify over 1,000 spatially variable transcript diversity events, primarily in synaptic signaling pathways linked to neuropsychiatric disorders, and uncover both known and novel regulatory relationships with region-specific RNA binding proteins. We further show that these patterns are evolutionarily conserved between mouse and human prefrontal cortex. Analysis of human glioblastoma highlights pervasive transcript diversity in antigen presentation and adhesion genes associated with specific microenvironmental conditions. Together, we present a comprehensive spatial splicing analysis in the brain under normal and neoplastic conditions. Highlights Multivariate tests of spatial variability and association for transcript usage Conserved isoform variability in synaptic pathways across mouse and human brains Coordinated RNA binding protein expression drives region-specific regulation Tumor microenvironment shapes spatial transcript landscapes in human glioma

Mitochondrial heteroplasmy, the co-existence of different mitochondrial genomes within a cell, is linked to aging and disease. Patients with heteroplasmy due to mitochondrial mutations experience multiple organ complications, particularly poor bone health and bone structure defects. However, the mechanisms involved are generally unknown, due largely to the difficulty of manipulating mtDNA in vivo. To overcome this, we leveraged a heteroplasmic mouse model and discovered that mitochondrial heteroplasmy affects a fundamental developmental process. Specifically, the differentiation of osteoclasts, which resorb bone tissue and maintain bone homeostasis. Mechanistically, there was a reduced localization of specifically respiratory complex I subunits in mitochondria in heteroplasmic mice, disrupting ATP production and osteoclast differentiation. In addition, autophagic flux is exhausted, and the autophagy inducer spermidine restores mitochondrial health and rescues osteoclast activity, both in mice and in cells from patients with primary mitochondrial disease. Together, we identify the mechanisms by which mitochondrial heteroplasmy impacts osteoclastogenesis and discover spermidine as a modulator of this process, which presents a potential treatment for human heteroplasmic conditions such as mitochondrial diseases, which are largely untreatable. Graphical

Oxidised low-density lipoprotein cholesterol (ox-LDL) is critical in the initiation and progression of atherosclerosis. While excessive atherogenic lipids in the arterial intima can trigger endothelial dysfunction in advanced lesions, the response of endothelial cells to ox-LDL in the early stages of atherogenesis remains unclear. Here, we conducted a comprehensive, genome-wide multi-omics characterisation of the cellular response to ox-LDL in primary human aortic endothelial cells (HAECs). Our results reveal that the exposure of HAECs to ox-LDL leads to pathogenic changes in metabolism, transcriptome and epigenome, but in the absence of a typical inflammatory endothelial phenotype. An integrative analysis implicates the role of AP-1, NFE-2 and CEBP transcription factors in regulating ox-LDL-induced transcription. We further demonstrate that ox-LDL activates endothelial cell migration through the epigenomic rewiring of transcription factor binding. Notably, these ox-LDL-induced dynamic binding sites are enriched for the genetic risk of coronary artery disease, enabling the discovery of the gene-environment interaction of rs62172376 and ox-LDL at the CALCRL / TFPI locus. Collectively, our findings provide an unbiased understanding of the transcriptional regulation in endothelial cells in response to ox-LDL, together with its interaction with the genetic element of coronary artery disease.

BACKGROUND: Coronary artery disease (CAD), the leading cause of death worldwide, is influenced by both environmental and genetic factors. Although over 250 genetic risk loci have been identified through genome-wide association studies, the specific causal variants and their regulatory mechanisms are still largely unknown, particularly in disease-relevant cell types such as macrophages. METHODS: We utilized single-cell RNA-seq and single-cell multiomics approaches in primary human monocyte–derived macrophages to explore the transcriptional regulatory network involved in a critical pathogenic event of coronary atherosclerosis—the formation of lipid-laden foam cells. The relative genetic contribution to CAD was assessed by partitioning disease heritability across different macrophage subpopulations. Meta-analysis of single-cell RNA-seq data sets from 38 human atherosclerotic samples was conducted to provide high-resolution cross-referencing to macrophage subpopulations in vivo. RESULTS: We identified 18 782 cis-regulatory elements by jointly profiling the gene expression and chromatin accessibility of >5000 macrophages. Integration with CAD genome-wide association study data prioritized 121 CAD-related genetic variants and 56 candidate causal genes. We showed that CAD heritability was not uniformly distributed and was particularly enriched in the gene programs of a novel CD52-hi lipid-handling macrophage subpopulation. These CD52-hi macrophages displayed significantly less lipoprotein accumulation and were also found in human atherosclerotic plaques. We investigated the cis-regulatory effect of a risk variant rs10488763 on FDX1 , implicating the recruitment of AP-1 and C/EBP-β in the causal mechanisms at this locus. CONCLUSIONS: Our results provide genetic evidence of the divergent roles of macrophage subsets in atherogenesis and highlight lipid-handling macrophages as a key subpopulation through which genetic variants operate to influence disease. These findings provide an unbiased framework for functional fine-mapping of genome-wide association study results using single-cell multiomics and offer new insights into the genotype-environment interactions underlying atherosclerotic disease.

Oxidative stress strongly influences the pathophysiology of erectile dysfunction (ED). In this study, we used the oxidative balance score (OBS), a composite index, to measure the effects of oxidative stress triggered by diet and lifestyle factors. Here, we conducted a cross-sectional study to determine the statistical relationship between OBS and ED among adult males in the U.S. The data from 3318 participants in the National Health and Nutrition Examination Survey (NHANES) 2001–2004 were analyzed. Weighted logistic regression was used to correct for confounding factors and acquire nationwide representative estimates. Generalized additive modeling was used to explore the nonlinear relationship. We also supplemented subgroup and sensitivity analysis to examine the robustness of the main results. Multivariate logistic regression indicated a consistent negative linear association between OBS and ED across all participants [OR (95% CI) = 0.96 (0.94, 0.98)]. After categorizing OBS into tertiles, participants in the highest tertile had 43% lower odds of having ED than those in the lowest tertile [OR (95% CI) = 0.57 (0.37, 0.87)]. The generalized additive model also visualized the linear trend of this association. Furthermore, this linear relationship remained relatively consistent, regardless of whether subgroup or sensitivity analyses were performed. Our findings suggest that adopting a lifestyle and diet pattern that promotes favorable OBS may effectively protect against the development of ED, regardless of the underlying causes.

Background: Coronary artery disease (CAD), the leading cause of death worldwide, is influenced by both environmental and genetic factors. While over 250 genetic risk loci have been identified through genome-wide association studies, the specific causal variants and their regulatory mechanisms are still largely unknown, particularly in disease-relevant cell types like macrophages. Methods: We utilized single-cell RNA-seq (scRNA-seq) and single-cell multi-omics approaches in primary human monocyte-derived macrophages to explore the transcriptional regulatory network involved in a critical pathogenic event of coronary atherosclerosis—the formation of lipid-laden foam cells. Meta-analysis of scRNA-seq datasets from 26 human plaque samples was undertaken to provide a comprehensive atlas of lesional macrophages and to correlate subpopulations in vivo and ex vivo . The genetic risk levels of CAD were assessed by partitioning disease heritability across different macrophage subpopulations. Results: We identified a novel macrophage subpopulation, termed lipid-handling macrophages, both ex vivo and in vivo , and identified associated marker genes, transcription regulators, and functional pathways. 18,782 cis-regulatory elements were identified by jointly profiling the gene expression and chromatin accessibility of >5000 macrophages. Integration with CAD GWAS data prioritized 121 CAD-related genetic variants and 56 candidate causal genes. We showed that CAD heritability was not uniformly distributed and was particularly enriched in the gene programs of lipid-handling macrophages. We investigated the cis-regulatory effect of a risk variant rs10488763 on FDX1, implicating the recruitment of AP-1 and C/EBP-beta in the causal mechanisms at this locus. Conclusions: Our results provide genetic evidence of the divergent roles of macrophage subsets in atherogenesis and highlight lipid-handling macrophages as a key sub-population through which genetic variants actively influence disease. These findings provide an unbiased framework for functional fine-mapping of GWAS results using single-cell multi-omics and offer new insights into the genotype-environment interactions underlying atherosclerotic disease.

Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution revealed plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allowed for spatial mapping of reference populations with significantly reduced ambiguity.