Biomedical subjects

Zhi Yu

Publications and source records attributed to Zhi Yu.

5 recordsLinked to original sources

PubMed2026

Machine learning-driven spleen imaging and genomics uncover a splenic connection to coronary artery disease.

Despite advances in managing traditional risk factors, coronary artery disease (CAD) remains the leading cause of mortality. Circulating hematopoietic cells influence risk for CAD separately from traditional risk factors, but the role of a key regulating organ, the spleen, is unknown. The understudied spleen is a representation of the hematopoietic system optimally suited for unbiased radiologic investigations toward mechanistic insights. Here, we leveraged deep learning to extract 107 splenic radiomic features from abdominal magnetic resonance imaging (MRI) scans of 42,059 UK Biobank participants and of 2745 Mass General Brigham Biobank (MGBB) participants. Of these, 10 features from UK Biobank were associated with CAD. Genome-wide association analysis of CAD-associated features identified 219 loci, including 9p21. Variants at 9p21, the strongest yet mechanistically elusive CAD locus, were associated with splenic features such as run-length nonuniformity, reflecting heterogeneity of continuous texture regions. Research MRI findings were consistent internally, but external clinical validation highlighted challenges in translating analyses of abdominal MRI scans to routine clinical practice because of variability in imaging protocols and greater clinical heterogeneity among patients. Our study, combining deep learning with genomics, presents a framework to uncover potential splenic involvement in CAD and emphasizes translational gaps between research and clinical radiomics.

Humans↗

PubMed2026

Impaired Glycolysis Leads to Defective Efferocytosis and Impaired Plaque Resolution in Tet2 Clonal Hematopoiesis.

BACKGROUND: Clonal hematopoiesis (CH) arising from mutations in hematopoietic genes has been identified as an important risk factor for atherosclerotic cardiovascular disease. Despite the established role of some CH mutations in promoting atherosclerosis progression, their role in clinically relevant LDL (low-density lipoprotein) lowering-induced plaque remodeling or regression has not been extensively studied. METHODS: To assess the effects of TET2 (tet methylcytosine dioxygenase 2) CH on plaque resolution, we prepared control or chimeric Tet2+/- CH mice with conditional deletion of Tet2 in hematopoietic stem cells during LDL lowering-induced plaque remodeling. After establishing atherosclerosis by Western diet feeding for 12 weeks in Ldlr-/- mice, Tet2 was deleted by tamoxifen injection, and hypercholesterolemia was either normalized to simulate clinical lipid management, or mice were continued on the Western diet. RESULTS: Unlike control mice, Tet2+/- CH mice failed to significantly reduce necrotic core area or increase fibrous cap thickness and showed impaired macrophage efferocytosis during LDL lowering. Single-cell RNA sequencing and gene set enrichment analysis of aortic cell populations revealed that Tet2 deficient monocyte/macrophage populations were defective in glycolysis, phagocytosis, and actin polymerization. Tet2-deficient bone marrow-derived macrophages and Tet2+/- induced pluripotent stem cell-derived human macrophages showed defective ability to sustain continuing rounds of efferocytosis. Bone marrow-derived macrophages displayed reduced apoptotic cell binding and internalization and impaired activity of Wiskott-Aldrich syndrome protein and SCAR (suppressor of cyclic AMP receptor) homolog complex mediated actin polymerization. We linked these defects to reduced anaerobic glycolysis and lactate levels and rescued them by lactate supplementation or by treatment with the HIF-1α (hypoxia-inducible factor 1α) activator molidustat. Molidustat treatment reversed the defects in necrotic core and fibrous cap formation during LDL lowering-induced plaque remodeling in Tet2+/- CH mice. Reduced plasma lactate levels were also shown in TET2 clonal hematopoiesis of indeterminate potential carriers in the UK Biobank. CONCLUSIONS: Our data identify impaired efferocytosis and glycolysis-lactate-actin polymerization pathways in advanced atherosclerosis as potential therapeutic targets to induce proresolving restructuring of the plaque immune cells and to promote beneficial atherosclerosis remodeling in subjects with TET2 CH.

LDL lowering↗

PubMed2026

Multi-omics insights into aroma formation in congou black tea during fermentation.

This study used multi-omics technologies to analyze aroma formation during Congou black tea fermentation. Volatile compounds were analyzed by headspace solid phase microextraction coupled with gas chromatography mass spectrometry using two columns of different polarity. Fermentation increased total volatile normalized peak area fivefold, with alcohols, aldehydes, and acids increasing over sevenfold. 29 differential metabolites were screened, including amino acid derived phenylacetaldehyde, phenylethanol, and 2-methylbutanal; fatty acid derived (E,E)-2,4-heptadienal, hexanal, and 1-hexanol; and isoprenoid derived linalool, geraniol, and beta ionone. Transcriptomic, proteomic, and enzyme analyses revealed that biosynthesis contributed to early accumulation of amino acid and isoprenoid derived aromas, whereas ortho quinone mediated Strecker degradation and free radical induced fatty acid auto oxidation dominated generation of amino and fatty acid derived aromas during middle and late fermentation. In conclusion, aroma formation during fermentation results from biosynthesis and non-enzymatic oxidation, with the latter possibly dominating amino and fatty acid derived aromas.

Fermentation↗

PubMed2026

The Biobank Rare Variant consortium powers the discovery of rare genetic associations through global collaboration.

Rare coding variants can have large effects on disease risk and provide direct routes from human genetics to disease mechanisms and therapeutic targets, but their discovery is constrained by sample size, particularly for low-prevalence diseases. Here we establish the Biobank Rare Variant Analysis (BRaVa) consortium, a global rare variant association resource that integrates sequencing and linked health-record data from ten biobanks and cohorts comprising over 1.2 million individuals across diverse ancestries. We performed gene-based meta-analyses of rare coding variation across 33 clinical endpoints and 11 quantitative traits. Aggregating evidence across biobanks and ancestries identified 514 gene-trait associations, including 31 not previously reported in prior studies or curated association resources following systematic literature review. Notably, 36.1% of gene-level associations were undetectable in any individual biobank, and 91 emerged only through cross-ancestry meta-analysis, demonstrating that federated integration enables discovery beyond the reach of single cohorts. Similar gains were observed at the variant level, where 25.0% of phenotype-locus associations were detectable only through meta-analysis. Effect size estimates were correlated across ancestries with concordant directions of effect, supporting the generalizability of rare variant associations. The identified signals implicate pathways involved in transcriptional and epigenetic regulation, metabolism, vascular and epithelial biology, and immune function, highlighting rare coding variation as an engine for biological discovery across medical record phenotypes. For example, damaging variation in ANKRD12 implicates inflammatory transcriptional dysregulation in asthma and chronic obstructive pulmonary disease, and ultra-rare predicted loss-of-function variants in NAA15 link protein acetylation processes to type 2 diabetes risk. BRaVa establishes a scalable framework and freely available community resource for rare variant meta-analysis across global biobanks. Public release of gene- and variant-level association summary statistics provides a reference map of rare coding variant associations to support disease gene discovery, biological interpretation, and therapeutic target prioritization as sequencing-linked health-record resources continue to expand.

Journal Article↗

PubMed2025

Deciphering Clonal Hematopoiesis of Indeterminate Potential: Methods, Mechanisms, and Implications for Kidney Diseases.

CKD afflicts over 10% of US adults, with its prevalence increasing sharply with age. Clonal hematopoiesis of indeterminate potential (CHIP) is a common, genetically heterogeneous blood cell disorder characterized by the age-related clonal expansion of hematopoietic cells driven by leukemogenic somatic mutations yet without hematologic malignancy or dysplasia. While CHIP is a strong risk factor of future hematologic malignancy (estimated at approximately 0.5% per year, compared with <0.1% for those without CHIP), it is also linked to two-fold higher cardiovascular disease in epidemiologic, cell-based, and murine studies. However, more recent work has implicated CHIP with kidney outcomes, such as CKD as well as AKI, independent of traditional risk factors. This review covers the observations and proposed hypotheses linking CHIP and kidney disease. The review also underscores the need for further research to elucidate the distinct pathways through which CHIP may contribute to CKD and its comorbidities, considering the heterogeneity within CKD stages and etiologies, as well as whether CHIP is a causal driver of kidney disease or a marker of aging and comorbidity. Finally, we discuss the potential of anti-inflammatory treatments to mitigate CHIP's adverse effects on kidney health, aiming to improve management strategies for patients with CHIP-associated kidney diseases.

Humans↗