Biology subjects

Ji, A.

Publications and source records attributed to Ji, A..

7 recordsLinked to original sources

bioRxiv2026

DNA methylation reveals molecular heterogeneity and urate excretion-associated subtypes of gout

Background: The molecular heterogeneity among gout patients remains largely unexplored, hindered the precise treatment for gout. Common indices for gout subtyping are cumbersome to measure, resulting in poor patient compliance. Methods: We elucidated the molecular heterogeneity of gout and developed a simple, reliable classification method for gout subtypes based on genome-wide DNA methylation, to facilitate individualized treatment. Genome-wide DNA methylation profiling was conducted in two independent cohorts, comprising a discovery cohort (n = 108) and a validation cohort (n = 100) representing four clinical gout subtypes. Results: We identified two gout subgroups associated with the fractional excretion of uric acid (FEUA) but not with 24-hour urinary uric acid levels (UUE) based on unsupervised clustering of whole-genome DNA methylation profiles, highlighting the contribution of epigenetic regulation to molecular heterogeneity in urate metabolism. Enrichment analysis links FEUA-associated subtypes to renal cell types, calcium related pathways and extended to the circulating immune compartment, with neutrophil- versus memory B cell-skewed leukocyte composition. A methylation-based classification model using 18 LASSO-selected CpGs with an XGBoost classifier effectively distinguished patients with high and low uric acid excretion, achieving excellent predictive performance (training cohort: AUC = 0.96, AP = 0.91; validation cohort: AUC = 0.86, AP = 0.85), outperforming the published model with clinical characteristics and SNPs. The signature site-associated genes NEK1 and TRPS1 display significant expression differences among urate-stratified patients and immune cells groups. TRPS1 may affect the AP-1/NF-{kappa}B inflammatory programme. Conclusions: These findings reveal distinct DNA methylation signatures underlying gout heterogeneity and demonstrate the feasibility of DNA methylation markers for gout subtype classification. The proposed methylation-based model provides a promising approach for personalized management of gout.

bioinformatics↗

bioRxiv2026

Accurate and scalable demultiplexing of single-cell RNA sequencing using BEACON

Barcode-based multiplexing strategies can significantly increase sample throughput and decrease costs, while mitigating batch effects of single-cell RNA sequencing experiments. However, these approaches can be limited by inaccurate or inefficient demultiplexing, resulting in cell loss and reduced statistical power. Here, we present BEACON, a novel sample demultiplexing method that efficiently learns the background count distribution from data and removes it from individual cells, thereby improving classification accuracy. BEACON outperforms other state-of-the-art methods on multiple human data sets. We apply it to cancer cell line time course experiments in vitro, enabling the identification of genes associated with aggressive tumors in vivo. Finally, we adapt BEACON to multimodal protein-transcriptome profiling, enhancing protein signal recovery to identify a CD161-positive effector memory CD4 T-cell population with a Th17-like phenotype, which we prospectively validate. BEACON can therefore be applied to other droplet-based single-cell sequencing methodologies.

bioinformatics↗

bioRxiv2026

Preserved CETP Activity and Early Serum Amyloid A are Associated with Improved Outcomes in Sepsis-Associated ARDS

Background: Sepsis is a life-threatening condition characterized by organ dysfunction resulting from a dysregulated host response to infection. It is a leading cause of in-hospital mortality. The multicenter Acute Respiratory Distress Syndrome Network Statins for Acutely Injured Lungs from Sepsis (ARDSNet-SAILS) trial found that rosuvastatin (RS) did not improve clinical outcomes in patients with sepsis-associated ARDS and may increase hepatic and renal dysfunction. We evaluated associations of plasma cholesterol ester transfer protein (CETP) activity and Serum Amyloid A (SAA) levels with survival and clinical outcomes using plasma samples and clinical data from ARDSNet-SAILS trial. Methods: This secondary analysis included clinical data and plasma samples from 471 ARDSNet-SAILS participants, randomized to placebo (PL) or RS. Plasma CETP activities and SAA levels were measured at enrollment (Day 0, n=466) and Days 3 (n=425) and 6 (n=342). Treatment effects were assessed using linear mixed models, and associations with survival and outcomes using Cox, linear, beta-binomial, and zero-inflated negative binomial regression models. Results: CETP activities were significantly higher in the survivors compared to non-survivors on days 0, 3, and 6 of analysis, in both the treatment groups (p<0.01). Higher Day 0 and Day 3 CETP activities in PL patients independently predicted improved survival, with every 3-unit increase in activity associated with 18 to 19% lower mortality risk. In the RS treatment group, higher CETP at Day 0, Day 3, and Day 6 was significantly associated with reduced hazard of mortality (p=0.039, 0.005, and 0.022, and hazard ratios = 0.87, 0.82, and 0.80, respectively, for Days 0, 3, and 6). Higher CETP values on Days 3 and 6 were also significantly negatively associated with APACHE score and positively associated with increased renal dysfunction-free days (p=0.001). Plasma SAA levels decreased significantly over time in both treatment groups (p<0.0001). In the PL group, higher plasma SAA levels were associated with a lower hazard of mortality. Accordingly, survivors had significantly higher plasma SAA levels than non-survivors at Day 0 (p=0.005). Higher SAA levels at Days 0 and 3 were also inversely correlated with APACHE scores, while Day 0 SAA levels were positively associated with overall organ dysfunction-free days (p=0.002). In contrast, in the RS group, higher plasma SAA levels were associated with an increased hazard of mortality, reaching statistical significance at Day 6 (p<0.01). Despite this, higher SAA levels in the RS group were positively associated with renal dysfunction-free days (Day 3, p=0.004; Day 6, p=0.006), hepatic dysfunction-free days (Days 0, 3, and 6; all p[≤]0.001), and overall organ dysfunction-free days (Day 0, p=0.017; Days 3 and 6, both p<0.001). Analysis of SAA levels in FPLC fractions demonstrated higher SAA levels in the HDL fraction among survivors compared with non-survivors in the PL group on Days 0 and 3; however, this difference was not observed in the RS group. Conclusion: Taken together, these findings identify plasma CETP activities and early SAA levels as stable prognostic biomarkers associated with improved survival and reduced disease severity in sepsis. However, while both CETP activity and SAA levels were unaffected by RS treatment, it appeared to modify the association between SAA and mortality.

biochemistry↗

bioRxiv2026

PRISMA: A tensor-based framework for deconstructing the genetic architecture of complex diseases, with application to diabetic retinopathy

Complex-disease GWAS compress heterogeneous, tissue-dependent genetic effects into global locus-level statistics, masking local regulatory routes through which polygenic risk contributes to disease architecture. Here we introduce PRISMA (Polygenic Risk Integration via Summary-statistics Multi-tissue Array-decomposition), a summary-statistics framework for quantifying tissue-resolved genetic heterogeneity hidden within aggregate GWAS signals. PRISMA integrates GWAS and multi-tissue cis-eQTL data using graph Laplacian-regularized block-wise factorization, preserving local linkage disequilibrium topology during decomposition. Applied to diabetic retinopathy, PRISMA deconvolved aggregated polygenic risk into three tissue-biased genetic axes corresponding to vascular-metabolic, systemic immune-inflammatory, and retina-specific neurodegenerative trajectories. The framework prioritized 549 axis-associated targets, including 403 below the conventional genome-wide significance threshold, and showed higher tissue-regulatory resolution than PCA, NMF, and K-means. A height GWAS negative-control analysis supported trait-dependent regulatory reprioritization within a shared eQTL-mappable framework. Independent single-cell transcriptomic analyses supported axis-specific enrichment across fibrovascular, immune, and retinal compartments. Exploratory vitreous humor proteomic and metabolomic profiling further nominated candidate molecular correlates of downstream convergence. PRISMA reframes complex-disease GWAS from aggregate locus discovery toward quantitative, LD-aware mapping of tissue-resolved genetic trajectories.

genomics↗

bioRxiv2026

Identification of scavenger receptor BI as a scavenger of free heme that is essential for protection against hemolysis

Severe hemolysis is a life-threatening condition with limited therapeutic options. Although haptoglobin and hemopexin sequester hemoglobin and heme, these protective systems are rapidly saturated during acute hemolysis, leading to the accumulation of cytotoxic free heme. In this study, we identify scavenger receptor BI (SR-BI) as a critical mediator of free heme clearance. SR-BI binds heme and facilitates its hepatic uptake under pathological conditions. Mice lacking hepatic SR-BI exhibit impaired heme clearance and increased susceptibility to heme- and hemolysis-induced lethality. Pharmacological upregulation of hepatic SR-BI via imatinib or adenoviral delivery confers protection against heme toxicity. Using a humanized model of sickle cell disease (SCD), we further demonstrate that sickle hepatopathy significantly reduces hepatic SR-BI expression compared to non-SCD littermates, potentially increasing vulnerability to heme-induced injury. Notably, adenoviral-mediated SR-BI upregulation rescues SCD mice from heme toxicity. These findings reveal a previously unrecognized mechanism of heme detoxification via hepatic SR-BI and identify a promising therapeutic target for hemolytic disorders. One-Sentence SummaryIdentification of scavenger receptor BI as a targetable scavenger of heme in hemolysis

physiology↗

bioRxiv2024

In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth

Cutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer deaths globally, making it the second-highest subtype of skin cancer. The prevalence of cSCC in humans, as well as the poor capacity for an efficient prognosis, highlights the need to uncover alternative actors and mechanisms at the foundation of skin cancer development. Significant advances have been made to better understand some key factors in cSCC progression. However, little is known about the role of noncoding RNAs, particularly of a specific category called long noncoding RNA (lncRNA). By performing pseudobulk analysis of single-cell sequencing data from normal and cSCC human skin tissues, we determined a global portfolio of lncRNAs specifically expressed in keratinocyte subpopulations. Integration of CRISPR interference screens in vitro and the xenograft model identified several lncRNAs impacting the growth of cSCC cancer lines both in vitro and in vivo. Among these, we further validated LINC00704 and LINC01116 as proliferation-regulating lncRNAs in cSCC lines and potential biomarkers of cSCC progression. Taken together, our study provides a comprehensive signature of lncRNAs with roles in regulating cSCC progression.

cancer biology↗

bioRxiv2023

Antisense Oligonucleotide Targeting Hepatic Serum Amyloid A Limits the Progression of Angiotensin II-Induced Abdominal Aortic Aneurysm Formation

Background and aimObesity increases the risk for abdominal aortic aneurysms (AAA) in humans and enhances angiotensin II (AngII)-induced AAA formation in C57BL/6 mice. We reported that deficiency of SAA significantly reduces AngII-induced inflammation and AAA in both hyperlipidemic apoE-deficient and obese C57BL/6 mice. The aim of this study is to investigate whether SAA plays a role in the progression of early AAA in obese C57BL/6 mice. MethodsMale C57BL/6J mice were fed a high-fat diet (60% kcal as fat) throughout the study. After 4 months of diet, the mice were infused with AngII until the end of the study. Mice with at least a 25% increase in the luminal diameter of the abdominal aorta after 4 weeks of AngII infusion were stratified into 2 groups. The first group received a control antisense oligonucleotide (Ctr ASO), and the second group received ASO that suppresses SAA (SAA-ASO) until the end of the study. ResultsPlasma SAA levels were significantly reduced by the SAA ASO treatment. While mice that received the control ASO had continued aortic dilation throughout the AngII infusion periods, the mice that received SAA-ASO had a significant reduction in the progression of aortic dilation, which was associated with significant reductions in matrix metalloprotease activities, decreased macrophage infiltration and decreased elastin breaks in the abdominal aortas. ConclusionsWe demonstrate for the first time that suppression of SAA protects obese C57BL/6 mice from the progression of AngII-induced AAA. Suppression of SAA may be a therapeutic approach to limit AAA progression.

pathology↗