Biomedical subjects

Hai Chen

Publications and source records attributed to Hai Chen.

3 recordsLinked to original sources

PubMed2026

Genetic Contributors to Postoperative Delirium and Their Implications for Dementia Outcomes.

BACKGROUND: Postoperative delirium (POD) is a perioperative neurocognitive disorder that substantially impairs patient recovery. Unfortunately, its genetic risk profile and relationship with subsequent dementia remain unclear. This study aimed to elucidate genetic contributors to POD identified via Hospital Episode Statistics codes and to examine its association with subsequent dementia. METHODS: The study included 230,179 noncardiac and 21,254 cardiac surgery subjects from the UK Biobank, defining POD using delirium codes from the International Classification of Diseases (10th revision) recorded within the first 7 postoperative days. Genome-wide association studies were performed in the noncardiac and cardiac cohorts and their prespecified subgroups, followed by functional annotation, gene prioritization and drug-target analyses. Associations between POD and subsequent dementia were estimated using Cox models. RESULTS: In the noncardiac cohort, one genome-wide significant locus was identified at the APOE region, with rs429358 as the lead variant ( P = 5.00 × 10 -28 ). Integrative gene prioritization analyses highlighted multiple genes within this locus. Exploratory drug-target analyses suggested potential subgroup-specific drug-target enrichment. In the cardiac cohort, no genome-wide significant signals were detected. POD was associated with all-cause dementia after both noncardiac (hazard ratio, 6.45; 95% CI, 5.45 to 7.63) and cardiac (hazard ratio, 2.95; 95% CI, 1.71 to 5.08) surgeries. CONCLUSIONS: This study demonstrates APOE as a genetic risk locus for International Classification of Diseases-coded POD in the noncardiac surgery setting and confirms an association between POD and subsequent dementia.

Humans↗

PubMed2026

Competing subclones and fitness diversity shape tumor evolution across cancer types.

MOTIVATION: Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited. RESULTS: We present estimating evolutionary events through single-timepoint sequencing (TEATIME), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric-fitness diversity-which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types. AVAILABILITY AND IMPLEMENTATION: R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).

Neoplasms↗

PubMed2024

Genome-wide screening and functional validation of methylation barriers near promoters.

CpG islands near promoters are normally unmethylated despite being surrounded by densely methylated regions. Aberrant hypermethylation of these CpG islands has been associated with the development of various human diseases. Although local genetic elements have been speculated to play a role in protecting promoters from methylation, only a limited number of methylation barriers have been identified. In this study, we conducted an integrated computational and experimental investigation of colorectal cancer methylomes. Our study revealed 610 genes with disrupted methylation barriers. Genomic sequences of these barriers shared a common 41-bp sequence motif (MB-41) that displayed homology to the chicken HS4 methylation barrier. Using the CDKN2A (P16) tumor suppressor gene promoter, we validated the protective function of MB-41 and showed that loss of such protection led to aberrant hypermethylation. Our findings highlight a novel sequence signature of cis-acting methylation barriers in the human genome that safeguard promoters from silencing.

Animals↗