黄琦雅
中国医学科学院阜外医院 心内科
BACKGROUND:DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation.RESULTS:Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation.CONCLUSIONS:Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.
Genome biology 2023
Background:Stroke ranks second worldwide and first in China as a leading cause of death and disability. It has a polygenic architecture and is influenced by environmental and lifestyle factors. However, it remains unknown as to whether and how much the genetic predisposition of stroke is associated with disease burden.Methods:Allele frequency from the whole genome sequencing data in the Chinese Millionome Database of 141,418 individuals and trait-specific polygenic risk score models were applied to estimate the provincial genetic predisposition to stroke, stroke-related risk factors and stroke-related drug response. Disease burden including mortality, disability-adjusted life years (DALYs), years of life lost(YLLs), years lived with disability (YLDs) and prevalence in China was collected from the Global Burden Disease study. The association between stroke genetic predisposition and the epidemiological burden was assessed and then quantified in both regression-based models and machine learning-based models at a provincial resolution.Findings:Among the 30 administrative divisions in China, the genetic predisposition of stroke was characterized by a north-higher-than-south gradient (p < 0.0001). Genetic predisposition to stroke, blood pressure, body mass index, and alcohol use were strongly intercorrelated (rho >0.6; p < 0.05 after Bonferroni correction for each comparison). Genetic risk imposed an independent effect of approximately 1-6% on mortality, DALYs and YLLs.Interpretation:The distribution pattern of stroke genetic predisposition is different at a macroscopic level, and it subtly but significantly impacts the epidemiological burden. Further research is warranted to identify the detailed aetiology and potential translation into public health measures.Funding:Beijing Municipal Science and Technology Commission (Z191100006619106), CAMS Innovation Fund for Medical Sciences (CAMS-I2M, 2023-I2M-1-001), the National High Level Hospital Clinical Research Funding (2022-GSP-GG-17), National Natural Science Foundation of China (32000398, 32171441 to X.J.), Natural Science Foundation of Guangdong Province, China (2017A030306026 to X.J.), and National Key R&D Program of China (2022YFC2502402).
The Lancet regional health. Western Pacific 2023
BACKGROUND:The presence of variants in OBSCN was identified to be linked to hypertrophic cardiomyopathy (HCM), but whether OBSCN truncating variants were associated with HCM remained unknown.METHODS:Whole-exome sequencing was performed in 986 patients with HCM and 761 non-HCM controls to search for OBSCN truncating variants, and the result was tested in a replication cohort consisting of 529 patients with HCM and 307 controls. The association of the OBSCN truncating variants with baseline characteristics and prognosis of patients with HCM were ascertained.RESULTS:There were 28 qualifying truncating variants in the OBSCN gene detected in 26 (2.6%) patients with HCM and 6 (0.8%) controls. The OBSCN truncating variants were more prevalent in patients with HCM than controls (odds ratio, 3.4, P=0.004). This association was confirmed in the replication cohort (odds ratio, 3.8, P=0.024). The combined effects of the two cohorts estimated the odds ratio to be 3.58 (P<0.001). Patients with or without OBSCN truncating variants shared similar demographic and echocardiographic variables at baseline. During 3.3±2.4 years (4795 patient-years) follow-up, the patients with OBSCN truncating variants were more likely to experience cardiovascular death (adjusted hazard ratio, 3.1 [95% CI, 1.40-6.70], P=0.005) and all-cause death (adjusted hazard ratio, 2.63 [95% CI, 1.21-5.71], P=0.015).CONCLUSIONS:Our data indicated that OBSCN truncating variants contributed to the disease-onset of HCM, and increased the risk of malignant events in patients with HCM.
Circulation. Genomic and precision medicine 2021
