Article
Cardiac & Cardiovascular Systems
Zirui Liu, Haocheng Wang, Zhengkai Yang, Yu Lu, Cao Zou
Summary: This MR study provides evidence for the causal effect of type 1 diabetes on peripheral atherosclerosis and coronary atherosclerosis, with hypertension mediating this effect partially. No significant causal relationships were found between other cardiovascular diseases and type 1 diabetes.
CARDIOVASCULAR DIABETOLOGY
(2023)
Article
Genetics & Heredity
Tongtong Hong, Na Qin, Xiaoyu Zhao, Cheng Wang, Yue Jiang, Hongxia Ma, Juncheng Dai
Summary: This study found no evidence to support a causal relationship between T2DM and lung cancer risk, with consistent results across different populations. Further large-scale prospective studies are needed to confirm these findings.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Linjing Zhang, Lu Tang, Tao Huang, Dongsheng Fan
Summary: The study found that there is a consistent association between type 2 diabetes and amyotrophic lateral sclerosis (ALS). The genetically predicted type 2 diabetes was associated with a significantly lower risk of ALS.
SCIENTIFIC REPORTS
(2022)
Article
Virology
Hongbao Cao, Ancha Baranova, Xuejuan Wei, Chun Wang, Fuquan Zhang
Summary: Observational studies have found a high comorbidity between T2D and COVID-19, and genetic correlation and MR analysis have shown a causal effect of T2D on hospitalized and critical COVID-19, as well as a causal effect of SARS-CoV-2 infection on T2D. Pathway analysis has also revealed potential mechanisms underlying the connection between T2D and COVID-19.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Immunology
Shan Lin, Xueyan Mao, Wanmei He
Summary: This genetic data analysis study using Mendelian Randomization (MR) framework explores the causal relationship between cytokines and sepsis. The study found that genetically predicted levels of RANTES, basic-FGF, and beta-NGF are associated with altered sepsis risk.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Maria C. Magnus, Maria Carolina Borges, Abigail Fraser, Deborah A. Lawlor
Summary: The age at natural menopause is associated with various health-related traits. This study conducted a Mendelian randomization phenome-wide association study to investigate these associations. The findings suggest that younger age at natural menopause may have potential causal effects on a range of health-related traits.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2022)
Article
Endocrinology & Metabolism
Jiahao Zhu, Huanling Zhao, Dingwan Chen, Lap Ah Tse, Sanjay Kinra, Yingjun Li
Summary: This study found significant genetic correlations between T2D, glycemic traits, and pulmonary function, with Mendelian randomization analyses suggesting a bidirectional causal association between T2D and pulmonary function.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Endocrinology & Metabolism
Mingkai Huang, Loum-Davadi Laina-Nicaise, Lingfeng Zha, Tingting Tang, Xiang Cheng
Summary: This study found causal effects of type 2 diabetes and glycemic traits on the risk of cardiovascular diseases and dyslipidemia using Mendelian randomization. Further investigations are needed to understand the underlying mechanisms.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Endocrinology & Metabolism
Li-Zhen Liao, Zhi-Chong Chen, Wei-Dong Li, Xiao-Dong Zhuang, Xin-Xue Liao
Summary: The study found that lower education levels were associated with an increased risk of type 2 diabetes, and body mass index may serve as a potential mediator between them.
WORLD JOURNAL OF DIABETES
(2021)
Article
Medicine, General & Internal
Xueying Zhu, Dan Cheng, Kaiming Ruan, Meixiao Shen, Yufeng Ye
Summary: This study used Mendelian randomization design to assess the potential causal relationships between type 2 diabetes, glycemic traits, and the risk of keratoconus. The findings suggest that higher fasting glucose levels are associated with a lower risk of keratoconus, while lower proinsulin levels may be linked to a higher risk. Additionally, genetically predicted type 2 diabetes is negatively correlated with keratoconus risk. These associations were supported by sensitivity analyses.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Chunyang Li, Yilong Chen, Yi Chen, Zhiye Ying, Yao Hu, Yalan Kuang, Huazhen Yang, Huan Song, Xiaoxi Zeng
Summary: This study aimed to identify novel associations between irritable bowel syndrome (IBS) and a broad range of outcomes. Using a genome-wide association study (GWAS) and polygenic risk score (PRS) analysis, the study found five diseases associated with genetically predicted IBS. Causal associations were observed in females only, not males.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Endocrinology & Metabolism
Masahiro Yoshikawa, Kensuke Asaba, Tomohiro Nakayama
Summary: Using a two-sample MR approach, the study found that T2DM has a significant causal effect on the risk of COVID-19 outcomes in the East Asian population, independent of the effect of BMI.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Genetics & Heredity
Yong-Bo Wang, Si-Yu Yan, Xu-Hui Li, Qiao Huang, Li-Sha Luo, Yun-Yun Wang, Jiao Huang, Ying-Hui Jin, Xian-Tao Zeng
Summary: This study using Mendelian randomization does not support a bidirectional causal association between periodontitis and type 2 diabetes.
FRONTIERS IN GENETICS
(2022)
Article
Endocrinology & Metabolism
Aiyong Cui, Peilun Xiao, Zhiqiang Fan, Jinlai Lei, Shuang Han, Danlong Zhang, Xing Wei, Pengfei Wang, Yan Zhuang
Summary: This study investigated the causal association between NAFLD and osteoporosis using a bidirectional two-sample Mendelian analysis. The results showed a causal relationship between NAFLD and osteoporosis, but no causal effect of osteoporosis on NAFLD. Furthermore, NAFLD did not have a causal effect on fracture and fall risk.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Public, Environmental & Occupational Health
Haoyang Zhang, Xuehao Xiu, Angli Xue, Yuedong Yang, Yuanhao Yang, Huiying Zhao
Summary: The study revealed a strong genetic correlation and potential causal effect of type 2 diabetes on cataract in East Asian population, while providing weak evidence on the genetic correlation and causal relationship between the two diseases in European population.
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
(2021)
Article
Biochemical Research Methods
Tianyi Zhao, Yang Hu, Liang Cheng
Summary: This study introduces a graph deep learning method, Deep-DRM, for identifying diseases-related metabolites. By calculating the similarities between metabolites and diseases, building networks, and applying a deep neural network, Deep-DRM shows outstanding performance in identifying true metabolite-disease pairs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Xudong Han, Qingfei Kong, Chonghui Liu, Liang Cheng, Junwei Han
Summary: SubtypeDrug is a software package based on systems biology that prioritizes subtype-specific drugs based on cancer expression data from samples of multiple subtypes. It uses a novel approach to identify subtype-specific drugs by considering the biological functions regulated by drugs at the subpathway level. Its capabilities include extraction of subpathways from biological pathways, identification of dysregulated subpathways induced by each drug, inference of sample-specific subpathway activity profiles, evaluation of drug-disease reverse association at the subpathway level, identification of cancer-subtype-specific drugs through subtype sample set enrichment analysis, and visualization of the results.
Article
Biochemical Research Methods
Yuqi Sheng, Ying Jiang, Yang Yang, Xiangmei Li, Jiayue Qiu, Jiashuo Wu, Liang Cheng, Junwei Han
Summary: Biological pathways are crucial in dictating disease states and drug responses, dysfunctional subpathways (SPs) have been associated with cancer, high-throughput sequencing allows for identification of dysfunctional SPs, a novel network-based method, CNA2Subpathway, integrates pathway topology information, multi-omics data, and SP crosstalk to identify cancer-relevant SPs driven by somatic CNAs. Validated in breast cancer and head and neck cancer datasets, CNA2Subpathway shows effectiveness in uncovering dysfunctional SPs associated with cancer immune response and patient prognosis.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Zijun Zhu, Xudong Han, Liang Cheng
Summary: This study integrates genetic mutation information and expression data to obtain a predictive signature for T2DM, which shows excellent performance and robustness.
CURRENT GENE THERAPY
(2022)
Review
Biochemistry & Molecular Biology
Haixiu Yang, Changlu Qi, Boyan Li, Liang Cheng
Summary: Recent studies have revealed the significant role of non-coding RNAs in regulating drug resistance in tumor cells. Understanding the relationship between ncRNAs and drug resistance can provide valuable insights into the mechanisms and biomarkers of chemoresistance, as well as facilitate personalized anticancer treatment regimens.
CURRENT MEDICINAL CHEMISTRY
(2022)
Letter
Infectious Diseases
Shizheng Qiu, Yang Hu, Liang Cheng
JOURNAL OF INFECTION
(2022)
Article
Biochemistry & Molecular Biology
Liang Cheng, Changlu Qi, Haixiu Yang, Minke Lu, Yiting Cai, Tongze Fu, Jialiang Ren, Qu Jin, Xue Zhang
Summary: gutMGene, a manually curated database, provides a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice. The database documents curated relationships between gut microbes, microbial metabolites and genes in both species. The user-friendly interface allows browsing and retrieval of entries, and also offers the option to download all entries and submit new validated associations.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Zijun Zhu, Sainan Zhang, Ping Wang, Xinyu Chen, Jianxing Bi, Liang Cheng, Xue Zhang
Summary: This article reviews the advantages and limitations of integrating omics data for SARS-CoV-2 and COVID-19, and summarizes the existing data analysis methods and research results. It also proposes research directions for the integration of SARS-CoV-2 (COVID-19) multi-omics data and presents a case study for deeper exploration of the disease mechanisms of COVID-19.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Changlu Qi, Chao Wang, Lingling Zhao, Zijun Zhu, Ping Wang, Sainan Zhang, Liang Cheng, Xue Zhang
Summary: SCovid is a comprehensive resource of single-cell data to explore the molecular characteristics of COVID-19 in different human tissues. It collects 21 single-cell datasets and reveals the molecular features of COVID-19 through manual annotation.
NUCLEIC ACIDS RESEARCH
(2022)
Editorial Material
Cell Biology
Liang Cheng, Lei Deng, Chuan-Xing Li, Yan Zhang
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Letter
Multidisciplinary Sciences
Zijun Zhu, Xinyu Chen, Chao Wang, Liang Cheng
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Junjie Wang, Jie Hu, Huiting Sun, MengDie Xu, Yun Yu, Yun Liu, Liang Cheng
Summary: In this study, we propose a multigranularity protein-ligand interaction model, which utilizes the Transformer model and convolutional neural network to accurately predict the binding affinity between drugs and protein targets.
Article
Biochemistry & Molecular Biology
Changlu Qi, Yiting Cai, Kai Qian, Xuefeng Li, Jialiang Ren, Ping Wang, Tongze Fu, Tianyi Zhao, Liang Cheng, Lei Shi, Xue Zhang
Summary: The gut microbiota plays a crucial role in maintaining health, and disruptions can lead to disorders. The gutMDisorder database provides a valuable resource for studying dysbiosis, and the latest version offers expanded data and improved features.
NUCLEIC ACIDS RESEARCH
(2023)
Letter
Gastroenterology & Hepatology
Zijun Zhu, Xinyu Chen, Chao Wang, Sainan Zhang, Liang Cheng
Article
Virology
Zijun Zhu, Xinyu Chen, Chao Wang, Sainan Zhang, Rui Yu, Yubin Xie, Shuofeng Yuan, Liang Cheng, Lei Shi, Xue Zhang
Summary: This study conducted a genome-wide association study (GWAS) to identify host genetic factors associated with COVID-19. The correlation between genetic variations and gene expression was assessed using expression quantitative trait locus (eQTL) analysis. The findings revealed 20 genes significantly associated with immunity and neurological disorders. Single-cell datasets were used to validate these findings and to explore the causal relationship between COVID-19 and neurological disorders. Cell experiments were conducted to investigate the effects of COVID-19-related protein-coding genes. This study provides important insights into the genetic architecture underlying the pathophysiology of COVID-19.
JOURNAL OF MEDICAL VIROLOGY
(2023)