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学者姓名：杨铁林
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| GB/T 7714 | Du, Mingfei , Wang, Yang , Gao, Wei -Hua et al. ASSOCIATION OF SERUM UROMODULIN AND GENETIC VARIANTS WITH BLOOD PRESSURE CHANGES, AND HYPERTENSION IN CHINESE ADULTS: RESULTS FROM TWO PROSPECTIVE COHORTS [J]. | JOURNAL OF HYPERTENSION , 2021 , 39 : E112-E112 . |
| MLA | Du, Mingfei et al. "ASSOCIATION OF SERUM UROMODULIN AND GENETIC VARIANTS WITH BLOOD PRESSURE CHANGES, AND HYPERTENSION IN CHINESE ADULTS: RESULTS FROM TWO PROSPECTIVE COHORTS" . | JOURNAL OF HYPERTENSION 39 (2021) : E112-E112 . |
| APA | Du, Mingfei , Wang, Yang , Gao, Wei -Hua , Sun, Yue , Zhang, Xiao -Yu , Zou, Ting et al. ASSOCIATION OF SERUM UROMODULIN AND GENETIC VARIANTS WITH BLOOD PRESSURE CHANGES, AND HYPERTENSION IN CHINESE ADULTS: RESULTS FROM TWO PROSPECTIVE COHORTS . | JOURNAL OF HYPERTENSION , 2021 , 39 , E112-E112 . |
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Genome-wide association studies (GWAS) have reproducibly associated the single nucleotide polymorphism (SNP) rs12454712 with waist-to-hip ratio adjusted for BMI (WHRadjBMI), but the functional role underlying this intronic variant is unknown. Integrative genomic and epigenomic analyses supported rs12454712 as a functional independent variant. We further demonstrated that rs12454712 acted as an allele-specific enhancer regulating expression of its located gene BCL2 by using dual-luciferase reporter assays and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Specifically, the rs12454712-C allele can bind transcription factor ZNF329, which efficiently elevates the enhancer activity and increases BCL2 expression. Knocking down Bcl2 in 3T3-L1 cells led to the downregulation of adipogenic differentiation marker genes and increased cell apoptosis. A significant negative correlation between BCL2 expression in subcutaneous adipose tissues and obesity was observed. Our findings illustrate the molecular mechanisms behind the intronic SNP rs12454712 for central obesity, which would be a potential and promising target for developing appropriate therapies.
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| GB/T 7714 | Dong, Shan-Shan , Zhu, Dong-Li , Zhou, Xiao-Rong et al. An Intronic Risk SNP rs12454712 for Central Obesity Acts As an Allele-Specific Enhancer To Regulate BCL2 Expression [J]. | DIABETES , 2021 , 70 (8) : 1679-1688 . |
| MLA | Dong, Shan-Shan et al. "An Intronic Risk SNP rs12454712 for Central Obesity Acts As an Allele-Specific Enhancer To Regulate BCL2 Expression" . | DIABETES 70 . 8 (2021) : 1679-1688 . |
| APA | Dong, Shan-Shan , Zhu, Dong-Li , Zhou, Xiao-Rong , Rong, Yu , Zeng, Mengqi , Chen, Jia-Bin et al. An Intronic Risk SNP rs12454712 for Central Obesity Acts As an Allele-Specific Enhancer To Regulate BCL2 Expression . | DIABETES , 2021 , 70 (8) , 1679-1688 . |
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The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and memory consuming. Here, we developed LDBlockShow, an open source software, for visualizing LD and haplotype blocks from variant call format files. It is time and memory saving. In a test dataset with 100 SNPs from 60 000 subjects, it was at least 10.60 times faster and used only 0.03-13.33% of physical memory as compared with other tools. In addition, it could generate figures that simultaneously display additional statistical context (e.g. association P-values) and genomic region annotations. It can also compress the SVG files with a large number of SNPs and support subgroup analysis. This fast and convenient tool will facilitate the visualization of LD and haplotype blocks for geneticists.
Keyword ：
haplotype block linkage disequilibrium VCF files visualization
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| GB/T 7714 | Dong Shan-Shan , He Wei-Ming , Ji Jing-Jing et al. LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. [J]. | Briefings in bioinformatics , 2021 , 22 (4) . |
| MLA | Dong Shan-Shan et al. "LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files." . | Briefings in bioinformatics 22 . 4 (2021) . |
| APA | Dong Shan-Shan , He Wei-Ming , Ji Jing-Jing , Zhang Chi , Guo Yan , Yang Tie-Lin . LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. . | Briefings in bioinformatics , 2021 , 22 (4) . |
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Although more than 80 psoriasis genetic risk loci have been reported through genome-wide association studies (GWASs), the genetic mechanism of psoriasis remains unclear. To identify novel candidate genes associated with psoriasis and reveal the potential effects of genetic factors in the development of psoriasis, we conducted a transcriptome-wide association study (TWAS) based on summary statistics from GWAS of psoriasis (5175 cases and 447 089 controls) and gene expression levels from six tissues datasets (blood and skin). We identified 11 conditionally independent genes for psoriasis after Bonferroni corrections, such as the most significant genes UBLCP1 (PYFS = 2.98 × 10-16), and LCE3C (PSNSE = 9.72 × 10-12, PSSE = 6.24 × 10-12). The omnibus test identified additional 5 genes associated with psoriasis via the joint association model from multiple reference tissues. Among the 16 identified genes, 5 genes (CTSW, E1F1AD, KLRC3, FIBP, and EFEMP2) were regarded as novel genes for psoriasis. We evaluated the 16 candidate genes by querying public databases and identified 11 differentially expressed genes and 8 genes proved by the knockout mice models. Through GO enrichment analyses, we found that TWAS genes were enriched in the known GO terms associated with skin development, such as cornified envelope (P = 4.80 × 10-8) and peptide cross-linking (P = 1.50 × 10-7). Taken together, our results detected multiple novel candidate genes for psoriasis, providing clues for understanding the genetic mechanism of psoriasis.
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| GB/T 7714 | Zhu Dongli , Yao Shi , Wu Hao et al. A transcriptome-wide association study identifies novel susceptibility genes for psoriasis. [J]. | Human molecular genetics , 2021 , 31 (2) : 300-308 . |
| MLA | Zhu Dongli et al. "A transcriptome-wide association study identifies novel susceptibility genes for psoriasis." . | Human molecular genetics 31 . 2 (2021) : 300-308 . |
| APA | Zhu Dongli , Yao Shi , Wu Hao , Ke Xin , Zhou Xiaorong , Geng Songmei et al. A transcriptome-wide association study identifies novel susceptibility genes for psoriasis. . | Human molecular genetics , 2021 , 31 (2) , 300-308 . |
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Objective: Pregnancy-associated plasma protein-A2 (PAPP-A2) is the homolog of PAPP-A in the vertebrate genome and its role in protecting against salt-induced hypertension in salt-sensitive rats has been confirmed. We sought to examine the associations of plasma PAPP-A2 levels and its genetic variants with salt sensitivity, blood pressure (BP) changes and hypertension incidence in humans. Methods: Eighty participants (18-65 years old) sequentially consuming a usual diet, a 7-day low-salt diet (3.0 g/day) and a 7-day high-salt diet (18 g/day). In addition, we studied participants of the original Baoji Salt-Sensitive Study, recruited from 124 families in Northern China in 2004 who received the same salt intake intervention, and evaluated them for the development of hypertension over 14 years. Results: The plasma PAPPA2 levels significantly decreased with the change from baseline to a low-salt diet and decreased further when converting from the low-salt to high-salt diet. SNP rs12042763 in the PAPP-A2 gene was significantly associated with systolic BP responses to both low-salt and high-salt diet while SNP rs2861813 showed a significant association with the changes in SBP and pulse pressure at 14-year follow-up. Additionally, SNPs rs2294654 and rs718067 demonstrated a significant association with the incidence of hypertension over the 14-year follow-up. Finally, the gene-based analysis found that Pappa2 was significantly associated with longitudinal SBP changes and the incidence of hypertension over the 14-year follow-up. Conclusions: This study shows that dietary salt intake affects plasma PAPP-A2 levels and that PAPP-A2 may play a role in salt sensitivity, BP progression and development of hypertension in the Chinese populations.
Keyword ：
blood pressure gene polymorphism pregnancy-associated plasma protein-A2 salt salt sensitivity
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| GB/T 7714 | Wang, Yang , Jia, Hao , Gao, Wei-Hua et al. Associations of plasma PAPP-A2 and genetic variations with salt sensitivity, blood pressure changes and hypertension incidence in Chinese adults [J]. | JOURNAL OF HYPERTENSION , 2021 , 39 (9) : 1817-1825 . |
| MLA | Wang, Yang et al. "Associations of plasma PAPP-A2 and genetic variations with salt sensitivity, blood pressure changes and hypertension incidence in Chinese adults" . | JOURNAL OF HYPERTENSION 39 . 9 (2021) : 1817-1825 . |
| APA | Wang, Yang , Jia, Hao , Gao, Wei-Hua , Zou, Ting , Yao, Shi , Du, Ming-Fei et al. Associations of plasma PAPP-A2 and genetic variations with salt sensitivity, blood pressure changes and hypertension incidence in Chinese adults . | JOURNAL OF HYPERTENSION , 2021 , 39 (9) , 1817-1825 . |
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Detecting SNPs associated with drug efficacy or toxicity is helpful to facilitate personalized medicine. Previous studies usually find SNPs associated with clinical outcome only in patients received a specific treatment. However, without information from patients without drug treatment, it is possible that the detected SNPs are associated with patients' clinical outcome even without drug treatment. Here we aimed to detect drug response SNPs based on data from patients with and without drug treatment through combing the cox proportional-hazards model and pairwise Kaplan-Meier survival analysis. A pipeline named Detection of Drug Response SNPs (DDRS) was built and applied to TCGA breast cancer data including 363 patients with doxorubicin treatment and 321 patients without any drug treatment. We identified 548 doxorubicin associated SNPs. Drug response score derived from these SNPs were associated with drug-resistant level (indicated by IC50) of breast cancer cell lines. Enrichment analyses showed that these SNPs were enriched in active epigenetic regulation markers (e.g., H3K27ac). Compared with random genes, the cis-eQTL genes of these SNPs had a shorter protein-protein interaction distance to doxorubicin associated genes. In addition, linear discriminant analysis showed that the eQTL gene expression levels could be used to predict clinical outcome for patients with doxorubicin treatment (AUC = 0.738). Specifically, we identified rs2817101 as a drug response SNP for doxorubicin treatment. Higher expression level of its cis-eQTL gene GSTA1 is associated with poorer survival. This approach can also be applied to identify new drug associated SNPs in other cancers. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
Keyword ：
Breast cancer Drug response Prognosis SNP
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| GB/T 7714 | Rong, Yu , Dong, Shan-Shan , Hu, Wei-Xin et al. DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment [J]. | COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL , 2021 , 19 : 3650-3657 . |
| MLA | Rong, Yu et al. "DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment" . | COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 19 (2021) : 3650-3657 . |
| APA | Rong, Yu , Dong, Shan-Shan , Hu, Wei-Xin , Guo, Yan , Chen, Yi-Xiao , Chen, Jia-Bin et al. DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment . | COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL , 2021 , 19 , 3650-3657 . |
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BackgroundChildhood obesity is reported to be associated with the risk of many diseases in adulthood. However, observational studies cannot fully account for confounding factors. We aimed to systematically assess the causal associations between childhood body mass index (BMI) and various adult traits/diseases using two-sample Mendelian randomization (MR).MethodsAfter data filtering, 263 adult traits genetically correlated with childhood BMI (P<0.05) were subjected to MR analyses. Inverse-variance weighted, MR-Egger, weighted median, and weighted mode methods were used to estimate the causal effects. Multivariable MR analysis was performed to test whether the effects of childhood BMI on adult traits are independent from adult BMI.ResultsWe identified potential causal effects of childhood obesity on 60 adult traits (27 disease-related traits, 27 lifestyle factors, and 6 other traits). Higher childhood BMI was associated with a reduced overall health rating (=-0.10, 95% CI -0.13 to -0.07, P=6.26x10(-11)). Specifically, higher childhood BMI was associated with increased odds of coronary artery disease (OR=1.09, 95% CI 1.06 to 1.11, P=4.28x10(-11)), essential hypertension (OR=1.12, 95% CI 1.08 to 1.16, P=1.27x10(-11)), type 2 diabetes (OR=1.36, 95% CI 1.30 to 1.43, P=1.57x10(-34)), and arthrosis (OR=1.09, 95% CI 1.06 to 1.12, P=8.80x10(-9)). However, after accounting for adult BMI, the detrimental effects of childhood BMI on disease-related traits were no longer present (P>0.05). For dietary habits, different from conventional understanding, we found that higher childhood BMI was associated with low calorie density food intake. However, this association might be specific to the UK Biobank population.ConclusionsIn summary, we provided a phenome-wide view of the effects of childhood BMI on adult traits. Multivariable MR analysis suggested that the associations between childhood BMI and increased risks of diseases in adulthood are likely attributed to individuals remaining obese in later life. Therefore, ensuring that childhood obesity does not persist into later life might be useful for reducing the detrimental effects of childhood obesity on adult diseases.
Keyword ：
Adult outcome Causal Childhood BMI Mendelian randomization
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| GB/T 7714 | Dong, Shan-Shan , Zhang, Kun , Guo, Yan et al. Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study [J]. | GENOME MEDICINE , 2021 , 13 (1) . |
| MLA | Dong, Shan-Shan et al. "Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study" . | GENOME MEDICINE 13 . 1 (2021) . |
| APA | Dong, Shan-Shan , Zhang, Kun , Guo, Yan , Ding, Jing-Miao , Rong, Yu , Feng, Jun-Cheng et al. Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study . | GENOME MEDICINE , 2021 , 13 (1) . |
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Background: Uromodulin, also named Tamm Horsfall protein, has been associated with renal function and regulation of sodium homeostasis. We aimed to examine the associations of serum uromodulin levels and its genetic variants with longitudinal blood pressure (BP) changes and hypertension incidence/risk.Methods: A total of 514 participants from the original Baoji Salt-Sensitive Study cohort were genotyped to examine the associations of genetic variations in uromodulin gene with the longitudinal BP changes and the incidence of hypertension over 8 years of follow-up. In addition, 2,210 subjects from the cohort of Hanzhong Adolescent Hypertension Study were used to investigate the relationships between serum uromodulin levels and the risk of hypertension.Results: SNPs rs12917707 and rs12708631 in the uromodulin gene were significantly associated with the longitudinal BP changes over 8 years of follow-up. SNP rs12708631 was significantly associated with the incidence of hypertension over 8 years. In addition, gene-based analyses supported the associations of uromodulin gene with the longitudinal BP changes and hypertension incidence in Baoji Salt-Sensitive Study cohort. Furthermore, serum uromodulin levels in the hypertensive subjects were lower than in the normotensive subjects (25.5 +/- 1.1 vs. 34.7 +/- 0.7 ng/mL). Serum uromodulin levels decreased gradually as BP levels increased (34.6, 33.2, 27.8, and 25.0 ng/mL for subjects with normotension, high-normal, grade 1 hypertension, and grade 2 hypertension, respectively). Serum uromodulin was significantly associated with the lower risk of hypertension [0.978 (0.972-0.984)] in Hanzhong Adolescent Hypertension Study cohort.Conclusion: This study shows that uromodulin is associated with blood pressure progression and development of hypertension.
Keyword ：
blood pressure gene polymorphism hypertension longitudinal change uromodulin (UMOD)
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| GB/T 7714 | Wang, Yang , Du, Ming-Fei , Yao, Shi et al. Associations of Serum Uromodulin and Its Genetic Variants With Blood Pressure and Hypertension in Chinese Adults [J]. | FRONTIERS IN CARDIOVASCULAR MEDICINE , 2021 , 8 . |
| MLA | Wang, Yang et al. "Associations of Serum Uromodulin and Its Genetic Variants With Blood Pressure and Hypertension in Chinese Adults" . | FRONTIERS IN CARDIOVASCULAR MEDICINE 8 (2021) . |
| APA | Wang, Yang , Du, Ming-Fei , Yao, Shi , Zou, Ting , Zhang, Xiao-Yu , Hu, Gui-Lin et al. Associations of Serum Uromodulin and Its Genetic Variants With Blood Pressure and Hypertension in Chinese Adults . | FRONTIERS IN CARDIOVASCULAR MEDICINE , 2021 , 8 . |
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The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people(1,2). Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.
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| GB/T 7714 | Wang, Chuan-Chao , Yeh, Hui-Yuan , Popov, Alexander N. et al. Genomic insights into the formation of human populations in East Asia [J]. | NATURE , 2021 , 591 (7850) : 413-+ . |
| MLA | Wang, Chuan-Chao et al. "Genomic insights into the formation of human populations in East Asia" . | NATURE 591 . 7850 (2021) : 413-+ . |
| APA | Wang, Chuan-Chao , Yeh, Hui-Yuan , Popov, Alexander N. , Zhang, Hu-Qin , Matsumura, Hirofumi , Sirak, Kendra et al. Genomic insights into the formation of human populations in East Asia . | NATURE , 2021 , 591 (7850) , 413-+ . |
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Aberrant telomerase reverse transcriptase (TERT) expression is crucial for tumor survival and cancer cells escaping apoptosis. Multiple TERT-locus variants at 5p15 have been discovered in association with cancer risk, yet the underlying mechanisms and clinical impacts remain unclear. Here, our association studies showed that the TERT promoter variant rs2853669 confers a risk of prostate cancer (PCa) in different ethnic groups. Further functional investigation revealed that the allele-specific binding of MYC and E2F1 at TERT promoter variant rs2853669 associates with elevated level of TERT in PCa. Mechanistically, androgen stimulations promoted the binding of MYC to allele T of rs2853669, thereby activating TERT, whereas hormone deprivations enhanced E2F1 binding at allele C of rs2853669, thus upregulating TERT expression. Notably, E2F1 could cooperate with AR signaling to regulate MYC expression. Clinical data demonstrated synergistic effects of MYC/E2F1/TERT expression or with the TT and CC genotype of rs2853669 on PCa prognosis and severity. Strikingly, single-nucleotide editing assays showed that the CC genotype of rs2853669 obviously promotes epithelial-mesenchymal transition (EMT) and the development of castration-resistant PCa (CRPC), confirmed by unbiased global transcriptome profiling. Our findings thus provided compelling evidence for understanding the roles of noncoding variations coordinated with androgen signaling and oncogenic transcription factors in mis-regulating TERT expression and driving PCa.
Keyword ：
AR signaling crpc E2F1 EMT MYC prostate cancer rs2853669 TERT
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| GB/T 7714 | Dong Xiaoming , Zhang Qin , Hao Jinglan et al. Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC. [J]. | Frontiers in oncology , 2021 , 11 : 754206 . |
| MLA | Dong Xiaoming et al. "Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC." . | Frontiers in oncology 11 (2021) : 754206 . |
| APA | Dong Xiaoming , Zhang Qin , Hao Jinglan , Xie Qianwen , Xu Binbing , Zhang Peng et al. Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC. . | Frontiers in oncology , 2021 , 11 , 754206 . |
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