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Wang X, Wang J, Xia X, Xu X, Li L, Cao S, Hao Y, Zhang L. Effect of genotyping errors on linkage map construction based on repeated chip analysis of two recombinant inbred line populations in wheat (Triticum aestivum L.). BMC Plant Biol 2024; 24:306. [PMID: 38644480 PMCID: PMC11034145 DOI: 10.1186/s12870-024-05005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/10/2024] [Indexed: 04/23/2024]
Abstract
Linkage maps are essential for genetic mapping of phenotypic traits, gene map-based cloning, and marker-assisted selection in breeding applications. Construction of a high-quality saturated map requires high-quality genotypic data on a large number of molecular markers. Errors in genotyping cannot be completely avoided, no matter what platform is used. When genotyping error reaches a threshold level, it will seriously affect the accuracy of the constructed map and the reliability of consequent genetic studies. In this study, repeated genotyping of two recombinant inbred line (RIL) populations derived from crosses Yangxiaomai × Zhongyou 9507 and Jingshuang 16 × Bainong 64 was used to investigate the effect of genotyping errors on linkage map construction. Inconsistent data points between the two replications were regarded as genotyping errors, which were classified into three types. Genotyping errors were treated as missing values, and therefore the non-erroneous data set was generated. Firstly, linkage maps were constructed using the two replicates as well as the non-erroneous data set. Secondly, error correction methods implemented in software packages QTL IciMapping (EC) and Genotype-Corrector (GC) were applied to the two replicates. Linkage maps were therefore constructed based on the corrected genotypes and then compared with those from the non-erroneous data set. Simulation study was performed by considering different levels of genotyping errors to investigate the impact of errors and the accuracy of error correction methods. Results indicated that map length and marker order differed among the two replicates and the non-erroneous data sets in both RIL populations. For both actual and simulated populations, map length was expanded as the increase in error rate, and the correlation coefficient between linkage and physical maps became lower. Map quality can be improved by repeated genotyping and error correction algorithm. When it is impossible to genotype the whole mapping population repeatedly, 30% would be recommended in repeated genotyping. The EC method had a much lower false positive rate than did the GC method under different error rates. This study systematically expounded the impact of genotyping errors on linkage analysis, providing potential guidelines for improving the accuracy of linkage maps in the presence of genotyping errors.
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Affiliation(s)
- Xinru Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jiankang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaowan Xu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Lingli Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shuanghe Cao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Yuanfeng Hao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Luyan Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Wu QH, Chen Q, Yang T, Chen J, Chen L, Xiang XL, Jia FY, Wu LJ, Hao Y, Li L, Zhang J, Ke XY, Yi MJ, Hong Q, Chen JJ, Fang SF, Wang YC, Wang Q, Li TY. [A survey on the current situation of serum vitamin A and vitamin D levels among children aged 2-<7 years of 20 cities in China]. Zhonghua Er Ke Za Zhi 2024; 62:231-238. [PMID: 38378284 DOI: 10.3760/cma.j.cn112140-20230923-00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Objective: To investigate serum vitamin A and vitamin D status in children aged 2-<7 years in 20 cities in China. Methods: A cross-sectional study was conducted. A total of 2 924 healthy children aged 2-<7 years were recruited from September 2018 to September 2019 from 20 cities in China, categorized by age groups of 2-<3 years, 3-<5 years, and 5-<7 years. The demographic and economic characteristics and health-related information of the enrolled children were investigated. Body weight and height were measured by professional staff members. The serum vitamin A and vitamin D levels were detected by high-performance liquid chromatography-tandem mass spectrometry. Chi-square test and Logistic regression were applied to analyze the association between vitamin A and vitamin D deficiency and insufficiency as well as their underlying impact factors. Results: The age of the 2 924 enrolled children was 4.33 (3.42, 5.17) years. There were 1 726 males (59.03%) and 1 198 females (40.97%). The prevalences of vitamin A and vitamin D deficiency in enrolled children were 2.19% (64/2 924) and 3.52% (103/2 924), respectively, and the insufficiency rates were 29.27% (856/2 924) and 22.20% (649/2 924), respectively. Children with both vitamin A and vitamin D deficiencies or insufficiencies were found in 10.50% (307/2 924) of cases. Both vitamin A (χ2=7.91 and 8.06, both P=0.005) and vitamin D (χ2=71.35 and 115.10, both P<0.001) insufficiency rates were higher in children aged 3-<5 and 5-<7 years than those in children aged 2-<3 years. Vitamin A and vitamin D supplementation in the last 3 months was a protective factor for vitamin A and D deficiency and insufficiency, respectively (OR=0.68 and 0.22, 95%CI 0.49-0.95 and 0.13-0.40, both P<0.05). The rates of vitamin A and D insufficiency was higher in children with annual household incomes <60 000 RMB than in those with annual household incomes ≥60 000 RMB (χ2=34.11 and 10.43, both P<0.01). Northwest and Southwest had the highest rates of vitamin A and vitamin D insufficiency in children aged 2-<7 yeas, respectively (χ2=93.22 and 202.54, both P<0.001). Conclusions: Among 20 cities in China, children aged 2-<7 years experience high rates of vitamin A and vitamin D insufficiency, which are affected by age, family economic level, vitamin A and vitamin D supplementation, and regional economic level. The current results suggest that high level of attention should be paid to vitamin A and vitamin D nutritional status of preschool children.
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Affiliation(s)
- Q H Wu
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
| | - Q Chen
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
| | - T Yang
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
| | - J Chen
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
| | - L Chen
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
| | - X L Xiang
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
| | - F Y Jia
- Department of Developmental and Behavioral Pediatrics, the First Hospital of Jilin University, Changchun 130031, China
| | - L J Wu
- Department of Children's and Adolescent Health, Public Health College of Harbin Medical University, Harbin 150001, China
| | - Y Hao
- Division of Child Healthcare, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - L Li
- Department of Children Rehabilitation, Hainan Women and Children's Medical Center, Haikou 570206, China
| | - J Zhang
- Children Health Care Center, Xi'an Children's Hospital, Xi'an 710003, China
| | - X Y Ke
- Child Mental Health Research Center, the Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing 210000, China
| | - M J Yi
- Department of Child Health Care, the Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Q Hong
- Department of Child Psychology and Behavior, Maternal and Child Health Hospital of Baoan, Shenzhen 518000, China
| | - J J Chen
- Department of Child Healthcare, Children's Hospital Affiliated to Shanghai Jiao Tong University, Children's Hospital of Shanghai, Shanghai 200000, China
| | - S F Fang
- Department of Child Health Care, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Y C Wang
- National Health Commission Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China
| | - Q Wang
- Department of Child Health Care, Deyang Maternity & Child Healthcare Hospital, Deyang 618000, China
| | - T Y Li
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Nutrition and Health, Chongqing 400014, China
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Chen J, Zhang Y, Wei J, Hu X, Yin H, Liu W, Li D, Tian W, Hao Y, He Z, Fernie AR, Chen W. Beyond pathways: Accelerated flavonoids candidate identification and novel exploration of enzymatic properties using combined mapping populations of wheat. Plant Biotechnol J 2024. [PMID: 38408119 DOI: 10.1111/pbi.14323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Although forward-genetics-metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co-mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare-activity-exhibiting flavonoid glycosyl- and methyl-transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward-genetics-metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics-assisted wheat crop improvement.
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Affiliation(s)
- Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Yazhouwan National Laboratory, Sanya, China
| | - Yueqi Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiaqi Wei
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huanran Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Ye B, Liu Y, Wang Z, Shen L, Yin C, Shen K, Sun J, Xu X, Sun M, Wu J, He Z, Yu X, Lu F, Hao Y, Guo Z. Genetic basis of geographical differentiation, breeding selection, domestication effects, and breeding application for TaJAZ1 in wheat. J Genet Genomics 2024:S1673-8527(24)00026-2. [PMID: 38295875 DOI: 10.1016/j.jgg.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 03/08/2024]
Affiliation(s)
- Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaowan Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; International Maize and Wheat Improvement Center China Office, c/o CAAS, Beijing 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Botanical Garden, Beijing 100093, China.
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Yin B, Jia J, Sun X, Hu X, Ao M, Liu W, Tian Z, Liu H, Li D, Tian W, Hao Y, Xia X, Sade N, Brotman Y, Fernie AR, Chen J, He Z, Chen W. Dynamic metabolite QTL analyses provide novel biochemical insights into kernel development and nutritional quality improvement in common wheat. Plant Commun 2024:100792. [PMID: 38173227 DOI: 10.1016/j.xplc.2024.100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/05/2024]
Abstract
Despite recent advances in crop metabolomics, the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown. Here, we performed widely targeted metabolite profiling of kernels from three developmental stages (grain-filling kernels [FKs], mature kernels [MKs], and germinating kernels [GKs]) using a population of 159 recombinant inbred lines. We detected 625 annotated metabolites and mapped 3173, 3143, and 2644 metabolite quantitative trait loci (mQTLs) in FKs, MKs, and GKs, respectively. Only 52 mQTLs were mapped at all three stages, indicating the high stage specificity of the wheat kernel metabolome. Four candidate genes were functionally validated by in vitro enzymatic reactions and/or transgenic approaches in wheat, three of which mediated the tricin metabolic pathway. Metabolite flux efficiencies within the tricin pathway were evaluated, and superior candidate haplotypes were identified, comprehensively delineating the tricin metabolism pathway in wheat. Finally, additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study. Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.
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Affiliation(s)
- Bo Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xu Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Min Ao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenfei Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanfeng Hao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nir Sade
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yariv Brotman
- School of Plant Sciences and Food Security, The Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Jie Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Yazhouwan National Laboratory, Sanya 572025, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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Liu J, Yang T, Dai L, Shi K, Hao Y, Chu B, Hu D, Bei Z, Yuan L, Pan M, Qian Z. Intravesical chemotherapy synergize with an immune adjuvant by a thermo-sensitive hydrogel system for bladder cancer. Bioact Mater 2024; 31:315-332. [PMID: 37663619 PMCID: PMC10468327 DOI: 10.1016/j.bioactmat.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/12/2023] [Accepted: 08/12/2023] [Indexed: 09/05/2023] Open
Abstract
Surgical resection remains the prefer option for bladder cancer treatment. However, the effectiveness of surgery is usually limited for the high recurrence rate and poor prognosis. Consequently, intravesical chemotherapy synergize with immunotherapy in situ is an attractive way to improve therapeutic effect. Herein, a combined strategy based on thermo-sensitive PLEL hydrogel drug delivery system was developed. GEM loaded PLEL hydrogel was intravesical instilled to kill tumor cells directly, then PLEL hydrogel incorporated with CpG was injected into both groins subcutaneously to promote immune responses synergize with GEM. The results demonstrated that drug loaded PLEL hydrogel had a sol-gel phase transition behavior in response to physiological temperature and presented sustained drug release, and the PLEL-assisted combination therapy could have better tumor suppression effect and stronger immunostimulating effect in vivo. Hence, this combined treatment with PLEL hydrogel system has great potential and suggests a clinically-relevant and valuable option for bladder cancer.
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Affiliation(s)
- J. Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - T.Y. Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - L.Q. Dai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - K. Shi
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Y. Hao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - B.Y. Chu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - D.R. Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Z.W. Bei
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - L.P. Yuan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - M. Pan
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Z.Y. Qian
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
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Gao HL, Hao Y, Chen WM, Li LD, Wang X, Qin YZ, Jiang Q. [Comparison of BCR::ABL (P210) mRNA levels detected by dPCR and qPCR methods in patients with chronic myeloid leukemia]. Zhonghua Xue Ye Xue Za Zhi 2023; 44:906-910. [PMID: 38185519 PMCID: PMC10753264 DOI: 10.3760/cma.j.issn.0253-2727.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 01/09/2024]
Abstract
Objective: To compare digital polymerase chain reaction (dPCR) and real-time quantitative PCR (qPCR) measurements of BCR::ABL (P210) mRNA expression in patients with chronic myeloid leukemia (CML) . Methods: In this non-interventional, cross-sectional study, BCR::ABL (P210) mRNA was simultaneously measured by dPCR and qPCR in peripheral blood samples collected from patients with CML who underwent tyrosine kinase inhibitor therapy and who achieved at least a complete cytogenetic response from September 2021 to February 2023 at Peking University People's Hospital. The difference, correlation, and agreement between the two methods were evaluated using the Wilcoxon signed-rank test, Spearman's correlation, and Bland-Altman analysis, respectively. Results: In total, 459 data pairs for BCR::ABL mRNA expression measured by dPCR and qPCR from 356 patients with CML were analyzed. There was a significant difference in BCR::ABL mRNA expression between the two methods (P<0.001). When analyzed by the depth of the molecular response (MR), a significant difference only existed for patients with ≥MR4.5 (P<0.001). No significant difference was observed for those who did not achieve a major MR (no MMR; P=0.922) or for those who achieved a major MR (MMR; P=0.723) or MR4 (P=0.099). There was a moderate correlation between the BCR::ABL mRNA expression between the two methods (r=0.761, P<0.001). However, the correlation gradually weakened or disappeared as the depth of the MR increased (no MMR: r=0.929, P<0.001; MMR: r=0.815, P<0.001; MR4: r=0.408, P<0.001; MR4.5: r=0.176, P=0.176). In addition, the agreement in BCR::ABL mRNA expression between the two methods in those with MR4.5 was weaker than other groups (no MMR: ▉= 0.042, P=0.846; MMR:▉=0.054, P=0.229; MR4:▉=-0.020, P=0.399; MR4.5:▉=-0.219, P<0.001) . Conclusions: dPCR is more accurate than qPCR for measuring BCR::ABL (P210) mRNA expression in patients with CML who achieve a stable deep MR.
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Affiliation(s)
- H L Gao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Y Hao
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - W M Chen
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - L D Li
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - X Wang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Y Z Qin
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
| | - Q Jiang
- Peking University People's Hospital, Peking University Institute of Hematology, Beijing 100044, China
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8
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Hao Y, Wu LN, Lyu YT, Liu YZ, Qin XS, Zheng R. [Evaluation of the application value of seven tumor-associated autoantibodies in non-small cell lung cancer based on machine learning algorithms]. Zhonghua Yu Fang Yi Xue Za Zhi 2023; 57:1827-1838. [PMID: 38008573 DOI: 10.3760/cma.j.cn112150-20221111-01099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Objective: Based on the diagnostic model established and validated by the machine learning algorithm, to investigate the value of seven tumor-associated autoantibodies (TAABs), namely anti-p53, PGP9.5, SOX2, GAGE7, GBU4-5, MAGEA1 and CAGE antibodies in the diagnosis of non-small cell lung cancer (NSCLC) and to differentiate between NSCLC and benign lung nodules. Methods: This was a retrospective study of clinical cases. Model building queue: a total of 227 primary patients who underwent radical lung cancer surgery in the Department of Thoracic Surgery, Shengjing Hospital of China Medical University, from November 2018 to June 2021 were collected as the NSCLC group, and 120 cases of benign lung nodules, 122 cases of pneumonia and 120 healthy individuals were selected as the control groups. External validation queue: a total of 100 primary patients who underwent radical lung cancer surgery in the Department of Thoracic Surgery, Shengjing Hospital of China Medical University, from May 2022 to December 2022 were collected as the NSCLC group, and 36 cases of benign lung nodules, 32 cases of pneumonia and 44 healthy individuals were selected as the control groups. In addition, NSCLC was divided into early (stage 0-ⅠB) and mid-to-late (stage ⅡA-ⅢB) subgroups. The levels of 7-TAABs were detected by enzyme immunoassay, and serum concentrations of CEA and CYFRA21-1 were detected by electrochemiluminescence. Four machine learning algorithms, XGBoost, Lasso logistic regression, Naïve Bayes, and Support Vector Machine are used to establish classification models. And the best performance model was chosen based on evaluation metrics and a multi-indicator combination model was established. In addition, an online risk evaluation tool was generated to assist clinical applications. Results: Except for p53, the levels of rest six TAABs, CEA and CYFRA21-1 were significantly higher in the NSCLC group (P<0.05). Serum levels of anti-SOX2 [1.50 (0.60, 10.85) U/ml vs. 0.8 (0.20, 2.10) U/ml, Z=2.630, P<0.05] and MAGEA1 antibodies [0.20 (0.10, 0.43) U/ml vs. 0.10 (0.10, 0.20) U/ml, Z=2.289, P<0.05], CEA [3.13 (2.12, 5.64) ng/ml vs. 2.11 (1.25, 3.09) ng/ml, Z=3.970, P<0.05] and CYFRA21-1 [4.31(2.37, 7.14) ng/ml vs. 2.53(1.92, 3.48) ng/ml, Z=3.959, P<0.05] were significantly higher in patients with mid-to late-stage NSCLC than in early stages. XGBoost model was used to establish a multi-indicator combined detection model (after removing p53). 6-TAABs combined with CYFRA21-1 was the best combination model for the diagnosis of NSCLC and early NSCLC. The optimal diagnostic thresholds were 0.410, 0.701 and 0.744, and the AUC was 0.828, 0.757 and 0.741, respectively (NSCLC vs. control, NSCLC vs. benign lung nodules, early NSCLC vs. benign lung nodules) in model building queue, and the AUC was 0.760, 0.710 and 0.660, respectively (NSCLC vs. control, NSCLC vs. benign lung nodules, early NSCLC vs. benign lung nodules) in external validation queue. Conclusion: In the diagnosis of NSCLC, 6-TAABs is superior to that of traditional tumor markers CEA and CYFRA21-1, and can compensate for the shortcomings of traditional tumor markers. For the differential diagnosis of NSCLC and benign lung nodule, "6-TAABs+CYFRA21-1" is the most cost-effective combination, and plays an important role in prevention and screening for early lung cancer.
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Affiliation(s)
- Y Hao
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, China Liaoning Clinical Research Center for Laboratory Medicine, Shenyang 110000, China
| | - L N Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, China Liaoning Clinical Research Center for Laboratory Medicine, Shenyang 110000, China
| | - Y T Lyu
- Biological Sciences, City University of Hong Kong, Hong Kong 999077, China
| | - Y Z Liu
- Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, China
| | - X S Qin
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, China Liaoning Clinical Research Center for Laboratory Medicine, Shenyang 110000, China
| | - R Zheng
- Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang 110000, China
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9
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Xu X, Sun D, Ni Z, Zou X, Xu X, Sun M, Cao Q, Tong J, Ding F, Zhang Y, Wang F, Dong Y, Zhang L, Wang J, Xia X, He Z, Hao Y. Molecular identification and validation of four stable QTL for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64. Theor Appl Genet 2023; 136:232. [PMID: 37875655 DOI: 10.1007/s00122-023-04481-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
KEY MESSAGE Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15 K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22 Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8 cM genetic intervals spanning 13.6 Mb (76.0-89.6 Mb) and 1.7 cM and 4.9 Mb (659.9-664.8 Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR.
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Affiliation(s)
- Xiaowan Xu
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Daojie Sun
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Zhongqiu Ni
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaoting Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Qiang Cao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Fugong Ding
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Shijiazhuang, 050035, Hebei, China
| | - Fengju Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Luyan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jiankang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Sun M, Luo Q, Zheng Q, Tong J, Wang Y, Song J, Zhang Y, Pu Z, Zheng J, Liu L, Zhou A, Rasheed A, Li M, Cao S, Xia X, He Z, Hao Y. Molecular characterization of stable QTL and putative candidate genes for grain zinc and iron concentrations in two related wheat populations. Theor Appl Genet 2023; 136:217. [PMID: 37782334 DOI: 10.1007/s00122-023-04467-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
KEY MESSAGE Major QTL for grain zinc and iron concentrations were identified on the long arm of chromosomes 2D and 6D. Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. Micronutrient malnutrition is one of the most common public health problems in the world. Biofortification, the most attractive and sustainable solution to surmount malnutrition requires the development of micronutrient enriched new crop cultivars. In this study, two recombinant inbred line (RIL) populations, ZM175/XY60 and ZM175/LX987, were used to identify QTL for grain zinc concentration (GZnC), grain iron concentration (GFeC) and thousand grain weight (TGW). Eight QTL for GZnC, six QTL for GFeC and five QTL for TGW were detected. Three QTL on chromosomes 2DL and 4BS and chromosome 6A showed pleiotropic effects on all three traits. The 4BS and 6A QTL also increased plant height and might be Rht-B1a and Rht25a, respectively. The 2DL locus within a suppressed recombination region was identified in both RIL populations and the favorable allele simultaneously increasing GZnC, GFeC and TGW was contributed by XY60 and LX987. A QTL on chromosome 6DL associated only with GZnC was detected in ZM175/XY60 and was validated in JD8/AK58 RILs using kompetitive allele-specific PCR (KASP) marker K_AX-110119937. Both the 2DL and 6DL QTL were new loci for GZnC. Based on gene annotations, sequence variations and expression profiles, the phytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. Their gene-based KASP markers were developed and validated in a cultivar panel of 343 wheat accessions. This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat.
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Affiliation(s)
- Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yue Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jie Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, 050031, Hebei, China
| | - Zongjun Pu
- Institute of Crop Sciences, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Jianmin Zheng
- Institute of Crop Sciences, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Lianzheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, Xinjiang, China
| | - Anding Zhou
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, Xinjiang, China
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ming Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shuanghe Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Dong Z, Hao Y, Laugeman E, Hugo GD, Samson P, Chen Y, Zhao T. Performance of Adaptive Deep Learning Models for Dose Predictions on High-Quality Cone-Beam Computed Tomography Images. Int J Radiat Oncol Biol Phys 2023; 117:e661. [PMID: 37785959 DOI: 10.1016/j.ijrobp.2023.06.2097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Online plan generation remains a patient-specific and time-consuming process that can place a significant burden on clinics strained with staffing shortages. As previous research show that dose-volume histogram (DVH) prediction plays a crucial role in automatic treatment planning, the objective of this study is to assess the capability of adaptive deep learning models in predicting dose information in volumetric modulation radiotherapy plans using the high-quality CBCT images and contour information of organs-at-risk (OARs). MATERIALS/METHODS The relationship between dose-volume histograms (DVHs) in radiotherapy plans and the geometric information of organs-at-risk (OAR) and planning target volume (PTV) has been well established. To evaluate the performance of the current state-of-the-art convolutional neural network (CNN) models including VIT3D and Unet3D, and intuitive machine learning methods (i.e., SVM and MLP), we implemented those models for dose prediction and conducted a comprehensive analysis with treatment plans created from images acquired from patients who consented to participate an IRB-approved imaging study designed to evaluate the imaging performance of the system. In total, 20 plans created by certified medical dosimetrists were employed in this study, with 15 used for training the machine-learning models and the remaining 5 used for performance testing. Two evaluation metrics were used: 1) root mean square error (RMSE) of the predicted dose and true dose and 2) time spent on dose prediction. RESULTS The results of the analysis showed that the ViT-3D (Transformer) model had the lowest RMSE of 3.682 ±0.010, followed by the Unet-3D (CNN) model with an RMSE of. 3.973 ±0.021 The MLP model had an RMSE of 8.007 ±0.019 while the SVM model had the highest RMSE of 9.156 ±0.032. For a fair comparison, we use 4-fold cross validation (each has 15 training plans and 5 testing plans), and report the mean value with standard deviation. All models are optimized with Adam optimizer of a learning rate 0.01, and the training process is stopped after 100 epochs. These findings indicate that the ViT-3D (Transformer) model performed the best in terms of predicting the dose information in volumetric modulation radiotherapy plans based on the CBCT images and contour information of OARs. For tested plan which contains 81 CT images (512 × 512 resolution), the inference time to predict dose information with a general CPU machine (6-Core Intel Core i7) is about 1.5 minutes. With GPU resources, such as NVIDIA A100, the inference process can be finished within seconds. CONCLUSION The study demonstrated that current state-of-the-art machine-learning models can achieve promising accuracy in dose prediction using high-quality CBCT images. A well-trained machine-learning model could offer clinicians a quick and reliable prediction of the true dose to patients in the case of significant anatomical changes or provide patient-specific optimization objectives if replanning is warranted.
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Affiliation(s)
- Z Dong
- Washington University in St. Louis, St. Louis, MO
| | - Y Hao
- Washington University in St. Louis, St. Louis, MO
| | - E Laugeman
- Washington University in St. Louis, St. Louis, MO
| | - G D Hugo
- Washington University in St. Louis, Saint Louis, MO
| | - P Samson
- Washington University in St. Louis, St. Louis, MO
| | - Y Chen
- Washington University in St. Louis, St. Louis, MO
| | - T Zhao
- Washington University in St. Louis, St. Louis, MO
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12
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Xie L, Liu S, Zhang Y, Tian W, Xu D, Li J, Luo X, Li L, Bian Y, Li F, Hao Y, He Z, Xia X, Song X, Cao S. Efficient proteome-wide identification of transcription factors targeting Glu-1: A case study for functional validation of TaB3-2A1 in wheat. Plant Biotechnol J 2023; 21:1952-1965. [PMID: 37381172 PMCID: PMC10502752 DOI: 10.1111/pbi.14103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/13/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
High-molecular-weight glutenin subunits (HMW-GS), a major component of seed storage proteins (SSP) in wheat, largely determine processing quality. HMW-GS encoded by GLU-1 loci are mainly controlled at the transcriptional level by interactions between cis-elements and transcription factors (TFs). We previously identified a conserved cis-regulatory module CCRM1-1 as the most essential cis-element for Glu-1 endosperm-specific high expression. However, the TFs targeting CCRM1-1 remained unknown. Here, we built the first DNA pull-down plus liquid chromatography-mass spectrometry platform in wheat and identified 31 TFs interacting with CCRM1-1. TaB3-2A1 as proof of concept was confirmed to bind to CCRM1-1 by yeast one hybrid and electrophoretic mobility shift assays. Transactivation experiments demonstrated that TaB3-2A1 repressed CCRM1-1-driven transcription activity. TaB3-2A1 overexpression significantly reduced HMW-GS and other SSP, but enhanced starch content. Transcriptome analyses confirmed that enhanced expression of TaB3-2A1 down-regulated SSP genes and up-regulated starch synthesis-related genes, such as TaAGPL3, TaAGPS2, TaGBSSI, TaSUS1 and TaSUS5, suggesting that it is an integrator modulating the balance of carbon and nitrogen metabolism. TaB3-2A1 also had significant effects on agronomic traits, including heading date, plant height and grain weight. We identified two major haplotypes of TaB3-2A1 and found that TaB3-2A1-Hap1 conferred lower seed protein content, but higher starch content, plant height and grain weight than TaB3-2A1-Hap2 and was subjected to positive selection in a panel of elite wheat cultivars. These findings provide a high-efficiency tool to detect TFs binding to targeted promoters, considerable gene resources for dissecting regulatory mechanisms underlying Glu-1 expression, and a useful gene for wheat improvement.
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Affiliation(s)
- Lina Xie
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
- College of AgronomyNorthwest A&F UniversityYanglingShaanxi ProvinceChina
| | - Siyang Liu
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Wenfei Tian
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
- International Maize and Wheat Improvement Center (CIMMYT) China OfficeChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Jihu Li
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lingli Li
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yingjie Bian
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Faji Li
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
- International Maize and Wheat Improvement Center (CIMMYT) China OfficeChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiyue Song
- College of AgronomyNorthwest A&F UniversityYanglingShaanxi ProvinceChina
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement CentreChinese Academy of Agricultural Sciences (CAAS)BeijingChina
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Xu X, Ni Z, Zou X, Zhang Y, Tong J, Xu X, Dong Y, Han B, Li S, Wang D, Xia X, He Z, Hao Y. QTL Mapping Reveals Both All-Stage and Adult-Plant Resistance to Powdery Mildew in Chinese Elite Wheat Cultivars. Plant Dis 2023; 107:3230-3237. [PMID: 37018212 DOI: 10.1094/pdis-02-23-0399-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Powdery mildew caused by Blumeria graminis f. sp. tritici is a threat to wheat production in China. Mapping quantitative trait loci (QTL) for resistance to powdery mildew and developing breeder-friendly markers are important initial steps in breeding resistant cultivars. An all-stage resistance gene and several QTL were identified using a population of 254 recombinant inbred lines developed from a Jingdong 8/Aikang 58 cross. The population was evaluated for powdery mildew resistance across six field environments over three consecutive growing seasons utilizing two different mixtures of B. graminis f. sp. tritici isolates, named #Bgt-HB and #Bgt-BJ. Using genotypic data obtained from the Wheat TraitBreed 50K single-nucleotide polymorphism array, seven stable QTL were identified on chromosome arms 1DL, 2AL, 2DS, 4DL, 5AL, 6BL.1, and 6BL.2. The QTL on 2AL conferred all-stage resistance to B. graminis f. sp. tritici race E20 in greenhouse tests and explained up to 52% of the phenotypic variance in field trials but was resistant only against #Bgt-HB. The gene involved in this QTL was predicted to be Pm4a based on genome location and gene sequence. QPmja.caas-1DL, QPmja.caas-4DL, and QPmja.caas-6BL.1 were identified as potentially new QTL for powdery mildew resistance. QPmja.caas-2DS and QPmja.caas-6BL.1 were effective against both B. graminis f. sp. tritici mixtures, indicating their probable broad-spectrum resistance. A Kompetitive allele-specific PCR marker closely linked to QPmja.caas-2DS was developed and validated in a panel of 286 wheat cultivars. Because both Jingdong 8 and Aikang 58 have been leading cultivars and breeding parents, the QTL and marker reported represent valuable resources for wheat researchers and breeders.
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Affiliation(s)
- Xiaoting Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhongqiu Ni
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xinyu Zou
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yelun Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang 050031, Hebei, China
| | - Jingyang Tong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xiaowan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Bin Han
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Simin Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Desen Wang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
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14
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Zhao T, Hilliard J, Lindsey A, Hao Y, Laugeman E, Samson P. Accuracy of Electron Density and Planning Dosimetry in a Novel High-Quality CBCT Imaging System. Int J Radiat Oncol Biol Phys 2023; 117:e749. [PMID: 37786168 DOI: 10.1016/j.ijrobp.2023.06.2292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) A high-quality Cone-Beam Computed Tomography (CBCT) imaging system has been FDA approved for imaging guidance and dose calculation in radiotherapy. This study aims to evaluate the accuracy of the relative electron density in CBCT images acquired in this CBCT imaging system in a phantom study and its dosimetric impact on treatment planning in a patient study. MATERIALS/METHODS Astoichiometric CT calibration was performed with a CIRS phantom (SunNuclear, Model 062M) to generate the HU-electron density curve for two tube voltages, 125kVp and 140 kVp, respectively. The phantom has a longitudinal length of 26.5 cm and is equipped with interchangeable inserts of various compositions, supplied by the vendor. Measurements were taken with solid water plates added to both ends of the phantom to allow adequate scattering and repeated for various clinical protocols with different combinations of tube voltages and exposures. The accuracy of the relative electron density of the CBCT imaging system was verified by comparing the calculated electron density from the Hounsfield Units (HU) measurements obtained from a Gammex phantom to the relative electron densities provided in vendor's specifications. To benchmark the relative electron density of the CBCT imaging system against a standard helical CT simulator, ten clinical plans that were created on CT simulation images were copied and recalculated on the CBCT images acquired immediately after the CT simulation, the latter of which was a standard procedure in current radiotherapy care for all patients who had given their consent to participate in the IRB-approved imaging study. The dose grids used in these calculations were 2.5mm x 2.5mm x 3mm. The Gamma passing rate was calculated using a standard 3mm/3% criterion with a 10% threshold. RESULTS Ourresults showed the difference between the averaged CBCT calibration curves acquired at tube voltages of 125 kVP and 140 kVp was less than 2%. The mean discrepancy of the relative electron densities from vendor's specification was 0.0045 with a range between -0.02 and 0.04. Relative electron densities in all inserts were within 2% from the vendor's specifications except the cortical bone insert. Gamma passing rate was between 96.02% and 98.49% with mean value of 97.4% and a standard deviation of 0.95%. We consider this reflects the fact that the CT simulation and CBCT imaging were performed in separated rooms, which resulted in slight anatomical deformation that could negatively impact the Gamma passing rate. CONCLUSION The CBCT imaging system provides sufficient accuracy of electron density for dose calculation, and the dose distribution calculated on the CBCT images is clinically equivalent to those calculated on helical CT images. The enhanced imaging quality of CBCT could further extend the role of imaging guidance to planning for adaptive radiotherapy, potentially reducing the need for re-simulation and interruptions in the radiotherapy course.
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Affiliation(s)
- T Zhao
- Washington University in St. Louis, St. Louis, MO
| | - J Hilliard
- Washington University in St. Louis, St. Louis, MO
| | - A Lindsey
- Washington University in St. Louis, St. Louis, MO
| | - Y Hao
- Washington University in St. Louis, St. Louis, MO
| | - E Laugeman
- Washington University in St. Louis, St. Louis, MO
| | - P Samson
- Washington University in St. Louis, St. Louis, MO
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Zhao T, Beckert R, Hilliard J, Laugeman E, Hao Y, Hunerkoch K, Miller K, Brunt L, Hong D, Schiff JP, Samson P. An In Silico study of a One-Day One-Machine Workflow for Definitive Radiotherapy Cases on a Novel Simulation and Treatment Platform. Int J Radiat Oncol Biol Phys 2023; 117:e749. [PMID: 37786169 DOI: 10.1016/j.ijrobp.2023.06.2291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The workflow in Radiotherapy (RT) has largely unchanged for the past three decades, despite increasing evidence suggesting that delayed access to RT, including the wait time between consultation, simulation, and treatment appointments, can negatively impact clinical outcomes. In this pilot study, we present preliminary results of an in silico study that demonstrate the feasibility of a novel RT platform, which integrates simulation into the treatment process and enables patients to receive immediate RT after their initial RT consultation. MATERIALS/METHODS A prospective clinical study has been approved to assess the capabilities of a novel RT platform with a high quality CBCT system for imaging guidance as well as planning. This new platform enables a novel clinical workflow that allows clinicians to review contours and plans created on diagnostic CT images prior to the initial RT consultation and allow them to approve new plans adapted on the actual simulation dataset acquired on the first treatment fraction. Four patients receiving standard of care RT (three abdomen and one thorax) consented for this study and underwent additional experimental CBCT simulation on the new platform in addition to their standard CT simulation. The CBCT simulation was taken in two setups: with a specific mold on a flat couch and without a mold on a curved couch. To demonstrate the equivalence of the new workflow to the current standard of care, the plan created on the most recent diagnostic CT images was compared to the plans adapted on the experimental simulation images and the standard CT simulation images, using a knowledge-based model. Contours were propagated from approved datasets to the new datasets through deformable image registration. RESULTS All experimental simulations were completed between 14 and 21 minutes with the assistance of two therapists. The contouring, editing, and replanning process took less than one hour in all cases, in line with our experience and peer-reviewed literature. Despite notable anatomical changes observed, the dose-volume histograms (DVH) were consistent, as shown in Table 1. CONCLUSION The novel workflow presented herein was feasible and demonstrates that the integration of simulation with image-guided RT on one single platform may unlock the potential of accelerating the RT workflow and reducing the wait time for treatment from weeks to hours.
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Affiliation(s)
- T Zhao
- Washington University in St. Louis, St. Louis, MO
| | - R Beckert
- Washington University in St. Louis, St. Louis, MO
| | - J Hilliard
- Washington University in St. Louis, St. Louis, MO
| | - E Laugeman
- Washington University in St. Louis, St. Louis, MO
| | - Y Hao
- Washington University in St. Louis, St. Louis, MO
| | - K Hunerkoch
- Washington University in St. Louis, St. Louis, MO
| | - K Miller
- Washington University in St. Louis, St. Louis, MO
| | - L Brunt
- Washington University in St. Louis, St. Louis, MO
| | - D Hong
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - J P Schiff
- Washington University in St. Louis, St. Louis, MO
| | - P Samson
- Washington University in St. Louis, St. Louis, MO
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Hao Y, Hugo GD, Zhao T. Proton Online Adaptation Using Novel Cone-Beam Computed Tomography System. Int J Radiat Oncol Biol Phys 2023; 117:e671. [PMID: 37785981 DOI: 10.1016/j.ijrobp.2023.06.2118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Cone beam computed tomography (CBCT) has been used in clinic frequently to provide quick, online, and handy three-dimensional images. However, due to its significant artifacts and inaccurate Hounsfield values (HU), CBCT based online proton adaptation is infeasible. Recently, a novel in-room imaging solution was developed to allow larger images, better contrast and faster CBCT imaging acquisition. Our work demonstrated for the first time the feasibility of using this novel CBCT images for direct intensity modulated proton planning. MATERIALS/METHODS Three patients and three CIRS phantoms were scanned using novel imaging technique (CBCTp) for this work. CT curves were acquired by scanning a CIRS electron density phantom. Stopping power ratio was computed using the stoichiometric method. Proton plans were made on treatment simulation CT and further evaluated on CBCTp to compare the differences. RESULTS The table below shows three patients and three phantoms plan comparisons. Multiple sites and dose levels were studied. The planning target volume (PTV) coverage (D95%) and mean dose difference between simulation CT and CBCTp are 0.8% and 0.3%, correspondingly. Dosimetrically, phantom and patient plans are almost identical between two imaging techniques. Lung patient plan show the largest variation due to patient tumor change and the quality of breathing. CONCLUSION The novel and high quality of CBCT is feasible for direct proton planning with accurate CT calibration. It provides a reliable alternative solution for proton online adaptive therapy.
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Affiliation(s)
- Y Hao
- Washington University School of Medicine, Department of Radiation Oncology, St. Louis, MO
| | - G D Hugo
- Washington University School of Medicine, Department of Radiation Oncology, St. Louis, MO
| | - T Zhao
- Washington University School of Medicine, Department of Radiation Oncology, St. Louis, MO
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Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li XY, Yang HF, Xiao JY, Hao Y, Xu B, Wu XY, Zhao XY, Ma TP, Lyu L, Feng WT, Li JY. [Association between different obesity measurement indexes and serum C-reactive protein in adult women]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1251-1256. [PMID: 37661617 DOI: 10.3760/cma.j.cn112338-20221122-00992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Objective: To explore the association of different obesity measurement indexes on serum C-reactive protein (CRP) in Chinese adult women. Methods: The data were obtained from baseline and follow-up surveys of the urban Breast Cancer Screening Program in Shuangliu District, Chengdu. A total of 441 adult women were included in the study. A questionnaire survey, physical examination, and laboratory testing were conducted on the subjects. Multivariate logistic regression model, two-level mixed effects logistic regression model, and restricted cubic spline method were used to investigate the linear and nonlinear correlation between different obesity measurement indexes and serum CRP in adult women. Results: For every 1 unit increase in BMI, waist circumference (WC), and adiposity, the risk of elevated serum CRP or exacerbation of chronic low-grade inflammation in adult women increased by 16.5%, 5.0%, and 11.1% (P<0.05), respectively. Both BMI and adiposity were nonlinear correlated with serum CRP. Using BMI=24.0 kg/m2 as the reference point, serum CRP level increased with the increase of BMI when BMI >24.0 kg/m2. Using adiposity=30% as the reference point, serum CRP level increased with the increase of adiposity when adiposity >30%. Conclusions: Overall, obesity reflected by BMI had the strongest association with serum CRP in adult women, followed by body fat content reflected by adiposity, and central obesity reflected by WC had the weakest association with CRP. Adult women with BMI >24.0 kg/m2 or adiposity >30% are at high risk for obesity-related inflammatory manifestations.
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Affiliation(s)
- X Y Li
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - H F Yang
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - J Y Xiao
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - Y Hao
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - B Xu
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - X Y Wu
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - X Y Zhao
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - T P Ma
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - L Lyu
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - W T Feng
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
| | - J Y Li
- West China School of Public Health/West China Forth Hospital, Sichuan University, Chengdu 610041, China
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Zhang H, Li FY, Hao Y, Wang XM, Zhang J, Ma YL, Zeng H, Lin J. [Identification and 3D architecture analysis of the LIPC gene mutation in a pedigree with familial hypercholesterolemia-like phenotype]. Zhonghua Xin Xue Guan Bing Za Zhi 2023; 51:716-721. [PMID: 37460425 DOI: 10.3760/cma.j.cn112148-20230601-00321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Objective: To identify and analyze 3D architecture of the mutational sites of susceptible genes in a pedigree with familial hypercholesterolemia-like phenotype (FHLP). Methods: This is a case series study. A pedigree with suspected familial hypercholesterolemia was surveyed. The proband admitted in Beijing Anzhen Hospital in April 2019. Whole-exome sequencing was performed to determine the mutational sites of susceptible genes in the proband. Polymerase chain reaction (PCR) sequencing was used to verify the pathogenic variant on proband's relatives. The structural and functional changes of the proteins were analyzed and predicted by Discovery Studio 4.0 and PyMol 2.0. Results: The patients in the pedigree showed abnormal lipid profiles, especially elevated levels of total cholesterol(TC). The genetic screening detected the c.1330C>T SNP in the exon 8 of lipase C (LIPC) gene, this mutation leads to an amino acid substitution from arginine to cysteine at position 444 (Arg444Cys), in the proband and proband's father and brother. In this family, members with this mutation exhibited elevated TC, whereas lipid profile was normal from the proband's mother without this mutation. This finding indicated that LIPC: c.1330C>T mutation might be the mutational sites of susceptible genes. The analysis showed that Arg444Cys predominantly affected the ligand-binding property of the protein, but had a limited impact on catalytic function. Conclusion: LIPC: c.1330C>T is a new mutational site of susceptible genes in this FHLP pedigree.
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Affiliation(s)
- H Zhang
- Department of Atherosclerosis, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing 100029, China
| | - F Y Li
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Peking University Ditan Teaching Hospital, Beijing 100015, China
| | - Y Hao
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - X M Wang
- College of Life Sciences, Yantai University, Yantai 264005, China
| | - J Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Y L Ma
- Institute of Basic Medical Theory of Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - H Zeng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Peking University Ditan Teaching Hospital, Beijing 100015, China
| | - J Lin
- Department of Atherosclerosis, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing 100029, China
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20
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Zhu Z, Cao Q, Han D, Wu J, Wu L, Tong J, Xu X, Yan J, Zhang Y, Xu K, Wang F, Dong Y, Gao C, He Z, Xia X, Hao Y. Molecular characterization and validation of adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895. Theor Appl Genet 2023; 136:142. [PMID: 37247049 DOI: 10.1007/s00122-023-04374-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/02/2023] [Indexed: 05/30/2023]
Abstract
KEY MESSAGE Adult-plant stripe rust resistance gene Yr86 in Chinese wheat cultivar Zhongmai 895 was mapped to the physical interval 710.2-713.2 Mb on the long arm of chromosome 2A. Adult-plant resistance to stripe rust is generally more durable than all-stage resistance. Chinese wheat cultivar Zhongmai 895 showed stable stripe rust resistance at the adult-plant stage. To map the genetic loci underlying its resistance, 171 doubled haploid (DH) lines from a Yangmai 16/Zhongmai 895 cross were genotyped with the wheat 660 K SNP chip. Disease severities of the DH population and parents were assessed in four environments. A major QTL designated QYryz.caas-2AL was mapped to interval 703.7-715.3 Mb on the long arm of chromosome 2A using both chip-based and KASP (kompetitive allele-specific PCR) marker-based methods, explaining 31.5 to 54.1% of the phenotypic variances. The QTL was further validated in an F2 population of cross Emai 580/Zhongmai 895 with 459 plants and a panel of 240 wheat cultivars using KASP markers. Three reliable KASP markers predicted a low frequency (7.2-10.5%) of QYryz.caas-2AL in the test panel and remapped the gene to the physical interval 710.2-713.2 Mb. Based on different physical positions or genetic effects from known genes or QTL on chromosome arm 2AL, the gene was predicted to be a new one for adult-plant stripe rust resistance and was named Yr86. Twenty KASP markers linked to Yr86 were developed in this study based on wheat 660 K SNP array and genome re-sequencing. Three of them are significantly associated with stripe rust resistance in natural population. These markers should be useful for marker-assisted selection and also provide a starting point for fine mapping and map-based cloning of the new resistance gene.
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Affiliation(s)
- Zhanwang Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, Hubei, China
| | - Qiang Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environment Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory, Chengdu, 610066, Sichuan, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xiaowan Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jun Yan
- Institute of Cotton Research, CAAS, Anyang, 455000, Henan, China
| | - Yong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Kaijie Xu
- Institute of Cotton Research, CAAS, Anyang, 455000, Henan, China
| | - Fengju Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Yachao Dong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chunbao Gao
- Food Crops Institute, Hubei Academy of Agricultural Sciences/Wheat Disease Biology Research Station for Central China, Wuhan, 430064, Hubei, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- CIMMYT-China Office, C/O CAAS, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
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Hao Y, Gao S, Zhang X, Cui M, Ding X, Wang H, Yang D, Ye H, Wang H. [Comparison of diagnostic performance of Clear Cell Likelihood Score v1.0 and v2.0 for clear renal cell carcinoma]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:800-806. [PMID: 37313822 DOI: 10.12122/j.issn.1673-4254.2023.05.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To compare the performance of Clear Cell Likelihood Score (ccLS) v1.0 and v2.0 in diagnosing clear cell renal cell carcinoma (ccRCC) from small renal masses (SRM). METHODS We retrospectively analyzed the clinical data and MR images of patients with pathologically confirmed solid SRM from the First Medical Center of the Chinese PLA General Hospital between January 1, 2018, and December 31, 2021, and from Beijing Friendship Hospital of Capital Medical University and Peking University First Hospital between January 1, 2019 and May 17, 2021. Six abdominal radiologists were trained for use of the ccLS algorithm and scored independently using ccLS v1.0 and ccLS v2.0. Random- effects logistic regression modeling was used to generate plot receiver operating characteristic curves (ROC) to evaluate the diagnostic performance of ccLS v1.0 and ccLS v2.0 for ccRCC, and the area under curve (AUC) of these two scoring systems were compared using the DeLong's test. Weighted Kappa test was used to evaluate the interobserver agreement of the ccLS score, and differences in the weighted Kappa coefficients was compared using the Gwet consistency coefficient. RESULTS In total, 691 patients (491 males, 200 females; mean age, 54 ± 12 years) with 700 renal masses were included in this study. The pooled accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of ccLS v1.0 for diagnosing ccRCC were 77.1%, 76.8%, 77.7%, 90.2%, and 55.7%, as compared with 80.9%, 79.3%, 85.1%, 93.4%, 60.6% with ccLS v2.0, respectively. The AUC of ccLS v2.0 was significantly higher than that of ccLS v1.0 for diagnosis of ccRCC (0.897 vs 0.859; P < 0.01). The interobserver agreement did not differ significantly between ccLS v1.0 and ccLS v2.0 (0.56 vs 0.60; P > 0.05). CONCLUSION ccLS v2.0 has better performance for diagnosing ccRCC than ccLS v1.0 and can be considered for use to assist radiologists with their routine diagnostic tasks.
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Affiliation(s)
- Y Hao
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Radiology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - S Gao
- Department of Radiology, Linyi Central Hospital, Linyi 276400, China
| | - X Zhang
- Department of Radiology, First Hospital of Shanxi Medical University, Taiyuan 030012, China
| | - M Cui
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Radiology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - X Ding
- Department of Pathology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - H Wang
- Department of Radiology, Peking University First Hospital, Beijing 100035, China
| | - D Yang
- Department of Radiology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - H Ye
- Department of Radiology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - H Wang
- Department of Radiology, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
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Liu Y, Shen K, Yin C, Xu X, Yu X, Ye B, Sun Z, Dong J, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Wang Z, Wu H, Liu D, Zhang L, Shen L, Hao Y, Lu F, Guo Z. Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits. Genome Biol 2023; 24:114. [PMID: 37173729 PMCID: PMC10176713 DOI: 10.1186/s13059-023-02932-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 04/10/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat (Triticum aestivum) breeding. The internode length of individual stems and tiller length of individual plants are important for the determination of plant architecture. However, few studies have explored the genetic basis of these traits. RESULTS Here, we conduct a genome-wide association study (GWAS) to dissect the genetic basis of geographical differentiation of these traits in 306 worldwide wheat accessions including both landraces and traditional varieties. We determine the changes of haplotypes for the associated genomic regions in frequency in 831 wheat accessions that are either introduced from other countries or developed in China from last two decades. We identify 83 loci that are associated with one trait, while the remaining 247 loci are pleiotropic. We also find 163 associated loci are under strong selective sweep. GWAS results demonstrate independent regulation of internode length of individual stems and consistent regulation of tiller length of individual plants. This makes it possible to obtain ideal haplotype combinations of the length of four internodes. We also find that the geographical distribution of the haplotypes explains the observed differences in internode length among the worldwide wheat accessions. CONCLUSION This study provides insights into the genetic basis of plant architecture. It will facilitate gene functional analysis and molecular design of plant architecture for breeding.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Xiaowan Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiayu Dong
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, 100049, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100010, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Koss KM, Son T, Li C, Hao Y, Cao J, Churchward MA, Zhang ZJ, Wertheim JA, Derda R, Todd KG. Toward discovering a novel family of peptides targeting neuroinflammatory states of brain microglia and astrocytes. J Neurochem 2023:10.1111/jnc.15840. [PMID: 37171455 PMCID: PMC10640667 DOI: 10.1111/jnc.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Microglia are immune-derived cells critical to the development and healthy function of the brain and spinal cord, yet are implicated in the active pathology of many neuropsychiatric disorders. A range of functional phenotypes associated with the healthy brain or disease states has been suggested from in vivo work and were modeled in vitro as surveying, reactive, and primed sub-types of primary rat microglia and mixed microglia/astrocytes. It was hypothesized that the biomolecular profile of these cells undergoes a phenotypical change as well, and these functional phenotypes were explored for potential novel peptide binders using a custom 7 amino acid-presenting M13 phage library (SX7) to identify unique peptides that bind differentially to these respective cell types. Surveying glia were untreated, reactive were induced with a lipopolysaccharide treatment, recovery was modeled with a potent anti-inflammatory treatment dexamethasone, and priming was determined by subsequently challenging the cells with interferon gamma. Microglial function was profiled by determining the secretion of cytokines and nitric oxide, and expression of inducible nitric oxide synthase. After incubation with the SX7 phage library, populations of SX7-positive microglia and/or astrocytes were collected using fluorescence-activated cell sorting, SX7 phage was amplified in Escherichia coli culture, and phage DNA was sequenced via next-generation sequencing. Binding validation was done with synthesized peptides via in-cell westerns. Fifty-eight unique peptides were discovered, and their potential functions were assessed using a basic local alignment search tool. Peptides potentially originated from proteins ranging in function from a variety of supportive glial roles, including synapse support and pruning, to inflammatory incitement including cytokine and interleukin activation, and potential regulation in neurodegenerative and neuropsychiatric disorders.
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Affiliation(s)
- K M Koss
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - T Son
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - C Li
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - Y Hao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - J Cao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - M A Churchward
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biology and Environmental Sciences, Concordia University of Edmonton, Alberta, Edmonton, Canada
| | - Z J Zhang
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - J A Wertheim
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - R Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - K G Todd
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biomedical Engineering, University of Alberta, Alberta, Edmonton, Canada
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Zhao C, Tong J, Gao Z, Liu J, Hao Y, Xia X, He Z, Zhang Y, Tian W. Genome-wide association study of alkylresorcinols content in 161 wheat cultivars. J Cereal Sci 2023. [DOI: 10.1016/j.jcs.2023.103679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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25
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis. Ann Bot 2023; 131:503-519. [PMID: 36655618 PMCID: PMC10072080 DOI: 10.1093/aob/mcad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. METHODS Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018-2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. KEY RESULTS These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = -0.63, P < 0.01), flag leaf angle (r = -0.49, P < 0.01) and spike number per square metre (r = -0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. CONCLUSIONS This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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26
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Hao Y, Si J, Wei J, Gu X, Wang W, Zhang Y, Guan Y, Huang H, Xu C, Song Z. 221P Comparison of efficacy and safety of carboplatin combined with nab-paclitaxel or paclitaxel as first-line therapy for advanced thymic epithelial tumors. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00474-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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27
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Hao Y, Si J, Jin J, Wei J, Xiang J, Xu C, Song Z. 220P Comparison of efficacy and safety of platinum-based chemotherapy as first-line therapy between B3 thymoma and thymic carcinoma. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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28
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Hao Y, Sun W, Zeng X, Shi Z, Wang W, Xu C, Song Z. 219P Clinical outcomes for advanced thymoma patients receiving platinum-based chemotherapy as first-line treatment. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00472-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, Zhang H, He Z, Reynolds M. Linking genetic markers with an eco-physiological model to pyramid favourable alleles and design wheat ideotypes. Plant Cell Environ 2023; 46:780-795. [PMID: 36517924 DOI: 10.1111/pce.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Genetic markers can be linked with eco-physiological crop models to accurately predict genotype performance and individual markers' contributions in target environments, exploring interactions between genotype and environment. Here, wheat (Triticum aestivum L.) yield was dissected into seven traits corresponding to cultivar genetic coefficients in an eco-physiological model. Loci for these traits were discovered through the genome-wide association studies (GWAS). The cultivar genetic coefficients were derived from the loci using multiple linear regression or random forest, building a marker-based eco-physiological model. It is then applied to simulate wheat yields and design virtual ideotypes. The results indicated that the loci identified through GWAS explained 46%-75% variations in cultivar genetic coefficients. Using the marker-based model, the normalized root mean square error (nRMSE) between the simulated yield and observed yield was 13.95% by multiple linear regression and 13.62% by random forest. The nRMSE between the simulated and observed maturity dates was 1.24% by multiple linear regression and 1.11% by random forest, respectively. Structural equation modelling indicated that variations in grain yield could be well explained by cultivar genetic coefficients and phenological data. In addition, 24 pleiotropic loci in this study were detected on 15 chromosomes. More significant loci were detected by the model-based dissection method than considering yield per se. Ideotypes were identified by higher yield and more favourable alleles of cultivar genetic traits. This study proposes a genotype-to-phenotype approach and demonstrates novel ideas and tools to support the effective breeding of new cultivars with high yield through pyramiding favourable alleles and designing crop ideotypes.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fulu Tao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - He Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Guo G, Xu S, Chen H, Hao Y, Mao H. QTL Mapping for Wheat Seed Dormancy in a Yangmai16/Zhongmai895 Double Haploid Population. Plants (Basel) 2023; 12:759. [PMID: 36840107 PMCID: PMC9967201 DOI: 10.3390/plants12040759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/04/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Pre-harvest sprouting (PHS) of wheat reduces grain yield and quality, and it is strongly affected by seed dormancy. Therefore, identification of quantitative trait loci (QTL) for seed dormancy is essential for PHS resistance breeding. A doubled haploid (DH) population, consisting of 174 lines from the cross between Yangmai16 (YM16) and Zhongmai895 (ZM895) was used to detect QTLs for seed dormancy and grain color. For seed dormancy, a total of seven QTLs were detected on chromosomes 2A, 3A, 3D, 4D, 5B and 5D over four environments, among which Qdor.hzau-3A, Qdor.hzau-3D.1 and Qdor.hzau-3D.2 were stably detected in more than two environments. For grain color, only two QTLs, Qgc.hzau-3A and Qgc.hzau-3D were detected on chromosomes 3A and 3D, which physically overlapped with Qdor.hzau-3A and Qdor.hzau-3D.1, respectively. Qdor.hzau-3D.2 has never been reported elsewhere and is probably a novel locus with allelic effect of seed dormancy contributed by weakly dormant parent ZM895, and a KASP marker was developed and validated in a wheat natural population. This study provides new information on the genetic dissection of seed dormancy, which may aid in further improvement for marker-assisted wheat breeding for PHS resistance.
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Affiliation(s)
- Gang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Zhao Q, Hao Y, Yang XQ, Yan XY, Qiu YL. [Preliminary study on the effect of fecal microbiota transplantation on neurobehavior and gut microbiota of offspring rats exposed to arsenic]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2023; 41:14-20. [PMID: 36725289 DOI: 10.3760/cma.j.cn121094-20220311-00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Objective: To explore the effects of fecal microbiota transplantation (FMT) on neurobehavior and gut microbiota of arsenic-exposed offspring rats. Methods: In April 2021, Thirty-six SPF SD rats aged 8 weeks were seleted, rats were ranked by weight and divided into four groups according to randomized block design, namely control group, arsenic exposure group (As group) , arsenic+normal saline group (As+NaCl group) and As+FMT group, 6 females and 3 males in each group. Fecal microbiota fluid were provided by feces of rats in control group. Rats drank tap water containing 75 mg/L sodium arsenite for one week and then were caged together. The arsenic exposure was terminated until the pups were born. Female rats with vaginal plug were treated with fecal microbiota fluid via gavage during neurodevelopmental teratogenic window period. The volume of gavage was 1 ml/100 g with once every two days, for a total of three times. Weight alterations of offspring rats were recorded every week after weaning, and when offspring rats grew up for 6 weeks, Morris test and open field experiment was used to observe learning and memory abilities, as well as neurobehavioral performance of autonomous exploration and tension, respectively. 16S rDNA sequencing technology was used to detect microbiota diversities in fecal samples of rats in As group and As+FMT group. Results: Compared with the control group, the ratio of swimming distance and staying time in the target quadrant and the times of crossing the platform of rats in As group decreased significantly, and the motor distance, times entering central zone and the number of grid crossing of rats decreased significantly (P<0.05) . Compared with As group, the ratio of swimming distance in target quadrant, the motor distance in central zone and times entering central zone of rats in As+FMT group were evidently increased (P<0.05) . The analysis of fecal microbiota diversities showed that, at the phyla level, the relative abundance of Bacteroidetes in feces of rats in As+FMT group was higher than that in As group (68.34% vs 60.55%) , while the relative abundance of Firmicutes was lower than that in As group (28.02% vs 33.48%) . At the genus level, the relative abundance of Prevotella in As+FMT group was significantly higher than that in As group, becoming the dominant genus (42.08% vs 21.78%) . Additionally, compared with As group, a total of 22 genus were increased with 21 decreased genus in As+FMT group (P<0.05) . LEfSe analysis showed that dominant genuses in As+FMT group were Prevotella and UCG_005, and their relative abundance was significantly higher than that of As group (P<0.05) . Conclusion: FMT may alleviate the impaired learning and memory ability and anxiety like behavior of the offspring rats exposed to arsenic, and improve the disrupted gut microbiota.
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Affiliation(s)
- Q Zhao
- Department of Health Toxicology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Y Hao
- Department of Health Toxicology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - X Q Yang
- Department of Health Toxicology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - X Y Yan
- Department of Health Toxicology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Y L Qiu
- Department of Health Toxicology, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
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Wang X, Jiang J, Hu W, Hu Y, Qin LQ, Hao Y, Dong JY. Dynapenic Abdominal Obesity and Risk of Heart Disease among Middle-Aged and Older Adults: A Prospective Cohort Study. J Nutr Health Aging 2023; 27:752-758. [PMID: 37754215 DOI: 10.1007/s12603-023-1975-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/29/2023] [Indexed: 09/28/2023]
Abstract
OBJECTIVES The vicious cycle of dynapenia and abdominal obesity may have synergistic detrimental impacts on health. We aim to investigate the prospective association between dynapenic abdominal obesity and the risk of heart disease among middle-aged and older adults. DESIGN A prospective cohort study. SETTING English Longitudinal Study of Ageing, 2002-2019. PARTICIPANTS A total of 4734 participants aged 50 years and older were included. MEASUREMENTS Individuals were divided into non-dynapenia/non-abdominal obesity (ND/NAO), non-dynapenia/abdominal obesity (ND/AO), dynapenia/non-abdominal obesity (D/NAO), and dynapenia/abdominal obesity (D/AO) according to grip strength and waist circumference at baseline. The Cox proportional hazards models were used to obtain the hazard ratios (HRs) of incident heart disease associated with dynapenia and abdominal obesity after adjusting for potential confounding factors. RESULTS During a median follow-up of 9.5 years, 1040 cases of heart disease were recorded. Compared with ND/NAO group, the multivariable HRs were 1.05 (0.92, 1.21) for ND/AO group, 1.31 (0.96, 1.81) for D/NAO group, and 1.39 (1.03, 1.88) for D/AO group. The significant association of D/AO with incident heart disease was detected in women but not in men [HR = 1.55 (1.07, 2.24) and 1.06 (0.60, 1.88), respectively]. Among middle-aged adults, significant associations of D/NAO and D/AO with incident heart disease were observed [HR = 2.46 (1.42, 4.29) and 1.74 (1.02, 2.97), respectively]. CONCLUSION Both D/NAO and D/AO might increase the risk of developing heart disease, highlighting the importance of dynapenia and obesity early screening for heart disease prevention.
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Affiliation(s)
- X Wang
- Yuantao Hao, Center for Public Health and Epidemic Preparedness and Response, Peking University, Beijing, 100191, China; Tel.: 010-82805061, E-mail: ; Jia-Yi Dong, Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Osaka 5650871, Japan; Tel: 06-6879-3911,
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Guo X, Liu C, Feng B, Hao Y. Evaluation of Membrane Fouling Control for Brackish Water Treatment Using a Modified Polyamide Composite Nanofiltration Membrane. Membranes (Basel) 2022; 13:38. [PMID: 36676845 PMCID: PMC9866803 DOI: 10.3390/membranes13010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
In northwest China, the limited amount of water resources are classified mostly as brackish water. Nanofiltration is a widely applied desalination technology used for brackish water treatment; however, membrane fouling restricts its application. Herein, we modified the membrane with triethanolamine (TEOA) and optimized the operating conditions (transmembrane pressure, temperature, and crossflow velocity) to control the nanofiltration membrane fouling by brackish water. Based on the physiochemical characteristics and desalination performance of the prepared membranes, the membrane modified with 2% TEOA (MPCM2) was identified as the optimal membrane, and 0.5 MPa, 25 °C, and 7 cm/s were identified as the optimal operating conditions through a series of nanofiltration experiments. Moreover, the membrane cleaning procedure for fouled MPCM2 was further determined, and a two-step cleaning procedure using ethylene diamine tetraacetic acid disodium followed by HCl with a permeance recovery rate of 98.77% was identified as the optimal cleaning procedure. Furthermore, the characterizations of the fouled and cleaned MPCM2 showed that the optimized cleaning procedure could recover the properties of MPCM2 to near virgin. This study is of great significance for the long-term stable operation of nanofiltration processes in brackish water treatment to ensure the supply of healthy water in the water-deficient areas of northwest China.
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Affiliation(s)
- Xuebai Guo
- Department of Environmental Engineering, Henan Vocational College of Water Conservancy and Environment, Zhengzhou 450008, China
| | - Cuixia Liu
- School of Energy & Environment, Zhongyuan University of Technology, Zhengzhou 450007, China
| | - Bin Feng
- CCTEG Chongqing Engineering (Group) Co., Ltd., Chongqing 401331, China
| | - Yuanfeng Hao
- Department of Environmental Engineering, Henan Vocational College of Water Conservancy and Environment, Zhengzhou 450008, China
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Hao Y, Zhu G, Yu L, Ren Z, Zhang P, Zhu J, Cao S. Extracellular vesicles derived from mesenchymal stem cells confer protection against intervertebral disc degeneration through a microRNA-217-dependent mechanism. Osteoarthritis Cartilage 2022; 30:1455-1467. [PMID: 36041665 DOI: 10.1016/j.joca.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 08/12/2022] [Accepted: 08/14/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Extracellular vesicles released by mesenchymal stem cells (MSC-EVs) can be applied to alleviate intervertebral disc degeneration (IVDD) by curbing apoptosis of nucleus pulposus cells (NPCs). The current study aims to evaluate the effect of MSC-EVs on NPC apoptosis and IVDD and the related regulatory mechanisms involving microRNA (miR)-217. METHOD Expression of miR-217 was examined in tumor necrosis factor-α (TNF-α)-induced NPCs and MSC-EVs, followed by identification in the relationship between miR-217, enhancer of zeste homolog 2 (EZH2) and forkhead box O-3 (FOXO3). After isolation of EVs from MSCs and subsequent co-culture with NPCs, we assessed effects of miR-217 on NPC viability, autophagy, senescence and apoptosis along with extracellular matrix (ECM) degradation. Further in vivo experiments were conducted in rat models of IVDD to substantiate the effect of miR-217 on IVDD. RESULTS Poor miR-217 expression was found in TNF-α-induced NPCs, while high miR-217 expression was identified in MSC-EVs (P < 0.05). MSC-EVs transferred miR-217 to NPCs and increased its expression, thus attenuating NPC apoptosis and ECM degradation (elevated collagen II and aggrecan but reduced MMP13 and ADAMTS5) (P < 0.05). miR-217 targeted EZH2, and EZH2 bound to the FOXO3 promoter and consequently downregulated its expression. FOXO3 restrained NPC apoptosis and ECM degradation by stimulating cell autophagy (P < 0.05). Furthermore, in vivo experimental results confirmed the suppressive role of miR-217 shuttled by MSC-EVs in IVDD. CONCLUSION Overall, the delivery of miR-217 may be a novel mechanism underlying the effect of MSC-EVs on NPC apoptosis and ECM degradation following IVDD.
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Affiliation(s)
- Y Hao
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China.
| | - G Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - L Yu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - Z Ren
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - P Zhang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - J Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| | - S Cao
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
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Lo W, Mulrow D, Hao Y, Bergom C, Rogers B, Sobotka L, Darafsheh A. Optimizing the Small Animal Radiation Research Platform (SARRP) for High-Dose Rate Focal Irradiation Studies. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.2149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Waters M, Price A, Laugeman E, Hugo G, Stowe H, Green O, Brenneman R, Hao Y, Gay H, Robinson C, Michalski J, Henke L, Baumann B. CT-Based Online Adaptive Prostate SBRT Improves Target Coverage and Reduces Rectal Dose. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.2265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Price A, Laugeman E, Hao Y, Stowe H, Henke L, Baumann B. Adaptive Workflow for Whole Bladder Radiation Therapy with Simultaneous Integrated Boost on a CBCT Adaptive AI-Driven System. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.2286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Wheat traits and the associated loci conferring radiation use efficiency. Plant J 2022; 112:565-582. [PMID: 36004546 DOI: 10.1111/tpj.15954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum L.) radiation use efficiency (RUE) must be raised through crop breeding to further increase the yield potential, as the harvest index is now close to its theoretical limit. Field experiments including 209 wheat cultivars which have been widely cultivated in China since the 1940s were conducted in two growing seasons (2018-2019 and 2019-2020) to evaluate the variations of phenological, physiological, plant architectural, and yield-related traits and their contributions to RUE and to identify limiting factors for wheat yield potential. The average annual genetic gain in grain yield was 0.60% (or 45.32 kg ha-1 year-1 ; R2 = 0.44, P < 0.01), mainly attributed to the gain in RUE (r = 0.85, P < 0.01). The net photosynthetic rates were positively and closely correlated with grain RUE and grain yield, suggesting source as a limiting factor to future yield gains. Thirty-four cultivars were identified, exhibiting not only high RUE, but also traits contributing to high RUE and 11 other critical traits - of known genetic basis - as potential parents for breeding to improve yield and RUE. Our findings reveal wheat traits and the associated loci conferring RUE, which are valuable for facilitating marker-assisted breeding to improve wheat RUE and yield potential.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fulu Tao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Zeng Z, Guo C, Yan X, Song J, Wang C, Xu X, Hao Y. QTL mapping and KASP marker development for seed vigor related traits in common wheat. Front Plant Sci 2022; 13:994973. [PMID: 36247615 PMCID: PMC9563228 DOI: 10.3389/fpls.2022.994973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Seed vigor is an important parameter of seed quality, and identification of seed vigor related genes can provide an important basis for highly efficient molecular breeding in wheat. In the present study, a doubled haploid (DH) population with 174 lines derived from a cross between Yangmai16 and Zhongmai 895 was used to evaluate 10 seed vigor related traits in Luoyang during the 2018-2019 cropping season and in Mengjin and Luoning Counties during 2019-2020 cropping season for three environments. Quantitative trait locus (QTL) mapping of 10 seed vigor related traits in the DH population resulted in the discovery/identification of 28 QTLs on chromosomes 2B, 3D, 4B, 4D, 5A, 5B, 6A, 6B, 6D, 7A and 7D, explaining 3.6-23.7% of the phenotypic variances. Among them, one QTL cluster for shoot length, root length and vigor index was mapped between AX-89421921 and Rht-D1_SNP on chromosome 4D in the physical intervals of 18.78-19.29 Mb (0.51 Mb), explaining 9.2-20.5% of the phenotypic variances. Another QTL for these traits was identified at the physical position 185.74 Mb on chromosome 5B, which was flanked by AX-111465230 and AX-109519938 and accounted for 8.0-13.3% of the phenotypic variances. Two QTLs for shoot length, shoot fresh weight and shoot dry weight were identified in the marker intervals of AX-109384026-AX-111120402 and AX-111651800-AX-94443918 on chromosomes 6A and 6B, explaining 8.2-11.7% and 3.6-10.3% of the phenotypic variance, respectively; both alleles for increasing phenotypic values were derived from Yangmai 16. We also developed the KASP markers for the QTL cluster QVI.haust-4D.1/QSL.haust-4D/QRL.haust-4D, and validated in an international panel of 135 wheat accessions. The germplasm, genes and KASP markers were developed for breeders to improve wheat varieties with seed vigor related traits.
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Affiliation(s)
- Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Cheng Guo
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Xuefang Yan
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Junqiao Song
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Xiaoting Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Ma QG, Hao Y, Xue YF, Niu YL, Chang XL. Removal of Formaldehyde from Aqueous Solution by Hydrogen Peroxide. J WATER CHEM TECHNO+ 2022. [DOI: 10.3103/s1063455x22040099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Garcia-Manero G, Bart S, McCloskey JK, Fenaux P, Selleslag D, Reda G, Valcárcel D, Santini V, Mayer J, Xicoy B, Yamaguchi H, Lübbert M, Miyazaki Y, Keer H, Hao Y, Azab M, Döhner H. P768: GUADECITABINE (SGI-110) VS. TREATMENT CHOICE (TC) IN RELAPSED/REFRACTORY(R/R) MYELODYSPLASTIC SYNDROME (MDS), RESULTS OF A GLOBAL, RANDOMIZED, PHASE 3 STUDY. Hemasphere 2022. [DOI: 10.1097/01.hs9.0000845956.26644.d0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Ji L, Gao D, Hao Y, Zhang Z. POS0720 LOW-DOSE GLUCOCORTICOIDS WITHDRAWN IN SYSTEMIC LUPUS ERYTHEMATOSUS: A DESIRABLE AND ATTAINABLE GOAL. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundProlonged use of GC may cause irreversible organ damage, leading to impaired quality of life and even increased mortality. However, many physicians are worried about severe flares after GC withdrawal in daily practice.ObjectivesTo assess the risk of flare in systemic lupus erythematosus (SLE) patients after low dose glucocorticoids (GC) discontinuation and evaluate the risk factors of flare.MethodsSLE patients who ever discontinued GC were identified from PKUFHS cohort. The disease flare profile after GC discontinuation were analyzed. Flare rate was analyzed using Kaplan-Meier analysis. COX regression was used to determine the effect of variables on SLE flare. A prognostic nomogram using Cox proportional hazards regression modeling were developed.Results132 SLE patients were eligible for the final analysis. They were followed up for a median (IQR) period of 21.8 (9.01, 36.7) months. The cumulative probability of flare after GC discontinuation was 8.3 % at 6 months, 16.8% at year 1 and 27.5% at year 2 (Figure 1A). In multivariate COX analysis, hypocomplementemia and serologically active clinically quiescent (SACQ) were independent risk factors of flare [HR 2.53, 95% CI (1.32, 4.88); HR 3.17, 95% CI (1.44, 6.97), respectively]. Age ≥ 40y at GC withdrawal and hydroxychloroquine usage were independent protective factors of flare [HR 0.53, 95% CI (0.29, 0.99); HR 0.32, 95% CI (0.17, 0.62), respectively] (Table 1). The protective effect of hydroxychloroquine was dosage related. From the prospective of different tapering strategies embodied as duration from prednisone 5mg/d to complete discontinuation, slower tapering strategy (12-24 months) significantly reduced the risk of flare compared to faster tapering strategy (< 3 months) [HR 0.30, 95% CI (0.11, 0.82), p=0.019]. The prognostic nomogram including aforementioned factors effectively predicted 1- and 2-year probability of flare-free (Figure 1B).Table 1.Predictors of flare by univariate and multivariate COX analysis.UnivariatepMultivariatepMultivariatepModel 1Model 2age≥40y at GC withdrawal0.59 (0.33,1.07)0.0840.53 (0.29, 0.99)0.0490.63 (0.33, 1.18)0.147Age at onset ≥18y2.03 (0.62, 6.66)0.2442.75 (0.77, 9.85)0.1212.88 (0.81, 10.2)0.103Remission duration≥60 months since the last flare0.66 (0.35, 1.27)0.2170.81 (0.41, 1.57)0.5260.73 (0.38, 1.41)0.346history of thrombocytopenia1.73 (0.94, 3.18)0.0771.36 (0.70, 2.65)0.3591.45 (0.74, 2.83)0.278history of lupus nephritis0.86 (0.47, 1.55)0.610////Hypocomplementemia1.97 (1.06, 3.66)0.0312.53 (1.32, 4.88)0.005//anti-dsDNA positive1.25 (0.70, 2.23)0.456////SACQ (both)2.91 (1.38, 6.15)0.005//3.17 (1.44, 6.97)0.004SACQ (or)1.29 (0.73, 2.30)0.380////Hydroxychloroquine or not0.29 (0.16, 0.53)<0.0010.29 (0.15, 0.56)<0.0010.32 (0.17, 0.62)0.001Immunosuppressant or not0.77 (0.40, 1.48)0.426////There was strong collinearity between hypocomplementemia and SACQ, so the two parameters were separated into two models. SACQ (both): anti-dsDNA positive and hypocomplementemia; SACQ (or): anti-dsDNA positive or hypocomplementemia; GC: glucocorticoids. Data were shown as HR (95% CI).Figure 1.ConclusionLow-dose GC is feasibly discontinued with infrequent flare in real-life setting. SACQ and younger age are potential risk factors of SLE flare, while hydroxychloroquine usage and slow GC tapering to withdrawal can reduce relapse. The visualized model we developed may help to predict risk of flare among SLE patients who discontinued GC.Disclosure of InterestsNone declared
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Gattlen C, Chriqui LE, Hao Y, Gonzalez M, Krueger T, Siankevich S, Dyson P, Cavin S, Perentes JY. The Prembion® pre-biotic improves the impact of anti-CTLA4 immune checkpoint inhibitor in a murine model of malignant pleural mesothelioma. Br J Surg 2022. [DOI: 10.1093/bjs/znac185.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Objective
Immune checkpoint inhibition (ICI) therapy has revolutionized the outcome of certain cancers such as malignant pleural mesothelioma (MPM). However, patient responsiveness to this treatment remains unpredictable. Recently, a role for the gut microbiota composition has emerged for patients to generate a robust immune response against their tumors, following immunotherapy. Here, we studied the impact of Prembion®, a pre-biotic and modulator of the gut microbiota, on tumor control and lymphocyte infiltration in a murine MPM model treated by ICI.
Methods
Prembion® (diluted into drinking water) was administrated to BALBc mice for 14 days. These animals were then inoculated orthotopically with a syngeneic MPM cell line (AB12-luc cells injected in the pleura) and followed by bioluminescence imaging. We determined the tumor growth and mouse survival in different groups: untreated control, Prembion®, IgG control, anti-PDL-1, anti-CTLA4, Prembion®+anti-PDL-1 and Prembion®+anti-CTLA4. A correlation between tumor response/animal survival and MPM infiltration with CD8+ lymphocytes was also performed by immunohistochemistry.
Results
Prembion® was well tolerated and did not affect animal weight or activity. Interestingly, Prembion® was as effective as anti-PDL1 and anti-CTLA4 monotherapy on tumor control, prolonging survival by 4.0 ± 1.1 days compared to controls (p<0.05). Moreover Prembion® potentiated anti-CTLA4 efficacy with a significant improvement in mouse survival of the Prembion®+anti-CTLA4 compared to controls (3.6 ± 1.1 days, p<0.05). Additionally, this finding correlated with enhanced MPM infiltration by CD8+ lymphocytes compared to controls (p<0.05).
Conclusion
Prembion® positively regulated the adaptive immune response against MPM and helped to improve the impact of anti-CTLA4 ICI on MPM. Further work focusing on the gut microbiome changes induced by Prembion® are ongoing to better understand the mechanisms involved.
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Affiliation(s)
- C Gattlen
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - L-E Chriqui
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - Y Hao
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - M Gonzalez
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - T Krueger
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - S Siankevich
- Embion Technologies, Embion Technologies , Etoy, Switzerland
| | - P Dyson
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - S Cavin
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - J-Y Perentes
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
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Golder V, Kandane-Rathnayake R, Louthrenoo W, Chen YH, Cho J, Lateef A, Hamijoyo L, Luo SF, Jan Wu YJ, Navarra S, Zamora L, LI Z, An Y, Sockalingam S, Katsumata Y, Harigai M, Hao Y, Zhang Z, Basnayake B, Chan M, Kikuchi J, Takeuchi T, Bae SC, O’neill S, Goldblatt F, Oon S, Gibson K, Ng K, Law A, Tugnet N, Kumar S, Tee C, Tee M, Tanaka Y, Lau CS, Nikpour M, Hoi A, Morand EF. OP0142 COMPARISON OF ATTAINMENT AND PROTECTIVE EFFECTS OF THE LUPUS LOW DISEASE ACTIVITY STATE IN PATIENTS WITH NEWLY DIAGNOSED VERSUS ESTABLISHED SLE - A MULTICENTRE PROSPECTIVE STUDY. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.3909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundLupus low disease activity state (LLDAS) attainment has been reported to be associated with reduced damage accrual, flare, and mortality, as well as improved quality of life, in cohorts of SLE patients with established disease. Whether these associations are present in recent-onset disease is less well known.ObjectivesTo evaluate the associations of LLDAS attainment with outcomes in patients with recent onset SLE.MethodsData from a 13-country longitudinal SLE cohort (ACR/SLICC criteria) were collected prospectively between 2013 and 2020 using standard templates. Organ damage and flare were captured using SLICC Damage Index and SELENA-SLEDAI Flare Index, respectively. LLDAS was defined as Golder et al., 2019 [1]. An inception cohort was defined based on duration since SLE diagnosis<1 year at enrolment. Patient characteristics between inception and non-inception cohorts were compared using Wilcoxon rank-sum (continuous variables) or Pearson’s Chi-squared tests (categorical variables). Survival analyses were performed to examine the association between LLDAS attainment and damage accrual and flare.ResultsThe study cohort included 4,106 patients of whom 680 (16%) were recruited within 1 year of SLE diagnosis (inception cohort). Compared to the non-inception cohort, inception cohort patients were significantly younger, had higher disease activity (SLEDAI-2K and physician global assessment), used more glucocorticoids and immunosuppressants but had less organ damage at enrolment and only 88 (13.6%) patients accrued damage during a median 2.2 years follow-up (Table 1).Table 1.Non-inception cohortInception cohortp-valuen=3426n=680Age at enrolment (years), median [IQR]40 [31, 51]33 [25, 44]<0.001Age at diagnosis (years), median [IQR]28 [21, 38]33 [25, 43]<0.001SLE duration at enrolment (years), median [IQR]10 [5, 16]1 [0, 1]<0.001Study duration (years), median [IQR]2.5 [1.0, 5.4]2.2 [0.9, 3.7]<0.001Females, n (%)3155 (92.1%)623 (91.6%)0.68Asian ethnicity, n (%)3037 (89.1%)595 (88.1%)0.49Prednisolone (PNL) use - ever, n (%)2865 (83.6%)620 (91.2%)<0.001Time adjusted mean (TAM)-PNL, median [IQR]5.0 [2.2, 8.6]6.2 [3.2, 10.3]<0.001Cumulative PNL (g), median [IQR]3.4 [0.5, 9.7]3.8 [1.1, 8.5]0.26Anti-Malarial use - ever, n (%)2669 (77.9%)569 (83.7%)<0.001Immunosupressant use -ever, n (%)2367 (69.1%)521 (76.6%)<0.001AMS (TAM-SLEDAI-2K), median [IQR]2.8 [1.2, 4.6]3.1 [1.6, 5.0]0.002TAM-PGA, median [IQR]0.4 [0.2, 0.7]0.4 [0.3, 0.8]<0.001Mild/moderate/severe flare ever, n (%)1789 (52.2%)391 (57.5%)0.012Organ damage accrual, n (%)629 (20.8%)88 (13.6%)<0.001LLDAS at baseline, n (%)1730 (50.5%)195 (28.7%)<0.001LLDAS-ever (at least once), n (%)2637 (78.2%)492 (73.9%)0.014≥50% time in LLDAS (LLDAS-5), n (%)1612 (50.6%)256 (41.1%)<0.001Significantly fewer inception cohort patients were in LLDAS at enrolment than the non-inception cohort (29% vs. 51%, p<0.001). However, 74% of inception and 78% of non-inception cohort patients achieved LLDAS at least once during follow-up. Limiting analysis only to patients not in LLDAS at enrolment, time to first LLDAS attainment was assessed: inception cohort patients were 60% more likely to attain their first LLDAS (HR = 1.60 (95%CI: 1.40, 1.82), p<0.001) than non-inception cohort patients. LLDAS attainment was significantly protective against flare in the inception (HR, 95% CI) and non-inception (HR, 95% CI) cohorts. Trends towards protection against damage accrual in association with LLDAS in the inception cohort were not significant.ConclusionLLDAS attainment is protective from flare in recent onset SLE. Significant protection from damage accrual was not observed, due to low rates of damage accrual in the first years after SLE diagnosis.References[1]Golder, V., et al., Lupus low disease activity state as a treatment endpoint for systemic lupus erythematosus: a prospective validation study. The Lancet Rheumatology, 2019. 1(2): p. e95-e102.AcknowledgementsWe thank all patients participating in the Asia Pacific Lupus Collaboration (APLC) cohort, and all data collectors for their ongoing support for APLC research activities.The APLC has received unrestricted project grants from AstraZeneca, BMS, Eli Lily, Janssen, Merck Serono, and UCB to support data collection contributing to this work.Disclosure of InterestsVera Golder: None declared, Rangi Kandane-Rathnayake: None declared, Worawit Louthrenoo: None declared, Yi-Hsing Chen Speakers bureau: Pfizer, Novartis, Abbvie, Johnson & Johnson, BMS, Roche, Lilly, GSK, Astra& Zeneca, Sanofi, MSD, Guigai, Astellas, Inova Diagnostics, UCB, Agnitio Science Technology, United Biopharma, Thermo Fisher, Consultant of: Pfizer, Novartis, Abbvie, Johnson & Johnson, BMS, Roche, Lilly, GSK, Astra and Zeneca, Sanofi, Guigai, Astellas, Inova Diagnostics, UCB, Agnitio Science Technology, United Biopharma, Thermo Fisher, Gilead, Grant/research support from: Yes. Clinical trials and/or research grants from Pfizer, Norvatis, BMS, Abbevie, Johnson & Johnson, Roche,Sanofi, Guigai, Roche, Boehringer Ingelheim, UCB, MSD, Astra-Zeneca,Astellas, Gilead, Jiacai Cho: None declared, Aisha Lateef: None declared, Laniyati Hamijoyo Speakers bureau: Pfizer, Novartis, Abbot, Shue Fen Luo: None declared, Yeong-Jian Jan Wu Speakers bureau: Pfizer, Lilly, Novartis, Abbvie, Sandra Navarra Speakers bureau: Pfizer, Johnson & Johnson, Novartis, Astellas, Grant/research support from: Astellas, Johnson & Johnson, Leonid Zamora: None declared, Zhanguo Li Speakers bureau: Eli, Lilly, Novartis, GSK, AbbVie, Paid instructor for: Pfizer, Roche, Johnson, Consultant of: Lilly, Pfizer, Grant/research support from: Pfizer, Yuan An: None declared, Sargunan Sockalingam Speakers bureau: Yes. Pfizer, Roche, Novartis, Grant/research support from: Roche and Novartis, Yasuhiro Katsumata Speakers bureau: Chugai Pharmaceutical Co., Ltd., Glaxo-Smithkline K.K., and Sanofi K.K., Masayoshi Harigai Speakers bureau: MH has received speaker’s fee from AbbVie Japan GK, Ayumi Pharmaceutical Co., Boehringer Ingelheim Japan, Inc.,Bristol Myers Squibb Co., Ltd., Chugai Pharmaceutical Co., Ltd., Eisai Co., Ltd., Eli Lilly Japan K.K., GlaxoSmithKline K.K., Kissei Pharmaceutical Co., Ltd., Pfizer Japan Inc., Takeda Pharmaceutical Co., Ltd., and Teijin Pharma Ltd, Consultant of: MH is a consultant for AbbVie, Boehringer-ingelheim, Bristol Myers Squibb Co., Kissei Pharmaceutical Co.,Ltd. and Teijin Pharma., Grant/research support from: MH has received research grants from AbbVie Japan GK, Asahi Kasei Corp., Astellas Pharma Inc., Ayumi Pharmaceutical Co., Bristol Myers Squibb Co., Ltd., Chugai Pharmaceutical Co., Daiichi-Sankyo, Inc.,Eisai Co., Ltd., Kissei Pharmaceutical Co., Ltd., Mitsubishi Tanabe Pharma Co., Nippon Kayaku Co., Ltd., Sekiui Medical, Shionogi & Co., Ltd., Taisho Pharmaceutical Co., Ltd., Takeda Pharmaceutical Co., Ltd., and Teijin Pharma Ltd., Yanjie Hao: None declared, Zhuoli Zhang Speakers bureau: Norvatis, GSK, Pfizer, BMDB Basnayake: None declared, Madelynn Chan Speakers bureau: AbbVie, Novartis, Consultant of: Advisory Board member for Pfizer, Eli-Lilly, Jun Kikuchi: None declared, Tsutomu Takeuchi Speakers bureau: AbbVie AYUMI Pharmaceutical Corp. Bristol-Myers Squibb Chugai Pharmaceutical Co, Ltd. Daiichi Sankyo Co., Ltd. Eisai Co., Ltd. Eli Lilly Japan, Gilead Sciences, Inc. Mitsubishi-Tanabe Pharma Corp. Pfizer Japan Inc. Sanofi K.K., Consultant of: Astellas Pharma, Inc. Chugai Pharmaceutical Co, Ltd. Eli Lilly Japan, Mitsubishi-Tanabe Pharma Corp., Grant/research support from: AbbVie Asahikasei Pharma Corp. Chugai Pharmaceutical Co, Ltd. Mitsubishi-Tanabe Pharma Corp. Sanofi K.K, Sang-Cheol Bae: None declared, Sean O’Neill Paid instructor for: Advisory board member for GSK, Fiona Goldblatt: None declared, Shereen Oon: None declared, Kathryn Gibson Speakers bureau: UCB, Consultant of: Novartis – co-chair for NSW and steering committee member for ARISE meeting Feb 2021Janssen Pharmaceuticals – advisory board, Grant/research support from: Novartis, Employee of: Eli Lilly, Kristine Ng Speakers bureau: speaker fees and advisory board (Abbvie, Novartis, Janssen), Annie Law: None declared, Nicola Tugnet: None declared, Sunil Kumar: None declared, Cherica Tee: None declared, Michael Tee: None declared, Yoshiya Tanaka Speakers bureau: Daiichi-Sankyo, Eli Lilly, Novartis, YL Biologics, Bristol-Myers, Eisai, Chugai, Abbvie, Astellas, Pfizer, Sanofi, Asahi-kasei, GSK, Mitsubishi-Tanabe, Gilead, Janssen, Grant/research support from: Daiichi-Sankyo, Eli Lilly, Novartis, YL Biologics, Bristol-Myers, Eisai, Chugai, Abbvie, Astellas, Pfizer, Sanofi, Asahi-kasei, GSK, Mitsubishi-Tanabe, Gilead, Janssen, C.S. Lau Shareholder of: Pfizer, Sanofi and Janssen, Mandana Nikpour Speakers bureau: Actelion, GSK, Janssen, Pfizer, UCB, Paid instructor for: UCB, Consultant of: Actelion, Boehringer Ingelheim, Certa Therapeutics, Eli Lilly, GSK, Janssen, Pfizer, UCB, Grant/research support from: Actelion, Astra Zeneca, BMS, GSK, Janssen, UCB, Alberta Hoi Consultant of: AH is on the advisory board for Abbvie and GSK, Grant/research support from: AH has received research support from AstraZeneca, GSK, BMS, Janssen, and Merck Serono, Eric F. Morand Speakers bureau: AstraZeneca, Paid instructor for: Eli Lilly, Consultant of: AstraZeneca, Amgen, Biogen, BristolMyersSquibb, Eli Lilly, EMD Serono, Genentech, Janssen, Grant/research support from: AstraZeneca, BristolMyersSquibb, Eli Lilly, EMD Serono, Janssen
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Zhang J, Ru J, Song J, Li H, Li X, Ma Y, Li Z, Hao Y, Chi Z, Hui D, Wan S. Increased precipitation and nitrogen addition accelerate the temporal increase in soil respiration during 8-year old-field grassland succession. Glob Chang Biol 2022; 28:3944-3959. [PMID: 35274404 DOI: 10.1111/gcb.16159] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/04/2022] [Indexed: 05/16/2023]
Abstract
Ecological succession after disturbance plays a vital role in influencing ecosystem structure and functioning. However, how global change factors regulate ecosystem carbon (C) cycling in successional plant communities remains largely elusive. As part of an 8-year (2012-2019) manipulative experiment, this study was designed to examine the responses of soil respiration and its heterotrophic component to simulated increases in precipitation and atmospheric nitrogen (N) deposition in an old-field grassland undergoing secondary succession. Over the 8-year experimental period, increased precipitation stimulated soil respiration by 11.6%, but did not affect soil heterotrophic respiration. Nitrogen addition increased both soil respiration (5.1%) and heterotrophic respiration (6.2%). Soil respiration and heterotrophic respiration linearly increased with time in the control plots, resulting from changes in soil moisture and shifts of plant community composition from grass-forb codominance to grass dominance in this old-field grassland. Compared to the control, increased precipitation significantly strengthened the temporal increase in soil respiration through stimulating belowground net primary productivity. By contrast, N addition accelerated temporal increases in both soil respiration and its heterotrophic component by driving plant community shifts and thus stimulating soil organic C. Our findings indicate that increases in water and N availabilities may accelerate soil C release during old-field grassland succession and reduce their potential positive impacts on soil C accumulation under future climate change scenarios.
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Affiliation(s)
- Jiajia Zhang
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Jingyi Ru
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Jian Song
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Heng Li
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Xiaoming Li
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Yafei Ma
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Zheng Li
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Yuanfeng Hao
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Zhensheng Chi
- School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - Shiqiang Wan
- School of Life Sciences, Henan University, Kaifeng, Henan, China
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
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Chriqui LE, Hao Y, Ortolini ME, Gattlen C, Gonzalez M, Krueger T, Perentes JY, Cavin S. Photodynamique therapy relieves tumor vascular anergy and promotes immune cell trafficking in an orthotopic mouse model of malignant pleural mesothelioma. Br J Surg 2022. [DOI: 10.1093/bjs/znac185.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Objective
Malignant pleural mesothelioma (MPM) is a deadly disease with limited treatment options. Recently, dual immune checkpoint inhibition therapy (ICI) showed improved patient survival. However, only a fraction of patients were responsive to immunotherapy. One potential mechanism of MPM resistance to ICIs could be their endothelial anergy that hampers leukocyte trafficking to the tumor bulk. Here, we hypothesized that vascular-targeted low dose photodynamic therapy (L-PDT), treatment of MPM could relieve tumor endothelial anergy and improve immunotherapy efficacy.
Methods
Using an orthotopic syngeneic MPM murine model (AB12 cells injected in the pleura of BALB/c mice), we determined the impact of L-PDT on the endothelial expression of E-Selectin, a key molecule involved in leukocyte diapedesis by immunohistochemistry. Furthermore, to confirm the role of E-selectin, we determined the extravasation of effector T cells (CD8+/CD4+) by immunostaining in L-PDT treated tumors in the presence or absence of an E-selectin blocking antibody. Finally, we assessed tumor growth/survival of our MPM murine model treated with L-PDT alone or combined to ICIs.
Results
L-PDT pre-treatment enhanced MPM endothelial E-Selectin expression in vivo. The latter was associated with increased CD4+ and CD8+ lymphocyte infiltration of MPM following L-PDT which did not occur after E-Selectin blockade. Also, L-PDT pre-treatment of MPM influenced favorably tumor control, mouse survival and the impact of ICIs compared to controls.
Conclusion
L-PDT pre-treatment relieves endothelial anergy in MPM which improves antitumor immunity and response to ICI. This approach could constitute a promising pre-treatment option, in combination with ICIs, for the management of this deadly disease.
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Affiliation(s)
- L E Chriqui
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - Y Hao
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - M E Ortolini
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - C Gattlen
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - M Gonzalez
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - T Krueger
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - J-Y Perentes
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
| | - S Cavin
- Department of Thoracic Surgery, Lausanne University Hospital , Lausanne, Switzerland
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Fernández I, T. Mozanzadeh M, Hao Y, Gisbert E. Editorial: Physiological Impacts of Global Warming in Aquatic Organisms. Front Physiol 2022; 13:914912. [PMID: 35615676 PMCID: PMC9125242 DOI: 10.3389/fphys.2022.914912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- I. Fernández
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO), Vigo, Spain
| | - M. T. Mozanzadeh
- South Iran Aquaculture Research Centre, Iranian Fisheries Science Institute (IFSRI), Agricultural Research Education and Extension Organization (AREEO), Ahwaz, Iran
| | - Y. Hao
- Institute of Hydrobiology, Chinese Academy of Sciences (CAS), Wuhan, China
| | - E. Gisbert
- Aquaculture Program, Institut de Recerca i Tecnología Agroalimentaries (IRTA), La Rápita, Spain
- *Correspondence: E. Gisbert,
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Chaudhry N, Muhammad H, Seidl C, Downes D, Young DA, Hao Y, Zhu L, Vincent TL. Highly efficient CRISPR-Cas9-mediated editing identifies novel mechanosensitive microRNA-140 targets in primary human articular chondrocytes. Osteoarthritis Cartilage 2022; 30:596-604. [PMID: 35074547 PMCID: PMC8987936 DOI: 10.1016/j.joca.2022.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE MicroRNA 140 (miR-140) is a chondrocyte-specific endogenous gene regulator implicated in osteoarthritis (OA). As mechanical injury is a primary aetiological factor in OA, we investigated miR-140-dependent mechanosensitive gene regulation using a novel CRISPR-Cas9 methodology in primary human chondrocytes. METHOD Primary (passage 1/2) human OA chondrocytes were isolated from arthroplasty samples (six donors) and transfected with ribonuclear protein complexes or plasmids using single guide RNAs (sgRNAs) targeting miR-140, in combination with Cas9 endonuclease. Combinations of sgRNAs and single/double transfections were tested. Gene editing was measured by T7 endonuclease 1 (T7E1) assay. miRNA levels were confirmed by qPCR in chondrocytes and in wild type murine femoral head cartilage after acute injury. Predicted close match off-targets were examined. Mechanosensitive miR-140 target validation was assessed in 42 injury-associated genes using TaqMan Microfluidic cards in targeted and donor-matched control chondrocytes. Identified targets were examined in RNAseq data from costal chondrocytes from miR-140-/- mice. RESULTS High efficiency gene editing of miR-140 (90-98%) was obtained when two sgRNAs were combined with double RNP-mediated CRISPR-Cas9 transfection. miR-140 levels fell rapidly after femoral cartilage injury. Of the top eight miR-140 gene targets identified (P < 0.01), we validated three previously identified ones (septin 2, bone morphogenetic protein 2 and fibroblast growth factor 2). Novel targets included Agrin, a newly recognised pro-regenerative cartilage agent, and proteins associated with retinoic acid signalling and the primary cilium. CONCLUSION We describe a highly efficient CRISPR-Cas9-mediated strategy for gene editing in primary human chondrocytes and identify several novel mechanosensitive miR-140 targets of disease relevance.
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Affiliation(s)
- N Chaudhry
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY, United Kingdom
| | - H Muhammad
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY, United Kingdom
| | - C Seidl
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY, United Kingdom
| | - D Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, United Kingdom
| | - D A Young
- Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - Y Hao
- Skeletal Research Group, Biosciences Institute, Newcastle University, Central Parkway, Newcastle Upon Tyne, NE1 3BZ, United Kingdom
| | - L Zhu
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY, United Kingdom
| | - T L Vincent
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, OX3 7FY, United Kingdom.
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Dong Y, Xu D, Xu X, Ren Y, Gao F, Song J, Jia A, Hao Y, He Z, Xia X. Fine mapping of QPm.caas-3BS, a stable QTL for adult-plant resistance to powdery mildew in wheat (Triticum aestivum L.). Theor Appl Genet 2022; 135:1083-1099. [PMID: 35006334 DOI: 10.1007/s00122-021-04019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
A stable QTL QPm.caas-3BS for adult-plant resistance to powdery mildew was mapped in an interval of 431 kb, and candidate genes were predicted based on gene sequences and expression profiles. Powdery mildew is a devastating foliar disease occurring in most wheat-growing areas. Characterization and fine mapping of genes for powdery mildew resistance can benefit marker-assisted breeding. We previously identified a stable quantitative trait locus (QTL) QPm.caas-3BS for adult-plant resistance to powdery mildew in a recombinant inbred line population of Zhou8425B/Chinese Spring by phenotyping across four environments. Using 11 heterozygous recombinants and high-density molecular markers, QPm.caas-3BS was delimited in a physical interval of approximately 3.91 Mb. Based on re-sequenced data and expression profiles, three genes TraesCS3B02G014800, TraesCS3B02G016800 and TraesCS3B02G019900 were associated with the powdery mildew resistance locus. Three gene-specific kompetitive allele-specific PCR (KASP) markers were developed from these genes and validated in the Zhou8425B derivatives and Zhou8425B/Chinese Spring population in which the resistance gene was mapped to a 0.3 cM interval flanked by KASP14800 and snp_50465, corresponding to a 431 kb region at the distal end of chromosome 3BS. Within the interval, TraesCS3B02G014800 was the most likely candidate gene for QPm.caas-3BS, but TraesCS3B02G016300 and TraesCS3B02G016400 were less likely candidates based on gene annotations and sequence variation between the parents. These results not only offer high-throughput KASP markers for improvement of powdery mildew resistance but also pave the way to map-based cloning of the resistance gene.
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Affiliation(s)
- Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- Shandong Provincial Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Xiaowan Xu
- College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yan Ren
- College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan, China
| | - Fengmei Gao
- Institute of Crop Germplasm Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Aolin Jia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Sun X, Hao Y, Emeis J, Steitz M, Breitenstein-Attach A, Berger F, Schmitt B, Kiekenap JF. Four-Dimensional Computed Tomography–Guided Valve Sizing for Transcatheter Pulmonary Valve Replacement. Thorac Cardiovasc Surg 2022. [DOI: 10.1055/s-0042-1742979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- X. Sun
- Charité – Universitätsmedizin Berlin, Deutsches Herzzentrum Berlin, Berlin, Deutschland
| | - Y. Hao
- Charité – Universitätsmedizin Berlin, Deutsches Herzzentrum Berlin, Berlin, Deutschland
| | - J. Emeis
- Charité – Universitätsmedizin Berlin, Berlin, Deutschland
| | - M. Steitz
- German Heart Institute Berlin, Berlin, Deutschland
| | | | - F. Berger
- Charité – Universitätsmedizin Berlin, Deutsches Herzzentrum Berlin, Berlin, Deutschland
| | - B. Schmitt
- Charité – Universitätsmedizin Berlin, Deutsches Herzzentrum Berlin, Berlin, Deutschland
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