1
|
Mak ACY, Sajuthi S, Joo J, Xiao S, Sleiman PM, White MJ, Lee EY, Saef B, Hu D, Gui H, Keys KL, Lurmann F, Jain D, Abecasis G, Kang HM, Nickerson DA, Germer S, Zody MC, Winterkorn L, Reeves C, Huntsman S, Eng C, Salazar S, Oh SS, Gilliland FD, Chen Z, Kumar R, Martínez FD, Wu AC, Ziv E, Hakonarson H, Himes BE, Williams LK, Seibold MA, Burchard EG. Lung Function in African American Children with Asthma Is Associated with Novel Regulatory Variants of the KIT Ligand KITLG/SCF and Gene-By-Air-Pollution Interaction. Genetics 2020; 215:869-886. [PMID: 32327564 PMCID: PMC7337089 DOI: 10.1534/genetics.120.303231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/22/2020] [Indexed: 01/12/2023] Open
Abstract
Baseline lung function, quantified as forced expiratory volume in the first second of exhalation (FEV1), is a standard diagnostic criterion used by clinicians to identify and classify lung diseases. Using whole-genome sequencing data from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine project, we identified a novel genetic association with FEV1 on chromosome 12 in 867 African American children with asthma (P = 1.26 × 10-8, β = 0.302). Conditional analysis within 1 Mb of the tag signal (rs73429450) yielded one major and two other weaker independent signals within this peak. We explored statistical and functional evidence for all variants in linkage disequilibrium with the three independent signals and yielded nine variants as the most likely candidates responsible for the association with FEV1 Hi-C data and expression QTL analysis demonstrated that these variants physically interacted with KITLG (KIT ligand, also known as SCF), and their minor alleles were associated with increased expression of the KITLG gene in nasal epithelial cells. Gene-by-air-pollution interaction analysis found that the candidate variant rs58475486 interacted with past-year ambient sulfur dioxide exposure (P = 0.003, β = 0.32). This study identified a novel protective genetic association with FEV1, possibly mediated through KITLG, in African American children with asthma. This is the first study that has identified a genetic association between lung function and KITLG, which has established a role in orchestrating allergic inflammation in asthma.
Collapse
Affiliation(s)
- Angel C Y Mak
- Department of Medicine, University of California, San Francisco, California 94143
| | - Satria Sajuthi
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206
| | - Jaehyun Joo
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan 48202
| | - Patrick M Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania, 19104
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Marquitta J White
- Department of Medicine, University of California, San Francisco, California 94143
| | - Eunice Y Lee
- Department of Medicine, University of California, San Francisco, California 94143
| | - Benjamin Saef
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, California 94143
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan 48202
| | - Kevin L Keys
- Department of Medicine, University of California, San Francisco, California 94143
- Berkeley Institute for Data Science, University of California, Berkeley, California 94720
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, Washington 98195
| | - Gonçalo Abecasis
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109
| | - Hyun Min Kang
- Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Northwest Genomics Center, Seattle, Washington, 98195
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195
| | | | | | | | | | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, California 94143
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, California 94143
| | - Sandra Salazar
- Department of Medicine, University of California, San Francisco, California 94143
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, California 94143
| | - Frank D Gilliland
- Department of Preventive Medicine, Division of Environmental Health, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Zhanghua Chen
- Department of Preventive Medicine, Division of Environmental Health, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611
| | - Fernando D Martínez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona 85721
| | - Ann Chen Wu
- Precision Medicine Translational Research (PRoMoTeR) Center, Department of Population Medicine, Harvard Medical School and Pilgrim Health Care Institute, Boston, Massachusetts 02215
| | - Elad Ziv
- Department of Medicine, University of California, San Francisco, California 94143
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania, 19104
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - L Keoki Williams
- Center for Individualized and Genomic Medicine Research, Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan 48202
| | - Max A Seibold
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, California 94143
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143
| |
Collapse
|
2
|
Navas LE, Martínez FD, Taverna ME, Fetherolf MM, Eltis LD, Nicolau V, Estenoz D, Campos E, Benintende GB, Berretta MF. A thermostable laccase from Thermus sp. 2.9 and its potential for delignification of Eucalyptus biomass. AMB Express 2019; 9:24. [PMID: 30756202 PMCID: PMC6372703 DOI: 10.1186/s13568-019-0748-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 11/25/2022] Open
Abstract
Laccases are multicopper oxidases that are being studied for their potential application in pretreatment strategies of lignocellulosic feedstocks for bioethanol production. Here, we report the expression and characterization of a predicted laccase (LAC_2.9) from the thermophilic bacterial strain Thermus sp. 2.9 and investigate its capacity to delignify lignocellulosic biomass. The purified enzyme displayed a blue color typical of laccases, showed strict copper dependence and retained 80% of its activity after 16 h at 70 °C. At 60 °C, the enzyme oxidized 2,2′-azino-di-(3-ethylbenzthiazoline sulfonate) (ABTS) and 2,6-dimethoxyphenol (DMP) at optimal pH of 5 and 6, respectively. LAC_2.9 had higher substrate specificity (kcat/KM) for DMP with a calculated value that accounts for one of the highest reported for laccases. Further, the enzyme oxidized a phenolic lignin model dimer. The incubation of steam-exploded eucalyptus biomass with LAC_2.9 and 1-hydroxybenzotriazole (HBT) as mediator changed the structural properties of the lignocellulose as evidenced by Fourier transform infrared (FTIR) spectroscopy and thermo-gravimetric analysis (TGA). However, this did not increase the yield of sugars released by enzymatic saccharification. In conclusion, LAC_2.9 is a thermostable laccase with potential application in the delignification of lignocellulosic biomass.
Collapse
|