|
1
|
Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare disease research resources at the Rat Genome Database. Genetics 2023; 224:iyad078. [PMID: 37119810 PMCID: PMC10411567 DOI: 10.1093/genetics/iyad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Rare diseases individually affect relatively few people, but as a group they impact considerable numbers of people. The Rat Genome Database (https://rgd.mcw.edu) is a knowledgebase that offers resources for rare disease research. This includes disease definitions, genes, quantitative trail loci (QTLs), genetic variants, annotations to published literature, links to external resources, and more. One important resource is identifying relevant cell lines and rat strains that serve as models for disease research. Diseases, genes, and strains have report pages with consolidated data, and links to analysis tools. Utilizing these globally accessible resources for rare disease research, potentiating discovery of mechanisms and new treatments, can point researchers toward solutions to alleviate the suffering of those afflicted with these diseases.
Collapse
Affiliation(s)
- Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Joint Department of Biomedical Engineering, Marquette University & Medical College of Wisconsin, Milwaukee, WI 53226, USA
| |
Collapse
|
|
2
|
Shu B, Fang Y, He W, Yang J, Dai C. Identification of macrophage-related candidate genes in lupus nephritis using bioinformatics analysis. Cell Signal 2018; 46:43-51. [PMID: 29458096 DOI: 10.1016/j.cellsig.2018.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 01/02/2023]
Abstract
Lupus nephritis (LN) is a chronic autoimmune disorder. Here we try to identify the candidate genes in macrophages related to LN. We performed a systematic search in the Gene Expression Omnibus (GEO) database for microarray in human mononuclear cells and mouse macrophages of LN. The results of clustering and venn analysis of different GEO datasets showed that 8 genes were up-regulated and 2 genes down-regulated in samples from both human and mouse LN. The data from gene network and GO analysis revealed that CD38 and CCL2 were localized in the core of the network. Immunofluorescence staining showed that CD38 expression was markedly increased in macrophages from kidneys with LN. Our study identifies the gene expression profile for macrophages and demonstrated the induction of CCL2 and CD38 in macrophages from patients with LN. However, regarding the limited patient number included in this study, the results are preliminary and more studies are still needed to further decipher the macrophage-related candidate genes for the pathogenesis of LN.
Collapse
Affiliation(s)
- Bingyan Shu
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Yi Fang
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Weichun He
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Junwei Yang
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Chunsun Dai
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China.
| |
Collapse
|