|
1
|
Wang J, Yang H, Chen S, Li W, Yu J, Hu Z, Zhuo Y, Huang Q, Liu Z, Zhou L, Wu J, Wang Z, Guo F, Yun P, Wang X, Liu JF. Genome-wide association study reveals candidate genes for pollution excreta traits in pigs. Anim Genet 2023. [PMID: 37040927 DOI: 10.1111/age.13323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/13/2022] [Accepted: 03/18/2023] [Indexed: 04/13/2023]
Abstract
Excreta traits comprise a very important characteristic in breeding that have been neglected for a long time. With the growth of intensive pig farming, plenty of environment problems have been raised, and people have begun to pay attention to pig excreta behaviors from genetics and breeding perspectives. However, the genetic architecture of excreta traits remains unclear. To investigate the genetic architecture of excreta traits in pigs, eight excreta traits and feed conversion ratio (FCR) were analyzed in this study. We performed genome-wide association studies (GWASs) on 213 Yorkshire pigs and estimated genetic parameters for a total number of 290 pigs, comprising 213 Yorkshire, 52 Landrace and 25 Duroc. After analysis, eight and 22 genome-wide significant SNPs were detected for FCR and the eight excreta traits in single-trait GWASs separately, and 18 were detected in a multi-trait meta-analysis for excreta traits, six of which were detected in both the single-trait and the multi-trait GWAS. Eighty, 182 and 133 genes were detected within 1 Mb of the genome-wide significant SNPs for FCR, excreta traits and multi-trait meta-analysis, respectively. Five candidate genes (BCKDC, DBT, ANKRD7, SHPRH and HCRT) with biochemical and physiological effects relevant to feed efficiency and excreta traits might be interesting markers for future breeding. Meanwhile, functional enrichment analysis indicates that most of the significant pathways are associated with the glutathione catabolic process, DNA topological change and replication fork protection complex. This study reveals the architecture of excreta traits in commercial pigs and offers an opportunity for decreasing the pollution from excreta using genomic selection in pigs.
Collapse
Affiliation(s)
- Junjian Wang
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huawei Yang
- Shenzhen Kingsino Technology Co., Ltd., 518107, Shenzhen, No.18 Guangdian North Rd, High-Tech Industrial Park, Guangming District, China
| | - Shaokang Chen
- Beijing General Station of Animal Husbandry, 100107, Beijing, China
| | - Weining Li
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Yu
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengzheng Hu
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yue Zhuo
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qianqian Huang
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Liu
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianliang Wu
- Beijing Zhongyu Pig Breeding Co. Ltd., 100194, Beijing, China
| | - Zhaojun Wang
- Beijing Zhongyu Pig Breeding Co. Ltd., 100194, Beijing, China
| | - Feng Guo
- Beijing General Station of Animal Husbandry, 100107, Beijing, China
| | - Peng Yun
- Beijing General Station of Animal Husbandry, 100107, Beijing, China
| | - Xiaofeng Wang
- Beijing General Station of Animal Husbandry, 100107, Beijing, China
| | - Jian-Feng Liu
- State Key Laboratory of animal Biotech Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
|
2
|
Kim HJ, Kim B, Byun HJ, Yu L, Nguyen TM, Nguyen TH, Do PA, Kim EJ, Cheong KA, Kim KS, Huy Phùng H, Rahman M, Jang JY, Rho SB, Kang GJ, Park MK, Lee H, Lee K, Cho J, Han HK, Kim SG, Lee AY, Lee CH. Resolvin D1 Suppresses H 2O 2-Induced Senescence in Fibroblasts by Inducing Autophagy through the miR-1299/ARG2/ARL1 Axis. Antioxidants (Basel) 2021; 10:1924. [PMID: 34943028 PMCID: PMC8750589 DOI: 10.3390/antiox10121924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 11/28/2021] [Indexed: 12/15/2022] Open
Abstract
ARG2 has been reported to inhibit autophagy in vascular endothelial cells and keratinocytes. However, studies of its mechanism of action, its role in skin fibroblasts, and the possibility of promoting autophagy and inhibiting cellular senescence through ARG2 inhibition are lacking. We induced cellular senescence in dermal fibroblasts by using H2O2. H2O2-induced fibroblast senescence was inhibited upon ARG2 knockdown and promoted upon ARG2 overexpression. The microRNA miR-1299 suppressed ARG2 expression, thereby inhibiting fibroblast senescence, and miR-1299 inhibitors promoted dermal fibroblast senescence by upregulating ARG2. Using yeast two-hybrid assay, we found that ARG2 binds to ARL1. ARL1 knockdown inhibited autophagy and ARL1 overexpression promoted it. Resolvin D1 (RvD1) suppressed ARG2 expression and cellular senescence. These data indicate that ARG2 stimulates dermal fibroblast cell senescence by inhibiting autophagy after interacting with ARL1. In addition, RvD1 appears to promote autophagy and inhibit dermal fibroblast senescence by inhibiting ARG2 expression. Taken together, the miR-1299/ARG2/ARL1 axis emerges as a novel mechanism of the ARG2-induced inhibition of autophagy. Furthermore, these results indicate that miR-1299 and pro-resolving lipids, including RvD1, are likely involved in inhibiting cellular senescence by inducing autophagy.
Collapse
Affiliation(s)
- Hyun Ji Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Boram Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Hyung Jung Byun
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Lu Yu
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Tuan Minh Nguyen
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Thi Ha Nguyen
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Phuong Anh Do
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Eun Ji Kim
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Kyung Ah Cheong
- Department of Dermatology, Dongguk University Ilsan Hospital, 814 Siksa-dong, Ilsandong-gu, Goyang-si 10326, Korea; (K.A.C.); (G.J.K.); (A.Y.L.)
| | - Kyung Sung Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Hiệu Huy Phùng
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Mostafizur Rahman
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Ji Yun Jang
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
- National Cancer Center, Goyang 10408, Korea; (S.B.R.); (H.L.)
| | - Seung Bae Rho
- National Cancer Center, Goyang 10408, Korea; (S.B.R.); (H.L.)
| | - Gyeoung Jin Kang
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Mi Kyung Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
- National Cancer Center, Goyang 10408, Korea; (S.B.R.); (H.L.)
| | - Ho Lee
- National Cancer Center, Goyang 10408, Korea; (S.B.R.); (H.L.)
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Jungsook Cho
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Hyo Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Sang Geon Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| | - Ai Young Lee
- Department of Dermatology, Dongguk University Ilsan Hospital, 814 Siksa-dong, Ilsandong-gu, Goyang-si 10326, Korea; (K.A.C.); (G.J.K.); (A.Y.L.)
| | - Chang Hoon Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Seoul 04620, Korea; (H.J.K.); (B.K.); (H.J.B.); (L.Y.); (T.M.N.); (T.H.N.); (P.A.D.); (K.S.K.); (H.H.P.); (M.R.); (J.Y.J.); (M.K.P.); (K.L.); (J.C.); (H.K.H.); (S.G.K.)
| |
Collapse
|
|
3
|
LW1497, an Inhibitor of Malate Dehydrogenase, Suppresses TGF-β1-Induced Epithelial-Mesenchymal Transition in Lung Cancer Cells by Downregulating Slug. Antioxidants (Basel) 2021; 10:antiox10111674. [PMID: 34829545 PMCID: PMC8615288 DOI: 10.3390/antiox10111674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/15/2021] [Accepted: 10/16/2021] [Indexed: 01/01/2023] Open
Abstract
LW1497 suppresses the expression of the hypoxia-inducing factor (HIF)-1α inhibiting malate dehydrogenase. Although hypoxia and HIF-1α are known to be important in cancer, LW1497 has not been therapeutically applied to cancer yet. Thus, we investigated the effect of LW1497 on the epithelial-mesenchymal transition (EMT) of lung cancer cells. A549 and H1299 lung cancer cells were induced to undergo via TGF-β1 treatment, resulting in the downregulation of E-cadherin and upregulation of N-cadherin and Vimentin concurrently with increases in the migration and invasion capacities of the cells. These effects of TGF-β1 were suppressed upon co-treatment of the cells with LW1497. An RNA-seq analysis revealed that LW1497 induced differential expression of genes related to hypoxia, RNA splicing, angiogenesis, cell migration, and metastasis in the A549 lung cancer cell lines. We confirmed the differential expression of Slug, an EMT-related transcription factor. Results from Western blotting and RT-PCR confirmed that LW1497 inhibited the expression of EMT markers and Slug. After orthotopically transplanting A549 cancer cells into mice, LW1497 was administered to examine whether the lung cancer progression was inhibited. We observed that LW1497 reduced the area of cancer. In addition, the results from immunohistochemical analyses showed that LW1497 downregulated EMT markers and Slug. In conclusion, LW1497 suppresses cancer progression through the inhibition of EMT by downregulating Slug.
Collapse
|
|
4
|
Xu M, Li J, Xiao Z, Lou J, Pan X, Ma Y. Integrative genomics analysis identifies promising SNPs and genes implicated in tuberculosis risk based on multiple omics datasets. Aging (Albany NY) 2020; 12:19173-19220. [PMID: 33051402 PMCID: PMC7732298 DOI: 10.18632/aging.103744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023]
Abstract
More than 10 GWASs have reported numerous genetic loci associated with tuberculosis (TB). However, the functional effects of genetic variants on TB remains largely unknown. In the present study, by combining a reported GWAS summary dataset (N = 452,264) with 3 independent eQTL datasets (N = 2,242) and other omics datasets downloaded from public databases, we conducted an integrative genomics analysis to highlight SNPs and genes implicated in TB risk. Based on independent biological and technical validations, we prioritized 26 candidate genes with eSNPs significantly associated with gene expression and TB susceptibility simultaneously; such as, CDC16 (rs7987202, rs9590408, and rs948182) and RCN3 (rs2946863, rs2878342, and rs3810194). Based on the network-based enrichment analysis, we found these 26 highlighted genes were jointly connected to exert effects on TB susceptibility. The co-expression patterns among these 26 genes were remarkably changed according to Mycobacterium tuberculosis (MTB) infection status. Based on 4 independent gene expression datasets, 21 of 26 genes (80.77%) showed significantly differential expressions between TB group and control group in mesenchymal stem cells, mice blood and lung tissues, as well as human alveolar macrophages. Together, we provide robust evidence to support 26 highlighted genes as important candidates for TB.
Collapse
Affiliation(s)
- Mengqiu Xu
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Jingjing Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China
| | - Zhaoying Xiao
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Jiongpo Lou
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Xinrong Pan
- Department of Infectious Diseases, Shengzhou People’s Hospital, The First Affiliated Hospital of Zhejiang University Shengzhou Branch, Shengshou 312400, Zhejiang, China
| | - Yunlong Ma
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China,School of Biomedical Engineering, School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| |
Collapse
|
|
5
|
Role of Sphingosylphosphorylcholine in Tumor and Tumor Microenvironment. Cancers (Basel) 2019; 11:cancers11111696. [PMID: 31683697 PMCID: PMC6896196 DOI: 10.3390/cancers11111696] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 12/25/2022] Open
Abstract
Sphingosylphosphorylcholine (SPC) is a unique type of lysosphingolipid found in some diseases, and has been studied in cardiovascular, neurological, and inflammatory phenomena. In particular, SPC’s studies on cancer have been conducted mainly in terms of effects on cancer cells, and relatively little consideration has been given to aspects of tumor microenvironment. This review summarizes the effects of SPC on cancer and tumor microenvironment, and presents the results and prospects of modulators that regulate the various actions of SPC.
Collapse
|