1
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You Y, Bai C, Wang W, Zhan T, Hu X, Hao F, Xia M, Liu Y, Ma T, Liu Y, Zheng C, Pu T, Zhang Y, Lu Y, Ding N, Li J, Yin Y, Chen Y, Wang L, Zhou J, Niu L, Xiu Y, Lu Y, Jia T, Liu X, Zhang C. Comparative proteomics in captive giant pandas to identify proteins involved in age-related cataract formation. Sci Rep 2023; 13:12722. [PMID: 37543644 PMCID: PMC10404263 DOI: 10.1038/s41598-023-40003-0] [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: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Approximately 20% of aged captive giant pandas (Ailuropoda melanoleuca) have cataracts that impair their quality of life. To identify potential biomarkers of cataract formation, we carried out a quantitative proteomics analysis of 10 giant pandas to find proteins differing in abundance between healthy and cataract-bearing animals. We identified almost 150 proteins exceeding our threshold for differential abundance, most of which were associated with GO categories related to extracellular localization. The most significant differential abundance was associated with components of the proteasome and other proteins with a role in proteolysis or its regulation, most of which were depleted in pandas with cataracts. Other modulated proteins included components of the extracellular matrix or cytoskeleton, as well as associated signaling proteins and regulators, but we did not find any differentially expressed transcription factors. These results indicate that the formation of cataracts involves a complex post-transcriptional network of signaling inside and outside lens cells to drive stress responses as a means to address the accumulation of protein aggregates triggered by oxidative damage. The modulated proteins also indicate that it should be possible to predict the onset of cataracts in captive pandas by taking blood samples and testing them for the presence or absence of specific protein markers.
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Affiliation(s)
- Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | - Chao Bai
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wei Wang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Tongtong Zhan
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Xin Hu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | | | - Yan Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Tao Ma
- Beijing Zoo, Beijing, China
| | | | | | | | | | | | | | | | | | - Yucun Chen
- Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China
| | | | | | | | - Yunfang Xiu
- Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China
| | - Yan Lu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | | | | | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
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2
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Li P, Chen J, Zhu C, Pan Z, Li Q, Wei H, Wang G, Cheng W, Fu B, Sun Y. DNA Methylation Difference between Female and Male Ussuri Catfish ( Pseudobagrus ussuriensis) in Brain and Gonad Tissues. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060874. [PMID: 35743904 PMCID: PMC9228513 DOI: 10.3390/life12060874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/27/2022]
Abstract
DNA methylation has been found to be involved in sex determination and differentiation in many aquaculture species. The Ussuri catfish (Pseudobagrus ussuriensis) is a popular aquaculture fish in China with high economic value in which male-biased sex dimorphism was observed in terms of body size and body weight. In this study, DNA methylation-sensitive RAD sequencing (Methyl-RAD) was used to explore the epigenetic difference between adult male and female samples in brain and gonad tissues. In brain tissues, 5,442,496 methylated cytosine sites were found and 9.94% of these sites were from symmetric CCGG or CCWGG sites. Among these sites, 321 differential DNA methylation sites (DMSs) in 171 genes were identified, while in gonad tissues, 4,043,053 methylated cytosines sites were found in total and 11.70% of them were from CCGG or CCWGG. Among these sites, 78 differential DNA methylation sites were found which were located in 64 genes. We also found several sex-determination genes among these differential methylated genes, such as amh, gsdf and hsd11b2 in brain tissues and slco3a1, socs2 and trim47 in gonad tissues. These results provided evidence for understanding the function of DNA methylation in the sex differentiation in Pseudobagrus ussuriensis, which further deepens the relationship between gene regulation and epigenetics.
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Affiliation(s)
- Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
| | - Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
| | - Chuankun Zhu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian 223300, China; (C.Z.); (Z.P.)
| | - Zhengjun Pan
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Jiangsu Engineering Laboratory for Breeding of Special Aquatic Organisms, Huaiyin Normal University, Huaian 223300, China; (C.Z.); (Z.P.)
| | - Qing Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
| | - Huijie Wei
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
| | - Guiying Wang
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
| | - Weiwei Cheng
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
| | - Beide Fu
- Ruibiao (Wuhan) Biotechnology Co., Ltd., Wuhan 430074, China;
| | - Yanhong Sun
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China; (P.L.); (J.C.); (Q.L.); (H.W.); wh (G.W.); (W.C.)
- Correspondence:
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3
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You Y, Bai C, Liu X, Lu Y, Jia T, Xia M, Yin Y, Wang W, Chen Y, Zhang C, Liu Y, Wang L, Pu T, Ma T, Liu Y, Zhou J, Niu L, Xu S, Ni Y, Hu X, Zhang Z. RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation. BMC Genom Data 2021; 22:44. [PMID: 34706646 PMCID: PMC8555103 DOI: 10.1186/s12863-021-00996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is an endangered mammalian species native to China. Fewer than 2500 giant pandas are known to exist, many of which are bred in captivity as a means to preserve and repopulate the species. Like other captive mammals, giant pandas acquire age-related cataracts, reducing their quality of life. Recent comparative genome-wide methylation analysis revealed 110 differentially methylated genes associated with cataract formation including six also associated with the formation of age-related cataracts in humans. RESULTS To investigate the pathological pathway in greater detail, here we used RNA-Seq analysis to investigate the differential expression profiles of genes in three giant pandas with cataracts and three healthy controls. We identified more than 700 differentially expressed genes, 29 of which were selected for further analysis based on their low q-value. We found that many of the genes encoded regulatory and signaling proteins associated with the control of cell growth, migration, differentiation and apoptosis, supporting previous research indicating a key role for apoptosis in cataract formation. CONCLUSION The identification of genes involved in the formation of age-related cataracts could facilitate the development of predictive markers, preventative measures and even new therapies to improve the life of captive animals.
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Affiliation(s)
- Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | - Chao Bai
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | - Yan Lu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | | | | | - Wei Wang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Yucun Chen
- Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Yan Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | | | - Tao Ma
- Beijing Zoo, Beijing, China
| | | | | | | | - Suhui Xu
- Strait (Fuzhou) Giant Panda Research and Exchange Centers, Fuzhou, China
| | | | - Xin Hu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
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4
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A novel missense mutation in the HSF4 gene of giant pandas with senile congenital cataracts. Sci Rep 2021; 11:5411. [PMID: 33686159 PMCID: PMC7940430 DOI: 10.1038/s41598-021-84741-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 02/16/2021] [Indexed: 11/23/2022] Open
Abstract
Cataracts are a common cause of visual impairment and blindness in mammals. They are usually associated with aging, but approximately one third of cases have a significant genetic component. Cataracts are increasingly prevalent among aging populations of captive giant pandas (Ailuropoda melanoleuca) and it is therefore important to identify genetic determinants that influence the likelihood of cataract development in order to distinguish between congenital and age-related disease. Here we screened for cataract-related genetic effects using a functional candidate gene approach combined with bioinformatics to identify the underlying genetic defect in a giant panda with congenital cataracts. We identified a missense mutation in exon 10 of the HSF4 gene encoding heat shock transcription factor 4. The mutation causes the amino acid substitution R377W in a highly conserved segment of the protein between the isoform-specific and downstream hydrophobic regions. Predictive modeling revealed that the substitution is likely to increase the hydrophobicity of the protein and disrupt interactions with spatially adjacent amino acid side chains. The mutation was not found in 13 unaffected unrelated animals but was found in an unrelated animal also diagnosed with senile congenital cataract. The novel missense mutation in the HSF4 gene therefore provides a potential new genetic determinant that could help to predict the risk of cataracts in giant pandas.
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Bai C, You Y, Liu X, Xia M, Wang W, Jia T, Pu T, Lu Y, Zhang C, Li X, Yin Y, Wang L, Zhou J, Niu L. A novel missense mutation in the gene encoding major intrinsic protein (MIP) in a Giant panda with unilateral cataract formation. BMC Genomics 2021; 22:100. [PMID: 33530927 PMCID: PMC7856726 DOI: 10.1186/s12864-021-07386-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 11/20/2022] Open
Abstract
Background Cataracts are defects of the lens that cause progressive visual impairment and ultimately blindness in many vertebrate species. Most cataracts are age-related, but up to one third have an underlying genetic cause. Cataracts are common in captive zoo animals, but it is often unclear whether these are congenital or acquired (age-related) lesions. Results Here we used a functional candidate gene screening approach to identify mutations associated with cataracts in a captive giant panda (Ailuropoda melanoleuca). We screened 11 genes often associated with human cataracts and identified a novel missense mutation (c.686G > A) in the MIP gene encoding major intrinsic protein. This is expressed in the lens and normally accumulates in the plasma membrane of lens fiber cells, where it plays an important role in fluid transport and cell adhesion. The mutation causes the replacement of serine with asparagine (p.S229N) in the C-terminal tail of the protein, and modeling predicts that the mutation induces conformational changes that may interfere with lens permeability and cell–cell interactions. Conclusion The c.686G > A mutation was found in a captive giant panda with a unilateral cataract but not in 18 controls from diverse regions in China, suggesting it is most likely a genuine disease-associated mutation rather than a single-nucleotide polymorphism. The mutation could therefore serve as a new genetic marker to predict the risk of congenital cataracts in captive giant pandas. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07386-8.
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Affiliation(s)
- Chao Bai
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Yuyan You
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China.
| | - Xuefeng Liu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | - Wei Wang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Ting Jia
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | - Yan Lu
- Beijing Zoo, Beijing, China
| | - Chenglin Zhang
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | | | | | | | - Jun Zhou
- , Chongqing Zoo, Chongqing, China
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6
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Huang X, Ouyang Q, Ran M, Zeng B, Deng L, Hu S, Yang M, Li G, Deng T, He M, Li T, Yang H, Zhang G, Zhang H, Zeng C, Wang J. The immune and metabolic changes with age in giant panda blood by combined transcriptome and DNA methylation analysis. Aging (Albany NY) 2020; 12:21777-21797. [PMID: 33188156 DOI: 10.18632/aging.103990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/14/2020] [Indexed: 11/25/2022]
Abstract
Giant panda (Ailuropoda melanoleuca) is an endangered mammalian species. Exploring immune and metabolic changes that occur in giant pandas with age is important for their protection. In this study, we systematically investigated the physiological and biochemical indicators in blood, as well as the transcriptome, and methylation profiles of young, adult, and old giant pandas. The white blood cell (WBC), neutrophil (NEU) counts and hemoglobin (HGB) concentrations increased significantly with age (young to adult), and some indicators related to blood glucose and lipids also changed significantly with age. In the transcriptome analysis, differentially expressed genes (DEGs) were found in comparisons of the young and adult (257), adult and old (20), young and old (744) groups. Separation of the DEGs into eight profiles according to the expression trend using short time-series expression miner (STEM) software revealed that most DEGs were downregulated with age. Functional analysis showed that most DEGs were associated with disease and that these DEGs were also associated with the immune system and metabolism. Furthermore, gene methylation in giant pandas decreased globally with age, and the expression of CCNE1, CD79A, IL1R1, and TCF7 showed a highly negative correlation with their degree of methylation. These results indicate that the giant panda's immune function improves gradually with age (young to adult), and that changes in the methylation profile are involved in the effects of age on immune and metabolic functions. These results have important implications for the understanding and conservation of giant pandas.
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Affiliation(s)
- Xiaoyu Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Qingyuan Ouyang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingxia Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Linhua Deng
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Guo Li
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Tao Deng
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Ming He
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Ti Li
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Haidi Yang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Guiquan Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Heming Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Changjun Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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