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Wu X, Yang C, Zou Y, Jones SE, Zhao X, Zhang L, Han Z, Hao Y, Xiao J, Xiao C, Zhang W, Yan P, Cui H, Tang M, Wang Y, Chen L, Zhang L, Yao Y, Liu Z, Li J, Jiang X, Zhang B. Using human genetics to understand the phenotypic association between chronotype and breast cancer. J Sleep Res 2024; 33:e13973. [PMID: 37380357 DOI: 10.1111/jsr.13973] [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: 04/03/2023] [Revised: 05/23/2023] [Accepted: 06/11/2023] [Indexed: 06/30/2023]
Abstract
Little is known regarding the shared genetic influences underlying the observed phenotypic association between chronotype and breast cancer in women. Leveraging summary statistics from the hitherto largest genome-wide association study conducted in each trait, we investigated the genetic correlation, pleiotropic loci, and causal relationship of chronotype with overall breast cancer, and with its subtypes defined by the status of oestrogen receptor. We identified a negative genomic correlation between chronotype and overall breast cancer (r g = -0.06, p = 3.00 × 10-4), consistent across oestrogen receptor-positive (r g = -0.05, p = 3.30 × 10-3) and oestrogen receptor-negative subtypes (r g = -0.05, p = 1.11 × 10-2). Five specific genomic regions were further identified as contributing a significant local genetic correlation. Cross-trait meta-analysis identified 78 loci shared between chronotype and breast cancer, of which 23 were novel. Transcriptome-wide association study revealed 13 shared genes, targeting tissues of the nervous, cardiovascular, digestive, and exocrine/endocrine systems. Mendelian randomisation demonstrated a significantly reduced risk of overall breast cancer (odds ratio 0.89, 95% confidence interval 0.83-0.94; p = 1.30 × 10-4) for genetically predicted morning chronotype. No reverse causality was found. Our work demonstrates an intrinsic link underlying chronotype and breast cancer, which may provide clues to inform management of sleep habits to improve female health.
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Affiliation(s)
- Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Epidemiology and Health Statistics, School of Public Health, Southwest Medical University, Luzhou, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Samuel E Jones
- Institute for Molecular Medicine, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Xunying Zhao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhitong Han
- School of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Hao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jinyu Xiao
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, School of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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Adam MAA, Robinson M, Schwartz AV, Wells G, Hoang A, Albekioni E, Chao G, Weeks J, George UZ, House CD, Turcan Ş, Sohl CD. Catalytically distinct IDH1 mutants tune phenotype severity in tumor models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590655. [PMID: 38712107 PMCID: PMC11071412 DOI: 10.1101/2024.04.22.590655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mutations in isocitrate dehydrogenase 1 (IDH1) impart a neomorphic reaction that produces the oncometabolite D-2-hydroxyglutarate (D2HG), which can inhibit DNA and histone demethylases to drive tumorigenesis via epigenetic changes. Though heterozygous point mutations in patients primarily affect residue R132, there are myriad D2HG-producing mutants that display unique catalytic efficiency of D2HG production. Here, we show that catalytic efficiency of D2HG production is greater in IDH1 R132Q than R132H mutants, and expression of IDH1 R132Q in cellular and mouse xenograft models leads to higher D2HG concentrations in cells, tumors, and sera compared to R132H-expressing models. Reduced representation bisulfite sequencing (RRBS) analysis of xenograft tumors shows expression of IDH1 R132Q relative to R132H leads to hypermethylation patterns in pathways associated with DNA damage. Transcriptome analysis indicates that the IDH1 R132Q mutation has a more aggressive pro-tumor phenotype, with members of EGFR, Wnt, and PI3K signaling pathways differentially expressed, perhaps through non-epigenetic routes. Together, these data suggest that the catalytic efficiency of IDH1 mutants modulate D2HG levels in cellular and in vivo models, resulting in unique epigenetic and transcriptomic consequences where higher D2HG levels appear to be associated with more aggressive tumors.
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Li X, Wang G, Wang X, Li W, Li N, Liu X, Fan W, He S, Han Y, Su G, Cao Q, Yang P, Hou S. OR11H1 Missense Variant Confers the Susceptibility to Vogt-Koyanagi-Harada Disease by Mediating Gadd45g Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306563. [PMID: 38168905 PMCID: PMC10953539 DOI: 10.1002/advs.202306563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/17/2023] [Indexed: 01/05/2024]
Abstract
Vogt-Koyanagi-Harada (VKH) disease is a severe autoimmune disease. Herein, whole-exome sequencing (WES) study are performed on 2,573 controls and 229 VKH patients with follow-up next-generation sequencing (NGS) in a collection of 2,380 controls and 2,278 VKH patients. A rare c.188T>C (p Val63Ala) variant in the olfactory receptor 11H1 (OR11H1) gene is found to be significantly associated with VKH disease (rs71235604, Pcombined = 7.83 × 10-30 , odds ratio = 3.12). Functional study showes that OR11H1-A63 significantly increased inflammatory factors production and exacerbated barrier function damage. Further studies using RNA-sequencing find that OR11H1-A63 markedly increased growth arrest and DNA-damage-inducible gamma (GADD45G) expression. Moreover, OR11H1-A63 activates the MAPK and NF-κB pathways, and accelerates inflammatory cascades. In addition, inhibiting GADD45G alleviates inflammatory factor secretion, likely due to the regulatory effect of GADD45G on the MAPK and NF-κB pathways. Collectively, this study suggests that the OR11H1-A63 missense mutation may increase susceptibility to VKH disease in a GADD45G-dependent manner.
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Affiliation(s)
- Xingran Li
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Guoqing Wang
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Xiaotang Wang
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Wanqian Li
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Na Li
- Department of Laboratory MedicineBeijing Tongren Hospital, Capital Medical UniversityBeijing100005China
| | - Xianyang Liu
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Wei Fan
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Siyuan He
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Yue Han
- Beijing Novogene Bioinformatics Technology Co.,LtdBeijing100600China
| | - Guannan Su
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Qingfeng Cao
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Peizeng Yang
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
| | - Shengping Hou
- Chongqing Branch of National Clinical Research Center for Ocular Diseases; Chongqing Key Laboratory of Ophthalmology; Chongqing Eye InstituteThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400042China
- Beijing Institute of OphthalmologyBeijing Tongren Eye CenterBeijing Ophthalmology & Visual Sciences Key LaboratoryBeijing Tongren HospitalCapital Medical UniversityBeijing100730China
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Zeng LP, Qin YQ, Lu XM, Feng ZB, Fang XL. Identify GADD45G as a potential target of 4-methoxydalbergione in treatment of liver cancer: bioinformatics analysis and in vivo experiment. World J Surg Oncol 2023; 21:324. [PMID: 37833694 PMCID: PMC10571512 DOI: 10.1186/s12957-023-03214-3] [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: 04/10/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The growth arrest and DNA damage-inducible gene gamma (GADD45G), an important member of GADD45 family, has been connected to the development of certain human cancers. Our previous studies have confirmed that GADD45G expression could be upregulated by 4-methoxydalbergione (4MOD) in liver cancer cells, but its potential pathological role in hepatocellular carcinoma (HCC) has not been fully understood. This study aimed to determine potential role of GADD45G in HCC, and the effects of 4-methoxydalbergione (4MOD) on the regulation of GADD45G expression in vivo were also analyzed. METHODS Publicly available data and in-house immunohistochemistry (IHC) experiments were utilized to explore the expression profiles and clinical significance of GADD45G in HCC samples. Functional enrichment analysis based on GADD45G co-expression genes was used to excavate the molecular mechanism of GADD45G in HCC. We also conducted in vivo experiment on BALB/c nude mice to excavate the inhibitory effect of 4MOD on HCC and to evaluate the differences in the expression of GADD45G in xenograft tissues between the 4MOD-treated and untreated groups. RESULTS GADD45G displayed significant low expression in HCC tissues. Downregulated expression of GADD45G was positively correlated with some high risk factors in HCC patients and predicted worse prognosis of HCC patients. There was a close association of GADD45G mRNA expression and immune cells, including neutrophils, NK cells, CD8 T cells, and macrophages. Co-expressed genes of GADD45G were involved in several pathways including cell cycle, carbon metabolism, and peroxisome. 4MOD could significantly suppress the growth of HCC in vivo, and this inhibitory effect was dependent on the upregulation of GADD45G expression. CONCLUSION GADD45G expression can be used as a new clinical biomarker for HCC and GADD45G may be a potential target for the anti-cancer effect of 4MOD in liver cancer.
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Affiliation(s)
- Li-Ping Zeng
- Department of Pathology, Hunan University of Medicine, 492 Jinxinan RD, Huaihua, Hunan, 418000, People's Republic of China
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong RD, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Yu-Qi Qin
- Department of Pathology, Jiangbin Hospital of Guangxi Zhuang Autonomous Region, 85 Hedi RD, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Xiao-Min Lu
- Department of Pathology, Hunan University of Medicine, 492 Jinxinan RD, Huaihua, Hunan, 418000, People's Republic of China
| | - Zhen-Bo Feng
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong RD, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China.
| | - Xian-Lei Fang
- Department of Pathology, Hunan University of Medicine, 492 Jinxinan RD, Huaihua, Hunan, 418000, People's Republic of China.
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You W, Liu S, Li J, Tu Y, Shan T. GADD45A regulates subcutaneous fat deposition and lipid metabolism by interacting with Stat1. BMC Biol 2023; 21:212. [PMID: 37807064 PMCID: PMC10561432 DOI: 10.1186/s12915-023-01713-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/26/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Obesity, characterized by excessive white adipose tissue expansion, is associated with several metabolic complications. Identifying new adipogenesis regulators may lead to effective therapies for obesity-induced metabolic disorders. RESULTS Here, we identified the growth arrest and DNA damage-inducible A (GADD45A), a stress-inducible histone-folding protein, as a novel regulator of subcutaneous adipose metabolism. We found that GADD45A expression was positively correlated with subcutaneous fat deposition and obesity in humans and fatty animals. In vitro, the gain or loss function of GADD45A promoted or inhibited subcutaneous adipogenic differentiation and lipid accumulation, respectively. Using a Gadd45a-/- mouse model, we showed that compared to wild-type (WT) mice, knockout (KO) mice exhibited subcutaneous fat browning and resistance to high-fat diet (HFD)-induced obesity. GADD45A deletion also upregulated the expression of mitochondria-related genes. Importantly, we further revealed that the interaction of GADD45A with Stat1 prevented phosphorylation of Stat1, resulting in the impaired expression of Lkb1, thereby regulating subcutaneous adipogenesis and lipid metabolism. CONCLUSIONS Overall, our results reveal the critical regulatory roles of GADD45A in subcutaneous fat deposition and lipid metabolism. We demonstrate that GADD45A deficiency induces the inguinal white adipose tissue (iWAT) browning and protects mice against HFD-induced obesity. Our findings provide new potential targets for combating obesity-related metabolic diseases and improving human health.
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Affiliation(s)
- Wenjing You
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Shiqi Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Jie Li
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Yuang Tu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Tizhong Shan
- College of Animal Sciences, Zhejiang University, Hangzhou, China.
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China.
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
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Han J, Li X, Liang B, Ma S, Pu Y, Yu F, Lu J, Ma Y, MacHugh DE, Jiang L. Transcriptome profiling of differentiating adipose-derived stem cells across species reveals new genes regulating adipogenesis. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159378. [PMID: 37572997 DOI: 10.1016/j.bbalip.2023.159378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
Adipose-derived stem cells (ADSCs) that are enriched in adipose tissue with multilineage differentiation potential have become an important tool in therapeutic research and tissue engineering. Certain breeds of sheep exhibit a unique fat tail trait such that tail tissue accounts for approximately 10 % of body weight and can provide an excellent source of ADSCs. Here, we describe isolation of primary ADSCs from ovine embryonic fat tail tissues that displayed high self-renewal capacity, multilineage differentiation and excellent adipogenic ability. Through transcriptome analysis covering ADSCs differentiating into adipocytes, 37 transcription factors were involved in early transcriptional events that initiate a regulatory cascade of adipogenesis; the entire adipogenic activity consists of a reduction in proliferation ability and upregulation of genes related to lipid generation and energy metabolism, as well as several genes associated with myogenesis. Furthermore, Comparative transcriptome analysis across species (sheep, human, and mouse) revealed enhanced basal metabolic ability in differentiating ovine ADSCs, which may relate to the excellent adipogenic capability of these cells. We also identified a small evolutionarily conserved gene set, consisting of 21 and 22 genes exhibiting increased and decreased expression, respectively. Almost half (20) of these genes have not previously been reported to regulate adipogenesis in mammals. In this study, we identified important regulators that trigger ovine adipocyte differentiation, main biological pathways involved in adipogenesis as well as the evolutionarily conserved genes governing adipogenic process across species. Our study provides a novel excellent biomaterial and novel genes regulating adipogenesis for cellular transplantation therapy and investigations of fat metabolism.
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Affiliation(s)
- Jiangang Han
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Xiaojie Li
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Benmeng Liang
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Sijia Ma
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; Agricultural College, Ningxia University, Yinchuan, Ningxia, China
| | - Yabin Pu
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuqing Yu
- National Animal Husbandry Service, Beijing 100193, China
| | - Jian Lu
- National Animal Husbandry Service, Beijing 100193, China
| | - Yuehui Ma
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8, Ireland.
| | - Lin Jiang
- Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China; National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
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Ma Q, Hu L, Luo Y, Wang M, Yu S, Lu A, Zhang L, Zeng H. Identification of apoptosis-related key genes and the associated regulation mechanism in thoracic aortic aneurysm. BMC Cardiovasc Disord 2023; 23:481. [PMID: 37770840 PMCID: PMC10540322 DOI: 10.1186/s12872-023-03516-0] [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: 03/27/2023] [Accepted: 09/17/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND This study investigated the role of apoptosis-related genes in thoracic aortic aneurysms (TAA) and provided more insights into TAA's pathogenesis and molecular mechanisms. MATERIAL/METHODS Two gene expression datasets (GSE9106 and GSE26155) were retrieved from the Gene Expression Omnibus (GEO) database. Apoptosis-related genes were obtained from the KEGG apoptosis pathway (hsa04210). Differentially expressed apoptosis-related genes were identified by performing differential expression analysis using limma for TAA blood and tissue samples. GO and KEGG enrichment analysis of the differentially expressed apoptosis genes was performed using the Metascape web tool. The miRNA-mRNA regulatory network was reconstructed using the ENCORI and miRDB databases, and functional enrichment analysis was performed on the related miRNAs using the miEAA tool. The correlation between the expression levels of differentially expressed apoptosis-related genes and genes involved in immune infiltration in TAA was calculated using the CIBERSORT algorithm. The apoptosis modification patterns mediated by differentially expressed apoptosis-related genes were systematically assessed in TAA samples. RESULTS A total of 9 differentially-expressed apoptosis-related genes were identified in TAA samples compared with normal samples. 150 miRNAs and 6 mRNAs regulatory networks were reconstructed using the ENCORI and miRDB databases. Immune infiltration analysis revealed that the GZMB had the strongest positive correlation with activated NK cells and the DFFA presented the strongest positive correlation with T cells follicular helper. 3 distinct apoptosis modification patterns mediated by 9 differentially-expressed apoptosis-related genes were identified. They differ in immune characteristics and drug sensitivity, and their biological functions in these subtypes were further studied. CONCLUSIONS This study identified key apoptosis-related genes related to TAA and evaluated the modification patterns of key apoptosis genes in TAA, providing insights into potential targets and mechanisms of TAA pathogenesis and progression.
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Affiliation(s)
- Qi Ma
- Department of Anesthesiology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Long Hu
- XJTLU Wisdom Lake Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Yingwan Luo
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Miao Wang
- Department of Pediatrics, Peking University People's Hospital, 11 Xizhimen South Street, Beijing, 100000, China
| | - Shui Yu
- Department of Pediatrics, Peking University People's Hospital, 11 Xizhimen South Street, Beijing, 100000, China
| | - Aidong Lu
- Department of Pediatrics, Peking University People's Hospital, 11 Xizhimen South Street, Beijing, 100000, China
| | - Leping Zhang
- Department of Pediatrics, Peking University People's Hospital, 11 Xizhimen South Street, Beijing, 100000, China
| | - Huimin Zeng
- Department of Pediatrics, Peking University People's Hospital, 11 Xizhimen South Street, Beijing, 100000, China.
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Zhang L, Wu L, Zhou D, Wang G, Chen B, Shen Z, Li X, Wu Q, Qu N, Wu Y, Yuan L, Gan Z, Zhou W. N76-1, a novel CDK7 inhibitor, exhibits potent anti-cancer effects in triple negative breast cancer. Eur J Pharmacol 2023; 955:175892. [PMID: 37429520 DOI: 10.1016/j.ejphar.2023.175892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Emerging evidence suggests that genetically highly specific triple-negative breast cancer (TNBC) possesses a relatively uniform transcriptional program that is abnormally dependent on cyclin-dependent kinase 7 (CDK7). In this study, we obtained an inhibitor of CDK7, N76-1, by attaching the side chain of the covalent CDK7 inhibitor THZ1 to the core of the anaplastic lymphoma kinase inhibitor ceritinib. This study aimed to elucidate the role and underlying mechanism of N76-1 in TNBC and evaluate its potential value as an anti-TNBC drug. The results of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and colony formation assays showed that N76-1 inhibited the viability of TNBC cells. Kinase activity and cellular thermal shift assays showed that N76-1 directly targeted CDK7. Flow cytometry results revealed that N76-1 induced apoptosis and cell cycle arrest in the G2/M phase. N76-1 also effectively inhibited the migration of TNBC cells by high-content detection. The RNA-seq analysis showed that the transcription of genes, especially those related to transcriptional regulation and cell cycle, was suppressed after N76-1 treatment. Moreover, N76-1 markedly inhibited the growth of TNBC xenografts and phosphorylation of RNAPII in tumor tissues. In summary, N76-1 exerts potent anticancer effects in TNBC by inhibiting CDK7 and provides a new strategy and research basis for the development of new drugs for TNBC.
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Affiliation(s)
- Limei Zhang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Lihong Wu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Duanfang Zhou
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Gang Wang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Bo Chen
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Zhengze Shen
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, 439 Xuanhua Road, Yongchuan District, Chongqing, 402160, China
| | - Xiaoli Li
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Qiuya Wu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Na Qu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Yuanli Wu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Lie Yuan
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China
| | - Zongjie Gan
- Department of Medicinal Chemistry, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China.
| | - Weiying Zhou
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China; Chongqing Key Laboratory of Drug Metabolism, Chongqing, 400016, China; Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, 400016, China.
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9
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Pan-cancer antagonistic inhibition pattern of ATM-driven G2/M checkpoint pathway vs other DNA repair pathways. DNA Repair (Amst) 2023; 123:103448. [PMID: 36657260 DOI: 10.1016/j.dnarep.2023.103448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/22/2022] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
DNA repair mechanisms keep genome integrity and limit tumor-associated alterations and heterogeneity, but on the other hand they promote tumor survival after radiation and genotoxic chemotherapies. We screened pathway activation levels of 38 DNA repair pathways in nine human cancer types (gliomas, breast, colorectal, lung, thyroid, cervical, kidney, gastric, and pancreatic cancers). We took RNAseq profiles of the experimental 51 normal and 408 tumor samples, and from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium databases - of 500/407 normal and 5752/646 tumor samples, and also 573 normal and 984 tumor proteomic profiles from Proteomic Data Commons portal. For all the samplings we observed a congruent trend that all cancer types showed inhibition of G2/M arrest checkpoint pathway compared to the normal samples, and relatively low activities of p53-mediated pathways. In contrast, other DNA repair pathways were upregulated in most of the cancer types. The G2/M checkpoint pathway was statistically significantly downregulated compared to the other DNA repair pathways, and this inhibition was strongly impacted by antagonistic regulation of (i) promitotic genes CCNB and CDK1, and (ii) GADD45 genes promoting G2/M arrest. At the DNA level, we found that ATM, TP53, and CDKN1A genes accumulated loss of function mutations, and cyclin B complex genes - transforming mutations. These findings suggest importance of activation for most of DNA repair pathways in cancer progression, with remarkable exceptions of G2/M checkpoint and p53-related pathways which are downregulated and neutrally activated, respectively.
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You W, Liu S, Ji J, Ling D, Tu Y, Zhou Y, Chen W, Valencak TG, Wang Y, Shan T. Growth arrest and DNA damage-inducible alpha regulates muscle repair and fat infiltration through ATP synthase F1 subunit alpha. J Cachexia Sarcopenia Muscle 2023; 14:326-341. [PMID: 36511343 PMCID: PMC9891974 DOI: 10.1002/jcsm.13134] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/06/2022] [Accepted: 11/10/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Skeletal muscle fat infiltration is a common feature during ageing, obesity and several myopathies associated with muscular dysfunction and sarcopenia. However, the regulatory mechanisms of intramuscular adipogenesis and strategies to reduce fat infiltration in muscle remain unclear. Here, we identified the growth arrest and DNA damage-inducible alpha (GADD45A), a stress-inducible histone folding protein, as a critical regulator of intramuscular fat (IMAT) infiltration. METHODS To explore the role of GADD45A on IMAT infiltration and muscle regeneration, the gain or loss function of GADD45A in intramuscular preadipocytes was performed. The adipocyte-specific GADD45A knock-in (KI) mice and high IMAT-infiltrated muscle model by glycerol injection (50 μL of 50% v/v GLY) were generated. RNA-sequencing, histological changes, gene expression, lipid metabolism, mitochondrial function and the effect of dietary factor epigallocatechin-3-gallate (EGCG) treatment (100 mg/kg) on IMAT infiltration were studied. RESULTS The unbiased transcriptomics data analysis indicated that GADD45A expression positively correlates with IMAT infiltration and muscle metabolic disorders in humans (correlation: young vs. aged people, Gadd45a and Cebpa, r2 = 0.20, P < 0.05) and animals (correlation: wild-type [WT] vs. mdx mice, Gadd45a and Cebpa, r2 = 0.38, P < 0.05; NaCl vs. GLY mice, Gadd45a and Adipoq/Fabp4, r2 = 0.80/0.71, both P < 0.0001). In vitro, GADD45A overexpression promotes intramuscular preadipocyte adipogenesis, upregulating the expression of adipogenic genes (Ppara: +47%, Adipoq: +28%, P < 0.001; Cebpa: +135%, Fabp4: +16%, P < 0.01; Pparg: +66%, Leptin: +77%, P < 0.05). GADD45A knockdown robustly decreased lipid accumulation (Pparg: -57%, Adipoq: -35%, P < 0.001; Fabp4: -37%, P < 0.01; Leptin: -28%, P < 0.05). GADD45A KI mice exhibit inhibited skeletal muscle regeneration (myofibres: -40%, P < 0.01) and enhanced IMAT infiltration (adipocytes: +20%, P < 0.05). These KI mice have impaired exercise endurance and mitochondrial function. Mechanistically, GADD45A affects ATP synthase F1 subunit alpha (ATP5A1) ubiquitination degradation (ubiquitinated ATP5A1, P < 0.001) by recruiting the E3 ubiquitin ligase TRIM25, which decreases ATP synthesis (ATP production: -23%, P < 0.01) and inactivates the cAMP/PKA/LKB1 signalling pathway (cAMP: -36%, P < 0.01; decreased phospho-PKA and phospho-LKB1 protein content, P < 0.01). The dietary factor EGCG can protect against muscle fat infiltration (triglyceride: -64%, P < 0.05) via downregulating GADD45A (decreased GADD45A protein content, P < 0.001). CONCLUSIONS Our findings reveal a crucial role of GADD45A in regulating muscle repair and fat infiltration and suggest that inhibition of GADD45A by EGCG might be a potential strategy to combat fat infiltration and its associated muscle dysfunction.
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Affiliation(s)
- Wenjing You
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | - Shiqi Liu
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | - Jianfei Ji
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, College of Life SciencesZhejiang UniversityHangzhouChina
| | - Defeng Ling
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | - Yuang Tu
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | - Yanbing Zhou
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | - Wentao Chen
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | | | - Yizhen Wang
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
| | - Tizhong Shan
- College of Animal SciencesZhejiang UniversityHangzhouZhejiangChina
- The Key Laboratory of Molecular Animal NutritionMinistry of EducationHangzhouChina
- Zhejiang Provincial Laboratory of Feed and Animal NutritionHangzhouChina
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11
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4-Methoxydalbergione Elicits Anticancer Effects by Upregulation of GADD45G in Human Liver Cancer Cells. JOURNAL OF HEALTHCARE ENGINEERING 2023; 2023:6710880. [PMID: 36776954 PMCID: PMC9908360 DOI: 10.1155/2023/6710880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 02/04/2023]
Abstract
Background 4-Methoxydalbergione (4MOD) is a flavonoid isolated from the heartwood of Dalbergia. Studies have demonstrated that 4MOD exerts anticancer activities on bladder cancer and astrocytoma. However, the anticancer activity of 4MOD in hepatocellular carcinoma (HCC) remains unknown. This study aims to examine its anticancer activities and mechanisms in human liver cancer cells. Methods CCK-8, colony forming, wound healing, transwell migration, and AnnexinV/PI assays were used to assess the anticancer effects of 4MOD in HCC cells. RNA sequencing (RNA-Seq) was selected to explore the possible mechanisms underlying the anti-HCC activity of 4MOD. The mRNA expression levels of target genes were verified through quantitative real-time PCR (qRT-PCR). A lentiviral shRNA interference technique was used to silence GADD45G expression. GADD45G knockdown was employed to confirm the crucial role of GADD45G in the 4MOD-mediatedanti-HCC effects. Results 4MOD inhibited HCC cells' proliferation and migration and promoted tumor cell apoptosis. RNA-Seq and qRT-PCR analyses revealed that 4MOD treatment increased GADD45G expression. Silencing GADD45G reversed 4MOD-mediated inhibition of proliferation, migration, and promotion of apoptosis. Conclusions Our findings show that 4MOD elicits anti-HCC effects by upregulating GADD45G expression and could be a valuable anticancer agent for liver cancer.
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12
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(–)-Xanthatin as a Killer of Human Breast Cancer MCF-7 Mammosphere Cells: A Comparative Study with Salinomycin. Curr Issues Mol Biol 2022; 44:3849-3858. [PMID: 36135176 PMCID: PMC9497939 DOI: 10.3390/cimb44090264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Experimental evidence accumulated by our research group and others strongly suggests that (–)-xanthatin, a xanthanolide sesquiterpene lactone, exhibits anti-proliferative effects on human breast cancer cells (in vitro) as well as anti-tumor effects in experimental animals (in vivo). In cancer biology, it is now critically important for anti-cancer agents to selectively target cancer stem cells (CSCs) in order to overcome cancer therapeutic resistance and recurrence. However, it has not yet been established whether (–)-xanthatin abrogates the formation of breast CSCs. In the present study, we utilized chemically synthesized pure (–)-xanthatin and a culture system to obtain mammospheres from human breast cancer MCF-7 cells, which are a CSC-enriched population. We herein demonstrated for the first time that (–)-xanthatin exhibited the ability to kill mammospheres, similar to salinomycin, an established selective killer of CSCs. A possible anti-proliferative mechanism toward mammospheres by (–)-xanthatin is discussed.
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13
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Hu F, Ma Y, Xu Z, Zhang S, Li J, Sun X, Wu J. Single-Cell RNA-Seq Reveals the Cellular Diversity and Developmental Characteristics of the Retinas of an Infant and a Young Child. Front Cell Dev Biol 2022; 10:803466. [PMID: 35386199 PMCID: PMC8979067 DOI: 10.3389/fcell.2022.803466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
The human retina, located in the innermost layer of the eye, plays a decisive role in visual perception. Dissecting the heterogeneity of retinal cells is essential for understanding the mechanism of visual development. Here, we performed single-cell RNA-seq to analyze 194,967 cells from the donors of infants and young children, resulting in 17 distinct clusters representing major cell types in the retina: rod photoreceptors (PRs), cone PRs, bipolar cells (BCs), horizontal cells (HCs), amacrine cells (ACs), retinal ganglion cells (RGCs), Müller glial cells (MGs), microglia, and astrocytes (ASTs). Through reclustering, we identified known subtypes of cone PRs as well as additional unreported subpopulations and corresponding markers in BCs. Additionally, we linked inherited retinal diseases (IRDs) to certain cell subtypes or subpopulations through enrichment analysis. We next constructed extensive intercellular communication networks and identified ligand-receptor interactions that play crucial roles in regulating neural cell development and immune homeostasis in the retina. Intriguingly, we found that the status and functions of PRs changed drastically between the young children and adult retina. Overall, our study offers the first retinal cell atlas in infants and young children dissecting the heterogeneity of the retina and identifying the key molecules in the developmental process, which provides an important resource that will pave the way for research on retinal development mechanisms and advancements in regenerative medicine concerning retinal biology.
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Affiliation(s)
- Fangyuan Hu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Yuting Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zaoxu Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shenghai Zhang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | | | - Xinghuai Sun
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Jihong Wu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China.,NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
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