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Wu M, Wu Z, Yan J, Zeng J, Kuang J, Zhong C, Zhu X, Mo Y, Guo Q, Li D, Tan J, Zhang T, Zhang J. Integrated analysis of single-cell and Bulk RNA sequencing reveals a malignancy-related signature in lung adenocarcinoma. Front Oncol 2023; 13:1198746. [PMID: 37427142 PMCID: PMC10327591 DOI: 10.3389/fonc.2023.1198746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD), the most common histotype of lung cancer, may have variable prognosis due to molecular variations. The research strived to establish a prognostic model based on malignancy-related risk score (MRRS) in LUAD. Methods We applied the single-cell RNA sequencing (scRNA-seq) data from Tumor Immune Single Cell Hub database to recognize malignancy-related geneset. Meanwhile, we extracted RNA-seq data from The Cancer Genome Atlas database. The GSE68465 and GSE72094 datasets from the Gene Expression Omnibus database were downloaded to validate the prognostic signature. Random survival forest analysis screened MRRS with prognostic significance. Multivariate Cox analysis was leveraged to establish the MRRS. Furthermore, the biological functions, gene mutations, and immune landscape were investigated to uncover the underlying mechanisms of the malignancy-related signature. In addition, we used qRT-PCR to explore the expression profile of MRRS-constructed genes in LUAD cells. Results The scRNA-seq analysis revealed the markers genes of malignant celltype. The MRRS composed of 7 malignancy-related genes was constructed for each patient, which was shown to be an independent prognostic factor. The results of the GSE68465 and GSE72094 datasets validated MRRS's prognostic value. Further analysis demonstrated that MRRS was involved in oncogenic pathways, genetic mutations, and immune functions. Moreover, the results of qRT-PCR were consistent with bioinformatics analysis. Conclusion Our research recognized a novel malignancy-related signature for predicting the prognosis of LUAD patients and highlighted a promising prognostic and treatment marker for LUAD patients.
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Affiliation(s)
- Mengxi Wu
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Zhenyu Wu
- Department of Urology, The First People’s Hospital of Foshan, Foshan, China
| | - Jun Yan
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jie Zeng
- Department of Thoracic Surgery, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, China
| | - Jun Kuang
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Chenghua Zhong
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xiaojia Zhu
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yijun Mo
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Quanwei Guo
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Dongfang Li
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jianfeng Tan
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Tao Zhang
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Jianhua Zhang
- Department of Thoracic Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, China
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Gu Y, Xu J, Sun F, Cheng J. Elevated intracellular pH of zygotes during mouse aging causes mitochondrial dysfunction associated with poor embryo development. Mol Cell Endocrinol 2023:111991. [PMID: 37336488 DOI: 10.1016/j.mce.2023.111991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
The mortality of preimplantation embryos is positively correlated with maternal age. However, the underlying mechanism for the poor quality of embryos remains unclear. Here, we found that aging caused elevated intracellular pH (pHi) in zygotes, which could trigger aberrant mitochondrial membrane potential, increased reactive oxygen species (ROS) levels, and poor embryo development. Moreover, single-cell transcriptome sequencing of mouse zygotes identified 120 genes that were significantly differentially expressed (DE) between young and older zygotes. These include genes such as Slc14a1, Fxyd5, CD74, and Bst, which are related to cell division, ion transporter, and cell differentiation. Further analysis indicated that these DE genes were enriched in apoptosis, the NF-kappa B signaling pathway, and the chemokine signaling pathway, which might be the key regulatory pathway affecting the quality of zygotes and subsequent embryo development. Taken together, our study helps elucidate the poor quality and development of older preimplantation embryos.
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Affiliation(s)
- Yimin Gu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Junjie Xu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China; Department of Obstetrics and Gynecology, The Second Hospital of Shanxi Medical University, 7, Taiyuan, 030001, China
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Jinmei Cheng
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
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He R, Ding X, Zhang T, Mei L, Zhu S, Wang C, Liao Y, Wang D, Wang H, Guo J, Guo X, Xing Y, Gu Z, Hu H. Study on myocardial toxicity induced by lead halide perovskites nanoparticles. Nanotoxicology 2023; 17:449-470. [PMID: 37688453 DOI: 10.1080/17435390.2023.2255269] [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: 01/29/2023] [Revised: 06/09/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Lead halide perovskites (LHPs) are outstanding candidates for next-generation optoelectronic materials, with considerable prospects of use and commercial value. However, knowledge about their toxicity is scarce, which may limit their commercialization. Here, for the first time, we studied the cardiotoxicity and molecular mechanisms of representative CsPbBr3 nanoparticles in LHPs. After their intranasal administration to Institute of Cancer Research (ICR) mice, using advanced synchrotron radiation, mass spectrometry, and ultrasound imaging, we revealed that CsPbBr3 nanoparticles can severely affect cardiac systolic function by accumulating in the myocardial tissue. RNA sequencing and Western blotting demonstrated that CsPbBr3 nanoparticles induced excessive oxidative stress in cardiomyocytes, thereby provoking endoplasmic reticulum stress, disturbing calcium homeostasis, and ultimately leading to apoptosis. Our findings highlight the cardiotoxic effects of LHPs and provide crucial toxicological data for the product.
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Affiliation(s)
- Rendong He
- Academician Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
| | - Xuefeng Ding
- Academician Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Critical Care Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
| | - Tingjun Zhang
- Academician Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Infectious Diseases, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
| | - Linqiang Mei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Shuang Zhu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Chinese Academy of Sciences, Beijing, P. R. China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Chengyan Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - You Liao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Dongmei Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Cardiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, P. R. China
| | - Junsong Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Cardiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, P. R. China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
| | - Yan Xing
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
| | - Zhanjun Gu
- Academician Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, P. R. China
- Center of Materials Science and Optoelectronics Engineering, College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Houxiang Hu
- Academician Workstation, Affiliated Hospital of North Sichuan Medical College, Nanchong, P. R. China
- Department of Cardiology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, P. R. China
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Richardson V, Engel N, Kulathinal RJ. Comparative developmental genomics of sex-biased gene expression in early embryogenesis across mammals. Biol Sex Differ 2023; 14:30. [PMID: 37208698 DOI: 10.1186/s13293-023-00520-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/15/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Mammalian gonadal sex is determined by the presence or absence of a Y chromosome and the subsequent production of sex hormones contributes to secondary sexual differentiation. However, sex chromosome-linked genes encoding dosage-sensitive transcription and epigenetic factors are expressed well before gonad formation and have the potential to establish sex-biased expression that persists beyond the appearance of gonadal hormones. Here, we apply a comparative bioinformatics analysis on a pair of published single-cell datasets from mouse and human during very early embryogenesis-from two-cell to pre-implantation stages-to characterize sex-specific signals and to assess the degree of conservation among early acting sex-specific genes and pathways. RESULTS Clustering and regression analyses of gene expression across samples reveal that sex initially plays a significant role in overall gene expression patterns at the earliest stages of embryogenesis which potentially may be the byproduct of signals from male and female gametes during fertilization. Although these transcriptional sex effects rapidly diminish, sex-biased genes appear to form sex-specific protein-protein interaction networks across pre-implantation stages in both mammals providing evidence that sex-biased expression of epigenetic enzymes may establish sex-specific patterns that persist beyond pre-implantation. Non-negative matrix factorization (NMF) on male and female transcriptomes generated clusters of genes with similar expression patterns across sex and developmental stages, including post-fertilization, epigenetic, and pre-implantation ontologies conserved between mouse and human. While the fraction of sex-differentially expressed genes (sexDEGs) in early embryonic stages is similar and functional ontologies are conserved, the genes involved are generally different in mouse and human. CONCLUSIONS This comparative study uncovers much earlier than expected sex-specific signals in mouse and human embryos that pre-date hormonal signaling from the gonads. These early signals are diverged with respect to orthologs yet conserved in terms of function with important implications in the use of genetic models for sex-specific disease.
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Affiliation(s)
- Victorya Richardson
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Nora Engel
- Department of Cancer Biology, Lewis Katz School of Medicine, Fels Cancer Institute for Personalized Medicine, Temple University, 3400 N. Broad Street, Philadelphia, PA, 19140, USA.
| | - Rob J Kulathinal
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA.
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA.
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Kim S, Koppitch K, Parvez RK, Guo J, Achieng M, Schnell J, Lindström NO, McMahon AP. Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.540880. [PMID: 37293066 PMCID: PMC10245679 DOI: 10.1101/2023.05.16.540880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.
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Cui L, Fang L, Zhuang L, Shi B, Lin CP, Ye Y. Sperm-borne microRNA-34c regulates maternal mRNA degradation and preimplantation embryonic development in mice. Reprod Biol Endocrinol 2023; 21:40. [PMID: 37101140 PMCID: PMC10131327 DOI: 10.1186/s12958-023-01089-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/05/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Studies have shown that sperm-borne microRNAs (miRNAs) are involved in mammalian preimplantation embryonic development. In humans, spermatozoan miR-34c levels are correlated with in vitro fertilization outcomes, such as embryo quality and the clinical pregnancy and live birth rates. In rabbits and cows, miR-34c improves the developmental competence of embryos generated by somatic cell nuclear transfer. However, the mechanisms underlying the regulation of embryonic development by miR-34c remain unknown. METHODS Female C57BL/6 mice (6-8 weeks old) were superovulated, and pronucleated zygotes were collected and microinjected with an miR-34c inhibitor or a negative-control RNA. The embryonic development of the microinjected zygotes was evaluated, and the messenger RNA (mRNA) expression profiles of the embryos at the two-cell, four-cell and blastocyst stages (five embryos per group) were determined by RNA sequencing analysis. Gene expression levels were verified by reverse transcription-quantitative polymerase chain reaction. Cluster analysis and heat map visualization were performed to detect differentially expressed mRNAs. Pathway and process enrichment analyses were performed using ontology resources. Differentially expressed mRNAs were systematically analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins database to determine their biological functions. RESULTS Embryonic developmental potential was significantly reduced in zygotes microinjected with the miR-34c inhibitor compared with those microinjected with a negative-control RNA. Two-cell stage embryos microinjected with an miR-34c inhibitor presented altered transcriptomic profiles, with upregulated expression of maternal miR-34c target mRNAs and classical maternal mRNAs. Differentially expressed transcripts were mainly of genes associated with lipid metabolism and cellular membrane function at the two-cell stage, with cell-cycle phase transition and energy metabolism at the four-cell stage; and with vesicle organization, lipid biosynthetic process and endomembrane system organization at the blastocyst stage. We also showed that genes related to preimplantation embryonic development, including Alkbh4, Sp1, Mapk14, Sin3a, Sdc1 and Laptm4b, were significantly downregulated after microinjection of an miR-34c inhibitor. CONCLUSIONS Sperm-borne miR-34c may regulate preimplantation embryonic development by affecting multiple biological processes, such as maternal mRNA degradation, cellular metabolism, cell proliferation and blastocyst implantation. Our data demonstrate the importance of sperm-derived miRNAs in the development of preimplantation embryos.
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Affiliation(s)
- Long Cui
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Li Fang
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Lili Zhuang
- Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200041, China
| | - Biwei Shi
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Chao-Po Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yinghui Ye
- Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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Li Q, Zhao L, Zeng Y, Kuang Y, Guan Y, Chen B, Xu S, Tang B, Wu L, Mao X, Sun X, Shi J, Xu P, Diao F, Xue S, Bao S, Meng Q, Yuan P, Wang W, Ma N, Song D, Xu B, Dong J, Mu J, Zhang Z, Fan H, Gu H, Li Q, He L, Jin L, Wang L, Sang Q. Large-scale analysis of de novo mutations identifies risk genes for female infertility characterized by oocyte and early embryo defects. Genome Biol 2023; 24:68. [PMID: 37024973 PMCID: PMC10080761 DOI: 10.1186/s13059-023-02894-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/01/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Oocyte maturation arrest and early embryonic arrest are important reproductive phenotypes resulting in female infertility and cause the recurrent failure of assisted reproductive technology (ART). However, the genetic etiologies of these female infertility-related phenotypes are poorly understood. Previous studies have mainly focused on inherited mutations based on large pedigrees or consanguineous patients. However, the role of de novo mutations (DNMs) in these phenotypes remains to be elucidated. RESULTS To decipher the role of DNMs in ART failure and female infertility with oocyte and embryo defects, we explore the landscape of DNMs in 473 infertile parent-child trios and identify a set of 481 confident DNMs distributed in 474 genes. Gene ontology analysis reveals that the identified genes with DNMs are enriched in signaling pathways associated with female reproductive processes such as meiosis, embryonic development, and reproductive structure development. We perform functional assays on the effects of DNMs in a representative gene Tubulin Alpha 4a (TUBA4A), which shows the most significant enrichment of DNMs in the infertile parent-child trios. DNMs in TUBA4A disrupt the normal assembly of the microtubule network in HeLa cells, and microinjection of DNM TUBA4A cRNAs causes abnormalities in mouse oocyte maturation or embryo development, suggesting the pathogenic role of these DNMs in TUBA4A. CONCLUSIONS Our findings suggest novel genetic insights that DNMs contribute to female infertility with oocyte and embryo defects. This study also provides potential genetic markers and facilitates the genetic diagnosis of recurrent ART failure and female infertility.
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Affiliation(s)
- Qun Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
- Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Lin Zhao
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Yang Zeng
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Yanping Kuang
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Yichun Guan
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Shiru Xu
- Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, 518001, Guangdong, China
| | - Bin Tang
- Reproductive Medicine Center, The First People's Hospital of Changde City, Changde, 415000, China
| | - Ling Wu
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Xiaoyan Mao
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Juanzi Shi
- Reproductive Medicine Center, Northwest Women's and Children's Hospital, Xi'an, 710000, China
| | - Peng Xu
- Hainan Jinghua Hejing Hospital for Reproductive Medicine, Haikou, 570125, China
| | - Feiyang Diao
- Reproductive Medicine Center, Jiangsu Province Hospital, Nanjing, 210036, China
| | - Songguo Xue
- Reproductive Medicine Center, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Shihua Bao
- Department of Reproductive Immunology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204, China
| | - Qingxia Meng
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000, China
| | - Ping Yuan
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Wenjun Wang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Ning Ma
- Reproductive Medical Center, Maternal and Child Health Care Hospital of Hainan Province, Haikou, 570206, Hainan Province, China
| | - Di Song
- Naval Medical University, Changhai Hospital, Shanghai, China
| | - Bei Xu
- Reproductive Medicine Centre, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jie Dong
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Mu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Zhihua Zhang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Huizhen Fan
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Hao Gu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Qiaoli Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Lin He
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Qing Sang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
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Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O’Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535726. [PMID: 37066300 PMCID: PMC10104014 DOI: 10.1101/2023.04.05.535726] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Riza M. Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Truc-Mai Le
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eva K. Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Megan L. Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Olivia Fulton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Saskia Ilcisin
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christine M. Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-cell genomics and Population dynamics, The Rockefeller University, New York, NY, USA
| | - Alexander F. Schier
- Biozentrum, University of Basel, Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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59
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Tommasini D, Fogel BL. multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data. BMC Bioinformatics 2023; 24:115. [PMID: 36964502 PMCID: PMC10039544 DOI: 10.1186/s12859-023-05233-z] [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: 08/16/2022] [Accepted: 03/15/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Gene co-expression networks represent modules of genes with shared biological function, and have been widely used to model biological pathways in gene expression data. Co-expression networks associated with a specific trait can be constructed and identified using weighted gene co-expression network analysis (WGCNA), which is especially useful for the study of transcriptional signatures in disease. WGCNA networks are typically constructed using both disease and wildtype samples, so molecular pathways associated with disease are identified. However, it would be advantageous to study such co-expression networks in their disease context across spatiotemporal conditions, but currently there is no comprehensive software implementation for this type of analysis. RESULTS Here, we introduce a WGCNA-based procedure, multiWGCNA, that is tailored to datasets with variable spatial or temporal traits. As well as constructing the combined network, multiWGCNA also generates a network for each condition separately, and subsequently maps these modules between and across designs, and performs relevant downstream analyses, including module-trait correlation and module preservation. When applied to astrocyte-specific RNA-sequencing (RNA-seq) data from various brain regions of mice with experimental autoimmune encephalitis, multiWGCNA resolved the de novo formation of the neurotoxic astrocyte transcriptional program exclusively in the disease setting. Using time-course RNA-seq from mice with tau pathology (rTg4510), we demonstrate how multiWGCNA can also be used to study the temporal evolution of pathological modules over the course of disease progression. CONCLUSION The multiWGCNA R package can be applied to expression data with two dimensions, which is especially useful for the study of disease-associated modules across time or space. The source code and functions are freely available at: https://github.com/fogellab/multiWGCNA .
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Affiliation(s)
- Dario Tommasini
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Gonda Room 6554A, Los Angeles, CA, 90095, USA
| | - Brent L Fogel
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angeles, 695 Charles E. Young Drive South, Gonda Room 6554A, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA.
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60
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Gawriyski L, Jouhilahti EM, Yoshihara M, Fei L, Weltner J, Airenne TT, Trokovic R, Bhagat S, Tervaniemi MH, Murakawa Y, Salokas K, Liu X, Miettinen S, Bürglin TR, Sahu B, Otonkoski T, Johnson MS, Katayama S, Varjosalo M, Kere J. Comprehensive characterization of the embryonic factor LEUTX. iScience 2023; 26:106172. [PMID: 36876139 PMCID: PMC9978639 DOI: 10.1016/j.isci.2023.106172] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/01/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
The paired-like homeobox transcription factor LEUTX is expressed in human preimplantation embryos between the 4- and 8-cell stages, and then silenced in somatic tissues. To characterize the function of LEUTX, we performed a multiomic characterization of LEUTX using two proteomics methods and three genome-wide sequencing approaches. Our results show that LEUTX stably interacts with the EP300 and CBP histone acetyltransferases through its 9 amino acid transactivation domain (9aaTAD), as mutation of this domain abolishes the interactions. LEUTX targets genomic cis-regulatory sequences that overlap with repetitive elements, and through these elements it is suggested to regulate the expression of its downstream genes. We find LEUTX to be a transcriptional activator, upregulating several genes linked to preimplantation development as well as 8-cell-like markers, such as DPPA3 and ZNF280A. Our results support a role for LEUTX in preimplantation development as an enhancer binding protein and as a potent transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Liangru Fei
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 14186 Stockholm, Sweden
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, 14186 Stockholm, Sweden
| | - Tomi T. Airenne
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Ras Trokovic
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mari H. Tervaniemi
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- IFOM-ETS, Milan, Italy
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Sini Miettinen
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | | | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Centre for Molecular Medicine Norway (NCMM), University of Oslo, 0349 Oslo, Norway
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory and InFLAMES Research Flagship Center, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
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61
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Dynamics of histone acetylation during human early embryogenesis. Cell Discov 2023; 9:29. [PMID: 36914622 PMCID: PMC10011383 DOI: 10.1038/s41421-022-00514-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/28/2022] [Indexed: 03/16/2023] Open
Abstract
It remains poorly understood about the regulation of gene and transposon transcription during human early embryogenesis. Here, we report that broad H3K27ac domains are genome-widely distributed in human 2-cell and 4-cell embryos and transit into typical peaks in the 8-cell embryos. The broad H3K27ac domains in early embryos before zygotic genome activation (ZGA) are also observed in mouse. It suggests that broad H3K27ac domains play conserved functions before ZGA in mammals. Intriguingly, a large portion of broad H3K27ac domains overlap with broad H3K4me3 domains. Further investigation reveals that histone deacetylases are required for the removal or transition of broad H3K27ac domains and ZGA. After ZGA, the number of typical H3K27ac peaks is dynamic, which is associated with the stage-specific gene expression. Furthermore, P300 is important for the establishment of H3K27ac peaks and the expression of associated genes in early embryos after ZGA. Our data also indicate that H3K27ac marks active transposons in early embryos. Interestingly, H3K27ac and H3K18ac signals rather than H3K9ac signals are enriched at ERVK elements in mouse embryos after ZGA. It suggests that different types of histone acetylations exert distinct roles in the activation of transposons. In summary, H3K27ac modification undergoes extensive reprogramming during early embryo development in mammals, which is associated with the expression of genes and transposons.
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62
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Anholt RRH, Mackay TFC. The genetic architecture of behavioral canalization. Trends Genet 2023:S0168-9525(23)00033-1. [PMID: 36878820 DOI: 10.1016/j.tig.2023.02.007] [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: 12/01/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/07/2023]
Abstract
Behaviors are components of fitness and contribute to adaptive evolution. Behaviors represent the interactions of an organism with its environment, yet innate behaviors display robustness in the face of environmental change, which we refer to as 'behavioral canalization'. We hypothesize that positive selection of hub genes of genetic networks stabilizes the genetic architecture for innate behaviors by reducing variation in the expression of interconnected network genes. Robustness of these stabilized networks would be protected from deleterious mutations by purifying selection or suppressing epistasis. We propose that, together with newly emerging favorable mutations, epistatically suppressed mutations can generate a reservoir of cryptic genetic variation that could give rise to decanalization when genetic backgrounds or environmental conditions change to allow behavioral adaptation.
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Affiliation(s)
- Robert R H Anholt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA.
| | - Trudy F C Mackay
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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63
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Coban O, Serdarogullari M, Pervaiz R, Soykok A, Yarkiner Z, Bankeroglu H. Effect of paternal age on assisted reproductive outcomes in ICSI donor cycles. Andrology 2023; 11:515-522. [PMID: 36482823 DOI: 10.1111/andr.13363] [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: 05/17/2022] [Revised: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Despite growing evidence suggesting age-related molecular changes in gametes, the impact of paternal age on clinical outcomes during infertility treatments has not been adequately assessed. OBJECTIVES This study aims to assess the correlation of paternal age to clinical pregnancy and live birth rates in egg donation cycles undergoing intracytoplasmic sperm injection. MATERIALS AND METHODS This retrospective cohort study includes 4930 fresh oocyte donation cycles from 3995 couples between April 2005 and February 2020 in a private IVF hospital. Clinical pregnancy and live birth rates were the primary outcome measures. The results were also assessed according to the paternal age groups, donor characteristics, semen parameters, fertilization rate, and quality of the transferred embryos. RESULTS The age and body mass index of the donors, oocyte maturation, fertilization rates, and the mean number of transferred embryo quality were comparable on day-3 but not on day-5 embryo transfers between paternal age groups (p > 0.05). Paternal age was found to be negatively correlated to the number of oocytes utilized, normal semen parameters, fertilization, clinical pregnancy, and live birth rates (p < 0.05). In day-5 embryo transfer cycles, only the rate of cycles with normal spermatozoa, number of allocated oocytes, and pregnancy were found to be statistically significant. DISCUSSION AND CONCLUSION Paternal age may influence reproductive outcomes and should be considered during infertility evaluations in intracytoplasmic sperm injection donor cycles. Further research is needed to confirm these findings.
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Affiliation(s)
- Onder Coban
- Department of Embryology, British Cyprus IVF Hospital, Nicosia, Cyprus
| | - Munevver Serdarogullari
- Department of Histology and Embryology, Faculty of Medicine, Cyprus International University, Nicosia, Cyprus
| | - Ruqiya Pervaiz
- Department of Zoology, Faculty of Chemical and Life Sciences, Abdul Wali Khan University, Mardan, Pakistan
| | - Afet Soykok
- Department of Embryology, British Cyprus IVF Hospital, Nicosia, Cyprus
| | - Zalihe Yarkiner
- Department of Basic Sciences and Humanities, Faculty of Arts and Sciences, Cyprus International University, Nicosia, Cyprus
| | - Hasan Bankeroglu
- Department of Obstetrics & Gynecology, British Cyprus IVF Hospital, Nicosia, Cyprus
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64
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Metabolism-based cardiomyocytes production for regenerative therapy. J Mol Cell Cardiol 2023; 176:11-20. [PMID: 36681267 DOI: 10.1016/j.yjmcc.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/17/2022] [Accepted: 01/14/2023] [Indexed: 01/19/2023]
Abstract
Human pluripotent stem cells (hPSCs) are currently used in clinical applications such as cardiac regenerative therapy, studying disease models, and drug screening for heart failure. Transplantation of hPSC-derived cardiomyocytes (hPSC-CMs) can be used as an alternative therapy for heart transplantation. In contrast to differentiated somatic cells, hPSCs possess unique metabolic programs to maintain pluripotency, and understanding their metabolic features can contribute to the development of technologies that can be useful for their clinical applications. The production of hPSC-CMs requires stepwise specification during embryonic development and metabolic regulation is crucial for proper embryonic development. These metabolic features have been applied to hPSC-CM production methods, such as mesoderm induction, specifications for cardiac progenitors, and their maturation. This review describes the metabolic programs in hPSCs and the metabolic regulation in hPSC-CM production for cardiac regenerative therapy.
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65
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Actin-driven chromosome clustering facilitates fast and complete chromosome capture in mammalian oocytes. Nat Cell Biol 2023; 25:439-452. [PMID: 36732633 PMCID: PMC10014578 DOI: 10.1038/s41556-022-01082-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
Accurate chromosome segregation during meiosis is crucial for reproduction. Human and porcine oocytes transiently cluster their chromosomes before the onset of spindle assembly and subsequent chromosome segregation. The mechanism and function of chromosome clustering are unknown. Here we show that chromosome clustering is required to prevent chromosome losses in the long gap phase between nuclear envelope breakdown and the onset of spindle assembly, and to promote the rapid capture of all chromosomes by the acentrosomal spindle. The initial phase of chromosome clustering is driven by a dynamic network of Formin-2- and Spire-nucleated actin cables. The actin cables form in the disassembling nucleus and migrate towards the nuclear centre, moving the chromosomes centripetally by interacting with their arms and kinetochores as they migrate. A cage of stable microtubule loops drives the late stages of chromosome clustering. Together, our data establish a crucial role for chromosome clustering in accurate progression through meiosis.
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66
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Asami M, Lam BYH, Hoffmann M, Suzuki T, Lu X, Yoshida N, Ma MK, Rainbow K, Gužvić M, VerMilyea MD, Yeo GSH, Klein CA, Perry ACF. A program of successive gene expression in mouse one-cell embryos. Cell Rep 2023; 42:112023. [PMID: 36729835 DOI: 10.1016/j.celrep.2023.112023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/26/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
At the moment of union in fertilization, sperm and oocyte are transcriptionally silent. The ensuing onset of embryonic transcription (embryonic genome activation [EGA]) is critical for development, yet its timing and profile remain elusive in any vertebrate species. We here dissect transcription during EGA by high-resolution single-cell RNA sequencing of precisely synchronized mouse one-cell embryos. This reveals a program of embryonic gene expression (immediate EGA [iEGA]) initiating within 4 h of fertilization. Expression during iEGA produces canonically spliced transcripts, occurs substantially from the maternal genome, and is mostly downregulated at the two-cell stage. Transcribed genes predict regulation by transcription factors (TFs) associated with cancer, including c-Myc. Blocking c-Myc or other predicted regulatory TF activities disrupts iEGA and induces acute developmental arrest. These findings illuminate intracellular mechanisms that regulate the onset of mammalian development and hold promise for the study of cancer.
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Affiliation(s)
- Maki Asami
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Brian Y H Lam
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Martin Hoffmann
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Regensburg, Germany
| | - Toru Suzuki
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Naoko Yoshida
- Department of Pathology, Kansai Medical University, Osaka 573-1010, Japan
| | - Marcella K Ma
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Kara Rainbow
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Miodrag Gužvić
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Matthew D VerMilyea
- Embryology and Andrology Laboratories, Ovation Fertility Austin, Austin, TX 78731, USA
| | - Giles S H Yeo
- Medical Research Council (MRC) Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Christoph A Klein
- Project Group Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Regensburg, Germany; Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany.
| | - Anthony C F Perry
- Laboratory of Mammalian Molecular Embryology, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.
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Khozyainova AA, Valyaeva AA, Arbatsky MS, Isaev SV, Iamshchikov PS, Volchkov EV, Sabirov MS, Zainullina VR, Chechekhin VI, Vorobev RS, Menyailo ME, Tyurin-Kuzmin PA, Denisov EV. Complex Analysis of Single-Cell RNA Sequencing Data. BIOCHEMISTRY (MOSCOW) 2023; 88:231-252. [PMID: 37072324 PMCID: PMC10000364 DOI: 10.1134/s0006297923020074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This approach provides information about molecular features (gene expression, mutations, chromatin accessibility, etc.) of cells, opens up the possibility to analyze the trajectories/phylogeny of cell differentiation and cell-cell interactions, and helps in discovery of new cell types and previously unexplored processes. From a clinical point of view, scRNA-seq facilitates deeper and more detailed analysis of molecular mechanisms of diseases and serves as a basis for the development of new preventive, diagnostic, and therapeutic strategies. The review describes different approaches to the analysis of scRNA-seq data, discusses the advantages and disadvantages of bioinformatics tools, provides recommendations and examples of their successful use, and suggests potential directions for improvement. We also emphasize the need for creating new protocols, including multiomics ones, for the preparation of DNA/RNA libraries of single cells with the purpose of more complete understanding of individual cells.
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Affiliation(s)
- Anna A Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia.
| | - Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Mikhail S Arbatsky
- Laboratory of Artificial Intelligence and Bioinformatics, The Russian Clinical Research Center for Gerontology, Pirogov Russian National Medical University, Moscow, 129226, Russia
- School of Public Administration, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Sergey V Isaev
- Research Institute of Personalized Medicine, National Center for Personalized Medicine of Endocrine Diseases, National Medical Research Center for Endocrinology, Moscow, 117036, Russia
| | - Pavel S Iamshchikov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
- Laboratory of Complex Analysis of Big Bioimage Data, National Research Tomsk State University, Tomsk, 634050, Russia
| | - Egor V Volchkov
- Department of Oncohematology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117198, Russia
| | - Marat S Sabirov
- Laboratory of Bioinformatics and Molecular Genetics, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russia
| | - Viktoria R Zainullina
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Vadim I Chechekhin
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Rostislav S Vorobev
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Maxim E Menyailo
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
| | - Pyotr A Tyurin-Kuzmin
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny V Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, 634050, Russia
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Wu X, Liu Y, Wang W, Crimmings K, Williams A, Mager J, Cui W. Early embryonic lethality of mice lacking POLD2. Mol Reprod Dev 2023; 90:98-108. [PMID: 36528861 PMCID: PMC9974775 DOI: 10.1002/mrd.23663] [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: 08/05/2022] [Revised: 11/09/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
As a highly conserved DNA polymerase (Pol), Pol δ plays crucial roles in chromosomal DNA synthesis and various DNA repair pathways. However, the function of POLD2, the second small subunit of DNA Pol δ (p50 subunit), has not been characterized in vivo during mammalian development. Here, we report for the first time, the essential role of subunit POLD2 during early murine embryogenesis. Although Pold2 mutant mouse embryos exhibit normal morphology at E3.5 blastocyst stage, they cannot be recovered at gastrulation stages. Outgrowth assays reveal that mutant blastocysts cannot hatch from the zona pellucida, indicating impaired blastocyst function. Notably, these phenotypes can be recapitulated by small interfering RNA (siRNA)-mediated knockdown, which also exhibit slowed cellular proliferation together with skewed primitive endoderm and epiblast allocation during the second cell lineage specification. In summary, our study demonstrates that POLD2 is essential for the earliest steps of mammalian development, and the retarded proliferation and embryogenesis may also alter the following cell lineage specifications in the mouse blastocyst embryos.
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Affiliation(s)
- Xiaoqing Wu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, Anhui, China
| | - Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, Anhui, China
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Wenying Wang
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Fuyang Normal University, Fuyang, Anhui, China
| | - Kate Crimmings
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Andrea Williams
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
- Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA
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Remodeling of maternal mRNA through poly(A) tail orchestrates human oocyte-to-embryo transition. Nat Struct Mol Biol 2023; 30:200-215. [PMID: 36646905 PMCID: PMC9935398 DOI: 10.1038/s41594-022-00908-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023]
Abstract
Poly(A)-tail-mediated post-transcriptional regulation of maternal mRNAs is vital in the oocyte-to-embryo transition (OET). Nothing is known about poly(A) tail dynamics during the human OET. Here, we show that poly(A) tail length and internal non-A residues are highly dynamic during the human OET, using poly(A)-inclusive RNA isoform sequencing (PAIso-seq). Unexpectedly, maternal mRNAs undergo global remodeling: after deadenylation or partial degradation into 3'-UTRs, they are re-polyadenylated to produce polyadenylated degradation intermediates, coinciding with massive incorporation of non-A residues, particularly internal long consecutive U residues, into the newly synthesized poly(A) tails. Moreover, TUT4 and TUT7 contribute to the incorporation of these U residues, BTG4-mediated deadenylation produces substrates for maternal mRNA re-polyadenylation, and TENT4A and TENT4B incorporate internal G residues. The maternal mRNA remodeling is further confirmed using PAIso-seq2. Importantly, maternal mRNA remodeling is essential for the first cleavage of human embryos. Together, these findings broaden our understanding of the post-transcriptional regulation of maternal mRNAs during the human OET.
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70
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Treen N, Chavarria E, Weaver CJ, Brangwynne CP, Levine M. An FGF timer for zygotic genome activation. Genes Dev 2023; 37:80-85. [PMID: 36801820 PMCID: PMC10069452 DOI: 10.1101/gad.350164.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/19/2023] [Indexed: 02/19/2023]
Abstract
Zygotic genome activation has been extensively studied in a variety of systems including flies, frogs, and mammals. However, there is comparatively little known about the precise timing of gene induction during the earliest phases of embryogenesis. Here we used high-resolution in situ detection methods, along with genetic and experimental manipulations, to study the timing of zygotic activation in the simple model chordate Ciona with minute-scale temporal precision. We found that two Prdm1 homologs in Ciona are the earliest genes that respond to FGF signaling. We present evidence for a FGF timing mechanism that is driven by ERK-mediated derepression of the ERF repressor. Depletion of ERF results in ectopic activation of FGF target genes throughout the embryo. A highlight of this timer is the sharp transition in FGF responsiveness between the eight- and 16-cell stages of development. We propose that this timer is an innovation of chordates that is also used by vertebrates.
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Affiliation(s)
- Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA;
| | - Emily Chavarria
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Claire J Weaver
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Clifford P Brangwynne
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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71
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Human zygotic genome activation is initiated from paternal genome. Cell Discov 2023; 9:13. [PMID: 36717546 PMCID: PMC9887001 DOI: 10.1038/s41421-022-00494-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/09/2022] [Indexed: 02/01/2023] Open
Abstract
Although parental genomes undergo extensive epigenetic reprogramming to be equalized after fertilization, whether they play different roles in human zygotic genome activation (ZGA) remains unknown. Here, we mapped parental transcriptomes by using human parthenogenetic (PG) and androgenetic (AG) embryos during ZGA. Our data show that human ZGA is launched at the 8-cell stage in AG and bi-parental embryos, but at the morula stage in PG embryos. In contrast, mouse ZGA occurs at the same stage in PG and AG embryos. Mechanistically, primate-specific ZNF675 with AG-specific expression plays a role in human ZGA initiated from paternal genome at the 8-cell stage. AG-specifically expressed LSM1 is also critical for human maternal RNA degradation (MRD) and ZGA. The allelic expressions of ZNF675 and LSM1 are associated with their allelically epigenetic states. Notably, the paternally specific expressions of ZNF675 and LSM1 are also observed in diploid embryos. Collectively, human ZGA is initiated from paternal genome.
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72
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Niu H, Lei A, Tian H, Yao W, Liu Y, Li C, An X, Chen X, Zhang Z, Wu J, Yang M, Huang J, Cheng F, Zhao J, Hua J, Liu S, Luo J. Scd1 Deficiency in Early Embryos Affects Blastocyst ICM Formation through RPs-Mdm2-p53 Pathway. Int J Mol Sci 2023; 24:ijms24021750. [PMID: 36675264 PMCID: PMC9864350 DOI: 10.3390/ijms24021750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Embryos contain a large number of lipid droplets, and lipid metabolism is gradually activated during embryonic development to provide energy. However, the regulatory mechanisms remain to be investigated. Stearoyl-CoA desaturase 1 (Scd1) is a fatty acid desaturase gene that is mainly involved in intracellular monounsaturated fatty acid production, which takes part in many physiological processes. Analysis of transcripts at key stages of embryo development revealed that Scd1 was important and expressed at an increased level during the cleavage and blastocyst stages. Knockout Scd1 gene by CRISPR/Cas9 from zygotes revealed a decrease in lipid droplets (LDs) and damage in the inner cell mass (ICM) formation of blastocyst. Comparative analysis of normal and knockout embryo transcripts showed a suppression of ribosome protein (RPs) genes, leading to the arrest of ribosome biogenesis at the 2-cell stage. Notably, the P53-related pathway was further activated at the blastocyst stage, which eventually caused embryonic development arrest and apoptosis. In summary, Scd1 helps in providing energy for embryonic development by regulating intra-embryonic lipid droplet formation. Moreover, deficiency activates the RPs-Mdm2-P53 pathway due to ribosomal stress and ultimately leads to embryonic development arrest. The present results suggested that Scd1 gene is essential to maintain healthy development of embryos by regulating energy support.
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Affiliation(s)
- Huimin Niu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Anmin Lei
- Shaanxi Stem Cell Engineering and Technology Research Center, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Huibin Tian
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Weiwei Yao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ying Liu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuetong An
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoying Chen
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhifei Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiao Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Min Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jiangtao Huang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fei Cheng
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jianqing Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jinlian Hua
- Shaanxi Stem Cell Engineering and Technology Research Center, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shimin Liu
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6018, Australia
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
- Correspondence:
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73
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Ko DK, Brandizzi F. Coexpression Network Construction and Visualization from Transcriptomes Underlying ER Stress Responses. Methods Mol Biol 2023; 2581:385-401. [PMID: 36413332 PMCID: PMC10500560 DOI: 10.1007/978-1-0716-2784-6_27] [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] [Indexed: 06/16/2023]
Abstract
Dynamic gene expression changes are primary cellular reactions in response to most stresses and developmental cues in all organisms, including plants. With the ever-decreasing cost and increasing access, high-throughput transcriptome analyses have become a significant research tool to understand a wide spectrum of complex gene regulatory mechanisms. However, it is still challenging to understand the complete picture of gene responses because of the interactive and dynamic nature of gene expression in biological networks. Coexpression network analyses followed by network mapping are being increasingly applied to overcome this challenge. In this chapter, we will introduce detailed instructions for performing a weighted coexpression network analysis (WGCNA) and network visualization using a transcriptome dataset obtained during recovery from endoplasmic reticulum (ER) stress in Arabidopsis thaliana. The streamlined workflow described here allows biologists to identify and visualize coexpression interactions among genes, accessing a comprehensive landscape of dynamic gene expression changes for further downstream analyses using their datasets.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI, USA.
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
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74
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Scheuren M, Möhner J, Zischler H. R-loop landscape in mature human sperm: Regulatory and evolutionary implications. Front Genet 2023; 14:1069871. [PMID: 37139234 PMCID: PMC10149866 DOI: 10.3389/fgene.2023.1069871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
R-loops are three-stranded nucleic acid structures consisting of an RNA:DNA hybrid and a displaced DNA strand. While R-loops pose a potential threat to genome integrity, they constitute 5% of the human genome. The role of R-loops in transcriptional regulation, DNA replication, and chromatin signature is becoming increasingly clear. R-loops are associated with various histone modifications, suggesting that they may modulate chromatin accessibility. To potentially harness transcription-coupled repair mechanisms in the germline, nearly the entire genome is expressed during the early stages of male gametogenesis in mammals, providing ample opportunity for the formation of a transcriptome-dependent R-loop landscape in male germ cells. In this study, our data demonstrated the presence of R-loops in fully mature human and bonobo sperm heads and their partial correspondence to transcribed regions and chromatin structure, which is massively reorganized from mainly histone to mainly protamine-packed chromatin in mature sperm. The sperm R-loop landscape resembles characteristic patterns of somatic cells. Surprisingly, we detected R-loops in both residual histone and protamine-packed chromatin and localize them to still-active retroposons, ALUs and SINE-VNTR-ALUs (SVAs), the latter has recently arisen in hominoid primates. We detected both evolutionarily conserved and species-specific localizations. Comparing our DNA-RNA immunoprecipitation (DRIP) data with published DNA methylation and histone chromatin immunoprecipitation (ChIP) data, we hypothesize that R-loops epigenetically reduce methylation of SVAs. Strikingly, we observe a strong influence of R-loops on the transcriptomes of zygotes from early developmental stages before zygotic genome activation. Overall, these findings suggest that chromatin accessibility influenced by R-loops may represent a system of inherited gene regulation.
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75
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Martin A, Mercader A, Dominguez F, Quiñonero A, Perez M, Gonzalez-Martin R, Delgado A, Mifsud A, Pellicer A, De Los Santos MJ. Mosaic results after preimplantation genetic testing for aneuploidy may be accompanied by changes in global gene expression. Front Mol Biosci 2023; 10:1180689. [PMID: 37122560 PMCID: PMC10140421 DOI: 10.3389/fmolb.2023.1180689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Aneuploidy in preimplantation embryos is a major cause of human reproductive failure. Unlike uniformly aneuploid embryos, embryos diagnosed as diploid-aneuploid mosaics after preimplantation genetic testing for aneuploidy (PGT-A) can develop into healthy infants. However, the reason why these embryos achieve full reproductive competence needs further research. Current RNA sequencing techniques allow for the investigation of the human preimplantation transcriptome, providing new insights into the molecular mechanisms of embryo development. In this prospective study, using euploid embryo gene expression as a control, we compared the transcriptome profiles of inner cell mass and trophectoderm samples from blastocysts with different levels of chromosomal mosaicism. A total of 25 samples were analyzed from 14 blastocysts with previous PGT-A diagnosis, including five low-level mosaic embryos and four high-level mosaic embryos. Global gene expression profiles visualized in cluster heatmaps were correlated with the original PGT-A diagnosis. In addition, gene expression distance based on the number of differentially expressed genes increased with the mosaic level, compared to euploid controls. Pathways involving apoptosis, mitosis, protein degradation, metabolism, and mitochondrial energy production were among the most deregulated within mosaic embryos. Retrospective analysis of the duration of blastomere cell cycles in mosaic embryos revealed several mitotic delays compared to euploid controls, providing additional evidence of the mosaic status. Overall, these findings suggest that embryos with mosaic results are not simply a misdiagnosis by-product, but may also have a genuine molecular identity that is compatible with their reproductive potential.
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Affiliation(s)
- A. Martin
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
| | - A. Mercader
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
- IVI-RMA Valencia, Valencia, Spain
| | - F. Dominguez
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
| | - A. Quiñonero
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
| | - M. Perez
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
| | | | | | | | - A. Pellicer
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
- IVI-RMA Rome, Rome, Italy
| | - M. J. De Los Santos
- IVI-RMA Foundation, Health Research Institute La Fe, Valencia, Spain
- IVI-RMA Valencia, Valencia, Spain
- *Correspondence: M. J. De Los Santos,
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76
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Charalambous C, Webster A, Schuh M. Aneuploidy in mammalian oocytes and the impact of maternal ageing. Nat Rev Mol Cell Biol 2023; 24:27-44. [PMID: 36068367 DOI: 10.1038/s41580-022-00517-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 11/09/2022]
Abstract
During fertilization, the egg and the sperm are supposed to contribute precisely one copy of each chromosome to the embryo. However, human eggs frequently contain an incorrect number of chromosomes - a condition termed aneuploidy, which is much more prevalent in eggs than in either sperm or in most somatic cells. In turn, aneuploidy in eggs is a leading cause of infertility, miscarriage and congenital syndromes. Aneuploidy arises as a consequence of aberrant meiosis during egg development from its progenitor cell, the oocyte. In human oocytes, chromosomes often segregate incorrectly. Chromosome segregation errors increase in women from their mid-thirties, leading to even higher levels of aneuploidy in eggs from women of advanced maternal age, ultimately causing age-related infertility. Here, we cover the two main areas that contribute to aneuploidy: (1) factors that influence the fidelity of chromosome segregation in eggs of women from all ages and (2) factors that change in response to reproductive ageing. Recent discoveries reveal new error-causing pathways and present a framework for therapeutic strategies to extend the span of female fertility.
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Affiliation(s)
- Chloe Charalambous
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandre Webster
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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77
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Li N, Cai Y, Zou M, Zhou J, Zhang L, Zhou L, Xiang W, Cui Y, Li H. CFIm-mediated alternative polyadenylation safeguards the development of mammalian pre-implantation embryos. Stem Cell Reports 2022; 18:81-96. [PMID: 36563685 PMCID: PMC9860127 DOI: 10.1016/j.stemcr.2022.11.016] [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: 03/06/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 12/24/2022] Open
Abstract
Alternative polyadenylation (APA) gives rise to transcripts with distinct 3' untranslated regions (3' UTRs), thereby affecting the fate of mRNAs. APA is strongly associated with cell proliferation and differentiation status, and thus likely plays a critical role in the embryo development. However, the pattern of APA in mammalian early embryos is still unknown. Here, we analyzed the 3' UTR lengths in human and mouse pre-implantation embryos using available single cell RNA-seq datasets and explored the underlying mechanism driving the changes. Although human and mouse early embryos displayed distinct patterns of 3' UTR changing, RNA metabolism pathways were involved in both species. The 3' UTR lengths are likely determined by the abundance of the cleavage factor I complex (CFIm) components NUDT21 and CPSF6 in the nucleus. Importantly, depletion of either component resulted in early embryo development arrest and 3' UTR shortening. Collectively, these data highlight an essential role for APA in the development of mammalian early embryos.
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Affiliation(s)
- Na Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Cai
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Min Zou
- Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430013, China
| | - Jian Zhou
- Wuhan Jianwen Biological Technology Co. LTD, Wuhan 430205, China
| | - Ling Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liquan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenpei Xiang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yan Cui
- International Center for Aging and Cancer, Hainan Medical University, Haikou 571199, China.
| | - Huaibiao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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78
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Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance. Commun Biol 2022; 5:1400. [PMID: 36543858 PMCID: PMC9772385 DOI: 10.1038/s42003-022-04338-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Posttranscriptional modification plays an important role in key embryonic processes. Adenosine-to-inosine RNA editing, a common example of such modifications, is widespread in human adult tissues and has various functional impacts and clinical consequences. However, whether it persists in a consistent pattern in most human embryos, and whether it supports embryonic development, are poorly understood. To address this problem, we compiled the largest human embryonic editome from 2,071 transcriptomes and identified thousands of recurrent embryonic edits (>=50% chances of occurring in a given stage) for each early developmental stage. We found that these recurrent edits prefer exons consistently across stages, tend to target genes related to DNA replication, and undergo organized loss in abnormal embryos and embryos from elder mothers. In particular, these recurrent edits are likely to enhance maternal mRNA clearance, a possible mechanism of which could be introducing more microRNA binding sites to the 3'-untranslated regions of clearance targets. This study suggests a potentially important, if not indispensable, role of RNA editing in key human embryonic processes such as maternal mRNA clearance; the identified editome can aid further investigations.
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79
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de Castro P, Vendrell X, Escrich L, Grau N, Gonzalez-Martin R, Quiñonero A, Dominguez F, Escribá MJ. Comparative single-cell transcriptomic profiles of human androgenotes and parthenogenotes during early development. Fertil Steril 2022; 119:675-687. [PMID: 36563838 DOI: 10.1016/j.fertnstert.2022.12.027] [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: 09/01/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To unravel the differential transcriptomic behavior of human androgenotes (AGs) and parthenogenotes (PGs) throughout the first cell cycles, analyze the differential expression of genes related to key biologic processes, and determine the time frame for embryonic genome activation (EGA) in AGs and PGs. DESIGN Laboratory study. SETTING Private fertility clinic. PATIENT(S) Mature oocytes were retrieved from healthy donors and subjected to artificial oocyte activation using calcium ionophore and puromycin to generate PGs (n = 6) or enucleated and subjected to intracytoplasmic sperm injection to generate AGs (n = 10). INTERVENTION(S) Uniparental constructs at different early stages of development were disaggregated into constituent single cells (we suggest the terms parthenocytes and androcytes) to characterize the single-cell transcriptional landscape using next-generation sequencing. MAIN OUTCOMES MEASURE(S) Transcriptomic profiles comparison between different stages of early development in AGs and PGs. RESULT(S) The uniparental transcriptomic profiles at the first cell cycle showed 68 down-regulated and 26 up-regulated differentially expressed genes (DEGs) in PGs compared with AGs. During the third cell cycle, we found 60 up-regulated and 504 down-regulated DEGs in PGs compared with AGs. In the fourth cell cycle, 1,771 up-regulated and 1,171 down-regulated DEGs were found in PGs compared with AGs. The AGs and PGs had reduced EGA profiles during the first 3 cell cycles, and a spike of EGA at the fourth cell cycle was observed in PGs. CONCLUSION(S) Transcriptomic analysis of AGs and PGs revealed their complementary behavior until the fourth cell cycle. Androgenotes undergo a low wave of transcription during the first cell cycle, which reflects the paternal contribution to cell cycle coordination, mechanics of cell division, and novel transcription regulation. Maternal transcripts are most prominent in the third and fourth cell cycles, with amplification of transcription related to morphogenic progression and embryonic developmental competence acquisition. Regarding EGA, in PGs, a primitive EGA begins at the 1-cell stage and gradually progresses until the 4-cell stage, when crucial epigenetic reprogramming (through methylation) is up-regulated. In addition, our longitudinal single-cell transcriptomic analysis challenges that the zygote and early cleavage stages are the only totipotent entities, by revealing potential totipotency in cleavage-stage AGs and implications of paternal transcripts.
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Affiliation(s)
- Pedro de Castro
- Grupo de Investigación en Medicina Reproductiva, Fundación FIVI, Instituto de Investigación Sanitaria La Fe (IIS LA FE), Valencia, Spain
| | | | | | | | - Roberto Gonzalez-Martin
- Grupo de Investigación en Medicina Reproductiva, Fundación FIVI, Instituto de Investigación Sanitaria La Fe (IIS LA FE), Valencia, Spain
| | - Alicia Quiñonero
- Grupo de Investigación en Medicina Reproductiva, Fundación FIVI, Instituto de Investigación Sanitaria La Fe (IIS LA FE), Valencia, Spain
| | - Francisco Dominguez
- Grupo de Investigación en Medicina Reproductiva, Fundación FIVI, Instituto de Investigación Sanitaria La Fe (IIS LA FE), Valencia, Spain.
| | - María José Escribá
- Grupo de Investigación en Medicina Reproductiva, Fundación FIVI, Instituto de Investigación Sanitaria La Fe (IIS LA FE), Valencia, Spain; IVI Valencia, Valencia, Spain
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80
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Sun H, Sun G, Zhang H, An H, Guo Y, Ge J, Han L, Zhu S, Tang S, Li C, Xu C, Guo X, Wang Q. Proteomic Profiling Reveals the Molecular Control of Oocyte Maturation. Mol Cell Proteomics 2022; 22:100481. [PMID: 36496143 PMCID: PMC9823227 DOI: 10.1016/j.mcpro.2022.100481] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/31/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Meiotic maturation is an intricate and precisely regulated process orchestrated by various pathways and numerous proteins. However, little is known about the proteome landscape during oocytes maturation. Here, we obtained the temporal proteomic profiles of mouse oocytes during in vivo maturation. We successfully quantified 4694 proteins from 4500 oocytes in three key stages (germinal vesicle, germinal vesicle breakdown, and metaphase II). In particular, we discovered the novel proteomic features during oocyte maturation, such as the active Skp1-Cullin-Fbox pathway and an increase in mRNA decay-related proteins. Using functional approaches, we further identified the key factors controlling the histone acetylation state in oocytes and the vital proteins modulating meiotic cell cycle. Taken together, our data serve as a broad resource on the dynamics occurring in oocyte proteome and provide important knowledge to better understand the molecular mechanisms during germ cell development.
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Affiliation(s)
- Hongzheng Sun
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Guangyi Sun
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Haotian Zhang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Huiqing An
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Juan Ge
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Shuai Zhu
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Shoubin Tang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Congyang Li
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Chen Xu
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China; Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine, Suzhou Municipal Hospital, Nanjing Medical University, Nanjing, China; Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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81
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Rabbani M, Zheng X, Manske GL, Vargo A, Shami AN, Li JZ, Hammoud SS. Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses. Annu Rev Genet 2022; 56:339-368. [PMID: 36070560 PMCID: PMC10722372 DOI: 10.1146/annurev-genet-080320-040045] [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] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a complex differentiation process coordinated spatiotemporally across and along seminiferous tubules. Cellular heterogeneity has made it challenging to obtain stage-specific molecular profiles of germ and somatic cells using bulk transcriptomic analyses. This has limited our ability to understand regulation of spermatogenesis and to integrate knowledge from model organisms to humans. The recent advancement of single-cell RNA-sequencing (scRNA-seq) technologies provides insights into the cell type diversity and molecular signatures in the testis. Fine-grained cell atlases of the testis contain both known and novel cell types and define the functional states along the germ cell developmental trajectory in many species. These atlases provide a reference system for integrated interspecies comparisons to discover mechanistic parallels and to enable future studies. Despite recent advances, we currently lack high-resolution data to probe germ cell-somatic cell interactions in the tissue environment, but the use of highly multiplexed spatial analysis technologies has begun to resolve this problem. Taken together, recent single-cell studies provide an improvedunderstanding of gametogenesis to examine underlying causes of infertility and enable the development of new therapeutic interventions.
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Affiliation(s)
- Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Gabe L Manske
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander Vargo
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Adrienne N Shami
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Urology, University of Michigan, Ann Arbor, Michigan, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
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82
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Niu Y, Yan J, Jiang H. Anesthesia and developing brain: What have we learned from recent studies. Front Mol Neurosci 2022; 15:1017578. [PMID: 36479527 PMCID: PMC9720124 DOI: 10.3389/fnmol.2022.1017578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2023] Open
Abstract
Anesthesia is unavoidable in surgical procedures. However, whether the general anesthetics are neurotoxic to immature brains remains undefined. Neurodevelopmental impairment induced by anesthesia has been a critical health issue and topic of concern. This review summarizes recent progress made in clinical and preclinical studies to provide useful suggestions and potential therapeutic targets for the protection of the immature brain. On the one hand, clinical researchers continue the debate about the effect of single and multiple exposures to anesthesia on developing brains. On the other hand, preclinical researchers focus on exploring the mechanisms of neurotoxic effects of general anesthesia on immature brains and seeking novel solutions. Rodent models have always been used in preclinical studies, but it is still unclear whether the mechanisms observed in rodent models have clinical relevance. Compared with these models, non-human primates (NHPs) are more genetically similar to humans. However, few research institutions in this area can afford to use NHP models in their studies. One way to address both problems is by combining single-cell sequencing technologies to screen differential gene expression in NHPs and perform in vivo validation in rodents. The mechanism of anesthesia-induced neurotoxicity still requires further elucidation in primates.
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Affiliation(s)
| | - Jia Yan
- Department of Anesthesiology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Jiang
- Department of Anesthesiology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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83
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Cao D, Wang S, Zhang D, Zhang Y, Cao J, Liu Y, Zhou H. KRAB family is involved in network shifts in response to osmotic stress in camels. Anim Cells Syst (Seoul) 2022; 26:348-357. [PMID: 36605583 PMCID: PMC9809417 DOI: 10.1080/19768354.2022.2143894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A feature of the camel is its tolerance to osmotic stress. However, few studies of osmotic stress in vivo or comparative analyses between different tissues of the camel have been performed. Here, we report the roles of Krüppel-associated box domain containing zinc-finger repressor proteins (KRAB-ZFPs) in transcriptional networks under osmotic stress in camels by analyzing transcriptomes of four different tissues under various osmotic conditions. We found that 273 of 278 KRAB-ZFPs were expressed in our data set, being involved in all of the 65 identified networks and exhibiting their extensive functional diversity. We also found that 110 KRAB-ZFPs were hub genes involved in more than half of the networks. We demonstrated that the osmotic stress response is involved in network shifts and that KRAB-ZFPs mediate this process. Finally, we presented the diverse mechanisms of osmotic stress responses in different tissues. These results revealed the genetic architecture of systematic physiological response in vivo to osmotic stress in camels. Our work will lead to new directions for studying the mechanism of osmotic stress response in anti-arid mammals.
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Affiliation(s)
- Dandan Cao
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Shenyuan Wang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China,Sheep Collaboration and Innovation Center, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Dong Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Yanru Zhang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Junwei Cao
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China
| | - Yongbin Liu
- Sheep Collaboration and Innovation Center, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Huanmin Zhou
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, People’s Republic of China,Sheep Collaboration and Innovation Center, Inner Mongolia University, Hohhot, People’s Republic of China, Huanmin Zhou College of Life Science, Inner Mongolia Agricultural University, No. 306 Zhaowuda Road, Hohhot, Inner Mongolia010018, People’s Republic of China; Sheep Collaboration and Innovation Center, Inner Mongolia University, No. 235 Daxue West Street, Hohhot, Inner Mongolia010021, People’s Republic of China
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84
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Li C, Zhang Y, Leng L, Pan X, Zhao D, Li X, Huang J, Bolund L, Lin G, Luo Y, Xu F. The single-cell expression profile of transposable elements and transcription factors in human early biparental and uniparental embryonic development. Front Cell Dev Biol 2022; 10:1020490. [PMID: 36438554 PMCID: PMC9691860 DOI: 10.3389/fcell.2022.1020490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/17/2022] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) and transcription factors (TFs) are involved in the precise regulation of gene expression during the preimplantation stage. Activation of TEs is a key event for mammalian embryonic genome activation and preimplantation early embryonic development. TFs are involved in the regulation of drastic changes in gene expression patterns, but an inventory of the interplay between TEs and TFs during normal/abnormal human embryonic development is still lacking. Here we used single-cell RNA sequencing data generated from biparental and uniparental embryos to perform an integrative analysis of TE and TF expression. Our results showed that endogenous retroviruses (ERVs) are mainly expressed during the minor embryonic genome activation (EGA) process of early embryos, while Alu is gradually expressed in the middle and later stages. Some important ERVs (e.g., LTR5_Hs, MLT2A1) and Alu TEs are expressed at significantly lower levels in androgenic embryos. Integrative analysis revealed that the expression of the transcription factors CTCF and POU5F1 is correlated with the differential expression of ERV TEs. Comparative coexpression network analysis further showed distinct expression levels of important TFs (e.g., LEUTX and ZSCAN5A) in dizygotic embryos vs. parthenogenetic and androgenic embryos. This systematic investigation of TE and TF expression in human early embryonic development by single-cell RNA sequencing provides valuable insights into mammalian embryonic development.
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Affiliation(s)
- Conghui Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yue Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Lizhi Leng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Xiaoguang Pan
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xuemei Li
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Jinrong Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lars Bolund
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Key Laboratory of Reproductive and Stem Cells Engineering, Ministry of Health, Changsha, China
- Reproductive & Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yonglun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Fengping Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI Cell, BGI-Shenzhen, Shenzhen, China
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85
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Wen L, Li G, Huang T, Geng W, Pei H, Yang J, Zhu M, Zhang P, Hou R, Tian G, Su W, Chen J, Zhang D, Zhu P, Zhang W, Zhang X, Zhang N, Zhao Y, Cao X, Peng G, Ren X, Jiang N, Tian C, Chen ZJ. Single-cell technologies: From research to application. Innovation (N Y) 2022; 3:100342. [PMID: 36353677 PMCID: PMC9637996 DOI: 10.1016/j.xinn.2022.100342] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
Abstract
In recent years, more and more single-cell technologies have been developed. A vast amount of single-cell omics data has been generated by large projects, such as the Human Cell Atlas, the Mouse Cell Atlas, the Mouse RNA Atlas, the Mouse ATAC Atlas, and the Plant Cell Atlas. Based on these single-cell big data, thousands of bioinformatics algorithms for quality control, clustering, cell-type annotation, developmental inference, cell-cell transition, cell-cell interaction, and spatial analysis are developed. With powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence, the molecular landscape at the single-cell level can be revealed. With spatial transcriptomics and single-cell multi-omics, even the spatial dynamic multi-level regulatory mechanisms can be deciphered. Such single-cell technologies have many successful applications in oncology, assisted reproduction, embryonic development, and plant breeding. We not only review the experimental and bioinformatics methods for single-cell research, but also discuss their applications in various fields and forecast the future directions for single-cell technologies. We believe that spatial transcriptomics and single-cell multi-omics will become the next booming business for mechanism research and commercial industry.
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Affiliation(s)
- Lu Wen
- Biomedical Pioneering Innovation Centre (BIOPIC), Peking University, Beijing 100871, China
| | - Guoqiang Li
- Biomedical Pioneering Innovation Centre (BIOPIC), Peking University, Beijing 100871, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Geng
- School of Chemical Engineering and Technology, Sun Yat-Sen University, Zhuhai 519082, China
| | - Hao Pei
- Mozhuo Biotech (Zhejiang) Co., Ltd., Tongxiang, Jiaxing 314500, China
| | | | - Miao Zhu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Pengfei Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Rui Hou
- Geneis (Beijing) Co., Ltd., Beijing 100102, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing 100102, China
| | - Wentao Su
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
| | - Dake Zhang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Pingan Zhu
- Department of Mechanical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Wei Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiuxin Zhang
- Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Ning Zhang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yunlong Zhao
- Advanced Technology Institute, University of Surrey, Guildford, Surrey, GU2 7XH, UK
- National Physical Laboratory, Teddington, Middlesex TW11 0LW, UK
| | - Xin Cao
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guangdun Peng
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xianwen Ren
- Biomedical Pioneering Innovation Centre (BIOPIC), Peking University, Beijing 100871, China
| | - Nan Jiang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
- Jinfeng Laboratory, Chongqing 401329, China
| | - Caihuan Tian
- Center of Peony, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Flower Crops (North China), Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, 250012, China
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86
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Moharrek F, Ingerslev LR, Altıntaş A, Lundell L, Hansen AN, Small L, Workman CT, Barrès R. Comparative analysis of sperm DNA methylation supports evolutionary acquired epigenetic plasticity for organ speciation. Epigenomics 2022; 14:1305-1324. [PMID: 36420698 DOI: 10.2217/epi-2022-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Aim: To perform a comparative epigenomic analysis of DNA methylation in spermatozoa from humans, mice, rats and mini-pigs. Materials & methods: Genome-wide DNA methylation analysis was used to compare the methylation profiles of orthologous CpG sites. Transcription profiles of early embryo development were analyzed to provide insight into the association between sperm methylation and gene expression programming. Results: We identified DNA methylation variation near genes related to the central nervous system and signal transduction. Gene expression dynamics at different time points of preimplantation stages were modestly associated with spermatozoal DNA methylation at the nearest promoters. Conclusion: Conserved genomic regions subject to epigenetic variation across different species were associated with specific organ functions, suggesting their potential contribution to organ speciation and long-term adaptation to the environment.
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Affiliation(s)
- Farideh Moharrek
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ali Altıntaş
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Leonidas Lundell
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ann N Hansen
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Lewin Small
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Christopher T Workman
- Department of Biotechnology & Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Romain Barrès
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.,Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur & Centre National pour la Recherche Scientifique (CNRS), Valbonne, 06560, France
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87
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Paloviita P, Vuoristo S. The non-coding genome in early human development - Recent advancements. Semin Cell Dev Biol 2022; 131:4-13. [PMID: 35177347 DOI: 10.1016/j.semcdb.2022.02.010] [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: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Not that long ago, the human genome was discovered to be mainly non-coding, that is comprised of DNA sequences that do not code for proteins. The initial paradigm that non-coding is also non-functional was soon overturned and today the work to uncover the functions of non-coding DNA and RNA in human early embryogenesis has commenced. Early human development is characterized by large-scale changes in genomic activity and the transcriptome that are partly driven by the coordinated activation and repression of repetitive DNA elements scattered across the genome. Here we provide examples of recent novel discoveries of non-coding DNA and RNA interactions and mechanisms that ensure accurate non-coding activity during human maternal-to-zygotic transition and lineage segregation. These include studies on small and long non-coding RNAs, transposable element regulation, and RNA tailing in human oocytes and early embryos. High-throughput approaches to dissect the non-coding regulatory networks governing early human development are a foundation for functional studies of specific genomic elements and molecules that has only begun and will provide a wider understanding of early human embryogenesis and causes of infertility.
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Affiliation(s)
- Pauliina Paloviita
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynaecology, University of Helsinki, 00014 Helsinki, Finland.
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88
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Pladevall-Morera D, Zylicz JJ. Chromatin as a sensor of metabolic changes during early development. Front Cell Dev Biol 2022; 10:1014498. [PMID: 36299478 PMCID: PMC9588933 DOI: 10.3389/fcell.2022.1014498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular metabolism is a complex network of biochemical reactions fueling development with energy and biomass; however, it can also shape the cellular epigenome. Indeed, some intermediates of metabolic reactions exert a non-canonical function by acting as co-factors, substrates or inhibitors of chromatin modifying enzymes. Therefore, fluctuating availability of such molecules has the potential to regulate the epigenetic landscape. Thanks to this functional coupling, chromatin can act as a sensor of metabolic changes and thus impact cell fate. Growing evidence suggest that both metabolic and epigenetic reprogramming are crucial for ensuring a successful embryo development from the zygote until gastrulation. In this review, we provide an overview of the complex relationship between metabolism and epigenetics in regulating the early stages of mammalian embryo development. We report on recent breakthroughs in uncovering the non-canonical functions of metabolism especially when re-localized to the nucleus. In addition, we identify the challenges and outline future perspectives to advance the novel field of epi-metabolomics especially in the context of early development.
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Affiliation(s)
| | - Jan J. Zylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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89
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Wang SH, Hao J, Zhang C, Duan FF, Chiu YT, Shi M, Huang X, Yang J, Cao H, Wang Y. KLF17 promotes human naive pluripotency through repressing MAPK3 and ZIC2. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1985-1997. [PMID: 35391627 DOI: 10.1007/s11427-021-2076-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
The pluripotent state of embryonic stem cells (ESCs) is regulated by a sophisticated network of transcription factors. High expression of KLF17 has recently been identified as a hallmark of naive state of human ESCs (hESCs). However, the functional role of KLF17 in naive state is not clear. Here, by employing various gain and loss-of-function approaches, we demonstrate that KLF17 is essential for the maintenance of naive state and promotes the primed to naive state transition in hESCs. Mechanistically, we identify MAPK3 and ZIC2 as two direct targets repressed by KLF17. Overexpression of MAPK3 or ZIC2 partially blocks KLF17 from promoting the naive pluripotency. Furthermore, we find that human and mouse homologs of KLF17 retain conserved functions in promoting naive pluripotency of both species. Finally, we show that Klf17 may be essential for early embryo development in mouse. These findings demonstrate the important and conserved function of KLF17 in promoting naive pluripotency and reveal two essential transcriptional targets of KLF17 that underlie its function.
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Affiliation(s)
- Shao-Hua Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Jing Hao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Chao Zhang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Fei-Fei Duan
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Ya-Tzu Chiu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Ming Shi
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Huiqing Cao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, 100871, China.
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90
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Perry ACF, Asami M, Lam BYH, Yeo GSH. The initiation of mammalian embryonic transcription: to begin at the beginning. Trends Cell Biol 2022; 33:365-373. [PMID: 36182534 DOI: 10.1016/j.tcb.2022.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
Gamete (sperm and oocyte) genomes are transcriptionally silent until embryonic genome activation (EGA) following fertilization. EGA in humans had been thought to occur around the eight-cell stage, but recent findings suggest that it is triggered in one-cell embryos, by fertilization. Phosphorylation and other post-translational modifications during fertilization may instate transcriptionally favorable chromatin and activate oocyte-derived transcription factors (TFs) to initiate EGA. Expressed genes lay on cancer-associated pathways and their identities predict upregulation by MYC and other cancer-associated TFs. One interpretation of this is that the onset of EGA, and the somatic cell trajectory to cancer, are mechanistically related: cancer initiates epigenetically. We describe how fertilization might be linked to the initiation of EGA and involve distinctive processes recapitulated in cancer.
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Affiliation(s)
- Anthony C F Perry
- Laboratory of Mammalian Molecular Embryology, Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK.
| | - Maki Asami
- Laboratory of Mammalian Molecular Embryology, Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Brian Y H Lam
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Giles S H Yeo
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
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91
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Luo C, He B, Shi P, Xi J, Gui H, Pang B, Cheng J, Hu F, Chen X, Lv Y. Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa. FRONTIERS IN PLANT SCIENCE 2022; 13:988845. [PMID: 36204077 PMCID: PMC9530330 DOI: 10.3389/fpls.2022.988845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2022] [Indexed: 06/01/2023]
Abstract
Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.
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Affiliation(s)
- Chuping Luo
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Pibiao Shi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinlong Xi
- Zhejiang Institute of Standardization, Hangzhou, China
| | - Hongbing Gui
- College of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Bingwen Pang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Cheng
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xi Chen
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Yuanda Lv
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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92
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Dynamic and aberrant patterns of H3K4me3, H3K9me3, and H3K27me3 during early zygotic genome activation in cloned mouse embryos. ZYGOTE 2022; 30:903-909. [DOI: 10.1017/s0967199422000454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Summary
Somatic cell nuclear transfer (NT) is associated with aberrant changes in epigenetic reprogramming that impede the development of embryos, particularly during zygotic genome activation. Here, we characterized epigenetic patterns of H3K4me3, H3K9me3, and H3K27me3 in mouse NT embryos up to the second cell cycle (i.e. four-celled stage) during zygotic genome activation. In vivo fertilized and parthenogenetically activated (PA) embryos served as controls. In fertilized embryos, maternal and paternal pronuclei exhibited asymmetric H3K4me3, H3K9me3, and H3K27me3 modifications, with the paternal pronucleus showing delayed epigenetic modifications. Higher levels of H3K4me3 and H3K9me3 were observed in NT and PA embryos than in fertilized embryos. However, NT embryos exhibited a lower level of H3K27me3 than PA and fertilized embryos from pronuclear stage 3 to the four-celled stage. Our finding that NT embryos exhibited aberrant H3K4me3, H3K9me3, and H3K27me3 modifications in comparison with fertilized embryos during early zygotic genome activation help to unravel the epigenetic mechanisms of methylation changes in early NT reprogramming and provide an insight into the role of histone H3 in the regulation of cell plasticity during natural reproduction and somatic cell NT.
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93
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Chen F, Ma B, Lin Y, Luo X, Xu T, Zhang Y, Chen F, Li Y, Zhang Y, Luo B, Zhang Q, Xie X. Comparative maternal protein profiling of mouse biparental and uniparental embryos. Gigascience 2022; 11:6691138. [PMID: 36056732 PMCID: PMC9440387 DOI: 10.1093/gigascience/giac084] [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: 04/22/2022] [Revised: 06/29/2022] [Accepted: 08/01/2022] [Indexed: 12/25/2022] Open
Abstract
Background Maternal proteins have important roles during early embryonic development. However, our understanding of maternal proteins is still very limited. The integrated analysis of mouse uniparental (parthenogenetic) and biparental (fertilized) embryos at the protein level creates a protein expression landscape that can be used to explore preimplantation mouse development. Results Using label-free quantitative mass spectrometry (MS) analysis, we report on the maternal proteome of mouse parthenogenetic embryos at pronucleus, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages and highlight dynamic changes in protein expression. In addition, comparison of proteomic profiles of parthenogenotes and fertilized embryos highlights the different fates of maternal proteins. Enrichment analysis uncovered a set of maternal proteins that are strongly correlated with the subcortical maternal complex, and we report that in parthenogenotes, some of these maternal proteins escape the fate of protein degradation. Moreover, we identified a new maternal factor-Fbxw24, and highlight its importance in early embryonic development. We report that Fbxw24 interacts with Ddb1-Cul4b and may regulate maternal protein degradation in mouse. Conclusions Our study provides an invaluable resource for mechanistic analysis of maternal proteins and highlights the role of the novel maternal factor Fbw24 in regulating maternal protein degradation during preimplantation embryo development.
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Affiliation(s)
- Fumei Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Buguo Ma
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yongda Lin
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Tao Xu
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yuan Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Fang Chen
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yanfei Li
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Yaoyao Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Bin Luo
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Qingmei Zhang
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
| | - Xiaoxun Xie
- Department of Histology and Embryology, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China.,Central Laboratory, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P. R. China
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94
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Mohanty G, Jena SR, Kar S, Samanta L. Paternal factors in recurrent pregnancy loss: an insight through analysis of non-synonymous single-nucleotide polymorphism in human testis-specific chaperone HSPA2 gene. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62219-62234. [PMID: 34845642 DOI: 10.1007/s11356-021-17799-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Heat shock protein A2 (HSPA2) is a testis-specific molecular chaperone of the 70 kDa heat shock protein (HSP70) family and reported to play a key role in spermatogenesis as well as in the remodelling of the sperm surface during capacitation. It is established that mice lacking HSPA2 gene are infertile and spermatozoa that fail to interact with the zona pellucida of the oocyte consistently lack HSPA2 protein expression. However, its role in post fertilization events is not fully understood. Owing to the importance of HSPA2 in male reproduction, the present study is undertaken to reveal the association between genetic mutation and phenotypic variation in recurrent pregnancy loss (RPL) patients through an in silico prediction analysis. In this study, we used different computational tools and servers such as SIFT, PolyPhen2, PROVEAN, nsSNPAnalyzer, and SNPs & GO to analyse the functional consequences of the nsSNPs in human HSPA2 gene. The most damaging amino acid variants generated were subjected to I-Mutant 2.0 and ConSurf. Post-translational modifications such as phosphorylation mediated by these deleterious nsSNPs were analysed using NetPhos 2.0, and gene-gene interaction study was conducted using GeneMANIA. Finally, in-depth studies of the nsSNPs were studied through Project HOPE. The findings of the study revealed 18 nsSNPs to be deleterious using a combinatorial bioinformatic approach. Further functional analysis suggests that screening of nsSNP variants of HSPA2 that tend to be conserved and has potential to undergo phosphorylation at critical positions (rs764410231, rs200951589, rs756852956) may be useful for predicting outcome in altered reproductive outcome. The physicochemical alterations and its impact on the structural and functional conformity were determined by Project HOPE. Gene-gene interaction depicts its close association with antioxidant enzyme (SOD1) strongly supporting an inefficient oxidative scavenging regulatory mechanism in the spermatozoa of RPL patients as reported earlier. The present study has thus identified high-risk deleterious nsSNPs of HSPA2 gene and would be beneficial in the diagnosis and prognosis of the paternal effects in RPL patients.
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Affiliation(s)
- Gayatri Mohanty
- Redox Biology & Proteomics Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
- Centre for Excellence in Environment and Public Health, Ravenshaw University, Cuttack, Odisha, India
| | - Soumya Ranjan Jena
- Redox Biology & Proteomics Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
- Centre for Excellence in Environment and Public Health, Ravenshaw University, Cuttack, Odisha, India
| | - Sujata Kar
- Department of Obstetrics & Gynaecology, Kar Clinic and Hospital Pvt. Ltd., Bhubaneswar, Odisha, India
| | - Luna Samanta
- Redox Biology & Proteomics Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India.
- Centre for Excellence in Environment and Public Health, Ravenshaw University, Cuttack, Odisha, India.
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95
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Chen F, Li C. Inferring structural and dynamical properties of gene networks from data with deep learning. NAR Genom Bioinform 2022; 4:lqac068. [PMID: 36110897 PMCID: PMC9469930 DOI: 10.1093/nargab/lqac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/22/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
The reconstruction of gene regulatory networks (GRNs) from data is vital in systems biology. Although different approaches have been proposed to infer causality from data, some challenges remain, such as how to accurately infer the direction and type of interactions, how to deal with complex network involving multiple feedbacks, as well as how to infer causality between variables from real-world data, especially single cell data. Here, we tackle these problems by deep neural networks (DNNs). The underlying regulatory network for different systems (gene regulations, ecology, diseases, development) can be successfully reconstructed from trained DNN models. We show that DNN is superior to existing approaches including Boolean network, Random Forest and partial cross mapping for network inference. Further, by interrogating the ensemble DNN model trained from single cell data from dynamical system perspective, we are able to unravel complex cell fate dynamics during preimplantation development. We also propose a data-driven approach to quantify the energy landscape for gene regulatory systems, by combining DNN with the partial self-consistent mean field approximation (PSCA) approach. We anticipate the proposed method can be applied to other fields to decipher the underlying dynamical mechanisms of systems from data.
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Affiliation(s)
- Feng Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhe Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China
- School of Mathematical Sciences, Fudan University, Shanghai 200433, China
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Bu G, Zhu W, Liu X, Zhang J, Yu L, Zhou K, Wang S, Li Z, Fan Z, Wang T, Hu T, Hu R, Liu Z, Wang T, Wu L, Zhang X, Zhao S, Miao YL. Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos. Genome Res 2022; 32:1487-1501. [PMID: 35868641 PMCID: PMC9435746 DOI: 10.1101/gr.276207.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 07/19/2022] [Indexed: 02/03/2023]
Abstract
Histone modifications are critical epigenetic indicators of chromatin state associated with gene expression. Although the reprogramming patterns of H3K4me3 and H3K27me3 have been elucidated in mouse and human preimplantation embryos, the relationship between these marks and zygotic genome activation (ZGA) remains poorly understood. By ultra-low-input native chromatin immunoprecipitation and sequencing, we profiled global H3K4me3 and H3K27me3 in porcine oocytes and in vitro fertilized (IVF) embryos. We observed sharp H3K4me3 peaks in promoters of ZGA genes in oocytes, and these peaks became broader after fertilization and reshaped into sharp peaks again during ZGA. By simultaneous depletion of H3K4me3 demethylase KDM5B and KDM5C, we determined that broad H3K4me3 domain maintenance impaired ZGA gene expression, suggesting its function to prevent premature ZGA entry. In contrast, broad H3K27me3 domains underwent global removal upon fertilization, followed by a re-establishment for H3K4me3/H3K27me3 bivalency in morulae. We also found that bivalent marks were deposited at promoters of ZGA genes, and inhibiting this deposition was correlated with the activation of ZGA genes. It suggests that promoter bivalency contributes to ZGA exit in porcine embryos. Moreover, we demonstrated that aberrant reprogramming of H3K4me3 and H3K27me3 triggered ZGA dysregulation in somatic cell nuclear transfer (SCNT) embryos, whereas H3K27me3-mediated imprinting did not exist in porcine IVF and SCNT embryos. Our findings highlight two previously unknown epigenetic reprogramming modes coordinated with ZGA in porcine preimplantation embryos. Finally, the similarities observed between porcine and human histone modification dynamics suggest that the porcine embryo may also be a useful model for human embryo research.
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Affiliation(s)
- Guowei Bu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Wei Zhu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Longtao Yu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Kai Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Shangke Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Zhekun Li
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Zhengang Fan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Tingting Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Taotao Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Zhiting Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Tao Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518120, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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97
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Ai Z, Xiang X, Xiang Y, Szczerbinska I, Qian Y, Xu X, Ma C, Su Y, Gao B, Shen H, Bin Ramli MN, Chen D, Liu Y, Hao JJ, Ng HH, Zhang D, Chan YS, Liu W, Liang H. Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency. Cell Rep 2022; 40:111240. [PMID: 36001968 DOI: 10.1016/j.celrep.2022.111240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.
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Affiliation(s)
- Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yangquan Xiang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Iwona Szczerbinska
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yuli Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Xiao Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Chenyang Ma
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yaqi Su
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Bing Gao
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Hao Shen
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Muhammad Nadzim Bin Ramli
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Di Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yue Liu
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Jia-Jie Hao
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Huck Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117597, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.
| | - Yun-Shen Chan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China; Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China.
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98
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Xu M, Cheng A, Yu L, Wei W, Li J, Cai C. AHNAK2 is a biomarker and a potential therapeutic target of adenocarcinomas. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1708-1719. [PMID: 36017889 PMCID: PMC9828698 DOI: 10.3724/abbs.2022112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Adenocarcinoma is the second largest histological type of cervical cancer, second only to cervical squamous cell carcinoma. At present, despite the clinical treatment strategies of cervical adenocarcinoma and cervical squamous cell carcinoma being similar, the outcome and prognosis of cervical adenocarcinoma are significantly poor. Therefore, it is urgent to find specific biomarker and therapeutic target for cervical adenocarcinoma. In this study, we aim to reveal and verify the potential biomarkers and therapeutic targets of cervical adenocarcinoma. Weighted correlation network analysis (WGCNA) reveals the differentially-expressed genes significantly related to the histological characteristics of the two cervical cancer subtypes. We select the genes with the top 20 significance for further investigation. Through microarray and immunohistochemical (IHC) analyses of a variety of tumor tissues, we find that among these 20 genes, AHNAK2 is highly expressed not only in cervical adenocarcinoma, but also in multiple of adenocarcinoma tissues, including esophagus, breast and colon, while not in normal gland tissues. In vitro, AHNAK2 knockdown significantly inhibits cell proliferation and migration of adenocarcinoma cell lines. In vivo, AHNAK2 knockdown significantly inhibits tumor progression and metastasis of various adenocarcinomas. RNA-sequencing and bioinformatics analyses suggest that the inhibitory effect of AHNAK2 knockdown on tumor progression is achieved by regulating DNA replication and upregulating Bim expression. Together, we demonstrate that AHNAK2 is a biomarker and a potential therapeutic target for adenocarcinomas.
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Affiliation(s)
- Meng Xu
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan University; Medical Research InstituteFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Anyi Cheng
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan University; Medical Research InstituteFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Liya Yu
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan University; Medical Research InstituteFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Wei Wei
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan University; Medical Research InstituteFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430071China
| | - Jinpeng Li
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan UniversityWuhan430071China,Correspondence address. Tel: +86-13917642692; (C.C.) / Tel: +86-18807162791; (J.L.) @126.com
| | - Cheguo Cai
- Department of Thyroid and Breast SurgeryZhongnan Hospital of Wuhan University; Medical Research InstituteFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430071China,Correspondence address. Tel: +86-13917642692; (C.C.) / Tel: +86-18807162791; (J.L.) @126.com
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99
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Liu Y, Chen L, Yu J, Ye L, Hu H, Wang J, Wu B. Advances in Single-Cell Toxicogenomics in Environmental Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11132-11145. [PMID: 35881918 DOI: 10.1021/acs.est.2c01098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The toxicity evaluation system of environmental pollutants has undergone numerous changes due to the application of new technologies. Single-cell toxicogenomics is rapidly changing our view on environmental toxicology by increasing the resolution of our analysis to the level of a single cell. Applications of this technology in environmental toxicology have begun to emerge and are rapidly expanding the portfolio of existing technologies and applications. Here, we first summarized different methods involved in single-cell isolation and amplification in single-cell sequencing process, compared the advantages and disadvantages of different methods, and analyzed their development trends. Then, we reviewed the main advances of single-cell toxicogenomics in environmental toxicology, emphatically analyzed the application prospects of this technology in identifying the target cells of pollutants in early embryos, clarifying the heterogeneous response of cell subtypes to pollutants, and finding pathogenic bacteria in unknown microbes, and highlighted the unique characteristics of this approach with high resolution, high throughput, and high specificity by examples. We also offered a prediction of the further application of this technology and the revolution it brings in environmental toxicology. Overall, these advances will provide practical solutions for controlling or mitigating exogenous toxicological effects that threaten human and ecosystem health, contribute to improving our understanding of the physiological processes affected by pollutants, and lead to the emergence of new methods of pollution control.
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Affiliation(s)
- Yuxuan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jing Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
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100
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Portela M, Jimenez-Carretero D, Labrador V, Andreu MJ, Arza E, Caiolfa VR, Manzanares M. Chromatin dynamics through mouse preimplantation development revealed by single molecule localisation microscopy. Biol Open 2022; 11:275915. [PMID: 35876820 PMCID: PMC9346283 DOI: 10.1242/bio.059401] [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: 04/19/2022] [Accepted: 06/30/2022] [Indexed: 01/07/2023] Open
Abstract
Most studies addressing chromatin behaviour during preimplantation development are based on biochemical assays that lack spatial and cell-specific information, crucial during early development. Here, we describe the changes in chromatin taking place at the transition from totipotency to lineage specification, by using direct stochastical optical reconstruction microscopy (dSTORM) in whole-mount embryos during the first stages of mouse development. Through the study of two post-translational modifications of Histone 3 related to active and repressed chromatin, H3K4me3 and H3K9me3 respectively, we obtained a time-course of chromatin states, showing spatial differences between cell types, related to their differentiation state. This analysis adds a new layer of information to previous biochemical studies and provides novel insight to current models of chromatin organisation during the first stages of development. SUMMARY: We have applied super-resolution microscopy to analyse changes in the state of chromatin during the first stages of mouse development, from the two-cell stage to the blastocyst.
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Affiliation(s)
- Marta Portela
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain.,Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Daniel Jimenez-Carretero
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Veronica Labrador
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Maria Jose Andreu
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Elvira Arza
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
| | - Valeria R Caiolfa
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.,Center for Experimental Imaging, Ospedale San Raffaele, Milan 20132, Italy
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid 28049, Spain.,Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain
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