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Korchivaia E, Ivanova A, Volodyaev I, Semenova M. Comparison of Preimplantation Mouse Embryos with Different Genetic Backgrounds as Models for Evaluating Human Embryo Culture Media Composition. Reprod Sci 2024:10.1007/s43032-024-01726-1. [PMID: 39390272 DOI: 10.1007/s43032-024-01726-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 10/03/2024] [Indexed: 10/12/2024]
Abstract
Can the best culture medium be determined by mouse embryo testing? Zygotes/embryos of four different mouse strains: inbred Balb/c (n = 79) and C57Bl/6 (n = 95), F1 hybrid DBA/2*C57Bl/6 (n = 133), and outbred ICR (n = 69) were incubated in vitro in four culture media: 1-Step Culture Medium (VitaVitro), CSC medium (Irvine Scientific), Sage 1-Step medium (Origio), G-TL medium (Vitrolife). The embryos were cultured under standard conditions at atmospheric oxygen: 37℃; 6% CO2, 100% humidity. Standard MEA-test parameters (number of expanded blastocysts on E4.5), as well as additional characteristics (embryo development on E2.5-E4.5, number of hatching and hatched blastocysts on E4.5, embryo arrest and degeneration) were assessed for each of the strain-medium combinations. The results were compared across strains as well as across media. Embryo development depended on both the media and the mouse strain. Embryos from inbred and outbred mice were more sensitive to suboptimal culture conditions compared to the hybrid strain; this was reflected in reduced blastocyst and hatching rates, as well as an increased percentage of arrested and degraded embryos. The choice of optimal media depended strongly on the strain: CSC was better for Balb/c, Sage 1-step for C57Bl/6, while both were preferred for hybrids, and G-TL for outbreds. VitaVitro was quite good for hybrids and performed worse for other strains. Overall, the embryos of each strain behaved differently in different media, and it was not possible to make a real preference for any of them over human embryos based on the results of any single mouse strain. Only a pooled sample of different mouse strains can be used for comprehensive media MEA testing. MEA testing with any strain of mice is doomed to error due to their specific culture requirements. Hybrid mice are too reproductively efficient and cannot be used to distinguish media based on their subtle differences. Outbred and inbred mice are too sensitive and may be delayed or degraded in culture media that is well suited to the requirements of human embryos. Combined analysis of multiple mouse strains should be used to test media more fully and may serve as a model for the heterogeneity of human embryos in IVF clinics.
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Affiliation(s)
- E Korchivaia
- Department of Embryology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, Bld 12, Moscow, 119991, Russia.
| | - A Ivanova
- Department of Embryology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, Bld 12, Moscow, 119991, Russia
| | - I Volodyaev
- Department of Embryology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, Bld 12, Moscow, 119991, Russia
- European Medical Center, Moscow, Russia
- ICARM (Interdisciplinary Clinical Association for Reproductive Medicine, www.medkarm.org), Moscow, Russia
| | - M Semenova
- Department of Embryology, Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, 1, Bld 12, Moscow, 119991, Russia
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Li N, Wang H, Zou S, Yu X, Li J. Perspective in the Mechanisms for Repairing Sperm DNA Damage. Reprod Sci 2024:10.1007/s43032-024-01714-5. [PMID: 39333437 DOI: 10.1007/s43032-024-01714-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 09/23/2024] [Indexed: 09/29/2024]
Abstract
DNA damage in spermatozoa is a major cause of male infertility. It is also associated with adverse reproductive outcomes (including reduced fertilization rates, embryo quality and pregnancy rates, and higher rates of spontaneous miscarriage). The damage to sperm DNA occurs during the production and maturation of spermatozoa, as well as during their transit through the male reproductive tract. DNA damage repair typically occurs during spermatogenesis, oocytes after fertilization, and early embryonic development stages. The known mechanisms of sperm DNA repair mainly include nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), and double-strand break repair (DSBR). The most severe type of sperm DNA damage is double-strand break, and it will be repaired by DSBR, including homologous recombination (HR), classical non-homologous end joining (cNHEJ), alternative end joining (aEJ), and single-strand annealing (SSA). However, the precise mechanisms of DNA repair in spermatozoa remain incompletely understood. DNA repair-associated proteins are of great value in the repair of sperm DNA. Several repair-related proteins have been identified as playing critical roles in condensing chromatin, regulating transcription, repairing DNA damage, and regulating the cell cycle. It is noteworthy that XRCC4-like factor (XLF) and paralog of XRCC4 and XLF (PAXX) -mediated dimerization promote the processing of populated ends for cNHEJ repair, which suggests that XLF and PAXX have potential value in the mechanism of sperm DNA repair. This review summarizes the classic and potential repair mechanisms of sperm DNA damage, aiming to provide a perspective for further research on DNA damage repair mechanisms.
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Affiliation(s)
- Nihong Li
- Chengdu Fifth People's Hospital, The Fifth People's Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 611130, China
| | - Hong Wang
- Chengdu Fifth People's Hospital, The Fifth People's Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 611130, China
| | - Siying Zou
- Chengdu Fifth People's Hospital, The Fifth People's Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 611130, China
| | - Xujun Yu
- College of Medicine and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Junjun Li
- Chengdu Fifth People's Hospital, The Fifth People's Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 611130, China.
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Yu T, Wang C, Fan J, Chen R, Liu G, Xu X, Ning J, Lu X. Single-cell RNA sequencing revealed the roles of macromolecule epidermal growth factor receptor (EGFR) in the hybrid sterility of hermaphroditic Argopecten scallops. Int J Biol Macromol 2024; 280:136062. [PMID: 39341320 DOI: 10.1016/j.ijbiomac.2024.136062] [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: 08/09/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 10/01/2024]
Abstract
The macromolecule epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein that belongs to the protein kinase superfamily, which plays versatile functions in cell proliferation, development and fertility regulation. Almost all F1 hybrids obtained from the hermaphroditic bay scallops and Peruvian scallops exhibit infertility, and the genetic mechanism remains unclear. In this study, the comprehensive scRNA-seq was first conducted in the gonads of hybrid scallops, deducing the developmental sequence of germ cells and identifying the critical regulators in hybrid sterility: epidermal growth factor receptor. During the development from oogenesis phase germ cells to oocytes, the expression of the EGFR gene gradually decreased in sterile hybrids but increased in fertile hybrids. The significantly lower EGFR expression and ATP content, but higher ROS production rate was detected in the gonad of sterile hybrids than that in fertile hybrids, which might cause slow development of oocytes, stagnation of cell cycle, insufficient energy supply, high level of apoptosis and final sterility. Specific knock-down of EGFR gene led to decreased ATP content, increased ROS production rate, and inhibited oocyte maturation and gonadal development. These findings provide new insights into the roles of EGFR in hybrid infertility of bivalves and the healthy development of scallop breeding.
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Affiliation(s)
- Tieying Yu
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunde Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Jiawei Fan
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongjie Chen
- Laizhou Marine Development and Fishery Service Center, Laizhou 261400, China
| | - Guilong Liu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai 264006, China
| | - Xin Xu
- Yantai Spring-Sea AquaSeed, Ltd., Yantai 264006, China
| | - Junhao Ning
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, China.
| | - Xia Lu
- School of Ocean, Yantai University, Yantai, Shandong 264005, China.
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Lei X, Mao S, Li Y, Huang S, Li J, Du W, Kuang C, Yuan K. ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer types. J Genet Genomics 2024:S1673-8527(24)00241-8. [PMID: 39265822 DOI: 10.1016/j.jgg.2024.09.004] [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: 05/13/2024] [Revised: 09/04/2024] [Accepted: 09/05/2024] [Indexed: 09/14/2024]
Abstract
Human endogenous retroviruses (HERVs) comprise approximately 8% of the human genome, co-opted into the dynamic regulatory network of cellular potency in early embryonic development. In recent studies, resurgent HERVs' transcriptional activity has been frequently observed in many types of human cancers, suggesting their potential functions in the occurrence and progression of malignancy. However, a dedicated web resource for querying the relationship between activation of HERVs and cancer development is lacking. Here, we have constructed a database to explore the sequence information, expression profiles, survival prognosis, and genetic interactions of HERVs in diverse cancer types. Our database currently contains RNA sequencing data of 580 HERVs across 16246 samples, including that of 6478 tumoral and 634 normal tissues, 932 cancer cell lines, as well as 151 early embryonic and 8051 human adult tissues. The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics, pathology, pharmacology, and related areas, enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance. The ERVcancer database is available at http://kyuanlab.com/ervcancer/.
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Affiliation(s)
- Xiaoyun Lei
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, the Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, China
| | - Song Mao
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yinshuang Li
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shi Huang
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, China
| | - Jinchen Li
- Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, China
| | - Wei Du
- Department of Pathology, Changde Hospital, Xiangya School of Medicine, Central South University, Changde, Hunan 415000, China
| | - Chunmei Kuang
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kai Yuan
- Hunan Key Laboratory of Molecular Precision Medicine, Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410000, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Furong Laboratory, Changsha, Hunan 410000, China; The Biobank of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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5
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Zhu Q, Li F, Wang H, Wang X, Xiang Y, Ding H, Wu H, Xu C, Weng L, Cai J, Xu T, Liang N, Hong X, Xue M, Ge H. Single-cell RNA sequencing reveals the effects of high-fat diet on oocyte and early embryo development in female mice. Reprod Biol Endocrinol 2024; 22:105. [PMID: 39164729 PMCID: PMC11334609 DOI: 10.1186/s12958-024-01279-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Obesity is a global health issue with detrimental effects on various human organs, including the reproductive system. Observational human data and several lines of animal experimental data suggest that maternal obesity impairs ovarian function and early embryo development, but the precise pathogenesis remains unclear. METHODS We established a high-fat diet (HFD)-induced obese female mouse model to assess systemic metabolism, ovarian morphology, and oocyte function in mice. For the first time, this study employed single-cell RNA sequencing to explore the altered transcriptomic landscape of preimplantation embryos at different stages in HFD-induced obese mice. Differential gene expression analysis, enrichment analysis and protein-protein interactions network analysis were performed. RESULTS HFD-induced obese female mice exhibited impaired glucolipid metabolism and insulin resistance. The ovaries of HFD mice had a reduced total follicle number, an increased proportion of atretic follicles, and irregular granulosa cell arrangement. Furthermore, the maturation rate of embryonic development by in vitro fertilization of oocytes was significantly decreased in HFD mice. Additionally, the transcriptional landscapes of preimplantation embryos at different stages in mice induced by different diets were significantly distinguished. The maternal-to-zygotic transition was also affected by the failure to remove maternal RNAs and to turn off zygotic genome expression. CONCLUSIONS HFD-induced obesity impaired ovarian morphology and oocyte function in female mice and further led to alterations in the transcriptional landscape of preimplantation embryos at different stages of HFD mice.
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Affiliation(s)
- Qi Zhu
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Nanjing Medical University, Nanjing, China
| | - Feng Li
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Hao Wang
- Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Xia Wang
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Yu Xiang
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Huimin Ding
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Honghui Wu
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Dalian Medical University, Dalian, China
| | - Cen Xu
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Linglin Weng
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China
| | - Jieyu Cai
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China
| | - Tianyue Xu
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China
| | - Na Liang
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Dalian Medical University, Dalian, China
| | - Xiaoqi Hong
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Nanjing Medical University, Nanjing, China
| | - Mingrui Xue
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
- Graduate School, Dalian Medical University, Dalian, China
| | - Hongshan Ge
- Reproductive Medicine Centre, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
- Graduate School, Nanjing Medical University, Nanjing, China.
- Graduate School, Nanjing University Of Chinese Medicine, Nanjing, China.
- Graduate School, Dalian Medical University, Dalian, China.
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Zhang C, Nie Y, Xu B, Mu C, Tian GG, Li X, Cheng W, Zhang A, Li D, Wu J. Luteinizing Hormone Receptor Mutation (LHR N316S) Causes Abnormal Follicular Development Revealed by Follicle Single-Cell Analysis and CRISPR/Cas9. Interdiscip Sci 2024:10.1007/s12539-024-00646-7. [PMID: 39150470 DOI: 10.1007/s12539-024-00646-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024]
Abstract
Abnormal interaction between granulosa cells and oocytes causes disordered development of ovarian follicles. However, the interactions between oocytes and cumulus granulosa cells (CGs), oocytes and mural granulosa cells (MGs), and CGs and MGs remain to be fully explored. Using single-cell RNA-sequencing (scRNA-seq), we determined the transcriptional profiles of oocytes, CGs and MGs in antral follicles. Analysis of scRNA-seq data revealed that CGs may regulate follicular development through the BMP15-KITL-KIT-PI3K-ARF6 pathway with elevated expression of luteinizing hormone receptor (LHR). Because internalization of the LHR is regulated by Arf6, we constructed LHRN316S mice by CRISPR/Cas9 to further explore mechanisms of follicular development and novel treatment strategies for female infertility. Ovaries of LHRN316S mice exhibited reduced numbers of corpora lutea and ovulation. The LHRN316S mice had a reduced rate of oocyte maturation in vitro and decreased serum progesterone levels. Mating LHRN316S female mice with ICR wild type male mice revealed that the infertility rate of LHRN316S mice was 21.4% (3/14). Litter sizes from LHRN316S mice were smaller than those from control wild type female mice. The oocytes from LHRN316S mice had an increased rate of maturation in vitro after progesterone administration in vitro. Furthermore, progesterone treated LHRN316S mice produced offspring numbers per litter equivalent to WT mice. These findings provide key insights into cellular interactions in ovarian follicles and provide important clues for infertility treatment.
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Affiliation(s)
- Chen Zhang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Hematology, Tangdu Hospital, Xi'an, 710032, China
| | - Yongqiang Nie
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bufang Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chunlan Mu
- School of Basic Medical Sciences, Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China
| | - Geng G Tian
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyong Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weiwei Cheng
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
| | - Aijun Zhang
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China.
- School of Basic Medical Sciences, Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China.
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Biswas B, Kumar N, Sugimoto M, Hoque MA. scHD4E: Novel ensemble learning-based differential expression analysis method for single-cell RNA-sequencing data. Comput Biol Med 2024; 178:108769. [PMID: 38897145 DOI: 10.1016/j.compbiomed.2024.108769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/14/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Differential expression (DE) analysis between cell types for scRNA-seq data by capturing its complicated features is crucial. Recently, different methods have been developed for targeting the scRNA-seq data analysis based on different modeling frameworks, assumptions, strategies and test statistic in considering various data features. The scDEA is an ensemble learning-based DE analysis method developed recently, yielding p-values using Lancaster's combination, generated by 12 individual DE analysis methods, and producing more accurate and stable results than individual methods. The objective of our study is to propose a new ensemble learning-based DE analysis method, scHD4E, using top performers in only 4 separate methods. The top performer 4 methods have been selected through an evaluation process using six real scRNA-seq data sets. We conducted comprehensive experiments for five experimental data sets to evaluate our proposed method based on the sample size effects, batch effects, type I error control, gene ontology enrichment analysis, runtime, identified matched DE genes, and semantic similarity measurement between methods. We also perform similar analyses (except the last 3 terms) and compute performance measures like accuracy, F1 score, Mathew's correlation coefficient etc. for a simulated data set. The results show that scHD4E is performs better than all the individual and scDEA methods in all the above perspectives. We expect that scHD4E will serve the modern data scientists for detecting the DEGs in scRNA-seq data analysis. To implement our proposed method, a Github R package scHD4E and its shiny application has been developed, and available in the following links: https://github.com/bbiswas1989/scHD4E and https://github.com/bbiswas1989/scHD4E-Shiny.
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Affiliation(s)
- Biplab Biswas
- Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj, 8100, Bangladesh; Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi, 6205, Bangladesh.
| | - Nishith Kumar
- Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj, 8100, Bangladesh.
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Md Aminul Hoque
- Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi, 6205, Bangladesh.
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8
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Rich A, Acar O, Carvunis AR. Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome. Genome Biol 2024; 25:183. [PMID: 38978079 PMCID: PMC11232214 DOI: 10.1186/s13059-024-03287-7] [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: 06/20/2023] [Accepted: 05/20/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficult to infer using conventional approaches because nORFs tend to be short, of recent de novo origins, and lowly expressed. Here we develop a dedicated coexpression analysis framework that accounts for low expression to investigate the transcriptional regulation, evolution, and potential cellular roles of nORFs in Saccharomyces cerevisiae. RESULTS Our results reveal that nORFs tend to be preferentially coexpressed with genes involved in cellular transport or homeostasis but rarely with genes involved in RNA processing. Mechanistically, we discover that young de novo nORFs located downstream of conserved genes tend to leverage their neighbors' promoters through transcription readthrough, resulting in high coexpression and high expression levels. Transcriptional piggybacking also influences the coexpression profiles of young de novo nORFs located upstream of genes, but to a lesser extent and without detectable impact on expression levels. Transcriptional piggybacking influences, but does not determine, the transcription profiles of de novo nORFs emerging nearby genes. About 40% of nORFs are not strongly coexpressed with any gene but are transcriptionally regulated nonetheless and tend to form entirely new transcription modules. We offer a web browser interface ( https://carvunislab.csb.pitt.edu/shiny/coexpression/ ) to efficiently query, visualize, and download our coexpression inferences. CONCLUSIONS Our results suggest that nORF transcription is highly regulated. Our coexpression dataset serves as an unprecedented resource for unraveling how nORFs integrate into cellular networks, contribute to cellular phenotypes, and evolve.
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Affiliation(s)
- April Rich
- Joint Carnegie Mellon University-University of Pittsburgh, University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM), University of Pittsburgh, Pittsburgh, PA, USA
| | - Omer Acar
- Joint Carnegie Mellon University-University of Pittsburgh, University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM), University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM), University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Liu W, Chen C, Gao Y, Cui X, Zhang Y, Gu L, He Y, Li J, Gao S, Gao R, Jiang C. Transcriptome Dynamics and Cell Dialogs Between Oocytes and Granulosa Cells in Mouse Follicle Development. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad001. [PMID: 38955498 PMCID: PMC11423849 DOI: 10.1093/gpbjnl/qzad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/17/2023] [Accepted: 09/20/2023] [Indexed: 07/04/2024]
Abstract
The development and maturation of follicles is a sophisticated and multistage process. The dynamic gene expression of oocytes and their surrounding somatic cells and the dialogs between these cells are critical to this process. In this study, we accurately classified the oocyte and follicle development into nine stages and profiled the gene expression of mouse oocytes and their surrounding granulosa cells and cumulus cells. The clustering of the transcriptomes showed the trajectories of two distinct development courses of oocytes and their surrounding somatic cells. Gene expression changes precipitously increased at Type 4 stage and drastically dropped afterward within both oocytes and granulosa cells. Moreover, the number of differentially expressed genes between oocytes and granulosa cells dramatically increased at Type 4 stage, most of which persistently passed on to the later stages. Strikingly, cell communications within and between oocytes and granulosa cells became active from Type 4 stage onward. Cell dialogs connected oocytes and granulosa cells in both unidirectional and bidirectional manners. TGFB2/3, TGFBR2/3, INHBA/B, and ACVR1/1B/2B of TGF-β signaling pathway functioned in the follicle development. NOTCH signaling pathway regulated the development of granulosa cells. Additionally, many maternally DNA methylation- or H3K27me3-imprinted genes remained active in granulosa cells but silent in oocytes during oogenesis. Collectively, Type 4 stage is the key turning point when significant transcription changes diverge the fate of oocytes and granulosa cells, and the cell dialogs become active to assure follicle development. These findings shed new insights on the transcriptome dynamics and cell dialogs facilitating the development and maturation of oocytes and follicles.
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Affiliation(s)
- Wenju Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Chuan Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuhan Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuanlin He
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Jing Li
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
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10
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Tian X, Qin B, Yang L, Li H, Zhou W. Association of phthalate exposure with reproductive outcomes among infertile couples undergoing in vitro fertilization: A systematic review. ENVIRONMENTAL RESEARCH 2024; 252:118825. [PMID: 38609072 DOI: 10.1016/j.envres.2024.118825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
Human fertility is impacted by changes in lifestyle and environmental deterioration. To increase human fertility, assisted reproductive technology (ART) has been extensively used around the globe. As early as 2009, the Endocrine Society released its first scientific statement on the potential adverse effects of environmental endocrine-disrupting chemicals (EDCs) on human health and disease development. Chemicals known as phthalates, frequently employed as plasticizers and additives, are common EDCs. Numerous studies have shown that phthalate metabolites in vivo exert estrogen-like or anti-androgenic effects in both humans and animals. They are associated with the progression of a range of diseases, most notably interference with the reproductive process, damage to the placenta, and the initiation of chronic diseases in adulthood. Phthalates are ingested by infertile couples in a variety of ways, including household products, diet, medical treatment, etc. Exposure to phthalates may exacerbate their infertility or poor ART outcomes, however, the available data on phthalate exposure and ART pregnancy outcomes are sparse and contradictory. Therefore, this review conducted a systematic evaluation of 16 papers related to phthalate exposure and ART pregnancy outcomes, to provide more aggregated results, and deepen our understanding of reproductive outcomes in infertile populations with phthalate exposure.
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Affiliation(s)
- Xiangming Tian
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Boyi Qin
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Li Yang
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Huanhuan Li
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Wenhui Zhou
- Medical Center for Human Reproduction, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China.
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11
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Santana PDPB, Pinheiro KDC, Pereira LCDS, Andrade SS, Aburjaile FF, Ramos PDCDA, de Souza EB, da Costa NN, Cordeiro MDS, Santos SDSD, Miranda MDS, Ramos RTJ, da Silva ALDC. RNA sequencing and gene co-expression network of in vitro matured oocytes and blastocysts of buffalo. Anim Reprod 2024; 21:e20230131. [PMID: 38912163 PMCID: PMC11192227 DOI: 10.1590/1984-3143-ar2023-0131] [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: 09/27/2023] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
In reproductive technologies, uncovering the molecular aspects of oocyte and embryo competence under different conditions is crucial for refining protocols and enhancing efficiency. RNA-seq generates high-throughput data and provides transcriptomes that can undergo additional computational analyses. This study presented the transcriptomic profiles of in vitro matured oocytes and blastocysts produced in vitro from buffalo crossbred (Bubalus bubalis), coupled with gene co-expression and module preservation analysis. Cumulus Oophorus Complexes, obtained from slaughterhouse-derived ovaries, were subjected to in vitro maturation to yield metaphase II oocytes (616) or followed in vitro fertilization and culture to yield blastocysts for sequencing (526). Oocyte maturation (72%, ±3.34 sd) and embryo development (21.3%, ±4.18 sd) rates were obtained from three in vitro embryo production routines following standard protocols. Sequencing of 410 metaphase II oocytes and 70 hatched blastocysts (grade 1 and 2) identified a total of 13,976 genes, with 62% being ubiquitously expressed (8,649). Among them, the differentially expressed genes (4,153) and the strongly variable genes with the higher expression (fold-change above 11) were highlighted in oocytes (BMP15, UCHL1, WEE1, NLRPs, KPNA7, ZP2, and ZP4) and blastocysts (APOA1, KRT18, ANXA2, S100A14, SLC34A2, PRSS8 and ANXA2) as representative indicators of molecular quality. Additionally, genes exclusively found in oocytes (224) and blastocysts (2,200) with specific biological functions were identified. Gene co-expression network and module preservation analysis revealed strong preservation of functional modules related to exosome components, steroid metabolism, cell proliferation, and morphogenesis. However, cell cycle and amino acid transport modules exhibited weak preservation, which may reflect differences in embryo development kinetics and the activation of cell signaling pathways between buffalo and bovine. This comprehensive transcriptomic profile serves as a valuable resource for assessing the molecular quality of buffalo oocytes and embryos in future in vitro embryo production assays.
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Affiliation(s)
| | | | | | - Soraya Silva Andrade
- Laboratório de Genômica e Bioinformática, Universidade Federal do Pará, Belém, PA, Brasil
| | | | | | - Eduardo Baia de Souza
- Laboratório de Fertilização In Vitro, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
| | - Nathalia Nogueira da Costa
- Laboratório de Fertilização In Vitro, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
| | | | | | - Moysés dos Santos Miranda
- Laboratório de Fertilização In Vitro, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil
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12
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Nguyen H, Nguyen H, Tran D, Draghici S, Nguyen T. Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges. Nucleic Acids Res 2024; 52:4761-4783. [PMID: 38619038 PMCID: PMC11109966 DOI: 10.1093/nar/gkae267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).
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Affiliation(s)
- Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Ha Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
| | - Duc Tran
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, Detroit, MI, USA
- Advaita Bioinformatics, Ann Arbor, MI, USA
| | - Tin Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, AL, USA
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13
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Sfakianoudis K, Zikopoulos A, Grigoriadis S, Seretis N, Maziotis E, Anifandis G, Xystra P, Kostoulas C, Giougli U, Pantos K, Simopoulou M, Georgiou I. The Role of One-Carbon Metabolism and Methyl Donors in Medically Assisted Reproduction: A Narrative Review of the Literature. Int J Mol Sci 2024; 25:4977. [PMID: 38732193 PMCID: PMC11084717 DOI: 10.3390/ijms25094977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
One-carbon (1-C) metabolic deficiency impairs homeostasis, driving disease development, including infertility. It is of importance to summarize the current evidence regarding the clinical utility of 1-C metabolism-related biomolecules and methyl donors, namely, folate, betaine, choline, vitamin B12, homocysteine (Hcy), and zinc, as potential biomarkers, dietary supplements, and culture media supplements in the context of medically assisted reproduction (MAR). A narrative review of the literature was conducted in the PubMed/Medline database. Diet, ageing, and the endocrine milieu of individuals affect both 1-C metabolism and fertility status. In vitro fertilization (IVF) techniques, and culture conditions in particular, have a direct impact on 1-C metabolic activity in gametes and embryos. Critical analysis indicated that zinc supplementation in cryopreservation media may be a promising approach to reducing oxidative damage, while female serum homocysteine levels may be employed as a possible biomarker for predicting IVF outcomes. Nonetheless, the level of evidence is low, and future studies are needed to verify these data. One-carbon metabolism-related processes, including redox defense and epigenetic regulation, may be compromised in IVF-derived embryos. The study of 1-C metabolism may lead the way towards improving MAR efficiency and safety and ensuring the lifelong health of MAR infants.
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Affiliation(s)
- Konstantinos Sfakianoudis
- Centre for Human Reproduction, Genesis Athens Clinic, 14-16, Papanikoli, 15232 Athens, Greece; (K.S.); (K.P.)
| | - Athanasios Zikopoulos
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
- Obstetrics and Gynecology, Royal Cornwall Hospital, Treliske, Truro TR1 3LJ, UK
| | - Sokratis Grigoriadis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - Nikolaos Seretis
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
| | - Evangelos Maziotis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - George Anifandis
- Department of Obstetrics and Gynecology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41222 Larisa, Greece;
| | - Paraskevi Xystra
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - Charilaos Kostoulas
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
| | - Urania Giougli
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
| | - Konstantinos Pantos
- Centre for Human Reproduction, Genesis Athens Clinic, 14-16, Papanikoli, 15232 Athens, Greece; (K.S.); (K.P.)
| | - Mara Simopoulou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.G.); (E.M.); (P.X.)
| | - Ioannis Georgiou
- Laboratory of Medical Genetics, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.Z.); (N.S.); (C.K.); (U.G.); (I.G.)
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14
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Wang Y, Zhang K, Chen D, Liu K, Chen W, He F, Tong Z, Luo Q. Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici. Arch Microbiol 2024; 206:241. [PMID: 38698267 DOI: 10.1007/s00203-024-03925-5] [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: 12/02/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 05/05/2024]
Abstract
The epidemic of stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are difficult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for efficiently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between low susceptibility and high susceptibility samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene co-expression network, identified the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the co-expression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that resistance-related genes such as TaPR1, TaWRKY18 and HSP70 were highly expressed in the network. They were likely to be involved in the biological processes of Pst infecting wheat. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.
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Affiliation(s)
- Yibo Wang
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, National Tobacco Genetic Engineering Research Centre, Kunming, 650021, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Zhang
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Dan Chen
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Kai Liu
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Wei Chen
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, 100101, China
| | - Zhijun Tong
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, National Tobacco Genetic Engineering Research Centre, Kunming, 650021, China.
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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15
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Liu M, Ding Z, Sun P, Zhou S, Wu H, Huo L, Yang L, Davis JS, Liang A. Neddylation inhibition affects early embryonic development by disrupting maternal-to-zygotic transition and mitochondrial function in mice. Theriogenology 2024; 220:1-11. [PMID: 38457854 DOI: 10.1016/j.theriogenology.2024.02.029] [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: 10/01/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Post-translational modifications (PTMs) are critical for early development in mice because early cleavage-stage embryos are characterized by transcriptional inactivity. Neddylation is an important ubiquitin-like PTM that regulates multiple biophysical processes. However, the exact roles of neddylation in regulating early embryonic development remain largely unknown. In the present study, we found that inhibition of neddylation by specific inhibitor MLN4924 led to severe arrest of early embryonic development. Transcriptomic analysis showed that neddylation inhibition changed the expression of 3959 genes at the 2-cell stage. Importantly, neddylation inhibition blocked zygotic genome activation and maternal mRNA degradation, thus disrupting the maternal-to-zygotic transition. Moreover, inhibition of neddylation induced mitochondrial dysfunction including aberrant mitochondrial distribution, decreased mitochondrial membrane potential, and reduced ATP content. Further analysis showed that inhibition of neddylation resulted in the accumulation of reactive oxygen species and superoxide anion, thereby resulting in oxidative stress and severe DNA damage at the 2-cell stage. Overall, this study demonstrates that neddylation is vital for early embryonic development in mice. Our findings suggest that proper neddylation regulation is essential for the timely inter-stage transition during early embryonic development.
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Affiliation(s)
- Mingxiao Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Zhiming Ding
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, 230032, PR China
| | - Peihao Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Shuo Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Hanxiao Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Lijun Huo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China; Frontiers Science Center for Animal Breeding and Sustainable Production (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, PR China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China; Frontiers Science Center for Animal Breeding and Sustainable Production (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, PR China
| | - John S Davis
- Olson Center for Women's Health, Department of Obstetrics and Gynecology, University of Nebraska Medical Center, and Veterans Affairs Medical Center, Omaha, NE, 68198, USA
| | - Aixin Liang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China; Frontiers Science Center for Animal Breeding and Sustainable Production (Huazhong Agricultural University), Ministry of Education, Wuhan, 430070, PR China.
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16
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Park Y, Hauschild AC. The effect of data transformation on low-dimensional integration of single-cell RNA-seq. BMC Bioinformatics 2024; 25:171. [PMID: 38689234 PMCID: PMC11059821 DOI: 10.1186/s12859-024-05788-5] [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: 11/02/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Recent developments in single-cell RNA sequencing have opened up a multitude of possibilities to study tissues at the level of cellular populations. However, the heterogeneity in single-cell sequencing data necessitates appropriate procedures to adjust for technological limitations and various sources of noise when integrating datasets from different studies. While many analysis procedures employ various preprocessing steps, they often overlook the importance of selecting and optimizing the employed data transformation methods. RESULTS This work investigates data transformation approaches used in single-cell clustering analysis tools and their effects on batch integration analysis. In particular, we compare 16 transformations and their impact on the low-dimensional representations, aiming to reduce the batch effect and integrate multiple single-cell sequencing data. Our results show that data transformations strongly influence the results of single-cell clustering on low-dimensional data space, such as those generated by UMAP or PCA. Moreover, these changes in low-dimensional space significantly affect trajectory analysis using multiple datasets, as well. However, the performance of the data transformations greatly varies across datasets, and the optimal method was different for each dataset. Additionally, we explored how data transformation impacts the analysis of deep feature encodings using deep neural network-based models, including autoencoder-based models and proto-typical networks. Data transformation also strongly affects the outcome of deep neural network models. CONCLUSIONS Our findings suggest that the batch effect and noise in integrative analysis are highly influenced by data transformation. Low-dimensional features can integrate different batches well when proper data transformation is applied. Furthermore, we found that the batch mixing score on low-dimensional space can guide the selection of the optimal data transformation. In conclusion, data preprocessing is one of the most crucial analysis steps and needs to be cautiously considered in the integrative analysis of multiple scRNA-seq datasets.
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Affiliation(s)
- Youngjun Park
- Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany
- International Max Planck Research Schools for Genome Science, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Anne-Christin Hauschild
- Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany.
- Campus-Institute Data Science (CIDAS), Georg-August-Universität Göttingen, Göttingen, Germany.
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17
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Zhang H, Wang Y, Hu Z, Wu Y, Chen N, Zhu Y, Yu Y, Fan H, Wang H. Zygotic Splicing Activation of the Transcriptome is a Crucial Aspect of Maternal-to-Zygotic Transition and Required for the Conversion from Totipotency to Pluripotency. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308496. [PMID: 38308190 PMCID: PMC11005748 DOI: 10.1002/advs.202308496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/27/2023] [Indexed: 02/04/2024]
Abstract
During maternal-to-zygotic transition (MZT) in the embryo, mRNA undergoes complex post-transcriptional regulatory processes. However, it is unclear whether and how alternative splicing plays a functional role in MZT. By analyzing transcriptome changes in mouse and human early embryos, dynamic changes in alternative splicing during MZT are observed and a previously unnoticed process of zygotic splicing activation (ZSA) following embryonic transcriptional activation is described. As the underlying mechanism of RNA splicing, splicing factors undergo dramatic maternal-to-zygotic conversion. This conversion relies on the key maternal factors BTG4 and PABPN1L and is zygotic-transcription-dependent. CDK11-dependent phosphorylation of the key splicing factor, SF3B1, and its aggregation with SRSF2 in the subnuclear domains of 2-cell embryos are prerequisites for ZSA. Isoforms generated by erroneous splicing, such as full-length Dppa4, hinder normal embryonic development. Moreover, alternative splicing regulates the conversion of early embryonic blastomeres from totipotency to pluripotency, thereby affecting embryonic lineage differentiation. ZSA is an essential post-transcriptional process of MZT and has physiological significance in generating new life. In addition to transcriptional activation, appropriate expression of transcript isoforms is also necessary for preimplantation embryonic development.
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Affiliation(s)
- Hua Zhang
- MOA Key Laboratory of Animal VirologyCenter for Veterinary SciencesZhejiang UniversityHangzhou310058China
- Department of Veterinary MedicineCollege of Animal SciencesZhejiang UniversityHangzhou310058China
| | - Yang Wang
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhe‐Wei Hu
- MOA Key Laboratory of Animal VirologyCenter for Veterinary SciencesZhejiang UniversityHangzhou310058China
| | - Yun‐Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Nuo Chen
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Yi‐Min Zhu
- Department of Reproductive EndocrinologyWomen's HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310002China
| | - Yuan‐Song Yu
- Savaid Stomatology SchoolHangzhou Medical CollegeHangzhou310053China
| | - Heng‐Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- Assisted Reproduction UnitDepartment of Obstetrics and GynecologySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
- Center for Biomedical ResearchShaoxing InstituteZhejiang UniversityShaoxing312000China
| | - Hua‐Nan Wang
- MOA Key Laboratory of Animal VirologyCenter for Veterinary SciencesZhejiang UniversityHangzhou310058China
- Department of Veterinary MedicineCollege of Animal SciencesZhejiang UniversityHangzhou310058China
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18
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Ma T, Zhou S, Xie X, Chen J, Wang J, Zhang G. A case report of a family with developmental arrest of human prokaryotic stage zygote. Front Cell Dev Biol 2024; 12:1280797. [PMID: 38606321 PMCID: PMC11006971 DOI: 10.3389/fcell.2024.1280797] [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: 08/21/2023] [Accepted: 02/19/2024] [Indexed: 04/13/2024] Open
Abstract
To study the genetic variation leading to the arrest phenotype of pronuclear (PN) zygotes. We recruited a family characterized by recurrent PN arrest during in vitro fertilization (IVF) and intracytoplasmic sperm injection cycles (ICSI) and performed whole-exome sequencing for 2 individuals. The transcriptome profiles of PN-arrest zygotes were assessed by single-cell RNA sequencing analysis. The variants were then validated by PCR amplification and Sanger sequencing in the affected individuals and other family members. A family characterized by recurrent PN arrest during IVF and ICSI cycles were enrolled after giving written informed consent. Peripheral blood samples were taken for DNA extraction. Three PN-arrest zygotes from patient III-3 were used for single-cell RNA-seq as described. This phenotype was reproduced after multiple cycles of egg retrieval and after trying different fertilization methods and multiple ovulation regimens. The mutant genes of whole exon sequencing were screened and verified. The missense variant c. C1630T (p.R544W) in RGS12 was responsible for a phenotype characterized by paternal transmission. RGS12 controls Ca2+ oscillation, which is required for oocyte activation after fertilization. Single-cell transcriptome profiling of PN-arrest zygotes revealed defective established translation, RNA processing and cell cycle, which explained the failure of complete oocyte activation. Furthermore, we identified proximal genes involved in Ca2+ oscillation-cytostatic factor-anaphase-promoting complex (Ca2+ oscillation-CSF-APC) signaling, including upregulated CaMKII, ORAI1, CDC20, and CDH1 and downregulated EMI1 and BUB3. The findings indicate abnormal spontaneous Ca2+ oscillations leading to oocytes with prolonged low CSF level and high APC level, which resulted in defective nuclear envelope breakdown and DNA replication. We have identified an RGS12 variant as the potential cause of female infertility characterized by arrest at the PN stage during multiple IVF and ICSI.
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Affiliation(s)
- Tianzhong Ma
- Reproductive Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Songxia Zhou
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Xuezhen Xie
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jingyao Chen
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jing Wang
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
| | - Guohong Zhang
- Department of Pathology, Shantou University Medical College, Shantou, Guangdong, China
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19
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Chen J, He Y, Chen L, Wu T, Yang G, Luo H, Hu S, Yin S, Qian Y, Miao H, Li N, Miao C, Feng R. Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals. iScience 2024; 27:109104. [PMID: 38433915 PMCID: PMC10904927 DOI: 10.1016/j.isci.2024.109104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 11/16/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
Alternative splicing (AS) as one of the important post-transcriptional regulatory mechanisms has been poorly studied during embryogenesis. In this study, we comprehensively collected and analyzed the transcriptome data of early embryos from human and mouse. We found that AS plays an important role in this process and predicted candidate RNA binding protein (RBP) regulators that are associated with reproductive development. The predicted RBPs such as EIF4A3, MAK16, SRSF2, and UTP23 were found to be associated with reproductive disorders. By Smart-seq2 sequencing analysis, we identified 5445 aberrant alternative splicing events in Eif4a3-knockdown embryos. These events were preferentially associated with RNA processing. In conclusion, our work on the landscape and potential function of alternative splicing events will boost further investigation of detailed mechanisms and key factors regulating mammalian early embryo development and promote the inspiration of pharmaceutical approaches for disorders in this crucial biology process.
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Affiliation(s)
- Jianhua Chen
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yanni He
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Liangliang Chen
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Tian Wu
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Guangping Yang
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Hui Luo
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Saifei Hu
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Siyue Yin
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yun Qian
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China
| | - Hui Miao
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China
| | - Na Li
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China
| | - Congxiu Miao
- Department of Reproductive Genetics, Heping Hospital of Changzhi Medical College, Key Laboratory of Reproduction Engineer of Shanxi Health Committee, Changzhi, Shanxi 046000, China
| | - Ruizhi Feng
- State Key Laboratory of Reproduction Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Reproductive Medical Center of Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China
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20
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Hu Y, Wang Y, He Y, Ye M, Yuan J, Ren C, Wang X, Wang S, Guo Y, Cao Q, Zhou S, Wang B, He A, Hu J, Guo X, Shu W, Huo R. Maternal KLF17 controls zygotic genome activation by acting as a messenger for RNA Pol II recruitment in mouse embryos. Dev Cell 2024; 59:613-626.e6. [PMID: 38325372 DOI: 10.1016/j.devcel.2024.01.013] [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: 10/13/2022] [Revised: 09/01/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Initiation of timely and sufficient zygotic genome activation (ZGA) is crucial for the beginning of life, yet our knowledge of transcription factors (TFs) contributing to ZGA remains limited. Here, we screened the proteome of early mouse embryos after cycloheximide (CHX) treatment and identified maternally derived KLF17 as a potential TF for ZGA genes. Using a conditional knockout (cKO) mouse model, we further investigated the role of maternal KLF17 and found that it promotes embryonic development and full fertility. Mechanistically, KLF17 preferentially binds to promoters and recruits RNA polymerase II (RNA Pol II) in early 2-cell embryos, facilitating the expression of major ZGA genes. Maternal Klf17 knockout resulted in a downregulation of 9% of ZGA genes and aberrant RNA Pol II pre-configuration, which could be partially rescued by introducing exogenous KLF17. Overall, our study provides a strategy for screening essential ZGA factors and identifies KLF17 as a crucial TF in this process.
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Affiliation(s)
- Yue Hu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | | | - Yuanlin He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Maosheng Ye
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Jie Yuan
- Bioinformatics Center of AMMS, Beijing, China
| | - Chao Ren
- Bioinformatics Center of AMMS, Beijing, China
| | - Xia Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Siqi Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Qiqi Cao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Shuai Zhou
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Bing Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Anlan He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | | | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Wenjie Shu
- Bioinformatics Center of AMMS, Beijing, China.
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Histology and Embryology, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China; Innovation Center of Suzhou Nanjing Medical University, Suzhou, China.
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21
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Gawriyski L, Tan Z, Liu X, Chowdhury I, Malaymar Pinar D, Zhang Q, Weltner J, Jouhilahti EM, Wei GH, Kere J, Varjosalo M. Interaction network of human early embryonic transcription factors. EMBO Rep 2024; 25:1589-1622. [PMID: 38297188 PMCID: PMC10933267 DOI: 10.1038/s44319-024-00074-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.
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Affiliation(s)
- Lisa Gawriyski
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Zenglai Tan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Xiaonan Liu
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | | | - Dicle Malaymar Pinar
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Qin Zhang
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Gong-Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
- Ministry of Education Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Juha Kere
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Folkhälsan Research Center, Helsinki, Finland
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Markku Varjosalo
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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22
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Zhang L, Zhao J, Lam SM, Chen L, Gao Y, Wang W, Xu Y, Tan T, Yu H, Zhang M, Liao X, Wu M, Zhang T, Huang J, Li B, Zhou QD, Shen N, Lee HJ, Ye C, Li D, Shui G, Zhang J. Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development. Nat Cell Biol 2024; 26:278-293. [PMID: 38302721 DOI: 10.1038/s41556-023-01341-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
Lipids are indispensable for energy storage, membrane structure and cell signalling. However, dynamic changes in various categories of endogenous lipids in mammalian early embryonic development have not been systematically characterized. Here we comprehensively investigated the dynamic lipid landscape during mouse and human early embryo development. Lipid signatures of different developmental stages are distinct, particularly for the phospholipid classes. We highlight that the high degree of phospholipid unsaturation is a conserved feature as embryos develop to the blastocyst stage. Moreover, we show that lipid desaturases such as SCD1 are required for in vitro blastocyst development and blastocyst implantation. One of the mechanisms is through the regulation of unsaturated fatty-acid-mediated fluidity of the plasma membrane and apical proteins and the establishment of apical-basal polarity during development of the eight-cell embryo to the blastocyst. Overall, our study provides an invaluable resource about the remodelling of the endogenous lipidome in mammalian preimplantation embryo development and mechanistic insights into the regulation of embryogenesis and implantation by lipid unsaturation.
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Affiliation(s)
- Ling Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jing Zhao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- LipidALL Technologies, Changzhou, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingzhuo Gao
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China
| | - Wenjie Wang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuyan Xu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyu Tan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Min Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xufeng Liao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengchen Wu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyun Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jie Huang
- College of Biomedical Engineering and Instrument Science, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, China
| | - Bowen Li
- LipidALL Technologies, Changzhou, China
| | - Quan D Zhou
- Institute of Immunology, Department of Surgical Oncology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ning Shen
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Hyeon Jeong Lee
- College of Biomedical Engineering and Instrument Science, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Da Li
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China.
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China.
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Center of Gene and Cell Therapy and Genome Medicine of Zhejiang Province, Hangzhou, China.
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23
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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 time-lapse of mouse prenatal development from gastrula to birth. Nature 2024; 626:1084-1093. [PMID: 38355799 PMCID: PMC10901739 DOI: 10.1038/s41586-024-07069-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
The house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans1,2. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells. Here, to establish a global framework for exploring mammalian development, we applied optimized single-cell combinatorial indexing3 to profile the transcriptional states of 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation (embryonic day 8) to birth (postnatal day 0). From these data, we annotate hundreds of cell types and explore the ontogenesis of the posterior embryo during somitogenesis and of kidney, mesenchyme, retina and early neurons. We leverage the temporal resolution and sampling depth of these whole-embryo snapshots, together with published data4-8 from earlier timepoints, to construct a rooted tree of cell-type relationships that spans the entirety of prenatal development, from zygote to birth. Throughout this tree, we systematically nominate genes encoding transcription factors and other proteins as candidate drivers of the in vivo differentiation of hundreds of cell types. Remarkably, the most marked temporal shifts in cell states are observed within one hour of birth and presumably underlie the massive physiological adaptations that must accompany the successful transition of a mammalian fetus to life outside the womb.
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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 and 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
- Brotman Baty Institute for Precision Medicine, 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 and 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
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
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24
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Karabekmez ME, Yarıcı M. Parameterization of asymmetric sigmoid functions in weighted gene co-expression network analysis. Comput Biol Chem 2024; 108:107998. [PMID: 38071762 DOI: 10.1016/j.compbiolchem.2023.107998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 11/22/2023] [Accepted: 12/03/2023] [Indexed: 01/22/2024]
Abstract
In most the biological contexts, examining gene expressions at the genomic level gives more accurate results than examining genes individually. It can improve understanding of the molecular mechanisms that cause molecular alterations. Weighted gene co-expression network analysis (WGCNA), which has recently been widely used to cluster transcriptomic datasets, implements a soft thresholding procedure using power function. However, these functions may sometimes exaggerate minor differences in expression correlations. We have previously proposed to use asymmetric sigmoid functions in soft thresholding as an alternative solution. However, the number of variables in asymmetric sigmoid functions may vary and parameterization can be problematic. In this study, we have introduced a systematic procedure for parameterizing asymmetric sigmoid function to ease using it as an alternative soft-thresholding solution in WGCNA. The efficiency of the employment was shown on four different COVID-19 datasets, on a yeast dataset, and on an E.Coli dataset. The results indicate that this approach provides biologically plausible associations for the resulting modules.
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Affiliation(s)
| | - Merve Yarıcı
- Istanbul Medeniyet University, Department of Bioengineering, Istanbul, Turkey
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25
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Wang C, Shi Z, Huang Q, Liu R, Su D, Chang L, Xiao C, Fan X. Single-cell analysis of isoform switching and transposable element expression during preimplantation embryonic development. PLoS Biol 2024; 22:e3002505. [PMID: 38363809 PMCID: PMC10903961 DOI: 10.1371/journal.pbio.3002505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 02/29/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Alternative splicing is an essential regulatory mechanism for development and pathogenesis. Through alternative splicing one gene can encode multiple isoforms and be translated into proteins with different functions. Therefore, this diversity is an important dimension to understand the molecular mechanism governing embryo development. Isoform expression in preimplantation embryos has been extensively investigated, leading to the discovery of new isoforms. However, the dynamics of isoform switching of different types of transcripts throughout the development remains unexplored. Here, using single-cell direct isoform sequencing in over 100 single blastomeres from the mouse oocyte to blastocyst stage, we quantified isoform expression and found that 3-prime partial transcripts lacking stop codons are highly accumulated in oocytes and zygotes. These transcripts are not transcription by-products and might play a role in maternal to zygote transition (MZT) process. Long-read sequencing also enabled us to determine the expression of transposable elements (TEs) at specific loci. In this way, we identified 3,894 TE loci that exhibited dynamic changes along the preimplantation development, likely regulating the expression of adjacent genes. Our work provides novel insights into the transcriptional regulation of early embryo development.
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Affiliation(s)
- Chaoyang Wang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingpei Huang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Rong Liu
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Dan Su
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Lei Chang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoying Fan
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
- The Bioland Laboratory (GuangZhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
- The Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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26
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Guo M, Wu J, Chen C, Wang X, Gong A, Guan W, Karvas RM, Wang K, Min M, Wang Y, Theunissen TW, Gao S, Silva JCR. Self-renewing human naïve pluripotent stem cells dedifferentiate in 3D culture and form blastoids spontaneously. Nat Commun 2024; 15:668. [PMID: 38253551 PMCID: PMC10803796 DOI: 10.1038/s41467-024-44969-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Human naïve pluripotent stem cells (hnPSCs) can generate integrated models of blastocysts termed blastoids upon switch to inductive medium. However, the underlying mechanisms remain obscure. Here we report that self-renewing hnPSCs spontaneously and efficiently give rise to blastoids upon three dimensional (3D) suspension culture. The spontaneous blastoids mimic early stage human blastocysts in terms of structure, size, and transcriptome characteristics and are capable of progressing to post-implantation stages. This property is conferred by the glycogen synthase kinase-3 (GSK3) signalling inhibitor IM-12 present in 5iLAF self-renewing medium. IM-12 upregulates oxidative phosphorylation-associated genes that underly the capacity of hnPSCs to generate blastoids spontaneously. Starting from day one of self-organization, hnPSCs at the boundary of all 3D aggregates dedifferentiate into E5 embryo-like intermediates. Intermediates co-express SOX2/OCT4 and GATA6 and by day 3 specify trophoblast fate, which coincides with cavity and blastoid formation. In summary, spontaneous blastoid formation results from 3D culture triggering dedifferentiation of hnPSCs into earlier embryo-like intermediates which are then competent to segregate blastocyst fates.
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Affiliation(s)
- Mingyue Guo
- Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China.
- Bioland Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China.
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Jinyi Wu
- Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
- Bioland Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
| | - Chuanxin Chen
- Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
- Bioland Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Xinggu Wang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
| | - An Gong
- Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
- Bioland Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Wei Guan
- Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
| | - Rowan M Karvas
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Kexin Wang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
| | - Mingwei Min
- Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China
| | - Yixuan Wang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Thorold W Theunissen
- Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shaorong Gao
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - José C R Silva
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong, China.
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27
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Guo ZH, Wang YB, Wang S, Zhang Q, Huang DS. scCorrector: a robust method for integrating multi-study single-cell data. Brief Bioinform 2024; 25:bbad525. [PMID: 38271483 PMCID: PMC10810333 DOI: 10.1093/bib/bbad525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/12/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The advent of single-cell sequencing technologies has revolutionized cell biology studies. However, integrative analyses of diverse single-cell data face serious challenges, including technological noise, sample heterogeneity, and different modalities and species. To address these problems, we propose scCorrector, a variational autoencoder-based model that can integrate single-cell data from different studies and map them into a common space. Specifically, we designed a Study Specific Adaptive Normalization for each study in decoder to implement these features. scCorrector substantially achieves competitive and robust performance compared with state-of-the-art methods and brings novel insights under various circumstances (e.g. various batches, multi-omics, cross-species, and development stages). In addition, the integration of single-cell data and spatial data makes it possible to transfer information between different studies, which greatly expand the narrow range of genes covered by MERFISH technology. In summary, scCorrector can efficiently integrate multi-study single-cell datasets, thereby providing broad opportunities to tackle challenges emerging from noisy resources.
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Affiliation(s)
- Zhen-Hao Guo
- College of Electronics and Information Engineering, Tongji University, Shanghai 200000, China
| | - Yan-Bin Wang
- College of Computer Science and Technology, Zhejiang University 310027, China
| | - Siguo Wang
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Tongxin Road No.568, Ningbo, Zhejiang 315201, China
| | - Qinhu Zhang
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Tongxin Road No.568, Ningbo, Zhejiang 315201, China
| | - De-Shuang Huang
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Tongxin Road No.568, Ningbo, Zhejiang 315201, China
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28
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Zheng D, Wondergem A, Kloet S, Willemsen I, Balog J, Tapscott SJ, Mahfouz A, van den Heuvel A, van der Maarel SM. snRNA-seq analysis in multinucleated myogenic FSHD cells identifies heterogeneous FSHD transcriptome signatures associated with embryonic-like program activation and oxidative stress-induced apoptosis. Hum Mol Genet 2024; 33:284-298. [PMID: 37934801 PMCID: PMC10800016 DOI: 10.1093/hmg/ddad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 09/22/2023] [Accepted: 10/21/2023] [Indexed: 11/09/2023] Open
Abstract
The sporadic nature of DUX4 expression in FSHD muscle challenges comparative transcriptome analyses between FSHD and control samples. A variety of DUX4 and FSHD-associated transcriptional changes have been identified, but bulk RNA-seq strategies prohibit comprehensive analysis of their spatiotemporal relation, interdependence and role in the disease process. In this study, we used single-nucleus RNA-sequencing of nuclei isolated from patient- and control-derived multinucleated primary myotubes to investigate the cellular heterogeneity in FSHD. Taking advantage of the increased resolution in snRNA-sequencing of fully differentiated myotubes, two distinct populations of DUX4-affected nuclei could be defined by their transcriptional profiles. Our data provides insights into the differences between these two populations and suggests heterogeneity in two well-known FSHD-associated transcriptional aberrations: increased oxidative stress and inhibition of myogenic differentiation. Additionally, we provide evidence that DUX4-affected nuclei share transcriptome features with early embryonic cells beyond the well-described cleavage stage, progressing into the 8-cell and blastocyst stages. Altogether, our data suggests that the FSHD transcriptional profile is defined by a mixture of individual and sometimes mutually exclusive DUX4-induced responses and cellular state-dependent downstream effects.
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Affiliation(s)
- Dongxu Zheng
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Annelot Wondergem
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Susan Kloet
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Iris Willemsen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Ahmed Mahfouz
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 2628 XE, Delft, The Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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29
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Wu Q, Zhou Z, Yan Z, Connel M, Garzo G, Yeo A, Zhang W, Su HI, Zhong S. A temporal extracellular transcriptome atlas of human pre-implantation development. CELL GENOMICS 2024; 4:100464. [PMID: 38216281 PMCID: PMC10794780 DOI: 10.1016/j.xgen.2023.100464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/09/2023] [Accepted: 11/19/2023] [Indexed: 01/14/2024]
Abstract
Non-invasively evaluating gene expression products in human pre-implantation embryos remains a significant challenge. Here, we develop a non-invasive method for comprehensive characterization of the extracellular RNAs (exRNAs) in a single droplet of spent media that was used to culture human in vitro fertilization embryos. We generate the temporal extracellular transcriptome atlas (TETA) of human pre-implantation development. TETA consists of 245 exRNA sequencing datasets for five developmental stages. These data reveal approximately 4,000 exRNAs at each stage. The exRNAs of the developmentally arrested embryos are enriched with the genes involved in negative regulation of the cell cycle, revealing an exRNA signature of developmental arrest. Furthermore, a machine-learning model can approximate the morphology-based rating of embryo quality based on the exRNA levels. These data reveal the widespread presence of coding gene-derived exRNAs at every stage of human pre-implantation development, and these exRNAs provide rich information on the physiology of the embryo.
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Affiliation(s)
- Qiuyang Wu
- Shu Chien-Gene Ley Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zixu Zhou
- Genemo, Inc., San Diego, CA 92130, USA
| | - Zhangming Yan
- Shu Chien-Gene Ley Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan Connel
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - Gabriel Garzo
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - Analisa Yeo
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - Wei Zhang
- Reproductive Partners San Diego, La Jolla, CA 92037, USA
| | - H Irene Su
- Reproductive Partners San Diego, La Jolla, CA 92037, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Sheng Zhong
- Shu Chien-Gene Ley Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Genemo, Inc., San Diego, CA 92130, USA.
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30
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Yu T, Zhang C, Song W, Zhao X, Cheng Y, Liu J, Su J. Single-cell RNA-seq and single-cell bisulfite-sequencing reveal insights into yak preimplantation embryogenesis. J Biol Chem 2024; 300:105562. [PMID: 38097189 PMCID: PMC10821408 DOI: 10.1016/j.jbc.2023.105562] [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: 03/24/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/13/2024] Open
Abstract
Extensive epigenetic reprogramming occurs during preimplantation embryonic development. However, the impact of DNA methylation in plateau yak preimplantation embryos and how epigenetic reprogramming contributes to transcriptional regulatory networks are unclear. In this study, we quantified gene expression and DNA methylation in oocytes and a series of yak embryos at different developmental stages and at single-cell resolution using single-cell bisulfite-sequencing and RNA-seq. We characterized embryonic genome activation and maternal transcript degradation and mapped epigenetic reprogramming events critical for embryonic development. Through cross-species transcriptome analysis, we identified 31 conserved maternal hub genes and 39 conserved zygotic hub genes, including SIN3A, PRC1, HDAC1/2, and HSPD1. Notably, by combining single-cell DNA methylation and transcriptome analysis, we identified 43 candidate methylation driver genes, such as AURKA, NUSAP1, CENPF, and PLK1, that may be associated with embryonic development. Finally, using functional approaches, we further determined that the epigenetic modifications associated with the histone deacetylases HDAC1/2 are essential for embryonic development and that the deubiquitinating enzyme USP7 may affect embryonic development by regulating DNA methylation. Our data represent an extensive resource on the transcriptional dynamics of yak embryonic development and DNA methylation remodeling, and provide new insights into strategies for the conservation of germplasm resources, as well as a better understanding of mammalian early embryonic development that can be applied to investigate the causes of early developmental disorders.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengtu Zhang
- Academician Zhang Yong Innovation Center, Xining Animal Disease Control Center, Xining, Qinghai, China
| | - Weijia Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyao Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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31
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Zhu W, Bu G, Hu R, Zhang J, Qiao L, Zhou K, Wang T, Li Q, Zhang J, Wu L, Xie Y, Hu T, Yang S, Guan J, Chu X, Shi J, Zhang X, Lu F, Liu X, Miao YL. KLF4 facilitates chromatin accessibility remodeling in porcine early embryos. SCIENCE CHINA. LIFE SCIENCES 2024; 67:96-112. [PMID: 37698691 DOI: 10.1007/s11427-022-2349-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/20/2023] [Indexed: 09/13/2023]
Abstract
Chromatin accessibility remodeling driven by pioneer factors is critical for the development of early embryos. Current studies have illustrated several pioneer factors as being important for agricultural animals, but what are the pioneer factors and how the pioneer factors remodel the chromatin accessibility in porcine early embryos is not clear. By employing low-input DNase-seq (liDNase-seq), we profiled the landscapes of chromatin accessibility in porcine early embryos and uncovered a unique chromatin accessibility reprogramming pattern during porcine preimplantation development. Our data revealed that KLF4 played critical roles in remodeling chromatin accessibility in porcine early embryos. Knocking down of KLF4 led to the reduction of chromatin accessibility in early embryos, whereas KLF4 overexpression promoted the chromatin openness in porcine blastocysts. Furthermore, KLF4 deficiency resulted in mitochondrial dysfunction and developmental failure of porcine embryos. In addition, we found that overexpression of KLF4 in blastocysts promoted lipid droplet accumulation, whereas knockdown of KLF4 disrupted this process. Taken together, our study revealed the chromatin accessibility dynamics and identified KLF4 as a key regulator in chromatin accessibility and cellular metabolism during porcine preimplantation embryo development.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Jixiang Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lianyong Qiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, 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
| | - 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
| | - Qiao 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
| | - 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
| | - 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
| | - Yali Xie
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, 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
| | - Shichun Yang
- 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
| | - Jiaqi Guan
- 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
| | - Xiaoyu Chu
- 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
| | - Juanjuan Shi
- 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
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, 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.
| | - 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.
- Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, 430070, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, China.
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32
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Sun C, Shao Y, Iqbal J. Insect Insights at the Single-Cell Level: Technologies and Applications. Cells 2023; 13:91. [PMID: 38201295 PMCID: PMC10777908 DOI: 10.3390/cells13010091] [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: 11/22/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Single-cell techniques are a promising way to unravel the complexity and heterogeneity of transcripts at the cellular level and to reveal the composition of different cell types and functions in a tissue or organ. In recent years, advances in single-cell RNA sequencing (scRNA-seq) have further changed our view of biological systems. The application of scRNA-seq in insects enables the comprehensive characterization of both common and rare cell types and cell states, the discovery of new cell types, and revealing how cell types relate to each other. The recent application of scRNA-seq techniques to insect tissues has led to a number of exciting discoveries. Here we provide an overview of scRNA-seq and its application in insect research, focusing on biological applications, current challenges, and future opportunities to make new discoveries with scRNA-seq in insects.
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Affiliation(s)
- Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junaid Iqbal
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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33
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Wang X, Pei J, Xiong L, Kang Y, Guo S, Cao M, Ding Z, Bao P, Chu M, Liang C, Yan P, Guo X. Single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics offer new insights into the etiological basis for male cattle-yak sterility. Int J Biol Macromol 2023; 253:126831. [PMID: 37716658 DOI: 10.1016/j.ijbiomac.2023.126831] [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: 05/26/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
The variety of species can be efficiently increased by interspecific hybridization. However, because the males in the hybrid progeny are usually sterile, this heterosis cannot be employed when other cattle and yaks are hybridized. While some system-level studies have sought to explore the etiological basis for male cattle-yak sterility, no systematic cellular analyses of this phenomenon have yet been performed. Here, single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics methods were used to study the differences in testicular tissue between 4-year-old male yak and 4-year-old male cattle-yak, providing new and comprehensive insights into the causes of male cattle-yak sterility. Cattle-yak testes samples detected 6 somatic cell types and one mixed germ cell type. Comparisons of these cell types revealed the more significant differences in Sertoli cells (SCs) and [Leydig cells and myoid cells (LCs_MCs)] between yak and cattle-yak samples compared to other somatic cell clusters. Even though the LCs and MCs from yaks and cattle-yaks were derived from the differentiation of the same progenitor cells, a high degree of overlap between LCs and MCs was observed in yak samples. Still, only a small overlap between LCs and MCs was observed in cattle-yak samples. Functional enrichment analyses revealed that genes down-regulated in cattle-yak SCs were primarily enriched in biological activity, whereas up-regulated genes in these cells were enriched for apoptotic activity. Furthermore, the genes of up-regulated in LCs_MCs of cattle-yak were significantly enriched in enzyme inhibitor and molecular function inhibitor activity. On the other hand, the genes of down-regulated in these cells were enriched for signal receptor binding, molecular function regulation, positive regulation of biological processes, and regulation of cell communication activity. The most significant annotated differences between yak and cattle-yak LCs_MCs were associated with cell-to-cell communication. While yak LCs_MCs regulated spermatogenic cells at spermatogonia, spermatocyte, and spermatid levels, no such relationships were found between cattle-yak LCs_MCs and germ cells. This may suggest that the somatic niche in male cattle-yak testes is a microenvironment that is ultimately not favorable for spermatogenesis.
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Affiliation(s)
- Xingdong Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Mengli Cao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ziqiang Ding
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China.
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Hornung BVH, Azmani Z, den Dekker AT, Oole E, Ozgur Z, Brouwer RWW, van den Hout MCGN, van IJcken WFJ. Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men. Genes (Basel) 2023; 14:2226. [PMID: 38137048 PMCID: PMC10743076 DOI: 10.3390/genes14122226] [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: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Single cell RNAseq has been a big leap in many areas of biology. Rather than investigating gene expression on a whole organism level, this technology enables scientists to get a detailed look at rare single cells or within their cell population of interest. The field is growing, and many new methods appear each year. We compared methods utilized in our core facility: Smart-seq3, PlexWell, FLASH-seq, VASA-seq, SORT-seq, 10X, Evercode, and HIVE. We characterized the equipment requirements for each method. We evaluated the performances of these methods based on detected features, transcriptome diversity, mitochondrial RNA abundance and multiplets, among others and benchmarked them against bulk RNA sequencing. Here, we show that bulk transcriptome detects more unique transcripts than any single cell method. While most methods are comparable in many regards, FLASH-seq and VASA-seq yielded the best metrics, e.g., in number of features. If no equipment for automation is available or many cells are desired, then HIVE or 10X yield good results. In general, more recently developed methods perform better. This also leads to the conclusion that older methods should be phased out, and that the development of single cell RNAseq methods is still progressing considerably.
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Affiliation(s)
- Bastian V. H. Hornung
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zakia Azmani
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Alexander T. den Dekker
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Edwin Oole
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zeliha Ozgur
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Mirjam C. G. N. van den Hout
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
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Full F, Walter S, Neugebauer E, Tan J, Drayman N, Franke V, Tay S, Landthaler M, Akalin A, Ensser A, Wyler E. Herpesviruses mimic zygotic genome activation to promote viral replication. RESEARCH SQUARE 2023:rs.3.rs-3125635. [PMID: 38168299 PMCID: PMC10760233 DOI: 10.21203/rs.3.rs-3125635/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DUX4 is a germline transcription factor and a master regulator of zygotic genome activation. During early embryogenesis, DUX4 is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In adult somatic cells, DUX4 expression is silenced and its activation in adult muscle cells causes the genetic disorder Facioscapulohumeral Muscular Dystrophy (FSHD). Here we show that herpesviruses from alpha-, beta- and gamma-herpesvirus subfamilies as well as papillomaviruses actively induce DUX4 expression to promote viral transcription and replication. We demonstrate that HSV-1 immediate early proteins directly induce expression of DUX4 and its target genes including endogenous retroelements, which mimics zygotic genome activation. We further show that DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for herpesvirus infection, since genetic depletion of DUX4 by CRISPR/Cas9 abrogates viral replication. Our results show that herpesviruses induce DUX4 expression and its downstream germline-specific genes and retroelements, thus mimicking an early embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.
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Affiliation(s)
- Florian Full
- University Medical Center, and Faculty of Medicine, Albert-Ludwig-University Freiburg
| | - Stephanie Walter
- Institute for Clinical and Molecular Virology, University Hospital Erlangen
| | - Eva Neugebauer
- Institute of Virology, University Medical Center, and Faculty of Medicine, Albert-Ludwig-University Freiburg
| | - Jiang Tan
- Institute of Virology, University Medical Center, and Faculty of Medicine, Albert-Ludwig-University Freiburg
| | - Nir Drayman
- The Department of Molecular Biology and Biochemistry, the Center for Virus Research and the Center for Complex Biological Systems, The University of California, Irvine
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36
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Tu S, Zuo J. Systematic single cell RNA sequencing analysis reveals unique transcriptional regulatory networks of Atoh1-mediated hair cell conversion in adult mouse cochleae. PLoS One 2023; 18:e0284685. [PMID: 38079436 PMCID: PMC10712870 DOI: 10.1371/journal.pone.0284685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/05/2023] [Indexed: 12/18/2023] Open
Abstract
Regeneration of mammalian cochlear hair cells (HCs) by modulating molecular pathways or transcription factors is a promising approach to hearing restoration; however, immaturity of the regenerated HCs in vivo remains a major challenge. Here, we analyzed a single cell RNA sequencing (scRNA-seq) dataset during Atoh1-induced supporting cell (SC) to hair cell (HC) conversion in adult mouse cochleae (Yamashita et al. (2018)) using multiple high-throughput sequencing analytical tools (WGCNA, SCENIC, ARACNE, and VIPER). Instead of focusing on differentially expressed genes, we established independent expression modules and confirmed the existence of multiple conversion stages. Gene regulatory network (GRN) analysis uncovered previously unidentified key regulators, including Nhlh1, Lhx3, Barhl1 and Nfia, that guide converted HC differentiation. Comparison of the late-stage converted HCs with the scRNA-seq data from neonatal mouse cochleae (Kolla et al. (2020)) revealed that they closely resemble postnatal day 1 wild-type OHCs, in contrast to other developmental stages. Using ARACNE and VIPER, we discovered multiple key regulators likely to promote conversion to a more mature OHC-like state, including Zbtb20, Nfia, Zmiz1, Gm14418, Bhlhe40, Six2, Fosb and Klf9. Our findings provide insights into the regulation of HC regeneration in adult mammalian cochleae in vivo and demonstrate an approach for analyzing GRNs in large scRNA-seq datasets.
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Affiliation(s)
- Shu Tu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States of America
| | - Jian Zuo
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, NE, United States of America
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37
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Kour R, Kim J, Roy A, Richardson B, Cameron MJ, Knott JG, Mazumder B. Loss of function of ribosomal protein L13a blocks blastocyst formation and reveals a potential nuclear role in gene expression. FASEB J 2023; 37:e23275. [PMID: 37902531 PMCID: PMC10999073 DOI: 10.1096/fj.202301475r] [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: 07/18/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023]
Abstract
Ribosomal proteins play diverse roles in development and disease. Most ribosomal proteins have canonical roles in protein synthesis, while some exhibit extra-ribosomal functions. Previous studies in our laboratory revealed that ribosomal protein L13a (RPL13a) is involved in the translational silencing of a cohort of inflammatory proteins in myeloid cells. This prompted us to investigate the role of RPL13a in embryonic development. Here we report that RPL13a is required for early development in mice. Crosses between Rpl13a+/- mice resulted in no Rpl13a-/- offspring. Closer examination revealed that Rpl13a-/- embryos were arrested at the morula stage during preimplantation development. RNA sequencing analysis of Rpl13a-/- morulae revealed widespread alterations in gene expression, including but not limited to several genes encoding proteins involved in the inflammatory response, embryogenesis, oocyte maturation, stemness, and pluripotency. Ex vivo analysis revealed that RPL13a was localized to the cytoplasm and nucleus between the two-cell and morula stages. RNAi-mediated depletion of RPL13a phenocopied Rpl13a-/- embryos and knockdown embryos exhibited increased expression of IL-7 and IL-17 and decreased expression of the lineage specifier genes Sox2, Pou5f1, and Cdx2. Lastly, a protein-protein interaction assay revealed that RPL13a is associated with chromatin, suggesting an extra ribosomal function in transcription. In summary, our data demonstrate that RPL13a is essential for the completion of preimplantation embryo development. The mechanistic basis of the absence of RPL13a-mediated embryonic lethality will be addressed in the future through follow-up studies on ribosome biogenesis, global protein synthesis, and identification of RPL13a target genes using chromatin immunoprecipitation and RNA-immunoprecipitation-based sequencing.
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Affiliation(s)
- Ravinder Kour
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Jaehwan Kim
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Antara Roy
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
| | - Brian Richardson
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mark J. Cameron
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jason G. Knott
- Developmental Epigenetics Laboratory, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
| | - Barsanjit Mazumder
- Center for Gene Regulation in Health and Disease, Department of Biological Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
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38
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Chen B, Pei D. Genetic clues to reprogramming power and formation of mouse oocyte. Curr Opin Genet Dev 2023; 83:102110. [PMID: 37722148 DOI: 10.1016/j.gde.2023.102110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/05/2023] [Accepted: 07/29/2023] [Indexed: 09/20/2023]
Abstract
Oocyte features the unique capacity to reprogram not only sperm but also somatic nuclei to totipotency, yet the scarcity of oocytes has hindered the exploration and application of their reprogramming ability. In the meanwhile, the formation of oocytes, which involves extensive intracellular alterations and interactions, has also attracted tremendous interest. This review discusses developmental principles and regulatory mechanisms associated with ooplasm reprogramming and oocyte formation from a genetic perspective, with knowledge derived from mouse models. We also discuss future directions, especially to address the lack of insight into the regulatory networks that shape the identity of female germ cells or drive transitions in their developmental programs.
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Tscherner AK, McClatchie T, Macaulay AD, Baltz JM. Relationship of quantitative reverse transcription polymerase chain reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome identifies mouse preimplantation embryo reference genes†. Biol Reprod 2023; 109:601-617. [PMID: 37669129 PMCID: PMC10651071 DOI: 10.1093/biolre/ioad107] [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: 05/16/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Numerous reference genes for use with quantitative reverse transcription polymerase chain reaction (RT-qPCR) have been used for oocytes, eggs, and preimplantation embryos. However, none are actually suitable because of their large variations in expression between developmental stages. To address this, we produced a standardized and merged RNA sequencing (RNAseq) data set by combining multiple publicly available RNAseq data sets that spanned mouse GV oocytes, MII eggs, and 1-cell, 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos to identify transcripts with essentially constant expression across all stages. Their expression was then measured using RT-qPCR, with which they did not exhibit constant expression but instead revealed a fixed quantitative relationship between measurements by the two techniques. From this, the relative amounts of total messenger RNA at each stage from the GV oocyte through blastocyst stages were calculated. The quantitative relationship between measurements by RNAseq and RT-qPCR was then used to find genes predicted to have constant expression across stages in RT-qPCR. Candidates were assessed by RT-qPCR to confirm constant expression, identifying Hmgb3 and Rb1cc1 or the geometric mean of those plus either Taf1d or Cd320 as suitable reference genes. This work not only identified transcripts with constant expression from mouse GV oocytes to blastocysts, but also determined a general quantitative relationship between expression measured by RNAseq and RT-qPCR across stages that revealed the relative levels of total mRNA at each stage. The standardized and merged RNA data set should also prove useful in determining transcript expression in mouse oocytes, eggs, and embryos.
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Affiliation(s)
- Allison K Tscherner
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | - Taylor McClatchie
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | | | - Jay M Baltz
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
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40
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Ishiuchi T, Sakamoto M. Molecular mechanisms underlying totipotency. Life Sci Alliance 2023; 6:e202302225. [PMID: 37666667 PMCID: PMC10480501 DOI: 10.26508/lsa.202302225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023] Open
Abstract
Numerous efforts to understand pluripotency in mammals, using pluripotent stem cells in culture, have enabled the generation of artificially induced pluripotent stem cells, which serve as a valuable source for regenerative medicine and the creation of disease models. In contrast to these tremendous successes in the pluripotency field in the past few decades, our understanding of totipotency, which is highlighted by its broader plasticity than pluripotency, is still limited. This is largely attributable to the scarcity of available materials and the lack of in vitro models. However, recent technological advances have unveiled molecular features that characterize totipotent cells. Single-cell or low-input sequencing technologies allow the dissection of pre- and post-fertilization developmental processes at the molecular level with high resolution. In this review, we describe some of the key findings in understanding totipotency and discuss how totipotency is acquired at the beginning of life.
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Affiliation(s)
- Takashi Ishiuchi
- https://ror.org/059x21724 Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Mizuki Sakamoto
- https://ror.org/059x21724 Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
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41
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Torre D, Francoeur NJ, Kalma Y, Gross Carmel I, Melo BS, Deikus G, Allette K, Flohr R, Fridrikh M, Vlachos K, Madrid K, Shah H, Wang YC, Sridhar SH, Smith ML, Eliyahu E, Azem F, Amir H, Mayshar Y, Marazzi I, Guccione E, Schadt E, Ben-Yosef D, Sebra R. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun 2023; 14:6902. [PMID: 37903791 PMCID: PMC10616205 DOI: 10.1038/s41467-023-42558-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023] Open
Abstract
Human preimplantation development involves extensive remodeling of RNA expression and splicing. However, its transcriptome has been compiled using short-read sequencing data, which fails to capture most full-length mRNAs. Here, we generate an isoform-resolved transcriptome of early human development by performing long- and short-read RNA sequencing on 73 embryos spanning the zygote to blastocyst stages. We identify 110,212 unannotated isoforms transcribed from known genes, including highly conserved protein-coding loci and key developmental regulators. We further identify 17,964 isoforms from 5,239 unannotated genes, which are largely non-coding, primate-specific, and highly associated with transposable elements. These isoforms are widely supported by the integration of published multi-omics datasets, including single-cell 8CLC and blastoid studies. Alternative splicing and gene co-expression network analyses further reveal that embryonic genome activation is associated with splicing disruption and transient upregulation of gene modules. Together, these findings show that the human embryo transcriptome is far more complex than currently known, and will act as a valuable resource to empower future studies exploring development.
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Affiliation(s)
- Denis Torre
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Yael Kalma
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Ilana Gross Carmel
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Betsaida S Melo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kimaada Allette
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ron Flohr
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel
| | - Maya Fridrikh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Kent Madrid
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shwetha H Sridhar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Foad Azem
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Hadar Amir
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel
| | - Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Ivan Marazzi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, University of California, Irvine, CA, 92697, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT); Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalit Ben-Yosef
- Fertility and IVF Institute, Tel-Aviv Sourasky Medical Center, Affiliated to Tel Aviv University, Tel Aviv, 64239, Israel.
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978, Israel.
- CORAL - Center Of Regeneration and Longevity, Tel-Aviv Sourasky Medical Center, Tel Aviv, 64239, Israel.
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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42
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Knoblochova L, Duricek T, Vaskovicova M, Zorzompokou C, Rayova D, Ferencova I, Baran V, Schultz RM, Hoffmann ER, Drutovic D. CHK1-CDC25A-CDK1 regulate cell cycle progression and protect genome integrity in early mouse embryos. EMBO Rep 2023; 24:e56530. [PMID: 37694680 PMCID: PMC10561370 DOI: 10.15252/embr.202256530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated and transcriptionally quiescent cells into early cleavage-stage blastomeres that are transcriptionally active and totipotent. This developmental transition is accompanied by cell cycle adaptation, such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in two-cell stage mouse embryos. Finally, Chk1 depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.
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Affiliation(s)
- Lucie Knoblochova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomas Duricek
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Michaela Vaskovicova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Chrysoula Zorzompokou
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Diana Rayova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Ivana Ferencova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Vladimir Baran
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of SciencesKosiceSlovakia
| | - Richard M Schultz
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
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43
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Ju LF, Xu HJ, Yang YG, Yang Y. Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:950-961. [PMID: 37075831 PMCID: PMC10928378 DOI: 10.1016/j.gpb.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination, ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation, several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages, including the 2- and 4-cell stages. The underlying mechanisms of early cell fate determination have long been an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis, as well as the current understanding of their regulatory roles in cell fate decisions. Moreover, as powerful tools for early embryogenesis research, single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators. Here, we summarize their applications in the research of preimplantation embryos, and provide new insights and perspectives on cell fate regulation.
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Affiliation(s)
- Lin-Fang Ju
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Heng-Ji Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yun-Gui Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ying Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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44
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Yang J, Cook L, Chen Z. Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558531. [PMID: 37781606 PMCID: PMC10541133 DOI: 10.1101/2023.09.19.558531] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we employed epigenome editing to perturb the long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in ~2667 insertions throughout the mouse genome. CRISPRi robustly repressed 2485 (~93%) MT2_Mm insertions and 1090 (~55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused down-regulation of hundreds of ZGA genes at the 2-cell stage and embryonic arrest mostly at the morula stage. Mechanistically, MT2_Mm/MT2C_Mm primarily served as alternative ZGA promoters activated by OBOX proteins. Thus, through unprecedented large-scale epigenome editing, we addressed to what extent MT2_Mm/MT2C_Mm regulates ZGA and preimplantation development. Our approach could be adapted to systematically perturb retrotransposons in other mammalian embryos as it doesn't require transgenic animals.
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Affiliation(s)
- Jian Yang
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, 45229, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, 45229, Ohio, USA
| | - Lauryn Cook
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, 45229, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, 45229, Ohio, USA
| | - Zhiyuan Chen
- Reproductive Sciences Center, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, 45229, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, 45229, Ohio, USA
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45
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Wang S, Zhang Y, Zhang Y, Wu W, Ye L, Li Y, Su J, Pang S. scASGC: An adaptive simplified graph convolution model for clustering single-cell RNA-seq data. Comput Biol Med 2023; 163:107152. [PMID: 37364529 DOI: 10.1016/j.compbiomed.2023.107152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is now a successful technique for identifying cellular heterogeneity, revealing novel cell subpopulations, and forecasting developmental trajectories. A crucial component of the processing of scRNA-seq data is the precise identification of cell subpopulations. Although many unsupervised clustering methods have been developed to cluster cell subpopulations, the performance of these methods is vulnerable to dropouts and high dimensionality. In addition, most existing methods are time-consuming and fail to adequately account for potential associations between cells. In the manuscript, we present an unsupervised clustering method based on an adaptive simplified graph convolution model called scASGC. The proposed method builds plausible cell graphs, aggregates neighbor information using a simplified graph convolution model, and adaptively determines the most optimal number of convolution layers for various graphs. Experiments on 12 public datasets show that scASGC outperforms both classical and state-of-the-art clustering methods. In addition, in a study of mouse intestinal muscle containing 15,983 cells, we identified distinct marker genes based on the clustering results of scASGC. The source code of scASGC is available at https://github.com/ZzzOctopus/scASGC.
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Affiliation(s)
- Shudong Wang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Yu Zhang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, 266590, China.
| | - Wenhao Wu
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Lan Ye
- Cancer Center, the Second Hospital of Shandong University, Jinan, 250033, China.
| | - YunYin Li
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
| | - Jionglong Su
- School of AI and Advanced Computing, XJTLU Entrepreneur College (Taicang), Xi'an Jiaotong-Liverpool University, Suzhou, 215123, China.
| | - Shanchen Pang
- College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, 266580, China.
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46
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Ross PJ, Goissis MD, Martins JPN, Chitwood JL, Pursley JR, Rosa GJM, Cibelli JB. Blastocyst Cell Number and Allocation Affect the Developmental Potential and Transcriptome of Bovine Somatic Cell Nuclear Transfer Embryos. Stem Cells Dev 2023; 32:515-523. [PMID: 37345692 DOI: 10.1089/scd.2022.0292] [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] [Indexed: 06/23/2023] Open
Abstract
Cloning cattle using somatic cell nuclear transfer (SCNT) is inefficient. Although the rate of development of SCNT embryos in vitro is similar to that of fertilized embryos, most fail to develop into healthy calves. In this study, we aimed to identify developmentally competent embryos according to blastocyst cell composition and perform transcriptome analysis of single embryos. Transgenic SCNT embryos expressing nuclear-localized HcRed gene at day 7 of development were imaged by confocal microscopy for cell counting and individually transferred to recipient heifers. Pregnancy rates were determined by ultrasonography. Embryos capable of establishing pregnancy by day 35 had an average of 117 ± 6 total cells, whereas embryos with an average of 128 ± 5 cells did not establish pregnancy (P < 0.05). A lesser average number of 41 ± 3 cells in the inner cell mass (ICM) also resulted in pregnancies (<0.05) than a greater number of 48 ± 2 cells in the ICM. Single embryos were then subjected to RNA sequencing for transcriptome analysis. Using weighted gene coexpression network analysis, we identified clusters of genes in which gene expression correlated with the number of total cells or ICM cells. Gene ontology analysis of these clusters revealed enriched biological processes in coenzyme metabolic process, intracellular signaling cascade, and glucose catabolic process, among others. We concluded that SCNT embryos with fewer total and ICM cell numbers resulted in greater pregnancy establishment rates and that these differences are reflected in the transcriptome of such embryos.
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Affiliation(s)
- Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Marcelo D Goissis
- Department of Animal Reproduction, College of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, Brazil
| | - João P N Martins
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - James L Chitwood
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - J Richard Pursley
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
| | - Guilherme J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Jose B Cibelli
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
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47
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Meng S, Liu X, Zhu S, Xie P, Fang H, Pan Q, Fang K, Li F, Zhang J, Che Z, Zhang Q, Mao G, Wang Y, Hu P, Chen K, Sun F, Xie W, Luo Z, Lin C. Young LINE-1 transposon 5' UTRs marked by elongation factor ELL3 function as enhancers to regulate naïve pluripotency in embryonic stem cells. Nat Cell Biol 2023; 25:1319-1331. [PMID: 37591949 DOI: 10.1038/s41556-023-01211-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
LINE-1s are the major clade of retrotransposons with autonomous retrotransposition activity. Despite the potential genotoxicity, LINE-1s are highly activated in early embryos. Here we show that a subset of young LINE-1s, L1Md_Ts, are marked by the RNA polymerase II elongation factor ELL3, and function as enhancers in mouse embryonic stem cells. ELL3 depletion dislodges the DNA hydroxymethylase TET1 and the co-repressor SIN3A from L1Md_Ts, but increases the enrichment of the Bromodomain protein BRD4, leading to loss of 5hmC, gain of H3K27ac, and upregulation of the L1Md_T nearby genes. Specifically, ELL3 occupies and represses the L1Md_T-based enhancer located within Akt3, which encodes a key regulator of AKT pathway. ELL3 is required for proper ERK activation and efficient shutdown of naïve pluripotency through inhibiting Akt3 during naïve-primed transition. Our study reveals that the enhancer function of a subset of young LINE-1s controlled by ELL3 in transcription regulation and mouse early embryo development.
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Affiliation(s)
- Siyan Meng
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Xiaoxu Liu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Shiqi Zhu
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Peng Xie
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Haitong Fang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Qingyun Pan
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Ke Fang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Fanfan Li
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Jin Zhang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zhuanzhuan Che
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Guangyao Mao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, China
| | - Fei Sun
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Wei Xie
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zhuojuan Luo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, China.
- Shenzhen Research Institute, Southeast University, Shenzhen, China.
| | - Chengqi Lin
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China.
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.
- Shenzhen Research Institute, Southeast University, Shenzhen, China.
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, China.
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48
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Chen F, Li MG, Hua ZD, Ren HY, Gu H, Luo AF, Zhou CF, Zhu Z, Huang T, Bi YZ. TET Family Members Are Integral to Porcine Oocyte Maturation and Parthenogenetic Pre-Implantation Embryogenesis. Int J Mol Sci 2023; 24:12455. [PMID: 37569830 PMCID: PMC10419807 DOI: 10.3390/ijms241512455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
The ten-eleven translocation (TET) enzyme family, which includes TET1/2/3, participates in active DNA demethylation in the eukaryotic genome; moreover, TET1/2/3 are functionally redundant in mice embryos. However, the combined effect of TET1/2/3 triple-gene knockdown or knockout on the porcine oocytes or embryos is still unclear. In this study, using Bobcat339, a specific small-molecule inhibitor of the TET family, we explored the effects of TET enzymes on oocyte maturation and early embryogenesis in pigs. Our results revealed that Bobcat339 treatment blocked porcine oocyte maturation and triggered early apoptosis. Furthermore, in the Bobcat339-treated oocytes, spindle architecture and chromosome alignment were disrupted, probably due to the huge loss of 5-hydroxymethylcytosine (5hmC)and concurrent increase in 5-methylcytosine (5mC). After Bobcat339 treatment, early parthenogenetic embryos exhibited abnormal 5mC and 5hmC levels, which resulted in compromised cleavage and blastocyst rate. The mRNA levels of EIF1A and DPPA2 (ZGA marker genes) were significantly decreased, which may explain why the embryos were arrested at the 4-cell stage after Bobcat339 treatment. In addition, the mRNA levels of pluripotency-related genes OCT4 and NANOG were declined after Bobcat339 treatment. RNA sequencing analysis revealed differentially expressed genes in Bobcat339-treated embryos at the 4-cell stage, which were significantly enriched in cell proliferation, cell component related to mitochondrion, and cell adhesion molecule binding. Our results indicated that TET proteins are essential for porcine oocyte maturation and early embryogenesis, and they act by mediating 5mC/5hmC levels and gene transcription.
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Affiliation(s)
- Fan Chen
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Ming-Guo Li
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Zai-Dong Hua
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Hong-Yan Ren
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Hao Gu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - An-Feng Luo
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Chang-Fan Zhou
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Zhe Zhu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
| | - Tao Huang
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China
| | - Yan-Zhen Bi
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430070, China; (F.C.); (M.-G.L.); (Z.-D.H.); (H.-Y.R.); (H.G.); (A.-F.L.); (C.-F.Z.); (Z.Z.)
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49
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Gu L, Li X, Zhu W, Shen Y, Wang Q, Liu W, Zhang J, Zhang H, Li J, Li Z, Liu Z, Li C, Wang H. Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition. J Pharm Anal 2023; 13:942-954. [PMID: 37719194 PMCID: PMC10499587 DOI: 10.1016/j.jpha.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 09/19/2023] Open
Abstract
Single-cell or low-input multi-omics techniques have revolutionized the study of pre-implantation embryo development. However, the single-cell or low-input proteomic research in this field is relatively underdeveloped because of the higher threshold of the starting material for mammalian embryo samples and the lack of hypersensitive proteome technology. In this study, a comprehensive solution of ultrasensitive proteome technology (CS-UPT) was developed for single-cell or low-input mouse oocyte/embryo samples. The deep coverage and high-throughput routes significantly reduced the starting material and were selected by investigators based on their demands. Using the deep coverage route, we provided the first large-scale snapshot of the very early stage of mouse maternal-to-zygotic transition, including almost 5,500 protein groups from 20 mouse oocytes or zygotes for each sample. Moreover, significant protein regulatory networks centered on transcription factors and kinases between the MII oocyte and 1-cell embryo provided rich insights into minor zygotic genome activation.
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Affiliation(s)
- Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wencheng Zhu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Yi Shen
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wenjun Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Junfeng Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Huiping Zhang
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ziyi Li
- Shanghai Applied Protein Technology Co., Ltd., Shanghai, 201100, China
| | - Zhen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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50
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Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu YC, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S, Hammoud SS. Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1. Nat Struct Mol Biol 2023; 30:1077-1091. [PMID: 37460896 PMCID: PMC10833441 DOI: 10.1038/s41594-023-01033-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 06/12/2023] [Indexed: 08/11/2023]
Abstract
Conventional dogma presumes that protamine-mediated DNA compaction in sperm is achieved by electrostatic interactions between DNA and the arginine-rich core of protamines. Phylogenetic analysis reveals several non-arginine residues conserved within, but not across species. The significance of these residues and their post-translational modifications are poorly understood. Here, we investigated the role of K49, a rodent-specific lysine residue in protamine 1 (P1) that is acetylated early in spermiogenesis and retained in sperm. In sperm, alanine substitution (P1(K49A)) decreases sperm motility and male fertility-defects that are not rescued by arginine substitution (P1(K49R)). In zygotes, P1(K49A) leads to premature male pronuclear decompaction, altered DNA replication, and embryonic arrest. In vitro, P1(K49A) decreases protamine-DNA binding and alters DNA compaction and decompaction kinetics. Hence, a single amino acid substitution outside the P1 arginine core is sufficient to profoundly alter protein function and developmental outcomes, suggesting that protamine non-arginine residues are essential for reproductive fitness.
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Affiliation(s)
- Lindsay Moritz
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Samantha B Schon
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Yi Sheng
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ritvija Agrawal
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Juniper Glass-Klaiber
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Caleb Sultan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences, and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Jourdan Clements
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Michael R Baldwin
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Adam G Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sy Redding
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Saher Sue Hammoud
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.
- Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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