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Choi JM, Park C, Chae H. moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud. PeerJ 2024; 12:e17006. [PMID: 38426141 PMCID: PMC10903350 DOI: 10.7717/peerj.17006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Single-cell omics sequencing has rapidly advanced, enabling the quantification of diverse omics profiles at a single-cell resolution. To facilitate comprehensive biological insights, such as cellular differentiation trajectories, precise annotation of cell subtypes is essential. Conventional methods involve clustering cells and manually assigning subtypes based on canonical markers, a labor-intensive and expert-dependent process. Hence, an automated computational prediction framework is crucial. While several classification frameworks for predicting cell subtypes from single-cell RNA sequencing datasets exist, these methods solely rely on single-omics data, offering insights at a single molecular level. They often miss inter-omic correlations and a holistic understanding of cellular processes. To address this, the integration of multi-omics datasets from individual cells is essential for accurate subtype annotation. This article introduces moSCminer, a novel framework for classifying cell subtypes that harnesses the power of single-cell multi-omics sequencing datasets through an attention-based neural network operating at the omics level. By integrating three distinct omics datasets-gene expression, DNA methylation, and DNA accessibility-while accounting for their biological relationships, moSCminer excels at learning the relative significance of each omics feature. It then transforms this knowledge into a novel representation for cell subtype classification. Comparative evaluations against standard machine learning-based classifiers demonstrate moSCminer's superior performance, consistently achieving the highest average performance on real datasets. The efficacy of multi-omics integration is further corroborated through an in-depth analysis of the omics-level attention module, which identifies potential markers for cell subtype annotation. To enhance accessibility and scalability, moSCminer is accessible as a user-friendly web-based platform seamlessly connected to a cloud system, publicly accessible at http://203.252.206.118:5568. Notably, this study marks the pioneering integration of three single-cell multi-omics datasets for cell subtype identification.
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Affiliation(s)
- Joung Min Choi
- Department of Computer Science, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States
| | - Chaelin Park
- Division of Computer Science, Sookmyung Women’s University, Seoul, South Korea
| | - Heejoon Chae
- Division of Computer Science, Sookmyung Women’s University, Seoul, South Korea
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Zhu Y, Liu H, Zheng L, Luo Y, Zhou G, Li J, Hou Y, Fu X. Vitrification of Mammalian Oocytes: Recent Studies on Mitochondrial Dysfunction. Biopreserv Biobank 2024. [PMID: 38227396 DOI: 10.1089/bio.2023.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Vitrification of reproductive cells is definitely essential and integral in animal breeding, as well as in assisted reproduction. However, issues accompanied with this technology such as decreased oocyte competency and relatively low embryo survival rates appear to be a tough conundrum that has long perplexed us. As significant organelles in cell metabolism, mitochondria play pivotal roles in numerous pathways. Nonetheless, extensive evidence has demonstrated that vitrification can seriously impair mitochondrial function in mammalian oocytes. Thus, in this article, we summarize the current progress in oocyte vitrification and particularly outline the common mitochondrial abnormalities alongside subsequent injury cascades seen in mammalian oocytes following vitrification. Based on existing literature, we tentatively come up with the potential mechanisms related to mitochondrial dysfunction and generalize efficacious ways which have been recommended to restore mitochondrial function.
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Affiliation(s)
- Yixiao Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Hongyu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Lv Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Yuwen Luo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guizhen Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
| | - Jun Li
- Department of Reproductive Medicine, Reproductive Medical Center, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yunpeng Hou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiangwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P. R. China
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Liang J, Lv C, Xiang D, Zhang Y, Zhang B, Raza SHA, Wu G, Quan G. The establishment of goat semen protein profile using a tandem mass tag-based proteomics approach. Res Vet Sci 2022; 150:22-32. [DOI: 10.1016/j.rvsc.2022.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/15/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
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Yang P, Chen X, Tian X, Zhou Z, Zhang Y, Tang W, Fu K, Zhao J, Ruan Y. A Proteomic Study of the Effect of N-acetylcysteine on the Regulation of Early Pregnancy in Goats. Animals (Basel) 2022; 12:ani12182439. [PMID: 36139298 PMCID: PMC9495164 DOI: 10.3390/ani12182439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Early pregnancy regulation is an extremely complex process that is influenced by various factors. We previously mined the differentially expressed genes affected by N-acetyl-L-cysteine (NAC) in early pregnancy in goats via transcriptome sequencing. We found that NAC increased the number of lambs by affecting the immune pathway in ewes and enhancing antioxidation. Based on this, we here explored the effect of NAC on early pregnancy in goats at the protein level. The results showed a difference in the expression of uterine keratin and increases in the levels of antioxidant indices and hormones in doe serum. Abstract Dietary supplementation with N-acetyl-L-cysteine (NAC) may support early pregnancy regulation and fertility in female animals. The purpose of this study was to investigate the effect of supplementation with 0.07% NAC on the expression of the uterine keratin gene and protein in Qianbei-pockmarked goats during early pregnancy using tandem mass spectrometry (TMT) relative quantitative proteomics. The results showed that there were significant differences in uterine keratin expression between the experimental group (NAC group) and the control group on day 35 of gestation. A total of 6271 proteins were identified, 6258 of which were quantified by mass spectrometry. There were 125 differentially expressed proteins (DEPs), including 47 upregulated and 78 downregulated proteins, in the NAC group. Bioinformatic analysis showed that these DEPs were mainly involved in the transport and biosynthesis of organic matter and were related to the binding of transition metal ions, DNA and proteins and the catalytic activity of enzymes. They were enriched in the Jak-STAT signalling pathway, RNA monitoring pathway, amino acid biosynthesis, steroid biosynthesis and other pathways that may affect the early pregnancy status of does through different pathways and thus influence early embryonic development. Immunohistochemistry, real-time quantitative PCR and Western blotting were used to verify the expression and localization of glial fibrillary acidic protein (GFAP) and pelota mRNA surveillance and ribosomal rescue factor (PELO) in uterine horn tissue. The results showed that both PELO and GFAP were localized to endometrial and stromal cells, consistent with the mass spectrometry data at the transcriptional and translational levels. Moreover, NAC supplementation increased the levels of the reproductive hormones follicle-stimulating hormone (FSH), luteinizing hormone (LH), oestradiol (E2), progesterone (P4), superoxide dismutase (SOD), glutamate peroxidase (GSH-Px) and nitric oxide (NO) in the serum of does. These findings provide new insight into the mechanism by which NAC regulates early pregnancy and embryonic development in goats.
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Affiliation(s)
- Peifang Yang
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Xiang Chen
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
- Correspondence:
| | - Xingzhou Tian
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Zhinan Zhou
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Yan Zhang
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wen Tang
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Kaibin Fu
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jiafu Zhao
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Yong Ruan
- Key Laboratory of Plateau Mountain Animal Genetics, Breeding and Reproduction of Ministry of Education, Guiyang 550025, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Guizhou Province, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China
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