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Jones ASK, Hannum DF, Machlin JH, Tan A, Ma Q, Ulrich ND, Shen YC, Ciarelli M, Padmanabhan V, Marsh EE, Hammoud S, Li JZ, Shikanov A. Cellular atlas of the human ovary using morphologically guided spatial transcriptomics and single-cell sequencing. SCIENCE ADVANCES 2024; 10:eadm7506. [PMID: 38578993 PMCID: PMC10997207 DOI: 10.1126/sciadv.adm7506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
The reproductive and endocrine functions of the ovary involve spatially defined interactions among specialized cell populations. Despite the ovary's importance in fertility and endocrine health, functional attributes of ovarian cells are largely uncharacterized. Here, we profiled >18,000 genes in 257 regions from the ovaries of two premenopausal donors to examine the functional units in the ovary. We also generated single-cell RNA sequencing data for 21,198 cells from three additional donors and identified four major cell types and four immune cell subtypes. Custom selection of sampling areas revealed distinct gene activities for oocytes, theca, and granulosa cells. These data contributed panels of oocyte-, theca-, and granulosa-specific genes, thus expanding the knowledge of molecular programs driving follicle development. Serial samples around oocytes and across the cortex and medulla uncovered previously unappreciated variation of hormone and extracellular matrix remodeling activities. This combined spatial and single-cell atlas serves as a resource for future studies of rare cells and pathological states in the ovary.
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Affiliation(s)
- Andrea S. K. Jones
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - D. Ford Hannum
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jordan H. Machlin
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Ansen Tan
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Qianyi Ma
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Nicole D. Ulrich
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Yu-chi Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Maria Ciarelli
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Erica E. Marsh
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Sue Hammoud
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Jun Z. Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
| | - Ariella Shikanov
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
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Jiang YR, Zhu L, Cao LR, Wu Q, Chen JB, Wang Y, Wu J, Zhang TY, Wang ZL, Guan ZY, Xu QQ, Fan QX, Shi SW, Wang HF, Pan JZ, Fu XD, Wang Y, Fang Q. Simultaneous deep transcriptome and proteome profiling in a single mouse oocyte. Cell Rep 2023; 42:113455. [PMID: 37976159 DOI: 10.1016/j.celrep.2023.113455] [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: 12/10/2022] [Revised: 09/23/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
Although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing, and mass spectrometry technology to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level, providing an important resource for understanding the relationship between transcription and translation in cells. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19,948 genes and 2,663 protein groups in single mouse oocytes. In particular, we analyzed the correlation of individual RNA and protein pairs, as well as the meiosis regulatory network with unprecedented depth, and identified 30 transcript-protein pairs as specific oocyte maturational signatures, which could be productive for exploring transcriptional and translational regulatory features during oocyte meiosis.
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Affiliation(s)
- Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Le Zhu
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China
| | - Lan-Rui Cao
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China
| | - Qiong Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | | | | | - Zhi-Ying Guan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Shao-Wen Shi
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Hui-Feng Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Xu-Dong Fu
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China; Center of Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310011, China.
| | - Yongcheng Wang
- School of Medicine, Liangzhu Laboratory, Zhejiang University, Hangzhou 311113, China; Department of Laboratory Medicine, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310011, China.
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China; Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou 310007, China.
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Bedenk J, Režen T, Jančar N, Geršak K, Virant Klun I. Effect of In Vitro Maturation of Human Oocytes Obtained After Controlled Ovarian Hormonal Stimulation on the Expression of Development- and Zona Pellucida-Related Genes and Their Interactions. Reprod Sci 2023; 30:667-677. [PMID: 35915350 DOI: 10.1007/s43032-022-01047-1] [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: 05/23/2022] [Accepted: 07/18/2022] [Indexed: 11/26/2022]
Abstract
In an in vitro fertilization program, approximately 10-15% of oocytes obtained after controlled ovarian stimulation are immature, with germinal vesicles (GVs). These oocytes are usually discarded in clinical practice; however, an in vitro maturation (IVM) procedure can be applied to mature them. There are scarce data in the literature on the effect of IVM on the expression of important development- and zona pellucida (ZP)-related genes in human oocytes; therefore, we wanted to determine this. One hundred nine human oocytes were collected from patients enrolled in an intracytoplasmic sperm injection program. The expression of the BMP4, GDF9, ZP1, ZP2, ZP3, and ZP4 genes was analyzed using RT-qPCR in oocytes matured in vitro with different reproductive hormones in the IVM medium (AMH, FSH + hCG, FSH + hCG + AMH), in in vivo matured oocytes and in immature oocytes with GVs. No statistically significant differences in the expression of selected genes in oocytes were observed among groups with different reproductive hormones in IVM medium. However, several interesting significant correlations were found between BMP4 and GDF9, and ZP1 and ZP4; between GDF9 and ZP1, and ZP2 and ZP4; and between ZP1 and ZP3 and ZP4 in the in vitro matured oocytes, while no such correlations were present in other groups of oocytes. The type of reproductive hormone in the maturation medium does not affect the expression of the analyzed genes in oocytes during the maturation process. However, the in vitro maturation procedure itself generated correlations among analyzed genes that were otherwise not present in in vivo matured and immature oocytes.
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Affiliation(s)
- Jure Bedenk
- Clinical Research Centre, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia.
| | - Tadeja Režen
- Institute of Biochemistry and Molecular Genetics, Centre for Functional Genomics and Bio-Chips, Faculty of Medicine, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Nina Jančar
- Department of Gynaecology and Obstetrics, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia
| | - Ksenija Geršak
- Faculty of Medicine, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Irma Virant Klun
- Clinical Research Centre, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia
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Tan TCY, Brown HM, Thompson JG, Mustafa S, Dunning KR. Optical imaging detects metabolic signatures associated with oocyte quality. Biol Reprod 2022; 107:1014-1025. [PMID: 35863764 PMCID: PMC9562116 DOI: 10.1093/biolre/ioac145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 06/02/2022] [Accepted: 07/11/2022] [Indexed: 11/14/2022] Open
Abstract
Oocyte developmental potential is intimately linked to metabolism. Existing approaches to measure metabolism in the cumulus oocyte complex (COC) do not provide information on the separate cumulus and oocyte compartments. Development of an assay that achieves this may lead to an accurate diagnostic for oocyte quality. Optical imaging of the autofluorescent cofactors NAD(P)H and FAD provides a spatially resolved indicator of metabolism via the optical redox ratio ($\mathrm{FAD}/\left[\mathrm{NAD}\left(\mathrm{P}\right)\mathrm{H}+\mathrm{FAD}\right]$). This may provide an assessment of oocyte quality. Here, we determined whether the optical redox ratio is a robust methodology for measuring metabolism in the cumulus and oocyte compartments compared with oxygen consumption in the whole COC. We also determined whether optical imaging could detect metabolic differences associated with poor oocyte quality (etomoxir-treated). We used confocal microscopy to measure NAD(P)H and FAD, and extracellular flux to measure oxygen consumption. We found that the optical redox ratio was an accurate reflection of metabolism in the oocyte compartment when compared with oxygen consumption (whole COC). Etomoxir-treated COCs showed significantly lower levels of NAD(P)H and FAD compared to control. While confocal imaging demonstrated the premise, we validated this approach using hyperspectral imaging, which is clinically compatible due to its low energy dose. This confirmed lower NAD(P)H and FAD in etomoxir-treated COCs. When comparing imaged vs non-imaged COCs, subsequent preimplantation development and post-transfer viability were comparable. Collectively, these results demonstrate that label-free optical imaging of metabolic cofactors is a safe and sensitive assay for measuring metabolism and has potential to assess oocyte developmental competence.
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Affiliation(s)
- Tiffany C Y Tan
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, South Australia, Australia.,Australian Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, South Australia, Australia.,Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
| | - Hannah M Brown
- Victorian Heart Institute, Monash University, Clayton, Victoria, Australia
| | - Jeremy G Thompson
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, South Australia, Australia.,Australian Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, South Australia, Australia.,Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia.,Fertilis Pty Ltd, Adelaide, South Australia, 5005, Australia
| | - Sanam Mustafa
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, South Australia, Australia.,Australian Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, South Australia, Australia.,Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kylie R Dunning
- Robinson Research Institute, School of Biomedicine, The University of Adelaide, Adelaide, South Australia, Australia.,Australian Research Council Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, South Australia, Australia.,Institute for Photonics and Advanced Sensing, The University of Adelaide, Adelaide, South Australia, Australia
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