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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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Song Y, Zhang N, Zhang Y, Wang J, Lv Q, Zhang J. Single-Cell Transcriptome Analysis Reveals Development-Specific Networks at Distinct Synchronized Antral Follicle Sizes in Sheep Oocytes. Int J Mol Sci 2024; 25:910. [PMID: 38255985 PMCID: PMC10815039 DOI: 10.3390/ijms25020910] [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: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The development of the ovarian antral follicle is a complex, highly regulated process. Oocytes orchestrate and coordinate the development of mammalian ovarian follicles, and the rate of follicular development is governed by a developmental program intrinsic to the oocyte. Characterizing oocyte signatures during this dynamic process is critical for understanding oocyte maturation and follicular development. Although the transcriptional signature of sheep oocytes matured in vitro and preovulatory oocytes have been previously described, the transcriptional changes of oocytes in antral follicles have not. Here, we used single-cell transcriptomics (SmartSeq2) to characterize sheep oocytes from small, medium, and large antral follicles. We characterized the transcriptomic landscape of sheep oocytes during antral follicle development, identifying unique features in the transcriptional atlas, stage-specific molecular signatures, oocyte-secreted factors, and transcription factor networks. Notably, we identified the specific expression of 222 genes in the LO, 8 and 6 genes that were stage-specific in the MO and SO, respectively. We also elucidated signaling pathways in each antral follicle size that may reflect oocyte quality and in vitro maturation competency. Additionally, we discovered key biological processes that drive the transition from small to large antral follicles, revealing hub genes involved in follicle recruitment and selection. Thus, our work provides a comprehensive characterization of the single-oocyte transcriptome, filling a gap in the mapping of the molecular landscape of sheep oogenesis. We also provide key insights into the transcriptional regulation of the critical sizes of antral follicular development, which is essential for understanding how the oocyte orchestrates follicular development.
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Affiliation(s)
| | | | | | | | | | - Jiaxin Zhang
- Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.S.)
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del Olmo I, Verdes A, Álvarez‐Campos P. Distinct patterns of gene expression during regeneration and asexual reproduction in the annelid Pristina leidyi. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:405-420. [PMID: 35604322 PMCID: PMC9790225 DOI: 10.1002/jez.b.23143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/03/2022] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Regeneration, the ability to replace lost body parts, is a widespread phenomenon in the animal kingdom often connected to asexual reproduction or fission, since the only difference between the two appears to be the stimulus that triggers them. Both developmental processes have largely been characterized; however, the molecular toolkit and genetic mechanisms underlying these events remain poorly unexplored. Annelids, in particular the oligochaete Pristina leidyi, provide a good model system to investigate these processes as they show diverse ways to regenerate, and can reproduce asexually through fission under laboratory conditions. Here, we used a comparative transcriptomics approach based on RNA-sequencing and differential gene expression analyses to understand the molecular mechanisms involved in anterior regeneration and asexual reproduction. We found 291 genes upregulated during anterior regeneration, including several regeneration-related genes previously reported in other annelids such as frizzled, paics, and vdra. On the other hand, during asexual reproduction, 130 genes were found upregulated, and unexpectedly, many of them were related to germline development during sexual reproduction. We also found important differences between anterior regeneration and asexual reproduction, with the latter showing a gene expression profile more similar to that of control individuals. Nevertheless, we identified 35 genes that were upregulated in both conditions, many of them related to cell pluripotency, stem cells, and cell proliferation. Overall, our results shed light on the molecular mechanisms that control anterior regeneration and asexual reproduction in annelids and reveal similarities with other animals, suggesting that the genetic machinery controlling these processes is conserved across metazoans.
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Affiliation(s)
- Irene del Olmo
- Department of Biology (Zoology)Universidad Autónoma de MadridMadridSpain
| | - Aida Verdes
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de MadridMadridSpain
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Worton LE, Shi YC, Smith EJ, Barry SC, Gonda TJ, Whitehead JP, Gardiner EM. Ectodermal-Neural Cortex 1 Isoforms Have Contrasting Effects on MC3T3-E1 Osteoblast Mineralization and Gene Expression. J Cell Biochem 2017; 118:2141-2150. [PMID: 27996212 DOI: 10.1002/jcb.25851] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 01/01/2023]
Abstract
The importance of Wnt pathway signaling in development of bone has been well established. Here we investigated the role of a known Wnt target, ENC1 (ectodermal-neural cortex 1; NRP/B), in osteoblast differentiation. Enc1 expression was detected in mouse osteoblasts, chondrocytes, and osteocytes by in situ hybridization, and osteoblastic expression was verified in differentiating primary cultures and MC3T3-E1 pre-osteoblast cells, with 57 kDa and 67 kDa ENC1 protein isoforms detected throughout differentiation. Induced knockdown of both ENC1 isoforms reduced alkaline phosphatase staining and virtually abolished MC3T3-E1 mineralization. At culture confluence, Alpl (alkaline phosphatase liver/bone/kidney) expression was markedly reduced compared with control cells, and there was significant and coordinated alteration of other genes involved in cellular phosphate biochemistry. In contrast, with 67 kDa-selective knockdown mineralized nodule formation was enhanced and there was a two-fold increase in Alpl expression at confluence. There was enhanced expression of Wnt/β-catenin target genes with knockdown of both isoforms at this time-point and a five-fold increase in Frzb (Frizzled related protein) with 67 kDa-selective knockdown at mineralization, indicating possible ENC1 interactions with Wnt signaling in osteoblasts. These results are the first to demonstrate a role for ENC1 in the control of osteoblast differentiation. Additionally, the contrasting mineralization phenotypes and transcriptional patterns seen with coordinate knockdown of both ENC1 isoforms vs selective knockdown of 67 kDa ENC1 suggest opposing roles for the isoforms in regulation of osteoblastic differentiation, through effects on Alpl expression and phosphate cellular biochemistry. This study is the first to report differential roles for the ENC1 isoforms in any cell lineage. J. Cell. Biochem. 118: 2141-2150, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Leah E Worton
- The University of Queensland, Brisbane, Queensland, Australia.,Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington
| | - Yan-Chuan Shi
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,Faculty of Medicine, University of New South Wales, New South Wales, Australia
| | - Elisabeth J Smith
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Simon C Barry
- The University of Adelaide, Adelaide, South Australia, Australia
| | - Thomas J Gonda
- The University of Queensland, Brisbane, Queensland, Australia
| | | | - Edith M Gardiner
- The University of Queensland, Brisbane, Queensland, Australia.,Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, Washington
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Kaminski HJ, Himuro K, Alshaikh J, Gong B, Cheng G, Kusner LL. Differential RNA Expression Profile of Skeletal Muscle Induced by Experimental Autoimmune Myasthenia Gravis in Rats. Front Physiol 2016; 7:524. [PMID: 27891095 PMCID: PMC5102901 DOI: 10.3389/fphys.2016.00524] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/24/2016] [Indexed: 01/14/2023] Open
Abstract
The differential susceptibility of skeletal muscle by myasthenia gravis (MG) is not well understood. We utilized RNA expression profiling of extraocular muscle (EOM), diaphragm (DIA), and extensor digitorum (EDL) of rats with experimental autoimmune MG (EAMG) to evaluate the hypothesis that muscles respond differentially to injury produced by EAMG. EAMG was induced in female Lewis rats by immunization with acetylcholine receptor purified from the electric organ of the Torpedo. Six weeks later after rats had developed weakness and serum antibodies directed against the AChR, animals underwent euthanasia and RNA profiling performed on DIA, EDL, and EOM. Profiling results were validated by qPCR. Across the three muscles between the experiment and control groups, 359 probes (1.16%) with greater than 2-fold changes in expression in 7 of 9 series pairwise comparisons from 31,090 probes were identified with approximately two-thirds being increased. The three muscles shared 16 genes with increased expression and 6 reduced expression. Functional annotation demonstrated that these common expression changes fell predominantly into categories of metabolism, stress response, and signaling. Evaluation of specific gene function indicated that EAMG led to a change to oxidative metabolism. Genes related to muscle regeneration and suppression of immune response were activated. Evidence of a differential immune response among muscles was not evident. Each muscle had a distinct RNA profile but with commonality in gene categories expressed that are focused on muscle repair, moderation of inflammation, and oxidative metabolism.
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Affiliation(s)
- Henry J Kaminski
- Department of Neurology, George Washington University Washington, DC, USA
| | - Keiichi Himuro
- Department of Neurology, Graduate School of Medicine, Chiba University Chiba, Japan
| | - Jumana Alshaikh
- Department of Neurology, George Washington University Washington, DC, USA
| | - Bendi Gong
- Department of Pediatrics, Washington University St. Louis, MO, USA
| | - Georgiana Cheng
- Department of Pathobiology, Cleveland Clinic Cleveland, OH, USA
| | - Linda L Kusner
- Pharmacology and Physiology, George Washington University Washington, DC, USA
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Degaki TL, Demasi MAA, Sogayar MC. Overexpression of Nrp/b (nuclear restrict protein in brain) suppresses the malignant phenotype in the C6/ST1 glioma cell line. J Steroid Biochem Mol Biol 2009; 117:107-16. [PMID: 19682578 DOI: 10.1016/j.jsbmb.2009.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 07/28/2009] [Accepted: 07/29/2009] [Indexed: 12/13/2022]
Abstract
Upon searching for glucocorticoid-regulated cDNA sequences associated with the transformed to normal phenotypic reversion of C6/ST1 rat glioma cells, we identified Nrp/b (nuclear restrict protein in brain) as a novel rat gene. Here we report on the identification and functional characterization of the complete sequence encoding the rat NRP/B protein. The cloned cDNA presented a 1767 nucleotides open-reading frame encoding a 589 amino acids residues sequence containing a BTB/POZ (broad complex Tramtrack bric-a-brac/Pox virus and zinc finger) domain in its N-terminal region and kelch motifs in its C-terminal region. Sequence analysis indicates that the rat Nrp/b displays a high level of identity with the equivalent gene orthologs from other organisms. Among rat tissues, Nrp/b expression is more pronounced in brain tissue. We show that overexpression of the Nrp/b cDNA in C6/ST1 cells suppresses anchorage independence in vitro and tumorigenicity in vivo, altering their malignant nature towards a more benign phenotype. Therefore, Nrp/b may be postulated as a novel tumor suppressor gene, with possible relevance for glioblastoma therapy.
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Affiliation(s)
- Theri Leica Degaki
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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