Histological analyses data for: Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures
Data files
Apr 07, 2025 version files 12.82 KB
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Paper_raw_data.xlsx
11.34 KB
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README.md
1.47 KB
May 19, 2025 version files 3.87 MB
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Aerobic_electron_transport_chain_heatmap.xlsx
15.37 KB
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apoptotic_cell_clearance_heatmap.xlsx
14.15 KB
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Immune_processes_heatmap.xlsx
15.77 KB
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mac_genes_heatmap.xlsx
11.52 KB
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MNGC_Mac_shared_gene_comparison.xlsx
348.70 KB
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MNGC_vs_Mac_DEGs_sig.xlsx
635.32 KB
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Paper_raw_data.xlsx
11.34 KB
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Pathway_Analysis_Mac_Unique.csv
119.16 KB
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Pathway_Analysis_MNGC_top_1000genes.csv
324.14 KB
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Pathway_Analysis_MNGC_Unique.csv
30.29 KB
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Pathway_Analysis_MNGC_vs_Mac_downreg.csv
113.28 KB
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Pathway_Analysis_MNGC_vs_Mac_upreg.csv
122.47 KB
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Proteolysis_heatmap.xlsx
15.54 KB
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README.md
8.78 KB
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Regulation_of_lipid_metabolic_processes_heatmap.xlsx
15.98 KB
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tcell_marker_heatmap.xlsx
11.70 KB
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Top_gene_lists.xlsx
2.02 MB
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Venn_Supplemental_F1.xls
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Abstract
The ovary is one of the first organs to exhibit signs of aging, characterized by reduced tissue function, chronic inflammation, and fibrosis. Multinucleated giant cells (MNGCs), formed by macrophage fusion, typically occur in chronic immune pathologies, including infectious and non-infectious granulomas and the foreign body response, but are also observed in the aging ovary. The function and consequence of ovarian MNGCs remain unknown as their biological activity is highly context-dependent, and their large size has limited their isolation and analysis through technologies such as single-cell RNA sequencing. In this study, we define ovarian MNGCs through a deep analysis of their presence across age and species using advanced imaging technologies as well as their unique transcriptome using laser capture microdissection. MNGCs form complex interconnected networks that increase with age in both mouse and nonhuman primate ovaries. MNGCs are characterized by high Gpnmb expression, a putative marker of ovarian and non-ovarian MNGCs. Pathway analysis highlighted functions in apoptotic cell clearance, lipid metabolism, proteolysis, immune processes, and increased oxidative phosphorylation and antioxidant activity. Thus, MNGCs have signatures related to degradative processes, immune function, and high metabolic activity. These processes were enriched in MNGCs compared to primary ovarian macrophages, suggesting discrete functionality. MNGCs express CD4 and colocalize with T-cells, which were enriched in regions of MNGCs, indicative of a close interaction between these immune cell types. These findings implicate MNGCs in modulation of the ovarian immune landscape during aging given their high penetrance and unique molecular signature that supports degradative and immune functions.
Dataset DOI: 10.5061/dryad.kh18932j4
Description of the data and file structure
Multinucleated giant cells are hallmarks of ovarian aging with unique immune and degradation-associated molecular signatures
https://doi.org/10.5061/dryad.kh18932j4
Description of the data and file structure
Includes data used to generate graphs related to transcriptomic data as well as histological quantification of MNGCs and postitive antibody staining was performed on tissue sections from mouse and non-human primate ovaries using ImageJ. Paper_raw_data.xlsx represents data from bar and line graphs (Fig 1 and Fig 4). For these data, to quantify the amount of ovarian area taken up by MNGCs (figure 1), the Trainable Weka Segmentation plugin in Fiji (NIH) was used to train the model on regions of non-ovary, non-MNGC ovary, and MNGCs. For figure 4, percent positive CD4 or CD3ε area was determined as DAB positive area over the total area of an ROI that included area of MNGCs, corpora lutea, or stroma.
Version changes
18 May 2025: Files related to transcriptomic data analyses in all figures have now been included. This includes top gene lists, DEGs, and the count values for heatmap generation, pathway analysis files, and gene comparison between group files.
Files and variables
File: Paper_raw_data.xlsx
Description: Raw data from ImageJ analysis of Figures 1C, 1D, 4F, 4G, 4H.
Variables
- Figure 1C and 1D
- Age in months (mouse) and age in years (non-human primate, NHP); RY refers to reproductively young 6-12 wks
- % multinucleated giant cell (MNGC) area
- Figure 4F
- % CD4 positive area
- Animal number, mouse
- Figure 4G and 4H
- % CD3 (4G) and % CD4 (4H) postitive area
- Ovarian structure (corpora lutea, CL; stroma; multinucleated giant cell, MNGC)
File: MNGC_vs_Mac_DEGs_sig.xlsx
Description: Significant differentially expressed genes (DEGs) between MNGC (multinucleated giant cell) and Mac (ovarian macrophage) sample groups. Data was generated from raw gene counts through DESeq2. This data was used to determine up and down regulated genes that were used for pathway analysis displayed in Fig. 3 F-G, and volcano plot shown in Fig. 3E. Log2FoldChange represents MNGC vs Mac.
Variables
- MNGC (multinucleated Giant cells) and Mac (ovarian macrophages)
File: Pathway_Analysis_MNGC_top_1000genes.csv
Description: Pathway analysis of top 1000 MNGC genes. Data table was obtained from Metascape (https://metascape.org/gp/index.html#/main/step1). Gene list for input was obtained from Top_gene_lists.xlsx, with the top 1000 genes from the MNGC group with the highest average expression serving as input. Data used to generate Fig 2D.
File: Pathway_Analysis_Mac_Unique.csv
Description: Pathway analysis of protein-coding genes that are expressed in MNGC samples but not Mac samples. Data table was obtained from Metascape (https://metascape.org/gp/index.html#/main/step1). Gene list (MNGC subset) for input was obtained from MNGC_Mac_shared_gene_comparison.xlsx. Data used to generate Fig. 4A.
File: Pathway_Analysis_MNGC_vs_Mac_upreg.csv
Description: Pathway analysis of genes that are upregulated in MNGC samples compared to Mac (Log2FoldChange>2, p<0.05). Data table was obtained from Metascape (https://metascape.org/gp/index.html#/main/step1). Gene list for input was obtained from MNGC_vs_Mac_DEGs_sig.xlsx, using the cutoffs stated above. Data used to generate Fig. 3F.
File: Top_gene_lists.xlsx
Description: Normalized gene count lists for all genes found in MNGC and Mac groups. Used to generate Fig. 2C (MNGC).
File: Pathway_Analysis_MNGC_vs_Mac_downreg.csv
Description: Pathway analysis of genes that are downregulated in MNGC samples compared to Mac (Log2FoldChange>2, p<0.05). Data table was obtained from Metascape (https://metascape.org/gp/index.html#/main/step1). Gene list for input was obtained from MNGC_vs_Mac_DEGs_sig.xlsx, using the cutoffs stated above. Data used to generate Fig. 3G.
File: Pathway_Analysis_MNGC_Unique.csv
Description: Pathway analysis of protein-coding genes that are expressed in Mac samples but not MNGC samples. Data table was obtained from Metascape (https://metascape.org/gp/index.html#/main/step1). Gene list (Mac subset) for input was obtained from MNGC_Mac_shared_gene_comparison.xlsx. Data used to generate Fig. 4B.
File: mac_genes_heatmap.xlsx
Description: Gene counts used to generate Fig. 3D. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages), Stroma (non-MNGC ovarian stroma)
File: Aerobic_electron_transport_chain_heatmap.xlsx
Description: Gene counts used to generate Aerobic electron transport chain panel in Fig. 3H. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages)
File: apoptotic_cell_clearance_heatmap.xlsx
Description: Gene counts used to generate apoptotic cell clearance panel in Fig. 3H. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages)
File: Immune_processes_heatmap.xlsx
Description: Gene counts used to generate immune processes panel in Fig. 3H. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages)
File: Proteolysis_heatmap.xlsx
Description: Gene counts used to generate proteolysis panel in Fig. 3H. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages)
File: Regulation_of_lipid_metabolic_processes_heatmap.xlsx
Description: Gene counts used to generate lipid metabolic processes panel in Fig. 3H. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages)
File: MNGC_Mac_shared_gene_comparison.xlsx
Description: Shared gene list used to determine MNGC and Mac unique genes for Fig 4 (A-C). Subset indicates if genes are “shared” by both MNGC and Mac samples, or only present in one sample type (“MNGC” or “Mac”).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages)
File: tcell_marker_heatmap.xlsx
Description: Gene counts used to generate Fig. 4D. Gene counts were used as input to generate a heatmap in SRplot (https://www.bioinformatics.com.cn/srplot).
Variables
- MNGC (multinucleated giant cells), Mac (ovarian macrophages), Stroma (non-MNGC ovarian stroma)
File: Venn_Supplemental_F1.xls
Description: Shared gene list used to determine how the top 100 compare between ovarian MNGCs and in vitro induced foreign body giant cells (FBGC), Osteoclasts (Osteo), and Langhans giant cells (LGC). Subset indicates if genes are “shared” by both all groups, or only present in one sample type (“Ovarian MNGC,” (“FBGC”, “Osteo”, or “LGC”). Comparison shown in Venn diagram in Supplemental Fig. 1. FBGC, Osteo, and LGC data was obtained from https://doi.org/10.15252/embr.202256310.
Variables
- Ovarian MNGC, foreign body giant cells (FBGC), osteoclasts (Osteo), and Langhans giant cells (LGC)
Access information
Other publicly accessible locations of the data:
Data was derived from the following sources:
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