Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models

doi:10.1038/s41597-023-02293-x

. 2023 Jun 16;10(1):387.

doi: 10.1038/s41597-023-02293-x.

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models

Jiehan Li^#^{1

2

3}, Christopher Jin^#¹, Stefan Gustafsson⁴, Abhiram Rao⁵, Martin Wabitsch⁶, Chong Y Park^{1

2

3}, Thomas Quertermous^{1

3}, Joshua W Knowles^{7

8

9

10}, Ewa Bielczyk-Maczynska^{11

12

13}

Affiliations

¹ Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
² Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA.
³ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
⁴ Clinical Epidemiology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
⁵ Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
⁶ Department of Pediatrics and Adolescent Medicine, Center for Rare Endocrine Diseases, Division of Pediatric Endocrinology and Diabetes, Ulm University Medical Centre, Ulm, 89075, Germany.
⁷ Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
⁸ Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
⁹ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
¹⁰ Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
¹¹ Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. ewabm@stanford.edu.
¹² Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA. ewabm@stanford.edu.
¹³ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA. ewabm@stanford.edu.

^# Contributed equally.

PMID: 37328521
PMCID: PMC10275883
DOI: 10.1038/s41597-023-02293-x

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models

Jiehan Li et al. Sci Data. 2023.

. 2023 Jun 16;10(1):387.

doi: 10.1038/s41597-023-02293-x.

Authors

Affiliations

¹ Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
² Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA.
³ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
⁴ Clinical Epidemiology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
⁵ Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
⁶ Department of Pediatrics and Adolescent Medicine, Center for Rare Endocrine Diseases, Division of Pediatric Endocrinology and Diabetes, Ulm University Medical Centre, Ulm, 89075, Germany.
⁷ Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
⁸ Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
⁹ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
¹⁰ Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA. knowlej@stanford.edu.
¹¹ Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. ewabm@stanford.edu.
¹² Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, 94305, USA. ewabm@stanford.edu.
¹³ Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA. ewabm@stanford.edu.

^# Contributed equally.

PMID: 37328521
PMCID: PMC10275883
DOI: 10.1038/s41597-023-02293-x

Abstract

Adipogenesis is a process in which fat-specific progenitor cells (preadipocytes) differentiate into adipocytes that carry out the key metabolic functions of the adipose tissue, including glucose uptake, energy storage, and adipokine secretion. Several cell lines are routinely used to study the molecular regulation of adipogenesis, in particular the immortalized mouse 3T3-L1 line and the primary human Simpson-Golabi-Behmel syndrome (SGBS) line. However, the cell-to-cell variability of transcriptional changes prior to and during adipogenesis in these models is not well understood. Here, we present a single-cell RNA-Sequencing (scRNA-Seq) dataset collected before and during adipogenic differentiation of 3T3-L1 and SGBS cells. To minimize the effects of experimental variation, we mixed 3T3-L1 and SGBS cells and used computational analysis to demultiplex transcriptomes of mouse and human cells. In both models, adipogenesis results in the appearance of three cell clusters, corresponding to preadipocytes, early and mature adipocytes. These data provide a groundwork for comparative studies on these widely used in vitro models of human and mouse adipogenesis, and on cell-to-cell variability during this process.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

**Fig. 1**
scRNA-Seq of mouse and human adipogenesis. (a) Schematic of the workflow. Human SGBS and mouse 3T3-L1 cells were analyzed at two time points, corresponding to before (D0) and during (D5 for 3T3-L1, D8 for SGBS) adipogenesis. At each time point, live cells were purified using exclusion of propidium iodide-stained cells by FACS. Equal numbers of SGBS and 3T3-L1 cells were then mixed and subjected to microfluidic single-cell capture with GelBeads-in-emulsion (GEMs) using 10X Chromium Controller. Single-cell cDNA libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit (10X Genomics), followed by sequencing on Illumina HiSeq 4000. Computational analysis involved barcode processing, UMI counting, demultiplexing, gene and cell filtering, normalization, and clustering. (b) Representative light microscopy images of differentiated cells, SGBS at day 8 (D8) and 3T3-L1 at day 5 (D5), show similar pattern of lipid deposition in adipocytes (arrows). Scale bar: 50 µm.

**Fig. 2**
Single-cell RNA-Seq dataset quality assessment following inferring the species from transcriptome. (a,b) Plots representing quantification of the alignment of individual cell’s transcriptomes to the human (hg19) and mouse (mm10) genomes at (a) D0 3T3-L1/D0 SGBS, and (b) D5 3T3-L1/D8 SGBS. (c,d) Violin plots of gene counts (nFeature_RNA) and UMI counts (nCount_RNA) after quality control filtering in (c) SGBS cells and (d) 3T3-L1 cells, separated by the day of differentiation.

**Fig. 3**
Clustering of scRNA-Seq data in human SGBS cells. (a) Primary component analysis (PCA) plot. (b) UMAP plot. (c) Pseudotime analysis. (d) t-SNE plot. (e) Assignment of cells by differentiation day (D0 vs. D8), superimposed on the t-SNE plot. (f) Heatmap showing the expression of top 10 enriched genes per cell cluster.

**Fig. 4**
Clustering of scRNA-Seq data in murine 3T3-L1 cells. (a) Primary component analysis (PCA) plot. (b) UMAP plot. (c) Pseudotime analysis. (d) t-SNE plot. (e) Assignment of cells by differentiation day (D0 vs. D5), superimposed on the t-SNE plot. (f) Heatmap showing the expression of top 10 enriched genes per cell cluster.

**Fig. 5**
Feature plots showing the expression of cluster marker genes for individual clusters in human SGBS cells. (a) Cluster 0 (preadipocytes); (b) Cluster 1 (differentiating); (c) Cluster 2 (adipocytes).

**Fig. 6**
Feature plots showing the expression of cluster marker genes for individual clusters in mouse 3T3-L1 cells. (a) Cluster 0 (preadipocytes); (b) Cluster 1 (differentiating); (c) Cluster 2 (adipocytes).

**Fig. 7**
Venn diagram representation of the number of unique and shared marker genes between SGBS and 3T3-L1 cell lines, separated by cell cluster.

See this image and copyright information in PMC

Update of

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models.
Li J, Jin C, Gustafsson S, Rao A, Wabitsch M, Park CY, Quertermous T, Bielczyk-Maczynska E, Knowles JW. Li J, et al. bioRxiv [Preprint]. 2023 Mar 29:2023.03.27.534456. doi: 10.1101/2023.03.27.534456. bioRxiv. 2023. Update in: Sci Data. 2023 Jun 16;10(1):387. doi: 10.1038/s41597-023-02293-x. PMID: 37034809 Free PMC article. Updated. Preprint.

Cited by

Loss of RREB1 reduces adipogenesis and improves insulin sensitivity in mouse and human adipocytes.
Yu GZ, Krentz NAJ, Bentley L, Zhao M, Paphiti K, Sun H, Honecker J, Nygård M, Dashti H, Bai Y, Reid M, Thaman S, Wabitsch M, Rajesh V, Yang J, Mattis KK, Abaitua F, Casero R, Hauner H, Knowles JW, Wu JY, Mandrup S, Claussnitzer M, Svensson KJ, Cox RD, Gloyn AL. Yu GZ, et al. bioRxiv [Preprint]. 2024 Jul 31:2024.07.30.605923. doi: 10.1101/2024.07.30.605923. bioRxiv. 2024. PMID: 39131393 Free PMC article. Preprint.
Tissue-Level Effect of Andrographis and Ashwagandha Metabolites on Metabolic and Inflammatory Gene Expression in Skeletal Muscle and Adipose Tissue: An Ex Vivo/In Vitro Investigation.
Lugtmeijer C, Bowtell JL, O'Leary M. Lugtmeijer C, et al. Nutrients. 2024 Jul 17;16(14):2291. doi: 10.3390/nu16142291. Nutrients. 2024. PMID: 39064738 Free PMC article.

References

1. Scheja L, Heeren J. The endocrine function of adipose tissues in health and cardiometabolic disease. Nat. Rev. Endocrinol. 2019;15:507–524. doi: 10.1038/s41574-019-0230-6. - DOI - PubMed
1. Frayn K, Karpe F, Fielding B, Macdonald I, Coppack S. Integrative physiology of human adipose tissue. Int. J. Obes. Relat. Metab. Disord. 2003;27:875–888. doi: 10.1038/sj.ijo.0802326. - DOI - PubMed
1. Tang W, et al. White fat progenitor cells reside in the adipose vasculature. Science. 2008;322:583–586. doi: 10.1126/science.1156232. - DOI - PMC - PubMed
1. Smith U, Kahn BB. Adipose tissue regulates insulin sensitivity: role of adipogenesis, de novo lipogenesis and novel lipids. J. Intern. Med. 2016;280:465–475. doi: 10.1111/joim.12540. - DOI - PMC - PubMed
1. Mackall J, Student A, Polakis SE, Lane M. Induction of lipogenesis during differentiation in a” preadipocyte” cell line. J. Biol. Chem. 1976;251:6462–6464. doi: 10.1016/S0021-9258(20)81883-3. - DOI - PubMed

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Grants and funding

LinkOut - more resources

Full Text Sources

[1] Scheja L, Heeren J. The endocrine function of adipose tissues in health and cardiometabolic disease. Nat. Rev. Endocrinol. 2019;15:507–524. doi: 10.1038/s41574-019-0230-6. - DOI - PubMed

[2] Scheja L, Heeren J. The endocrine function of adipose tissues in health and cardiometabolic disease. Nat. Rev. Endocrinol. 2019;15:507–524. doi: 10.1038/s41574-019-0230-6. - DOI - PubMed

[3] Frayn K, Karpe F, Fielding B, Macdonald I, Coppack S. Integrative physiology of human adipose tissue. Int. J. Obes. Relat. Metab. Disord. 2003;27:875–888. doi: 10.1038/sj.ijo.0802326. - DOI - PubMed

[4] Frayn K, Karpe F, Fielding B, Macdonald I, Coppack S. Integrative physiology of human adipose tissue. Int. J. Obes. Relat. Metab. Disord. 2003;27:875–888. doi: 10.1038/sj.ijo.0802326. - DOI - PubMed

[5] Tang W, et al. White fat progenitor cells reside in the adipose vasculature. Science. 2008;322:583–586. doi: 10.1126/science.1156232. - DOI - PMC - PubMed

[6] Tang W, et al. White fat progenitor cells reside in the adipose vasculature. Science. 2008;322:583–586. doi: 10.1126/science.1156232. - DOI - PMC - PubMed

[7] Smith U, Kahn BB. Adipose tissue regulates insulin sensitivity: role of adipogenesis, de novo lipogenesis and novel lipids. J. Intern. Med. 2016;280:465–475. doi: 10.1111/joim.12540. - DOI - PMC - PubMed

[8] Smith U, Kahn BB. Adipose tissue regulates insulin sensitivity: role of adipogenesis, de novo lipogenesis and novel lipids. J. Intern. Med. 2016;280:465–475. doi: 10.1111/joim.12540. - DOI - PMC - PubMed

[9] Mackall J, Student A, Polakis SE, Lane M. Induction of lipogenesis during differentiation in a” preadipocyte” cell line. J. Biol. Chem. 1976;251:6462–6464. doi: 10.1016/S0021-9258(20)81883-3. - DOI - PubMed

[10] Mackall J, Student A, Polakis SE, Lane M. Induction of lipogenesis during differentiation in a” preadipocyte” cell line. J. Biol. Chem. 1976;251:6462–6464. doi: 10.1016/S0021-9258(20)81883-3. - DOI - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models

Affiliations

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Update of

Similar articles

Cited by

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Abstract

Conflict of interest statement

Figures

Update of

Similar articles

Cited by

References

Publication types

MeSH terms

Related information

Grants and funding

LinkOut - more resources

Full Text Sources