A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle
Deposition of intramuscular fat (IM), also known as marbling, is the deciding factor of beef quality grade in the U.S. Defining molecular mechanisms underlying the differential deposition of adipose tissue in distinct anatomical areas in beef cattle is key to the development of strategies for marbli...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-07-01
|
| Series: | Agriculture |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2077-0472/15/14/1545 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849304129433763840 |
|---|---|
| author | Mollie M. Green Hunter R. Ford Alexandra P. Tegeler Oscar J. Benitez Bradley J. Johnson Clarissa Strieder-Barboza |
| author_facet | Mollie M. Green Hunter R. Ford Alexandra P. Tegeler Oscar J. Benitez Bradley J. Johnson Clarissa Strieder-Barboza |
| author_sort | Mollie M. Green |
| collection | DOAJ |
| description | Deposition of intramuscular fat (IM), also known as marbling, is the deciding factor of beef quality grade in the U.S. Defining molecular mechanisms underlying the differential deposition of adipose tissue in distinct anatomical areas in beef cattle is key to the development of strategies for marbling enhancement while limiting the accumulation of excessive subcutaneous adipose tissue (SAT). The objective of this exploratory study was to define the IM and SAT transcriptional heterogeneity at the whole tissue and single-nuclei levels in beef steers. Longissimus dorsi muscle samples (9–11th rib) were collected from two finished beef steers at harvest to dissect matched IM and adjacent SAT (backfat). Total RNA from IM and SAT was isolated and sequenced in an Illumina NovaSeq 6000. Nuclei from the same samples were isolated by dounce homogenization, libraries generated with 10× Genomics, and sequenced in an Illumina NovaSeq 6000, followed by analysis via Cell Ranger pipeline and Seurat in RStudio (v4.3.2) By the expression of signature marker genes, single-nuclei RNA sequencing (snRNAseq) analysis identified mature adipocytes (AD; <i>ADIPOQ</i>, <i>LEP</i>), adipose stromal and progenitor cells (ASPC; <i>PDGFRA</i>), endothelial cells (EC; <i>VWF</i>, <i>PECAM1</i>), smooth muscle cells (SMC; <i>NOTCH3</i>, <i>MYL9</i>) and immune cells (IMC; <i>CD163</i>, <i>MRC1</i>). We detected six cell clusters in SAT and nine in IM. Across IM and SAT, AD was the most abundant cell type, followed by ASPC, SMC, and IMC. In SAT, AD made up 50% of the cellular population, followed by ASPC (31%), EC (14%), IMC (1%), and SMC (4%). In IM depot, AD made up 23% of the cellular population, followed by ASPC at 19% of the population, EC at 28%, IMC at 7% and SMC at 12%. The abundance of ASPC and AD was lower in IM vs. SAT, while IMC was increased, suggesting a potential involvement of immune cells on IM deposition. Accordingly, both bulk RNAseq and snRNAseq analyses identified activated pathways of inflammation and metabolic function in IM. These results demonstrate distinct transcriptional cellular heterogeneity between SAT and IM depots in beef steers, which may underly the mechanisms by which fat deposits in each depot. The identification of depot-specific cell populations in IM and SAT via snRNAseq analysis has the potential to reveal target genes for the modulation of fat deposition in beef cattle. |
| format | Article |
| id | doaj-art-6f4ed776ae454ec58c4fc40973556e4d |
| institution | Kabale University |
| issn | 2077-0472 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj-art-6f4ed776ae454ec58c4fc40973556e4d2025-08-20T03:55:49ZengMDPI AGAgriculture2077-04722025-07-011514154510.3390/agriculture15141545A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef CattleMollie M. Green0Hunter R. Ford1Alexandra P. Tegeler2Oscar J. Benitez3Bradley J. Johnson4Clarissa Strieder-Barboza5Department of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USADepartment of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USADepartment of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USADepartment of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USADepartment of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409, USADepartment of Veterinary Sciences, Texas Tech University, Lubbock, TX 79409, USADeposition of intramuscular fat (IM), also known as marbling, is the deciding factor of beef quality grade in the U.S. Defining molecular mechanisms underlying the differential deposition of adipose tissue in distinct anatomical areas in beef cattle is key to the development of strategies for marbling enhancement while limiting the accumulation of excessive subcutaneous adipose tissue (SAT). The objective of this exploratory study was to define the IM and SAT transcriptional heterogeneity at the whole tissue and single-nuclei levels in beef steers. Longissimus dorsi muscle samples (9–11th rib) were collected from two finished beef steers at harvest to dissect matched IM and adjacent SAT (backfat). Total RNA from IM and SAT was isolated and sequenced in an Illumina NovaSeq 6000. Nuclei from the same samples were isolated by dounce homogenization, libraries generated with 10× Genomics, and sequenced in an Illumina NovaSeq 6000, followed by analysis via Cell Ranger pipeline and Seurat in RStudio (v4.3.2) By the expression of signature marker genes, single-nuclei RNA sequencing (snRNAseq) analysis identified mature adipocytes (AD; <i>ADIPOQ</i>, <i>LEP</i>), adipose stromal and progenitor cells (ASPC; <i>PDGFRA</i>), endothelial cells (EC; <i>VWF</i>, <i>PECAM1</i>), smooth muscle cells (SMC; <i>NOTCH3</i>, <i>MYL9</i>) and immune cells (IMC; <i>CD163</i>, <i>MRC1</i>). We detected six cell clusters in SAT and nine in IM. Across IM and SAT, AD was the most abundant cell type, followed by ASPC, SMC, and IMC. In SAT, AD made up 50% of the cellular population, followed by ASPC (31%), EC (14%), IMC (1%), and SMC (4%). In IM depot, AD made up 23% of the cellular population, followed by ASPC at 19% of the population, EC at 28%, IMC at 7% and SMC at 12%. The abundance of ASPC and AD was lower in IM vs. SAT, while IMC was increased, suggesting a potential involvement of immune cells on IM deposition. Accordingly, both bulk RNAseq and snRNAseq analyses identified activated pathways of inflammation and metabolic function in IM. These results demonstrate distinct transcriptional cellular heterogeneity between SAT and IM depots in beef steers, which may underly the mechanisms by which fat deposits in each depot. The identification of depot-specific cell populations in IM and SAT via snRNAseq analysis has the potential to reveal target genes for the modulation of fat deposition in beef cattle.https://www.mdpi.com/2077-0472/15/14/1545single-celltranscriptomebeef cattlemarblingadipose tissuefat |
| spellingShingle | Mollie M. Green Hunter R. Ford Alexandra P. Tegeler Oscar J. Benitez Bradley J. Johnson Clarissa Strieder-Barboza A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle Agriculture single-cell transcriptome beef cattle marbling adipose tissue fat |
| title | A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle |
| title_full | A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle |
| title_fullStr | A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle |
| title_full_unstemmed | A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle |
| title_short | A Single-Cell Assessment of Intramuscular and Subcutaneous Adipose Tissue in Beef Cattle |
| title_sort | single cell assessment of intramuscular and subcutaneous adipose tissue in beef cattle |
| topic | single-cell transcriptome beef cattle marbling adipose tissue fat |
| url | https://www.mdpi.com/2077-0472/15/14/1545 |
| work_keys_str_mv | AT molliemgreen asinglecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT hunterrford asinglecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT alexandraptegeler asinglecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT oscarjbenitez asinglecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT bradleyjjohnson asinglecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT clarissastriederbarboza asinglecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT molliemgreen singlecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT hunterrford singlecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT alexandraptegeler singlecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT oscarjbenitez singlecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT bradleyjjohnson singlecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle AT clarissastriederbarboza singlecellassessmentofintramuscularandsubcutaneousadiposetissueinbeefcattle |