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Updated: Jan 15, 2026
Isolation of Adipose Tissue Nuclei for Single-Cell Genomic Applications
Published on: June 12, 2020
Decoding adipocyte heterogeneity through single-nucleus transcriptomics unveils subtype-specific adipocytes
Yiwei Tong1, Zheng Wang1, Niu Qiao2
1Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
Background:
While adipose tissue constitutes a substantial proportion of breast composition, the functional characteristics and pathological relevance of the adipocyte microenvironment in breast carcinogenesis remain undercharacterized. This study employs single-nucleus RNA sequencing (snRNA-seq) to establish a comprehensive cellular atlas of adipocyte heterogeneity across molecular subtypes of breast cancer, aiming to elucidate subtype-specific adipocyte contributions to tumor microenvironment modulation.
Methods:
snRNA-seq was performed on breast adipose tissues isolated from individuals without cancer and treatment-naïve breast cancer. Various adipocyte and pre-adipocyte subclusters were identified. Comparative analyses of cellular distribution and transcriptional profiles were performed across disease states and molecular subtypes. Pseudotime, cell communication, and immunofluorescence analyses were further implemented to investigate cellular dynamics and microenvironment interactions.
Results:
snRNA-seq data of 86,529 nuclei were obtained. Three adipocyte and seven pre-adipocyte subclusters were identified, of which Adi_LDLR, Pre_Adi_LDLR, and Pre_Adi_LGR4_TGFBR1 were restricted to cancer-associated adipose (CAAs). Adi_LDLR and Pre_Adi_LDLR were enriched in estrogen receptor (ER)-positive CAAs and related to cell senescence and immunosuppression. Pre_Adi_LGR4_TGFBR1 was predominantly present in triple-negative breast cancer, functionally pro-proliferative, immunosuppressive, and lacked normal adipose function. The immunofluorescence intensity of LDLR (p=0.031) and TGFBR1 (p=0.038) was positively associated with disease recurrence, suggesting the formation of immunosuppressive niches by these cancer-specific adipose subsets in both subtypes. Cell communication analyses revealed a specific (pre-) adipocyte-macrophage interaction via ligand-receptor pairs involved in stromal remodeling and tumor migration for ER-positive tumors, whereas tumor proliferation and metastasis for triple-negative ones likely contribute to tumor progression.
Conclusions:
This study delineated a distinct adipocyte landscape in breast cancer and subtype-specific immunosuppressive niches fostered by CAAs and (pre-) adipocyte-macrophage interactions. These findings provide novel therapeutic targets for microenvironment-directed interventions in breast oncology.
