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This publication describes a protocol for the isolation of nuclei from mature adipocytes, purification by fluorescence-activated sorting, and single-cell level transcriptomics.
Brown and beige fat are specialized adipose tissues that dissipate energy for thermogenesis by UCP1 (Uncoupling Protein-1)-dependent and independent pathways. Until recently, thermogenic adipocytes were considered a homogeneous population. However, recent studies have indicated that there are multiple subtypes or subpopulations that are distinct in developmental origin, substrate use, and transcriptome. Despite advances in single-cell genomics, unbiased decomposition of adipose tissues into cellular subtypes has been challenging because of the fragile nature of lipid-filled adipocytes. The protocol presented was developed to circumvent these obstacles by effective isolation of single nuclei from adipose tissue for downstream applications, including RNA sequencing. Cellular heterogeneity can then be analyzed by RNA sequencing and bioinformatic analyses.
Studies have shown that brown adipose tissue (BAT) has a remarkable capacity to dissipate energy. Two types of thermogenic adipocytes with distinct developmental features exist in both rodents and humans: beige adipocytes and classical brown adipocytes. While classical brown adipocytes are located mostly in interscapular BAT depots, beige adipocytes sporadically emerge in white adipose tissue (WAT) in response to certain physiological cues, such as chronic cold exposure, a process referred to as "browning" or "beiging". Through the use of advanced imaging, it is now clear that adult humans have substantial depots of UCP1+ BAT, especially in ....
Animal care and experimentation were performed according to procedures approved by the Institutional Animal Care and Use Committee at the Albert Einstein College of Medicine.
1. Preparation of tissue digestion and lysis buffers
Unsorted adipocyte nuclei contain debris and doublets that create noise and high background in downstream single-cell RNA sequencing. The representative FACS gate strategy is shown in Figure 1. The nuclei were first selected based on forward scatter (FSC) and side scatter (SSC) (A), then, only singlets were selected based on the combination of width and heights of SSC (B). Finally, only DAPI-positive events were selected and .......
A straightforward and robust method to isolate single nuclei and study adipose tissue heterogeneity is presented. Compared to whole tissue RNA sequencing, this workflow offers an unbiased view of cellular heterogeneity and population-specific markers. This is significant and innovative for the advancement of adipocyte biology, molecular metabolism, and obesity research.
This protocol is particularly optimized for downstream application of snRNA-seq. The "cleanup" step to achieve isolat.......
We would like to thank David Reynolds from the Albert Einstein Genomics core and Jinghang Zhang from the Flow Cytometry Core for technical support. We acknowledge support from the National Institutes of Health (NIH) (DK110426) and Pilot and Feasibility Grants from the Einstein-Mount Sinai Diabetes Research Center (DK020541), and New York Obesity Research Center (DK026687) (all to K.S.). We also would like to thank Albert Einstein Cancer Center (CA013330) for core support.
....Name | Company | Catalog Number | Comments |
autoMACS Rinsing Solution | Miltenyi Biotec | 130-091-222 | PBS with EDTA; sterile-filtered |
BSA | Sigma | A1595 | |
CaCl2 | Sigma | 21115 | |
Cell filter 100 μm | Corning | 431752 | |
Cell filter 40μm | Corning | 431750 | |
CellTrics (30 μm) | Sysmex | 04-004-2326 | |
Collagenase D | Roche | 11088866001 | |
Countess II FL Automated Cell Counter | Invitrogen | AMQAF1000 | |
DAPI | Sigma | D9542 | |
Dispase II | Roche | 4942078001 | |
HEPES | Sigma | H4034 | |
KCl | Fisher | P217-3 | |
MACS SmartStrainers (30 µm) | Miltenyi Biotec | 130-098-458 | Stackable filters |
MgCl2 | Sigma | M1028 | |
MoFloXDP Cell Sorter | Beckman Coulter | ML99030 | |
NP-40 | Sigma | 74385 | |
Protector RNase Inhibitor | Roche | 3335402001 | |
Sucrose | Fisher | S5-3 |
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