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Method Article
We describe a method for the isolation of endocrine cells from embryonic, neonatal and postnatal pancreases followed by single-cell RNA sequencing. This method allows analyses of pancreatic endocrine lineage development, cell heterogeneity and transcriptomic dynamics.
Pancreatic endocrine cells, which are clustered in islets, regulate blood glucose stability and energy metabolism. The distinct cell types in islets, including insulin-secreting β cells, are differentiated from common endocrine progenitors during the embryonic stage. Immature endocrine cells expand via cell proliferation and mature during a long postnatal developmental period. However, the mechanisms underlying these processes are not clearly defined. Single-cell RNA-sequencing is a promising approach for the characterization of distinct cell populations and tracing cell lineage differentiation pathways. Here, we describe a method for the single-cell RNA-sequencing of isolated pancreatic β cells from embryonic, neonatal and postnatal pancreases.
The pancreas is a vital metabolic organ in mammals. The pancreas is comprised of endocrine and exocrine compartments. Pancreatic endocrine cells, including insulin-producing β cells and glucagon-producing α cells, cluster together in the islets of Langerhans and coordinately regulate systemic glucose homeostasis. Dysfunction of the endocrine cells results in diabetes mellitus, which has become a major public health issue worldwide.
Pancreatic endocrine cells are derived from Ngn3+ progenitors during embryogenesis1. Later, during the perinatal period, the endocrine cells proliferate to form immature islets. These immature cells continue to develop and gradually become mature islets, which become richly vascularized to regulate blood glucose homeostasis in adults2.
Although a group of transcriptional factors has been identified that regulate β cell differentiation, the precise maturation pathway of β cells is still unclear. Moreover, the β cell maturation process also involves the regulation of cell number expansion3,4 and the generation of cellular heterogeneity5,6. However, the regulatory mechanisms of these processes have not been well studied.
Single-cell RNA-sequencing is a powerful approach that can profile cell subpopulations and trace cell lineage developmental pathways7. Taking advantage of this technology, the key events that occur during pancreatic islet development can be deciphered at the single-cell level8. Among the single-cell RNA-sequencing protocols, Smart-seq2 allows the generation of full-length cDNA with improved sensitivity and accuracy, and the use of standard reagents at lower cost9. Smart-seq2 takes approximately two days to construct a cDNA library for sequencing10.
Here, we propose a method for the isolation of fluorescence-labeled β cells from the pancreases of fetal to adult Ins1-RFP transgenic mice11, using fluorescence-activated cell sorting (FACS), and the performance of transcriptomic analyses at the single-cell level, using Smart-seq2 technology (Figure 1).This protocol can be extended to analyze the transcriptomes of all pancreatic endocrine cell types in normal, pathological and aging states.
All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of Peking University.
1. Pancreas Isolation
2. Collagenase Digestion and Islet Isolation
3. Trypsin Digestion of Pancreatic Tissue or Islets
4. Single-cell Lysis
5. Single-cell cDNA Amplification
6. cDNA Library Construction
7. DNA Sequencing
8. Bioinformatics Analyses
Pancreases were dissected from embryonic, neonatal and postnatal mice (Figure 2A and 2B). For mice older than postnatal day 18, the digestive effect depends on the degree of perfusion; therefore, the injection is the most important step for islet isolation (Figure 2C-2E and Table 6). As much collagenase was injected as was possible to fill the pancreas during thi...
In this protocol, we demonstrated an effective and easy-to-use method for studying the single-cell expression profiles of pancreatic β cells. This method could be used to isolate endocrine cells from embryonic, neonatal and postnatal pancreases and to perform single-cell transcriptomic analyses.
The most critical step is the isolation of single β cells in good condition. Fully perfused pancreases respond better to subsequent digestion. Insufficient perfusion, which usually occurs in ...
The authors have nothing to disclose.
We thank the National Center for Protein Sciences, Beijing (Peking University) and the Peking-Tsinghua Center for the Life Science Computing Platform. This work was supported by the Ministry of Science and Technology of China (2015CB942800), the National Natural Science Foundation of China (31521004, 31471358, and 31522036), and funding from Peking-Tsinghua Center for Life Sciences to C.-R.X.
Name | Company | Catalog Number | Comments |
Collagenase P | Roche | 11213873001 | |
Trypsin-EDTA (0.25 %), phenol red | Thermo Fisher Scientific | 25200114 | |
Fetal bovine serum (FBS) | Hyclone | SH30071.03 | |
Dumont #4 Forceps | Roboz | RS-4904 | |
Dumont #5 Forceps | Roboz | RS-5058 | |
30 G BD Needle 1/2" Length | BD | 305106 | |
Stereo Microscope | Zeiss | Stemi DV4 | |
Stereo Fluorescence microscope | Zeiss | Stereo Lumar V12 | |
Centrifuge | Eppendorf | 5810R | |
Centrifuge | Eppendorf | 5424R | |
Polystyrene Round-Bottom Tube with Cell-Strainer Cap | BD-Falcon | 352235 | |
96-Well PCR Microplate | Axygen | PCR-96-C | |
Silicone Sealing Mat | Axygen | AM-96-PCR-RD | |
Thin Well PCR Tube | Extragene | P-02X8-CF | |
Cell sorter | BD Biosciences | BD FACSAria | |
Capillary pipette | Sutter | B100-58-10 | |
RNaseZap | Ambion | AM9780 | |
ERCC RNA Spike-In Mix | Life Technologies | 4456740 | |
Distilled water | Gibco | 10977 | |
Triton X-100 | Sigma-Aldrich | T9284 | |
dNTP mix | New England Biolabs | N0447 | |
Recombinant RNase Inhibitor | Takara | 2313 | |
Superscript II reverse transcriptase | Invitrogen | 18064-014 | |
First-strand buffer (5x) | Invitrogen | 18064-014 | |
DTT | Invitrogen | 18064-014 | |
Betaine | Sigma-Aldrich | 107-43-7 | |
MgCl2 | Sigma-Aldrich | 7786-30-3 | |
Nuclease-free water | Invitrogen | AM9932 | |
KAPA HiFi HotStart ReadyMix (2x) | KAPA Biosystems | KK2601 | |
VAHTS DNA Clean Beads XP beads | Vazyme | N411-03 | |
Qubit dsDNA HS Assay Kit | Invitrogen | Q32854 | |
AceQ qPCR SYBR Green Master Mix | Vazyme | Q121-02 | |
TruePrep DNA Library Prep Kit V2 for Illumina | Vazyme | TD502 | Include 5x TTBL, 5x TTE, 5x TS, 5x TAB, TAE |
TruePrep Index Kit V3 for Illumina | Vazyme | TD203 | Include 16 N6XX and 24 N8XX |
High Sensitivity NGS Fragment Analysis Kit | Advanced Analytical Technologies | DNF-474 | |
1x HBSS without Ca2+ and Mg2+ | 138 mM NaCl; 5.34 mM KCl 4.17 mM NaHCO3; 0.34 mM Na2HPO4 0.44 mM KH2PO4 | ||
Isolation buffer | 1 × HBSS containing 10 mM HEPES, 1 mM MgCl2, 5 mM Glucose, pH 7.4 | ||
FACS buffer | 1 × HBSS containing 15 mM HEPES, 5.6 mM Glucose, 1% FBS, pH 7.4 | ||
NaCl | Sigma-Aldrich | S5886 | |
KCl | Sigma-Aldrich | P9541 | |
NaHCO3 | Sigma-Aldrich | S6297 | |
Na2HPO4 | Sigma-Aldrich | S5136 | |
KH2PO4 | Sigma-Aldrich | P5655 | |
D-(+)-Glucose | Sigma-Aldrich | G5767 | |
HEPES | Sigma-Aldrich | H4034 | |
MgCl2 | Sigma-Aldrich | M2393 | |
Oligo-dT30VN primer | 5'-AAGCAGTGGTATCAA CGCAGAGTACT30VN-3' | ||
TSO | 5'-AAGCAGTGGTATCAAC GCAGAGTACATrGrG+G-3' | ||
ISPCR primers | 5'-AAGCAGTGGTAT CAACGCAGAGT-3' | ||
Gapdh Forward primer | 5'-ATGGTGAAGGTC GGTGTGAAC-3' | ||
Gapdh Reverse primer | 5'-GCCTTGACT GTGCCGTTGAAT-3' | ||
Ins2 Forward primer | 5'-TGGCTTCTTC TACACACCCA-3' | ||
Ins2 Reverse primer | 5'-TCTAGTTGCA GTAGTTCTCCA-3' |
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