Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Summary

We provide a protocol for isolation of microglia from different dissected regions of an adult mouse brain hemisphere, followed by semi-automated library preparation for deep single-cell RNA sequencing of full-length transcriptomes. This method will help to elucidate functional heterogeneity of microglia in health and disease.

Abstract

As resident macrophages in the central nervous system, microglia actively control brain development and homeostasis, and their dysfunctions may drive human diseases. Considerable advances have been made to uncover the molecular signatures of homeostatic microglia as well as alterations of their gene expression in response to environmental stimuli. With the advent and maturation of single-cell genomic methodologies, it is increasingly recognized that heterogenous microglia may underlie the diverse roles they play in different developmental and pathological conditions. Further dissection of such heterogeneity can be achieved through efficient isolation of microglia from a given region of interest, followed by sensitive profiling of individual cells. Here, we provide a detailed protocol for the rapid isolation of microglia from different brain regions in a single adult mouse brain hemisphere. We also demonstrate how to use these sorted microglia for plate-based deep single-cell RNA sequencing. We discuss the adaptability of this method to other scenarios and provide guidelines for improving the system to accommodate large-scale studies.

Introduction

Microglia, representing 5%−10% of all neural cells, are resident macrophages scattered throughout the central nervous system (CNS)¹. Protected behind blood-brain barrier, typical microglia in a healthy adult brain contain many fine processes that rapidly extend and retract to interact with neurons and other glial cells in the parenchyma. Microglia can also adopt the amoeboid morphology associated with increased phagocytic function during specific developmental stages or upon immune challenges in injury and disease^1,2,3,4. Recent exciting discoveries have clearly demonstrated that microglia are by no means passive bystanders to brain-derived or pathological signals, but play pivotal roles in controlling brain development and homeostasis, for instance, by supporting neuronal survival, pruning immature synapses, promoting oligodendrocyte lineage cells differentiation as well as angiogenesis¹. As more functions of microglia are elucidated, the excitement is further fueled by human genetics studies, which showed that many neurodegenerative disease risk genes, such as TREM2, are predominantly or exclusively expressed by microglia^5,6,7. Given their significance in development and plausible disease-driving roles, tremendous effort has recently been put towards our understanding of microglial gene regulation and function in hope of finding new therapeutic targets for neurodegenerative diseases^1,8.

RNA sequencing (RNA-seq) allows unbiased characterization of cell type-specific gene expression, which in turn guides scientists to investigate gene functions in dense cellular networks⁷. RNA-seq had been mostly done on bulk samples, leading to the discovery of a homeostatic microglial gene signature that distinguishes them from other neural and immune cells⁹. However, such an approach could overlook molecular and functional differences among microglia, especially those transiently present in development, or associated with aging and disease. Indeed, single-cell RNA-seq (scRNA-seq) offers the sensitivity and resolution that have revolutionized the field by revealing previously underappreciated heterogeneity of microglia in a variety of contexts^2,3,10. In addition, due to the presence of other similar immune cells at the CNS-circulation interface, scRNA-seq provides information aiding the design of new tools to separate and functionally dissect these related cells with little prior knowledge^2,11.

A diverse array of scRNA-seq platforms have been invented, each suitable for certain applications¹². In general, droplet-based methods, such as 10x Genomics, are higher in throughput with (tens of) thousands of cells sequenced in each run, and they are less selective for the input which may contain mixed cell populations requiring broad categorization. Plate-based methods provide higher sensitivity and read depth^13,14, usually targeting specific populations from cell sorting to reveal subtle differences or rare transcripts. Given the small percentage of microglial cells, particularly those development- or disease-associated subpopulations, among all CNS cell types, it is often desirable to isolate microglia from a specific region of interest and obtain deep and full-length transcriptomic information in order to understand their heterogeneity.

Here, we provide details on how to isolate microglia from different mouse brain regions dissected from a single hemisphere, which are used for single-cell (or bulk) RNA-seq following a semi-automated plate-based library preparation procedure. The other hemisphere can then be used for histological validation. Streamlined from a previously published method⁹, this isolation protocol aims to maximize the yield from small amount of starting materials, and meanwhile maintain endogenous microglial gene expression profiles. We use fluorescence-activated cell sorting (FACS) to enrich microglia (or other related immune cells of interest) into 96-well plates and miniaturize the volumes of reagents for library preparation in order to increase throughput. We highlight this sensitive scRNA-seq platform, although other plate-based strategies may be applied. This method can be easily adapted to isolate microglia from other dissected tissues, such as injury or disease foci, and the age of the mouse can vary across almost any postnatal stages. Efficient isolation of regional microglia for single-cell transcriptomics studies will facilitate better understanding of their functions in health and disease.

Protocol

All procedures involving rodents conformed to Stanford University guidelines, which comply with national and state laws and policies. All animal procedures were approved by Stanford University's Administrative Panel on Laboratory Animal Care.

NOTE: All solution and buffer compositions are provided in Table of Materials.

1. Preparation on the Day of Cell Isolation

1. Prepare the following reagents and chill them on ice: medium A (50 mL), magnetic-activated cell sorting (MCS) buffer (30 mL), FACS buffer (25 mL), phosphate-buffered saline (PBS; 30 mL), DNase (320 µL), and RNase inhibitor (30 µL).
   NOTE: The volumes provided here are sufficient to isolate microglia from 4 brain regions (e.g., cortex, cerebellum, hippocampus and striatum) of a single mouse brain hemisphere. Scale up if more tissues are used.
2. Place four clean 2 mL Dounce homogenizers on ice and add 2 mL of medium A with 80 µL of DNase (12,500 units/mL) and 5 µL of RNase inhibitor into each Dounce homogenizer. Chill the pistons in 15 mL tubes.
3. Label four 6 cm Petri dishes with brain regions for tissue collection and add 200 µL of cold medium A into each dish on ice. Add about 5 mL of medium A into a 6 cm Petri dish for dissection.
   NOTE: Prior to use, make sure all reagents are sterile and suitable for RNA applications. Bench and dissection tools need to be clean and sprayed with RNase decontamination solution (Table of Materials).

2. Brain Region Dissection

NOTE: This step should take ~30 min.

1. Inject 400−500 µL of ketamine/xylazine (24 mg/mL ketamine and 2.4 mg/mL xylazine) into the peritoneum of a juvenile to adult stage mouse (>1 month old).
   NOTE: A male mouse is used here for illustration, but either gender is suitable.
2. Wait for 5 min and pinch a hind paw to ensure lack of retraction.
3. Immediately use a 26 G x 3/8 needle to perform transcardial perfusion with 20−30 mL of ice-cold PBS until buffer runs out with no visible blood.
4. Decapitate the mouse with a pair of surgical scissors. Use small scissors to cut open the skin to expose the underneath skull, and then cut through the sagittal suture, lambdoidal suture and coronal suture. Use forceps to pull off both sides of parietal bone and interparietal bone without damaging the tissue, and carefully move the brain into the dissection Petri dish with medium A.
5. Use a pre-chilled blade to cut the brain through midline into two hemispheres.
   NOTE: The four brain regions described here from a single hemisphere yield sufficient numbers of microglia for single-cell or bulk RNA-seq applications. The other hemisphere can be used for immunohistochemistry or RNA in situ validation.
6. Separate the cerebellum from the cortical lobe and the brain stem with #55 forceps and transfer the tissue into a collection Petri dish.
7. Use #55 forceps to carefully dissect out the hippocampus and the striatum from the cortex and transfer each tissue into a collection Petri dish.

3. Mechanical Tissue Dissociation

NOTE: Keep cells and reagents cool all the time except during staining steps. This step should take ~30 min.

1. Chop each brain tissue with a razor blade into <1 mm³ fine pieces.
2. Use 1 mL pipette (with tips cut off) to transfer tissue pieces into the pre-chilled Dounce homogenizers, each containing 2 mL of medium A with DNase and RNase inhibitor.
3. Homogenize the tissue by slowly twisting the piston in and out of the Dounce homogenizer for 6−10 full strokes, until no visible chunks are present.
   NOTE: Douncing kills neurons and most other glial cells but leave microglial cells rather intact. Both insufficient and over-douncing can lead to low yield of cells.
4. Transfer dissociated tissues into 50 mL tubes through 70 µm strainers.
5. Rinse each Dounce homogenizer and piston with a total of 6 mL of cold medium A and filter the rinsing solution through the same strainer into the corresponding tube.
6. Transfer the single cell suspensions (about 8 mL each) into 15 mL conical tubes and centrifuge at 400 x g for 5 min at 4 °C with brake = 5.

4. Myelin Removal

NOTE: This step should take ~60 min.

1. Prepare 1 large depletion (LD) column (for cortex) and 3 large selection (LS) columns (for the other 3 regions) in a magnetic separator (Table of Materials). Rinse each column with 3 mL of MCS buffer.
2. Once centrifugation is finished, pipette out and discard the supernatant without disturbing the pellet. For the cortex and cerebellum tissues, resuspend cells in 850 µL of MCS buffer with 1.8 µL of RNase inhibitor. For hippocampus and striatum tissues, resuspend cells in 400 µL of MCS buffer with 0.9 µL of RNase inhibitor.
   NOTE: The columns (LD vs. LS) and the volume used for resuspension are optimized based on the amount of myelin present in the tissue. If other brain regions are assayed, these conditions may need to be adjusted depending on the size of the tissue and how much myelin may exist. Effectiveness of myelin removal can be estimated in step 4.9.
3. Add 100 µL of myelin removal beads each into cells from cortex and cerebellum and add 50 µL of myelin removal beads each into cells from hippocampus and striatum.
4. Gently mix the cells with beads and incubate the tubes on ice for 10 min.
5. Bring the volume of the tube with cortical cells to 2 mL with MCS buffer, and all others to 1 mL (i.e., add 1 mL for cortical cells; 500 µL for hippocampal and striatal cells; no need to add buffer to cerebellar cells).
6. Once columns are empty of rinsing buffer, place a 15 mL tube below each column. Load cortical cells (2 mL) onto the LD column, and all others (1 mL each) onto the LS columns. Immediately use 1 mL of MCS buffer each to wash the original tubes and load the solution onto the corresponding columns.
7. Wash the LD column once with 1 mL of MCS buffer and wash each LS column twice with 1 mL of MCS buffer each wash. Continue to collect the flow-through solution during washing.
8. Filter cells into round bottom FACS tubes through 35 µm strainer caps.
   NOTE: Each tube should collect about 4 mL of single cell suspension depleted of myelin.
9. Optionally, take 10 µL of the cell suspension and mix it with 10 µL of 0.4% trypan blue solution. Examine the cells under a 10x bright field microscope to estimate the yield, survival rate and the level of residual myelin.
   NOTE: A successful preparation should generate over 90% live cells (round in shape and excluding the blue dye) with little to no myelin debris.
10. Pellet cells in the FACS tubes at 400 x g for 5 min at 4 °C, with brake = 5. Slowly pour out supernatant and dab the edge of the tube on tissue paper. Resuspend cells in each tube with 300 µL of FACS buffer.
    NOTE: If MCS sorting is preferred, CD11b beads can be used to select microglia and other myeloid cells following myelin removal. These cells can then be used for non-plate-based scRNA-seq as well as bulk RNA-seq. The caveat of this alternative approach is that CD11b beads do not separate microglia from other related immune cells which are also positive for this antigen.

5. Staining for Fluorescence-activated Cell Sorting

NOTE: This step should take ~40 min.

1. Add 5 µL of mouse Fc receptors block reagent (Table of Materials) into each tube. Incubate for 5 min on ice.
2. Add 1 µL of CD45-PE-Cy7 and 1 µL of CD11b-BV421 into each tube.
   NOTE: Antibodies with other conjugated fluorophores may be used. Antibodies against TMEM119, a specific marker for homeostatic microglia⁹, can also be included, but it is recommended to be used together with CD45 and CD11b, because certain microglia subpopulations may lose TMEM119 surface expression.
3. Incubate the tubes on a shaker for 10 min at room temperature (RT).
4. Add 2 mL of FACS buffer to wash.
5. Pellet cells at 4 °C, 400 x g for 5 min. Slowly pour out supernatant and dab the edge of the tube on tissue paper. Resuspend cells in each tube using 400 µL of FACS buffer with 1 µL of RNase inhibitor and 0.5 µL of propidium iodide (PI, 1:1,000 dilution).

6. Index FACS Sorting

NOTE: This step should take ~1 h.

1. Following standard FACS procedure, draw gates based on scatter (excluding debris), single cells, live cells (PI negative), microglia and myeloid cells (CD45⁺, CD11b⁺).
   NOTE: Typical microglial cells express CD45 at lower levels compared with other border-associated macrophages, such as perivascular and meningeal macrophages, and therefore gating on CD45 low CD11b⁺ should be sufficient if the focus of the research is gene expression profiles in these classical microglia^1,2. However, certain subsets of microglia may have higher CD45 expression and this is particularly true during development or in disease conditions. To ensure unbiased analysis of microglial gene expression, CD45 high and CD45 low immunophenotypes can be recorded through index sorting setting and both populations collected for sequencing and downstream analysis. In addition, TMEM119 surface expression may be used to target the homeostatic microglial population (see step 5.2) and analyzed together with CD45 levels and the sequencing results.
2. Sort single microglia (with a 100 µm nozzle) into 96-well polymerase chain reaction (PCR) plates, containing 4 µL of lysis buffer each well (see the published protocol¹⁴ for details).
   NOTE: The External RNA Control Consortium (ERCC) RNA spike-in mix (Table of Materials) can be added at 1:2.4 x 10⁷ in the lysis buffer for quality control and normalization purposes².
3. Briefly vortex the plates and spin down using a bench-top centrifuge.
4. Immediately freeze the samples on dry ice. Store the plates at -80 °C until library preparation.
   NOTE: Alternatively, more cells can be collected into 1.5 mL tubes with RNA extraction buffer for bulk RNA-seq. According to authors' experience, 3,000 cells are sufficient to generate good quality libraries following the published protocol^2,14.

7. Single-cell RNA-sequencing Library Preparation

NOTE: Here, the published protocol¹⁴ is followed to generate scRNA-seq libraries with the aid of liquid handling robotics and a few modifications. In this article, the procedure is only briefly described, and the differences are highlighted. Processing 4 plates simultaneously takes about 2.5 days.

1. Thaw plates on ice and perform reverse transcription with Oligo-dT30VN primer (in the lysis buffer) to generate cDNA with thermal cyclers (Table 1): 42 °C 90 min; 70 °C 5 min; 4 °C hold. Then amplify cDNA with an additional exonuclease digestion step at the beginning (Table 2) using the PCR master mix and in situ PCR (ISPCR) primers (Table of Materials) and the following PCR condition: 37 °C 30 min; 95 °C 3 min; 23 cycles of 98 °C 20 s, 67 °C 15 s, 72 °C 4 min; 72 °C 5 min.
2. Purify cDNA using 18 µL of magnetic beads per well (0.7:1 ratio). Incubate the plate on a magnetic stand for 5 min and wash samples twice with freshly made 80% ethanol, 80 µL per well each time. After drying the plate for 15-20 min, elute cDNA with 20 µL of elution buffer per well.
   NOTE: For quality control, use a fragment analyzer (high sensitivity next-generation sequencing [NGS] fragment analysis, 1−6,000 bp) to check size distributions and concentrations of cDNA, and only further process samples with a smear between 500−5,000 bp, and higher than 0.05 ng/µL.
3. To generate libraries, mix 0.4 µL of each cDNA sample with 1.2 µL of Tn5 tagmentation reagents from the library preparation kit (Table of Materials) in a 384-well plate with the aid of a nanoliter pipetting machine, at 55 °C 10 min.
   NOTE: Here, 1/12.5 of the suggested reaction volume (5 µL sample and 15 µL of tagmentation reagents) is added in order to reduce cost and meanwhile increase throughput. A nanoliter pipetting machine (Table of Materials) is used to transfer reagents (this and following steps) from and to 384-well plates.
4. Add 0.4 µL of neutralization buffer to stop the tagmentation reaction at RT for 5 min.
5. Add 384 indexes (Table of Materials, 0.4 µL forward and 0.4 µL reverse), 1.2 µL of PCR mix to samples (2 µL each), and amplify the libraries using the following condition: 72 °C 3 min; 95 °C 30 s; 10 cycles of 95 °C 10 s, 55 °C 30 s, 72 °C 1 min; 72 °C 5 min.
6. Pool all individual libraries (take 1 µL each) from the same 384-well plate together, and use magnetic beads (Table of Materials, 0.7:1 ratio) to purify the final pooled libraries.
7. Use a fluorometer (Table of Materials) to measure the concentrations and a bioanalyzer (Table of Materials) to examine the size distributions of pooled libraries before sequencing. Target the sequencing depth at 1 million raw reads per cell.
8. Follow standard bioinformatic procedures to filter and trim sequencing reads and perform alignment². Use the count table and meta data as inputs to do clustering analysis with the Seurat package¹⁵.

Results

This protocol describes a method to isolate and sort microglia from different brain regions in one adult perfused brain hemisphere, followed by scRNA-seq. We use douncing to create single cell suspension and also as a first step to enrich microglia. Insufficient or over-douncing reduces the yield. In addition, adult mouse brains contain high levels of myelin, which can also reduce sorting efficiency and yield if not removed properly. Therefore, we examine the cell suspension under microscope by using trypan blue and a he...

Discussion

Microglia actively interact with other cell types in the CNS, and they are very sensitive to environmental stimuli. In order to minimize inflammatory responses and aberrant changes in their gene expression during the isolation process, this protocol has been streamlined from a previously published method⁹, and it is now suitable to isolate microglia from multiple regions of a single mouse brain hemisphere in parallel. The tissues and reagents are kept at cold temperature and experiments are perfor...

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
5 M Betaine	Sigma-Aldrich	Cat# B0300-5VL
10 mM dNTP mix	Thermo Fisher Scientific	Cat# R0192
0.5 M EDTA, pH 8.0	Thermo Fisher Scientific	Cat# 15575020
10X Hanks’ Balanced Salt Solution	Thermo Fisher Scientific	Cat# 14185-052
1 M HEPES	Thermo Fisher Scientific	Cat# 15630080
1X KAPA HIFI Hotstart Master Mix	Kapa Biosciences	Cat# KK2602
5 mL Round Bottom Polystyrene Tube, with Cell Strainer Cap	Corning	Cat# 352235
AATI, High Sensitivity NGS Fragment Analysis Kit (1 bp – 6,000 bp)	Advanced Analytical	Cat# DNF-474-1000
Bovine Serum Albumin	Sigma Aldrich	Cat# A8806
DNase I	Worthington	Cat# LS002007	Working solution: 12500 units/ml
DTT, Molecular Grade	Promega	Cat# P1171
ERCC RNA Spike-In Mix	Thermo Fisher Scientific	Cat# 4456740
Fetal Bovine Serum	Thermo Fisher Scientific	Cat# 10437-028
Illumina XT Index Kit v2 Set A (96 indexes)	Illumina	Cat# FC-131-2001
Illumina XT Index Kit v2 Set B (96 indexes)	Illumina	Cat# FC-131-2002
Illumina XT Index Kit v2 Set C (96 indexes)	Illumina	Cat# FC-131-2003
Illumina XT Index Kit v2 Set D (96 indexes)	Illumina	Cat# FC-131-2004
Lambda Exonuclease (5 U/μl)	New England BioLabs	Cat# M0262S
Mouse Fc block	BD Pharmingen	Cat# 553142
Myelin removal beads	Miltenyl Biotec	Cat# 130-096-433
Nextera XT DNA Sample Prep Kit	Illumina	Cat# FC-131-1096
NextSeq 500/550 High Output Kit v2.5 (150 Cycles)	Illumina	Cat# 20024907
PBS (10X), pH 7.4	Thermo Fisher Scientific	Cat# 70011044
PCRClean DX beads	Aline Biosciences	Cat# C-1003-50
Propidium Iodide	Thermo Fisher Scientific	Cat# P3566	Staining: 1:1000
Qubit dsDNA HS Assay Kit	Thermal Fisher Scientific	Cat# Q32851
Rat monoclonal anti mouse/human CD11b, Brilliant Violet 421 (clone M1/70)	BioLegend	Cat# 101236; RRID: AB_11203704	Staining: 1:300
Rat monoclonal anti mouse CD45, PE/Cy7 (clone 30-F11)	Thermo Fisher Scientific	Cat# 25-0451-82; RRID: AB_469625	Staining: 1:300
Recombinant RNase Inhibitor	Takara Bio	Cat# 2313B
SMARTScribe Reverse Transcriptase (100 U/μl)	Clontech	Cat# 639538	Containing 5x First strand buffer
Oligonucleotides
0.1 μM ISPCR Oligo: 5' - AAGCAGTGGTATCAA CGCAGAGT-3'			(Picelli et al., 2014)
Oligo-dT30VN primer: 5' - AAGCAGTGGTATCAACGCA GAGTACT 30 VN-3'			(Picelli et al., 2014)
TSO 5' - AAGCAGTGGTATCAACGCAGA GTACATrGrG+G-3' ("r" is forribobases and "+" is for an LNA base)			(Picelli et al., 2014)
Solutions
FACS buffer			Recipe: sterile-filtered 1% FBS, 2 mM EDTA, 25 mM HEPES in 1X PBS
MCS buffer			Recipe: sterile-filtered 0.5% BSA, 2 mM EDTA in 1X PBS
Medium A			Recipe: 15 mM HEPES, 0.5% glucose in 1X HBSS without phenol red
Plates
384-well Rigi-Plate PCR Microplates, Axygen Scientific	VWR	89005-556
Hard-shell 96-well PCR plates	Bio-Rad	HSP9631
Others
Dumont #55 forceps	Fine Science Tools	11295-51
Dounce homogenizer, 2 ml	Wheaton	357422
Large depletion column	Miltenyi Biotec	130-042-901
Large selection column	Miltenyi Biotec	130-042-401
MACS MultiStand	Miltenyi Biotec	130-042-303
QuadroMACS Separator	Miltenyi Biotec	130-090-976
RNAzap	Thermo Fisher Scientific	AM9780
Strainer (70 μm)	Falcon	352350
Equipment
BD FACSAria II	BD Biosciences	http://www.bdbiosciences.com/
Bioanalyzer	Agilent	2100
Fragment Analyzer	Agilent	5300
Mosquito HTS nanoliter pipetting robot	TTP Labtech	https://www.ttplabtech.com/
Qubit 4 Fluorometer	Thermo Fisher Scientific	Q33226