Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School
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Veremeyko, T., Starossom, S. C., Weiner, H. L., Ponomarev, E. D. Detection of MicroRNAs in Microglia by Real-time PCR in Normal CNS and During Neuroinflammation. J. Vis. Exp. (65), e4097, doi:10.3791/4097 (2012).
Microglia are cells of the myeloid lineage that reside in the central nervous system (CNS)1. These cells play an important role in pathologies of many diseases associated with neuroinflammation such as multiple sclerosis (MS)2. Microglia in a normal CNS express macrophage marker CD11b and exhibit a resting phenotype by expressing low levels of activation markers such as CD45. During pathological events in the CNS, microglia become activated as determined by upregulation of CD45 and other markers3. The factors that affect microglia phenotype and functions in the CNS are not well studied. MicroRNAs (miRNAs) are a growing family of conserved molecules (~22 nucleotides long) that are involved in many normal physiological processes such as cell growth and differentiation4 and pathologies such as inflammation5. MiRNAs downregulate the expression of certain target genes by binding complementary sequences of their mRNAs and play an important role in the activation of innate immune cells including macrophages6 and microglia7. In order to investigate miRNA-mediated pathways that define the microglial phenotype, biological function, and to distinguish microglia from other types of macrophages, it is important to quantitatively assess the expression of particular microRNAs in distinct subsets of CNS-resident microglia. Common methods for measuring the expression of miRNAs in the CNS include quantitative PCR from whole neuronal tissue and in situ hybridization. However, quantitative PCR from whole tissue homogenate does not allow the assessment of the expression of miRNA in microglia, which represent only 5-15% of the cells of neuronal tissue. Hybridization in situ allows the assessment of the expression of microRNA in specific cell types in the tissue sections, but this method is not entirely quantitative. In this report we describe a quantitative and sensitive method for the detection of miRNA by real-time PCR in microglia isolated from normal CNS or during neuroinflammation using experimental autoimmune encephalomyelitis (EAE), a mouse model for MS. The described method will be useful to measure the level of expression of microRNAs in microglia in normal CNS or during neuroinflammation associated with various pathologies including MS, stroke, traumatic injury, Alzheimer's disease and brain tumors.
1. Isolation of Microglia from Normal CNS
Isolation of microglia is performed as was described previously with modifications3.
2. Control of Purity of Microglia by Flow Cytometry
Staining with antibodies is performed as previously described with modifications7,8.
3. Isolation of Microglia and Peripheral Macrophages from Inflamed CNS in Mouse Model of Neuroinflammation
Experimental autoimmune encephalitis (EAE) is induced as was previously described in our paper7; FACS sorting is performed similarly to published protocol8.
4. Isolation of RNA
RNA will be isolated using the mirVana kit according to the manufacturer's instructions with modifications.
5. Detection of miRNA in Microglia and Macrophages
For analysis of miRNA expression, real-time quantitative reverse transcriptase PCR (qRT-PCR) analyses is carried out using TaqMan assays with primers and fluorescent probes for particular microRNA of interest and one of the ubiquitously expressed short RNAs (e.g. snoRNA-55, snoRNA-135 or U6) for normalization. Primers and fluorescent probes for particular sets of human or mouse miRNA can be purchased from Life Technologies Inc. Here we will use miR-124 as an example for miRNA of interest and snoRNA-55 as an example for normalization.
|Item||Volume (μl) per sample|
|5x RT Primer||1.00|
|RT Enzyme Mix|
|25 mM each (100 mM total) dNTPs||0.050|
|MultiScribe Reverse Transcriptase)||0.333|
|10X RT Buffer||0.500|
|AB RNase Inhibitor||0.063|
Dilute RNA samples to concentration 3 ng/μl. Prepare RT Enzyme Mix and put 3.33 μL to PCR tubes and add 1.67 μl of RNA sample. Incubate in PCR Instrument (BioRad) at 16 °C for 30 min, 42 °C for 30 min, 85 °C for 5 min, and set at 4° C on hold.
|Item||Volume (μl) per sample|
|2X TaqMan Master Mix||5.0|
Use a 384-well clear optical reaction plate (Life Technologies) for each reaction and real-time PCR instrument AB 7900 HT. Cycling conditions: 95 °C for 10 min, [95 °C for 5 sec, 60 °C for 60 sec] x 40 cycles.
6. Normalization and Data Analysis
Relative expression levels for miRNA of interest (miR-124) are calculated using the ΔΔCT method as previously described7,9 using snoRNA-55 for normalization of the initial amount of RNA.
7. Representative Results
Typical curves for real-time PCR and CT values for miR-124 (microRNA of interest) and snoRNA-55 (normalization) as well as relative levels of expression of miR-124 are shown in Fig. 4 and Table I. In our experiments we used snoRNA-55 as a control for normalization. As we mentioned above, other ubiquitous RNAs can be also used for normalization such as snoRNA-135 and U6.
The examples of the expression of miR-124 in adult microglia vs. bone-marrow derived macrophages (BMDMs) are shown in Fig. 5a (BMDMs were grown in the presence of M-CSF as described7). In Fig. 5b, we compared the expression of miR-124 in sorted populations of CD45low microglia vs. CD45hi macrophages. In both of these experiments we demonstrated that microglia are different from other macrophages by expressing higher levels of miR-124. Similar experiments can be performed in the future for kinetics of microglia activation in vivo or in vitro.
Expression of miR-124 in microglia isolated from CNS of C57BL/6 mice at different stages of development is shown in Fig. 5c. This data demonstrate that microglia in early stages of development express lower levels of miR-124, which correlated with their activated phenotype7. Similar analysis can be performed to study the functions of microglia in normal CNS such as comparison of expression of particular miRNAs in microglia isolated from different areas of the CNS: the cerebellum, spinal cord, hippocampus etc.
Figure 1. The examples of good and bad preparations of microglia as determined by flow cytometry. In the case of "good" isolation of microglia from normal CNS, 95-98% of the cells represent CD11b+CD45low microgla with 2-5% of CD11b+CD45hi perivascular macrophages. Less than 1% of CD11b-CD45hi lymphocytes or CD11b-CD45- astroglial or oligodendroglial cells or cell fragments should be present (a). The case of "bad" preparation is shown here (b) where 18% of contaminating CD11b-CD45- cells is present (b, lower left quadrant) suggesting insufficient Percoll gradient separation. In the case of good preparation, 95-98% of the cells should represent CD11b+CD45low microglia (a, upper left quadrant) , 2-5% of all cells should represent CD11b+CD45hi perivascular macrophages (a, upper right quadrant), and less than 1% of all cells should represent CD11b negative contaminating cells (a, lower left quadrant). In the case of "bad preparation", significant contamination of CD11b-CD45- cells or cell fragments (astroglia, myelin particles etc.) are present (b, lower left quadrant), which makes preparation of the cells unsuitable for RNA isolation and further analysis. In addition, CD11b-CD45hi cells could be also present in the case of "bad preparation" (b, lower right quadrant) indicating contamination by blood lymphocytes due to insufficient perfusion.
Figure 2. Flow cytometry analysis and sorting of populations of microglia and peripheral macrophages from diseased CNS. (a) During neuroinflammation three populations of the cells are present in the CNS: CD11b+CD45low (microglia), CD11b+CD45hi (macrophages), and CD11b-CD45hi (lymphocytes), as shown in the upper left, upper right and lower right quadrants, respectively. Gates for sorting populations of CD11b+CD45low microglia and CD11b+CD45hi macrophages are shown in (b) and the purities of reanalyzed sorted populations are shown in (c,d). Preliminary gating on viable cells based on FSC/SSC parameters was implemented.
Figure 3. Examples of "good" and "bad" qualities of RNAs isolated from microglia and analyzed by gel electrophoresis. In the case of good quality, RNA ladder and ribosomal RNA is evident (a). In the case of bad quality, smear, and low molecular weight degradation products are evident (b).
Figure 4. Real-time qRT-PCR curves for fluorescently labeled miR-124 and snoRNA-55 PCR products. Curves for snoRNA-55 (a) and miR-124 (b) are shown for microglia and bone-marrow derived macrophages (BMDMs). The experiment was performed in duplicates. Ct values were determined by the intersection of the baseline with the lower part of linear range of qRT-PCR curves as shown in (b). Click here to view larger figure.
|snoRNA-55||miR-124||DCt=Ct(Exp)-Ct(Norm)||DDCt=DCt-DCt(Ref)||Relative Level of Expression=2-DDCt|
|Ct (Norm)||Ct(Exp)||DCt||DDCt||miR-124 Expression|
|Microglia from normal CNS||24.082||24.572||0.49(Ref)||0||1.0|
|Bone-marrow derived macrophages (BMDMs)||26.879||32.231||5.352||5.317||0.025|
Table I. Calculation of relative levels of miR-124 expression in microglia vs. bone marrow derived macrophages based of Ct values for miR-124 (microRNA of interest) and snoRNA-55 (control for normalization).
Figure 5. Analysis of miR-124 expression in microglia and macrophages. Comparison of miR-124 expression in microglia from normal CNS vs. bone marrow derived macrophages (BMDMs) is shown in (a). Comparison of miR-124 in microglia vs. peripheral macrophages isolated from CNS of in mice with neuroinflammation is shown in (b). Changes in the level of expression of miR-124 in microglia during development in mice of 1, 2, and 4 weeks old when compared to adult mice (at 8 weeks old) is shown in (c). In (a, b) the experiment was performed in triplicate with mean ± S.D. of three separate PCR reactions shown. In (c) experiment was performed in duplicates as indicated.
Recently significant interest was given to microglia and involvement of these cells in many pathologies associated with neuroinflammation and neurodegeneration. In addition, the role of microRNAs in the differentiation of immune and cancer cells has dramatically grown over the last several years5,10. We have previously reported the role of miR-124 in the maintenance of non-activated or resting phenotype of microglia in normal CNS7, but the role of the other types of microRNAs in microglia phenotype and activation state remains to be discovered. This will require development of new methods for measuring miRNA expression specifically in microglia.
Microglia are difficult cells to handle in experiments since they become activated and significantly altered after their isolation from CNS. The protocols for isolation of microglia from normal CNS were previously published11,12. Although these protocols could be useful for RNA isolation, we believe that these protocols are more suitable for mRNA expression rather than for the assessment of microRNA expression. First, many investigators use enzymatic digestion of homogenized tissue or magnetic bead purification that activate microglia and result in significant changes in microRNA expression (not published observation). Second, the authors use Trizol-based methods for RNA isolation11 which is not optimal for microRNA analysis in a small number of microglial cells, especially for those populations that were sorted from CNS by FACS. Here, we present a quick and simple protocol with minimal manipulations during isolation of microglia from CNS. This method allows the receiving of pure populations of microglia with minimal levels of spontaneous activation combined with a technique for effective isolation of RNA from a small number of cells. In addition, we used the protocol for the isolation of RNA which will be particularly enriched with short non-coding RNAs and microRNA.
Besides the purity of isolated microglia, it is also important to make sure that the quality of RNA is suitable. Without proper separation of microglia on the Percoll gradient the result is the contamination of RNA samples with myelin debris, which would make miRNA profiling in microglia not only difficult to interpret, but also decreases the quality of the RNA rather drastically due to a high concentration of nucleic acids, proteins, and lipids in myelin particles.
As we mentioned above, a substantial difficulty in measuring miRNA expression in microglia is the small number of the cells and low amount of the RNA obtained even from a large group of mice (10 or more). Therefore we would recommend making a short list of 10-30 microRNAs and look separately at the level of expression of each of one using singleplex qRT-PCR rather than using less sensitive multiplex PCR assays or arrays that require a rather high amount of RNA. After assessment of the expression of several microRNAs by singleplex qRT-PCR as we described, other large scale miRNA profiling methods could be used after their careful validation. Recently, there was a report about a more sensitive method for multiplex analysis of microRNAs on microfluidics platforms13, which could potentially be adopted for large scale microRNA expression profiling in microglia.
No conflicts of interest declared.
The work was supported by the NIH R01 NS071039-01A1 research grant.
|1X PBS||GIBCO||14190||Can be prepared from dry components in the laboratory, pH: 7.2-7.4|
|10X PBS||Thermo Scientific||SH30258.02||Can be prepared from dry components in the laboratory, pH: 7.2-7.4|
|DMEM; FBS||GBCO||11965; 10438|
|Percoll||Sigma||P4937-500 ml||100 ml of 100% Percoll is prepared by mixing 10 ml of 10X PBS and 90 ml of Percoll from Sigma. 50 ml of 70% Percoll is prepared by mixing of 35 ml of 100% Percoll and 15 ml of DMEM 50 ml of 40% Percoll is prepared by mixing 20 ml of 100% Percoll and 30 ml of 1X PBS|
|MOG35-55 peptide||AnaSpec Inc||60130-5|
|FcR blocking antibodies||BD Biosciences||553142||Clone 2.4G2|
|Anti-CD11b-PE mAb||BD Biosciences||553311||Can be used with different fluorophores (e.g. AF488)|
|Anti-CD45-APC-Cy7 mABs||Biolegend||103116||Can be used with different fluorophores (e.g. APC)|
|Paraformaldehyde (16%)||EMS Inc||15710||Dilute 1:15 in 1X PBS|
|15% TBE-Urea Gel||Life Technologies Inc.||EC68855BOX|
|TaqMan MicroRNA Reverse Transcription Kit||Life Technologies Inc||4366596|
|TaqMan Universal PCR Master Mix||Life Technologies Inc||4304437|
|TaqMan MicroRNA Assays mmu-miR-124a||Life Technologies Inc||4427975 ID 001182|
|TaqMan MicroRNA Assays snoRNA-55||Life Technologies Inc||4427975 ID 001228|
|Nuclease-free water||Life Technologies Inc||AM9937||Nuclease-free water|
|384-well clear optical reaction plate||Life Technologies Inc.||4309849||Can be substituted with other plates (e.g. 96 well plate) in different real-time PCR instruments|
|Dounce homogenizer (15 ml)||Wheaton Science Products.||358044||Teflon/glass|
|40 μ nylon cell strainer||Falcon||352340|
|Big centrifuge||Sorval||RT 6000B||Rotor diameter 18.5 cm|
|Small centrifuge||Eppendorf||5415 R||Rotor diameter 6.5 cm|
|Real-time PCR Instrument||Life Technologies Inc.||AB 7900 HT||Can be substituted with other instruments|
|Flow cytometer||BD Biosciencess||LSR II||Can be substituted with other instruments|
|FACS||BD Biosciences||FACSAria||Can be substituted with other instruments|
|Nanodrop spectrophotometer||Thermo Scientific||Nanodrop 1000|