In situ hybridization for miR-146a was performed using a 5′ fluorescein-labelled 19mer antisense oligonucleotide containing locked nucleic acid and 2′OME RNA moieties (FAM – AacCcaTggAauTcaGuuCucA, capitals indicate LNA, lower case indicates 2′OME RNA). The oligonucleotides were synthesized by Ribotask ApS, Odense, Denmark. The hybridizations were done on 6-μm sections of paraffin-embedded materials described previously (Budde et al., 2008). The hybridization signal was detected using a rabbit polyclonal anti-fluorescein/Oregon green antibody (A21253, Molecular Probes, Invitrogen) and a horseradish peroxidase-labelled goat anti-rabbit polyclonal antibody (P0448 Dako, Glostrup Denmark) as secondary antibody. Signal was detected with chromogens 3-amino-9-ethyl carbazole (St Louis, MO, USA) or Vector NovaRed (Vector Laboratories, Burlingame, CA, USA), and the nuclei were stained with haematoxylin. Slides were sealed with glycerol-gelatin (St Louis, MO, USA). As control for non-specific binding, other similarly modified oligonucleotides were used. These probes were specific for other human transcripts (miR-338, MIMAT0004701; miR-218, MIMAT0000275; miR-204, MIMAT0000265; miR-134, MIMAT0000447). These oligonucleotides showed different staining patterns (no expression in glial cells). Additionally negative control assays were performed without probes and without primary antibody (sections were blank). For the double-staining, combining immunocytochemistry with in situ hybridization, sections were first processed for immunocytochemistry as previously described (Aronica et al., 2001a, 2003) with glial fibrillary acidic protein (GFAP; polyclonal rabbit; DAKO, Glostrup, Denmark; 1 : 4000), neuronal nuclear protein (NeuN; mouse clone MAB377; Chemicon, Temecula, CA, USA; 1 : 2000), HLA-DR [anti-human leukocyte antigen (HLA)-DP, DQ, DR (mouse clone CR3/43); DAKO, Glostrup, Denmark; 1 : 400], CFH (polyclonal goat; Quidel, San Diego, CA, USA; 1 : 100) or the biotinylated lectin Ricinus Communis Agglutinin I (RCA 120; Vector Laboratories, Burlingame, CA, USA; 1 : 500, for the visualization of microglial cells on rat tissue), using Fast Blue B salt (St Louis, MO, USA) or Vector Blue substrate (Vector Laboratories) as chromogen. After washing, sections were processed for in situ hybridization as described above. Images were captured with an Olympus microscope (BX41, Tokyo, Japan) equipped with a digital camera (DFC500, Leica Microsystems-Switzerland, Heerbrugg, Switzerland).
To analyse the percentage of double-labelled cells positive for miR-146a and GFAP, or for the microglia marker (HLA-DR, human; lectin, rat), digital photomicrographs were obtained from five hippocampal samples. Images of three representative fields (CA3 and DG) per section were collected (Leica DM5000B). Images were analysed with a Nuance VIS-FL Multispectral Imaging System (Cambridge Research Instrumentation, Woburn, MA, USA). Spectra were acquired from 460–660 nm at 10-nm intervals, and Nuance software (version 2.4) was used for analysis, as previously described (Boer et al., 2008; van der Loos, 2008). The total number of cells stained with miR-146a and GFAP (or HLA-DR or lectin), as well as the number of cells double-labelled, were counted visually and percentages were calculated (expressed as mean ± SEM) of cells co-expressing miR-146a and GFAP (or HLA-DR or lectin) in two regions of prominent gliosis (CA3 and DG of rat, at 1 week post-SE, and of human hippocampus). Sections incubated without the primary Ab or with pre-immune serum were blank, and when processed for in situ hybridization showed only the in situ hybridization signal.