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. 2017 Apr 11;8(4):1046-1061.
doi: 10.1016/j.stemcr.2017.02.012. Epub 2017 Mar 16.

Synergic Functions of miRNAs Determine Neuronal Fate of Adult Neural Stem Cells

Meritxell Pons-Espinal  1 , Emanuela de Luca  1 , Matteo Jacopo Marzi  2 , Ruth Beckervordersandforth  3 , Andrea Armirotti  4 , Francesco Nicassio  2 , Klaus Fabel  5 , Gerd Kempermann  5 , Davide De Pietri Tonelli  6
Affiliations

Synergic Functions of miRNAs Determine Neuronal Fate of Adult Neural Stem Cells

Meritxell Pons-Espinal et al. Stem Cell Reports. .

Abstract

Adult neurogenesis requires the precise control of neuronal versus astrocyte lineage determination in neural stem cells. While microRNAs (miRNAs) are critically involved in this step during development, their actions in adult hippocampal neural stem cells (aNSCs) has been unclear. As entry point to address that question we chose DICER, an endoribonuclease essential for miRNA biogenesis and other RNAi-related processes. By specific ablation of Dicer in aNSCs in vivo and in vitro, we demonstrate that miRNAs are required for the generation of new neurons, but not astrocytes, in the adult murine hippocampus. Moreover, we identify 11 miRNAs, of which 9 have not been previously characterized in neurogenesis, that determine neurogenic lineage fate choice of aNSCs at the expense of astrogliogenesis. Finally, we propose that the 11 miRNAs sustain adult hippocampal neurogenesis through synergistic modulation of 26 putative targets from different pathways.

Keywords: DICER; adult neurogenesis; astrogliogenesis; fate choice; hippocampus; microRNAs; mouse; neural stem cells; synergy.

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Figures

None
Graphical abstract
Figure 1
Figure 1
Split-Cre Virus-Mediated Dicer Ablation In Vivo Impairs Neuronal Differentiation and Survival but Not Astrogliogenesis (A) Schematic representation of the experiment. (B) qRT-PCR quantification of Dicer mRNA from FACS-sorted Td-Tomato+ aNSCs 2 months after split-Cre virus injection. (C and E) Representative micrographs showing recombined Td-Tomato/BrdU double-positive cells from Dicer WT and cKO mice 1 month after BrdU injection (C), co-expressing NeuN (E, left panel), GFAP (E, middle panel) and S100b (E, right panel). Yellow arrowheads show Td-Tomato/BrdU double-positive cells co-expressing NeuN, GFAP, or S100b. (D) Percentage of Td-Tomato+ cells expressing BrdU after 10 days, or 1 month after BrdU injections. (F–H) Percentage of Td-Tomato/BrdU double-positive cells co-expressing NeuN (F), DCX (G), or S100b (H) 10 days or 1 month after BrdU injections. ML, molecular layer; GCL, granular cell layer; SGZ, subgranular zone; H, Hilus. Data are expressed as mean ± SEM, n = 4–6 mice per group. Unpaired t test was used for Dicer mRNA expression analysis. One-way ANOVA Bonferroni as post hoc was used to analyze cell marker quantification. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Scale bars, 20 μm.
Figure 2
Figure 2
Dicer and miRNAs Are Depleted after Recombination of Dicerflox Allele in Hippocampal aNSCs In Vitro (A) Representative micrographs showing Td-Tomato+ aNSCs from Dicer WT, Dicer HT, and Dicer cKO mice after nucleofection with Cre recombinase. (B) PCR Genotyping of Cre-recombined aNSCs, showing the three Dicer genotypes. (C) qRT-PCR quantification of Dicer mRNA in Cre-recombined aNSCs. (D) Average of all miRNAs quantified from recombined aNSCs. Data are expressed as mean ± SEM, n = 3 independent experiments containing three replicates. One-way ANOVA Bonferroni as post hoc: ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Scale bar, 50 μm.
Figure 3
Figure 3
Loss of Dicer-Dependent miRNA in aNSCs Impairs Neurogenesis and Neuronal Maturation In Vitro (A) Schematic representation of the protocol and experiment. (B) Representative micrographs showing recombined Td-Tomato+ aNSCs from Dicer WT, Dicer HT, and Dicer cKO mice after 6 DIV with growth factors titration expressing DCX. (C) Percentage of Td-Tomato+ cells expressing DCX. (D) Representative micrographs showing dendritic morphology of immature newly formed neurons expressing DCX. Data are expressed as mean ± SEM, n = 3 independent experiments containing three replicates. One-way ANOVA Bonferroni as post hoc: ∗p < 0.05, ∗∗∗p < 0.001. Scale bars, 50 μm.
Figure 4
Figure 4
Loss of Dicer-Dependent miRNAs Does Not Affect Astrogliogenesis of aNSCs In Vitro (A) Schematic representation of the protocol and experiment. (B) Representative micrographs showing recombined Td-Tomato+ aNSCs from Dicer WT, Dicer HT, and Dicer cKO mice after 6 DIV with 10% fetal bovine serum expressing S100b (upper panels) and GFAP (bottom panels). (C) Percentage of Td-Tomato+ cells expressing astrocyte markers (GFAP and S100b). (D–F) Relative Nestin (D), GFAP (E), and S100b (F) mRNA quantification with qRT-PCR. (G–I) Protein quantification of NESTIN (H) and GFAP (I). Data are expressed as mean ± SEM, n = 3 independent experiments containing three replicates. One-way ANOVA Bonferroni as post hoc: ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Scale bar, 50 μm.
Figure 5
Figure 5
Profiling of miRNA Expression during Neuronal Differentiation of aNSCs In Vitro (A) Schematic representation of the neuronal differentiation protocol with inducible retrovirus expressing ASCL1 (Ascl1-ERT2-IRES-GFP) and the experiment. Cells were collected during proliferation (P) or differentiation after 7 (D7), 14 (D14), and 21 (D21) DIV. (B) Heatmap representing the set of miRNAs dynamically regulated upon neuronal differentiation at 7, 14, and 21 DIV. Red indicates high expression and green, low expression. (C) Fold change of selected miRNAs during differentiation over proliferating cells. (D) Fold change expression of miRNAs in vivo in FACS-sorted Td-Tomato+ cells from ten adult Dicer WT and ten Dicer cKO mice 2 months after split-Cre recombinase virus injection into the DG. n = 3 independent experiments containing three replicates. Data are expressed as mean ± SEM. Paired t test: ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.
Figure 6
Figure 6
A Pool of 11 miRNAs Synergistically Rescues Dicer cKO Impairment of Adult Neurogenesis, at the Expense of Astrogliogenesis, In Vitro (A) Representative micrographs showing aNSCs from Dicer WT and Dicer cKO mice transfected with 250 nM scrambled RNA or total pool (25 nM of each miRNA) after 6 DIV of growth factors withdrawal expressing DCX (upper panel), MAP2 (middle panel), and S100b (bottom panel). Scale bar, 50 μm. (B) Percentage of DCX-, MAP2-, and S100b-positive aNSCs with respect to DAPI in WT and KO aNSCs transfected with scrambled RNA or total pool. (C) Proportion of KO aNSCs expressing DCX upon transfection of 250 nM subpool 1 (mir-124-3p + mir-135a-5p), subpool 2 (mir-139-5p + mir-218-5p + mir-411-5p + mir-134-5p + mir-370-3p + mir-382-5p + mir-708-5p), subpool 3 (mir-127-3p + miR-376b-3p), or each miRNA alone with respect to KO control. (D) Percentage of DCX-positive aNSCs with respect to DAPI after 6 DIV from WT or KO mice transfected with scrambled RNA, total pool, or a pool with ten miRNAs by the withdrawal of individual miRNAs. (E) mRNA quantification with qRT-PCR from recombined KO aNSCs after 6 DIV. Data are expressed as mean ± SEM, n ≥ 3 independent experiments containing three replicates. One-way ANOVA with Bonferroni as post hoc test: ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.
Figure 7
Figure 7
Convergence of the 11 miRNAs on Neurogenesis-Related Biological Processes (A) Representative micrographs showing aNSCs from Dicer WT mice transfected with 250 nM scrambled RNA or a pool of miRNA inhibitors (antagomir) (25 nM of each miRNA inhibitor) after 6 DIV of growth factor withdrawal expressing DCX (upper panel), MAP2 (middle panel), and S100b (bottom panel). (B) Percentage of DCX-, MAP2-, and S100b-positive aNSCs with respect to DAPI in WT aNSCs transfected with scrambled RNA or pool inhibitor. (C) Expression proteomics profile of miRNA inhibitor with respect to control group at 6 DIV. (D) Venn diagram showing the putative predicted targets by at least two miRNAs from the in silico analysis that are significantly dysregulated in the proteomics analysis upon miRNA inhibitor administration. (E) Dysregulated proteins that are putatively targeted by at least two miRNAs. Fold change and SD for WT aNSCs transfected with a pool of inhibitors versus control RNA for each protein expression and predicted targeting miRNAs are shown. A.C, absent in control samples; A.I, absent in miRNA inhibitor samples. (F) Gene ontology (GO) analysis significantly represented for the 26 predicted common targets dysregulated upon miRNA inhibition. Data are expressed as mean ± SEM, n = 3 independent experiments containing three replicates. Unpaired t test: ∗p < 0.05, ∗∗p < 0.01. Scale bar, 50 μm.
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