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Therapeutically viable generation of neurons with antisense oligonucleotide suppression of PTB

Abstract

Methods to enhance adult neurogenesis by reprogramming glial cells into neurons enable production of new neurons in the adult nervous system. Development of therapeutically viable approaches to induce new neurons is now required to bring this concept to clinical application. Here, we successfully generate new neurons in the cortex and dentate gyrus of the aged adult mouse brain by transiently suppressing polypyrimidine tract binding protein 1 using an antisense oligonucleotide delivered by a single injection into cerebral spinal fluid. Radial glial-like cells and other GFAP-expressing cells convert into new neurons that, over a 2-month period, acquire mature neuronal character in a process mimicking normal neuronal maturation. The new neurons functionally integrate into endogenous circuits and modify mouse behavior. Thus, generation of new neurons in the dentate gyrus of the aging brain can be achieved with a therapeutically feasible approach, thereby opening prospects for production of neurons to replace those lost to neurodegenerative disease.

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Fig. 1: Application of an ASO catalyzing PTB mRNA degradation is sufficient to induce new neurons in a mature human organoid model.
Fig. 2: Injection of an ASO into the CSF to suppress PTB is sufficient to induce new neurons in the adult and aged mouse brain.
Fig. 3: Transition of GFAP:tdTomato+ cells into new neurons results in no depletion in the total GFAP cell number.
Fig. 4: Newly generated neurons follow canonical neurogenesis in the dentate gyrus.
Fig. 5: Radial glial-like cells are the main cell origin for newly generated neurons in dentate gyrus, after PTB reduction using ASO.
Fig. 6: Newly generated neurons have intrinsic membrane properties of mature granule neurons.
Fig. 7: Generation of new functional neurons in aged mouse dentate gyrus.

Data availability

Data are available on request from the authors.

Code availability

No codes were used for this study.

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Acknowledgements

This work was supported by a grant from the Nomis Foundation to D.W.C., by grant no. NS27036 from the N.I.H. to D.W.C. and S.D.C., by a Veteran’s Administration grant to T.S.H, and by grants no. MH109885, no. MH100175, no. MH108528 and no. NS105969 from the NIH to A.R.M. Some of the microscopy utilized the UCSD Microscopy Core, supported by NIH grant NS047101. D.W.C. receives salary support from the Ludwig Institute for Cancer Research. R.M. is the recipient of a postdoctoral fellowship from the Hereditary Disease Foundation. We also thank A. Roberts and the mouse phenotyping facility of the Scripps Research Institute for performing the behavioral tests in this manuscript.

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Contributions

R.M., C.C.-M., S.D.C. and D.W.C. conceived the study. R.M., C.C.-M., C.E.S., S.M.S., K.L., F.R., C.F.B., S.D.C., T.S.H., A.R.M. and D.W.C. designed the study. R.M., C.C.-M., C.E.S., S.M.S., M.M.-D. and K.L. performed the experiments. R.M., C.C.-M. and S.M.S. analyzed the data. R.M., C.C.-M., C.E.S., S.M.S., F.R., C.F.B., S.D.C., T.S.H., A.R.M. and D.W.C. wrote the manuscript. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Don W. Cleveland.

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Competing interests

C.F.B., F.R. and K.L. are employees of, and D.W.C. is a consultant for, Ionis Pharmaceuticals. A.R.M. is a cofounder and has an equity interest in TISMOO, a company dedicated to genetic analysis and brain organoid modeling focusing on therapeutic applications customized for autism spectrum disorder and other neurological disorders with genetic origins. The terms of this arrangement have been reviewed and approved by the University of California San Diego by its conflict of interest policies.

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Peer review information Nature Neuroscience thanks the anonymous reviewers for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 PTB and neuronal PTB (nPTB) mRNA levels 3 days post-ICV injection of PTB-ASO2.

a, PTB mRNA levels in the hippocampus, motor cortex, and striatum measured by qPCR, 3 days post ICV injection of 500 μg PTB or control ASOs into 3-months-old mouse brain. Data are presented as fold change mean +/− s.e.m. (Hippocampus: control mean: 1 +/− 0.01; PTB-ASO mean: 0.5 +/− 0.07; n = 3,n = 2 biological repeats; respectively; Motor cortex: control mean: 1 +/− 0.09; PTB-ASO mean: 0.65 +/− 0.05; n = 3 biological repeats; Striatum: control mean: 1 +/− 0.03; PTB-ASO mean: 0.86 +/− 0.04; n = 3 biological repeats). b, PTB mRNA levels in the hippocampus measured by qPCR 3 days and 15 days post ICV injection of 500 mg PTB or control ASOs into 3-month-old mouse brain. Data are presented as fold change mean +/− s.e.m. (control mean: 1 +/− 0.04; 3 days post PTB-ASOs mean: 0.61 +/− 0.08; 15 days post PTB-ASOs mean: 1.18 +/− 0.24; n = 3 biological repeats. c, Neuronal PTB (nPTB) mRNA levels in the hippocampus measured by qPCR 3 days and 15 days post ICV injection of 500 mg PTB or control ASOs into 3-month-old mouse brain. Data are presented as fold change mean +/− s.e.m. (control mean: 1 +/− 0.03; 3 days post PTB-ASOs mean: 0.63 +/− 0.04; 15 days post PTB-ASOs mean: 1.75 +/− 0.33; n = 3 biological repeats).

Extended Data Fig. 2 ASOs efficiently penetrate into and regulate gene expression in 3D human organoids in culture.

a, Representative immunofluorescence images from a 5-month-old human organoid taken 1-week post Cy3-Malat1-ASO addition to the culture medium. Images show a view of (red) Cy3-Malat1-ASO (visualized by direct immunofluorescence) or (blue) DAPI staining for DNA; experiment was reproduced two times, independently, with similar results. b, Malat1 mRNA levels measured by qPCR 2 or 4 weeks after addition to human organoid cultures or either 10 μM Malat1-ASO or control, non-targeting ASO. Data are presented as fold change mean +/− s.e.m. (2 weeks control mean: 1 +/− 0.04; 2 weeks post Malat1-ASOs mean: 0.11 +/− 0.03; 4 weeks control mean: 1 +/− 0.1; 4 weeks post Malat1-ASOs mean: 0.1 +/− 0.02; n = 3 biological repeats). c, Representative immunofluorescence images from 5-month-old human organoids taken 1-month post-Malat1-ASO application to the organoid culture medium. Images show a view of (green) a Malat1-ASO (visualized by immunofluorescence) or (blue) DAPI staining for DNA; experiment was reproduced three times, independently, with similar results.

Extended Data Fig. 3 PTB-ASO application into human organoid cultures leads to increase levels of TuJ1 protein with no alterations in SOX2 or caspase 3 markers.

a, Representative images of 5 months old human organoid taken 1-month post-PTB-ASO2 or control treatment. Images show a view of the axonal marker (green) TUJ1 (visualized by immunofluorescence); DAPI staining for DNA; experiment was reproduced three times, independently, with similar results. b, Total TuJ1 area in PTB-ASO treated organoids compared to control ASO. Data are presented as fold change mean +/− SEM (control mean: 1 +/− 0.21; PTB-ASO mean: 1.73 +/− 0.33; n = 3 biological repeats). c, Representative images and from 5 months old human organoid taken 1-month post-PTB-ASO2 application to the culture medium. Images show a view of (green) SOX2 (visualized by immunofluorescence); experiment was reproduced three times, independently, with similar results. d, Quantification of the total SOX2 positive cells per organoid area treated with PTB-ASO compared to ASO control. Data are presented as mean +/− s.e.m. (control mean: 436.7 +/− 17.82; PTB-ASO mean: 406.3 +/− 19.89; n = 3 biological repeats). e, Total caspase 3 (CC3) protein area in PTB-ASO treated organoids compared to control ASO. Data are presented as fold change mean +/− s.e.m. (control mean: 1 +/− 0.21; PTB-ASO mean: 0.79 +/− 0.19; n = 4 biological repeats).

Extended Data Fig. 4 Morphology of newly generated neurons in different brain regions, 2 months post-PTB-ASO ICV administration.

Representative images of (left) granule cell layer, (middle) CA1, and (right) cortex, 2 months post-ICV injection of PTB-ASO2 into mice carrying both a CAG-lox-stop-lox-tdTomato gene and a tamoxifen-inducible GFAP-CreERT2 transgene. (Red) tdTomato (visualized by direct fluorescence); (blue) DAPI staining for DNA; experiment was reproduced three times, independently, with similar results.

Extended Data Fig. 5 New neurons along the dentate gyrus were not detected in 1.2 years old control injected mice.

a, Representative image from (left) 5 months and (right) 1.2 years old mouse dentate gyrus taken 2 months post-ICV injection of control-ASO into mice carrying both a CAG-lox-stop-lox-tdTomato gene and a tamoxifen-inducible GFAP-CreERT2 transgene. (Green) NeuN and (red) tdTomato (visualized by immunofluorescence and direct fluorescence, respectively); b, Quantification of the tdTomato + & NeuN+ neurons (iNeurons) in the granule cell layer 2 months post ICV injection of control-ASO at 5 months or 1.2 years old mice. Data are presented as fold change mean +/− s.e.m. (control 5 months mean: 1 +/− 0.35; Control 1.2 years old mean: 0 +/− 0; n = 8, n = 5 brain slides per each condition, n = 3, n = 1, respectively).

Extended Data Fig. 6 Injection of ASO to suppress PTB into the cerebral spinal fluid induces a low number of new neurons in the aged mouse cortex.

a,b, Representative image (a) from 1.2 year old mouse cortex taken 2 months post-ICV injection of PTB-ASO2 into mice carrying both a CAG-lox-stop-lox-tdTomato gene and a tamoxifen-inducible GFAP-CreERT2 transgene. b, high-magnification views of newly induced neurons (iNeurons) in the cortex expressing (green) NeuN and (red) tdTomato (visualized by immunofluorescence and direct fluorescence, respectively); (blue) DAPI staining for DNA; experiment was reproduced three times, independently, with similar results.

Extended Data Fig. 7 ICV delivery of PTB-ASO facilitate Ki67 expression in the mouse dentate gyrus and in human brain organoids.

a,b, Representative images from (a) 5 months and (b) 1.2 years old mouse dentate gyrus taken 2 months post-ICV injection of control ASO or PTB-ASO2. (Red) Ki67 (visualized by immunofluorescence); (blue) DAPI staining for DNA; experiment was reproduced three times, independently, with similar results. c, Total Ki67 positive cells per dentate gyrus of a 5 months old mouse 2 months post ICV delivery of PTB-ASO or control ASO. Data are presented as mean +/− SEM (control: 1.25 +/− 0.75; PTB-ASO mean: 5.75 +/− 2.3; n = 4 biological repeats). d, Ki67 mRNA levels measured by qPCR, 1 month after the addition of either PTB-ASO2 or control ASO to the human organoid culture medium. Data are presented as fold change mean +/− s.e.m. (control: 1 +/− 0.35; PTB-ASO mean: 4.193 +/− 1.19; n = 3 biological repeats).

Extended Data Fig. 8 DCX expression levels 2 weeks post-PTB-ASO ICV delivery into 1.5 years old mice.

Four representative images and insets of 1.5 years old mice dentate gyrus at 2 weeks post ICV delivery of (upper) control or (lower) PTB-ASO. (Green) DCX (visualized by immunofluorescence); (blue) DAPI stain for DNA; experiment was reproduced three times, independently, with similar results.

Extended Data Fig. 9 DCX protein expression levels 1 month post PTB-ASO treatment in human organoid cultures.

a, Representative images of a 5-month-old human organoid taken a 1-month post PTB or control ASO treatment. (Green) DCX visualized by immunofluorescence; (blue) DAPI to stain DNA; experiment was reproduced four times, independently, with similar results. b, Total DCX area in either PTB-ASO or control treated organoids. Data are presented as fold change mean +/− s.e.m. (control: 1 +/− 0.09; PTB-ASO mean: 1.43 +/− 0.13; n = 4 biological repeats, two tailed t test *p = 0.042).

Extended Data Fig. 10 tdTomato + , DCX + cells convert to expression of NeuN within 2 months of PTB ASO injection.

Quantification of total tdTomato + , NeuN+ positive cells per dentate gyrus area of 5 months old mice 2 weeks or 2 months post PTB-ASO or control ICV injection into mice Data are presented as mean +/− s.e.m. (control: 1.33 +/− 0.66; 2 weeks PTB-ASO mean: 3.16 +/− 1.59; 2 months PTB-ASO mean: 28.88 +/− 4.87; n = 3, n = 3, n = 4, respectively; **, One way ANOVA with Tukey’s multiple comparisons, **p = 0.0013).

Supplementary information

Reporting Summary

Supplementary Video 1

PTB-ASO-dependent iNeurons generated in the mouse dentate gyrus. High-magnification Z-stacks of an area of the dentate gyrus granule cell layer, 2 months post intracerebroventricular (ICV) injection of (video 1) control or (video 2) PTB-ASO2 into 3-month-old mice carrying both a CAG-lox-stop-lox-tdTomato gene (integrated at the Rosa locus) and a tamoxifen-inducible GFAP-CreERT2 transgene. (Green) NeuN visualized by immunofluorescence; (red) tdTomato visualized by direct fluorescence; the experiment was reproduced four times, independently, with similar results.

Supplementary Video 2

PTB-ASO-dependent iNeurons generated in the mouse dentate gyrus. High-magnification Z-stacks of an area of the dentate gyrus granule cell layer, 2 months post intracerebroventricular (ICV) injection of (video 1) control or (video 2) PTB-ASO2 into 3-month-old mice carrying both a CAG-lox-stop-lox-tdTomato gene (integrated at the Rosa locus) and a tamoxifen-inducible GFAP-CreERT2 transgene. (Green) NeuN visualized by immunofluorescence; (red) tdTomato visualized by direct fluorescence; the experiment was reproduced four times, independently, with similar results.

Supplementary Video 3

Unbiased quantification method to measure the number of total new neurons and total GFAP-positive cell number in the mouse dentate gyrus. Representative image of the output mask image created by the algorithm used to quantify the number of total tdTomato+, NeuN+ cells and the number of GFAP+ cells in the dentate gyrus area 2 months post PTB-ASO injection.

Supplementary Video 4

PTB-ASO-dependent iNeurons expressing MAP2, a marker of mature dendrites. High-magnification Z-stacks of an area of the dentate gyrus granule cell layer, 2 months post intracerebroventricular (ICV) injection of PTB-ASO2 into 3-month-old mice carrying both a CAG-lox-stop-lox-tdTomato gene (integrated at the Rosa locus) and a tamoxifen-inducible GFAP-CreERT2 transgene. (Green) MAP2 visualized by immunofluorescence; (red) tdTomato visualized by direct fluorescence; the experiment was reproduced three times, independently, with similar results.

Supplementary Video 5

PTB-ASO-dependent immature neurons expressing DCX do not colocalize with GFAP marker. High-magnification 3D video of an area of the dentate gyrus granule cell layer 2 weeks post intracerebroventricular (ICV) injection of PTB-ASO2 into 3-month-old mice. (Green) GFAP; (red) DCX (both visualized by immunofluorescence); the experiment was reproduced three times, independently, with similar results.

Supplementary Video 6

Radial glial-like cells exhibit hybrid cell markers and morphology 1week post PTB-ASO delivery. 1 week post (ICV) injection of PTB-ASO2 into 3-month-old mice carrying both a CAG-lox-stop-lox-tdTomato gene (integrated at the Rosa locus) and a tamoxifen-inducible GFAP-CreERT2 transgene. (Green) GFAP; (magenta) DCX (both visualized by immunofluorescence). (Red) tdTomato visualized by direct fluorescence; the experiment was reproduced three times, independently, with similar results.

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Maimon, R., Chillon-Marinas, C., Snethlage, C.E. et al. Therapeutically viable generation of neurons with antisense oligonucleotide suppression of PTB. Nat Neurosci (2021). https://doi.org/10.1038/s41593-021-00864-y

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