Cited by 213Pluripotent Stem Cells ResearchGenetics, Aging, and Longevity in Model OrganismsTelomeres, Telomerase, and Senescence

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Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts

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Abstract

Aging is a major risk factor in many forms of late-onset neurodegenerative disorders. The ability to recapitulate age-related characteristics of human neurons in culture will offer unprecedented opportunities to study the biological processes underlying neuronal aging. Here, we show that using a recently demonstrated microRNA-based cellular reprogramming approach, human fibroblasts from postnatal to near centenarian donors can be efficiently converted into neurons that maintain multiple age-associated signatures. Application of an epigenetic biomarker of aging (referred to as epigenetic clock) to DNA methylation data revealed that the epigenetic ages of fibroblasts were highly correlated with corresponding age estimates of reprogrammed neurons. Transcriptome and microRNA profiles reveal genes differentially expressed between young and old neurons. Further analyses of oxidative stress, DNA damage and telomere length exhibit the retention of age-associated cellular properties in converted neurons from corresponding fibroblasts. Our results collectively demonstrate the maintenance of age after neuronal conversion.

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Figure 1. MicroRNA-mediated direct neuronal conversion applied to fibroblasts across the age spectrum. (A) Schematic diagram of neuronal conversion of human fibroblast samples from individuals ranging from three days to 96 years of age. Primary fibroblasts were transduced with microRNA-9/9*-124 and the transcription factor cocktail CTIP2, DLX1/2, MYT1L (CDM) and analyzed for neuronal properties after 30 days. (B) Expression of pan-neuronal markers MAP2 (top) and TUBB3 (bottom) after neuronal conversion of human fibroblasts ranging in age. Scale bar = 50 µm. (C) Expression of pan-neuronal marker NeuN and medium spiny neuron-specific markers GABA and DARPP32 in reprogrammed neurons from fibroblasts aged 91-, 72-, 92-years respectively. (D) Immunostaining analysis of percentage of reprogrammed neurons positive for neuronal markers TUBB3 and MAP2 over DAPI signals (n = 200–300 per cell line). (E) Representative whole-cell current clamp recording of converted neurons from young (29 years old, left) and old (94 year old donor, right) donors. Converted human neurons in monoculture displayed multiple action potentials in response to step current injections at four weeks post-transduction. All reprogrammed neurons from old fibroblasts recorded (n = 11) fired APs in response to current injections (top). Representative traces of fast-inactivating inward currents recorded in voltage-clamp mode. Voltage steps ranged from +10 to +70 mV (bottom). DOI: http://dx.doi.org/10.7554/eLife.18648.003
Figure 1. MicroRNA-mediated direct neuronal conversion applied to fibroblasts across the age spectrum. (A) Schematic diagram of neuronal conversion of human fibroblast samples from individuals ranging from three days to 96 years of age. Primary fibroblasts were transduced with microRNA-9/9*-124 and the transcription factor cocktail CTIP2, DLX1/2, MYT1L (CDM) and analyzed for neuronal properties after 30 days. (B) Expression of pan-neuronal markers MAP2 (top) and TUBB3 (bottom) after neuronal conversion of human fibroblasts ranging in age. Scale bar = 50 µm. (C) Expression of pan-neuronal marker NeuN and medium spiny neuron-specific markers GABA and DARPP32 in reprogrammed neurons from fibroblasts aged 91-, 72-, 92-years respectively. (D) Immunostaining analysis of percentage of reprogrammed neurons positive for neuronal markers TUBB3 and MAP2 over DAPI signals (n = 200–300 per cell line). (E) Representative whole-cell current clamp recording of converted neurons from young (29 years old, left) and old (94 year old donor, right) donors. Converted human neurons in monoculture displayed multiple action potentials in response to step current injections at four weeks post-transduction. All reprogrammed neurons from old fibroblasts recorded (n = 11) fired APs in response to current injections (top). Representative traces of fast-inactivating inward currents recorded in voltage-clamp mode. Voltage steps ranged from +10 to +70 mV (bottom). DOI: http://dx.doi.org/10.7554/eLife.18648.003CC BY · PubMed Central
Figure 1—figure supplement 1. Transcriptome analyses between converted neurons and fibroblasts of young and old age groups. (A) Volcano plots show global transcriptomic differences between reprogrammed neurons compared to starting human fibroblasts from young (three day, five month and one year-old, top) and old (90, 92 and 92 year-old, bottom) donors. Upregulated DEGs (in red) and downregulated DEGs (in blue) after direct neuronal reprogramming are shown. (B) Heatmap of representative DEGs: upregulation of neuronal genes (top) and downregulation of fibroblast associated genes (bottom) in reprogrammed neurons from both young and old fibroblasts (right) when compared to corresponding fibroblasts (left). DOI: http://dx.doi.org/10.7554/eLife.18648.004
Figure 1—figure supplement 1. Transcriptome analyses between converted neurons and fibroblasts of young and old age groups. (A) Volcano plots show global transcriptomic differences between reprogrammed neurons compared to starting human fibroblasts from young (three day, five month and one year-old, top) and old (90, 92 and 92 year-old, bottom) donors. Upregulated DEGs (in red) and downregulated DEGs (in blue) after direct neuronal reprogramming are shown. (B) Heatmap of representative DEGs: upregulation of neuronal genes (top) and downregulation of fibroblast associated genes (bottom) in reprogrammed neurons from both young and old fibroblasts (right) when compared to corresponding fibroblasts (left). DOI: http://dx.doi.org/10.7554/eLife.18648.004CC BY · PubMed Central
Figure 2. Conservation of the epigenetic clock of reprogrammed neurons from human fibroblasts. (A) Schematic diagram representing the hypothesis that the epigenetic clock of fibroblasts from different age groups is conserved in reprogrammed neurons after miR-mediated neuronal conversion. (B) Top: Predicted ages based on the methylation status (DNAm age) of fibroblasts plotted against the actual ages of fibroblasts (correlation = 0.75, p=9.1e-08). Middle: Predicted DNAm ages of reprogrammed neurons against actual ages of starting fibroblast, correlation = 0.82, p=1e-04. Bottom: Combined plot of DNAm ages of fibroblasts and DNAm ages of reprogrammed neurons against actual ages (correlation = 0.77, p=1.6e-11). (C) DNAm age of reprogrammed neurons plotted against the DNAm ages of the corresponding, starting fibroblast ages, correlation = 0.91 p=2.5e-06. DOI: http://dx.doi.org/10.7554/eLife.18648.005
Figure 2. Conservation of the epigenetic clock of reprogrammed neurons from human fibroblasts. (A) Schematic diagram representing the hypothesis that the epigenetic clock of fibroblasts from different age groups is conserved in reprogrammed neurons after miR-mediated neuronal conversion. (B) Top: Predicted ages based on the methylation status (DNAm age) of fibroblasts plotted against the actual ages of fibroblasts (correlation = 0.75, p=9.1e-08). Middle: Predicted DNAm ages of reprogrammed neurons against actual ages of starting fibroblast, correlation = 0.82, p=1e-04. Bottom: Combined plot of DNAm ages of fibroblasts and DNAm ages of reprogrammed neurons against actual ages (correlation = 0.77, p=1.6e-11). (C) DNAm age of reprogrammed neurons plotted against the DNAm ages of the corresponding, starting fibroblast ages, correlation = 0.91 p=2.5e-06. DOI: http://dx.doi.org/10.7554/eLife.18648.005CC BY · PubMed Central
Figure 3. Age-associated changes in transcriptome and microRNA profiles in reprogrammed neurons. (A) Principle component analysis (PCA) of transcriptome profiling of reprogrammed neurons from young fibroblasts aged three days, five months one year (green) and from old fibroblasts aged 90, 92, and 92 years (blue) alongside corresponding young fibroblasts (black) and old fibroblasts (red) (FDR < 0.05). (B) Differentially expressed genes (DEGs) with age in fibroblasts (x axis) and in reprogrammed neurons (y axis). Age-associated DEGs in reprogrammed neurons shown in green, DEGs in fibroblasts shown in red, and commonly shared DEGs with age in both fibroblasts and reprogrammed neurons shown in blue. (C) PCA of miRNA profile in reprogrammed neurons from young fibroblasts aged three days, five months one year (green) and from old fibroblasts aged 90, 92, and 92 years (bue) alongside the corresponding young fibroblasts (black) and old fibroblasts (red) (FDR < 0.05). (D) MicroRNAs that are differentially regulated with age in both fibroblasts (red) and reprogrammed neurons (blue). Four microRNAs, miR-10a, miR-497, miR-10b, and miR-195, are upregulated with age, while 10 microRNAs are shown to be downregulated with age, p<0.05. (E) Validation of expression of miRNA expression upregulated with aging (miR-10a, miR-497, miR-195) in reprogrammed neurons from old fibroblasts over reprogrammed neurons from young fibroblasts (left). Validation of expression changes of miR-10a, miR-497, miR-195 in human striatum slices (middle) and human cortex slices (right) from old individuals compared to young individuals. DOI: http://dx.doi.org/10.7554/eLife.18648.007
Figure 3. Age-associated changes in transcriptome and microRNA profiles in reprogrammed neurons. (A) Principle component analysis (PCA) of transcriptome profiling of reprogrammed neurons from young fibroblasts aged three days, five months one year (green) and from old fibroblasts aged 90, 92, and 92 years (blue) alongside corresponding young fibroblasts (black) and old fibroblasts (red) (FDR < 0.05). (B) Differentially expressed genes (DEGs) with age in fibroblasts (x axis) and in reprogrammed neurons (y axis). Age-associated DEGs in reprogrammed neurons shown in green, DEGs in fibroblasts shown in red, and commonly shared DEGs with age in both fibroblasts and reprogrammed neurons shown in blue. (C) PCA of miRNA profile in reprogrammed neurons from young fibroblasts aged three days, five months one year (green) and from old fibroblasts aged 90, 92, and 92 years (bue) alongside the corresponding young fibroblasts (black) and old fibroblasts (red) (FDR < 0.05). (D) MicroRNAs that are differentially regulated with age in both fibroblasts (red) and reprogrammed neurons (blue). Four microRNAs, miR-10a, miR-497, miR-10b, and miR-195, are upregulated with age, while 10 microRNAs are shown to be downregulated with age, p<0.05. (E) Validation of expression of miRNA expression upregulated with aging (miR-10a, miR-497, miR-195) in reprogrammed neurons from old fibroblasts over reprogrammed neurons from young fibroblasts (left). Validation of expression changes of miR-10a, miR-497, miR-195 in human striatum slices (middle) and human cortex slices (right) from old individuals compared to young individuals. DOI: http://dx.doi.org/10.7554/eLife.18648.007CC BY · PubMed Central
Figure 3—figure supplement 1. Gene ontology of DEGs in reprogrammed neurons. (A) GO analysis of age-downregulated transcripts (top) and upregulated transcipts (bottom) in reprogrammed neurons, log fc > 1, FDR < 0.01 using BiNGO from Cytoscape version 3.3.0. (FDR 0.05). GO terms related to aging-associated processes are represented here. DOI: http://dx.doi.org/10.7554/eLife.18648.010
Figure 3—figure supplement 1. Gene ontology of DEGs in reprogrammed neurons. (A) GO analysis of age-downregulated transcripts (top) and upregulated transcipts (bottom) in reprogrammed neurons, log fc > 1, FDR < 0.01 using BiNGO from Cytoscape version 3.3.0. (FDR 0.05). GO terms related to aging-associated processes are represented here. DOI: http://dx.doi.org/10.7554/eLife.18648.010CC BY · PubMed Central
Figure 3—figure supplement 2. Gene ontology of predicted targets of age-resulted microRNAs. (A) GO analysis of list of age-downregulated transcripts predicted to be targeted by upregulated microRNAs, miR-10a-5p (top) and miR-497-5p (bottom). A list of original downregulated transcripts were filtered by fc<-1.5, FDR < 0.05. Target prediction analysis with Ingenuity Pathway Analysis, MicroRNA-mRNA Interactions. DOI: http://dx.doi.org/10.7554/eLife.18648.011
Figure 3—figure supplement 2. Gene ontology of predicted targets of age-resulted microRNAs. (A) GO analysis of list of age-downregulated transcripts predicted to be targeted by upregulated microRNAs, miR-10a-5p (top) and miR-497-5p (bottom). A list of original downregulated transcripts were filtered by fc<-1.5, FDR < 0.05. Target prediction analysis with Ingenuity Pathway Analysis, MicroRNA-mRNA Interactions. DOI: http://dx.doi.org/10.7554/eLife.18648.011CC BY · PubMed Central
Figure 4. Analysis of cellular biomarkers of age reveals conservation of neuron-specific aging in reprogrammed neurons. (A) ROS levels visualized by MitoSOX and analyzed by FACs. Representative dot plot of reprogrammed neuron from 1-year-old fibroblast (left) and from 91-year-old fibroblast (right), y axis = FL2 channel (MitoSOX), x axis = FSC. Quantification of percent of cells positive for MitoSOX reveals a significant difference in fibroblasts with age in addition to reprogrammed neurons with age. ***p-value=0.0008; *p-value=0.019. (B) Representative images of comets indicating DNA damage from five month old fibroblasts (top left) versus old fibroblasts (top right) alongside reprogrammed neurons from 5-month-old fibroblasts (bottom left) and 92-year-old fibroblasts (bottom right). Quantification of tail lengths in fibroblasts and reprogrammed neurons with age *p-value=0.013, **p-value=0.004. (C) Telomere length analyses of reprogrammed neurons are maintained from corresponding starting fibroblasts from one year old, 56 year old, and 86 year old donors. DOI: http://dx.doi.org/10.7554/eLife.18648.012
Figure 4. Analysis of cellular biomarkers of age reveals conservation of neuron-specific aging in reprogrammed neurons. (A) ROS levels visualized by MitoSOX and analyzed by FACs. Representative dot plot of reprogrammed neuron from 1-year-old fibroblast (left) and from 91-year-old fibroblast (right), y axis = FL2 channel (MitoSOX), x axis = FSC. Quantification of percent of cells positive for MitoSOX reveals a significant difference in fibroblasts with age in addition to reprogrammed neurons with age. ***p-value=0.0008; *p-value=0.019. (B) Representative images of comets indicating DNA damage from five month old fibroblasts (top left) versus old fibroblasts (top right) alongside reprogrammed neurons from 5-month-old fibroblasts (bottom left) and 92-year-old fibroblasts (bottom right). Quantification of tail lengths in fibroblasts and reprogrammed neurons with age *p-value=0.013, **p-value=0.004. (C) Telomere length analyses of reprogrammed neurons are maintained from corresponding starting fibroblasts from one year old, 56 year old, and 86 year old donors. DOI: http://dx.doi.org/10.7554/eLife.18648.012CC BY · PubMed Central
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Metadata

Authors
Huh, C. J., Zhang, B., Victor, M. B., Dahiya, S., Batista, L. F., Horvath, S., & Yoo, A. S.
Affiliations
  • Washington University in St. Louis (US)
  • Department of Developmental Biology, Washington University School of Medicine, St. Louis, United States
  • University of California, Los Angeles (US)
Corresponding author
Yoo, Andrew S
Venue
eLife
Published
2016-09-20
Volume
5
ISSN
2050-084X (ISSN-L)
OpenAlex
W2521543069
Cited by
213
References
57
Citations by year
2026: 16 · 2025: 18 · 2024: 23 · 2023: 22 · 2022: 17 · 2021: 33 · 2020: 29 · 2019: 17 · 2018: 26 · 2017: 11
FWCI
9.35
Type
journal article
Language
en
Open access
Locations
  • eLife (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • National Institute on Drug Abuse (R25 DA027995)
  • National Institutes of Health (K99/R00, 4R00HL114732-03, 1U34AG051425-01, 5R01, AG042511-02, DP2NS083372-01)
  • Washington University in St. Louis (DDRCC, NIDDK P30 DK052574)
  • Ellison Medical Foundation (AG-NS-0878-12)
  • Cure Alzheimer's Fund
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Aging › Genetics, Aging, and Longevity in Model Organisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Telomeres, Telomerase, and Senescence
Keywords
neuronal aging, fibroblast-to-neuron conversion, epigenetic clocks, DNA methylation, age-related gene expression, oxidative stress, DNA damage, telomere length, neurodegenerative diseases, human neurons
MeSH terms
Aging, Cytological Techniques, DNA Damage, Fibroblasts, Humans, Neurons, Telomere, Oxidative Stress, Gene Expression Profiling, MicroRNAs, Epigenesis, Genetic, Cell Transdifferentiation

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