The neuron-specific IIS/FOXO transcriptome in aged animals reveals regulatory mechanisms of cognitive aging
- Department of Molecular Biology, Princeton University, United States
- Princeton University, United States
Figures
Figure 1 with 2 supplements
Identifying neuronal aging targets in wild-type (WT) worms using neuron-specific RNA-sequencing.
(a) Wild-type learning and 1 hr memory results on Day 1 and Day 7. Learning and memory results are represented as learning index (LI). Details of the LI calculation are explained in the methods. …
Figure 1—figure supplement 1
Aged neuron-specific sequencing.
(a–b) FACS results of neuron isolation. Over 99.94% of the cells collected are GFP + neurons. 100,000 cells are collected for each biological replicate, six biological replicates for each condition. …
Figure 1—figure supplement 2
Whole-worm RNA-sequencing identifies whole-body changes during aging.
(a) Volcano plot of Day 1 vs Day 8 differentially-expressed genes during aging. 264 genes are expressed at higher levels in young worms, 1626 genes are higher in aged worms (log2[Fold-change (Day 1 …
Figure 2
Genes that increase with age cause behavioral defects.
(a) Tissue prediction score for wild-type genes expressed at higher levels in aged worms. (b) Gene ontology (GO) terms of genes expressed higher in aged neurons highlight transcription regulation …
Figure 3 with 3 supplements
Identifying neuronal IIS/FOXO targets in aged worms using neuron-specific RNA-sequencing.
(a) daf-2 mutants show better learning maintenance with age compared to N2 and daf-16;daf-2 worms. n=10 plates in each condition. (b) daf-2 mutants show better memory maintenance with age compared …
Figure 3—figure supplement 1
Neuron-specific sequencing of Day 8 daf-2 and daf-16;daf-2 mutants.
(a–b) FACS results of neuron isolation. Over 99% of the cells collected are GFP + neurons. 100,000 cells are collected for each biological replicate, six replicates for each genotype. (c) …
Figure 3—figure supplement 2
Whole-worm RNA-sequencing identifies changes in aged daf-2 mutants.
(a–b) Gene ontology (GO) term analysis of whole-worm daf-2-regulated genes shows enrichment in stress-resistant genes. (c) Comparison of neuronal and whole-worm Day 8 daf-2 differentially-expressed …
Figure 3—figure supplement 3
DAF-16-dependent and -independent daf-2-regulated genes show different features.
(a) Volcano plot of daf-2 vs N2 differentially expressed genes during aging. 1036 genes are more highly expressed in daf-2 mutants, 1285 genes are higher in N2 (log2[Fold-change(daf-2 vs N2)]>0.5, …
Figure 4
Neuronal IIS/FOXO aging targets regulate memory decline with age in daf-2 worms.
(a) Comparison of neuronal Day 1 and Day 8 daf-2 vs daf-16;daf-2 upregulated genes. All shared genes and top Day 8-specific daf-2 upregulated genes are labeled. (b) daf-2-regulated fold-change …
Figure 5 with 1 supplement
Aged daf-2 neurons upregulate neuroprotective genes to maintain improved cognitive behaviors.
During normal neuronal aging, neuron-specific genes decrease in expression, while proteolysis and epigenetic regulators are upregulated, resulting in neuron dysfunction and cognitive function loss. …
Figure 5—figure supplement 1
Comparison with recent sequencing datasets.
(a) Comparison with CeNGEN (L4 stage) gene expression data (Taylor et al., 2021) shows a high correlation, with many genes only detected in our isolated neuron bulk-sequencing dataset (orange; …
Tables
Table 1
List of top daf-2 vs daf-16;daf-2 upregulated genes with orthologs that have neuroprotective functions.
| Gene name | Full name | log2(FC) | p-adj | Mammalian ortholog | Ortholog full name | Inferred function |
|---|---|---|---|---|---|---|
| Neuroprotective against Neurodegenerative Diseases | ||||||
| cpi-1 | Cysteine Protease Inhibitor 1 | 2.07 | 7.80E-19 | CST3 | Cystatin C | Protease inhibitor, suppresses AD pathology Gauthier et al., 2011 |
| alh-2 | ALdehyde deHydrogenase 2 | 1.83 | 2.65E-05 | ALDH1A1 | Aldehyde dehydrogenase 1 | Expressed in dopaminergic neurons. Regulates dopamine release in Parkinson’s Disease Carmichael et al., 2021 |
| ttr-41,45,2 | TransThyretin-Related family domain 41,45,2 | 1.68 | 3.98E-06 | Inhibits Aβ fibril formation, and suppresses the AD pathology Li et al., 2011 | ||
| cyp-33B1 | CYtochrome P450 family 33B1 | 1.34 | 2.04E-03 | CYP2J2 | Cytochrome P450 2J2 | Protective against Parkinson’s Disease through altered metabolism Li et al., 2018; Ferguson and Tyndale, 2011 |
| spin-2 | SPINster (Dm lysosomal permease) homolog 2 | 1.27 | 6.20E-04 | SPNS2 | Spinster homolog 2 | Sphingosine-1-phosphate Transporter, neuroprotective in AD Zhong et al., 2019 |
| gpx-5 | Glutathione PeroXidase 5 | 1.27 | 3.99E-04 | GPX3,5,6 | glutathione peroxidase 3,5,6 | Protects again lipid peroxidation, protects against neurodegeneration Lee et al., 2020; Hambright et al., 2017 |
| cpr-2 | Cysteine PRotease related 2 | 1.25 | 5.01E-03 | CTSB | Cathepsin B | Lysosomal Protease, Involved in Aβ and APP protein degradation Cermak et al., 2016 |
| djr-1.2 | DJ-1 (mammalian transcript’l regulator) Related 1.2 | 1.09 | 3.90E-03 | PARK7 | Parkinsonism associated deglycase | Neuroprotective against Parkinson’s Disease; Prevents accumulation of harmful metabolites Heremans et al., 2022 |
| Synaptic Organization Maintenance | ||||||
| dod-24 | Downstream Of DAF-16 (regulated by DAF-16) 24 | 1.93 | 1.39E-07 | Cub-like Domain Containing Protein | Clustering of neurotransmitter receptor proteins González-Calvo et al., 2022 | |
| ptr-19,15 | PaTched Related family 19,15 | 1.21 | 1.72E-05 | PTCHD1,3,4 | Patched domain-containing 1,3,4 | Synaptic organization, autism risk factor Ung et al., 2018; Pastore et al., 2022 |
| hbl-1 | HunchBack Like (fly gap gene-related) 1 | 1.16 | 6.47E-06 | hb | Hunchback (fly) | Regulate synapse number and locomotor circuit function Lee et al., 2022 |
| cutl-4 | CUTiclin-Like 4 | 1.08 | 2.74E-02 | pio | Piopio (fly) | ECM protein for axonal growth and synapse formation Broadie et al., 2011 |
| lron-2 | eLRR (extracellular Leucine-Rich Repeat) ONly 2 | 1.06 | 8.70E-05 | LGI1,2 | Leucine-Rich Glioma Inactivated protein 1 | Modulation of trans-synaptic proteins. Protection against seizure Fels et al., 2021 |
| Neuronal Homeostasis Maintenance | ||||||
| mocs-1 | MOlybdenum Cofactor Sulfurase 1 | 1.05 | 1.17E-04 | MOCOS | Molybdenum cofactor sulfurase | Regulation of redox homeostasis and synaptogenesis. Down in ASD Rontani et al., 2021 |
| plep-1 | PLugged Excretory Pore 1 | 1.12 | 2.92E-03 | MFSD11 | Major facilitator superfamily domain 11 | Putative SLC solute carrier protein, involved in brain energy homeostasis Perland et al., 2016 |
| cky-1 | CKY homolog 1 | 1.08 | 1.58E-04 | NPAS4 | Neuronal PAS Domain Protein 4 | Calcium-dependent transcription factor, neuronal homeostasis maintenance Fu et al., 2020; Shan et al., 2018 |
| Neuronal Injury Repair facilitation | ||||||
| F08H9.4, hsp-12.3,12.6 | small HSP domain-containing protein | 1.94 | 7.33E-06 | HSPB2 | Heat-shock Protein Beta 2 | Facilitates PNS injury regeneration, suppresses inflammation Huang et al., 2023 |
| sod-3 | SOD superoxide dismutase 3 | 1.66 | 3.05E-09 | SOD2 | superoxide dismutase2 | Converts superoxide to the less reactive hydrogen peroxide (H2O2). Protects neurons from injury. Flynn and Melov, 2013 |
| Normal Neuronal Activity Maintenance | ||||||
| lgc-28 | Ligand-Gated ion Channel 28 | 1.38 | 7.29E-04 | CHRNA6,3 | Neuronal acetylcholine receptor subunit alpha-6,3 | Nicotinic receptor. Regulates cognitive functions and addiction Koukouli and Changeux, 2020; Zeiger et al., 2008 |
| F22B7.9 | 1.33 | 8.91E-15 | METTL23 | methyltransferase like 23 | Interacts with GABPA; disruption causes intellectual disability Bernkopf et al., 2014; Reiff et al., 2014 | |
| fat-5 | FATty acid desaturase 5 | 1.31 | 3.40E-03 | SCD5 | StearoylCoA Desaturase-5 | Neuronal Cell Proliferation and Differentiation Sinner et al., 2012 |
| slc-36.3 | SLC (SoLute Carrier) homolog 36.3 | 1.25 | 2.88E-03 | SLC36A4 | Solute Carrier Family36 Member4 | amino acid transporter, transports Trp, involved in kynurenic acid pathway Lautrup et al., 2019 |
| lin-42 | abnormal cell LINeage 42 | 1.15 | 1.66E-04 | PER1,2 | Period 1,2 | Phosphorylates CREB, modulates CREB-mediated memory consolidation Smies et al., 2022 |
| ctsa-1.1 | CaThepSin A homolog 1.1 | 1.07 | 4.97E-05 | CTSA | Lysosomal Ser carboxy-peptidase Cathepsin A | Involved in normal neuronal development De Pasquale et al., 2020; Hsu et al., 2018; |
| gsnl-1 | GelSoliN-Like 1 | 1.06 | 2.93E-04 | AVIL | advillin | Facilitates somatosensory neuron axon regeneration Chuang et al., 2018 |
Additional files
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Supplementary file 1
Whole-worm DEseq2 results.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp1-v1.xlsx
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Supplementary file 2
Neuronal WT Day 1 vs Day 8 DEseq2.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp2-v1.xlsx
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Supplementary file 3
Neuronal Day 8 daf-2 vs daf-16;daf-2 DEseq2.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp3-v1.xlsx
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Supplementary file 4
Neuronal Day 8 daf-2 vs N2 DEseq2.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp4-v1.xlsx
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Supplementary file 5
Neuronal Day 8 daf-16;daf-2 vs N2 DEseq2.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp5-v1.xlsx
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Supplementary file 6
Number of sequencing reads.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp6-v1.xlsx
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Supplementary file 7
Raw behavioral data.
- https://cdn.elifesciences.org/articles/95621/elife-95621-supp7-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/95621/elife-95621-mdarchecklist1-v1.pdf
