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A multiregional proteomic survey of the postnatal human brain

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Abstract

Detailed observations of transcriptional, translational and post-translational events in the human brain are essential to improving our understanding of its development, function and vulnerability to disease. Here, we exploited label-free quantitative tandem mass-spectrometry to create an in-depth proteomic survey of regions of the postnatal human brain, ranging in age from early infancy to adulthood. Integration of protein data with existing matched whole-transcriptome sequencing (RNA-seq) from the BrainSpan project revealed varied patterns of protein–RNA relationships, with generally increased magnitudes of protein abundance differences between brain regions compared to RNA. Many of the differences amplified in protein data were reflective of cytoarchitectural and functional variation between brain regions. Comparing structurally similar cortical regions revealed significant differences in the abundances of receptor-associated and resident plasma membrane proteins that were not readily observed in the RNA expression data.

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Acknowledgements

We thank S. Leslie and D. Li for discussions. Data were generated as part of the PsychENCODE Consortium, supported by U01MH103339, U01MH103365, U01MH103392, U01MH103340, U01MH103346, R01MH105472, R01MH094714, R01MH105898, R21MH102791, R21MH105881, R21MH103877 and P50MH106934 awarded to S. Akbarian (Icahn School of Medicine at Mount Sinai), G. Crawford (Duke University), S. Dracheva (Icahn School of Medicine at Mount Sinai), P. Farnham (University of Southern California), M.B.G. (Yale University), D. Geschwind (University of California, Los Angeles), T.M. Hyde (Lieber Institute for Brain Development), A. Jaffe (Lieber Institute for Brain Development), J.A. Knowles (University of Southern California), C. Liu (University of Illinois at Chicago), D. Pinto (Icahn School of Medicine at Mount Sinai), N.S. (Yale University), P. Sklar (Icahn School of Medicine at Mount Sinai), M. State (University of California, San Francisco), P. Sullivan (University of North Carolina), F. Vaccarino (Yale University), S. Weissman (Yale University), K. White (University of Chicago) and P. Zandi (Johns Hopkins University). This work was supported by the Yale/NIDA Neuroproteomics Centre (DA018343-12), by NIA grant AG047270-02, by NIMH grant MH110926, by NIH SIG grants 1S10OD019967-0 and 1S10ODOD018034-01, and by the State of Connecticut, Department of Mental Health & Addiction Services. B.C.C. was supported by a 2014 NARSAD Young Investigator Grant from the Brain & Behavior Research Foundation.

Author information

Author notes

  1. Becky C. Carlyle and Robert R. Kitchen contributed equally to this work.

Affiliations

  1. Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA

    • Becky C. Carlyle
    • , Robert R. Kitchen
    •  & Angus C. Nairn
  2. Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA

    • Robert R. Kitchen
    • , TuKiet T. Lam
    •  & Mark B. Gerstein
  3. W.M. Keck Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT, USA

    • Jean E. Kanyo
    • , Edward Z. Voss
    •  & TuKiet T. Lam
  4. Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA

    • Mihovil Pletikos
    • , André M. M. Sousa
    •  & Nenad Sestan
  5. Departments of Genetics and Psychiatry, Section of Comparative Medicine, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA

    • Nenad Sestan
  6. Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT, USA

    • Nenad Sestan
    •  & Angus C. Nairn

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Contributions

B.C.C. designed the experiments, performed the experiments, analyzed the data and wrote the manuscript. R.R.K. designed the experiments, analyzed the data and wrote the manuscript. J.E.K. performed the experiments. E.Z.V. performed the experiments. M.P. contributed to tissue and sample processing. A.M.M.S. contributed to tissue and sample processing. T.T.L. designed the experiments and wrote the manuscript. M.B.G. contributed to RNA-seq data generation and provided computational resources. N.S. designed the experiments, contributed to tissue and sample processing, contributed to RNA-seq data generation and wrote the manuscript. A.C.N. designed the experiments and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Nenad Sestan or Angus C. Nairn.

Integrated supplementary information

  1. Supplementary Figure 1: Number of proteins detected by highly fractionated proteomics across all regions

  2. Supplementary Figure 2: Number of peptides detected per protein shows no clear inter-regional variability

  3. Supplementary Figure 3: Numbers of proteins detected in each single shot sample. The use of “match between runs” results in an approximately 50% increase in the number of proteins identified by single shot proteomics

  4. Supplementary Figure 4: Batch effect identified by sample correlations is corrected by ComBat

  5. Supplementary Figure 5: Clustering all samples subjected to MS/MS using proteins significantly differentially expressed between brain regions revealed expected bulk differences between brain regions

  6. Supplementary Figure 6: Clustering all proteins significantly differentially expressed between regions reveals consistent patterns of expression that favour region-specific enrichment or region-specific depletion in abundance

  7. Supplementary Figure 7: Clustering all proteins significantly differentially expressed between regions reveals consistent patterns of expression that favour region-specific enrichment or region-specific depletion in abundance

  8. Supplementary Figure 8: Striatally enriched clusters contain interacting proteins with roles in dopaminergic signalling and drug addiction

  9. Supplementary Figure 9: Clustering all proteins significantly differentially expressed over developmental period reveals proteins enriched shortly after birth (period 8) and proteins more gently increasing or decreasing in abundance over the time-course

  10. Supplementary Figure 10a: RNA vs protein fold-change comparison of all pairs of brain regions

  11. Supplementary Figure 10b: RNA vs protein fold-change comparison of all pairs of brain regions

  12. Supplementary Figure 10c: RNA vs protein fold-change comparison of all pairs of brain regions

  13. Supplementary Figure 10d: RNA vs protein fold-change comparison of all pairs of brain regions

  14. Supplementary Figure 10e: RNA vs protein fold-change comparison of all pairs of brain regions

  15. Supplementary Figure 10f: RNA vs protein fold-change comparison of all pairs of brain regions

  16. Supplementary Figure 10g: RNA vs protein fold-change comparison of all pairs of brain regions

  17. Supplementary Figure 10h: RNA vs protein fold-change comparison of all pairs of brain regions

  18. Supplementary Figure 11: Summary quantifications of all RNA vs protein fold-change scatter plots

  19. Supplementary Figure 12: DFC/V1C comparison in detail

  20. Supplementary Figure 13: Summary quantifications of all fold-change scatter plots for human vs mouse

  21. Supplementary Figure 14a: Human protein vs mouse protein fold-change comparison of all pairs of brain regions

  22. Supplementary Figure 14b: Human protein vs mouse protein fold-change comparison of all pairs of brain regions

  23. Supplementary Figure 14c: Human protein vs mouse protein fold-change comparison of all pairs of brain regions

  24. Supplementary Figure 14d: Human protein vs mouse protein fold-change comparison of all pairs of brain regions

  25. Supplementary Figure 14e: Human protein vs mouse protein fold-change comparison of all pairs of brain regions

  26. Supplementary Figure 15: Un-cropped versions of the immunoblots in Figure S12

Supplementary Information

  1. Supplementary Text and Figures

    Supplementary Figures 1–15 and Supplementary Table 11

  2. Life Sciences Reporting Summary

  3. Supplementary Table 1

    Metadata for all 77 BrainSpan samples subjected to MS/MS for this study.

  4. Supplementary Table 2

    Peptide-level data obtained from heavily fractionated per-region MS/MS.

  5. Supplementary Table 3

    Protein-level summary of the fractionated per-region and single-shot MS/MS.

  6. Supplementary Table 4

    Label-free protein quantification (LFQ) of all single-shot samples.

  7. Supplementary Table 5

    Results of the proteomic spatiotemporal differential expression analysis.

  8. Supplementary Table 6

    Protein and RNA expression data for genes expressed in both datasets.

  9. Supplementary Table 7

    Inter-regional protein and RNA abundance and differential expression summary.

  10. Supplementary Table 8

    Summary of the RNA vs. protein differential consistency of each gene in accordance with the definitions introduced in Fig. 5.

  11. Supplementary Table 9

    Complete ontology and gene-set enrichment analysis results consistent with the definitions introduced in Fig. 5.

  12. Supplementary Table 10

    Inter-regional human and mouse protein abundance summary.

  13. Supplementary Software

    Supplementary Software