TAGC Meeting 2016

This presentation describes published pQTL data from the liver and compares it to *new* pQTL data from the kidney. Note: Conclusions about the tissue comparison are preliminary.

Transcript

1. The effects of natural genetic variation
   on transcript and protein abundance.
   Steve Munger
   The Jackson Laboratory
   Free your slides! https://speakerdeck.com/stevemunger
   Twitter: @stevemunger
   

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2. How does genetic variation impact
   transcript and protein abundance?
   DNA RNA Protein
   DNA RNA Protein
   Transcrip)on Transla)on
   DNA RNA Protein
   Francis Crick 1956
   

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3. Diversity Outbred (DO) mice:
   A designed discovery population.
   -  45M+ SNPS
   -  2M+ indels
   -  Balanced popula)on
   structure
   -  Each individual unique
   -  400+ recombina)ons
   in each animal
   - High heterozygosity
   

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4. 192 DO Mice
   Transcripts
   Short Reads
   RNA-Seq
   eQTL pQTL
   eQTL Mapping pQTL Mapping
   Proteins
   Peptides
   MS/MS
   Compare
   ?
   Munger et al. 2014 Chick*, Munger* et al. Nature, 2016
   How does genetic variation influence transcript
   and protein abundance in the liver and kidney?
   Compare kidney to liver
   

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5. Genetic variation affects protein abundance.
   Liver Kidney
   

   View Slide

6. Liver
   Protein Location
   pQTL Location
   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 1819 X
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   Transcriptional mechanisms underlie most local pQTL.
   Half of local pQTL affect both liver and kidney.
   QTL RNA Protein
   cis cis
   Kidney
   

   View Slide

7. Example: DHTKD1– Cis pQTL liver, Cis pQTL kidney
   Liver
   Kidney
   

   View Slide

8. Genetic variant(s) with conserved effects in liver & kidney.
   Founder strain coefficients
   at peak QTL SNP
   r = 0.99
   

   View Slide

9. Example: LDHA – Cis pQTL liver, Cis pQTL kidney
   Kidney
   Liver
   

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10. Local variant(s) cause opposite tissue effects on LDHA expression.
    r = -0.88
    

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11. Example: MESDC2 – Cis pQTL liver, No pQTL kidney
    Liver
    Kidney
    

    View Slide

12. No cis pQTL in kidney, but …
    Kidney founder coefficients
    match what we see in the liver.
    Effects are subtle, but there.
    r = 0.93
    

    View Slide

13. Distant pQTL are abundant.
    Liver Kidney
    

    View Slide

14. Post-transcriptional mechanisms underlie
    nearly all distant pQTL.
    Protein Location
    pQTL Location
    1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 1819 X
    1
    2
    3
    4
    5
    6
    7
    8
    9
    10
    11
    12
    13
    14
    15
    16
    17
    18
    19
    X
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    Liver Kidney
    cis
    RNA Protein
    QTL
    trans
    

    View Slide

15. Post-transcriptional mechanisms underlie distant pQTL.
    Almost no overlap between liver and kidney.
    RNA Protein
    QTL
    trans
    Liver Kidney
    

    View Slide

16. Searching for protein and transcript mediators
    of distant pQTL –> Mediation Analysis
    RNA Protein
    QTL
    trans
    cis
    RNA Protein
    Target
    Causal Intermediates
    RNA Protein
    trans
    QTL
    cis
    Target
    Target Protein ~ pQTLdistant
    Target Protein ~ pQTLdistant
    + MediatorProtein
    x 8000 proteins
    Target Protein ~ pQTLdistant
    + MediatorRNA
    x 21000 Transcripts
    X
    

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17. Mediation analysis reveals causal intermediates.
    pQTLD
    Tmem68 TMEM68
    trans
    13
    Target
    3 cis
    

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18. Tmem68 TMEM68
    trans
    13
    cis
    Target
    3 cis
    cis
    Nnt NNT
    Mediation analysis reveals causal intermediates.
    

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19. “Pulling the (genetic) weeds” to identify
    mediators of subthreshold pQTL.
    PRODH2
    “Weeds”
    Step 1: Condi)on out the giant cis effect.
    

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20. Mediation analysis to identify subtle genetic interactions
    Step 2: Mediate all subthreshold peaks LOD > 5.
    Aka “Pull the weeds”.
    Step 3: Repeat process for all 8k proteins.
    Step 4: Find proteins that share same
    subthreshold peak and mediator
    

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21. Lpgat1
    Dync1h1
    Actr1a
    Nup210
    Arl6ip5
    Dync1li2
    Prodh2
    Wbscr16
    Etfa
    Ywhah
    Rock2
    Ctsf
    Mcm2
    Myo9b
    Ehd4
    Mcm5
    Frmd8
    Mrps18c
    Maoa
    Ttll12
    Actr1b
    Apba3
    Lrrc59
    Cdc34
    Uaca
    Ptcd2
    Dctn1
    Tmem63a
    Nfkb2
    Plcb3
    Ap3b1
    Rnf135
    Ccdc6
    Trap1
    Yars2
    Ggct
    Mtpap
    Dctn3
    Diap1
    Etnppl
    Cps1
    Usp40
    Aass
    Etfb
    Dctn2
    Rbm25
    Ptk2b
    Mme
    Mkl2
    Ube2l3
    Actr10
    Ccdc91
    Ebna1bp2
    Cecr5
    Tgfbrap1
    Dync1i2
    Lyrm4
    Dctn4
    Klc4
    Sin3a
    Psmg1
    Cpsf7
    Clpp
    Slco2a1
    Mapkapk2
    Dync1li1
    Smu1
    Naga
    Scpep1
    Step 5: Look for enriched annota)ons among list.
    Dynein complex, mitochondria, amine catabolism.
    

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22. Natural gene)c perturba)ons +
    Media)on analysis = Predic)ve
    Protein Network
    Cytoscape Visualiza)on
    

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23. Conclusions
    •  Transcriptional mechanisms are responsible for most local
    pQTL, but…
    –  Most local variants that affect transcript levels do not
    affect protein levels.
    •  Post-transcriptional mechanisms underlie all but a few of
    distant pQTL.
    –  Very few distant pQTL shared by liver and kidney.
    •  Mediation analysis can identify protein intermediates that
    confer significant or subtle effects on protein abundance.
    •  Tissue-specific local e/pQTL drive tissue-specific distant
    pQTL.
    

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24. Acknowledgments
    

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25. View Slide

26. Slides can be downloaded at https://speakerdeck.com/stevemunger
    Lab website: mungerlab.com
    Twitter: @stevemunger
    

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