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de Klein N, Tsai EA, Vochteloo M, Baird D, Huang Y, Chen CY, van Dam S, Oelen R, Deelen P, Bakker OB, El Garwany O, Ouyang Z, Marshall EE, Zavodszky MI, van Rheenen W, Bakker MK, Veldink J, Gaunt TR, Runz H, Franke L, Westra HJ. Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases. Nat Genet 2023; 55:377-388. [PMID: 36823318 PMCID: PMC10011140 DOI: 10.1038/s41588-023-01300-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/17/2023] [Indexed: 02/25/2023]
Abstract
Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis- and trans-expression quantitative trait locus (eQTL) meta-analyses in multiple brain region- and ancestry-specific datasets (n ≤ 2,759). Many of the 16,169 cortex cis-eQTLs were tissue-dependent when compared with blood cis-eQTLs. We inferred brain cell types for 3,549 cis-eQTLs by interaction analysis. We prioritized 186 cis-eQTLs for 31 brain-related traits using Mendelian randomization and co-localization including 40 cis-eQTLs with an inferred cell type, such as a neuron-specific cis-eQTL (CYP24A1) for multiple sclerosis. We further describe 737 trans-eQTLs for 526 unique variants and 108 unique genes. We used brain-specific gene-co-regulation networks to link GWAS loci and prioritize additional genes for five central nervous system diseases. This study represents a valuable resource for post-GWAS research on central nervous system diseases.
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Affiliation(s)
- Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Ellen A Tsai
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Martijn Vochteloo
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Denis Baird
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Yunfeng Huang
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Sipko van Dam
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Ancora Health, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Groningen, The Netherlands
| | - Olivier B Bakker
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | - Omar El Garwany
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Wellcome Sanger Institute, Hinxton, UK
| | | | - Eric E Marshall
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Maria I Zavodszky
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jan Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Heiko Runz
- Translational Biology, Research and Development, Biogen Inc., Cambridge, MA, USA.
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Groningen, The Netherlands.
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Abstract
We describe a Fourier transform spectroscopy technique for directly measuring band structures, and apply it to a spin-1 spin-orbit coupled Bose-Einstein condensate. In our technique, we suddenly change the Hamiltonian of the system by adding a spin-orbit coupling interaction and measure populations in different spin states during the subsequent unitary evolution. We then reconstruct the spin and momentum resolved spectrum from the peak frequencies of the Fourier transformed populations. In addition, by periodically modulating the Hamiltonian, we tune the spin-orbit coupling strength and use our spectroscopy technique to probe the resulting dispersion relation. The frequency resolution of our method is limited only by the coherent evolution timescale of the Hamiltonian and can otherwise be applied to any system, for example, to measure the band structure of atoms in optical lattice potentials.
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Affiliation(s)
| | | | | | - IB Spielman
- Author to whom any correspondence should be addressed.
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Jackels SC, Marshall EE, Omaiye AG, Gianan RL, Lee FT, Jackels CF. GCMS investigation of volatile compounds in green coffee affected by potato taste defect and the Antestia bug. J Agric Food Chem 2014; 62:10222-10229. [PMID: 25284290 DOI: 10.1021/jf5034416] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Potato taste defect (PTD) is a flavor defect in East African coffee associated with Antestiopsis orbitalis feeding and 3-isopropyl-2-methoxypyrazine (IPMP) in the coffee. To elucidate the manifestation of PTD, surface and interior volatile compounds of PTD and non-PTD green coffees were sampled by headspace solid phase microextraction and analyzed by gas chromatography mass spectrometry. Principal component analysis of the chromatographic data revealed a profile of surface volatiles distinguishing PTD from non-PTD coffees dominated by tridecane, dodecane, and tetradecane. While not detected in surface volatiles, IPMP was found in interior volatiles of PTD coffee. Desiccated antestia bugs were analyzed by GCMS, revealing that the three most prevalent volatiles were tridecane, dodecane, and tetradecane, as was found in the surface profile PTD coffee. Coffee having visible insect damage exhibited both a PTD surface volatile profile and IPMP in interior volatiles, supporting the hypothesis linking antestia bug feeding activity with PTD profile compounds on the surface and IPMP in the interior of the beans.
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Affiliation(s)
- Susan C Jackels
- Chemistry Department, Seattle University , 901 12th Avenue, Seattle, Washington 98122-1090, United States
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