eQTL in diseased colon tissue identifies novel target genes associated with IBD Article Swipe
Nina C. Nishiyama
,
Sophie Silverstein
,
Kimberly Darlington
,
Meaghan M. Kennedy Ng
,
Katelyn Clough
,
Mikaela J. Bauer
,
Caroline Beasley
,
Akshatha Bharadwaj
,
Rajee Ganesan
,
Muneera R. Kapadia
,
Gwen Lau
,
Grace Lian
,
Reza Rahbar
,
Timothy S. Sadiq
,
Matthew R. Schaner
,
Jonathan Stem
,
Jessica Friton
,
William A. Faubion
,
Shehzad Z. Sheikh
,
Terrence S. Furey
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.10.14.618229
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.10.14.618229
Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14 , and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.
Related Topics
Concepts
Gene
Expression quantitative trait loci
Biology
Computational biology
Genetics
Single-nucleotide polymorphism
Genotype
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.10.14.618229
- OA Status
- green
- References
- 81
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4403506392
All OpenAlex metadata
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https://doi.org/10.1101/2024.10.14.618229Digital Object Identifier
- Title
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eQTL in diseased colon tissue identifies novel target genes associated with IBDWork title
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preprintOpenAlex work type
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enPrimary language
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2024Year of publication
- Publication date
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2024-10-17Full publication date if available
- Authors
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Nina C. Nishiyama, Sophie Silverstein, Kimberly Darlington, Meaghan M. Kennedy Ng, Katelyn Clough, Mikaela J. Bauer, Caroline Beasley, Akshatha Bharadwaj, Rajee Ganesan, Muneera R. Kapadia, Gwen Lau, Grace Lian, Reza Rahbar, Timothy S. Sadiq, Matthew R. Schaner, Jonathan Stem, Jessica Friton, William A. Faubion, Shehzad Z. Sheikh, Terrence S. FureyList of authors in order
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https://doi.org/10.1101/2024.10.14.618229Publisher landing page
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://doi.org/10.1101/2024.10.14.618229Direct OA link when available
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.252 | 40 |
| abstract_inverted_index.300 | 8 |
| abstract_inverted_index.ABO | 91 |
| abstract_inverted_index.IBD | 41, 74, 79 |
| abstract_inverted_index.and | 50, 92, 95, 114, 139, 143 |
| abstract_inverted_index.are | 23 |
| abstract_inverted_index.but | 17 |
| abstract_inverted_index.for | 21, 68, 78, 86, 132 |
| abstract_inverted_index.had | 111 |
| abstract_inverted_index.key | 146 |
| abstract_inverted_index.the | 12, 27, 124 |
| abstract_inverted_index.two | 57 |
| abstract_inverted_index.GWAS | 70, 80 |
| abstract_inverted_index.IBD. | 54, 150 |
| abstract_inverted_index.eQTL | 60, 72, 106, 127 |
| abstract_inverted_index.from | 39 |
| abstract_inverted_index.gene | 48 |
| abstract_inverted_index.have | 5 |
| abstract_inverted_index.loci | 9, 33, 81 |
| abstract_inverted_index.most | 22 |
| abstract_inverted_index.over | 7 |
| abstract_inverted_index.such | 89 |
| abstract_inverted_index.were | 76 |
| abstract_inverted_index.with | 11, 56, 117 |
| abstract_inverted_index.bowel | 14 |
| abstract_inverted_index.colon | 37, 59 |
| abstract_inverted_index.eQTL. | 104 |
| abstract_inverted_index.genes | 20, 67, 88, 99, 147 |
| abstract_inverted_index.loci. | 71 |
| abstract_inverted_index.novel | 84 |
| abstract_inverted_index.these | 122 |
| abstract_inverted_index.trait | 32 |
| abstract_inverted_index.using | 36 |
| abstract_inverted_index.(GWAS) | 4 |
| abstract_inverted_index.(IBD), | 16 |
| abstract_inverted_index.(eQTL) | 34 |
| abstract_inverted_index.causal | 19 |
| abstract_inverted_index.effect | 119 |
| abstract_inverted_index.sizes. | 120 |
| abstract_inverted_index.target | 66, 98 |
| abstract_inverted_index.tissue | 38, 75, 103, 110, 131 |
| abstract_inverted_index.unique | 107 |
| abstract_inverted_index.effects | 46 |
| abstract_inverted_index.genetic | 45, 137 |
| abstract_inverted_index.largest | 28 |
| abstract_inverted_index.non-IBD | 58, 102 |
| abstract_inverted_index.studies | 3, 128 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Combined | 55 |
| abstract_inverted_index.TNFRSF14 | 93 |
| abstract_inverted_index.analysis | 35 |
| abstract_inverted_index.compared | 100 |
| abstract_inverted_index.diseased | 109, 130 |
| abstract_inverted_index.diseases | 15 |
| abstract_inverted_index.distinct | 112 |
| abstract_inverted_index.enriched | 77 |
| abstract_inverted_index.evidence | 85 |
| abstract_inverted_index.involved | 148 |
| abstract_inverted_index.patients | 42 |
| abstract_inverted_index.provided | 83 |
| abstract_inverted_index.putative | 18 |
| abstract_inverted_index.studies, | 61 |
| abstract_inverted_index.unknown. | 24 |
| abstract_inverted_index.Together, | 121 |
| abstract_inverted_index.conducted | 26 |
| abstract_inverted_index.determine | 44 |
| abstract_inverted_index.highlight | 123 |
| abstract_inverted_index.increased | 118 |
| abstract_inverted_index.molecular | 141 |
| abstract_inverted_index.potential | 51, 65 |
| abstract_inverted_index.variants, | 138 |
| abstract_inverted_index.additional | 97 |
| abstract_inverted_index.associated | 10 |
| abstract_inverted_index.expression | 30, 49 |
| abstract_inverted_index.functional | 115, 134 |
| abstract_inverted_index.identified | 6, 63, 96 |
| abstract_inverted_index.importance | 125 |
| abstract_inverted_index.mechanisms | 142 |
| abstract_inverted_index.regulation | 144 |
| abstract_inverted_index.regulatory | 113 |
| abstract_inverted_index.Genome-wide | 1 |
| abstract_inverted_index.association | 2 |
| abstract_inverted_index.elucidating | 140 |
| abstract_inverted_index.consequences | 135 |
| abstract_inverted_index.contribution | 52 |
| abstract_inverted_index.inflammatory | 13 |
| abstract_inverted_index.quantitative | 31 |
| abstract_inverted_index.understanding | 133 |
| abstract_inverted_index.IBD-associated | 87, 105 |
| abstract_inverted_index.characteristics | 116 |
| abstract_inverted_index.disease-focused | 29 |
| abstract_inverted_index.colocalizations, | 82 |
| cited_by_percentile_year | |
| countries_distinct_count | 1 |
| institutions_distinct_count | 20 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.5199999809265137 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.23541766 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |