Evidence map›Paper›PMID 34301333›Full record

ArticleHuman genomics2021

Altered splicing associated with the pathology of inflammatory bowel disease.

Kiera Berger, Hari Somineni, Jarod Prince, Subra Kugathasan, Greg Gibson

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Human genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.6field-weighted citation impact, top 33% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Review
  3. Review
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 2 institutions in 1 country.

Kiera BergerSchool of Biological Sciences and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA.ORCID 0000-0002-3995-7892
Hari SomineniDepartment of Pediatrics, Emory University, Atlanta, GA, 30322, USA.
Jarod PrinceDepartment of Pediatrics, Emory University, Atlanta, GA, 30322, USA.
Subra KugathasanDepartment of Pediatrics, Emory University, Atlanta, GA, 30322, USA.
Greg GibsonSchool of Biological Sciences and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, 30332, USA. greg.gibson@biology.gatech.edu.
Emory University · USGeorgia Institute of Technology · US

Funding

Gene discoveries in subjects with Crohn's disease of African descentR01DK087694 · NIDDK · EMORY UNIVERSITY · PI KUGATHASAN, SUBRA · 2011 to 2023
$10.3M
New computational, transcriptional, and genome editing approaches to the biology of inflammatory bowel diseaseR01DK119991 · NIDDK · GEORGIA INSTITUTE OF TECHNOLOGY · PI GIBSON, GREGORY C · 2018 to 2021
$692k
NIDDK NIH HHS R01 DK087694NIDDK NIH HHS R01 DK119991
6 · The paper itself

Abstract

backgroundAberrant splicing of individual genes is a well-known mechanism promoting pathology for a wide range of conditions, but disease is less commonly attributed to global disruption of exon usage. To explore the possible association of aberrant splicing with inflammatory bowel disease, we developed a pipeline for quantifying transcript abundance and exon inclusion transcriptome-wide and applied it to a dataset of ileal and rectal biopsies, both obtained in duplicate from 34 pediatric or young adult cases of ulcerative colitis and Crohn's disease.

resultsExpression and splicing covary to some extent, and eight individuals exhibited aberrant profiles that can be explained by altered ratios of epithelial to stromal and immune cells. Ancestry-related biases in alternative splicing accounting for 5% of the variance were also observed, in part also related to cell-type proportions. In addition, two individuals were identified who had 284 exons with significantly divergent percent spliced in exons, including in the established IBD risk gene CEACAM1, which caused their ileal samples to resemble the rectum.

conclusionsThese results imply that quantitative differences in splice usage contribute to the pathology of inflammatory bowel disease in a previously unrecognized manner.

Indexed as

AdolescentAdultAlternative SplicingAntigens, CDCell Adhesion MoleculesChildColitis, UlcerativeCrohn DiseaseExonsFemaleGene Expression RegulationHumansInflammatory Bowel DiseasesMaleRNA SplicingTranscriptomeAntigens, CDCD66 antigensCell Adhesion MoleculesGene expressionInflammatory bowel diseasePercent spliced inRNA-seqSplicing

Identifiers

PMID34301333
PMCPMC8305504
OpenAlexW3185228885

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.