Evidence map›Paper›PMID 41573945›Full record

ArticlebioRxiv : the preprint server for biology2026

High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk.

Valeriya Malysheva, Helen Ray-Jones, Nora Lakes, Rachel A Brown, Tareian A Cazares, Owen Clay, David E Ohayon, Pavel Artemov, Joseph A Wayman, Zi F Yang and 25 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

35 authors.

Valeriya MalyshevaMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0002-0919-7845
Helen Ray-JonesMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0002-8884-6865
Nora LakesImmunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0002-8398-9680
Rachel A BrownDepartment of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA.ORCID 0000-0001-5201-1420
Tareian A CazaresImmunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0003-4624-6156
Owen ClayDivision of Human Genetics and Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
David E OhayonDivision of Human Genetics and Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.ORCID 0000-0002-5226-5110
Pavel ArtemovMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0001-6699-6400
Joseph A WaymanDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Zi F YangDivision of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Monica Della RosaMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0002-0626-4598
Carmen PetitjeanMRC Laboratory of Medical Sciences, London W12 0HS, UK.
Clarissa BoothCenter for Genetics and Rare Diseases, Sanford Research, Sioux Falls, SD 57104, USA.
Joseph I J EllawayMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0002-6670-5391
Jenna R BarnesMedical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
Andrew W DangelDepartment of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA.
Ankita SainiDepartment of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA.
William R OrchardMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0001-8329-5577
Xiaoting ChenDivision of Human Genetics and Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.ORCID 0000-0002-3782-3962
Sreeja ParameswaranDivision of Human Genetics and Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
Frances BurdenDepartment of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
Mattia FrontiniDepartment of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.ORCID 0000-0001-8074-6299
Takashi NaganoThe Babraham Institute, Cambridge, CB22 3AT, UK.
Peter FraserThe Babraham Institute, Cambridge, CB22 3AT, UK.
Stefan SchoenfelderThe Babraham Institute, Cambridge, CB22 3AT, UK.ORCID 0000-0002-3200-8133
Matthew T WeirauchImmunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0001-7977-9122
Leah C KottyanImmunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0003-3979-2220
David F SmithDepartment of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0002-0048-4012
Nick PowellDepartment of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK.
Jill M WeimerCenter for Genetics and Rare Diseases, Sanford Research, Sioux Falls, SD 57104, USA.ORCID 0000-0003-2504-4942
Eugene M OltzDepartment of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA.ORCID 0000-0002-2513-7156
Chris WallaceMRC Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge CB2 0SR, UK.ORCID 0000-0001-9755-1703
Emily R MiraldiImmunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0002-0232-3116
Stephen WaggonerImmunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.ORCID 0000-0001-9658-2874
Mikhail SpivakovMRC Laboratory of Medical Sciences, London W12 0HS, UK.ORCID 0000-0002-0383-3943

Funding

TSLP, IL-9-producing mucosal mast cells, and allergic inflammationU19AI070235 · NIAID · CINCINNATI CHILDRENS HOSP MED CTR · PI Gurjit K. Khurana Hershey · 2006 to 2026
$31.3M
Stem Cell/Organoid and Genome Editing CoreP30DK078392 · NIDDK · CINCINNATI CHILDRENS HOSP MED CTR · PI LEE ARMISTEAD DENSON · 2007 to 2026
$24.4M
Research Project 3: Role of Posttranslational Protein Modifications in the Pathogenesis of Ebola Virus DiseaseP01AI150585 · NIAID · UNIVERSITY OF TEXAS MED BR GALVESTON · PI BUKREYEV, ALEXANDER, GARCIA-BLANCO, MARIANO A. · 2021 to 2025
$11.3M
Molecular Epidemiology in Children's Environmental Health Training Program (MECEH)T32ES010957 · NIEHS · UNIVERSITY OF CINCINNATI · PI Kelly J Brunst · 2001 to 2026
$11.1M
HLA GENE COMPLEMENTATION IN PRIMARY SJOGREN'S AND LUPUSR01AI024717 · NIAID · OKLAHOMA MEDICAL RESEARCH FOUNDATION · PI KOTTYAN, LEAH CLAIRE, WEIRAUCH, MATTHEW TYSON · 1987 to 2025
$7.8M
Tissue Repository CoreP30AR070549 · NIAMS · CINCINNATI CHILDRENS HOSP MED CTR · PI Leah Claire Kottyan · 2016 to 2026
$7.7M
Polygenic Risk Scores for Healthier African American FamiliesU01HG011172 · NHGRI · CINCINNATI CHILDRENS HOSP MED CTR · PI Leah Claire Kottyan, LISA J MARTIN · 2020 to 2026
$7.2M
Gene Regulation as a Foundation for Autoimmune Disease PreventionU01AI130830 · NIAID · CINCINNATI CHILDRENS HOSP MED CTR · PI WEIRAUCH, MATTHEW TYSON · 2017 to 2021
$7.2M
BIOCHEMICAL AND GENETIC ANALYSIS OF NOTCH SIGNALINGR01GM055479 · NIGMS · WASHINGTON UNIVERSITY · PI KOPAN, RAPHAEL, WEIRAUCH, MATTHEW TYSON · 1996 to 2021
$6.4M
Dynamic regulatory network models of human response to influenza virusU01AI150748 · NIAID · UNIVERSITY OF CALIFORNIA-IRVINE · PI MARAZZI, IVAN, MIRALDI, EMILY · 2020 to 2024
$5.8M
CIS-REGULATORY CIRCUITS FOR ILC FUNCTION AND PLASTICITYR01AI134035 · NIAID · WASHINGTON UNIVERSITY · PI MARCO COLONNA, Eugene M Oltz · 2018 to 2026
$4.8M
Binding of Epstein Barr Virus EBNA2 Unifies Multiple Sclerosis Genetic MechanismsR01NS099068 · NINDS · CINCINNATI CHILDRENS HOSP MED CTR · PI Leah Claire Kottyan, Matthew Tyson Weirauch · 2017 to 2026
$4.2M
NHGRI NIH HHS R01 HG010730NHGRI NIH HHS U01 HG011172NHLBI NIH HHS K08 HL148551NIAID NIH HHS P01 AI150585NIAID NIH HHS R01 AI024717NIAID NIH HHS R01 AI134035NIAID NIH HHS R01 AI141569NIAID NIH HHS R01 AI148276NIAID NIH HHS R01 AI153442NIAID NIH HHS R21 AI156185NIAID NIH HHS U01 AI130830NIAID NIH HHS U01 AI150748NIAID NIH HHS U19 AI070235NIAMS NIH HHS P30 AR070549NIAMS NIH HHS R01 AR073228NIAMS NIH HHS T32 AR069512NIDDK NIH HHS P30 DK078392NIDDK NIH HHS R01 DK107502NIEHS NIH HHS T32 ES010957NIGMS NIH HHS R01 GM055479NINDS NIH HHS R01 NS099068Wellcome Trust
6 · The paper itself

Abstract

Innate lymphoid cells (ILCs) are rare, tissue-resident innate lymphocytes that functionally mirror CD4+ T helper cell lineages but lack antigen receptors. Type 3 ILCs (ILC3s) are enriched in the gut, airways, and mucosal lymphoid tissues, where they regulate inflammation and promote barrier integrity. To define the regulatory architecture of primary human ILC3s, we map promoter-anchored chromosomal contacts using high-resolution, low-input Promoter Capture Hi-C (PCHi-C) in these cells alongside CD4+ T cells. By combining statistical detection with a PCHi-C-adapted Activity-by-Contact approach, we link promoters to distal regulatory elements, identifying hundreds of ILC3-specific contacts. We use these maps to connect genome-wide association study (GWAS) risk variants for Crohn's disease to target genes using multiCOGS, a Bayesian framework that integrates PCHi-C with summary-statistic imputation and multivariate fine-mapping. This analysis highlights both known and unanticipated candidates, including

Identifiers

PMID41573945
PMCPMC12821085

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Read underepoch 390

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.