Gastroenterology

Gastroenterology

Volume 151, Issue 4, October 2016, Pages 710-723.e2
Gastroenterology

Original Research
Full Report: Basic and Translational—Alimentary Tract
A Frameshift in CSF2RB Predominant Among Ashkenazi Jews Increases Risk for Crohn's Disease and Reduces Monocyte Signaling via GM-CSF

https://doi.org/10.1053/j.gastro.2016.06.045Get rights and content

Background & Aims

Crohn’s disease (CD) has the highest prevalence in Ashkenazi Jewish populations. We sought to identify rare, CD-associated frameshift variants of high functional and statistical effects.

Methods

We performed exome sequencing and array-based genotype analyses of 1477 Ashkenazi Jewish individuals with CD and 2614 Ashkenazi Jewish individuals without CD (controls). To validate our findings, we performed genotype analyses of an additional 1515 CD cases and 7052 controls for frameshift mutations in the colony-stimulating factor 2–receptor β common subunit gene (CSF2RB). Intestinal tissues and blood samples were collected from patients with CD; lamina propria leukocytes were isolated and expression of CSF2RB and granulocyte-macrophage colony–stimulating factor–responsive cells were defined by adenomatous polyposis coli (APC) time-of-flight mass cytometry (CyTOF analysis). Variants of CSF2RB were transfected into HEK293 cells and the expression and functions of gene products were compared.

Results

In the discovery cohort, we associated CD with a frameshift mutation in CSF2RB (P = 8.52 × 10-4); the finding was validated in the replication cohort (combined P = 3.42 × 10-6). Incubation of intestinal lamina propria leukocytes with granulocyte-macrophage colony–stimulating factor resulted in high levels of phosphorylation of signal transducer and activator of transcription (STAT5) and lesser increases in phosphorylation of extracellular signal–regulated kinase and AK straining transforming (AKT). Cells co-transfected with full-length and mutant forms of CSF2RB had reduced pSTAT5 after stimulation with granulocyte-macrophage colony–stimulating factor, compared with cells transfected with control CSF2RB, indicating a dominant-negative effect of the mutant gene. Monocytes from patients with CD who were heterozygous for the frameshift mutation (6% of CD cases analyzed) had reduced responses to granulocyte-macrophage colony–stimulating factor and markedly decreased activity of aldehyde dehydrogenase; activity of this enzyme has been associated with immune tolerance.

Conclusions

In a genetic analysis of Ashkenazi Jewish individuals, we associated CD with a frameshift mutation in CSF2RB. Intestinal monocytes from carriers of this mutation had reduced responses to granulocyte-macrophage colony–stimulating factor, providing an additional mechanism for alterations to the innate immune response in individuals with CD.

Section snippets

Human Subjects

Written informed consent for genetic analyses was obtained from all subjects through the respective Institutional Review Boards from the contributing institutions (Supplementary Table 1). Resected terminal ileal tissues and blood samples from Crohn’s patients were obtained after written informed consent under the guidelines of the Human Investigations Committee (Institutional Review Board) of the Icahn School of Medicine at Mount Sinai. IBD patients had diagnoses confirmed at each recruiting

Exome Sequencing and Association Studies

Exome sequencing detected a total of 371 frameshift mutations in 47 CD patients and 3 controls with full AJ ancestry.19 Of these, 224 mutations passed the Illumina design filters for custom content and were added to the HumanExome beadchip. Using this array, we performed association analyses in 1477 unrelated CD cases and 2614 independent healthy controls passing quality filters with full AJ ancestry genetically validated using PCA (discovery cohort). Sequencing 94 independent chromosomes would

Conclusions

In this study, we surveyed the role of uncommon frameshift mutations in Ashkenazi Jewish CD. For most common variants reported in GWAS, the genetic architecture among Ashkenazim is similar to non-Jewish European ancestry populations, with similar directions of risk alleles observed for the large majority of loci.19 Rare variant analyses focused on Jewish populations may be particularly fruitful because of the higher CD prevalence and unique population history of the Ashkenazim. Although the

Acknowledgments

The authors thank the patients who participated in this study and the staff that assisted in their recruitment. The authors appreciate the sample contribution of The Charles Bronfman Institute for Personalized Medicine’s Biobank at Mount Sinai. The Flow Cytometry CORE at the Icahn School of Medicine at Mount Sinai provided training, consultation, and technical assistance for CyTOF and flow cytometry. Microscopy was performed at the Microscopy CORE at the Icahn School of Medicine at Mount Sinai.

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    Conflicts of interest The authors disclose no conflicts.

    Funding Supported by the National Institutes of Health (DK092235), Inflammatory Bowel Disease Genetics Consortium (DK062429), Genetic Research Center at the Icahn School of Medicine (DK062422), New York Crohn’s Foundation, Consortium ancillary RO1 (DK099097) and U01 (DK062431), Inflammatory Bowel Disease Genetic Research Chair, RO1 (DK062420) and RO1 (CA141743), the Atran Foundation, and the Sanford J. Grossman Charitable Trust. Researchers at University College of London were funded by the Wellcome Trust, Charles Wolfson Charitable Trust, and the Irwin Joffe Memorial Fellowship. Inflammatory bowel disease Research at Cedars-Sinai is supported by U.S. Public Health Service grant PO1 (DK046763) and the Cedars-Sinai F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute Research Funds. Project investigators are supported by The Helmsley Charitable Trust (D.P.B.M.), The European Union (D.P.B.M.), The Crohn's and Colitis Foundation of America (D.P.B.M.), The Joshua L. and Lisa Z. Greer Chair in Inflammatory Bowel Disease Genetics (D.P.B.M.), and grants DK062413, DK046763-19, AI067068, and HS021747 (D.P.B.M.).

    Author names in bold designate shared co-first authorship.

    Authors share co-first authorship.

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