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Epigenetic and genetic variation in GATA5 is associated with gastric disease risk

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An Erratum to this article was published on 14 July 2016

Abstract

Gastric cancer incidence varies considerably among populations, even those with comparable rates of Helicobacter pylori infection. To test the hypothesis that genetic variation plays a role in gastric disease, we assessed the relationship between genotypes and gastric histopathology in a Colombian study population, using a genotyping array of immune-related single nucleotide polymorphisms (SNPs). Two synonymous SNPs (rs6061243 and rs6587239) were associated with progression of premalignant gastric lesions in a dominant-effects model after correction for multiple comparisons (p = 2.63E−07 and p = 7.97E−07, respectively); effect sizes were β = −0.863 and β = −0.815, respectively, where β is an estimate of effect on histopathology scores, which ranged from 1 (normal) to 5 (dysplasia). In our replication cohort, a second Colombian population, both SNPs were associated with histopathology when additively modeled (β = −0.256, 95 % CI = −0.47, −0.039; and β = −0.239, 95 % CI = −0.45, −0.024), and rs6587239 was significantly associated in a dominant-effects model (β = −0.330, 95 % CI = −0.66, 0.00). Because promoter methylation of GATA5 has previously been associated with gastric cancer, we also tested for the association of methylation status with more advanced histopathology scores in our samples and found a significant relationship (p = 0.001). A multivariate regression model revealed that the effects of both the promoter methylation and the exonic SNPs in GATA5 were independent. A SNP-by-methylation interaction term was also significant. This interaction between GATA5 variants and GATA5 promoter methylation indicates that the association of either factor with gastric disease progression is modified by the other.

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Acknowledgments

We wish to acknowledge Ms. Jacki Sands (Qiagen) for assistance in assay design for Pyrosequencing. This study was supported by the National Center for Advancing Translational Sciences, Grant 5UL1TR000445; and Grant 2P01CA028842 from the National Cancer Institute. This work was supported by Public Health Service award 5T32 GM007347 from the National Institute of General Medical Sciences for the Vanderbilt Medical-Scientist Training Program. SMW, RSS and NK were partially supported by National Institutes of Health Grant 5P20 GM103534.

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    Authors and Affiliations

    1. Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA

      Rafal S. Sobota & Nuri Kodaman

    2. Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA

      Nuri Kodaman & Scott M. Williams

    3. Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA

      Nuri Kodaman & Scott M. Williams

    4. Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, 2215 Garland Avenue, Nashville, TN, 37232, USA

      Robertino Mera, M. Blanca Piazuelo, Alberto G. Delgado, Douglas R. Morgan, Keith T. Wilson, Pelayo Correa & Barbara G. Schneider

    5. Department of Pathology, School of Medicine, Universidad del Valle, Cali, 760043, Colombia

      Luis E. Bravo

    6. Department of Biology, University of Nariño, Pasto, 520002, Colombia

      Alvaro Pazos

    7. Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA

      Jovanny Zabaleta

    8. Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA

      Wael El-Rifai

    9. Department of Veterans Affairs, Veterans Affairs Tennessee Valley Healthcare System and Office of Medical Research, Nashville, TN, USA

      Wael El-Rifai & Keith T. Wilson

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    R. S. Sobota and N. Kodaman contributed equally to this work.

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    Sobota, R.S., Kodaman, N., Mera, R. et al. Epigenetic and genetic variation in GATA5 is associated with gastric disease risk. Hum Genet 135, 895–906 (2016). https://doi.org/10.1007/s00439-016-1687-1

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