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Volume 7, Issue 11

Genome-wide association study of gastric cancer- and duodenal ulcer-derived strains reveals discriminatory genetic variations and novel oncoprotein candidates Open Access

Abstract

Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as , which causes gastric cancer. We conducted a small-sample GWAS (125 gastric cancer cases and 115 controls) followed by prediction of gastric cancer and control (duodenal ulcer) strains. We identified 11 single nucleotide polymorphisms (eight amino acid changes) and three DNA motifs that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into gastric cancer pathogenesis and a basis for identifying a set of biomarkers for distinguishing these -related diseases.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): duodenal ulcer , gastric cancer , GWAS , Helicobacter pylori , population genomics and recombination
Funding
This study was supported by the:
  • ministry of education, culture, sports, science and technology (Award 18KK0266)
    • Principle Award Recipient: YoshioYamaoka
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Erratum

An erratum has been published for this content:
Corrigendum: ‘Genome-wide association study of gastric cancer- and duodenal ulcer-derived strains reveals discriminatory genetic variations and novel oncoprotein candidates’
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2021-11-30
2024-04-18
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References

  1. Falush D, Bowden R. Genome-wide association mapping in bacteria?. Trends Microbiol 2006; 14:353–355 [View Article] [PubMed]
     [Google Scholar]
  2. Jaillard M, Lima L, Tournoud M, Mahe P, van Belkum A et al. A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet 2018; 14:11 [View Article]
     [Google Scholar]
  3. Lees JA, Galardini M, Bentley SD, Weiser JN, Corander J. pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics 2018; 34:4310–4312 [View Article] [PubMed]
     [Google Scholar]
  4. Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci USA 2013; 110:11923–11927 [View Article] [PubMed]
     [Google Scholar]
  5. Yahara K, Meric G, Taylor AJ, de Vries SP, Murray S. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. Environ Microbiol 2017; 19:361–380 [View Article] [PubMed]
     [Google Scholar]
  6. Suzuki M, Shibayama K, Yahara K. A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains. Sci Rep 2016; 6:37811 [View Article] [PubMed]
     [Google Scholar]
  7. Earle SG, C-H W, Charlesworth J, Stoesser N, Gordon NC. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat Microbiol 2016; 1:16041 [View Article] [PubMed]
     [Google Scholar]
  8. Berthenet E, Yahara K, Thorell K, Pascoe B, Meric G et al. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. BMC Biol 2018; 16:84 [View Article] [PubMed]
     [Google Scholar]
  9. Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T et al. Chromosome painting in silico in a bacterial species reveals fine population structure. Mol Biol Evol 2013; 30:1454–1464 [View Article] [PubMed]
     [Google Scholar]
  10. Linz B, Balloux F, Moodley Y, Manica A, Liu H. An African origin for the intimate association between humans and Helicobacter pylori. Nature 2007; 445:915–918 [View Article] [PubMed]
     [Google Scholar]
  11. Takahashi-Kanemitsu A, Knight CT, Hatakeyama M. Molecular anatomy and pathogenic actions of Helicobacter pylori CagA that underpin gastric carcinogenesis. Cell Mol Immunol 2020; 17:50–63 [View Article] [PubMed]
     [Google Scholar]
  12. Breurec S, Guillard B, Hem S, Brisse S, Dieye FB. Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia. PloS one 2011; 6:e22058 [View Article] [PubMed]
     [Google Scholar]
  13. Furuta Y, Yahara K, Hatakeyama M, Kobayashi I. Evolution of cagA oncogene of Helicobacter pylori through recombination. PloS one 2011; 6:e23499 [View Article] [PubMed]
     [Google Scholar]
  14. Hatakeyama M. Structure and function of Helicobacter pylori CagA, the first-identified bacterial protein involved in human cancer. Proc Jpn Acad, Ser B, Phys Biol Sci 2017; 93:196–219 [View Article]
     [Google Scholar]
  15. Yamaoka Y. Mechanisms of disease: Helicobacter pylori virulence factors. Nat Rev Gastroenterol Hepatol 2010; 7:629–641 [View Article]
     [Google Scholar]
  16. Kusters JG, van Vliet AH, Kuipers EJ. Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev 2006; 19:449–490 [View Article] [PubMed]
     [Google Scholar]
  17. Correa P, Haenszel W, Cuello C, Tannenbaum S, Archer M. A model for gastric cancer epidemiology. Lancet 1975; 2:58–60 [View Article] [PubMed]
     [Google Scholar]
  18. Hansson LE, Nyren O, Hsing AW, Bergstrom R, Josefsson S. The risk of stomach cancer in patients with gastric or duodenal ulcer disease. N Engl J Med 1996; 335:242–249 [View Article] [PubMed]
     [Google Scholar]
  19. Uemura N, Okamoto S, Yamamoto S, Matsumura N, Yamaguchi S. Helicobacter pylori infection and the development of gastric cancer. N Engl J Med 2001; 345:784–789 [View Article] [PubMed]
     [Google Scholar]
  20. Lu H, Hsu PI, Graham DY, Yamaoka Y. Duodenal ulcer promoting gene of Helicobacter pylori. Gastroenterology 2005; 128:833–848 [View Article] [PubMed]
     [Google Scholar]
  21. El Khadir M, Alaoui Boukhris S, Benajah DA, El Rhazi K, Ibrahimi SA. VacA and CagA Status as Biomarker of Two Opposite End Outcomes of Helicobacter pylori Infection (Gastric Cancer and Duodenal Ulcer) in a Moroccan Population. PloS one 2017; 12: [View Article] [PubMed]
     [Google Scholar]
  22. Shiota S, Matsunari O, Watada M, Hanada K, Yamaoka Y. Systematic review and meta-analysis: the relationship between the Helicobacter pylori dupA gene and clinical outcomes. Gut Pathog 2010; 2:13 [View Article] [PubMed]
     [Google Scholar]
  23. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  25. Lawson DJ, Hellenthal G, Myers S, Falush D. Inference of population structure using dense haplotype data. PLoS Genet 2012; 8:e1002453 [View Article] [PubMed]
     [Google Scholar]
  26. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
     [Google Scholar]
  27. Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM et al. Phandango: an interactive viewer for bacterial population genomics. bioRxiv [Preprint] 2017 [View Article]
     [Google Scholar]
  28. Kawai M, Furuta Y, Yahara K, Tsuru T, Oshima K. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiol 2011; 11:104 [View Article] [PubMed]
     [Google Scholar]
  29. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PloS one 2010; 5:e11147 [View Article]
     [Google Scholar]
  30. Earle SG, CH W, Charlesworth J, Stoesser N, Gordon NC. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat Microbiol 2016; 1:16041 [View Article] [PubMed]
     [Google Scholar]
  31. Ma KC, Mortimer TD, Hicks AL, Wheeler NE, Sanchez-Buso L. Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae. Nat Commun 2020; 11:4126 [View Article] [PubMed]
     [Google Scholar]
  32. Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biol 2020; 21:180 [View Article] [PubMed]
     [Google Scholar]
  33. Robin X, Turck N, Hainard A, Tiberti N, Lisacek F. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 2011; 12:77 [View Article] [PubMed]
     [Google Scholar]
  34. Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010; 464:250–255 [View Article] [PubMed]
     [Google Scholar]
  35. Li L, Huang D, Cheung MK, Nong W, Huang Q et al. BSRD: a repository for bacterial small regulatory rna. Nucleic Acids Res 2013; 41:238
     [Google Scholar]
  36. Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J et al. Rapid evolution of distinct helicobacter pylori subpopulations in the americas. PLoS Genet 2017; 13:e1006546
     [Google Scholar]
  37. Lees JA, Ferwerda B, Kremer PHC, Wheeler NE, Seron MV. Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis. Nat Commun 2019; 10:2176 [View Article] [PubMed]
     [Google Scholar]
  38. Machuca MA, Johnson KS, Liu YC, Steer DL, Ottemann KM. Helicobacter pylori chemoreceptor TlpC mediates chemotaxis to lactate. Sci Rep 2017; 7:14089 [View Article] [PubMed]
     [Google Scholar]
  39. Keilberg D, Steele N, Fan S, Yang C, Zavros Y et al. Gastric metabolomics detects h. pylori correlated loss of numerous metabolites in both the corpus and antrum. Infect Immun 2020; 89:e00690-20
     [Google Scholar]
  40. Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M et al. Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori. Front Microbiol 2020; 11:1628
     [Google Scholar]
  41. Liu YP, Tang Q, Zhang JZ, Tian LF, Gao P. Structural basis underlying complex assembly and conformational transition of the type I R-M system. Proc Natl Acad Sci USA 2017; 114:11151–11156 [View Article] [PubMed]
     [Google Scholar]
  42. Kelleher JE, Daniel AS, Murray NE. Mutations that confer de novo activity upon a maintenance methyltransferase. J Mol Biol 1991; 221:431–440 [View Article] [PubMed]
     [Google Scholar]
  43. Backert S, Bernegger S, Skorko-Glonek J, Wessler S. Extracellular HtrA serine proteases: An emerging new strategy in bacterial pathogenesis. Cell Microbiol 2018; 20:e12845 [View Article] [PubMed]
     [Google Scholar]
  44. Zurawa-Janicka D, Wenta T, Jarzab M, Skorko-Glonek J, Glaza P. Structural insights into the activation mechanisms of human HtrA serine proteases. Arch Biochem Biophys 2017; 621:6–23 [View Article] [PubMed]
     [Google Scholar]
  45. Wilken C, Kitzing K, Kurzbauer R, Ehrmann M, Clausen T. Crystal structure of the DegS stress sensor: How a PDZ domain recognizes misfolded protein and activates a protease. Cell 2004; 117:483–494 [View Article] [PubMed]
     [Google Scholar]
  46. Lee JH, Jun SH, Baik SC, Kim DR, Park JY. Prediction and screening of nuclear targeting proteins with nuclear localization signals in Helicobacter pylori. J Microbiol Methods 2012; 91:490–496 [View Article] [PubMed]
     [Google Scholar]
  47. Li X, Wang J, Shi Y. Structural mechanisms of DIAP1 auto-inhibition and DIAP1-mediated inhibition of drICE. Nat Commun 2011; 2:408 [View Article] [PubMed]
     [Google Scholar]
  48. Zanotti G, Papinutto E, Dundon W, Battistutta R, Seveso M. Structure of the neutrophil-activating protein from Helicobacter pylori. J Mol Biol 2002; 323:125–130 [View Article] [PubMed]
     [Google Scholar]
  49. Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. DNA Res 2016; 23:135–143 [View Article] [PubMed]
     [Google Scholar]
  50. Waldman T. Emerging themes in cohesin cancer biology. Nat Rev Cancer 2020; 20:504–515 [View Article] [PubMed]
     [Google Scholar]
  51. Cheng H, Zhang N, Pati D. Cohesin subunit RAD21: From biology to disease. Gene 2020; 758:144966 [View Article] [PubMed]
     [Google Scholar]
  52. Bischler T, Tan HS, Nieselt K, Sharma CM. Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori. Methods 2015; 86:89–101 [View Article] [PubMed]
     [Google Scholar]
  53. Stingl K, Brandt S, Uhlemann EM, Schmid R, Altendorf K. Channel-mediated potassium uptake in Helicobacter pylori is essential for gastric colonization. EMBO J 2007; 26:232–241 [View Article] [PubMed]
     [Google Scholar]
  54. Mechold U, Potrykus K, Murphy H, Murakami KS, Cashel M. Differential regulation by ppGpp versus pppGpp in Escherichia coli. Nucleic Acids Res 2013; 41:6175–6189 [View Article] [PubMed]
     [Google Scholar]
  55. Hauryliuk V, Atkinson GC, Murakami KS, Tenson T, Gerdes K. Recent functional insights into the role of (p)ppGpp in bacterial physiology. Nat Rev Microbiol 2015; 13:298–309 [View Article] [PubMed]
     [Google Scholar]
  56. Yamamoto K, Yamanaka Y, Shimada T, Sarkar P, Yoshida M. Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome. mSystems 2018; 3: [View Article] [PubMed]
     [Google Scholar]
  57. Winkler W, Nahvi A, Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002; 419:952–956 [View Article] [PubMed]
     [Google Scholar]
  58. Rodionov DA, Arzamasov AA, Khoroshkin MS, Iablokov SN, Leyn SA et al. Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome. Front Microbiol 2019; 10:1316 [View Article]
     [Google Scholar]
  59. Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR. Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet 2014; 10:e1004547 [View Article] [PubMed]
     [Google Scholar]
  60. San JE, Baichoo S, Kanzi A, Moosa Y, Lessells R. Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls. Front Microbiol 2019; 10:3119 [View Article] [PubMed]
     [Google Scholar]
  61. Kim N, Weeks DL, Shin JM, Scott DR, Young MK. Proteins released by Helicobacter pylori in vitro. J Bacteriol 2002; 184:6155–6162 [View Article] [PubMed]
     [Google Scholar]
  62. Kaakoush NO, Kovach Z, Mendz GL. Potential role of thiol:disulfide oxidoreductases in the pathogenesis of Helicobacter pylori. FEMS Immunol Med Microbiol 2007; 50:177–183 [View Article] [PubMed]
     [Google Scholar]
  63. Lester J, Kichler S, Oickle B, Fairweather S, Oberc A. Characterization of Helicobacter pylori HP0231 (DsbK): role in disulfide bond formation, redox homeostasis and production of Helicobacter cystein-rich protein HcpE. Mol Microbiol 2015; 96:110–133 [View Article] [PubMed]
     [Google Scholar]
  64. Hudak L, Jaraisy A, Haj S, Muhsen K. An updated systematic review and meta-analysis on the association between Helicobacter pylori infection and iron deficiency anemia. Helicobacter 2017; 22:e12330 [View Article] [PubMed]
     [Google Scholar]
  65. Torti SV, Manz DH, Paul BT, Blanchette-Farra N, Torti FM. Iron and Cancer. Annu Rev Nutr 2018; 38:97–125 [View Article] [PubMed]
     [Google Scholar]
  66. Beckett AC, Loh JT, Chopra A, Leary S, Lin AS. Helicobacter pylori genetic diversification in the Mongolian gerbil model. PeerJ 2018; 6:e4803 [View Article] [PubMed]
     [Google Scholar]
  67. Heitzmann D, Warth R. Physiology and pathophysiology of potassium channels in gastrointestinal epithelia. Physiol Rev 2008; 88:1119–1182 [View Article] [PubMed]
     [Google Scholar]
  68. King CR, Zhang A, Tessier TM, Gameiro SF, Mymryk JS. Hacking the Cell: Network Intrusion and Exploitation by Adenovirus E1A. mBio 2018; 9: [View Article] [PubMed]
     [Google Scholar]
  69. Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ et al. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet 2018; 14: [View Article] [PubMed]
     [Google Scholar]
  70. Lebeuf-Taylor E, McCloskey N, Bailey SF, Hinz A, Kassen R. The distribution of fitness effects among synonymous mutations in a gene under directional selection. Elife 2019; 8: [View Article] [PubMed]
     [Google Scholar]
  71. Zwart MP, Schenk MF, Hwang S, Koopmanschap B, de Lange N et al. Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase. Heredity (Edinb) 2018; 121:406–421 [View Article] [PubMed]
     [Google Scholar]
  72. Olbermann P, Josenhans C, Moodley Y, Uhr M, Stamer C. A global overview of the genetic and functional diversity in the Helicobacter pylori cag pathogenicity island. PLoS Genet 2010; 6: [View Article] [PubMed]
     [Google Scholar]
  73. Zhang Y, Zhao F, Kong M, Wang S, Nan L et al. Validation of a high-throughput multiplex genetic detection system for helicobacter pylori identification, quantification, virulence, and resistance analysis. Front Microbiol 2016; 7:1401
     [Google Scholar]
  74. Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res 2009; 37:762–770 [View Article] [PubMed]
     [Google Scholar]
  75. Sohn J, Grant RA, Sauer RT. Allostery is an intrinsic property of the protease domain of DegS: implications for enzyme function and evolution. J Biol Chem 2010; 285:34039–34047 [View Article] [PubMed]
     [Google Scholar]
  76. Tsuruta O, Yokoyama H, Fujii S. A new crystal lattice structure of Helicobacter pylori neutrophil-activating protein (HP-NAP. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:134–140 [View Article] [PubMed]
     [Google Scholar]
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Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates
M Gen 7, 000680 (2021); https://doi.org/10.1099/mgen.0.000680
/content/journal/mgen/10.1099/mgen.0.000680
/content/journal/mgen/10.1099/mgen.0.000680
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