title: Helicobacter pylori CagA protein polymorphisms and their lack of association with pathogenesis.
abstract: OBJECTIVE
  To investigate Helicobacter pylori (H. pylori) CagA diversity and to evaluate the association between protein polymorphisms and the occurrence of gastric pathologies.
  
  
  METHODS
  One hundred and twenty-two clinical isolates of H. pylori cultured from gastric biopsies obtained from Colombian patients with dyspepsia were included as study material. DNA extracted from isolates was used to determine cagA status, amplifying the C-terminal cagA gene region by polymerase chain reaction. One hundred and six strains with a single amplicon were sequenced and results were used to characterize the 3' variable region of the cagA gene. To establish the number and type of tyrosine phosphorylation motifs Glutamine acid-Proline-Isoleucine-Tyrosine-Alanine (EPIYA) bioinformatic analysis using Amino Acid Sequence Analyzer-Amino Acid Sequence Analyzer software was conducted. Analysis of the association between the number of EPIYA motifs and the gastric pathology was performed using chi(2) test and analysis of the presence of EPIYA-C motifs in relation to the pathology was made by logistic regression odds ratios. Comparisons among EPIYA types found and those reported in GenBank were performed using a proportion test in Statistix Analytical Software version 8.0.
  
  
  RESULTS
  After amplification of the 3' of the cagA gene, 106 from 122 isolates presented a single amplicon and 16 showed multiple amplicons. As expected, diversity in the size of the cagA unique fragments among isolates was observed. The 106 strains that presented a single amplicon after 3' cagA amplification came from patients with gastritis (19 patients), atrophic gastritis (21), intestinal metaplasia (26), duodenal ulcer (22) and gastric cancer. DNA sequence analysis showed that the differences in size of 3' cagA unique fragments was attributable to the number of EPIYA motifs: 1.9% had two EPIYA motifs, 62.3% had three, 33.0% had four and 2.8% had five motifs. The majority of tested clinical strains (62.3%) were found to harbor the ABC combination of EPIYA motifs and a significant statistical difference was observed between the frequencies of ABCC tyrosine phosphorylation motifs and Western strains sequences deposited in GenBank.
  
  
  CONCLUSIONS
  The present report describes a lack of association between H. pylori CagA-protein polymorphisms and pathogenesis. ABCC high frequency variations compared with Western-strains sequences deposited in GenBank require more investigation.
authors: Molecular Diagnostics and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 # 18A-10, Bogotá, Colombia.
authors: Nicole
authors: N
authors: Acosta
authors: Andrés
authors: A
authors: Quiroga
authors: Pilar
authors: P
authors: Delgado
authors: María-Mercedes
authors: MM
authors: Bravo
authors: Carlos
authors: C
authors: Jaramillo
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000942:Antigens, Bacterial / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D001706:Biopsy; D016009:Chi-Square Distribution; D003105:Colombia; D004381:Duodenal Ulcer / Q000382:microbiology; D005756:Gastritis / Q000382:microbiology; D005757:Gastritis, Atrophic / Q000382:microbiology; D005767:Gastrointestinal Diseases / Q000382:microbiology* / Q000473:pathology; D016481:Helicobacter Infections / Q000382:microbiology* / Q000473:pathology; D016480:Helicobacter pylori / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D006801:Humans; D016015:Logistic Models; D008679:Metaplasia; D008969:Molecular Sequence Data; D016017:Odds Ratio; D011110:Polymorphism, Genetic; D018570:Risk Assessment; D012307:Risk Factors; D012720:Severity of Illness Index; D013270:Stomach / Q000382:microbiology* / Q000473:pathology; D013274:Stomach Neoplasms / Q000382:microbiology
chemical_list: D000942:Antigens, Bacterial; D001426:Bacterial Proteins; C080866:cagA protein, Helicobacter pylori