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Series GSE45979 Query DataSets for GSE45979
Status Public on Jan 05, 2018
Title A HUS-associated STEC expressing a dicA transcriptional module is related to gene network dysregulation in Caco-2
Platform organisms Homo sapiens; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655
Sample organisms Escherichia coli; Homo sapiens
Experiment type Expression profiling by array
Summary We conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from hemolytic-uremic syndrome patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. Conversely, global gene expression comparison of both strains cultured in conditioned medium revealed a gene set exclusively expressed in EH41, which includes the dicA putative virulence factor regulator. Network analysis showed that this set of genes constitutes an EH41 specific transcriptional module. The GCNs of Caco-2 cells exposed to EH41 or to Ec472/01 presented a major transcriptional module containing many hubs related to inflammatory response that was not found in the GCN of control cells. Moreover, EH41 seems to cause gene network dysregulation in Caco-2. Therefore, EH41 virulence may be derived from its capacity for dysregulating enterocyte genome functioning and its enhanced enteric survival due to slow growth.
 
Overall design [EH41]: Caco-2 transcriptomic profiles after 3 hrs of interaction with STEC strain EH41 and without interaction (control) were compared in order to identify differentially expressed transcripts
[EC472]: Caco-2 transcriptomic profiles after 3 hrs of interaction with STEC strain EC472/01 and without interaction (control) were compared in order to identify differentially expressed transcripts
[COND]: STEC transcriptomic profiles after 3 hrs incubation in conditioned Caco-2 cell medium: STEC strain EH41 (isolated from patient with HUS) and STEc strain EC472/01 (isolated from cattle) were compared in order to identify differentially expressed transcripts
[FRESH]: STEC transcriptomic profiles after 3 hrs incubation in fresh medium: STEC strain EH41 (isolated from patient with HUS) and STEc strain EC472/01 (isolated from cattle) were compared in order to identify differentially expressed transcripts
 
Contributor(s) Bando SY, Iamashita P, Guth BE, dos Santos LF, Fujita A, Abe CM, Ferreira LR, Moreira-Filho CA
Citation(s) 29253906
Submission date Apr 11, 2013
Last update date Jan 23, 2019
Contact name Carlos Alberto Moreira-Filho
E-mail(s) carlos.moreira@hc.fm.usp.br
Phone 55-11-26618606
Organization name Faculdade de Medicina da Universidade de Sao Paulo
Department Departments of Pediatrics
Lab LIM36
Street address Av. Dr. Eneas Carvalho de Aguiar 647
City Sao Paulo
State/province SP
ZIP/Postal code 05403-900
Country Brazil
 
Platforms (2)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
GPL13359 Agilent-020097 E. coli Gene Expression Microarray (Probe Name version)
Samples (32)
GSM1120930 Caco after 3 hrs interaction with STEC EH41, replicate 1 [EH41]
GSM1120931 Caco after 3 hrs interaction with STEC EH41, replicate 2 [EH41]
GSM1120932 Caco after 3 hrs interaction with STEC EH41, replicate 3 [EH41]
Relations
BioProject PRJNA196853

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Supplementary file Size Download File type/resource
GSE45979_RAW.tar 163.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data included within Sample table

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