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Series GSE2596 Query DataSets for GSE2596
Status Public on Oct 24, 2005
Title Heart transplant biopsies
Organism Homo sapiens
Experiment type Expression profiling by array
Summary MOLECULAR PROFILING IMPROVES DIAGNOSES OF REJECTION AND INFECTION IN TRANSPLANTED ORGANS.
The monitoring of transplanted hearts is currently based on histological evaluation of endomyocardial biopsies, a method that is fairly insensitive and that does not always accurately discriminate between rejection and infection in the heart. Accurate diagnosis of rejection and infection is absolutely crucial, however, as the respective treatments are completely different.
Using microarrays we analyzed gene expression in 76 cardiac biopsies from 40 heart recipients undergoing rejection, no rejection, or T. cruzi infection. We found a set of 98 genes whose expression patterns were typical of acute rejection, and 87 genes that discriminated between rejection and T. cruzi infection. These sets revealed acute rejection episodes up to two weeks earlier, and trypanosome infection up to two months earlier than did histological evaluation. When applied to raw data from other institutions, the two sets of predictive genes were also able to accurately pinpoint acute rejection of lung and kidney transplants, as well as bacterial infections in kidneys. In addition to their usefulness as diagnostic tools, the data suggest that there are similarities in the biology of the processes involved in rejection of different grafts and also in the tissue responses to pathogens as diverse as bacteria and protozoa.

pre-rejection:
GSM47949, GSM48048, GSM49625

non-rejection:
GSM47957, GSM48045, GSM48049, GSM48057, GSM48072, GSM48089, GSM48092, GSM49624, GSM49654, GSM49656, GSM49657, GSM49658, GSM49661, GSM49666, GSM49748, GSM49750, GSM49751, GSM49752, GSM49754, GSM49756, GSM49757, GSM49758, GSM49762, GSM49765, GSM49766, GSM49767, GSM49769, GSM49771, GSM49773, GSM49774, GSM49781, GSM49782, GSM49783, GSM49784

acute rejection:
GSM48040, GSM48043, GSM48046, GSM48047, GSM48050, GSM48053, GSM48056, GSM49655, GSM49747, GSM49749, GSM49755, GSM49759, GSM49761, GSM49763, GSM49764, GSM49780

pre-Chagas disease reactivation:
GSM48089, GSM49756, GSM49757, GSM49758, GSM49767, GSM49769, GSM49771

Chagas disease reactivation:
GSM49753, GSM49760, GSM49768, GSM49772, GSM49775, GSM49776, GSM49777, GSM49778

Toxoplasma myocarditis:
GSM48058

first subset ("summer"):
GSM47949, GSM47957, GSM48040, GSM48043, GSM48045, GSM48046, GSM48047, GSM48048, GSM48049, GSM48050, GSM48053, GSM48056, GSM48057, GSM48058, GSM48072, GSM48089, GSM48092, GSM49624, GSM49625, GSM49654, GSM49655, GSM49656, GSM49657, GSM49658, GSM49661, GSM49666, GSM49747, GSM49748, GSM49749, GSM49750, GSM49751, GSM49752

second subset ("winter"):
GSM49753, GSM49754, GSM49755, GSM49756, GSM49757, GSM49758, GSM49759, GSM49760, GSM49761, GSM49762, GSM49763, GSM49764, GSM49765, GSM49766, GSM49767, GSM49768, GSM49769, GSM49770, GSM49771, GSM49772, GSM49773, GSM49774, GSM49775, GSM49776, GSM49777, GSM49778, GSM49780, GSM49781, GSM49782, GSM49783, GSM49784
Keywords = cardiac transplant
Keywords = acute rejection
Keywords = infection
Keywords: repeat sample
 
Overall design This is a series that includes training and first test set of samples. Number of biological samples: 52. Eleven samples were done in replicates as identified below.
RNA was isolated from endomyocardial biopsies, amplified and labeled with Cy3. Reference RNA was labeled with Cy5.
 
Contributor(s) Morgun A, Shulzhenko N, Perez-Diez A, Diniz RV, Sanson GF, Almeida DR, Matzinger P, Gerbase-DeLima M
Citation(s) 16794196
Submission date Apr 28, 2005
Last update date Jan 18, 2013
Contact name Natalia Shulzhenko
E-mail(s) anemorgun@hotmail.com, shulzhenkon@niaid.nih.gov
Phone 1 301 4355817
Fax 1 301 4964286
Organization name NIH
Department NIAID
Lab Ghost Lab, LCMI
Street address 9000 Rockville Pike, Building 4, room 111
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL1053 NIAID - Hsab
Samples (63)
GSM47949 28 (pre-R) Hsab-03-28
GSM47957 22 (N) Hsab-03-30
GSM48040 14 (R) Hsab-03-31
Relations
BioProject PRJNA92007

Clinical Data header descriptions
GEO Accession
GEO Title
aRNA
replicate array
Patient&sample ID (letter=patient ID, number=days after Tx):
Sex:
Basic disease:
Days after Tx:
Histology:
Clinical history notes:
Final Clinical diagnosis (R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas):

Data table
GEO Accession GEO Title aRNA replicate array Patient&sample ID (letter=patient ID, number=days after Tx): Sex: Basic disease: Days after Tx: Histology: Clinical history notes: Final Clinical diagnosis (R=rejection; Ch=Chagas disease reactivation; N=non-rejection&non-Chagas):
GSM48058 29 Hsab-03-58 29 N W63 male dilated cardiomyopathy 63 toxoplasma myocarditis anti-toxoplasma treatment toxoplasma myocarditis
GSM48040 14 (R) Hsab-03-31 14 N B10 female Chagas cardiomyopathy 10 3A R
GSM48043 15 (R) Hsab-03-36 15 Y N25 female ischemic cardiomyopathy 25 3A R
GSM49655 15 (R) Hsab-03-71 15 Y N25 female ischemic cardiomyopathy 25 3A R
GSM48050 16 (R) Hsab-03-51 16 Y Y90 male dilated cardiomyopathy 90 3A 1 month after anti-rejection pulse R
GSM49747 16 (R) Hsab-04-50 16 Y Y90 male dilated cardiomyopathy 90 3A 1 month after anti-rejection pulse R
GSM48053 17 (R) Hsab-03-53 17 N A105 male Chagas cardiomyopathy 105 3A R
GSM48056 18 (R) Hsab-03-54 18 N Z15 male dilated cardiomyopathy 15 3B anti-rejection treatment R
GSM48046 19 (R) Hsab-03-46 19 N D119 female Chagas cardiomyopathy 119 1B 2 months after starting treatment for Chagas R
GSM48047 20 (R) Hsab-03-47 20 N W97 male dilated cardiomyopathy 97 2 R
GSM49749 24 (R) Hsab-04-54 24 N Y538 male dilated cardiomyopathy 538 0 patient presented clinical sign of rejection (flutter), anti-rejection treatment R
GSM49755 50 (R) Hsab-08-41 50 Y J111 male dilated cardiomyopathy 111 3A R
GSM49761 50 (R) Hsab-08-58 50 Y J111 male dilated cardiomyopathy 111 3A R
GSM49780 51 (R) Hsab-08-93 51 N G108 male Chagas cardiomyopathy 108 3A anti-rejection pulse R
GSM49764 56 (R) Hsab-08-71 56 N AC55 male ischemic cardiomyopathy 55 3A R
GSM49759 US1 (R) Hsab-08-47 US1 Y US11 female ischemic cardiomyopathy 11y 3A transplanted more than 11 years ago, patient stopped to take immunosuppression for about 1 year before this rejection R
GSM49763 US1 (R) Hsab-08-62 US1 Y US11 female ischemic cardiomyopathy 11y 3A transplanted more than 11 years ago, patient stopped to take immunosuppression for about 1 year before this rejection R
GSM48048 27 (pre-R) Hsab-03-48 27 N D185 female Chagas cardiomyopathy 185 0 3 weeks before clinical sign of rejection (flutter); 3 months after starting treatment of Chagas Pre-R
GSM47949 28 (pre-R) Hsab-03-28 28 Y AE41 male Chagas cardiomyopathy 41 0 14days before Quilty B and 1B rejection Pre-R
GSM49625 28 (Pre-R) Hsab-03-69 28 Y AE41 male Chagas cardiomyopathy 41 0 14days before Quilty B and 1B rejection Pre-R

Total number of rows: 63

Table truncated, full table size 6 Kbytes.




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