Gene Expression Profile Score Research Articles

Gene expression profiling to study racial differences after heart transplantation

BackgroundThe basis for increased mortality after heart transplantation in African Americans and other non-Caucasian racial groups is poorly defined. We hypothesized that increased risk of adverse events is driven by biological factors. To test this hypothesis in the IMAGE study, we determined whether the event rate of the primary outcome of acute rejection, graft dysfunction, death, or re-transplantation varied by race as a function of calcineurin inhibitor levels and gene expression profile (GEP) scores.MethodsWe determined the event rate of the primary outcome, comparing racial groups, stratified by time post-transplant. Logistic regression was used to compute the relative risk across racial groups and linear modeling was used to measure the dependence of CNI levels and GEP score on race.ResultsIn 580 patients followed for a median of 19 months, the incidence of the primary endpoint in African Americans, other non-Caucasians, and Caucasians was 18.3%, 22.2%, and 8.5%, respectively (p<0.001). There were small but significant correlations of race and tacrolimus trough levels to GEP score. Tacrolimus levels were similar between races. Of patients receiving tacrolimus, other non-Caucasians had higher GEP scores than the other racial groups. African American recipients demonstrated a unique decrease in expression of the FLT3 gene in response to higher tacrolimus levels.ConclusionsAfrican Americans and other non-Caucasian heart transplant recipients were 2.5–3 times more likely than Caucasians to experience outcome events in IMAGE. The increased risk of adverse outcomes may be partly due to the biology of the alloimmune response, which is less effectively inhibited at similar tacrolimus levels in minority racial groups.

(357) - Gene Expression Profile Score Variability Characteristics: Analysis of 49,836 Tests From 12,177 Heart Transplant Patients

Gene expression profile (GEP) is a commercially available blood test which is noninferior to endomyocardial biopsy in detecting rejections after orthotopic heart transplant (OHT). A reference value below 34 in patients (pts) at least 6 months post OHT is associated with a very low risk of rejection. The variability of serial GEP scores has been shown to independently predict future hemodynamic compromise or death. The purpose of this study is to characterize the within pt GEP score variability in a large population over 4 periods of time post OHT.

Racial Disparities after Heart Transplant: Evidence from IMAGE

Purpose The basis for increased mortality after heart transplant in non-Caucasians is poorly defined. We hypothesized that increased risk of adverse events is due to biological factors related to the alloimmune response. To test this hypothesis in the IMAGE study, we determined whether the event rate of the primary outcome (rejection with hemodynamic compromise, graft dysfunction, death, or retransplantation) varied by race in heart transplant recipients. We explored whether racial differences may be due to differences in levels of calcineurin inhibitors (CNI) or gene expression profile (GEP) scores. Methods and Materials We studied the event rate of the primary outcome, comparing racial groups in the IMAGE population, stratified by time post-transplant. We assessed whether differences in event rate varied as a function of CNI levels and GEP score. Logistic regression was used to compute the relative risk across racial groups and linear modeling was used to measure the dependence of GEP score and CNI on race. Results We found increased incidence of the primary endpoint in African Americans and other non-Caucasians, compared to Caucasians (18.3% and 22.2% vs. 8.5% respectively). African Americans had higher GEP score than Caucasians on CSA (p=0.01) despite similar levels. GEP score was higher, albeit tacrolimus blood level was lower, for other non-Caucasians than Caucasians. Conclusions Non-Caucasian heart transplant patients are 2.5-3 times more likely than Caucasians to experience rejection with hemodynamic compromise or death. Our data suggest that the increased risk of adverse outcomes may be due to the biology of the alloimmune response, which is less effectively abrogated by immunosuppression in non-Caucasians. Group Month post-tx Events/pt/yr Tac median trough CSA median trough GEP score mean (Tac) GEP score mean (CSA) Caucasian 7-12 0.09 8.8 167 28.8 26.1 13-36 0.07 8.2 144 30 30.1 >36 0.05 7.0 118 30 30 African American 7-12 0.27 9.3 141 30.5 32.2 13-36 0.18 8.4 120 29.8 32.2 >36 0.14 7.1 111 29.4 30.5 Other non-Caucasian 7-12 0.87 8.2 183 29.7 28.5 13-36 0.21 7.0 173 31.8 29.4 >36 0.07 5.7 122 29.6 28.0

The Impact of Time Post Cardiac Transplant on Gene Expression Profile Scores, an Analysis of 32,043 Tests

Background: Gene Expression Profiling (GEP) has been used since 2005 to identify Orthotopic Heart Transplant (OHT) recipients at low risk of allograft rejection. A rise in GEP scores during the first year post OHT has been previously reported. The purpose of this study is to confirm and better characterize this effect of time post-transplant in a larger, unselected cohort. Methods: All commercially obtained GEP scores (XDx Inc., Brisbane, CA) collected between January 2005 and September 2011 were included. Clinical data were available for patient age, gender and dates of transplantation and tests. Results: There were 32,043 GEP tests from 9,272 patients at 108 transplant centers (mean age at testing 54.2 ± 14.7 yrs, 25% women). There was a significant effect of time post transplant on GEP, which rose from 24.7 ± 7.8 at 2-6 months to 28.8 ± 5.8 at 7-12 months (p<0.0001) and 29.6 ± 5.0 (p<0.0001) at 13-24 months, after which it remained stable. Conclusions: A rise in GEP scores is seen during the first year following OHT, which parallels the time frame of decreased corticosteroid dosing. Further study of this test characteristic may better inform clinical use of GEP testing in conjunction with endomyocardial biopsy.

78 Do Longitudinal Stable Lower AlloMap® Scores Portend Better Outcomes after Heart Transplantation?

Purpose AlloMap® is a non-invasive gene expression profile (GEP) test with a high negative predictive value for moderate/severe cellular rejection. We have observed a cohort of patients with consistently low GEP scores. Whether this reflects a group of patients with unique characteristics and a more quiescent immunological state manifest by improved outcomes is of interest in this study. Methods and Materials A low GEP score was defined within the lowest quartile of all GEP scores from a large database of all patients with at least 3 tests performed at the reference lab. Two groups from the IMAGE multicenter clinical outcomes study were retrospectively defined: Group 1 had a mean score in the lowest quartile (GEP ≤27.5), and patients with scores greater than 2 standard deviations from the mean were excluded; Group 2 had mean scores <34, the clinically accepted threshold for low rejection risk, that did not meet Group 1 criteria. Clinical outcomes of interest included a composite primary endpoint (rejection with hemodynamic compromise, graft dysfunction due to other causes, and death/retransplantation), any treated rejection, left ventricular ejection fraction (LVEF), and hospitalizations. Results We evaluated 1684 scores from 353 patients from IMAGE. Group 1 had 59 patients with 250 scores; Group 2 had 294 patients with 1434 scores. Basic demographics including age, gender, and race were similar between groups. Mean time since transplant was 21 months in both groups. Outcomes are shown below. Table 1. Outcomes (events) Group 1 (GEP ≤27.5) Group 2 (GEP <34) p value Primary Endpoint 1 53 0.027 Treated Rejection 2 66 0.017 Average LVEF (%) 63.7 62.4 0.001 Hospitalizations 21 180 0.16 Full-size table Table options View in workspace Download as CSV Conclusions Patients with consistently low GEP scores have a significantly lower incidence of adverse outcomes compared to patients in Group 2 despite similar demographics. With further characterization of this group, and if validated on a larger scale, more personalized post-transplant care to tailor immunosuppression down may be possible.

Comparative Genomic Hybridization, Gene Expression Profiling and Whole Genome Sequencing Analysis of Disease Progression in Myeloma Reveals Vigorous Clonal Evolution in Patients with High Baseline Genetic Risk.

Abstract 2810Poster Board II-786We wished to explore the genetic events associated with disease progression and development of drug resistance in multiple myeloma (MM). To do so 11 patients were studied in whom at least two (range 2-3) temporally distinct samples of tumor DNA and RNA were available. The baseline genetic initiating event was defined for all patients (3 were genetic high risk; one with t(14;16) two with t(4;14)) as well as the gene expression profile (GEP) defined risk score using the Little Rock 70 or 17 gene panel (only one, the t(14;16) was GEP defined high risk). High resolution array CGH and gene expression were then performed on each sample. Of the 8 patients with a “low risk” tumor initiating event and low risk GEP score, 6 patients had no, or only one, copy number abnormality (CNA) change between the two temporally distinct MM samples. In stark contrast the 3 genetic high risk at baseline had between 17 and 40 distinct CNA changes at the time of progression. For all 11 patients 89 CNA were acquired with progression whereas 19 previously abnormal regions disappeared suggesting clones with these abnormalities were extinguished by the therapy received. In total we detected 0-40 CNA changes between the various timepoints, median 1, mean 10.7. The acquisition of new CNA was much more common than the loss of CNA. We then focused more specifically on the t(4;14) patient with the highest number of CNA changes. This patient has a well documented clinical course of having a sustained two year VGPR to Len/dex and then progressing while still taking Len/dex. Comparison of the pre and post-Len/dex samples identified 40 CNA changes(the most of any pair studied to date). Only six CNA were shared between the two samples, which included deletions of chr4, 9, 12, 13, and X plus a t(4;14) translocation. These likely represent the initiating “driver” tumor events. The new CNA we identified originated from both remodeled genomic changes and the emergence of unique changes, indicating a new tumor clone had emerged while the previously dominant clone had regressed (e.g. a deletion of a large segment of chromosome 8 at diagnosis was no longer observed in the relapse sample). The newly acquired CNA encompassed 3968 genes (13.7% of the genes in the genome), however, only 1235 of these genes (4%) were expressed in this patient at diagnosis (1188 in the typical myeloma patient). Since 1235 genes is still a large number we hypothesized that whole genome sequencing (WGS) would help elucidate the mechanism of lenalidomide resistance. We isolated DNA from germline tissue and CD138 purified tumor cells including: diagnostic, first relapse and second relapse samples. Utilizing SOLiD (Applied Biosystems, Foster City, CA) sequencing technology, we have completed fragment library WGS on both the germline and the final tumor samples. Quality control measures report the average number of sequence reads per start point to be less than 1.2, indicating the library is primarily composed of unique molecules. In addition, approximately 40% of the sequence reads map uniquely to the genome. Together these quality measures indicate our sample libraries are complex and provide good representation of the genome. Data on the whole genome sequence of myeloma at diagnosis and at the time of progression will be presented. Disclosures:Bergsagel:Celgene: Consultancy.

Treatment of Symptomatic Cartilage Defects of the Knee

Background Damaged articular cartilage has limited capacity for self-repair. Autologous chondrocyte implantation using a characterized cell therapy product results in significantly better early structural repair as compared with microfracture in patients with symptomatic joint surface defects of the femoral condyles of the knee. Purpose To evaluate clinical outcome at 36 months after characterized chondrocyte implantation (CCI) versus microfracture (MF). Study Design Randomized controlled trial; Level of evidence, 1. Methods Patients aged 18 to 50 years with single International Cartilage Repair Society (ICRS) grade III/IV symptomatic cartilage defects of the femoral condyles were randomized to CCI (n = 57) or MF (n = 61). Clinical outcome was measured over 36 months by the Knee injury and Osteoarthritis Outcome Score (KOOS). Serial magnetic resonance imaging (MRI) scans were scored using the Magnetic resonance Observation of Cartilage Repair Tissue (MOCART) system and 9 additional items. Gene expression profile scores associated with ectopic cartilage formation were determined by RT-PCR. Results Baseline mean overall KOOS (±SE) was comparable between the CCI and MF groups (56.30 ± 1.91 vs 59.46 ± 1.98, respectively). Mean improvement (±SE) from baseline to 36 months in overall KOOS was greater in the CCI group than the MF group (21.25 ± 3.60 vs 15.83 ± 3.48, respectively), while in a mixed linear model analysis with time as a categorical variable, significant differences favoring CCI were shown in overall KOOS (P = .048) and the subdomains of Pain (P = .044) and QoL (P = .036). More CCI- than MF-treated patients were treatment responders (83% vs 62%, respectively). In patients with symptom onset of <2 years, the mean improvement (±SE) from baseline to 36 months in overall KOOS was greater with CCI than MF (24.98 ± 4.34 vs 16.50 ± 3.99, respectively) and even greater in patients with symptom onset of <3 years (26.08 ± 4.10 vs 17.09 ± 3.77, respectively). Characterized chondrocyte implantation patients with high (>2) versus low (<2) gene profile scores showed greater improvement from baseline in mean overall KOOS (±SE) at 36 months (28.91 ± 5.69 vs 18.18 ± 5.08, respectively). Subchondral bone reaction significantly worsened over time with MF compared with CCI (P < .05). Conclusion Characterized chondrocyte implantation for the treatment of articular cartilage defects of the femoral condyles of the knee results in significantly better clinical outcome at 36 months in a randomized trial compared with MF. Time to treatment and chondrocyte quality were shown to affect outcome.