Abnormal Gene Expression as an Early Indicator of Relapse in Acute Myelogenous Leukemia (AML)

Author(s):  
M. J. Evinger-Hodges ◽  
J. A. Spinolo ◽  
I. Cox ◽  
K. A. Dicke
Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 883-883 ◽  
Author(s):  
TzuChieh Ho ◽  
Mark W LaMere ◽  
Kristen O'Dwyer ◽  
Jason H. Mendler ◽  
Jane L. Liesveld ◽  
...  

Abstract Acute Myelogenous Leukemia (AML) is a disease that clinically evolves over time as many patients who are responsive to therapy upfront acquire resistance to the same agents when applied in the relapse setting. The stem cell model for AML has been invoked to explain primary resistance to standard therapy; the leukemia stem cell (LSC) population representing a therapy-refractory reservoir for relapse. There have been no prospective efforts to formally assess the evolution of the LSC population during patients’ clinical course. We performed a prospective characterization of specimens from a well-defined cohort of patients with AML at diagnosis and relapse to assess the frequency and phenotype of functionally defined LSCs. Methods Primary bone marrow and peripheral blood samples were collected on IRB approved protocols from patients with newly diagnosed AML undergoing induction therapy. Twenty-five patients who relapsed after achieving a complete remission were selected for further study. Screening studies identified seven patients whose pre-therapy samples demonstrated sustained engraftment of NSG mice following transplantation. Pre-therapy and post-relapse LSC frequencies were assessed using xenotransplantation limiting dilution analyses (LDA). We assessed the frequencies of CD45RA, CD32, TIM-3, CD96, CD47, and CD97 expressing populations that have been previously published to possess LSC activity. Functionally validated pre-therapy and post-relapse LSC populations were identified using fluorescent labeled cell sorting and NSG xenotransplantation. LSC activity was confirmed for each population using secondary xenotransplantation. Gene expression analysis of highly enriched LSC populations from pre-therapy and post-relapse samples was performed using ABI TILDA qPCR analyses following pre-amplification. Results We demonstrated by LDA an 8 to 42-fold increase in LSC frequency between diagnosis and relapse in paired primary patient samples. The increase in LSC activity was not associated with an increase in frequency for phenotypically-defined populations previously reported to possess LSC activity. Rather, we found that LSC activity expanded at relapse to immunophenotypic populations of leukemic cells that did not possess LSC activity prior to treatment. Moreover, in all patients, the number of phenotypically distinct LSC populations (as defined by CD34 and CD38 or CD32 and CD38) detectable at relapse was dramatically expanded. Further, while the majority of the LSC populations’ gene expression profile remained stable between diagnosis and relapse, a subset of genes were enriched in defined LSC populations at relapse including IL3-receptor alpha and IL1-RAP, both previously demonstrated to play a role in LSC biology. Conclusions This study is the first to characterize the natural evolution of LSCs in vivo following treatment and relapse. We demonstrate an increase in LSC activity and greatly increased phenotypic diversity of the LSC population, suggesting a loss of hierarchical organization following relapse. These findings demonstrate that treatment of AML patients with conventional chemotherapy regimens can promote quantitative and qualitative expansion of the LSC compartment. Further, the data indicate that surface antigen immune-phenotype is not predictive of function in relapse and suggest a major limitation to efforts targeting specific surface antigens in the relapse setting. Understanding the mechanisms by which LSC expansion occurs and how to target it will likely improve our currently poor treatment options for patients who relapse. Disclosures: Becker: Millenium: Research Funding.


2004 ◽  
Vol 28 (2) ◽  
pp. 149-157 ◽  
Author(s):  
Akihiro Yokoyama ◽  
Takuya Yamashita ◽  
Eisuke Shiozawa ◽  
Atsuko Nagasawa ◽  
Junko Okabe-Kado ◽  
...  

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4266-4266 ◽  
Author(s):  
Tzu-Chieh Ho ◽  
Craig T Jordan ◽  
Mark W. LaMere ◽  
John M. Ashton ◽  
Kristen O'Dwyer ◽  
...  

Abstract Background Acute Myelogenous Leukemia (AML) evolves as many patients who are responsive to therapy upfront are resistant to the same agents when applied at relapse. We previously reported the results of our prospective efforts to formally assess the evolution of the leukemia stem cell (LSC) population(s) during patients' clinical courses. We identified a 9-90 fold increase in LSC activity and greatly increased phenotypic diversity of the LSC population. To identify the potential mechanisms underlying these changes we further characterized functionally-defined LSC populations from paired diagnosis and relapse samples. Methods Primary bone marrow and peripheral blood samples were collected on IRB approved protocols from patients with newly diagnosed AML undergoing induction therapy as well as normal donors. Twenty-five patients who relapsed after achieving a complete remission were selected for further study. Screening studies identified seven patients whose pre-therapy samples demonstrated sustained engraftment of NSG mice following transplantation. Transcriptional profiling of highly enriched LSC populations from seven patients was performed using ABI TaqMan® Low Density Array (TLDA) qPCR analyses following pre-amplification using a novel 153 gene expression platform. Protein expression levels of interleukin-1 receptor accessory protein (IL1RAP) on bulk leukemia cells and LSC populations from 25 patients were assessed by flow cytometry. The impact of loss of IL1RAP was assessed using lentiviral based shRNA targeting all IL1RAP isoforms followed by assessment of proliferation, apoptosis, colony forming unit (CFU) activity and NSG engraftment capacity in human cell lines as well as in primary patient samples. Downstream signaling events for IL1RAP were probed using a small molecule inhibitor approach. Results While the majority of the LSC populations' gene expression profile remained stable, twelve genes were differentially expressed between pre-treatment and relapsed LSC populations including IL1RAP. Flow cytometric analyses confirmed that IL1RAP is overexpressed on both bulk leukemia populations as well as LSC populations at diagnosis and relapse in comparison to normal hematopoietic stem cell (HSC) populations. Targeting ILRAP1 using shRNA in both cell lines and primary AML samples resulted in impaired proliferation, increased apoptosis, a marked loss of CFU capacity and impaired NSG engraftment. IL1 signaling is known to involve both the MAPkinase and NFKappB pathways. To determine which pathways are involved in IL1RAP mediated LSC survival, we performed a small molecule inhibitor screen targeting elements in both signaling cascades. Established inhibitors of the NFKappaB pathway resulted in loss in loss of leukemic cell function while MAPK signaling inhibition had minimal to no effect. Conclusions We identified IL1RAP as being overexpressed in both bulk leukemia and functionally defined LSC populations from pre-treatment and relapsed AML samples. Loss of IL1RAP was associated with a marked decline in LSC function. Preliminary studies support a primary role for the NF Kappa B pathway in LSC function. Our findings support a critical role for IL1RAP in LSC function and support its development as a target for AML therapy in both the upfront and relapse setting. Disclosures Wang: Immunogen: Research Funding. Calvi:Fate Therapeutics: Patents & Royalties. Becker:Millenium: Research Funding.


2009 ◽  
Vol 106 (9) ◽  
pp. 3396-3401 ◽  
Author(s):  
R. Majeti ◽  
M. W. Becker ◽  
Q. Tian ◽  
T.-L. M. Lee ◽  
X. Yan ◽  
...  

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3018-3018 ◽  
Author(s):  
Jonathan Ben-Ezra ◽  
Amy C. Ladd ◽  
Catherine I. Dumur ◽  
Kellie J. Archer ◽  
Alden Chesney ◽  
...  

Abstract Cryopreservation of patient bone marrow specimens allows for future purification of tumor cells for research or diagnostic purposes. It has not been determined whether this practice causes significant changes in gene expression. In order to evaluate this, we performed microarray analysis (Affymetrix U133A and U133A 2.0 gene chips) on mononuclear cells from 5 acute myelogenous leukemia (AML) patient samples (>70% blast count) that had been either a) cryopreserved, b) snap frozen, or c) resuspended in TRIzol and stored at −80°C. Samples remained frozen for a period of 1–4 weeks. While gene expression changes between groups were minor, there were some differences. Thirteen probe sets between TRIzol and cryopreserved samples, and 60 probe sets between TRIzol and snap frozen samples, varied significantly (>2-fold difference and p<0.01; t-test). While both non-TRIzol samples lost transcripts associated with mature, contaminating granulocytes, the snap frozen samples also lost transcripts associated with cell growth and metabolism. To determine whether the observed changes were enough to cause a misclassification of AML subtypes, we performed an unsupervised cluster analysis on the 15 original samples plus 15 new AML samples (13 unique cases), all of varying subtypes. RNA from all of these samples was undegraded. All samples passed strict quality control parameters, not limited to but including tumor content, % rRNA, cDNA and cRNA synthesis product size, and GAPDH 3′-5′ ratios. Differentially preserved samples originating from the same patient segregated together during the clustering process regardless of preservation method. Three main clusters emerged; cluster #1 (FAB-M0 and -M1, n=3), cluster #2 (FAB-M3, n=5), and cluster #3 (FAB-M2, -M4 and -M5b, n=22). In cluster #3, there were three sub-groupings. One group contained only M4 and M5b subtypes, another contained only the M2 subtype, and the third contained both M2 and M4 subtypes. RNA isolated from snap frozen samples was sometimes moderately to severely degraded. When we examined three snap frozen samples, not part of the above data set, exhibiting moderate RNA degradation, they all clustered incorrectly according to the above established groups. Given these results, we conclude that cryopreservation is an acceptable method of cell preservation for gene expression analysis, but snap frozen samples should be closely evaluated for RNA degradation before using in microarray analyses.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2986-2986
Author(s):  
Laura Bystrom ◽  
Hsiao-Ting Hsu ◽  
Catherine Neto ◽  
Gail J. Roboz ◽  
Duane C Hassane ◽  
...  

Abstract Abstract 2986 Acute myelogenous leukemia (AML) is a fatal disease in which the majority of patients relapse and die even after attaining initial complete remission. AML is thought to be initiated and maintained by chemoresistant leukemia stem cells (AML-SCs). Therefore, identifying therapies that can eliminate AML-SCs is a priority. Iron is crucial to normal cell metabolism and plays a role in multiple cellular activities, including promotion of processes required for maintenance of malignancy, such oxidative phosphorylation, nucleotide synthesis, and Wnt signaling. An important regulator of intracellular iron is ferroportin, an iron exporter. Using a publicly available gene expression dataset for AML patients (GEO accession #GSE6891), we found that low levels of ferroportin correlate with poor outcomes (p = 0.018). We investigated the levels of ferroportin in AML-SCs and discovered that ferroportin levels are significantly lower in AML-SCs than in their normal counterparts (p=0.008). Based on these findings, we hypothesized that aberrant iron metabolism may be an important feature of LSC biology that could be targeted by a novel therapeutic agent. To this end, we investigated the activity of known natural products with iron chelation activity in AML-SCs, specifically focusing on proanthocyanidins found in cranberry extracts. Many of the reported health benefits of cranberries, including their antimicrobial functions, are associated with a unique class of proanthocyanidins referred to as A–type PACs (A-PACs). We tested the effects of a commercially available cranberry extract (Cysticran 40; CYS) and A-PACs in 15 primary AML and 5 normal CD34+ cord blood specimens and found potent and specific anti-LSC activity. Primary AML samples were shown to be highly sensitive to CYS, with a mean LD50 of 180.6 μg/ml (110.2 – 251.1 μg/ml, 95% CI; n=9). Purified PACs demonstrated even greater potency (mean LD50= 82.51 μg/mL; 57.07–107.9, 95% CI; n=11). The sensitivity to PACs and CYS was also observed in phenotypically described progenitor and stem cell populations from the AML samples. Sensitivity to CYS and A-PACs was not confined to AML with specific cytogenetic abnormalities or known mutations, suggesting potency across AML subtypes. Importantly, we did not observe any overt effects on purified CD34+ cells from healthy cord blood samples. Functional stem cell assays showed ablation of AML-SCs with A-PAC treatment. Specifically, primary AML samples treated with 62.5μg/ml demonstrated more than 75% decrease in colony forming activity relative to vehicle control (n=5). In contrast, there was less than 2 fold decrease in colony formation in CD34+ CB cells treated with 125μg/ml of PACs (n=4). Xenotransplant assays showed significantly decreased human AML engraftment after treatment with 62.5μg/ml A-PAC (90.6% decreased engraftment, n=3, p<0.001), while normal CD34+ cells retained engraftment capability in immunodeficient mice (n=4). We observed that treatment with CYS and PACs resulted in caspase-3 activation, evaluated by immunoblots and flow cytometry. Furthermore, pre-treatment with antioxidants or holo-transferrin partially protected AML cells from A-PAC induced cell death (p<0.01). In addition, A-PAC treatment induced changes in cellular iron metabolism and increased ROS levels. Interestingly, gene expression analysis revealed that A-PACs upregulated chemokine and NF-kB pathways (p= 1.2 × 10−9), which is uncharacteristic of anti-LSC compounds discovered to date and suggests a novel mode of AML-SC ablation that bypasses NF-kB signaling to achieve AML-SC ablation. Together, our results suggest that cranberry A-PACs represent a novel class of compounds with therapeutic potential to ablate leukemia stem and progenitor cells, with minimal effects on normal hematopoietic stem cells. Disclosures: No relevant conflicts of interest to declare.


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