Identification of Gene Expression Based Prognostic Markers in the Hematopoietic Stem Cells of Patients with Myelodysplastic Syndromes

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3857-3857
Author(s):  
Andrea Pellagatti ◽  
Axel Benner ◽  
Ken I Mills ◽  
Mario Cazzola ◽  
Aristoteles Giagounidis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Principal Components ◽  
Myelodysplastic Syndromes ◽  
Expression Profiling ◽  
Mononuclear Cells ◽  
Patient Survival ◽  
Gene Signature ◽  
Bone Marrow Mononuclear Cells ◽  
Cd34 Cells

Abstract Abstract 3857 The diagnosis of patients with myelodysplastic syndromes (MDS) is largely dependent on morphologic examination of bone marrow aspirates. Several criteria that form the basis of the classifications and scoring systems most commonly used in clinical practice are affected by operator-dependent variation. In order to identify more standardized molecular markers that would allow a more reliable prediction of prognosis, we have used gene expression profiling (GEP) data on CD34+ cells from MDS patients to determine the relationship between gene expression levels and prognosis in this disorder. GEP data on CD34+ cells from 125 MDS patients with a minimum 12-month follow-up since date of bone marrow sample collection were included in this study. Prediction for overall survival was performed using supervised principal components (“SuperPC”) and lasso penalized Cox proportional hazards regression applying the “Coxnet” algorithm. Supervised principal components analysis was performed on patients randomly split in a training set (n=84) and a test set (n=41), and 139 genes were identified the expression of which was significantly associated with MDS patient survival, including LEF1, CDH1, WT1 and MN1. In order to identify a smaller set of genes associated with patient survival, a second approach aiming at building sparse prediction models was used. A model was generated using the Coxnet algorithm and a predictor consisting of 20 genes was identified. Eight genes identified by the supervised principal components method were in common with the genes identified by the Coxnet model: ADHFE1, BTBD6, CPT1B, LEF1, FRMD6, GPR114, C7orf58 and LOC100286844. The Coxnet predictor outperformed other predictors including one which additionally used clinical information. To validate our findings, we evaluated the performance of our prognostic Coxnet gene signature in an independent gene expression profiling dataset on MDS bone marrow mononuclear cells (Mills et al, Gene Expression Omnibus series GSE15061). Our Coxnet gene signature based on CD34+ cells significantly identified a low-risk patient group in this independent GEP dataset based on unsorted bone marrow mononuclear cells, demonstrating that our signature is robust and may be applicable to bone marrow cells without the need to isolate CD34+ cells. These GEP-based signatures correlating with clinical outcome may significantly contribute to a refined risk classification of MDS. Disclosures: No relevant conflicts of interest to declare.

Research of Gene Expression in Patients with Myelodysplastic Syndromes.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4433-4433
Author(s):  
Bao-An Chen ◽  
Bo Zhang ◽  
Chong Gao ◽  
Guo-Hua Xia ◽  
Ze-ye Shao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Clinical Significance ◽  
Myelodysplastic Syndromes ◽  
Mononuclear Cells ◽  
Conflicts Of Interest ◽  
Bone Marrow Mononuclear Cells ◽  
Rt Pcr ◽  
Normal People ◽  
Significant Difference

Abstract Abstract 4433 Object This study was aimed to investigate the expression of c-FLIPL, c-FLIPS and DLK1 mRNA in Myelodysplastic Syndromes (MDS) patients, as compared with normal people and AML patients, and to find its clinical significance. Methods The expression of c-FLIPL, c-FLIPS and DLK1 mRNA in bone marrow mononuclear cells (BMNNC) of 16 patients with MDS, 8 patients with AML and 3 controls were detected by RT-PCR. Results The expression of DLK1 mRNA was up-regulated in MDS, including RA and RAEB, as compared with controls(P<0.05). There was no significant difference in expression of DLK1 between RA and RAEB(P>0.05). The expression of DLK1 was significant higher in AML patients, compared with controls(P<0.05). There was no significant difference between MDS and AML patients(P>0.05). The expression of c-FLIPL mRNA was higher than that in controls, both in RA and RAEB(P<0.05). There was no significant difference in expression of c-FLIPL between RA and RAEB(P>0.05). In eight AML patients, c-FLIPL gene's expression was up-regulated, as compared with controls(P<0.05). Between AML and MDS patients, there was no significant difference(P>0.05); The expression of c-FLIPS mRNA had no significant difference between MDS patients and controls(P>0.05), but its expression in RAEB was significant higher as compared with RA patients and controls(P<0.05). And in AML patients, the expression of c-FLIPS was higher than that in controls(P<0.05), but there was no significant difference between AML and MDS patients(P>0.05). Conclusion It is concluded that the expressions of DLK1, c-FLIPL and c-FLIPS mRNA in MDS/AML patients are abnormal as compared with normal people, although there are no significant difference have been found between AML and MDS. These genes may play critical roles in escaping malignant clone of MDS from apoptosis and acquiring the ability to divide unlimitedly, they can become important indexes for evaluating of development in MDS. Disclosures: No relevant conflicts of interest to declare.

Identification of Gene Expression–Based Prognostic Markers in the Hematopoietic Stem Cells of Patients With Myelodysplastic Syndromes

2013 ◽  
Vol 31 (28) ◽  
pp. 3557-3564 ◽  
Author(s):  
Andrea Pellagatti ◽  
Axel Benner ◽  
Ken I. Mills ◽  
Mario Cazzola ◽  
Aristoteles Giagounidis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Myelodysplastic Syndromes ◽  
Mononuclear Cells ◽  
Bone Marrow Cells ◽  
Cox Proportional Hazards ◽  
Sample Collection ◽  
Data Set ◽  
Hematopoietic Stem ◽  
Cd34 Cells

Purpose The diagnosis of patients with myelodysplastic syndromes (MDS) is largely dependent on morphologic examination of bone marrow aspirates. Several criteria that form the basis of the classifications and scoring systems most commonly used in clinical practice are affected by operator-dependent variation. To identify standardized molecular markers that would allow prediction of prognosis, we have used gene expression profiling (GEP) data on CD34+ cells from patients with MDS to determine the relationship between gene expression levels and prognosis. Patients and Methods GEP data on CD34+ cells from 125 patients with MDS with a minimum 12-month follow-up since date of bone marrow sample collection were included in this study. Supervised principal components and lasso penalized Cox proportional hazards regression (Coxnet) were used for the analysis. Results We identified several genes, the expression of which was significantly associated with survival of patients with MDS, including LEF1, CDH1, WT1, and MN1. The Coxnet predictor, based on expression data on 20 genes, outperformed other predictors, including one that additionally used clinical information. Our Coxnet gene signature based on CD34+ cells significantly identified a separation of patients with good or bad prognosis in an independent GEP data set based on unsorted bone marrow mononuclear cells, demonstrating that our signature is robust and may be applicable to bone marrow cells without the need to isolate CD34+ cells. Conclusion We present a new, valuable GEP-based signature for assessing prognosis in MDS. GEP-based signatures correlating with clinical outcome may significantly contribute to a refined risk classification of MDS.

scholarly journals DNA methylation identifies genetically and prognostically distinct subtypes of myelodysplastic syndromes

2019 ◽  
Vol 3 (19) ◽  
pp. 2845-2858 ◽  
Author(s):  
Brian Reilly ◽  
Tiffany N. Tanaka ◽  
Dinh Diep ◽  
Huwate Yeerna ◽  
Pablo Tamayo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bone Marrow ◽  
Myelodysplastic Syndromes ◽  
Mononuclear Cells ◽  
Scoring Systems ◽  
Bone Marrow Mononuclear Cells ◽  
Key Points ◽  
Prognostic Scoring Systems

Key Points Targeted DNAm profiling of MDS patient bone marrow mononuclear cells identifies several distinct DNAm clusters. Clusters enrich for specific genetic lesions and show differences in survival independent of clinical prognostic scoring systems..

scholarly journals Interferon-gamma gene expression in unstimulated bone marrow mononuclear cells predicts a good response to cyclosporine therapy in aplastic anemia

Blood ◽  
1992 ◽  
Vol 79 (10) ◽  
pp. 2532-2535 ◽  
Author(s):  
S Nakao ◽  
M Yamaguchi ◽  
S Shiobara ◽  
T Yokoi ◽  
T Miyawaki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Aplastic Anemia ◽  
Interferon Gamma ◽  
Messenger Rna ◽  
Mononuclear Cells ◽  
Bone Marrow Mononuclear Cells ◽  
Ifn Gamma ◽  
Exact Test ◽  
Transfusion Independence

Cyclosporine (CyA) therapy has been shown to be effective in some patients with aplastic anemia. In an attempt to characterize aplastic patients likely to benefit from CyA therapy, we examined bone marrow mononuclear cells (BMMC) obtained before therapy from 23 patients with aplastic anemia, who were treated with CyA alone. Expression of four myelosuppressive cytokines, including tumor necrosis factor (TNF), lymphotoxin, macrophage inflammatory protein-1 alpha (MIP-1 alpha), and interferon-gamma (IFN-gamma) was examined using polymerase chain reaction (PCR)-assisted messenger RNA (mRNA) amplification. mRNA for TNF, lymphotoxin, and MIP-1 alpha was readily detectable at variable levels in BMMC from normal and transfused controls as well as in BMMC from aplastic patients. In contrast, IFN-gamma mRNA was only demonstrable in BMMC from some patients with aplastic anemia, irrespective of a history of transfusions. Of 13 patients who responded to CyA therapy and achieved transfusion-independence, IFN-gamma mRNA was detected in 12 patients, whereas the mRNA was only detectable in 3 of 10 patients refractory to CyA therapy (P = .003, Fisher's exact test). Follow-up examination of BMMC obtained from seven CyA-responding patients after hematologic remission showed disappearance of IFN-gamma mRNA in four patients. These results suggest that detection of IFN- gamma gene expression in pretreatment BMMC from aplastic patients using PCR may be helpful in predicting a good response to CyA therapy.

scholarly journals Mechanism of Action of Azacytidine in Myelodysplastic Syndromes (MDS)

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4315-4315
Author(s):  
Niraja Dighe ◽  
Subhashree Venkatesan ◽  
Poon Zhiyong ◽  
William YK Hwang
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Stem Cell ◽  
Mechanism Of Action ◽  
Stromal Cells ◽  
Expression Profiling ◽  
Healthy Controls ◽  
Singapore General Hospital ◽  
Cd34 Cells ◽  
Stem Cell Niches

Abstract Introduction: Myelodysplastic syndromes (MDS) have historically been classified as a set of heterogeneous hematopoietic stem cell (HSC) disorders, which are characterized clinically by abnormalities in the hematopoietic system. However, several recent landmark studies have now demonstrated that the pathogenesis of MDS is not confined to HSCs, and mesenchymal stromal cells (MSCs) in the bone marrow also play important contributing roles in sustaining the disorder. Treatment for MDS using hypomethylating agents such as azacytidine is effective, with patients showing recovery of blood counts and long-term restoration of normal hematopoiesis - an outcome that is plausibly brought about only by the reversal of abnormalities the bone marrow stem cell niches. In this work, we investigate the use of azacytidine in both HSCs and MSCs of MDS patients in order to better understand its therapeutic mechanism on stem cell niches, as well as to inform strategies for the development of future therapies for similar hematopoietic disorders. Methods: Cryopreserved BM MDS samples (n=20) were obtained from the Department of Hematology repository at Singapore General Hospital. Healthy MSCs were derived from bone marrow aspirates of healthy donors, obtained at Singapore General Hospital. Healthy CD34+ HSCs were purchased from Lonza. Osteogeneic and adipogeneic differentiation capabilities and proliferation capacities were performed on MSCs. Proliferation, cell cycling and apoptosis in HSCs were analysed. Gene expression profiling for MDS candidate genes was performed by quantitative PCR on both MSCs and HSCs. Co-culture experiments with healthy CD34+ cells on MDS MSCs were investigated. All assays were performed on both MSCs and HSCs, before and after azacytidine treatment. Results: MDS MSCs have significantly reduced proliferative capacities (p=0.02) and osteogeneic differentiation potentials (p=0.0006) compared to healthy MSCs. Gene expression profiling of MDS MSCs showed a 4.6-fold (n=17; p=0.0002) and 6.2-fold (n=15; p=0.0002) reduction in osteogeneic markers like Runx2 and Osterix respectively. Hematopoietic growth factors and chemokines such as IGF1, IL-8 and Angiopoietin-1 are 5.35-fold (n=17; p<0.0001), 3.36-fold (n=20; p=0.02) and 1.45-fold (n=15; p=0.2) lower than healthy controls. After treatment with azacytidine, MDS MSCs demonstrated significant increased proliferative capacities (n=4; p<0.0001) and differentiation potentials (n=3; p<0.0001) in comparison to healthy MSCs. Significant increase in gene expression of Osterix (n=5; p<0.0001) was seen in comparison to healthy controls. In MDS HSCs, expression of hematopoietic, cell cycling and apoptosis genes such as CXCR4, CCL3, Cyclin D1 and BCL2 are significantly different from healthy HSC - 13 fold (n=15; p=0.1005), 6.8 fold (n=15; p=0.014), 20 fold (n=19; p=0.2673) and 5.26 fold (n=19; p=0.0478) lower than healthy HSCs, respectively. Proliferation of MDS HSCs in culture was 3.3 fold higher than healthy HSCs but treatment with azacytidine of 1µM and 5µM reduced the growth advantage of MDS HSCs to 3 fold and 4.2 fold in comparison with similarly treated healthy controls. Co-culture experiments of healthy CD34+ cells on MDS MSCs, induced a gene expression profile in healthy HSCs similar to MDS HSC. After treatment of MDS MSCs with azacytidine, the gene expression of expanded healthy CD34+ cells was normal. Conclusion: MDS stromal cells are functionally abnormal and have the ability to instruct healthy HSCs to adopt genetic features that resemble MDS HSCs. Treatment with azacytidine restores normal function to MDS MSCs while conferring a growth disadvantage to MDS HSCs but not healthy HSCs. These observations help elucidate for the first time a possible mechanism of action by azacytidine on stromal cells in the treatment of MDS and further suggest that therapies which also target stromal elements in bone marrow niches may be necessary in achieving more favorable outcomes for hematopoieic disorders such as MDS. Disclosures Hwang: Janssen-Cilag, Singapore: Honoraria, Other: Travel Support; Celgene, Singapore: Honoraria, Other: Travel Support; Roche, Singapore: Honoraria, Other: Travel Support; Pfizer, Singapore: Honoraria, Other: Travel Support; Novartis, Singapore: Honoraria, Other: Travel Support; BMS, Singapore: Honoraria, Other: Travel Support; MSD, Singapore: Honoraria, Other: Travel Support; Sanofi, Singapore: Honoraria, Other: Travel Support.

Individual Gene Expression Profiling of Bone Marrow CD34 Cells in Acquired Severe Aplastic Anemia (aSAA) in Children.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 978-978 ◽  
Author(s):  
Bernd Hubner ◽  
Sylvia Merk ◽  
Sonja Rauhut ◽  
Martin Dugas ◽  
Torsten Haferlach ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Differentially Expressed Genes ◽  
Expression Profiling ◽  
Cell Metabolism ◽  
Cell Communication ◽  
Differentially Expressed ◽  
Cd34 Cells ◽  
The Individual

Abstract Acquired SAA in children is a rare, life-threatening disease characterized by pancytopenia and bone marrow hypocellularity. There is good clinical and laboratory evidence that a T-cell mediated immune attack against stem and progenitor cells plays an important role in the pathogenesis of SAA. However, due to the paucity of residual CD34 positive cells at diagnosis still only little is known about the stem cells and their response to the autoimmune attack in SAA in children. To further investigate the characteristics of CD34 cells in SAA we compared the individual transcriptomes of CD34 cells of 9 newly diagnosed, untreated pediatric SAA patients with 8 pediatric healthy controls. Hematopoietic stem cells were isolated with high efficiency from bone marrow by Ficoll density centrifugation and subsequent affinity purification using Dynabeads (Dynal, Invitrogen). Expression profiling experiments were performed using the two cycle amplification system and the HG-U133 plus 2.0 array (Affymetrix). Gene expression data were analyzed using R 2.3.0 and Bioconductor 1.8. packages (Affymetrix, multtest). Raw data were normalized using robust multiarray average (RMA) algorithm. Probe sets with “absent” calls in more than 50% of samples in the smaller group were identified and omitted from further analysis. To determine differentially expressed genes, t-test was applied. P value adjustments for multiple comparisons were done using the step-up false discovery rate (FDR) controlling method proposed by Benjamini and Hochberg. Overall 402 genes were differentially expressed in children with SAA compared to controls (p &lt; 0.05), 288 genes were downregulated and 114 were upregulated. Gene ontology analyses (FatiGO) indicated that biological processes in CD34 cells are significantly affected in pediatric SAA by mainly downregulation of genes for cell metabolism (78 down, 30 up), cell communication/adhesion (48 down, 25 up), growth and differentiation (15 down, 4 up) and stress response (16 down, 3 up). Unexpectedly only very few genes involved in cell death/apoptosis (5 down, 4 up) were differentially expressed. Genes encoding for DNA/RNA binding proteins (28 down, 14 up) and ion binding proteins (47 down, 18 up) were also mainly downregulated. Despite the extremely low numbers of residual CD34 cells present in the bone marrow of children with untreated SAA we were able to analyze the individual transcriptome pattern of single patients. These patterns showed homogeneously and significantly different gene expressions in the group of affected children when compared to controls. Genes involved in apoptosis seem to be less altered in there expression than expected from adult data. These observation might be consistent with the major clinical finding in these children of almost empty bone marrows where most of the apoptotic cell death has already taken place. In the tiny population of “survivors” most of the differentially expressed genes are involved in cell metabolism and cell communication or adhesion. These unexpected results provide new hints for further investigations regarding the involvement of CD34 cells in the pathogenesis of childhood aSAA.

Efficacy of Bone Marrow Mononuclear Cells to Promote Bone Regeneration Compared With Isolated CD34+ Cells From the Same Volume of Aspirate

2010 ◽  
Vol 34 (7) ◽  
pp. 594-599 ◽  
Author(s):  
Shinji Yasuhara ◽  
Yuji Yasunaga ◽  
Takashi Hisatome ◽  
Masakazu Ishikawa ◽  
Takuma Yamasaki ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Bone Regeneration ◽  
Mononuclear Cells ◽  
Bone Marrow Mononuclear Cells ◽  
Cd34 Cells

scholarly journals Paracrine Effects of Bone Marrow Mononuclear Cells in Survival and Cytokine Expression after 90% Partial Hepatectomy

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Carlos Oscar Kieling ◽  
Carolina Uribe-Cruz ◽  
Mónica Luján López ◽  
Alessandro Bersch Osvaldt ◽  
Themis Reverbel da Silveira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Liver Failure ◽  
Acute Liver Failure ◽  
Partial Hepatectomy ◽  
Mononuclear Cells ◽  
Bone Marrow Mononuclear Cells ◽  
Remnant Liver ◽  
Promising Alternative ◽  
Paracrine Effects

Acute liver failure is a complex and fatal disease. Cell-based therapies are a promising alternative therapeutic approach for liver failure due to relatively simple technique and lower cost. The use of semipermeable microcapsules has become an interesting tool for evaluating paracrine effects in vivo. In this study, we aimed to assess the paracrine effects of bone marrow mononuclear cells (BMMC) encapsulated in sodium alginate to treat acute liver failure in an animal model of 90% partial hepatectomy (90% PH). Encapsulated BMMC were able to increase 10-day survival without enhancing liver regeneration markers. Gene expression of Il-6 and Il-10 in the remnant liver was markedly reduced at 6 h after 90% PH in animals receiving encapsulated BMMC compared to controls. This difference, however, was neither reflected by changes in the number of CD68+ cells nor by serum levels of IL6. On the other hand, treated animals presented increased caspase activity and gene expression in the liver. Taken together, these results suggest that BMMC regulate immune response and promote apoptosis in the liver after 90% PH by paracrine factors. These changes ultimately may be related to the higher survival observed in treated animals, suggesting that BMMC may be a promising alternative to treat acute liver failure.

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