scholarly journals Identification of Endogenous Control miRNAs for RT-qPCR in T-Cell Acute Lymphoblastic Leukemia

2018 ◽  
Vol 19 (10) ◽  
pp. 2858 ◽  
Author(s):  
Monika Drobna ◽  
Bronisława Szarzyńska-Zawadzka ◽  
Patrycja Daca-Roszak ◽  
Maria Kosmalska ◽  
Roman Jaksik ◽  
...  

Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. Universal endogenous controls are lacking, thus candidate normalizers must be evaluated individually for each experiment. Here we present a strategy that we applied to the identification of optimal control miRNAs for RT-qPCR profiling of miRNA expression in T-cell acute lymphoblastic leukemia (T-ALL) and in normal cells of T-lineage. First, using NormFinder for an iterative analysis of miRNA stability in our miRNA-seq data, we established the number of control miRNAs to be used in RT-qPCR. Then, we identified optimal control miRNAs by a comprehensive analysis of miRNA stability in miRNA-seq data and in RT-qPCR by analysis of RT-qPCR amplification efficiency and expression across a variety of T-lineage samples and T-ALL cell line culture conditions. We then showed the utility of the combination of three miRNAs as endogenous normalizers (hsa-miR-16-5p, hsa-miR-25-3p, and hsa-let-7a-5p). These miRNAs might serve as first-line candidate endogenous controls for RT-qPCR analysis of miRNAs in different types of T-lineage samples: T-ALL patient samples, T-ALL cell lines, normal immature thymocytes, and mature T-lymphocytes. The strategy we present is universal and can be transferred to other RT-qPCR experiments.

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1439-1439 ◽  
Author(s):  
Hamilton L. Gimenes-Teixeira ◽  
Guilherme A. dos Santos ◽  
Dalila L. Zanette ◽  
Priscila S Scheucher ◽  
Luciana Correa Oliveira de Oliveira ◽  
...  

Abstract Abstract 1439 T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of immature T cells that accounts about 15% of pediatric and 25% of adult ALL cases. In the last years, several clinical and laboratory features have been described as prognostic markers; nevertheless, with intensification of therapy most of them have lost their predictive value. MicroRNA (miRNA) expression analysis has proved to be an useful tool for identifying specific subsets of cancer patients with relevant cytogenetic, laboratorial and clinical features. The aim of the present study was to determine if miRNAs may be useful markers in T-ALL. First, we performed a supervised analysis comparing the miRNA expression profile of T-ALL blasts from 36 T-ALL/CD56− and 12 T-ALL/CD56+. We selected CD56 as prognostic marker based on our previous report showing that the disease-free survival (DFS) of T-ALL/CD56+ patients was of 28.5 months compared to 69.8 in the CD56− group. Also patients tended to be older and to present normal platelet counts in the T-LLA/CD56+ group. We used the Taqman MicroRNA Assay Human Panel (Applied Biosystems) to perform a screening of 164 knowledge mature miRNA sequences using specific primers and probes according to manufacturer instructions. Total RNA input was normalized based on the geometric means of Ct values obtained from four endogenous RNAs. All reactions were run in duplicate and a coefficient of variation greater than 5% was used as an exclusion factor (seven miRNAs were excluded). The fold change was calculated using comparative 2−δCt method. We have identified a set of 14 miRNAs differentially expressed, of which miR-374 and miR-221 best distinguished T-ALL/CD56+ from T-ALL/CD56− blasts. Based on this profile, we selected miR-221 and miR-374 as potential markers and quantified their expression in the same samples using RQ-PCR. Patients were stratified as high and low expression using the median value as cut off. We detected a significant association between the miR-221 high expression and poorer treatment outcome. On the contrary, miR-374 expression levels were not associated with treatment outcome. We evaluate the impact of age, white blood cell counts, CD56 and miR221 expression on overall survival (OS). Age and miR-221 were the only ones found to be significant. The estimate 5-year OS (mean and confidence interval 95%) was of 67.0 ± 10.3% in the group of patients expressing miR-221 below the cut-off value, whereas this value was of 28.5 ± 14.5% in the alternative group. Even among T-ALL/CD56− patients, the higher expression of miR-221 was significantly associated with poorer outcome. Our data suggest that miR-221 play an important role in T-ALL and its regulation may represent a potential therapeutic intervention. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1296-1296
Author(s):  
Marc R Mansour ◽  
Takaomi Sanda ◽  
Lee N Lawton ◽  
Xiaoyu Li ◽  
Taras Kreslavsky ◽  
...  

Abstract Abstract 1296 The oncogenic transcription factor TAL1/SCL is aberrantly expressed in over 40% of cases of human T-cell acute lymphoblastic leukemia (T-ALL) and causes T-ALL in murine transgenic models, emphasizing its importance in the molecular pathogenesis of this disease. However, the mechanism by which TAL1 leads to transformation of thymocytes is unclear. Dysregulation of miRNAs play an important role in tumorigenesis in diverse cancer types. A recent study identified miR-223 as the most abundant miRNA in T-ALL patient samples and was oncogenic by virtue of its ability to accelerate Notch-induced T-ALL in a murine model (Mavrakis et al. Nature Genetics 2011). However, the underlying mechanisms leading to dysregulated miRNA expression in T-ALL remain poorly understood. In order to explore the hypothesis that aberrant expression of miRNAs is mediated by the TAL1 oncogene in T-ALL, we generated high-resolution maps of the genome-wide occupancy of the TAL1 complex, including E2A, HEB, GATA3, LMO2 and RUNX1 by chromatin immunoprecipitation coupled to massively parallel DNA sequencing (ChIP-seq). Analysis of binding sites in two TAL1-positive T-ALL cell lines (Jurkat and CCRF-CEM cells) and two primary T-ALL samples identified 54 miRNAs where binding of the TAL1 complex was within 10 kb of either the transcriptional start sites or the start sites of genes that contain miRNAs in their intronic regions. To determine which of these miRNAs were not only directly bound, but also regulated by the TAL1 complex, we analyzed global changes in miRNAs after knockdown of TAL1 in Jurkat cells using two independent shRNAs. By miRNA expression profiling, we identified significant changes in expression of 25 miRNAs, of which nine were down-regulated on TAL1 knockdown (and thus positively regulated by TAL1) and 16 were up-regulated on TAL1 knockdown (and thus negatively regulated by TAL1). Of these 25 miRNAs, four (miR-223, miR181a*, miR-26a and miR-29c) were shown to be direct targets of the TAL1 complex based on our ChIP-seq data. We chose to focus on miR-223 because it exhibited the most dynamic down-regulation after TAL1 knockdown. ChIP-qPCR validated binding of the TAL1 complex to a region within 4 kb of the miR-223 transcriptional start site. Analysis of RNA polymerase II and CBP binding showed significant enrichment, and high levels of H3K4M3 and H3K79M2 modification were detected indicative of transcriptional initiation and elongation of this locus. Furthermore, expression of miR-223 was significantly higher in the TAL1-positive cell lines (n=13) as compared to the TAL1-low cells (n=10) (P<0.0001). miR-223 levels also closely mirrored TAL1 levels in murine thymic subsets, with marked down-regulation after the DN2 stage, suggesting miR-223 is a physiological target of TAL1 during normal thymic development, and that its overexpression in TAL1-positive T-ALL cells, arrested at the double-positive (DP) stage, is aberrant compared to their normal DP counterpart. To test the hypothesis that the growth inhibition observed after TAL1 knockdown is mediated by decreases in miR-223 expression, we retrovirally infected Jurkat and RPMI-8402 T-ALL cell lines with a miR-223 construct, such that miR-223 expression was no longer under the control of TAL1 in these cells. Forced expression of miR-223 partially rescued the growth inhibitory effects induced by TAL1 knockdown, in both a lentiviral and doxycycline-inducible shRNA system. Additionally, inhibition of mature miR-223 by lentiviral infection of a miR-223 shRNA construct led to significant growth inhibition of TAL1-positive cell lines through the induction of apoptosis. Thus, maintenance of miR-223 expression is required for optimal growth of TAL1-positive T-ALL cells. The highest ranked predicted target of miR-223 by Targetscan is the FBXW7 tumor suppressor, a ubiquitin ligase that is mutated in a significant proportion of T-ALL patients and targets oncogenes such as c-MYC, NOTCH and mTOR for degradation. Accordingly, overexpression of miR-223 in TAL1-low miR-223-low T-ALL cells markedly down-regulated FBXW7 protein expression. Furthermore, the up-regulation of FBXW7 protein expression observed on knockdown of TAL1 in TAL1-positive cell lines could be prevented by retroviral miR-223 expression. Thus, miR-223 is an important target of TAL1 and links the TAL1 oncogene to repression of the FBXW7 tumor suppressor. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2822-2822
Author(s):  
Daniel Ribeiro ◽  
Inês Lopes ◽  
Marta Abreu ◽  
Carlos Custódia ◽  
Joao Barata

Abstract T-cell acute lymphoblastic leukemia (T-ALL), an aggressive and common childhood hematological malignancy, arises from clonal expansion of T-cell progenitors. Autophagy is a homeostatic process characterized by the sequestration of cytoplasmic compartments within double-membrane vesicles (autophagosomes) to promote their degradation. Importantly, autophagy is upregulated during starvation and cellular stress, as a compensatory mechanism to provide nutrients and stress relief. By mitigating stress and allowing cell survival, autophagy may serve as a pro-tumoral mechanism. On the other hand, persistent autophagy can lead to cell death and thereby prevent tumor growth. Interleukin-7 (IL-7), a cytokine produced by the bone marrow and thymic stroma, is essential for normal T-cell development. However, IL-7-mediated signaling can also contribute to leukemogenesis. A majority of T-ALL patients (~70%) expresses the IL-7 receptor and IL-7 accelerates T-ALL progression in vivo and promotes T-ALL cell proliferation, survival and metabolic activation in vitro via PI3K/Akt/mTOR pathway (a master negative regulator of autophagy). IL-7 can also activate MEK/Erk pathway (which has been implicated in promotion of autophagy). Because IL-7 has the ability to activate signaling pathways with potentially opposing roles in autophagy regulation, we explored whether IL-7 impacted on the autophagic process in T-ALL cells and sought to elucidate the molecular mechanisms and functional consequences of IL-7-mediated autophagy regulation under different culture conditions: a) medium with 10% serum - a scenario where cells have optimal growth conditions, b) medium with low (1%) serum - to mimic a milieu with nutrient stress (which may happen in densely populated leukemic niches in vivo), and c) regular medium plus asparaginase (ASNase) - to induce treatment-imposed stress. Using IL-7-responsive T-ALL cell lines and patient-derived xenograft (PDX) samples, we show that, in optimal culture conditions, IL-7 leads to a decrease in LC3-I/-II conversion and a reduction in both LC3 puncta and autophagosome/autolysosome formation, as determined by immunoblot, confocal microscopy, flow cytometry and electron microscopy - indicating that IL-7 inhibits autophagy in T-ALL. Using signaling-specific small molecule inhibitors (UO126 for MEK/Erk; LY294002 and rapamycin for PI3K/Akt/mTOR) we found that IL-7-mediated regulation of autophagy occurs in a complex manner that involves concomitant triggering of both pro- (via MEK/Erk) and anti- (via PI3K/Akt/mTOR) autophagic signaling, with the effects of the latter prevailing over the former. In this scenario, IL-7-mediated viability relies on PI3K/Akt/mTOR pathway and, as expected, autophagy inhibition (using MRT68921) does not prevent the ability of IL-7 to promote leukemia cell survival. In contrast, under serum starvation IL-7 promotes autophagy, and IL-7-mediated leukemia cell viability partially relies on autophagy activation, and strictly requires MEK/Erk activation. Mechanistically, we provide evidence that depending on the culture conditions, IL-7 can balance the relative activation of PI3K/Akt/mTOR and MEK/Erk pathways, inhibiting or facilitating autophagy, in order to consistently promote T-ALL cell viability. We further extended our studies to a therapy-related scenario and found that under ASNase treatment, IL-7 still promotes increased survival of leukemic cells, a possible mechanism of treatment resistance. Functionally, we demonstrate that the IL-7-mediated increase in survival under ASNase treatment is, in part, mediated via activation of autophagy, suggesting that combining ASNase administration with autophagy inhibitors may be an attractive strategy to prevent resistance. In summary, our results indicate that IL-7 makes use of a 'flexible strategy' to promote T-ALL cell viability by activating both pro- and anti-autophagic pathways, which are differentially recruited, depending on the microenvironmental conditions, to prevent tumor cell death. Moreover, our findings strengthen the notion that combination therapies against PI3K/Akt/mTOR and MEK/Erk pathways may constitute a valid therapeutic avenue and highlight the potential of using autophagy inhibitors to prevent microenvironment-induced chemotherapy resistance in T-ALL. Disclosures Barata: Instituto de Medicina Molecular João Lobo Antunes: Patents & Royalties: Patents.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3065-3065
Author(s):  
Hamilton L. Gimenes-Teixeira ◽  
Dalila L. Zanette ◽  
Guilherme Augusto S. dos Santos ◽  
Priscila S. Scheucher ◽  
Leandro F. Dalmazzo ◽  
...  

Abstract Abstract 3065 Poster Board III-2 Deregulations of miRNA expression and function in B-cell acute lymphoblastic leukemia (B-ALL) have been associated with specific recurrent citogenetic abnormalities and clinical outcomes. In contrast, there is few data about miRNAs in T-cell acute lymphoblastic leukemia (T-ALL). We have determined the miRNA expression profile of 48 T-ALL patients' blasts and compared with normal mature T cells. We used the Taqman MicroRNA Assay Human Panel to screen 164 known mature miRNA sequences. Normal CD3+ cells were isolated from peripheral blood of four healthy subjects by immunomagnetic labeling. Total RNA was pooled and reverse transcribed with specific looped RT primers, and expression was evaluated by quantitative real-time PCR (RQ-PCR). Reactions were performed in duplicates and samples with a coefficient of variation greater than 5% were excluded. Furthermore, we considered as differentially expressed those miRNAs with fold change values higher than 10 or lower than 0.1. With this strategy we identified four miRNAs that were hyper-expressed (miR-181a, miR-181b, miR-213 and miR-29b) and three hypo-expressed (miR-150, miR-95, miR-338) in the leukemic pool. In order to confirm our findings, we then performed the analysis of miR-181a, miR-181b and miR-29b expression on 52 individual samples (48 T-ALL and 4 normal T cell samples) using RQ-PCR. Forty-five (93.7%) and 46 (95.8%) of the T-ALL samples presented expression levels of miR-29b and of miRs 181a/181b higher than the maximum detected in the normal samples. The analysis of the predicted targets for these three miRNAs was performed using miRNApath. MAPK signaling was the pathway with the highest number of target genes with 60 genes, of which MAP4K4, FOS, RAP1B, AKT3 and NLK were commonly targeted by all three miRNAs. As deregulation of the MAPK pathway in T-ALL has been previously described, we hypothesized that the hyper-expression of miR-29b, miR-181a and miR181b may be associated with this aberrant MAPK signaling. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Kehan Li ◽  
Cunte Chen ◽  
Rili Gao ◽  
Xibao Yu ◽  
Youxue Huang ◽  
...  

AbstractT-cell acute lymphoblastic leukemia (T-ALL) is an aggressive subtype of leukemia with poor prognosis, and biomarkers and novel therapeutic targets are urgently needed for this disease. Our previous studies have found that inhibition of the B-cell leukemia/lymphoma 11B (BCL11B) gene could significantly promote the apoptosis and growth retardation of T-ALL cells, but the molecular mechanism underlying this effect remains unclear. This study intends to investigate genes downstream of BCL11B and further explore its function in T-ALL cells. We found that PTK7 was a potential downstream target of BCL11B in T-ALL. Compared with the healthy individuals (HIs), PTK7 was overexpressed in T-ALL cells, and BCL11B expression was positively correlated with PTK7 expression. Importantly, BCL11B knockdown reduced PTK7 expression in T-ALL cells. Similar to the effects of BCL11B silencing, downregulation of PTK7 inhibited cell proliferation and induced apoptosis in Molt-4 cells via up-regulating the expression of tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and p27. Altogether, our studies suggest that PTK7 is a potential downstream target of BCL11B, and downregulation of PTK7 expression via inhibition of the BCL11B pathway induces growth retardation and apoptosis in T-ALL cells.


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