scholarly journals Identification and Validation of Novel Reference Genes in Acute Lymphoblastic Leukemia for Droplet Digital PCR

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 376 ◽  
Author(s):  
Vanessa Villegas-Ruíz ◽  
Karina Olmos-Valdez ◽  
Kattia Alejandra Castro-López ◽  
Victoria Estefanía Saucedo-Tepanecatl ◽  
Josselen Carina Ramírez-Chiquito ◽  
...  

Droplet digital PCR is the most robust method for absolute nucleic acid quantification. However, RNA is a very versatile molecule and its abundance is tissue-dependent. RNA quantification is dependent on a reference control to estimate the abundance. Additionally, in cancer, many cellular processes are deregulated which consequently affects the gene expression profiles. In this work, we performed microarray data mining of different childhood cancers and healthy controls. We selected four genes that showed no gene expression variations (PSMB6, PGGT1B, UBQLN2 and UQCR2) and four classical reference genes (ACTB, GAPDH, RPL4 and RPS18). Gene expression was validated in 40 acute lymphoblastic leukemia samples by means of droplet digital PCR. We observed that PSMB6, PGGT1B, UBQLN2 and UQCR2 were expressed ~100 times less than ACTB, GAPDH, RPL4 and RPS18. However, we observed excellent correlations among the new reference genes (p < 0.0001). We propose that PSMB6, PGGT1B, UBQLN2 and UQCR2 are housekeeping genes with low expression in childhood cancer.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1826-1826
Author(s):  
Stuart S. Winter ◽  
Hadya Khawaja ◽  
Zeyu Jiang ◽  
Timothy Griffin ◽  
Barbara Asselin ◽  
...  

Abstract The clinical features of age, white count, and presence of extramedullary disease cannot predict risk for induction failure (IF) in patients who present with T-cell acute lymphoblastic leukemia (T-ALL). On the basis of recent observations that gene expression profiles can distinguish clinicopathologic cohorts of patients with acute leukemia, we hypothesized that microarray analyses performed on diagnostic T-ALL bone marrow samples might identify a genomic classifier for IF patients. Using a case-control study design for children and young adults treated for T-ALL on Children’s Oncology Group Study 9404, we analyzed 50 cryopreserved T-ALL samples using Affymetrix U133A Plus 2 genechips, which have 54,000 genes, ESTs and genomic classifiers. Following RMA normalization, we used Prognostic Multi-array Analysis (PAM) to identify a 116-member genomic classifier that could accurately identify all 6 IF cases from the 44 patients who achieved remission. Within the IF cohort, 37 genes were up-regulated and 79 were down-regulated in comparison to other outcome groups. To further investigate the genetic mechanisms governing IF, we developed four cell lines with acquired drug resistance: Jurkat and Sup T1; each having resistance to daunorubicin (DNR) and asparaginase (ASP). Using a comparative analysis for fold-change in gene expression among 6 IF patients and the T-ALL DNR and ASP-resistant cell lines, we identified seven genes that were up-regulated, and another set of seven genes that were commonly down-regulated. To validate the potential use of our 116-member gene set in predicting IF in T-ALL, we tested our genomic classifier in 42 cases which were treated on COG study 8704 and hybridized to the Affymetrix U133Av.2 chip. Because only 85 probes were shared between U133A Plus 2 and U133Av. 2 chips, we employed shrunken class centroids to constrain our classifier to 25 rank-ordered probes. This smaller classifier correctly identified the single IF case in 8704, as well as another patient who was an early treatment failure, indicating that similar genomic classifiers may identify IF patients in different clinical trials. These results indicate that genetic profiling may be useful in prospectively identifying IF patients in T-ALL. In addition, we identified genes that were commonly upregulated in IF patients and T-ALL cell lines with intrinsic drug resistance.


Leukemia ◽  
2018 ◽  
Vol 32 (10) ◽  
pp. 2117-2125 ◽  
Author(s):  
Rebeqa Gunnarsson ◽  
Sebastian Dilorenzo ◽  
Kristina B Lundin-Ström ◽  
Linda Olsson ◽  
Andrea Biloglav ◽  
...  

Hematology ◽  
2014 ◽  
Vol 20 (7) ◽  
pp. 377-383 ◽  
Author(s):  
Jun Li ◽  
Xiaowen Zhai ◽  
Hongsheng Wang ◽  
Xiaowen Qian ◽  
Hui Miao ◽  
...  

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 453-453
Author(s):  
Gianluigi Zaza ◽  
Meyling Cheok ◽  
Wenjian Yang ◽  
Pei Deqing ◽  
Cheng Cheng ◽  
...  

Abstract Thioguanine nucleotides (TGN) are considered the principal active metabolites exerting the antileukemic effects of mercaptopurine (MP). Numerous clinical studies have reported substantial inter-patient variability in intracellular TGN concentrations during continuation therapy of acute lymphoblastic leukemia (ALL). To identify genes whose expression is related to the intracellular accumulation of TGN in leukemia cells after in vivo treatment with MP alone (MP) or in combination with MTX (MP+MTX), we used oligonucleotide microarrays (Affymetrixâ HG-U95Av2) to analyze the expression of approximately 9,670 genes in bone marrow leukemic blasts obtained at diagnosis from 82 children with ALL. TGN levels were determined in bone marrow aspirates of these patients 20 hours after mercaptopurine infusion (1 g/m2 I.V). Because, as previously reported, patients treated with MP alone achieved higher levels of intracellular TGN compared to those treated with the combination, we used Spearman’s rank correlation to identify genes associated with TGN levels separately for the 33 patients treated with MP alone and the 49 with the combination (MP: median TGN: 2.46 pmol/5x106 cells, range: 0.01–19.98; and MTX+MP: median TGN: 0.55 pmol/5x106 cells, range: 0.005–3.31). Hierarchical clustering using these selected probe sets clearly separated the 33 patients treated with MP alone into two major groups according to TGN concentration (< 2.46 and > 2.46 pmol/5x106 cells; n=60 genes) and two major branches were also found for patients treated with the combination (< 0.55 and > 0.55 pmol/5x106 cells; n=75 genes). Interestingly, there was no overlap between the two sets of genes, indicating that different genes influence the accumulation of TGN when this drug is given alone or in combination with MTX. The association between gene expression profiles and TGN levels determined by leave-one-out cross-validation using support vector machine (SVM) based on Spearman correlation, was rho=0.60 (p<0.001) for MP alone and rho=0.65 (p<0.001) for MTX+MP, with false discovery rate (FDR) computed using Storey’s q-value (MP: 50% true positive, MTX+MP: 70% true positive respectively). Genes highly associated with the post-treatment TGN level in ALL patients treated with MP alone encode transporters, enzymes involved in the MP metabolic pathway and cell proliferation. Genes associated with post-treatment levels of TGN after combined therapy have been implicated in protein and ATP biosynthesis. Together, these in vivo data provide new insights into the basis of inter-patient differences in TGN accumulation in ALL cells, revealing significant differences between treatment with MP alone or in combination with MTX.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4282-4282
Author(s):  
Ronald W. Stam ◽  
Stefan Bohlander ◽  
Renate Kirschner-Schwabe ◽  
Susan Arentsen-Peters ◽  
Rob Pieters ◽  
...  

Abstract Gene expression profiles (GEPs) are becoming increasingly more important for diagnostic procedures, allowing clinical predictions including treatment response and outcome for various types of cancer. However, established gene signatures not always appear helpful in understanding underlying disease mechanisms. Therefore, we explored an alternative approach for analyzing GEPs of a group of t(4;11) positive infant acute lymphoblastic leukemia patients (n=15), a highly aggressive type of MLL rearranged leukemia. We developed a method that uses a relational database program in combination with a normalization approach and specific discriminators. For normalization, every GEP of a given t(4;11) positive ALL sample was compared with 3 GEPs of normal bone marrow aspirates derived from healthy donors. Using the GeneChip Analysis Suite 5.0 program for single comparison analysis, the resulting gene lists were then compared with each other and only consistently identified genes (present on all three gene lists) were used for further analysis. This noise reduction decreased the amount of potentially deregulated target genes to about 30–40%. The remaining gene lists represented highly significant target genes that were then incorporated into a relational database program using specific discriminators. These discriminators were: upregulation of HOXA9 and HOXA10, presence/absence of the AF4-MLL fusion transcripts in addition to the MLL-AF4 fusion, and the localization of the genomic breakpoint within the MLL gene. This pilot study led to promising results, surprisingly classifying individual t(4;11) positive ALL patients into two distinct subgroups. Both subgroups share about 80 target genes, but also display particular sets of subgroup specific target genes. Importantly, these identified target genes can directly be linked to biological properties of t(4;11) positive leukemia cells, and therefore, allow important novel insights into this aggressive type of leukemia in infants.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1074-1074
Author(s):  
Ying Cheng ◽  
Kudakwashe Chikwava ◽  
Chao Wu ◽  
Anchit Bhagat ◽  
John K. Choi ◽  
...  

Abstract B-precursor acute lymphoblastic leukemia (B-ALL) is the leading cause of cancer-related deaths in children and commonly has a poor outcome in adults. Gene profiling and exome sequencing of high-risk ALLs led to the recent identification of the Philadelphia chromosome (Ph)-like ALL subtype. These leukemias have gene expression profiles similar to BCR-ABL1-positive (Ph+) ALL, but lack a BCR-ABL1 rearrangement, and often result in poor outcomes. Many Ph-like ALL-associated mutations identified to date are known or predicted to activate oncogenic cytokine receptor signaling pathways, particularly those associated with JAK. The lymphocyte adaptor protein LNK (also called SH2B3) has emerged as a powerful negative regulator of cytokine-mediated JAK2 signaling in hematopoietic stem cells (HSCs). Loss-of-function LNK mutations and deletions have recently been described in B-ALL, and germline loss of LNK contributes to pediatric ALL development. However, the mechanisms by which LNK alterations impact leukemogenesis remain poorly understood. Here we show that LNK synergizes with TP53 and INK4a in suppressing B-ALL development in mice. Tp53-/-Lnk-/- mice developed highly aggressive and transplantable B-ALL with 100% penetrance in contrast to T-lymphoma or sarcoma development observed in Tp53-/- mice. Importantly, gene expression profiles of Tp53-/-Lnk-/- B-ALL blasts were similar to those of human Ph-like B-ALLs, validating the relevance of this model for preclinical studies. Tp53-/-Lnk-/- pro-B progenitors initiated B-ALL in the transplanted recipients, and Lnk loss-of-heterozygosity (LOH) was found exclusively in B-ALL cells from Tp53-/-Lnk+/- mice, but not in HSCs, common lymphoid progenitors, or cells of myeloid/T cell lineages, attesting that LNK is a bona fide tumor suppressor in the committed B-cell precursors. Mechanistically, we found that pre-leukemic Lnk-/-Tp53-/- pro-B progenitors were hypersensitive to IL-7 and showed markedly enhanced self-renewal ability in vitro and in vivo. Our genetic studies revealed that LNK controls normal B cell and B-ALL development independently of its effects on HSCs and specifically regulates pro-B cell homeostasis. A novel phosphoflow cytometry approach in freshly isolated BM cells that combines the surface marker B220, intracellular mu-heavy chain detection, and phospho-specific antibodies enabled separation of subpopulations of B progenitors with distinct IL-7 responsiveness. Using this approach, we demonstrated that LNK deficiency potentiated STAT5 activation in response to IL-7 in pre-leukemic pro-B cells. Of note, Lnk-/-p53-/- leukemic blasts with elevated pSTAT5, were less sensitive to JAK inhibitors than pre-leukemic B progenitors, in part due to constitutive activation of MAPK and AKT/mTOR pathways. Our results invoke the targeting of these pathways as novel therapeutic approaches in B-ALL. In sum, we have developed a novel B-ALL mouse model suitable for preclinical studies aimed at further deciphering the pathogenic mechanisms underlying this disease and exploring new therapeutic strategies. Disclosures No relevant conflicts of interest to declare.


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