bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Critical Role of Peptidyl-Prolyl cis/trans Isomerase, Pin1 in Acute Myeloid Leukemia with C/EBPalpha Mutations.
Authors: Pulikkan J. , Zada A. Peer , Geletu M. , Dengler V. , Tenen Daniel G. , Behre G. 
Published: October 2019

Abstract
CCAAT enhancer binding protein alpha (C/EBPα) is a myeloid specific transcription factor that coordinates cellular differentiation and cell cycle arrest. Loss of C/EBPα expression or function in leukemic blasts contributes to a block in myeloid cell differentiation. C/EBPα is mutated in around 9% of acute myeloid leukemia (AML). The mutations reported in C/EBPα are frame shift mutations and point mutations at basic region Leucine zipper. The mutant form of C/EBPα ie C/EBPα-p30 exhibits dominant negative function over the wild type protein. The role of peptidyl-prolyl cis/trans isomerase, Pin1 in tumorogenesis and its overexpression in many cancers led us to investigate its role in acute myeloid leukemia with C/EBPα mutation. Here we show that Pin1 is upregulated in patients with acute myeloid leukemia by affymetrix analysis. By quantitative Real-Time RT-PCR analysis, we show C/EBPα-p30 could induce Pin1 transcription, while the wild type C/EBPα downregulates Pin1 expression. Luciferase promoter assay for the Pin1 promoter shows that wild type C/EBPα is able to block Pin1 promoter activity. Mean while, C/EBPα-p30 couldn’t block Pin1 promotor activity. By silencing Pin1 by RNA Interference as well as with inhibitor against Pin1 (PiB) we could show myeloid differentiation in human CD34+ cord blood cells as well as in Kasumi-6 cells as assessed by FACS analysis with granulocytic markers. We investigated the mechanism underlying the dominant negative action of C/EBPα-p30 over the wild type protein. We report that Pin1 increases the transcriptional activity of the oncogene c-jun. We also show that c-jun blocks the DNA binding and transactivation of C/EBPα protein as assessed by gel shift assay and promoter assay respectively. We have previously shown that c-jun expression is high in AML patients with C/EBPα mutation and c-jun could block C/EBPα function by protein-protein interaction. Quantitative Real-Time RT-PCR analysis shows that inhibition of Pin1 by the inhibitor PiB downregulates c-jun mRNA expression. In conclusion, inhibition of Pin1 leads to granulocytic differentiation. Our results show Pin1 as a novel target in treating AML patients with C/EBPα mutation.
Hypermethylation of FANCC and FANCL Resulting in a Mitomycine-C (MMC) Sensitive Cellular Phenotype in Sporadic Acute Leukemia.
Authors: Hess Corine J. , Ameziane Najim , Schuurhuis Gerrit Jan , Errami Abdellatif , Denkers Fedor , Hubeek Isabelle , Kaspers Gertjan J.L. , Joenje Hans , Reinhardt Dirk , Ossenkoppele Gert J. , Zwaan Christian M. , Waisfisz Quinten 
Published: October 2019

Abstract
The proteins of the Fanconi anemia/BRCA pathway are thought to function in specific DNA repair processes. Disruption of these genes results in genomic instability and hypersensitivity to DNA cross-linking agents. As illustrated by patients with Fanconi anemia (FA) [OMIM#227650] this cellular phenotype confers an increased risk for the development of malignancies, in particular acute myeloid leukemia (AML). In the past years several studies have shown that inherited and somatic abnormalities in individual FA genes play a role in the development of sporadic cancers. To study the involvement of the FA genes in sporadic cases of leukemia we analyzed the presence of aberrant promoter methylation of the 11 known FA genes by Methylation Specific-Multiplex Ligation dependent Probe Amplification (MS-MLPA).
We studied 119 unselected adult AML bone marrow samples and 20 pediatric AML samples that were selected on the bases of a complex karyotype. A single adult patient sample, diagnosed biphenotypic AML, showed aberrant methylation of the promoter region of the FANCC gene. The aberrant methylation pattern was also present at relapse. Another four biphenotypic AML samples, together with 15 adult and 82 pediatric ALL samples were subsequently analyzed. In this group, one adult ALL sample showed FANCL promoter methylation and three pediatric ALL samples showed FANCC promoter methylation. Phenotypically all four ALL samples were classified as hyperdiploid B-cell precursor ALL. Sodium bisulphite sequencing confirmed hypermethylation of the respective genes in all cases. Colony Forming Unit (CFU) assays were performed to analyze whether hypermethylation of FANCC and FANCL result in an FA-like phenotype of DNA cross-linker sensitivity. Colony formation in the methylated samples as well as control leukemic samples, i.e. without FA-gene methylation, was scored after proliferation in the absence or presence of MMC. Two pediatric ALL samples with FANCC hypermethylation did not show colony formation in the CFU assay. The other four samples with FA gene methylation, including the relapse sample from the biphenotypic AML patient, demonstrated hypersensitivity to MMC in a CFU assay when compared to the controls.
In summary, this is the first report showing FANCC and FANCL promoter hypermethylation in acute leukemia with either partial or complete lymphoid differentiation. Silencing of the corresponding FA genes may contribute to the leukemogenic process by imposing an increased level of spontaneous genomic instability. Cross-linkers may thus be of therapeutic use in these selected patients.
DNA Methylation Independent Silencing of the RARα Gene Expression in Acute Myeloid Leukemia.
Authors: Glasow Annegret , Barrett Angela , Chornet Manuel Boix , Gupta Rajeev , Zhou Da-cheng , Gallagher Robert , von Lindern Marieke , Waxman Samuel , Enver Tariq , Hildebrandt Guido , Zelent Arthur 
Published: October 2019

Abstract
All-trans-retinoic acid (ATRA) and the gene encoding retinoic acid receptor-α (RARα) have been implicated in the pathogenesis and treatment of acute promyelocytic leukemia (APL). Nevertheless, the role of these molecules in the pathogenesis and therapy of non-APL acute myeloid leukemias (AMLs) remains unclear. Previously we have shown that expression of the ATRA-inducible RARα2 isoform is downregulated in a variety of AML cell lines and increases with hematopoietic differentiation along the myelomonocytic lineage. Using quantitative real-time PCR we have now investigated expression of the RARα gene in primary AML cells (n=23) and report that as in AML cell lines the levels of RARα2 mRNAs are markedly reduced (by 48 fold in APL, p≤0.05, and by 52 fold in non-APL AML, p≤0.01) relative to cord blood (CB) derived CD33 (or CD34) positive cell population (n=4). However, in contrast to the AML cell lines and normal hematopoietic progenitors, the expression of the RARα1 isoform was also significantly reduced in primary AML samples (up to 26 fold, p≤0.05). Examination of potential mechanisms underlying the silencing of the RARα gene expression in AML revealed that the RARα2 promoter possesses two small CpG islands that are fully methylated in all AML cell lines examined. Consistent with the expression pattern of RARα1 a single CpG island in the RARα1 promoter region was unmethylated in all these samples. As expected from such results expression of RARα2, but not RARα1, could be stimulated with a DNA demethylating agent 5-aza-2′deoxycytidine and synergistic effects between 5-aza-2′deoxycytidine and ATRA were observed on both RARα2 expression and cellular differentiation of APL and non-APL AML cell lines. Extending this analysis to clinical material we have surprisingly discovered that RARα1 and RARα2 CpG islands are unmethylated in all AML patient samples, including 3 APL cases, suggesting that DNA methylation may not play a significant role in silencing of the RARα gene expression in primary AML cells. Chromatin immunoprecipitation of the RARα2 regulatory region with antibodies to specific histone modifications revealed presence of other negatively acting chromatin states in primary AML samples (relative to normal CD33 positive CB cells), including decreased histone H3 acetylation as well as decreased di- and tri-methylation of histone H3 lysine 4. A possibility that microRNAs targeting sequences in the common 3′-UTR regions of the RARα1 and α2 isoforms may also contribute to silencing of both RARα1 and α2 expression in AML cannot be excluded. These results underscore the complexities of mechanisms that are responsible for silencing of gene expression in AML and support the notion that diminished RARα expression contributes to leukemogenesis.
Identification of Oncogenic Pathways of T-Acute Lymphoblastic Leukemia (T-ALL) through Gene Expression Profiling of Mouse Tumor Models.
Authors: Sulis Maria Luisa , Palomero Teresa , Real Pedro J. , Barnes Kelly C. , Aplan Peter , Copeland Neal , Utpal Dave , Gounari Fotini , Grosveld Gerald , Kappes Dietmar J. , Kee Barbara , Kelliher Michelle , Lenz Jack , Richardson Christine , Ferrando Adolfo 
Published: October 2019

Abstract
Transgenic mouse models of T-cell oncogenes such as TAL1 and LMO1, have confirmed their critical role in the development of T-lymphoblastic lymphoma (T-LL). In addition, retroviral insertional mutagenesis (RIM) in mice is a powerful system for the identification of genes involved in T-cells leukemogenesis. However, incomplete knowledge of the pathogenesis of T-ALL limits the ability to stratify patients and to deliver tailored therapy accordingly. Thus, a major goal is to identify common oncogenic pathways downstream of T-cell oncogenes that can serve as therapeutic targets for the treatment of T-ALL. We hypothesize that T-cell oncogenes operate through a limited number of oncogenic pathways with distinct gene expression profiles. Furthermore, we propose that gene expression profiling of murine models of T-cell lymphomas, which harbor specific genetic lesions, will serve to identify such oncogenic pathways and to establish a molecular classification of T-ALL. To test this hypothesis we have analyzed normal thymus and mouse T-cell lymphomas originated from retroviral insertional mutagenesis (n=11) and transgenic and knock-outs models (n=30) using Affymetrix 430A2.0 microarrays. Unsupervised analysis clearly distinguishes tumor samples from normal thymus and clusters the tumors into three major groups. TAL1, LMO2 and E2 proteins are known to be part of a transcriptional complex and to cooperate in T-cell leukemogenesis by suppressing E2A function. Accordingly, mouse tumors originating in TAL1, TAL1/LMO2 transgenic and E2A knock-out mice share a common gene expression signature and cluster together. Supervised analysis of tumors generated by retroviral mutagenesis showed increased expression of the proviral tagged genes and identified corresponding known downstream targets. Nearest neighbor analysis identified high levels of Notch1 expression in tumors with proviral insertion in the Notch1 locus and in tumors generated in the TAL1/, TAL1/LMO2, OLIG2/LMO1, ThPOK and Ikaros mouse models, which harbored activating mutations in NOTCH1. Our results demonstrate that gene expression profiling identifies common oncogenic pathways in T-cell tumors generated in mice, establishes common mechanisms of transformation for several T-ALL oncogenes and allows coupling of poorly characterized genes identified in proviral insertional sites with well characterized oncogenes and downstream molecular pathways. The identification of mechanisms of T-cell transformation common to tumors of different origin lays the ground for the identification of new therapeutic targets for the treatment of T-ALL.
Identification of Normal and Neoplastic Human Mature B Cells “miRome”.
Authors: Basso Katia , Morozov Pavel , Califano Andrea , Rosolen Angelo , Chau Jacqueline , Chen Chang-Zheng , Dalla-Favera Riccardo 
Published: October 2019

Abstract
The recent discovery of microRNAs (miRs) has added a new dimension to the mechanisms that regulate gene expression in normal cell development. Initial evidence also suggests that structural or functional alterations of miRs are associated with tumorigenesis. Nonetheless, the full set of genomic miRs is not known for any eukaryotic species including humans, since presently known miRs have been identified by virtue of their expression in only a few cell types. Analogous to other transcriptional units, it is conceivable that a significant part of the entire miR genomic pool may display tissue-specific expression. In order to understand the role of miRs in mature B cell function and lymphomagenesis, we planned the isolation of the full set of miRs (miRome) expressed in germinal center (GC) B cells and in GC-derived B cell lymphomas. Toward this end, we constructed libraries representative of all miRs expressed in normal GC B cells isolated from human tonsils and in a Burkitt lymphoma cell line (Ramos). Short RNAs were gel purified and linked to adaptor oligonucleotides, reverse transcribed, PCR amplified, cloned into an expression vector, and subjected to sequencing. Candidate miRs have been aligned to the human genome to retrieve their potential precursor sequences, whose folding characteristics have been analyzed in order to identify bona fide precursors. The cloned and structurally validated miR precursors have been matched to the public miR database to detect previously identified miR sequences. Initial results show that 453 miRs cloned from GC B cells correspond to 99 precursors (59 previously known and 40 newly discovered), while 233 miRs cloned from Ramos cell line identified 42 known and 46 new precursors. Overall, this initial analysis led to the discovery of 76 not previously reported miR precursors. Since less than a third of the available clones have been analyzed, it is expected that a significantly larger number of novel miRs will be identified by our method. A comprehensive analysis of miR expression profiles of normal versus neoplastic GC B cells will be obtained using a dedicated miR chip. Interestingly, initial results indicate that a set of miRs is expressed in normal GC cells, but not in Ramos and other GC-derived Burkitt lymphoma cell lines, suggesting that structural and/or functional alterations of miRs occur during lymphomagenesis.
HOX Expression Patterns Identify Major Cytogenetic Groups and Are of Prognostic Importance in Adult AML.
Authors: Andreeff Michael , Ruvolo Vivian , Gadgil Sharvari , Chen Wenjing , Coombes Kevin , Zeng Chan , Baron Anna , Drabkin Harry 
Published: October 2019

Abstract
Naturally occurring and experimentally-induced deregulation of HOX genes has been causally linked to leukemia and myeloproliferative states. We developed and validated SYBR-green based real-time qRT-PCR assays for the clustered HOXA-D genes as well as other selected homeodomain, trithorax and polycomb genes. These were used to examine 120 cases of adult AML (median age 58 y) with the following cytogenetic classifications: favorable (FAV) 17, intermediate (INT) 53, unfavorable (UNFAV) 46, no analyzable metaphases 4, plus normal CD34+ sorted cells from 4 bone marrow donors. HOX expression patterns were intimately linked to the major cytogenetic subsets and provide a unifying feature for some AML subsets, particularly within the favorable prognostic group. Twenty genes were identified, with a 95% confidence of no false positives, that distinguished the major cytogenetic groups. In general, levels of HOXA genes and MEIS1 distinguished FAV vs. INT and FAV vs. UNFAV groups, while the HOXB and PBX3 levels distinguished either all three groups or INT vs. UNFAV. Comparing 68 patients who achieved a complete response with 49 patients who had resistant disease (or failed induction therapy), 11 genes were differentially expressed with parametric p-values < 0.05. Based on permutation distribution with a 95% confidence level, there were no more than 5 false positives among these 11 genes. Using a COX proportional hazards model and patients for whom survival data were available, HOXA9 and HOXA10 were predictive of overall survival, with parametric p-values <0.05. Lastly, compared to normal CD34+ cells, homeodomain gene expression was abnormal in nearly every AML. Based on these results and the role of HOX deregulation in experimental leukemogenesis, we propose that differences in HOX expression may be responsible for some of the biological differences observed among major cytogenetic subsets in human AML.
The mTOR Inhibitor Temsirolimus (CCI-779) Induces Cell Cycle Arrest and Autophagy in Hodgkin Lymphoma (HL) Cell Lines and Enhances the Effect of the PI3-Kinase Inhibitor LY294002.
Authors: Georgakis Georgios V. , Yazbeck Victor Y. , Li Yang , Younes Anas 
Published: October 2019

Abstract
The PI3K/AKT/mTOR pathway is frequently activated in a variety of cancers giving hope that that this pathway may prove to be a good target for cancer therapy. We and others have recently reported that primary and cultured Hodgkin and Reed-Sternberg cells of HL express the active phosphorylated form of Akt (pAkt) which contribute to their survival. Furthermore, we have demonstrated that inhibition of PI3K by the small molecule LY294002 or Akt inhibition induced cell cycle arrest and apoptosis. However, at the present time there is no PI3K or Akt inhibitors in clinical trials. Instead, several inhibitors of the downstream mTOR kinase are already being evaluated in patients with cancer. Temsirolimus (CCI-779) is an mTOR inhibitor that demonstrated promising clinical activity in patients with relapsed mantle cell lymphoma. To explore the potential clinical activity of Temsirolimus in HL, we examined its efficacy in HL-derived cell lines (HD-LM2, L-428, and KM-H2). Here, we demonstrate that CCI-779 inhibited mTOR, as evident by the inhibition of ribosomal S6 phosphorylation as early as 6 hours, with a dose as low as 1 nM. Temsirolimus induced antiproliferative cytostatic effect in the same dose (1nM) in all HL cell lines, and this effect did not improve with higher concentrations (up to 1000 nM). Furthermore, the effect was predominantly cytostatic with little or no induction of apoptosis. This antiproliferative effect was predominantly due to cell cycle arrest in G0/G1 phase, and was associated with upregulation of p27 cell cycle protein. Although temsirolimus did not induce apoptosis, it induced autophagy, as determined by Acridine Orange staining of the acidic autophagic intracellular organelles and FACS analysis. Combination of 1nM CCI-779 with increasing concentrations of the PI3K inhibitor LY294002 showed a profound decrease in the IC50 of LY294002 in all 3 cell lines. Moreover, the combination of CCI-779 and LY294002 blocked cell cycle at G0/G1 phase more efficiently and significantly increased autophagic cells when compared with each agent alone, but failed to induce apoptosis. This effect was mediated in part by inhibiting a negative feedback loop involving AKT phosphorylation. Collectively, our data suggest that temsirolimus may have a therapeutic value in HL.
Genetic Polymorphisms in the Folate Pathway and Risk of Childhood Acute Lymphoblastic Leukemia (ALL): MTHFR, MTHFD1, RFC1 and TS.
Authors: Yeoh Allen Eng-Juh , Kham Shirley Kow-Yin , Lu Yi , Foo Toon-Chai , Ariffin Hany , Quah Thuan-Chong 
Published: October 2019

Abstract
Folate is critical for DNA synthesis and methylation; dysfunction in methylating enzymes may result in genomic instability and DNA damage via the nucleotide synthesis pathways. We hypothesize that perturbation in the folate metabolism pathway may alter the risk of developing childhood leukaemia. We recently reported that methylenetetrahydrofolate reductase (MTHFR 677C>T) was associated with reduced risk in childhood ALL.
We aim to explore the value of a pathway approach, in this case exploring the impact of polymorphisms in multiple enzymes involved in the folate pathway, to determine its role in development of childhood ALL. As childhood ALL is highly heterogeneous and that some like TEL-AML1 and hyperdiploid subgroups have in utero origin, we postulated that the impact of folate metabolism may be greatest for in utero onset ALL. We analyzed the methylenetetrahydrofolate dehydrogenase (MTHFD1), reduced folate carrier (RFC1) and thymidylate synthase (TSER 5′-UTR 28bp repeat, TSER 3′-UTR 6bp deletion) in 360 children with ALL and 433 controls of Chinese and Malay origin (Ch=221, Mal=212). Genotyping was performed by RFLP-PCR, TEL-AML1 by RT-PCR, and hyperdiploidy either DNA index (≥1.16) or karyotyping. The latter was only available in some patients, especially in the Chinese.
Using logistic regression model analysis, MTHFR 677C>T and MTHFD1 1958G>A showed significant influence on leukemia susceptibility in the Chinese (n=235, p=0.005) and Malays (n=125, p=0.032) respectively.
In the Chinese cohort, MTHFR 677 CT and TT genotypes significantly decreased risk of childhood ALL as compared to CC wild type (p=0.004, OR=0.57, 95%CI=0.39–0.83), as well as in the hyperdiploidy subgroup (n=35, p=0.002, OR=0.28, 95%CI=0.12–0.65). The combined effect of RFC 80GA and AA genotypes with MTHFR 677CC wild type also decreased risk of childhood ALL in Chinese (p=0.05, OR=0.47, 95%CI=0.22–1.0). In the Malay cohort, the MTHFR 677 CT and TT genotypes played a protective role only in the TEL-AML1 subgroup (n=27) as compared to CC wild type (p=0.05, OR=0.24, 95%CI=0.06–1.0). However, interestingly MTHFD1 1958GG wild type decreased risk of childhood ALL as compared to MTHFD1 1958GA or AA genotypes (p=0.02, OR=0.54, 95%CI=1.11–3.05) when combined with MTHFR 677CC genotype. Haplotype analysis of TSER variants showed no significant effect in the 2 races.
Using a candidate pathway approach, we showed that polymorphisms in the folate pathway significantly modified the risk of developing childhood ALL especially the MTHFR, MTHFD1 and RFC1. This effect may arise from different genes of the same pathway and this may be different for different races. This supports a pathway way rather than a single-gene approach towards elucidation of cancer risk in childhood ALL.