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It is well documented that over-expression of the c-myc proto-oncogene occurs in the vast majority of mouse thymic lymphomas induced by γ-irradiation, evidencing the importance of this gene in T-cell lymphomagenesis. However, it remains unknown whether elevated levels of c-myc expression are driven by extra c-myc copy numbers. Here we use a quantitative test on the basis of real-time PCR to determine the cellular copy number of c-myc in a set of 14 g-radiation-induced thymic lymphomas obtained from (C57BL/6J x BALB/cJ) F1 hybrid mice with increased mRNA c-myc expression. Since 5 out of 14 (35.7%) cases had no extra copy numbers of c-myc, gene amplification was obviously not the cause of c-myc over-expression in these tumours. In the remaining 9 tumours, c-myc over-expression was also accompanied with extra DNA copy numbers. Therefore, c-myc amplification might be a consequence of the genomic instability subsequent to the up-regulation of c-myc. However, linear regression analysis showed a lack of correlation between increasing DNA copy numbers and mRNA over expression of c-myc in these tumours (r =0.029, p=0.94). De-regulation of c-myc does not necessarity imply amplification of this gene in these tumours. This report is, to our knowledge, the first one comparing c-myc amplification with expression in lymphomas of the T-cell lineage. [ABSTRACT FROM AUTHOR]

This pilot study tested the gender-specificity of the association between suicide attempts and a polymorphism in the promoter area of the serotonin transporter with two allelic variants, a long (1) variant and a short (s) variant. In a Spanish general hospital, 180 suicide attempters (121 women and 59 men) and 212 control blood donors (93 women and 119 men) were recruited. Subjects were classified as S individuals (s/s or s/l) with low expression of the serotonin transporter, and L individuals (l/l) with high expression. S individuals were significantly overrepresented (or L, underrepresented) in female attempters when compared with female controls and male attempters. Lethality appeared to have a significant influence on the effects of the genotype in suicide since S females were overrepresented among non-lethal female attempters. Further studies are needed to replicate that the serotonin genotype polymorphism may influence suicide attempts only in females. [Copyright &y& Elsevier]

The INK4a/ARF locus encodes two different proteins involved in cell cycle control. Both molecules, p16INK4a and p19ARF, inhibit cell cycle progression and have been shown to act as tumor suppressors in a variety of models. Their expression is controlled by separate promoters responding to different stimuli and they therefore show independent transcriptional regulation. We have cloned and characterized a 2.5 kb region upstream of the murine p19ARF gene to determine the role of DNA methylation in suppressing p19ARF transcription in a wide panel of murine primary T cell lymphomas. This region contains a DNA fragment with the characteristics of a CpG island similar to those described for the murine p16INK4a and p15INK4b genes. Expression of p19ARF is decreased in a significant number (20%) of the murine lymphomas analyzed. Overexpression of the p19ARF transcript is also frequent, suggesting alterations in molecules of the retinoblastoma or p53 pathways that are involved in p19ARF regulation. Although hypermethylation of the INK4a and INK4b promoters is frequently involved in murine lymphomas, the p19ARF CpG island is infrequently methylated in the murine primary lymphomas studied in this work. Since loss of p19ARF expression cannot be explained as the result of homozygous deletions or hypermethylation of the ARF gene, other regulatory mechanisms seem to be altered in these malignancies. [ABSTRACT FROM PUBLISHER]

Changes in the isozyme profiles of peroxidases (POX, EC 1.11.1.7), glutamate oxaloacetate transaminase (GOT, EC 2.6.1 .1) and esterases (EST, EC 3.1.1.1) have been studied in leaves of Chenopodium foetidum S. treated with ethrel. Different systems for administration of the ethrel led to different responses. In intact plants., treatment of the complete surface of leaves or local administration by pricking the leaves induced senescence and wilting as well as quick changes, characteristic of ageing, in the isozyme patterns of the treated leaves. isolated leaves treated with ethrel in vitro also showed. a senescence response, but this was followed by a necrosis that displayed an isozyme pattern highly similar to that of necrotic lesions induced by plum pox virus (PPV) infection. An accelerated senescence process seems to be involved in the induction of changes in the isozyme patterns of expression during the hypersensitive response of Chenopodium foetidum to PPV infection, and ethylene could participate in this process. However, other factors may also be required for necrotization. [ABSTRACT FROM AUTHOR]

The cyclin-dependent kinase inhibitor p15INK4b has been shown to be involved in human and rodent tumors and seems to act as a tumor suppressor gene in hematological malignancies. Alterations of this gene in tumors include mainly homozygous deletions and hypermethylation of the CpG island in the promoter region. In this work, we describe a new area sensitive to methylation in the 3′ untranslated region (UTR) of the murine p15INK4b gene. This region shows different levels of methylation depending on the tissues, being relatively highly methylated in brain and gut, and weakly methylated in liver, spleen or thymus. DNA methylation and expression is similar in both maternal and paternal alleles indicating no imprinting effect. Although methylation of the p15INK4b 3′-UTR is low in normal thymus, increased levels (up to 100%) of specific methylation in this region are found in up to 30% of radiation- or carcinogen-induced thymic lymphomas, correlating with decreased gene expression. Hypermethylation of the p15INK4b 3′-UTR frequently occurs in tumors with loss of heterozygosity (LOH) but without methylation of the promoter CpG island or intragenic mutations. Furthermore, in vitro CpG methylation of the 3′-UTR produces reduced levels of a luciferase reporter in cultured cells. Methylation of two CpG sites in a 120 bp region is sufficient to interfere with transcription of the reporter gene. These data suggest that although the levels of p15INK4b in normal tissues can be mainly determined by promoter regulatory elements, strong hypermethylation of the 3′-UTR can interfere with transcription. Thus, hypermethylation of the 3′-UTR may explain the lack of p15INK4b gene expression in a subset of tumors with no promoter methylation and could be a new alternative mechanism for tumor suppressor gene inactivation in tumorigenesis. [ABSTRACT FROM AUTHOR]

A wide panel of murine induced T-cell lymphomas have been analysed for p16INK4a or p15INK4b alterations. Only one γ-radiation-induced lymphoma showed p16INK4a homozygous deletion and no other intragenic mutations were found in these INK4 genes. However, de novo methylation of the 5′ CpG islands of the murine p15INK4b and p16INK4a genes was found to be highly frequent. While p16INK4a hypermethylation was found in 36% of the neutron-radiation-induced lymphomas and 15% of the γ-radiation-induced lymphomas, de novo methylation of p15INK4b occurs in 88% and 42% of these tumors respectively, correlating with deficient expression of the corresponding mRNA and allelic losses in the p15INK4b and p16INK4a chromosome location. These data represent, to our knowledge, the first report on the significant involvement of hypermethylation of these INK4 genes in murine primary tumors. Moreover, they show the importance of allelic losses and CpG island methylation of p15INK4b gene inactivation and support a tumor suppressor role for p15INK4b in T-cell lymphomas independent of p16INK4a . [ABSTRACT FROM AUTHOR]

The cyclin-dependent kinase inhibitors p15 INK4b and p16 INK4a are involved in the development of a wide range of human and murine tumors. These tumor suppressor genes are inactivated by deletions frequently associated to point mutations in the coding regions or hypermethylation of their promoters. In this work, we describe a simple-sequence length polymorphism located in mouse Chromosome (Chr) 4, between the Cdkn2B (p15 INK4b ) and Cdkn2A (p16 INK4a ) genes, only 700 bp downstream of the Cdkn2B locus. This DNA region was analyzed in different inbred strains showing a variable AC-repetitive DNA sequence. We used this microsatellite to detect loss of heterozygosity of the Cdkn2A and Cdkn2B loci in γ-irradiation-induced thymic lymphomas of C57BL/6J × RF/J F1 hybrids. Using this specific marker, we were able to locate additional allelic losses not detected by other microsatellites. Since the allelic losses can be detected by a simple PCR amplification, this AC-repetitive sequence is specially useful as a genetic marker for these Cdkn2 genes and specifically for the p15 INK4b cell cycle inhibitor. [ABSTRACT FROM AUTHOR]

(E) Cell growth analysis of Jurkat, K562 and Ba/F3 cells transduced with SEPTIN6:ABL2 (Ba/F3-SA) treated with Imatinib (0.1, 0.5 or 1 M; left), Nilotinib (10, 50, 100 nM; middle) and Dasatinib (1, 5, 10 nM; right) and referred to DMSO-treated cells. T-cell acute lymphoblastic leukaemia (T-ALL) arises from the malignant transformation of T-cell progenitors.[[1]] Current standard-of-care treatment for T-ALL consists of high-dose multi-agent chemotherapy followed by haematopoietic stem cell transplantation (HSCT) in standard-high risk patients.[3] Despite reasonable rates of initial complete responses (CR), patients who relapse or do not respond to first-line treatments show a dismal outcome with cure rates below 10% and limited therapeutic options.[2] Actually, since the approval of nelarabine in 2005 no pharmacological inhibitors have been approved for relapsed/refractory T-ALL patients.[4] Therefore, there is an urgent need to identify the molecular alterations that are present in such patients and that promote leukemogenesis in order to implement personalized-therapies with higher efficacy and fewer adverse effects.[5] Here, we identify and comprehensively characterize a novel, oncogenic and targetable I SEPTIN6 i : I ABL2 i fusion in a 16-year-old boy with T-ALL (Figure 1A). M07e cells transduced with I SEPTIN6 i : I ABL2 i showed significantly higher levels of cell growth and viability compared to cells transduced with the empty-vector or with I ABL2 i SP WT sp in the absence of cytokines (Figure 2A). We evaluated the mutational profile of the patient in matched tumour samples at diagnosis (Patient Dx) and relapse (Patient Rx) by paired-end 2 × 150 bp exome sequencing analysis. [Extracted from the article]

Summary: Despite the Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway being frequently altered in T‐ALL/LBL, no specific therapy has been approved for T‐ALL/LBL patients with constitutive signalling by JAK/STAT, so there is an urgent need to identify pathway members that may be potential therapeutic targets. In the present study, we searched for JAK/STAT pathway members potentially modulated through aberrant methylation and identified SOCS3 hypermethylation as a recurrent event in T‐ALL/LBL. Additionally, we explored the implications of SOCS3 deregulation in T‐ALL/LBL and demonstrated that SOCS3 counteracts the constitutive activation of the JAK/STAT pathway through different molecular mechanisms. Therefore, SOCS3 emerges as a potential therapeutic target in T‐ALL/LBL. [ABSTRACT FROM AUTHOR]

A reduction in FADD levels has been reported in precursor T-cell neoplasms and other tumor types. Such reduction would impact on the ability of tumor cells to undergo apoptosis and has been associated with poor clinical outcomes. However, FADD is also known to participate in non-apoptotic functions, but these mechanisms are not well-understood. Linking FADD expression to the severity of precursor T-cell neoplasms could indicate its use as a prognostic marker and may open new avenues for targeted therapeutic strategies. Using transcriptomic and clinical data from patients with precursor T-cell neoplasms, complemented by in vitro analysis of cellular functions and by high-throughput interactomics, our results allow us to propose a dual role for FADD in precursor T-cell neoplasms, whereby resisting cell death and chemotherapy would be a canonical consequence of FADD deficiency in these tumors, whereas deregulation of the cellular metabolism would be a relevant non-canonical function in patients expressing FADD. These results reveal that evaluation of FADD expression in precursor T-cell neoplasms may aid in the understanding of the biological processes that are affected in the tumor cells. The altered biological processes can be of different natures depending on the availability of FADD influencing its ability to exert its canonical or non-canonical functions. Accordingly, specific therapeutic interventions would be needed in each case. [ABSTRACT FROM AUTHOR]

In the quest for more effective radiation treatment options that can improve both cell killing and healthy tissue recovery, combined radiation therapies are lately in the spotlight. The molecular response to a combined radiation regime where exposure to an initial low dose (priming dose) of ionizing radiation is administered prior to a subsequent higher radiation dose (challenging dose) after a given latency period have not been thoroughly explored. In this study we report on the differential response to either a combined radiation regime or a single challenging dose both in mouse in vivo and in human ex vivo thymocytes. A differential cell cycle response including an increase in the subG1 fraction on cells exposed to the combined regime was found. Together with this, a differential protein expression profiling in several pathways including cell cycle control (ATM, TP53, p21CDKN1A), damage response (γH2AX) and cell death pathways such as apoptosis (Cleaved Caspase-3, PARP1, PKCδ and H3T45ph) and ferroptosis (xCT/GPX4) was demonstrated. This study also shows the epigenetic regulation following a combined regime that alters the expression of chromatin modifiers such as DNMTs (DNMT1, DNMT2, DNMT3A, DNMT3B, DNMT3L) and glycosylases (MBD4 and TDG). Furthermore, a study of the underlying cellular status six hours after the priming dose alone showed evidence of retained modifications on the molecular and epigenetic pathways suggesting that the priming dose infers a "radiation awareness phenotype" to the thymocytes, a sensitization key to the differential response seen after the second hit with the challenging dose. These data suggest that combined-dose radiation regimes could be more efficient at making cells respond to radiation and it would be interesting to further investigate how can these schemes be of use to potential new radiation therapies. [ABSTRACT FROM AUTHOR]

Full differentiation potential along with self‐renewal capacity is a major property of pluripotent stem cells (PSCs). However, the differentiation capacity frequently decreases during expansion of PSCs in vitro. We show here that transient exposure to a single microRNA, expressed at early stages during normal development, improves the differentiation capacity of already‐established murine and human PSCs. Short exposure to miR‐203 in PSCs (miPSCs) induces a transient expression of 2C markers that later results in expanded differentiation potency to multiple lineages, as well as improved efficiency in tetraploid complementation and human–mouse interspecies chimerism assays. Mechanistically, these effects are at least partially mediated by direct repression of de novo DNA methyltransferases Dnmt3a and Dnmt3b, leading to transient and reversible erasure of DNA methylation. These data support the use of transient exposure to miR‐203 as a versatile method to reset the epigenetic memory in PSCs, and improve their effectiveness in regenerative medicine. Synopsis: Long‐term expansion of pluripotent stem cells (PSC) frequently results in decreased differentiation potential diminishing their utility. Here, a miRNA‐based strategy is shown to enhance PSC potency via resetting their epigenetic state, suggesting new opportunities for improved stem cell therapies. Developmental miR‐203 improves potential and plasticity of mouse and human PSCs in vivo.miR‐203 increases human‐mouse interspecies chimera competency.miR‐203 targets de novo DNA methyltransferases Dnmt3a/b inducing global and reversible DNA hypomethylation.Transient miR‐203 enhances PSC maturation into cardiomyocytes. [ABSTRACT FROM AUTHOR]

Background: Precursor T-cell lymphoblastic lymphomas (T-LBL) are rare aggressive hematological malignancies that mainly develop in children. As in other cancers, the loss of cell cycle control plays a prominent role in the pathogenesis in these malignancies that is primarily attributed to loss of CDKN2A (encoding protein p16INK4A). However, the impact of the deregulation of other genes such as CDKN1C, E2F1, and TP53 remains to be clarified. Interestingly, experiments in mouse models have proven that conditional T-cell specific deletion of Cdkn1c gene may induce a differentiation block at the DN3 to DN4 transition, and that the loss of this gene in the absence of Tp53 led to aggressive thymic lymphomas.Results: In this manuscript, we demonstrated that the simultaneous deregulation of CDKN1C, E2F1, and TP53 genes by epigenetic mechanisms and/or the deregulation of specific microRNAs, together with additional impairing of TP53 function by the expression of dominant-negative isoforms are common features in primary human T-LBLs.Conclusions: Previous experimental work in mice revealed that T-cell specific deletion of Cdkn1c accelerates lymphomagenesis in the absence of Tp53. If, as expected, the consequences of the deregulation of the CDKN1C-E2F1-TP53 axis were the same as those experimentally demonstrated in mouse models, the disruption of this axis might be useful to predict tumor aggressiveness, and to provide the basis towards the development of potential therapeutic strategiesin human T-LBL. [ABSTRACT FROM AUTHOR]

Abstract: Background: Complex behaviors such as suicidal behavior likely exhibit gene–gene interactions. The main aim of this study is to explore potential single nucleotide polymorphisms combinations with epistatic effect in suicidal behavior using a data mining tool (Multifactor Dimensionality Reduction). Methods: Genomic DNA from peripheral blood samples was analyzed using SNPlex Technology. Multifactor Dimensionality Reduction was used to detect epistatic interactions between single nucleotide polymorphisms from the main central nervous system (CNS) neurotransmitters (dopamine: 9; noradrenaline: 19; serotonin: 23; inhibitory neurotransmitters: 60) in 889 individuals (417 men and 472 women) aged 18years or older (585 psychiatric controls without a history of suicide attempts, and 304 patients with a history of suicide attempts). Individual analysis of association between single nucleotide polymorphisms and suicide attempts was estimated using logistic regression models. Results: Multifactor Dimensionality Reduction showed significant epistatic interactions involving four single nucleotide polymorphisms in female suicide attempters with a classification test accuracy of 60.7% (59.1%–62.4%, 95% CI): rs1522296, phenylalanine hydroxylase gene (PAH); rs7655090, dopamine receptor D5 gene (DRD5); rs11888528, chromosome 2 open reading frame 76, close to diazepam binding inhibitor gene (DBI); and rs2376481, GABA-A receptor subunit γ3 gene (GABRG3). The multivariate logistic regression model confirmed the relevance of the epistatic interaction [OR(95% CI)=7.74(4.60–13.37)] in females. Conclusions: Our results suggest an epistatic interaction between genes of all monoamines and GABA in female suicide attempters. [Copyright &y& Elsevier]

Background: Acute T-cell lymphoblastic leukaemia (T-ALL) is an aggressive disorder derived from immature thymocytes. The variability observed in clinical responses on this type of tumours to treatments, the high toxicity of current protocols and the poor prognosis of patients with relapse or refractory make it urgent to find less toxic and more effective therapies in the context of a personalized medicine of precision.Methods: Whole exome sequencing and RNAseq were performed on DNA and RNA respectively, extracted of a bone marrow sample from a patient diagnosed with tumour primary T-ALL and double negative thymocytes from thymus control samples. We used PanDrugs, a computational resource to propose pharmacological therapies based on our experimental results, including lists of variants and genes. We extend the possible therapeutic options for the patient by taking into account multiple genomic events potentially sensitive to a treatment, the context of the pathway and the pharmacological evidence already known by large-scale experiments.Results: As a proof-of-principle we used next-generation-sequencing technologies (Whole Exome Sequencing and RNA-Sequencing) in a case of diagnosed Pro-T acute lymphoblastic leukaemia. We identified 689 disease-causing mutations involving 308 genes, as well as multiple fusion transcript variants, alternative splicing, and 6652 genes with at least one principal isoform significantly deregulated. Only 12 genes, with 27 pathogenic gene variants, were among the most frequently mutated ones in this type of lymphoproliferative disorder. Among them, 5 variants detected in CTCF, FBXW7, JAK1, NOTCH1 and WT1 genes have not yet been reported in T-ALL pathogenesis.Conclusions: Personalized genomic medicine is a therapeutic approach involving the use of an individual's information data to tailor drug therapy. Implementing bioinformatics platform PanDrugs enables us to propose a prioritized list of anticancer drugs as the best theoretical therapeutic candidates to treat this patient has been the goal of this article. Of note, most of the proposed drugs are not being yet considered in the clinical practice of this type of cancer opening up the approach of new treatment possibilities. [ABSTRACT FROM AUTHOR]