Toward a Molecular Classification of Peripheral T-Cell Lymphomas: The Role of Gene Expression Profiling

Peripheral T-cell lymphomas-not otherwise specified (PTCL/NOS) are the most common T-cell neoplasms. This study sought to reshape the PTCL/NOS sub-classification (including its two main morphological variants, Lennert lymphoma, LL, and Follicular variant, F-PTCL) based on the correspondence between their molecular features and those of different functional T-cell subsets, also assessing the clinical impact of such an approach. We found that PTCLs/NOS could be divided into groups corresponding to T-cell subsets differently reliant on transcription regulators including mTOR and FOXP3, and identified minimal gene sets discriminating among these groups. Notably, by grouping tumors according to their dependency on master regulators of T-lymphocyte fate, we identified three groups (T-cytotoxic, Treg/TFH, and other-T-helper) characterized by specific genetic patterns and significantly different clinical outcomes. Immunohistochemistry partially substituted for the molecular analysis by consistently recognizing only Treg and TFH cases. Finally, targeted inhibition of MTOR in T-helper cases (that were characterized by genetic lesions targeting the pathway) was proved to be effective ex vivo. We conclude that PTCL/NOS can be divided into subgroups corresponding to different cellular counterparts, characterized by different genetic patterns and possibly sensitivity to specific therapeutic approaches. Furthermore, we identified different gene and microRNA signatures for LL capable of differentiating it from other PTCL/NOS and enriched in cytotoxic function. Moreover, PI3K/Akt/mTOR pathway emerged as novel therapeutic targets for LL. Additionally, LL showed some differences with other PTCL/NOS in terms of clinical features, all supporting its recognition as a distinct entity. Besides, we found that F-PTCL has a distinct molecular signature more similar to PTCL/NOS rather than AITL, and therefore cannot be included among AITLs at least based on GEP, although this necessities more genetic studies. Overall, these results may impact on PTCL classification as well as on future studies aimed to define the more appropriate therapeutic strategy for each identified subgroup/entity

Pathobiologic roles of epstein–barr virus-encoded microRNAs in human lymphomas

Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating role—are of great importance. The genome of EBV encodes 44 mature microRNAs belonging to two different classes, including BamHI-A rightward transcript (BART) and Bam HI fragment H rightward open reading frame 1 (BHRF1), with different expression levels in different EBV latency types. These microRNAs might contribute to the pathogenetic effects exerted by EBV through targeting self mRNAs and host mRNAs and interfering with several important cellular mechanisms such as immunosurveillance, cell proliferation, and apoptosis. In addition, EBV microRNAs can regulate the surrounding microenvironment of the infected cells through exosomal transportation. Moreover, these small molecules could be potentially used as molecular markers. In this review, we try to present an updated and extensive view of the role of EBV-encoded miRNAs in human lymphomas

SNPs Array Karyotyping in Non-Hodgkin Lymphoma

The traditional methods for detection of chromosomal aberrations, which included cytogenetic or gene candidate solutions, suffered from low sensitivity or the need for previous knowledge of the target regions of the genome. With the advent of single nucleotide polymorphism (SNP) arrays, genome screening at global level in order to find chromosomal aberrations like copy number variants, DNA amplifications, deletions, and also loss of heterozygosity became feasible. In this review, we present an update of the knowledge, gained by SNPs arrays, of the genomic complexity of the most important subtypes of non-Hodgkin lymphomas

SNPs Array Karyotyping in Non-Hodgkin Lymphoma

The traditional methods for detection of chromosomal aberrations, which included cytogenetic or gene candidate solutions, suffered from low sensitivity or the need for previous knowledge of the target regions of the genome. With the advent of single nucleotide polymorphism (SNP) arrays, genome screening at global level in order to find chromosomal aberrations like copy number variants, DNA amplifications, deletions, and also loss of heterozygosity became feasible. In this review, we present an update of the knowledge, gained by SNPs arrays, of the genomic complexity of the most important subtypes of non-Hodgkin lymphomas

Effects of Artemisia annua L. (Asteracea) on nutritional physiology and enzyme activities of elm leaf beetle, Xanthogaleruca luteola Mull. (Coleoptera: Chrysomellidae)

Methanolic extract of Artemisia annua L., a weed collected around paddy fields in north of Iran, was investigated for its toxic effects on: feeding, growth, fecundity, fertility including the biochemical characteristics of elm leaf beetle Xanthogaleruca luteola Mull. The toxicity tests indicate that insecticidal effect was 2.4-fold higher in 3rd instar larvae than in adults. The LC 50 was 48% and 43.77% of a methanolic leaf extract at 24 and 48 h, respectively. The feeding deterrence was highest at 10% concentration and lowest at 0.625% for 3rd instar larvae and adults during the first 24 h and decreased thereafter. Larval duration significantly increased at higher concentrations. Larval treatment with 10% methanolic extract resulted in deformed adults (adultoids) with drastic changes in gross morphology of female reproductive system. Food digestion and assimilation significantly decreased in adults. Larval duration and adult fecundity and fertility were also significantly reduced. Twenty-four hours after treating 3rd instar larva with the extract the levels of glucose, protein, urea, uric acid, α-amylase, alkaline phosphatase, alanine amino transferase and aspartate amino transferase significantly changed. However, at 48 h the extract lost its potency. The extract did not effect the level of cholesterol in treated larva. These results indicate that Artemisia annua L. extract contains inhibitors of key metabolic pathways that may be useful in future control of the elm leaf beetle

Protective role of Lactobacillus plantarum A7 against irinotecan-induced genotoxicity

Objective: Irinotecan is a botanical derivative and an anti-cancer drug with cytotoxic and genotoxic effects. The present study evaluated the effect of Lactobacillus plantarum A7 on the genotoxic activity of irinotecan in a hepatocellular carcinoma cell line (HepG2) by comet assay. Materials and Methods: HepG2 were incubated with irinotecan (100 µM), heat-killed cells (0.025 µg/ml) + irinotecan (100 µM), and cell-free supernatants (0.5 and 1 µg/ml) of L. plantarum A7 + irinotecan (100 µM). Phosphate buffered saline (PBS) was used as negative control. Results: Irinotecan was shown to induce DNA damage in HepG2 cells. The results showed that heat-killed cells (0.025 µg/ml) and cell-free supernatants (0.5 and 1 µg/ml) of L. plantarum significantly reduce irinotecan- induced DNA damage. Conclusion: Our results indicate that L. plantarum A7 can decrease the genotoxic effects of irinotecan in HepG2 cells, in vitro. This finding may be supportive for the optimization of therapeutic efficacy in irinotecan treatment

Single-Step IGHV Next-Generation Sequencing Detects Clonality and Somatic Hypermutation in Lymphoid Malignancies: A Phase III Diagnostic Accuracy Study

Background: Multiplex PCR based on consensus primers followed by capillary electrophoresis and Sanger sequencing are considered as the gold standard method for the evaluation of clonality and somatic hypermutation in lymphoid malignancies. As an alternative, the next-generation sequencing (NGS) of immune receptor genes has recently been proposed as a solution, due to being highly effective and sensitive. Here, we designed a phase III diagnostic accuracy study intended to compare the current gold standard methods versus the first commercially available NGS approaches for testing immunoglobulin heavy chain gene rearrangements. Methods: We assessed IGH rearrangements in 68 samples by means of both the NGS approach (LymphoTrack® IGH assay, and LymphoTrack® IGH somatic hypermutation assay, run on Illumina MiSeq) and capillary electrophoresis/Sanger sequencing to assess clonality and somatic hypermutations (SHM). Results: In comparison to the routine capillary-based analysis, the NGS clonality assay had an overall diagnostic accuracy of 96% (63/66 cases). Other studied criteria included sensitivity (95%), specificity (100%), positive predictive value (100%) and negative predictive value (75%). In discrepant cases, the NGS results were confirmed by a different set of primers that provided coverage of the IGH leader sequence. Furthermore, there was excellent agreement of the SHM determination with both the LymphoTrack® FR1 and leader assays when compared to the Sanger sequencing analysis (84%), with NGS able to assess the SHM rate even in cases where the conventional approach failed. Conclusion: Overall, conventional Sanger sequencing and next-generation-sequencing-based clonality and somatic hypermutation analyses gave comparable results. For future use in a routine diagnostic workflow, NGS-based approaches should be evaluated prospectively and an analysis of cost-effectiveness should be performed

Increased angiogenesis seems to correlate with inferior overall survival in myeloid sarcoma patients

Myeloid sarcomas (MS) are tumors composed by myeloid elements and developing outside bone marrow. The prognosis is overall poor, only stem cell transplantation being consistently reposted as a potentially curative approach. In this study we explored whether microvessel density, a biomarker of angiogenesis, might be relevant in MS. We studied 60 MS, 24 acute myeloid leukemia, 5 normal bone marrow samples and 2 cases of extramedullary hemopoiesis in patients without evidence of hematological malignancy. We used immunohistochemistry (anti-CD34) to identify and quantify micro-vessel density (MVD) and micro-vessel grading (MVG). We found that MS had significantly higher MVD and MVG than normal bone marrow (p = 0.0002 and p < 0.001, respectively). We then found that cases with monocytic morphology had significantly higher MVD than myelo-monocytic and blastic ones (p = 0.005), while no differences were recorded based on extramedullary site. Finally, we found that higher MVD and higher MVG were associated with inferior outcome in terms of overall survival in multivariate analysis (p = 0.05 and p = 0.02, respectively), when censoring for stem cell transplantation was undertaken. In conclusion, we documented for the first time that increased angiogenesis is characteristic of MS and correlates with survival, suggesting that anti-angiogenic approaches might deserve a clinical evaluation in this setting

SF3B1 Gene Abnormalities are Not Common in Peripheral T-Cell Lymphomas-Not Otherwise Specified

The molecular basis of Peripheral T cell lymphoma not otherwise specified (PTCL/ NOS) has remained essentially elusive, due to heterogeneous nature of this malignancy. Recently recurrent genetic lesions affecting normal RNA splicing have been described in different hematological malignancies. Therefore, this study aimed to investigate the possible role of SF3B1 gene, the core component of splicing machinery, in PTCL/NOS pathogenesis

Burkitt lymphoma beyond MYC translocation: N-MYC and DNA methyltransferases dysregulation

BACKGROUND: The oncogenic transcription factor MYC is pathologically activated in many human malignancies. A paradigm for MYC dysregulation is offered by Burkitt lymphoma, where chromosomal translocations leading to Immunoglobulin gene-MYC fusion are the crucial initiating oncogenic events. However, Burkitt lymphoma cases with no detectable MYC rearrangement but maintaining MYC expression have been identified and alternative mechanisms can be involved in MYC dysregulation in these cases. METHODS: We studied the microRNA profile of MYC translocation-positive and MYC translocation-negative Burkitt lymphoma cases in order to uncover possible differences at the molecular level. Data was validated at the mRNA and protein level by quantitative Real-Time polymerase chain reaction and immunohistochemistry, respectively. RESULTS: We identified four microRNAs differentially expressed between the two groups. The impact of these microRNAs on the expression of selected genes was then investigated. Interestingly, in MYC translocation-negative cases we found over-expression of DNA-methyl transferase family members, consistent to hypo-expression of the hsa-miR-29 family. This finding suggests an alternative way for the activation of lymphomagenesis in these cases, based on global changes in methylation landscape, aberrant DNA hypermethylation, lack of epigenetic control on transcription of targeted genes, and increase of genomic instability. In addition, we observed an over-expression of another MYC family gene member, MYCN that may therefore represent a cooperating mechanism of MYC in driving the malignant transformation in those cases lacking an identifiable MYC translocation but expressing the gene at the mRNA and protein levels. CONCLUSIONS: Collectively, our results showed that MYC translocation-positive and MYC translocation-negative Burkitt lymphoma cases are slightly different in terms of microRNA and gene expression. MYC translocation-negative Burkitt lymphoma, similarly to other aggressive B-cell non Hodgkin’s lymphomas, may represent a model to understand the intricate molecular pathway responsible for MYC dysregulation in cancer. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12885-015-1661-7) contains supplementary material, which is available to authorized users