Bitter Taste Receptor Agonist Denatonium Inhibits Stemness Characteristics in Hematopoietic Stem/Progenitor Cells

Bone marrow microenvironmental stimuli profoundly impact hematopoietic stem cell fate and biology. As G protein-coupled receptors, the bitter taste receptors (TAS2Rs) are key in transmitting extracellular stimuli into an intracellular response, within the oral cavity but also in extraoral tissues. Their expression in the bone marrow (BM)-derived cells suggests their involvement in sensing the BM microenvironmental fluctuation. In the present study, we demonstrated that umbilical cord blood (UCB)-derived CD34+ cells express fully functional TAS2Rs along with the signal transduction cascade components and their activation by the prototypical agonist, denatonium benzoate, significantly modulated genes involved in stemness maintenance and regulation of cell trafficking. The activation of these specific pathways was confirmed in functional in vitro experiments. Denatonium exposure exerted an antiproliferative effect on UCB-derived CD34+ cells, mainly affecting the most undifferentiated progenitor frequency. It also reduced their clonogenicity and repopulating potential in vitro. In addition, the TAS2R signaling activation impaired the UCB-derived CD34+ cell trafficking, mainly reducing the migration toward the chemoattractant agent CXCL12 and modulating the expression of the adhesion molecules CD62L, CD49d, and CD29. In conclusion, our results in UCB-derived CD34+ cells expand the observation of TAS2R expression in the setting of BM-resident cells and shed light on the role of TAS2Rs in the extrinsic regulation of hematopoietic stem cell functions.

IDH mutations in G2-3 conventional central bone chondrosarcoma: a mono institutional experience

BACKGROUND

Heterozygous isocitrate dehydrogenase (IDH) mutations occur in about half of conventional central bone chondrosarcomas (CCBC). Aim of this study was to assess the frequency and prognostic impact of IDH mutations in high grade CCBC patients.

METHODS

64 patients with G2 and G3 CCBC were included. DNA extraction, PCR amplification of IDH1/2 exon 4s, and sequencing analysis with Sanger were performed.

RESULTS

IDH mutations were detected in 24/54 patients (44%): IDH1 in 18, IDH2 in 4, and both IDH1/2 in 2 patients. The frequency of mutations was 37% in G2 vs. 69% in G3 (p = 0.039), and 100% in three Ollier disease associated chondrosarcoma. 5-year overall survival (OS) at 124 months (range 1-166) was 51%, with no significant difference based on the IDH mutational status: 61% in IDHmut vs. 44% in IDH wild type (IDHwt). The 5-year relapse free survival (RFS) was 33% (95% CI:10-57) for IDHmut vs. 57% (95%CI: 30-77) for IDHwt. Progression free survival (PFS) was 25% (95%CI:1-65) IDHmut vs. 16% (95%CI: 0.7-52) IDHwt. 55% (5/9) of IDHmut G2 became higher grade at the recurrence, as compared with 25% (3/12) of G2 IDHwt.

CONCLUSIONS

This study shows a higher frequency of IDH mutations in G3 CCBC as compared with G2. No significant differences in OS, RFS, and PFS by mutational status were detected. After relapse, a higher rate of G3 for IDH mutated CCBC was observed.

Extracellular vesicle-associated IGF2BP3 tunes Ewing sarcoma cell migration and affects PI3K/Akt pathway in neighboring cells

Ewing sarcoma (EWS) is a challenging pediatric cancer characterized by vast intra-tumor heterogeneity. We evaluated the RNA-binding protein IGF2BP3, whose high expression correlates with a poor prognosis and an elevated tendency of metastases, as a possible soluble mediator of inter-cellular communication in EWS. Our data demonstrate that (i) IGF2BP3 is detected in cell supernatants, and it is released inside extracellular vesicles (EVs); (ii) EVs from IGF2BP3-positive or IGF2BP3-negative EWS cells reciprocally affect cell migration but not the proliferation of EWS recipient cells; (iii) EVs derived from IGF2BP3-silenced cells have a distinct miRNA cargo profile and inhibit the PI3K/Akt pathway in recipient cells; (iv) the 11 common differentially expressed miRNAs associated with IGF2BP3-positive and IGF2BP3-negative EVs correctly group IGF2BP3-positive and IGF2BP3-negative clinical tissue specimens. Overall, our data suggest that IGF2BP3 can participate in the modulation of phenotypic heterogeneity.

Oncogenic Vav1-Myo1f induces therapeutically targetable macrophage-rich tumor microenvironment in peripheral T cell lymphoma

Peripheral T cell lymphoma not otherwise specified (PTCL-NOS) comprises heterogeneous lymphoid malignancies characterized by pleomorphic lymphocytes and variable inflammatory cell-rich tumor microenvironment. Genetic drivers in PTCL-NOS include genomic alterations affecting the VAV1 oncogene; however, their specific role and mechanisms in PTCL-NOS remain incompletely understood. Here we show that expression of Vav1-Myo1f, a recurrent PTCL-associated VAV1 fusion, induces oncogenic transformation of CD4⁺ T cells. Notably, mouse Vav1-Myo1f lymphomas show T helper type 2 features analogous to high-risk GATA3⁺ human PTCL. Single-cell transcriptome analysis reveals that Vav1-Myo1f alters T cell differentiation and leads to accumulation of tumor-associated macrophages (TAMs) in the tumor microenvironment, a feature linked with aggressiveness in human PTCL. Importantly, therapeutic targeting of TAMs induces strong anti-lymphoma effects, highlighting the lymphoma cells' dependency on the microenvironment. These results demonstrate an oncogenic role for Vav1-Myo1f in the pathogenesis of PTCL, involving deregulation in T cell polarization, and identify the lymphoma-associated macrophage-tumor microenvironment as a therapeutic target in PTCL.

Integrated Molecular Characterization of Patient-Derived Models Reveals Therapeutic Strategies for Treating CIC-DUX4 Sarcoma

Capicua-double homeobox 4 (CIC-DUX4)-rearranged sarcomas (CDS) are extremely rare, highly aggressive primary sarcomas that represent a major therapeutic challenge. Patients are treated according to Ewing sarcoma protocols, but CDS-specific therapies are strongly needed. In this study, RNA sequencing was performed on patient samples to identify a selective signature that differentiates CDS from Ewing sarcoma and other fusion-driven sarcomas. This signature was used to validate the representativeness of newly generated CDS experimental models-patient-derived xenografts (PDX) and PDX-derived cell lines-and to identify specific therapeutic vulnerabilities. Annotation analysis of differentially expressed genes and molecular gene validation highlighted an HMGA2/IGF2BP/IGF2/IGF1R/AKT/mTOR axis that characterizes CDS and renders the tumors particularly sensitive to combined treatments with trabectedin and PI3K/mTOR inhibitors. Trabectedin inhibited IGF2BP/IGF2/IGF1R activity, but dual inhibition of the PI3K and mTOR pathways was required to completely dampen downstream signaling mediators. Proof-of-principle efficacy for the combination of the dual AKT/mTOR inhibitor NVP-BEZ235 (dactolisib) with trabectedin was obtained in vitro and in vivo using CDS PDX-derived cell lines, demonstrating a strong inhibition of local tumor growth and multiorgan metastasis. Overall, the development of representative experimental models (PDXs and PDX-derived cell lines) has helped to identify the unique sensitivity of the CDS to AKT/mTOR inhibitors and trabectedin, revealing a mechanism-based therapeutic strategy to fight this lethal cancer.

SIGNIFICANCE

This study identifies altered HMGA2/IGF2BP/IGF2 signaling in CIC-DUX4 sarcomas and provides proof of principle for combination therapy with trabectedin and AKT/mTOR dual inhibitors to specifically combat the disease.

Targeting CD99 Compromises the Oncogenic Effects of the Chimera EWS-FLI1 by Inducing Reexpression of Zyxin and Inhibition of GLI1 Activity

Ewing sarcoma, a highly aggressive pediatric tumor, is driven by EWS-FLI1, an oncogenic transcription factor that remodels the tumor genetic landscape. Epigenetic mechanisms play a pivotal role in Ewing sarcoma pathogenesis, and the therapeutic value of compounds targeting epigenetic pathways is being identified in preclinical models. Here, we showed that modulation of CD99, a cell surface molecule highly expressed in Ewing sarcoma cells, may alter transcriptional dysregulation in Ewing sarcoma through control of the zyxin-GLI1 axis. Zyxin is transcriptionally repressed, but GLI1 expression is maintained by EWS-FLI1. We demonstrated that targeting CD99 with antibodies, including the human diabody C7, or genetically inhibiting CD99 is sufficient to increase zyxin expression and induce its dynamic nuclear accumulation. Nuclear zyxin functionally affects GLI1, inhibiting targets such as NKX2-2, cyclin D1, and PTCH1 and upregulating GAS1, a tumor suppressor protein negatively regulated by SHH/GLI1 signaling. We used a battery of functional assays to demonstrate (i) the relationship between CD99/zyxin and tumor cell growth/migration and (ii) how CD99 deprivation from the Ewing sarcoma cell surface is sufficient to specifically affect the expression of some crucial EWS-FLI1 targets, both in vitro and in vivo, even in the presence of EWS-FLI1. This article reveals that the CD99/zyxin/GLI1 axis is promising therapeutic target for reducing Ewing sarcoma malignancy.

Corrigendum: Denatonium as a Bitter Taste Receptor Agonist Modifies Transcriptomic Profile and Functions of Acute Myeloid Leukemia Cells

[This corrects the article DOI: 10.3389/fonc.2020.01225.].

Restriction Factors expression decreases in HIV-1 patients after cART

Activation of interferon (IFN) mediated responses and the consequent expression of restriction factors (RFs) represent an early line of defense against HIV-1 infection. The levels of viral replication and the antiviral are among the determinants influencing RFs' expression pattern. A deeper understanding of the molecular mechanisms regulating RFs activity and their relationship with viral replication factors might lead to new therapeutic strategies based on the enhancement of immune response against the virus. The aim of this study is to perform a longitudinal evaluation of the variations in the levels of a group of selected RFs (APOBEC3G, BST2, TRIM5α, MX2, SAMHD1, SERINC3/5, IFI16 and STING) to determine the impact of cART on their expression in HIV-1 positive patients. Together with RFs expression, immunological and virological parameters (plasma HIV1-RNA load and total HIV1-DNA) were longitudinally evaluated in a cohorts fourteen HIV-1 cART na ve patients, who were evaluated at diagnosis (T0) and followed at 4 (T1) and 8 (T2) months after starting cART. Fourteen long-term treated patients who achieved sustained undetectable viremia for at least 2 years were also included in the study as a reference group. We observed a restoration of immunological conditions during cART, together with a progressive decrease of HIV1-RNA load, which became undetectable at 8 months after starting treatment. On the other hand, despite showing a trend towards decrease, total HIV1-DNA remained detectable after reaching viral suppression, similarly to what observed in long term treated patients. The expression of APOBEC3G, SAMHD1, BST2, IFI16, SERINC3, and SERINC5 was higher at the time of diagnosis and decreased significantly during therapy, reaching levels similar to the ones observed in virally suppressed patients. On the other hand, MX2 and TRIM5a high expression values up to T0, reaching lower levels immediately after the initiation of cART treatment. Correlation analysis showed a positive association between the expression levels of APOBEC3G, IFI16, MX2, SAMHD1, SERINC3 and TRIM5α with the HIV-1 viral load. On the contrary, no significant association was observed for BST2, SERINC5 and STING, even BST2 expression showed a tendency to correlate with viral load. We observed a tendency for a positive association of MX2, SAMHD1 and SERINC5 with the size of viral reservoir and a trend for a negative association for STING. STING appeared also as the only one factor whose expression correlates with the CD4 count and the CD4/CD8 ratio. Our data confirm the correlation between viral replication and expression of RFs, with, the levels of cellular defense proteins decreasing in parallel to the reduction of viral replication.

Denatonium as a Bitter Taste Receptor Agonist Modifies Transcriptomic Profile and Functions of Acute Myeloid Leukemia Cells

The contribution of cell-extrinsic factors in Acute Myeloid Leukemia (AML) generation and persistence has gained interest. Bitter taste receptors (TAS2Rs) are G protein-coupled receptors known for their primary role as a central warning signal to induce aversion toward noxious or harmful substances. Nevertheless, the increasing amount of evidence about their extra-oral localization has suggested a wider function in sensing microenvironment, also in cancer settings. In this study, we found that AML cells express functional TAS2Rs. We also highlighted a significant association between the modulation of some TAS2Rs and the poor-prognosis AML groups, i.e., TP53- and TET2-mutated, supporting a potential role of TAS2Rs in AML cell biology. Gene expression profile analysis showed that TAS2R activation with the prototypical agonist, denatonium benzoate, significantly modulated a number of genes involved in relevant AML cellular processes. Functional assay substantiated molecular data and indicated that denatonium reduced AML cell proliferation by inducing cell cycle arrest in G0/G1 phase or induced apoptosis via caspase cascade activation. Moreover, denatonium exposure impaired AML cell motility and migratory capacity, and inhibited cellular respiration by decreasing glucose uptake and oxidative phosphorylation. In conclusion, our results in AML cells expand the observation of cancer TAS2R expression to the setting of hematological neoplasms and shed light on a role of TAS2Rs in the extrinsic regulation of leukemia cell functions.

Correction: Whole exome sequencing reveals mutations in FAT1 tumor suppressor gene clinically impacting on peripheral T-cell lymphoma not otherwise specified

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Abstract 1805: Integrative analysis of microRNAs in blastic plasmacytoid dendritic cell neoplasm

Background:

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an extremely rare and aggressive hematological disease, deriving from the malignant transformation of plasmacytoid, alpha-interferon producing dendritic cells (pDCs). Recent studies shed new light on BPDCN genomic and trascriptomic alterations, but the microRNA (miRNA) profile is still largely unknown.

We analyzed the miRNA expression profile of BPDCN patients to enhance our understanding of the molecular mechanisms driving this disease and to identify new potential diagnostic and therapeutic biomarkers.

Methods:

We performed the miRNA profiling (NanoString Technologies) of 26 BPDCN patients and 4 normal pDCs samples as controls. To better investigate the functional consequences of miRNAs dysregulation, 9 BPDCN patients, were also analyzed at the transcriptomic level.

We applied a Moderated t-test to find genes and miRNAs differentially expressed between BPDCNs and pDCs. The most deregulated miRNAs and mRNAs were validated by qRT-PCR and immunohistochemistry and analyzed by miRNET, a bioinformatic tool for statistical analysis and functional interpretation of miRNA and mRNA data.

Results:

We found that, according to the supervised clustering analysis of miRNAs, tumor samples display a molecular signature well distinct from their normal counterpart. Indeed, BPDCN patients expressed a set of 175 miRNAs significantly deregulated and potentially involved in essential biological processes and therefore in malignant transformation. Thus, to evaluate the impact of these miRNAs on the BPDCN transcriptome, miRNAs and mRNAs expression profiles were analyzed by miRNET tool.

Thanks to this integrative approach, we uncovered the most relevant miRNA-mRNA networks in BPDCN setting and in particular we identified 9 up-regulated hub miRNAs, targeting multiple genes and synergistically inter-connected: hsa-mir-93-5p, hsa-mir-106b-5p, hsa-mir-19b-3p, hsa-mir-19a-3p, hsa-mir-21-5p, hsa-mir-181a-5p, hsa-mir-25-3p, hsa-mir-155-5p, hsa-mir-17-3p (in order of relevance). These 9 hub miRNAs regulate the expression of genes already described as relevant in BPDCN patients (ex. TCF4, RHOA, EP300) and, according to functional enrichment analysis, that could aberrantly interfere with TLR signaling, protein translation and DNA transcription regulation.

Of interest, most of these hub miRNAs are classified as oncomir (OncoMir Cancer Database) and, if validated in an extended number of cases, promising targets for anti-miRNA based therapy.

In conclusion, we identified a panel of miRNAs that regulate relevant cancer-related pathways and can be also used as new potential biomarkers and therapeutic targets in BPDCN.

Citation Format: Maria Rosaria Sapienza, Manuela Ferracin, Fabio Fuligni, Federica Melle, Giovanna Motta, Maria Antonella Laginestra, Maura Rossi, Luciano Cascione, Alessandro Laganà, Claudio Agostinelli, Elena Sabattini, Alessandro Pileri, Carlo Maria Croce, Stefano Aldo Pileri. Integrative analysis of microRNAs in blastic plasmacytoid dendritic cell neoplasm [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1805.

Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery

Background

Aneuploidy occurs in more than 20% of acute myeloid leukemia (AML) cases and correlates with an adverse prognosis.

Methods

To understand the molecular bases of aneuploid acute myeloid leukemia (A‐AML), this study examined the genomic profile in 42 A‐AML cases and 35 euploid acute myeloid leukemia (E‐AML) cases.

Results

A‐AML was characterized by increased genomic complexity based on exonic variants (an average of 26 somatic mutations per sample vs 15 for E‐AML). The integration of exome, copy number, and gene expression data revealed alterations in genes involved in DNA repair (eg, SLX4IP, RINT1, HINT1, and ATR) and the cell cycle (eg, MCM2, MCM4, MCM5, MCM7, MCM8, MCM10, UBE2C, USP37, CK2, CK3, CK4, BUB1B, NUSAP1, and E2F) in A‐AML, which was associated with a 3‐gene signature defined by PLK1 and CDC20 upregulation and RAD50 downregulation and with structural or functional silencing of the p53 transcriptional program. Moreover, A‐AML was enriched for alterations in the protein ubiquitination and degradation pathway (eg, increased levels of UHRF1 and UBE2C and decreased UBA3 expression), response to reactive oxygen species, energy metabolism, and biosynthetic processes, which may help in facing the unbalanced protein load. E‐AML was associated with BCOR/BCORL1 mutations and HOX gene overexpression.

Conclusions

These findings indicate that aneuploidy‐related and leukemia‐specific alterations cooperate to tolerate an abnormal chromosome number in AML, and they point to the mitotic and protein degradation machineries as potential therapeutic targets.

Aneuploid acute myeloid leukemia (A‐AML) is associated with genomic and transcriptional alterations in the cell cycle and protein degradation pathways. The upregulation of PLK1 and CDC20 and the downregulation of RAD50 and of a p53‐related signature are hallmarks of A‐AML.

Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy for which there is still no effective therapy. In order to identify genetic alterations useful for a new treatment design, we used whole-exome sequencing to analyze 14 BPDCN patients and the patient-derived CAL-1 cell line. The functional enrichment analysis of mutational data reported the epigenetic regulatory program to be the most significantly undermined (P<0.0001). In particular, twenty-five epigenetic modifiers were found mutated (e.g. ASXL1, TET2, SUZ12, ARID1A, PHF2, CHD8); ASXL1 was the most frequently affected (28.6% of cases). To evaluate the impact of the identified epigenetic mutations at the gene-expression and Histone H3 lysine 27 trimethylation/acetylation levels, we performed additional RNA and pathology tissue-chromatin immunoprecipitation sequencing experiments. The patients displayed enrichment in gene signatures regulated by methylation and modifiable by decitabine administration, shared common H3K27-acetylated regions, and had a set of cell-cycle genes aberrantly up-regulated and marked by promoter acetylation. Collectively, the integration of sequencing data showed the potential of a therapy based on epigenetic agents. Through the adoption of a preclinical BPDCN mouse model, established by CAL-1 cell line xenografting, we demonstrated the efficacy of the combination of the epigenetic drugs 5’-azacytidine and decitabine in controlling disease progression in vivo.

LncRNAs as novel players in hepatocellular carcinoma recurrence

Long non-coding RNAs (lncRNAs) are ncRNAs more than 200 nucleotides long that participate to a wide range of biological functions. However, their role in cancer is poorly known. By using an NGS-based approach we analyzed the intragenic and poliA-lncRNAs in hepatocellular carcinoma (HCC) and we assayed the relationships between their deregulated expression and clinical-pathological characteristics. The expression profile of lncRNAs was studied in a discovery series of 28 HCC and matched cirrhosis and was validated in an independent cohort of 32 HCC patients both in tissue and serum. The correlation between lncRNA expression and clinical-pathological variables, EMT markers and putative sponged microRNAs level were investigated. Functional experiments were performed in HCC-derived cell lines to clarify the role of selected lncRNAs in HCC. A panel of deregulated lncRNAs differentiated HCC from cirrhotic tissue. CASC9 and LUCAT1 were up-regulated in a subset of HCC-derived cell lines and in half of HCCs which displayed a lower recurrence after surgery. LUCAT1 and CASC9 silencing increased cell motility and invasion capability in HCC cells and influenced the EMT phenotype. LUCAT1 was demonstrated to directly sponge the onco-miR-181d-5p. Both LUCAT1 and CASC9 were secreted in exosomes, and higher circulating CASC9 levels were associated with tumor size and HCC recurrence after surgery, suggesting its potential usage as putative non-invasive prognostic biomarker of recurrence.

The emerging role of GSK-3β in the pathobiology of classical Hodgkin lymphoma

AIMS

Glycogen synthase kinase-3 beta (GSK-3β) is a serine/threonine kinase involved in glycogen metabolism, cell cycle progression, differentiation, embryogenesis, migration, metabolism, survival and cellular senescence. Its main biological function is to inhibit β-catenin by sequestration and promotion of its proteasomal degradation in the Wnt canonical pathway; however, GSK-3β interacts with multiple signalling pathways, and aberrant expression of the enzyme was reported in many solid neoplasms. This study aimed to investigate the biological relevance of GSK-3β in classical Hodgkin lymphomas (cHL).

METHODS AND RESULTS

We analysed the functional status of GSK-3β enzyme in cHL by using antibodies raised against fixation-resistant epitopes of phospho Y216 GSK-3β (active form), phospho S9 GSK-3β (inactive form) and β-catenin protein. We first detected the pY216 GSK-3β active form of the enzyme in 100 of 100 (100%) of the cases, and in line with the latter expression profile, the β-catenin protein was found in only 12 of 100 (12%) of the samples. As reported previously in bladder cancer, pancreatic adenocarcinoma and chronic lymphocytic leukaemia, we showed an aberrant nuclear localization in the neoplastic clone of active pY216 GSK-3β in 78 of 100 (78%) of cHL cases.

CONCLUSIONS

We demonstrated the activation of GSK-3β in cHL resulting in inhibition of the Wnt/β-catenin signal cascade and the aberrant accumulation of its activated form in nuclei of Hodgkin Reed-Sternberg and Hodgkin cells. These findings may be relevant for future clinical studies, identifying GSK-3β as a potential therapeutic target for cHL.

Virus-encoded microRNA contributes to the molecular profile of EBV-positive Burkitt lymphomas

Burkitt lymphoma (BL) is an aggressive neoplasm characterized by consistent morphology and phenotype, typical clinical behavior and distinctive molecular profile. The latter is mostly driven by the MYC over-expression associated with the characteristic translocation (8;14) (q24; q32) or with variant lesions. Additional genetic events can contribute to Burkitt Lymphoma pathobiology and retain clinical significance. A pathogenetic role for Epstein-Barr virus infection in Burkitt lymphomagenesis has been suggested; however, the exact function of the virus is largely unknown.

In this study, we investigated the molecular profiles (genes and microRNAs) of Epstein-Barr virus-positive and -negative BL, to identify specific patterns relying on the differential expression and role of Epstein-Barr virus-encoded microRNAs.

First, we found significant differences in the expression of viral microRNAs and in selected target genes. Among others, we identified LIN28B, CGNL1, GCET2, MRAS, PLCD4, SEL1L, SXX1, and the tyrosine kinases encoding STK10/STK33, all provided with potential pathogenetic significance. GCET2, also validated by immunohistochemistry, appeared to be a useful marker for distinguishing EBV-positive and EBV-negative cases. Further, we provided solid evidences that the EBV-encoded microRNAs (e.g. BART6) significantly mold the transcriptional landscape of Burkitt Lymphoma clones.

In conclusion, our data indicated significant differences in the transcriptional profiles of EBV-positive and EBV-negative BL and highlight the role of virus encoded miRNA.

Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma

Endemic Burkitt lymphoma (eBL) is primarily found in children in equatorial regions and represents the first historical example of a virus-associated human malignancy. Although Epstein-Barr virus (EBV) infection and MYC translocations are hallmarks of the disease, it is unclear whether other factors may contribute to its development. We performed RNA-Seq on 20 eBL cases from Uganda and showed that the mutational and viral landscape of eBL is more complex than previously reported. First, we found the presence of other herpesviridae family members in 8 cases (40%), in particular human herpesvirus 5 and human herpesvirus 8 and confirmed their presence by immunohistochemistry in the adjacent non-neoplastic tissue. Second, we identified a distinct latency program in EBV involving lytic genes in association with TCF3 activity. Third, by comparing the eBL mutational landscape with published data on sporadic Burkitt lymphoma (sBL), we detected lower frequencies of mutations in MYC, ID3, TCF3 and TP53, and a higher frequency of mutation in ARID1A in eBL samples. Recurrent mutations in two genes not previously associated with eBL were identified in 20% of tumors: RHOA and cyclin F (CCNF). We also observed that polyviral samples showed lower numbers of somatic mutations in common altered genes in comparison to sBL specimens, suggesting dual mechanisms of transformation, mutation versus virus driven in sBL and eBL respectively.

Burkitt lymphoma is endemic in sub-Saharan Africa and affects primarily children of age 4–7 years. Historically, it was one of the first tumors associated with a virus (EBV) and bearing a translocation involving an oncogene, i.e. MYC. There are three distinct clinical variants of Burkitt lymphoma according to the World Health Organization: sporadic, endemic and immunodeficiency-related. Although there has been some recent work on the molecular characterization of sporadic Burkitt lymphomas, little is known about the pathogenesis of endemic cases. In this work, we analyzed 20 samples of RNASeq from Burkitt lymphoma collected in Lacor Hospital (Uganda, Africa) and validated in an extension panel of 73 samples from Uganda and Kenya. We identify the presence in the adjacent non-neoplastic tissue of other herpesviridae family members in 53% of the cases, namely cytomegalovirus (CMV) and Kaposi sarcoma herpesvirus (KSHV). We also demonstrate expression of EBV lytic genes in primary tumor samples and find an inverse association between EBV lytic expression and TCF3 activity. When studying the mutational profile of endemic Burkitt tumors, we find recurrent alterations in genes rarely mutated in sporadic Burkitt lymphomas, i.e. ARID1A, CCNF and RHOA, and lower numbers of mutations in genes previously reported to be commonly mutated in sporadic cases, i.e. MYC, ID3, TCF3, TP53. Together, these results illustrate a distinct genetic and viral profile of endemic Burkitt lymphoma, suggesting a dual mechanism of transformation (mutation versus virus driven in sBL and eBL respectively).

Abstract 2362: Identification and characterization of pathogenetic pathways and potential therapeutic targets in tumors derived from histiocytes and follicular dendritic cells

Tumors derived from histiocytes and follicular dendritic cells (FDC) are extremely rare, constituting less than 1% of hematopoietic tumors. Among others, follicular dendritic cell sarcoma (FDC-S), histiocytic sarcoma (HS) , and Langerhans histiocytosis (LH) are the commonest types. The clinical course is variable from indolent to aggressive; however, the disease is more often incurable. Further, probably due to their rarity and complexity, the pathobiology of these tumor is nearly unknown at present, with only scattered studies being reported.

In this study, we investigated by gene expression profiling (GEP) and extensive immunohistochemistry (IHC) a relatively large series of cases, aiming 1) to identify and characterize functional pathways possibly involved in the pathogenesis of the disease, and 2) to unveil potential targets for novel treatments.

We studied by GEP FDC-S (N=30), LH (N=9), and HS (N=4) as well as non neoplastic cells including tissue microdissected FDC (N=5), CD1c+ myeloid dendritic cells (N=4), peripheral blood monocytes (N=8), and human cultured fibroblasts (N=3). All cases were studied with the Illumina DASL whole genome microarray. The same cases as well as and independent cohort was then used for IHC validation studies.

First, unsupervised approaches (principal component analysis and hierarchical clustering) indicated that tissue samples were distinct from cellular ones, while the different entities could not be clearly separated. Second, we found by supervised comparison (ANOVA, p&lt;0.05, fold change ≥2, FDR according to Benjamini-Hockeberg), the 3 tumor types could be discriminated. Particularly, the tumors differed for genes related to immune response (consistent with their histogenesis) and to intracellular signaling. In this regard, we found several oncogenic pathways to be differentially activated while others were consistently deregulated including those related to cellular adhesion, chemotaxis, angiogenesis and response to growth factors.

We then compared each tumor type with the specific supposed counterpart (i.e. FDC-s vs. FDC; LH vs. myeloid DC; HS vs. monocytes) and identified genes and cellular programs deregulated in each of them. Interestingly, all tumors presented with consistent deregulation of previously unknown potential therapeutic targets, including PDGF/PDGFRs, PTEN, JAK/STAT, mTOR/AKT, and EGFR. Importantly, IHC confirmed GEP data and confirmed the activation of these selected pathways.

We defined for the first time the cellular programs deregulated in tumors derived from histiocytes and FDC and identified remarkable potential therapeutic targets. As appropriate experimental models (i.e. cell lines, animal models) are not available at present, international collaboration would be advisable to confirm these observation in large series before eventually moving to early phase clinical trials.

Citation Format: Pier-Paolo Piccaluga, Maura Rossi, Giovanna Motta, Sylvia Hartmann, Claudia Doering, Fabio Fuligni, Claudio Agostinelli, Maria Rosaria Sapienza, Maria Antonella Laginestra, Federica Melle, Maryam Etebari, Mohsen Navari, Anna Gazzola, Claudia Mannu, Clara Bertuzzi, Claudio Tripodo, Martin L. Hansmann, Fabio Facchetti, Stefano A Pileri. Identification and characterization of pathogenetic pathways and potential therapeutic targets in tumors derived from histiocytes and follicular dendritic cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2362. doi:10.1158/1538-7445.AM2014-2362

Abstract 5173: Identification of single-nucleotide variants by high-throughput RNA sequencing in endemic Burkitt Lymphoma

Endemic Burkitt lymphoma (eBL) constitutes the commonest cancer in children in Developing Countries, while the sporadic (sBL) and immunodeficiency associated BL (ID-BL) forms are mainly encountered in Western Countries. The molecular hallmark of three BL variants is the translocation of MYC proto-oncogene to the immunoglobulin-heavy [t(8;14)(q24;q32)] or one of the light chain genes [t(2;8)(p12; q24) and t(8;22)(q24; q11)], leading to constitutive MYC activation. However, additional genetic events contributes to BL pathogenesis, most of which have been studies in sBL only.

Here, we performed RNA Sequencing aiming to identify genetic changes possibly cooperating with MYC in the pathogenesis of eBL. We studied by RNA Sequencing (Illumina HiScanSQ) 21 eBL cases, collected at different African Institutions as discovery set. Total RNA was extracted with Trizol and libraries were prepared according to TruSeq RNA sample preparation v2 protocol. Sequence variants were obtained using the SAVI (Statistical Algorithm for Variant Identification) algorithm independently for each sample. Candidate somatic mutations were obtained by eliminating common germline variants and recurrence. To validate single-nucleotide variants (SNVs) we performed Sanger sequencing on these 21 cases. Further, we studied these SNVs by Sequenom Technology and Sanger sequencing on additional 24 eBL cases as validation set. 41 sBL and 8 ID-BL were also considered as controls.

We found 66 genes affected by 219 total SNVs with different frequency in 21 samples (range 2-22 for sample). We then focused on genes mutated in at least three samples and predicted to induce somatic protein-changing. We identified 25 genes affected by 172 total SNVs, that were recurrently mutated (min. 3/21 samples; max 11/21 samples). These included genes previously known to be involved in sBL, such as TP53, MYC, ID3, PCBP1 and TCF3 as well as genes involved in other lymphomas such as DDX3X and RHOA. The remaining 18 genes (AGAP6, APBB1IP, ARID1A, ASPSCR1, AVEN, CAD, CCNF, GPATCH4, HERC2, KPNA2, MTBP, MTERFD1, NEK9, NUP133,

PARP1, POLQ, SCFD2, TIGD1) were previously not related to BL, and resulted to be involved in several important molecular pathways as cell cycle progression, apoptosis, matrix remodelling, angiogenesis.

Sanger sequencing confirmed such SNVs with 100% accuracy in 21 cases of discovery set. Subsequently, we studied them in 24 independent cases of validation set by both Sanger sequencing and by mass spectrometry (Sequenom). We found that most eBL cases carried additional SNVs rather than MYC translocations. Noteworthy, we failed to find these mutations in sBL, confirming the concept that different pathogenetic events may contribute to the pathogenesis of BL subtypes.

In conclusion , we discovered new SNVs that might have a significant role in the pathogenesis of eBL. Functional experiments are required to definitely assess their impact.

Citation Format: Maria Antonella Laginestra, Francesco Abate, Maryam Etebari, Giulia De Falco, Fabio Fuligni, Maura Rossi, Sakellarios Zairis, Maria Rosaria Sapienza, Anna Gazzola, Claudia Mannu, Federica Melle, Claudio Agostinelli, Mohsen Navari, Cristiana Bellan, Sara Gazaneo, Lucia Mundo, Martin Ogwang, Valeria Calbi, Lorenzo Leoncini, Stefano A. Pileri, Raul Rabadan, Pier Paolo Piccaluga. Identification of single-nucleotide variants by high-throughput RNA sequencing in endemic Burkitt Lymphoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5173. doi:10.1158/1538-7445.AM2014-5173

The evolution of clonality testing in the diagnosis and monitoring of hematological malignancies

Currently, distinguishing between benign and malignant lymphoid proliferations is based on a combination of clinical characteristics, cyto/histomorphology, immunophenotype and the identification of well-defined chromosomal aberrations. However, such diagnoses remain challenging in 10-15% of cases of lymphoproliferative disorders, and clonality assessments are often required to confirm diagnostic suspicions. In recent years, the development of new techniques for clonality detection has allowed researchers to better characterize, classify and monitor hematological neoplasms. In the past, clonality was primarily studied by performing Southern blotting analyses to characterize rearrangements in segments of the IG and TCR genes. Currently, the most commonly used method in the clinical molecular diagnostic laboratory is polymerase chain reaction (PCR), which is an extremely sensitive technique for detecting nucleic acids. This technique is rapid, accurate, specific, and sensitive, and it can be used to analyze small biopsies as well as formalin-fixed paraffin-embedded samples. These advantages make PCR-based approaches the current gold standard for IG/TCR clonality testing. Since the completion of the first human genome sequence, there has been a rapid development of technologies to facilitate high-throughput sequencing of DNA. These techniques have been applied to the deep characterization and classification of various diseases, patient stratification, and the monitoring of minimal residual disease. Furthermore, these novel approaches have the potential to significantly improve the sensitivity and cost of clonality assays and post-treatment monitoring of B- and T-cell malignancies. However, more studies will be required to demonstrate the utility, sensitivity, and benefits of these methods in order to warrant their adoption into clinical practice. In this review, recent developments in clonality testing are examined with an emphasis on highly sensitive systems for improving diagnostic workups and minimal residual disease assessments.

Molecular profiling of blastic plasmacytoid dendritic cell neoplasm reveals a unique pattern and suggests selective sensitivity to NF-kB pathway inhibition

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare disease of controversial origin recently recognized as a neoplasm deriving from plasmacytoid dendritic cells (pDCs). Nevertheless, it remains an orphan tumor with obscure biology and dismal prognosis. To better understand the pathobiology of BPDCN and discover new targets for effective therapies, the gene expression profile (GEP) of 25 BPDCN samples was analyzed and compared with that of pDCs, their postulated normal counterpart. Validation was performed by immunohistochemistry (IHC), whereas functional experiments were carried out ex vivo. For the first time at the molecular level, we definitely recognized the cellular derivation of BPDCN that proved to originate from the myeloid lineage and in particular, from resting pDCs. Furthermore, thanks to an integrated bioinformatic approach we discovered aberrant activation of the NF-kB pathway and suggested it as a novel therapeutic target. We tested the efficacy of anti-NF-kB-treatment on the BPDCN cell line CAL-1, and successfully demonstrated by GEP and IHC the molecular shutoff of the NF-kB pathway. In conclusion, we identified a molecular signature representative of the transcriptional abnormalities of BPDCN and developed a cellular model proposing a novel therapeutic approach in the setting of this otherwise incurable disease.

Molecular profiling improves classification and prognostication of nodal peripheral T-cell lymphomas: results of a phase III diagnostic accuracy study

PURPOSE

The differential diagnosis among the commonest peripheral T-cell lymphomas (PTCLs; ie, PTCL not otherwise specified [NOS], angioimmunoblastic T-cell lymphoma [AITL], and anaplastic large-cell lymphoma [ALCL]) is difficult, with the morphologic and phenotypic features largely overlapping. We performed a phase III diagnostic accuracy study to test the ability of gene expression profiles (GEPs; index test) to identify PTCL subtype.

METHODS

We studied 244 PTCLs, including 158 PTCLs NOS, 63 AITLs, and 23 ALK-negative ALCLs. The GEP-based classification method was established on a support vector machine algorithm, and the reference standard was an expert pathologic diagnosis according to WHO classification.

RESULTS

First, we identified molecular signatures (molecular classifier [MC]) discriminating either AITL and ALK-negative ALCL from PTCL NOS in a training set. Of note, the MC was developed in formalin-fixed paraffin-embedded (FFPE) samples and validated in both FFPE and frozen tissues. Second, we found that the overall accuracy of the MC was remarkable: 98% to 77% for AITL and 98% to 93% for ALK-negative ALCL in test and validation sets of patient cases, respectively. Furthermore, we found that the MC significantly improved the prognostic stratification of patients with PTCL. Particularly, it enhanced the distinction of ALK-negative ALCL from PTCL NOS, especially from some CD30+ PTCL NOS with uncertain morphology. Finally, MC discriminated some T-follicular helper (Tfh) PTCL NOS from AITL, providing further evidence that a group of PTCLs NOS shares a Tfh derivation with but is distinct from AITL.

CONCLUSION

Our findings support the usage of an MC as additional tool in the diagnostic workup of nodal PTCL.

Abstract 1951: miRNA expression profile of Blastic plasmacytoid dendritic cell neoplasm

Background:

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare neoplasm currently included among acute myeloid leukemias in the WHO classification. BPDCN is an orphan tumor characterized by an unknown biology with clinical aggressive course and dismal prognosis.

Only few studies explored its genetics, documenting a complex karyotype and sporadic genetic alterations. Unfortunately, data were based on a limited number of patients and lacked functional elucidation. Conversely, studies on the transcriptome only compared BPDCN with other leukemias, failing to identify pathogenetic events.

In this study we aimed to assess whether miRNA deregulation contribute to BPDCN pathogenesis and clinical behaviour.

Methods:

We studied by miRNA profiling (NanoString Technologies) 30 BPDCN samples, 9 normal plasmacytoid dendritic cell (pDCs) samples and the CAL-1 tumor cell line. In addition, 25 independent BPDCN cases were studied by qRT-PCR and IHC as validation. To investigate the functional consequences of miRNA deregulation, we also performed a global gene expression profile (GEP) analysis on the same cases by using the Illumina Whole Genome DASL Assay. We applied ANOVA and Student t-test to find genes and miRNAs differentially expressed between BPDCNs and normal pDCs. The selected miRNAs were further filtered based on their predicted impact on the GEP using Linear Discriminant Analysis, Spearman correlation and Gene Set Enrichment Analysis. Finally, the functional effects of selected miRNAs were assessed ex vivo on CAL-1 cell line.

Results:

We found that, according to the unsupervised analysis of miRNAs, BPDCN patients have a molecular signature well distinct from their normal counterpart.

The following supervised analysis identified a set of 114 miRNAs significantly deregulated whose aberrant expression might have a relevant impact on cancer-related cellular pathways.

Therefore, after validating their expression in an independent set of cases, we integrated the miRNA and mRNA expression profiles on the same patients, in order to assess the functional impact of deregulated miRNAs on gene expression profile.

Pathway analysis of the predicted miRNA target genes, revealed that most of them were involved in the same gene ontology category: miRNAs synergic action appeared to strongly affect the biological process of programmed cell death.

We thus focused on miRNA-mRNA anti-correlations affecting the apoptotic pathway: we transfected specific mimics and inhibitors into CAL-1 cell line; we evaluated their functional impact by gene expression profile and, finally, we confirmed their relation with specific targets by Luciferase assay.

In conclusion, for the first time we investigated the miRNA profile of BPDCN, defining previously uncovered molecular mechanisms underlying the pathogenesis of the disease. Specifically, we found a subset of miRNAs significantly deregulated and highly affecting the apoptotic pathway.

Citation Format: Maria Rosaria Sapienza, Fabio Fuligni, Maria Antonella Laginestra, Maura Rossi, Luciano Cascione, Alessandro Laganà, Claudio Agostinelli, Maryam Etebari, Anna Gazzola, Claudia Mannu, Elena Sabattini, Francesco Bacci, Carlo Maria Croce, Stefano Aldo Pileri, Pier Paolo Piccaluga. miRNA expression profile of Blastic plasmacytoid dendritic cell neoplasm. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1951. doi:10.1158/1538-7445.AM2013-1951

Abstract 5275: miRNA profiling of peripheral T-cell lymphomas

Background: Peripheral T cell lymphomas not otherwise specified (PTCLs/NOS) are rare and aggressive tumors, whose molecular pathogenesis is poorly known and whose diagnosis is quite difficult. In fact, both morphology and phenotype largely overlap with those of other nodal PTCLs, including angioimmunoblastic T cell lymphoma (AITL) and anaplastic large cell lymphomas (ALCLs).

Here, we performed an extensive miRNA profiling of PTCLs in order to identify differentially expressed miRNA, either involved in their pathogenesis or potentially useful for their differential diagnosis.

Methods: We studied by miRNA profiling (TaqMan Array MicroRNA Cards A) 60 samples including PTCLs/NOS (N=25), AITLs (N=10), ALCLs (N=12) and normal T cells (N=13); in addition, 40 independent PTCL cases were studied by qRT-PCR as validation. Further, to assess the functional impact of deregulated miRNAs, we performed a global gene expression profile (GEP) analysis in the same cases by using the Illumina Whole Genome DASL Assay. ANOVA and Student t-test were performed to find genes and miRNAs differentially expressed between PTCLs and normal T cells or among PTCL subtypes, respectively. Differentially expressed miRNAs were further filtered based on their predicted impact on the GEP using Linear Discriminant Analysis, Spearman correlation and Gene Set Enrichment Analysis. A discriminant function based on linear combination of GEP signatures was then used to better distinguish different PTCLs subtypes. Finally, the functional effects of selected miRNA were assessed by transfection of specific mimic and inhibitors into PTCL cells and then evaluating the GEPs (functional GEP).

Findings: First, unsupervised analyses clearly discriminated PTCLs and normal T cells based on the miRNA expression patterns. Second, supervised analysis identified 256 miRNA differentiating the two groups (p&lt;0.05, FC ≥2, Bonferroni correction). To identify those miRNA more likely to impact the GEP of the tumors, we then performed a multi-step analysis integrating miRNA and GEP data. We identified 4 highly discriminant miRNA inversely correlated with different potential target genes. All 4 miRNA were confirmed by qPCR in a validation set, while their target genes were assessed by functional GEP confirming their impact.

Thereafter, we sought miRNAs differentially expressed in the PTCL subtypes, to be used as diagnostic markers. Based on ANOVA and subsequent linear discriminant analysis we identified 3 sets of miRNA able to efficiently distinguish PTCL/NOS vs. ALK-/ALCL (N=5 miRNA), ALK+/ALCL vs. ALK-/ALCL (N=4), and PTCL/NOS vs. AITL (N=8). Noteworthy, this novel molecular diagnostic tool was validated by qPCR in independent cases, demonstrating a remarkable diagnostic accuracy ranging between 85% and 95%.

In conclusion, miRNA profiling allowed to identify miRNA possibly involved in PTCL pathogenesis and to develop a novel diagnostic tool for the differential diagnosis of the commonest subtypes.

Citation Format: Maria Antonella Laginestra, Fabio Fuligni, Maura Rossi, Davide Gibellini, Maria Rosaria Sapienza, Anna Gazzola, Claudia Mannu, Elena Sabattini, Francesco Bacci, Claudio Agostinelli, Stefano Aldo Pileri, Pier Paolo Piccaluga. miRNA profiling of peripheral T-cell lymphomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5275. doi:10.1158/1538-7445.AM2013-5275

Use of IGK gene rearrangement analysis for clonality assessment of lymphoid malignancies: a single center experience

Diagnosis of B-non Hodgkin lymphomas (NHLs) is based on clinical, morphological and immunohistochemi-cal features. However, in up to 10-15% of cases, analysis of immunoglobulin heavy (IGH) or light (IGK/IGL) chains genes is required to discriminate between malignant and reactive lymphoid proliferations. In this study, we evaluated the feasibility and efficiency of IGK analysis in the routine diagnostic of B-cell lymphoproliferative disorders (B-LD) when applied to formalin-fixed paraffin-embedded (FFPE) tissues. Clonality patterns were studied in 59 B-LD using the BIOMED-2 protocol for IGK assays, after failure of the IGH assay. PCR products were evaluated by both heterodu-plex and GeneScan analysis. IGK analysis was technically successful in all cases. Overall, it supported the histopa-thological suspicion in 52/59 cases (88%), the sensitivity and specificity being 83% and 80%, respectively. Further, positive and negative predictive values were 95% and 50%, respectively. Interestingly, among various lymphoma subtypes, marginal zone lymphoma and follicular lymphoma most frequently required IGK analysis. In conclusion, IGK study according to the BIOMED-2 protocol resulted feasible and extremely useful in supporting challenging diagnosis of B-LD even if applied on FFPE samples. Accordingly, when NHL is suspected, negative results at IGH analysis should not be considered as conclusive and further investigation of IGK is appropriate.