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Introduction: Venetoclax has emerged as a breakthrough treatment which has revolutionized the therapeutic paradigm of chronic lymphocytic leukemia (CLL). This is primarily attributed to the efficacy of venetoclax as a time-limited, chemo-free, therapy in a field dominated by targeted agents given on a continuous schedule. Furthermore, compelling clinical data support the use of venetoclax in combination with other targeted agents in the hope of preventing drug resistance due to the emergence of acquired mutations.Areas covered: This paper provides an overview of clinical results of newly approved or investigational venetoclax-based therapies for CLL. In view of current and potential roles in CLL care, the strengths and disadvantages of venetoclax-combinations are discussed. The MEDLINE database, ClinicalTrials.gov and conference proceedings were all reviewed to select the relevant literature.Expert opinion: While the advent of venetoclax-based combinations has significantly expanded the therapeutic options for patients with CLL, further research with longer follow-up is required to address remaining open questions such as (I) the role of venetoclax as fixed duration therapy(II) timing and threshold of minimal residual disease (MRD) assessment for therapy discontinuation, (III) the efficacy of novel triplet combinations with venetoclax as backbone therapy, (IV) indications for the re-initiation of therapy with venetoclax.

The treatment landscape for chronic lymphocytic leukaemia (CLL) is rapidly evolving, with several targeted agents recently approved. These compounds have dramatically changed the natural history of the disease. However, with the array of effective therapies commercially available, the challenge is to define tailored treatment strategies able to realize a balance between treatment efficacy and toxicity or tolerance. New algorithms of treatment are being developed, and it appears that minimal residual disease (MRD) directed therapy will become the norm in the future. Clinical trials are looking at various combinations of novel therapies given with a defined, fixed-period of treatment based on MRD analysis. This approach enables patients to have a period of treatment-free remission instead of continuous therapy. In this review, we summarize this evolution of targeted therapies in CLL.

To shed light onto the molecular basis of Philadelphia chromosome-positive acute lymphoblastic leukemia and to investigate the prognostic role of additional genomic lesions, we analyzed copy number aberrations using the Cytoscan HD Array in 116 newly diagnosed adult patients with Philadelphia chromosome-positive acute lymphoblastic leukemia enrolled in four different GIMEMA protocols, all based on a chemotherapy-free induction strategy. This analysis showed that patients with Philadelphia chromosome-positive acute lymphoblastic leukemia carry an average of 7.8 lesions/case, with deletions outnumbering gains (88% versus 12%). The most common deletions were those targeting IKZF1, PAX5 and CDKN2A/B, which were detected in 84%, 36% and 32% of cases, respectively. Patients carrying simultaneous deletions of IKZF1 plus CDKN2A/B and/or PAX5 had a significantly lower disease-free survival rate (24.9% versus 43.3%; P=0.026). The only IKZF1 isoform affecting prognosis was the dominant negative one (P=0.003). Analysis of copy number aberrations showed that 18% of patients harbored MEF2C deletions, which were of two types, differing in size: the longer deletions were associated with the achievement of a complete molecular remission (P=0.05) and had a favorable impact on disease-free survival (64.3% versus 32.1% at 36 months; P=0.031). These findings retained statistical significance also in multivariate analysis (P=0.057). KRAS deletions, detected in 6% of cases, were associated with the achievement of a complete molecular remission (P=0.009). These results indicate that in adults with Philadelphia chromosome-positive acute lymphoblastic leukemia a detailed evaluation of additional deletions - including CDKN2A/B, PAX5, IKZF1, MEF2C and KRAS - has prognostic implications and should be incorporated in the design of more personalized treatment strategies.

The co-occurrence of BCR-ABL1 fusion and core-binding factor (CBF) rearrangements is uncommonly reported in AML. Although CBF rearrangements carry a favorable prognosis, the coexistence of BCR-ABL1 is associated with aggressive disease suggesting a potential advantage of high-intensity chemotherapy in association with tyrosine kinase inhibitors. Herein, we describe a refractory AML patient harboring BCR-ABL1 fusion and CBFB rearrangement that was successfully treated with a combination of venetoclax and hypomethylating agent.

Given the immunosuppression of chronic lymphocytic leukemia (CLL), this disease represents a challenging model for assessing the extent of serologic response to mRNA vaccination against severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). In this perspective, we assessed the efficacy of the BNT162b2 mRNA COVID-19 vaccine in 70 CLL pts followed up at single hematological institution. The study was approved by the Institutional Review Board. Serologic testing for SARS Cov2 IgG was performed using the LIAISON® SARS-CoV-2 S1/S2 IgG test (DiaSorin; Saluggia, Italy), a chemiluminescence immunoassay for the quantitative determination of anti-S1 and anti-S2 specific IgG antibodies to SARS-CoV-2. Clinical sensitivity and specificity of assay were 98.7% and 99.5% respectively. Samples were considered negative for antibody titers below 13 AU/ml. Results were compared with those of an age-matched group of subjects with no hematological malignancy (n=57). Patient samples for serology testing were obtained after median time of 14 days (range, 14-28) from the second vaccine dose. Median age of CLL pts was 72 years (range, 63-88) and 71.4% were males. The median time from CLL diagnosis to vaccination was 82.5 mo. (range, 1-280). Twenty-three pts (32.9%) were treatment naïve (TN), 36 (51.4%) on active therapy (i.e., BTKi, 22; anti-BCL2 12; PI3Ki,1; cyclophosphamide,1) and 11 (15.7%) off-therapy (i.e., 8 in complete [CR] or partial remission [PR], and 3 in CLL relapse). Of note, 9 (25.7%) of 35 pts on therapy with a pathway inhibitor (PI) at the time of vaccination had been given an anti-CD20 antibody. The vaccine elicited an antibody-mediated response in 41 (58.5%) of the 70 CLL pts. An inferior response rate [RR] (58.5% vs 100%, OR, 0.012 [0.0007-0.206];P=0.02) and a lower antibody titers (median, 58 AU/ml; range, 1.8-800 vs. 284 AU/ml; range, 14-800; P< 0.0001) were observed in CLL pts in comparison to age-matched subjects with no hematological malignancy. The RR was higher in TN (87%) or off-therapy pts with sustained clinical response (87.5%) in comparison to pts on therapy at the time of vaccination (41.7%)( In univariate analysis, the following variables were significantly associated with serological response to SARS-CoV-2 vaccination: early Rai stage (i.e.,0-I) (OR, 0.36 [0.13-0.97];P=0.04), mutated IGHV status (OR,0.30 [0.10-0.88]; P=0.02), lack of active therapy - which comprised TN and off-therapy pts with sustained response - (OR,0.09 [0.03-0.32];P In agreement with results of recent studies (Herishanu et al, Blood 2021; Roeker et al, Leukemia 2021;Perry et al, Blood Cancer J. 2021; Benjamini O et al, Haematologica 2021 ) our findings suggest that antibody-mediated response to COVID-19 vaccination is significantly reduced in CLL and influenced by disease activity and treatment status. The serological response to SARS-CoV-2 vaccination observed in pts. with early disease with no need of therapy may help to identify CLL pts who are expected to achieve an optimal response to COVID-19 vaccine similarly to age- and sex-matched controls. Figure 1 Figure 1. Disclosures Molica: Astrazeneca: Honoraria; Abbvie: Consultancy, Honoraria; Janssen: Consultancy, Honoraria.

Summary Copy number aberrations (CNAs) represent cooperating events in B-lineage acute lymphoblastic leukaemia (B-ALL); however, their clinical relevance across different age cohorts is unclear. We analysed the recurrent CNAs in 157 age-stratified B-ALL negative cases for recurrent rearrangements (B-NEG ALL), and their association with patients’ clinico-biological features. We found that: (i) CDKN2A/RB1-deleted and EBF1-deleted adults had a shorter disease-free survival than those with wild-type, (ii) among the unfavourable markers, CDKN2A/RB1 deletions and K/NRAS mutations retained their impact in multivariate analysis, encouraging the evaluation of CDKN2A/RB1 deletions and RAS mutations in the diagnostic/prognostic workflow to refine ALL risk assessment.

Introduction: In the last few years, the expansion of therapy with pathway inhibitors has revolutionized the treatment landscape of chronic lymphocytic leukemia (CLL). As a matter of fact, ibrutinib, the first-in-class Bruton tyrosine kinase (BTK) inhibitor, became a milestone in the treatment of both naive or relapsed/refractory CLL patients. Most patients treated with such an agent achieve durable clinical response; however, a deeper response is rarely reached and continuous treatment is required. Since ibrutinib-resistant CLL clones can develop in about 20% of patients and toxicities, leading to drug discontinuation, occur in about 30% of patients treated with ibrutinib, several new BTK inhibitors have been developed in order to lower off-target effects and overcome ibrutinib resistance.Areas covered: In this review, we summarize the main English publications exploring efficacy and side effects of first and next-generation BTK inhibitors. Results of clinical trials evaluating these novel agents are presented and critically discussed.Expert opinion: Efforts in the development of highly specific second-generation BTK inhibitors and combination strategies provide challenging options to overcome limitations of therapy with ibrutinib. It is also crucial to identify additional risk factors and to understand disease biology underlying clonal evolution of CLL in the context of novel agents.

The IL7 receptor α chain, encoded by the IL7R gene, heterodimerizes with the IL-2Rγ (common gamma) chain to form the IL7 receptor, or with the cytokine receptor-like factor 2 (CRLF2) for the thymic...

BCR/ABL1-like acute lymphoblastic leukaemia (ALL) is a subgroup of B-lineage acute lymphoblastic leukaemia that occurs within cases without recurrent molecular rearrangements. Gene expression profiling (GEP) can identify these cases but it is expensive and not widely available. Using GEP, we identified 10 genes specifically overexpressed by BCR/ABL1-like ALL cases and used their expression values - assessed by quantitative real time-polymerase chain reaction (Q-RT-PCR) in 26 BCR/ABL1-like and 26 non-BCR/ABL1-like cases to build a statistical "BCR/ABL1-like predictor", for the identification of BCR/ABL1-like cases. By screening 142 B-lineage ALL patients with the "BCR/ABL1-like predictor", we identified 28/142 BCR/ABL1-like patients (19·7%). Overall, BCR/ABL1-like cases were enriched in JAK/STAT mutations (P < 0·001), IKZF1 deletions (P < 0·001) and rearrangements involving cytokine receptors and tyrosine kinases (P = 0·001), thus corroborating the validity of the prediction. Clinically, the BCR/ABL1-like cases identified by the BCR/ABL1-like predictor achieved a lower rate of complete remission (P = 0·014) and a worse event-free survival (P = 0·0009) compared to non-BCR/ABL1-like ALL. Consistently, primary cells from BCR/ABL1-like cases responded in vitro to ponatinib. We propose a simple tool based on Q-RT-PCR and a statistical model that is capable of easily, quickly and reliably identifying BCR/ABL1-like ALL cases at diagnosis.

Over the past two decades, hematologic malignancies have been extensively evaluated due to the introduction of powerful technologies, such as conventional karyotyping, FISH analysis, gene and microRNA expression profiling, array comparative genomic hybridization and SNP arrays, and next-generation sequencing (including whole-exome sequencing and RNA-seq). These analyses have allowed for the refinement of the mechanisms underlying the leukemic transformation in several oncohematologic disorders and, more importantly, they have permitted the definition of novel prognostic algorithms aimed at stratifying patients at the onset of disease and, consequently, treating them in the most appropriate manner. Furthermore, the identification of specific molecular markers is opening the door to targeted and personalized medicine. The most important findings on novel acquisitions in the context of acute lymphoblastic leukemia of both B and T lineage and de novo acute myeloid leukemia are described in this review.

Since the discovery of the BCR-ABL1 fusion gene in chronic myeloid leukemia, many more fusion genes resulting from chromosomal rearrangements have been identified and characterized. The study of these fusion genes has been extremely important for our understanding of the role of chromosomal rearrangements in leukemogenesis and in oncology in general. In chronic myeloid leukemia, or related myeloproliferative malignancies caused by the expression of oncogenic fusion kinases, tyrosine kinase inhibitors are now successfully used to treat these diseases. In acute myeloid leukemias, the presence of chromosomal rearrangements, oncogenic fusion genes and point mutations in key oncogenic drivers has important prognostic value and determines the choice of therapy. In this review, the authors provide an overview of the important fusion genes present in various myeloid malignancies and their importance for clinical practice.

MLLT10 (also known as AF10 ), at chromosome 10 band p12, is emerging as a promiscuous gene. Six partners have been reported to date: PICALM(CALM )/11q14, MLL /11q23, NAP1L1 /12q21, HNRNPH1 /5q35, DDX3X /Xp11.3 and NUP98 /11p15.[1][1],[2][2] All fusions retain the MLLT10 octapeptide motif-leucine

The mammalian target of rapamycin (mTOR) is a central processor of intra- and extracellular signals, regulating many fundamental cellular processes such as metabolism, growth, proliferation, and survival. Strong evidences have indicated that mTOR dysregulation is deeply implicated in leukemogenesis. This has led to growing interest in the development of modulators of its activity for leukemia treatment. This review intends to provide an outline of the principal biological and molecular functions of mTOR. We summarize the current understanding of how mTOR interacts with microRNAs, with components of cell metabolism, and with controllers of apoptotic machinery. Lastly, from a clinical/translational perspective, we recapitulate the therapeutic results in leukemia, obtained by using mTOR inhibitors as single agents and in combination with other compounds.

// Monica Messina 1,* , Sabina Chiaretti 1,* , Jiguang Wang 2,* , Anna Lucia Fedullo 1 , Nadia Peragine 1 , Valentina Gianfelici 1 , Alfonso Piciocchi 3 , Fulvia Brugnoletti 1 , Filomena Di Giacomo 4 , Simona Pauselli 1 , Antony B. Holmes 5 , Maria Cristina Puzzolo 1 , Giulia Ceglie 1 , Valerio Apicella 1 , Marco Mancini 1 , Geertruy te Kronnie 6 , Anna Maria Testi 1 , Antonella Vitale 1 , Marco Vignetti 3 , Anna Guarini 1 , Raul Rabadan 2 and Robin Foa 1 1 Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy 2 Department of Systems Biology, Biomedical Informatics and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA 3 GIMEMA Data Center, Rome, Italy 4 Department of Molecular Biotechnology and Health Science, and Center for Experimental Research and Medical Studies (CeRMS), University of Torino, Torino, Italy 5 Institute for Cancer Genetics and The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA 6 Department of Women’s and Children’s Health, University of Padova, Padova, Italy * These authors have contributed equally to this work Correspondence to: Robin Foa, email: // Keywords : acute lymphoblastic leukemia, next generation sequencing, copy number aberrations, novel prognostic markers, genetic-driven targeted therapy Received : October 23, 2015 Accepted : January 28, 2016 Published : February 12, 2016 Abstract To shed light into the molecular bases of B-lineage acute lymphoblastic leukemia lacking known fusion transcripts, i.e. BCR-ABL1 , ETV6-RUNX1 , E2A-PBX1 , and MLL rearrangements (B-NEG ALL) and the differences between children, adolescents/young adults (AYA) and adults, we analyzed 168 B-NEG ALLs by genome-wide technologies. This approach showed that B-NEG cases carry 10.5 mutations and 9.1 copy-number aberrations/sample. The most frequently mutated druggable pathways were those pertaining to RAS/RTK (26.8%) and JAK/STAT (12.5%) signaling. In particular, FLT3 and JAK/STAT mutations were detected mainly in AYA and adults, while KRAS and NRAS mutations were more frequent in children. RAS/RTK mutations negatively affected the outcome of AYA and adults, but not that of children. Furthermore, adult B-NEG ALL carrying JAK/STAT mutations had a shorter survival. In vitro experiments showed that FLT3 inhibitors reduced significantly the proliferation of FLT3 -mutated primary B-NEG ALL cells. Likewise, PI3K/mTOR inhibitors reduced the proliferation of primary cells harboring RAS and IL7R mutations. These results refine the genetic landscape of B-NEG ALL and suggest that the different distribution of lesions and their prognostic impact might sustain the diverse outcome between children, adults and partly AYA - whose genomic scenario is similar to adults - and open the way to targeted therapeutic strategies.

Recurrent deletions of the long arm of chromosome 5 were detected in 23/200 cases of T-cell acute lymphoblastic leukemia. Genomic studies identified two types of deletions: interstitial and terminal. Interstitial 5q deletions, found in five cases, were present in both adults and children with a female predominance (chi-square, P=0.012). Interestingly, these cases resembled immature/early T-cell precursor acute lymphoblastic leukemia showing significant down-regulation of five out of the ten top differentially expressed genes in this leukemia group, including TCF7 which maps within the 5q31 common deleted region. Mutations of genes known to be associated with immature/early T-cell precursor acute lymphoblastic leukemia, i.e. WT1, ETV6, JAK1, JAK3, and RUNX1, were present, while CDKN2A/B deletions/mutations were never detected. All patients had relapsed/resistant disease and blasts showed an early differentiation arrest with expression of myeloid markers. Terminal 5q deletions, found in 18 of patients, were more prevalent in adults (chi-square, P=0.010) and defined a subgroup of HOXA-positive T-cell acute lymphoblastic leukemia characterized by 130 up- and 197 down-regulated genes. Down-regulated genes included TRIM41, ZFP62, MAPK9, MGAT1, and CNOT6, all mapping within the 1.4 Mb common deleted region at 5q35.3. Of interest, besides CNOT6 down-regulation, these cases also showed low BTG1 expression and a high incidence of CNOT3 mutations, suggesting that the CCR4-NOT complex plays a crucial role in the pathogenesis of HOXA-positive T-cell acute lymphoblastic leukemia with terminal 5q deletions. In conclusion, interstitial and terminal 5q deletions are recurrent genomic losses identifying distinct subtypes of T-cell acute lymphoblastic leukemia.

Despite therapeutic improvements, a sizable number of patients with T-cell acute lymphoblastic leukemia still have a poor outcome. To unravel the genomic background associated with refractoriness, we evaluated the transcriptome of 19 cases of refractory/early relapsed T-cell acute lymphoblastic leukemia (discovery cohort) by performing RNA-sequencing on diagnostic material. The incidence and prognostic impact of the most frequently mutated pathways were validated by Sanger sequencing on genomic DNA from diagnostic samples of an independent cohort of 49 cases (validation cohort), including refractory, relapsed and responsive cases. Combined gene expression and fusion transcript analyses in the discovery cohort revealed the presence of known oncogenes and identified novel rearrangements inducing overexpression, as well as inactivation of tumor suppressor genes. Mutation analysis identified JAK/STAT and RAS/PTEN as the most commonly disrupted pathways in patients with chemorefractory disease or early relapse, frequently in association with NOTCH1/FBXW7 mutations. The analysis on the validation cohort documented a significantly higher risk of relapse, inferior overall survival, disease-free survival and event-free survival in patients with JAK/STAT or RAS/PTEN alterations. Conversely, a significantly better survival was observed in patients harboring only NOTCH1/FBXW7 mutations: this favorable prognostic effect was abrogated by the presence of concomitant mutations. Preliminary in vitro assays on primary cells demonstrated sensitivity to specific inhibitors. These data document the negative prognostic impact of JAK/STAT and RAS/PTEN mutations in T-cell acute lymphoblastic leukemia and suggest the potential clinical application of JAK and PI3K/mTOR inhibitors in patients harboring mutations in these pathways.

JAK3 is a tyrosine kinase that associates with the common γ chain of cytokine receptors and is recurrently mutated in T-cell acute lymphoblastic leukemia (T-ALL). We tested the transforming properties of JAK3 pseudokinase and kinase domain mutants using in vitro and in vivo assays. Most, but not all, JAK3 mutants transformed cytokine-dependent Ba/F3 or MOHITO cell lines to cytokine-independent proliferation. JAK3 pseudokinase mutants were dependent on Jak1 kinase activity for cellular transformation, whereas the JAK3 kinase domain mutant could transform cells in a Jak1 kinase-independent manner. Reconstitution of the IL7 receptor signaling complex in 293T cells showed that JAK3 mutants required receptor binding to mediate downstream STAT5 phosphorylation. Mice transplanted with bone marrow progenitor cells expressing JAK3 mutants developed a long-latency transplantable T-ALL-like disease, characterized by an accumulation of immature CD8(+) T cells. In vivo treatment of leukemic mice with the JAK3 selective inhibitor tofacitinib reduced the white blood cell count and caused leukemic cell apoptosis. Our data show that JAK3 mutations are drivers of T-ALL and require the cytokine receptor complex for transformation. These results warrant further investigation of JAK1/JAK3 inhibitors for the treatment of T-ALL. ispartof: Blood vol:124 issue:20 pages:3092-3100 ispartof: location:United States status: published

Endometrial stromal sarcomas (ESSs) are a genetically heterogeneous group of rare uterine neoplasms that are commonly driven by recurrent gene rearrangements. In conventional low-grade ESS, JAZF1-SUZ12, PHF1-JAZF1, EPC1-PHF1 and MEAF6-PHF1, and recently described ZC3H7-BCOR chimeric fusions have been reported in > 50% of cases. Conversely, oncogenic t(10;17)(q22;p13) translocation yields YWHAE-FAM22A/B chimeric proteins that are associated with histologically high-grade and clinically more aggressive ESS. Integrating whole-transcriptome paired-end RNA sequencing with fluorescence in situ hybridization (FISH) and banding cytogenetics, we identified MBTD1 (malignant brain tumor domain-containing 1) and CXorf67 (chromosome X open reading frame 67) as the genes involved in the novel reciprocal t(X;17)(p11.2;q21.33) translocation in two independent low-grade ESS of classical histology. The presence of the MBTD1-CXorf67 fusion transcript was validated in both cases using reverse-transcription polymerase chain reaction followed by Sanger sequencing. A specific FISH assay was developed to detect the novel t(X;17) translocation in formalin-fixed paraffin-embedded material, and resulted in identification of an additional low-grade ESS case positive for the MBTD1-CXorf67 fusion among 25 uterine stromal tumors [14 ESS and 11 undifferentiated endometrial sarcomas (UESs)] that were negative for JAZF1 and YWHAE rearrangements. Gene expression profiles of seven ESS (including three with YWHAE and two with JAZF1 rearrangements) and four UES without specific chromosomal aberrations indicated clustering of tumors with MBTD1-CXorf67 fusion together with low-grade JAZF1-associated ESS. The chimeric MBTD1-CXorf67 fusion identifies yet another cytogenetically distinct subgroup of low-grade ESS and offers the opportunity to shed light on the functions of two poorly characterized genes.

Introduction. T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous malignancy associated with a high risk of treatment failure. Efforts to improve outcomes have focused on underlying genetic defects. However, new evidence suggests that the microenvironment can foster drug resistance/relapses. Identification of factors that contribute to microenvironment-mediated chemo-refractoriness remains an important challenge. Here, we sought to construct an in vitro platform to dissect tumor-host interactions and to optimize drug treatments using Patient-Derived Tumor Xenograft models (PDTX) of high risk adult T-ALL and engineered human endothelial cells. Methods. T-ALL PDTX were established and serially passaged in NSG mice. Engraftment was monitored by flow cytometry of peripheral blood and/or MRI. Mice were sacrificed and leukemic cells were harvested from the spleen/bone marrow. To determine the ex vivo growing conditions, we first cultured a panel of 8 "bona fide" T-ALL cell lines and 11 PDTX cells alone in complete RPMI 20% FCS supplemented with IL2, IL12, IL15 and IL7; or co-cultured with human E4-ORF1 endothelial cells (ECs) without ILs in complete RPMI 20% FCS or serum/cytokine-free media. CDK4/6, MEK, PI3K and JAK inhibitors were used at 0.1 and 1 µM alone and in combination. Cell titer glo, cell titer blue, Annexin-V and S-cell cycle analysis were used as readouts. Total RNA from cells before and after co-culture was extracted for paired-end RNA sequencing on an Illumina HiSeq2500. Results. To study the supporting role of ECs, we first co-cultured ECs with T-ALL cell lines in vitro (serum/cytokine free co-culture) and showed that ECs could reproducibly sustain the viability of 3/8 cell lines (Loucy, KOPTK1, P12 Ichikawa) serum/cytokine-free media. A partial rescue was seen with 3 additional lines (HPB-ALL, CCRF-CEM, CUTLL1), while 2 (KE37, DND41) underwent massive cell death. We next tested whether either ILs or CXCL12 could provide anti-apoptotic signals and demonstrated that KOPTK1 and Loucy were only partially rescued by IL15 or CXCL12. Conversely, IL7, although capable of inducing a robust upregulation of pSTAT5, had no effect (CCRF-CEM and CUTLL1). We then characterized 11 PDTX from 15 high-risk adult T-ALL patients. All PDTX were serially propagated and caused T-ALL in subsequent NSG mice (massive spleen and bone marrow infiltration with extensive paravertebral mass associated with paralysis and multi-organ involvement). Genomic analysis (RNA-seq) demonstrated a high concordance between primary (pre-implant) and PDTX samples. All of them were extensively studied ex vivo, demonstratingthat T-ALL PDTX cells could only survive in ILs supplemented media, even better if enriched of growth factors and supplements for the expansion of human hematopoietic cells. However, when PDTX cells were treated with targeting compounds they all underwent massive apoptosis. Conversely, individual PDTX T-ALL could be selectively rescued by ECs, allowing the construction of individual drug response profile. To extend these data, 7 PDX T-ALL samples were screened against a 430-targeted compound library in supplemented RPMI or Stem Span media. Results indicated differential cell killing and gain (NFKB, BTK) and loss (TP-53, IGF-1R) of targets. Conclusions. These data clearly demonstrate a key role of aberrantly activated vascular niche in T-ALL cell maintenance and drug resistance. We envisage that drug screening of EC+T-ALL will lead to the identification of actionable targets in each individual patient. Our report supports the potential for future personalized curative strategies aimed at targeting both tumor cells and host tissue supporting niche elements disrupting pro-tumorigenic signals within leukemia cell niches. Disclosures Foà: Roche: Consultancy, Speakers Bureau; Genentech: Consultancy; Janssen: Consultancy, Speakers Bureau; Gilead: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau; Celgene: Consultancy, Speakers Bureau; BMS: Consultancy; Pfizer: Speakers Bureau; Ariad: Speakers Bureau. Rafii:Angiocrine Bioscience: Equity Ownership, Other: Non-paid consultant.

Trisomy 12, the third most frequent chromosomal aberration in chronic lymphocytic leukemia (CLL), confers an intermediate prognosis. In our cohort of 104 untreated patients carrying +12, NOTCH1 mutations occurred in 24% of cases and were associated to unmutated IGHV genes (P=0.003) and +12 as a sole cytogenetic abnormality (P=0.008). NOTCH1 mutations in +12 CLL associated with an approximately 2.4 fold increase in the risk of death, a significant shortening of survival (P0.01) and proved to be an independent predictor of survival in multivariate analysis. Analogous to +12 CLL with TP53 disruption or del(11q), NOTCH1 mutations in +12 CLL conferred a significantly worse survival compared to that of +12 CLL with del(13q) or +12 only. The overrepresentation of cell cycle/proliferation related genes of +12 CLL with NOTCH1 mutations suggests the biological contribution of NOTCH1 mutations to determine a poor outcome. NOTCH1 mutations refine the intermediate prognosis of +12 CLL.

The protein tyrosine phosphatase CD45, encoded by the PTPRC gene, is well known as a regulator of B- and T-cell receptor signaling. In addition, CD45 negatively regulates JAK family kinases downstream of cytokine receptors. Here, we report the presence of CD45 inactivating mutations in T-cell acute lymphoblastic leukemia. Loss-of-function mutations of CD45 were detected in combination with activating mutations in IL-7R, JAK1, or LCK, and down-regulation of CD45 expression caused increased signaling downstream of these oncoproteins. Furthermore, we demonstrate that down-regulation of CD45 expression sensitizes T cells to cytokine stimulation, as observed by increased JAK/STAT signaling, whereas overexpression of CD45 decreases cytokine-induced signaling. Taken together, our data identify a tumor suppressor role for CD45 in T-cell acute lymphoblastic leukemia.

With the advent of whole-genome and whole-exome sequencing, high-quality catalogs of recurrently mutated cancer genes are becoming available for many cancer types. Increasing access to sequencing technology, including bench-top sequencers, provide the opportunity to re-sequence a limited set of cancer genes across a patient cohort with limited processing time. Here, we re-sequenced a set of cancer genes in T-cell acute lymphoblastic leukemia (T-ALL) using Nimblegen sequence capture coupled with Roche/454 technology. First, we investigated how a maximal sensitivity and specificity of mutation detection can be achieved through a benchmark study. We tested nine combinations of different mapping and variant-calling methods, varied the variant calling parameters, and compared the predicted mutations with a large independent validation set obtained by capillary re-sequencing. We found that the combination of two mapping algorithms, namely BWA-SW and SSAHA2, coupled with the variant calling algorithm Atlas-SNP2 yields the highest sensitivity (95%) and the highest specificity (93%). Next, we applied this analysis pipeline to identify mutations in a set of 58 cancer genes, in a panel of 18 T-ALL cell lines and 15 T-ALL patient samples. We confirmed mutations in known T-ALL drivers, including PHF6, NF1, FBXW7, NOTCH1, KRAS, NRAS, PIK3CA, and PTEN. Interestingly, we also found mutations in several cancer genes that had not been linked to T-ALL before, including JAK3. Finally, we re-sequenced a small set of 39 candidate genes and identified recurrent mutations in TET1, SPRY3 and SPRY4. In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations. ispartof: PLoS One vol:7 issue:6 ispartof: location:United States status: published

We investigated TET2 deletion in 418 patients with hematological malignancies. Overall interphase FISH detected complete or partial TET2 monoallelic deletion (TET2del) in 20/418 cases (4.7%). TET2del was very rare in lymphoid malignancies (1/242 cases; 0.4%). Among 19 positive myeloid malignancies TET2del was associated with a 4q24 karyotypic abnormality in 18 cases. In AML, TET2del occurred in CD34-positive hematopoietic precursors and preceded established genomic abnormalities, such as 5q− and −7/7q−, which were the most frequent associated changes (Fisher's exact test P = 0.000).

Little is known about the incidence and clinical impact of cytomegalovirus (CMV) infection in patients with acute myeloid leukemia at the time of diagnosis and during chemotherapy. The aims of the present study were to assess prospectively the incidence of active CMV infection in 69 consecutive patients with acute myeloid leukemia and to describe the outcomes of treatment. pp65 antigenemia was monitored at diagnosis, post-induction and post-consolidation chemotherapy, and whenever CMV reactivation was suspected. Patients with pp65 antigenemia received pre-emptive anti-CMV treatment. Fifty-nine patients achieved complete remission. Baseline CMV serology results were available for 56 of the 59 patients: 52 patients (93%) were IgG positive. The overall incidence of pp65 antigenemia in patients in complete remission after chemotherapy was 35% (21/59): 9 patients after induction and 12 post-consolidation. Sixteen of the 21 pp65-positive patients received anti-CMV treatment: 15 as pre-emptive therapy and 1 for interstitial CMV pneumonitis. Five patients received no anti-CMV treatment and did not develop CMV disease. Patients with pp65 antigenemia had more hospital admissions (2.57 vs. 2.16; P = 0.009), while patients with >10 pp65-positive cells had more clinical complications (8/9 vs. 2/12; P = 0.002). In conclusion, patients with acute myeloid leukemia receiving chemotherapy should be monitored for active CMV infection. CMV reactivation in these patients was associated with an increased number of hospital admissions, and high levels of pp65 antigenemia were associated with more clinical complications. Controlled studies are needed to assess the relevance of pre-emptive anti-CMV therapy in patients with acute myeloid leukemia receiving chemotherapy.

The lymphoid tissues of Waldeyer's ring, including the nasopharynx, are rarely involved in Hodgkin's disease (HD). Between March 1977 and July 2001, about 2150 patients affected by HD were observed in our institute; 7 of them (0.32%), all male patients, had HD of the nasopharynx. They had no symptoms and blood tests were normal. All patients were treated with chemotherapy and/or radiotherapy and achieved complete remission. At a median follow-up of 72 months, they are alive and in continuous complete remission. We conclude that Hodgkin's disease of the nasopharynx is a rare and predominantly male disease with a particularly favorable prognosis. Bone marrow biopsy could be avoided. We believe that two to four cycles of a chemotherapeutic regimen and involved field radiotherapy at an intermediate-high dosage (25–30 Gy) could be the first line treatment for these patients.

Nucleophosmin (NPM1) gene mutations represent the most common genetic alterations in adult acute myeloid leukemia (AML), accounting for about 30% of cases and 50–60% of AML with normal karyotype. In addition to their recognized prognostic value (when combined with analysis of the FLT3 gene), NPM1 mutations represent an ideal marker for monitoring of minimal residual disease (MRD) since they are very stable during the course of the disease. PCR quantitative monitoring of NPM1 mutant copies has been mainly restricted to patients treated with conventional chemotherapy. In our study, we retrospectively analyzed, by RQ-PCR, MRD in 12 consecutive NPM1-mutated AML patients who underwent an autologous peripheral blood stem cell transplantation (PBSCT) between September 2000 and March 2008 at the Division of Hematology, “Sapienza” University of Rome. By sequencing of the region encompassing NPM1 exon 12, we demonstrated the presence of a type A mutation in 10/12 patients and of a type B in the remaining 2. Moreover, at diagnosis molecular analysis of the FLT3 gene revealed an internal tandem duplication (ITD) in 7/12 patients. Cytogenetic analysis showed a normal karyotype in 11/12, whereas 1 patient presented a minor karyotype aberration (trisomy 4). RQ-PCR was retrospectively performed on bone marrow samples in all patients at diagnosis, in 11/12 patients before the transplant and in 9/12 after the graft. Six of the 12 patients are at present in continuous complete remission (CCR) with a median follow-up of 54 months (range 4–89), 1 patient has died in CCR 55 months after PBSCT due to a pancreatic carcinoma and 5/12 have relapsed. Four of the latter 5 patients relapsed shortly after the transplant (range 3–10 months); 2 of them died of disease progression and 2 of salvage chemotherapy toxicity. One patient, who relapsed 92 months from PBSCT, is alive in second hematological remission following re-induction and consolidation chemotherapy. No significant differences in median levels of transcript at diagnosis were found between relapsing and non-relapsing patients (93,000 and 68,000; range: 86,000–103,000 and 37,000–116,000, respectively). Nine patients were analyzed after PBSCT: 3 persistently positive relapsed and the copy number of the transcript was always higher than at diagnosis. In the other 6 patients, the transcript was undetectable (3 of them were already in molecular remission pre-transplant): 5 are still in CCR while 1 patient relapsed 92 months after the graft. Regarding the FLT3-ITD status at diagnosis, 3/7 patients are in CCR whereas 4 have relapsed. The retention of NPM1 mutations even at relapse further confirms that NPM1 alterations are highly stable, pointing to this event as critical for leukemia growth and survival. Moreover, in our study long-term survival was always associated with a copy number of NPM1 mutant transcripts below the detectable level of the method, suggesting that disappearance of the transcript should be the primary clinical endpoint. Prospective studies and larger case series are necessary in an attempt to identify a cut-off level during treatment which could be predictive of the clinical outcome of AML patients harboring NPM1 mutations and help in therapeutic choices.

Introduction: Among B-lineage ALL, BCR/ABL1-like cases have clearly emerged as a subgroup with peculiar features. By gene expression profiling (GEP), they have a transcriptional signature similar to that of BCR/ABL1+ cases. Moreover, these cases often have IKZF1 deletions and CRLF2 deregulation, and harbor several lesions involving tyrosine kinases (TKs) that may be patient specific. The incidence varies with age (from 10% of B-lineage ALL in children, to 27% in adolescents/young adults, with a decrease in adults) and they are usually characterized by an inferior outcome, though risk-directed therapy based on minimal residual disease levels has improved prognosis in childhood. Even if GEP promptly recognizes these patients, this technique is expensive, not readily available and not applicable to all centers. Aims: To generate a simple and reliable tool, based on a Q-RT-PCR approach, aimed at the rapid identification of BCR/ABL1-like cases, and to build a statistical predictive model. Finally, to correlate the results obtained with the clinico-biologic features and outcome. Methods and patients: Through a meta-analysis of previously published GEP data focused on BCR/ABL1-like cases, and on our in house results, 9 commonly overexpressed genes were selected and evaluated by Q-RT-PCR; CRLF2 was also included, because of its association with this signature (total=10 genes). Q-RT-PCR was performed using the ABI PRISM 7300 Sequence Detection System and FastStart Universal SYBR Green Master (Rox). Overall, 149 B-lineage ALL cases, negative for known major rearrangements, i.e. BCR/ABL1, ETV6/RUNX1, E2A/PBX1 and ALL1 (B-NEG ALL), were tested. Median age was 28.8 years (range 1-78), 59 were females and 90 males. To generate a predictive model for BCR/ABL1-like identification, one round of cross-validation was performed; the full dataset was divided into two panels (discovery and screening). The discovery panel included 52 cases previously evaluated for GEP analysis and comprised 26 BCR/ABL1-like and 26 B-NEG ALL samples, while the screening panel (n=97) was based on 81 cases including 16 B-NEG ALL samples harboring JAK2, IL7R or CRLF2 mutations, tested as internal control, given their association with a BCR/ABL1-like signature. Results: The statistical model was built on the discovery panel and was validated, in terms of sensitivity and specificity, on the screening panel. Q-RT-PCR values of the 10 genes were grouped in the discovery panel according to principal component analysis to reduce multicollinearity and a logistic regression model was used to examine the association among the first three principal components (accounting for more than 80% of the total variance) and BCR/ABL1-like cases. Finally, a score was computed and validated in the screening panel. The model had a sensitivity and specificity of 93.8% and 93.8%, respectively, with a positive predictive value of 75%. Within the screening panel, 10/81 (12.3%) and 6/16 JAK2, IL7R or CRLF2 mutated cases (37.5%) were predicted as BCR/ABL1-like (total=16.5%). GEP was performed on 14/16 BCR/ABL1-like samples and confirmed the similarity with BCR/ABL1+ ALL cases by unsupervised and supervised analysis. Molecular screening, comprising the screening of JAK1/2, CRLF2, IL7R (JAK/STAT pathway) mutations and IKZF1 deletions, confirmed a significant enrichment of the JAK/STAT pathway (48% vs 15%, p=0.001) and of IKZF1 deletions (82 vs 46%, p=0.006) in BCR-ABL1-like cases as opposed to the other B-NEG ALL cases. Finally, BCR-ABL1 -like patients showed a significantly higher white blood cells (WBC) count (46x109/l vs 12.8x109/l, p=0.003) and poorer prognosis compared to the other B-NEG ALL patients, in terms of complete remission achievement (70.3 vs 87%, p=0.07), overall survival (41.1% vs 59.1%, p=0.06) and disease-free survival (DFS) (31.1 % vs 46%, p=0.008). Conclusions: We describe a Q-RT-PCR approach and a statistical model capable of rapidly identifying BCR-ABL1-like cases. We confirm a significant association with JAK/STAT mutations, IKZF1 deletions and poorer outcome. The prompt recognition of BCR-ABL1-like ALL at presentation can: i) identify cases in which additional lesion/s involving a TK - that might sustain the BCR/ABL1-like signature - should be further investigated; ii) drive therapeutic decisions, since these patients might benefit by the addition of targeted therapies, particularly TK inhibitors. Disclosures Foà: Roche: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau.

T-cell acute lymphoblastic leukemia (T-ALL) is a malignancy of the lymphoblasts committed to the T-cell lineage. Despite the therapeutic improvements witnessed over the years, ∼25% of children and ∼50% of adults still show a poor long-term outcome. While many recurrent oncogenic lesions have been identified through the characterization of chromosomal aberrations and candidate gene sequencing, several observations indicate that additional genetic alterations, not evident by conventional cytogenetics, might influence leukemogenesis and treatment outcome. Improvement of our knowledge in the identification and characterization of new oncogenic genome variations is expected to lead to a better prognostic classification and should also allow the design of tailored therapeutic strategies. To get further insights into the molecular pathogenesis of T-ALL and to identify novel markers for risk stratification and treatment improvement, we performed whole transcriptome sequencing (RNA-seq) on 18 refractory T-ALL cases sampled at diagnosis (median age 37.5 years, range 11-55). A pool of normal thymus cells was used as negative control. Next generation sequencing libraries were constructed from the mRNA fraction, followed by paired-end sequencing on a HiSeq2000 (Illumina). Sequence reads were aligned to the reference genome and were processed to identify gene expression levels, gene fusion transcripts and single nucleotide variations (SNVs). We first determined accurate gene expression levels from the RNA-seq data and used them to classify patients into T-ALL subtypes. Next, we applied the deFuse algorithm to detect fusion transcripts. Fusion transcripts detected also in normal thymus cells were filtered out, as well as fusions involving ribosomal genes. After applying these filters, we obtained 407 fusion transcripts (average: 22.6/sample, range: 0-84) predominantly involving genes localized on the same chromosome and mostly generated by deletion (306/407). Novel candidate fusion transcripts were confirmed by RT-PCR and Sanger sequencing. The SET-NUP214 fusion was identified in 2 cases, as well as 2 novel fusion transcripts involving the T-cell receptor (TCR) genes and not detected by conventional cytogenetics: the first fusion resulted in a chromosomal rearrangement between HOXA-AS4 and TRBC2 (also accompanied by overexpression of the HOXA genes) and the second between TRAC and SOX8 (associated with SOX8 overexpression). Interestingly, we also found out-of-frame fusion transcripts leading to the potential inactivation of tumor suppressor genes, such as PTEN-FAS and MAST3-C19orf10. Finally, we performed SNV calling on our dataset. After removing the most common polymorphisms, we obtained 1,483 protein-altering SNVs (missense, nonsense mutations and mutations affecting splicing), ranging between 30 and 131 per sample, with 85 genes that contain a protein-altering mutation in at least 3 of the 18 samples (i.e. 16% of cohort). Members or modulators of NOTCH and JAK/STAT pathways were the most recurrently mutated, each accounting for ∼38% of cases. In particular, 7/18 samples showed previously reported lesions in the NOTCH1 (n=5) and FBXW7 (n=1) genes but also in novel candidates as NOTCH2 (n=1), NOTCH3 (n=1) and SPEN (n=1). Interestingly, 1 patient showed 2 different mutations in the exon 26 of NOTCH1, while in 2 samples NOTCH1 mutation was associated with mutations in NOTCH2 or NOTCH3. Similarly, the JAK/STAT pathway was affected in 7/18 samples, including JAK1 (n=2), JAK3 (n=5), TYK2 (n=1) but also the novel candidates STAT5A (n=2) and STAT6 (n=1). Four of the 5 JAK3-positive patients showed also a mutation in another gene of the same pathway, such as JAK1 (n=1), STAT5A (n=2) and STAT6 (n=1). Thus, mutational screening of both the NOTCH and JAK/STAT pathway shows that mutations can occur simultaneously and suggests that more than one lesion is required for leukemic transformation. In conclusion, RNA-seq appears as a promising tool to dissect the heterogeneity of T-ALL and to identify targets that might be useful for tailored therapeutic interventions. Further investigations are ongoing to determine the recurrence and specificity of these lesions, and their potential in inducing a refractory phenotype. Finally, in vitro experiments will be carried out to investigate the transforming capability of specific lesions and the targettability of the recurrently impaired pathways. Disclosures: No relevant conflicts of interest to declare.