Antonella Padella

Chromothripsis in acute myeloid leukemia: biological features and impact on survival

Chromothripsis is a one-step genome-shattering catastrophe resulting from disruption of one or few chromosomes in multiple fragments and consequent random rejoining and repair. This study define incidence of chromothripsis in 395 newly-diagnosed adult acute myeloid leukemia (AML) patients from three institutions, its impact on survival and its genomic background. SNP 6.0 or CytoscanHD Array (Affymetrix®) were performed on all samples. We detected chromothripsis with a custom algorithm in 26/395 patients. Patients harboring chromothripsis had higher age (p=.002), ELN high risk (HR) (p<.001), lower white blood cell (WBC) count (p=.040), TP53 loss and/or mutations (p<.001) while FLT3 (p=.025) and NPM1 (p=.032) mutations were mutually exclusive with chromothripsis. Chromothripsis-positive patients showed a worse overall survival (OS) (p<.001) compared with HR patients (p=.011) and a poor prognosis in a COX-HR optimal regression model. Chromothripsis presented the hallmarks of chromosome instability [i.e. TP53 alteration, 5q deletion, higher mean of copy number alteration (CNA), complex karyotype, alterations in DNA repair and cell cycle] and focal deletions on chromosomes 4, 7, 12, 16, 17. CBA. FISH showed that chromothripsis is associated with marker, derivative and ring chromosomes. In conclusion, chromothripsis frequently occurs in AML (6.6%) and influences patient prognosis and disease biology.

SETD2 and histone H3 lysine 36 methylation deficiency in advanced systemic mastocytosis

The molecular basis of advanced systemic mastocytosis (SM) is not fully understood and despite novel therapies the prognosis remains dismal. Exome sequencing of an index-patient with mast cell leukemia (MCL) uncovered biallelic loss-of-function mutations in the SETD2 histone methyltransferase gene. Copy-neutral loss-of-heterozygosity at 3p21.3 (where SETD2 maps) was subsequently found in SM patients and prompted us to undertake an in-depth analysis of SETD2 copy number, mutation status, transcript expression and methylation levels, as well as functional studies in the HMC-1 cell line and in a validation cohort of 57 additional cases with SM, including MCL, aggressive SM and indolent SM. Reduced or no SETD2 protein expression—and consequently, H3K36 trimethylation—was found in all cases and inversely correlated with disease aggressiveness. Proteasome inhibition rescued SETD2 expression and H3K36 trimethylation and resulted in marked accumulation of ubiquitinated SETD2 in SETD2-deficient patients but not in patients with near-normal SETD2 expression. Bortezomib and, to a lesser extent, AZD1775 alone or in combination with midostaurin induced apoptosis and reduced clonogenic growth of HMC-1 cells and of neoplastic mast cells from advanced SM patients. Our findings may have implications for prognostication of SM patients and for the development of improved treatment approaches in advanced SM.

Aneuploidy: Cancer strength or vulnerability?

Aneuploidy is a very rare and tissue‐specific event in normal conditions, occurring in a low number of brain and liver cells. Its frequency increases in age‐related disorders and is one of the hallmarks of cancer. Aneuploidy has been associated with defects in the spindle assembly checkpoint (SAC). However, the relationship between chromosome number alterations, SAC genes and tumor susceptibility remains unclear. Here, we provide a comprehensive review of SAC gene alterations at genomic and transcriptional level across human cancers and discuss the oncogenic and tumor suppressor functions of aneuploidy. SAC genes are rarely mutated but frequently overexpressed, with a negative prognostic impact on different tumor types. Both increased and decreased SAC gene expression show oncogenic potential in mice. SAC gene upregulation may drive aneuploidization and tumorigenesis through mitotic delay, coupled with additional oncogenic functions outside mitosis. The genomic background and environmental conditions influence the fate of aneuploid cells. Aneuploidy reduces cellular fitness. It induces growth and contact inhibition, mitotic and proteotoxic stress, cell senescence and production of reactive oxygen species. However, aneuploidy confers an evolutionary flexibility by favoring genome and chromosome instability (CIN), cellular adaptation, stem cell‐like properties and immune escape. These properties represent the driving force of aneuploid cancers, especially under conditions of stress and pharmacological pressure, and are currently under investigation as potential therapeutic targets. Indeed, promising results have been obtained from synthetic lethal combinations exploiting CIN, mitotic defects, and aneuploidy‐tolerating mechanisms as cancer vulnerability.

Abstract 294: Override the doxorubicin-induced G2/M checkpoint using cell-cycle checkpoint inhibitors on acute lymphoblastic leukemia

The topoisomerase 2 inhibitor, doxorubicin, has been showed by different groups to induce cell cycle arrest in various kind of tumor cells. Specifically doxorubicin-treated cells activate the G2/M cell cycle checkpoint as a consequence of the induction of DNA damages. During the last years many studies have been showed the efficacy of different cell cycle checkpoint inhibitors in single agent or in combination with various DNA damaging agents. These studies showed that the inhibition of key proteins of the cell cycle, like Chk1 and Wee1, deeply sensitize tumor cells to the treatment with genotoxic agent. On these bases, the aim of the study was to evaluate the efficacy of a selective Chk1/Chk2 inhibitor and a Wee1 inhibitor in combination with doxorubicin for the treatment of acute lymphoblastic leukemia. Firstly we evaluate the effect of doxorubicin treatment on a panel of human B and T ALL cell lines in term of reduction of the cell viability, modification of cell cycle profile and activation of the DNA damage response. For this reason the cells were treated with doxorubicin (0.25, 0.5 and 1uM) for 24 and 48 hours and the reduction of the cell viability was quantified using WST-1 reagents. In all the cell lines treated the cytotoxic effect of doxorubicin was time and dose dependent. Then the induction of the apoptosis (Pi/Annexin V) and the effect on cell cycle profile (Pi staining) was evaluated in all the cell lines. In line with the literature the treatment with doxorubicin arrested the cells in G2/M phase. Then the effect of the combinations between doxorubicin and the two checkpoint kinase inhibitor was assessed in all the cell lines. Different cell lines were treated with doxorubicin (5, 10, 25 and 50 nM for the more sensitive cell lines; 50, 100, 250 and 500 nM for the less sensitive cell lines) in combination with the Chk1/Chk2 inhibitor (2, 5 and 10 nM) for 24 and 48 hours. The combination showed a additively effect in term of reduction of the cell viability and induction of apoptosis. Different cell lines were pre-treated for 18 hours with doxorubicin and then with Chk1/Chk2 inhibitor for different time points. Interestingly the inhibition of both Chk1/Chk2 proteins removed the G2/M arrest induced by the pre-treatment with doxorubicin, progressively reducing the number of cells in G2/M phase, increasing the percentage of cells in sub-G1 phase. Similar results were seen combining a Wee1 inhibitor with doxorubicin on several ALL cell lines. In our opinion the combination between the cell cycle checkpoint inhibitors and doxorubicin could be a promising strategy for the treatment of B/T-ALL. Supported by ELN, AIL, AIRC, progetto Regione-Universita 2010-12 (L. Bolondi), FP7 NGS-PTL project. Citation Format: Andrea Ghelli Luserna di Rora, Ilaria Iacobucci, Enrica Imbrogno, Anna Ferrari, Valentina Robustelli, Cristina Papayannidis, Maria Chiara Abbenante, Antonella Padella, Giovanni Marconi, Sandro Grilli, Giovanni Martinelli. Override the doxorubicin-induced G2/M checkpoint using cell-cycle checkpoint inhibitors on acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 294. doi:10.1158/1538-7445.AM2017-294

Abstract 3472: Separase overexpression defines a new subset of acute myeloma leukemia patients characterized by high CD34 and MYC levels

The endopeptidase Separase, encoded by the ESPL1 gene, plays a key role in faithful segregation of sister chromatids by cleaving the cohesin complex at the metaphase to anaphase transition. Its overexpression associates with aneuploidy and bad prognosis in solid tumors. Little is known in Acute Myeloid Leukemia (AML). We profiled the genomic landscape of 405 and 78 AML cases by SNP array (SNP 6.0 and Cytoscan HD, Affymetrix) and whole exome sequencing (100 bp, paired-end, Illumina), respectively. Bone marrow blasts from 61 patients were analyzed by gene expression profiling (HTA 2.0, Affymetrix). Separase expression was determined by Immunohistochemistry (1:600 antibody dilution Abnova, clone 6H6) in 44 AML and 4 control bone marrow specimens. One patient exhibited a nonsynonimous mutation in ESPL1 (1.3%), which was predicted to alter the protein function. Moreover, ESPL1 copy number gain was observed in 5/405 cases (1.2%): 2 hyperdiploid AML, one trisomy 12 and 2 cases with a short gain at 12q. Notably, protein level detection in one of the 12q-gain cases confirmed Separase overexpression. To determine the incidence of Separase overexpression, we performed Immunohistochemistry on additional 43 AML. Separase was overexpressed in 29/44 AML (66%, Separase-high), being comparable to control marrow biopsies in the remaining 15 samples (Separase-low). Sixty-two percent of Separase-high AML were aneuploid. However, no significative association was observed, as previously reported for mutations in the cohesin genes in AML. Separase overexpression correlated with increased patients’ age (median age 64 vs. 57 years, p=.01), 17-fold upregulation of CD34 (p=.004) and a trend towards reduced overall survival (6-years follow-up). Separase overexpression was not mutually esclusive with cohesin gene mutations, it co-occurred with NPM1 and FLT3 lesions and frequent mutations in genes involved in protein post-translational modification and ubiquitination (p=.04). Separase-low cases were enriched for mutations in RAS signaling pathway (NRAS, KRAS, NF1, RIT1, GRAP2, RALGDS; p=4.5x10-5) and in cell migration-related genes (LIMS2, S1PR1, PPIA, PLXNB1, FAT1). Separase-high cases also showed a defined transcriptomic profile, characterized by reduced expression of HOXA/B family genes, the DNA damage repair gene ATM, the p53 regulator MDM2 and forced expression of the cell cycle markers CDC20, AURKB, NUSAP1 and of MYC, independently of chromosome 8 gain. Taken together, our data suggest that genomic lesions targeting ESPL1 are a rare event in AML. However, Separase overexpression is a common feature and defines a new subset of AML cases with a distinct gene expression profile, which may benefit of innovative targeted therapies including CDC20 and bromodomain inhibitors. Supported by: ELN, AIL, AIRC, progetto Regione-Universita 2010-12 (L. Bolondi), FP7 NGS-PTL project. Citation Format: Giorgia Simonetti, Antonella Padella, Simona Righi, Maria Chiara Fontana, Marco Manfrini, Cristina Papayannidis, Giovanni Marconi, Carmen Baldazzi, Marianna Garonzi, Alberto Ferrarini, Massimo Delledonne, Nicoletta Testoni, Elena Sabattini, Giovanni Martinelli. Separase overexpression defines a new subset of acute myeloma leukemia patients characterized by high CD34 and MYC levels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3472. doi:10.1158/1538-7445.AM2017-3472

Abstract 2451: Genomic wide microarray analysis identifies novel copy number alterations in adult acute myeloid leukemia

Introduction: Novel array-based technique as SNP microarray can detect losses or gains of chromosomic material, which could be predictive of response and can help define therapeutic strategies. The aim of this study is to improve conventional cytogenetic analysis and identify new genetic alterations relevant to leukemogenesis, by a SNP array-based genotyping approach. Materials and Methods: We performed SNP 6.0 or Cytoscan HD (Affymetrix) in 235 Acute Myeloid Leukemia (AML) patients at diagnosis. Seventy-eight/235 samples were also performed by Whole Exome Sequencing, WES (HiSeq,Illumina). SNP Array data were analyzed by Nexus Copy Number v8.0 (BioDiscovery) and R Core Team. Results: Copy Number Alterations (CNAs) were scattered across all chromosomes and all pts showed CNA events. SNP array analysis showed that several genes were preferentially deleted, including MRPS5 (14.8%), PHF6 (9.3%), SCAPER (7.2%), CASK (5.9%), WNK (4.6%), STAG2 (4.2%), LRRK1 (3.4%), PALB2 (3.4%), while the genes preferentially amplified were RABL2B (16.1%), NF2 (10.2%), NBPF9 (7.6%), JAK2 (6.8%), RB1, NF1 and KMT2A (4.2%), PTEN (3.4%), TP73 and SMAD2 (2.5%). Single-copy losses and deletions were enriched (p Conclusion: We have identified new CNAs and pathways involving novel potential leukemia-related genes. Our results suggest that the comparison between SNP and WES data could provide important findings on prognosis of AML patients. Minimal deleted regions of genes implicated in deregulated pathways deserve further investigation in order to identify new candidate genes which could be relevant AML biomarkers. Acknowledgements: ELN,AIL,AIRC,progetto Regione-Universita 2010-12 (L. Bolondi),FP7 NGS-PTL project,HARMONY. Citation Format: Maria Chiara Fontana, Giovanni Marconi, Cristina Papayannidis, Eugenio Fonzi, Giorgia Simonetti, Antonella Padella, Anna Ferrari, Emanuela Ottaviani, Silvia Lo Monaco, Stefania Paolini, Simona Soverini, Giovanni Martinelli. Genomic wide microarray analysis identifies novel copy number alterations in adult acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2451. doi:10.1158/1538-7445.AM2017-2451

Abstract 515: Alterations in phosphatidylinositol 3-phosphate (PI3P) pathway and cAMP pathway confirm poor prognosis and reduced overall survival (OS) in a series of 209 acute myeloid leukemia patients

Introduction PI3P is a molecule that regulate cell growth and mediates cell proliferation via PI3K/AKT/mTOR in response to various growth signals. Abnormal activation of genes in its pathway is associated to oncogenic activity and poor Overall Survival (OS). AMPK plays a role as a regulator of cellular energy homeostasis. Aims The aim of the this study is to define the role of PI3P pathways and AMPK pathway in AML. Methods In this work we analyzed 208 consecutive newly diagnosed non M3 AML patients, screened for TP53, FLT3, NMP1, IDH1, IDH2, and DNMT3A mutations. Remission status was assessed with bone marrow biopsy. We performed Microarray-based Comparative Genomic Hybridization with Affymetrix SNP array 6.0 or Cytoscan HD in all the patients; we performed Whole Exome Sequencing (WES)in 80/208 patients. Survival data were collected prospectively, with a median follow-up of 18 months. Survival analysis was performed with Kaplan Meyer method using log rank test. Univariate and multivariable regression and Cox Hazard Ratio(HR) model was performed. Correlation between variables was assessed with Fisher’s exact test. Results We selected genes in pathways basing on literature and GO data. Alterations in these pathways involved 103/209 patients (48%). We analyzed the gene in two different pathways. PI3K/AKT/mTOR pathway includes the following genes: pik3ca, cdkn1a, akt1, akt3, mtor and pten, pdk1,pik3r1 and irs1. The second one is AMPK pathway and it include: sesn, prkaa1, prkab1, prkag1, prkag3. Alterations in PI3K/AKT/mTOR pathway confer worst OS (p = .035) when compared with unaltered patient, but events in these pathways did not affect therapy response. Alterations in AMPK pathway confer worst OS (p Conclusions Our work investigates the role of PI3P and cAMP pathways in AML. Surprisingly, it showed that alterations in these pathways are associated with poor prognosis. Significantly, alterations in cAMP pathways were associated with therapy resistance. Acknowledgement: ELN, AIL, AIRC, PRIN, Progetto Regione-Universita 2010-12, FP7 NGS-PTL project, HARMONY Citation Format: Mariachiara Abbenante, Mariachiara Fontana, Giovanni Marconi, Giorgia Simonetti, Antonella Padella, Elena Tenti, Eugenia Franchini, Anna Ferrari, Sarah Parisi, Emanuela Ottaviani, Nicoletta Testoni, Viviana Guadagnuolo, Chiara Sartor, Silvia Lo Monaco, Cristina Papayannidis, Giovanni Martinelli. Alterations in phosphatidylinositol 3-phosphate (PI3P) pathway and cAMP pathway confirm poor prognosis and reduced overall survival (OS) in a series of 209 acute myeloid leukemia patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 515. doi:10.1158/1538-7445.AM2017-515

Abstract A27: European Network NGS-PTL preliminary data: Whole exome sequencing identifies mutations of ALDH2, RETSAT, HSPG2, CHPF and other metabolic genes as a novel functional category in acute myeloid leukemia

Next Generation Sequencing (NGS) studies identified 9 functional categories of mutations in acute myeloid leukemia (AML), with >99% of cases having at least one of those mutations ( Ley et al. NEJM 2013). However, multiple genetic hits participate to AML pathogenesis, and metabolic dysregulations, as the one induced by IDH1/2 mutations, play oncogenic functions ( Ward et al. Cancer Cell 2010). Aim of the study was to define novel functional categories of AML mutations affecting relevant and druggable biological processes, with focus on genetic determinants of metabolic plasticity. Out of 455 whole exome sequencing (WES) cases from onco-hematological patients collected in the NGS-PTL project, we analyzed 37 AML cases, belonging to our cohort of 239 FLT3 -WT samples (886 AML total). We performed 100 bp paired-end WES (HiSeq2000, Illumina) and mapped the sequenced reads with Burrows-Wheeler Aligner. Variants where called with MuTect or GATK for single nucleotide variant (SNV) and indels detection, respectively (>90% confidence). Gene expression profiling was performed using HTA2.0 microarray (Affymetrix) on 56 bone marrow samples, including AML (≥80% blasts) and healthy controls. By WES analysis, we detected an average of 26 somatic variants per patient (range, 7 to 65). Gene ontology annotation identified 8 novel relevant functional categories of mutated genes: transcription, translation and post-translational modifications, protein degradation, cytoskeleton, cell cycle, DNA damage, cell survival and metabolism. Since metabolic pathways are promising targets for tailored therapies (e.g. IDH1/2 and glutaminase inhibitors), we focused our analysis on them. We identified 82 variants (74 SNVs, 2 frameshift and 4 nonframeshift deletions, 2 stopgains) targeting 70 genes involved in metabolism, with 78% of patients carrying at least one mutation in a metabolic gene and 35 variants rated as damaging by CONDEL algorithm. Among mutations in metabolic genes, the most represented pathways according to Recon X database were amino acids, lipids, CoA and nucleotides metabolism, transport and bioenergetics pathways. Notably, IMPDH2 , a mediator of MYC-induced proliferation involved in nucleotide interconversion, was mutated and overexpressed in our AML cohort ( p=0.01 ), suggesting a potential oncogenic function. Moreover, ALDH2 , a regulator of hematopoietic stem cell functions which is involved in multiple metabolic pathways and associates with metabolic remodeling, was mutated and 2-fold downregulated in AML blasts. Seven genes were mutated in 5-8% of samples: RETSAT , HSPG2 , CHPF , ABCA2 , ND1 , APOBR , NAAA . Among them, RETSAT , HSPG2 , CHPF mutations were also predicted as “drivers” by DOTS-Finder tool. Bioenergetics pathways were affected by mutations in glycolysis and gluconeogenesis ( GPI , ITPA ), oxidative phosphorylation ( ND1 , ND4 , ND5 , CYTB ), pentose phosphate pathway ( H6PD , PGLS ). Patients carrying mutations in the bioenergetics pathway showed a strong trend towards reduced overall survival, which did not associate with unfavorable molecular mutations. In conclusion, metabolism is the most represented class of mutated genes (8.6% of variants) in our FLT3 -WT AML cohort after signaling, leading us to propose a novel functional category. Our data suggest that, along with mutations in established oncogenes and tumor suppressors involved in metabolic control ( KRAS , TP53 , MYC pathway), a number of genetic determinants participate to leukemia metabolic plasticity and oncogenic mutations of metabolic enzymes may drive leukemogenesis, impact on patient9s survival and become novel targets for personalized therapies. Acknowledgements: ELN, AIL, AIRC, progetto Regione-Universita 2010-12 (L. Bolondi), FP7 NGS-PTL project. GS and AP equally contributed to this work. Citation Format: Giorgia Simonetti, Antonella Padella, Ilaria Iacobucci, Italo Do Valle, Gabriele Fontanarosa, Elisa Zago, Francesca Griggio, Marianna Garonzi, Simona Bernardi, Cristina Papayannidis, Maria Chiara Abbenante, Giovanni Marconi, Giorgio Melloni, Laura Riva, Viviana Guadagnuolo, Mariachiara Fontana, Samantha Bruno, Elisa Zuffa, Eugenia Franchini, Annalisa Astolfi, Carmen Baldazzi, Elisa Dan, Barbara Sinigaglia, Michele Cavo, Nicoletta Testoni, Emanuela Ottaviani, Pier Giuseppe Pelicci, Marco Sazzini, Alberto Ferrarini, Massimo Delledonne, Daniel Remondini, Giovanni Martinelli. European Network NGS-PTL preliminary data: Whole exome sequencing identifies mutations of ALDH2, RETSAT, HSPG2, CHPF and other metabolic genes as a novel functional category in acute myeloid leukemia. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr A27.

Abstract 3582: Chromothripsis in AML patients: A new mechanism of cancer initiation and progression

Introduction: Genomic rearrangements can drive the development of cancer through different mechanisms: chromothripsis, a catastrophic mechanism of genomic instability, could be relevant for hematological disease. Aim: To discover the mechanisms underlying the pathogenesis of Acute Myeloid Leukemia (AML), we studied chromothripsis in our cohort of patients (pts). Methods: We perform SNP Array 6.0 or Cytoscan HD Array (Affymetrix) in a cohort of 104 AML pts at diagnosis. SNP Array data were analyzed by Nexus Copy Number™ v7.5 (BioDiscovery). Results: Seven/104 pts (6.7%) showed chromothripsis events involving different chromosomes (8, 17, 11, 5 and 16). These pts had median age of 68.5 years (range 56-76), complex karyotype and high risk disease according to ELN definition. Among the pts showing chromothripsis, we compared chromosomic abnormalities of pts with de novo (5/7) and secondary (2/7) AML. De novo AML showed a prevalence of trisomy of chromosome 8 in a non-statistical way (4/5 vs 0/2), due to the low number of cases. However, we identified significant differences in the pattern of genes altered in the two groups. De novo AML had copy number gain of PEX1, ANK1, NCOA2, ESRP1, TPD52, ESRP1, ZFPM2 and MITF (p Conclusion: Our data suggest that different pathways and genomic alterations are involved in chromothripsis events in de novo and secondary AML, which could be explained by the repeated rounds of stress underwent by leukemic cells in secondary AML cases. Cytoskeleton and microtubules formation pathways appear to be the main cellular processes implicated in chromothripsis genesis, while alterations of histone acetyltransferase, immune response and antigen presentation pathways could sustain leukemic cells after chromothripsis. Acknowledgement: ELN, AIL, AIRC, PRIN, progetto Regione-Universita 2010-12(L. Bolondi), FP7 NGS-PTL project. Citation Format: Maria Chiara Fontana, Viviana Guadagnuolo, Cristina Papayannidis, Giovanni Marconi, Giorgia Simonetti, Antonella Padella, Marco Manfrini, Barbara Santacroce, Margherita Perricone, Silvia Lo Monaco, Emanuela Ottaviani, Simona Soverini, Michele Cavo, Giovanni Martinelli. Chromothripsis in AML patients: A new mechanism of cancer initiation and progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3582.

Abstract 368: Specific chromosomic alterations confer therapy resistance in a cohort of 49 patients with newly diagnosed acute myeloid leukemia treated with intensive chemotherapy

Introduction. Intensive induction chemotherapy in non-M3 young Acute Myeloid Leukemia (AML) patients is represented by the association of an antracycline and Cytarabine. Some treatment regimens including fludarabine or the addition of Gemtuzumab Ozogamicin (GO) as a third or fourth drug, proved to give a benefit in terms of CR rates. Aims of the study. In a group of 49 patients treated with intensive chemotherapy, we evaluated chromosomal abnormalities with SNP 6.0 and Cytoscan HD (Affymetrix) in order to improve conventional cytogenetic analysis and discover novel chromosomic aberrations related to clinical data and therapy response. Patients and Methods. From 2001 to 2014, 489 patients were treated in our Institution. Among those, in 49 newly diagnosed AML patients (median age 54 (range 19-71)), SNP microarray based-genotyping were performed and then analyzed by Nexus Copy Number™ v7.5 (BioDiscovery) and R Development Core Team. According to karyotype, FLT3 and NPM1 mutational status, 55.9% of the patients were considered at High Risk (HR) and 4.1% at low risk (LR). Ten patients had secondary AML. Patients were treated with induction schemes including MyFLAI, MyAIE, FLAI, FLAN, FLAG, 3+7 or DAE. Results. The CR rate after induction was 87.8% (43/49 patients). Deaths during induction (DDI), occurring in the first 50 days from 1st line therapy, were 1/49. The median OS was 135 months, the 5-years OS in our patients was 55,1%. Patients treated with GO showed a non-statistical trend toward a better OS than patients treated with other regimens (median OS not reached vs 133 months, respectively). We explored the alterations found by SNP array in our patients searching for novel markers of therapy resistance. We found a median of 192,5 total copy number aberrations (range 72- 1071): a median of 145,5 total copy number aberrations in responding patients group (RPG), and a median of 361 total copy number aberrations (p = ns) in non-responding patients group (NRPG). We compared the frequency of detected aberrations in RPG and in NRPG with Fisher9s exact test. We found that PIK3CA, Gain chr3:178,927,088-178,929,550 (p = 0,0016), SMAD4, Gain chr18:48,573,154-48,573,255 (p = 0,0166) and several other gene9s loci (CASC18, TCF12, UTY, GRB10, ZFY) are significant aberrations in NRPG compared with RPG. Conclusions. We identified a number of genes with significant aberrations in NRPG, particularly PIK3CA, a protein-coding gene involved in cell proliferation and metabolic pathway with interaction with HRAS/KRAS and EGF, and SMAD4, a transcription factor activated by TGF-beta. Those 2 genes were found overexpressed in other solid tumors. We suppose that those genes may be involved in a hyper-proliferative pathway that underlies a mechanism of chemo-resistance. Acknowledgments Work supported by ELN, AIL, AIRC, Progetto Regione-Universit⁁ 2010-12 (L.Bolondi), FP7 NGS-PTL project. Citation Format: Cristina Papayannidis, Maria Chiara Fontana, Giovanni Marconi, Viviana Guadagnuolo, Giorgia Simonetti, Antonella Padella, Simona Soverini, Stefania Paolini, Maria Chiara Abbenante, Sarah Parisi, Chiara Sartor, Silvia Lo Monaco, Marco Manfrini, Elisa Zuffa, Eugenia Franchini, Claudia Venturi, Maria Teresa Bochicchio, Andrea Ghelli Luserna di Rora, Emanuela Ottaviani, Giovanni Martinelli. Specific chromosomic alterations confer therapy resistance in a cohort of 49 patients with newly diagnosed acute myeloid leukemia treated with intensive chemotherapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 368.