scholarly journals Single-Strand Breaks at Genome Initiate FLT3-ITD Formation

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4333-4333
Author(s):  
Shota Yokoyama ◽  
Masahiro Onozawa ◽  
Daisuke Hidaka ◽  
Daigo Hashimoto ◽  
Masao Nakagawa ◽  
...  
Keyword(s):  
Pharmaceutical Company ◽  
Cell Line ◽  
Board Of Directors ◽  
Genomic Dna ◽  
Research Funding ◽  
Strand Break ◽  
Single Strand ◽  
Repeated Sequences ◽  
Advisory Committees ◽  
Dna Break

Abstract The fms-like tyrosine kinase 3 internal tandem duplication (FLT3-ITD) is the most common recurrent mutation in acute myeloid leukemia (AML). FLT3-ITD varies in size from 3 to over 200 bp, resulting in elongation of juxtamembrane domain coded by exon 14 and constitutive kinase activation. The FLT3-ITD is a poor prognostic marker found in 20-30% of AML. However, molecular mechanisms underlying ITD formation are remained to be elucidated. We have analyzed FLT3-ITD mutation-positive AML cases using next-generation sequencing (NGS) and speculated that DNA breakage initiates ITD formation. We developed artificial FLT3-ITD formation assay using CRISPR/Cas9 system. First, genomic DNA from 25 cases with FLT3-ITD mutation-positive AML was used to PCR-amplify the ITD cluster region (ICR; FLT3 exon 14-15) and sequenced by NGS. We extracted more than 3 bp of deletion and insertion. Total 139 independent ITD sequences were identified at varied variant allele frequency (VAF) (0.0005%-45.7%). Each case had 1 to 13 ITDs (median 4 clones). The length of ITDs was 6 to 201 bp (median 48 bp) and 135 (97.1%) unique ITDs showed length with a multiple of 3 bp. In addition, we found 32 clones with Complex ITD, which is considered to have multiple ITD events. Simple FLT3-ITD showed consecutive two repeated sequences with or without filler sequence between the repeated sequences (Fig. Ai). However, some clones showed three or four repetitive sequences (Fig. Aii, Aiii). Furthermore, some clones had sequential second ITD including parts of the first ITD (Fig. Aiv), and some clones had two ITDs at adjacent or distant locations (Fig. Av). These "Complex ITD" was seen in 18 (72%) cases and always accompanying originated "Simple ITD" clones with higher VAF. Total 59 independent deletion sequences were identified in 24 out of 25 (96%) cases. Length of deletion of ICR is 3 to 204 bp (median 4.5 bp). Deletion clone is always rare clone which had a few reads. Non-ITD insertions were found only in 5 clones. The presence of multiple ITD clones in a single case, Complex ITD clones, and deletion clones in the ICR suggest that the ICR is prone to genomic damage, and the mutation process is ongoing in each AML case creating various ITD/deletions. Based on the observation of clinical samples, we investigated whether artificially induced DNA break at ICR repaired as ITDs in the human cell line. The FLT3 ICR was TA-cloned into the pGEM-T easy vector. FLT3 exon 14-targeted guide RNA and Cas9 protein were incubated with the vector in vitro and transfected to HEK293T cells. We compared conventional Cas9 inducing double-strand break (DSB) and Cas9-nickase inducing single-strand break (SSB) to determine the efficacy of ITD formation depending on the different DNA break modes. Genomic DNA was extracted from transfected HEK293T and successfully repaired ICR was amplified with primers annealing to pGEM-T easy vector flanking the cloning site. The amplified PCR product was analyzed by NGS with a 250 bp pair-end read. We extracted 545 and 353 miss repair events from DSB and SSB experiments respectively. The DSB of ICR was repaired as ITDs 1.1%, non-ITD insertions 7.5%, and deletions 91.4% (Fig. B). On the other hand, SSB of ICR was repaired as ITDs 7.3%, non-ITD insertions 1.4%, and deletions 91.2% (Fig. B). Within insertion event, ITD frequency was significantly higher in SSB compared to DSB. (p<0.001; chi-square test). Length of ITDs were 3 to 13 bp (median 3.5 bp) in DSB and 3 to 75 bp (median 28 bp) in SSB experiment (Fig. C). The ITD formed by the SSB was significantly longer than that formed by the DSB (p=0.0013; Mann-Whitney U test) and similar to observation in clinical simple ITD (Fig. C, D). Furthermore, we induced in-vivo SSB at endogenous FLT3 exon14 in HEK293T cells and successfully detected in situ ITDs. Using CRISPR induced SSB, we might develop a cell line with artificial FLT3-ITD which would contribute to deepen understanding of FLT3 biology. SSBs at FLT3 ICR could be a key initiator of FLT3-ITD formation. Progress in understanding the molecular mechanism of FLT3-ITD formation may lead to the development of therapeutic agents in the future. Figure 1 Figure 1. Disclosures Nakagawa: AbbVie GK: Research Funding; Takeda Pharmaceutical Company: Research Funding. Kondo: Astellas Pharma Inc.: Consultancy, Honoraria; Sanwa Kagaku Kenkyusho CO.,LTD: Consultancy; Sumitomo Dainippon Pharma: Honoraria; Bristol-Myers Squibb Company: Honoraria; Novartis Pharma KK: Honoraria; Otsuka Pharmaceutical: Consultancy, Honoraria, Research Funding; Abbvie: Honoraria; Pfizer: Honoraria. Teshima: Astellas Pharma Inc.: Research Funding; Takeda Pharmaceutical Company: Honoraria, Membership on an entity's Board of Directors or advisory committees; Kyowa Kirin Co.,Ltd.: Honoraria, Research Funding; Merck Sharp & Dohme: Membership on an entity's Board of Directors or advisory committees; Fuji pharma CO.,Ltd: Research Funding; Pfizer Inc.: Honoraria; TEIJIN PHARMA Limited: Research Funding; Gentium/Jazz Pharmaceuticals: Consultancy; Novartis International AG: Membership on an entity's Board of Directors or advisory committees, Other, Research Funding; Nippon Shinyaku Co., Ltd.: Research Funding; Janssen Pharmaceutical K.K.: Other; Bristol Myers Squibb: Honoraria; CHUGAI PHARMACEUTICAL CO., LTD.: Research Funding; Sanofi S.A.: Research Funding.

The Interaction of Bortezomib with P-Gp, MRP-1 and BCRP Drug Transporters: Implications for Therapeutic Applications of Bortezomib in Advanced Multiple Myeloma and Other Neoplasias.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 1729-1729
Author(s):  
Melissa G Ooi ◽  
Robert O'Connor ◽  
Jana Jakubikova ◽  
Justine Meiller ◽  
Steffen Klippel ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Multiple Myeloma ◽  
Cell Line ◽  
Board Of Directors ◽  
Cell Lines ◽  
Research Funding ◽  
Significant Activity ◽  
Cancer Resistance ◽  
Advisory Committees ◽  
Bortezomib Treatment

Abstract Abstract 1729 Poster Board I-755 Background Multidrug transporters are energy-dependent transmembrane proteins which can efflux a broad range of anticancer drugs and thereby play a role in resistance to the actions of substrate agents. Classically, three transporters, p-glycoprotein (Pgp; MDR-1; ABCB1), multidrug resistant protein-1 (MRP-1; ABCC1) and breast cancer resistance protein (BCRP; MXR; ABCG2), have been found to have the broadest substrate specificity and a strong correlation with drug resistance in vitro and in vivo in many models and forms of cancer. We have sought to characterize the interaction of bortezomib with these transporters and thereby explore the potential for these agents to play a role in resistance. Bortezomib is a novel proteosome inhibitor with significant activity in multiple myeloma, although subsets of patients remain refractory to the activity of the drug. Hence, better characterization of the interactions of this drug with classical resistance mechanisms may identify improved treatment applications. Methods and Results We investigated the role of these transporters by using isogenic cell line models which are resistant due to overexpression of a particular transporter: DLKP lung cancer cell line that overexpresses MRP-1; DLKP-A which overexpresses Pgp; and DLKP-SQ-Mitox which overexpresses BCRP. DLKP-A cells exhibited a 4.6-fold decrease in responsiveness to bortezomib compared to parental DLKP cells. In DLKP-SQ-Mitox, bortezomib-induced cytotoxicity was comparable to DLKP. When bortezomib was combined with elacridar, a Pgp and BCRP inhibitor, significant synergy was evident in DLKP-A (100% viable cells with single agent treatment versus 11% with the combination), but not DLKP-SQ-Mitox. Sulindac, an MRP-1 inhibitor, combined with bortezomib failed to produce any synergy in MRP-1 positive DLKP cells. Conversely, combination assays of Pgp substrate cytotoxics such as doxorubicin with Bortezomib were largely additive in nature. This indicates that bortezomib has little, if any, direct Pgp inhibitory activity, as combinations of a traditional Pgp inhibitor (such as elacridar) and doxorubicin would show marked synergy rather than just an additive effect in Pgp positive cells. To further characterize the extent of this interaction with Pgp, we conducted cytotoxicity assays in cell lines with varying levels of Pgp overexpression. NCI/Adr-res (ovarian cancer, high Pgp overexpression), RPMI-Dox40 (multiple myeloma, moderate Pgp overexpression) and A549-taxol (lung cancer, low Pgp overexpression). The combination of bortezomib and elacridar that produced the most synergy was in cell lines expressing moderate to high levels of Pgp expression. Cell lines with lower Pgp expression produced an additive cytotoxicity. We next examined whether bortezomib had any direct effect on Pgp expression. In RPMI-Dox40 cells, Pgp expression is reduced in a time-dependent manner with bortezomib treatment. Conclusions Our studies therefore show that bortezomib is a substrate for Pgp but not the other drug efflux pumps. In tumor cells expressing high levels of Pgp, the efficacy of bortezomib is synergistically enhanced by combinations with a Pgp inhibitor, while bortezomib treatment itself can reduce the expression of Pgp. This study suggests that in the subset of patients with advanced multiple myeloma or solid tumors which express high levels of Pgp, inhibition of its function could contribute to enhanced responsiveness to bortezomib. Disclosures Richardson: millenium: Membership on an entity's Board of Directors or advisory committees, Research Funding; celgene: Membership on an entity's Board of Directors or advisory committees, speakers bureau up to 7/1/09; MLNM: speakers bureau up to 7/1/09. Mitsiades:Millennium Pharmaceuticals : Consultancy, Honoraria; Novartis Pharmaceuticals : Consultancy, Honoraria; Bristol-Myers Squibb : Consultancy, Honoraria; Merck &Co: Consultancy, Honoraria; Kosan Pharmaceuticals : Consultancy, Honoraria; Pharmion: Consultancy, Honoraria; PharmaMar: licensing royalties ; Amgen Pharmaceuticals: Research Funding; AVEO Pharma: Research Funding; EMD Serono : Research Funding; Sunesis Pharmaceuticals: Research Funding. Anderson:Celgene: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Millennium: Consultancy, Research Funding; Biotest AG: Consultancy, Research Funding.

CYC065, a Potent Derivative of Seliciclib Is Active In Multiple Myeloma In Preclinical Studies

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2999-2999 ◽  
Author(s):  
Samantha Pozzi ◽  
Diana Cirstea ◽  
Loredana Santo ◽  
Doris M Nabikejje ◽  
Kishan Patel ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Multiple Myeloma ◽  
Cell Line ◽  
Board Of Directors ◽  
Cell Lines ◽  
Preliminary Data ◽  
Research Funding ◽  
Preclinical Studies ◽  
Dependent Manner ◽  
Advisory Committees

Abstract Abstract 2999 Multiple myeloma (MM) is a treatable but incurable hematological malignancy and novel targeted therapies are under investigation. MM is characterized by dysregulation of the cell cycle, consequent to the overexpression of cyclins and their related kinases, the cyclins dependent kinases (CDK), a group of Ser/Thr proteine kinases. CDKs represent a promising therapeutic target, and inhibitors have been developed for anticancer treatment. We have previously studied seliciclib in the context of MM. CYC065, a second generation CDK inhibitor is the more potent derivative of seliciclib. It is mainly active on CDK 2, 5 and 9, involved in progression of the cell cycle and protein transcription. It has already shown promising results in preclinical studies in breast cancer and acute leukemia. We tested CYC065 in in vitro experiments in MM. Our preliminary data in 7 MM cell lines showed cytotoxicity of CYC065, both in MM cell lines sensitive as well as resistant to conventional chemotherapy, with an IC50 ranging between 0.06 and 2μ M, at 24 and 48h. Tritiated thymidine uptake assay confirmed the antiproliferative effects of CYC065 in MM, and its ability to overcome the growth advantage conferred by co-culture with bone marrow stromal cells derived from MM patients, and cytokines like interleukin 6 (10ng/ml) and insulin like growth factor-1 (50ng/ml). The anti-proliferative effect was evident both at 24 and 48h, starting at concentrations as low as 0.015μ M. The AnnexinV/PI assay in the MM1.s cell line confirmed CYC065's ability to induce apoptosis in a time dependent manner starting at 9 hours of treatment, at a concentration of 0.125 μ M, inducing 82% of apoptosis after 48h of exposure. Cell cycle analysis in the same MM1.s cell line showed an increase of subG1 phase, starting at 9 hours of treatment, at 0.125 μ M of CYC065. Preliminary results of western blot analysis confirmed the apoptotic effect of CYC065 in the MM1s cell line, highlighted by the cleavage of caspase 3, 8, 9 and PARP. The compound was tested in primary CD138+ cells isolated from three refractory MM patients, confirming its efficacy at 0.125 μ M, both at 24 and 48h. Comparative analysis in PBMCs from normal donors, for the evaluation of the drug toxicity is ongoing and will be presented. In conclusion our preliminary data confirm the efficacy of CYC065 in MM cell lines and primary MM cells, at nanomolar concentrations. Ongoing mechanistic and in vivo studies will delineate its role in the now increasing spectrum of CDK inhibitors in MM and better define its potential for clinical development in MM. Disclosures: Green: Cyclacel: Employment. Anderson:Millennium Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau. Scadden:Fate Therapeutics: Consultancy, Equity Ownership, Patents & Royalties. Raje:Celgene: Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Research Funding; Acetylon: Research Funding.

An Update On The Clinical Activity Of Resimmune, a Targeted Therapy Directed To CD3 Receptor, In Patients With Cutaneous T Cell Lymphomas--CTCL

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4381-4381 ◽  
Author(s):  
Arthur E. Frankel ◽  
Jung H Woo ◽  
Jeremy P Mauldin ◽  
Francine M. Foss ◽  
Madeleine Duvic ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Pichia Pastoris ◽  
Cell Line ◽  
Board Of Directors ◽  
Research Funding ◽  
Response Rate ◽  
The United States ◽  
Advisory Committees ◽  
Systemic Therapies

Abstract Cutaneous T cell lymphoma—CTCL is a malignancy of skin-tropic T cells. CTCL cells have ubiquitous overexpression of CD3. Although uncommon, CTCL has been estimated to affect 1,500 patients per year in the United States. There are multiple approved systemic therapies for CTCL, but responses are brief lasting months. Allogeneic stem cell transplantation may provide long-term remissions, but is suitable for only rare CTCL patients. Overall, CTCL has a long clinical course with relentless progression over months to years with estimated median survival of 3-5 years for stage IB-IIB patients. The CD3 targeted agent, Resimmune, was synthesized and prepared for clinical use. It consists of the catalytic and translocation domains of diphtheria toxin fused to two anti-human CD3 Fv fragments. DNA encoding Resimmune protein was integrated into the Pichia pastoris genome, and recombinant protein was produced in Pichia pastoris via the secretory route (Woo, Protein Expr Purif 25, 270, 2002). Protein was purified by anion exchange and size exclusion chromatography. The CD3+ Jurkat cell line incubated with Resimmune yielded an IC50 for protein synthesis inhibition of 0.017pM. The CD3- Vero cell line incubated with Resimmune showed an IC50 >10pM. Mice, rats, and monkeys given total doses of >200mg/kg over four days showed only transient transaminasemia without histopathologic tissue injury or clinical signs or symptoms (Woo, Cancer Immunol Immunother 57, 1225, 2008). In a mouse model with human CD3e transfected lymphocytes, four logs of antigen positive cells were reproducibly depleted from nodes and spleen with 100mg/kg total dose of Resimmune (Thompson, Protein Eng 14, 1035, 2001). Based on these findings, a phase 1 study was initiated and this report serves to update the results of a single cycle of Resimmune given at 2.5-11.25mg/kg 15 min IV infusion twice daily for 8 doses to 18 CTCL patients. There were 10 females and 8 males with ages 20-81 years. Two patients were naïve to systemic therapies, and all others had failed 1-4 prior treatments including interferon, bexarotene, gemcitabine, vorinostat, chlorambucil, etoposide, pralatrexate, doxil, romidepsin, methotrexate, CHOP, and brentuximab vedotin. None of the Resimmune treated CTCL patients had dose-limiting toxicities. Side effects were mild-moderate and transient with fevers, chills, nausea, transaminasemia, hypoalbuminemia, lymphopenia, reactivation of EBV and CMV, and hypophosphatemia. Toxicities responded to antipyretics, anti-emetics, albumin infusions, rituximab treatment and valgancyclovir. Among measured patients, there was a 3 log decline in normal, circulating T cells by day 5 that recovered by day 14. Because of vascular leak syndrome toxicities in non-CTCL patients, the MTD was defined as 7.5mg/kg x 8 doses. Cmax ranged from 1.9-40.7ng/mL and half-life from 5-66min. Pretreatment anti-DT titers were 0.9-251mg/mL and day 30 post-therapy increased to 5-4059 mg/mL. 17 CTCL patients were evaluable for response. There were six responses for a response rate of 35%. There were four CRs (24% CR rate). Three of the CRs are over 4-years duration. Patients with IB or IIB disease and mSWAT<50 had an overall response rate of 86% and CR rate of 56%. The long time required to convert from a PR to a CR in the absence of any additional therapy beyond the four treatment days suggest an additional anti-tumor mechanism beyond immunotoxin-induced killing such as immunomodulation. Accrual of patients with mSWAT scores of 50 or less is ongoing. Disclosures: Woo: Angimmune: Patents & Royalties, Research Funding. Foss:celgene: Honoraria, Research Funding; millenium: Honoraria, Membership on an entity’s Board of Directors or advisory committees; eisai: Membership on an entity’s Board of Directors or advisory committees; spectrum: Research Funding; merck: Research Funding; seattle genetics: Research Funding. Neville:Angimmune: Employment, Equity Ownership, Patents & Royalties.

a Phase 1b/2 Study of TAK-659, an Investigational Dual SYK and FLT-3 Inhibitor, in Patients (Pts) with Relapsed or Refractory Acute Myelogenous Leukemia (R/R AML)

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2834-2834 ◽  
Author(s):  
Jason B Kaplan ◽  
Dale L. Bixby ◽  
John C Morris ◽  
Olga Frankfurt ◽  
Jessica Altman ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Pharmaceutical Company ◽  
Board Of Directors ◽  
Dose Escalation ◽  
Research Funding ◽  
Advisory Committees ◽  
Company Limited ◽  
Safety Population ◽  
Wholly Owned Subsidiary ◽  
Phase 1B

Abstract Background Spleen tyrosine kinase (SYK) is a nonreceptor cytoplasmic protein kinase and a key mediator of immunoreceptor signaling that has been shown to play an important role in the pathogenesis of both B-cell and myeloid malignancies. SYK has also been shown to directly bind and activate FMS-like tyrosine kinase 3 (FLT-3), a Class III receptor tyrosine kinase that is commonly mutated in approximately 30% of pts with AML (Puissant et al. Cancer Cell 2014;25:226-42). TAK-659 is an investigational, reversible, and potent dual inhibitor of SYK and FLT-3. Preclinical studies with TAK-659 have demonstrated growth inhibition of cell lines and xenograft tumor models of B-cell lymphoma or AML origin. Moreover, TAK-659 has exhibited antitumor activity in lymphoma pts in an ongoing clinical trial (Petrich et al. Blood 2015;126:2693). The primary objectives of the phase 1b dose-finding portion of this study are to evaluate the safety, tolerability, and maximum tolerated dose (MTD)/recommended phase 2 dose (RP2D) of TAK-659, as well as preliminary efficacy in the phase 2 expansion study. Secondary objectives include evaluation of TAK-659 pharmacokinetics (PK) in this pt population. Methods During dose escalation using a 3x3 schema, adult pts with R/R AML received oral TAK-659 daily (QD) in 28-d cycles (C) starting with a dose of 60 mg. Adverse events (AEs) were assessed per NCI-CTCAE v4.03. Response per IWG criteria for AML was assessed between d22 and d28 of C1, C2, and C4. Blood samples for plasma pharmacokinetic (PK) assessments were collected pre-dose and at multiple times post-dose on d1 and d15 of C1. The pharmacodynamic effect of TAK-659 was assessed at multiple time points by measuring the phosphorylation of ribosomal protein S6 (pS6) in peripheral AML blasts using flow cytometry. FLT-3 mutation status (wild type [FLT-3-WT], FLT-3-ITD, or point mutation [FLT-3-D835Y]) was assessed using a PCR-based assay at a central laboratory. The effect of TAK-659 treatment on FLT-3-ITD phosphorylation was evaluated using a plasma inhibitory assay (PIA) as previously described (Levis et al. Blood 2006;108:3477-83). Results At data cut-off (June 9, 2016), 15 pts had been enrolled at TAK-659 QD 60 mg (n=4), 100 mg (n=7), or 120 mg (n=4). No dose-limiting toxicity per protocol has been observed. Dose escalation is currently ongoing at 160 mg QD. In the safety population (n=13), median age was 67 yrs (range 25-86), 69% of pts were male, and 38% had received ≥4 prior lines of therapy. Baseline mutation data was available for 12 pts: 6 pts were FLT-3-WT, 3 pts had FLT-3-ITD, 1 pt had FLT-3-D835Y, and 2 pts had concurrent FLT-3-ITD/D835Y mutations. In the safety population, all-grade drug-related AEs occurred in 12 (92%) pts overall; the most common were elevated AST (31%), ALT (23%), and amylase levels (23%). Grade ≥3 drug-related AEs occurred in 7 (54%) pts including: increased ALT, AST, and amylase levels, cataract, positive fungal test, macular fibrosis, pancreatitis, pneumocystis jirovecii pneumonia, rash, and fungal sinusitis (each 1pt). Blood LDH levels were increased in almost all pts (significance unknown). Three pts discontinued TAK-659 due to AEs and 3 pts died on study; none of these events were considered related to the study drug. Preliminary plasma PK of TAK-659 (n=11, 60-100 mg) was characterized by rapid absorption (median Tmax of 2 hours), moderate variability in steady-state exposures (42% coefficient of variation for C1 d15 dose-normalized AUCtau), and mean accumulation of 2.1-fold after repeated QD dosing for 15 days. Of 9 pts evaluated to date, pS6 was detected at baseline and reduced after dosing in 4 pts (2 FLT-3-ITD; 2 FLT-3-WT). At 60 mg and 100 mg TAK-659, up to 70% inhibition of FLT-3-ITD phosphorylation was observed as assessed by PIA. Early signs of clinical activity were observed, with decreases in peripheral blood myeloblasts observed in some pts. Assessment is ongoing and preliminary efficacy data will be presented. Conclusions TAK-659 has a unique mechanism of action with dual inhibition of SYK and FLT-3. Dose escalation to determine the MTD/RP2D is ongoing. TAK-659 exhibits an acceptable PK profile in R/R AML pts, supporting continuous oral QD dosing. Disclosures Kaplan: Seattle Genetics: Research Funding; Janssen: Research Funding. Morris:Boehringer-Ingelheim: Speakers Bureau. Altman:Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Syros: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees. Wise-Draper:Merck: Research Funding. Collins:Millennium Pharmaceuticals Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Kannan:Millennium Pharmaceuticals Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Wang:Millennium Pharmaceuticals Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Faucette:Millennium Pharmaceuticals Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Lee:Millennium Pharmaceuticals Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Shou:Millennium Pharmaceuticals Inc., Cambridge, MA, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited: Employment. Levis:Millennium: Consultancy, Research Funding; Astellas: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Daiichi-Sankyo: Consultancy, Honoraria.

scholarly journals Tolinapant (ASTX660), a Non-Peptidomimetic Antagonist of cIAP1/2 and XIAP, and the HDAC Inhibitor Romidepsin Are Synergistic in in Vitro Models of T Cell Lymphoma

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4356-4356
Author(s):  
John S Manavalan ◽  
Ipsita Pal ◽  
Aidan Pursley ◽  
George A. Ward ◽  
Tomoko Smyth ◽  
...  
Keyword(s):  
T Cell ◽  
Cell Line ◽  
Board Of Directors ◽  
Cell Lines ◽  
Research Funding ◽  
Cell Lymphoma ◽  
T Cell Lymphoma ◽  
Tnf Alpha ◽  
Sensitive Cell ◽  
Advisory Committees

Abstract Background: The PTCL are a heterogeneous group of non-Hodgkin lymphomas originating from mature T-lymphocytes. They are aggressive diseases, often resistant to conventional chemotherapy. Despite the fact that a number of new agents have been approved, treatment paradigms tailored to the biology of the disease have yet to emerge. Tolinapant (ASTX660) is a potent antagonist of both cellular and X-linked inhibitors of apoptosis proteins (cIAP1/2 and XIAP), and is presently in phase I/II trials in patients with advanced solid tumors and lymphomas (NCT02503423). IAP antagonists enhance tumor necrosis factor (TNF) receptor superfamily mediated apoptosis (Ward GA, et al. Mol Cancer Ther. 2018), are potent anti-tumor immune enhancers and induce markers of immunogenic cell death such as damage associated molecular patterns (DAMPs; Ye W, et al, Oncoimmunology, 2020). Objectives: We explored the sensitivity of a range of T-cell lymphoma (TCL) cell lines to tolinapant. We establish the synergy coefficient between tolinapant and the HDAC inhibitor, romidepsin, and interrogated the molecular basis of their synergistic interaction. Methods: A panel of human T-cell lymphoma cell lines were tested in proliferation assays (CellTiterGlo) for sensitivity to tolinapant in the presence or absence of 10ng/ml of TNF alpha. For combination studies, with tolinapant and romidepsin, each drug was tested at the IC10 and IC40 concentrations in the presence or absence of TNF alpha. Synergy scores using the Excess over Bliss (EOB) model were calculated using SynergyFinder (Aleksandr Ianevski et al; Nucleic Acids Research, 2020). Additionally, the effects of tolinapant and romidepsin on the IAPs and caspases were analyzed by western blots. TNFR1 receptor expression and induction of DAMPs were also analyzed by flow cytometry. Results: TCL Lines demonstrated varying sensitivities to tolinapant in the presence or absence of TNF alpha. The most sensitive cell lines, ALK+ ALCL and SUP-M2, had IC50 concentrations ranging from 200nM ± 100nM to 20nM ± 1nM in the absence or presence of TNF alpha, respectively, at 24, 48 and 72hrs, while a resistant CTCL cell line HH had an IC50 concentration of over 20mM, even in the presence of TNF alpha. Interestingly, using western blot analysis, we found that the presence of TNF alpha increased the levels of cIAP1 in the tolinapant sensitive SUP-M2 cell line, but not in the resistant HH cell line. However, there was a concentration dependent decrease in cIAP1 but not in XIAP in both cell lines treated with tolinapant. Flow cytometry analysis demonstrated that tolinapant increases the expression of TNFR1 and DAMPs in a dose dependent manner on the sensitive SUP-M2, but not in the resistant HH cells. In combination experiments, using the EOB model, tolinapant plus romidepsin was found to be synergistic in the absence of TNF alpha, at 36hrs, in both the sensitive cell line SUP-M2 and the resistant cell line HH. In the presence of TNF alpha, synergism was seen only in the sensitive cell line SUP-M2 and antagonistic in the HH cell line (Fig. 3). In the tolinapant plus romidepsin treated samples, cIAP1 levels decreased in the SUP-M2 cell line, in the absence of TNF alpha, however, addition of TNF alpha did not alter the levels of cIAP1 in the SUP-M2 cells. The cIAP1 levels decreased in the HH cells treated with the combination, in both the presence or absence of TNF alpha (Figure). Our findings indicate that the synergy of the tolinapant plus romidepsin is not dependent on the presence of TNF alpha. Conclusion: Tolinapant has demonstrated potent cytotoxic effects against a broad range of TCL lines both as a monotherapy and in combination with the HDAC Inhibitor, romidepsin. In in vitro studies, T cell lymphoma cell lines demonstrated varying sensitivity to tolinapant with certain cell lines being more resistant, even in the presence of TNF alpha. Interestingly, the addition of romidepsin appeared to overcome the intrinsic resistance to tolinapant in the absence of TNF alpha. These data provide the rationale to continue to explore the combination of tolinapant and romidepsin in vivo and to investigate additional combinations with T-cell specific agents (e.g. pralatrexate, belinostat, azacitidine and decitabine). Figure 1 Figure 1. Disclosures Smyth: Astex Pharmaceuticals: Current Employment. Sims: Astex Pharmaceuticals: Current Employment. Loughran: Kymera Therapeutics: Membership on an entity's Board of Directors or advisory committees; Bioniz Therapeutics: Membership on an entity's Board of Directors or advisory committees; Keystone Nano: Membership on an entity's Board of Directors or advisory committees; Dren Bio: Membership on an entity's Board of Directors or advisory committees. Marchi: Kyowa Kirin: Honoraria; Myeloid Therapeutics: Honoraria; Astex: Research Funding; BMS: Research Funding; Merck: Research Funding; Kymera Therapeutics: Other: Scientific Advisor.

scholarly journals Genotype-Phenotype Relationships and Therapeutic Targets in Acute Erythroid Leukemia

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 17-18
Author(s):  
June Takeda ◽  
Kenichi Yoshida ◽  
Akinori Yoda ◽  
Lee-Yung Shih ◽  
Yasuhito Nannya ◽  
...  
Keyword(s):  
Cell Line ◽  
Board Of Directors ◽  
Research Funding ◽  
Pharmaceutical Research ◽  
Private Company ◽  
Advisory Committees ◽  
Otsuka Pharmaceutical ◽  
Group A ◽  
Genetic Profiles ◽  
Stat Pathway

Background: Acute erythroid leukemia (AEL) is a rare subtype of AML characterized by erythroid predominant proliferation and classified into two subtypes with pure erythroid (PEL) and myeloid/erythroid (MEL) phenotypes. Although gene mutations in AEL have been described in several reports, genotype phenotype correlations are not fully understood with little knowledge about the feasible molecular targets for therapy. Methods: To understand the mechanism of the erythroid dominant phenotype of AEL and identify potential therapeutic targets for AEL, we analyzed a total of 105 AEL cases with the median age of 60 (23-86), using targeted-capture sequencing of commonly mutated genes in myeloid neoplasms, together with 1,279 SNPs for copy number measurements. Among these 105 cases, 13 were also analyzed by RNA sequencing. Genetic profiles of these 105 AEL cases were compared to those of 775 cases with non-erythroid AML (NEL) including 561 cases from The Cancer Genome Atlas and Beat AML study. An immature erythroid cell line (TF1) and three patient-derived xenografts (PDX) established from AEL with JAK2 and/or EPOR amplification. Cell line and samples from patients were inoculated into immune-deficient mice and tested for their response to JAK1/2 inhibitor. Results: According to unique genetic alterations, AEL was classified into 4 subgroups (A-D). Characterized by TP53 mutations and complex karyotype, Group A was the most common subtype and showed very poor prognosis. Remarkably, all PEL cases were categorized into Group A. Conspicuously, 80% of PEL cases had amplifications of JAK2 (6/10; 60%), EPOR (7/10;70%), and ERG (6/10;60%) loci on chromosomes 9p, 19q, and 21q, respectively, frequently in combination, although they were rarely seen in NEL cases. All cases in Group B (n=19, 18%), another prevalent form of AEL, had STAG2 mutations and classified in MEL. To further characterize this subgroup, we compared genetic profiles of STAG2-mutated AEL and NEL. Prominently, 70% (14/20) of STAG2-mutated cases in AEL had KMT2A-PTD, whereas it was found only in 8.8% (3/34) of NEL. CEBPA mutations were also more common in AEL (6/21; 29%) than NEL (4/34; 12%). While Group C was characterized by frequent NPM1 mutations, in contrast to the frequent co-mutation of FLT3 in the corresponding subgroup of NPM1-mutated cases in NEL, NPM1-mutated patents in this subgroup lacked FLT3 mutations but had frequent PTPN11 mutations (8/16; 50%), which were much less common in NEL (25/209; 12%). The remaining cases were categorized into Group D, which was enriched for mutations in ASXL1, BCOR, PHF6, U2AF1 and KMT2C. Recurrent loss-of-function mutations in USP9X were unique to this subtype, although USP9X mutations have been reported in ALL with upregulation of JAK-STAT pathway. In RNA sequencing analysis, AEL cases exhibited gene expression profiles implicated in an upregulated STAT5 signaling pathway, which was seen not only those cases with JAK2 or EPOR amplification, but also those without, suggesting that aberrantly upregulated STAT5 activation might represent a common defect in AEL. Based on this finding, we evaluated the effect of a JAK inhibitior, ruxolitinib, on an AEL-derived cell line and three PDX models established from AEL having TP53 mutations and JAK2 and EPOR mutation/amplification. Of interest, ruxolitinib significantly suppressed cell growth and prolonged overall survival in mice engrafted with TF1 and 2 PDX models with STAT5 downregulation, although the other model was resistant to JAK2 inhibition with persistent STAT5 activation. Conclusion: AEL is a heterogeneous group of AML, of which PEL is characterized by frequent amplifications/mutations in JAK2, EPOR and/or ERG. Frequent involvement of EPOR/JAK/STAT pathway is a common feature of AEL, in which a role of JAK inhibition was suggested. Disclosures Yoda: Chordia Therapeutics Inc.: Research Funding. Shih:Novartis: Research Funding; Celgene: Research Funding; PharmaEssentia: Consultancy, Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Consultancy, Membership on an entity's Board of Directors or advisory committees. Ishiyama:Alexion: Research Funding; Novartis: Honoraria. Miyazaki:Astellas Pharma Inc.: Honoraria; Sumitomo Dainippon Pharma Co., Ltd.: Honoraria; NIPPON SHINYAKU CO.,LTD.: Honoraria; Celgene: Honoraria; Otsuka Pharmaceutical: Honoraria; Chugai Pharmaceutical Co., Ltd.: Honoraria; Novartis Pharma KK: Honoraria; Kyowa Kirin Co., Ltd.: Honoraria. Nakagawa:Sumitomo Dainippon Pharma Co., Ltd.: Research Funding. Takaori-Kondo:Celgene: Honoraria, Research Funding; Ono Pharmaceutical: Research Funding; Thyas Co. Ltd.: Research Funding; Takeda: Research Funding; CHUGAI: Research Funding; OHARA Pharmaceutical: Research Funding; Sanofi: Research Funding; Novartis Pharma: Honoraria; Bristol-Myers Squibb: Honoraria, Research Funding; Pfizer: Research Funding; Otsuka Pharmaceutical: Research Funding; Eisai: Research Funding; Astellas Pharma: Honoraria, Research Funding; Kyowa Kirin: Honoraria, Research Funding; Nippon Shinyaku: Research Funding; MSD: Honoraria. Kataoka:Asahi Genomics: Current equity holder in private company; Otsuka Pharmaceutical: Research Funding; Takeda Pharmaceutical Company: Research Funding; CHUGAI PHARMACEUTICAL CO., LTD.: Research Funding. Usuki:Alexion: Research Funding, Speakers Bureau; Apellis: Research Funding; Novartis: Research Funding, Speakers Bureau; Chugai: Research Funding. Maciejewski:Novartis, Roche: Consultancy, Honoraria; Alexion, BMS: Speakers Bureau. Ganser:Novartis: Consultancy; Celgene: Consultancy. Thol:Daiichi Sankyo: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Ogawa:Sumitomo Dainippon Pharma Co., Ltd.: Research Funding; Otsuka Pharmaceutical Co., Ltd.: Research Funding; Asahi Genomics Co., Ltd.: Current equity holder in private company; Eisai Co., Ltd.: Research Funding; Chordia Therapeutics, Inc.: Membership on an entity's Board of Directors or advisory committees, Research Funding; KAN Research Institute, Inc.: Membership on an entity's Board of Directors or advisory committees, Research Funding. OffLabel Disclosure: Ruxolitinib is used for drug efficacy test using patient-derived xenografts established from acute erythroid leukemia.

scholarly journals CD38low Natural Killer Cells Transiently Expressing CD16F158V m-RNA Potentiates the Therapeutic Activity of Daratumumab Against Multiple Myeloma with Minimal Effector NK Cell Fratricide

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3199-3199 ◽  
Author(s):  
Subhashis Sarkar ◽  
Sachin Chauhan ◽  
Arwen Stikvoort ◽  
Alessandro Natoni ◽  
John Daly ◽  
...  
Keyword(s):  
Nk Cells ◽  
Cell Line ◽  
Board Of Directors ◽  
Cell Lines ◽  
Research Funding ◽  
Nk Cell ◽  
Ex Vivo ◽  
Advisory Committees ◽  
Cd38 Expression ◽  
Rpmi 8226

Abstract Introduction: Multiple Myeloma (MM) is a clonal plasma cell malignancy typically associated with the high and uniform expression of CD38 transmembrane glycoprotein. Daratumumab is a humanized IgG1κ CD38 monoclonal antibody (moAb) which has demonstrated impressive single agent activity even in relapsed refractory MM patients as well as strong synergy with other anti-MM drugs. Natural Killer (NK) cells are cytotoxic immune effector cells mediating tumour immunosurveillance in vivo. NK cells also play an important role during moAb therapy by inducing antibody dependent cellular cytotoxicity (ADCC) via their Fcγ RIII (CD16) receptor. Furthermore, 15% of the population express a naturally occurring high affinity variant of CD16 harbouring a single point polymorphism (F158V), and this variant has been linked to improved ADCC. However, the contribution of NK cells to the efficacy of Daratumumab remains debatable as clinical data clearly indicate rapid depletion of CD38high peripheral blood NK cells in patients upon Daratumumab administration. Therefore, we hypothesize that transiently expressing the CD16F158V receptor using a "safe" mRNA electroporation-based approach, on CD38low NK cells could significantly enhance therapeutic efficacy of Daratumumab in MM patients. In the present study, we investigate the optimal NK cell platform for generating CD38low CD16F158V NK cells which can be administered as an "off-the-shelf"cell therapy product to target both CD38high and CD38low expressing MM patients in combination with Daratumumab. Methods: MM cell lines (n=5) (MM.1S, RPMI-8226, JJN3, H929, and U266) and NK cells (n=3) (primary expanded, NK-92, and KHYG1) were immunophenotyped for CD38 expression. CD16F158V coding m-RNA transcripts were synthesized using in-vitro transcription (IVT). CD16F158V expression was determined by flow cytometry over a period of 120 hours (n=5). 24-hours post electroporation, CD16F158V expressing KHYG1 cells were co-cultured with MM cell lines (n=4; RPMI-8226, JJN3, H929, and U266) either alone or in combination with Daratumumab in a 14-hour assay. Daratumumab induced NK cell fratricide and cytokine production (IFN-γ and TNF-α) were investigated at an E:T ratio of 1:1 in a 14-hour assay (n=3). CD38+CD138+ primary MM cells from newly diagnosed or relapsed-refractory MM patients were isolated by positive selection (n=5), and co-cultured with mock electroporated or CD16F158V m-RNA electroporated KHYG1 cells. CD16F158V KHYG1 were also co-cultured with primary MM cells from Daratumumab relapsed-refractory (RR) patients. Results: MM cell lines were classified as CD38hi (RPMI-8226, H929), and CD38lo (JJN3, U266) based on immunophenotyping (n=4). KHYG1 NK cell line had significantly lower CD38 expression as compared to primary expanded NK cells and NK-92 cell line (Figure 1a). KHYG1 electroporated with CD16F158V m-RNA expressed CD16 over a period of 120-hours post-transfection (n=5) (Figure 1b). CD16F158V KHYG1 in-combination with Daratumumab were significantly more cytotoxic towards both CD38hi and CD38lo MM cell lines as compared to CD16F158V KHYG1 alone at multiple E:T ratios (n=4) (Figure 1c, 1d). More importantly, Daratumumab had no significant effect on the viability of CD38low CD16F158V KHYG1. Moreover, CD16F158V KHYG1 in combination with Daratumumab produced significantly higher levels of IFN-γ (p=0.01) upon co-culture with CD38hi H929 cell line as compared to co-culture with mock KHYG1 and Daratumumab. The combination of CD16F158V KHYG1 with Daratumumab was also significantly more cytotoxic to primary MM cell ex vivo as compared to mock KHYG1 with Daratumumab at E:T ratio of 0.5:1 (p=0.01), 1:1 (p=0.005), 2.5:1 (p=0.003) and 5:1 (p=0.004) (Figure 1e). Preliminary data (n=2) also suggests that CD16F158V expressing KHYG1 can eliminate 15-17% of primary MM cells from Daratumumab RR patients ex vivo. Analysis of more Daratumumab RR samples are currently ongoing. Conclusions: Our study provides the proof-of-concept for combination therapy of Daratumumab with "off-the-shelf" CD38low NK cells transiently expressing CD16F158V for treatment of MM. Notably, this approach was effective against MM cell lines even with low CD38 expression (JJN3) and primary MM cells cultured ex vivo. Moreover, the enhanced cytokine production by CD16F158V KHYG1 cells has the potential to improve immunosurveillance and stimulate adaptive immune responses in vivo. Disclosures Sarkar: Onkimmune: Research Funding. Chauhan:Onkimmune: Research Funding. Stikvoort:Onkimmune: Research Funding. Mutis:Genmab: Research Funding; OnkImmune: Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Gilead: Research Funding; Celgene: Research Funding; Novartis: Research Funding. O'Dwyer:Abbvie: Membership on an entity's Board of Directors or advisory committees; Celgene: Research Funding; BMS: Research Funding; Glycomimetics: Research Funding; Onkimmune: Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding.

scholarly journals Multiomic Mapping of Copy Number and Structural Variation on Chromosome 1 (Chr1) Highlights Multiple Recurrent Disease Drivers

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 721-721
Author(s):  
Patrick Blaney ◽  
Eileen M Boyle ◽  
Yubao Wang ◽  
Hussein Ghamlouch ◽  
Jinyoung Choi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Board Of Directors ◽  
Cell Lines ◽  
Chromatin Structure ◽  
Copy Number ◽  
Research Funding ◽  
Chromosome 1 ◽  
Structural Variants ◽  
Advisory Committees

Abstract Introduction Copy number abnormalities (CNA) and structural variants (SV) are crucial to driving cancer progression and in multiple myeloma (MM). Chr1 CNA are seen in up to 40% of cases and associate with poor prognosis. Variants include deletions, gains, translocations and complex SV events such as chromothripsis (CT), chromoplexy (CP) and templated insertions (TI) which result in aberrant transcriptional patterns. Abnormal expression of genes on chr1 lead to the adverse clinical outcome and studies focussed on 1p12, 1p32.3 and 1q12-21 identified potential causal genes including TENT5C, CDKN2C, CKS1B, PDZK1, BCL9, ANP32E, ILF2, ADAR, MDM2 and MCL1 but none fully explain the clinical behavior. To address this deficiency and to relate chromatin structure to gene deregulation we present a multiomic bioinformatic analysis of SV, CNA, mutation and expression changes in relation to the chromatin structure of chr1. Methods We analysed data derived from 1,154 CoMMpass trial patients. We analyzed 972 NDMM patients with whole exome for mutations, and 752 whole genomes for copy number, translocations, complex rearrangements such as CP, CT and TI as previously described. Using GISTIC 2.0, we identified hotspots of CNA. This information was then analyzed in conjunction to the RNA-seq data derived from 643 patients to determine the aberrant transcriptional landscape of chr1. Using HiC data derived from U266 MM cell line, we associated these changes with TAD structures, A/B compartments, and histone marks along chr1, to gene expression changes, and recurrent SV. Using the cell line dependency map for CRISPR knockdown of the gene set on chr1 derived from 20 MM cell lines we related cell viability to chr1 copy number status. Results We identified 7 hotspots of deletion, 9 of gain, 3 of CT and 2 of templated-insertion across chr1. We mapped these regions to epigenetic plots and show that gained regions are hypomethylated compared to the rest of chr1 (Wilcoxon, p=0.0002). Overall 69% of gain(1q) and 45% of the non-gained hotspots were in A compartments (χ 2=11, p=0.0009) and had an overall higher compartment score (p=0.01).The recurrent regions of loss on 1p confirm the clinical relevance of this region. The critical importance of TENT5C, CDKN2C and RPL5 is identified by the impact of deletion, mutation and the rearrangement of superenhancers. Further this convergence of multiple oncogeneic mechanisms to a single locus points to a number of novel candidate drivers including FUB1 and NTRK1.We provide important new information on 1q21.1-1q25.2 encompassing 145-180Mb a transcriptionally dense region containing 6 GISTIC 2.0 hotspots of gain (G2-G7). The hotspots occur within TAD structures that correlate upregulation of known drivers listed above and also identified novel potential upregulated drivers including POU2F1, a transcription factor, CREG1, an adenovirus E1A protein that both activates and represses gene expression promoting proliferation and inhibiting differentiation (G6) and BTG2 a G1/S transition regulator (G8). These data for copy number gain provides strong evidence for the prognostic relevance of of multiple drivers within deregulated TADs rather than single candidate genes. It also highlights the importance of the chromatin structure of Chr1 in the generation of these events.Using dependency map CRISPR data we identified 320 essential genes for at least one cell line (&gt;1). A common set of 31 genes were identified including 3 proteasome subunits (PSMA5, PSMB2, PSMB4), three regulators of ubiquitin-protein transferase activity (RPL5, RPL11, CDC20), splicing (SF3B4, SF3A3, SFPQ, RNPC3, SRNPE, PRPF38A, PRPF38B) and DTL. A common dependency for 1q+ or 1p- was not identified but a number of dependencies were identified in more than one cell line including UQCRH, SLCA1, CLSPN in 1p- cell lines and IPO9, PPIAL4G, and MRPS2 in 1q+. Conclusion We present an elegant anatomic map of chr1 at the genetic and epigenetic levels providing an unprecedented level of resolution for the relationships of structural variants to epigenetic, expression and mutation status. The analysis highlights the importance of active chromatin in gene deregulation by SV and CNA where the importance of multiple gene deregulation within TAD structures is critical to MM pathogenesis. The implications are that we could improve prognostic assignment and identify new targets for therapy by further characterizing these relationships. Figure 1 Figure 1. Disclosures Braunstein: Jansen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Adaptive: Membership on an entity's Board of Directors or advisory committees; AstraZeneca: Membership on an entity's Board of Directors or advisory committees; Epizyme: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees. Davies: Takeda: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Oncopeptides: Membership on an entity's Board of Directors or advisory committees; Constellation: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Celgene/BMS: Consultancy, Membership on an entity's Board of Directors or advisory committees.

scholarly journals Whole-Exome Sequencing in Myelodysplastic Syndromes with 5q Deletion

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4635-4635
Author(s):  
Vera Adema ◽  
Laura Palomo ◽  
María Díez-Campelo ◽  
Mar Mallo ◽  
Leonor Arenillas ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Board Of Directors ◽  
Whole Exome Sequencing ◽  
Myelodysplastic Syndromes ◽  
Genomic Dna ◽  
Research Funding ◽  
Sequencing Data ◽  
Advisory Committees ◽  
Whole Exome ◽  
Increased Risk

Abstract INTRODUCTION Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal myeloid stem cell disorders that are highly prevalent in elderly populations. MDS are characterized by inefficient hematopoiesis, peripheral blood (PB) cytopenias, and increased risk of transformation to acute myeloid leukemia (AML; 20–30% of patients with MDS). Around 50% of MDS patients carry at least one karyotypic aberration. The interstitial deletion of the long arm of chromosome 5 ([del(5q)] is the most common aberration, accounting for almost 30% of abnormal MDS karyotype. Various studies supports a favorable prognosis of MDS with isolated del(5q) with an excellent response to lenalidomide treatment. In order to describe the molecular events associated with MDS and del(5q) we performed whole-exome sequencing (WES)(assessing 334,378 exons) of tumor-normal paired samples from 20 MDS patients to unravel the genetic basis of MDS with del(5q). The analysis is ongoing and the complete results will be presented in the meeting. METHODS A total of 50 samples from 20 patients with MDS, with del(5q) were collected. For each diagnostic sample, we performed Conventional G-banding cytogenetics and fluorescence in situ hybridization (FISH, to confirm or dismiss del(5q)) and SNP arrays with Cytoscan HD (Affymetrix). These samples included: 20 tumor samples at diagnosis, 20 control samples and 10 samples after diagnosis, during lenalidomide treatment (5) or at the moment of relapse (5) in order to compare the genetic status before and during the treatment. Genomic DNA from tumor cells was obtained from bone marrow (BM) samples or from PB granulocytes. As a source of constitutional DNA we used CD3+T cells from each patient by isolating by magnetic-activated cell sorting. WES targeted capture was carried out on 7μg of genomic DNA, using the SureSelect Human Exome Kit 51Mb version 4.Libraries were sequenced on an Illumina HiSeq2000. Sequencing data will be analyzed using an in-house bioinformatics pipeline as previously reported. RESULTS Our preliminary analysis of these 20 new patients by WES confirmed our previous analyses with mutations in well described genes as ASXL1, JAK2 and TET2, but not in genes RUNX1, SF3B1 and SRSF2. In those patients we found two patients with missense mutation in TP53, one of the patients had an isolated del(5q) and is receiving lenalidomide treatment, and the other one had a complex karyotype. According to our prior analyses, in which 249 non-silent somatic variants were detected, we look forward to validate these mutations in this new series of patients. CONCLUSIONS We envision to validate these previous results with the new sequencing data of more patients with MDS and del(5q). We expect to measure somatic mutations that vary in abundance after lenalidomide treatment, potentially identifying mutations associated with resistance or relapse. ACKNOWLEDGEMENTS: This work has been supported (in part) by a grants from Instituto de Salud Carlos III, Ministerio de Sanidad y Consumo, Spain (PI 11/02010); by Red Temática de Investigación Cooperativa en Cáncer (RTICC, FEDER) (RD07/0020/2004; RD12/0036/0044); 2014 SGR225 (GRE) Generalitat de Catalunya; Fundació Internacional Josep Carreras; Obra Social “la Caixa”; Sociedad Española de Hematología y Hemoterapia (SEHH)and Celgene Spain. FOOTNOTES Rafael Bejar and Francesc Sole contributed equally. Disclosures Díez-Campelo: Novartis, Celgene: Honoraria, Research Funding. Xicoy:Celgene: Honoraria. Cañizo:Celgene, Jansen-Cilag, Arry, Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. sanchez-Garcia:Celgene: Honoraria, Research Funding. Bejar:Celgene: Membership on an entity's Board of Directors or advisory committees; Genoptix Medical Laboratory: Consultancy, Honoraria, Licensed IP, no royalties Patents & Royalties, Membership on an entity's Board of Directors or advisory committees. Sole:Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding.

scholarly journals Ultra-Sensitive Detection of Circulating Serum microRNAs (miRNAs) in Diffuse Large B-Cell Lymphoma (DLBCL) Patient-Derived Xenograft (PDX) Models and Correlation with Disease Status in DLBCL Patient

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2973-2973
Author(s):  
Afshin Beheshti ◽  
Kristen E. Stevenson ◽  
Ravi Dashnamoorthy ◽  
Charles Vanderburg ◽  
David M Weinstock ◽  
...  
Keyword(s):  
Cell Line ◽  
Board Of Directors ◽  
Research Funding ◽  
Healthy Controls ◽  
Mirna Signature ◽  
Advisory Committees ◽  
Dlbcl Patient ◽  
Wilcoxon Rank Sum Test ◽  
Circulating Levels ◽  
Pdx Models

Abstract Background: MiRNAs are small non-coding RNAs that regulate post-transcriptional gene expression, contribute to various facets of cancer pathogenesis, and may serve as a sensitive diagnostic platform as well as potential novel therapeutic targets. We recently identified a 9 miRNA (miR-15a, let-7c, let-7b, miR-27a, miR10b, miR-18a, miR130a, miR24, and miR155) signature in serum of Smurf2T/T mice that was detectable many months prior to the formation of visible DLBCL (Beheshti A et al PLOS One, 2017). We hypothesized that this circulating miRNA signature would also correlate with DLBCL status in PDX models and ultimately patients (pts). Methods: We performed droplet digital PCR (ddPCR), which allows for rapid quantification of single miRNA molecules. First, we examined the 9 aforementioned miRNAs in serum collected from mice xenografted with 5 DLBCL PDXs (Townsend et al. Cancer Cell 2016) and age-matched NSG mice without xenografts as controls. We also quantified the amount of miRNAs directly from all PDX cell lines utilized and 2 commercially available DLBCL cell lines for comparison. Next, we collected and analyzed serum from 86 pts with DLBCL in the following conditions: pre-treatment with first-line therapy (n=11); progression after treatment (n=7); during treatment (n=16); and in complete remission (n=52). Seventeen healthy non-tumor bearing individuals were used as controls. Median age of healthy controls was 52 years (range, 29-70) vs 64 years (range, 21-87) for DLBCL pts (p<0.001; Wilcoxon rank-sum test). 69% of DLBCL pts were male vs 35% of healthy controls (p=0.012; Fisher exact test). Results: The miRNA signature was enriched in DLBCL PDX mice with high expression confirmed in the 9 miRNAs, including MYC single and double hit models. The overall mean amounts of the miRNAs present in the serum of PDX bearing mice were mostly equivalent to the amount present in the original PDX cell line (Fig 1), with exception of one PDX cell line (DFBL-75549) that consistently had 100x more miRNA present in the serum of the mice vs associated cell line. In addition, we identified significantly increased circulating levels of the same miRNA signature in the serum of DLBCL pts (Table 1) (two-sided Wilcoxon rank-sum test, p<0.05) with similar patterns of change as seen in the murine models. Interestingly, higher circulating levels of let-7b were associated with a higher stage at diagnosis (stage I-II vs III-IV, median 54.0 vs. 163.2; P=0.007) and higher levels of both miR-27a and miR-24 were associated with having a MYC rearrangement (median 20.0 vs. 4.8; P=0.003; median 58.4 vs. 24.4; P=0.046). Higher levels of miR-18a were associated with Myc positivity by immunohistochemistry (0-9% of cells vs. 10-59% vs. ≥60%, median 3.3 vs. 2.8 vs. 8.8; P=0.030) as well as having received a prior therapy for DLBCL (median 4.8 for previously treated vs. 1.1 for untreated; P=0.016). Using the 23 on-treatment and progression samples compared with healthy samples, we selected cut-points based on the Youden Index from receiver operating curve (ROC) analysis and were able to classify the remission samples with an accuracy of 46%-88%. miR-24 performed the best in classification with a sensitivity of 85% and a specificity of 100%, while 6 of the 9 miRs had a classification rate >80%. Using a 5 miR signature with cut-points selected from recursive partitioning, we were able to classify remission samples with an accuracy of 91% (sensitivity 90%, specificity 94%). Conclusions: Altogether, ultrasensitive detection of circulating miRNAs originally identified in a lymphoma xenograft knockout model was readily detectable and highly elevated in DLBCL PDX models. Additionally, there were significantly increased circulating levels of the miRNA signature from the serum of DLBCL pts. Particular miRs were associated with pt stage and the presence of MYC overexpression or rearrangement in pts with DLBCL. Furthermore, circulating miRNAs were able to reliably distinguish DLBCL pts in remission from healthy controls based on a novel 5 miR signature. Validation in additional cohorts is needed to confirm whether miRNA quantification from serum may be a broadly applicable strategy for diagnosis, classification and response assessment among pts with DLBCL. Disclosures Weinstock: Astra Zeneca, JAX, Samumed, Regeneron, Sun Pharma, Prescient: Patents & Royalties; Genentech/Roche, Monsanto: Consultancy; Novartis: Consultancy, Research Funding; Novartis, Astra Zeneca, Abbvie, Aileron, Surface Oncology, Daiichi Sankyo: Research Funding; Novartis, Dragonfly, Travera, DxTerity, Travera: Consultancy; Travera: Equity Ownership. Evens:Pharmacyclics International DMC: Membership on an entity's Board of Directors or advisory committees; Bayer: Consultancy; Seattle Genetics, Inc.: Membership on an entity's Board of Directors or advisory committees, Research Funding; Affimed: Consultancy; Abbvie: Consultancy; Tesaro: Research Funding; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Consultancy; Novartis: Consultancy; Acerta: Consultancy.

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