DNA Damage Repair Pathway Alterations in Multiple Myeloma Predict Poor Prognosis, but Correlate with Sensitivity to IGF1R-PI3K-mTOR and HDAC Inhibitors

Abstract Introduction Although several novel drugs have recently been approved or are in development for multiple myeloma (MM), there are few molecular indicators to guide treatment selection. In addition, the impact of recurrent myeloma alterations on drug response is often unclear. To address these limitations and elucidate genotype to phenotype relationships in myeloma, we comprehensively analyzed 100 MM samples and compared genomic, transcriptomic, and cytogenetic information to ex vivo drug response profiles and clinical outcome of individual MM patients. Our results reveal novel insights on i) drug response and resistance mechanisms, ii) biomarkers for drug response, and iii) potential treatment combinations to overcome drug resistance. Methods Bone marrow aspirates were collected from MM patients (n=100; newly diagnosed n=34; relapsed/refractory n=66) and healthy individuals (n=14). CD138+ plasma cells were enriched from the mononuclear cell fraction by immunomagnetic bead selection. Cells were screened against 142 oncology drugs tested in a 10,000-fold concentration range and 12 different drug combinations Somatic alterations were identified by exome sequencing of DNA from CD138+ cells and skin biopsies from each patient (n=85). RNA sequencing derived read counts from CD138+ cells of MM samples (n=67) were used for differential gene expression. Karyotype was determined by fluorescence in situ hybridization. Results For most drugs tested, no significant difference in response was observed between samples from newly diagnosed and relapsed refractory patients except for signal transduction inhibitors targeting IGF1R-PI3K-mTOR, MAPK and HSP90. A positive correlation was observed between mutational burden and sensitivity to targeted therapies. The median number of somatic alterations was 118 in sensitive compared to 50 in resistant samples. 14% of the samples exhibited a multidrug resistant phenotype and were resistant to proteasome inhibitors, immunomodulatory drugs and glucocorticoids. 30% of the resistant samples were from del(17p) patients. In addition, gene expression analysis revealed elevated expression of cell adhesion and integrin signaling molecules including ITGB3, ITGA2B, VCL, TLN1, MMP8, MMP9, plus ABCC3, which encodes a transporter protein shown to be associated with multidrug resistance. A combination of the protein kinase C inhibitor bryostatin-1 and pan-BCL2 inhibitor navitoclax was highly effective against the resistant samples. 26% of the patient samples harbored mutations in genes involved in DNA damage repair signaling, namely TP53, TP73, ATM and BAX, in a mutually exclusive pattern. In addition, patients with these mutations had a high relapse rate and poor overall survival (HR=7.2,95%CI 3.2-16.08). Interestingly, CD138+ cells from these patients showed activation of IGF1R-PI3K-mTOR signaling and were highly susceptible to inhibitors targeting this signaling axis. These samples were also highly sensitive to HDAC inhibitors. While no strong correlation between RAS pathway mutations (NRAS, KRAS, NF1, BRAF) and MEK inhibitor sensitivity was observed, samples with clonal RAS mutations tended to be more sensitive to MEK inhibitors compared to samples with subclonal mutations. Summary Our results suggest that drug resistance in myeloma may occur either via accumulation of somatic alterations or via cell adhesion mediated cytoprotection. Driver alterations in DNA damage signaling pathways were found to contribute to poor prognosis, but samples with these mutations showed enhanced sensitivity to IGF1R-PI3K-mTOR and HDAC inhibitors. Using genomic and transcriptomic data we identified molecular events that may shape the drug response landscape and found drug combinations that can overcome resistance mechanisms. Our results demonstrate that molecular information and ex vivo drug profiling may be useful to develop tailored treatment strategies and guide treatment decision, especially for relapsed/refractory myeloma patients. Disclosures Silvennoinen: Sanofi: Honoraria, Other: Lecture fee; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Lecture fee; Janssen: Honoraria, Research Funding; Celgene: Honoraria, Research Funding. Porkka:Bristol-Myers Squibb: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Novartis: Honoraria, Research Funding. Heckman:Pfizer: Research Funding; Celgene: Research Funding.

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Therapy-Related Myeloid Neoplasm Has a Distinct Pro-Inflammatory Bone Marrow Microenvironment and Delayed DNA Damage Repair

Blood ◽

10.1182/blood-2020-137277 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 37-38

Author(s):

Monika M Kutyna ◽

Li Yan A Wee ◽

Sharon Paton ◽

Dimitrios Cakouros ◽

Agnieszka Arthur ◽

...

Keyword(s):

Dna Damage ◽

Board Of Directors ◽

Research Funding ◽

High Dose ◽

Cytotoxic Therapy ◽

Advisory Committees ◽

Myeloid Neoplasm ◽

Myeloid Neoplasms ◽

Damage Repair

Introduction: Therapy-related myeloid neoplasms (t-MN) are associated with extremely poor clinical outcomes in otherwise long-term cancer survivors. t-MN accounts for ~20% of cases of myeloid neoplasms and is expected to rise due to the increased use of chemotherapy/radiotherapy (CT/RT) and improved cancer survivorship. Historically, t-MN was considered a direct consequence of DNA damage induced in normal hematopoietic stem cells (HSC) by DNA damaging cytotoxics. However, these studies have largely ignored the bone marrow (BM) microenvironment and the effects of age and concurrent/previous cancers. Aim: We performed an exhaustive functional study of mesenchymal stromal cells (MSC) obtained from a comparatively large cohort of t-MN patients and carefully selected control populations to evaluate the long-term damage induced by cytotoxic therapy to BM microenvironment and its impact on malignant and normal haematopoiesis. Methods: Four different cohorts were used: (1) t-MN, in which myeloid malignancy occurred after CT/RT for a previous cancer (n=18); (2) patients with multiple cancer and in which a myeloid neoplasm developed following an independent cancer which was not treated with CT/RT (MC-MN; n=10); (3) primary MN (p-MN; n=7) untreated and without any prior cancer or CT/RT; (4) age-matched controls (HC; n=17). Morphology, proliferation, cellular senescence, differentiation potential and γH2AX DNA damage response was performed. Stem/progenitor supportive capacity was assessed by co-culturing haematopoietic stem cells on MSC feeder-layer in long-term culture initiating assay (LTC-IC). Cytokine measurements were performed using 38-plex magnetic bead panel (Millipore) and RNA sequencing libraries were prepared with Illumina TruSeq Total RNA protocol for 150bp paired-end sequencing on a NextSeq500 instrument. Functional enrichment analysis was performed using EnrichR software. Results: MSC cultured from t-MN patients were significantly different from HC, p-MN and MC-MN MSC according to multiple parameters. They exhibited aberrant morphology consisting of large, rounded and less adhesive cells compared to typical spindle-shaped morphology observed with controls. MSC from myeloid neoplasm also showed impaired proliferation, senescence, osteo- and adipogenic differentiation with t-MN MSC showing the greatest differences. DNA repair was dramatically impaired compared to p-MN and HC (Fig.1A). Importantly, these aberrant t-MN MSC were not able to support normal or autologous in vitro long-term haematopoiesis (Fig.1B). The biological characteristic and poor haematopoietic supportive capacity of MSC could be "cell-intrinsic" or driven by an altered paracrine inflammatory microenvironment. Interestingly, several inflammatory cytokines were higher in t-MN compared with marrow interstitial fluid obtained from p-MN patients (Fig.1Ci) and many of these including Fractalkine, IFNα2, IL-7 and G-CSF were also significantly higher in t-MN MSC conditional media (Fig.1Cii). Together, this data suggest that t-MN microenvironment is distinct from p-MN with paracrine production of pro-inflammatory milieu that may contribute to poor HSC supportive capacity. Preliminary whole transcriptome analysis revealed differential gene expression between t-MN and HC (Fig.1Di) and p-MN MSC. Importantly, the deregulated genes play critical role in cell cycle, DNA damage repair, and cellular senescence pathways explaining phenotypical characteristic of t-MN MSC (Fig.1Dii). Moreover CXCL12 expression, a key regulator of haematopoiesis, was significantly lower in t-MN compared to HC (p=0.002) and p-MN MSC (p=0.009), thus explaining poor HSC supportive capacity. The key difference between the p-MN, MC-MN and t-MN is prior exposure to CT/RT. To study this we obtained MSC from two t-MN patients for whom we had samples at the time of their primary cancer, post high-dose chemotherapy and at the time of t-MN. MSC displayed aberrant proliferation and differentiation capacity after high-dose cytotoxic therapy (2 to 4 years prior to developing t-MN) and remained aberrant at t-MN diagnosis (Fig.1E). Conclusions: BM-MSC from t-MN patients are significantly abnormal compared with age-matched controls and typical myeloid neoplasm. Importantly, prior CT/RT leads to long-term irreversible damage to the BM microenvironment which potentially contributes to t-MN pathogenesis. Disclosures Hughes: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Hiwase:Novartis Australia: Research Funding.

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Landscape of Recurrent Mutations in Non-Coding Genome with Functional Implications in Newly-Diagnosed Multiple Myeloma

Blood ◽

10.1182/blood-2018-190 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 190-190 ◽

Cited By ~ 1

Author(s):

Mehmet Kemal Samur ◽

Chandraditya Chakraborty ◽

Raphael Szalat ◽

Anil Aktas Samur ◽

Mariateresa Fulciniti ◽

...

Keyword(s):

Board Of Directors ◽

Research Funding ◽

P Value ◽

Newly Diagnosed ◽

Rna Seq ◽

Coding Region ◽

Advisory Committees ◽

Coding Regions ◽

Somatic Alterations ◽

Equity Ownership

Abstract Multiple Myeloma (MM) is a complex disease with distinct molecular and clinical characteristics. Recent large collaborative efforts have identified number of driver genes. However over 95% of all somatic alterations occur in non-coding regions and very little is known about how they affect the disease. We performed a deep (average coverage > 80X) whole genome sequencing (WGS) on 260 MM samples (208 newly diagnosed and 52 first relapse after uniform treatment) to comprehensively analyze recurrent somatic alterations in non-coding regions. We detected median 11,852 (Range 4,802-87,396) mutations and indels per sample with overall more than 3.9M total somatic mutations. Introns (3.6 mutations/per Mb) and intergenic regions (4.06 mutations/per Mb) had significantly higher number of mutations per megabase compared to Exons (2.7 mutations/per Mb) (p < 1e-5). Mutations in coding regions in our data was similar to published whole exome sequencing studies. We observed 46 [range 7 - 219] structural variants (SVs) per sample with 98% involving non-coding regions. We found that number of SVs significantly correlated with overall survival (p value = 1.7e-5). We detected chromothripsis (>=7 oscillating copy number change and significant clustered SVs and/or clustered translocations) in 24% of newly diagnosed samples; and kataegis hotspots on chromosome 3q27-3q28 (24%), 11q13 (5.8%) and 12q24 (5.3%). By clustering SV breakpoints across the genome we have identified 3 SV hotspots on chromosome 17q21, 7q34, and 11q13. We next interrogated the non-coding regions to identify genomic loci with higher than expected mutation count compared to background mutation rate. We have identified 456 loci that are significantly enriched in non-coding regions (5' UTR, 3'UTR, promoter, intergenic, intronic, and distal regulatory regions) [adjusted p value < 1e-5 and observed in >=10% newly diagnosed MM]. These loci are then assigned to genes or gene neighborhoods to evaluate their potential impact. We have identified the most frequently involved genes affected by perturbation in neighboring non-coding region and integrate their expression using our matching deep RNA-seq data from the same patients. Of these the most prominent examples are 1.) 3'UTR mutations are enriched in CD93 gene, which plays critical role in B cell development with loss of expression in CD138+ MM cells compared to normal plasma cells (p value < 1e-5); 2.) Promoter region - we have identified 635 mutations in 2kb region in BCL6 coming from 76% of all newly diagnosed samples. BCL6 (p value < 1e-5) has significantly downregulated expression in MM. Interestingly, but not surprisingly this hypermutated region showed high intensity of H3K27Ac activity in normal cells; 3.) 5'UTR - BCL7A (27.9%) and LPP (11.7%) were top two 5' UTR mutated target genes and RNA-seq data confirmed significant downregulation of their expression (p values < 1e-5 and 0.0048 respectively) in the MM cells. Additionally, BCL7A (48%) also showed significant enrichment of intronic mutations. A similar mutational hotspots were observed within the vicinity of additional functionally important genes in myeloma including ROBO1/2, ILF2, IRF8 and BCL2A1. Our data also showed that these frequent mutations have higher cancer cell fraction (CCF) [median CCF > 0.75] suggesting their occurrence earlier in the disease development. To validate the function of these mutations, we have started to carry out gain/loss of function studies. Our analysis with BCL7A shows that BCL7A knockdown increases the cell viability while its overexpression decreased growth, colony formation and increased apoptosis. This tumor suppressor function of BCL7A is being further analyzed in light of our mutational data in the nearby non-coding region. In conclusion, this large deep whole genome sequencing data from newly-diagnosed MM patients identifies a vast majority of non-coding mutations with potentially significant functional and biological role in MM. Our integrative approach using both WGS and RNA-seq data from the patients now provides us important tools to further characterize the impact of these mutations and develop opportunities for targeted therapeutics. Disclosures Richardson: Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Membership on an entity's Board of Directors or advisory committees; BMS: Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Karyopharm: Membership on an entity's Board of Directors or advisory committees. Moreau:Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees. Thakurta:Celgene Corporation: Employment, Equity Ownership. Anderson:Millennium Takeda: Consultancy; Gilead: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Consultancy; OncoPep: Equity Ownership, Other: Scientific founder; C4 Therapeutics: Equity Ownership, Other: Scientific founder; Celgene: Consultancy. Avet-Loiseau:Amgen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Abbvie: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Sanofi: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding. Munshi:OncoPep: Other: Board of director.

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Comparative Analysis of Independent Ex Vivo functional Drug Screens Identifies Predictive Biomarkers of BCL-2 Inhibitor Response in AML

Blood ◽

10.1182/blood-2018-99-111916 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 2763-2763 ◽

Cited By ~ 1

Author(s):

Brian S. White ◽

Suleiman A. Khan ◽

Muhammad Ammad-ud-din ◽

Swapnil Potdar ◽

Mike J Mason ◽

...

Keyword(s):

Gene Expression ◽

Board Of Directors ◽

Research Funding ◽

Drug Response ◽

Ex Vivo ◽

Predictive Performance ◽

Data Sets ◽

Advisory Committees ◽

Data Set ◽

Equity Ownership

Abstract Introduction: Therapeutic options for patients with AML were recently expanded with FDA approval of four drugs in 2017. As their efficacy is limited in some patient subpopulations and relapse ultimately ensues, there remains an urgent need for additional treatment options tailored to well-defined patient subpopulations to achieve durable responses. Two comprehensive profiling efforts were launched to address this need-the multi-center Beat AML initiative, led by the Oregon Health & Science University (OHSU) and the AML Individualized Systems Medicine program at the Institute for Molecular Medicine Finland (FIMM). Methods: We performed a comparative analysis of the two large-scale data sets in which patient samples were subjected to whole-exome sequencing, RNA-seq, and ex vivo functional drug sensitivity screens: OHSU (121 patients and 160 drugs) and FIMM (39 patients and 480 drugs). We predicted ex vivo drug response [quantified as area under the dose-response curve (AUC)] using gene expression signatures selected with standard regression and a novel Bayesian model designed to analyze multiple data sets simultaneously. We restricted analysis to the 95 drugs in common between the two data sets. Results: The ex vivo responses (AUCs) of most drugs were positively correlated (OHSU: median Pearson correlation r across all pairwise drug comparisons=0.27; FIMM: median r=0.33). Consistently, a samples's ex vivo response to an individual drug was often correlated with the patient's Average ex vivo Drug Sensitivity (ADS), i.e., the average response across the 95 drugs (OHSU: median r across 95 drugs=0.41; FIMM: median r=0.58). Patients with a complete response to standard induction therapy had a higher ADS than those that were refractory (p=0.01). Further, patients whose ADS was in the top quartile had improved overall survival relative to those having an ADS in the bottom quartile (p<0.05). Standard regression models (LASSO and Ridge) trained on ADS and gene expression in the OHSU data set had improved ex vivo response prediction performance as assessed in the independent FIMM validation data set relative to those trained on gene expression alone (LASSO: p=2.9x10-4; Ridge: p=4.4x10-3). Overall, ex vivo drug response was relatively well predicted (LASSO: mean r across 95 drugs=0.62; Ridge: mean r=0.62). The BCL-2 inhibitor venetoclax was the only drug whose response was negatively correlated with ADS in both data sets. We hypothesized that, whereas the predictive performance of many other drugs was likely dependent on ADS, the predictive performance of venetoclax (LASSO: r=0.53, p=0.01; Ridge: r=0.63, p=1.3x10-3) reflected specific gene expression biomarkers. To identify biomarkers associated with venetoclax sensitivity, we developed an integrative Bayesian machine learning method that jointly modeled both data sets, revealing several candidate biomarkers positively (BCL2 and FLT3) or negatively (CD14, MAFB, and LRP1) correlated with venetoclax response. We assessed these biomarkers in an independent data set that profiled ex vivo response to the BCL-2/BCL-XL inhibitor navitoclax in 29 AML patients (Lee et al.). All five biomarkers were validated in the Lee data set (Fig 1). Conclusions: The two independent ex vivo functional screens were highly concordant, demonstrating the reproducibility of the assays and the opportunity for their use in the clinic. Joint analysis of the two data sets robustly identified biomarkers of drug response for BCL-2 inhibitors. Two of these biomarkers, BCL2 and the previously-reported CD14, serve as positive controls credentialing our approach. CD14, MAFB, and LRP1 are involved in monocyte differentiation. The inverse correlation of their expression with venetoclax and navitoclax response is consistent with prior reports showing that monocytic cells are resistant to BCL-2 inhibition (Kuusanmäki et al.). These biomarker panels may enable better selection of patient populations likely to respond to BCL-2 inhibition than would any one biomarker in isolation. References: Kuusanmäki et al. (2017) Single-Cell Drug Profiling Reveals Maturation Stage-Dependent Drug Responses in AML, Blood 130:3821 Lee et al. (2018) A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia, Nat Commun 9:42 Disclosures Druker: Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees; ALLCRON: Consultancy, Membership on an entity's Board of Directors or advisory committees; Fred Hutchinson Cancer Research Center: Research Funding; Celgene: Consultancy; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Aileron Therapeutics: Consultancy; Third Coast Therapeutics: Membership on an entity's Board of Directors or advisory committees; Oregon Health & Science University: Patents & Royalties; Patient True Talk: Consultancy; Millipore: Patents & Royalties; Monojul: Consultancy; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; GRAIL: Consultancy, Membership on an entity's Board of Directors or advisory committees; Beta Cat: Membership on an entity's Board of Directors or advisory committees; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Henry Stewart Talks: Patents & Royalties; Bristol-Meyers Squibb: Research Funding; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Aptose Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; McGraw Hill: Patents & Royalties; ARIAD: Research Funding; Novartis Pharmaceuticals: Research Funding. Heckman:Orion Pharma: Research Funding; Novartis: Research Funding; Celgene: Research Funding. Porkka:Novartis: Honoraria, Research Funding; Celgene: Honoraria, Research Funding. Tyner:AstraZeneca: Research Funding; Incyte: Research Funding; Janssen: Research Funding; Leap Oncology: Equity Ownership; Seattle Genetics: Research Funding; Syros: Research Funding; Takeda: Research Funding; Gilead: Research Funding; Genentech: Research Funding; Aptose: Research Funding; Agios: Research Funding. Aittokallio:Novartis: Research Funding. Wennerberg:Novartis: Research Funding.

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BRCA1/2 Containing Complex 3 (BRCC36) Is Recurrently Mutated in AML with t(8;21) and Associated with Increased Sensitivity to Chemotherapy through Impairment of the DNA Damage Repair Pathway

Blood ◽

10.1182/blood-2018-99-114143 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 1487-1487

Author(s):

Tatjana Meyer ◽

Nikolaus Jahn ◽

Anna Dolnik ◽

Peter Paschka ◽

Verena I. Gaidzik ◽

...

Keyword(s):

Dna Damage ◽

Board Of Directors ◽

Cell Lines ◽

Research Funding ◽

De Novo ◽

Dna Damage Repair ◽

Advisory Committees ◽

Data Set ◽

Damage Repair ◽

De Novo Aml

Abstract Introduction BRCA1/BRCA2-containing complex 3 (BRCC36) is a Lys63-specific deubiquitinating enzyme (DUB) involved in DNA damage repair. Mutations in BRCC36 have been identified in 2-3% of patients with myelodysplastic syndromes (MDS) and secondary AML (sAML). The role of BRCC36 mutations in de novo AML and their impact on DNA damage-inducing cytotoxic chemotherapy sensitivity is not clear. Aim We aimed to determine the incidence of BRCC36 mutations in AML and their impact on outcome and drug sensitivity in vitro. Methods We analyzed the entire coding region of BRCC36 for mutations in 191 AML cases with t(8;21) (q22;q22.1) and 95 cases with inv(16) (p13.1q22) using a customized targeted sequencing panel. Data for de novo AML was derived from The Cancer Genome Atlas Research Network (TCGA) data set (NEJM 2013). Lentiviral CRISPR/Cas9 was used to inactivate BRCC36 in t(8;21)-positive AML cell lines - Kasumi-1 and SKNO-1 - and murine hematopoietic stem and progenitor cells (LSKs). Knockout was confirmed by a cleavage assay as well as Western blot. AML1-ETO-9a was expressed by a retroviral vector. Cell lines and LSK cells were treated with different concentrations of doxorubicin or cytarabine and their viability was assessed seven days post treatment. DNA damage was assessed through phospho-γH2AX staining using flow-cytometry. Results BRCC36 mutations were identified in 7 out of 191 patients (3.7%) with t(8;21) AML and none of 95 patients with inv(16). In the TCGA data set one out of 200 patients (0.5%) with de novo AML had a BRCC36 mutation. This patient had a complex karyotype and would be considered as secondary AML with myelodysplastic-associated changes according to the 2016 WHO classification. Six of the 7 mutations were missense or nonsense mutations that were predicted to be deleterious to BRCC36 function. One mutation affected a splice site at exon 6, resulting in an impaired splicing capability. With intensive standard chemotherapy all patients with BRCC36 mutations achieved a complete remission and had an estimated relapse-free and overall survival of 100% after a median follow up of 4.2 years. Given its role in DNA damage repair, we hypothesized that BRCC36 inactivation sensitizes AML cells to DNA-damage inducing drugs. In order to test this, we generated BRCC36 knockout Kasumi-1 and SKNO-1 cell lines using CRISPR-Cas9. BRCC36 inactivation had no impact on cell growth on either of the cell lines. However, we found that BRCC36 knockout cells were significantly more sensitive to doxorubicin as compared to the parental cells with normal BRCC36. This was accompanied by a significant increase in DNA damage as assessed by phospho-γH2AX in BRCC36 knockout vs control cells after doxorubicin treatment. In contrast, BRCC36 inactivation had no impact on cytarabine sensitivity. We next assessed drug sensitivity in primary murine leukemic cells expressing AML1-ETO-9a. Again, inactivation of BRCC36 resulted in a significant higher sensitivity to doxorubicin but not cytarabine. Conclusion We found BRCC36 to be recurrently mutated in t(8;21)-positive AML Inactivation of BRCC36 was associated with impairment of the DNA damage repair pathway and thus higher sensitivity to DNA damage-inducing chemotherapy. This might be also reflected by the favorable clinical outcome of patients with BRCC36 mutated t(8;21)-positive AML, a finding which has to be confirmed in a large patient cohort. Disclosures Paschka: Pfizer: Membership on an entity's Board of Directors or advisory committees; Takeda: Other: Travel support; Novartis: Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Speakers Bureau; Otsuka: Membership on an entity's Board of Directors or advisory committees; Sunesis: Membership on an entity's Board of Directors or advisory committees; Jazz: Speakers Bureau; Amgen: Other: Travel support; Janssen: Other: Travel support; Bristol-Meyers Squibb: Other: Travel support, Speakers Bureau; Celgene: Membership on an entity's Board of Directors or advisory committees, Other: Travel support, Speakers Bureau; Astellas: Membership on an entity's Board of Directors or advisory committees, Travel support; Astex: Membership on an entity's Board of Directors or advisory committees; Agios: Membership on an entity's Board of Directors or advisory committees. Bullinger:Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Pfizer: Speakers Bureau; Bayer Oncology: Research Funding; Sanofi: Research Funding, Speakers Bureau; Janssen: Speakers Bureau; Bristol-Myers Squibb: Speakers Bureau; Amgen: Honoraria, Speakers Bureau; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Döhner:Novartis: Consultancy, Honoraria, Research Funding; Jazz: Consultancy, Honoraria; Jazz: Consultancy, Honoraria; AROG Pharmaceuticals: Research Funding; Janssen: Consultancy, Honoraria; Celator: Consultancy, Honoraria; Pfizer: Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Astex Pharmaceuticals: Consultancy, Honoraria; AROG Pharmaceuticals: Research Funding; Janssen: Consultancy, Honoraria; Seattle Genetics: Consultancy, Honoraria; Sunesis: Consultancy, Honoraria, Research Funding; Astellas: Consultancy, Honoraria; Astex Pharmaceuticals: Consultancy, Honoraria; Bristol Myers Squibb: Research Funding; Pfizer: Research Funding; Agios: Consultancy, Honoraria; Novartis: Consultancy, Honoraria, Research Funding; AbbVie: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Agios: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria; Celator: Consultancy, Honoraria; Astellas: Consultancy, Honoraria; Bristol Myers Squibb: Research Funding; Seattle Genetics: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Sunesis: Consultancy, Honoraria, Research Funding.

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STAG2 Mutations Alter Cohesin Ring Function and Provide Therapeutic Vulnerabilities in Acute Myeloid Leukemia

Blood ◽

10.1182/blood-2018-99-117480 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 940-940

Author(s):

Zuzana Tothova ◽

John M. Krill-Burger ◽

Daniel S. Day ◽

J. Erika Haydu ◽

Brian J. Abraham ◽

...

Keyword(s):

Dna Damage ◽

Board Of Directors ◽

Research Funding ◽

Dna Damage Repair ◽

Cohesin Complex ◽

Advisory Committees ◽

Damage Repair ◽

Equity Ownership ◽

Mutant Cells ◽

Splicing Machinery

Abstract Recurrent somatic mutations in core components and modulators of the cohesin ring - a multimeric protein complex that forms a ring structure around DNA and provides spatial genome organization - have been identified across multiple cancer types, including acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), where they are associated with poor overall survival. Cohesin proteins are involved in sister chromatid cohesion, chromatin organization into loops, transcriptional activation, and DNA damage repair. The mechanisms underlying clonal expansion of these driver mutations are unknown and no therapies have selective efficacy in cohesin-mutant cancers. We sought to determine the effects of mutations in the most frequently mutated cohesin subunit, STAG2, on cohesin complex composition using immunoprecipitation followed by quantitative mass spectrometry (IP-MS), genetic dependencies of STAG2-mutant cells by genome-wide CRISPR screening, and mutant cohesin association with chromatin using chromatin immunoprecipitation followed by sequencing (ChIP-Seq). Our goal was to understand how these mutations contribute to cellular transformation and to identify possible therapeutic targets. Applying IP-MS in AML cell lines engineered with different STAG2 mutations, we identified and validated a switch from STAG2- to its paralog STAG1-containing cohesin complexes. In addition, we observed changes in the interaction of the mutant cohesin complex with proteins involved in DNA repair and replication, including PARP1, and RNA-mediated interaction with RNA splicing machinery, including SF3B family members. We next hypothesized that these cohesin-dependent alterations could lead to shifts in genetic dependencies. Using genome-scale CRISPR-Cas9 screens, we identified preferential dependency of STAG2-mutant cells on STAG1, consistent with our proteomics studies. We also found a striking concordance between additional cellular processes highlighted by IP-MS experiments and observed increased dependency of STAG2-mutant cells on DNA damage repair and mRNA processing. Therefore, STAG2 mutations lead to changes in cohesin complex structure and alter interactions with proteins involved in DNA damage, replication, and RNA modification, which become genetic dependencies in this context. Prompted by this concordance, we evaluated DNA replication, DNA damage and splicing in cohesin-mutant cells. We observed a 4-fold increase in replication fork stalling in STAG2-mutant cells, which was associated with accumulation of double strand DNA breaks and activation of the ATR and ATM DNA damage checkpoints. STAG2-mutant cells demonstrated ~100-fold increased sensitivity to the PARP inhibitor talazoparib, which was consistent across models of other cohesin-mutant subunits. In addition, cohesin-mutant cells showed aberrant splicing and increased sensitivity to treatment with SF3B1 inhibitors E7107 and H3B-8800. In aggregate, genetic or pharmacologic perturbation of DNA damage repair or splicing created a synthetic vulnerability for cohesin-mutant cells in vitro and in vivo. Finally, we explored how STAG1-containing complexes alter cohesin-mediated genome compartmentalization in cohesin-mutant cells. Using ChIP-Seq, we observed that STAG2 loss leads to a global decrease in cohesin binding to chromatin, including at sites of insulated neighborhood boundaries, with subsequent gene expression changes. Loss of cohesin binding was associated with increased enhancer activity and super-enhancer expansion in STAG2-mutant cells. In addition, we identified changes in the co-localization of the mutant cohesin complex with super-enhancer enriched factors, DNA damage repair and splicing machinery. These findings are consistent with a model in which wild type and mutant cohesin complexes, defined by their unique composition and patterns of chromatin binding and architecture, have differential abilities to maintain chromatin organization as it relates to spatial organization of super-enhancers, coactivators and transcription factors, as well as DNA damage repair and splicing machinery. Perturbation of any of these components, which have been recently proposed to form phase-separated nuclear bodies, creates vulnerabilities that may be exploited therapeutically with existing drugs in patients with cohesin-mutated malignancies. Disclosures Abraham: Syros Pharmaceuticals: Equity Ownership. Seiler:H3 Biomedicine: Employment. Buonamici:H3 Biomedicine: Employment. D'Andrea:Intellia Therapeutics: Consultancy; Cedilla Therpeutics: Consultancy, Equity Ownership; EMD-Serono: Consultancy, Research Funding; Sierra: Consultancy, Research Funding; Ideaya: Consultancy, Equity Ownership; Lilly: Consultancy, Research Funding; Formation Biologics: Consultancy. Young:Omega Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Syros Pharmaceuticals: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Camp4 Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

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The Synergistic Effect of Melphalan and XPO1 Inhibition in Pre-Clinical Models of Multiple Myeloma

Blood ◽

10.1182/blood.v128.22.5662.5662 ◽

2016 ◽

Vol 128 (22) ◽

pp. 5662-5662 ◽

Cited By ~ 2

Author(s):

Yan Cui ◽

Joel G Turner ◽

Jana L Dawson ◽

Juan A Gomez ◽

Kenneth H. Shain ◽

...

Keyword(s):

Multiple Myeloma ◽

Dna Damage ◽

Western Blot ◽

Board Of Directors ◽

Cell Lines ◽

Research Funding ◽

Single Agent ◽

Newly Diagnosed ◽

Advisory Committees ◽

Genetics Research

Abstract Introduction:Multiple myeloma (MM) is an incurable cancer of plasma cells. It accounts for approximately 10% of all hematologic malignancies. In the US, it is estimated that there will be approximately 30,330 new cases and 12,650 deaths in 2016. In the past decade, responses/survivals have been significantly increased by newer therapies. However, almost all of the patients will eventually die from multi-drug resistant disease. Materials and Methods:Weused XPO1 inhibitors (XPO1i) selinexor (300nM) or KPT-8602 (300nM) +/- melphalan (15 μM) to treat human MM parental RPMI8226 and U266 cells, and melphalan resistant LR5 and LR6 cell lines for 20 hours and then assayed for apoptosis and viability by flow cytometry. DNA damage was assayed by the comet assay and phospho-H2AX protein expression in H929 human myeloma cells. p53, NFkB, IKKα, FANCF, and FANCL were assayed by Western blot in H929 MM cells. We also treated cells from patients with newly diagnosed or relapsed/refractory MM with the XPO1i (300nM)/ melphalan (10μM) combination and assayed for apoptosis. In addition, selinexor/melphalan treated NOD/SCID-gamma mice with U226 MM tumors were assayed for tumor growth, survival, and toxicity. Results:Cell viability of all tested MM cell lines was decreased synergistically and apoptosis increased by XPO1i/melphalan treatment (selinexor/melphalan, P = 2.2x10E-6 to 0.0032, KPT-8602/ melphalan, P = 1.2X10E-7 to 0.0031). Comet assays showed that the XPO1i/ melphalan drug combination increased DNA damage more than single agent melphalan or XPO1i alone. Phospho-H2AX expression also was increased (selinexor/ melphalan, P = 0.005 and KPT-8602/melphalan, P = 0.001). Western blot analysis showed that XPO1i treatment can increase p53 and decrease NFkB, IKKα, FANCF, and FANCL in MM cells. Apoptosis assays showed that both melphalan-resistant and parental MM cell lines were sensitized to melphalan by XPO1i. In addition, CD138+/light chain+ MM cells from newly diagnosed and relapsed/refractory MM patients were sensitized (20-fold and 5 to10-fold respectively) by XPO1i to melphalan. XPO1i/melphalan combination treatment demonstrated a strong synergistic anti-tumor effect when compared to single-agent melphalan (selinexor, P = 0.0024 and KPT-8602, P = 0.0030) in NOD/SCID-gamma mice challenged with U266 MM tumors. XPO1i/ melphalan treated mice had increased survival and no significant toxicity. Conclusions:XPO1i's can improve the response of human MM cell lines and patient MM cells to melphalan both in vitro and ex vivo. The mechanism of this synergy reversing melphalan resistance may be due to increased nuclear p53, in combination with decreased NFkB and IKKα, and decreased DNA repair proteins FANCL and FANCF of the Fanconi Anemia/BRCA pathway. Our preliminary data suggest that the synergistic cell kill may be because XPO1i's increase melphalan-induced DNA damage and block the repair of the DNA damage. Thus using combination therapies of XPO1i, especially the clinical compounds selinexor and KPT-8602 +/- melphalan may have potential to improve the treatment outcomes of MM. Based on these promising pre-clinical data, we designed a phase 1/2 clinical trial evaluating the combination of selinexor and high-dose melphalan as a conditioning regimen for autologous hematopoietic cell transplantation in patients with multiple myeloma (NCT02780609). Disclosures Shain: Novartis: Speakers Bureau; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Signal Genetics: Research Funding; Takeda/Millennium: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Amgen/Onyx: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Baloglu:Karyopharm Therapeutics Inc: Employment, Other: stockholder. Nishihori:Signal Genetics: Research Funding; Novartis: Research Funding.

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A Phase 3 Randomized Study (PRIMULA) of the Epigenetic Combination of Pracinostat, a Pan-Histone Deacetylase (HDAC) Inhibitor, with Azacitidine (AZA) in Patients with Newly Diagnosed Acute Myeloid Leukemia (AML) Unfit for Standard Intensive Chemotherapy (IC)

Blood ◽

10.1182/blood-2019-125924 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 2652-2652

Author(s):

Guillermo Garcia-Manero ◽

Maciej Kaźmierczak ◽

Chun Yew Fong ◽

Pau Montesinos ◽

Adriano Venditti ◽

...

Keyword(s):

Overall Survival ◽

Board Of Directors ◽

Research Funding ◽

Hdac Inhibitors ◽

Newly Diagnosed ◽

Research Support ◽

Phase 3 ◽

Advisory Committees ◽

To Receive ◽

Support Research

Background: AML is associated with poor survival rates in patients ineligible for IC or stem cell transplant due to advanced age, comorbidities, and/or disease and patient-specific risk factors. Non-intensive therapies, including the hypomethylating agent (HMA) AZA, have historically been used in this setting; however, response rates and survival remain dismal. Pre-clinical studies in myeloid malignancies indicate that the epigenetic combination of HMAs and HDAC inhibitors induce re-expression of silenced genes in a synergistic fashion. Pracinostat, an oral pan-HDAC (class I, II, and IV isoforms) inhibitor, has shown superior pharmacokinetic and pharmacodynamic properties compared with other HDAC inhibitors. The activity of pracinostat has been shown in xenograft tumor models of AML and synergistic interactions have been observed with multiple cytotoxic and targeted anti-cancer therapeutics, including AZA. In a Phase 2 study in AML patients ≥65 years not eligible for IC, the epigenetic combination of pracinostat and AZA showed promising efficacy (Garcia Manero, Blood 2016) with a 64% overall response rate and 19.1 months median overall survival. Favorable responses were also seen in patients with high risk molecular features and adverse prognostic factors. The safety profile of pracinostat/AZA is comparable to each administered as monotherapy, with no significant added toxicity. Study Design and Methods: The Phase 3, multicenter, double-blind, randomized PRIMULA study (NCT03151408) evaluates the efficacy and safety of pracinostat administered with AZA in adult patients with newly diagnosed AML who are ineligible to receive IC based on either 1) age ≥75 years or 2) age <75 years plus a protocol-defined comorbidity. A total of 500 patients (randomized 1:1 to either pracinostat/AZA or placebo/AZA) are planned to be enrolled at ~140 study centers worldwide. Randomization is stratified by cytogenetic risk (intermediate vs. unfavorable-risk) and ECOG Performance Status (0-1 vs. 2). Treatments are administered as 28-day cycles, with pracinostat given orally as a 60 mg capsule QD, 3x/week for 3 weeks followed by one week off, and AZA administered for 7 days of each cycle. Patients are to receive a minimum of 6 cycles as long as there is no evidence of disease progression or non-manageable toxicity. The primary endpoint is overall survival; secondary efficacy endpoints include morphologic and cytogenetic complete remission (CR) rates, CR without minimal residual disease and transfusion independence ≥8 weeks. Safety is assessed primarily through treatment-emergent adverse events. Overall survival will be tested for superiority of pracinostat/AZA over placebo/AZA using the stratified log-rank test at the alpha = 0.025 level of significance (one-sided). One interim analysis is planned when 260 events (i.e., deaths due to any cause) have occurred. Enrollment is open and as of July 8, 2019 257 patients have been randomized. Disclosures Garcia-Manero: Amphivena: Consultancy, Research Funding; Helsinn: Research Funding; Novartis: Research Funding; AbbVie: Research Funding; Celgene: Consultancy, Research Funding; Astex: Consultancy, Research Funding; Onconova: Research Funding; H3 Biomedicine: Research Funding; Merck: Research Funding. Fong:Amgen: Consultancy, Research Funding, Speakers Bureau; Astellas: Consultancy; Pfizer: Consultancy, Speakers Bureau; Novartis: Speakers Bureau. Montesinos:Pfizer: Membership on an entity's Board of Directors or advisory committees, Other: Research support, Research Funding, Speakers Bureau; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: Research support, Speakers Bureau; Incyte: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Teva: Membership on an entity's Board of Directors or advisory committees, Other: Research support, Research Funding, Speakers Bureau; Novartis: Membership on an entity's Board of Directors or advisory committees, Other: Research support, Research Funding, Speakers Bureau; Karyopharm: Membership on an entity's Board of Directors or advisory committees, Other: Research support; Janssen: Membership on an entity's Board of Directors or advisory committees, Other: Research support, Research Funding, Speakers Bureau; Daiichi Sankyo: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: Research support, Speakers Bureau; Abbvie: Membership on an entity's Board of Directors or advisory committees. Venditti:Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Abbvie: Consultancy; Astellas: Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees. Mappa:Helsinn Healthcare SA: Employment; Helsinn Healthcare SA: Patents & Royalties. Spezia:Helsinn Healthcare: Employment. Ades:Helsinn Healthcare: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Silence Therapeutics: Membership on an entity's Board of Directors or advisory committees; Agios: Membership on an entity's Board of Directors or advisory committees; Jazz: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Amgen: Research Funding. OffLabel Disclosure: Pracinostat is an HDAC inhibitor not yet approved by the FDA

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Predicting Response to Dasatinib Using a Computational Model and Its Validation: A Beat AML Project Study

Blood ◽

10.1182/blood-2018-99-115678 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 1541-1541

Author(s):

Jeffrey W. Tyner ◽

Brian J. Druker ◽

Cristina E. Tognon ◽

Stephen E Kurtz ◽

Leylah M. Drusbosky ◽

...

Keyword(s):

Bone Marrow ◽

Computational Biology ◽

Board Of Directors ◽

Research Funding ◽

Drug Response ◽

Drug Sensitivity ◽

Ex Vivo ◽

Patient Specific ◽

Advisory Committees ◽

Equity Ownership

Abstract Background: New prognostic factors have been recently identified in AML patient population that include frequent mutations of receptor tyrosine kinases (RTK) including KIT, PDGFR, FLT3, that are associated with higher risk of relapse. Thus, targeting RTKs could improve the therapeutic outcome in AML patients. Aim: To create a digital drug model for dasatinib and validate the predicted response in AML patient samples with ex vivo drug sensitivity testing. Methods: The Beat AML project (supported by the Leukemia & Lymphoma Society) collects clinical data and bone marrow specimens from AML patients. Bone marrow samples are analyzed by conventional cytogenetics, whole-exome sequencing, RNA-seq, and an ex vivo drug sensitivity assay. For 50 randomly chosen patients, every available genomic abnormality was inputted into a computational biology program (Cell Works Group Inc.) that uses PubMed and other online resources to generate patient-specific protein network maps of activated and inactivated pathways. Digital drug simulations with dasatinib were conducted by quantitatively measuring drug effect on a composite AML disease inhibition score (DIS) (i.e., cell proliferation, viability, and apoptosis). Drug response was determined based on a DIS threshold reduction of > 65%. Computational predictions of drug response were compared to dasatinib IC50 values from the Beat AML ex vivo testing. Results: 23/50 (46%) AML patients had somatic mutations in an RTK gene (KIT, PDGFR, FLT3 (ITD (n=15) & TKD (n=4)), while 27/50 (54%) were wild type (WT) for the RTK genes. Dasatinib showed ex vivo cytotoxicity in 9/50 (18%) AML patients and was predicted by CBM to remit AML in 9/50 AML patients with 4 true responders and 5 false positive. Ex vivo dasatinib responses were correctly matched to the CBM prediction in 40/50 (80%) of patients (Table1), with 10 mismatches due to lack of sufficient genomic information resulting in profile creation issues and absence of sensitive loops in the profile. Only 4/23 (17%) RTK-mutant patients and 5/27(19%) RTK-WT patients were sensitive to dasatinib ex vivo, indicating that presence of somatic RTK gene mutations may not be essential for leukemia regression in response to dasatinib. Co-occurrence of mutations in NRAS, KRAS and NF1 seemed to associate with resistance as seen in 10 of the 14 profiles harboring these mutations. Conclusion: Computational biology modeling can be used to simulate dasatinib drug response in AML with high accuracy to ex vivo chemosensitivity. DNA mutations in RTK genes may not be required for dasatinib response in AML. Co-occurrence of NRAS, KRAS and NF1gene mutations may be important co-factors in modulating response to dasatinib. Disclosures Tyner: Leap Oncology: Equity Ownership; Syros: Research Funding; Seattle Genetics: Research Funding; Janssen: Research Funding; Incyte: Research Funding; Gilead: Research Funding; Genentech: Research Funding; AstraZeneca: Research Funding; Aptose: Research Funding; Takeda: Research Funding; Agios: Research Funding. Druker:Third Coast Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novartis Pharmaceuticals: Research Funding; Millipore: Patents & Royalties; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Oregon Health & Science University: Patents & Royalties; McGraw Hill: Patents & Royalties; Celgene: Consultancy; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; GRAIL: Consultancy, Membership on an entity's Board of Directors or advisory committees; Bristol-Meyers Squibb: Research Funding; Amgen: Membership on an entity's Board of Directors or advisory committees; Aptose Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Henry Stewart Talks: Patents & Royalties; Patient True Talk: Consultancy; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; ARIAD: Research Funding; Fred Hutchinson Cancer Research Center: Research Funding; Beta Cat: Membership on an entity's Board of Directors or advisory committees; Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; ALLCRON: Consultancy, Membership on an entity's Board of Directors or advisory committees; Aileron Therapeutics: Consultancy; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Monojul: Consultancy. Sahu:Cellworks Research India Private Limited: Employment. Vidva:Cellworks Research India Private Limited: Employment. Kapoor:Cellworks Research India Private Limited: Employment. Azam:Cellworks Research India Private Limited: Employment. Kumar:Cellworks Research India Private Limited: Employment. Chickdipatti:Cellworks Research India Private Limited: Employment. Raveendaran:Cellworks Research India Private Limited: Employment. Gopi:Cellworks Research India Private Limited: Employment. Abbasi:Cell Works Group Inc.: Employment. Vali:Cell Works Group Inc.: Employment. Cogle:Celgene: Other: Steering Committee Member of Connect MDS/AML Registry.

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Salicylates Potentiate and Broaden CRM1 Inhibitor Anti-Tumor Activity Via S-Phase Arrest and Impaired DNA-Damage Repair

Blood ◽

10.1182/blood-2020-138619 ◽

2020 ◽

Vol 136 (Supplement 1) ◽

pp. 17-18

Author(s):

Jithma P. Abeykoon ◽

Xiaosheng Wu ◽

Kevin E. Nowakowski ◽

Surendra Dasari ◽

Jonas Paludo ◽

...

Keyword(s):

Dna Damage ◽

Research Funding ◽

Antitumor Effect ◽

Cell Lymphoma ◽

Ex Vivo ◽

Dna Damage Repair ◽

Hematologic Malignancies ◽

Damage Repair ◽

Cellular Pathways

Chromosome region maintenance protein1 (CRM1) mediates protein export from the nucleus and is a new target for anti-cancer therapeutics. Broader application of KPT-330 (selinexor), a first in class CRM1 inhibitor recently approved for multiple myeloma and diffuse large B-cell lymphoma (DLBCL), has been limited by substantial adverse effects (AEs). To address this clinical problem, we focused on identifying novel strategies to boost the potency, reduce toxicity, and broaden the applicability of CRM1 inhibitors to a wider range of malignancies. We discovered that salicylates could markedly enhance the anti-tumor activity of CRM1 inhibitors by extending the mechanisms of action beyond CRM1 inhibition. KPT-330 was chosen as the prototypical CRM1 inhibitor given its current FDA approval status and characterized pharmacokinetics; and choline salicylate (CS) was chosen as the prototypical salicylate given its favorable pharmacokinetics and reduced antiplatelet, renal, neurological and gastrointestinal AEs in humans compared to other salicylates. By using cell lines belonging to different hematologic malignancies and solid tumors, we demonstrated ex vivo that the combination of KPT-330 and CS (K+CS) could induce unique and significant antitumor effect at much lower dose of KPT-330 (at 25% of the dose used in the clinic), thereby potentially mitigating prohibitive clinical AEs (Figure 1a-d, and e-g). This significant synergetic antitumor effect observed with K+CS ex vivo was also validated in vivo by using an NSG mouse model of mantle cell lymphoma (Figure 1h). Moreover, the K+CS combination did not show this potent toxic effect on non-malignant cells in vivo and was safe without inducing toxicity to normal organs in NSG mice. Mechanistically, protein profiling through mass spectroscopy revealed that K+CS uniquely affects the cellular pathways of DNA damage repair, DNA synthesis and cell cycle progression. Studies involving immunoblotting, cell cycle analysis, immunofluorescence microscopy assessing nucleocytoplasmic molecular export and DNA damage, reporter assay to assess homologous recombination repair proficiency and immunohistochemistry showed that, compared to KPT-330 treatment alone, K+CS decreased the expression of CRM1, Rad51 and thymidylate synthase proteins in vitro and in vivo, leading to more efficient inhibition of CRM1-mediated nuclear export, impairment of DNA-damage repair, reduced pyrimidine synthesis, and importantly a unique cell cycle arrest in S-phase, thus leading to cell apoptosis. These effects on cellular proteins and pathways were unique to K+CS treatment and were not observed with KPT-330 or CS single agent treatment. Pathway analyses through RNA sequencing also paralleled the findings of proteomic studies thus further validating the unique effect of K+CS treatment on the aforementioned cellular pathways. Importantly, K+CS treatment exerted unique and significant antitumor effect ex vivo on primary malignant cells obtained from patient's with high-risk hematologic malignancies such as double hit DLBCL, BTK and BCL2 inhibitor resistant mantle cell lymphoma, TP53 deleted/mutated chronic lymphocytic leukemia and high-risk multiple myeloma thus signifying its broader applicability as a treatment option for these aggressive hematologic malignancies where there is a dire need to find new treatment strategies (Figure 1i). In summary, we describe a unique all-oral drug combination with a novel constellation of mechanisms of action on cellular pathways that are exploited by cancer cells. K+CS represents a new class of therapy for multiple cancer types and will stimulate future investigations to exploit DNA-damage repair and nucleocytoplasmic transport for therapy of blood cancers. Disclosures Witzig: Karyopharm Therapeutics: Research Funding; Acerta: Research Funding; Incyte: Consultancy; AbbVie: Consultancy; Celgene: Consultancy, Research Funding; MorphSys: Consultancy; Immune Design: Research Funding; Spectrum: Consultancy.

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Distinct Senescent Bone Marrow Microenvironment in Therapy-Related Myeloid Neoplasms

Blood ◽

10.1182/blood-2021-148215 ◽

2021 ◽

Vol 138 (Supplement 1) ◽

pp. 2585-2585

Author(s):

Monika M Kutyna ◽

Chung Hoow Kok ◽

Sharon Paton ◽

Dimitrios Cakouros ◽

Agnieszka Arthur ◽

...

Keyword(s):

Dna Damage ◽

Board Of Directors ◽

Transcriptome Analysis ◽

Research Funding ◽

Differentially Expressed ◽

Advisory Committees ◽

Irreversible Damage ◽

Myeloid Neoplasms ◽

Damage Repair

Abstract Background: Therapy-related myeloid neoplasms (tMN) is a second haematological malignancy associated with distinct molecular profile (Singhal et al Leukemia 2019) and dismal outcome. tMN is believed to arise from cytotoxic DNA damage to haematopoietic stem cells (HSC). Although, cytotoxic therapy (CT) can damage bone marrow (BM) microenvironment, its role in tMN pathogenesis remains unknown. Aim and Methods: We performed comprehensive multiomic profiling (transcriptomic, cytokine quantification, phenotype, DNA damage) of BM stromal cells (BMSC) from (i) tMN patients previously exposed to CT. Critically, we compared it with (ii) patients with MN and a history of another cancer without CT (pMN+Ca), (iii) primary MN (pMN) and (iv) age-matched controls (Healthy). Results: To decipher microenvironmental changes induced by CT from that of MN and age-related changes, whole transcriptome analysis was performed on BMSC isolated from tMN and compared with all control cohorts. Twenty-nine genes were differentially expressed in tMN compared to Healthy (FDR < 0.1, P < 0.05). Unexpectedly 146 genes were differentially expressed in tMN BMSC compared to other MN and interestingly, ~90% of differentially expressed genes were involved in senescence. Moreover, functional enrichment and GO analysis suggest DNA damage repair, cell cycle regulation, and senescence pathways were deregulated in tMN BMSC (Fig. 1A). Genes such as CDKN1A (a critical cyclin dependent kinase inhibitor orchestrating cell cycle arrest), TNFRSF10D (senescence associated), and FGF-2 (a key player in cell proliferation) were highly expressed (P < 0.001). These findings were validated by demonstrating other features of senescence in tMN BMSC: (i) enlarged/flattened cellular morphology, (ii) decreased cell proliferation and colony-forming potential, (iii) increased β-galactosidase expression, and (iv) defective DNA damage repair (Fig. 1Bi-iv). Interestingly, within the tMN cohort there was no correlation between latency period (the interval between completion of CT until tMN diagnosis) and senescence, indicating that higher senescence is persistent even after several years of CT. Senescence associated secretory phenotype (SASP), a mixture of inflammatory cytokines and chemokines such as IL-7, IL-1β, IL-13, and IL-6, were significantly higher in conditioned media of tMN BMSC (9/14, 64%) (Fig. 1 Bv). Despite reduced proliferation and senescence, transcriptome analysis showed enrichment of metabolic and energy production pathways in tMN BMSC compared to controls. TXNRD1, regulator of glucose and lipid metabolism, and BNIP3, a negative regulator of mitochondrial potential, were highly expressed in tMN BMSC (P < 0.001). These findings were further verified by Seahorse bioenergetic analyses. The overall energetic rate (as assessed by ATP production) was higher in tMN compared to Healthy BMSC (P = 0.002), with higher proportion of ATP generated by glycolysis (77% versus 35.5%) (Fig. 1C). Adipogenic differentiation potential of senescent BMSC is not well known. Transcriptome analysis showed reduced expression of genes involved in adipogenesis in tMN BMSC. This was further validated by two independent in vitro assays showing reduced adipogenesis (Fig. 1D). Interestingly, PNPLA2, a catalyst of the first lipolysis reaction, were significantly de-regulated in tMN BMSC (P < 0.001). The key difference in tMN and other MN is prior exposure to CT. Hence, we hypothesise that prior CT leads to long-term irreversible damage to BM microenvironment and induced senescence, which in turn propagate senescence in surrounding normal cells and promote clonal abnormalities in HSC. Other possibility is that tMN clone can induce these changes in BM microenvironment. To decipher it, we assessed serial BMSC. We observed aberrant stroma proliferation and bi-differentiation capacity, following CT, well before the diagnosis of tMN. Conclusions: By multiple orthogonal indices, our results show that tMN BMSC lie on an extreme trajectory away from normal and typical MN, with massive defect in senescence and distinct metabolic phenotype. Importantly, prior CT leads to long-term irreversible damage to the BM microenvironment which potentially contributes to tMN pathogenesis. Together, these data provide a valuable resource for future strategies to delay or prevent the onset of tMN and assist in marrow regeneration in patients undergoing CT. Figure 1 Figure 1. Disclosures Hughes: BMS: Research Funding; Novartis: Honoraria, Research Funding; Takeda: Honoraria. Hiwase: Novartis: Membership on an entity's Board of Directors or advisory committees; AbbVie: Membership on an entity's Board of Directors or advisory committees.

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