Abstract: The CC-chemokine eotaxin is a potent eosinophil chemoattractant that stimulates recruitment of eosinophils from the blood to sites of allergic inflammation. Mobilization from the bone marrow is an important early step in eosinophil trafficking during the allergic inflammatory response. In this paper we examine the potential of eotaxin to mobilize eosinophils and their progenitors from bone marrow. Eotaxin stimulated selective, dose-dependent chemotaxis of guinea pig bone marrow eosinophils in vitro. Intravenous injection of eotaxin (1 nmol/kg) into guinea pigs in vivo stimulated a rapid blood eosinophilia (from 3.9 ± 1.2 to 28 ± 9.9 × 104eosinophils/mL at 30 minutes) and a corresponding decrease in the number of eosinophils retained in the femoral marrow (from 9.0 ± 0.8 to 4.8 ± 0.8 × 106 eosinophils per femur). To show a direct release of eosinophils from the bone marrow an in situ perfusion system of the guinea pig femoral bone marrow was developed. Infusion of eotaxin into the arterial supply of the perfused femoral marrow stimulated a rapid and selective release of eosinophils into the draining vein. In addition, eotaxin stimulated the release of colony-forming progenitor cells. The cytokine interleukin-5 was chemokinetic for bone marrow eosinophils and exhibited a marked synergism with eotaxin with respect to mobilization of mature eosinophils from the femoral marrow. Thus, eotaxin may be involved in both the mobilization of eosinophils and their progenitors from the bone marrow into the blood and in their subsequent recruitment into sites of allergic inflammation.

Abstract: The CC-chemokine eotaxin is a potent eosinophil chemoattractant that stimulates recruitment of eosinophils from the blood to sites of allergic inflammation. Mobilization from the bone marrow is an important early step in eosinophil trafficking during the allergic inflammatory response. In this paper we examine the potential of eotaxin to mobilize eosinophils and their progenitors from bone marrow. Eotaxin stimulated selective, dose-dependent chemotaxis of guinea pig bone marrow eosinophils in vitro. Intravenous injection of eotaxin (1 nmol/kg) into guinea pigs in vivo stimulated a rapid blood eosinophilia (from 3.9 ± 1.2 to 28 ± 9.9 × 104eosinophils/mL at 30 minutes) and a corresponding decrease in the number of eosinophils retained in the femoral marrow (from 9.0 ± 0.8 to 4.8 ± 0.8 × 106 eosinophils per femur). To show a direct release of eosinophils from the bone marrow an in situ perfusion system of the guinea pig femoral bone marrow was developed. Infusion of eotaxin into the arterial supply of the perfused femoral marrow stimulated a rapid and selective release of eosinophils into the draining vein. In addition, eotaxin stimulated the release of colony-forming progenitor cells. The cytokine interleukin-5 was chemokinetic for bone marrow eosinophils and exhibited a marked synergism with eotaxin with respect to mobilization of mature eosinophils from the femoral marrow. Thus, eotaxin may be involved in both the mobilization of eosinophils and their progenitors from the bone marrow into the blood and in their subsequent recruitment into sites of allergic inflammation.

Abstract: Background. Acute Myeloid Leukemia (AML) is genetically and epigenetically heterogeneous. Most AML samples display clonal heterogeneity at presentation, which evolves with therapeutic interventions. To better understand the epigenetic consequences of clonal heterogeneity, we are using single-cell RNA-sequencing (scRNA-seq) to characterize expression heterogeneity in AML. To date, scRNA-seq has had limited utility in applications where it is essential to link transcriptional heterogeneity to genetic variation, because it has been difficult to identify specific mutations in individual cells using scRNA-seq data alone. To address this limitation, we developed an approach to use scRNA-seq data to identify expressed mutations in individual AML cells, and link these variants to the expression heterogeneity in the same samples. Methods. We generated duplicate cDNA libraries for each of 5 cryopreserved bone marrow samples from adult patients with de novo AML, using the 10x Genomics Chromium Single Cell 5' Gene Expression workflow for Single Cell RNA Sequencing. Single cell libraries were sequenced to yield a median of 20,474 cells per sample, and 192,427 reads per cell. Transcript alignment, counting, and inter-library normalization were performed using the Cell Ranger pipeline (10x Genomics). The Seurat R package was used for further normalization, filtering, principal component analysis, clustering, and t-SNE visualization. A nearest-neighbor algorithm was developed to assign each cell in the data set to the most transcriptionally similar hematopoietic lineage. For each case, we performed whole genome sequencing (WGS) to identify germline and somatic variants, and define clonal architecture. We then developed bioinformatic methods to determine which cells harbor these mutations, assign those cells to mutationally-defined subclones, and link mutations to defined expression clusters. Results. WGS identified 25-56 coding mutations per sample; we were able to identify 22%-46% of these mutations in at least one cell in the scRNA-seq data, including point mutations (e.g. DNMT3A, U2AF1, TP53, IDH1, IDH2, SRSF2, CEBPA, and others) and indels (e.g. FLT3-ITD, NPMc). Although the libraries were 5' biased, expressed mutations could be identified at long distances from the 5' end of transcripts; for example, an expressed DNMT3AR882H mutation (2.646 Kb from the initiating codon) was easily detected (Fig 1c). The frequency of detected mutations in the single-cell data varied widely (range: 1-1564 cells; median: 11 cells), and as expected, depended heavily on the expression level of the gene, and the size of the clone containing the mutation. Regardless, a median of 1378 cells (6.7%) had at least one identifiable mutation in the 5 samples. Using these data, we were able to 1) distinguish AML cells from normal cells in bone marrow samples (Fig 1a/b), 2) identify major subclones within the AML samples (Fig 1c/d), and 3) identify mutation-specific and subclone-specific expression profiles. In 2 samples with mutationally-defined subclones (one with a CEBPAR142fs mutation, and the other with a GATA2R361C mutation), subclone-specific gene expression profiles were clearly detected in the scRNA-seq data, and could be directly associated with cells containing the mutant transcription factors. In the case with the subclonal GATA2R361C mutation, cells with that mutation were restricted to a subset of expression clusters (Fig 1d). In this subset, we identified an expression signature that is supported by pre-existing knowledge of the GATA2/SPI1 transcriptional regulatory circuit. In addition, we observed that expression heterogeneity frequently occurs independent of mutations defined by specific subclones. For instance, the GATA2R361C subclone contained additional heterogeneity (5 independent expression clusters) that could not be accounted for by mutations (Fig 1a/d). Moreover, the other 3 cases exhibited extensive expression heterogeneity within the AML cells that was not explained by genetically defined subclones. In sum, scRNA-seq data, when adapted to detect mutations, has dramatically improved our understanding of the expression heterogeneity of AML, which arises from two main sources: 1) cell-type composition of the sample, and 2) expression variation among the AML cells themselves (caused by both mutation-associated and mutation-independent factors). Disclosures Williams: 10x Genomics: Employment, Equity Ownership. Fiddes:10x Genomics: Employment, Equity Ownership. Church:10x Genomics: Employment, Equity Ownership.

Abstract: We conducted a genome-wide association study to identify novel associations between genetic variants and circulating plasminogen activator inhibitor-1 (PAI-1) concentration, and examined functional implications of variants and genes that were discovered. A discovery meta-analysis was performed in 19 599 subjects, followed by replication analysis of genome-wide significant (P 〈 5 × 10−8) single nucleotide polymorphisms (SNPs) in 10 796 independent samples. We further examined associations with type 2 diabetes and coronary artery disease, assessed the functional significance of the SNPs for gene expression in human tissues, and conducted RNA-silencing experiments for one novel association. We confirmed the association of the 4G/5G proxy SNP rs2227631 in the promoter region of SERPINE1 (7q22.1) and discovered genome-wide significant associations at 3 additional loci: chromosome 7q22.1 close to SERPINE1 (rs6976053, discovery P = 3.4 × 10−10); chromosome 11p15.2 within ARNTL (rs6486122, discovery P = 3.0 × 10−8); and chromosome 3p25.2 within PPARG (rs11128603, discovery P = 2.9 × 10−8). Replication was achieved for the 7q22.1 and 11p15.2 loci. There was nominal association with type 2 diabetes and coronary artery disease at ARNTL (P 〈 .05). Functional studies identified MUC3 as a candidate gene for the second association signal on 7q22.1. In summary, SNPs in SERPINE1 and ARNTL and an SNP associated with the expression of MUC3 were robustly associated with circulating levels of PAI-1.

Abstract: IBR+VEN combination was designed to overcome resistance to IBR, but CLL and MCL samples ex vivo show resistance even to this combination. Microenvironmental agonists (IL-10, soluble CD40L, CpG-ODN) generate resistance via NF-κB–dependent expression of Mcl-1/Bcl-xL/survivin.

Abstract: Ibrutinib (IBR), an inhibitor of Bruton's Tyrosine Kinase (BTK), has been FDA approved for Chronic Lymphocytic Leukemia (CLL) and Mantle Cell Lymphoma (MCL). However, IBR responses are incomplete in most cases, and of short duration for MCL and higher-risk CLL subtypes. We hypothesize that intrinsic resistance, incomplete responses, and rapid recurrence can be due to adaptive signaling that should be co-targeted with BTK inhibition to achieve deeper and more durable responses. We previously showed that venetoclax (VEN), an inhibitor of Bcl-2, generated synergistic cytotoxicity with IBR in MCL lines as well as circulating leukemic B cells in 13/19 CLL and 4/5 MCL patient samples treated ex vivo (Jayappa KD et al. ASH 2015; Portell CA et al. ASH 2014). However, the sensitivity to VEN or IBR+VEN was highly variable among patient samples, and did not correlate with the diagnostic genetic lesions in the CLL/MCL cells or clinical characteristics of the patients. Here, we show that resistance to IBR+VEN can be induced by interaction with soluble factors found in the in vivo "macroenvironment" of the circulating cancer cells. To gain insight into changes in signaling pathways that might underlie mechanisms of drug synergy and resistance, we analyzed drug resistant MCL lines treated with IBR, VEN, and the combination by Reverse Phase Protein Arrays. We observed downregulation of PI3K-Akt, MAPK, JAK-STAT, and NOTCH signaling after IBR and IBR+VEN treatment, cleavage of caspases and PARP after VEN-treatment, and greatly enhanced cleavage of caspases and PARP after IBR+VEN treatment. A notable exception was significantly increased phosphorylation on p65 S536 of the NF-kB pathway at longer times after IBR+VEN treatment, indicating a possible role of NF-kB signalling in generating resistance to IBR and VEN in cells that survived treatment. To determine whether extrinsic factors in the cancer cell environment might be able to induce a drug-resistant phenotype, we co-cultured or pre-incubated PBMC with a diverse panel of stromal cells, cytokines, and other agonists. We found that the combination of soluble CD40L, IL-10, and CpG DNA (agonist mix) generated nearly complete resistance to IBR+VEN in CLL and MCL patient samples, with CpG DNA being the most effective single agent. Every sample treated with agonist mix displayed increased resistance to IBR+VEN drug combination, suggesting that responsiveness transcends genetic heterogeneity and reflects the developmental lineage of the cancer cells. We investigated whether the extrinsic agonists induce drug resistance by activating the NF-κB pathway, by analyzing nuclear localization of NF-kB transcription factors RelA and RelB using ImageStream and cell fractionation. We observed robust activation of alternative-NF-kB signaling in primary CLL and MCL cells treated with agonist mix, with little effect on canonical NF-κB. PKC, MAPK and PI3K-Akt signaling also showed evidence of activation by agonist mix. Agonist mix treatment also caused significant overexpression of anti-apoptotic proteins Mcl-1, Bcl-xL, and survivin, but not Bcl-2. Inhibitors of NF-κB blocked RelB translocation and overexpression of Mcl-1, Bcl-xL and survivin. Inhibitors of NF-kB or of upregulated anti-apoptotic proteins overcame drug resistance induced by agonist mix. Inhibitors of the other activated pathways (MAPK, PI3K-Akt, PKC) did not block agonist-induced drug resistance at pharmacologically relevant concentrations. To determine whether extra-nodal agonists in the blood of patients could generate resistance to IBR and VEN, we analyzed drug cytotoxicity in CLL patient PBMCs cultured with autologous plasma. We found that autologous plasma was able to induce increased resistance to IBR+VEN in 3/7 CLL samples and this resistance was blocked by treatment with an NF-kB inhibitor. In conclusion, soluble agonists in the patient macroenvironment of circulating CLL/MCL cells can generate resistance to IBR+VEN by activating alternative-NF-kB signaling and over-expression of multiple anti-apoptotic proteins. Inhibitors of NF-kB or of the upregulated anti-apoptotic proteins overcame IBR+VEN resistance generated by these extrinsic factors. We suggest that survival signals generated by extra-nodal agonists in the patient macroenvironment generate drug resistance in CLL and MCL, and that improved responses could occur with interventions that block these survival signals. Disclosures Portell: AbbVie: Research Funding; Roche/Genentech: Research Funding; Infinity: Research Funding; Acerta: Research Funding. Wulfkuhle:Theranostics Health, LLC: Equity Ownership. Petricoin:Perthera, Inc.: Consultancy, Equity Ownership; Ceres Nanosciences, Inc.: Consultancy, Equity Ownership, Patents & Royalties; Avant Diagnostics, Inc.: Equity Ownership. Williams:University of Virginia: Employment; Janssen and Pharmacyclics: Research Funding.

Abstract: Responses to single-agent ibrutinib (IBR) or venetoclax (VEN) in Chronic Lymphocytic Leukemia (CLL) or Mantle Cell Lymphoma (MCL) are often incomplete suggesting drug combinations are needed to overcome de novo and acquired resistance. We previously reported synergistic cytotoxicity for the IBR+VEN combination in CLL/MCL cells ex vivo and have initiated an IBR+VEN clinical trial in MCL (NCT02419560). However, ex vivo analysis of patient samples showed de novo resistance even to the IBR+VEN combination in some samples, consistent with recent clinical experience (Tam et al. N Engl J Med, 2018). We noted that sensitivity to IBR+VEN was lower in CLL cells showing an "activation" phenotype (CD5+/19+/69+) that can be induced by extracellular factors in vivo, suggesting that the microenvironment could induce drug tolerance in the cancer cells.This was supported by our finding that ex vivo exposure of CLL/MCL samples to a mixture of microenvironmental agonists (CpG-ODN, sCD40L, and IL10; "agonist mix") induced significant loss of sensitivity to IBR+VEN (Jayappa et al. Blood Adv., 2017). Here we show that various microenvironmental agonists, including of innate immunity, are able to reduce sensitivity to IBR+VEN as well as other pro-apoptotic drugs, generating a multi-drug tolerant phenotype. To explore drug tolerance, we performed flow cytometric analysis of apoptosis induced by IBR+VEN in CD5+/19+cancer cells in CLL/MCL PBMCs cultured with agonists of TLRs, NOD1/2, CD40, and IL10R and various stromal cells. Tolerance to IBR+VEN as determined by resistance to apoptosis was noted in most samples cultured with TLR9 agonist CpG-ODN, sCD40L, or Jurkat cells expressing CD40L. IL10 and HUVEC induced modest levels of drug tolerance in a few CLL/MCL samples, and TLR1/2, TLR7, and NOD1/2 agonists were effective only in MCL samples. Prior exposure to CpG-ODN enhanced the ability of sCD40L to induce proliferation and drug tolerance and vice versa in CLL/MCL, predicting mutually reinforcing interactions in vivo. We noted that CLL cells exposed to CpG-ODN displayed higher levels of CD40 and downstream signaling proteins (TRAF2, RelB, and p100/52). Conversely, CD40L induced a modest increase in NF-kB transcription factors, providing a possible mechanism for mutual reinforcement. Using flow cytometric analysis of apoptosis, we noted tolerance to several pro-apoptotic agents (bendamustine, fludarabine, and inhibitors of Mcl-1, Bcl-xL, Bcl-2, and Bcl-2/Bcl-xL) including IBR+VEN in CD5+/19+cells from CLL samples treated with agonist mix, showing development of multi-drug tolerance in these cells. CpG-ODN or agonist mix induced NFkB-dependent over-expression of pro-survival proteins (Mcl-1 and Bcl-xL), and increased ratio of these to cognate pro-apoptotic proteins. This increased expression of pro-survival proteins underlies the multi-drug tolerant phenotype. Consistently, multi-drug tolerance was rescued with inhibitors of NFkB (BMS345541 or Bortezomib) or drug combinations simultaneously inhibiting multiple anti-apoptotic proteins (inhibition of Mcl-1 with Bcl-2, Bcl-xL, or Bcl-2 and Bcl-xL). CLL cells with activation phenotype (CD5+/19+/69+) in patient PBMCs cultured without the agonist mix also showed tolerance to several apoptotic protein inhibitors ex vivo, and this was also effectively rescued with NF-kB inhibition or combination of apoptotic protein inhibitors ex vivo. These results suggest that the cancer cells with activation phenotype exist in vivo anddisplay multi-drug tolerant phenotype consistent with the drug tolerance induced by agonist mix ex vivo. In conclusion, several microenvironmental factors, particularly agonists of TLR9 and CD40, induce tolerance to IBR+VEN and cell proliferation in CLL/MCL, and response to these agonists is enhanced by combinatorial exposure. These agonists generate tolerance to several apoptosis-inducing agents beyond IBR+VEN. This microenvironment-induced multi-drug tolerance is mediated by NFkB dependent over-expression of multiple pro-survival proteins. Inhibitors of NFkB, or drug combinations targeting multiple pro-survival proteins, overcame multi-drug tolerance in agonist mix-treated samples and in CD69+CLL cells in patient PBMCs that represent multi-drug tolerant cells in vivo. Thus, more complete and durable responses might be achieved in MCL/CLL with therapies that target multi-drug tolerant persister cells. Disclosures Williams: Celgene: Consultancy, Research Funding; Kite: Consultancy; Juno: Consultancy; Seattle Genetics: Consultancy; Gilead: Consultancy, Research Funding; Novartis: Research Funding; TG Therapeutics: Consultancy; Sandoz: Consultancy; Astra-Zeneca: Consultancy; Abbvie: Consultancy; Takeda: Research Funding; Pharmacyclics: Research Funding; Janssen: Consultancy, Honoraria, Research Funding; Verastem: Consultancy. Portell:AbbVie: Research Funding; Infinity: Research Funding; Genentech/Roche: Consultancy, Research Funding; Acerta: Research Funding; BeiGene: Research Funding; Kite: Research Funding; Amgen: Consultancy; TG therapeutics: Research Funding.

Abstract: The Bcl-2 inhibitor venetoclax has yielded exceptional clinical responses in chronic lymphocytic leukemia (CLL). However, de novo resistance can result in failure to achieve negative minimal residual disease and predicts poor treatment outcomes. Consequently, additional proapoptotic drugs, such as inhibitors of Mcl-1 and Bcl-xL, are in development. By profiling antiapoptotic proteins using flow cytometry, we find that leukemic B cells that recently emigrated from the lymph node (CD69+/CXCR4Low) in vivo are enriched for cell clusters simultaneously overexpressing multiple antiapoptotic proteins (Mcl-1High/Bcl-xLHigh/Bcl-2High) in both treated and treatment-naive CLL patients. These cells exhibited antiapoptotic resistance to multiple BH-domain antagonists, including inhibitors of Bcl-2, Mcl-1, and Bcl-xL, when tested as single agents in a flow cytometry–based functional assay. Antiapoptotic multidrug resistance declines ex vivo, consistent with resistance being generated in vivo by extrinsic microenvironmental interactions. Surviving “persister” cells in patients undergoing venetoclax treatment are enriched for CLL cells displaying the functional and molecular properties of microenvironmentally induced multidrug resistance. Overcoming this resistance required simultaneous inhibition of multiple antiapoptotic proteins, with potential for unwanted toxicities. Using a drug screen performed using patient peripheral blood mononuclear cells cultured in an ex vivo microenvironment model, we identify novel venetoclax drug combinations that induce selective cytotoxicity in multidrug-resistant CLL cells. Thus, we demonstrate that antiapoptotic multidrug-resistant CLL cells exist in patients de novo and show that these cells persist during proapoptotic treatment, such as venetoclax. We validate clinically actionable approaches to selectively deplete this reservoir in patients.

Abstract: BACKGROUND: E4402 was a randomized phase III study comparing two different rituximab dosing strategies for patients with previously untreated, low tumor burden follicular lymphoma (FL). The primary endpoint was time to treatment failure. The initial publication (Kahl, JCO 2014) demonstrated that a retreatment strategy utilized less drug and produced comparable time to treatment failure compared to a maintenance strategy. Here we provide long term follow up results, focusing on response duration, time to first cytotoxic therapy, overall survival, and risk of histologic transformation. METHODS: Eligible patients had untreated, low tumor burden (GELF criteria) FL. Patients received R 375 mg/m 2 weekly x 4 and responders were randomized to maintenance rituximab (MR) (single dose R q 3 months) or retreatment rituximab (RR) (R weekly x 4 doses at disease progression). Each strategy was continued until treatment failure. The primary endpoint, time to treatment failure, was defined as progression within 6 months of last R, no response to R retreatment, initiation of alternative therapy, or inability to complete protocol therapy. Secondary endpoints included time to first cytotoxic therapy, quality of life and safety. The ECOG Data Monitoring Committee recommended release of study results at a planned interim analysis in September 2011 and patients and providers were notified of results. Time to treatment failure data collection halted with release of the results but limited data collection on time to first cytotoxic therapy, response duration, and risk of histologic transformation continued. INITITIAL RESULTS: From 11/03 to 9/08, 384 patients with FL were enrolled. Complete or partial response was achieved in 289 patients (71%), who were then randomized to MR (n=146) or RR (n=143). Demographic features were similar in the two arms: median age 59 years; ECOG PS 0-1 in all patients, and FLIPI low-risk (14.9 vs. 16.4%), intermediate-risk (46.3 vs. 42.9%) and high-risk (38.8 vs. 40.7%) for MR vs. RR, respectively. At initial publication, with a median follow-up of 3.8 years, the time to treatment failure was 3.9 years for MR vs. 3.6 years for RR (p=NS). LONG TERM FOLLOW UP RESULTS: Immunoglobulin levels and risks for serious infections/late complications in MR patients will be updated at the annual meeting. For the endpoint of time to first cytotoxic therapy, the median follow up is 8.7 years. At 7 years, 83% of MR and 63% of RR remained free from first cytotoxic therapy (HR 2.37; 95% CI 1.50 - 3.76) [Figure 1]. For the endpoint of response duration, the median follow up is 12.1 years. At 10 years, 66% of the MR patients remained in their 1 st remission compared to 30% of the RR patients who remained in their 1 st remission [Figure 2] . The median response duration for RR patients receiving a single 4-week course of rituximab was 3.25 years. There was no difference in the overall survival at 10 years, 84% for MR vs. 83% for RR. There was a trend towards a lower risk of histologic transformation for patients receiving MR (n = 4) compared to RR (n = 11) (p = 0.11). CONCLUSIONS: With long term follow up, the RESORT data indicates that in previously untreated, low tumor burden, follicular lymphoma, MR was superior to RR for delaying time to first cytotoxic therapy and for response duration, with a trend towards reducing the risk of histologic transformation. MR did not improve the overall survival. The original publication concluded that the time to treatment failure is similar between the two dosing strategies. Due to study design, time to treatment failure could not be analyzed in this long term follow up analysis. Compared to the historical benchmark of 3 years median time to first cytotoxic therapy when watch and wait is utilized, single agent rituximab, administered by either dosing strategy, was highly effective at delaying the time to first cytotoxic therapy. Figure 1 Figure 1. Disclosures Kahl: AbbVie, Adaptive, ADCT, AstraZeneca, Bayer, BeiGene, Bristol-Myers Squibb, Celgene, Genentech, Incyte, Janssen, Karyopharm, Kite, MEI, Pharmacyclics, Roche, TG Therapeutics, and Teva: Consultancy; AbbVie, Acerta, ADCT, AstraZeneca, BeiGene, Genentech: Research Funding. Habermann: Incyte: Other: Scientific Advisory Board; Tess Therapeutics: Other: Data Monitoring Committee; Seagen: Other: Data Monitoring Committee; Morphosys: Other: Scientific Advisory Board; Loxo Oncology: Other: Scientific Advisory Board; Eli Lilly & Co.,: Other: Scientific Advisor. Schuster: Abbvie: Consultancy, Research Funding; Acerta Pharma: Consultancy; AstraZeneca: Consultancy; Adaptive Biotechnologies: Research Funding; BeiGene: Consultancy; Celgene: Consultancy, Honoraria, Research Funding; DTRM: Research Funding; Genetech: Consultancy, Research Funding; Roche: Consultancy, Research Funding; Incyte: Research Funding; Juno Theraputics: Consultancy, Research Funding; Loxo Oncology: Consultancy; Merck: Research Funding; Nordic Nanovector: Consultancy; Novartis: Consultancy, Honoraria, Patents & Royalties, Research Funding; Pharmaclcyclics: Research Funding; Tessa Theraputics: Consultancy; TG Theraputics: Research Funding. Fenske: TG Therapeutics: Consultancy, Speakers Bureau; Servier Pharmaceuticals: Consultancy; Seattle Genetics: Speakers Bureau; Sanofi: Speakers Bureau; Pharmacyclics: Consultancy; MorphoSys: Consultancy; Kite (Gilead): Speakers Bureau; KaryoPharm: Consultancy; CSL Therapeutics: Consultancy; Bristol-Myers Squibb: Speakers Bureau; Biogen: Consultancy; Beigene: Consultancy; AstraZeneca: Speakers Bureau; ADC Therapeutics: Consultancy; Adaptive Biotechnologies: Consultancy; AbbVie: Consultancy.

Abstract: Introduction: Multiple myeloma (MM) is a genetically heterogeneous disease where risk stratification and outcomes are associated with translocations involving the immunoglobulin (Ig) loci and MYC, copy number abnormalities including gain(1q), del(1p), and del(17p), as well as mutations. Additionally, MM tumors may harbor rare mutations in genes that are targetable in other tumors, such as in IDH1 and IDH2. Therefore, we designed a comprehensive MM targeted sequencing panel to interrogate the common genomic abnormalities in MM and validated it against known standards. Methods: The targeted panel was designed to include the exons of 228 genes which are either frequently mutated, associated with prognosis or risk stratification, clinically actionable, or sites of important copy number abnormalities. Additional targets were added across the genome to identify hyperdiploidy. These targeted regions encompass the mutation detection part of the panel and involve approximately 990 kb. The Ig loci and region surrounding MYC were tiled to capture translocations and copy number changes. In total, this translocation part of the panel involves approximately 4.7 Mb. The mutation and translocation panels are manufactured separately and combined during the assay resulting in a 5:1 sequencing ratio, respectively, which prevents over-sequencing of the large translocation panel. 100 ng DNA extracted from CD138+ bone marrow cells (n=223) and from non-tumor tissue (peripheral blood or saliva) was processed using the HyperCap workflow (KAPA Biosystems). Of the 223, 48 samples were processed in a clinical diagnostic laboratory. Adapter ligated DNA was hybridized with a mixture of the mutation and translocation panel and purified, amplified libraries were sequenced using 75 bp paired end reads. Sequences were aligned to hg19 and mutations and translocations identified using Strelka and Manta. Copy number was determined using the ratio of non-tumor to tumor reads in each targeted region. Data were validated using clinical FISH (translocations, n=116), MLPA (copy number, n=101), known standards (mutations), ddPCR (mutations), and whole genome sequencing (WGS; translocations and copy number, n=122). Results: Canonical IgH translocations were detected in 43.2% of patients by the panel, and all agreed with WGS. FISH detected one additional "variant" t(4;14), but did not detect 4 translocations detected by both sequencing methods. In the remainder of the samples no canonical IgH translocation was detected, agreeing with FISH results. Non-canonical translocations were detected in 14.5% of samples, 43% of which were to the MYC locus. MYC translocations were detected in 37.3% of samples with copy number abnormalities occurring surrounding MYC in 32.7% of samples. Overall, MYC abnormalities were detected in 46.4% of samples. Copy number was determined by panel sequencing and MLPA for 22 regions that were directly comparable between the technologies in 101 patient samples and 13 myeloma cell lines. The copy number concordance between the technologies was 96.9% and 99.6% in patient samples and cell lines, respectively. For the important prognostic regions, the concordance was R 2=0.962 (CDKN2C), R 2=0.986 (CKS1B), and R 2=0.973 (TP53). Panel copy number data were also compared to WGS data and showed complete concordance across the three prognostic regions, which the exception of 2 samples. In these 2 samples a homozygous deletion was detected by the panel but not by WGS. The deletions were 6.2 and 8.0 kb in size, one encompassing the coding sequencing of TP53 and the other exons 1-4 of TP53. A larger homozygous deletion of 36.3 kb was detected by both sequencing methods. Mutation detection validation was performed using Horizon Discovery samples with known variant allele frequencies (VAF) for common mutations. We were able to determine the sequencing VAF for 74 mutations across 5 samples which had a concordance of R 2=0.9849 between the expected and observed frequencies. The minimum detected VAF was 1.3% at an average depth of 891x. We also performed ddPCR on 6 patient samples with the common KRAS, NRAS and BRAF mutations which resulted in a VAF concordance of R 2=0.9983. Conclusion: We have developed a targeted sequencing panel for MM patient samples that is as robust or better than both FISH and WGS. A full protocol for sample processing and analysis is available, and has been used in a clinical diagnostic laboratory. Disclosures Ahsan: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Abu Zaid: Pieris: Current equity holder in publicly-traded company; Incyte: Research Funding; Pharamcyclic: Research Funding; Syndax: Consultancy, Research Funding. Ramasamy: Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; Celgene (BMS): Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel, Conference registration, Research Funding; GSK: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive biotech: Honoraria, Membership on an entity's Board of Directors or advisory committees; Karyopharm: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees; Sanofi: Honoraria, Membership on an entity's Board of Directors or advisory committees. Yong: GSK: Honoraria; Amgen: Honoraria; BMS: Research Funding; Sanofi: Honoraria, Research Funding; Takeda: Honoraria; Autolus: Research Funding; Janssen: Honoraria, Research Funding. Morgan: Takeda: Honoraria. Abonour: Celgene-BMS: Membership on an entity's Board of Directors or advisory committees, Research Funding; Takeda: Research Funding; Jensen: Honoraria, Research Funding; GSK: Consultancy, Honoraria, Research Funding. Flynt: Bristol Myers Squibb: Current Employment. Ansari-Pour: Bristol Myers Squibb: Consultancy. Gooding: Bristol Myers Squibb: Research Funding. Thakurta: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Walker: Bristol Myers Squibb: Research Funding; Sanofi: Speakers Bureau.