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Complex karyotype, defined as ≥3 cytogenetic abnormalities, is prognostic of survival in patients treated with ibrutinib or venetoclax in relapsed/refractory (RR) chronic lymphocytic leukemia (CLL). Recent studies re-evaluating this dichotomous variable have shown that higher numbers of cytogenetic abnormalities (ie, ≥5) have a worse overall survival in patients treated with chemoimmunotherapy. We sought to determine if increasing karyotypic complexity, treated as a continuous variable, was prognostic of survival for patients treated with ibrutinib for CLL. We conducted a retrospective analysis of all patients with CLL treated with single-agent ibrutinib or in combination with an anti–CD20 antibody at our institution. We included 456 patients with both treatment-naive and RR disease. Median number of prior therapies was 2 (range, 0-13), 30% of patients had presence of del(17p), and 75% expressed unmutated IGHV. Fifty percent had ≥3 cytogenetic abnormalities, including 30% with ≥5. In a multivariable analysis, increasing karyotypic complexity was an independent predictor of shorter progression-free survival (hazard ratio, 1.07; 95% confidence interval, 1.04-1.10; P < .0001) and overall survival (hazard ratio, 1.09; 95% confidence interval, 1.05-1.12; P < .0001). Furthermore, we found that presence of clonal evolution determined by cytogenetic analysis at progression was prognostic of subsequent survival (P = .02). This solidifies karyotypic complexity as an important prognostic factor for patients with CLL treated with ibrutinib. Further research should consider sequential karyotypic analysis as a determination of risk of progression and death in patients with CLL.

Somatic variants, primarily fusion genes and single-nucleotide variants (SNVs) or insertions/deletions (indels), are prevalent among sarcomas. In many cases, accurate diagnosis of these tumors incorporates genetic findings that may also carry prognostic or therapeutic significance. Using the anchored multiplex PCR-based FusionPlex system, a custom RNA sequencing panel was developed that simultaneously detects fusion genes, SNVs, and indels in 112 genes found to be recurrently mutated in solid tumors. Using this assay, a retrospective analysis was conducted to identify somatic variants that may have assisted with classifying a cohort of 90 previously uncharacterized primarily pediatric sarcoma specimens. In total, somatic variants were identified in 45.5% (41/90) of the samples tested, including 22 cases with fusion genes and 19 cases with SNVs or indels. In addition, two of these findings represent novel alterations: a WHSC1L1/NCOA2 fusion and a novel in-frame deletion in the NRAS gene (NM_002524: c.174_176delAGC p.Ala59del). These sequencing results, taken in context with the available clinical data, indicate a potential change in the initial diagnosis, prognosis, or management in 27 of the 90 cases. This study presents a custom RNA sequencing assay that detects fusion genes and SNVs in tandem and has the ability to identify novel fusion partners. These features highlight the advantages associated with utilizing anchored multiplex PCR technology for the rapid and highly sensitive detection of somatic variants.

Hematopoiesis is hierarchical, and it has been postulated that acute myeloid leukemia (AML) is organized similarly with leukemia stem cells (LSCs) residing at the apex. Limited cells acquired by fluorescence activated cell sorting in tandem with targeted amplicon-based sequencing (LC-FACSeq) enables identification of mutations in small subpopulations of cells, such as LSCs. Leveraging this, we studied clonal compositions of immunophenotypically-defined compartments in AML through genomic and functional analyses at diagnosis, remission and relapse in 88 AML patients. Mutations involving DNA methylation pathways, transcription factors and spliceosomal machinery did not differ across compartments, while signaling pathway mutations were less frequent in putative LSCs. We also provide insights into TP53-mutated AML by demonstrating stepwise acquisition of mutations beginning from the preleukemic hematopoietic stem cell stage. In 10 analyzed cases, acquisition of additional mutations and del(17p) led to genetic and functional heterogeneity within the LSC pool with subclones harboring varying degrees of clonogenic potential. Finally, we use LC-FACSeq to track clonal evolution in serial samples, which can also be a powerful tool to direct targeted therapy against measurable residual disease. Therefore, studying clinically significant small subpopulations of cells can improve our understanding of AML biology and offers advantages over bulk sequencing to monitor the evolution of disease.

Introduction: It is well established that genetic prognostication using fluorescence in situ hybridization (FISH) for the common recurrent abnormalities deletion 13q, trisomy 12, deletion 11q, and deletion 17p hierarchically stratifies time to first treatment (TTFT) and overall survival (OS) for chronic lymphocytic leukemia (CLL) patients (pts). Approximately 20% of CLL pts are negative for each of these abnormalities (normal 12/13/11/17), which is considered a favorable prognostic finding. Although favorable, outcomes within this group are heterogeneous, with limited information as to the importance of other simultaneous factors. Limited studies have shown a subset of these pts have complex karyotypes, suggesting standard CLL FISH may be insufficient for prognostication of this group, prompting a need for studies focusing specifically on this subset of pts (Haferlach et. al. Leukemia 2007; Baliakas et. al. Blood 2019). Here, we investigated the normal 12/13/11/17 pts to interrogate the utility of additional genetic testing and identify prognostically important variables. Methods: We conducted a retrospective analysis of all treatment-naïve CLL pts with cytogenetics performed at The Ohio State University Cytogenetics Laboratory from 2008 to 2018 for whom standard 12/13/11/17 CLL FISH were normal on their first cytogenetic analysis at our institution. Chromosome banding analysis was performed on cells stimulated with CpG oligonucleotides, phorbol-12-myristate-13-acetate, and pokeweed mitogen and analyzed according to standard laboratory procedures. FISH using probes for the standard CLL panel, D13S319, D12Z3 , ATM, TP53, and an expanded panel including BCL6, MYC, REL, SEC63/MYB, CDKN2A, and IGH were done according to manufacturer's recommendations. PCR was used to determine IGHV mutational status. TTFT and OS were both measured from diagnosis; pts not starting treatment were censored at death or last follow-up for TTFT, and pts who were alive were censored at last follow-up for OS. Cox regression models were used to evaluate TTFT and OS. A multiple imputation procedure was used to impute missing data and obtain regression estimates from combining results across 30 imputed datasets. Results: We analyzed 280 pts with a median follow up of 6.1 years among survivors since diagnosis. Median age at diagnosis was 58, and 63% were men. 95% of pts had low to intermediate Rai stage at diagnosis, 49% were IGHV unmutated, and 6% expressed IGHV3-21. 35% of pts showed an abnormal karyotype, with 8% being complex (3 or more abnormalities). Additional FISH testing showed 7% had deletion of IGH, 5% had BCL6 gain/rearrangement, 5% had deletion 6q, 4% had gain/rearrangement of MYC, 4% had gain of REL (limited subset tested, n=180), and 3% had IGH rearrangement. None of the tested pts (limited subset tested, n=115) had CDKN2A deletion. 144 pts (51%) progressed to requiring treatment, with a median TTFT of 6.5 years (95% CI 5-7.6). On univariable analysis, male sex, advanced Rai stage, increasing Beta-2-microglobulin (B2M), unmutated IGHV, increasing karyotypic complexity, gain of REL, and deletion 6q by FISH were significant predictors of shorter TTFT. However, only increasing B2M (p=0.03, HR 1.15 (95% CI 1.01-1.32)) and unmutated IGHV (p Conclusions: Additional cytogenetic testing demonstrates alternative genetic alterations are common in normal 12/13/11/17 CLL pts, however, our data do not show that these alterations are significant independent predictors of TTFT or OS. While normal FISH CLL is a relatively heterogeneous group, pts with mutated IGHV represent a subset of pts with very low risk disease. Figure 1 Figure 1. Disclosures Ruppert: Telios Pharma: Consultancy. Byrd: Novartis, Trillium, Astellas, AstraZeneca, Pharmacyclics, Syndax: Consultancy, Honoraria; Vincerx Pharmaceuticals: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Newave: Membership on an entity's Board of Directors or advisory committees. Bhat: Beigene: Consultancy; Aptitude Health: Honoraria; Onclive: Honoraria; AstraZeneca: Consultancy. Kittai: Janssen: Consultancy; Abbvie: Consultancy; Bristol-Meyers Squibb: Consultancy. Rogers: Acerta Pharma: Consultancy; Pharmacyclics LLC: Consultancy; Innate Pharma: Consultancy; Genentech: Consultancy, Research Funding; AstraZeneca: Consultancy; Janssen Pharmaceuticals, Inc: Research Funding; AbbVie Inc.: Consultancy, Research Funding; ovartis Pharmaceuticals Corporation: Research Funding. Woyach: AbbVie Inc, ArQule Inc, AstraZeneca Pharmaceuticals LP, Janssen Biotech Inc, Pharmacyclics LLC, an AbbVie Company,: Consultancy; AbbVie Inc, ArQule Inc, Janssen Biotech Inc, AstraZeneca, Beigene: Other: Advisory Committee; AbbVie Inc, Loxo Oncology Inc, a wholly owned subsidiary of Eli Lilly & Company: Research Funding; Gilead Sciences Inc: Other: Data & Safety.

Introduction: Our group and others have previously shown that the presence of complex karyotype (>/= 3 cytogenetic abnormalities) is an important prognostic factor in relapsed/refractory (RR) chronic lymphocytic leukemia (CLL) patients treated with ibrutinib (Woyach JCO 2017, Thompson Cancer 2015, Maddocks JAMA Oncology 2015). It has been shown recently that increasing karyotypic complexity is a prognostic marker (Baliakis Blood 2019), but whether this is relevant for patients treated with novel therapies is unclear. Here, we aimed to determine whether the degree of karyotypic complexity beyond the dichotomy of complex versus not is a prognostic variable for patients with CLL treated with ibrutinib. Methods: We conducted a retrospective analysis of all patients with CLL treated with ibrutinib as a single agent or in combination with a monoclonal anti-CD20 antibody (MOAB) from 2010 through 2019 at The Ohio State University. We included patients with both treatment-naïve (TN) and RR disease. To determine karyotype, cells were stimulated with mitogen cocktail (PWM/PMA/CpG-ODN) and analyzed according to standard laboratory procedures. FISH using probes for D13S319, D12Z3, ATM, and TP53 were done according to manufacturer's recommendations. PCR was used to determine IGHV mutational status. Cytogenetic testing was included in the analysis if done Results: We analyzed 561 patients with a median age of 65 (range 26-91). 86% were treated with ibrutinib monotherapy, 22% were TN, and median number of prior therapies was 2 (range 0-13). 96% had an ECOG performance status (PS) of 0 or 1. Median LDH, WBC, HgB and PLT were 213 U/L, 23.2 K/uL, 11.2 g/dL, and 115 K/uL respectively. With available data, del13q14, trisomy 12, del11q22, and del17p13 was present in 50%, 22%, 30%, and 29% of patients respectively; 74% of patients were IGHV unmutated. 63 patients were excluded from cytogenetic analyses as the test was not done during the specified time window. Of the 458 evaluable, 50% had >3 cytogenetic abnormalities including 30% with >5 abnormalities. After a median follow up of 55.5 months, for the entire cohort estimated median PFS was 61.6 months (95% CI 56.1-69.5), and estimated median OS was 95.4 months (95% CI 86.3-not reached). On univariable analysis, older age, RR status, higher ECOG PS and LDH, lower HgB and PLT, presence of del17p13 and increasing karyotypic complexity were found to be statistically significant predictors of worse PFS and OS. To illustrate the relationship between increasing karyotypic complexity and clinical outcome, Kaplan-Meier plots are provided grouping pts with 0-2, 3-4, and 5 or higher aberrations (Figure 1). Accounting for statistically and clinically important factors on multivariate analysis (MVA, Table 1), increasing karyotypic complexity continued to be a statistically significant predictor of both PFS (p=0.01, HR 1.08 (95% CI 1.02-1.15)) and OS (p=0.001, HR 1.14 (95% CI 1.05-1.23)). Del17p13 did not retain statistical significance independently of karyotypic complexity on MVA. The interaction effect between prior treatment status and karyotypic complexity term was not significant for OS (p=0.89) and PFS (p=0.46), suggesting the prognostic effect of karyotypic complexity is similar across TN and RR cohorts. Conclusions: In this single center retrospective analysis, we found that increasing karyotypic complexity predicts inferior survival for patients with CLL treated with ibrutinib. This highlights that it is not only important to dichotomize presence of complex karyotype as >3 abnormalities, but to describe the number of karyotypic abnormalities in subsequent studies. Disclosures Bond: Seattle Genetics: Honoraria. Byrd:Acerta Pharma: Research Funding; Trillium: Research Funding; Pharmacyclics LLC, an AbbVie Company, Janssen, Novartis, Gilead, TG Therapeutics: Other; Pharmacyclics LLC, an AbbVie Company, Gilead, TG Therapeutics, Novartis, Janssen: Speakers Bureau; Pharmacyclics LLC, an AbbVie Company, Gilead, TG Therapeutics, BeiGene: Research Funding; Janssen: Consultancy; Leukemia and Lymphoma Society: Other; Novartis: Research Funding; Kartos Therapeutics: Research Funding; Vincera: Research Funding; Syndax: Research Funding. Rogers:AstraZeneca: Other: Travel; Abbvie, Acerta, AstraZeneca, Pharmacyclics: Consultancy; Abbvie, Genetech, Janssen: Research Funding. Woyach:Pharmacyclics: Consultancy, Research Funding; AbbVie: Research Funding; Janssen: Consultancy, Research Funding; Karyopharm: Research Funding; Morphosys: Research Funding; Loxo: Research Funding; Verastem: Research Funding.

CD19 is an attractive therapeutic target as it is highly expressed in CLL. Tafasitamab (Taf) is an Fc-engineered, humanized anti-CD19 monoclonal antibody with efficacy in CLL as a single agent. Compared to non-engineered antibodies, Taf shows significantly increased antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis, and direct cytotoxic effects (apoptosis) on tumor cells. With the addition of lenalidomide (Len), ADCC can be further augmented in vitro. Given the potential synergy of these agents, acceptable individual safety profiles, and efficacy as single agents, we conducted a study of Taf in combination with Len in patients (pts) with treatment-naïve (TN) and relapsed/refractory (RR) CLL, and included a pilot cohort of ibrutinib (IB)-treated pts with resistance mutations, but no clinical relapse, with Taf added to IB. We present the final results of this single institution phase II trial. In combination with Len, Taf was given at a dose of 1 mg/kg on cycle(C) 1 day(D) 1, 9 mg/kg on C1 D 2, 8, 15, and 22, and D1 of C2-12. Len 2.5 mg began daily on C1D8 and was given continuously. Len was escalated to 10 mg daily in pts without toxicity. After C12, Len could continue indefinitely in responding pts. In combination with IB, Taf was given at 1 mg/kg on C1D1, 12 mg/kg on C1 D2, 8, 15, and 22, weekly during C2-3, and every other week through C12. IB continued at 420 mg daily. The primary endpoint for Phase II was overall response rate (ORR) after C6. Based on previous studies with single agent Len, we tested whether the combination could improve ORR, from 50% to 80% in the TN cohort, and from 30% to 60% in the RR cohort. Using single stage designs, 19 pts per cohort provided at least 90% power to detect an increase in ORR (type I error rate 10%). By design, 13 and 9 responses were needed in the TN and RR cohorts, respectively, to warrant further study. A secondary endpoint was ORR after 12 cycles of therapy. Twelve pts were enrolled in the TN cohort; median age was 62 (range 44-75). Six pts were Rai stage III/IV, and 1 had both del(17p) and del(11q). Nine pts had ZAP 70-methylated disease. After C6, ORR was 67% [1 complete response (CR), 7 partial responses (PR); 90% confidence interval (CI): 39-88]; responses remained the same after C12. Three pts completed treatment per protocol, 3 discontinued treatment for progressive disease (PD) and 6 for AEs. Thirteen pts were enrolled in the RR cohort, median age was 70 (range 62-75). Eight pts were Rai stage III/IV, 4 had del(17p) and 2 had del(11q). Eleven pts had ZAP 70-methylated disease. After C6, ORR was 15% (all PRs - 90% CI: 3-41), and responses improved to 38% after C12 (90% CI: 17-65). Additional 1 pt had stable disease (SD). Five pts completed treatment per protocol, 6 discontinued treatment for PD, 1 for alternative therapy, and 1 continues on treatment. Nine pts with molecular progression on IB were enrolled; median age was 62 (range 45-87). Seven pts had del(17p) and 1 pt had del(11q). Eight pts had ZAP 70-methylated disease. After C6, only 1 pt (11%) responded with a PR; 3 additional pts had SD. Two pts completed treatment per protocol criteria, 3 discontinued treatment for AEs, 2 for alternative therapy and 1 pt each for PD and increased C481S allelic frequency. Figure shows Progression-free Survival (PFS) and Overall Survival (OS) for the 3 cohorts. Taf plus Len was well tolerated. Grade(gr)≥3 AEs included: infections [4: I each of lung infection, sinusitis, upper respiratory tract infection (URTI) and appendicitis], decreased neutrophil count (3) and infusion related reactions (2) in TN pts and decreased neutrophil count (10), infections [7: 2 catheter related urinary tract infections, 1 each with URTI, lung infection and soft tissue infection, 2 unspecified], diarrhea (3), hyponatremia (3) and hypophosphatemia (3) in RR pts. In the Taf plus IB cohort most common gr≥3 AEs included infections (4: 2 lung infections, 1 URTI and I unspecified), hyperglycemia (3) and hyponatremia (3). Gr≥3 atrial fibrillation was seen in 1 pt. In conclusion, although the trial did not fully accrue as planned, Taf in combination with Len appeared safe and demonstrated promising activity in TN CLL, warranting further investigation, and has similar efficacy to rituximab plus Len in RR CLL. Taf plus IB was less effective in pts with resistance to IB. Disclosures Blachly: AbbVie, AstraZeneca, KITE Pharma: Consultancy. Rogers:AbbVie: Consultancy, Research Funding; Genentech: Research Funding; Janssen: Research Funding; Pharmacyclics: Consultancy; Acerta Pharma: Consultancy; AstraZeneca: Consultancy, Other: Travel Funding. Lozanski:Genentech, Novartis, Beckman Coulter: Research Funding. Byrd:Syndax: Research Funding; Vincera: Research Funding; Acerta Pharma: Research Funding; Novartis: Research Funding; Kartos Therapeutics: Research Funding; Trillium: Research Funding; Leukemia and Lymphoma Society: Other; Janssen: Consultancy; Pharmacyclics LLC, an AbbVie Company, Gilead, TG Therapeutics, BeiGene: Research Funding; Pharmacyclics LLC, an AbbVie Company, Gilead, TG Therapeutics, Novartis, Janssen: Speakers Bureau; Pharmacyclics LLC, an AbbVie Company, Janssen, Novartis, Gilead, TG Therapeutics: Other. Woyach:Karyopharm: Research Funding; Morphosys: Research Funding; Pharmacyclics: Consultancy, Research Funding; Verastem: Research Funding; AbbVie: Research Funding; Janssen: Consultancy, Research Funding; Loxo: Research Funding. OffLabel Disclosure: Lenalidomide off label use for CLL

Ibrutinib is a highly effective targeted therapy for chronic lymphocytic leukemia (CLL). However, ibrutinib must be discontinued in a subset of patients due to progressive CLL or transformation to aggressive lymphoma (Richter transformation). Transformation occurs early in the course of therapy and has an extremely poor prognosis. Thus, identification of prognostic markers associated with transformation is of utmost importance. Near-tetraploidy (4 copies of most chromosomes within a cell) has been reported in various lymphomas, but its incidence and significance in CLL has not been described. Using fluorescence in situ hybridization, we detected near-tetraploidy in 9 of 297 patients with CLL prior to beginning ibrutinib treatment on 1 of 4 clinical trials (3.0%; 95% confidence interval [CI], 1.4%-5.7%). Near-tetraploidy was associated with aggressive disease characteristics: Rai stage 3/4 ( P = .03), deletion 17p ( P = .03), and complex karyotype ( P = .01). Near-tetraploidy was also associated with ibrutinib discontinuation due to Richter transformation ( P P = .41). Of the 9 patients with near-tetraploidy, 6 had Richter transformation with diffuse large B-cell lymphoma. In a multivariable model, near-tetraploidy (hazard ratio [HR], 8.66; 95% CI, 3.83-19.59; P P = .01) were independent risk factors for discontinuing ibrutinib due to transformation. Our results suggest that near-tetraploidy is a potential prognostic marker for Richter transformation to assess in patients going on ibrutinib.

Chronic lymphocytic leukemia (CLL) is a highly heterogeneous disease and biomarkers are integral to predicting outcomes. In the past, cytogenetics in CLL typically utilized fluorescence in situ hybridization to detect abnormalities due to the low mitotic index of CLL hampering metaphase karyotyping. Recently, stimulation of CLL cells with CpG oligodeoxynucleotides has largely overcome this challenge. CpG oligodeoxynucleotides enhance the detection of karyotypic abnormalities in CLL by stimulating leukemic cells that normally do not proliferate in culture. Karyotyping has identified complex karyotype as a prognostic marker associated with poor outcome in CLL. Karyotyping has also uncovered novel chromosomal abnormalities including trisomies, dicentric chromosomes, and jumping translocations. CpG oligodeoxynucleotide stimulation significantly improves the ability to detect chromosomal abnormalities via karyotyping in CLL. Karyotyping has proven to be an important diagnostic tool in CLL and contributes to the discovery of novel recurrent chromosomal abnormalities.

Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.

Chromosome analysis of chronic lymphocytic leukemia (CLL) is an important clinical tool for evaluating prognosis and disease progression. Visualizing chromosomes microscopically using traditional cytogenetic techniques requires dividing cells to be arrested during metaphase. The major challenge for performing this analysis on CLL samples is stimulating the cells to divide in culture. Stimulation of CLL cells with CpG oligodeoxynucleotides has improved our ability to perform chromosome analysis for this leukemia. This protocol should help the reader successfully culture CLL samples for clinical chromosome analysis.

Chromosome analysis of chronic lymphocytic leukemia (CLL) is an important clinical tool for evaluating prognosis and disease progression. Visualizing chromosomes microscopically using traditional cytogenetic techniques requires dividing cells to be arrested during metaphase. The major challenge for performing this analysis on CLL samples is stimulating the cells to divide in culture. Stimulation of CLL cells with CpG oligodeoxynucleotides has improved our ability to perform chromosome analysis for this leukemia. This protocol should help the reader successfully culture CLL samples for clinical chromosome analysis.

A jumping translocation (JT) is a rare cytogenetic aberration that can occur in haematological malignancy. It involves the translocation of the same fragment of donor chromosome onto two or more recipient chromosomes, typically in different cells. In this study, we describe the first series of chronic lymphocytic leukaemia (CLL) patients with JTs reported to date. Following a review of 878 CLL patient karyotypes, we identified 26 patients (3%) with 97 JTs. The most commonly occurring breakpoint in these translocations was 17p11.2. Loss of TP53 was identified prior to or at the same time as JT in 23 of 26 patients (88%). All patients eventually developed a complex karyotype. All but one patient has required treatment for CLL, with estimated median time to treatment of 11.5 months. This study establishes JTs as a recurrent abnormality found in CLL patients with aggressive disease. JTs contribute to complex karyotypes and, in many cases, are involved in chromosomal rearrangements that result in loss of the tumour suppressor gene TP53.

Significance B-cell chronic lymphocytic leukemia (CLL) is the most common adult leukemia. We previously found that dysregulation of the T-cell leukemia/lymphoma 1 ( TCL1 ) oncogene is a critical contributing event in the pathogenesis of this disease. In this study we investigated molecular causes of TCL1 overexpression in CLL. We identified miR-3676 as a powerful regulator of TCL1 expression. We found that miR-3676 is down-regulated on all groups of CLLs and mutated in 1% of CLLs. Interestingly, miR-3676 is located at 17p13, only 500-kb centromeric of tumor protein p53 ( Tp53 ), and is codeleted with Tp53 in 17p-deleted CLL. Loss of miR-3676 causes high levels of TCL1 expression contributing to CLL progression. Thus, this study uncovers a major mechanism in the pathogenesis of CLL.

Ibrutinib is a promising targeted therapy for chronic lymphocytic leukemia (CLL). However, a small subset of patients progress on ibrutinib either through progressive CLL or Richter's transformation. Patients responding to ibrutinib and then progressing with Richter's transformation do so most commonly within the first 2 years of treatment and have an extremely poor prognosis. Identifying biomarkers associated with this transformation is of utmost importance. Near-tetraploidy (4 copies of most chromosomes within a cell) has been reported in various lymphomas; however, its incidence in CLL has not been described. We investigated the prevalence of near-tetraploidy in CLL patients prior to starting ibrutinib and identified it as a pre-treatment biomarker for Richter's transformation. We examined near-tetraploidy in a large series of CLL patients enrolled across four ibrutinib clinical trials at the Ohio State University, for which extensive correlative studies and follow up data are available (previously described by Maddocks et al., JAMA Oncol, 2015). We identified this abnormality in 9 of 300 patients (3.0%, 95% CI: 1.4-5.6) in blood or bone marrow samples taken prior to starting therapy. Near-tetraploidy was detected by the presence of four signals with four or more fluorescence in situ hybridization (FISH) probes and confirmed in the metaphase karyotype of each patient in at least one cell. Near-tetraploidy was associated with aggressive disease characteristics including: Rai stage 3/4 (p=0.03), deletion 17p (p=0.03), and complex karyotype (p=0.01), as well as trisomy 12 (p=0.05). With a median follow-up time of 40.5 months, in patients positive with near-tetraploidy, one patient (11%) progressed with CLL on ibrutinib, six patients (67%) progressed with Richter's transformation, and two patients (22%) were still on treatment. Cumulative incidence of Richter's transformation was significantly higher in patients with near-tetraploidy (Figure; p Our results suggest that near-tetraploidy is a distinct biomarker to assess in patients initiating ibrutinib which would predict a high risk for Richter's transformation. As a biomarker it will be important to confirm this association in a second independent data set as well as interrogate the distinct pathophysiology of this genomic subset of CLL. Figure Figure. Disclosures Lozanski: Stemline Therapeutics Inc.: Research Funding; Boehringer Ingelheim: Research Funding; Genentech: Research Funding; Beckman Coulter: Research Funding. Jones:Pharmacyclics, LLC, an AbbVie Company: 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, Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding. Andritsos:Hairy Cell Leukemia Foundation: Research Funding. Awan:Novartis Oncology: Consultancy; Pharmacyclics: Consultancy; Innate Pharma: Research Funding. Blum:Pharmacyclics: Research Funding. Woyach:Acerta: Research Funding; Morphosys: Research Funding; Karyopharm: Research Funding.

Enhancer of Zeste Homolog 2 (EZH2) is a catalytic core subunit of the Polycomb repressive complex 2, PRC2. EZH2 catalyzes the tri-methylation of lysine 27 on histone H3 (H3K27me3) which often results in the silencing of associated gene promoters. The over-expression of EZH2 is associated with cancer progression and poor prognosis in solid tumors and hematological malignances. EZH2 mutations in lymphoma generally are activating whereas those in myelodysplasia and acute myeloid leukemia are typically loss of function. Additionally, EZH2 mutations are not isolated to a hotspot and therefore discerning phenotype is challenging. The purpose of this study was to determine if the inhibition of EZH2 induces cell differentiation or apoptosis in AML, and to determine the significance of EZH2 mutations in AML patients. As H3K27me3 deposition is catalyzed by EZH2, we hypothesized that analysis of H3K27me3 levels could differentiate an inactivating EZH2 mutation. We analyzed H3K27me3 levels in AML patient samples with wild type (N = 5) and mutant (N = 3) EZH2, and found that overall H3K27me3 is reduced in the mutant patient samples. Furthermore, the sample with the highest variant allele frequency (VAF) of the EZH2 mutation had noticeably lower levels of H3K27me3 compared to those that had a lower VAF. This finding demonstrates that diminished H3K27me3 levels can predict the presence of an inactivating EZH2 mutation in AML cells. We next assessed if the EZH2 tool molecule EPZ011989 produced a similar phenotype in wild-type EZH2 AML cell lines (Kasumi-1, MOLM-13, and MV4-11). EPZ011989 inhibited H3K27me3 in all of the cell lines at a concentration of 0.625 μM after only four days of treatment. At these concentrations and this time point we demonstrated no change in viability among these three cell lines and only minimal proliferation inhibition in MV4-11 and MOLM-13 cells. Longer time points are currently being investigated as EZH2 inhibitors often induce anti-proliferative effects only after longer incubation periods. Therefore, our results support that inactivation of EZH2 with EZP011989 in AML cell lines induces the same cell-biochemical consequence (i.e. H3K27me3 loss) associated with EZH2 mutations in AML patients. This potentially will allow diverse pharmacologic studies in cell lines relative to gene targets and also synergistic lethality studies utilizing genetic and pharmacologic screening techniques to potentially develop therapeutic agents to treat this subtype of AML. Citation Format: Sydney Fobare, Cecelia Miller, Shelley J. Orwick, Heike Keilhack, Erin Hertlein, John C. Byrd. The effect of EPZ011989, an enhancer of Zeste homolog 2 inhibitor, in acute myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4520.

Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression, and dysregulated expression of lncRNAs has been reported in many cancers. One of the most documented ways by which lncRNAs can contribute to cancer aggressiveness is by altering gene expression through associations with chromatin modifying proteins. However, the vast majority of lncRNAs dysregulated in cancer remain to be functionally characterized. Specifically, there have been few studies investigating the role of lncRNAs in chronic lymphocytic leukemia (CLL). Numerous studies have been published documenting the role of micro RNAs (miRs) in CLL, indicating that non-coding RNAs can play a significant role in this disease. Therefore we hypothesize that dysregulated lncRNA expression in CLL contributes to aggressive disease. We performed microarray analysis using Arraystar Human LncRNA Array v2.0, a platform that analyzes over 30,000 lncRNA transcripts in addition to 30,000 coding transcripts. We found that many lncRNAs are aberrantly expressed in CLL compared to healthy donor B cells. We identified the lncRNA treRNA (TRERNA1) as overexpressed in CLL cells (p = .0014). treRNA has been previously described to have enhancer-like function (Ørom et al., 2010) as well as translational regulatory functions (Gummireddy et al., 2013). It has been reported as overexpressed in breast cancer lymph-node metastases and colon cancer (Gummireddy et al., 2013). In addition to expressing spliced treRNA, CLL cells contain a transcript that retains the intron between the two coding exons due to insufficient splicing. Therefore we investigated the prognostic significance of both spliced and retained intron treRNA (ri-treRNA) in subsequent studies. We obtained 144 well-characterized CLL patient samples from the CLL Research Consortium (CRC) and measured transcript expression by quantitative reverse transcription PCR (qRT-PCR). We separated patients into high or low expressers of treRNA relative to the overall median expression and found that patients with higher expression of treRNA have significantly shorter time to treatment (p = .04). High expression of treRNA also correlates with the poor prognostic indicators unmutated IGHV (p < .0001) and low ZAP70 methylation (p Disclosures Flinn: Celgene Corporation: Research Funding.