Smoley, Stephanie A.

Abstract Abstract 3605 CLL is a malignant B-cell disorder characterized by the accumulation of small B lymphocytes with a mature appearance in blood, marrow and lymph nodes. Despite effective treatment options, all patients with CLL will eventually relapse after therapy. This could be due in part to the presence of subclones of the CLL cell population that harbor genetic abnormalities, which confer resistance to treatment. The aims of this study were to investigate the clonal evolution in longitudinal samples of CLL patients and to identify genetic alterations associated with disease progression and resistance to therapy. Sequential analyses were performed in 51 samples from 23 patients who were included in a previously reported clinical trial of pentostatin, cyclophosphamide and rituximab (PCR) given every 3 weeks for 6 cycles in previously untreated CLL (Blood 109:2007). In all cases the first sample analyzed was prior to therapy. In 5 of 23 patients, three time points were analyzed: >6 months prior to entry onto PCR trial (time point A), just before starting with the PCR regimen (time point B), and the time of relapse after PCR trial (time point C). Seven patients were analyzed at time points A and B; 9 at time points B and C and 2 at time points A and C. The median time between points A and B was 17.5 months (range 8–48 months) and between points B and C was 20.5 months (7–60 m). All samples were examined by array-based comparative genomic hybridization (aCGH) using the Agilent Sureprint G3 (1 million probe) array. aCGH findings were confirmed by interphase FISH using probes for D13S319 (MIR16–1/MIR15A), RB1, MDM2, CEP12, CEP6, MYB, TP53, NFKBIA, PERP and FGFR1 loci. Overall, we observed a small increase in the number of copy-number abnormalities (CNA) with disease progression. Twenty-two of the 23 patients with paired samples harbored at least one CNA that persisted in all samples, indicating clonal relationship between the sequential samples. In 15 of the 23 patients the tumor clone was stable and no CNA differences between time points were identified. Conversely, genomic evolution was found in 8 patients. In 3 cases the genetic differences were observed pre treatment (between time points A and B) and in the other 5 cases, the observed changes were found after therapy (between time points A and C or between B and C). One remarkable case with genome evolution exhibited two subclones sharing trisomies 12 and 19, but with several unique CNA confined to each subclone. The first subclone was characterized by deletions of 6q, RB1, MIR16-1/MIR15A and 3 other losses, while the second subclone showed homozygous deletion of MIR16–1/MIR15A and 5 other monoallelic deletions. The first subclone was predominant at time points A and B (60–70% of cells), but was present in only 10–20% of cells at time point C as confirmed by FISH. Conversely, the second subclone was observed in ~20% of cells at time points A and B and became predominant after therapy, found in ~80% of cells at time point C. Another case was characterized by deletion 11q32 (including ATM and others) as the sole abnormality at time point B. Significant genomic complexity was observed at time point C, including deletions of 11q32, 9p21 (CDKN2A), 9q12-q33, 14q13.2 (NFKBIA) and 17p (TP53), and gains of 2p16 (REL) and 9q34. Interestingly, the deletion 11q32 from both time points arose independently at each time point, as they exhibited different chromosomal breakpoints and copy number variants. Moreover, the other CNA found at relapse were not identified at diagnosis (confirmed by aCGH and FISH). For evolution of specific CNA, trisomy 12 was found in 5 cases at the first sample analyzed and was stable with no changes between time points. The frequency of deletions 13q14.3 (MIR16-1/MIR15A) and 17p increased at the later time points. Conversely, –6q decreased in frequency across time points (3 cases in time points A–B and 1 case in time point C). In summary, at least 35% of CLL patients exhibited clonal evolution and at least 9% showed evidence of multiple subclones. This subgroup of CLL patients provides an exceptional framework for comprehensive analysis of genome evolution during disease progression before and after therapy. Our observations also support the hypothesis of a common CLL progenitor cell can give rise to clonally related, but genetically evolving subpopulations of tumor cells. Finally, this study may bring novel information regarding the drug resistance pathways utilized by CLL B cell clones post therapy. Disclosures: Kipps: GlaxoSmithKline: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Genentech: Research Funding; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Research Funding; Genzyme: Research Funding; Memgen: Research Funding; Igenica: Consultancy, Membership on an entity's Board of Directors or advisory committees; Sanofi Aventis: Research Funding; Abbott Laboratories: Research Funding. Fonseca:Genzyme: Consultancy; Medtronic: Consultancy; BMS: Consultancy; AMGEN: Consultancy; Otsuka: Consultancy; Celgene: Consultancy, Research Funding; Intellikine: Consultancy; Cylene: Research Funding; Onyx: Research Funding; FISH probes prognostication in myeloma: Patents & Royalties.

Abstract Abstract 2486 In patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL), deletion of 17p13 (17p-) resulting in loss of one allele of TP53 and 11q22 (11q-) resulting in loss of one allele of ATM predicts a significantly poorer prognosis. These lesions are nearly always monoallelic in patients with CLL and their consequences are considerably influenced by the integrity of the remaining allele. A dysfunctional mutation in the remaining allele, resulting in more aggressive disease, ultimately occurs in most patients with 17p- (> 80%) but fewer patients with 11q- (30%). Because ATM and TP53 are integral components of the p53 pathway, we hypothesize that patients with clonal 17p- and 11q- in the same CLL cell would have a worse prognosis than patients with only one of these deletions. To test this hypothesis, we compared the clinical outcomes (overall survival (OS) and time to treatment (TTT)) of patients with 17p- and 11q- in the same cell to patients with either 17p- or 11q- or neither defect. Methods: We used the Mayo Clinic CLL Database and the Cytogenetics laboratory database to identify all CLL patients seen in the Division of Hematology from 1/1/1995-3/29/2012 who had FISH analysis. Data was extracted on demographics, date of first (sentinel) occurrence of 11q- and 17p-, treatment, and vital status. FISH studies were performed on uncultured blood or bone marrow by standard methods using the Mayo Clinic CLL FISH panel of centromere specific control probes and probes for 6q (MYB), 11q (ATM), 13q14, and 17p (TP53) deletions, trisomy 12 and IGH. Patients with both 11q- and 17p- were further tested with the Abbott Molecular (Des Plaines, IL) ATM/TP53 combination probe set, to determine if the 11q and 17p deletions were present in the same cells. Patients were grouped into 4 cohorts: 1) clonal 17p- and 11q-; 2) 17p- only; 3) 11q- only; and 4) neither 17p- nor 11q-. OS and TTT were calculated and Kaplan-Meier curves were drawn from sentinel FISH date until their last known alive date or death date for OS and until treatment or last known untreated date for TTT. We censored all data on 3/29/2012 and analyzed using log-rank tests from date of sentinel FISH. Sanger sequencing of exons 4–9 of TP53 was done in samples from 15 patients with clonal 17p- and 11q- with an available sample collected within 1 year of the sentinel FISH test and without treatment in that interval. All mutations were confirmed by a repeat assay and analyzed for their predicted effect using the UMD p53 database. Results: We studied 2234 CLL patients with a median follow-up of 4.8 years (range 0 – 29.6 years). Twenty (1%) patients had clonal 17p- and 11q-, 159 (7%) had 17p-, 251 (11%) had 11q-, and 1804 (81%) had neither 17p- nor 11q-. Median OS from sentinel FISH study (Figure 1) was significantly shorter in the clonal 17p- and 11q- group (1.9 years), 17p- group (3.2 y), and 11q- group (4.7 y) compared to the patients with neither 17p- nor 11q- (9.2 y) (p < 0.0001). OS was significantly shorter in the patients with clonal 17p- and 11q- cells vs those with 17p- (p=0.048). TTT was also significantly different among the 4 groups (p<0.0001) with median time to treatment of 0.07 y in the clonal 17p- and 11q-, 0.2 y in 17p-, 0.7 y in 11q-, and 5.6 y in the neither 17p- nor 11q- group. TP53 analysis performed in samples from 15 patients with clonal 17p- and 11q- showed that 10 patients had mutations in the remaining TP3 allele predicted to be deleterious to normal p53 protein function. Median OS was 2.1 years for those with TP53 mutations and 0.9 years for those without mutations (p = 0.03) and median TTT was 0.25 years for those with TP53 mutations and 0.05 years for those without mutations (p = 0.049). Conclusion: “Double hit” clonal deletions of 17p and 11q occurred in 1% of this large cohort of CLL patients and were associated with a significantly poorer prognosis. We recommend that testing for this “double hit” phenomenon, by use of an ATM/TP53 combination probe set, should thus be performed in all patients with 17p- and 11q- on FISH analysis because these patients have a poorer prognosis than those with either 17p- or 11q- and could be candidates for novel therapies. The finding that dysfunctional TP53 mutations in the remaining allele did not worsen prognosis in patients with clonal 17p- and 11q- suggests that monoallelic deletion of both ATM and TP53 in a clone of CLL cells is sufficient to disable p53 pathway function in these patients. Future study of clonal 17p- and 11q- CLL could thus be informative in this regard. Disclosures: Kay: Celgene: Research Funding. Shanafelt:Genentech: Research Funding; Glaxo-Smith-Kline: Research Funding; Cephalon: Research Funding; Hospira: Research Funding; Celgene: Research Funding; Polyphenon E International: Research Funding. Zent:Biothera: Research Funding; Genzyme: Research Funding; Genentech: Research Funding; Novartis: Research Funding; GlaxoSmithKline: Research Funding.

Abstract Abstract 3606 Background: Cytogenetic abnormalities are important prognostic indicators in CLL. At Mayo Clinic, CLL FISH analyses are derived from buffy coat samples not purified for lymphocytes. Scoring is therefore performed on consecutive qualifying nuclei regardless of cell size, shape or morphology. This scoring may not reflect the percent of abnormal nuclei of the affected cell type, but rather the entire population of cells present in the sample. We sought to determine whether the percent abnormal nuclei in only the affected cell type (e.g. lymphocytes) of patients with CLL differed from that of the general cell population. Scoring only B-lymphocytes could increase the sensitivity of the test in patients with low B-cell counts, either early in their disease or after treatment. Cell sorting techniques could be used to reach this goal but can be expensive, labor intensive and add to completion time. We propose a “Poor Man's Cell Sorting” technique based on cell morphology when stained with 4',6-diamidino-2-phenylindole (DAPI). In CLL samples, both round and so called “lobed” cells are seen by DAPI staining but we hypothesize that the CLL B-cells typically present as perfectly round in shape (Fig. 1). Thus our hypothesis: if only the round cells are scored for a genetic defect, would this more accurately represent the malignant leukemic B-cell population and allow for enhanced disease status by FISH? Methods: After IRB approval, we identified 87 CLL patients (75% male; 25% female, mean age 62.4 y, range 43–89 y) in the Mayo Clinic CLL Database, who were seen at Mayo Clinic between March, 2002 - July, 2010. We selected patients known to have low level FISH abnormalities and who therefore should have a significant population of both lymphocytes and neutrophils. Selection criteria included <20×106 B-cells per microliter (by flow cytometry) of peripheral blood and ≤40% of interphase nuclei expressing a specific FISH abnormality. Although most of the 87 patients exhibited more than one FISH abnormality, we focused on only one FISH defect per patient for this study. The original specimen (slide or fixed cell pellet) was rescored for % abnormal nuclei among 100 consecutive round and 100 consecutive lobed (or multilobular) nuclei, using DAPI to identify nuclear architecture. These scores were compared to each other and to the original clinical FISH analysis (scored for 200 consecutive nuclei and not selected for nuclear morphology). Results: Among 87 cases, FISH signals were scored for 6q-(1), 11q-(9), +12(15), 13q-(58), 17p-(2) and 2 IGH rearrangements. In 86/87 cases, the abnormal lobed nuclei did not have FISH defects. One patient exhibited 35% +12 by clinical assay, 52% +12 in the round nuclei, and 11% by lobed nuclei. For all cases, the mean percentage of abnormal nuclei was greater in the round cells (46%) vs original scoring (23.6%). In 79/87 patients (91%), the % of abnormal nuclei was greater in the round cells vs original FISH (mean increase 24.3%; range 1.5–57%). One patient's score was the same in round cells vs original, and 7 patients exhibited fewer abnormal nuclei in the round cells vs original. For these 7 cases, the mean % abnormal nuclei was 5.6% for round nuclei vs 8.4% for original score (score differences ranged from 1 – 5.5%). Overall, by univariate regression analysis, round cells (p=0.0043) have a better correlation with % B-cells, ascertained by flow cytometry, than either the current clinical approach (p=0.0462) or the lobed-cell approach (p=0.4058). Discussion: In virtually all cases (99%), the abnormal FISH patterns were confined to the round nuclei, and the lobed nuclei were virtually always normal by FISH. For patients with <20×106 lymphocytes, selecting for round nuclei uniformly resulted in identification of a higher percentage of abnormal cells. Further studies, including comparison of our round nucleus approach to CLL FISH analysis to actual sorted B-lymphocyte cell selection and the association of this leukemic restricted estimation of abnormal FISH levels to clinical outcome are necessary. Given our findings, we believe that estimating FISH defects restricted to the leukemic B-cell population will become an important adjunct to cytogenetic analysis for patients with low lymphocyte counts, including those in clinical remission and those with minimal residual disease. Disclosures: No relevant conflicts of interest to declare.

Abstract Genetic analysis has an increasing role in the diagnosis, classification, and management of patients with CLL. Although translocations involving the IgH locus are well characterized in B-cell malignancies such as follicular cell lymphoma, their frequency and significance in CLL are less well defined. We studied a series of patients with a clinical diagnosis of CLL using a FISH probe set including IgH. Methods: FISH was performed on blood using a DNA probe set designed to detect common chromosome anomalies associated with CLL and translocations involving IgH. Patients with an IgH abnormality were further studied using FISH probes sets for IgH and cyclin D1, BCL-2, BCL-3, BCL-6, BCL-11a, c-MYC, MALT-1, c-MAF, FGFR-3 or PAX-5. The clinical presentation, pathology, and flow cytometric immunophenotype was reviewed in patients with various translocations involving IgH. Results: Between 1/1/03 and 6/15/04, samples from 1032 patients with a clinical diagnosis of CLL were analyzed by FISH. Of these, 76 patients (7%) had translocations involving the IgH locus. Sixty one patients had a single translocation partner gene (cyclin D1 45%, BCL-2 24%, BCL-3 8%, c-MYC 2.5%, or BCL-11a 1.3%). Two patients had two independent clones (cyclin D1 and BCL-2; BCL-3 and BCL-11a). In 13 pts (17%) we could not identify the translocation partner. Thirty five (46%) of the 76 patients with IgH translocations had been seen at Mayo Clinic Rochester and had clinical and laboratory data for detailed review. Among these 35 patients, 16 (45%) had fusion of IgH and cyclin D1 and were diagnosed with mantle cell lymphoma (MCL). The immunophenotype of the monoclonal B cells was typical of MCL (CD5+, CD23-) in 6 patients and typical of CLL (CD5+, CD23+) in 4 patients. Six MCL patients had non-diagnostic immunophenotypes: CD5-, CD 23+ (n = 3) and CD5-, CD23- (n = 3). Twelve (34%) of the 35 patients had the IGH/BCL-2 fusion gene. Of these, 3 patients had leukemic phase follicular lymphoma, one had both CLL and MCL, and 8 had the diagnostic immunophenotype of CLL. The remaining 7 patients (19%) had a variety of translocation partners: BCL-3 (n = 1), BCL-3 and BCL-11a (n = 1), c-MYC (n = 2), and unknown (n = 3). The patients with a translocation involving BCL-3 had a typical CLL immunophenotype. Discussion: The IgH FISH probe detected a molecular defect in 7% of patients with a circulating monoclonal B cell population. In patients with a CLL immunophenotype, use of the IgH probe identified the IgH/cyclin D1 translocation characteristic of MCL in 4 patients, a finding of major clinical significance. Interestingly, after exclusion of MCL patients, more than 4% patients with CLL had other translocations involving IgH, a proportion comparable with other better defined chromosomal abnormalities in CLL. Although IgH/BCL-2 translocation is usually associated with follicular lymphoma, we identified 8 patients with CLL and this translocation. Translocations involving BCL-3 had been described before in CLL with an “atypical” immunophenotype. In contrast both of our patients with BCL-3 had typical phenotypes. Translocations involving IgH and BCL-11a have not been previously described. We conclude that FISH studies using the IgH probe improve the precision of diagnosis in CLL and could also have prognostic value.

Abstract Background Although the clinical importance of del 17p13 in patients with chronic lymphocytic leukemia (CLL) is well recognized, the implications of when this defect is identified are less clearly defined. In particular, the distinction between the identification of del 17p13 at the time of diagnosis and secondary acquisition of del 17p13 during the course of the disease are poorly characterized. Methods We identified all patients with CLL cared for at the Mayo Clinic between 1/1/2000 and 12/31/2012 who underwent baseline fluorescence in-situ hybridization (FISH) testing prior to receiving treatment. The Results of repeat FISH testing were reviewed to identify cases with clinically ascertained clonal evolution. Results A total of 1757 patients with newly diagnosed CLL were seen at Mayo Clinic prior to receiving treatment. Among these, 1243 had FISH testing performed prior to treatment and within 36 months of diagnosis. The median time from diagnosis to initial FISH was 0.8 months (11.5 to 35.4 months). The Results of baseline FISH testing among these patients is as follows: 486 (39%) had del 13q14, 234 (19%) had trisomy 12, 115 (9%) had del 11q23, 59 (5%) had del 17p13, 15 (1%) had other (e.g., del6q) and 334 (37%) had no abnormalities detected. Among these patients, 344 (28%) underwent repeat FISH testing during the course of their disease. Repeat FISH testing was typically performed for clinical suspicion of karyotype evolution or prior to therapy selection in patients with a long time interval between first prognostic FISH and initiation of treatment. Among these 344 patients, 41 (12%) acquired new cytogenetic abnormalities on repeat FISH. Classification of these 344 patients by the Dohner classification at diagnosis and time of follow-up FISH is shown in Table 1. Among the 41 pts who acquired a new FISH detectable genetic abnormality, the newly acquired defect resulted in a change in Dohner FISH risk category for 39 patients including 15/41 (37%) who acquired a del 17p13. Baseline clinical and prognostic characteristics of patients who developed clonal evolution to those who did not are shown in Table 2. Patients with unmutated immunoglobulin heavy chain (IGHV) gene mutation status (p<0.0001) and CD49d (p=0.003) expression were more likely to experience clonal evolution. Among the 319 patients who did not have del 17p13 on baseline FISH, 15 (5%) acquired del 17p13 during the course of their disease. The overall survival from the date del 17p13 was identified is shown for those with del 17p13 at diagnosis (n=59) compared to those who acquired del 17p13 later in the course of the disease (n=15) in Figure 1A. Similarly, among 339 patients who did not have del 6q23 on baseline FISH, 9 (3%) acquired del 6q23 during the course of their disease. The overall survival from the date del 6q23 was identified is shown for those with del 6q23 at diagnosis (n=11) and those who acquired del 6q23 later in the course of the disease (n=9) in Figure 1B. Conclusion Acquired cytogenetic evolution is clinically ascertained by FISH during the course of the disease in approximately 12% of patients. The newly acquired defects in these patients result in a change in Dohner classification for in >90% of these patients including ∼37% who acquire del 17p13. The clinical implications of del 17p13 is influenced by the timing of ascertainment with markedly shorter survival for those who acquire del 17p13 during the course of the disease relative to those with this defect at diagnosis. Disclosures: Shanafelt: Genentech: Research Funding; Glaxo-Smith-Kline: Research Funding; Cephalon: Research Funding; Hospira: Research Funding; Celgene: Research Funding; Polyphenon E International: Research Funding.

Abstract Background: In 2006 Lenalidomide received FDA approval for myelodysplasia (MDS) with interstitial deletion 5q [del(5q)] based on conventional cytogenetic (CC) results before and after treatment. In clinical practice, FISH studies of interphase nuclei with probes for EGR1 are widely used to detect del(5q), but it is not known whether this method has similar efficacy as CC. Thus, we compared CC and FISH results for various forms of del(5q). Methods: We selected 145 patients (pts) in our cytogenetic database with del(5q). These pts had various forms of del(5q) and were representative of our clinical practice. This series included 9 pts with MDS that were studied before and after treatment with Lenalidomide. CC studies were done using standard procedures to analyze 20 metaphases from bone marrow. FISH studies were done on the same specimens using stored left-over cells and standard procedures for EGR1 (5q31.2) and D5S23/D5S721 (5p15.2). The cutoff for del(5q) for FISH was <6.0% based on 200 nuclei. Results: Among 145 pts, 104 were referred for MDS, 9 acute myeloid leukemia, 9 lymphoproliferative disorders, 7 myeloproliferative disorders and 16 without clinical information. A total of 116 pts had breakpoints at del(5)(q13q33), 17 del(5)(q15q33), 8 del(5)(q11.2~q31q31~q35), 3 del(5)(q22q33) and 1 del(5)(q13q22). Del(5q) was detected in 144 pts by both CC and FISH. One pt had del(5)(q13q22) in 20/20 metaphases but was normal by FISH. Percent abnormal cells by FISH was lower in 135/145 pts compared to CC (mean difference 22.5 ± 19.6, range −42 to 98). For 9 pts with MDS, 29 specimens were collected before and after treatment with Lenalidomide: 7 achieved complete cytogenetic remission (four relapsed) and 2 showed a decrease in percent abnormal metaphases. Results of CC and FISH for these 9 pts were concordant for detection of del(5q) and trend of tumor burden due to treatment for 28/29 specimens. The discordant specimen was collected 222 days after treatment; results of CC were normal but FISH was abnormal in 19% of nuclei. Among the 29 specimens, percent abnormal cells by FISH was lower than CC in 27 (mean difference 13.9% ± 22.5, range −19.0 to 73.5). Each of the 9 treated pts had only del(5q) prior to treatment, and was detected by both FISH and CC. After treatment, FISH did not detect a separate cytogenetic clone involving deletion 20q without del(5q) in 2 pts nor did it identify development of other anomalies in 3 pts. Conclusions: Results of CC and FISH were mostly concordant, but differed in 4 respects. First, 1/145 pts was normal by FISH but had del(5q) by CC. This pt had unusual breakpoints that did not result in loss of EGR1. Second, percentage of cells with del(5q) was usually lower by FISH than CC. This observation is likely related to a different mitotic rate of cells with del(5q) versus normal cells. Third, 1 specimen was abnormal by FISH but normal by CC after treatment, but 2 subsequent specimens were concordant. This discrepancy was likely due to interference of mitosis of del(5q) cells and residual non-proliferating disease. Fourth, 2 treated pts developed a separate cytogenetic clone without del(5q) and 3 developed other anomalies that could not be detected by FISH. We believe FISH for EGR1 is useful in clinical practice, but not a substitute for CC.

Abstract Introduction We have previously developed a primary human bone marrow model in CLL which allows us to study marrow derived mesenchymal stroma cells (MSC) and mimic in vivoMSC-leukemic interactions in CLL (Ding, Blood, 2010) These interactions proved to be bidirectional with functional implications for both cell types. However the biologic and clinical implications of these bilateral cellular interactions in relation to MSC function in CLL patients have not been completely studied. MSC are clearly established as an essential component in forming supportive marrow niches for hematopoiesis. Our focus in this study thus was to further investigate on the status of CLL MSC function in comparison with normal MSC and the impact of the leukemic CLL B cell on MSC function and its role in forming marrow niches in CLL. Methods Bone marrow (BM) aspirates of CLL patients or normal age-matched subjects were used to generate MSC and these MSC were then assessed for various functions. Specifically we assessed the growth, differentiation capacity, gene expression, cytokine secretion profile and transcriptome analysis of CLL and normal MSC using colony forming unit (CFU) assay, MSC differentiation assay, Affymetrix U133 2.0 plus array and RNA sequencing respectively. To determine MSC CFU frequency, fixed number of nucleated cells (5 or 10 million) from BM aspirates were added in MSC growth medium for 10 days to form CFU. CFU frequency was then calculated by dividing the number of MSC colonies by the fixed number of inputted nucleated cells. In order to test the specific gene changes that occurred in MSC after their interaction with CLL leukemic cells, normal MSC were co-cultured with CLL cells for 1 week and subsequently followed by cell growth, gene expression analysis with RNA sequencing and cytokine profiles using a multiplex assay. Results CLL MSC generated significantly lower CFU colonies compared to normal subjects (CLL [n=24] vs normal [n=6] mean: 2.2 vs. 22 CFU per million nucleated cells, p=0.01). In order to test if the lower number of CLL MSC CFU was due to their reduced growth capacity or lower frequency, we then performed the CFU assay using identical numbers of CLL and normal MSC at the start of culture. CLL MSC was found to have significantly lower CFU capacity compared to normal MSC (mean: 2.1 [CLL] vs 4.5 [normal] CFU/10 input cell, n=7 in each group, p=0.03). To investigate the mechanism(s) for the reduced growth capacity of CLL MSC, we compared the gene expression profiles of non-stimulated CLL vs. normal MSC (n=10 for each group) with the following outcomes: CLL MSC had increased expression of cell cycle inhibitor: p16(Ink4a) and p57, both key markers of cell senescence (Baker, Nature, 2011); CLL MSC overexpressed homeobox B cluster of transcription factors, key regulator for cell development and differentiation. Wnt inhibitors DKK1/DKK2 and non-canonical Wnt 5b known to be associated with aging were found to be 10 and 2 fold more elevated in CLL MSC. In addition, MSC abundantly produced a milieu of the cytokines MCP-1/IL-8/IL-6/IL-1Ra after interaction with CLL leukemic cells. These cytokines are associated with a senescent associated secretory phenotype (SASP). Co-culture experiments of normal MSC with CLL Leukemic cells revealed significant impact of leukemic cells on normal MSC functions. Co-culture with a low density of CLL leukemic cells (CLL to MSC ratio: ≤10,000/1) increased MSC growth (1.2 fold). However, high density co-culture of CLL cells with MSC (CLL to MSC ratio of 100,000/1) inhibited MSC growth (0.8 fold). Transcriptome analysis of normal MSC before and after one week of co-culture with CLL leukemic cells showed that normal MSC had alteration of ~1500 genes. Many of the modified genes (CDKN2B, DKK2, LIF, HGF, FOXQ1 etc) are known to be involved in regulation of cell growth and senescence. Conclusion Collectively, these results demonstrated that bone marrow derived CLL MSC have decreased proliferative potential and possess senescent phenotypes. Importantly these senescent features were inducible in normal MSC after their interaction with CLL leukemic cells implying that leukemic B cells can educate MSC to become senescent. The implications of the CLL MSC senescence status are multiple and include: defective hematopoietic niches due to dysfunctional MSC, immune dysregulation and the enhanced nurturing of CLL B cell by these MSC. We are now investigating several of these latter features in our current work. Disclosures Shanafelt: Genentech: Research Funding; GlaxoSmithKline: Research Funding; Celegene: Research Funding; Cephalon: Research Funding; Pharmacyclics/Jannsen: Research Funding; Hospira: Research Funding; Polyphenon E Int'l: Research Funding. Kay:Genetech: Research Funding; Pharmacyclics: Research Funding; Hospira: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees.

Abstract Abstract 873 Introduction: Clonal chromosomal anomalies have been well-characterized in the blood cells of patients with Chronic Lymphocytic Leukemia (CLL) and other hematological malignancies. However, the frequencies and types of chromosomal anomalies found in “normal” people (i.e. no history of hematological cancer) are much less well known. Here we compare chromosomal anomalies in untreated CLL patients with those found in a large sample of people (n>50,000) recruited for genome-wide association studies in the Gene Environment Association Studies (GENEVA) consortium. This comparison provides information about the extent to which people without a prior history of hematological cancer have chromosomal anomalies that are characteristic of CLL. Methods and Results: The anomaly detection method focused on acquired, rather than inherited, chromosomal anomalies identified in whole blood samples. The method and results for the GENEVA subjects were published recently (Laurie et al. 2012, Nat. Gen. 44:642–650). The same method was applied to pre-treatment samples from 220 CLL patients from US Intergroup Trial E2997 of the Eastern Cooperative Oncology Group (ECOG). Acquired anomalies were detected as mosaic mixtures of normal disomic cells along with cells containing autosomal anomalies consisting of large (generally > 1 Mb) deletions, duplications and/or acquired uniparental disomy (UPD). Detection requires a large fraction of cells with the same abnormal karyotype (>5–10%), which is presumably of clonal origin. The subjects (of all ages) came from 12 different GENEVA studies, which addressed a variety of health conditions not directly related to hematological cancer (e.g. addiction and glaucoma). DNA was extracted mainly from blood samples (or, in 8% of subjects, from buccal/saliva samples) and genotyped on Illumina SNP mircroarrays. Clonal mosaic anomalies were detected from change points in intensity and genotype data (B Allele Frequency and Log R Ratio). We found 514 anomalies in 404 GENEVA subjects out of 50,222 examined (0.8% of subjects), although the prevalence increased with age. Clinical data from about 75% of subjects with a clonal chromosomal abnormality revealed that only a small fraction (2.8%, 95% CI=1.0 – 4.7%) had a record of prior hematological cancer. In the ECOG study, blood samples from 220 CLL patients enrolled in protocol E2997 were genotyped on the Illumina HumanOmni1-Quad_v1 array and clonal mosaic chromosome anomalies were detected using the GENEVA method. Chromosomal anomalies typical of CLL also were identified using interphase FISH (i.e. 6q23.3-, 11q22-, 12q15+, 13q14-, 17p13-) as previously reported (Grever, JCO 25:799-804). We found 489 anomalies in 148 patients of the 220 examined (67% of patients). The anomalies detected by FISH and SNP microarray were highly concordant (>98%). Although, the most common recurrent anomalies occurred on chromosomes 6, 11, 12, 13 and 17 in regions that span the FISH probes (except for chromosome 6), a majority of the anomalies detected by SNP data (74% of 489) were not detected by the CLL FISH panel. The frequency of large chromosomal anomalies was much higher in CLL patients than in GENEVA (67% versus 0.8% of subjects) and the overall composition of anomaly types found was also different. The fraction of anomalies consisting of acquired UPD was substantially higher in GENEVA subjects than in ECOG (34.0% versus 10.6%), while deletions were less common in GENEVA (50.1% versus 72.4%) and duplications were similar (15.6% versus 17.0%) (Chi-squared test p-value=3 × 10−18). We compared the most commonly deleted regions (CDR) on each chromosome across studies. In the ECOG CLL patients, four chromosomes each had 10 or more overlapping deletions in their top CDR (6, 11, 13 and 17), which span the FISH probes (except for chromosome 6). The GENEVA subjects also had CDR on chromosomes 11, 13 and 17, which overlap those in ECOG. In addition, GENEVA had CDR spanning genes or regions implicated in myeloid malignancies, including DNMT3a on 2p, TET2 on 4q, PRAME on 22q, and a region on 20q13. Conclusions: These genotyping results of >50,000 subjects suggest clonal chromosomal anomalies may represent precursor states, or perhaps undiagnosed or unrecorded cases, of a variety of hematological malignancies. Further studies to validate these findings and explore the natural history of these genetic defects in individuals without hematologic malignancy are warranted. Disclosures: Shanafelt: Genentech: Research Funding; Glaxo-Smith-Kline: Research Funding; Cephalon: Research Funding; Hospira: Research Funding; Celgene: Research Funding; Polyphenon E International: Research Funding.

Abstract Abstract 1614 Poster Board I-640 Background Cytogenetic abnormalities in B-cell CLL are important prognostic indicators for predicting disease progression and treatment response. Until recently, only interphase cytogenetics has been readily applicable to clinical use in CLL due to the inability of traditional mitogens to promote effective metaphase cytogenetic identification. Recently, cytokine or CpG oligonucleotide stimulation has been utilized to promote efficient metaphase analysis. One concern with this approach is the actual clonality and reproducibility of such clones when examined by different cytogenetic laboratories. The CLL Research Consortium (CRC) conducted a prospective trial to test (1) whether CpG would enhance detection of abnormal clones and (2) whether the CRC cytogenetic laboratories would achieve similar results when testing the same patient samples. Methods Initially, one laboratory compared stimulation of CLL cells using CpG versus pokeweed mitogen (PWM) + 12-O-tetradecanoyl-phorbol-13-acetate (TPA) in the same samples. To test the reproducibility of CpG stimulation, fresh blood samples from 1 normal control and 12 CLL patients were collected at one site and distributed (blinded to phenotype and prior cytogenetic results) to 5 CRC cytogenetic laboratories where they were cultured for 3 days using CpG stimulation, harvested, banded and analyzed utilizing standard laboratory procedures. When possible, each laboratory analyzed 20 metaphases per case. Interphase FISH analysis for CLL (including probes for chromosomes 6q, 11q, 12, 13q, 17p, and IGH/CCND1) was also done on each sample. Results In the PWM+TPA versus CpG comparison, more cases were found to have clonal abnormalities with CpG stimulation (147 of 229, 64%) than with PWM+TPA (110 of 229, 48%; P=0.0005). All clonal abnormalities detected in the PWM+TPA cultures were also observed in the CpG cultures. In the 5-laboratory CpG comparison, the results were compiled and compared to the concurrent FISH results. The CpG karyotypes were concordant with the FISH results. The control case had a normal CpG-stimulated karyotype in all 5 laboratories. Three cases exhibited a complex karyotype; one of these also exhibited 11q-, one had 17p-, and one had neither. The cytogenetic descriptions varied modestly among labs, but all identified the complex clones. Every case including the control exhibited some nonclonal abnormal cells, but no pattern was detected among the 5 labs. When an abnormal clone was found by only 1 or 2 labs, it was present in only a very small number of cells. A small 13q- clone was observed in 2 cases in 1 and 2 labs (3 of 20 and 5 of 50 cells, respectively), and was confirmed by interphase FISH. A single lab found 2 of 30 cells with a t(12;15) in one case. Conclusions Abnormal clones in CLL are more readily detected with CpG stimulation than with traditional B-cell mitogens. The clonal abnormalities revealed by CpG stimulation are consistent with the “gold standard” interphase FISH results, and are reproducible among different cytogenetic laboratories. We have no evidence that CpG oligonucleotides create new clonal B-cell populations in vitro during 3 days of cell culture. CpG stimulation in vitro reveals clonal cytogenetic abnormalities and complexity in CLL that should be evaluated as potential independent prognostic parameters. Disclosures Kay: Biogenc-Idec, Celgene, Genentech, genmab: Membership on an entity's Board of Directors or advisory committees; Genentech, Celgene, Hospira, Polyphenon Pharma, Sanofi-Aventis: Research Funding.

Key Points This article characterizes a cryptic IGH/CCND1 rearrangement in MCL by NGS. Mate-pair sequencing can help in accurately diagnosing MCL in cases of cyclin-D1–positive B-cell lymphoma with negative CCND1 FISH studies.