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  • 1
    Publication Date: 2007-11-16
    Description: We examined a large cohort (N=2,457) of chronic lymphocytic leukemia (CLL) patients evaluated by the CLL Research Consortium (CRC) and found 63 (2.6%) used IGHV3-21. Comparing the Ig heavy chain third complementarity determining region (HCDR3) of the IGHV3-21 cases: 25/63 cases (39.7%) had a conserved amino acid motif (motif 1: DANGMDV) in the otherwise highly variable Ig HCDR3, as described by Tobin et al. Blood 2003. All but one of these Ig heavy chains (IgH) were paired with a lambda light chain encoded by IGLV3-21. In addition, we found that 3/63 cases (4.8%) had a previously unrecognized conserved HCDR3 amino acid motif (motif 2: DPSFYSSSWTLFDY). In contrast, these IgH invariably were paired with kappa immunoglobulin light chains (IgL) encoded by IGKV3-20. Similarly to that noted for CLL cases that use IgH encoded by unmutated IGHV1-69 (Widhopf et al. Blood Epub First Edition 2007), the pairing of IgH encoded by IGHV3-21 with IgL appears governed by the HCDR3. The non-stochastic pairing of IgH with IgL argues strongly that antigen plays a role in selecting the Ig expressed in CLL. To examine for the antigen(s) recognized by the most common Ig encoded by IGHV3-21, we isolated IgH and IgL genes expressed by IGHV3-21/IGLV3-21 CLL cases and generated recombinant antibodies, which we examined for binding to antigen(s) present on microarray of self or environmental antigens. We found that Ig encoded by IGHV3-21/IGLV3-21 had apparent specific binding for protein L, a multi-domain cell-wall protein isolated from Peptostreptococcus magnus, a Gram-positive commensal bacteria that comprise a large portion of the human bacterial gut flora. Prior studies identified that protein L is a superantigen capable of binding human Ig kappa light chains encoded by IGKV genes of the I, III, and IV subgroups, but not human Ig lambda light chains. The specific binding of IGHV3-21/IGLV3-21 to protein L suggested that protein L might play a role in the development of CLL cells that express such Ig. To test this hypothesis, we examined the capacity of various recombinant antibodies to bind protein L by ELISA. We found that lambda IgL encoded by IGLV3-21 could bind to protein L with similar activity, independent of whether this lambda IgL paired with the native IgH, IgH encoded by IGHV3-21 lacking the DANGMDV HCDR3 motif, or even irrelevant IgH encoded by IGHV4-39 that are not found paired with IGLV3-21 in the Ig expressed in CLL. Moreover, Ig formed by pairing IgH encoded by IGHV3-21 that has the DANGMDV HCDR3 motif with an IgL encoded by an IGLV that was irrelevant to IGLV3-21 did not bind protein L. These results reveal a previously unrecognized capacity of human IgL encoded by IGLV3-21 to bind the protein L superantigen of Peptostreptococcus magnus, a bacteria commonly found in the human gastrointestinal tract. However, because the binding of IGLV3-21 does not depend upon the non-stochaistic pairing of IgH and IgL observed in CLL, we reason that the capacity of IGLV3-21 to bind protein L cannot account for the selected Ig repertoire expressed in CLL, suggesting that it actually does not play a role in CLL leukemogenesis. This finding suggests that caution should be exercised when defining an antigen that is found capable of binding the restricted Ig expressed in CLL as the driving factor responsible for leukemogenesis.
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  • 2
    Publication Date: 2007-11-16
    Description: Introduction: Fludarabine treatment has been shown to be beneficial for patients with Chronic Lymphocytic Leukemia (CLL), and fludarabine-based combinations may even further improve outcomes in patients with CLL. However, most CLL patients eventually become fludarabine refractory, a state which is associated with a relatively short survival. Treatment of fludarabine-refractory patients is challenging, with a median survival of about 10 months. Recently, 2 phase II clinical trials (Chanan-Khan et al. JCO 2006 and Ferrajoli et al. ASH 2006) demonstrated the clinical efficacy of lenalidomide, an immunomodulatory agent, in relapsed/refractory CLL patients. We conducted a subset analysis to examine the efficacy of lenalidomide in patients who are fludarabine refractory. Methods: All patients enrolled on the 2 phase II single agent lenalidomide clinical trials were evaluated and patients with fludarabine-refractory disease (progressed while on or within 6 months of fludarabine-based therapy) were assessed for clinical efficacy of lenalidomide. Lenalidomide was given orally either at 10 mg daily for 28 days followed by 5 mg increments every 28 days to a maximum dose of 25 mg or given at 25 mg on days 1–21 of each 28-day cycle. Response was assessed using the NCI-WG 1996 criteria. Results: A total of 80 patients were collectively enrolled in these clinical studies. Among these, 29 were identified to have fludarabine-refractory disease. Important clinical characteristics of these patients are reported in Table 1. The overall response rate in fludarabine-refractory patients was 34.5% (10/29). Complete remission was observed in 2 (6.8%) patients. Conclusion: Lenalidomide is a novel agent with immunomodulating properties demonstrating clinical efficacy in relapsed or refractory CLL patients. Interestingly, clinical responses to single agent lenalidomide were noted despite refractoriness to fludarabine (a subset of CLL patients with poor survival and limited therapeutic options). This observation of the clinical benefit of lenalidomide independent of responsiveness to prior fludarabine is encouraging and warrants further evaluation. Table 1 Ferrajoli et al. Chanan-Khan et al. Fludarabine-refractory (N=12) Fludarabine-refractory (N=17) ORR, overall response rate; PFS, progression-free survival; OS, overall survival. Median age, years (range) 62 (51–82) 68 (53–75) Sex, female/male 4/8 4/13 Median no. prior therapies (range) 4 (3–15) 4 (1–10) Median beta microglobulin (range) 5 (3–10) 5 (2–10) Advance Rai Stage (III/IV), n (%) 7 (58.3) 13 (76.4) ORR, n (%) 3 (25.0) 7 (41.2) Median PFS, months 12 14.9 Median OS, months All alive (range, 7–19) 23
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  • 3
    Publication Date: 2019-11-13
    Description: Human pentraxins are a family of proteins with a unique pentameric structure. Unlike C-reactive protein (CRP), serum amyloid P (SAP) and pentraxin-3 (PTX3) play an opposite role in tissue remodeling. PTX3 induces whereas SAP inhibits the differentiation of CD14+ monocytes into fiborcytes. While in patients with CLL CRP levels are high and were found to be associated with poor overall survival (OS) (Herishanu et al. Ann Med 2017), little is known about the plasma levels or clinical significance of other pentraxins in CLL. Therefore, we obtained plasma sample from 36 randomly chosen treatment-naïve CLL patients and 12 age-matched healthy individuals and, using an enzyme linked immuno-sorbent assay, found that PTX3, CRP and SAP plasma levels were significantly higher in CLL patients than in healthy individuals (P
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  • 4
    Publication Date: 2014-12-06
    Description: Background. Lenalidomide (Len) is an immunomodulatory drug with single agent activity in patients (pts) with treatment-naïve (TN) CLL, (overall response rate (ORR) 56-65%, Chen JCO 2011, Ferrajoli Blood 2011). Given the encouraging results of the combination of Len and rituximab (R) in relapsed CLL, we explored this combination as initial therapy. TN pts could derive greater benefit than relapsed pts from Len + R given their less compromised immune function. Methods. Fifty-eight pts were enrolled between 01/2012 and the present time. All patients had treatment indications per IWCLL 2008 criteria, WHO performance status ≤2 and adequate hepatic and renal function. Patients with HIV, hepatitis B or C infection were excluded. Treatment consisted of R 375 mg/m2 IV given weekly for 4 weeks then monthly during months (mo) 3-12 and Len 10 mg PO/day from day 9 for 24 mo. Allopurinol 300 mg PO daily was given for the first 2 weeks. No pts received antibiotic or DVT prophylaxis. Use of growth factors was allowed according to ASCO guidelines. Responses were assessed (2008 IWG criteria) at mo 3, 6 and every 6mo thereafter. Results. Forty-eight patients are evaluable for response and toxicity (8 too early, 1 lost to follow-up and 1 diagnosed with metastatic colonic adenocarcinoma within 1 week of study entry). Median age was 66 yrs (42-79). 29 (59%) pts were ≥age 65. 22 pts (46%) had Rai stage III-IV disease. Median β2M level was 3.8 mg/dL (1.4-10.5). 24/37 pts (65%) had unmutated IGHV gene and 31 pts (65%) expressed ZAP-70. 4 pts (8%) had del(17p) and 15 pts (32%) del(11q). Forty pts responded (ORR 83%). 7 pts (14.6%) achieved CR (1 MRD negative) and 33 (68.8%) achieved PR (including 7 nodular PRs). Median time to CR was 11mo (range 5-27). 5 pts discontinued therapy before the 3mo evaluation (4 due to toxicity and 1 due to unrelated co-morbidities). Six pts discontinued between 3 and 6mo (4 for refractory disease and 2 for toxicity after achieving PR). ORR was similar for patients with mutated and unmutated IGHV gene (85 vs 83%, p=0.96), age ≥65 and
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  • 5
    Publication Date: 2018-11-29
    Description: Introduction. In the context of chemoimmunotherapy, complete remission (CR) is more common and is associated with improved survival in patients with chronic lymphocytic leukemia (CLL). CR is less frequent in CLL patients treated with ibrutinib, and the prognostic significance of achieving CR with ibrutinib is indeterminate. Methods. We prospectively analyzed 208 CLL patients treated on a phase 2 study (NCT02007044) of first-line (deletion 17p only; n=27) or salvage ibrutinib (n=181), with or without rituximab, between 12/2013 and 01/2018. Response was assessed by international workshop on CLL 2018 guidelines. Categorical variables were compared using the χ2 or Fisher exact tests. Progression-free survival (PFS) was defined as time from treatment initiation to disease progression and/or death, and Kaplan-Meier curves compared using the log-rank test. A landmark analysis at median time of CR achievement (best response) was performed for PFS. Results. After a median follow-up of 34 months (range, 3-48 months), response was evaluable in 194 patients, overall response rate (ORR) was 99%, and CR rate was 24%, with negative minimal residual disease (MRD) in 3% of patients; median time to response was 10 months (range, 3-45 months) and median time to CR was 21 months (5-45 months). None of the patients' baseline characteristics associated with achievement of CR (Table). Among the 47 patients in CR, 7 (15%) discontinued treatment, after a median time from treatment initiation of 19 months (range, 10-39); the main cause of discontinuation was toxicity (5 patients), with second cancer (metastatic melanoma) and disease progression prompting treatment discontinuation only in 2 patients. Among the 145 patients in PR, 50 (34%) discontinued treatment, after a median time from treatment initiation of 14 months (range, 4-45 months); while the main cause of discontinuation was again toxicity (26 patients), 2nd cancers and progressive disease prompted treatment discontinuation in 5 and 14 patients, respectively. Remaining causes of treatment discontinuation among patients in PR were loss to follow-up (3 patients) and consolidation therapy (2 patients). Median PFS was not reached and 28 patients (13%) progressed and/or died. Achievement of CR significantly associated with prolonged PFS (4-year PFS 98% vs 78%, p=0.03)(Figure). The association between CR and prolonged PFS was also confirmed on a landmark analysis (21 months)(p=0.05). Among baseline characteristics shown in the Table, the only factor associated with prolonged PFS was absence of complex karyotype (4-year PFS 80% vs 40%, p=0.05). Median OS has not been reached and 16 (8%) patients have died; of these, only 1 patient was in CR (and cause of death was metastatic melanoma), whereas the remaining 15 were in PR. Among patients in PR, causes of death were: infections in 7 patients, 2nd cancers in 2 patients, Richter transformation in 2 patients and other in 4 patients (small bowel obstruction, colon perforation, intracranial hemorrhage, bradyarrhythmia). Conclusions. This is the first study showing that achievement of CR is a desirable endpoint for patients with CLL treated with ibrutinib, associating with prolonged PFS. Our results support the development of future combination studies, aimed at achieving higher rates of CR in patients treated with ibrutinib. Figure. Figure. Disclosures Wierda: AbbVie, Inc: Research Funding; Genentech: Research Funding. Jain:Infinity: Research Funding; Novimmune: Honoraria, Membership on an entity's Board of Directors or advisory committees; Genentech: Research Funding; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; BMS: Research Funding; Infinity: Research Funding; ADC Therapeutics: Research Funding; Astra Zeneca: Research Funding; Cellectis: Research Funding; Verastem: Research Funding; Servier: Honoraria, Membership on an entity's Board of Directors or advisory committees; Incyte: Research Funding; ADC Therapeutics: Research Funding; BMS: Research Funding; ADC Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pfizer: Research Funding; Pharmacyclics: Research Funding; Genentech: Research Funding; Abbvie: Research Funding; Celgene: Research Funding; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologies: Honoraria, Membership on an entity's Board of Directors or advisory committees; Servier: Research Funding; Pharmacyclics: Research Funding; Seattle Genetics: Research Funding; Seattle Genetics: Research Funding; Abbvie: Research Funding; Pfizer: Research Funding; Incyte: Research Funding; Adaptive Biotechnologioes: Research Funding; Celgene: Research Funding; Pharmacyclics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Research Funding; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Honoraria, Membership on an entity's Board of Directors or advisory committees; Servier: Research Funding; Verastem: Honoraria, Membership on an entity's Board of Directors or advisory committees; Verastem: Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; ADC Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Cellectis: Research Funding; Pfizer: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologioes: Research Funding; Servier: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pharmacyclics: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novimmune: Honoraria, Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologies: Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Astra Zeneca: Honoraria, Membership on an entity's Board of Directors or advisory committees; Verastem: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees. Thompson:Adaptive Biotechnologies: Research Funding; Genentech: Honoraria, Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria, Research Funding; Gilead Sciences: Honoraria, Membership on an entity's Board of Directors or advisory committees; Pharmacyclics: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding.
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  • 6
    Publication Date: 2009-11-20
    Description: Abstract 2381 Poster Board II-358 The natural history of patients (pts) who fail or relapse after chemoimmunotherapy with fludarabine, cyclophosphamide, and rituximab (FCR) has not been established. Three hundred pts received FCR as initial therapy for progressive or advanced chronic lymphocytic leukemia (CLL) (Tam CS; Blood 112(4):975-980, 2008). Fifteen (5%) pts failed to respond, 72% achieved a CR and 22% a PR. Treatment failure occurred in 18 pts because of the development of AML, MDS or Richter's transformation and there were 15 deaths in remission (infection (7), cancer (6), or cardiac events (2)). Fourteen relapsed pts have not received therapy and are considered to be “watch and wait.” One hundred and twelve pts have received therapy. A large variety of treatment programs were administered at time of relapse during the ten years of the study. The most commonly used were FCR-like regimens (33) with or without lumiliximab or bevacizumab, FCR + alemtuzumab (CFAR) 9 pts, rituximab-based regimens (28) +/- GMCSF or steroids, Campath-based regimens (16) +/- rituximab, and a variety of other phase I and miscellaneous salvage treatments. 79 pts received salvage therapy at M. D. Anderson Cancer Center (MDACC) and the 33 others in their local community. 17 patients (16%) achieved a CR and 46 a PR (4%). CR rates were 15% for FCR, 56% for CFAR, 4% for rituximab regimens, 31% for alemtuzumab regimens and 4% for other regimens. While higher CR rates were noted in alemtuzumab regimens, no difference in time-to-treatment failure or survival was noted. The median overall survival was 33 months with a 40% five-year survival rate. A number of characteristics shown in Table 1 associated with complete remission and overall response rate. Outcome of 1st Salvage – FCR Relapsed/Refractory (112 pts) Characteristic Value Patients %CR %OR Med Surv (Mths) Age / years
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  • 7
    Publication Date: 2009-11-20
    Description: Abstract 2347 Poster Board II-324 The human T cell leukemia/lymphoma 1 (TCL1) oncogene was initially identified as a target of chromosomal translocations and inversions at the 14q32.1 chromosome breakpoint region in T-cell prolymphocytic leukemia (T-PLL). Increased TCL1 expression is seen in follicular lymphoma, Burkitt lymphoma, diffuse large B-cell lymphoma, and chronic lymphocytic leukemia (CLL). Transgenic mice over-expressing TCL1 under control of the mu immunoglobulin gene enhancer develop a CD5+ B cell lymphoproliferative disorder that mimics human CLL, indicating that TCL1 plays a central and/or causal role in the pathogenesis of CLL. However, chromosome aberrations that constitutively activate TCL1 have not (yet) been identified in the vast majority of CLL patients, and therefore the oncogenic mechanism(s) of TCL1 activation in CLL remain unclear. There is growing evidence that external signals from the microenvironment control and regulate the survival and proliferation of CLL cells. Marrow stromal cells (MSC) are highly effective in protecting CLL cells from spontaneous and drug-induced apoptosis, and are used as a model system to study the marrow microenvironment. In order to explore the molecular cross talk between CLL cells and MSC, we co-cultured CLL cells with different MSC and analyzed gene expression changes induced by co-cultures with MSC, an approach similar to our recent study with nurselike cells (Blood 113:3050-8, 2009). For this, RNA was extracted from 19-purified CLL cells from 10 different patients (baseline expression, day 0). Also, the same patients' samples were co-cultured on stroma cells (KUSA-H1, NK-Tert) for 2 and 7 days. At these time points, RNA again was isolated after CD19-purification. Then, gene expression was determined using HG U133 plus 2.0 oligonucleotide arrays from Affymetrix. Gene expression changes were analyzed in individual patients' samples, comparing baseline samples' gene expression to samples after 2 and 7 of co-culture on MSC. We observed relatively homogeneous gene expression changes in CLL cells after co-culture with MSC. We found that TCL1 was among the top 5 genes that were most highly up-regulated by MSC, based on at least 3-fold up-regulation in at least 6 of the paired samples. We also found an up-regulation of TCL1 at the protein level when assessed by immunoblotting and flow cytometry in CLL samples after co-culture with MSC. These findings indicate that MSC can induce and regulate TCL1 expression in CLL, suggesting that the microenvironment plays an even greater role in the pathogenesis of this disease than previously recognized. Disclosures: No relevant conflicts of interest to declare.
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  • 8
    Publication Date: 2008-11-16
    Description: The majority of patients with acute myelogenous leukemia (AML) who achieve complete remission (CR) with initial chemotherapy will eventually relapse. Most relapses occur in the first three years and rare patients relapse after being in CR for more than 5 years. We have reviewed retrospectively 2347 patients with AML treated at M D Anderson Cancer Center from January 1980 to July 2008. Of the total cohort, 1366 patients achieved CR and among these 942 patients relapsed. We identified 11 patients (1.16%) who relapsed after being in CR 〉5 years; these patients are the focus of this analysis. There were 4 females and 7 males. Their median age was 66 years (range 37–79), and their median presentation white blood cell (WBC) count was 2.3 x109/L (range, 1.1–92.3). The FAB classification was M2 in 5 patients, M1, M4, M5, M6 in 1 patient each, and unknown in 2 patients. Initial cytogenetics were diploid in 6, del(7q) in one, miscellaneous in 1, and unavailable in 3 patients. Initial therapy was with combination of idarubicin (Ida) and cytarabine (Ara-C) in 4 patients (1 with additional fludarabine), amsacrine based in 3, daunorubicin (Dauno) single agent in 2 and other agents in 2 patients. All patients except one achieved CR after the first induction course; one patient needed 2 cycles of induction to achieve CR. None underwent an allogeneic stem cell transplant in first CR. The median duration of CR was 81 months (range, 60–137). At the time of relapse, median WBC count was 4.4 x109/L (range 1.7–48.8). Karyotype at relapse was diploid in 2, del(5)del(7) in 1, del(6)del(7) in 1, trisomy 8 in 1, hyperdiploid in 2, add(2q) and add(6q) in 1 each and unavailable in 2 patients. The karyotype at relapse was different from the initial finding in 8 of 8 patients with available data at both time points. Treatment for relapse included Ida (or Dauno) with Ara-C in 8 patients (1 with additional fludarabine), and other agents in 3 patients. The response to treatment was CR in 4, partial remission in 2, resistant in 4 and unknown in 1. No patient underwent an allogeneic stem cell transplant in second CR. The median duration of the second CR was 2 months (range 0–37). The median survival after relapse was 6.4 months (range 1–39). Median survival from initial diagnosis of AML was 107 months (range 68–143). We conclude that late relapses in AML (〉5 years after CR) are infrequent (1.16% of all relapses) and response to their subsequent therapy is poor; best responses occur with a regimen similar to the initial induction regimen. The karyotype at relapse is frequently different raising the question of a second AML versus relapse with the original clone.
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  • 9
    Publication Date: 2012-11-16
    Description: Abstract 2885 MicroRNAs (miRs) are involved in the initiation, progression and dissemination of CLL cells (Calin GA, Croce CM. Blood 114:4761, 2009). Recent studies showed that high levels of miR-155, previously shown to regulate hematopoietic cell development, are expressed in CLL cells. Because transgenic miR-155 overexpression in the mouse stimulates B-cell proliferation, it is thought that miR-155 plays a role in the pathogenesis of CLL (Calin GA et al. N Engl J Med 353:1793, 2005). STAT3 is constitutively activated in CLL and induces the transcription of several STAT3-regulated genes. A recent study demonstrated that STAT3 activates miR-21 and miR-181b-1 (Iliopolus D. et al. Mol Cell 39:493, 2010). Therefor we wondered whether STAT3 enhances the expression of miR-155 in CLL cells. Because a sequence analysis revealed that the promoter of miRNA-155 harbors γ-interferon activation sequence-like elements typically activated by STAT3, we sought to determine whether STAT3 directly activates miR-155 expression. We generated truncated constructs of the miR-155 promoter, co-transfected them into MM1 cells together with STAT3 small interfering (si) RNA (siRNA), and assessed their luciferase activity. The luciferase activity data suggested that of the two putative STAT3 binding sites only one site is involved in STAT3 induced transcription because STATR3-siRNA reduced the activity of miRNA-155 promoter of constructs that harbor this site. To confirm these data we performed an electrophoretic mobility shift assay (EMSA) and chromatin immune-precipitation (ChIP). The EMSA confirmed that STAT3 bound the miR-155 promoter in fresh CLL cells, and ChIP confirmed that STAT3 bound one putative STAT3-binding site in the miR-155 promoter but not to the other, as demonstrated by the luciferase assay; STAT3 co-immuno-precipitated only one putative STAT3 binding region of miR-155 promoter and other STAT3-regulated genes. Finally, STAT3-small hairpin RNA (shRNA) downregulated miR-155 and other STAT3-regulated genes, suggesting that constitutively activated STAT3, binds miR-155 promoter and induces miR-155 transcription in CLL cells. Disclosures: Keating: Celgene Corporation: Consultancy, Research Funding; Roche: Consultancy, Research Funding; Xcenda: Consultancy, Speakers Bureau.
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  • 10
    Publication Date: 2012-11-16
    Description: Abstract 2886 Non-coding RNAs regulate the expression of more than 30% of protein-coding genes both at a post-transcriptional and translational level. Although approximately 1000 microRNAs (miRs) have been identified in the human genome, little is known about the mechanisms that regulate miR expression. STAT3 regulates the transcription of miR-21, and miR181b-1, binds to their promoter and induce neoplastic cell transformation (Iliopoulos, Jaeger et al. 2010). Because STAT3 is constitutively activated in CLL cells (Hazan-Halevy, Harris et al. 2010) we sought to investigate how STAT3 affects non-coding RNA gene expression in CLL cells. We transfected peripheral blood CLL cells from 3 different patients with STAT3-shRNA and assessed non-coding RNA levels using a non-coding RNA array containing 2277 human miR probes, 960 from ultra-conserved genes and 3540 of long non-coding RNAs. When compared to transfection control, 152 probes from 78 non-coding RNA genes were differentially expressed (134 down-regulated and 18 up-regulated), suggesting that STAT3 affects the non-coding RNA network in CLL cells. Supervised clustering analysis was used to select genes for validation. By using quantitative RT-PCR we validated our gene array analysis. Similar to the data obtained by the non-coding RNA array, we found that transfection of CLL cells with STAT3- down-regulated the levels of miR-21, miR-155, and miR-320b. Binding site prediction programs and ChIP-seq data embedded in the UCSC genome browser determined that in 5 of 7 genes, down-regulated by STAT3-shRNA transfection, were either putative or experimentally confirmed STAT3-binding sites, indication that STAT3 directly regulates the transcription of those miRs. It has been shown that the interaction between miRs and single stranded RNA is dependent on base pairing in a seed region at positions 2 to 8. High levels of 4.8kb single stranded STAT3 RNA transcripts, present in CLL cells, provide a substrate for such paring. Therefore, we assumed that STAT3 functions as a “RNA sponge” soaking up miRs and altering their effective levels and function. To test this hypothesis we used the pattern-based RNA22 algorithm and identified potential miR targets. We than calculated the energy that would be released if the corresponding RNA/RNA complexes are saturated. We found that the energy released from binding of miRs to STAT3 sequences would be higher than energy released from binding to a random sequence with same length and base content suggesting that STAT3 “sponges out” miRs in a sequence specific manner. Thus, CLL cells are characterized by an ongoing interaction between STAT3-mediated transcriptional regulation of non-coding RNA and miR-mediated translational regulation of coding genes. Disclosures: No relevant conflicts of interest to declare.
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