Ara-C Arm Research Articles

AraC Functional Suppressors of Mutations in the C-Terminal Domain of the RpoA Subunit of the Escherichia coli RNA Polymerase.

In E. coli, transcriptional activation is often mediated by the C-terminal domain of RpoA, the α subunit of RNA polymerase. Random mutations that prevent activation of the arabinose PBAD promoter are clustered in the RpoA C-terminal domain (α-CTD). We have isolated functional suppressors of rpoA α-CTD mutations that map to araC, the main transcriptional regulator of ara genes, or to the PBAD promoter. No mutation was found in the DNA regulatory region between araC and PBAD. Most suppressors that improve PBAD transcription are localized to the N-terminal domain of AraC. One class of araC mutations generates substitutions in the core of the N-terminal domain, suggesting that they affect its conformation. Other suppressors localize to the flexible N-terminal arm of AraC. Some, but not all, suppressors confer an arabinose constitutive phenotype. Suppression by both classes of araC mutations requires the α-CTD to stimulate expression from PBAD. Surprisingly, in rpoA+ strains lacking Crp, the cAMP receptor protein, these araC mutations largely restore arabinose gene expression and can essentially bypass Crp activation. Thus, the N-terminal domain of AraC exhibits at least three distinct activities: dimerization, arabinose binding, and transcriptional activation. Finally, one mutation maps to the AraC C-terminal domain and can synergize with AraC mutations in the N-terminal domain.

Personalization of Induction Therapy for Pediatric AML to Ara-C+Dauno+ Etoposide (ADE) or Clofarabine+Ara-C According to a Polygenic Ara-C SNP Score- ACS10

Acute myeloid leukemia (AML) is a heterogenous disease with overall suboptimal outcome. Although chemotherapy regimens that include cytarabine (ara-C) induce remission in a majority of pediatric AML patients, approximately 30% relapse and subsequently have very dismal outcome. Ara-C is a prodrug requiring activation to ara-CTP which induces leukemic cell death. Thus, inter-patient variation in each patient's ability to activate ara-C is a significant contributor to clinical outcomes. We recently performed a comprehensive pharmacogenomics evaluation of SNPs in ara-C metabolism pathway genes and developed a polygenic ara-C 10-SNP genotype (ACS10) score based on association with leukemic intracellular ara-CTP levels and clinical outcome (Elsayed et al, 2022, JCO1). Our results demonstrated that patients with low ACS10 score had poor outcomes when given standard induction including low-dose ara-C, daunorubicin and etoposide (ADE); however their outcomes were much better by augmenting therapy with either an increased dose of ara-C or the addition of gemtuzumab ozogamicin1. Conversely, patients with a high ACS10 score fared worse when given high-dose ara-C than low ara-C dose-based ADE induction (LDAC). These results suggest that pediatric AML patients may benefit from pharmacogenetic personalization of ADE therapy according to their ACS10 scores. Additionally, these results motivate research regarding the utility of ACS10 for pharmacogenetic personalization of other therapies for pediatric AML. Clofarabine is another nucleoside analog that inhibits both DNA polymerase as well as ribonucleotide reductase, thus enhancing the activity of ara-C. Recent data from the AML08 clinical trial [NCT00703820] has shown promising results with use of clofarabine with cytarabine during remission induction in pediatric AML patients.2 Therefore, we evaluated the association of ACS10 score with outcomes among 91 patients randomly assigned standard ADE induction on the AML02 clinical trial (LDAC arm) [NCT00136084] and 117 patients randomly assigned an induction of clofarabine and ara-C (Clo+Ara-C arm) on the AML08 trial [NCT00703820] (Figure 1A shows the study design). 5-year event-free survival (EFS) and overall survival (OS) of patients treated with ADE improved with increasing ACS10 score; however, for patients treated with Clo+Ara-C, improvement with increasing ACS10 score was not observed (OS shown in Figure 1A). This differential outcome association pattern suggests that thresholding the ACS10 score at 0 could be used to classify patients into low (<=0) and high (>0) ACS10 groups. Patients within low ACS10 score group had a better outcome with Clo+AraC whereas the high ACS10 score patient group fared better with ADE. In particular, there is significant improvement in EFS and OS within the low-ACS10 score patients when treated with Clo+Ara-C as compared to ADE (Clo+AraC vs. ADE; EFS HR=0.45, 95% CI: 0.23-0.82; p=0.01; OS HR=0.45, 95% CI: 0.19-0.93, p=0.028; Figure 1B). In contrast, patients with a high ACS10 score had worse EFS and OS with Clo+AraC induction than with ADE induction (EFS HR= 1.84, 95% CI: 0.99-3.41, p=0.05; OS HR= 2.40, 95%CI: 1.13-5.13; p=0.02, Figure 1B). These results are unlikely to suffer from a strong historical comparison bias because there are not statistically significant differences in the outcomes of the randomly assigned therapies of the AML02 and AML08 trials as well as outcome by the clinical trial (EFS/OS of each arm of the two trials as well as between AML02 and AML08 trials; p=0.8, data not shown). In summary, consistent with our recent report, these results show that for patients with Low-ACS10 genetic score prognosis is poor with standard ADE induction. However, therapy augmentation options such as Clo+AraC, ADE with high-dose Ara-C, and ADE+gemtuzumab may improve the prognosis. This calls for an action on using preemptive genotyping for selection of the most effective induction 1 chemotherapy regimen to achieve maximum clinical benefit. References. 1. Elsayed AH, et al: Polygenic Ara-C Response Score Identifies Pediatric Patients With Acute Myeloid Leukemia in Need of Chemotherapy Augmentation. JCO 2022, PMID:34990262 2. Rubnitz JE, et al: Clofarabine Can Replace Anthracyclines and Etoposide in Remission Induction Therapy for Childhood Acute Myeloid Leukemia: The AML08 Multicenter, Randomized Phase III Trial. JCO 2019, PMID:3124652 Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Addition of High-Dose Cytarabine to Immunochemotherapy before Autologous Stem-Cell Transplantation in Patients Aged 65 Years or Younger with Mantle Cell Lymphoma (MCL Younger): A Long-Term Follow-up of the Randomized, Open-Label, Phase 3 Trial of the European Mantle Cell Lymphoma Network

Addition of High-Dose Cytarabine to Immunochemotherapy before Autologous Stem-Cell Transplantation in Patients Aged 65 Years or Younger with Mantle Cell Lymphoma (MCL Younger): A Long-Term Follow-up of the Randomized, Open-Label, Phase 3 Trial of the European Mantle Cell Lymphoma Network

Myeloablative versus non-myeloablative consolidative chemotherapy for newly diagnosed primary central nervous system lymphoma: Results of CALGB 51101 (Alliance).

7506 Background: Optimal consolidative therapy for primary central nervous system lymphoma (PCNSL) is not defined. Avoidance of whole brain radiation may reduce risk of neurotoxicity. Non-radiation consolidative options include myeloablative chemotherapy with autologous stem cell transplantation (HDT/ASCT) or non-myeloablative chemotherapy. Methods: This is a randomized phase 2, National Clinical Trials Network study of induction methotrexate (MTX) (8 g/m2 days 1, 15), temozolomide (TMZ) (150-200 mg/m2 D7-11), and rituximab (RTX) (C1 D3, 10, 17, 24 and C2 D3, 10 ) in four 28-day cycles followed by one cycle of cytarabine (ARA-C) (2 g/m2 BID, D1, 2) (MTRA). After induction, patients (pts) received consolidation with thiotepa (5 mg/kg BID, D -5, -4) plus carmustine (400 mg/m2, day -6) and ASCT (Arm A) or one cycle of ARA-C (2 g/m2 BID, D1-4) plus infusional etoposide (40 mg/kg over 96h) (Arm B). Pts were stratified on age and performance status and randomized 1:1 before induction. The primary endpoint was progression-free survival (PFS) from randomization. With 110 pts, there was 84% power to detect an improvement in PFS using a log-rank test (1-sided α= 10%), assuming a median PFS of 3 months for pts who progress during induction, and a median PFS of 2 years (yrs) for Arm B and 4.5 yrs for Arm A consolidation. This report includes the results for the primary endpoint analysis. Results: 113 pts (median age 61 yrs, range 33-75) were randomized (Arm A: 57, Arm B: 56) across 27 centers. 108 eligible pts who received induction therapy were included in the primary endpoint analysis (Arm A: 54, Arm B: 54). 72/108 pts started consolidation and 70/72 completed consolidation per protocol (Arm A: 36, Arm B: 34). With a median follow-up of 3.8 years, median PFS from randomization was 6 yrs (95% CI 3.9-not reached) in Arm A vs 2.4 yrs (95% CI 0.6-not reached) in Arm B (p = 0.02). However, more pts randomized to Arm B went off treatment before consolidation due to progression or death (28% vs 11%, p = 0.05). PFS landmarked at start of consolidation demonstrated a trend for improved PFS favoring Arm A (HR 0.58, 95% CI 0.25-1.36; p = 0.21). Median OS was not reached in either arm, and 3-yr estimates were 83% (95% CI 69-91; Arm A) vs 72% (95% CI 57-82; Arm B). Toxicities were similar between arms with no treatment-related mortality during consolidation. Conclusions: MTRA induction followed by myeloablative consolidation (Arm A) had improved PFS vs MTRA induction followed by non-myeloablative consolidation (Arm B), though more progressions or deaths leading to treatment discontinuation prior to consolidation in Arm B were noted. Both consolidation regimens were well-tolerated with encouraging PFS and OS in newly-diagnosed PCNSL. Support: U10CA180821, U10CA180882; https://acknowledgments.alliancefound.org . Clinical trial information: NCT01511562.

Myeloablative versus non-myeloablative consolidative chemotherapy for newly diagnosed primary central nervous system lymphoma: Results of induction therapy in Alliance 51101.

8042 Background: Optimal consolidative therapy for primary central nervous system lymphoma (PCNSL) is not defined. Avoidance of whole brain radiation may reduce risk of neurotoxicity. Non-radiation consolidative options include myeloablative chemotherapy followed by autologous stem cell transplantation (HDT/ASCT) or non-myeloablative chemotherapy. Methods: This is a randomized phase 2, National Clinical Trials Network study of induction methotrexate (MTX) (8 g/m2days 1, 15), temozolomide (TMZ) (150-200 mg/m2 D7-11), and rituximab (RTX) (C1 D3, 10, 17, 24 and C2 D3, 10) in four 28-day cycles followed by one cycle of cytarabine (ARA-C) (2 g/m2 BID, D1, 2) (MTRA). Following induction, patients (pts) received consolidation with thiotepa (5 mg/kg BID, D -5, -4) plus carmustine (400 mg/m2, day -6) and ASCT (Arm A) or one cycle of ARA-C (2 g/m2 BID, D1-4) plus infusional etoposide (40 mg/kg over 96h) (Arm B). The primary endpoint was median progression-free survival (PFS), designed to compare consolidation regimens. This report describes the results of the 5 cycles of induction therapy. Results: 113 pts (median age 61 years, range 33-75) were randomized (Arm A: 57, Arm B: 56) across 27 centers. 108 eligible pts who received induction therapy were evaluated. 36 pts (33.3%) did not proceed to consolidation, mainly due to disease progression (17), pt withdrawal (8), or adverse events including death (6). Grade 3 or 4 febrile neutropenia occurred in 12 pts (11.1%) during induction. Dose modifications of MTX were required in 75% of pts and 63.3% of cycles, mainly due to renal adjustments. Dose delays of MTX were required in 52.8% of pts and 22.2% of cycles. Overall response rate (CR, CRu, PR) at the end of induction was 65.7% (95% CI, 56%, 74.6%). Conclusions: While MTRA is feasible and active a significant proportion of pts did not receive consolidation, supporting the need to develop more effective induction strategies. Clinical trial information: NCT01511562 .

Computational and experimental investigation of constitutive behavior in AraC

Many mutations in the N-terminal arm of AraC result in constitutive behavior in which transcription of the araBAD genes occurs even in the absence of arabinose. To begin to understand the mechanism underlying this class of mutations, we used molecular dynamics with self-guided Langevin dynamics to simulate (1) wild-type (WT) AraC, (2) known constitutive mutants resulting from alterations in the regulatory arm, particularly alanine and glycine substitutions at residue 8 because P8G is constitutive, whereas P8A behaves like wild type, and (3) selected variant AraC proteins containing alterations in the dimerization core. In all of the constitutive arm mutants, but not the WT protein, residues 37-42, which are located in the core of the dimerization domain, became restructured. This raised the question of whether or not these structural changes are an obligatory component of constitutivity. Using molecular dynamics, we identified alterations in the core that produced a similar restructuring. The corresponding mutants were constructed and their ara constitutivity status was determined experimentally. Because the core mutants were not found to be constitutive, we conclude that restructuring of core residues 37-42 does not, itself, lead to constitutivity of AraC. The available data lead to the hypothesis that the interaction of the N-terminal arm with something other than the front lip is the primary determinant of the inducing versus repressing state of AraC.

Consolidation Chemotherapy for Adults With AML in First Remission: Is There a Best Choice?

Consolidation Chemotherapy for Adults With AML in First Remission: Is There a Best Choice?

Clofarabine Plus Cytarabine Compared With Cytarabine Alone in Older Patients With Relapsed or Refractory Acute Myelogenous Leukemia: Results From the CLASSIC I Trial

To compare the receipt of clofarabine plus cytarabine (Clo+Ara-C arm) with cytarabine (Ara-C arm) in patients ≥ 55 years old with refractory or relapsed acute myelogenous leukemia (AML). Patients were randomly assigned to receive either clofarabine (Clo) 40 mg/m(2) or a placebo followed by Ara-C 1 g/m(2) for five consecutive days. The primary end point was overall survival (OS). Secondary end points included event-free survival (EFS), 4-month EFS, overall remission rate (ORR; complete remission [CR] plus CR with incomplete peripheral blood count recovery), disease-free survival (DFS), duration of remission (DOR), and safety. Among 320 patients with confirmed AML (median age, 67 years), the median OS was 6.6 months in the Clo+Ara-C arm and 6.3 months in the Ara-C arm (hazard ratio [HR], 1.00; 95% CI, 0.78 to 1.28; P = 1.00). The ORR was 46.9% in the Clo+Ara-C arm (35.2% CR) versus 22.9% in the Ara-C arm (17.8% CR; P < .01). EFS (HR: 0.63; 95% CI, 0.49 to 0.80; P < .01) and 4-month EFS (37.7% v 16.6%; P < .01) favored the Clo+Ara-C arm compared with Ara-C arm, respectively. DFS and DOR were similar in both arms. Overall 30-day mortality was 16% and 5% for CLO+Ara-C and Ara-C arms, respectively. In the Clo+Ara-C and Ara-C arms, the most common grade 3 to 4 toxicities were febrile neutropenia (47% v 35%, respectively), hypokalemia (18% v 11%, respectively), thrombocytopenia (16% v 17%, respectively), pneumonia (14% v 10%, respectively), anemia (13% v 0%, respectively), neutropenia (11% v 9%, respectively), increased AST (11% v 2%, respectively), and increased ALT (10% v 3%, respectively). Although the primary end point of OS did not differ between arms, Clo+Ara-C significantly improved response rates and EFS. Study follow-up continues, and the role of clofarabine in the treatment of adult patients with AML continues to be investigated.

Computational Predictions of the Mutant Behavior of AraC

An algorithm implemented in Rosetta correctly predicts the folding capabilities of the 17-residue N-terminal arm of the AraC gene regulatory protein when arabinose is bound to the protein and the dramatically different structure of this arm when arabinose is absent. The transcriptional activity of 43 mutant AraC proteins with alterations in the arm sequences was measured in vivo and compared with their predicted folding properties. Seventeen of the mutants possessed regulatory properties that could be directly compared with folding predictions. Sixteen of the 17 mutants were correctly predicted. The algorithm predicts that the N-terminal arm sequences of AraC homologs fold to the Escherichia coli AraC arm structure. In contrast, it predicts that random sequences of the same length and many partially randomized E. coli arm sequences do not fold to the E. coli arm structure. The high level of success shows that relatively “simple” computational methods can in some cases predict the behavior of mutant proteins with good reliability.

Optimaization of Imatinib Therapy by Combination. 5 Year Survival and Response Results of the Pilot Phase of the Randomized German CML STUDY IV.

Abstract 862Rapid relapse after discontinuation of imatinib, the need for indefinite therapy and residual disease in most patients are the major challenges in management of CML. Combinations of imatinib with IFN simultaneously, or consecutively preceding imatinib, or with araC may improve treatment outcome. The German CML Study Group therefore designed a randomized trial to compare standard imatinib vs. imatinib + interferon alpha (IFN) vs. imatinib + low dose araC vs. imatinib after IFN failure (for low- and intermediate-risk patients, high risk patients received imatinib 800 mg instead). The current evaluation represents the prefinal results of the pilot phase of the trial. Inclusion criteria were newly diagnosed BCR/ABL positive CML in chronic phase (CP). Primary aims are: prolongation of survival (overall, OS, and progression free, PFS), determination of rates of hematologic, cytogenetic and molecular remissions, adverse events (AE) and role of allografting. By the end of 2005, 670 patients were randomized, 13 had to be excluded (no CML (n=3), pregnancy, no CP (n=1 each), imatinib 800 mg (n=8)). Analysis was according to intention to treat. 657 patients were evaluable (174 with imatinib 400 mg, 196 with imatinib+IFN, 158 with imatinib+araC and 129 with imatinib after IFN-failure). 656 patients were evaluable for hematologic, 611 for cytogenetic, and 618 for molecular responses. Patient characteristics of treatment arms were similar for age (median 53 years), sex (40% female), median values for Hb (12.6 g/dl), WBC (66.2/μl), platelets (383/μl) and for Euro risk score (low 35%, intermediate 54%, high 10%). The median dose of imatinib was 400mg/die in all arms, of araC 10 mg per treatment day and of IFN 4.2 Mio I.U./die in the imatinib after IFN arm and 1.8 Mio I.U./die in the imatinib+IFN arm. Median observation time was 57.3 months. 55 patients died, 73 patients were transplanted in 1st CP, 81 patients progressed, 59 patients were switched to second generation TKIs. After 3 years 126 patients (72%) of the imatinib 400mg arm still received the initial therapy as well as 60 patients (30%) of the imatinib+IFN arm and 53 patients (34%) of the imatinib+araC arm. 9 patients (7%) of the imatinib after IFN arm are still on IFN. 5-year OS of all patients is 91%. 5-year PFS of all patients (no death, patient still in first chronic phase) is 87%. 5-year-OS and PFS according to treatment arm are shown in the Table. At 5 years, the cumulative incidences of achieving complete cytogenetic remission or major molecular remission (MMR) as determined by competing risks (death, progression) are not different (Table). Type and severity of adverse events (AE) over a 5-years period did not differ from those reported previously (Table). Hematologic AEs grade III/IV were similar in all therapy arms except leukopenia grade III/IV, which was more frequently observed in the imatinib after IFN arm (14%). Non hematologic AEs were mainly fluid retention, neurological and gastrointestinal symptoms and fatigue. Neurologic symptoms and fatigue were more often reported for the therapy arms with IFN.Imatinib 400mgImatinib+IFNImatinib+AraCImatinib after IFN5-Year Survival and Response RatesOS87%93%92%92%PFS84%91%88%84%CCR92%92 %89%83%MMR83%78%80%70%Adverse Events, WHO Grade III/IVAnemia7%1%3%3%Leukopenia4%5%2%14%Thrombocytopenia5%6%6%6%WHO Grade I-IVEdema15%13%5%0%Neurological5%15%5%22%Gastrointestinal17%27%21%15%Fatigue8%13%9%23%This analysis shows excellent survival and durable response rates in all arms. Currently, survival in all treatment arms is equal to, or better than in IRIS. To verify possible differences in survival, e.g. imatinib 400 mg vs. imatinib + IFN, longer observation is planned. Although cytogenetic and molecular responses in the imatinib after IFN failure arm at 5 years are inferior to that in the other treatment arms, the question of whether the consecutive therapy with IFN first and imatinib after IFN-failure provides a survival advantage requires long term follow-up. Imatinib in combination with, or after IFN, or with low dose araC are feasible and safe treatment modalities. We expect that the study will optimize and improve therapy outcome in CML. Disclosures:German CML Study Group:Deutsche Krebshilfe: Research Funding; Novartis: Research Funding; German Competence Net : Research Funding; European LeukemiaNet: Research Funding; Roche: Research Funding; Essex: Research Funding.

Randomized phase II trial on primary chemotherapy with high-dose methotrexate (HD-MTX) alone or associated with high-dose cytarabine (HD-araC) for patients with primary CNS lymphoma (I.E.L.S.G. #20 Trial): Tolerability, activity, and survival analyses

8545 Background: HD-MTX-based chemotherapy (cht) is the conventional approach to primary CNS lymphoma (PCNSL), but superiority of polycht over HD-MTX alone is unproven. A benefit of adding HD-araC to MTX has been suggested. This is a randomized phase II trial comparing HD-MTX monocht versus HD-MTX plus HD-araC as primary cht in immunocompetent patients (pts) with PCNSL. Methods: 79 HIV- pts with newly diagnosed PCNSL, age 18–75 ys, ECOG-PS≤3, and measurable disease were randomly assigned to receive 4 courses (interval 3 weeks) of MTX 3.5 g/mq (control arm; n=40) or MTX (same dose) + araC 2 g/mq × 2/d, d 2–3 (experimental arm; n=39). Cht was followed by whole-brain irradiation. Pts were stratified based on IELSG score and centre irradiation policy for pts &gt;60 ys in complete remission (CR) after cht. CR rate (CRR) after cht was the primary endpoint; planned accrual (α=.05 β=.2) for P0 30% and P1 50% was 39 pts/arm. Results: Median age of the 79 entered pts was 58 ys (range 25–74). No differences in clinical presentation between arms were observed. Two hundred thirty-one (73%) of the 316 planned courses were actually delivered (MTX 71%; MTX+araC 76%). Causes of cht interruption were: progressive disease in 20 MTX and 8 MTX+araC pts, toxicity in 1 MTX and 7 MTX+araC pts and refusal in 2 MTX+araC pts. As expected, neutropenia, thrombocytopenia and infections were more common in MTX+araC arm. All G3–4 non-hematological toxicities were &lt;5%. One MTX pt and 3 MTX+araC pts died of toxicity. CRR was 18% after MTX and 46% after MTX+araC (p=0.006), with an ORR of 40% and 69% (p=0.009), respectively. At a median follow-up of 30 m., 31 MTX and 22 MTX+araC pts experienced failure, with a 3-yr FFS of 21±6% and 38±8% (p=0.01), respectively. No differences in relapse sites or salvage efficacy between treatment arms were observed. Twelve MTX and 20 MTX+araC pts are alive, with a 3-yr OS of 32±8% and 46±9% (p=0.07). Conclusions: This is the first randomized trial on PCNSL with completed accrual. The addition of HD-araC to HD-MTX resulted in significantly better outcome and acceptable toxicity. MTX+araC may be the cht combination used as control arm in future randomized trials. No significant financial relationships to disclose.

Constitutive Mutations in theEscherichia coliAraC Protein

The Escherichia coli AraC protein represses and induces the araBAD operon in response to the absence or presence of l-arabinose. Constitutive mutations in the AraC gene no longer require the presence of l-arabinose to convert AraC from its repressing to its inducing state. Such mutations were isolated directly by virtue of their constitutivity or by their resistance to the nonmetabolizable arabinose analog, d-fucose. The majority of the constitutive mutations lie within the same residues of the N-terminal regulatory arm of AraC. Two, however, were found in the core of the dimerization domain. As predicted by the light switch mechanism of AraC, constitutive mutations increase the susceptibility of the N-terminal arms to digestion by trypsin or chymotrypsin, suggesting that these mutations weaken or disrupt the arm structure required for repression by AraC. Fluorescence, circular dichroism, and cysteine reactivity measurements show that the constitutive mutations in the core of the dimerization domain lead to a weakening of the support for the arms and reduce the stability of the minus-arabinose arm structure. These mutations also weaken the interaction between the two-helix bundle and the beta-barrel subdomains of the dimerization domain and reduce the structural stability of the beta-barrels.

Randomized Phase II Trial on Primary Chemotherapy with High-Dose Methotrexate Alone or Associated with High-Dose Cytarabine for Patients with Primary CNS Lymphoma (IELSG #20 Trial): Tolerability, Activity and Event-Free Survival Analysis

Background: High-dose methotrexate (HD-MTX)-based chemotherapy is the conventional approach to primary CNS lymphomas (PCNSL), but superiority of polychemotherapy over HD-MTX alone is unproven. A benefit of adding high-dose cytarabine (araC) to MTX has been suggested by a meta-analysis and a large retrospective series. This is a randomized phase II trial comparing HD-MTX monochemotherapy versus HD-MTX plus HD-araC as primary chemotherapy in immunocompetent patients (pts) with PCNSL.Patients: HIV-negative pts with newly diagnosed PCNSL, age 18–75 ys, ECOG-PS≤3, and measurable disease were randomly assigned to receive 4 courses (interval 3 weeks) of MTX 3.5 g/mq (control arm) or MTX (same dose) + araC 2 g/mq × 2/d, d 2–3 (experimental arm). Chemotherapy was followed by complementary whole-brain irradiation (WBRT). Pts were stratified based on IELSG score and centre WBRT policy for pts >60 ys in complete remission (CR) after chemotherapy. Complete remission rate (CRR) after chemotherapy was the primary endpoint; planned accrual (a=.05 b=.2) for P0 30% and P1 50% was 39 pts/arm.Results: 79 pts (median age 58 ys; range 25–74) were randomly assigned to receive MTX (n=40) or MTX+araC (n=39). IELSG risk was low in 22 (28%) pts, intermediate in 48 (61%) and high in 9; 7 (9%) pts had ocular lesions and 7 (9%) had meningeal disease; no differences in clinical presentation between arms were observed. Two hundred thirty-one (73%) of the 316 planned courses were actually delivered (MTX 71%; MTX+araC 76%). Causes of chemotherapy interruption were: progressive disease (PD) in 20 (50%) MTX and 8 (21%) MTX+araC pts (p<0.001), toxicity in 1 (3%) MTX and 7 (18%) MTX+araC pts (p=0.009) and refusal in 2 MTX+araC pts. Dose reduction ≥25% was indicated in 1 MTX and 17 MTX+araC pts. G4 neutropenia (10% vs. 74%), G4 thrombocytopenia (5% vs. 64%) and infections (3% vs. 23%) were significantly higher in MTX+araC arm. All G3–4 non-hematological toxicities were <5%. One MTX pt (3%, cardiotoxicity) and 3 MTX+araC pts (8%, sepsis - hepatotoxicity) died of toxicity.After chemotherapy, 7 MTX and 18 MTX+araC pts achieved CR (18% vs. 46%; p=0.0002); 9 MTX and 9 MTX+araC pts achieved PR (ORR: 40% vs. 69%; p=0.0002). After conclusion of the whole upfront treatment, 11 MTX and 25 MTX+araC pts achieved CR (28% vs. 64%; p<0.0001).At a median follow-up of 25 months, 31 MTX and 22 MTX+araC pts experienced failure (PD, relapse, death), with a 3-yr event-free survival (EFS) of 20% and 38% (p=0.01), respectively. Relapse/progression involved the brain, alone (n=34) or associated with eyes or meninges (n=8) in 42 (88% of relapses) cases, while it involved meninges, with or without eyes, in 4 (8%) cases; a systemic dissemination was detected in 2 (4%) pts. No differences in relapse sites between treatment arms were observed. Salvage with MTX+araC in 6 pts relapsed after MTX was invariably followed by PD. Conversely, 8 of 12 pts with PD after primary chemotherapy treated with salvage WBRT achieved an objective response, with a median response duration of 10 months (1–51+). Treatment arm and IELSG risk score were the two variables independently associated with EFS. Fifteen MTX and 21 MTX+araC pts are alive, with a 3-yr OS of 34% vs. 47% (p=0.12).Conclusions: This is the first randomized trial on PCNSL with completed accrual. The addition of HD-araC to HD-MTX resulted in significantly better outcome and acceptable toxicity. MTX+araC may be the chemotherapy combination used as control arm in future randomized trials.

Functional modes of the regulatory arm of AraC

One of the two crystal structures of the arm-dimerization domain determined in the absence of arbinose fails to show the arm, whereas the other structure does show it. The two structures lead to different pictures for the regulatory behavior of the arms. Trypsin digestion, fluorescence anisotropy, and NMR experiments presented here were designed to resolve the issue and show that in arm-dimerization domain, the arms are structured, although differently, in the presence and absence of arabinose. The arms have also been shown to interact with the DNA binding domains of AraC by their requirement for the immobilization of the DNA binding domains that is necessary for DNA looping and repression. The binding of arabinose has been shown to release the DNA binding domains and looping ceases. The picture resulting from the new experiments and the crystal structures of the arm-dimerization domain is that in the absence of arabinose, the arm adopts one structure on the dimerization domain and that the DNA binding domain then binds to this complex. Upon binding arabinose, the arm restructures and as a result, no longer serves as a gasket between the DNA binding domain and dimerization domain. The DNA binding domain is then released, subject only to the constraints imposed by the flexible linker connecting it to dimerization domain, and the protein relocates on the DNA and activates transcription.

Specific interactions by the N‐terminal arm inhibit self‐association of the AraC dimerization domain

Deletion of the regulatory N-terminal arms of the AraC protein from its dimerization domain fragments increases the susceptibility of the dimerization domain to form a series of higher order polymers by indefinite self-association. We investigated how the normal presence of the arm inhibits this self-association. One possibility is that arms can act as an entropic bristles to interfere with the approach of other macromolecules, thereby decreasing collision frequencies. We examined the repulsive effect of flexible arms by measuring the rate of trypsin cleavage of a specially constructed ubiquitin-arm protein. Adding an arm to ubiquitin or increasing its length produced only a modest repulsive effect. This suggests that arms such as the N-terminal arm of AraC do not reduce self-association by entropic exclusion. We consequently tested the hypothesis that the arm on AraC reduces self-association by binding to the core of the dimerization domain even in the absence of arabinose. The behaviors of dimerization domain mutants containing deletions or alterations in the N-terminal arms substantiate this hypothesis. Apparently, interactions between the N-terminal arm and the dimerization domain core position the arm to interfere with the protein-protein contacts necessary for self-association.

The K247R Substitution in ABL Tyrosine Kinase Domain Is Not a Mutation Leading to Imatinib Resistance but a Polymorphism Rarely Present in CML Patients and in Normal Subjects.

Abstract The major mechanism for resistance to imatinib mesylate (IM) is the onset of ABL point mutations altering functional inhibition of the tyrosine kinase activity by IM. Biochemical, cellular assays and clinical studies have demonstrated that different BCR-ABL mutations exhibit various degrees of resistance, and mutations occurring in the ATP-binding loop may be correlated with subsequent disease progression. In this study, we investigated the status of the K247R ABL polymorphism and correlated it to disease outcome. Patients and methods: Two patients (P1 and P2) were diagnosed with CML based on peripheral blood findings, karyotyping analysis (showing t(9;22)(q34;q11)) and molecular analysis for BCR-ABL (indicating M-BCR fusion transcripts) in 2,000 and 1,994, respectively. P1, a 54 years old male, enrolled in the Novartis IRIS study, was randomly assigned to the interferon + AraC arm after informed consent. The patient achieved a complete hematologic remission (CHR) at 3 months and a complete cytogenetic response (CCR) at 24 months. At time of cytogenetic relapse (2 years later), P1 had never received IM which was introduced in April 2,005. P2 received IM (400mg to 600mg/day) during 82 months and had shown only CHR during 14 months with no MCR. Epithelial cells were collected in the mouth through sterile foam tipped applicators for both patients. DNA was obtained from blood samples of 232 individuals, including 124 patients with CML, 72 patients with acute myeloid leukemias (AML) and 36 normal healthy donors. The K247R change was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique (AluI restriction enzymatic site abolished) and was confirmed by direct sequencing. Results: Both patients, showing the K247R substitution located close to the P-loop, were retrospectively investigated during disease progression. We found that this change accounted for 100% of the BCR-ABL transcripts at CML diagnosis (and in all the further samples) for P1 (no material was yet available from P2 at this time) and for 50% of the ABL gene in extracted DNA from epithelial cells in the 2 patients. P1, despite of the K247R substitution received IM (400 mg/day) and achieved a CHR, a CCR and a good molecular response (one log reduction after two months of IM). IM resistance observed in P2 was probably due to the presence of an additional F317L mutation, known to induce a very strong resistance to IM. The F317L mutation accounted for 100% of the BCR-ABL transcripts at the resistance, was absent in DNA from epithelial cells. The screening showed the K247R exchange in 1 normal subject (heterozygote), in 2 CML patients (P1 and P2: at heterozygous state in normal cells and at homozygous state in BCR-ABL transcripts) and in none AML samples. According to that, the incidence of this polymorphism seems to reach nearly 1 to 1.5%. Conclusion: This study demonstrates that the K247R substitution in ABL tyrosine kinase domain is not a mutation leading to IM resistance but only a rare polymorphism. Detailed analysis of this polymorphism status will be reported.

Concept, Feasibility and Results of the Randomized Comparison of Imatinib Combination Therapies for Chronic Myeloid Leukemia: The German CML-Study IV.

Targeted therapy with the BCR-ABL tyrosine kinase inhibitor imatinib induces high response rates in chronic myeloid leukemia (CML) patients (pts). Nevertheless, residual disease remains in virtually all pts on imatinib monotherapy as a potential cause of relapse. In July 2002, the German CML-Study Group activated the four-armed randomized controlled trial comparing imatinib 400mg/d with imatinib+IFN, imatinib+Ara-C, and imatinib after IFN failure in newly diagnosed pts with chronic phase CML. Randomization is stratified according to prognostic risk groups and not biased by consecutive allogeneic stem cell transplantation (SCT). High-risk pts are randomly assigned to primary imatinib-based therapies including a treatment arm with 800mg/d imatinib. By 7/05, 632 pts were randomized: imatinib 400mg/d (n=129), imatinib+IFN (n=179), imatinib+Ara-C (n=156), imatinib after IFN failure (n=157), and imatinib 800mg/d (n=11). According to the Hasford score, 35% of pts were low risk, 54% intermediate risk, and 11% high risk. At baseline, median WBC count was 67/nl (3–529), median platelet count 391/nl (34–2,799) and median hemoglobin 12.6 g/dl (6.1–16.6). We sought to evaluate results of pts with a >12 months follow-up (n=416), recruited between 7/02 and 6/04 (imatinib 400mg/d, n=102; imatinib+IFN, n=126; imatinib+Ara-C, n=104; imatinib after IFN failure, n=81; imatinib 800mg/d, n=3) and of pts with a >24 months follow-up (n=232), recruited between 7/02 and 6/03 (imatinib 400mg/d, n=55; imatinib+IFN, n=74; imatinib+Ara-C, n=54; imatinib after IFN failure, n=49) with respect to response, resistance, and progression. After 12 months of treatment cytogenetic data are available from 238/335 pts (71%) randomized to primary imatinib based therapies. 209 pts (63%) achieved a major cytogenetic remission (MCR; Ph+<35%), being complete in 53%. Q-PCR data were available in 270 pts (81%). 89 pts (27%) achieved a major molecular response (MMR; ratio BCR-ABL/ABL <0.12%). After 24 months cytogenetic data are available from 141/183 pts (77%). 126 pts (69%) achieved a MCR, being complete in 60%. Q-PCR data were available in 149 pts (81%). 73 pts (40%) achieved a MMR. 12/177 pts lost CCR (7%) during the 1st year and 6/110 pts (5%) during the 2nd year of treatment. Within the 1st year 13/335 pts (6 low, 3 intermediate, 4 high risk; 4%) progressed to blast crisis, 4 of them revealed clonal evolution (complex aberrant karyotype, n=3; +8, n=1), two others BCR-ABL mutations (E355G and M244V). Within the 2nd year 3/232 pts (1 each low, intermediate, and high risk; 1%) progressed to blast crisis. During the 1st year of treatment imatinib therapy was stopped due to side effects or resistance in 6% of pts in the imatinib 400mg arm, in 2% of pts in the imatinib+IFN, and in 2% of pts in the imatinib+Ara-C arm. IFN was stopped in 21%, Ara-C in 18% of pts. This interim analysis of a prospective randomized trial with imatinib and imatinib in combination for newly diagnosed pts with CML has proven feasibility of imatinib combinations in addition to high response and low progression rates. Long-term observation will demonstrate whether the promising results will be maintained and will improve survival.

Phase I Study of Clofarabine Plus Idarubicin and Clofarabine Plus Idarubicin Plus Cytarabine (ARA-C) in Patients (PTS) with Relapsed and Primary Refractory Acute Myeloid Leukemia (AML), Myelodysplastic Syndrome (MDS), and Myeloid Blast Phase of Chronic Myeloid Leukemia (CML).

Phase I and II clinical studies demonstrated activity of Clofarabine in acute leukemias. In previous studies we have investigated clofarabine, plus ara-C combinations and reported a CR rate of 24% in relapsed AML and 52% in previously untreated AML ≥ 50 years (yrs) with acceptable toxicity profile. Anthracyclines are active in AML. To explore clofarabine further in AML combinations we conducted a phase I study of clofarabine with idarubicin with or without ara-C in pts with relapsed AML, MDS, and CML. Considered as dose-limiting toxicities (DLT) are ≥ grade 3 drug-related toxicities. Maximum tolerated dose (MTD) will be determined by “3+3” dose escalation scheme. On the clofarabine (C)/idarubicin (I) combination (CI), 9 AML pts are enrolled (2 primary refractory, 7 first relapse). Median age: 58 yrs (range 24–71). Median first remission duration (CRD1): 3.1 mos. (0–7.6). For the first dose level, C was given at 22.5mg/m2 i.v. daily x 5d and I at 12mg/m2 i.v. daily x 3d. Among the first 6 pts, 2 ≥ gr. 3 toxicities (diarrhea, rash, ↑ bili) occurred necessitating dose de-escalation of C to 15mg/m2 i.v. daily x 5 and I 8mg/m2 i.v. daily x 3. Among 3 pts, 1 ≥ gr.3 toxicity (↑ bili) was observed. No responses occurred. On the CI + ara-C arm (CIA), 7 AML pts are enrolled (1 primary refractory, 6 first relapse). Median age: 58 yrs. (24–78). Median CRD1: 11.2 mos. (0–13.1). First dose level: C 22.5mg/m2 i.v. daily x 5d, I 8mg/m2 i.v. daily x 3d, A 1g/m2 i.v. daily x 5d. Of 3 pts, 2 developed ≥ gr.3 toxicities (↑ bili, diarrhea) leading to the following de-escalation: C 15mg/m2 i.v. daily x 5d, I 6mg/m2 i.v. daily x 3d, A 0.75g/m2 i.v. daily x 5d. Of 4 pts (1 ≥ gr. 3 rash, ↑ bili), 3 pts achieved CR. The phase I study is ongoing until determination of DLT and MTD for each arm. Our preliminary results indicate clinical activity of CIA even at the low dose level.

Low Dose Ara-C Versus Hydroxyurea with or without Retinoid in Older Patients Not Considered Fit for Intensive Chemotherapy: The UK NCRI AML14 Trial.

There is no adequate treatment for older patients with AML who are not considered fit for intensive chemotherapy who comprise a significant proportion of the AML population. As part of the ongoing NCRI (formerly MRC) AML14 Trial in patients over 60 years patients were randomised to Low Dose Ara-C (20mg bd for 10 days every 4–6 weeks) versus Hydroxycarbamide (Hydroxyurea). Because of preclinical studies showing sensitization to Ara-C, patients were in addition randomised to receive All-transretinoic acid or not (45mgs/m2 for 60 days).Two hundred and four patients entered; 129 had a WHO score of <2; 155 patients were >65 yrs; 108 had do novo, 53 secondary disease and 28 had high risk MDS (blasts >10%). One hundred and ninety-nine patients entered the HU vs LD-Ara-C randomisation and 204 entered the ATRA randomisation. The arms were balanced with respect to age; sex; disease type; WBC and performance score.Complete remission was seen in 1 of 92 (1%) patients in the HU arm and 15 of 94 (17%) in the LD Ara-C arm (P=0003). Overall survival was considerably improved (hazard ratio 0.61, 95% Cl 0.45 to 0.82, p=0.001). This improvement in outcome was not obtained at the expense of less well tolerated treatment: toxicity and supportive care requirements were similar between the two groups. However, there were no significant differences in outcome between patients given ATRA or not overall or within the treatment arms, although numbers were too small to rule out moderate benefits or disbenefits of treatment (hazard ratio for OS 0.97, 95% Cl 0.73 to 1.28, p=0.8).We conclude that LD-Ara-C in the schedule chosen could be adopted as a standard of care for older patients not fit for intensive chemotherapy but the outcome remains poor. Future strategies could combine Low Dose Ara-C with novel agents. This trial received a research grant from the UK Leukaemia Research Fund.

Mutational Analysis of Residue Roles in AraC Function

The previously isolated hemiplegic, induction-negative, repression-positive mutants, H80R and Y82C, were found to be defective in the binding of arabinose. Randomization of other residues close to arabinose in the three-dimensional structure of AraC or that make strong interactions with arabinose yielded induction-negative, repression-positive mutants. The induction and repression properties of mutants obtained by randomizing individual residues of the N-terminal arm of AraC allowed identification of the domain with which that residue very likely makes its predominant interactions. Residues 8–14 of the arm appear to make their predominant interaction with the DNA-binding domain. Although the side-chain of residue 15 interacts directly with arabinose bound to the N-terminal dimerization domain, the properties of mutant F15L indicate that this mutation increases the affinity of the arm for the DNA-binding domain.