ALBERT

Description: Background: Pralatrexate (PDX) is a novel targeted antifolate that is designed to accumulate preferentially in cancer cells. Pralatrexate has demonstrated activity at a range of doses in patients (pts) with relapsed/refractory T-cell lymphoma. The maximum tolerated dose (MTD) in a trial of pts with aggressive lymphomas was 30 mg/m2 weekly for 6 of 7 weeks. In that Phase 1 study, responses were seen in pts with cutaneous T-cell lymphoma (CTCL). To further explore this activity, we designed PDX-010, a multi-center, open-label, Phase 1 study of pralatrexate with vitamin B12 and folic acid in pts with relapsed/refractory CTCL. As CTCL is often a more indolent disease than peripheral T-cell lymphoma and treatment paradigms use maintenance approaches, we sought to identify the least toxic dose and schedule with activity for this distinct pt population through a dose de-escalation scheme. Methods: Eligible pts were required to have mycosis fungoides (MF), Sézary syndrome (SS), or cutaneous anaplastic large cell lymphoma (ALCL), and progression of disease (PD) after ≥ 1 systemic therapy. The dosing scheme employed 2 schedules: a 3 out of 4 week schedule and a 2 out of 3 week schedule. Doses are reduced in sequential cohorts based on toxicity. Optimal dose and schedule is defined as evidence of anti-tumor activity without Grade (Gr) 4 hematological toxicity, Gr 3–4 infection, or febrile neutropenia. Responses in skin are investigator-assessed using the modified severity weighted assessment tool (mSWAT). Results: From August 2007 to August 2008, 23 pts have enrolled, 17 of whom are evaluable for safety and response. The 17 evaluable pts, 15 with MF, 1 with SS, and 1 with ALCL, were enrolled into 4 cohorts: 30 mg/m2 3 of 4 weeks (n=2), 20 mg/m2 3 of 4 weeks (n=3), 20 mg/m2 2 of 3 weeks (n=7), and 15 mg/m2 3 of 4 weeks (n=5). These pts were heavily pretreated with a median of 6 prior regimens (range 1–25), and a median of 3.5 prior systemic regimens (range 1–9). Dose-limiting toxicities (DLTs) to date have included Gr 2 acute renal failure (1), Gr 3 joint stiffness/muscle weakness (1), and Gr 2–3 stomatitis/mucositis (4). The most common treatment-related AEs include mucositis (10 patients [59%]), nausea (8 patients [47%]), and fatigue (7 patients [41%]). Treatment-related SAEs occurred in 3 pts: stomatitis (Gr 2) at pralatrexate 20 mg/m2 2 of 3 weeks; chills (Gr 1) and exfoliative dermatitis (Gr 2) at pralatrexate 20 mg/m2 2 of 3 weeks; and hypoalbuminemia (Gr 3) and tumor lysis syndrome (Gr 3) at pralatrexate 20 mg/m2 3 of 4 weeks. To date of the 17 evaluable pts, 9 have achieved a response (53%), including partial response (PR) in 7 pts, and complete response (CR) in 2 pts (1 progressed rapidly off treatment). In addition, 6 pts had SD. Eight of the responding pts had MF, and the pt with ALCL had a CR. Seven of the 17 pts remain on treatment, including 3 pts who have been on treatment for 8, 8, and 9 months, respectively. Conclusion: In this preliminary report, pralatrexate shows marked clinical activity in the treatment of CTCL at much lower doses than those used for aggressive lymphomas. Responses have been observed in pts who had previously received up to 8 prior treatment regimens. This study is ongoing to identify a dose and schedule of pralatrexate that can result in maintained responses with minimal toxicity for pts with CTCL.

Description: Background: Pralatrexate (PDX) is a novel targeted antifolate that is designed to accumulate preferentially in cancer cells. Pralatrexate has demonstrated activity in the treatment of non-Hodgkin’s lymphoma (NHL). Single-agent gemcitabine (Gem) has demonstrated promising activity in relapsed Hodgkin’s lymphoma, T-cell lymphoma, and select sub-types of B-cell NHL. Based on pre-clinical data demonstrating a schedule dependent synergy for this combination (pralatrexate + Gem) (Clin Cancer Res2006; 12(3):924–932), a Phase 1/2a, non-randomized, open-label, multi-center trial was designed to assess the potential co-administration of these 2 agents. The primary objective of the study is to determine the maximum tolerated dose (MTD) and recommended Phase 2 dose when pralatrexate and Gem are administered with vitamin B12 and folic acid supplementation to patients (pts) with relapsed/refractory lymphoma. Methods: Initially, pts were assigned to a schedule of pralatrexate, followed the next day by Gem, once weekly for 3 of 4 weeks (Treatment group A). When this schedule was poorly tolerated, new cohorts were enrolled in a dose escalating fashion: Treatment group B – pralatrexate (10 mg/m2) followed the next day by Gem (300–400 mg/m2) once every 2 weeks (q 2 weeks); and Treatment group C – pralatrexate (10 mg/m2) followed 1 hour later by Gem (300–400 mg/m2) q 2 weeks. Eligibility criteria include histologically confirmed lymphoma, documented disease progression (PD) after 3 1 prior treatment, and ECOG PS £ 2. Results: As of August 2008, 20 pts have been treated on this study, including 11 males (55%) and 9 females (45%). Pt histology is as follows: 8 pts [40%] diffuse large B-cell lymphoma [DLBCL]; 1 pt [5%] follicular lymphoma, Hodgkin lymphoma (HL) (5 pts [26%]), T/NK-cell (5 pts [26%]), and composite DLBCL and PTCL (1 pt [5%]). Pts were heavily pre-treated having received a median of 4 prior regimens (range 3–12) with a median of 3 prior systemic regimens (range 2–10). Treatment group A was not well tolerated as evidenced by the incidence of Grade (Gr) 3–4 hematological toxicities. In comparison pts in treatment groups B and C had far fewer adverse events (AEs) with lower severity toxicities. Across all dose cohorts and treatment groups, the most frequently reported Gr 3–4 AEs considered to be treatment related have been neutropenia (9 pts [45%]) thrombocytopenia (9 pts [45%]), and anemia (8 pts [40%]). Preliminary efficacy data show 6 pts (30%) with partial response (PR): 4 with HL, 1 with DLBCL, and 1 with composite DLBCL and PTCL. PRs occurred on both the sequential dosing schedule (5 pts) and the same-day dosing schedule (1 pt). The HL pts with a PR were heavily pretreated (7, 8, 11, and 12 prior therapies) and all had received previous Gem, 3 of the 4 without response. Conclusion: The combination of pralatrexate and Gem can be safely administered on a q 2 week schedule. The MTD was established for the sequential day schedule as pralatrexate 10/Gem 300 (mg/m2). Dose escalation continues on the same day schedule. Pralatrexate and Gem administration at a frequency of 3/4 weeks is not feasible in heavily pretreated pts due to hematologic toxicity; however, when administered on a 2 q week schedule, the combination has shown a favorable safety profile. The combination of pralatrexate and Gem has shown encouraging activity in pts with heavily pre-treated, refractory lymphomas and enrollment in the study is ongoing to define the MTD on a same day schedule. Cohort Number of Pts Dose Pralatrexate/Gem (mg/m2) Schedule #DLTs DLT (Grade) A1 2 15/400 Sequential days, 3/4 weeks 2 Thrombocytopenia (Gr 4); Neutropenia (Gr 3) & Thrombocytopenia (Gr 3) A-1 2 10/400 Sequential days, 3/4 weeks 2 Neutropenia (Gr 3) Thrombocytopenia Gr 3) A-2 3 10/300 Sequential days, 3/4 weeks 2 Thrombocytopenia (Gr 3) Neutropenia (Gr 3) B1 3 10/300 Sequential days, q 2 weeks 0 B2 3 10/400 Sequential days, q 2 weeks 0 B3 2 15/400 Sequential days, q 2 weeks 2 Cellulitis (Gr 3) Pulmonary embolus (Gr 3) C1 3 10/300 Same day, q 2 weeks 0 C2 2 10/400 Same day, q 2 weeks 1 Hypoxia (Gr 3) &

Description: Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of $$upalpha$$ α -helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.

Description: Organic and inorganic molecules, neutral and ions have been observed in the interstellar medium. A few anions of organic molecules have also been observed recently. The Cassini spacecraft in the upper atmosphere of Titan has observed anions of large organic molecules. In this project we have studied the physical and spectroscopic properties of C4H3-, C6H3-, and C6H5-. We have optimized the geometrical structures of all low-lying isomers of the anions, calculated rotational, and harmonic vibrational frequencies of the anions mentioned above using the B3LYP density functional along with the augmented correlation consistent polar valence triple zeta (aug-cc-pVTZ) basis set. We have found many low-lying isomers on the potential energy surface of these anions.

Description: Marine imaging studies have unique constraints on the data collected requiring a tool for defining the biological scope to facilitate data discovery, quality evaluation, sharing and reuse. Defining the ‘target population’ is way of scoping biological sampling or observations by setting the pool of organisms to be observed or sampled. It is used in survey design and planning, to determine statistical inference, and is critical for data interpretation and reuse (both images and derived data). We designed a set of attributes for defining and recording the target population in biological studies using marine photography, incorporating ecological and environmental delineation and marine imaging method constraints. We describe how this definition may be altered and recorded at different phases of a project. The set of attributes records the definition of the target population in a structured metadata format to enhance data FAIRness. It is designed as an extension to the image FAIR Digital Objects metadata standard, and we map terms to other biological data standards where possible. This set of attributes serves a need to update ecological metadata to align with new remotely-sensed data, and can be applied to other remotely-sensed ecological image data.