Small Cell Lung Cancer Plasticity Enables NFIB-Independent Metastasis

Metastasis is a major cause of morbidity and mortality in patients with cancer, highlighting the need to identify improved treatment and prevention strategies. Previous observations in preclinical models and tumors from patients with small cell lung cancer (SCLC), a fatal form of lung cancer with high metastatic potential, identified the transcription factor NFIB as a driver of tumor growth and metastasis. However, investigation into the requirement for NFIB activity for tumor growth and metastasis in relevant in vivo models is needed to establish NFIB as a therapeutic target. Here, using conditional gene knockout strategies in genetically engineered mouse models of SCLC, we found that upregulation of NFIB contributes to tumor progression, but NFIB is not required for metastasis. Molecular studies in NFIB wild-type and knockout tumors identified the pioneer transcription factors FOXA1/2 as candidate drivers of metastatic progression. Thus, while NFIB upregulation is a frequent event in SCLC during tumor progression, SCLC tumors can employ NFIB-independent mechanisms for metastasis, further highlighting the plasticity of these tumors.

SIGNIFICANCE

Small cell lung cancer cells overcome deficiency of the prometastatic oncogene NFIB to gain metastatic potential through various molecular mechanisms, which may represent targets to block progression of this fatal cancer type.

A Randomized Trial Evaluating Patient Experience and Preference Between Octreotide Long-Acting Release and Lanreotide for Treatment of Well-Differentiated Neuroendocrine Tumors

PURPOSE

Somatostatin analogs octreotide long-acting release (octLAR) and lanreotide are equally acceptable in National Comprehensive Cancer Network guidelines for neuroendocrine tumors (NETs). Lanreotide is more expensive and given by deep subcutaneous injection, whereas octLAR is given intramuscularly. We evaluated patient preference between these agents in terms of injection site pain.

MATERIALS AND METHODS

Randomized, single-blinded study. Patients with NETs received injections every 4 weeks. Arm 1: octLAR × 3, then lanreotide × 3; arm 2: reverse order. Self-reported injection site pain scores (range, 0-10) were obtained after each of the first three injections. Primary end point was comparison of mean pain scores over the first three injections. Secondary end points included patient-reported preference.

RESULTS

Fifty-one patients enrolled (26 in arm 1 and 25 arm 2), all evaluable for primary end point. No significant difference was identified in the mean pain score over the first three injections (2.4 ± 1.9 v 1.9 ± 1.5, P = .5). Thirty-four of 51 (67%) patients (15 in arm 1 and 19 in arm 2) completed post-therapy questionnaires and were evaluable for secondary end points. Seven patients (47%) in arm 1 and eight patients (42%) in arm 2 indicated no drug preference at the end of treatment. In the other 19 patients, more patients indicated mild or strong preference for octLAR over lanreotide.

CONCLUSION

We found minimal pain with octLAR and lanreotide and no significant pain score differences between the two. Patients indicating a drug preference trended toward favoring octLAR.

Early-onset well differentiated pancreatic neuroendocrine tumors: Clinical presentation, pathologic features, and oncological outcomes

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Background: Young onset of several gastrointestinal cancers is associated with more advanced disease and poor oncological outcomes, however, this association has not been fully investigated for well differentiated pancreatic neuroendocrine tumors (PanNET). Our study aimed to evaluate clinical and pathological differences as well as disease outcomes between young-onset PanNET (YO-PanNET) and late-onset PanNET (LO-PanNET). Methods: Patients with localized PanNET who underwent surgery at Memorial Sloan Kettering Cancer Center between 2000 to 2017 were identified. Those with hereditary syndromes, metastatic disease, and postoperative mortality were excluded. YO-PanNET was defined as <50 and LO-PanNET >50 years of age at time of diagnosis. Family history, clinical and pathology characteristics, were recorded. Fisher’s exact test was used to detect difference between the age groups. Kaplan-Meier method was used to investigate age prognostic significance. Results: A total of 366 patients were identified, 84 (23%) with YO-PanNET. Compared with LO-PanNET, YO-PanNET were less likely to have a personal history of another cancer (p<0.001) and a first-line relative with cancer (p<0.015). We did not observe any significant differences between YO-PanNET and LO-PanNET with regards to pathology features such as tumor grade (p=0.7), size (p=0.5), nodal metastases (p=0.8), and stage of disease (p=0.7). With a median follow-up of 68 months (range 0-238), 5-year recurrence-free survival was 76% and 83%, and 10-year RFS was 69% and 78%, respectively, in YO-PanNET and LO-PanNET (p=0.12; see Table) with similar 5- and 10-year overall survival (p=0.31). Conclusions: In this large retrospective surgical series, we found that YO-PanNET is not associated with an increased rate of personal or familial history of cancer. Pathological characteristics and long-term oncological outcomes do not significantly differ between YO-PanNET and LO-PanNET. Current efforts include next-generation sequencing analysis in the resected surgical specimens to evaluate for genomic biomarkers of recurrence.[Table: see text]

Treatment response and clinical outcomes of neuroendocrine neoplasms treated with immune checkpoint inhibitors: A single-institution experience

506

Background: Immune checkpoint inhibitors (ICIs) have antitumor activity in some solid tumors, however a role for ICI’s in the treatment of neuroendocrine neoplasms (NENs) is uncertain. We analyzed response and outcomes of NENs, both well differentiated neuroendocrine tumors (WDNET) and poorly differentiated neuroendocrine carcinomas (PDNEC), treated with ICIs at Memorial Sloan Kettering Cancer Center during the past decade. Methods: Patients with NENs who received ICIs between 2010-2021 were identified. Demographics, pathology characteristics, treatment response and outcomes were recorded. Progression-free survival (PFS) and overall survival (OS) were estimated using Kaplan-Meier methods. Analysis of next-generation sequencing (NGS) results from archival tumor tissue was performed. Results: 57 patients with NENs treated with ICIs were identified (WDNET-16; PDNEC-41). All patients had heavily-treated metastatic disease (median number of prior systemic treatments, WDNET-4, PDNEC-2). Median time from diagnosis to ICI treatment was 41.5 months in WDNET, 8 months in PDNEC. WDNET response: 1 (6%) partial response (PR), 4 (25%) stable disease (SD), 10 (63%) progressive disease (PD). PDNEC response: 6 (15%) PR (5 microsatellite stable, 1 unknown), 3 (7%) SD, 32 (78%) PD. Median duration of ICI treatment: 2 months (range 0-27) in WDNET, 1 month (range 0-16) in PDNEC; median duration of treatment for the 7 responders was 11 months (range 2-27). While receiving ICIs, 3 PDNEC responders developed PD in an escape lesion (2 brain, 1 nodal) after response in all other disease sites and successfully continued ICI treatment post-RT of escape lesion. Six-month PFS was 20% [95%CI: 7%-55%] and 9.8% [95%CI: 4%-25%], OS 60% [95%CI: 40%-91%] and 37% [95%CI: 25%-56%], respectively in WDNET and PDNEC. NGS results were available in archival tumor tissue of 35 patients (61%); most common alterations were TP53 (20/26, 77%) and RB1 (14/26, 54%) in PDNEC versus ATM, SMAD4, CREBBP, and IRS2 (all 1/9, 11%) in WDNET. Conclusions: We observed limited activity for ICI’s in NEN treatment, primarily restricted to a subset of PDNEC. PFS/OS findings were consistent with historical data, reflecting the pathogenesis of distinct NEN subtypes.

Randomized blinded study comparing injection site pain from octreotide long-acting-release (LAR) versus lanreotide during the treatment of well differentiated neuroendocrine tumors (WDNETs)

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Background: The somatostatin analogs (SSAs) octreotide LAR and lanreotide are equally acceptable in the NCCN guidelines to treat WDNETs. Average Sales Price for 1 year of lanreotide at 120mg is $106,802 versus $53,471 for 1 year of octreotide LAR 20mg and $80,206 for 1 year of 30mg. Lanreotide is given by “deep subcutaneous injection” while octreotide LAR is given intramuscularly. We conducted a randomized, blinded trial evaluating patient (pt) experience, as measured by injection site pain, with octreotide LAR and lanreotide, during the treatment of advanced, nonfunctional, WDNETs. We also investigated drug preference and financial toxicity in this pt population. Methods: This randomized single-blinded pilot study enrolled 51 pts recommended to begin SSA therapy. Pts received injections q 4 weeks and received 6 injections on study; Arm 1: octreotide LAR for 3 injections then lanreotide for 3 injections; Arm 2: lanreotide for 3 injections then octreotide LAR for 3 injections. Pts were blinded as to which agent they received throughout the study. Self-reported injection site pain scores were obtained after each of the first 3 injections using a 0 to 10 scale (0: “I didn’t feel it”; 10: “worst pain ever”). Primary endpoint was comparison of mean pain scores over the first 3 injections of octreotide LAR (Arm 1) or lanreotide (Arm 2). Secondary endpoints, evaluated with descriptive statistics, included pt-reported preference of octreotide LAR versus lanreotide, and willingness to pay for the preferred therapy, both assessed after 6 months of therapy by questionnaire. Results: 51 pts were enrolled (Arm 1: N = 26, Arm 2: N = 25). All pts were evaluable for the study primary endpoint. All pts received lanreotide at a dose of 120mg monthly; among those pts (49) receiving octreotide LAR, 30 (61%) received 20mg, 18 (37%) received 30mg, 1 (2%) received 10mg. No significant difference was identified in mean pain scores over the first 3 SSA injections; Arm 1: mean 2.4, standard deviation 1.9 versus Arm 2: mean 1.9, standard deviation 1.5 (p = 0.5). 34/51 (67%) pts (15 pts in Arm 1; 19 pts in Arm 2) were evaluated for secondary endpoints and completed post-therapy questionnaires. 7 (47%) in Arm 1 and 8 (42%) in Arm 2 indicated no drug preference at the end of the 6 months. There was a trend towards preference for octreotide LAR versus lanreotide in both arms, with more pts indicating mild or strong preference for octreotide LAR. 7 (50%) and 10 (56%) of pts in Arms 1 and 2, respectively, were unwilling to pay more for their preferred SSA; the rest of the cohort was willing to experience increased financial toxicity to receive their preferred SSA. Conclusions: This randomized, blinded study evaluating pt comfort with SSAs found minimal pain with both agents and no significant differences in pain scores between octreotide LAR versus lanreotide. Clinical trial information: NCT03289741.

Ribociclib and everolimus in well-differentiated foregut neuroendocrine tumors

The mammalian target of rapamycin inhibitor everolimus is an established therapy for well-differentiated (WD) foregut neuroendocrine tumors (NETs). Pre-clinical data demonstrates a potential synergistic role for cyclin dependent kinase 4/6 inhibition and everolimus to treat this disease. In this phase II multicenter study, patients with advanced foregut WDNETs received combination ribociclib and everolimus until confirmed disease progression or unacceptable toxicity. The first 12 patients received ribociclib 300 mg three weeks in a row with a 1 week break and everolimus 2.5 mg daily (recommended phase II dose). Due to unexpected hematologic and infectious toxicities, the trial was put on hold, modified, and an additional 9 patients received ribociclib 200 mg and everolimus 2.5 mg daily. The primary end point was progression-free survival. Archived pre-treatment tumor was profiled by next-generation sequencing to evaluate for genomic markers of drug response. Twenty-one patients were treated (median age, 56; range, 24 to 77). The study did not meet the pre-specified criteria to advance to stage two. No patients experienced an objective response. Thirteen patients (62%) experienced stable disease. Median progression-free survival was 7.7 months (95% CI, 2.8 months to not reached). Eleven of the first 12 patients (92%) developed grade 2 or more myelosuppression. Ten patients (84%) experienced treatment interruption and 8 patients (67%) required dose reduction. Genetic testing in archival tumor tissue samples failed to identify a predictive biomarker of disease stabilization. The combination of ribociclib and everolimus had insufficient activity to warrant further investigation in foregut WDNETs.

Genomic stratification beyond Ras/B-Raf in colorectal liver metastasis patients treated with hepatic arterial infusion

Background

Resection of colorectal liver metastases (CLM) can cure disease, but many patients with extensive disease cannot be fully resected and others recur following surgery. Hepatic arterial infusion (HAI) chemotherapy can convert extensive liver disease to a resectable state or decrease recurrence risk, but response varies and no biomarkers currently exist to identify patients most likely to benefit.

Methods

We performed a retrospective cohort study of CLM patients receiving HAI chemotherapy whose tumors underwent MSK‐IMPACT sequencing. The frequency of oncogenic alterations and their association with overall survival (OS) and objective response rate were analyzed at the individual gene and signaling pathway levels.

Results

Three hundred and seventy patients met inclusion criteria: 189 (51.1%) who underwent colorectal liver metastasectomy followed by HAI + systemic therapy (Adjuvant cohort), and 181 (48.9%) with unresectable CLM (Metastatic cohort) who received HAI + systemic therapy, consisting of 63 (34.8%) with extrahepatic disease and 118 (65.2%) with liver‐restricted disease. Genomic alterations were similar in each cohort, and no individual gene or pathway was significantly associated with objective response. Patients in the adjuvant cohort with concurrent Ras/B‐Raf alteration and SMAD4 inactivation had worse prognosis while in the metastatic cohort patients with co‐alteration of Ras/B‐Raf and TP53 had worse OS. Similar findings were observed in a validation cohort.

Conclusions

Concurrently altered Ras/B‐Raf and SMAD4 mutations were associated with worse survival in resectable patients, while concurrent Ras/B‐Raf and TP53 alterations were associated with worse survival in unresectable patients. The mutual exclusivity of Ras/B‐Raf, SMAD4, and TP53 may have prognostic value for CLM patients receiving HAI.

A soft matter computer for soft robots

Despite the growing interest in soft robotics, little attention has been paid to the development of soft matter computational mechanisms. Embedding computation directly into soft materials is not only necessary for the next generation of fully soft robots but also for smart materials to move beyond stimulus-response relationships and toward the intelligent behaviors seen in biological systems. This article describes soft matter computers (SMCs), low-cost, and easily fabricated computational mechanisms for soft robots. The building block of an SMC is a conductive fluid receptor (CFR), which maps a fluidic input signal to an electrical output signal via electrodes embedded into a soft tube. SMCs could perform both analog and digital computation. The potential of SMCs is demonstrated by integrating them into three soft robots: (i) a Softworm robot was controlled by an SMC that generated the control signals necessary for three distinct gaits; (ii) a soft gripper was given a set of reflexes that could be programmed by adjusting the parameters of the CFR; and (iii) a two-degree of freedom bending actuator was switched between three distinct behaviors by varying only one input parameter. SMCs are a low-cost way to integrate computation directly into soft materials and an important step toward entirely soft autonomous robots.

Randomized phase II trial of adjuvant hepatic arterial infusion (HAI) + systemic FOLFIRI +/- panitumumab (Pmab) in patients with resected RAS wild type colorectal cancer hepatic metastases (CRLM)

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Background: HAI therapy has improved recurrence free (RF) survival in several randomized trials after resection of CRLM. The purpose of this trial was to determine whether systemic Pmab added to adjuvant HAI + FOLFIRI in RAS WT pts increases 15 months RF survival (RFS) after liver resection. Secondary endpoints are evaluation of overall survival, toxicity, and predictive biomarkers. Methods: RAS WT pts with resected liver mets were randomized to HAI + SYS (+/-) Pmab after stratification by clinical risk score (≥ 3 or < 3) and previous chemotherapy (Y/N). For a particular arm, if 24 or more patients (pts) were alive and RF at 15 months, the regimen in that arm would be considered worthy of further investigation. The initial dose of HAI FUDR 0.12mg/Kg + dexamethasone was infused over the first 2 weeks of a 5-week cycle. Systemic chemotherapy was delivered on days 15 and 29 (irinotecan 125 mg/m2, LV 400 mg/ m2, 5FU 1000 mg/m2 48-hour continuous infusion and +/- Pmab 6mg/kg). Patient characteristics were compared between arms using Fisher’s exact test and Wilcoxon rank-sum test. Survival curves were estimated using the Kaplan-Meier method and compared by the log-rank test. Results: After randomization of 75 pts, the arm receiving + Pmab met the decision rule of having ≥ 24 patients alive and RF at 15 months. The two arms had similar pt characteristics and toxicity, with the exception of Pmab related rash (Table). The 15-month RFS is 79% and 67% in +/- Pmab arms, respectively. With a median follow-up of 45 months, 3-year RFS is 65% [CL 0.45-0.78] and 42% [CL 0.24-0.57], and 3-year survival is 96% and 90% in +/-Pmab arms, respectively. Conclusions: In this trial, the addition of Pmab to HAI and SYS showed promising activity without increase in biliary toxicity and should be further investigated in a larger study. Predictive biomarkers will be presented. Clinical trial information: NCT01312857. [Table: see text]

A retrospective study of hepatic arterial infusion (HAI) FUDR/Dex and mitomycin C (MMC) for chemotherapy refractory unresectable intrahepatic cholangiocarcinomas (ICC)

432

Background: ICC are aggressive tumors with approximately 6,000 cases a year in US. The 5-year survival rate is less than 30% even for localized disease. There is only one approved line of systemic (SYS) treatment and further treatment options are necessary. HAI chemotherapy is an option to treat liver predominant cancers. Methods: After obtaining IRB approval, we retrospectively reviewed patients (pts) with ICC chemo refractory unresectable liver limited (LL) or liver dominant (LD) disease who received intrahepatic chemotherapy with HAI MMC. Baseline characteristics, previous lines of therapy, toxicity profile, combinations and radiographic responses were reviewed. Tumor genomic analyses were performed on samples using an on-site next generation sequencing (NGS) assay. Results: Between January 2011 and October 2018, 19 patients ICC with LL or LD disease were treated with HAI FUDR/Dex/MMC at Memorial Sloan Kettering Cancer Center. Disease was confined to the liver in 58% of the pts. All pts had previous chemotherapy (1-4 lines) and 14 (74%) previously had HAI FUDR/Dex. Of the 19 pts, 56% had HAI with FUDR/Dex and MMC, 43% had FUDR/Dex, MCC and SYS and 5% had HAI MMC and SYS. Seventeen patients were evaluable for response, two are being treated and will have response assessment for the meeting. Response was noted in 4 (23.5%), stable disease in 6 (35.5%) and progressive disease in 7 (41%) pts. Median overall survival from treatment was 6.1months (0.36-26). Median progression free survival was 3.65 months (0.36-9.53). Four patients had dose reductions. Common toxicity attributed to MMC was grade (G) one fatigue (32%), thrombocytopenia G1(16%) and G2 (5%). Of the 12 tumors analyzed to date the most 92% of tumors harbored at least one (0-10) genomic alteration. Common genomic alterations were ARID1 (25%), RASA1 (25%), IDH1(16.6%), NTRK (16.6%), TERT (16.6%), NRAS (16.6%), CDKN2 (16. 6%). FGFR2-FOXP1 and GTL2MEt fusions were found in one patient each. Conclusions: HAI FUDR/Dex/MMC containing regimens are active in pts with heavily pretreated refractory unresectable ICC. This strategy should be further investigated. Translational data will be presented.

Abstract P6-03-02: Independent evaluation of prognostic value of residual cancer burden (RCB) score on disease free and overall survival of breast cancer patients treated with neoadjuvant systemic treatment at a single institution

Introduction: Among the various approaches to measure response to neoadjuvant chemotherapy in breast cancer patients a significant relationship to overall (OS) and disease-free survival (DFS) has been recently demonstrated for the residual cancer burden (RCB) score. The calculated RCB- index provides additional prognostic information independently of TNM categories and stage, respectively[1]. The goal of our study was to validate the prognostic impact of the RCB score for OS and DFS on a cohort of patients selected for neoadjuvant treatment and treated either with chemotherapy with or without Her2 targeted therapy or endocrine therapy. We hypothesised that accross all histological breast cancer subtypes, the RCB-score will show significant impact on OS and DFS.

Methods: All surgical specimens (n =212) were processed according to the same protocol in a single institution. The RCB score was calculated according to Symmans et al. using the MD Anderson website. Pathologic complete remission is designated RCB 0, residual disease is based on its extent categorized as RCB I-III. Additional information such as histological and molecular subtypes, therapy regimen, as well as follow up information were collected prospectively from paper based patient files. The impact of the RCB score on OS and DFS were estimated with Kaplan-Mayer curves were compared by using long rank test statistics.

Results: The RCB score showed a significant correlation to DFS (p=0.000006) and OS (p=0.000306) The correlation between molecular subtypes (Luminal A, luminal B, Her2 positive and triple negative) and neoadjuvant treatment is ongoing and will be presented at the meeting.

Conclusion: We were able to show a general prognostic value of the RCB-Score in a series of 212 patients with neoadjuvant treatment, without consideration of the histological and molecular subtypes and adjuvant treatment. We were further able to confirm the reproducibility of the RCB Score by a standardized pathological procedure at a single institution. Further independent evaluation of the histological and molecular subtypes as well as the therapy regimens is ongoing.

[1] Loibel S.;How much information do we need to know after neoadjuvant Chemotherapy for Breast Cancer; American Society of Clinical Oncology, 24.Feb.2017.

Citation Format: Balic M, Mueller DH, Hammer R, Gumpoldsberger M, Suppan C, Posch F, Stoeger H, Dandachi N, Prein K, Hauser H, Lax S. Independent evaluation of prognostic value of residual cancer burden (RCB) score on disease free and overall survival of breast cancer patients treated with neoadjuvant systemic treatment at a single institution [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-03-02.

Recovery-Koeffizienten zur Quantifizierung der arteriellen Inputfunktion aus dynamischen PET-Messungen: experimentelle und theoretische Bestimmung

Aim: For kinetic modelling of dynamic PET data, the arterial input function can be determined directly from the PET scans if a large artery is visualized on the images. It was the purpose of this study to experimentally and theoretically determine recovery coefficients for cylinders as a function of the diameter and level of background activity. Methods: The measurements were performed using a phantom with seven cylinder inserts (Ø = 5-46 mm). The cylinders were filled with an aqueous 68Ga solution while the main chamber was filled with a 18F solution in order to obtain a varying concentration ratio between the cylinders and the background due to the different isotope half lives. After iterative image reconstruction, the activity concentrations were measured in the center of the cylinders and the recovery coefficients were calculated as a function of the diameter and the background activity. Based on the imaging properties of the PET system, we also developed a model for the quantitative assessment of recovery coefficients. Results: The functional dependence of the measured recovery data from the cylinder diameter and the concentration ratio is well described by our model. For dynamic PET measurements, the recovery correction must take into account the decreasing concentration ratio between the blood vessel and the surrounding tissue. Under the realized measurement and data analysis conditions, a recovery correction is required for vessels with a diameter of up to 25 mm. Conclusions: Based on the experimentally verified model, the activity concentration in large arteries can be calculated from the measured activity concentration in the blood vessel and the background activity. The presented approach offers the possibility to determine the arterial input function for pharmacokinetic PET studies non-invasively from large arteries (especially the aorta).

Laparoscopic versus open appendectomy for complicated appendicitis in high risk patients

INTRODUCTION

Laparoscopic appendectomy is widely used for the treatment of complicated appendicitis. Its use in patients with high operative risk is still on debate. The aim of the presented study was to investigate the benefits of laparoscopic appendectomy in patients with high peri- and postoperative risk factors.

METHODS

We performed a retrospective analysis of all patients who underwent appendectomy in our center between 2006 and 2013. Patients were classified according to their preoperative risk (classification of the American Society of Anesthesia--ASA score). Only patients with ASA 3 and 4 were included and were divided into two groups--open appendectomy (OA group) and laparoscopic appendectomy (LA group).

RESULTS

The operation time was slightly longer in the LA group (p = 0.05), but hospital stay was shorter (p = 0.05). Complications graded according to the Clavien Dindo classification were slightly more frequent in patients after LA, whereas severe complications occurred more frequently in patients after OA (p = 0.01). The postoperative WBC decreased steadily and significantly in patients after OA, whereas the decrease in patients after LA was delayed (p = 0.03). CRP slightly increased after OA and decreased thereafter, whereas it steadily decreased after LA (p = 0.05).

CONCLUSION

Laparoscopic appendectomy can be recommended for patients with complicated appendicitis even with higher risk categories.

Exploiting short-term memory in soft body dynamics as a computational resource

Soft materials are not only highly deformable, but they also possess rich and diverse body dynamics. Soft body dynamics exhibit a variety of properties, including nonlinearity, elasticity and potentially infinitely many degrees of freedom. Here, we demonstrate that such soft body dynamics can be employed to conduct certain types of computation. Using body dynamics generated from a soft silicone arm, we show that they can be exploited to emulate functions that require memory and to embed robust closed-loop control into the arm. Our results suggest that soft body dynamics have a short-term memory and can serve as a computational resource. This finding paves the way towards exploiting passive body dynamics for control of a large class of underactuated systems.

Separation of 90Nb from zirconium target for application in immuno-PET

Fast progressing immuno-PET asks to explore new radionuclides. One of the promising candidates is 90Nb. It has a half-life of 14.6 h that allows visualizing and quantifying biological processes with medium and slow kinetics, such as tumor accumulation of antibodies and antibodies fragments or drug delivery systems and nanoparticles. 90Nb exhibits a positron branching of 53% and an average kinetic energy of emitted positrons of E mean =0.35 MeV. Currently, radionuclide production routes and Nb V labeling techniques are explored to turn this radionuclide into a useful imaging probe. However, efficient separation of 90Nb from irradiated targets remains in challenge. Ion exchange based separation of 90Nb from zirconium targets was investigated in systems AG 1 × 8 – HCl/H2O2 and UTEVA-HCl. 95Nb (t 1/2 = 35.0 d), 95Zr (t 1/2 = 64.0 d) and 92m Nb (t 1/2 = 10.15 d) were chosen for studies on distribution coefficients. Separation after AG 1 × 8 anion exchange yields 99% of 90/95Nb. Subsequent use of a solid-phase extraction step on UTEVA resin further decontaminates 90/95Nb from traces of zirconium with yields 95% of 90/95Nb. A semi-automated separation takes one hour to obtain an overall recovery of 90/95Nb of 90%. The amount of Zr was reduced by factor of 108. The selected separation provides rapid preparation (< 1 h) of high purity 90Nb appropriate for the synthesis of 90Nb-radiopharmaceuticals, relevant for purposes of immuno-PET. Applying the radioniobium obtained, 90/95Nb-labeling of a monoclonal antibody (rituximab) modified with desferrioxamine achieved labeling yields of >90% after 1 h incubation at room temperature.

Representative Factor Generation for the Interactive Visual Analysis of High-Dimensional Data

Datasets with a large number of dimensions per data item (hundreds or more) are challenging both for computational and visual analysis. Moreover, these dimensions have different characteristics and relations that result in sub-groups and/or hierarchies over the set of dimensions. Such structures lead to heterogeneity within the dimensions. Although the consideration of these structures is crucial for the analysis, most of the available analysis methods discard the heterogeneous relations among the dimensions. In this paper, we introduce the construction and utilization of representative factors for the interactive visual analysis of structures in high-dimensional datasets. First, we present a selection of methods to investigate the sub-groups in the dimension set and associate representative factors with those groups of dimensions. Second, we introduce how these factors are included in the interactive visual analysis cycle together with the original dimensions. We then provide the steps of an analytical procedure that iteratively analyzes the datasets through the use of representative factors. We discuss how our methods improve the reliability and interpretability of the analysis process by enabling more informed selections of computational tools. Finally, we demonstrate our techniques on the analysis of brain imaging study results that are performed over a large group of subjects.

DNA-Based Vaccination with Polycistronic Expression Plasmids

DNA-based vaccination is a potent technique to prime cellular (T-cell mediated) immune responses (reviewed in 1). Many details of the priming of T-cell precursors by antigen translated from injected expression plasmid DNA are unknown. The relevant cell that is transfected in situ after DNA vaccination and that can process and present the protein in an immunogenic form has not yet been identified. Alternatively, the transfected cell may initiate 'cross-priming' in vivo by transferring processed antigen to a professional antigen-presenting cell (APC).

90Nb – a potential PET nuclide: production and labeling of monoclonal antibodies

Fast progressing immuno-PET gives reasons to develop new potential medium-long and long-lived radioisotopes. One of the promising candidates is 90Nb. It has a half-life of 14.6 h, which allows visualizing and quantifying processes with medium and slow kinetics, such as tumor accumulation of antibodies and antibodies fragments or polymers and other nanoparticles. 90Nb exhibits a high positron branching of 53% and an optimal energy of β + emission of E mean=0.35 MeV only. Consequently, efficient radionuclide production routes and NbV labeling techniques are required.

90Nb was produced by the 90Zr(p,n) 90Nb nuclear reaction on natural zirconium targets. No-carrier-added (n.c.a.) 90Nb was separated from the zirconium target via a multi-step separation procedure including extraction steps and ion-exchange chromatography. Protein labeling was exemplified using the bifunctional chelator desferrioxamine attached to the monoclonal antibody rituximab. Desferrioxamine was coupled to rituximab via two different routes, by the use of N-succinyl-desferrioxamine (N-suc-Df) and by means of the bifunctional derivative p-isothiocyanatobenzyl-desferrioxamine B (Df-Bz-NCS), respectively. Following antibody modification, labeling with 90Nb was performed in HEPES buffer at pH 7 at room temperature. In vitro stability of the radiolabeled conjugates was tested in saline buffer at room temperature and in fetal calf serum (FCS) at 37 ºC.

The selected production route led to a high yield of 145 ± 10 MBq/μA h of 90Nb with high radioisotopic purity of >97%. This yield may allow for large scale production of about 10 GBq 90Nb. The separation procedure resulted in 76–81% yield. The Zr/90Nb decontamination factor reaches 107. Subsequent radiolabeling of the two different conjugates with 90Nb gave high yields; after one hour incubation at room temperature, more than 90% of 90Nb-Df-mAb was formed in both cases. At room temperature in aqueous solution, both 90Nb-Df-mAb constructs were more than 99% stable over a period of 18 d.

The developed production and separation strategy provided 90Nb with purity appropriate for radiolabeling applications. Labeling and stability studies proved the applicability of 90Nb as a potential positron emitter for immuno-PET.

Genetic aspects of cell line development from a synthetic biology perspective

Animal cells can be regarded as factories for the production of relevant proteins. The advances described in this chapter towards the development of cell lines with higher productivity capacities, certain metabolic and proliferation properties, reduced apoptosis and other features must be regarded in an integrative perspective. The systematic application of systems biology approaches in combination with a synthetic arsenal for targeted modification of endogenous networks are proposed to lead towards the achievement of a predictable and technologically advanced cell system with high biotechnological impact.

Manipulation of culture conditions for BHK cell growth inhibition by IRF-1 activation

The activation of interferon-regulatory-factor-1 (IRF-1) hasbeen applied to regulate the cell growth of BHK cells. Theconstitutively expressed IRF-1-estrogen receptor fusion protein(IRF-1-hER) activated by the addition to the culture medium ofan estrogen analogue (estradiol), enabled IRF-1 to gain itstranscriptional activator function. By using a dicistronicstabilised self-selecting construct it was possible to controlcell proliferation. With the addition of 100 nM of estradiol at the beginning of the exponential phase, the IRF-1 activationled to a rapid cell growth inhibition. Two days after estradioladdition cell concentration was still maintained but a decreasein cell viability was observed. This cell response isindependent on clone (producer and non-producer) and culturesystem (static and stirred cultures). Specificrecombinant-protein productivity of the producer clone was notsignificantly altered. Control experiments confirmed that IRF-1activation effect was not due to the addition of estradiol per se, estradiol solvent or serum concentration. The extent ofcell growth inhibition is dependent on estradiol concentrationand estradiol addition time, although a decrease in cellviability was always observed. Reducing the time span ofestradiol exposure allowed the decrease in the cell viability tobe controlled and the stationary inhibited phase to be extended:when the time of contact between the cells and estradiol isreduced cell viability increases, archieving values similar tothose obtained if no estradiol is added. During this recoveryphase the cells passed two different phases: first a stationaryphase extension where cell growth was still inhibited, followedby an increase of cell concentration. The IRF-1 system isreversible. This pattern can be repeated for an extended period when estradiol addition and removal are repeated, showing acyclic response. Thus, it is possible to modulate the IRF-1effect by manipulating cycles of addition/removal of estradioland in this way the stationary phase can be maintained.

Separation and purification of no-carrier-added arsenic from bulk amounts of germanium for use in radiopharmaceutical labelling

Radioarsenic labelled radiopharmaceuticals could add special features to molecular imaging with positron emission tomography (PET). For example the long physical half-lives of 72As (T 1/2=26 h) and 74As (T 1/2=17.8 d) in conjunction with their high positron branching rates of 88% and 29%, respectively, allow the investigation of slow physiological or metabolical processes, like the enrichment and biodistribution of monoclonal antibodies in tumour tissue or the characterization of stem cell trafficking. A method for separation and purification of no-carrier-added (nca) arsenic from irradiated metallic germanium targets based on distillation and anion exchange is developed. It finally converts the arsenic into an *As(III) synthon in PBS buffer and pH 7 suitable for labelling of proteins via As-S bond formations. The method delivers radioarsenic in high purity with separation factors of 106 from germanium and an overall yield from target to labelling synthon of >40%. In a proof-of-principle experiment, the monoclonal antibody Bevacizumab, directed against the human VEGF receptor, was labelled with a radiochemical yield >90% within 1 h at room temperature with nca 72/74/77As.

Relevance of an academic GMP Pan-European vector infra-structure (PEVI)

In the past 5 years, European investigators have played a major role in the development of clinical gene therapy. The provision of substantial funds by some individual member states to construct GMP facilities makes it an opportune time to network available gene therapy GMP facilities at an EU level. The integrated coordination of GMP production facilities and human skills for advanced gene and genetically-modified (GM) cell therapy, can dramatically enhance academic-led "First-in-man" gene therapy trials. Once proof of efficacy is gathered, technology can be transferred to the private sector which will take over further development taking advantage of knowledge and know-how. Complex technical challenges require existing production facilities to adapt to emerging technologies in a coordinated manner. These include a mandatory requirement for the highest quality of production translating gene-transfer technologies with pharmaceutical-grade GMP processes to the clinic. A consensus has emerged on the directions and priorities to adopt, applying to advanced technologies with improved efficacy and safety profiles, in particular AAV, lentivirus-based and oncolytic vectors. Translating cutting-edge research into "First-in-man" trials require that pre-normative research is conducted which aims to develop standard assays, processes and candidate reference materials. This research will help harmonise practices and quality in the production of GMP vector lots and GM-cells. In gathering critical expertise in Europe and establish conditions for interoperability, the PEVI infrastructure will contribute to the demands of the advanced therapy medicinal products* regulation and to both health and quality of life of EU-citizens.

Strict control of transgene expression in a mouse model for sensitive biological applications based on RMCE compatible ES cells

Recombinant mouse strains that harbor tightly controlled transgene expression proved to be indispensible tools to elucidate gene function. Different strategies have been employed to achieve controlled induction of the transgene. However, many models are accompanied by a considerable level of basal expression in the non-induced state. Thereby, applications that request tight control of transgene expression, such as the expression of toxic genes and the investigation of immune response to neo antigens are excluded. We developed a new Cre/loxP-based strategy to achieve strict control of transgene expression. This strategy was combined with RMCE (recombinase mediated cassette exchange) that facilitates the targeting of genes into a tagged site in ES cells. The tightness of regulation was confirmed using luciferase as a reporter. The transgene was induced upon breeding these mice to effector animals harboring either the ubiquitous (ROSA26) or liver-specific (Albumin) expression of CreER^T2, and subsequent feeding with Tamoxifen. Making use of RMCE, luciferase was replaced by Ovalbumin antigen. Mice generated from these ES cells were mated with mice expressing liver-specific CreER^T2. The transgenic mice were examined for the establishment of an immune response. They were fully competent to establish an immune response upon hepatocyte specific OVA antigen expression as indicated by a massive liver damage upon Tamoxifen treatment and did not show OVA tolerance. Together, this proves that this strategy supports strict control of transgenes that is even compatible with highly sensitive biological readouts.

Stabilization of lipid bilayer vesicles by sucrose during freezing

The freeze-induced fusion and leakage of small unilamellar vesicles (SUV) of natural and synthetic phosphatidylcholines and the suppression of these processes by sucrose was studied by electron microscopy, by high-resolution NMR, and by ESR techniques. During slow freezing of SUV suspensions in water, the lipid was compressed into a small interstitial volume and transformed into a multilamellar aggregate without vesicular structure. When frozen in sucrose solution, the lipid also was compressed between the ice crystals but remained in the form of vesicles. The fractional amount of lipid remaining as SUV after freezing was found to increase significantly only at sucrose/lipid molar ratios above 0.4. Eu(3+) displaced sucrose from the lipid by competitive binding. During freezing in the absence of sucrose, the vesicles became transiently permeable to ions. ESR studies showed that fusion of vesicles in the absence of sucrose is far more extensive when they are frozen while above their phase-transition temperature (t(c)) than when frozen while below their t(c). It is concluded that the extent of membrane disruption depends on the membrane mobility at the moment of freezing and that sucrose exerts its protective effect by binding to the membrane interface and/or by affecting the water structure.

Toxin-antitoxin based transgene expression in mammalian cells

Long-term, recombinant gene expression in mammalian cells depends on the nature of the transgene integration site and its inherent properties to modulate transcription (epigenetic effects). Here we describe a method by which high transgene expression is achieved and stabilized in extensively proliferating cultures. The method is based on strict co-expression of the transgene with an antitoxin in cells that express the respective toxin. Since the strength of antitoxin expression correlates with an advantage for cell growth, the cells with strong antitoxin expression are enriched over time in cultures of heterogeneous cells. This principle was applied to CHO cell lines that conditionally express the toxin kid and that are transduced to co-express the antitoxin kis together with different transgenes of interest. Cultivation of pools of transfectants that express the toxin steadily increase their transgene expression within several weeks to reach a maximum that is up to 120-fold over the initial status. In contrast, average transgene expression drops in the absence of toxin expression. Together, we show that cells conditionally expressing kid can be employed to create overexpressing cells by a simple coupling of kis to the transgene of interest, without further manipulation and in absence of selectable drugs.

GARP: a key receptor controlling FOXP3 in human regulatory T cells

Recent evidence suggests that regulatory pathways might control sustained high levels of FOXP3 in regulatory CD4(+)CD25(hi) T (T(reg)) cells. Based on transcriptional profiling of ex vivo activated T(reg) and helper CD4(+)CD25(-) T (T(h)) cells we have identified GARP (glycoprotein-A repetitions predominant), LGALS3 (lectin, galactoside-binding, soluble, 3) and LGMN (legumain) as novel genes implicated in human T(reg) cell function, which are induced upon T-cell receptor stimulation. Retroviral overexpression of GARP in antigen-specific T(h) cells leads to an efficient and stable re-programming of an effector T cell towards a regulatory T cell, which involves up-regulation of FOXP3, LGALS3, LGMN and other T(reg)-associated markers. In contrast, overexpression of LGALS3 and LGMN enhance FOXP3 and GARP expression, but only partially induced a regulatory phenotype. Lentiviral down-regulation of GARP in T(reg) cells significantly impaired the suppressor function and was associated with down-regulation of FOXP3. Moreover, down-regulation of FOXP3 resulted in similar phenotypic changes and down-regulation of GARP. This provides compelling evidence for a GARP-FOXP3 positive feedback loop and provides a rational molecular basis for the known difference between natural and transforming growth factor-beta induced T(reg) cells as we show here that the latter do not up-regulate GARP. In summary, we have identified GARP as a key receptor controlling FOXP3 in T(reg) cells following T-cell activation in a positive feedback loop assisted by LGALS3 and LGMN, which represents a promising new system for the therapeutic manipulation of T cells in human disease.

[CT coronary angiogram: state of the art in 2009]

Thanks to 64 multi-detector CT-scan it is nowadays possible to visualise non invasively the coronary arteries: the recently published series have shown excellent sensitivity and specificity in the detection of coronary artery disease. Actually, the principal interest of the technique is the excellent negative predictive value which is very useful to rule out a significant coronary artery stenosis. For the time being, the angio CT is recommended for symptomatic patients with low to intermediate probability of coronary artery disease with inconclusive functional test. Despite some technical ameliorations, the irradiation doses delivered by multi-detector CT are significant and should restrict its indications specifically in women and young patients, in whom a late radio-induced cancer may be a concern.

The genome of the simian and human malaria parasite Plasmodium knowlesi

Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.

A New Generation of Retroviral Producer Cells: Predictable and Stable Virus Production by Flp-Mediated Site-Specific Integration of Retroviral Vectors

We developed a new strategy that provides well-defined high-titer producer cells for recombinant retroviruses in a minimum amount of time. The strategy involves the targeted integration of the retroviral vector into a chromosomal locus with favorable properties. For proof of concept we established a novel HEK293-based retroviral producer cell line, called Flp293A, with a single-copy retroviral vector integrated at a selected chromosomal locus. The vector was flanked by noninteracting Flp-recombinase recognition sites and was exchanged for different retroviral vectors via Flp-mediated cassette exchange. All analyzed cell clones showed correct integration and identical titers for each of the vectors, confirming that the expression characteristics from the parental cell were preserved. Titers up to 2.5 x 10(7) infectious particles/10(6) cells were obtained. Also, high-titer producer cells for a therapeutic vector that encodes the 8.9-kb collagen VII cDNA in a marker-free cassette were obtained within 3 weeks without screening. Thus, we provide evidence that the precise integration of viral vectors into a favorable chromosomal locus leads to high and predictable virus production. This method is compatible with other retroviral vectors, including self-inactivating vectors and marker-free vectors. Further, it provides a tool for evaluation of different retroviral vector designs.

The use of recombinase mediated cassette exchange in retroviral vector producer cell lines: predictability and efficiency by transgene exchange

Currently, retroviral vector producer cell lines must be established for the production of each gene vector. This is done by transfection of a packaging cell line with the gene of interest. In order to find a high-titer retroviral vector producer clone, exhaustive clone screening is necessary, as the random integration of the transgene gives rise to different expression levels. We established a virus producing packaging cell line, the 293 FLEX, in which the viral vector is flanked by two different FRT sites and a selection trap. Using Flp recombinase mediated cassette exchange; this vector can be replaced by another compatible retroviral vector. The first step was the tagging of 293 cells with a lacZ reporter gene, which allowed screening and choosing a high expressing chromosomal locus. After checking that, a single copy of the construct was integrated, cassette exchangeability was confirmed with a reporter targeting construct. Subsequently gag-pol and GaLV envelope genes were stably transfected. The lacZ transgene was replaced by a GFP transgene and the 293 FLEX producer cell line maintained the titer, thus validating the flexibility and efficacy of this producer cell line. The tagged retroviral producer cell clone should constitute a highly advantageous cell line since it has a predictable titer and can be rapidly used for different therapeutic applications.

The genome of the social amoeba Dictyostelium discoideum

The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

Secretory heat-shock protein as a dendritic cell-targeting molecule: a new strategy to enhance the potency of genetic vaccines

DNA vaccines are an appealing strategy for inducing cytotoxic T-lymphocyte and antibody responses against tumor cells as well as infectious agents. Dendritic cells (DCs) play a critical role in inducing immune responses, but their potential is not fully utilized in the DNA vaccine setting since they take up only a minor fraction of the injected DNA. Here we describe a novel DNA vaccination strategy based on the targeting of a modified tumor-associated antigen, the human papilloma virus (HPV) type 16 E7 protein, to DCs by a heat-shock protein (HSP) to enhance antigen presentation and immune responses. Specifically, a chimerical HPV-E7 and HSP70 fusion gene preceded with a leader sequence was constructed. When mice were immunized with this construct, the DNA is taken up by various types of cells, which then produce and secrete an HPV-E7-HSP70 fusion protein that is targeted to DCs by the HSP70 portion of the chimerical molecule for antigen presentation. In studies to test the efficacy of this strategy, we demonstrated that DNA vaccination with this secretory HPV-E7-HSP70 construct strongly enhanced an antigen-specific CD8+ T-cell response as well as a specific B-cell response in mice. Furthermore, this immunization approach not only protected mice against lethal challenge with an HPV E7-expressing tumor line (TC-1), but also showed a therapeutic effect against established tumors. The results of this study indicate that secretory HSPs can be broadly used to target tumor-associated antigens to DCs to enhance antigen-specific immune responses.

Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors

The bacterial family Enterobacteriaceae is notable for its well studied human pathogens, including Salmonella, Yersinia, Shigella, and Escherichia spp. However, it also contains several plant pathogens. We report the genome sequence of a plant pathogenic enterobacterium, Erwinia carotovora subsp. atroseptica (Eca) strain SCRI1043, the causative agent of soft rot and blackleg potato diseases. Approximately 33% of Eca genes are not shared with sequenced enterobacterial human pathogens, including some predicted to facilitate unexpected metabolic traits, such as nitrogen fixation and opine catabolism. This proportion of genes also contains an overrepresentation of pathogenicity determinants, including possible horizontally acquired gene clusters for putative type IV secretion and polyketide phytotoxin synthesis. To investigate whether these gene clusters play a role in the disease process, an arrayed set of insertional mutants was generated, and mutations were identified. Plant bioassays showed that these mutants were significantly reduced in virulence, demonstrating both the presence of novel pathogenicity determinants in Eca, and the impact of functional genomics in expanding our understanding of phytopathogenicity in the Enterobacteriaceae.

[Recovery coefficients for the quantification of the arterial input functions from dynamic PET measurements: experimental and theoretical determination]

AIM

For kinetic modelling of dynamic PET data, the arterial input function can be determined directly from the PET scans if a large artery is visualized on the images. It was the purpose of this study to experimentally and theoretically determine recovery coefficients for cylinders as a function of the diameter and level of background activity.

METHODS

The measurements were performed using a phantom with seven cylinder inserts (Ø = 5-46 mm). The cylinders were filled with an aqueous 68Ga solution while the main chamber was filled with a 18F solution in order to obtain a varying concentration ratio between the cylinders and the background due to the different isotope half lives. After iterative image reconstruction, the activity concentrations were measured in the center of the cylinders and the recovery coefficients were calculated as a function of the diameter and the background activity. Based on the imaging properties of the PET system, we also developed a model for the quantitative assessment of recovery coefficients.

RESULTS

The functional dependence of the measured recovery data from the cylinder diameter and the concentration ratio is well described by our model. For dynamic PET measurements, the recovery correction must take into account the decreasing concentration ratio between the blood vessel and the surrounding tissue. Under the realized measurement and data analysis conditions, a recovery correction is required for vessels with a diameter of up to 25 mm.

CONCLUSIONS

Based on the experimentally verified model, the activity concentration in large arteries can be calculated from the measured activity concentration in the blood vessel and the background activity. The presented approach offers the possibility to determine the arterial input function for pharmacokinetic PET studies non-invasively from large arteries (especially the aorta).

Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.