De novo assembly and annotation of Popillia japonica's genome with initial clues to its potential as an invasive pest

BACKGROUND

The spread of Popillia japonica in non-native areas (USA, Canada, the Azores islands, Italy and Switzerland) poses a significant threat to agriculture and horticulture, as well as to endemic floral biodiversity, entailing that appropriate control measures must be taken to reduce its density and limit its further spread. In this context, the availability of a high quality genomic sequence for the species is liable to foster basic research on the ecology and evolution of the species, as well as on possible biotechnologically-oriented and genetically-informed control measures.

RESULTS

The genomic sequence presented and described here is an improvement with respect to the available draft sequence in terms of completeness and contiguity, and includes structural and functional annotations. A comparative analysis of gene families of interest, related to the species ecology and potential for polyphagy and adaptability, revealed a contraction of gustatory receptor genes and a paralogous expansion of some subgroups/subfamilies of odorant receptors, ionotropic receptors and cytochrome P450s.

CONCLUSIONS

The new genomic sequence as well as the comparative analyses data may provide a clue to explain the staggering invasive potential of the species and may serve to identify targets for potential biotechnological applications aimed at its control.

Effect of space flight on the behavior of human retinal pigment epithelial ARPE-19 cells and evaluation of coenzyme Q10 treatment

Astronauts on board the International Space Station (ISS) are exposed to the damaging effects of microgravity and cosmic radiation. One of the most critical and sensitive districts of an organism is the eye, particularly the retina, and > 50% of astronauts develop a complex of alterations designated as spaceflight-associated neuro-ocular syndrome. However, the pathogenesis of this condition is not clearly understood. In the current study, we aimed to explore the cellular and molecular effects induced in the human retinal pigment ARPE-19 cell line by their transfer to and 3-day stay on board the ISS in the context of an experiment funded by the Agenzia Spaziale Italiana. Treatment of cells on board the ISS with the well-known bioenergetic, antioxidant, and antiapoptotic coenzyme Q10 was also evaluated. In the ground control experiment, the cells were exposed to the same conditions as on the ISS, with the exception of microgravity and radiation. The transfer of ARPE-19 retinal cells to the ISS and their living on board for 3 days did not affect cell viability or apoptosis but induced cytoskeleton remodeling consisting of vimentin redistribution from the cellular boundaries to the perinuclear area, underlining the collapse of the network of intermediate vimentin filaments under unloading conditions. The morphological changes endured by ARPE-19 cells grown on board the ISS were associated with changes in the transcriptomic profile related to the cellular response to the space environment and were consistent with cell dysfunction adaptations. In addition, the results obtained from ARPE-19 cells treated with coenzyme Q10 indicated its potential to increase cell resistance to damage.

EZmito: a simple and fast tool for multiple mitogenome analyses

Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.

Improved tolerability of neratinib in patients with HER2-positive early-stage breast cancer: the CONTROL trial

BACKGROUND

Neratinib is an irreversible pan-HER tyrosine kinase inhibitor approved for extended adjuvant treatment in early-stage HER2-positive breast cancer based on the phase III ExteNET study. In that trial, in which no antidiarrheal prophylaxis was mandated, grade 3 diarrhea was observed in 40% of patients and 17% discontinued due to diarrhea. The international, open-label, sequential-cohort, phase II CONTROL study is investigating several strategies to improve tolerability.

PATIENTS AND METHODS

Patients who completed trastuzumab-based adjuvant therapy received neratinib 240 mg/day for 1 year plus loperamide prophylaxis (days 1-28 or 1-56). Sequential cohorts evaluated additional budesonide or colestipol prophylaxis (days 1-28) and neratinib dose escalation (DE; ongoing). The primary end point was the incidence of grade ≥3 diarrhea.

RESULTS

Final data for loperamide (L; n = 137), budesonide + loperamide (BL; n = 64), colestipol + loperamide (CL; n = 136), and colestipol + as-needed loperamide (CL-PRN; n = 104) cohorts, and interim data for DE (n = 60; completed ≥six cycles or discontinued; median duration 11 months) are available. No grade 4 diarrhea was observed. Grade 3 diarrhea rates were lower than ExteNET in all cohorts and lowest in DE (L 31%, BL 28%, CL 21%, CL-PRN 32%, DE 15%). Median number of grade 3 diarrhea episodes was one; median duration per grade 3 episode was 1.0-2.0 days across cohorts. Most grade 3 diarrhea and diarrhea-related discontinuations occurred in month 1. Diarrhea-related discontinuations were lowest in DE (L 20%, BL 8%, CL 4%, CL-PRN 8%, DE 3%). Decreases in health-related quality of life did not cross the clinically important threshold.

CONCLUSIONS

Neratinib tolerability was improved with preemptive prophylaxis or DE, which reduced the rate, severity, and duration of neratinib-associated grade ≥3 diarrhea compared with ExteNET. Lower diarrhea-related treatment discontinuations in multiple cohorts indicate that proactive management can allow patients to stay on neratinib for the recommended time period. CLINICALTRIALS.GOV: NCT02400476.

A randomized, open-label, multicenter, phase 3 study to compare the efficacy and safety of eribulin to treatment of physician's choice in patients with advanced non-small cell lung cancer

BACKGROUND

Eribulin is a microtubule dynamics inhibitor with a novel mechanism of action. This phase 3 study aimed to compare overall survival (OS) in patients with heavily pretreated non-small cell lung cancer (NSCLC) receiving eribulin to treatment of physician's choice (TPC).

PATIENTS AND METHODS

Patients with advanced NSCLC who had received ≥2 prior therapies, including platinum-based doublet and epidermal growth factor receptor tyrosine kinase inhibitor, were randomly assigned to receive eribulin or TPC (gemcitabine, pemetrexed, vinorelbine, docetaxel). The primary endpoint was OS. Secondary endpoints were progression-free survival and objective response rate.

RESULTS

Five hundred and forty patients were randomized to either eribulin (n = 270) or TPC (n = 270). Median OS for eribulin and TPC was the same: 9.5 months [hazard ratio (HR): 1.16; 95% confidence interval: 0.95-1.41; P = 0.13]. Progression-free survival for eribulin and TPC was 3.0 and 2.8 months, respectively (HR: 1.09; 95% confidence interval: 0.90-1.32; P = 0.39). The objective response rate was 12% for eribulin and 15% for TPC. Clinical benefit rate (eribulin, 57%; TPC, 55%) and disease control rate (eribulin, 63%; TPC, 58%) were similar between treatment arms. The most common adverse event was neutropenia, which occurred in 57% of eribulin patients and 49% of TPC patients at all grades. Other non-hematologic side-effects were manageable and similar in both groups except for peripheral sensory neuropathy (all grades; eribulin, 16%; TPC, 9%).

CONCLUSION

This phase 3 study did not demonstrate superiority of eribulin over TPC with regard to overall survival. However, eribulin does show activity in the third-line setting for NSCLC.

TRIAL REGISTRATION ID

www.ClinicalTrials.gov; NCT01454934.

Relationship among circulating tumor cells, CEA and overall survival in patients with metastatic colorectal cancer

BACKGROUND

We previously reported results of a prospective trial evaluating the significance of circulating tumor cells (CTCs) in patients with metastatic colorectal cancer (mCRC). This secondary analysis assessed the relationship of the CTC number with carcinoembryonic antigen (CEA) and overall survival.

PATIENTS AND METHODS

Patients with mCRC had CTCs measured at baseline and specific time points after the initiation of new therapy. Patients with a baseline CEA value ≥ 10 ng/ml and CEA measurements within ± 30 days of the CTC collection were included.

RESULTS

We included 217 patients with mCRC who had a CEA value of ≥ 10 ng/ml. Increased baseline CEA was associated with shorter survival (15.8 versus 20.7 months, P = 0.012). Among all patients with a baseline CEA value of ≥ 25 ng/ml, patients with low baseline CTCs (<3, n = 99) had longer survival than those with high CTCs (≥ 3, n = 58; 20.8 versus 11.7 months, P = 0.001). CTCs added prognostic information at the 3-5- and 6-12-week time points regardless of CEA. In a multivariate analysis, CTCs at baseline but not CEA independently predicted survival and both CTCs and CEA independently predicted survival at 6-12 weeks.

CONCLUSIONS

This study demonstrates that both CEA and CTCs contribute prognostic information for patients with mCRC.

Final STEPP results of prophylacatic versus reactive skin toxicity (ST) treatment (tx) for panitumumab (pmab)-related ST in patients (pts) with metastatic colorectal cancer (mCRC)

CRA4027

Background: Pmab, a fully human monoclonal antibody targeting the epidermal growth factor receptor (EGFR), is approved as monotherapy in the US for mCRC following disease progression (PD) and in the EU and Canada for tumors bearing wild-type (WT) KRAS. The most common toxicity with anti-EGFR inhibitors are ST. This study of pmab+ chemotherapy (CT) estimates the difference in the incidence of specific ≥ grade 2 ST of interest between pts receiving prophylactic (P) or reactive (R) skin tx. Methods: Pts had unresectable mCRC after PD with 1st-line fluoropyrimidine and oxaliplatin-based CT ± bevacizumab. Pts received either pmab 6.0mg/kg/FOLFIRI Q2W or pmab 9 mg/kg/irinotecan Q3W. Within each stratum, pts were randomized 1:1 to either P ST tx 24 hrs before the 1st dose daily for 6 wks or R ST tx after ST occurred. Tx for ST included: moisturizers, sunscreen, topical steroid, and doxycycline. Efficacy and safety were evaluated by P vs R tx groups, KRAS status (mutant [MT] vs WT), and chemotherapy status. Responses were assessed using modified RECIST with confirmation. Quality of life was assessed using the Dermatology Life Quality Index at screening, wks 2–7, and follow-up. Results: 95 pts were enrolled and randomized: 48 pts to P and 47 pts to R. During the 6 wk ST tx period, 29% of pts in the P group vs 62% of pts in the R group had protocol-specified ≥grade 2 ST. Of the 87 KRAS evaluable pts, 49 (56%) pts had WT KRAS and 38 (44%) pts had MT KRAS. Efficacy and safety are shown. Mean (SD) change in DLQI from baseline was 1.3 (2.6) for P and 4.2 (5.8) for R at wk 3 (when the median time to 1st ≥grade 2 ST was reached in the R group) and was 2.0 (2.8) for P and 2.6 (4.4) for R at wk 7. Conclusions: Prophylactic use of the skin tx regimen resulted in >50% reduction in the rate of specific ≥ grade 2 STs and improved QOL during the 6-week skin tx period vs R use. Numerical differences in favor of the P group were observed for all endpoints.

[Table: see text]

[Table: see text]

Final STEPP results of prophylacatic versus reactive skin toxicity (ST) treatment (tx) for panitumumab (pmab)-related ST in patients (pts) with metastatic colorectal cancer (mCRC)

CRA4027

The full, final text of this abstract will be available in Part II of the 2009 ASCO Annual Meeting Proceedings, distributed onsite at the Meeting on May 30, 2009, and as a supplement to the June 20, 2009, issue of the Journal of Clinical Oncology.

[Table: see text]

Prognostic significance of circulating tumor cells in patients with metastatic colorectal cancer

BACKGROUND

We demonstrated that circulating tumor cell (CTC) number at baseline and follow-up is an independent prognostic factor in metastatic colorectal cancer (mCRC). This analysis was undertaken to explore whether patient and treatment characteristics impact the prognostic value of CTCs.

PATIENTS AND METHODS

CTCs were enumerated with immunomagnetic separation from the blood of 430 patients with mCRC at baseline and on therapy. Patients were stratified into unfavorable and favorable prognostic groups based on CTC levels of > or = 3 or <3 CTCs/7.5 ml, respectively. Subgroups were analyzed by line of treatment, liver involvement, receipt of oxaliplatin, irinotecan, or bevacizumab, age, and Eastern Cooperative Oncology Group performance status (ECOG PS).

RESULTS

Seventy-one percent of deaths have occurred. Median follow-up for living patients is 25.8 months. For all patients, progression-free survival (PFS) and overall survival (OS) for unfavorable compared with favorable baseline CTCs is shorter (4.4 versus 7.8 m, P = 0.004 for PFS; 9.4 versus 20.6 m, P < 0.0001 for OS). In all patient subgroups, unfavorable baseline CTC was associated with inferior OS (P < 0.001). In patients receiving first- or second-line therapy (P = 0.003), irinotecan (P = 0.0001), having liver involvement (P = 0.002), >/=65 years (P = 0.0007), and ECOG PS of zero (P = 0.04), unfavorable baseline CTC was associated with inferior PFS.

CONCLUSION

Baseline CTC count is an important prognostic factor within specific subgroups defined by treatment or patient characteristics.

Circulating tumor cells (CTC) predict progression free (PFS) and overall survival (OS) in patients with metastatic colorectal cancer

4010

Background: Treatment options for patients with metastatic colorectal cancer (mCRC) have recently expanded. However, the introduction of new regimens has highlighted the need for biomarkers to guide and monitor therapy. This study investigates the hypothesis that CTC levels can predict clinical outcomes in patients with mCRC. Methods: In a prospective multi-center study, 7.5 mL of blood from 456 patients with mCRC were tested for CTC using immunomagnetic separation before starting 1st, 2nd or 3rd line therapy and at subsequent radiographic follow-up timepoints. Response on imaging was determined by participating centers. Results: Patients were stratified into unfavorable and favorable prognostic groups based on levels of =3 or <3 CTC per 7.5mL, respectively. Median PFS, OS and significance between the two groups (log rank test) at different timepoints after the initiation of therapy is indicated in the table . The OS of patients converting to or maintaining unfavorable CTC at follow up timepoints was worse than for patients maintaining favorable CTC (12.6, 7.0 vs. 21.1 months, respectively, p<0.0001). In multivariate analyses, which included age, ECOG performance status, and the line and type of therapy, CTC remained the most significant independent predictor of outcome. Conclusions: CTC levels before treatment and at subsequent timepoints are an independent predictor of PFS and OS in patients with mCRC. CTC levels of =3 per 7.5mL of blood after initiation of therapy are highly predictive of shorter PFS and OS. A large randomized phase III study to confirm these findings in mCRC patients receiving first line therapy recently completed accrual (DCCG CAIRO- 2).

[Table: see text]

No significant financial relationships to disclose.

A phase II study of a novel anti-tubulin, E7389, in patients with advanced non-small cell lung cancer (NSCLC)

7106

Background: E7389, a synthetic analog of halichondrin B that was isolated from a marine sponge, has broad anti-proliferative activity at nanomolar levels and a unique profile of tubulin interactions. Methods: This is an open-label, single-arm, stratified phase II study of E7389 in patients with measurable, recurrent and/or metastatic NSCLC who progressed during or after platinum-based doublet chemotherapy. E7389 (1.4 mg/m2) was administered as a bolus IV on days 1, 8, and 15 of a 28-day cycle to 72 patients (cohort 1) in stratum I (55 taxane pretreated patients) and stratum II (17 taxane-naive patients) and on Days 1 and 8 of a 21-day cycle (cohort 2), providing an additional 22 patients in stratum I. The primary efficacy endpoint was objective response rate to E7389 monotherapy. Results: As of 9 December 2005, 94 evaluable patients received E7389. Nineteen tumors were classified as squamous cell carcinomas, 39 as adenocarcinomas, and 36 were large cell carcinomas or unclassified. The median number of cycles completed was 3. Fifteen patients completed 6 or more cycles and 75 patients underwent tumor assessments after cycle 2. Major toxicities related to study drug included myelosuppression, nausea, fatigue, dehydration, arthralgias, dyspnea, and peripheral neuropathy. Based on RECIST criteria, 6 partial responses (PR) were observed among 94 evaluable patients (PR rate = 6.4%, 95% CI: 2.8%, 12.8%). For 33 patients the best response was stable disease (SD rate = 35.1%, 95% CI: 25.5%, 45.1%). Disease control rate (PR + SD) was 41.5% (95% CI: 31.4%, 51.7%). For cohort 1, the 12-week progression free survival rate was 57.2%. As of 9 December 2005, median PFS time was 108 days (95% CI = 55, min-max = 1–239+). Cohort 2 is being followed to estimate their 12-week PFS. The correlation of beta tubulin isotype, stathmin, microtubule-associated protein 4 (MAP4) and tau protein mRNA expression with tumor responses is on-going. Conclusions: Based on this data, E7389 has been shown to be safe and effective in the treatment of NSCLC patients. Updated information and results of molecular correlations of responses will be presented.

[Table: see text]

Phase-1 trial of high-dose intravenous cisplatin with simultaneous intravenous sodium thiosulfate

Previous pharmacological and clinical data have suggested that it is possible to increase significantly the dose of "active" cisplatin delivered systemically by the simultaneous administration of intravenous sodium thiosulfate. In order to define more critically the toxicity and potential efficacy of this therapeutic approach, 36 patients with a variety of solid tumors and limited pretreatment were entered into a phase-1 trial of high-dose intravenous cisplatin plus sodium thiosulfate. The maximally tolerated dose of cisplatin was found to be 200 mg/m2, excessive renal toxicity being observed at a dose of 225 mg/m2 (6/14 courses associated with serum creatinine rise to greater than 2.0 mg-%). Following several courses of high-dose cisplatin, peripheral neuropathy becomes the limiting toxicity (9/15 patients receiving at least three courses of cisplatin at greater than or equal to 150 mg/m2 experienced at least grade-1 neuropathy). Significant ototoxicity developed after only one or two treatment courses, but with continued treatment hearing loss appeared to stabilize in the moderately severe range in most patients. Major responses (PR/CR) were observed in 7/27 evaluable patients. We conclude that cisplatin can be administered at a dose at 200 mg/m2 as a 2-h infusion (with simultaneous sodium thiosulfate) with significant but acceptable toxicities and without evidence of loss of anti-neoplastic activity (secondary to the presence of thiosulfate). However, owing to the development of neurotoxicity most patients will be unable to receive more than three courses of this high-dose treatment regimen.