Description: Effector-triggered immunity (ETI) is activated when plant disease resistance (R) proteins recognize the presence of pathogen effector proteins delivered into host cells. The ETI response generally encompasses a defensive ‘hypersensitive response’ (HR) that involves programmed cell death at the site of pathogen recognition. While many R protein and effector protein pairs are known to trigger HR, other components of the ETI signaling pathway remain elusive. Effector genes regulated by inducible promoters cause background HR due to leaky protein expression, preventing the generation of relevant transgenic plant lines. By employing the HyP5SM suicide exon, we have developed a strategy to tightly regulate effector proteins such that HR is chemically inducible and non-leaky. This alternative splicing-based gene regulation system was shown to successfully control Bs2/AvrBs2-dependent and RPP1/ATR151-dependent HR in Nicotiana benthamiana and Nicotiana tabacum , respectively. It was also used to generate viable and healthy transgenic Arabidopsis thaliana plants that inducibly initiate HR. Beyond enabling studies on the ETI pathway, our regulatory strategy is generally applicable to reduce or eliminate undesired background expression of transgenes.

Description: Motivation: With improvements in next-generation sequencing technologies and reductions in price, ordered RNA-seq experiments are becoming common. Of primary interest in these experiments is identifying genes that are changing over time or space, for example, and then characterizing the specific expression changes. A number of robust statistical methods are available to identify genes showing differential expression among multiple conditions, but most assume conditions are exchangeable and thereby sacrifice power and precision when applied to ordered data. Results: We propose an empirical Bayes mixture modeling approach called EBSeq-HMM. In EBSeq-HMM, an auto-regressive hidden Markov model is implemented to accommodate dependence in gene expression across ordered conditions. As demonstrated in simulation and case studies, the output proves useful in identifying differentially expressed genes and in specifying gene-specific expression paths. EBSeq-HMM may also be used for inference regarding isoform expression. Availability and implementation: An R package containing examples and sample datasets is available at Bioconductor. Contact: kendzior@biostat.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Leishmania braziliensis are intracellular parasites that cause unique clinical forms of cutaneous leishmaniasis. Previous studies with other leishmania species demonstrated that reactive oxygen species (ROS) control promastigotes, the infective stage of the parasite, but not the amastigote form that exists in the mammalian host. Here we show that ROS inhibits growth of L. braziliensis amastigotes in resting monocytes, and that classical monocytes are primarily responsible for this control. ROS, but not nitric oxide, also contributed to killing of L. braziliensis by IFN- activated monocytes. Furthermore, by gene expression profiling of human lesions we found greater expression of genes associated with ROS, but not nitric oxide, compared to normal skin. This study shows that ROS are important for control of L. braziliensis both at the initial stages of infection, as well as at later time points, and highlights that monocyte subsets may play different roles during leishmaniasis.

Description: Background Growth modulation index (GMI), the ratio of two times to progression measured in patients receiving two successive treatments (GMI = TTP2/TTP1), has been proposed as a criterion of phase II clinical trials. Nevertheless, its use has been limited until now. Patients and methods We carried out a retrospective multicentre study in soft tissue sarcoma patients receiving a second-line treatment after doxorubicin-based regimens to evaluate the link between overall survival and GMI. Second-line treatments were classified as ‘active’ according to the EORTC-STBSG criteria (3-month progression-free rate 〉40% or 6-month PFR 〉14%). Comparisons used chi-squared and log-rank tests. Results The population consisted in 106 men and 121 women, 110 patients (48%) received ‘active drugs’. Median OS from the second-line start was 317 days. Sixty-nine patients experienced GMI 〉1.33 (30.4%). Treatments with ‘active drug’ were not associated with OS improvement: 490 versus 407 days ( P = 0.524). Median OS was highly correlated with GMI: 324, 302 and 710 days with GMI 〈1, GMI = [1.00–1.33], and GMI 〉1.33, respectively ( P 〈 0.0001). In logistic regression analysis, the sole predictive factor was the number of doxorubicin-based chemotherapy cycles. Conclusion GMI seems to be an interesting end point that provides additional information compared with classical criteria. GMI 〉1.33 is associated with significant OS improvement.

Description: Background This phase III open-label trial investigated the efficacy of nilotinib in patients with advanced gastrointestinal stromal tumors following prior imatinib and sunitinib failure. Patients and methods Patients were randomized 2 : 1 to nilotinib 400 mg b.i.d. or best supportive care (BSC; BSC without tyrosine kinase inhibitor, BSC + imatinib, or BSC + sunitinib). Primary efficacy end point was progression-free survival (PFS) based on blinded central radiology review (CRR). Patients progressing on BSC could cross over to nilotinib. Results Two hundred and forty-eight patients enrolled. Median PFS was similar between arms (nilotinib 109 days, BSC 111 days; P  = 0.56). Local investigator-based intent-to-treat (ITT) analysis showed a significantly longer median PFS with nilotinib (119 versus 70 days; P  = 0.0007). A trend in longer median overall survival (OS) was noted with nilotinib (332 versus 280 days; P  = 0.29). Post hoc subset analyses in patients with progression and only one prior regimen each of imatinib and sunitinib revealed a significant difference in median OS of 〉4 months in favor of nilotinib (405 versus 280 days; P  = 0.02). Nilotinib was well tolerated. Conclusion In the ITT analysis, no significant difference in PFS was observed between treatment arms based on CRR. In the post hoc subset analyses, nilotinib provided significantly longer median OS.

Description: Background Masitinib is a highly selective tyrosine kinase inhibitor with activity against the main oncogenic drivers of gastrointestinal stromal tumor (GIST). Masitinib was evaluated in patients with advanced GIST after imatinib failure or intolerance. Patients and methods Prospective, multicenter, randomized, open-label trial. Patients with inoperable, advanced imatinib-resistant GIST were randomized (1 : 1) to receive masitinib (12 mg/kg/day) or sunitinib (50 mg/day 4-weeks-on/2-weeks-off) until progression, intolerance, or refusal. Primary efficacy analysis was noncomparative, testing whether masitinib attained a median progression-free survival (PFS) (blind centrally reviewed RECIST) threshold of 〉3 months according to the lower bound of the 90% unilateral confidence interval (CI). Secondary analyses on overall survival (OS) and PFS were comparative with results presented according to a two-sided 95% CI. Results Forty-four patients were randomized to receive masitinib ( n = 23) or sunitinib ( n = 21). Median follow-up was 14 months. Patients receiving masitinib experienced less toxicity than those receiving sunitinib, with significantly lower occurrence of severe adverse events (52% versus 91%, respectively, P = 0.008). Median PFS (central RECIST) for the noncomparative primary analysis in the masitinib treatment arm was 3.71 months (90% CI 3.65). Secondary analyses showed that median OS was significantly longer for patients receiving masitinib followed by post-progression addition of sunitinib when compared against patients treated directly with sunitinib in second-line [hazard ratio (HR) = 0.27, 95% CI 0.09–0.85, P = 0.016]. This improvement was sustainable as evidenced by 26-month follow-up OS data (HR = 0.40, 95% CI 0.16–0.96, P = 0.033); an additional 12.4 months survival advantage being reported for the masitinib treatment arm. Risk of progression while under treatment with masitinib was in the same range as for sunitinib (HR = 1.1, 95% CI 0.6–2.2, P = 0.833). Conclusions Primary efficacy analysis ensured the masitinib treatment arm could satisfy a prespecified PFS threshold. Secondary efficacy analysis showed that masitinib followed by the standard of care generated a statistically significant survival benefit over standard of care. Encouraging median OS and safety data from this well-controlled and appropriately designed randomized trial indicate a positive benefit–risk ratio. Further development of masitinib in imatinib-resistant/intolerant patients with advanced GIST is warranted.

Description: Gene transfer in inner ear cells: a challenging race Gene Therapy 20, 237 (March 2013). doi:10.1038/gt.2012.51 Authors: R Sacheli, L Delacroix, P Vandenackerveken, L Nguyen & B Malgrange