Unique genetic profiles from cerebrospinal fluid cell-free DNA in leptomeningeal metastases of EGFR-mutant non-small-cell lung cancer: a new medium of liquid biopsy.

Background: Leptomeningeal metastases (LM) are more frequent in non-small-cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations. Due to limited access to leptomeningeal lesions, the purpose of this study was to explore the potential role of cerebrospinal fluid (CSF) as a source of liquid biopsy in patients with LM. Patients and methods: Primary tumor, CSF, and plasma in NSCLC with LM were tested by next-generation sequencing. In total, 45 patients with suspected LM underwent lumbar puncture, and those with EGFR mutations diagnosed with LM were enrolled. Results: A total of 28 patients were enrolled in this cohort; CSF and plasma were available in 26 patients, respectively. Driver genes were detected in 100% (26/26), 84.6% (22/26), and 73.1% (19/26) of samples comprising CSF cell-free DNA (cfDNA), CSF precipitates, and plasma, respectively; 92.3% (24/26) of patients had much higher allele fractions in CSF cfDNA than the other two media. Unique genetic profiles were captured in CSF cfDNA compared with those in plasma and primary tissue. Multiple copy number variations (CNVs) were mainly identified in CSF cfDNA, and MET copy number gain identified in 47.8% (11/23) of patients was the most frequent one, while other CNVs included ERBB2, KRAS, ALK, and MYC. Moreover, loss of heterozygosity (LOH) of TP53 was identified in 73.1% (19/26) CSF cfDNA, which was much higher than that in plasma (2/26, 7.7%; P < 0.001). There was a trend towards a higher frequency of concomitant resistance mutations in patients with TP53 LOH than those without (70.6% versus 33.3%; P = 0.162). EGFR T790M was identified in CSF cfDNA of 30.4% (7/23) of patients who experienced TKI progression. Conclusion: CSF cfDNA could reveal the unique genetic profiles of LM and should be considered as the most representative liquid biopsy medium for LM in EGFR-mutant NSCLC.

A phase III randomised controlled trial of erlotinib vs gefitinib in advanced non-small cell lung cancer with EGFR mutations.

BACKGROUND: A phase III trial was conducted to compare the safety and efficacy of erlotinib with that of gefitinib in advanced non-small cell lung cancer harbouring epidermal growth factor receptor mutations in exon 19 or 21. METHODS: Eligible patients were randomised to receive erlotinib (150 mg per day) or gefitinib (250 mg per day) orally until disease progression or unacceptable toxicity. We aimed to determine whether erlotinib is superior to gefitinib in efficacy. The primary end point was progression-free survival. RESULTS: A total of 256 patients were randomised to receive erlotinib (N=128) or gefitinib (N=128). Median progression-free survival was not better with erlotinib than with gefitinib (13.0 vs 10.4 months, 95% confidence interval (CI) 0.62-1.05, P=0.108). The corresponding response rates and median overall survival were 56.3% vs 52.3% (P=0.530) and 22.9 vs 20.1 months (95% CI 0.63-1.13, P=0.250), respectively. There were no significant differences in grade 3/4 toxicities between the two arms (P=0.172). CONCLUSIONS: The primary end point was not met. Erlotinib was not significantly superior to gefitinib in terms of efficacy in advanced non-small cell lung cancer with epidermal growth factor receptor mutations in exon 19 or 21, and the two treatments had similar toxicities.

[The effect of preoperative induction chemotherapy on long-term survival of patients with advanced squamous cell carcinoma of the oral cavity tongue].

Objective:To discuss the long term efficency of preoperative induction chemotherapy(IC)±radiotherapy on patients with resectable stage Ⅲ or Ⅳ squamous cell carcinoma of the oral cavity tongue(SCCOT).Method:During June 1996 to December 2005, 73 patients with locally advanced SCCOT treated preoperatively with IC(3 cycle of cisplatin and 5 fluorouracil) followed by surgery(resection of the primary tumor and neck)±radiotherapy in the Cancer Center of Sun Yat-sen University were enrolled in our study. Five-year overall survival rates(OS), local control rate and reasons of treatment failure were analyzed retrospectively.Result:The follow-up time was 1.9 to 188.0 months, and the median follow-up time was 70.9 months.Among that, 24 cases(32.9%) were still alive, of which 23 patients survival time is more than 10 years until the deadline of the follow-up. After IC, 17 patients(23.3%) had clinical complete response; 44 patients(60.3%) had a clinical partial response; 12 patients(16.4%) had no response or progression, and an overall response rate was 83.6%(65/73). On final surgical pathology, 14 patients(19.2%) had pathological complete response; 59 patients(80.8%) had histological incomplete response(residual tumor). Univariate analysis showed that the tumor size(P< 0.05), cervical lymphatic metastasis(P< 0.05),clinical stage(P< 0.05), the different clinical remissions(P< 0.05), had or not pathological complete remission(P< 0.05) were risk factors affecting prognosis(P< 0.05).Multivariate analysis indicated that cervical lymphatic metastasis cervical lymphatic metastasis(P< 0.05), the different clinical remissions (P< 0.05), had or not pathological complete remission(P< 0.05) were independent factors for prognosis. Five-year OS of clinical effective of IC was 62.5%, apparently higher than the invalid effect 41.7% (P< 0.05). Five-year OS of pCR was 92.9%, while have no pCR was 47.9%(P< 0.05). A significant difference between the two groups was also found. During whole follow-up time, 22 patients developed recurrence. Five-year OS was 59.8%, local control rate were 69.9%.Conclusion:IC plus surgery with or without postoperative radiotherapy was a treatment modality that was tolerated with encouraging activity and survival outcome in patients with advanced resectable SCCOT. Response rate with this IC regimen was limited, but the responders were associated with excellent prognosis.

Pemetrexed versus gefitinib as a second-line treatment in advanced nonsquamous nonsmall-cell lung cancer patients harboring wild-type EGFR (CTONG0806): a multicenter randomized trial.

BACKGROUND: CTONG0806 assessed the efficacy of pemetrexed versus gefitinib as second-line treatment in advanced nonsquamous nonsmall-cell lung cancer (NSCLC) harboring wild-type epidermal growth factor receptor (EGFR). PATIENTS AND METHODS: Patients with locally advanced or metastatic nonsquamous NSCLC harboring wild-type EGFR, detected by direct sequencing, and previously treated with platinum-based chemotherapy were randomized to receive gefitinib (250 mg/day) orally or pemetrexed (500 mg/m(2)) i.v. on day 1 of a 21-day cycle until disease progression or unacceptable toxicity. The primary end point was progression-free survival (PFS). The Independent Review Committee (IRC) evaluated all pictorial data. RESULTS: From February 2009 to August 2012, 161 patients were enrolled, and 157 were assessable (81 in the gefitinib arm, 76 in the pemetrexed arm). Baseline characteristics were balanced between the two arms. The median PFSs were 4.8 versus 1.6 months in the pemetrexed and gefitinib arms, respectively [hazard ratio (HR) 0.54, 95% confidence interval (CI) 0.40-0.75, P < 0.001] as confirmed by IRC evaluation (5.6versus 1.7 months, HR 0.53, 95% CI 0.38-0.75, P < 0.001). The median overall survival (OS) showed a trend of superiority in the pemetrexed arm (12.4 versus 9.6 months, HR 0.72, 95% CI 0.49-1.04, P = 0.077). Quality-of-life assessment showed no marked difference between the arms. No unexpected adverse events were found. Of 108 patients with sufficient DNA samples, EGFR mutation status was re-tested by Scorpion amplification refractory mutation system (ARMS); 32 (29.6%) tested positive (19 in the pemetrexed arm, 13 in the gefitinib arm; median PFS: 8.1 versus 7.0 months, HR 0.94, 95% CI 0.43-2.08, P = 0.877). CONCLUSIONS: CTONG0806 is the first trial to show significant improvement in PFS and an improved OS trend with pemetrexed compared with gefitinib as second-line setting treatment of EGFR wild-type advanced nonsquamous NSCLC. ARMS is superior to direct sequencing in excluding false-negative patients. CLINICALTRIALSGOV IDENTIFIER: NCT00891579.

Emissions of halocarbons from mobile vehicle air conditioning system in Hong Kong.

During the implementation of Montreal Protocol, emission inventories of halocarbons in different sectors at regional scale are fundamental to the formulation of relevant management strategy and inspection of the implementation efficiency. This study investigated the emission profile of halocarbons used in the mobile vehicle air conditioning system, the leading sector of refrigeration industry in terms of the refrigerant bank, market and emission, in the Hong Kong Special Administrative Region, using a bottom-up approach developed by 2006 IPCC Good Practice Guidance. The results showed that emissions of CFC-12 peaked at 53 tons ODP (Ozone Depletion Potential) in 1992 and then gradually diminished, whereas HFC-134a presented an increasing emission trend since 1990s and the emissions of HFC-134a reached 65,000 tons CO2-equivelant (CO2-eq) by the end of 2011. Uncertainty analysis revealed relatively high levels of uncertainties for special-purpose vehicles and government vehicles. Moreover, greenhouse gas (GHG) abatements under different scenarios indicated that potential emission reduction of HFC-134a ranged from 4.1 to 8.4 × 10(5)tons CO2-eq. The findings in this study advance our knowledge of halocarbon emissions from mobile vehicle air conditioning system in Hong Kong.

Lower Ras expression as an independent predictor of patient outcomes in lung cancer treated with bevacizumab plus chemotherapy.

The objective of this study was to analyze the predictive roles of VEGF/KDR/Ras/MAPK gene expression in patients with advanced non-small-cell lung cancer (NSCLC) treated with bevacizumab plus chemotherapy. Twenty-five patients participating in an open-label phase IV trial (SAiL, MO19390) with available tumor tissues were analyzed. The mRNA expression levels of VEGF, kinase insert domain receptor (KDR), Ras, and mitogen-activated protein kinase (MAPK) in tumor tissues were detected using real-time quantitative PCR methods. The relationships between gene expression and disease control rate (DCR), progression-free survival (PFS), and overall survival (OS) were assessed. Patients with lower Ras expression had a longer PFS and OS than patients with higher expression (median PFS, 9.9 vs 5.5 months, χ(2)=3.944, P=0.047; OS, 19.3 vs 7.1 months, χ(2)=9.384, P=0.002). The PFS and OS of patients with lower and higher MAPK expression exhibited a marginal and significant difference (median PFS, 9.9 vs 5.5 months, χ(2)=3.464, P=0.063; OS, 19.3 vs 9.7 months, χ(2)=5.298, P=0.021), respectively. Multivariate analyses using Cox's proportional hazards model showed that Ras is an independent predictor of OS (χ(2)=9.384, P=0.002). No differences in DCR were found according to Ras expression level. The results indicate that Ras is an independent predictor of OS. Thus, patients with lower Ras expression are most likely to benefit from bevacizumab plus chemotherapy treatment regimen. Patients with higher levels of Ras should receive other inhibitors that target Ras. The results also suggest that gene therapies that decrease RAS expression combined with bevacizumab may improve lung cancer treatment. Although there is a very important implication to patient selection in the target therapy, the data in this study are very preliminary owing to the too small sample size. Therefore, further research involving large numbers of patients and a prospective assessment of low and high RAS mRNA expressions getting the same treatments need to be done before conclusions can be made.

Rhizoctonia solani Identified as the Disease Causing Agent of Peanut Leaf Rot in China.

Peanut (Arachis hypogaea L.) is one of the most economically important oil crops in the world. Since the 1990s, the peanut industry has developed rapidly in China. However, because of the use of high-yield varieties and increased plant density, a peanut leaf rot disease occurred in Laixi Experimental Fields in Shandong Province, China in 2007. Leaves had nearly circular, brown lesions that enlarged quickly developing yellow-brown halos at the edges of the lesions. High relative humidity under field conditions led to complete necrosis of the leaves with cotton wool-like mycelia observed followed by the development of sclerotia on the leaf surface. Symptomatic plants were observed between 2007 and 2010, and symptomatic leaf tissue was collected from the Laixi Experimental Fields. An isolate (designated YF-1) from symptomatic peanut leaves was isolated and purified on potato dextrose agar (PDA) and water agar (WA) medium. On PDA, the colony appeared initially as colorless and grew to the diameter of a 9-cm petri dish within 3 days. As the mycelium aged, the colony color gradually became light brown, and sclerotia developed on the surface of the colony. YF-1 was identified as Rhizoctonia solani Kühn based on the number of nuclei per cell ranging from 4 to 13 (average 6.1), hyphal diameter being 7.5 to 12.9 µm (average 8.3 µm), branching at right angles, a septum was present near each hyphal branch with a slight constriction, and no clamp connection structures or conidia were ever observed (4). To further confirm the identity of isolate YF-1, genomic DNA was extracted using the DNeasy Plant Mini DNA Extraction Kit (Shanghai Leifeng Biotechnol. Co., Ltd.), and the complete internal transcribed spacer (ITS) region of ribosomal DNA was amplified and sequenced with a pair of primers ITS1/ITS4 (2). A GenBank BLAST search produced an exact match for the sequences of R. solani (AY154301), with 100% sequence similarity. To estimate the mode of anastomosis, YF-1 was paired on WA medium with each reference strain belonging to anastomosis groups (AGs) 1 through 8 (provided by Shandong Agriculture University) (1,3). The results indicated that YF-1 belonged to group AG-1, subgroup AG-1-IA of R. solani. Pathogenicity tests were conducted by inoculating 10 peanut leaves using a colonized paper disc method (filter paper 1 cm in diameter suspended in the mycelia suspension). Ten control leaves received paper discs without mycelium. Inoculated and non-inoculated plants were kept in humid chambers for 24 h at 25°C. Three days after inoculation, the leaves developed typical brown lesions that were similar to those of naturally diseased plants. Koch's postulates were fulfilled by reisolation of R. solani from symptomatic leaves. No symptoms were observed on control leaves. To our knowledge, this is the first report of peanut leaf rot caused by R. solani. Occurrence of the disease in China is a new threat to the health of peanut. References: (1) Y. X. Chen et al. Acta Phytopathol. Sin. 3:139, 1985. (2) T. Misawa and S. Kuninaga. J. Gen. Plant Pathol. 76:310, 2010. (3) A. Ogoshi. Ann. Phytopathol. Soc. Jpn. 38:117, 1972. (4) J. R. Jr. Pameter and H. S. Whitmey. UC Press. 135, 1970.

Erlotinib as second-line treatment in patients with advanced non-small-cell lung cancer and asymptomatic brain metastases: a phase II study (CTONG-0803).

BACKGROUND: This phase II, open-label study evaluated the efficacy and safety of erlotinib as second-line therapy in non-small-cell lung cancer (NSCLC) patients with brain metastases (BM). PATIENTS AND METHODS: Forty-eight patients aged 18-75 years with Eastern Cooperative Oncology Group performance status 0-2, confirmed adenocarcinoma or activating epidermal growth factor receptor (EGFR) mutation-positive NSCLC, and asymptomatic BM without extracranial progressive disease after first-line platinum-doublet chemotherapy were recruited. Treatment comprised erlotinib 150 mg/day. The primary end point was progression-free survival (PFS) determined by RECIST. RESULTS: The median PFS was 10.1 months [95% confidence interval (CI) 7.1-12.3] for intracranial progression and 9.7 months (95% CI 2.5-17.8) for intracranial and systemic progression. Patients with EGFR mutation-positive disease had significantly longer median PFS versus EGFR wild-type disease [15.2 months (95% CI 8.3-22.2) versus 4.4 months (95% CI 0.0-11.6); P = 0.02]. The median overall survival was 18.9 months (95% CI 14.4-23.4); 6-month and 1-year survival rates were 85% and 73%, respectively. Overall response rate was 58.3%. Most common adverse events were rash (77.1%), paronychia (20.8%), hyperbilirubinemia (16.7%), and diarrhea (14.6%); these were predominantly of grade 1/2. CONCLUSIONS: Single-agent erlotinib was active and well tolerated in NSCLC patients with BM. Further studies are warranted.

Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana.

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.

Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana.

A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago truncatula (Mt) and Glycine max (soybean), and also among homoeologous segments of soybean, we used a hybridization strategy involving bacterial artificial chromosome (BAC) contigs. A Mt BAC library consisting of 30,720 clones was screened with a total of 187 soybean BAC subclones and restriction fragment length polymorphism (RFLP) probes. These probes came from 50 soybean contig groups, defined as one or more related BAC contigs anchored by the same low-copy probe. In addition, 92 whole soybean BAC clones were hybridized to filters of HindIII-digested Mt BAC DNA to identify additional cases of cross-hybridization after removal of those soybean BACs found to be repetitive in Mt. Microsynteny was inferred when at least two low-copy probes from a single soybean contig hybridized to the same Mt BAC or when a soybean BAC clone hybridized to three or more low-copy fragments from a single Mt BAC. Of the 50 soybean contig groups examined, 54% showed microsynteny to Mt. The degree of conservation among 37 groups of soybean contigs was also investigated. The results indicated substantial conservation among soybean contigs in the same group, with 86.5% of the groups showing at least some level of microsynteny. One contig group was examined in detail by a combination of physical mapping and comparative sequencing of homoeologous segments. A TBLASTX similarity search was performed between 1,085 soybean sequences on the 50 BAC contig groups and the entire Arabidopsis genome. Based on a criterion of sequence homologues <100 kb apart, each with an expected value of < or =1e-07, seven of the 50 soybean contig groups (14%) exhibited microsynteny with Arabidopsis.

A genome-specific repetitive DNA sequence from Oryza eichingeri: characterization, localization, and introgression to O. sativa.

In the course of transferring the brown planthopper resistance from a diploid, CC-genome wild rice species, Oryza eichingeri (IRGC acc. 105159 and 105163), to the cultivated rice variety 02428, we have isolated many alien addition and introgression lines. The O. eichingeri chromatin in some of these lines has previously been identified using genomic in situ hybridization and molecular-marker analysis. Here we cloned a tandemly repetitive DNA sequence from O. eichingeri IRGC acc105163, and detected it in 25 introgression lines. This repetitive DNA sequence showed high specificity to the rice CC genome, but was absent from all the four tetraploid species with BBCC or CCDD genomes. The monomer in this repetitive DNA sequence is 325-366-bp long, with a copy number of about 5,000 per 1 C of the O. eichingerigenome, showing 88% homology to a repetitive DNA sequence isolated from Oryza officinalis(2n=2 x=24, CC). Fluorescent in situ hybridization revealed 11 signals distributed over eight O. eichingeri chromosomes, mostly in terminal or subterminal regions.