Reporting 678 putative cSNPs from full-length enriched cDNA sequences of the Korean native pig

Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomic studies. We have analysed 1970 high-quality chromatograms (Phred value >or= 30) that were obtained from sequencing the 5' ends of brainstem, liver, neocortex and spleen clones derived from full-length enriched cDNA libraries from Korean native pigs. In addition, 50,000 pig expressed sequence tag (EST) sequence trace files were obtained from Genbank and combined with our sequencing information to facilitate SNP identification in silico. The process generated 8118 contigs, of which 239 included minimum one sequence from Korean native pig and contained 678 putative coding single nucleotide polymorphisms (cSNPs). Of these, 33 putative cSNPs were randomly selected for confirmatory analysis and validated using 20 pigs from four different breeds (Duroc, Landrace, Yorkshire, Korean native pig). Of the 33 putative cSNPs, 20 were confirmed (61%), which was similar to the frequency reported in other studies. We also identified 15 new cSNPs from the validation process, which were not detected by our in silico analysis. Our study shows that analysing genetically diverse pig breeds including the Korean native pig could serve as a useful strategy for generating a large number of cSNPs.

A randomized phase II study of perifosine (P) plus imatinib for patients with imatinib-resistant gastrointestinal stromal tumor (GIST)

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Background: P inhibits activation of the Akt pathway which results in apoptosis and block cancer cell proliferation. Since AKT is a molecule downstream of Kit, its inhibition may overcome Kit-dependent imatinib resistance. We performed a phase II trial to assess antitumor activity of perifosine in patients with advanced GIST who were refractory to imatinib mesylate. Methods: Pts with Kit(+) advanced GIST who have PD on IM were eligible. Pts continued their current dose of IM and were randomized to one of two dosing schedules of P (Arm A: 100 mg p.o. qd x 28 + IM or Arm B: 900 mg [300 mg p.o tid] qweekly + qd IM). A Bayesian approach was utilized to assess a target response rate or 20% with an unacceptable toxicity rate of 15% or less. Response was measured at q8 wk intervals by RECIST and Choi criteria. The primary endpoint was to determine the efficacy of P with IM in pts with advanced GIST with PD while receiving IM. Results: From 8/2005 to 7/2008, 41 pts were accrued. After 1 pt exclusion and 2 cross-overs, 22 pts were in Arm A and 18 pts in Arm B. Median age was 58 (range, 32–82), 51% were male, and median ECOG PS was 1. The most common primary site of disease and metastasis was the stomach (29%) and liver (66%), respectively. KIT genotype was available for 22 pts(54%); 5(12%) WT, 13(32%) exon 11 mutations, and 4(10%) exon 9 mutations. The median number of cycles was 2 (range, 1–24). By Choi and RECIST, 30 pts(73%) and 36 pts(87%) were available for response, respectively. No CR was identified but the PR rate was 4/36 (11%) by Choi (4 PR, 9 SD) and 0/36 (0%) by RECIST (16 SD). 4/5 (80%) of pts with WT KIT appeared to benefit (Choi: 1 PR, 3 SD; RECIST: 4 SD). Median PFS and OS for 40 pts were 2.2 months and 18.3 months. No difference in PFS was noted for the 2 schedules. Toxicity was assessed in 39 pts; 46 grade 3 events and 4 grade 4 events (ALT elevation, blurred vision, fatigue, and mood alteration) were noted. The most common grade 3 event was fatigue (20%). Three pts (7%) were removed from the study for toxicity (Arm A:1 pt, Arm B:2 pts). Conclusions: The addition of P to IM has minimal activity in IM-refractory GIST although its activity in GIST with WT KIT may be further investigated.

No significant financial relationships to disclose.

Neoadjuvant therapy of gastric cancer with cetuximab added to both irinotecan and cisplatin, followed by surgical resection and adjuvant chemoradiation

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Background: We previously demonstrated the efficacy of irinotecan (CPT) and cisplatin (Cis) combination therapy as neoadjuvant therapy for locally advanced gastric cancer [Newman E et al. J Gastrointest Surg. 2002.]. This trial was designed to add cetuximab (C) to both induction treatment and adjuvant chemoradiation (CRT) with bolus 5-FU/LV. Methods: Pts with untreated locally advanced (T3, T4 or N+) gastric/GE cancers were eligible. Neoadjuvant therapy consisted of Cis 25mg/m2 + CPT 75mg/m2 on d1,8 q21d x 4, C 400mg/m2 on d1, then 250mg/m2 qwk. Curative (R0) resection was performed 4–6 wks later. Adjuvant CRT with 5-FU/LV (425/20/m2 qd x 5 on wks 1,14,19; 400/20/m2 qd x 4 on wk 5, x 3 on wk 9) was given with C 250mg/m2 qwk. Results: Since 11/05, 21 pts [median age 59 (32–82); 9 Caucasian, 11 Asian, 1 Hispanic; 15 male, 20 PS 0–1] received neoadjuvant therapy. The most common toxicities were gr 3 neutropenia (38%), gr 2 rash (33%), gr 2 fatigue (29%); gr 4 included 1 pt each of diarrhea, neutropenia, & hypomagnesemia. 3 did not complete neoadjuvant therapy, due to gr 3 rash, diarrhea and GI bleeding (2 had gastrectomy; 1 lost to f/u). All 18 pts who completed neoadjuvant therapy were surgically explored. 4 had occult metastases, and went off study. 14 underwent R0 gastrectomy (see table); 8 were downstaged, 2 had stable disease, 4 were upstaged compared to the preoperative EUS. There was no postoperative mortality. Of 14 resected pts, 2 did not receive adjuvant therapy (prolonged postoperative recovery), 1 too early to assess, and 11 remaining receiving CRT. The most common toxicities for CRT were gr 3 nausea, gr 3 emesis, gr 2 and 3 fatigue, 3 pts each and 1 each of gr 4 neutropenia and thrombocytopenia. Among the 18 pts who completed neoadjuvant therapy, 5 died of disease, 1 is alive with disease, 12 remain NED with median f/u of 11.6mos (4.1–27.7mos). Conclusions: The addition of C to CPT/Cis as neoadjuvant therapy and to postoperative adjuvant CRT is well tolerated. The regimen induces a favorable pathologic response on the primary tumor. Ongoing evaluation includes K-ras mutation status on outcome and survival benefit. [Supported in part by a grant from BMS.]

[Table: see text]

Activity and tolerance of biweekly CapeOx-cetuximab in 1st line therapy of metastatic colorectal cancer (mCRC): Relation to K-ras mutation status

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Background: This novel q2w schedule trial combined oxaliplatin (Ox), flat dose capecitabine (Cape) and cetuximab(C) in first line therapy of mCRC. C was given weekly initially and then q2w. We report the response rate, toxicity and influence of K-ras mutation status in first-line patients treated with biweekly CapeOx-C in this phase II trial. Methods: Pts with previously untreated, histologically confirmed, metastatic colon adenocarcinoma, ECOG PS 0–1, and adequate organ function were eligible. Pts were treated with C (initially 250mg/m2 q week and later amended to 500mg/m2 q2w) and Ox (85mg/m2) combined with flat dose Cape (2500mg po bid x 7days) q2w. Endpoints included response (RECIST), toxicity (CTCAE v3) and relationship to K-ras mutation status as determined in codons 12/13 of exon 2 in genomic tumor DNA by PCR, blinded to clinical data. Results: Between 8/04 and 8/08, 27 pts were enrolled. One pt failed screening, 1 withdrew prior to rx and 2 too early for assessment. 25 pts were treated: M/F (15/10), PS 0/1 (13/12), median age 65 yrs (37–80). 12 pts were treated weekly with C and 13 q2w. 23 pts were eligible for both toxicity and efficacy analysis. The most common grade 3/4 toxicities (N=23) were diarrhea (26%), thrombosis (22%), neuropathy (17%), rash (13%), hand-foot syndrome (9%), hypersensitivity reaction (9%), stomatitis (9%). Toxicity profiles between the two C schedules were comparable. Of 23 pts evaluable for response, there were 2 CR, 12 PR, and 3 SD (ORR 61%; disease control rate (DCR) 74%). K-ras status was determined in 18 pts: 9 were K-ras wild-type (WT) and 9 mutant (MT) with ORR and DCR = 66%, 89% for WT vs. 44%, 44% MT. Time on study was 6 mon for WT vs 3 mon for MT (p<0.05). Grade 0–1 vs. 2–3 skin rash was 33% vs. 67% for WT and. 89% vs. 11% in MT pts. Conclusions: The novel combination of biweekly CapeOx-C, with flat dose Cape was well tolerated and very active (regardless of K-ras status) as first line treatment in mCRC. C 500 mg/m2 q2w appears equal to weekly dosing. Analysis of the K-ras mutation status showed a trend toward increased benefit by response rate and time on study, with more cutaneous toxicity in K-ras WT pts. [Supported in part by grant from BMS.]

[Table: see text]

Predictive and prognostic functions of microtubule-associated protein-tau and topoisomerase IIα protein in early breast cancer

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Background: Topoisomerase IIα protein(topo II) is the molecular target of topo II inhibitors such as anthracyclines and Microtubule-Associated Protein(MAP)-tau protein is associated with taxane sensitivity. Anthracyclins and taxanes are major cytotoxic agents of breast cancer in the adjuvant setting. The aim of this study was to evaluate the predictive and prognostic functions of MAP-tau and topo II in early breast cancers. Methods: Representative breast tumor sections were constructed from paraffin embedded specimens from 78 node positive breast cancer patients. MAP-tau and topo II protein were assessed by immunochemistry using antibody clone 4F1(Affinity BioReagents,USA) and clone Ki-S1 antibody(Dakocytomation,USA). MAP-tau staining of tumor cells was semiquantatively scored as 0, 1+, 2+, 3+ and cases with 0 or 1+ staining intensity were considered MAP-tau negative. Topo II protein over- expression was defined as the detection of nuclear staining in more than median value of evaluated cells. Results: Thirty- four cases (43.6%) of 78 samples showed topo II overexpression and 35 cases(44.9%) showed MAP-tau overexpression in node positive breast cancers. HER2 overexpression was noted in 28 samples (35.9%) and 56 cases (71.8%) were compatible with the luminal type. In 43 patients (55.1%), anthracyclin and taxane were used as adjuvant therapy and in this group, both MAP-tau and topo II overexpression showed lower disease-free survival (DFS) than the others, but statistically not significant. In luminal type, MAP-tau overexpression was poor prognostic factor on DFS in Cox regression.(HR 5.644, 95% CI 1.14–28.07, p=0.034) Conclusions: Topo II overexpression and MAP-tau overexpression in node positive breast cancers were not significant predictive factors for anthracyclin and taxane therapies. As several investigators reported, MAP-tau is associated endocrine therapy sensitivity in patients without chemotherapy, but higher MAP-tau in luminal type was a strong poor prognostic factor in patients who were given chemotherapy and hormonal therapy.

No significant financial relationships to disclose.

Does hormone receptor (HR) positivity affect the prognosis in breast cancers with human epidermal growth factor receptor 2 (HER2) overexpression?

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Background: Biologically, there is an unclear issue about the role of HR positivity in HER2 positive breast cancer. These HER2(+)/ HR(+) pts were grouped into luminal B type apart from HER2(+)/ HR(-) pts in molecular profiling. However, from the clinical point of view, these pts have been categorized and been treated as either the only HER2(+) disease regardless of HR status or vice versa. Thus, we investigated the impact of HR status on clinical outcomes in HER2-overexpressed breast cancers. Methods: We retrospectively reviewed medical charts of HER2-positive breast cancer pts who underwent curative surgical resection from 1996 to 2001 in the Severance hospital, Korea. Demographic comparisons were performed by Chi-square tests. Tumor size, nodal stage, TNM stage, HR status, and adjuvant tamoxifen use were included in the Cox proportional hazards model. Results: Among the total 174 HER2-positive pts, HR (n=93) was positive in 53.5% (n = 93) and HR-positive tumors were more likely to be premenopausal (73% v 52%; P=0.01) and well- differentiated (grade 1or 2; 77% v 62%; P=0.04). There were no significant differences according to HR status in terms of tumor size, nodal stage, TNM stage, operation methods, and chemotherapy regimen. In these HER2-positive pts, the 5-year disease free survival (DFS) was longer in HR(+) pts than in HR(-) pts (DFS; 82.9% v 61.5%; P= 0.01). In a subset analysis, the 5-year DFS of HER2(+)/ER(+) pts without adjuvant tamoxifen (n=26) was not different from that of HER2(+)/ ER(-) pts (DFS; 57.7% v 61.5%; P= 0.32). However, the 5-year DFS of HER2(+)/ ER(+) pts with adjuvant tamoxifen was significantly prolonged compared with that of HER2(+)/ ER(-) pts (DFS; 91.5% v 61.5%; P< 0.001). In a multivariate analysis of DFS, tumor size and adjuvant tamoxifen use significantly affected DFS with an adjusted hazard ratio of 2.56 (95% CI, 1.2–4.9; P= 0.01) and 6.58 (95% CI, 2.8–20.3; P< 0.001), respectively. Conclusions: In an analysis of HER2-overexpressed breast cancer, the presence of HR itself did not affect the prognosis. However, most of the survival benefit seems to be driven from adjuvant tamoxifen therapy not the HR status itself.

No significant financial relationships to disclose.

Reporting disease activity in clinical trials of patients with rheumatoid arthritis: EULAR/ACR collaborative recommendations

OBJECTIVE

To make recommendations on how to report disease activity in clinical trials of rheumatoid arthritis (RA) endorsed by the European League Against Rheumatism (EULAR) and the American College of Rheumatology (ACR).

METHODS

The project followed the EULAR standardised operating procedures, which use a three-step approach: (1) expert-based definition of relevant research questions (November 2006); (2) systematic literature search (November 2006 to May 2007); and (3) expert consensus on recommendations based on the literature search results (May 2007). In addition, since this is the first joint EULAR/ACR publication on recommendations, an extra step included a meeting with an ACR panel to approve the recommendations elaborated by the expert group (August 2007).

RESULTS

Eleven relevant questions were identified for the literature search. Based on the evidence from the literature the expert panel recommended that each trial should report the following items: (1) disease activity response and disease activity states; (2) appropriate descriptive statistics of the baseline, the endpoints and change of the single variables included in the core set; (3) baseline disease activity levels (in general); (4) the percentage of patients achieving a low disease activity state and remission; (5) time to onset of the primary outcome; (6) sustainability of the primary outcome; (7) fatigue.

CONCLUSIONS

These recommendations endorsed by EULAR and ACR will help harmonise the presentations of results from clinical trials. Adherence to these recommendations will provide the readership of clinical trials with more details of important outcomes, while the higher level of homogeneity may facilitate the comparison of outcomes across different trials and pooling of trial results, such as in meta-analyses.

Anomalous attenuation of transverse sound in 3He

We present the first measurements of the attenuation of transverse sound in superfluid 3He-B. We use fixed path length interferometry combined with the magnetoacoustic Faraday effect to vary the effective path length by a factor of 2, resulting in absolute values of the attenuation. We find that attenuation is significantly larger than expected from the theoretical dispersion relation, in contrast with the phase velocity of transverse sound. We suggest that the anomalous attenuation can be explained by surface Andreev bound states.

Hyperlipidaemia, statin use and the risk of developing rheumatoid arthritis

OBJECTIVE

To evaluate whether statins are associated with a protective effect on the development of rheumatoid arthritis (RA).

METHODS

A nested case-control study was conducted using data from the General Practice Research Database. A study population consisting of three groups of subjects aged 40-89 years was identified: (1) patients exposed to a statin or other lipid-lowering agent (LLA); (2) patients with a diagnosis of hyperlipidaemia in the absence of lipid-lowering drug treatment and (3) a random sample of 25 000 individuals with no diagnosis of hyperlipidaemia nor a prescription for a LLA. From this population incident cases of RA and up to four controls for each case were identified, matched on age, sex, general practice, number of years of recorded history in the database and index date. The independent effects of hyperlipidaemia and statins on the development of RA were evaluated using conditional logistic regression.

RESULTS

313 cases of RA and 1252 matched controls were identified. Compared with patients with untreated hyperlipidaemia, or hyperlipidaemia treated with LLA other than statins, the adjusted odds ratio for patients with no hyperlipidaemia was 0.68 (95% CI 0.50 to 0.91). When those with hyperlipidaemia who received statins were compared with those with hyperlipidaemia who did not use statins (ie, untreated hyperlipidaemia patients or those treated with non-statin LLA) the OR was 0.59 (95% CI 0.37 to 0.96).

CONCLUSION

These data provide evidence to support the hypothesis that statins may be protective against the development of RA in patients with hyperlipidaemia.

Sudden high concentration of TSP affected by atmospheric boundary layer in Seoul metropolitan area during duststorm period

Hourly concentrations of TSP, PM(10), PM(2.5) near the surface at Seoul city were examined from March 20 to March 25, 2001 (duststorm event) in order to investigate the effect of a duststorm generated in China on the local aerosol concentration in Korea, The ratios of fine to coarse particles such as TSP to PM(10), TSP to PM(2.5) and PM(10)-PM(2.5) to PM(2.5) showed that a great amount of dust transported from the origin of the duststorm was remarkable with a maximum ratio of 9.77 between TSP and PM(2.5). Back trajectories every 6 h showed the movement of dust particles in the lower atmosphere near 500 m to 1500 m (atmospheric boundary layer), which implied transport from Baotou in inner Mongolia of northern China to the direction of Seoul city in Korea and then the back trajectories passed near the southern border of Mongolia and Baotou through Zengzhou in the midlevels (3000 m) and low levels (500 m) of China, finally reaching Seoul city. So, the TSP concentration at Seoul city was partially influenced by the duststorm, under the prevailing westerly wind and the transported aerosols could influence high concentrations of pollutants of TSP, PM(10) and PM(2.5) in Seoul. The sudden high concentrations of TSP and PM(10) were found for a few hours, especially at 1500 to 1800 LST, March 22. At 1200 LST, before the passage of a cold front through the Korean peninsula, the convective boundary layer (CBL) near Seoul was not shallow, but at 1500 LST, under the frontal passage, the CBL was remarkably thinner (less than 300 m), due to the compression of the boundary layer by the intrusion of cold air. This resulted in the increase of the TSP concentration, even though the mixed layer above maintained almost the same depth. At 1800 LST shortly after the frontal passage, that is, near sunset, the nocturnal cooling of the ground caused air parcels to cool, thereby enhancing the shallower nocturnal surface inversion layer and producing the maximum concentration of TSP of 1388 microg/m(3) near Seoul city.

Covalent regulation of ULVWF string formation and elongation on endothelial cells under flow conditions

BACKGROUND AND OBJECTIVES

The adhesion ligand von Willebrand factor (VWF) is a multimeric glycoprotein that mediates platelet adhesion to exposed subendothelium. On endothelial cells, freshly released ultra-large (UL) VWF multimers form long string-like structures to which platelets adhere.

METHODS

The formation and elongation of ULVWF strings were studied in the presence of the thiol-blocking N-ethylmaleimide (NEM). The presence of thiols in ULVWF and plasma VWF multimers was determined by maleimide-PEO(2)-Biotin labeling and thiol-chromatography. Finally, covalent re-multimerization of ULVWF was examined in a cell- and enzyme-free system.

RESULTS

We found that purified plasma VWF multimers adhere to and elongate ULVWF strings under flow conditions. The formation and propagation of ULVWF strings were dose-dependently reduced by blocking thiols on VWF with NEM, indicating that ULVWF strings are formed by the covalent association of perfused VWF to ULVWF anchored to endothelial cells. The association is made possible by the presence of free thiols in VWF multimers and by the ability of (UL) VWF to covalently re-multimerize.

CONCLUSION

The data provide a mechanism by which the thrombogenic ULVWF strings are formed and elongated on endothelial cells. This mechanism suggests that the thiol-disulfide state of ULVWF regulates the adhesion properties of strings on endothelial cells.