TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

Transcription factors (TFs) are major trans-acting factors in transcriptional regulation. Therefore, elucidating TF-target interactions is a key step toward understanding the regulatory circuitry underlying complex traits such as human diseases. We previously published a reference TF-target interaction database for humans-TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining)-which was constructed using sentence-based text mining, followed by manual curation. Here, we present TRRUST v2 (www.grnpedia.org/trrust) with a significant improvement from the previous version, including a significantly increased size of the database consisting of 8444 regulatory interactions for 800 TFs in humans. More importantly, TRRUST v2 also contains a database for TF-target interactions in mice, including 6552 TF-target interactions for 828 mouse TFs. TRRUST v2 is also substantially more comprehensive and less biased than other TF-target interaction databases. We also improved the web interface, which now enables prioritization of key TFs for a physiological condition depicted by a set of user-input transcriptional responsive genes. With the significant expansion in the database size and inclusion of the new web tool for TF prioritization, we believe that TRRUST v2 will be a versatile database for the study of the transcriptional regulation involved in human diseases.

The Use of Clinician-Performed Ultrasonography to Determine the Treatment Method for Suspected Paediatric Appendicitis

Objective

To investigate whether the clinician-performed ultrasonography based on the specific criteria for paediatric appendicitis could decrease the negative appendectomy rate without treatment failure.

Methods

The study was a retrospective review of paediatric patients with suspected appendicitis who presented at the emergency department of a teaching hospital over a period of 18 months. The clinicians performed the ultrasound and decided whether the patients with suspected appendicitis should be referred to surgery or managed conservatively. The determinative ultrasound criteria were the presence of periappendiceal fat infiltration and/or an obstructing appendicolith.

Results

The 166 paediatric patients with suspected appendicitis underwent ultrasonography performed by clinicians on weekdays; forty (24.1%) cases with an obstructing appendicolith and/or periappendiceal fat infiltration were treated surgically, and none had a pathologically negative appendectomy, which was significantly lower than the number in the computed tomography scan group (10.4%, 11/106) on weeknights or weekends. The remaining 126 (75.8%) patients without obstructing appendicolith or periappendiceal fat infiltration were treated conservatively, regardless of their appendiceal diameter, and no patients experienced a treatment failure.

Conclusions

The clinician-performed ultrasonography bases on the strict use of above specific ultrasound criteria to determine treatment strategies for suspected paediatric appendicitis can reduce the negative appendectomies without treatment failure. (Hong Kong j.emerg.med. 2015;22:31-40)

Effect of an obesity prevention program focused on motivating environments in childhood: a school-based prospective study

BACKGROUND/OBJECTIVES

There has been an increasing global recognition of the need for effective strategies to prevent and control childhood obesity. In this study, we aimed to identify the effectiveness of an obesity prevention program focused on motivating environments in school.

SUBJECTS/METHODS

In this school-based, prospective, quasi-experimental study, we enrolled three elementary (fourth graders) and two middle (seventh graders) schools located in Chungju, Korea. We assigned three of the schools to the intervention group and two schools to the control group. The intervention group received 1 year of environmental intervention. Diet- and exercise-related educational video content was provided by internet protocol television services during rest time, and various design materials were painted along the school staircase and hallway to encourage physical activities. Overweight and obese students were recommended to join the summer vacation obesity care program.

RESULTS

The final number of total participants was 768 (control 350 and intervention 418). After 1 year of follow-up, there was no significant difference in the overweight/obesity incidence rates and remission rates between the two groups. However, the intervention group showed a greater decrease in the body mass index (BMI) z-score (-0.11 (95% confidence interval (CI) -0.16 to -0.06), P<0.001), increase in height (1.1 cm (95% CI 0.8 to 1.4), P<0.001), reduction of body fat, and increase in muscle mass compared with the control group. In addition, blood pressure (BP) was significantly reduced, and significant improvement in physical fitness followed. In subgroup analysis, students of normal weight, boys and younger participants showed the most beneficial results in weight-related outcomes. In addition, the BP reduction was more pronounced in the higher BMI group, boys and older children.

CONCLUSIONS

A simple environmental intervention could effectively influence children. By adding to previously studied strategies, we can develop a more effective obesity prevention program for children.

Primary male development of two sequentially hermaphroditic groupers, Epinephelus akaara and Epinephelus awoara (Perciformes: Epinephelidae)

Gonad ontogeny of the Hong Kong grouper Epinephelus akaara (a bi-directional sex changer) and the yellow grouper Epinephelus awoara (a protogynous hermaphrodite) was examined for the first time from post-larval phase until first sexual maturation, by histology. Approximately 20 specimens of each species were collected randomly every 2-7 weeks from rearing tanks with natural sea water and temperature between June 2013 and June 2014. The paired gonadal primordia (GP) were observed at 6 weeks after hatching (wah) for both species; however, gonia were first observed in GP at 16 wah for E. akaara and at 8 wah for E. awoara. The timings for the appearance of primary-growth stage oocytes (O1) and the completion of ovarian lumen (OL) varied; both at 27 wah for E. akaara, and at 18 and 23 wah for E. awoara respectively. A bisexual-phase gonad with an OL, O1 and scattered spermatogenic cysts (SC) was observed at 27-29 wah for both E. akaara and E. awoara. Sexual differentiation was subsequently observed from the bisexual-phase gonad at 34 wah for E. akaara, and 41 wah for E. awoara, with the appearance of cortical-alveolus stage oocytes (O2) for developing female and the proliferation of SC for developing primary male (i.e. from juvenile directly). Ovaries of mature females contained the vitellogenic stage oocytes (O3) and scattered SC; testes of mature primary males had sperm in sperm sinuses within the gonadal wall and remained O1. Minimum age of first sexual maturation for both female and primary male of E. akaara was at 41 wah; minimum total length (LT ) of female (143 mm) was larger than that of primary male (137 mm L(T)). Minimum age and size of first sexual maturation for female of E. awoara (47 wah and 149 mm L(T), respectively) were larger than those of E. akaara. Developing primary males of E. awoara were found at 41-58 wah, however, mature males were not observed, indicating inconsistency in first sexual maturation for E. awoara. This study provided strong evidences of primary male pathway in E. akaara and E. awoara; the latter is confirmed to be diandric.

Abstract P4-14-01: Trastuzumab emtansine improves overall survival versus capecitabine plus lapatinib in patients with previously treated HER2-positive advanced breast cancer: Final results from the phase 3 EMILIA study

Introduction

T-DM1 is indicated for the treatment of advanced HER2-positive MBC in patients who previously received trastuzumab and a taxane (separately or in combination) based on data from the phase 3 EMILIA study (BO21977/TDM4370g; NCT00829166). In the primary PFS and second interim OS analyses, respectively, T-DM1 significantly improved PFS (median 9.6 vs 6.4 months; HR=0.65; 95% CI, 0.55–0.77; p&lt;0.0001) and OS (median 30.9 vs 25.1 months; HR=0.68; 95% CI, 0.55–0.85; p&lt;0.0006) compared with capecitabine (X) plus lapatinib (L). T-DM1 treatment was associated with fewer grade ≥3 AEs (41% vs 57%) vs XL. Here we present the final OS analysis from EMILIA.

Methods

EMILIA was a randomized, open-label study of patients with centrally confirmed HER2-positive (IHC3+ and/or FISH amplification ratio ≥2.0), unresectable, locally advanced or MBC, previously treated with trastuzumab and a taxane. Patients were randomized 1:1 to T-DM1 (3.6 mg/kg IV every 3 weeks) or X (1000 mg/m2 PO twice daily, days 1–14 every 3 weeks) plus L (1250 mg PO daily). The final OS analysis was to be conducted following 632 events, and these results are descriptive only. Since the OS efficacy boundary (HR&lt;0.71, p=0.0025) was crossed in the second interim analysis, a protocol amendment allowed crossover from XL to T-DM1.

Results

From Feb 2009 to Oct 2011, 991 patients were randomized to T-DM1 (n=495) or XL (n=496). Patient disposition by the data cutoff (31 Dec 2014) is shown in Table 1. OS was longer with T-DM1 vs XL (median OS 29.9 vs 25.9 months; HR=0.75; 95% CI, 0.64–0.88; p=0.0003). In a sensitivity analysis, which censored crossover patients at the time of switching from XL to T-DM1, the HR was 0.69 (95% CI, 0.59–0.82; p&lt;0.0001). The overall safety profile was similar to previous analyses (Table 2). More grade ≥3 thrombocytopenia occurred with T-DM1 vs XL (14.3% vs 0.4%). Cardiac dysfunction occurred in 2.7% of T-DM1 patients vs 3.5% of XL patients.

Table 1. Patient disposition. T-DM1 (n=495)XL (n=496)Median treatment duration, months7.6X: 5.3  L: 5.5Median duration of follow-up, months47.841.9Discontinued study, n (%)364 (74)404 (82)Crossover, n (%)  Per protocolaNot applicable136 (27)Non-protocol therapybX: 252 (54)X: 53 (11) L: 224 (48)L: 74 (15)aMedian duration of follow-up among per-protocol crossover patients was 24.1 months.bBy investigator choice after study treatment discontinuation; X or L could be given in combination with each other or other agents after progression.

Table 2. Safety summary in patients who received ≥1 dose of study treatment.n (%)T-DM1 (n=490)XL (n=488)Grade ≥3 AEs233 (47.6)291 (59.6)Serious AEs91 (18.6)99 (20.3)AEs leading to dose reduction91 (18.6)X: 205 (42.0)  L: 98 (20.1)

Conclusions

This final analysis of EMILIA shows an OS benefit of T-DM1 compared with XL. While median drug exposure was longer with T-DM1 than XL, T-DM1 was associated with fewer grade ≥3 AEs and AEs leading to dose reduction compared with XL. These final OS results confirm that T-DM1 treatment improved survival, even in the presence of treatment crossover, and reaffirm T-DM1 as the standard of care in patients with previously treated HER2-positive MBC.

Citation Format: Diéras V, Miles D, Verma S, Pegram M, Welslau M, Baselga J, Krop I, Blackwell K, Kang B, Xu J, Green M, Gianni L. Trastuzumab emtansine improves overall survival versus capecitabine plus lapatinib in patients with previously treated HER2-positive advanced breast cancer: Final results from the phase 3 EMILIA study. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-14-01.

MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates

Laboratory mouse, Mus musculus, is one of the most important animal tools in biomedical research. Functional characterization of the mouse genes, hence, has been a long-standing goal in mammalian and human genetics. Although large-scale knockout phenotyping is under progress by international collaborative efforts, a large portion of mouse genome is still poorly characterized for cellular functions and associations with disease phenotypes. A genome-scale functional network of mouse genes, MouseNet, was previously developed in context of MouseFunc competition, which allowed only limited input data for network inferences. Here, we present an improved mouse co-functional network, MouseNet v2 (available at http://www.inetbio.org/mousenet), which covers 17 714 genes (>88% of coding genome) with 788 080 links, along with a companion web server for network-assisted functional hypothesis generation. The network database has been substantially improved by large expansion of genomics data. For example, MouseNet v2 database contains 183 co-expression networks inferred from 8154 public microarray samples. We demonstrated that MouseNet v2 is predictive for mammalian phenotypes as well as human diseases, which suggests its usefulness in discovery of novel disease genes and dissection of disease pathways. Furthermore, MouseNet v2 database provides functional networks for eight other vertebrate models used in various research fields.

The Introduction of Human Heme Oxygenase-1 and Soluble Tumor Necrosis Factor-α Receptor Type I With Human IgG1 Fc in Porcine Islets Prolongs Islet Xenograft Survival in Humanized Mice

Apoptosis during engraftment and inflammation induce poor islet xenograft survival. We aimed to determine whether overexpression of human heme oxygenase-1 (HO-1) or soluble tumor necrosis factor-α receptor type I with human IgG1 Fc (sTNF-αR-Fc) in porcine islets could improve islet xenograft survival. Adult porcine islets were transduced with adenovirus containing human HO-1, sTNF-αR-Fc, sTNF-αR-Fc/HO-1 or green fluorescent protein (control). Humanized mice were generated by injecting human cord blood-derived CD34(+) stem cells into NOD-scid-IL-2Rγ(null) mice. Both HO-1 and sTNF-αR-Fc reduced islet apoptosis under in vitro hypoxia or cytokine stimuli and suppressed RANTES induction without compromising insulin secretion. Introduction of either gene into islets prolonged islet xenograft survival in pig-to-humanized mice transplantation. The sTNF-αR-Fc/HO-1 group showed the best glucose tolerance. Target genes were successfully expressed in islet xenografts. Perigraft infiltration of macrophages and T cells was suppressed with decreased expression of RANTES, tumor necrosis factor-α and IL-6 in treatment groups; however, frequency of pig-specific interferon-γ-producing T cells was not decreased, and humoral response was not significant in any group. Early apoptosis of islet cells was suppressed in the treatment groups. In conclusion, overexpression of HO-1 or sTNF-αR-Fc in porcine islets improved islet xenograft survival by suppressing both apoptosis and inflammation. HO-1 or sTNF-αR-Fc transgenic pigs have potential for islet xenotransplantation.

Lower serum zinc levels are associated with unhealthy metabolic status in normal-weight adults: The 2010 Korea National Health and Nutrition Examination Survey

AIM

This study investigated whether serum zinc concentration is associated with glucose tolerance, insulin resistance and metabolic health status in Korean adults.

METHODS

Subjects with available serum zinc levels were recruited from the fifth Korea National Health and Nutrition Examination Survey (KNHANESV) cohort. Those in the highest quartile on homoeostasis model assessment for insulin resistance (HOMA-IR) and with a body mass index (BMI) of 18.5-25kg/m(2) were classified as metabolically obese and normal weight (MONW).

RESULTS

A total of 1813 subjects with a mean age of 45.2±0.5 years and a mean BMI of 24.01±0.11kg/m(2) were enrolled. Those in the lower serum zinc quartiles exhibited higher levels of fasting blood glucose and insulin resistance indices compared with those in the higher quartiles. However, these associations were positive only in normal-weight subjects. Those categorized as MONW exhibited significantly lower serum zinc levels than the metabolically healthy and normal weight (MHNW) subjects (131.6±3.0μg/dL vs 141.7±2.8μg/dL, respectively; P=0.0026), whereas serum zinc levels did not differ according to metabolic health in obese subjects. The odds ratio for being categorized as MONW was 4.12 (95% CI: 1.75, 9.72) among those in the lowest serum zinc quartile compared with those in the highest quartile even after adjusting for possible confounding factors.

CONCLUSION

Lower serum zinc levels were associated with unhealthy metabolic status in normal-weight adults. Further prospective studies are required to define the role of zinc in metabolic health.