Abstract P6-03-08: Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting

Background: Recent discoveries of recurrent and targetable gene fusions in breast cancer suggest the need to characterize the functional significance of such genomic aberrations within larger cohorts. We quantified fusion transcript expression in patient samples using RNASeq to identify recurrent gene fusion events in breast cancer as well as study the fusions post-brief exposure to mono-therapy.

Methods: We sequenced transcriptomes of core biopsy RNA from 130 breast tumors obtained from brief-exposure preoperative clinical trials BrUOG 211A/211B. HER2- patients were treated with brief exposure to bevacizumab (B) or nab-paclitaxel (nP) followed by treatment with B/nP/carboplatin while HER2+ patients received brief exposure to trastuzumab (T) or nP followed by T/nP/carboplatin. Paired-end sequencing on 75 baseline biopsies and 55 post-exposure biopsies using amplified total RNA yielded 55 million reads on average perlsample. Fusion transcript abundance was evaluated using 2 pipelines, TopHat-Fusion and deFuse, due to their complementary strategies in fusion detection. We eliminated gene-pseuodogene fusion pairs as likely false positives arising due to alignment artifacts. Fusions that met 1 or more of the following 3 criteria were considered high confidence:

i) Called by both deFuse and TopHat. ii) Called by deFuse with probability >95% iii) Called by TopHat with > 15 reads supporting the fusion.

Results: We identified high confidence gene fusions, detected by both TopHat and deFuse, in 73 of the 75 baseline biopsies with 16 fusions on average per sample. We looked for modulation of gene fusions upon brief exposure to therapy in 55 patients that had post exposure biopsy data and found that out of the 545 high confidence fusions detected across these patients, 62 (11.37%) of the fusions were found to be still present after the therapy exposure. For the recurrent fusion analyses, we considered the 75 baseline samples. We found a total of 1158 unique candidate fusions. Out of these, 116 (10%) were recurrent in more than 1 patient. After further filtering, we were able to narrow down to 9 (0.77%) fusions that were reliable since they were predicted by both the algorithms in different patients. 2 of these 9 fusions involved GAS5 as a partner gene. GAS5 have been studied to have a role in apoptosis and its down-regulation has been associated with cell proliferation, which makes it a very interesting fusion candidate.

Conclusions: We find that gene fusions in breast cancer are highly heterogeneous but are enriched with cancer-related pathway genes. This is the first study to report 2 novel gene-lincRNA fusion transcripts: MDN1-GAS5 and GABRB3-GAS5. Both these fusions are called in the baseline & post-therapy for atleast 1 patient (different patients each). GAS5 has been found as participating in a fusion in B-cell lymphoma. We are currently in the process of validating the fusion calls using qRT-PCR. The heterogeneity of detected fusions suggests that multiple mechanisms could underlie the selective advantage of tumor cells expressing fusion transcripts. The brief-exposure preoperative paradigm provides a unique opportunity to evaluate modulation of fusion transcripts that can shed light on their functional importance.

Citation Format: Agrawal V, Varadan V, Banerjee N, Miskimen K, Vadodkar A, Abu-Khalaf M, Sikov W, Harris L, Dimitrova N. Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting. [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 P6-03-08.

IFPA meeting 2015 workshop report III: nanomedicine applications and exosome biology, xenobiotics and endocrine disruptors and pregnancy, and lipid

Workshops are an important part of the IFPA annual meeting, as they allow for discussion of specialized topics. At the IFPA meeting 2015 there were twelve themed workshops, three of which are summarized in this report. These workshops were related to various aspects of placental biology but collectively covered areas of pregnancy pathologies and placental metabolism: 1) nanomedicine applications and exosome biology; 2) xenobiotics and endocrine disruptors and pregnancy; 3) lipid mediators and placental function.

A qualitative study exploring why adults with intellectual disabilities and obesity want to lose weight and views of their carers

Background

Obesity is more prevalent in adults with intellectual disabilities (ID) compared to the general population. Motivations for weight loss may influence engagement with weight management programmes and have only been studied in adults without ID. Aims: To determine reasons given by adults with ID and obesity for seeking weight loss and whether these reasons differ from those of their carers.

Methods

Prior to a multi-component weight management intervention, participants were asked “why do you want to lose weight?” Carers were asked their views and these were compared to the answers given by the adult with ID. Responses were themed. The Fisher’s Exact analysis was used to test for any relationship between reasons for seeking weight loss and participants’ level of ID, age, gender and BMI.

Results

Eighteen men and 32 women; age 41.6 SD 14.6 years; BMI 40.8 SD 7.5 kg/m²; Level ID Mild (28 %), Moderate (42 %), Severe (22 %), Profound (8 %). Eleven were unable to respond. Six themes emerged; Health; Fitness / Activity / Mobility; Appearance / Clothes; Emotional / Happiness; For Others; Miscellaneous. The most frequent reason given overall and by women was “appearance.” Carers cited “health” most frequently and “appearance” least, rarely agreeing with participants. “Health” was given as a reason more from older adults and those with milder ID. No statistically significant associations were found between reasons for seeking weight loss and BMI age, gender or level of ID but the differing views of adults with ID and their carers were clear.

Conclusions

Views of adults with obesity and mild or moderate ID can be collected. The opposing views of adults and their carers may affect motivation for weight loss.

The effects of physical activity interventions on preventing weight gain and the effects on body composition in young adults with intellectual disabilities: systematic review and meta-analysis of randomized controlled trials

The aim of this study was to examine the literature on randomized controlled trials examining the efficacy of physical activity interventions to prevent weight gain and the effects on body composition in young adults with intellectual disabilities.A systematic search of Medline, Emabse, CINHAL, PsychINFO, Cochrane library and ERIC was conducted from 1946 to September 2014. Eligibility criteria included; randomized controlled trials of a physical activity intervention: objective measure of body weight and body composition; young adults (age range 16-24 years) with intellectual disabilities. Six studies met the eligibility criteria. The interventions varied in their prescription of physical activity including aerobic and strength-based activities. The mean duration of the interventions was 15.3 (range 10-21 weeks). There was no significant effect of physical activity interventions on body weight (weighted mean difference: -0.17 kg, 95% confidence interval, -1.04 kg to 0.72 kg) and body composition outcomes. The meta-analysis showed that physical activity interventions did not prevent weight gain in young adults with intellectual disabilities. Published studies are inadequate to form firm conclusions. Future longer term studies of interventions specifically designed for this population group are required to elucidate the effects of physical activity interventions on body composition and the prevention of weight gain in young adults with intellectual disabilities.

Microbial water quality communication: public and practitioner insights from British Columbia, Canada

This work examines the communication interactions of water suppliers and health authorities with the general public regarding microbial source water quality for recreational and drinking water. We compare current approaches to risk communication observable in British Columbia (BC), Canada, with best practices derived from the communications literature, finding significant gaps between theory and practice. By considering public views and government practices together, we identify key disconnects, leading to the conclusion that at present, neither the public's needs nor public health officials' goals are being met. We find: (1) there is a general lack of awareness and poor understanding by the public of microbial threats to water and the associated health implications; (2) the public often does not know where to find water quality information; (3) public information needs are not identified or met; (4) information sharing by authorities is predominantly one-way and reactive (crisis-oriented); and (5) the effectiveness of communications is not evaluated. There is a need for both improved public understanding of water quality-related risks, and new approaches to ensure information related to water quality reaches audiences. Overall, greater attention should be given to planning and goal setting related to microbial water risk communication.