A guide to creating an effective big data management framework

Abstract Many agencies and organizations, such as the U.S. Geological Survey, handle massive geospatial datasets and their auxiliary data and are thus faced with challenges in storing data and ingesting it, transferring it between internal programs, and egressing it to external entities. As a result, these agencies and organizations may inadvertently devote unnecessary time and money to convey data without existing or outdated standards. This research aims to evaluate the components of data conveyance systems, such as transfer methods, tracking, and automation, to guide their improved performance. Specifically, organizations face the challenges of slow dispatch time and manual intervention when conveying data into, within, and from their systems. Conveyance often requires skilled workers when the system depends on physical media such as hard drives, particularly when terabyte transfers are required. In addition, incomplete or inconsistent metadata may necessitate manual intervention, process changes, or both. A proposed solution is organization-wide guidance for efficient data conveyance. That guidance involves systems analysis to outline a data management framework, which may include understanding the minimum requirements of data manifests, specification of transport mechanisms, and improving automation capabilities

Abstract PD5-8: <i>HER2/PIK3CAH1047R</i> transgenic mammary tumors develop acquired resistance to triple therapy with trastuzumab, pertuzumab and PI3K inhibitors via multiple mechanisms

Abstract HER2 amplification and activating mutations in PIK3CA, the gene encoding the p110α subunit of PI3K, often co-occur in breast cancer. We generated a transgenic mouse model of HER2-overexpressing (HER2+), PIK3CAH1047R-mutant breast cancer. In these mice, PIK3CAH1047R accelerates HER2-mediated mammary epithelial transformation and metastatic progression, confers stem cell-like properties to HER2-overexpressing cancers and generates resistance to the combination of trastuzumab and pertuzumab (Hanker et al. PNAS 2013). HER2+/PIK3CA tumor growth was inhibited by treatment with the HER2 antibodies trastuzumab and pertuzumab in combination with the pan-PI3K inhibitor BKM120 (TPB). We sought to discover mechanisms of acquired resistance to the triple therapy by long-term treatment of established HER2+/PIK3CA tumors. We used tumor transplants derived from two HER2+/PIK3CA transgenic mice, #564 and #635. Tumor transplants from model 564 were initially growth inhibited by TPB, but did not regress. A subset of 564 transplants (3/11) resumed growth in the presence of continuous TPB therapy. All transplants (n=9) from model 635 regressed to a volume of &amp;lt;100 mm3 within 6 weeks of treatment. All tumors recurred and 2 tumors continued growth when re-treated with TPB. Resistance was maintained following passaging in mice and tumors were cross-resistant to trastuzumab/pertuzumab/BYL719, a p110α-specific inhibitor. TPB-resistant tumor 635-2 expressed p95 HER2, which was not detected in untreated tumors. In contrast, HER2 expression was significantly reduced in TPB-resistant tumor 635-3. P-AKT remained suppressed in some resistant tumors, but was restored in others. Short-term TPB treatment strongly suppressed P-S6 in sensitive tumors, whereas P-S6 was no longer inhibited in all TPB-resistant tumors from both models. We are currently performing whole-exome sequencing and RNA-sequencing on TPB-resistant vs. untreated tumors in order to identify additional mechanisms of resistance. In parallel, we established human HER2+, PIK3CA-mutant cell lines (MDA-MB 453, UACC893, and HCC1954) resistant to TPB by long-term treatment (&amp;gt;5 months) in the presence of the three drugs. Similar to the TPB-resistant tumors, P-S6 was no longer inhibited following TPB treatment in the resistant cell lines. Treatment with the TORC1/2 inhibitor MLN0128 abolished levels of P-S6 in HER2+/PIK3CAH1047R tumors. Combined treatment with MLN0128 and TPB inhibited growth of the drug-resistant tumors. Interestingly, Both TPB-resistant HER2+/PIK3CAH1047R tumor lines displayed resistance to the antibody-drug conjugate trastuzumab-DM1 (T-DM1) in vitro and in vivo, despite maintenance of HER2 overexpression. In addition, HCC1954 cells selected for resistance to TPB in culture were 66-fold less sensitive to T-DM1 than parental cells, despite maintaining equal levels of HER2 by western blot. These data suggest that multiple mechanisms may contribute to resistance to dual HER2 and PI3K blockade, including re-activation of mTOR signaling. We speculate that a similar heterogeneity of resistance mechanisms may occur in HER2+/PIK3CA-mutant metastases in patients. Citation Format: Ariella B Hanker, Benjamin Bulen, Monica Red Brewer, Christian D Young, Kirsten M Farrar, Rebecca S Cook, Thomas P Stricker, Carlos L Arteaga. HER2/PIK3CAH1047R transgenic mammary tumors develop acquired resistance to triple therapy with trastuzumab, pertuzumab and PI3K inhibitors via multiple mechanisms [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD5-8.</jats:p

Abstract S3-03: Nuclear FGFR1 interaction with estrogen receptor (ER) α is associated with resistance to endocrine therapy in ER+/FGFR1-amplified breast cancer

Abstract Background: Estrogen receptor (ER)-positive breast cancers (BC) initially respond to antiestrogens but eventually become hormone-independent and recur. FGFR1 is amplified in ∼10% of ER+ BC and is associated with early recurrence on antiestrogen therapy. Notably, one third of FGFR1-amplified tumors have simultaneous amplification of CCND1, FGF3, FGF4 and FGF19 on chromosome 11q12-14. Herein, we investigated the mechanisms by which FGFR1 amplification confers resistance to antiestrogen therapy in ER+ BC cells. Results: We performed whole exome sequencing in tumor biopsies from 130 patients with an operable ER+/HER2- BC who had received letrozole for 10-21 days prior to surgery. Tumors were categorized by the natural log (ln) of post-letrozole Ki67 as sensitive (ln ≤1 or ≤2.7% Ki67+ cells; n=68) or resistant (ln ≥2 or ≥7.4%; n=18). We found amplifications in FGFR1 and/or 11q12-14 in 6/11 (55%) resistant tumors compared with 5/34 (15%) in sensitive tumors (p=0.006); all cases were confirmed by FGFR1-fluorescence in situ hydridization (FISH). Resistant tumors with FGFR1 and/or 11q12-14-amplification showed a marked increase in nuclear FGFR1 with letrozole. ER+/FGFR1-amplified CAMA1 and MDA134 cell lines also exhibited co-localization of ER and FGFR1 in the nucleus. Cell proliferation was partially reduced by estrogen deprivation, and FGFR1 siRNA further reduced cell growth in hormone-depleted medium. We generated CAMA1 and MDA134 cells resistant to long-term estrogen deprivation (LTED). These cells exhibited overexpression of FGF3/4/19 and ERα with a concomitant increase in ligand-independent ER transcriptional activity and growth. An ER-FGFR1 interaction was observed in the nucleus and cytosol of CAMA1 parental cells with enhanced interaction in CAMA1 LTED cells. Genetic (with siRNA) and pharmacologic (with lucitinib) inhibition of FGFR1 reduced a) nuclear localization of FGFR1; b) ER transcriptional activity; and c) cell proliferation. Nuclear localization and ER-FGFR1 interaction were disrupted by a kinase-deficient FGFR1. Conversely, addition of FGF3 ligand stimulated ER-FGFR1 interaction and ER transcriptional activity, suggesting FGFR activation can regulate ER function. Inhibition of FGF receptor-specific substrate (FRS2), a principal mediator of FGFR1 signal transduction to the MAPK and PI3K pathways, with siRNA or pharmacologic inhibition of PI3K with buparlisib or MEK with GSK1120212 did not reduce ER transcriptional activity suggesting that, in ER+/FGFR1-amplified cancer cells, ER function is not modulated by FGFR signal transducers. Finally, using chromatin immunoprecipitation (ChIP) we showed that FGFR1 binds directly to estrogen response elements (ERE). This association was reduced with lucitanib. We are currently investigating genes modulated by ER/FGFR1 in ER+ BC and the in vivo anti-tumor efficacy of dual inhibition of FGFR1 and ER in ER+/FGFR1-amplified patient-derived breast cancer xenografts. Conclusions: These data support a critical role of ER and FGFR1 interaction in endocrine resistance in ER+/FGFR1-amplified breast cancer. Targeting of FGFR1 in combination with antiestrogens may abrogate resistance to endocrine therapy in these tumors and is worthy of clinical investigation. Citation Format: Formisano L, Young CD, Bhola NE, Bulen B, Estrada VM, Wagle N, Van Allen E, Red Brewer ML, Jansen VM, Guerrero AL, Giltnane JM, Strcker T, Arteaga CL. Nuclear FGFR1 interaction with estrogen receptor (ER) α is associated with resistance to endocrine therapy in ER+/FGFR1-amplified breast cancer. [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 S3-03.</jats:p