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Ants are some of the most abundant and familiar animals on Earth, and they play vital roles in most terrestrial ecosystems. Although all ants are eusocial, and display a variety of complex and fascinating behaviors, few genomic resources exist for them. Here, we report the draft genome sequence of a particularly widespread and well-studied species, the invasive Argentine ant ( Linepithema humile ), which was accomplished using a combination of 454 (Roche) and Illumina sequencing and community-based funding rather than federal grant support. Manual annotation of >1,000 genes from a variety of different gene families and functional classes reveals unique features of the Argentine ant's biology, as well as similarities to Apis mellifera and Nasonia vitripennis . Distinctive features of the Argentine ant genome include remarkable expansions of gustatory (116 genes) and odorant receptors (367 genes), an abundance of cytochrome P450 genes (>110), lineage-specific expansions of yellow/major royal jelly proteins and desaturases, and complete CpG DNA methylation and RNAi toolkits. The Argentine ant genome contains fewer immune genes than Drosophila and Tribolium , which may reflect the prominent role played by behavioral and chemical suppression of pathogens. Analysis of the ratio of observed to expected CpG nucleotides for genes in the reproductive development and apoptosis pathways suggests higher levels of methylation than in the genome overall. The resources provided by this genome sequence will offer an abundance of tools for researchers seeking to illuminate the fascinating biology of this emerging model organism.

First two authors contributed equally Last two authors contributed equally Recent studies have shown that ex vivo propagation of normal tissues or patient-derived tumor cells in presence of irradiated fibroblast feeder cells and ROCK inhibitor can rapidly establish conditionally reprogramed cells (CRCs). In case of normal tissues, the induction of CRCs was reversible when the ROCK inhibitor and the feeder cells were removed, resulting in CRCs differentiating to its tissue origin (Liu et al.2012). Previous publications suggested that the establishment of such cell models provides new strategies to understand acquired resistance during treatment (Crystal et al 2015) and to predict treatment response (Liu et al. 2014). However, gene expression modulations and genomic drifting during the establishment of CRC propagation have not been thoroughly studied. The primary goal of this study is to molecularly characterize alterations between the original tumor tissues and the derived models growing with or without ROCK inhibitor. Understanding in-depth molecular fluctuations in this patient-derived ex vivo system will facilitate its appropriate use for tumor biology experimentation. Herein, tumors from prostate cancer and breast cancer patients were surgical removed and cryopreserved at the clinical site then processed and cultured as previously described (Liu et al. 2012). Gene expression profiling and next-generation sequencing were carried out on the original tumor tissues and cellular models passaged during the CRC propagation in the presence or absence of ROCK inhibitor. Gene expression analysis of the prostate cancer cells and the breast cancer cells were carried out using a 93-gene prostate cancer-focused Fluidigm panel and a 800 gene NanoString breast cancer-focused panel, respectively. Cancer hotspot mutations were analyzed using the Ion Torrent Cancer Hotspot v2 NGS assay. Through aforementioned genomic and transcriptomic interrogations, we demonstrated the extent of indication-relevant gene expression modulation during establishment and propagation of these cells. We also characterize cancer hotspot mutations in the primary tumor cells and the stability of those mutations during ex vivo propagation. These results should begin to inform the appropriate use of the CRC model for tumor biology experimentation. Citation Format: Jessica Li, Bonnie Liu, Rin Nakamura, Heidi Savage, Shoji Ikeda, Timothy Wilson, Teiko Sumiyoshi, Garret Hampton, Lukas Amler, Mark Lackner, Shih-Min A. Huang, Walter C. Darbonne. Gene expression and genomic drift comparative analysis between patient-derived conditionally reprogrammed cells and original tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4257.

Accurately measuring the expression of genes in formalin-fixed paraffin embedded (FFPE) tumor tissues has long been a struggle due to the inherent degradation of RNA isolated from these materials. Accurate quantification of gene expression levels in FFPE samples can enable the testing of biomarker hypotheses in the clinic and can potentially be used for patient stratification or selection in clinical trials. Platforms such as Fluidigm, Nanostring and microarrays are currently the high-throughput technologies utilized. Each of these platforms has different drawbacks and challenges such as lack of sensitivity, reproducibility or dynamic range when working with degraded FFPE samples. Currently, whole transcriptome RNA sequencing (RNA-Seq) is the only platform that offers a truly high-throughput, sensitive, and reproducible method to accurately quantify mRNA levels in RNA derived from FFPE samples. RNA-Seq, however has not yet been widely evaluated and adapted for use with degraded FFPE samples. Here we report the direct comparison of whole transcriptome RNA-Seq with two platforms that are currently compatible with FFPE derived RNA, Fluidigm and Nanostring, to determine the accuracy and feasibility of using this technology on degraded RNA. Utilizing a collection of matched fresh frozen (FF) and FFPE samples we analyzed gene expression using all three platforms to allow for a direct evaluation of each technology. By comparing the results to the matching FF sample, we were able to determine the accuracy and sensitivity of each platform when using degraded FFPE derived RNA. By titrating down the input of FFPE RNA into the RNA-Seq library prep we were also able to define the optimal input of FFPE RNA needed to accurately and reproducibly quantify gene expression. This work allows for a systematic comparison of different gene expression platforms for their use with degraded FFPE RNA. Citation Format: Erica B. Schleifman, Maipelo Motlhabi, Craig Cummings, Rin Nakamura, Linda Bosch, Rajesh Patel, An Do, Andrew Watson, Thomas Sandmann, Walter Darbonne, Ian McCaffery, Eric Peters, Rajiv Raja. Comparison of gene expression platforms: RNA-Seq, Fluidigm, and Nanostring. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4901. doi:10.1158/1538-7445.AM2015-4901