Transcriptome and proteome profiling reveals stress-induced expression signatures of imiquimod-treated Tasmanian devil facial tumor disease (DFTD) cells

As a topical cancer immunotherapy, the toll-like receptor 7 ligand imiquimodactivates tumor regression via stimulation of immune cell infiltration and cytotoxicresponses. Imiquimod also exerts direct pro-apoptotic effects on tumor cells invitro, but a role for these effects in imiquimod-induced tumor regression remainsundefined. We previously demonstrated that cell lines derived from devil facial tumordisease (DFTD), a transmissible cancer threatening the survival of the Tasmaniandevil (Sarcophilus harrisii), are sensitive to imiquimod-induced apoptosis. In thisstudy, the pro-apoptotic effects of imiquimod in DFTD have been investigated usingRNA-sequencing and label-free quantitative proteomics. This analysis revealedthat changes to gene and protein expression in imiquimod treated DFTD cells areconsistent with the onset of oxidative and endoplasmic reticulum stress responses,and subsequent activation of the unfolded protein response, autophagy, cell cyclearrest and apoptosis. Imiquimod also regulates the expression of oncogenic pathways,providing a direct mechanism by which this drug may increase tumor susceptibilityto immune cytotoxicity in vivo. Our study has provided the first global analysis ofimiquimod-induced effects in any tumor cell line. These findings have highlightedthe potential of cell stress pathways as therapeutic targets in DFTD, and will allowfor improved mechanistic use of imiquimod as a therapy in both the Tasmanian deviland human cancers

Epithelial-to-mesenchymal transition supports ovarian carcinosarcoma tumorigenesis and confers sensitivity to microtubule-targeting with eribulin

Ovarian carcinosarcoma (OCS) is an aggressive and rare tumour type with limited treatment options. OCS is hypothesised to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analysed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumours. Preclinical OCS models were used to test the efficacy of microtubule-targeting drugs, including eribulin, which has previously been shown to reverse EMT characteristics in breast cancers and induce differentiation in sarcomas. Vinorelbine and eribulin more effectively inhibited OCS growth than standard-of-care platinum-based chemotherapy, and treatment with eribulin reduced mesenchymal characteristics and N-MYC expression in OCS patient-derived xenografts (PDX). Eribulin treatment resulted in an accumulation of intracellular cholesterol in OCS cells, which triggered a down-regulation of the mevalonate pathway and prevented further cholesterol biosynthesis. Finally, eribulin increased expression of genes related to immune activation and increased the intratumoral accumulation of CD8+ T cells, supporting exploration of immunotherapy combinations in the clinic. Together, these data indicate EMT plays a key role in OCS tumourigenesis and support the conversion theory for OCS histogenesis. Targeting EMT using eribulin could help improve OCS patient outcomes

Regression of devil facial tumour disease following immunotherapy in immunised Tasmanian devils

Devil facial tumour disease (DFTD) is a transmissible cancer devastating the Tasmanian devil (Sarcophilus harrisii) population. The cancer cell is the 'infectious' agent transmitted as an allograft by biting. Animals usually die within a few months with no evidence of antibody or immune cell responses against the DFTD allograft. This lack of anti-tumour immunity is attributed to an absence of cell surface major histocompatibility complex (MHC)-I molecule expression. While the endangerment of the devil population precludes experimentation on large experimental groups, those examined in our study indicated that immunisation and immunotherapy with DFTD cells expressing surface MHC-I corresponded with effective anti-tumour responses. Tumour engraftment did not occur in one of the five immunised Tasmanian devils, and regression followed therapy of experimentally induced DFTD tumours in three Tasmanian devils. Regression correlated with immune cell infiltration and antibody responses against DFTD cells. These data support the concept that immunisation of devils with DFTD cancer cells can successfully induce humoral responses against DFTD and trigger immune-mediated regression of established tumours. Our findings support the feasibility of a protective DFTD vaccine and ultimately the preservation of the species.Research support was provided by the Australian Research Council (ARC Linkage grant #LP0989727, ARC Discovery grant #DP130100715), University of Tasmania Foundation through funds raised by the Save the Tasmanian Devil Appeal. J.M.M. acknowledges fellowship support (APP1105754) and L.M.C. Program Grant funding (APP1054925) from NHMRC. J.M.M. and L.M.C. acknowledge NHMRC IRIISS (9000220) and Victorian Government Operational Infrastructure Support. Y.C. and K.B. are supported by the Australian Research Council (ARC Discovery grant #DP140103260). K.B. is funded by an ARC Future Fellowship. J.K. is supported by a Wellcome Trust programme Grant (089305)

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat

Background The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. With Ebola virus, Marburg virus is a member of the family Filoviridae that causes severe hemorrhagic fever disease in humans and nonhuman primates, but results in little to no pathological consequences in bats. Understanding host-pathogen interactions within reservoir host species and how it differs from hosts that experience severe disease is an important aspect of evaluating viral pathogenesis and developing novel therapeutics and methods of prevention. Results Progress in studying bat reservoir host responses to virus infection is hampered by the lack of host-specific reagents required for immunological studies. In order to establish a basis for the design of reagents, we sequenced, assembled, and annotated the R. aegyptiacus transcriptome. We performed de novo transcriptome assembly using deep RNA sequencing data from 11 distinct tissues from one male and one female bat. We observed high similarity between this transcriptome and those available from other bat species. Gene expression analysis demonstrated clustering of expression profiles by tissue, where we also identified enrichment of tissue-specific gene ontology terms. In addition, we identified and experimentally validated the expression of novel coding transcripts that may be specific to this species. Conclusion We comprehensively characterized the R. aegyptiacus transcriptome de novo. This transcriptome will be an important resource for understanding bat immunology, physiology, disease pathogenesis, and virus transmission

Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail

This corrects the article DOI: 10.1038/ncomms15451

Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.

MOTIVATION: A challenge for computational biologists is to make our analyses reproducible-i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. RESULTS: We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. AVAILABILITY AND IMPLEMENTATION: BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662)

The life history of neochromosomes revealed

Neochromosomes are a little-studied class of chromosome-scale mutations that drive some cancers. By sequencing isolated neochromosomes from liposarcomas, we recently defined their structure at single-nucleotide resolution and proposed a model for their life history. Here, we summarize that work, highlighting significant aspects and providing historical context and insight into the discovery process