Oncolytic virus treatment differentially affects the CD56dim and CD56bright NK cell subsets in vivo and regulates a spectrum of human NK cell activity

Natural killer (NK) cells protect against intracellular infection and cancer. These properties are exploited in oncolytic virus (OV) therapy, where antiviral responses enhance anti-tumour immunity. We have analysed the mechanism by which reovirus, an oncolytic dsRNA virus, modulates human NK cell activity. Reovirus activates NK cells in a type I interferon (IFN-I) dependent manner, inducing STAT1 and STAT4 signalling in both CD56dim and CD56bright NK cell subsets. Gene expression profiling revealed the dominance of IFN-I responses and identified induction of genes associated with NK cell cytotoxicity and cell cycle progression, with distinct responses in the CD56dim and CD56bright subsets. However, reovirus treatment inhibited IL-15 induced NK cell proliferation in an IFN-I dependent manner and was associated with reduced AKT signalling. In vivo, human CD56dim and CD56bright NK cells responded with similar kinetics to reovirus treatment, but CD56bright NK cells were transiently lost from the peripheral circulation at the peak of the IFN-I response, suggestive of their redistribution to secondary lymphoid tissue. Coupled with the direct, OV-mediated killing of tumour cells, the activation of both CD56dim and CD56bright NK cells by antiviral pathways induces a spectrum of activity that includes the NK cell-mediated killing of tumour cells and modulation of adaptive responses via the trafficking of IFN-γ expressing CD56bright NK cells to lymph nodes.

ETS transcription factor ELF3 (ESE-1) is a cell cycle regulator in benign and malignant prostate

This study aimed to elucidate the role of ELF3, an ETS family member in normal prostate growth and prostate cancer. Silencing ELF3 in both benign prostate (BPH-1) and prostate cancer (PC3) cell lines resulted in decreased colony forming ability, inhibition of cell migration and reduced cell viability due to cell cycle arrest, establishing ELF3 as a cell cycle regulator. Increased ELF3 expression in more advanced prostate tumours was shown by immunostaining of tissue microarrays and from analysis of gene expression and genetic alteration studies. This study indicates that ELF3 functions as part of normal prostate epithelial growth but also as a potential oncogene in advanced prostate cancers.

Notch signalling is a potential resistance mechanism of progenitor cells within patient-derived prostate cultures following ROS-inducing treatments

Low Temperature Plasma (LTP) generates reactive oxygen and nitrogen species, causing cell death, similarly to radiation. Radiation resistance results in tumour recurrence, however mechanisms of LTP resistance are unknown. LTP was applied to patient-derived prostate epithelial cells and gene expression assessed. A typical global oxidative response (AP-1 and Nrf2 signalling) was induced, whereas Notch signalling was activated exclusively in progenitor cells. Notch inhibition induced expression of prostatic acid phosphatase (PAP), a marker of prostate epithelial cell differentiation, whilst reducing colony forming ability and preventing tumour formation. Therefore, if LTP is to be progressed as a novel treatment for prostate cancer, combination treatments should be considered in the context of cellular heterogeneity and existence of cell type-specific resistance mechanisms.

Genetic and Environmental Determinants of Immune Response to Cutaneous Melanoma

The immune response to melanoma improves the survival in untreated patients and predicts the response to immune checkpoint blockade. Here, we report genetic and environmental predictors of the immune response in a large primary cutaneous melanoma cohort. Bioinformatic analysis of 703 tumor transcriptomes was used to infer immune cell infiltration and to categorize tumors into immune subgroups, which were then investigated for association with biological pathways, clinicopathologic factors, and copy number alterations. Three subgroups, with "low", "intermediate", and "high" immune signals, were identified in primary tumors and replicated in metastatic tumors. Genes in the low subgroup were enriched for cell-cycle and metabolic pathways, whereas genes in the high subgroup were enriched for IFN and NF-κB signaling. We identified high MYC expression partially driven by amplification, HLA-B downregulation, and deletion of IFNγ and NF-κB pathway genes as the regulators of immune suppression. Furthermore, we showed that cigarette smoking, a globally detrimental environmental factor, modulates immunity, reducing the survival primarily in patients with a strong immune response. Together, these analyses identify a set of factors that can be easily assessed that may serve as predictors of response to immunotherapy in patients with melanoma. SIGNIFICANCE: These findings identify novel genetic and environmental modulators of the immune response against primary cutaneous melanoma and predict their impact on patient survival.See related commentary by Anichini, p. 2457.

Abstract 3696: RNAseq of patient-derived cancer stem-like cells and exosomes provides new insights into Ewing's sarcoma

Background

Cancer stem-like cells (CSCs) are responsible for disease progression and relapse (Schatton et al, Bioessays 2009, 31:1038-49). Therefore, the eradication of Ewing's sarcoma (ES)-CSCs is expected to improve outcome for patients. Since the transfer of exosome cargo between cells drives ES progression (Ventura et al, Oncogene, 2016, 35:3944-54) or can be exploited as biomarker (Miller et al, Biology of the Cell 2013, 105:289-303; Tsugita et al, PLoS ONE 2013, 8:e77416) we have characterized primary patient-derived ES, paired ES-CSCs, and the exosomal cargo from these cultures to identify potential prognostic biomarkers of risk and targets for the development of new treatments.

Methods

ES taken at diagnosis and resection were collected following patient consent (GenoEwing; IRAS-167880). ES-CSCs were isolated using a functional self-renewing assay. EWSR1 translocations were confirmed by FISH using a break-apart probe and RT-PCR. Exosomes were collected after incubation of cultures in serum-free media for 48h, isolated using exoEasy Maxi kit (Qiagen) and characterized by Nanoparticle tracking, Western blot and flow cytometry. The expression of the ES-marker CD99 was investigated by immunocytochemistry, Western blot and flow cytometry. RNA was extracted from ES cells and paired exosomes using the miRNeasy Micro kit (Qiagen) and RNA quality confirmed employing the Agilent Bioanalyser. Total RNA libraries were prepared and sequenced using the HiSeq3000 (Illumina®). Reads were processed using fqtools (Droop, Bioinformatics 2016, 32:1883-4), aligned by STAR (Dobin et al, Bioinformatics 2013, 29:15-21) and differential expression was determined by DESeq2 (Anders et al, Genome Biology 2010, 11:R106). Genes were ranked on adjusted p value and log2 fold change; candidates were validated by RTqPCR.

Results

ES patient-derived cells expressed CD99 and contained an EWSR1 gene translocation (23/23). The median size of isolated ES exosomes was 84nm (range 32-132nm). Exosomes were enriched for small RNA (53±5% in exosomes vs 12±3% in cells). The optimal protein panel to identify ES exosomes is CD81, CD63 and TSG-101; CD9 was not detected. Consistent with the exosomal cell of origin, expression of CD99 was detected in 71-79% of isolated vesicles.

The RNA profile of parental cultures and daughter ES-CSCs was compared and two genes with increased expression in ES-CSCs were validated by RTqPCR (p<0.0001). Using a novel experimental approach in ES, we have sequenced the total RNA profile of paired exosomes from patient-derived ES cultures and confirmed the expression of CD99 and one putative ES-CSC biomarker in exosomes.

Conclusions

For the first time, we have sequenced paired exosomes and patient-derived ES cells to identify a potential prognostic biomarker and novel target for therapy.

Work funded by University of Leeds, Ewing's Sarcoma Research Trust (ESRT) and Bone Cancer Research Trust (BCRT).

Citation Format: Mariona Chicón Bosch, Elizabeth A. Roundhill, Alastair P. Droop, Michael Parry, Lee Jeys, Susan A. Burchill. RNAseq of patient-derived cancer stem-like cells and exosomes provides new insights into Ewing's sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3696.

fqtools: an efficient software suite for modern FASTQ file manipulation

Summary: Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines.

Availability and implementation: fqtools is open source and is available at: https://github.com/alastair-droop/fqtools.

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:a.p.droop@leeds.ac.uk

qsubsec: a lightweight template system for defining sun grid engine workflows

Summary: The Sun Grid Engine (SGE) high-performance computing batch queueing system is commonly used in bioinformatics analysis. Creating re-usable scripts for the SGE is a common challenge. The qsubsec template language and interpreter described here allow researchers to easily create generic template definitions that encapsulate a particular computational job, effectively separating the process logic from the specific run details. At submission time, the generic template is filled in with specific values. This system provides an intermediate level between simple scripting and complete workflow management tools.

Availability and implementation: Qsubsec is open-source and is available at https://github.com/alastair-droop/qsubsec.

Contact: a.p.droop@leeds.ac.uk

Supplementary information:Supplementary data are available at Bioinformatics online.

DNA hypermethylation in prostate cancer is a consequence of aberrant epithelial differentiation and hyperproliferation

Prostate cancer (CaP) is mostly composed of luminal-like differentiated cells, but contains a small subpopulation of basal cells (including stem-like cells), which can proliferate and differentiate into luminal-like cells. In cancers, CpG island hypermethylation has been associated with gene downregulation, but the causal relationship between the two phenomena is still debated. Here we clarify the origin and function of CpG island hypermethylation in CaP, in the context of a cancer cell hierarchy and epithelial differentiation, by analysis of separated basal and luminal cells from cancers. For a set of genes (including GSTP1) that are hypermethylated in CaP, gene downregulation is the result of cell differentiation and is not cancer specific. Hypermethylation is however seen in more differentiated cancer cells and is promoted by hyperproliferation. These genes are maintained as actively expressed and methylation-free in undifferentiated CaP cells, and their hypermethylation is not essential for either tumour development or expansion. We present evidence for the causes and the dynamics of CpG island hypermethylation in CaP, showing that, for a specific set of genes, promoter methylation is downstream of gene downregulation and is not a driver of gene repression, while gene repression is a result of tissue-specific differentiation.

Abstract B25: DNA hypermethylation in prostate cancer is a consequence of aberrant epithelial differentiation and hyperproliferation

Prostate cancer (CaP) is mostly composed of differentiated luminal cells, but contains a small subpopulation of undifferentiated basal cells (including stem-like cells), which is thought to be the driving force of CaP. In cancers, CpG island hypermethylation has been associated with gene downregulation, but the causal relationship between the two phenomena is still debated. This study aimed to understand the function and origin of CpG island hypermethylation in CaP, in the context of cancer hierarchy and differentiation. We have analyzed separately primary prostate basal and luminal cells derived from BPH and CaP. This allowed us to dissect the intra-tumor heterogeneity, and to understand the origin of gene downregulation and hypermethylation in CaP. We report that a set of genes commonly hypermethylated in CaP (including GSTP1) is: (i) downregulated as a result of prostate-specific epithelial differentiation in both CaP and benign prostatic hyperplasia (BPH); (ii) selectively hypermethylated in differentiated (luminal) cancer cells, process promoted by the hyperproliferating phenotype of these cells; (iii) actively expressed and methylation free in undifferentiated (basal) CaP cells. Downregulation and hypermethylation of these genes is not essential for tumor development or tumor expansion. Moreover, for all these genes, downregulation induced by prostate-specific differentiation, is independent of DNA hypermethylation, and is associated with detachment of RNA PolII from their promoter and reduction in histone marks associated with active transcription.

Citation Format: Davide Pellacani, Dimitra Kestoras, Alastair P. Droop, Fiona M. Frame, Paul A. Berry, Mitchell G. Lawrence, Michael J. Stower, Matthew S. Simms, Vincent M. Mann, Anne T. Collins, Gail P. Risbridger, Norman J. Maitland. DNA hypermethylation in prostate cancer is a consequence of aberrant epithelial differentiation and hyperproliferation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B25.

Retinoic acid and androgen receptors combine to achieve tissue specific control of human prostatic transglutaminase expression: a novel regulatory network with broader significance

In the human prostate, expression of prostate-specific genes is known to be directly regulated by the androgen-induced stimulation of the androgen receptor (AR). However, less is known about the expression control of the prostate-restricted TGM4 (hTGP) gene. In the present study we demonstrate that the regulation of the hTGP gene depends mainly on retinoic acid (RA). We provide evidence that the retinoic acid receptor gamma (RAR-G) plays a major role in the regulation of the hTGP gene and that presence of the AR, but not its transcriptional transactivation activity, is critical for hTGP transcription. RA and androgen responsive elements (RARE and ARE) were mapped to the hTGP promoter by chromatin immunoprecipitation (ChIP), which also indicated that the active ARE and RARE sites were adjacent, suggesting that the antagonistic effect of androgen and RA is related to the relative position of binding sites. Publicly available AR and RAR ChIP-seq data was used to find gene potentially regulated by AR and RAR. Four of these genes (CDCA7L, CDK6, BTG1 and SAMD3) were tested for RAR and AR binding and two of them (CDCA7L and CDK6) proved to be antagonistically regulated by androgens and RA confirming that this regulation is not particular of hTGP.

Abstract 5209: Prostate cancer progenitor cells have distinct DNA methylation profile which changes upon differentiation

Prostate cancer is phenotypically, genetically and epigenetically heterogeneous. In the present study we have dissected the epigenetic heterogeneity of prostate cancer by analyzing DNA methylation patterns in pure subpopulations of primary cancer cells, on the basis of their differentiation status. GSTP1, an enzyme involved in intracellular detoxification, is highly expressed in prostate basal epithelial cells but is down-regulated in luminal cells by a mechanism independent of DNA methylation. The GSTP1 promoter becomes frequently hypermethylated in prostate cancer, where the majority of cells bear a luminal-like phenotype. However, a small subpopulation of basal cells (<1%) persists within prostate cancer and is hypothesized to contain stem-like cells that give rise to aberrantly differentiated cancer cells. By analyzing the DNA methylation patterns in basal and luminal like prostate cancer cells, it has been possible to unveil the origin of promoter hypermethylation in prostate cancer that ultimately leads to epigenetic heterogeneity. In established cell lines, GSTP1 was actively transcribed (measured by RT-PCR) and not hypermethylated (measured by pyrosequencing methylation assay) in basal-like cancer cells, while it was hypermethylated and down-regulated in luminal-like cancer cells. MACs selection of Lin−/CD31−/CD24+ cells from prostate primary tissues highly enriched for AR+/KRT8+/GSTP1low cells bearing a luminal-like phenotype, while generation of prostate primary epithelial cultures gave rise to cells with basal phenotype. In luminal-like cells, GSTP1 was hypermethylated in cancer samples compared to benign controls. However, no significant hypermethylation of GSTP1 was found in the basal-like cells, where the gene was actively expressed in both benign and cancer samples. Lack of GSTP1 promoter methylation was also found in tumor xenografts generated in Rag2−/+gammaC−/+ mice from primary prostate cancer tissues. These xenografts do not undergo complete differentiation and show an intermediate phenotype expressing both basal and luminal markers. Moreover, in BPH-1 cells, a fast cycling immortalized cell line, expression and promoter methylation of GSTP1 correlated with the differentiation status of the cells, being hypermethylated in more differentiated cells. Our results strongly indicate that within prostate cancer there is a subpopulation of undifferentiated basal-like cells that do not hypermethylate the GSTP1 promoter. We hypothesize that these cells can differentiate into luminal-like cancer cells, which down-regulate GSTP1 and hypermethylate its promoter as a consequence of aberrant proliferation. Future work will include determination of the mechanism of GSTP1 down-regulation in normal and malignant prostate epithelial differentiation, and whether this mechanism is shared with other genes frequently hypermethylated in prostate cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5209. doi:1538-7445.AM2012-5209

Abstract 5198: Elucidation of dynamic prostate epithelial hierarchy: Insights into transcriptional and epigenetic regulatory mechanisms

The aim of present investigation is to elucidate the complex stem cell dynamics within prostate cancer, which can be utilized to design novel diagnostic and therapeutic strategies for the management of prostate cancer. In order to determine precise transcriptional and microRNA regulatory mechanisms modulating stem cell self-renewal and differentiation, unique cellular assays have been developed in our lab that utilize homogeneous fractionated cell populations enriched from primary patient prostate cultures. Using a prospective bioinformatic analysis of gene expression data from Birnie et. al., 2008, we have identified LCN2, CEACAM6, and S100p as candidate genes for regulation of prostate stem cell differentiation. Their over-expression in differentiated cells, as compared to stem cells, was validated in respective cells enriched from cultures obtained from BPH, cancer and castration resistant prostate cancer samples and from primary human prostate cancer xenografts. Interestingly, the analysis of 25,000 published human Affymetrix microarray chips revealed that LCN2, CEACAM6, and S100p have a more similar expression pattern than that of any other genes in the entire human genome, suggesting that they may have common function and are co-regulated. Indeed, the promoter analysis showed that the promoters (1kb from TSS) of all these genes have common binding sites for 40 transcription factors with very high affinity and P < 0.001. Most of these transcription factors have a well-documented role in cell differentiation (RA, AR, and NANOG) and prostate carcinogenesis (NF-kB). Significant up-regulation in the expression of these genes in prostate cell lines after treatment with all-trans retinoic acid and androgen analogue R1881 further suggested the role of AR and RA in prostate differentiation. Along with transcriptional regulation, Agilent v3 miRNA microarray data revealed obviously distinct miRNA expression profiles in stem and differentiated prostate epithelial cells, confirming crucial role of miRNA in main taining epithelial hierarchies, in prostate. We anticipate that evaluation of integrative transcriptional (LCN2-CEACAM6-S100p)-microRNA regulatory network, with further functional studies, will comprehensively establish a detailed knowledge base for potential regulatory mechanisms involved in prostate stem cell and prostate cancer stem cell differentiation. These insights will be valuable to formulate efficient ‘differentiation therapy’ for the management of prostate cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5198. doi:1538-7445.AM2012-5198

The calcium sensor STIM1 is regulated by androgens in prostate stromal cells

BACKGROUND

Prostate development and maintenance in the adult results from an interaction of stromal and glandular components. Androgens can drive this process by direct action on the stroma. We investigated whether there was a direct link between androgens and another key regulator of stromal cells, intracellular Ca2+ ([Ca2+ ]i ).

METHODS

Prostate stromal cells were freshly obtained and cultures derived from patients with benign prostatic hyperplasia. Gene expression in dihydrotestosterone treated and untreated cells was compared using Affymetrix gene expression arrays and Ca2+ regulated features were identified by Gene Ontology (GO). Changes in [Ca2+]i were determined in Fluo-4 loaded cells. Androgen regulation was confirmed by chromatin immunoprecipitaion.

RESULTS

Stromal cell cultures were sorted for expression of integrin α1 β1 , which enriched for cells expressing the androgen receptor (AR). We identified key functional categories, within the androgen-induced gene expression signature, focusing on genes involved in calcium signaling. From this analysis, stromal interaction molecule-1 (STIM1) was identified as a significantly differentially expressed gene with four relevant associated GO terms. DNA sequence analysis showed that the promoter region of STIM1 contained putative androgen response element sequences in which AR binding ability of STIM1 was confirmed. Androgens directly regulated STIM1 expression and STIM1 effects on store-operated calcium entry were inhibited by STIM1 knock-down. Reduced STIM1 expression in prostate stromal cells led to a reduction in basal Ca2+ levels, the amount of Ca2+ released by thapsigargin and a reduction in store filling following TG-induced store depletion.

CONCLUSIONS

These results indicate that androgens modulate [Ca2+]i through the direct regulation of the STIM1 gene by AR binding to the STIM1 promoter.

Properties of biological mutation networks and their implications for ALife

We report a study of networks constructed from mutation patterns observed in biology. These networks form evolutionary trajectories, which allow for both frequent substitution of closely related structures, and a small evolutionary distance between any two structures. These two properties define the small-world phenomenon. The mutation behavior between tokens in an evolvable artificial chemistry determines its ability to explore evolutionary space. This concept is underrepresented in previous work on string-based chemistries. We argue that small-world mutation networks will confer better exploration of the evolutionary space than either random or fully regular mutation strategies. We calculate network statistics from two data sets: amino acid substitution matrices, and codon-level single point mutations. The first class are observed data from protein alignments; while the second class is defined by the standard genetic code that is used to translate RNA into amino acids. We report a methodology for creating small-world mutation networks for artificial chemistries with arbitrary node count and connectivity. We argue that ALife systems would benefit from this approach, as it delivers a more viable exploration of evolutionary space.

Yeast ntr1/spp382 mediates prp43 function in postspliceosomes

The Ntr1 and Ntr2 proteins of Saccharomyces cerevisiae have been reported to interact with proteins involved in pre-mRNA splicing, but their roles in the splicing process are unknown. We show here that they associate with a postsplicing complex containing the excised intron and the spliceosomal U2, U5, and U6 snRNAs, supporting a link with a late stage in the pre-mRNA splicing process. Extract from cells that had been metabolically depleted of Ntr1 has low splicing activity and accumulates the excised intron. Also, the level of U4/U6 di-snRNP is increased but those of the free U5 and U6 snRNPs are decreased in Ntr1-depleted extract, and increased levels of U2 and decreased levels of U4 are found associated with the U5 snRNP protein Prp8. These results suggest a requirement for Ntr1 for turnover of the excised intron complex and recycling of snRNPs. Ntr1 interacts directly or indirectly with the intron release factor Prp43 and is required for its association with the excised intron. We propose that Ntr1 promotes release of excised introns from splicing complexes by acting as a spliceosome receptor or RNA-targeting factor for Prp43, possibly assisted by the Ntr2 protein.