ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements.

Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.

An Essential Role of Maspin in Embryogenesis and Tumor Suppression.

Maspin (SerpinB5) is an epithelial-specific tumor suppressor gene product that displays context-dependent cellular functions. Maspin-deficient mouse models created to date have not definitively established maspin functions critical for cancer suppression. In this study, we generated a mouse strain in which exon 4 of the Maspin gene was deleted, confirming its essential role in development but also enabling a breeding scheme to bypass embryonic lethality. Phenotypic characterization of this viable strain established that maspin deficiency was associated with a reduction in maximum body weight and a variety of context-dependent epithelial abnormalities. Specifically, maspin-deficient mice exhibited pulmonary adenocarcinoma, myoepithelial hyperplasia of the mammary gland, hyperplasia of luminal cells of dorsolateral and anterior prostate, and atrophy of luminal cells of ventral prostate and stratum spinosum of epidermis. These cancer phenotypes were accompanied by increased inflammatory stroma. These mice also displayed the autoimmune disorder alopecia aerate. Overall, our findings defined context-specific tumor suppressor roles for maspin in a clinically relevant model to study maspin functions in cancer and other pathologies. Cancer Res; 77(4); 886-96. ©2017 AACR.

The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera: Figitidae), a parasitoid wasp of Drosophila.

The partial mitochondrial genome sequence of Leptopilina boulardi (Hymenoptera: Figitidae) was characterized. Illumina sequencing was used yielding 35,999,679 reads, from which 102,482 were utilized in the assembly. The length of the sequenced region of this partial mitochondrial genome is 15,417 bp, consisting of 13 protein-coding, two rRNA, and 21tRNA genes (the trnaM failed to be sequenced) and a partial A+T-rich region. All protein-coding genes start with ATN codons. Eleven protein-coding genes presented TAA stop codons, whereas ND6 and COII that presented TA, and T nucleotides, respectively. The gene pattern revealed extensive rearrangements compared to the typical pattern generally observed in insects. These rearrangements involve two protein-coding and two ribosomal genes, along with the 16 tRNA genes. This gene order is different from the pattern described for Ibalia leucospoides (Ibaliidae, Cynipoidea), suggesting that this particular gene order can be variable among Cynipoidea superfamily members. A maximum likelihood phylogenetic analysis of the main groups of Apocrita was performed using amino acid sequence of 13 protein-coding genes, showing monophyly for the Cynipoidea superfamily within the Hymenoptera phylogeny.

Gene expression analysis of bone metastasis and circulating tumor cells from metastatic castrate-resistant prostate cancer patients.

BACKGROUND: Characterization of genes linked to bone metastasis is critical for identification of novel prognostic or predictive biomarkers and potential therapeutic targets in metastatic castrate-resistant prostate cancer (mCRPC). Although bone marrow core biopsies (BMBx) can be obtained for gene profiling, the procedure itself is invasive and uncommon practice in mCRPC patients. Conversely, circulating tumor cells (CTCs), which are likely to stem from bone metastases, can be isolated from blood. The goals of this exploratory study were to establish a sensitive methodology to analyze gene expression in BMBx and CTCs, and to determine whether the presence or absence of detectable gene expression is concordant in matching samples from mCRPC patients. METHODS: The CellSearch(®) platform was used to enrich and enumerate CTCs. Low numbers of PC3 prostate cancer (PCa) cells were spiked into normal blood to assess cell recovery rate. RNA extracted from recovered PC3 cells was amplified using an Eberwine-based procedure to obtain antisense mRNA (aRNA), and assess the linearity of the RNA amplification method. In this pilot study, RNAs extracted from CTCs and PCa cells microdissected from formalin-fixed paraffin-embedded BMBx, were amplified to obtain aRNA and assess the expression of eight genes functionally relevant to PCa bone metastasis using RT-PCR. RESULTS: RNAs were successfully extracted from as few as 1-5 PCa cells in blood samples. The relative expression levels of reference genes were maintained after RNA amplification. The integrity of the amplified RNA was also demonstrated by RT-PCR analysis using primer sets that target the 5'-end, middle, and 3'-end of reference mRNA. We found that in 21 out of 28 comparisons, the presence or absence of detectable gene expression in CTCs and PCa cells microdissected from single bone lesions of the same patients was concordant. CONCLUSIONS: This exploratory analysis suggests that aRNA amplification through in vitro transcription may be useful as a method to detect gene expression in small numbers of CTCs and tumor cells microdissected from bone metastatic lesions. In some cases, gene expression in CTCs and BMBxs was not concordant, raising questions about using CTC gene expression to make clinical decisions.

The mouse prostate: a basic anatomical and histological guideline.

Despite substantial similarities in embryological, cellular and molecular biology features, human and mouse prostates differ in organ morphology and tissue architecture. Thus, a clear understanding of the anatomy and histology of the mouse prostate is essential for the identification of urogenital phenotypes in genetically engineered mice, as well as for the study of the etiology, development, and treatment of human prostatic diseases for which mouse models are used. The purpose of this manuscript is to provide a brief guide for the dissection of the mouse prostate and the identification of its different lobes and histology, to both basic researchers and medical pathologists who are unfamiliar with mouse tissues.

Tumor suppressor maspin as a modulator of host immune response to cancer.

Despite the promising clinical outcome, the primary challenge of the curative cancer immunotherapy is to overcome the dichotomy of the immune response: tumor-evoked immunostimulatory versus tumor-induced immunosuppressive. The goal needs to be two-fold, to re-establish sustainable antitumor-cancer immunity and to eliminate immunosuppression. The successful elimination of cancer cells by immunosurveillance requires the antigenic presentation of the tumor cells or tumor-associated antigens and the expression of immunostimulatory cytokines and chemokines by cancer and immune cells. Tumors are heterogeneous and as such, some of the tumor cells are thought to have stem cell characteristics that enable them to suppress or desensitize the host immunity due to acquired epigenetic changes. A central mechanism underlying tumor epigenetic instability is the increased histone deacetylase (HDAC)-mediated repression of HDAC-target genes regulating homeostasis and differentiation. It was noted that pharmacological HDAC inhibitors are not effective in eliminating tumor cells partly because they may induce immunosuppression. We have shown that epithelial-specific tumor suppressor maspin, an ovalbumin-like non-inhibitory serine protease inhibitor, reprograms tumor cells toward better differentiated phenotypes by inhibiting HDAC1. Recently, we uncovered a novel function of maspin in directing host immunity towards tumor elimination. In this review, we discuss the maspin and maspin/HDAC1 interplay in tumor biology and immunology. We propose that maspin based therapies may eradicate cancer.

Cross-cultural adaptation and validation of the episodic autobiographic memory interview for Brazilian Portuguese / Validação e adaptação transcultural da entrevista para avaliação da memória episódica autobiográfica para o português brasileiro

Episodic memory enables the storage of personal events with specific temporal and spatial details, and their retrieval through a sensory experience, usually visual, which is called autonoetic consciousness. While, in Brazil, several scales for the evaluation of anterograde episodic memory have been validated, there is not yet an instrument to assess the episodic autobiographical memory. The aim of this study is thus to make a cross-cultural adaptation and validation of the Episodic Autobiographic Memory Interview (EAMI) for Brazilian Portuguese. Altogether, 11 patients with Alzheimer’s disease (AD) and 10 healthy controls (CTs) were evaluated. EAMI scores for AD patients were lower than those of CTs, and these scores also correlated positively with the Remember-Know coefficient. The intraclass correlation coefficient indicated a good inter-rater reliability. The Portuguese version of EAMI showed a good reliability and validity, which suggests that it is a useful tool for evaluation of autobiographical memory in Brazilian patients.

A memória episódica possibilita o arquivamento de eventos pessoais, com seus detalhes temporais e espaciais, e sua recuperação através de uma experiência sensorial, geralmente visual, chamada de consciência autonoética. No Brasil, foram validados vários instrumentos para avaliação da memória episódica anterógrada, porém não há ainda uma escala para avaliar a memória episódica autobiográfica. O objetivo deste estudo é realizar uma validação e adaptação transcultural da Entrevista para avaliação da Memória Episódica Autobiográfica (EMEA) para o português brasileiro. Onze pacientes com doença de Alzheimer (DA) e 10 controles normais foram avaliados. Os escores dos pacientes com DA na EMEA foram menores do que nos controles saudáveis. Estes escores se correlacionaram positivamente com o coeficiente Lembrar-Saber. O coeficiente de correlação intraclasse indicou uma confiabilidade inter-examinadores adequada. A EMEA demonstrou uma boa validade e confiabilidade, sugerindo que ela é um instrumento útil para a avaliação da memória autobiográfica em pacientes brasileiros.

Cross-cultural adaptation and validation of the episodic autobiographic memory interview for Brazilian Portuguese.

Episodic memory enables the storage of personal events with specific temporal and spatial details, and their retrieval through a sensory experience, usually visual, which is called autonoetic consciousness. While, in Brazil, several scales for the evaluation of anterograde episodic memory have been validated, there is not yet an instrument to assess the episodic autobiographical memory. The aim of this study is thus to make a cross-cultural adaptation and validation of the Episodic Autobiographic Memory Interview (EAMI) for Brazilian Portuguese. Altogether, 11 patients with Alzheimer's disease (AD) and 10 healthy controls (CTs) were evaluated. EAMI scores for AD patients were lower than those of CTs, and these scores also correlated positively with the Remember-Know coefficient. The intraclass correlation coefficient indicated a good inter-rater reliability. The Portuguese version of EAMI showed a good reliability and validity, which suggests that it is a useful tool for evaluation of autobiographical memory in Brazilian patients.