A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells

In humans, more than 30,000 chimeric transcripts originating from 23,686 genes have been identified. The mechanisms and association of chimeric transcripts arising from chromosomal rearrangements with cancer are well established, but much remains unknown regarding the biogenesis and importance of other chimeric transcripts that arise from nongenomic alterations. Recently, a SLC45A3–ELK4 chimera has been shown to be androgen-regulated, and is overexpressed in metastatic or high-grade prostate tumors relative to local prostate cancers. Here, we characterize the expression of a KLK4 cis sense–antisense chimeric transcript, and show other examples in prostate cancer. Using non-protein-coding microarray analyses, we initially identified an androgen-regulated antisense transcript within the 3′ untranslated region of the KLK4 gene in LNCaP cells. The KLK4 cis-NAT was validated by strand-specific linker-mediated RT-PCR and Northern blotting. Characterization of the KLK4 cis-NAT by 5′ and 3′ rapid amplification of cDNA ends (RACE) revealed that this transcript forms multiple fusions with the KLK4 sense transcript. Lack of KLK4 antisense promoter activity using reporter assays suggests that these transcripts are unlikely to arise from a trans-splicing mechanism. 5′ RACE and analyses of deep sequencing data from LNCaP cells treated ±androgens revealed six high-confidence sense–antisense chimeras of which three were supported by the cDNA databases. In this study, we have shown complex gene expression at the KLK4 locus that might be a hallmark of cis sense–antisense chimeric transcription.

Narrative therapy for adults with major depressive disorder: Improved symptom and interpersonal outcomes

Abstract This study investigated depressive symptom and interpersonal relatedness outcomes from eight sessions of manualized narrative therapy for 47 adults with major depressive disorder. Post-therapy, depressive symptom improvement (d=1.36) and proportions of clients achieving reliable improvement (74%), movement to the functional population (61%), and clinically significant improvement (53%) were comparable to benchmark research outcomes. Post-therapy interpersonal relatedness improvement (d=.62) was less substantial than for symptoms. Three-month follow-up found maintenance of symptom, but not interpersonal gains. Benchmarking and clinical significance analyses mitigated repeated measure design limitations, providing empirical evidence to support narrative therapy for adults with major depressive disorder. RÉSUMÉ Cette étude a investigué les symptômes dépressifs et les relations interpersonnels d'une thérapie narrative en huit séances chez 47 adultes souffrant d'un trouble dépressif majeur. Après la thérapie, l'amélioration des symptômes dépressifs (d=1.36) et la proportion de clients atteignant un changement significatif (74%), le mouvement vers la population fonctionnelle (61%), enfin l'amélioration clinique significative (53%) étaient comparables aux performances des études de résultats. L'amélioration des relations interpersonnelles (d=0.62) était inférieure à l'amélioration symptomatique. Le suivi à trois mois montrait un maintien des gains symptomatiques mais pas pour les relations interpersonnelles. L’évaluation des performances et les analyses de significativité clinique modèrent les limitations du plan de recherche à mesures répétées et apportent une preuve empirique qui étaie l'efficacité des thérapies narratives pour des adultes avec un trouble dépressif majeur. Este estudo investigou sintomas depressivos e resultados interpessoais relacionados em oito sessões de terapia narrativa manualizada para 47 adultos com perturbação depressiva major. No pós terapia, melhoria de sintomas depressivos (d=1,36) e proporção de clientes que alcançam melhoria válida (74%), movimento para a população funcional (61%) e melhoria clinicamente significativa (53%) foram comparáveis com os resultados da investigação reportados. As melhorias pós terapia nos resultados interpessoais relacionados (d=.62) foi menos substancial do que para os sintomas. Aos três meses de seguimento houve a manutenção dos sintomas mas não dos ganhos interpessoais. As análises de benchemarking e de melhoria clinicamente significativas atenuam as limitações de um design de medidas repetidas, fornecendo evidência empírica para a terapia narrativa para adultos com perturbação depressiva major. Questo lavoro ha valutato i sintomi depressivi e gli outcome nella capacità di relazionarsi a livello interpersonale in 8 sedute di psicoterapia narrativa manualizzata in un gruppo di 47 adulti con depressione maggiore. I risultati ottenuti relativamente a: post terapy, miglioramento dei sintomi depressivi (d_1.36), proporzione di pazienti che hanno raggiunto un miglioramento affidabile e consistente (74%), movimento verso il funzionamento atteso nella popolazione (61%) e miglioramento clinicamente significativo (53%) sono paragonabili ai valori di riferimento della ricerca sull'outcome. I miglioramento della capacità di relazionarsi valutata alla fine del trattamento (d_.62) si è rivelata meno sostanziale rispetto ai sintomi. Un follow-up dopo 3 mesi ha dimostrato che il miglioramento sintomatologico è stato mantenuto, ma non quello degli obiettivi interpersonali. Valori di riferimento e analisi della significatività clinica hanno fatto fronte ai limiti del disegno a misure ripetute, offrendo prove empiriche sulla rilevanza della terapia narrativa in pazienti adulti con depressione maggiore

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

Expression of PSA-RP2, an alternatively spliced variant from the PSA gene, is increased in prostate cancer tissues but the protein is not secreted from prostate cancer cells

PSA-RP2 is a variant transcript expressed from the PSA gene that is conserved in gorillas, chimpanzees and humans suggesting a particular relevance for this transcript in these primates. We demonstrated by qRT-PCR that PSA-RP2 is upregulated in prostate cancer compared with benign prostatic hyperplasia tissues. The PSA-RP2 protein was not detected in seminal fluid and was cytoplasmically localised but not secreted from LNCaP or transfected PC3 prostate cells, despite secretion from transfected Cos-7 and HEK293 kidney cell lines. PSA-RP2-transfected PC3 cells showed slightly decreased proliferation and increased migration towards PC3-conditioned medium that could suggest a functional role in prostate cancer.

Myocyte enhancer factor 2C : an osteoblast transcription factor identified by DMSO enhanced mineralization

Rapid mineralization of cultured osteoblasts could be a useful characteristic in stem-cell mediated therapies for fracture and other orthopaedic problems. Dimethyl sulfoxide (DMSO) is a small amphipathic solvent molecule capable of simulating cell differentiation. We report that, in primary human osteoblasts, DMSO dose-dependently enhanced the expression of osteoblast differentiation markers alkaline phosphatase (ALP) activity and extracellular matrix mineralization. Furthermore, similar DMSO mediated mineralization enhancement was observed in primary osteoblast-like cells differentiated from mouse mesenchymal cells derived from fat, a promising source of starter cells for cell-based therapy. Using a convenient mouse pre-osteoblast model cell line MC3T3-E1 we further investigated this phenomenon showing that numerous osteoblast-expressed genes were elevated in response to DMSO treatment and correlated with enhanced mineralization. Myocyte enhancer factor 2c (Mef2c) was identified as the transcription factor most induced by DMSO, among numerous DMSO-induced genes, suggesting a role for Mef2c in osteoblast gene regulation. Immunohistochemistry confirmed expression of Mef2c in osteoblast-like cells in mouse mandible, cortical and trabecular bone. shRNAi-mediated Mef2c gene silencing resulted in defective osteoblast differentiation, decreased ALP activity and matrix mineralization and knockdown of osteoblast specific gene expression, including osteocalcin and bone sialoprotein. Flow on knockdown of bone specific transcription factors, Runx2 and osterix by shRNAi knockdown of Mef2c suggests that Mef2c lies upstream of these two important factors in the cascade of gene expression in osteoblasts.