CircSERPINA3 regulates SERPINA3-mediated apoptosis, autophagy and aerobic glycolysis of prostate cancer cells by competitively binding to MiR-653-5p and recruiting BUD13

Background Prostate cancer (PCa) belongs to an epithelial malignancy that occurs in the prostate gland and is the most common malignancy of the male genitourinary system. Referring to related literature, circSERPINA3 has been reported to be up-regulated in PCa. However, its biological function remains unclear. Purpose This study aimed to reveal the specific role and relevant molecular mechanism of circSERPINA3 in PCa. Methods RT-qPCR was used to examine gene expression and functional analyses were conducted to verify the effect of circSERPINA3 on cell apoptosis, autophagy and aerobic glycolysis in PCa cells. Mechanism assays were applied to evaluate the relationship among circSERPINA3/miR-653-5p/SERPINA3/BUD13. Results CircSERPINA3 was verified to be up-regulated in PCa cells and to inhibit cell apoptosis while promoting aerobic glycolysis and autophagy in PCa cells. CircSERPINA3 and SERPINA3 were also testified to bind to miR-653-5p through a line of mechanism experiments. Moreover, it was discovered that circSERPINA3 could stabilize SERPINA3 mRNA via recruiting BUD13. Additionally, SERPINA3 was verified to inhibit cell apoptosis, while promoting aerobic glycolysis and autophagy in PCa cells. Conclusions Our study suggested that circSERPINA3 regulated apoptosis, autophagy and aerobic glycolysis of PCa cells by competitively binding to miR-653-5p and recruiting BUD13. Graphic abstract

Patterns of regulatory divergence and gene expression in hybrids are associated with molecular evolution in species undergoing gene flow

The extent to which hybridization disrupts a gene's pattern of expression likely governs its propensity for introgression, while its extent of molecular divergence can itself underlie such disruption. Together, these phenomena shape the landscape of sequence and transcriptional divergence across the genome as species diverge. To understand this process, we examine gene expression inheritance, regulatory and molecular divergences in the reproductive transcriptomes of species linked by gene flow. The fruit flies Anastrepha fraterculus and A. obliqua show evidence of gene flow despite clear evolutionary divergence and incomplete reproductive isolation. We find that their transcriptional patterns are a mosaic between those typically observed within and between allopatric species. Genes showing transgressive expression in hybrids or cis-regulatory divergence between species are associated with greater molecular divergence. This may reflect pleiotropic constraints that make them more resistant to gene flow or they may be more likely to experience divergent selection. However, while these highly divergent genes are likely to be important contributors to species differences, they are relatively rare. Instead, most differentially regulated genes, including those linked to reproduction, show high degrees of dominance in hybrids and trans-regulated divergence between species, suggesting widespread genetic compatibility that allowed for the identified introgression. These findings provide insights into how postzygotic isolating mechanisms might evolve in the presence of gene flow: regions showing cis-regulatory divergence or transgressive expression contribute to reproductive isolation, while regions with dominant expression and trans-regulatory divergence act as a buffer of hybrid breakdown, facilitating introgression, and leading to a genomic mosaic of expression and sequence divergence.

Gene Expression Analysis in Four Dogs With Canine Pemphigus Clinical Subtypes Reveals B Cell Signatures and Immune Activation Pathways Similar to Human Disease

Pemphigus is a group of autoimmune-mediated mucocutaneous blistering diseases characterized by acantholysis. Pemphigus has also been recognized in dogs and shares similar clinical characteristics and variants with human pemphigus. While relationships between human and canine pemphigus have been reported, gene expression patterns across species have not been described in the literature. We sought to perform gene expression analysis of lesional skin tissue from four dogs with various forms of pemphigus to examine gene expression during spontaneous disease in dogs. We found increased T and B cell signatures in canine pemphigus lesions compared to controls, as well as significant upregulation of CCL3, CCL4, CXCL10, and CXCL8 (IL8), among other genes. Similar chemokine/cytokine expression patterns and immune infiltrates have been reported in humans, suggesting that these genes play a role in spontaneous disease. Direct comparison of our dataset to previously published human pemphigus datasets revealed five conserved differentially expressed genes: CD19, WIF1, CXCL10, CD86, and S100A12. Our data expands our understanding of pemphigus and facilitates identification of biomarkers for prediction of disease prognosis and treatment response, which may be useful for future veterinary and human clinical trials.

Evolution of gene expression across species and specialized zooids in Siphonophora

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

Tissue-specific transcriptomics reveal functional differences in maize floral development

Flowers are produced by floral meristems, groups of stem cells that give rise to floral organs. In grasses, including the major cereal crops, flowers (florets) are contained in spikelets, which contain one to many florets, depending on the species. Importantly, not all grass florets are developmentally equivalent, and one or more florets are often sterile or abort in each spikelet. Members of the Andropogoneae tribe, including maize, produce spikelets with two florets; the upper and lower florets are usually dimorphic and the lower floret greatly reduced compared to the upper floret. In maize ears, early development appears identical in both florets but the lower floret ultimately aborts. To gain insight into the functional differences between florets of different fates, we used laser capture microdissection coupled with RNA-seq to globally examine gene expression in upper and lower floral meristems in maize. Differentially expressed genes were involved in hormone regulation, cell wall, sugar and energy homeostasis. Furthermore, cell wall modifications and sugar accumulation differed between the upper and lower florets. Finally, we identified a novel boundary domain between upper and lower florets, which we hypothesize is important for floral meristem activity. We propose a model in which growth is suppressed in the lower floret by limiting sugar availability and upregulating genes involved in growth repression. This growth repression module may also regulate floret fertility in other grasses and potentially be modulated to engineer more productive cereal crops.

Evaluation of blood gene expression levels in facioscapulohumeral muscular dystrophy patients

Facioscapulohumeral muscular dystrophy (FSHD) is caused by the expression of DUX4 in skeletal muscles. A number of therapeutic approaches are being developed to antagonize the events preceding and following DUX4 expression that leads to muscular dystrophy. Currently, the possibility to evaluate treatment response in clinical trials is hampered by the lack of objective molecular biomarkers connecting the disease cause to clinical performance. In this study we employed RNA-seq to examine gene expression in PAXgene tubes obtained from two independent cohorts of FSHD patients. Analysis of gene expression profiles did not lead to the identification of genes or pathways differentially expressed in FSHD patients, or associated with disease severity. In particular, we did not find evidence that the DUX4 and PAX7 signatures were differentially expressed. On the other hand, we were able to improve patient classification by including single genes or groups of genes in classification models. The best classifier was ROPN1L, a gene known to be expressed in testis, coincidentally the typical location of DUX4 expression. These improvements in patient classification hold the potential to enrich the FSHD clinical trial toolbox.

0024 PTSD with Concurrent Excessive Daytime Sleepiness Alters Gene Expression in Military Personnel and Veterans; An RNA-Sequencing Study

Introduction Up to 91% of military personnel and veterans with posttraumatic stress disorder (PTSD) report co-occurring sleep disturbances, including. insomnia and excessive daytime sleepiness (EDS). Sleep disturbances have been shown not only to increase the risk of developing PTSD, but to exacerbate and maintain PTSD symptomology. The aim of this study was to examine gene expression in active duty military personnel and veterans with PTSD, with and without EDS. Participants were categorized into three groups; 1) PTSD with EDS (PTSDwEDS; n=21), 2) PTSD without EDS (PTSDnoEDS; n=25), or 3) Controls (no PTSD and no EDS; n=57). Methods Participants were 79% male, mean age of 37.6years (SD=11.2years). PTSD symptoms were measured using the PTSD checklist for civilians (PCL-C); participants were classified as PTSD-present using DSM-IV-TR criteria of “moderate-to-severe”. Daytime sleepiness was assessed using the Epworth Sleepiness Scale (ESS), high sleepiness was indicated by an ESS score >13. We performed RNA-seq with Illumina’s HiSeq 2500 in paired-end. We conducted quality control using FastQC and aligned to GRCh38 reference genome using STAR (v2.5.3a). Differentially expressed genes identified using DESeq2 (v1.20.0) with False Discovery Rate of 0.10. Finally, Ingenuity Pathway Analysis (IPA) was conducted to identify dysregulated gene networks. Results Between the Controls and PTSDnoEDS groups, two genes were significantly dysregulated. In controls and PTSDwEDS groups, 251 genes were dysregulated. The IPA networks showed that genes associated with inflammation were significantly dysregulated. Finally, between PTSDwEDS and PTSDnoEDS there were 1,873 significantly dysregulated genes. The IPA networks identified dysregulation of genes related to sleep, fatigue, circadian, and mitochondrial function. Conclusion Taken together this data indicates that EDS that is co-morbidly experienced with PTSD is associated with significant gene dysregulation, above and beyond that observed in participants with PTSD without significant EDS and controls. Treating EDS in military personnel and veterans with PTSD is important. Support This work was supported by the Center for Neuroscience and Regenerative Medicine (CNRM)

The Drosophila Post-mating Response: Gene Expression and Behavioral Changes Reveal Perdurance and Variation in Cross-Tissue Interactions

Examining cross-tissue interactions is important for understanding physiology and homeostasis. In animals, the female gonad produces signaling molecules that act distally. We examine gene expression in Drosophila melanogaster female head tissues in 1) virgins without a germline compared to virgins with a germline, 2) post-mated females with and without a germline compared to virgins, and 3) post-mated females mated to males with and without a germline compared to virgins. In virgins, the absence of a female germline results in expression changes in genes with known roles in nutrient homeostasis. At one- and three-day(s) post-mating, genes that change expression are enriched with those that function in metabolic pathways, in all conditions. We systematically examine female post-mating impacts on sleep, food preference and re-mating, in the strains and time points used for gene expression analyses and compare to published studies. We show that post-mating, gene expression changes vary by strain, prompting us to examine variation in female re-mating. We perform a genome-wide association study that identifies several DNA polymorphisms, including four in/near Wnt signaling pathway genes. Together, these data reveal how gene expression and behavior in females are influenced by cross-tissue interactions, by examining the impact of mating, fertility, and genotype.

Development of 3D human kidney model using Urine-Derived Epithelial Cells and HUVECs

Background and Hypothesis: Development of realistic, scaffold-free 3D organoids/tubuloids such as renal-like tissue, can serve as models for study of renal drug toxicity/screening, tissue repair, and renal disease. Previous studies utilized urine-derived epithelial cells (UDEpCs) to create viable tubuloid structures suspended in 3D Matrigel, displaying renal epithelial gene expression and functionality. Alternatively, renal proximal tubule epithelial cells (PTECs) with HUVECs were co-cultured in a monolayer to improve the model. Therefore, we hypothesized that the addition of HUVECs will help to establish and optimize growth conditions of UDEpCs in a 3D environment. Experimental design: UDEpCs were isolated and co-cultured with tdTomatoHUVECs in Matrigel with different combinations of growth media. Cell growth and endothelial cell tube formation were examined daily. PTECs and tdTomatoHUVECs were also used to make spheroids in low-binding plates. Real-time PCR analysis was performed to examine gene expression for epithelial markers (ABCC4, PAX8), an endothelial marker (PECAM1), and TGF-β in spheroids. Results: A single cell-derived colony was isolated from human urine and was double positive for CD10 and CD13, two renal PTEC markers. Co-culture of UDEpCs and tdTomato-HUVECs in Matrigel dramatically increased the growth, survival, and tubuloid formation of both cell types, for up to 12 days. Total RNA from spheroids showed a decline over time in all conditions. Gene expression was decreased in co-culture conditions, but patterns of gene expression were maintained. Conclusions and Potential Impact: Future studies will examine gene expression in Matrigel cells, further optimize conditions for growth of UDEpCs, and perform functional assays, such as brush border enzyme activity. Improved methods to develop 3D kidney organoids/tubuloids will produce more accurate models for renal function studies. Developing a functional model mimicking in vivo processes can lead to new applications for creating novel therapies and treatment strategies.

A Portal to Visualize Transcriptome Profiles in Mouse Models of Neurological Disorders

Target nomination for drug development has been a major challenge in the path to finding a cure for several neurological disorders. Comprehensive transcriptome profiles have revealed brain gene expression changes associated with many neurological disorders, and the functional validation of these changes is a critical next step. Model organisms are a proven approach for the elucidation of disease mechanisms, including screening of gene candidates as therapeutic targets. Frequently, multiple models exist for a given disease, creating a challenge to select the optimal model for validation and functional follow-up. To help in nominating the best mouse models for studying neurological diseases, we developed a web portal to visualize mouse transcriptomic data related to neurological disorders: http://mmad.nrihub.org. Users can examine gene expression changes across mouse model studies to help select the optimal mouse model for further investigation. The portal provides access to mouse studies related to Alzheimer’s diseases (AD), Parkinson’s disease (PD), Huntington’s disease (HD), Amyotrophic Lateral Sclerosis (ALS), Spinocerebellar ataxia (SCA), and models related to aging.