Project description:Accurate embryo selection is vital for successful in vitro fertilization (IVF), but current morphological scoring methods are somewhat subjective and do not reflect molecular changes. This study employs ultra-sensitive Pandora sequencing to detect highly modified rsRNAs in culture media, aiming to identify molecular markers for non-invasive embryo quality assessment. Machine learning identified four candidate rsRNAs (5S, 5.8S, 28-1S, 28-2S) associated with embryo quality, with cross-validation demonstrating high predictive accuracy (AUC = 0.955). Quantitative RT-PCR further confirmed that 5.8S and 28-2S levels were significantly higher in the culture media of high-quality embryos. These findings suggest that specific rsRNAs could serve as non-invasive markers for embryo selection, offering new insights into rsRNA functions in embryo development.
2025-12-09 | GSE278434 | GEO
Project description:Saliva as a non-invasive specimen for COPD assessment
Project description:In this study, we investigated the changes in phosphorylation of proteins in urinary extracellular vesicles from dogs with invasive urothelial carcinoma compared to control dogs.
Project description:Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy and, low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR=8.42, CI=3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for the majority of disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.
Project description:Screening for urinary bladder cancer was performed in dogs in a breed (Scottish Terriers) with a very high inherited risk for bladder cancer. Naturally-occurring urothelial carcinoma in dogs serves as a relevant model for muscle invasive bladder cancer in humans. Urothelial carcinoma was detected in dogs with no outward evidence of the cancer. RNAseq data analyses were performed on these "early" tumors, and the sequencing files are included here. RNA-seq data from additional dogs has been deposited in the NCI Integrated Canine Data Commons (ICDC UBC02).
Project description:The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease influenced human evolution, we studied changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 was 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observed multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in several non-immune tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.
Project description:In dogs, a species for which markers of cell populations are often limiting, we sought to evaluate in an unbiased way the heterogeneity of cell subpopulations in the bronchoalveolar lavage fluid of healthy dogs, by single-cell RNA-sequencing.
