Konnaris, M. A. (+), Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Statistics, Penn State University, University Park, Pennsylvania, USA; Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, USA. Mouratidis, I. (*,+), Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA. Chantzi, N. (+), Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA. Chan, C. S.Y. (+), Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA. Montgomery A., Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA. Baltoumas F.A., Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari 16672 Greece. Pavlopoulos G.A., Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari 16672 Greece. Chartoumpekis D.V., Service of Endocrinology Diabetology and Metabolism Lausanne University Hospital Lausanne Switzerland. Georgakopoulos-Soares I. (*), Institute for Personalized Medicine Department of Biochemistry and Molecular Biology The Pennsylvania State University College of Medicine Hershey PA USA. * Corresponding authors +These authors contributed equally
Poster # 34
Despite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. The identification of the shortest species-specific nucleic sequences can provide insights into species evolution and can potentially have practical applications in agriculture, wildlife conservation, and healthcare. We propose a new method for sequence analysis termed nucleic "quasi-primes", the shortest occurring sequences in each of 45,785 organismal reference genomes present in one species and absent from every other examined genome. In the human genome, we find that the genomic loci of nucleic quasi-primes are most enriched for genes associated with brain development and cognitive function. In a single-cell case study focusing on the human primary motor cortex, nucleic quasi-prime genes account for 22.1% of the variation among the top 2000 selected genes based on average gene expression (p-value: 1.613 x 10-173. Effect size: 0.165). This further suggests that these genes may play an important role in distinguishing different cell types in the primary motor cortex. Gene set enrichment, gene ontology and KEGG analysis were conducted to highlight cell-type specific functional differences in differentially expressed quasi-prime genes (log 2-fold change > 2 and p-value < 0.05). Five non-neuronal cell-types (Astrocytes, Endothelial cells, Microglia, Oligodendrocytes, and Vascular and leptomeningeal cells) traditionally involved in maintaining the cellular environment for different regions of the brain to provide homeostatic regulation, protecting from injury and disease, and affecting neural transmission show significant differences among quasi-prime genes. Finally, disease ontology and DisGeNET analysis validate our findings of cognitive relationships and cancer associations. This analysis shows that the five cell-types mentioned have activated quasi-prime gene associations of neoplasms and cancers and suppressed quasi-prime gene associations of cognitive, mental, and developmental disorders. Somatostatin chondrolectin, an GABAergic interneuron, is also most associated with quasi-prime genes activating seizure related processes.
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