The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia PatientsResearch in Context
Tian Tian,
Zhi Wei,
Xiao Chang,
Yichuan Liu,
Raquel E. Gur,
Patrick M.A. Sleiman,
Hakon Hakonarson
Affiliations
Tian Tian
Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA
Zhi Wei
Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA; Corresponding author at: Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA.
Xiao Chang
Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Yichuan Liu
Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Raquel E. Gur
Neuropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Patrick M.A. Sleiman
Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Hakon Hakonarson
Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Correspondence to: Hakon Hakonarson Center for Applied Genomics, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, Pennsylvania 19104, USA.
To date, most transcriptome studies of schizophrenia focus on the analysis of protein-coding genes. Long noncoding RNAs (lncRNAs) are emerging as key tissue-specific regulators of cellular and disease processes. The amygdala brain region has been implicated in the pathophysiology of schizophrenia. We performed unbiased whole transcriptome profiling of amygdala tissues from 22 schizophrenia patients and 24 non-psychiatric controls using RNA-seq. We reconstructed amygdala transcriptome and employed systems biology approaches to annotating the functional roles of lncRNAs. As a result, we identified 839 novel lncRNAs in amygdala. We found in amygdala lncRNAs are more subtype-specific than protein-coding genes. We identified functional modules associated with “synaptic transmission”, “ribosome”, and “immune responses” which were related to schizophrenia pathophysiology that involved lncRNAs. Integrative functional analyses associating individual lncRNAs with specific pathways and functions further show that amygdala lncRNAs are connected with all of these pathways. Our study presents the first systematic landscape of lncRNAs in amygdala tissue from schizophrenia cases. Keywords: Schizophrenia, Next-generation sequencing, Transcriptome, Systems biology