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European Archives of Psychiatry and Clinical Neuroscience
Published in: European Archives of Psychiatry and Clinical Neuroscience 8/2023

03-04-2023 | Schizophrenia | Original Paper

Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case–control association study

Authors: Anirban Mukhopadhyay, Smita N. Deshpande, Triptish Bhatia, B. K. Thelma

Published in: European Archives of Psychiatry and Clinical Neuroscience | Issue 8/2023

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Abstract

Genetic etiology of schizophrenia is poorly understood despite large genome-wide association data. Long non-coding RNAs (lncRNAs) with a probable regulatory role are emerging as important players in neuro-psychiatric disorders including schizophrenia. Prioritising important lncRNAs and analyses of their holistic interaction with their target genes may provide insights into disease biology/etiology. Of the 3843 lncRNA SNPs reported in schizophrenia GWASs extracted using lincSNP 2.0, we prioritised n = 247 based on association strength, minor allele frequency and regulatory potential and mapped them to lncRNAs. lncRNAs were then prioritised based on their expression in brain using lncRBase, epigenetic role using 3D SNP and functional relevance to schizophrenia etiology. 18 SNPs were finally tested for association with schizophrenia (n = 930) and its endophenotypes—tardive dyskinesia (n = 176) and cognition (n = 565) using a case–control approach. Associated SNPs were characterised by ChIP seq, eQTL, and transcription factor binding site (TFBS) data using FeatSNP. Of the eight SNPs significantly associated, rs2072806 in lncRNA hsaLB_IO39983 with regulatory effect on BTN3A2 was associated with schizophrenia (p = 0.006); rs2710323 in hsaLB_IO_2331 with role in dysregulation of ITIH1 with tardive dyskinesia (p < 0.05); and four SNPs with significant cognition score reduction (p < 0.05) in cases. Two of these with two additional variants in eQTL were observed among controls (p < 0.05), acting likely as enhancer SNPs and/or altering TFBS of eQTL mapped downstream genes. This study highlights important lncRNAs in schizophrenia and provides a proof of concept of novel interactions of lncRNAs with protein-coding genes to elicit alterations in immune/inflammatory pathways of schizophrenia.
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Metadata
Title
Significance of an altered lncRNA landscape in schizophrenia and cognition: clues from a case–control association study
Authors
Anirban Mukhopadhyay
Smita N. Deshpande
Triptish Bhatia
B. K. Thelma
Publication date
03-04-2023
Publisher
Springer Berlin Heidelberg
Keyword
Schizophrenia
Published in
European Archives of Psychiatry and Clinical Neuroscience / Issue 8/2023
Print ISSN: 0940-1334
Electronic ISSN: 1433-8491
DOI
https://doi.org/10.1007/s00406-023-01596-9

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