21 CHARACTERIZATION OF THE micro-RNA TRANSCRIPTOME IN LUNG TISSUES OF CLONED CALVES SUFFERING FROM RESPIRATORY DISTRESS SYNDROME

Abstract

Developmental deficiency leads to low survival rates of newborns, especially in cloned animals. Alveoli collapse leading to respiratory failure is one of the major causes of death in newborn cloned calves. The present study provides an insight into the expression pattern of micro-RNAs (miRNAs) in lung tissues and their role in the respiratory distress syndrome (RDS) in the cloned calves. Short RNA high-throughput sequencing and bioinformatic analysis from small RNA libraries created from collapsed lung tissues from 4 newborn cloned calves with RDS and normal lung tissues from 4 age-matched healthy individuals were implemented. Lung tissues were collected by dissection from newborns that died due to RDS and from healthy individuals on the first day after birth. RNA samples from the lung tissues were processed to generate small RNA libraries that were further used for deep sequencing. Expression profiles of surfactant-associated protein B (SPB), surfactant-associate protein C (SPC), and their key transcription regulator thyroid transcription factor-1 (TTF-1), which are responsible for stabilising alveolar surface, reducing surface tension, and thus preventing alveoli collapse, were verified through real-time RT-PCR, Western blot, and immunohistochemistry (IHC). Differentially expressed (DE) miRNAs were quantified by edgeR (empirical analysis of digital gene expression data in R), and their target genes were predicted by both TargetScan and miRanda software. Only miRNAs with P values <0.05 were considered statistically significant (Fisher exact test). Sequence analysis revealed the presence of 1592 and 1777 miRNAs in the RDS and healthy groups, respectively. A total of 326 miRNAs were DE between the two groups according to our criteria, of which 179 miRNAs were up-regulated and 147 were down-regulated in the RDS group. Gene ontological analysis showed that the DE miRNAs had a primary role in DNA-dependent regulation of transcription, cytoplasm biosynthesis, and nucleotide binding. Eleven miRNAs (bta-miR-186, bta-miR-2284x_R+1, bta-miR-24–3p_R-2, bta-miR-424–3p, bta-miR-592_L-1, bta-miR-660, bta-miR-150_R-1, bta-miR-2478_L-2, bta-miR-450b_R-1, bta-miR-134_L+2R-2 and bta-miR-326_R+1) were DE between the 2 groups and were predicted to target SPB, SPC, and TTF-1, respectively. Among these DE miRNAs, 5 miRNAs (bta-miR-134_L+2R-2, bta-miR-424–3p, bta-miR-660, bta-miR-2478_L-2, bta-miR-450b_R-1) were up-regulated in the RDS group. Western blot and IHC confirmed the down-regulation of SPB, SPC, and TTF-1 at the protein level in RDS group. This increase in abundance of miRNAs targeting key regulatory genes in lung of newborn cloned calves may take part in the dysregulation of alveolus development leading to alveoli collapse and RDS. The assay for target gene verification and analysis of gene transcription profile are under study.

Y. Liu and Y. Zhang contributed equally to this work. This project was supported by the National Natural Science Foundation of China (No. 31301977) and the National Nonprofit Institute Research Grant (No. 2011cj-11).