Singhal Richa, Lukose Rachel, Carr Gwenyth, Moktar Afsoon, Gonzales-Urday Ana Lucia, Rouchka Eric C, Vajravelu Bathri N
Department of Biochemistry and Molecular Genetics, KY IDeA Networks of Biomedical Research Excellence Bioinformatics Core, University of Louisville, Louisville, KY, United States.
Department of Physician Assistant Studies, Massachusetts College of Pharmacy and Health Sciences, Boston, MA, United States.
JMIR Bioinform Biotechnol. 2022 Jun 17;3(1):e33186. doi: 10.2196/33186.
Long noncoding RNAs (lncRNAs) are noncoding RNA transcripts greater than 200 nucleotides in length and are known to play a role in regulating the transcription of genes involved in vital cellular functions. We hypothesized the disease process in dysferlinopathy is linked to an aberrant expression of lncRNAs and messenger RNAs (mRNAs).
In this study, we compared the lncRNA and mRNA expression profiles between wild-type and dysferlin-deficient murine myoblasts (C2C12 cells).
LncRNA and mRNA expression profiling were performed using a microarray. Several lncRNAs with differential expression were validated using quantitative real-time polymerase chain reaction. Gene Ontology (GO) analysis was performed to understand the functional role of the differentially expressed mRNAs. Further bioinformatics analysis was used to explore the potential function, lncRNA-mRNA correlation, and potential targets of the differentially expressed lncRNAs.
We found 3195 lncRNAs and 1966 mRNAs that were differentially expressed. The chromosomal distribution of the differentially expressed lncRNAs and mRNAs was unequal, with chromosome 2 having the highest number of lncRNAs and chromosome 7 having the highest number of mRNAs that were differentially expressed. Pathway analysis of the differentially expressed genes indicated the involvement of several signaling pathways including PI3K-Akt, Hippo, and pathways regulating the pluripotency of stem cells. The differentially expressed genes were also enriched for the GO terms, developmental process and muscle system process. Network analysis identified 8 statistically significant (P<.05) network objects from the upregulated lncRNAs and 3 statistically significant network objects from the downregulated lncRNAs.
Our results thus far imply that dysferlinopathy is associated with an aberrant expression of multiple lncRNAs, many of which may have a specific function in the disease process. GO terms and network analysis suggest a muscle-specific role for these lncRNAs. To elucidate the specific roles of these abnormally expressed noncoding RNAs, further studies engineering their expression are required.
长链非编码RNA（lncRNA）是长度超过200个核苷酸的非编码RNA转录本，已知其在调节参与重要细胞功能的基因转录中发挥作用。我们推测肢带型肌营养不良症的疾病过程与lncRNA和信使RNA（mRNA）的异常表达有关。
在本研究中，我们比较了野生型和缺乏dysferlin的小鼠成肌细胞（C2C12细胞）之间的lncRNA和mRNA表达谱。
使用微阵列进行lncRNA和mRNA表达谱分析。使用定量实时聚合酶链反应验证了几种差异表达的lncRNA。进行基因本体（GO）分析以了解差异表达的mRNA的功能作用。进一步的生物信息学分析用于探索差异表达的lncRNA的潜在功能、lncRNA-mRNA相关性和潜在靶标。
我们发现了3195个差异表达的lncRNA和1966个差异表达的mRNA。差异表达的lncRNA和mRNA的染色体分布不均等，2号染色体上差异表达的lncRNA数量最多，7号染色体上差异表达的mRNA数量最多。差异表达基因的通路分析表明，包括PI3K-Akt、Hippo以及调节干细胞多能性的通路在内的几种信号通路参与其中。差异表达的基因在GO术语“发育过程”和“肌肉系统过程”中也富集。网络分析从上调的lncRNA中鉴定出8个具有统计学意义（P<0.05）的网络对象，从下调的lncRNA中鉴定出3个具有统计学意义的网络对象。
我们目前的结果表明，肢带型肌营养不良症与多种lncRNA的异常表达有关，其中许多可能在疾病过程中具有特定功能。GO术语和网络分析表明这些lncRNA具有肌肉特异性作用。为了阐明这些异常表达的非编码RNA的具体作用，需要进一步研究对其表达进行调控。
