Spatial transcriptome analysis of long non-coding RNAs reveals tissue specificity and functional roles in cancer.

Kang XU; Xiyun Jin; Ya Luo; Haozhe Zou; Dezhong LV; Liping Wang; Limei FU; Yangyang Cai; Tingting Shao; Yongsheng LI; Juan XU

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Spatial transcriptome analysis of long non-coding RNAs reveals tissue specificity and functional roles in cancer.

Author: Kang XU ¹ ; Xiyun JIN ¹ ; Ya LUO ¹ ; Haozhe ZOU ¹ ; Dezhong LV ¹ ; Liping WANG ¹ ; Limei FU ¹ ; Yangyang CAI ¹ ; Tingting SHAO ¹ ; Yongsheng LI ² ; Juan XU ³
Author Information

1. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
2. Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China. xujuanbiocc@ems.hrbmu.edu.cn, liyongsheng@hainmc.edu.cn.
3. College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. xujuanbiocc@ems.hrbmu.edu.cn.
Publication Type:Journal Article
Keywords: Biomarker; Cancer; Long non-coding RNA; Spatial expression; Transcriptome
MeSH: Humans; Gene Expression Profiling; Neoplasms/genetics*; Organ Specificity; RNA, Long Noncoding/genetics*; Transcriptome
From: Journal of Zhejiang University. Science. B 2023;24(1):15-31
CountryChina
Language:English
Abstract: Long non-coding RNAs (lncRNAs) play a significant role in maintaining tissue morphology and functions, and their precise regulatory effectiveness is closely related to expression patterns. However, the spatial expression patterns of lncRNAs in humans are poorly characterized. Here, we constructed five comprehensive transcriptomic atlases of human lncRNAs covering thousands of major tissue samples in normal and disease states. The lncRNA transcriptomes exhibited high consistency within the same tissues across resources, and even higher complexity in specialized tissues. Tissue-elevated (TE) lncRNAs were identified in each resource and robust TE lncRNAs were refined by integrative analysis. We detected 1 to 4684 robust TE lncRNAs across tissues; the highest number was in testis tissue, followed by brain tissue. Functional analyses of TE lncRNAs indicated important roles in corresponding tissue-related pathways. Moreover, we found that the expression features of robust TE lncRNAs made them be effective biomarkers to distinguish tissues; TE lncRNAs also tended to be associated with cancer, and exhibited differential expression or were correlated with patient survival. In summary, spatial classification of lncRNAs is the starting point for elucidating the function of lncRNAs in both maintenance of tissue morphology and progress of tissue-constricted diseases.