2. Academic Validation
  3. Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells

Nanopore long-read RNA sequencing reveals functional alternative splicing variants in human vascular smooth muscle cells

  • Commun Biol. 2023 Oct 31;6(1):1104. doi: 10.1038/s42003-023-05481-y.
Hao Wu # 1 2,  Yicheng Lu # 2,  Zhenzhen Duan # 2,  Jingni Wu 2,  Minghui Lin 2,  Yangjun Wu 3,  Siyang Han 4,  Tongqi Li 4,  Yuqi Fan 5,  Xiaoyuan Hu 6,  Hongyan Xiao 7,  Jiaxuan Feng 8,  Zhiqian Lu 9,  Deping Kong 10,  Shengli Li 11
Affiliations

Affiliations

  • 1 Department of Cardiovascular Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
  • 2 Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
  • 3 Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
  • 4 Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
  • 5 North Cross School Shanghai, Shanghai, China.
  • 6 H. Milton Stewart School of Industrial and Systems Engineering, College of Engineering, Geogia Institute of Technology, Atlanta, GA, USA.
  • 7 Department of Cardiac Surgery, Wuhan Asia Heart Hospital, Wuhan University of Science and Technology, Wuhan, China.
  • 8 Department of Vascular Surgery and Intervention Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
  • 9 Department of Cardiovascular Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. 18930177678@163.com.
  • 10 Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. deping.kong@shsmu.edu.cn.
  • 11 Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. shengli.li@sjtu.edu.cn.
  • # Contributed equally.
PMID: 37907652 DOI: 10.1038/s42003-023-05481-y
Abstract

Vascular smooth muscle cells (VSMCs) are the major contributor to vascular repair and remodeling, which showed high level of phenotypic plasticity. Abnormalities in VSMC plasticity can lead to multiple cardiovascular diseases, wherein alternative splicing plays important roles. However, alternative splicing variants in VSMC plasticity are not fully understood. Here we systematically characterized the long-read transcriptome and their dysregulation in human aortic smooth muscle cells (HASMCs) by employing the Oxford Nanopore Technologies long-read RNA Sequencing in HASMCs that are separately treated with platelet-derived growth factor, transforming growth factor, and hsa-miR-221-3P transfection. Our analysis reveals frequent alternative splicing events and thousands of unannotated transcripts generated from alternative splicing. HASMCs treated with different factors exhibit distinct transcriptional reprogramming modulated by alternative splicing. We also found that unannotated transcripts produce different open reading frames compared to the annotated transcripts. Finally, we experimentally validated the unannotated transcript derived from gene CISD1, namely CISD1-u, which plays a role in the phenotypic switch of HASMCs. Our study characterizes the phenotypic modulation of HASMCs from an insight of long-read transcriptome, which would promote the understanding and the manipulation of HASMC plasticity in cardiovascular diseases.

Figures
Products