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Clinical challenges of tissue preparation for spatial transcriptome.

Xiaoxia Liu1, Yujia Jiang2,3, Dongli Song1,4

  • 1Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics, Zhongshan Hospital of Fudan University, Shanghai Engineering Research for AI Technology for Cardiopulmonary Diseases, Shanghai, China.

Clinical and Translational Medicine
|January 27, 2022
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Summary

Optimizing sample handling is crucial for high-quality spatial transcriptomics. Keeping human lung tissue samples dry and processed within 30 minutes significantly improves results for disease research.

Keywords:
clinical challengecritical factorspatial transcriptomicsspatiotemporal molecular imagespatiotemporal molecular medicine

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Area of Science:

  • Molecular Biology
  • Pathology
  • Bioinformatics

Background:

  • Spatial transcriptomics integrates molecular data with clinical imaging for spatiotemporal insights.
  • High-quality human sample preparation is essential for reliable spatial transcriptome data.
  • Understanding factors influencing spatial transcriptomics quality in lung cancer is critical.

Purpose of the Study:

  • To identify factors affecting spatial transcriptomics quality in lung, para-cancer, and normal tissues.
  • To assess the impact of clinical and pathological variables on RNA integrity and unique molecular identifier (UMI) counts.
  • To optimize clinical sample preparation for enhanced spatial transcriptome sequencing.

Main Methods:

  • Categorization of potential influencing factors: patient selection, pathology, surgery, sample harvest, preservation, transport, and storage.
  • Evaluation of histological scores, RNA integrity number (RIN), and unique molecular identifier (UMI) for quality assessment.
  • Analysis of sample isolation time and preservation conditions (e.g., 'dry' status).

Main Results:

  • No significant correlation found between histological scores, RIN, and UMI.
  • Sample isolation time and maintaining 'dry' conditions are critical for UMI and overall spatial transcriptomic quality.
  • Optimal temporary preservation in the operation room is within 30 minutes and in a 'dry' state.

Conclusions:

  • Clinical sample preparation procedures require standardization for reliable spatial transcriptomics.
  • Direct cryo-preservation in OCT media is recommended for human lung samples.
  • Optimized clinical spatial transcriptomics will advance spatiotemporal molecular imaging and disease mechanism understanding.