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<p>Over the past five decades, gene expression analysis has evolved from classical methods such as Northern blot and in situ hybridization to high-resolution sequencing techniques. For the first time, modern technologies, such as spatial transcriptomics, now allow the simultaneous analysis of histology and (sub-)cellular gene expression.</p><p>The aim of this work is to present the methodological development of gene expression analysis and to evaluate current platforms such as Visium HD, GeoMx, CosMx, and Xenium in terms of resolution, applicability, and challenges when analyzing FFPE and postmortem tissue.</p><p>Based on a&#xa0;literature review, classical and modern methods are compared, with a&#xa0;focus on cell type-specific and spatial expression patterns as well as RNA quality.</p><p>While traditional approaches mainly provide quantitative information, currently available technologies enable high-resolution mapping of gene expression down to a&#xa0;single-cell or subcellular level. However, RNA quality proves to be a&#xa0;critical factor for the reliability of analyses, especially in FFPE and postmortem samples. Spatial transcriptomics provides unprecedented insights into cellular interactions and molecular pathomechanisms. For valid results, standardized sample preparation, RNA quality control, and close collaboration with a (neuro-)pathologist are essential.</p>

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Ein halbes Jahrhundert Genexpressionsanalyse

  • 期刊论文

  • 发表日期：

    2026年4月14日

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  • Torben Redmer,
  • Josefine Radke,
  • Helena Radbruch

摘要

Over the past five decades, gene expression analysis has evolved from classical methods such as Northern blot and in situ hybridization to high-resolution sequencing techniques. For the first time, modern technologies, such as spatial transcriptomics, now allow the simultaneous analysis of histology and (sub-)cellular gene expression.

The aim of this work is to present the methodological development of gene expression analysis and to evaluate current platforms such as Visium HD, GeoMx, CosMx, and Xenium in terms of resolution, applicability, and challenges when analyzing FFPE and postmortem tissue.

Based on a literature review, classical and modern methods are compared, with a focus on cell type-specific and spatial expression patterns as well as RNA quality.

While traditional approaches mainly provide quantitative information, currently available technologies enable high-resolution mapping of gene expression down to a single-cell or subcellular level. However, RNA quality proves to be a critical factor for the reliability of analyses, especially in FFPE and postmortem samples. Spatial transcriptomics provides unprecedented insights into cellular interactions and molecular pathomechanisms. For valid results, standardized sample preparation, RNA quality control, and close collaboration with a (neuro-)pathologist are essential.