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<p>This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers—<i>ESR1</i>,<i> PGR</i>,<i> AR</i>,<i> MKI67</i>,<i> ERBB2</i>,<i> CD274</i>,<i> CDX2</i>,<i> KRT7</i>, and <i>KRT20</i>—were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman’s correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores. The results revealed strong correlations for most biomarkers, with coefficients ranging from 0.53 to 0.89. RNA-seq thresholds were confirmed across internal and external cohorts, demonstrating high diagnostic accuracy (up to 98%) and precision in identifying biomarker expression levels. The analysis also highlighted the influence of tumor microenvironment and purity, particularly in the moderate correlation of 0.63 observed for PD-L1. Our study demonstrates that RNA-seq can serve as a robust complementary tool to IHC, offering objective and high-throughput biomarker assessment. The RNA-seq thresholds established provide a reliable method for determining biomarker positivity, supporting the integration of RNA-seq in clinical diagnostics to enhance precision, especially where tumor purity and microenvironment factors are significant.</p>

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RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年8月2日

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  • Vladimir Kushnarev,
  • Danil Stupichev,
  • Suren Davitavyan,
  • Kirill Kriukov,
  • Basavaraja U. Shanthappa,
  • Anna Butusova,
  • Sofia Menshikova,
  • Anna Belozerova,
  • Anastasia Shvyrkova,
  • Arina Tkachuk,
  • Olga Khatenkova,
  • Linda Balabanian,
  • Ekaterina Postovalova,
  • Jochen K. Lennerz,
  • Funda Meric-Bernstam,
  • Alexander Bagaev

摘要

This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers—ESR1, PGR, AR, MKI67, ERBB2, CD274, CDX2, KRT7, and KRT20—were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman’s correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores. The results revealed strong correlations for most biomarkers, with coefficients ranging from 0.53 to 0.89. RNA-seq thresholds were confirmed across internal and external cohorts, demonstrating high diagnostic accuracy (up to 98%) and precision in identifying biomarker expression levels. The analysis also highlighted the influence of tumor microenvironment and purity, particularly in the moderate correlation of 0.63 observed for PD-L1. Our study demonstrates that RNA-seq can serve as a robust complementary tool to IHC, offering objective and high-throughput biomarker assessment. The RNA-seq thresholds established provide a reliable method for determining biomarker positivity, supporting the integration of RNA-seq in clinical diagnostics to enhance precision, especially where tumor purity and microenvironment factors are significant.