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Cross-cancer transcriptomic integration identifies a core immune-signaling network in hormone-driven malignancies

Prasanna Kumar Selvam1, Supraja Mohan1, Karthick Vasudevan1

  • 1Manipal Academy of Higher Education (MAHE), Manipal, India; Institute of Bioinformatics, International Technology Park, Bangalore, India.

Advances in Protein Chemistry and Structural Biology
|July 14, 2026
PubMed

Insights

This study found a shared immune-signaling transcriptional program in breast, ovarian, and thyroid cancers. Prostate cancer showed less overlap, suggesting distinct molecular drivers in hormone-driven malignancies.

Area of Science:

  • Genomics and Molecular Biology
  • Cancer Research
  • Endocrinology

Background:

  • Hormone-dependent cancers (breast, ovarian, thyroid, prostate) are driven by endocrine signaling but show molecular heterogeneity.
  • Understanding shared transcriptional programs across these cancers is crucial for developing targeted therapies.
  • Existing research has not fully elucidated conserved gene expression signatures in hormone-driven malignancies.

Purpose of the Study:

  • To identify conserved gene expression signatures across hormone-driven cancers using a systematic transcriptomic framework.
  • To investigate the degree of transcriptional overlap and directionality of gene dysregulation among breast, ovarian, thyroid, and prostate cancers.
  • To define a core pan-hormone transcriptional signature and analyze its functional characteristics.

Main Methods:

  • Applied a direction-aware transcriptomic framework to RNA-sequencing data from hormone-driven cancers and matched controls.
  • Performed differential gene expression analysis using DESeq2 for each cancer type.
  • Integrated differentially expressed genes (DEGs) across cancers using a presence-direction matrix and conducted leave-one-out sensitivity analysis.

Main Results:

  • Identified 15,648 significant DEGs across the four cancer types, with limited universal overlap (only one gene shared across all four).
  • Prostate cancer exhibited lower transcriptional concordance; excluding it revealed 10,948 shared DEGs across breast, ovarian, and thyroid cancers.
  • A core pan-hormone signature of 270 genes was defined for breast, ovarian, and thyroid cancers, enriched for immune signaling and cytokine-related functions.

Conclusions:

  • A conserved, immune-signaling-centric transcriptional program is shared among breast, ovarian, and thyroid cancers.
  • Prostate cancer displays distinct transcriptional patterns compared to the other hormone-dependent malignancies studied.
  • These findings highlight potential common therapeutic targets and underscore the importance of considering cancer-specific molecular profiles.
Keywords:
Breast cancerCross-cancer transcriptomicsHormone-dependent cancersOvarian cancerProstate cancerThyroid cancer

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