Nature Communications (Apr 2023)

Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients

  • Pei-Chen Tsai,
  • Tsung-Hua Lee,
  • Kun-Chi Kuo,
  • Fang-Yi Su,
  • Tsung-Lu Michael Lee,
  • Eliana Marostica,
  • Tomotaka Ugai,
  • Melissa Zhao,
  • Mai Chan Lau,
  • Juha P. Väyrynen,
  • Marios Giannakis,
  • Yasutoshi Takashima,
  • Seyed Mousavi Kahaki,
  • Kana Wu,
  • Mingyang Song,
  • Jeffrey A. Meyerhardt,
  • Andrew T. Chan,
  • Jung-Hsien Chiang,
  • Jonathan Nowak,
  • Shuji Ogino,
  • Kun-Hsing Yu

DOI
https://doi.org/10.1038/s41467-023-37179-4
Journal volume & issue
Vol. 14, no. 1
pp. 1 – 13

Abstract

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Abstract Histopathologic assessment is indispensable for diagnosing colorectal cancer (CRC). However, manual evaluation of the diseased tissues under the microscope cannot reliably inform patient prognosis or genomic variations crucial for treatment selections. To address these challenges, we develop the Multi-omics Multi-cohort Assessment (MOMA) platform, an explainable machine learning approach, to systematically identify and interpret the relationship between patients’ histologic patterns, multi-omics, and clinical profiles in three large patient cohorts (n = 1888). MOMA successfully predicts the overall survival, disease-free survival (log-rank test P-value<0.05), and copy number alterations of CRC patients. In addition, our approaches identify interpretable pathology patterns predictive of gene expression profiles, microsatellite instability status, and clinically actionable genetic alterations. We show that MOMA models are generalizable to multiple patient populations with different demographic compositions and pathology images collected from distinctive digitization methods. Our machine learning approaches provide clinically actionable predictions that could inform treatments for colorectal cancer patients.