A Metastatic Cancer Expression Generator (MetGen): A Generative Contrastive Learning Framework for Metastatic Cancer Generation

Zhentao Liu, Yu Chiao Chiu, Yidong Chen, Yufei Huang

Research output: Contribution to journalArticlepeer-review

Abstract

Despite significant advances in tumor biology and clinical therapeutics, metastasis remains the primary cause of cancer-related deaths. While RNA-seq technology has been used extensively to study metastatic cancer characteristics, challenges persist in acquiring adequate transcriptomic data. To overcome this challenge, we propose MetGen, a generative contrastive learning tool based on a deep learning model. MetGen generates synthetic metastatic cancer expression profiles using primary cancer and normal tissue expression data. Our results demonstrate that MetGen generates comparable samples to actual metastatic cancer samples, and the cancer and tissue classification yields performance rates of 99.8 ± 0.2% and 95.0 ± 2.3%, respectively. A benchmark analysis suggests that the proposed model outperforms traditional generative models such as the variational autoencoder. In metastatic subtype classification, our generated samples show 97.6% predicting power compared to true metastatic samples. Additionally, we demonstrate MetGen’s interpretability using metastatic prostate cancer and metastatic breast cancer. MetGen has learned highly relevant signatures in cancer, tissue, and tumor microenvironments, such as immune responses and the metastasis process, which can potentially foster a more comprehensive understanding of metastatic cancer biology. The development of MetGen represents a significant step toward the study of metastatic cancer biology by providing a generative model that identifies candidate therapeutic targets for the treatment of metastatic cancer.

Original languageEnglish (US)
Article number1653
JournalCancers
Volume16
Issue number9
DOIs
StatePublished - May 2024

Keywords

  • contrastive learning
  • deep learning
  • metastatic cancer
  • tumor microenvironment

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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