GCN2 eIF2 kinase promotes prostate cancer by maintaining amino acid homeostasis

  1. Ricardo A Cordova
  2. Jagannath Misra
  3. Parth H Amin
  4. Anglea J Klunk
  5. Nur P Damayanti
  6. Kenneth R Carlson
  7. Andrew J Elmendorf
  8. Hyeong-Geug Kim
  9. Emily T Mirek
  10. Bennet D Elzey
  11. Marcus J Miller
  12. X Charlie Dong
  13. Liang Cheng
  14. Tracy G Anthony
  15. Robero Pili  Is a corresponding author
  16. Ronald C Wek  Is a corresponding author
  17. Kirk A Staschke  Is a corresponding author
  1. Indiana University, United States
  2. Rutgers, The State University of New Jersey, United States
  3. Purdue University West Lafayette, United States
  4. Indiana University School of Medicine, United States
  5. University at Buffalo, State University of New York, United States

Abstract

A stress adaptation pathway termed the integrated stress response has been suggested to be active in many cancers including prostate cancer (PCa). Here, we demonstrate that the eIF2 kinase GCN2 is required for sustained growth in androgen-sensitive and castration-resistant models of PCa both in vitro and in vivo, and is active in PCa patient samples. Using RNA-seq transcriptome analysis and a CRISPR-based phenotypic screen, GCN2 was shown to regulate expression of over 60 solute-carrier (SLC) genes, including those involved in amino acid transport and loss of GCN2 function reduces amino acid import and levels. Addition of essential amino acids or expression of 4F2 (SLC3A2) partially restored growth following loss of GCN2, suggesting that GCN2 targeting of SLC transporters is required for amino acid homeostasis needed to sustain tumor growth. A small molecule inhibitor of GCN2 showed robust in vivo efficacy in androgen-sensitive and castration-resistant mouse models of PCa, supporting its therapeutic potential for the treatment of PCa.

Data availability

The authors declare that all data generated or analyzed in this study are included in the published article, its supplementary information and source files, or are publicly available. The CHARGE-seq and RNA-seq datasets generated in this study have been deposited in the NCBI Gene Expression Omnibus (GEO) database under the ascension codes GSE196251 and GSE196252, respectively. The custom python script used in the analysis of our Charge-seq study is available on GitHub (https://github.com/carlsonkPhD/tRNA_Charge-Seq/). Gene expression data from prostate cancer patients (PRAD) in the TCGA database used for correlation analysis is publicly available.

The following data sets were generated

Article and author information

Author details

  1. Ricardo A Cordova

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  2. Jagannath Misra

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  3. Parth H Amin

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  4. Anglea J Klunk

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  5. Nur P Damayanti

    Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  6. Kenneth R Carlson

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  7. Andrew J Elmendorf

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  8. Hyeong-Geug Kim

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  9. Emily T Mirek

    Department of Nutritional Sciences, Rutgers, The State University of New Jersey, New Brunswick, United States
    Competing interests
    No competing interests declared.
  10. Bennet D Elzey

    5Department of Comparative Pathology, Purdue University West Lafayette, West Lafayette, United States
    Competing interests
    No competing interests declared.
  11. Marcus J Miller

    Indiana University School of Medicine, Indianapolis, United States
    Competing interests
    No competing interests declared.
  12. X Charlie Dong

    1Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  13. Liang Cheng

    Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, United States
    Competing interests
    No competing interests declared.
  14. Tracy G Anthony

    Department of Nutritional Sciences, Rutgers, The State University of New Jersey, New Brunswick, United States
    Competing interests
    Tracy G Anthony, is a consultant for HiberCell, Inc..
  15. Robero Pili

    Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, United States
    For correspondence
    rpili@buffalo.edu
    Competing interests
    No competing interests declared.
  16. Ronald C Wek

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    For correspondence
    rwek@iu.edu
    Competing interests
    Ronald C Wek, is a member of the advisory board and holds equity in HiberCell, Inc..
  17. Kirk A Staschke

    Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, United States
    For correspondence
    kastasch@iu.edu
    Competing interests
    Kirk A Staschke, is a consultant for HiberCell, Inc. and receives research support from HiberCell, Inc..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8722-9585

Funding

NIH Office of the Director (GM136331)

  • Ronald C Wek

NIH Office of the Director (DK109714)

  • Tracy G Anthony

National Cancer Institute (R21CA221942)

  • Robero Pili

Indiana University Melvin and Bren Simon Comprehensive Cancer Center (P30CA082709)

  • Kirk A Staschke

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All animal experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at Indiana University School of Medicine (Protocol #21014) and comply with all regulations for ethical conduct of animal research. Human prostate core needle biopsy specimens were obtained from the Indiana University Comprehensive Cancer Center Tissue Procurement and Distribution Core and approval was granted by the Institutional Review Board (IRB #1796) at the Office of Research Administration at Indiana University.

Reviewing Editor

  1. Nima Sharifi, Cleveland Clinic, United States

Publication history

  1. Received: June 15, 2022
  2. Accepted: September 14, 2022
  3. Accepted Manuscript published: September 15, 2022 (version 1)

Copyright

© 2022, Cordova et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 503
    Page views
  • 272
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ricardo A Cordova
  2. Jagannath Misra
  3. Parth H Amin
  4. Anglea J Klunk
  5. Nur P Damayanti
  6. Kenneth R Carlson
  7. Andrew J Elmendorf
  8. Hyeong-Geug Kim
  9. Emily T Mirek
  10. Bennet D Elzey
  11. Marcus J Miller
  12. X Charlie Dong
  13. Liang Cheng
  14. Tracy G Anthony
  15. Robero Pili
  16. Ronald C Wek
  17. Kirk A Staschke
(2022)
GCN2 eIF2 kinase promotes prostate cancer by maintaining amino acid homeostasis
eLife 11:e81083.
https://doi.org/10.7554/eLife.81083

Further reading

    1. Cancer Biology
    2. Computational and Systems Biology
    Pan Cheng, Xin Zhao ... Teresa Davoli
    Research Article

    How cells control gene expression is a fundamental question. The relative contribution of protein-level and RNA-level regulation to this process remains unclear. Here, we perform a proteogenomic analysis of tumors and untransformed cells containing somatic copy number alterations (SCNAs). By revealing how cells regulate RNA and protein abundances of genes with SCNAs, we provide insights into the rules of gene regulation. Protein complex genes have a strong protein-level regulation while non-complex genes have a strong RNA-level regulation. Notable exceptions are plasma membrane protein complex genes, which show a weak protein-level regulation and a stronger RNA-level regulation. Strikingly, we find a strong negative association between the degree of RNA-level and protein-level regulation across genes and cellular pathways. Moreover, genes participating in the same pathway show a similar degree of RNA- and protein-level regulation. Pathways including translation, splicing, RNA processing, and mitochondrial function show a stronger protein-level regulation while cell adhesion and migration pathways show a stronger RNA-level regulation. These results suggest that the evolution of gene regulation is shaped by functional constraints and that many cellular pathways tend to evolve one predominant mechanism of gene regulation at the protein level or at the RNA level.

    1. Cancer Biology
    2. Chromosomes and Gene Expression
    Arnaud Carrier, Cécile Desjobert ... Paola B Arimondo
    Research Article

    Aberrant DNA methylation is a well‑known feature of tumours and has been associated with metastatic melanoma. However, since melanoma cells are highly heterogeneous, it has been challenging to use affected genes to predict tumour aggressiveness, metastatic evolution, and patients' outcomes. We hypothesized that common aggressive hypermethylation signatures should emerge early in tumorigenesis and should be shared in aggressive cells, independent of the physiological context under which this trait arises. We compared paired melanoma cell lines with the following properties: (i) each pair comprises one aggressive counterpart and its parental cell line, and (ii) the aggressive cell lines were each obtained from different host and their environment (human, rat, and mouse), though starting from the same parent cell line. Next, we developed a multi-step genomic pipeline that combines the DNA methylome profile with a chromosome cluster-oriented analysis. A total of 229 differentially hypermethylated genes were commonly found in the aggressive cell lines. Genome localization analysis revealed hypermethylation peaks and clusters, identifying eight hypermethylated gene promoters for validation in tissues from melanoma patients. Five CpG identified in primary melanoma tissues were transformed into a DNA methylation score that can predict survival (Log-rank test, p=0.0008). This strategy is potentially universally applicable to other diseases involving DNA methylation alterations.