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Oncogenesis induced by combined Phf6 and Idh2 mutations through increased oncometabolites and impaired DNA repair

Oncogene volume 41, pages 1576–1588 (2022)Cite this article

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Abstract

The pathogenesis of acute leukemia involves interaction among genetic alterations. Mutations of IDH1/2 and PHF6 are common and co-exist in some patients of hematopoietic malignancies, but their cooperative effects remain unexplored. In this study, we addressed the question by characterizing the hematopoietic phenotypes of mice harboring neither, Phf6 knockout, Idh2 R172K, or combined mutations. We found that the combined Phf6KOIdh2R172K mice showed biased hematopoietic differentiation toward myeloid lineages and reduced long-term hematopoietic stem cells. They rapidly developed neoplasms of myeloid and lymphoid lineages, with much shorter survival compared with single mutated and wild-type mice. The marrow and spleen cells of the combined mutated mice produced a drastically increased amount of 2-hydroxyglutarate compared with mice harboring Idh2 R172K. Single-cell RNA sequencing revealed distinct patterns of transcriptome of the hematopoietic stem/progenitor cells from the combined mutated mice, including aberrant expression of metabolic enzymes, increased expression of several oncogenes, and impairment of DNA repairs, as confirmed by the enhanced γH2AX expression in the marrow and spleen cells. We conclude that Idh2 and Phf6 mutations are synergistic in leukemogenesis, at least through overproduction of 2-hydroxyglutarate and impairment of DNA repairs.

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Fig. 1: Combined Phf6KO and Idh2R172K resulted in chronic myelomonocytic leukemia-like phenotypes with marked cytopenia in vivo at 8–12 weeks.
Fig. 2: Combined Phf6KO and Idh2R172K mutations altered hematopoietic differentiation and reduced LT-HSC at 8–12 weeks.
Fig. 3: Early onset of hematopoietic neoplasms in the Phf6KOIdh2R172K mice.
Fig. 4: Drastic elevation of oncometabolites 2-HG resulted from higher expression of mutant Idh2R172K mRNA and protein in the Phf6KOIdh2R172K mice.
Fig. 5: Single-cell transcriptomic profiling of mice from four genotypes revealed altered hematopoiesis and expression of metabolic enzymes.
Fig. 6: Distinct transcriptional pattern of the HSC/MPP cluster in the Phf6KOIdh2R172K mice, compared with WT mice.
Fig. 7: Increased γH2AX in the young Phf6KOIdh2R172K mice.

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Acknowledgements

We thank the technical services provided by the Transgenic Mouse Model Core Facility of the National Core Facility Program for Biotechnology, Ministry of Science and Technology, the Animal Resources Laboratory of National Taiwan University Centers of Genomic and Precision Medicine, the Metabolomics Core Laboratory of National Taiwan University Center of Genomic Medicine, and the National Center for Genome Medicine. We thank the technical help from the Genomics Core Facility of the Institute of Molecular Biology, Academia Sinica. We would like to acknowledge the service provided by the Flow Cytometric Analyzing and Sorting Core Facilities at National Taiwan University Hospital and First Core Laboratory of National Taiwan University College of Medicine. The study was supported by research grants including TCVGH-1093702B, TCVGH-1103701B, Ministry of Science and Technology of Taiwan (MOST 106-2314-B-002-224-MY3, MOST 106-2314-B-002-152-, MOST 107-2314-B-075A-010-, MOST 108-2314-B-075A-007-, MOST 109-2314-B-002 −221- and MOST 109-2314-B-075A-008-MY2-), and Ministry of Health and Welfare (MOHW109-TDU-B-211-134009).

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Authors and Affiliations

  1. Division of Hematology/Medical Oncology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan

    Tsung-Chih Chen

  2. Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan

    Tsung-Chih Chen, Chi-Yuan Yao, Chang-Tsu Yuan, Chien-Chin Lin & Po-Han Chuang

  3. Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan

    Chi-Yuan Yao, Yu-Ren Chen, Chien-Chin Lin, Yueh-Chwen Hsu, Po-Han Chuang, Chein-Jun Kao & Wen-Chien Chou

  4. Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan

    Chang-Tsu Yuan & Wen-Chien Chou

  5. Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan

    Chang-Tsu Yuan

  6. Department of Animal Science, Chinese Culture University, Taipei, Taiwan

    Yi-Hung Li

  7. Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan

    Hsin-An Hou & Hwei-Fang Tien

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Contributions

T-CC, W-CC and H-FT wrote the paper, performed the experiments and analyzed the data. C-YY performed the bioinformatics analysis. Y-RC performed the animal experiments. C-TY interpreted the tissue sections. W-CC planned, designed, coordinated the research. C-CL, Y-CH, P-HC, C-JK, Y-HL and H-AH provided important materials and help in the study.

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Correspondence to Wen-Chien Chou.

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Chen, TC., Yao, CY., Chen, YR. et al. Oncogenesis induced by combined Phf6 and Idh2 mutations through increased oncometabolites and impaired DNA repair. Oncogene 41, 1576–1588 (2022). https://doi.org/10.1038/s41388-022-02193-1

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