All Publications

  • The AMBRA1 E3 ligase adaptor regulates the stability of cyclinD. Nature Chaikovsky, A. C., Li, C., Jeng, E. E., Loebell, S., Lee, M. C., Murray, C. W., Cheng, R., Demeter, J., Swaney, D. L., Chen, S., Newton, B. W., Johnson, J. R., Drainas, A. P., Shue, Y. T., Seoane, J. A., Srinivasan, P., He, A., Yoshida, A., Hipkins, S. Q., McCrea, E., Poltorack, C. D., Krogan, N. J., Diehl, J. A., Kong, C., Jackson, P. K., Curtis, C., Petrov, D. A., Bassik, M. C., Winslow, M. M., Sage, J. 2021


    The initiation of cell division integrates a large number of intra- and extracellular inputs. D-type cyclins (hereafter, cyclinD) couple these inputs to the initiation of DNA replication1. Increased levels of cyclinD promote cell division by activating cyclin-dependent kinases4 and 6 (hereafter, CDK4/6), which in turn phosphorylate and inactivate the retinoblastoma tumour suppressor. Accordingly, increased levels and activity of cyclinD-CDK4/6 complexes are strongly linked to unchecked cell proliferation and cancer2,3. However, the mechanisms that regulate levels of cyclinD are incompletely understood4,5. Here we show that autophagy and beclin1 regulator1 (AMBRA1) is the main regulator of the degradation of cyclinD. We identified AMBRA1 in a genome-wide screen to investigate the genetic basis of the response to CDK4/6 inhibition. Loss of AMBRA1 results in high levels of cyclinD in cells and in mice, which promotes proliferation and decreases sensitivity to CDK4/6 inhibition. Mechanistically, AMBRA1 mediates ubiquitylation and proteasomal degradation of cyclinD as a substrate receptor for the cullin4 E3 ligase complex. Loss of AMBRA1 enhances the growth of lung adenocarcinoma in a mouse model, and low levels of AMBRA1 correlate with worse survival in patients with lung adenocarcinoma. Thus, AMBRA1 regulates cellular levels of cyclinD, and contributes to cancer development and the response of cancer cells to CDK4/6 inhibitors.

    View details for DOI 10.1038/s41586-021-03474-7

    View details for PubMedID 33854239

  • The Long-Lost Ligase: CRL4AMBRA1 Regulates the Stability of D-Type Cyclins. DNA and cell biology Chaikovsky, A. C., Sage, J., Pagano, M., Simoneschi, D. 2021


    D-type cyclins (cyclin D1, D2, and D3, together cyclin D) are central drivers of the cell division cycle and well-described proto-oncoproteins. Rapid turnover of cyclin D is critical for its regulation, but the underlying mechanism has remained a matter of debate. Recently, AMBRA1 was identified as the major regulator of the stability of all three D-type cyclins. AMBRA1 serves as the substrate receptor for one of ∼40 CUL4-RING E3 ubiquitin ligase (CRL4) complexes to mediate the polyubiquitylation and subsequent degradation of cyclin D. Consequently, AMBRA1 regulates cell proliferation to impact tumor growth and the cellular response to cell cycle-targeted cancer therapies. Here we discuss the findings that implicate AMBRA1 as a core member of the cell cycle machinery.

    View details for DOI 10.1089/dna.2021.0659

    View details for PubMedID 34495753

  • RB1 deletion in RB-pathway disrupted cells results in DNA damage and cancer progression. Molecular and cellular biology Marshall, A. E., Roes, M. V., Passos, D. T., DeWeerd, M. C., Chaikovsky, A. C., Sage, J., Howlett, C. J., Dick, F. A. 2019


    Proliferative control in cancer cells is frequently disrupted by mutations in the RB-pathway. Intriguingly, RB1 mutations can arise late in tumorigenesis in cancer cells whose RB-pathway is already compromised by another mutation. In this study, we present evidence for increased DNA damage and instability in cancer cells with RB-pathway defects when RB1 mutations are induced. We generated isogenic RB1 mutant genotypes with CRISPR/Cas9 in a number of cell lines. Cells with even one mutant copy of RB1 have increased basal levels of DNA damage and increased mitotic errors. Elevated levels of reactive oxygen species as well as impaired homologous recombination repair underlie this DNA damage. When xenografted into immune compromised mice RB1 mutant cells exhibit an elevated propensity to seed new tumors in recipient lungs. This study offers evidence that late arising RB1 mutations can facilitate genome instability and cancer progression that are beyond the pre-existing proliferative control deficit.

    View details for DOI 10.1128/MCB.00105-19

    View details for PubMedID 31138663

  • E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family. Nature communications Hsu, J. n., Arand, J. n., Chaikovsky, A. n., Mooney, N. A., Demeter, J. n., Brison, C. M., Oliverio, R. n., Vogel, H. n., Rubin, S. M., Jackson, P. K., Sage, J. n. 2019; 10 (1): 2939


    E2F transcription factors are central regulators of cell division and cell fate decisions. E2F4 often represents the predominant E2F activity in cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. This role for E2F4 is independent of the RB family. Furthermore, E2F4 functionally interacts with chromatin regulators associated with gene activation and we observed decreased histone acetylation at the promoters of cell cycle genes and E2F targets upon loss of E2F4 in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that provide insights into the biology of rapidly dividing cells.

    View details for DOI 10.1038/s41467-019-10901-x

    View details for PubMedID 31270324

  • Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin CANCER DISCOVERY Yang, D., Denny, S. K., Greenside, P. G., Chaikovsky, A. C., Brady, J. J., Ouadah, Y., Granja, J. M., Jahchan, N. S., Lim, J., Kwok, S., Kong, C. S., Berghoff, A. S., Schmitt, A., Reinhardt, H., Park, K., Preusser, M., Kundaje, A., Greenleaf, W. J., Sage, J., Winslow, M. M. 2018; 8 (10): 1316–31
  • Beyond the Cell Cycle: Enhancing the Immune Surveillance of Tumors Via CDK4/6 Inhibition MOLECULAR CANCER RESEARCH Chaikovsky, A. C., Sage, J. 2018; 16 (10): 1454-1457
  • Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. Cancer discovery Yang, D., Denny, S. K., Greenside, P. G., Chaikovsky, A. C., Brady, J. J., Ouadah, Y., Granja, J. M., Jahchan, N. S., Lim, J. S., Kwok, S., Kong, C. S., Berghoff, A. S., Schmitt, A., Reinhardt, H. C., Park, K., Preusser, M., Kundaje, A., Greenleaf, W. J., Sage, J., Winslow, M. M. 2018


    The extent to which early events shape tumor evolution is largely uncharacterized, even though a better understanding of these early events may help identify key vulnerabilities in advanced tumors. Here, using genetically defined mouse models of small cell lung cancer (SCLC), we uncovered distinct metastatic programs attributable to the cell type of origin. In one model, tumors gain metastatic ability through amplification of the transcription factor NFIB and a widespread increase in chromatin accessibility, whereas in the other model, tumors become metastatic in the absence of NFIB-driven chromatin alterations. Gene-expression and chromatin accessibility analyses identify distinct mechanisms as well as markers predictive of metastatic progression in both groups. Underlying the difference between the two programs was the cell type of origin of the tumors, with NFIB-independent metastases arising from mature neuroendocrine cells. Our findings underscore the importance of the identity of cell type of origin in influencing tumor evolution and metastatic mechanisms.SIGNIFICANCE: We show that SCLC can arise from different cell types of origin, which profoundly influences the eventual genetic and epigenetic changes that enable metastatic progression. Understanding intertumoral heterogeneity in SCLC, and across cancer types, may illuminate mechanisms of tumor progression and uncover how the cell type of origin affects tumor evolution. Cancer Discov; 8(10); 1-16. ©2018 AACR.See related commentary by Pozo et al., p. 1216.

    View details for PubMedID 30228179



    Inhibitors of the cyclin-dependent kinases 4 and 6 (CDK4/6) were originally designed to block proliferation and cell cycle progression of cancer cells in which the activity of these kinases is dysregulated. CDK4/6 inhibitors have already been FDA-approved for the treatment of estrogen receptor (ER)-positive breast cancer and are being tested in numerous other cancer types. However, several recent studies have identified novel effects of CDK4/6 inhibitors on tumor growth, most notably an indirect effect resulting from the activation of immune surveillance. This Perspective discusses these recent observations, including the effects that CDK4/6 inhibitors may have on immune cells themselves. It is likely that CDK4/6 inhibitors will have a broader impact than their expected induction of cell cycle arrest in the treatment of human cancers.

    View details for PubMedID 29934327