University of Pennsylvania (Doctor of Philosophy) 2010 Cancer Biology
Fudan University, Shanghai, China (Bachelor of Science) 2004 Biological Science

Research Experience

2016.9-present Assistant Professor
Department of Radiation Oncology, Stanford University
Research interests: The interaction between metabolic stress and chromatin remodeling.

2011-2016 Research Scholar
Memorial Sloan Kettering Cancer Center
Laboratory of Craig B. Thompson, M.D.
Research interests: Serine and one-carbon unit metabolism in cancer; Nutrient-sensing mechanisms in mammalian cells.

2010-2011 Postdoctoral Fellow
Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Laboratory of Craig B. Thompson, M.D.

2005-2010 Graduate Student
Department of Cancer Biology, Wake Forest University (2005-2006) and Department of Radiation Oncology, University of Pennsylvania School of Medicine (2006-2010), Laboratory of Constantinos Koumenis, Ph.D

Administrative Appointments

  • Affiliated Faculty, Stanford Bio-X (2016 - Present)
  • Member, The Child Health Research Institute (CHRI) at Stanford (2016 - Present)
  • Member, The American Association for the Advancement of Science (2016 - Present)
  • Member, Cancer Epigenetics Society (2017 - Present)
  • Associate Member, Canary Center at Stanford for Cancer Early Detection (2018 - Present)
  • Member, American Association of Cancer Research (2018 - Present)

Research & Scholarship

Current Research and Scholarly Interests

One hallmark of cancer is that malignant cells modulate metabolic pathways to promote cancer progression. My professional interest is to investigate the causes and consequences of the abnormal metabolic phenotypes of cancer cells in response to microenvironmental stresses such as hypoxia and nutrient deprivation, with the prospect that therapeutic approaches might be developed to target these metabolic pathways to improve cancer treatment.


2019-20 Courses

Stanford Advisees

  • Doctoral Dissertation Reader (AC)
    David Armenta
  • Postdoctoral Faculty Sponsor
    Haowen Jiang
  • Doctoral Dissertation Advisor (AC)
    Albert Li

Graduate and Fellowship Programs


All Publications

  • ATF4 couples MYC-dependent translational activity to bioenergetic demands during tumour progression. Nature cell biology Tameire, F., Verginadis, I. I., Leli, N. M., Polte, C., Conn, C. S., Ojha, R., Salas Salinas, C., Chinga, F., Monroy, A. M., Fu, W., Wang, P., Kossenkov, A., Ye, J., Amaravadi, R. K., Ignatova, Z., Fuchs, S. Y., Diehl, J. A., Ruggero, D., Koumenis, C. 2019; 21 (7): 889?99


    The c-Myc oncogene drives malignant progression and induces robust anabolic and proliferative programmes leading to intrinsic stress. The mechanisms enabling adaptation to MYC-induced stress are not fully understood. Here we reveal an essential role for activating transcription factor 4 (ATF4) in survival following MYC activation. MYC upregulates ATF4 by activating general control nonderepressible 2 (GCN2) kinase through uncharged transfer RNAs. Subsequently, ATF4 co-occupies promoter regions of over 30 MYC-target genes, primarily those regulating amino acid and protein synthesis, including eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1), a negative regulator of translation. 4E-BP1 relieves MYC-induced proteotoxic stress and is essential to balance protein synthesis. 4E-BP1 activity is negatively regulated by mammalian target of rapamycin complex 1 (mTORC1)-dependent phosphorylation and inhibition of mTORC1 signalling rescues ATF4-deficient cells from MYC-induced endoplasmic reticulum stress. Acute deletion of ATF4 significantly delays MYC-driven tumour progression and increases survival in mouse models. Our results establish ATF4 as a cellular rheostat of MYC activity, which ensures that enhanced translation rates are compatible with survival and tumour progression.

    View details for DOI 10.1038/s41556-019-0347-9

    View details for PubMedID 31263264

  • p53 Suppresses Metabolic Stress-Induced Ferroptosis in Cancer Cells CELL REPORTS Tarangelo, A., Magtanong, L., Bieging-Rolett, K. T., Li, Y., Ye, J., Attardi, L. D., Dixon, S. J. 2018; 22 (3): 569?75


    How cancer cells respond to nutrient deprivation remains poorly understood. In certain cancer cells, deprivation of cystine induces a non-apoptotic, iron-dependent form of cell death termed ferroptosis. Recent evidence suggests that ferroptosis sensitivity may be modulated by the stress-responsive transcription factor and canonical tumor suppressor protein p53. Using CRISPR/Cas9 genome editing, small-molecule probes, and high-resolution, time-lapse imaging, we find that stabilization of wild-type p53 delays the onset of ferroptosis in response to cystine deprivation. This delay requires the p53 transcriptional target CDKN1A (encoding p21) and is associated with both slower depletion of intracellular glutathione and a reduced accumulation of toxic lipid-reactive oxygen species (ROS). Thus, the p53-p21 axis may help cancer cells cope with metabolic stress induced by cystine deprivation by delaying the onset of non-apoptotic cell death.

    View details for PubMedID 29346757

  • GCN2 sustains mTORC1 suppression upon amino acid deprivation by inducing Sestrin2 GENES & DEVELOPMENT Ye, J., Palm, W., Peng, M., King, B., Lindsten, T., Li, M. O., Koumenis, C., Thompson, C. B. 2015; 29 (22): 2331-2336


    Mammalian cells possess two amino acid-sensing kinases: general control nonderepressible 2 (GCN2) and mechanistic target of rapamycin complex 1 (mTORC1). Their combined effects orchestrate cellular adaptation to amino acid levels, but how their activities are coordinated remains poorly understood. Here, we demonstrate an important link between GCN2 and mTORC1 signaling. Upon deprivation of various amino acids, activated GCN2 up-regulates ATF4 to induce expression of the stress response protein Sestrin2, which is required to sustain repression of mTORC1 by blocking its lysosomal localization. Moreover, Sestrin2 induction is necessary for cell survival during glutamine deprivation, indicating that Sestrin2 is a critical effector of GCN2 signaling that regulates amino acid homeostasis through mTORC1 suppression.

    View details for DOI 10.1101/gad.269324.115

    View details for Web of Science ID 000365333700002

    View details for PubMedID 26543160

  • Translational Upregulation of an Individual p21(Cip1) Transcript Variant by GCN2 Regulates Cell Proliferation and Survival under Nutrient Stress PLOS GENETICS Lehman, S. L., Cerniglia, G. J., Johannes, G. J., Ye, J., Ryeom, S., Koumenis, C. 2015; 11 (6)


    Multiple transcripts encode for the cell cycle inhibitor p21(Cip1). These transcripts produce identical proteins but differ in their 5' untranslated regions (UTRs). Although several stresses that induce p21 have been characterized, the mechanisms regulating the individual transcript variants and their functional significance are unknown. Here we demonstrate through (35)S labeling, luciferase reporter assays, and polysome transcript profiling that activation of the Integrated Stress Response (ISR) kinase GCN2 selectively upregulates the translation of a p21 transcript variant containing 5' upstream open reading frames (uORFs) through phosphorylation of the eukaryotic translation initiation factor eIF2?. Mutational analysis reveals that the uORFs suppress translation under basal conditions, but promote translation under stress. Functionally, ablation of p21 ameliorates G1/S arrest and reduces cell survival in response to GCN2 activation. These findings uncover a novel mechanism of p21 post-transcriptional regulation, offer functional significance for the existence of multiple p21 transcripts, and support a key role for GCN2 in regulating the cell cycle under stress.

    View details for DOI 10.1371/journal.pgen.1005212

    View details for Web of Science ID 000357341600006

    View details for PubMedID 26102367

  • Serine Catabolism Regulates Mitochondrial Redox Control during Hypoxia CANCER DISCOVERY Ye, J., Fan, J., Venneti, S., Wan, Y., Pawel, B. R., Zhang, J., Finley, L. W., Lu, C., Lindsten, T., Cross, J. R., Qing, G., Liu, Z., Simon, M. C., Rabinowitz, J. D., Thompson, C. B. 2014; 4 (12): 1406-1417


    The de novo synthesis of the nonessential amino acid serine is often upregulated in cancer. In this study, we demonstrate that the serine catabolic enzyme, mitochondrial serine hydroxymethyltransferase (SHMT2), is induced when MYC-transformed cells are subjected to hypoxia. In mitochondria, SHMT2 can initiate the degradation of serine to CO2 and NH4+, resulting in net production of NADPH from NADP+. Knockdown of SHMT2 in MYC-dependent cells reduced cellular NADPH:NADP+ ratio, increased cellular reactive oxygen species, and triggered hypoxia-induced cell death. In vivo, SHMT2 suppression led to impaired tumor growth. In MYC-amplified neuroblastoma patient samples, there was a significant correlation between SHMT2 and hypoxia-inducible factor-1 ? (HIF1?), and SHMT2 expression correlated with unfavorable patient prognosis. Together, these data demonstrate that mitochondrial serine catabolism supports tumor growth by maintaining mitochondrial redox balance and cell survival.In this study, we demonstrate that the mitochondrial enzyme SHMT2 is induced upon hypoxic stress and is critical for maintaining NADPH production and redox balance to support tumor cell survival and growth.

    View details for DOI 10.1158/2159-8290.CD-14-0250

    View details for Web of Science ID 000346501900025

    View details for PubMedID 25186948

  • Quantitative flux analysis reveals folate-dependent NADPH production (vol 510, pg 298, 2014) NATURE Fan, J., Ye, J., Kamphorst, J. J., Shlomi, T., Thompson, C. B., Rabinowitz, J. D. 2014; 513 (7519): 574-574
  • Induction of sarcomas by mutant IDH2 GENES & DEVELOPMENT Lu, C., Venneti, S., Akalin, A., Fang, F., Ward, P. S., DeMatteo, R. G., Intlekofer, A. M., Chen, C., Ye, J., Hameed, M., Nafa, K., Agaram, N. P., Cross, J. R., Khanin, R., Mason, C. E., Healey, J. H., Lowe, S. W., Schwartz, G. K., Melnick, A., Thompson, C. B. 2013; 27 (18): 1986-1998


    More than 50% of patients with chondrosarcomas exhibit gain-of-function mutations in either isocitrate dehydrogenase 1 (IDH1) or IDH2. In this study, we performed genome-wide CpG methylation sequencing of chondrosarcoma biopsies and found that IDH mutations were associated with DNA hypermethylation at CpG islands but not other genomic regions. Regions of CpG island hypermethylation were enriched for genes implicated in stem cell maintenance/differentiation and lineage specification. In murine 10T1/2 mesenchymal progenitor cells, expression of mutant IDH2 led to DNA hypermethylation and an impairment in differentiation that could be reversed by treatment with DNA-hypomethylating agents. Introduction of mutant IDH2 also induced loss of contact inhibition and generated undifferentiated sarcomas in vivo. The oncogenic potential of mutant IDH2 correlated with the ability to produce 2-hydroxyglutarate. Together, these data demonstrate that neomorphic IDH2 mutations can be oncogenic in mesenchymal cells.

    View details for DOI 10.1101/gad.226753.113

    View details for Web of Science ID 000324872100004

    View details for PubMedID 24065766

  • SnapShot: Cancer Metabolism Pathways CELL METABOLISM Finley, L. W., Zhang, J., Ye, J., Ward, P. S., Thompson, C. B. 2013; 17 (3): 466-?

    View details for DOI 10.1016/j.cmet.2013.02.016

    View details for Web of Science ID 000326265400018

    View details for PubMedID 23473039

  • Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ye, J., Mancuso, A., Tong, X., Ward, P. S., Fan, J., Rabinowitz, J. D., Thompson, C. B. 2012; 109 (18): 6904-6909


    Despite the fact that most cancer cells display high glycolytic activity, cancer cells selectively express the less active M2 isoform of pyruvate kinase (PKM2). Here we demonstrate that PKM2 expression makes a critical regulatory contribution to the serine synthetic pathway. In the absence of serine, an allosteric activator of PKM2, glycolytic efflux to lactate is significantly reduced in PKM2-expressing cells. This inhibition of PKM2 results in the accumulation of glycolytic intermediates that feed into serine synthesis. As a consequence, PKM2-expressing cells can maintain mammalian target of rapamycin complex 1 activity and proliferate in serine-depleted medium, but PKM1-expressing cells cannot. Cellular detection of serine depletion depends on general control nonderepressible 2 kinase-activating transcription factor 4 (GCN2-ATF4) pathway activation and results in increased expression of enzymes required for serine synthesis from the accumulating glycolytic precursors. These findings suggest that tumor cells use serine-dependent regulation of PKM2 and GCN2 to modulate the flux of glycolytic intermediates in support of cell proliferation.

    View details for DOI 10.1073/pnas.1204176109

    View details for Web of Science ID 000303602100035

    View details for PubMedID 22509023

  • Modulation of CCAAT/Enhancer Binding Protein Homologous Protein (CHOP)-dependent DR5 Expression by Nelfinavir Sensitizes Glioblastoma Multiforme Cells to Tumor Necrosis Factor-related Apoptosis-inducing Ligand (TRAIL) JOURNAL OF BIOLOGICAL CHEMISTRY Tian, X., Ye, J., Alonso-Basanta, M., Hahn, S. M., Koumenis, C., Dorsey, J. F. 2011; 286 (33): 29408-29416


    Human glioblastoma multiforme cells demonstrate varying levels of sensitivity to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis. Endoplasmic reticulum (ER) stress has been shown to trigger cell death through apoptosis. We therefore pursued a strategy of integrating clinically relevant investigational agents that cooperate mechanistically through the regulation of ER stress and apoptosis pathways. Nelfinavir belongs to the protease inhibitor class of drugs currently used to treat patients with HIV and is in clinical trials as an anti-tumor agent. We found that Nelfinavir treatment led to ER stress-induced up-regulation of the DR5 receptor. This transactivation was mediated by the transcription factor CCAAT/enhancer binding protein homologous protein (CHOP). We also determined that ER stress-induced ATF4 up-regulation was responsible for modulation of CHOP. In contrast, DR4 receptor expression was unchanged by Nelfinavir treatment. Combining Nelfinavir with TRAIL led to a significantly enhanced level of apoptosis that was abrogated by siRNA silencing of DR5. We provide evidence that Nelfinavir-induced ER stress modulates DR5 expression in human glioblastoma multiforme cells and can enhance TRAIL efficacy. These studies provide a potential mechanistic rationale for the use of the Food and Drug Administration-approved agent Nelfinavir in combination with DR5 agonists to induce apoptosis in human malignancies.

    View details for DOI 10.1074/jbc.M110.197665

    View details for Web of Science ID 000293837000075

    View details for PubMedID 21697087

  • PERK promotes cancer cell proliferation and tumor growth by limiting oxidative DNA damage ONCOGENE Bobrovnikova-Marjon, E., Grigoriadou, C., Pytel, D., Zhang, F., Ye, J., Koumenis, C., Cavener, D., Diehl, J. A. 2010; 29 (27): 3881-3895


    To proliferate and expand in an environment with limited nutrients, cancer cells co-opt cellular regulatory pathways that facilitate adaptation and thereby maintain tumor growth and survival potential. The endoplasmic reticulum (ER) is uniquely positioned to sense nutrient deprivation stress and subsequently engage signaling pathways that promote adaptive strategies. As such, components of the ER stress-signaling pathway represent potential antineoplastic targets. However, recent investigations into the role of the ER resident protein kinase, RNA-dependent protein kinase (PKR)-like ER kinase (PERK) have paradoxically suggested both pro- and anti-tumorigenic properties. We have used animal models of mammary carcinoma to interrogate the contribution of PERK in the neoplastic process. The ablation of PERK in tumor cells resulted in impaired regeneration of intracellular antioxidants and accumulation of reactive oxygen species triggering oxidative DNA damage. Ultimately, PERK deficiency impeded progression through the cell cycle because of the activation of the DNA damage checkpoint. Our data reveal that PERK-dependent signaling is used during both tumor initiation and expansion to maintain redox homeostasis, thereby facilitating tumor growth.

    View details for DOI 10.1038/onc.2010.153

    View details for Web of Science ID 000279603200002

    View details for PubMedID 20453876

  • The GCN2-ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation EMBO JOURNAL Ye, J., Kumanova, M., Hart, L. S., Sloane, K., Zhang, H., De Panis, D. N., Bobrovnikova-Marjon, E., Diehl, J. A., Ron, D., Koumenis, C. 2010; 29 (12): 2082-2096


    The transcription factor ATF4 regulates the expression of genes involved in amino acid metabolism, redox homeostasis and ER stress responses, and it is overexpressed in human solid tumours, suggesting that it has an important function in tumour progression. Here, we report that inhibition of ATF4 expression blocked proliferation and survival of transformed cells, despite an initial activation of cytoprotective macroautophagy. Knockdown of ATF4 significantly reduced the levels of asparagine synthetase (ASNS) and overexpression of ASNS or supplementation of asparagine in trans, reversed the proliferation block and increased survival in ATF4 knockdown cells. Both amino acid and glucose deprivation, stresses found in solid tumours, activated the upstream eukaryotic initiation factor 2alpha (eIF2alpha) kinase GCN2 to upregulate ATF4 target genes involved in amino acid synthesis and transport. GCN2 activation/overexpression and increased phospho-eIF2alpha were observed in human and mouse tumours compared with normal tissues and abrogation of ATF4 or GCN2 expression significantly inhibited tumour growth in vivo. We conclude that the GCN2-eIF2alpha-ATF4 pathway is critical for maintaining metabolic homeostasis in tumour cells, making it a novel and attractive target for anti-tumour approaches.

    View details for DOI 10.1038/emboj.2010.81

    View details for Web of Science ID 000278832100014

    View details for PubMedID 20473272

  • ATF4, an ER Stress and Hypoxia-Inducible Transcription Factor and its Potential Role in Hypoxia Tolerance and Tumorigenesis CURRENT MOLECULAR MEDICINE Ye, J., Koumenis, C. 2009; 9 (4): 411-416


    Hypoxia/anoxia promotes tumor aggressiveness and negatively impacts tumor response to therapy. Coordinate regulation of HIF-dependent and HIF-independent pathways has been shown to contribute to cellular adaptation to hypoxic stress, and to couple macromolecular synthesis rates to reduced energy availability. An important component of this type of adaptation is the activation of the endoplasmic reticulum kinase PERK by acute or prolonged hypoxia. Activated PERK subsequently induces phosphorylation of the translation initiation factor eIF2alpha and translational upregulation of the transcription factor ATF4. ATF4 is a basic leucine-zipper (bZip) transcription factor, which regulates amino acid metabolism, cellular redox state, and anti-stress responses. ATF4 expression can be regulated at transcriptional, translational, and post-translational levels. The functional activation of ATF4 under hypoxia and the overexpression of ATF4 in hypoxic areas of clinical samples of human tumors suggest that ATF4 plays a role in tumor hypoxic adaptation. Here we summarize recent findings regarding the regulation of ATF4 in transformed cells, clinical tumor samples and tumor models, and speculate on its potential role in tumor progression and chemoresistance.

    View details for Web of Science ID 000265697200003

    View details for PubMedID 19519398

  • Preferential Cytotoxicity of Bortezomib toward Hypoxic Tumor Cells via Overactivation of Endoplasmic Reticulum Stress Pathways CANCER RESEARCH Fels, D. R., Ye, J., Segan, A. T., Kridel, S. J., Spiotto, M., Olson, M., Koong, A. C., Koumenis, C. 2008; 68 (22): 9323-9330


    Hypoxia is a dynamic feature of the tumor microenvironment that contributes to drug resistance and cancer progression. We previously showed that components of the unfolded protein response (UPR), elicited by endoplasmic reticulum (ER) stress, are also activated by hypoxia in vitro and in vivo animal and human patient tumors. Here, we report that ER stressors, such as thapsigargin or the clinically used proteasome inhibitor bortezomib, exhibit significantly higher cytotoxicity toward hypoxic compared with normoxic tumor cells, which is accompanied by enhanced activation of UPR effectors in vitro and UPR reporter activity in vivo. Treatment of cells with the translation inhibitor cycloheximide, which relieves ER load, ameliorated this enhanced cytotoxicity, indicating that the increased cytotoxicity is ER stress-dependent. The mode of cell death was cell type-dependent, because DLD1 colorectal carcinoma cells exhibited enhanced apoptosis, whereas HeLa cervical carcinoma cells activated autophagy, blocked apoptosis, and eventually led to necrosis. Pharmacologic or genetic ablation of autophagy increased the levels of apoptosis. These results show that hypoxic tumor cells, which are generally more resistant to genotoxic agents, are hypersensitive to proteasome inhibitors and suggest that combining bortezomib with therapies that target the normoxic fraction of human tumors can lead to more effective tumor control.

    View details for DOI 10.1158/0008-5472.CAN-08-2873

    View details for Web of Science ID 000261136600029

    View details for PubMedID 19010906

  • Hypoxia and the unfolded protein response OXYGEN BIOLOGY AND HYPOXIA Koumenis, C., Bi, M., Ye, J., Feldman, D., Koong, A. C. 2007; 435: 275-?


    Tumor hypoxia refers to the development of regions within solid tumors in which the oxygen concentration is lower (0-3%) compared to that in most normal tissues (4-9%) (Vaupel and Hockel, 2000). Considerable experimental and clinical evidence exists supporting the notion that hypoxia fundamentally alters the physiology of the tumor towards a more aggressive phenotype (Hockel and Vaupel, 2001). Therefore, delineating the mechanisms by which hypoxia affects tumor physiology at the cellular and molecular levels will be crucial for a better understanding of tumor development and metastasis and for designing better antitumor modalities.

    View details for DOI 10.1016/S0076-6879(07)35014-3

    View details for Web of Science ID 000251162300014

    View details for PubMedID 17998059

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