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
Dissertation: The role of the transcription factor ATF4 in tumor progression under nutrient deprivation and hypoxia.

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)

Honors & Awards

  • Solutions Innovation Research Award, Agilent (2023)
  • MCR Michael B. Kastan Award for Research Excellence, AACR (2022)
  • Faculty scholar award, Stanford MCHRI (2020)
  • Research Scholar Award, American Cancer Society (2020)
  • Innovative Cancer Research Award, Mary Kay Foundation (2017)
  • NIH Pathway to Independence Award, National Cancer Institute (2015)
  • AACR Scholar-in-Training Award, AACR (2015)
  • People's Scholarship, First Class, Fudan University (2004)
  • People's Scholarship, First Class, Fudan University (2003)
  • Freshman Scholarship, First Class, Fudan University (2000)
  • Silver Medal, International Biology Olympiad (2000)

Boards, Advisory Committees, Professional Organizations

  • Member, Cancer Epigenetics Society (2016 - Present)
  • Member, American Association for Cancer Research (AACR) (2007 - Present)

Professional Education

  • Ph.D, University of Pennsylvania, Cancer Biology (2010)
  • B.S, Fudan University, Biological Science (2004)

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.

2023-24 Courses

Stanford Advisees

Graduate and Fellowship Programs

All Publications

  • The Warburg effect drives dedifferentiation through epigenetic reprogramming. Cancer biology & medicine Jiang, H., Jedoui, M., Ye, J. 2024; 20 (12)
  • Epigenetic priming targets tumor heterogeneity to shift transcriptomic phenotype of pancreatic ductal adenocarcinoma towards a Vitamin D susceptible state. Cell death & disease He, B., Stoffel, L., He, C. J., Cho, K., Li, A. M., Jiang, H., Flowers, B. M., Nguyen, K. T., Wang, K. W., Zhao, A. Y., Zhou, M. N., Ferreira, S., Attardi, L. D., Ye, J. 2024; 15 (1): 89


    As a highly heterogeneous tumor, pancreatic ductal adenocarcinoma (PDAC) exhibits non-uniform responses to therapies across subtypes. Overcoming therapeutic resistance stemming from this heterogeneity remains a significant challenge. Here, we report that Vitamin D-resistant PDAC cells hijacked Vitamin D signaling to promote tumor progression, whereas epigenetic priming with glyceryl triacetate (GTA) and 5-Aza-2'-deoxycytidine (5-Aza) overcame Vitamin D resistance and shifted the transcriptomic phenotype of PDAC toward a Vitamin D-susceptible state. Increasing overall H3K27 acetylation with GTA and reducing overall DNA methylation with 5-Aza not only elevated the Vitamin D receptor (VDR) expression but also reprogrammed the Vitamin D-responsive genes. Consequently, Vitamin D inhibited cell viability and migration in the epigenetically primed PDAC cells by activating genes involved in apoptosis as well as genes involved in negative regulation of cell proliferation and migration, while the opposite effect of Vitamin D was observed in unprimed cells. Studies in genetically engineered mouse PDAC cells further validated the effects of epigenetic priming for enhancing the anti-tumor activity of Vitamin D. Using gain- and loss-of-function experiments, we further demonstrated that VDR expression was necessary but not sufficient for activating the favorable transcriptomic phenotype in respond to Vitamin D treatment in PDAC, highlighting that both the VDR and Vitamin D-responsive genes were prerequisites for Vitamin D response. These data reveal a previously undefined mechanism in which epigenetic state orchestrates the expression of both VDR and Vitamin D-responsive genes and determines the therapeutic response to Vitamin D in PDAC.

    View details for DOI 10.1038/s41419-024-06460-9

    View details for PubMedID 38272889

    View details for PubMedCentralID 5858034

  • Mitochondrial uncoupler and retinoic acid synergistically induce differentiation and inhibit proliferation in neuroblastoma. bioRxiv : the preprint server for biology Jiang, H., Tiche, S. J., He, C. J., Jedoui, M., Forgo, B., Zhao, M., He, B., Li, Y., Li, A. M., Truong, A. T., Ho, J., Simmermaker, C., Yang, Y., Zhou, M., Hu, Z., Cuthbertson, D. J., Svensson, K. J., Hazard, F. K., Shimada, H., Chiu, B., Ye, J. 2024


    Neuroblastoma is a leading cause of death in childhood cancer cases. Unlike adult malignancies, which typically develop from aged cells through accumulated damage and mutagenesis, neuroblastoma originates from neural crest cells with disrupted differentiation. This distinct feature provides novel therapeutic opportunities beyond conventional cytotoxic methods. Previously, we reported that the mitochondrial uncoupler NEN (niclosamide ethanolamine) activated mitochondria respiration to reprogram the epigenome, promoting neuronal differentiation. In the current study, we further combine NEN with retinoic acid (RA) to promote neural differentiation both in vitro and in vivo. The treatment increased the expression of RA signaling and neuron differentiation-related genes, resulting in a global shift in the transcriptome towards a more favorable prognosis. Overall, these results suggest that the combination of a mitochondrial uncoupler and the differentiation agent RA is a promising therapeutic strategy for neuroblastoma.

    View details for DOI 10.1101/2024.01.22.576741

    View details for PubMedID 38328117

  • Metabolic reprogramming by histone deacetylase inhibition preferentially targets NRF2-activated tumors. Cell reports Karagiannis, D., Wu, W., Li, A., Hayashi, M., Chen, X., Yip, M., Mangipudy, V., Xu, X., Sánchez-Rivera, F. J., Soto-Feliciano, Y. M., Ye, J., Papagiannakopoulos, T., Lu, C. 2023; 43 (1): 113629


    The interplay between metabolism and chromatin signaling is implicated in cancer progression. However, whether and how metabolic reprogramming in tumors generates chromatin vulnerabilities remain unclear. Lung adenocarcinoma (LUAD) tumors frequently harbor aberrant activation of the NRF2 antioxidant pathway, which drives aggressive and chemo-resistant disease. Using a chromatin-focused CRISPR screen, we report that NRF2 activation sensitizes LUAD cells to genetic and chemical inhibition of class I histone deacetylases (HDACs). This association is observed across cultured cells, mouse models, and patient-derived xenografts. Integrative epigenomic, transcriptomic, and metabolomic analysis demonstrates that HDAC inhibition causes widespread redistribution of H4ac and its reader protein, which transcriptionally downregulates metabolic enzymes. This results in reduced flux into amino acid metabolism and de novo nucleotide synthesis pathways that are preferentially required for the survival of NRF2-active cancer cells. Together, our findings suggest NRF2 activation as a potential biomarker for effective repurposing of HDAC inhibitors to treat solid tumors.

    View details for DOI 10.1016/j.celrep.2023.113629

    View details for PubMedID 38165806

  • Uridine Synthesis Is the Metabolic Vulnerability in Relapse-Associated B-ALL Cells with Active Pre-BCR Signaling Liu, Y., Jiang, H., Stuani, L., Sarno, J., Domizi, P., Merchant, M., Jedoui, D., Jager, A., Huang, M., Lacayo, N. J., Sakamoto, K. M., Ye, J., Davis, K. L. AMER SOC HEMATOLOGY. 2023
  • Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proceedings of the National Academy of Sciences of the United States of America Li, A. M., He, B., Karagiannis, D., Li, Y., Jiang, H., Srinivasan, P., Ramirez, Y., Zhou, M. N., Curtis, C., Gruber, J. J., Lu, C., Rankin, E. B., Ye, J. 2023; 120 (38): e2302489120


    Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.

    View details for DOI 10.1073/pnas.2302489120

    View details for PubMedID 37695911

  • Mitochondrial uncoupling inhibits reductive carboxylation in cancer cells. Molecular cancer research : MCR Jiang, H., He, C. J., Li, A. M., He, B., Li, Y., Zhou, M., Ye, J. 2023


    When the electron transport chain (ETC) function is impaired, cancer cells rely on reductive carboxylation (RC) to convert alpha-ketoglutarate (alphaKG) to citrate for macromolecular synthesis, thereby promoting tumor growth. Currently, there is no viable therapy to inhibit RC for cancer treatment. In this study, we demonstrate that the mitochondrial uncoupler treatment effectively inhibits RC in cancer cells. Mitochondrial uncoupler treatment activates the ETC and increases the NAD+/NADH ratio. Using U-13C-glutamine and 1-13C-glutamine tracers, we show that mitochondrial uncoupling accelerates the oxidative TCA cycle and blocks RC under hypoxia, in von Hippel-Lindau (VHL) tumor suppressor-deficient kidney cancer cells, or under anchorage-independent growth condition. Together, these data demonstrate that mitochondrial uncoupling redirects alpha-KG from RC back to the oxidative TCA cycle, highlighting that the NAD+/NADH ratio is one key switch that determines the metabolic fate of alpha-KG. Inhibiting RC could be a key mechanism by which mitochondrial uncouplers inhibit tumor growth.

    View details for DOI 10.1158/1541-7786.MCR-23-0049

    View details for PubMedID 37358566

  • Differential effects of SARM1 inhibition in traumatic glaucoma and EAE optic neuropathies. Molecular therapy. Nucleic acids Liu, P., Chen, W., Jiang, H., Huang, H., Liu, L., Fang, F., Li, L., Feng, X., Liu, D., Dalal, R., Sun, Y., Jafar-Nejad, P., Ling, K., Rigo, F., Ye, J., Hu, Y. 2023; 32: 13-27


    Optic neuropathy is a group of optic nerve (ON) diseases withprogressive degeneration of ON and retinal ganglion cells(RGCs). The lack of neuroprotective treatments is a central challenge for this leading cause of irreversible blindness. SARM1 (sterile alpha and TIR motif-containing protein 1) has intrinsic nicotinamide adenine dinucleotide (NAD+) hydrolase activity that causes axon degeneration by degrading axonal NAD+ significantly after activation by axon injury. SARM1 deletion is neuroprotective in many, but not all, neurodegenerative disease models. Here, we compare two therapy strategies for SARM1 inhibition, antisense oligonucleotide (ASO) and CRISPR, with germline SARM1 deletion in the neuroprotection of three optic neuropathy mouse models. This study reveals that, similar to germline SARM1 knockout in every cell, local retinal SARM1 ASO delivery and adeno-associated virus (AAV)-mediated RGC-specific CRISPR knockdown of SARM1 provide comparable neuroprotection to both RGC somata and axons in the silicone oil-induced ocular hypertension (SOHU) glaucoma model but only protect RGC axons, not somata, after traumatic ON injury. Surprisingly, neither of these two therapy strategies of SARM1 inhibition nor SARM1 germline knockout (KO) benefits RGC or ON survival in the experimental autoimmune encephalomyelitis (EAE)/optic neuritis model. Our studies therefore suggest that SARM1 inhibition by local ASO delivery or AAV-mediated CRISPR is a promising neuroprotective gene therapy strategy for traumatic and glaucomatous optic neuropathies but not for demyelinating optic neuritis.

    View details for DOI 10.1016/j.omtn.2023.02.029

    View details for PubMedID 36950280

  • PHGDH-mediated endothelial metabolism drives glioblastoma resistance to chimeric antigen receptor T cell immunotherapy. Cell metabolism Zhang, D., Li, A. M., Hu, G., Huang, M., Yang, F., Zhang, L., Wellen, K. E., Xu, X., Conn, C. S., Zou, W., Kahn, M., Rhoades, S. D., Weljie, A. M., Fuchs, S. Y., Amankulor, N., Yoshor, D., Ye, J., Koumenis, C., Gong, Y., Fan, Y. 2023


    The efficacy of immunotherapy is limited by the paucity of T cells delivered and infiltrated into the tumors through aberrant tumor vasculature. Here, we report that phosphoglycerate dehydrogenase (PHGDH)-mediated endothelial cell (EC) metabolism fuels the formation of a hypoxic and immune-hostile vascular microenvironment, driving glioblastoma (GBM) resistance to chimeric antigen receptor (CAR)-T cell immunotherapy. Our metabolome and transcriptome analyses of human and mouse GBM tumors identify that PHGDH expression and serine metabolism are preferentially altered in tumor ECs. Tumor microenvironmental cues induce ATF4-mediated PHGDH expression in ECs, triggering a redox-dependent mechanism that regulates endothelial glycolysis and leads to EC overgrowth. Genetic PHGDH ablation in ECs prunes over-sprouting vasculature, abrogates intratumoral hypoxia, and improves T cell infiltration into the tumors. PHGDH inhibition activates anti-tumor T cell immunity and sensitizes GBM to CAR T therapy. Thus, reprogramming endothelial metabolism by targeting PHGDH may offer a unique opportunity to improve T cell-based immunotherapy.

    View details for DOI 10.1016/j.cmet.2023.01.010

    View details for PubMedID 36804058

  • Small-molecule toosendanin reverses macrophage-mediated immunosuppression to overcome glioblastoma resistance to immunotherapy. Science translational medicine Yang, F., Zhang, D., Jiang, H., Ye, J., Zhang, L., Bagley, S. J., Winkler, J., Gong, Y., Fan, Y. 2023; 15 (683): eabq3558


    T cell-based immunotherapy holds promise for treating solid tumors, but its therapeutic efficacy is limited by intratumoral immune suppression. This immune suppressive tumor microenvironment is largely driven by tumor-associated myeloid cells, including macrophages. Here, we report that toosendanin (TSN), a small-molecule compound, reprograms macrophages to enforce antitumor immunity in glioblastoma (GBM) in mouse models. Our functional screen of genetically probed macrophages with a chemical library identifies that TSN reverses macrophage-mediated tumor immunosuppression, leading to enhanced T cell infiltration, activation, and reduced exhaustion. Chemoproteomic and structural analyses revealed that TSN interacts with Hck and Lyn to abrogate suppressive macrophage immunity. In addition, a combination of immune checkpoint blockade and TSN therapy induced regression of syngeneic GBM tumors in mice. Furthermore, TSN treatment sensitized GBM to Egfrviii chimeric antigen receptor (CAR) T cell therapy. These findings suggest that TSN may serve as a therapeutic compound that blocks tumor immunosuppression and circumvents tumor resistance to T cell-based immunotherapy in GBM and other solid tumors that warrants further investigation.

    View details for DOI 10.1126/scitranslmed.abq3558

    View details for PubMedID 36791206

  • The magic bullet: Niclosamide. Frontiers in oncology Jiang, H., Li, A. M., Ye, J. 2022; 12: 1004978


    The term 'magic bullet' is a scientific concept proposed by the German Nobel laureate Paul Ehrlich in 1907, describing a medicine that could specifically and efficiently target a disease without harming the body. Oncologists have been looking for a magic bullet for cancer therapy ever since. However, the current therapies for cancers-including chemotherapy, radiation therapy, hormone therapy, and targeted therapy-pose either pan-cytotoxicity or only single-target efficacy, precluding their ability to function as a magic bullet. Intriguingly, niclosamide, an FDA-approved drug for treating tapeworm infections with an excellent safety profile, displays broad anti-cancer activity in a variety of contexts. In particular, niclosamide inhibits multiple oncogenic pathways such as Wnt/β-catenin, Ras, Stat3, Notch, E2F-Myc, NF-κB, and mTOR and activates tumor suppressor signaling pathways such as p53, PP2A, and AMPK. Moreover, niclosamide potentially improves immunotherapy by modulating pathways such as PD-1/PDL-1. We recently discovered that niclosamide ethanolamine (NEN) reprograms cellular metabolism through its uncoupler function, consequently remodeling the cellular epigenetic landscape to promote differentiation. Inspired by the promising results from the pre-clinical studies, several clinical trials are ongoing to assess the therapeutic effect of niclosamide in cancer patients. This current review summarizes the functions, mechanism of action, and potential applications of niclosamide in cancer therapy as a magic bullet.

    View details for DOI 10.3389/fonc.2022.1004978

    View details for PubMedID 36479072

    View details for PubMedCentralID PMC9720275

  • Mitochondrial uncoupling induces epigenome remodeling and promotes differentiation in neuroblastoma. Cancer research Jiang, H., Greathouse, R. L., Tiche, S. J., Zhao, M., He, B., Li, Y., Li, A. M., Forgo, B., Yip, M., Li, A., Shih, M., Banuelos, S., Zhou, M., Gruber, J. J., Rankin, E. B., Hu, Z., Shimada, H., Chiu, B., Ye, J. 2022


    The Warburg effect is the major metabolic hallmark of cancer. According to Warburg himself, the consequence of the Warburg effect is cell dedifferentiation. Therefore, reversing the Warburg effect might be an approach to restore cell differentiation in cancer. In this study, we used a mitochondrial uncoupler, niclosamide ethanolamine (NEN), to activate mitochondrial respiration, which induced neural differentiation in neuroblastoma cells. NEN treatment increased the nicotinamide adenine dinucleotide (NAD)+/NADH and pyruvate/lactate ratios and also the alpha-ketoglutarate (alpha-KG)/2- hydroxyglutarate (2-HG) ratio. Consequently, NEN treatment induced promoter CpG island demethylation and epigenetic landscape remodeling, activating the neural differentiation program. In addition, NEN treatment upregulated p53 but downregulated N-Myc and beta-catenin signaling in neuroblastoma cells. Importantly, even under hypoxia, NEN treatment remained effective in inhibiting 2-HG generation, promoting DNA demethylation, and suppressing hypoxia-inducible factor signaling. Dietary NEN intervention reduced tumor growth rate, 2-HG levels, and expression of N-Myc and beta-catenin in tumors in an orthotopic neuroblastoma mouse model. Integrative analysis indicated that NEN treatment upregulated favorable prognosis genes and downregulated unfavorable prognosis genes, which were defined using multiple neuroblastoma patient datasets. Altogether, these results suggest that mitochondrial uncoupling is an effective metabolic and epigenetic therapy for reversing the Warburg effect and inducing differentiation in neuroblastoma.

    View details for DOI 10.1158/0008-5472.CAN-22-1029

    View details for PubMedID 36318118

  • Use of Niclosamide Ethanolamine as a Mitochondrial Decoupler in Neuroblastoma Rafeeqi, T., Jiang, H., Greathouse, R., He, B., Li, A., Shimada, H., Ye, J., Chiu, B. LIPPINCOTT WILLIAMS & WILKINS. 2022: S194-S195
  • A stromal integrated stress response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumor progression Verginadis, I. I., Avgousti, H., Kim, K., Skoufos, G., Chinga, F., Leli, N., Karagounis, I. V., Bell, B. I., Velalopoulou, A., Wu, V. S., Li, Y., Ye, J., Scott, D. A., Osterman, A. L., Sengupta, A., Weljie, A., Hatzigeorgiou, A. G., Ryeom, S., Diehl, A. J., Fuchs, S. Y., Pure, E., Koumenis, C. AMER ASSOC CANCER RESEARCH. 2022
  • Serine starvation silences estrogen receptor signaling through histone hypoacetylation Li, A. M., Li, Y., He, B., Jiang, H., Lu, C., Gruber, J. J., Rankin, E. B., Ye, J. AMER ASSOC CANCER RESEARCH. 2022
  • Deciphering the Warburg effect: Redox is the key to tumor differentiation Jiang Haowen, Greathouse, R. L., He, B., Li, Y., Li, A. M., Forgo, B., Banuelos, S., Gruber, J., Shimada, H., Chiu, B., Ye, J. AMER ASSOC CANCER RESEARCH. 2022
  • A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression. Nature cell biology Verginadis, I. I., Avgousti, H., Monslow, J., Skoufos, G., Chinga, F., Kim, K., Leli, N. M., Karagounis, I. V., Bell, B. I., Velalopoulou, A., Salinas, C. S., Wu, V. S., Li, Y., Ye, J., Scott, D. A., Osterman, A. L., Sengupta, A., Weljie, A., Huang, M., Zhang, D., Fan, Y., Radaelli, E., Tobias, J. W., Rambow, F., Karras, P., Marine, J., Xu, X., Hatzigeorgiou, A. G., Ryeom, S., Diehl, J. A., Fuchs, S. Y., Pure, E., Koumenis, C. 2022


    Bidirectional signalling between the tumour and stroma shapes tumour aggressiveness and metastasis. ATF4 is a major effector of the Integrated Stress Response, a homeostatic mechanism that couples cell growth and survival to bioenergetic demands. Using conditional knockout ATF4 mice, we show that global, or fibroblast-specific loss of host ATF4, results in deficient vascularization and a pronounced growth delay of syngeneic melanoma and pancreatic tumours. Single-cell transcriptomics of tumours grown in Atf4Delta/Delta mice uncovered a reduction in activation markers in perivascular cancer-associated fibroblasts (CAFs). Atf4Delta/Delta fibroblasts displayed significant defects in collagen biosynthesis and deposition and a reduced ability to support angiogenesis. Mechanistically, ATF4 regulates the expression of the Col1a1 gene and levels of glycine and proline, the major amino acids of collagen. Analyses of human melanoma and pancreatic tumours revealed a strong correlation between ATF4 and collagen levels. Our findings establish stromal ATF4 as a key driver of CAF functionality, malignant progression and metastasis.

    View details for DOI 10.1038/s41556-022-00918-8

    View details for PubMedID 35654839

  • NMNAT2 and NAD(+) are Downregulated in Glaucomatous RGCs and Overexpression of NMNAT2 Rescues Glaucomatous Neurodegeneration Liu, D., Fang, F., Zhuang, P., Feng, X., Liu, P., Huang, H., Li, L., Chen, W., Liu, L., Sun, Y., Jiang, H., Ye, J., Hu, Y. ASSOC RESEARCH VISION OPHTHALMOLOGY INC. 2022
  • Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype. PNAS nexus Viswanathan, V., Cao, H., Saiki, J., Jiang, D., Mattingly, A., Nambiar, D., Bloomstein, J., Li, Y., Jiang, S., Chamoli, M., Sirjani, D., Kaplan, M., Holsinger, F. C., Liang, R., Von Eyben, R., Jiang, H., Guan, L., Lagory, E., Feng, Z., Nolan, G., Ye, J., Denko, N., Knox, S., Rosen, D., Le, Q. 2022; 1 (2): pgac056


    Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures postradiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from Aldh3a1 -/- mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels, depletes glutathione pool, and accumulates ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.

    View details for DOI 10.1093/pnasnexus/pgac056

    View details for PubMedID 35707206

  • beta-Cell Succinate Dehydrogenase Deficiency Triggers Metabolic Dysfunction and Insulinopenic Diabetes. Diabetes Lee, S., Xu, H., Van Vleck, A., Mawla, A. M., Li, A. M., Ye, J., Huising, M. O., Annes, J. P. 2022


    Mitochondrial dysfunction plays a central role in Type 2 Diabetes (T2D); however, the pathogenic mechanisms in pancreatic beta-cells are incompletely elucidated. Succinate dehydrogenase (SDH) is a key mitochondrial enzyme with dual functions in the TCA cycle and electron transport chain (ETC). Using human diabetic samples and a mouse model of beta-cell-specific SDH ablation (SDHBbetaKO), we define SDH deficiency as a driver of mitochondrial dysfunction in beta-cell failure and insulinopenic diabetes. beta-Cell SDH deficiency impairs glucose-induced respiratory oxidative phosphorylation and mitochondrial membrane potential (DeltaPsim) collapse, thereby compromising glucose-stimulated ATP production, insulin secretion and beta-cell growth. Mechanistically, metabolomic and transcriptomic studies reveal that the loss of SDH causes excess succinate accumulation, which inappropriately activates mTORC1-regulated metabolic anabolism, including increased SREBP-regulated lipid synthesis. These alterations, which mirror diabetes-associated human beta-cell dysfunction, are partially reversed by acute mTOR inhibition with rapamycin. We propose SDH deficiency as a contributing mechanism to the progressive beta-cell failure of diabetes and identify mTORC1 inhibition as a potential mitigation strategy.

    View details for DOI 10.2337/db21-0834

    View details for PubMedID 35472723

  • NMNAT2 Is Downregulated in Glaucomatous RGCs and RGC-Specific Gene Therapy Rescues Neurodegeneration and Visual Function. Molecular therapy : the journal of the American Society of Gene Therapy Fang, F., Zhuang, P., Feng, X., Liu, P., Liu, D., Huang, H., Li, L., Chen, W., Liu, L., Sun, Y., Jiang, H., Ye, J., Hu, Y. 1800


    The lack of neuroprotective treatments for retinal ganglion cells (RGCs) and optic nerve (ON) is a central challenge for glaucoma management. Emerging evidence suggests that redox factor NAD+ decline is a hallmark of aging and neurodegenerative diseases. Supplementation with NAD+ precursors and overexpression of NMNAT1, the key enzyme in the NAD+ biosynthetic process, have significant neuroprotective effects. We first profile the translatomes of RGCs in naive mice and mice with silicone oil-induced ocular hypertension (SOHU)/glaucoma by RiboTag mRNA sequencing. Intriguingly, only NMNAT2, but not NMNAT1 or NMNAT3, is significantly decreased in SOHU glaucomatous RGCs, which we confirm by in situ hybridization. We next demonstrate that AAV2 intravitreal injection-mediated overexpression of long half-life NMNAT2 mutant driven by RGC-specific mouse gamma-synuclein (mSncg) promoter restores decreased NAD+ levels in glaucomatous RGCs and ONs. Moreover, this RGC-specific gene therapy strategy delivers significant neuroprotection of both RGC soma and axon and preservation of visual function in the traumatic ON crush model and the SOHU glaucoma model. Collectively, our studies suggest that the weakening of NMNAT2 expression in glaucomatous RGCs contributes to a deleterious NAD+ decline and that modulating RGC intrinsic NMNAT2 levels by AAV2-mSncg vector is a promising gene therapy for glaucomatous neurodegeneration.

    View details for DOI 10.1016/j.ymthe.2022.01.035

    View details for PubMedID 35114390

  • Mitochondria-Rich Extracellular Vesicles From Autologous Stem Cell-Derived Cardiomyocytes Restore Energetics of Ischemic Myocardium. Journal of the American College of Cardiology Ikeda, G. n., Santoso, M. R., Tada, Y. n., Li, A. M., Vaskova, E. n., Jung, J. H., O'Brien, C. n., Egan, E. n., Ye, J. n., Yang, P. C. 2021; 77 (8): 1073–88


    Mitochondrial dysfunction results in an imbalance between energy supply and demand in a failing heart. An innovative therapy that targets the intracellular bioenergetics directly through mitochondria transfer may be necessary.The purpose of this study was to establish a preclinical proof-of-concept that extracellular vesicle (EV)-mediated transfer of autologous mitochondria and their related energy source enhance cardiac function through restoration of myocardial bioenergetics.Human-induced pluripotent stem cell-derived cardiomyocytes (iCMs) were employed. iCM-conditioned medium was ultracentrifuged to collect mitochondria-rich EVs (M-EVs). Therapeutic effects of M-EVs were investigated using in vivo murine myocardial infarction (MI) model.Electron microscopy revealed healthy-shaped mitochondria inside M-EVs. Confocal microscopy showed that M-EV-derived mitochondria were transferred into the recipient iCMs and fused with their endogenous mitochondrial networks. Treatment with 1.0 × 108/ml M-EVs significantly restored the intracellular adenosine triphosphate production and improved contractile profiles of hypoxia-injured iCMs as early as 3 h after treatment. In contrast, isolated mitochondria that contained 300× more mitochondrial proteins than 1.0 × 108/ml M-EVs showed no effect after 24 h. M-EVs contained mitochondrial biogenesis-related messenger ribonucleic acids, including proliferator-activated receptor γ coactivator-1α, which on transfer activated mitochondrial biogenesis in the recipient iCMs at 24 h after treatment. Finally, intramyocardial injection of 1.0 × 108 M-EVs demonstrated significantly improved post-MI cardiac function through restoration of bioenergetics and mitochondrial biogenesis.M-EVs facilitated immediate transfer of their mitochondrial and nonmitochondrial cargos, contributing to improved intracellular energetics in vitro. Intramyocardial injection of M-EVs enhanced post-MI cardiac function in vivo. This therapy can be developed as a novel, precision therapeutic for mitochondria-related diseases including heart failure.

    View details for DOI 10.1016/j.jacc.2020.12.060

    View details for PubMedID 33632482

  • Developing metabolic intervention strategies to reprogram neuroblastoma epigenome and overcome tumor resistance to differentiation therapy Jiang, H., Li, Y., Yip, M., Gruber, J., Li, A., Ye, J. AMER ASSOC CANCER RESEARCH. 2020
  • Deciphering Warburg effect: hypoxia inhibits tumor cell differentiation through reducing acetyl-CoA generation and chromatin accessibility Ye, J., Li, Y., Gruber, J. J., Litzenburger, U. M., Zhou, Y., Miao, Y. R., LaGory, E. L., Li, A. M., Hu, Z., Hart, L. S., Maris, J. M., Chang, H. Y., Giaccia, A. J. AMER ASSOC CANCER RESEARCH. 2020
  • Reprogramming of serine metabolism during breast cancer progression Li, A., Ducker, G. S., Li, Y., Seoane, J. A., Xiao, Y., Melemenidis, S., Zhou, Y., Liu, L., Vanharanta, S., Graves, E. E., Rankin, E. B., Curtis, C., Massague, J., Rabinowitz, J. D., Thompson, C. B., Ye, J. AMER ASSOC CANCER RESEARCH. 2020
  • Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia. Cell death & disease Li, Y. n., Gruber, J. J., Litzenburger, U. M., Zhou, Y. n., Miao, Y. R., LaGory, E. L., Li, A. M., Hu, Z. n., Yip, M. n., Hart, L. S., Maris, J. M., Chang, H. Y., Giaccia, A. J., Ye, J. n. 2020; 11 (2): 102


    Despite the fact that Otto H. Warburg discovered the Warburg effect almost one hundred years ago, why cancer cells waste most of the glucose carbon as lactate remains an enigma. Warburg proposed a connection between the Warburg effect and cell dedifferentiation. Hypoxia is a common tumor microenvironmental stress that induces the Warburg effect and blocks tumor cell differentiation. The underlying mechanism by which this occurs is poorly understood, and no effective therapeutic strategy has been developed to overcome this resistance to differentiation. Using a neuroblastoma differentiation model, we discovered that hypoxia repressed cell differentiation through reducing cellular acetyl-CoA levels, leading to reduction of global histone acetylation and chromatin accessibility. The metabolic switch triggering this global histone hypoacetylation was the induction of pyruvate dehydrogenase kinases (PDK1 and PDK3). Inhibition of PDKs using dichloroacetate (DCA) restored acetyl-CoA generation and histone acetylation under hypoxia. Knocking down PDK1 induced neuroblastoma cell differentiation, highlighting the critical role of PDK1 in cell fate control. Importantly, acetate or glycerol triacetate (GTA) supplementation restored differentiation markers expression and neuron differentiation under hypoxia. Moreover, ATAC-Seq analysis demonstrated that hypoxia treatment significantly reduced chromatin accessibility at RAR/RXR binding sites, which can be restored by acetate supplementation. In addition, hypoxia-induced histone hypermethylation by increasing 2-hydroxyglutarate (2HG) and reducing α-ketoglutarate (αKG). αKG supplementation reduced histone hypermethylation upon hypoxia, but did not restore histone acetylation or differentiation markers expression. Together, these findings suggest that diverting pyruvate flux away from acetyl-CoA generation to lactate production is the key mechanism that Warburg effect drives dedifferentiation and tumorigenesis. We propose that combining differentiation therapy with acetate/GTA supplementation might represent an effective therapy against neuroblastoma.

    View details for DOI 10.1038/s41419-020-2303-9

    View details for PubMedID 32029721

  • Reprogramming of serine, glycine and one-carbon metabolism in cancer. Biochimica et biophysica acta. Molecular basis of disease Li, A. M., Ye, J. n. 2020: 165841


    Metabolic pathways leading to the synthesis, uptake, and usage of the nonessential amino acid serine are frequently amplified in cancer. Serine encounters diverse fates in cancer cells, including being charged onto tRNAs for protein synthesis, providing head groups for sphingolipid and phospholipid synthesis, and serving as a precursor for cellular glycine and one-carbon units, which are necessary for nucleotide synthesis and methionine cycle reloading. This review will focus on the participation of serine and glycine in the mitochondrial one-carbon (SGOC) pathway during cancer progression, with an emphasis on the genetic and epigenetic determinants that drive SGOC gene expression. We will discuss recently elucidated roles for SGOC metabolism in nucleotide synthesis, redox balance, mitochondrial function, and epigenetic modifications. Finally, therapeutic considerations for targeting SGOC metabolism in the clinic will be discussed.

    View details for DOI 10.1016/j.bbadis.2020.165841

    View details for PubMedID 32439610

  • The PHGDH enigma: do cancer cells only need serine or also a redox modulator? Cancer letters Li, A. M., Ye, J. n. 2020


    Upregulation of serine biosynthesis pathway activity is an increasingly apparent feature of many cancers. Most notably, the first rate-limiting enzyme of the pathway, phosphoglycerate dehydrogenase (PHGDH), is genomically amplified in some melanomas and breast cancers and can be transcriptionally regulated by various tumor suppressors and oncogenes. Yet emerging evidence suggests that serine-in particular, serine biosynthetic pathway activity-may promote cancer in ways beyond providing the building blocks to support cell proliferation. Here, we summarize how mammalian cells tightly control serine synthesis before discussing alternate ways in which increased serine synthetic flux through PHGDH may benefit cancer cells, such as maintenance of TCA cycle flux through alpha-ketoglutarate (αKG) and modulation of cellular redox balance. We will also provide an overview of the current landscape of therapeutics targeting serine synthesis and offer a perspective on future strategies.

    View details for DOI 10.1016/j.canlet.2020.01.036

    View details for PubMedID 32032680

  • The m6A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor. Proceedings of the National Academy of Sciences of the United States of America Xiao, Y. n., Thakkar, K. N., Zhao, H. n., Broughton, J. n., Li, Y. n., Seoane, J. A., Diep, A. N., Metzner, T. J., von Eyben, R. n., Dill, D. L., Brooks, J. D., Curtis, C. n., Leppert, J. T., Ye, J. n., Peehl, D. M., Giaccia, A. J., Sinha, S. n., Rankin, E. B. 2020


    Loss of the von Hippel-Lindau (VHL) tumor suppressor is a hallmark feature of renal clear cell carcinoma. VHL inactivation results in the constitutive activation of the hypoxia-inducible factors (HIFs) HIF-1 and HIF-2 and their downstream targets, including the proangiogenic factors VEGF and PDGF. However, antiangiogenic agents and HIF-2 inhibitors have limited efficacy in cancer therapy due to the development of resistance. Here we employed an innovative computational platform, Mining of Synthetic Lethals (MiSL), to identify synthetic lethal interactions with the loss of VHL through analysis of primary tumor genomic and transcriptomic data. Using this approach, we identified a synthetic lethal interaction between VHL and the m6A RNA demethylase FTO in renal cell carcinoma. MiSL identified FTO as a synthetic lethal partner of VHL because deletions of FTO are mutually exclusive with VHL loss in pan cancer datasets. Moreover, FTO expression is increased in VHL-deficient ccRCC tumors compared to normal adjacent tissue. Genetic inactivation of FTO using multiple orthogonal approaches revealed that FTO inhibition selectively reduces the growth and survival of VHL-deficient cells in vitro and in vivo. Notably, FTO inhibition reduced the survival of both HIF wild type and HIF-deficient tumors, identifying FTO as an HIF-independent vulnerability of VHL-deficient cancers. Integrated analysis of transcriptome-wide m6A-seq and mRNA-seq analysis identified the glutamine transporter SLC1A5 as an FTO target that promotes metabolic reprogramming and survival of VHL-deficient ccRCC cells. These findings identify FTO as a potential HIF-independent therapeutic target for the treatment of VHL-deficient renal cell carcinoma.

    View details for DOI 10.1073/pnas.2000516117

    View details for PubMedID 32817424

  • Metabolic Profiling Reveals a Dependency of Human Metastatic Breast Cancer on Mitochondrial Serine and One-Carbon Unit Metabolism. Molecular cancer research : MCR Li, A. M., Ducker, G. S., Li, Y. n., Seoane, J. A., Xiao, Y. n., Melemenidis, S. n., Zhou, Y. n., Liu, L. n., Vanharanta, S. n., Graves, E. E., Rankin, E. B., Curtis, C. n., Massague, J. n., Rabinowitz, J. D., Thompson, C. B., Ye, J. n. 2020


    Breast cancer is the most common cancer among American women and a major cause of mortality. To identify metabolic pathways as potential targets to treat metastatic breast cancer, we performed metabolomics profiling on breast cancer cell line MDA-MB-231 and its tissue-tropic metastatic subclones. Here, we report that these subclones with increased metastatic potential display an altered metabolic profile compared to the parental population. In particular, the mitochondrial serine and one-carbon (1C) unit pathway is upregulated in metastatic subclones. Mechanistically, the mitochondrial serine and 1C unit pathway drives the faster proliferation of subclones through enhanced de novo purine biosynthesis. Inhibition of the first rate-limiting enzyme of the mitochondrial serine and 1C unit pathway, serine hydroxymethyltransferase (SHMT2), potently suppresses proliferation of metastatic subclones in culture and impairs growth of lung metastatic subclones at both primary and metastatic sites in mice. Some human breast cancers exhibit a significant association between the expression of genes in the mitochondrial serine and 1C unit pathway with disease outcome and higher expression of SHMT2 in metastatic tumor tissue compared to primary tumors. In addition to breast cancer, a few other cancer types, such as adrenocortical carcinoma (ACC) and kidney chromophobe cell carcinoma (KICH), also display increased SHMT2 expression during disease progression. Together, these results suggest that mitochondrial serine and 1C unit plays an important role in promoting cancer progression, particularly in late stage cancer. Implications: This study identifies mitochondrial serine and 1C unit metabolism as an important pathway during the progression of a subset of human breast cancers.

    View details for DOI 10.1158/1541-7786.MCR-19-0606

    View details for PubMedID 31941752

  • p53 deficiency triggers dysregulation of diverse cellular processes in physiological oxygen. The Journal of cell biology Valente, L. J., Tarangelo, A. n., Li, A. M., Naciri, M. n., Raj, N. n., Boutelle, A. M., Li, Y. n., Mello, S. S., Bieging-Rolett, K. n., DeBerardinis, R. J., Ye, J. n., Dixon, S. J., Attardi, L. D. 2020; 219 (11)


    The mechanisms by which TP53, the most frequently mutated gene in human cancer, suppresses tumorigenesis remain unclear. p53 modulates various cellular processes, such as apoptosis and proliferation, which has led to distinct cellular mechanisms being proposed for p53-mediated tumor suppression in different contexts. Here, we asked whether during tumor suppression p53 might instead regulate a wide range of cellular processes. Analysis of mouse and human oncogene-expressing wild-type and p53-deficient cells in physiological oxygen conditions revealed that p53 loss concurrently impacts numerous distinct cellular processes, including apoptosis, genome stabilization, DNA repair, metabolism, migration, and invasion. Notably, some phenotypes were uncovered only in physiological oxygen. Transcriptomic analysis in this setting highlighted underappreciated functions modulated by p53, including actin dynamics. Collectively, these results suggest that p53 simultaneously governs diverse cellular processes during transformation suppression, an aspect of p53 function that would provide a clear rationale for its frequent inactivation in human cancer.

    View details for DOI 10.1083/jcb.201908212

    View details for PubMedID 32886745

  • Novel Aza-podophyllotoxin derivative induces oxidative phosphorylation and cell death via AMPK activation in triple-negative breast cancer. British journal of cancer Tailor, D. n., Going, C. C., Resendez, A. n., Kumar, V. n., Nambiar, D. K., Li, Y. n., Dheeraj, A. n., LaGory, E. L., Ghoochani, A. n., Birk, A. M., Stoyanova, T. n., Ye, J. n., Giaccia, A. J., Le, Q. T., Singh, R. P., Sledge, G. W., Pitteri, S. J., Malhotra, S. V. 2020


    To circumvent Warburg effect, several clinical trials for different cancers are utilising a combinatorial approach using metabolic reprogramming and chemotherapeutic agents including metformin. The majority of these metabolic interventions work via indirectly activating AMP-activated protein kinase (AMPK) to alter cellular metabolism in favour of oxidative phosphorylation over aerobic glycolysis. The effect of these drugs is dependent on glycaemic and insulin conditions.  Therefore, development of small molecules, which can activate AMPK, irrespective of the energy state, may be a better approach for triple-negative breast cancer (TNBC) treatment.Therapeutic effect of SU212 on TNBC cells was examined using in vitro and in vivo models.We developed and characterised the efficacy of novel AMPK activator (SU212) that selectively induces oxidative phosphorylation and decreases glycolysis in TNBC cells, while not affecting these pathways in normal cells.   SU212 accomplished this metabolic reprogramming by activating AMPK independent of energy stress and irrespective of the glycaemic/insulin state. This leads to mitotic phase arrest and apoptosis in TNBC cells. In vivo, SU212 inhibits tumour growth, cancer progression and metastasis.SU212 directly activates AMPK in TNBC cells, but does not hamper glucose metabolism in normal cells. Our study provides compelling preclinical data for further development of SU212 for the treatment of TNBC.

    View details for DOI 10.1038/s41416-020-01137-4

    View details for PubMedID 33139797

  • Acetate supplementation eliminates hypoxia mediated resistance to differentiation therapy in neuroblastoma cells Li, Y., Zhou, Y., Maris, J. M., Giaccia, A. J., Ye, J. AMER ASSOC CANCER RESEARCH. 2019
  • 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 eIF2α. 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 α (HIF1α), 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

    View details for PubMedCentralID PMC3617567

  • 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